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the circadian functionality of a brain region. The presence of different putative retinoid-and clock-responsive elements on the CAT and GPx gene upstream regions shown in Figure 5, would explain, at least in part, a differential regulation of these genes at transcriptional level as well as the distinct response to the vitamin A deficiency seen in this study. Thus, CAT promoter seems more responsive and sensitive to clock control through its five E-boxes. Shallower daily CAT expression and activity could be either a consequence of the loss of BMAL1 and PER1 rhythmicity or, taking into account Hirayama et al. (2007) findings, either the cause of the loss of clock proteins oscillation. In the case of GPx upstream region, besides a larger number of RXR sites, it has only one Ebox and one RORE sites. RORa in the SCN or other brain regions is a retinoid-related orphan receptor recently incorporated to the molecular clock machinery (Sato et al., 2004), which activates BMAL1 transcription in a 24-h cycle. It has been shown that RORamediated transcription is activated synergistically by RAR in Pukinje cerebellar cells (Matsui, 1997), evidencing a functional interaction between RORa and RAR transcription factors. RARs operate as heterodimers with RXRs (Soprano et al., 2004). In these studies, vitamin A deficiency had no effect on the RARα mRNA expression but significantly reduced the RXRβ transcript level ( Figure 6). Taking into account the presence of RXR responsive sites on CAT and GPx genes upstream region ( Figure 5), the lower availability of RXRβ might affect some necessary transcriptional | 3,069,400 | 21239645 | 0 | 16 |
interactions to maintain rhythmic expression of antioxidant enzymes genes; for example, affecting either RXR heterodimerization, either RORa-mediated transcriptional activation of clock (BMAL1) or clock-controlled (GPx) cycling genes. These last questions led us to test whether vitamin A deprivation modifies the circadian expression of key endogenous clock proteins such as BMAL1 and PER1, a positive and a negative clock transcription factor, respectively. Interestingly, we observed vitamin A deficiency was able to reduce in a 20 and 37% the BMAL1 and PER1 rhythms amplitude. Even thought there are many reports that associate vitamin deficiencies with altered daily expression patterns, just a very few report the effect of nutritional deficiencies on circadian clock gene expression, and only one determines the effect of vitamin A deficiency on the oscillating Bmal1 and Per2 gene expression (Shiari et al., 2006). Conversely to what we observed in the hippocampus of vitamin A deficient rats, Shirai et al. (2006) found that circadian expression of clock genes is maintained in the liver of Vitamin A-deficient mice. This lead us to suggest a tissue-specific role for vitamin A given by a tissue-specific distribution of its nuclear receptors, that is RXRα, RARα and RARβ being the most abundant in the liver (Ulven et al., 1998) and RXRβ, RARα, and RARγ, being the ones in the hippocampus (Krezel et al., 1999, Zetterstrom et al. 1999). Thus, vitamin A deficiency might affect transcriptional and/or post-transcriptional processes, either by affecting RARs-or RXRs-mediated transcriptional regulation of CAT and GPx, either by affecting the formation of BMAL1:CLOCK heterodimer or its interaction with | 3,069,401 | 21239645 | 0 | 16 |
the antioxidant enzymes promoters. Recovering of daily clock proteins and antioxidant enzymes expression rhythms in the hippocampus of vitamin A-refed rats Even thought refeeding vitamin A-deficient animals with the control diet during 15 days was not enough to restore the mRNA expression of RXRβ to control level (Figure 6), it was sufficient for recovering daily rhythmicity of BMAL1 and PER1 protein levels (Figure 7). These observations would allow us to explain the, in some cases complete in other partial, recovering of vitamin A-refed rats. Interestingly, CAT circadian rhythms were almost completely recovered after refeeding with the vitamin A-sufficient (control) diet. In this case, a higher number of Ebox sites on the CAT gene 5′ regulatory region is in agreement with the recovering of BMAL1 and PER1 circadian patterns (Figure 7). On the other hand, studies of RAR null and RXR mutations, have shown a compensatory activity of other RARs or RXRs when one RAR is not produced (Krezel et al., 1996) or one RXR is mutated and not functional (Vivat-Hannah et al., 2003). In our case, vitamin A refeeding increased RARα mRNA level and, as shown in Figure 5, CAT gene has, besides two RXREs, a RARE site on its promoter. All above observations could explain daily CAT recovering from vitamin A deficiency when animals were refed with the control diet. However, lipoperoxidation and GPx circadian patterns were half-a-way restored in the vitamin A-refed group, as expected since GPx gene promoter is richer in RXRE but lacks of RARE sites and thereafter, it is probably more | 3,069,402 | 21239645 | 0 | 16 |
sensitive to the significant lowered and unrecovered RXRs levels. Conclusion Throughout a whole 24-h cycle, our study shows that CAT and GPx expression and activity present a daily rhythmicity in the rat hippocampus. This might reveal an interesting strategy to respond to the challenge of daily oxidative stress in this brain region. Temporal patterns of lipoperoxidation, CAT and GPx expression and activity, as well as daily oscillation of clock BMAL1 and PER1 proteins, showed dramatic changes under the nutritional vitamin A deficiency. Thus, the daily variation of physiological parameters and functions might be under the control of both endogenous and external factors such as environmental or nutritional ones. The presence of an endogenous biological clock is fundamental for life at all levels of an organism and as we and others have shown hippocampus does not run away from this. Taken together, the results presented here would contribute to define, for the first time, a possible role for vitamin A as a rhythm regulator in the establishment of circadian clock and antioxidant enzyme systems. On the other hand, learning how vitamin A deficiency affects the circadian expression of genes involved in the antioxidant defense system in the hippocampus may have an impact on the neurobiology, nutritional, and chronobiology fields, emphasizing for the first time the importance of nutritional factors such as dietary micronutrients in the regulation of circadian parameters in the brain memory-and-learningrelated regions. We would also expect that emerging data from this and future studies would highlight retinoid signalling pathways as potential novel therapeutic targets for | 3,069,403 | 21239645 | 0 | 16 |
cognitive as well as for clock-related deficits. Figure 1. CAT and GPx mRNA levels in the hippocampus of control, vitamin A-deficient and vitamin A-refed rats Bars represent mean ± standard error of four animals per group performed in duplicates. Statistical analysis was performed using one-way ANOVA followed by Tukey test. *P<0,02; **P<0,05. MDA was measured by the thiobarbituric acid method. Each value represents the mean ± SE of two pools of three left hippocampi each. Horizontal bars represent the distribution of light (open) and dark (closed) phases of the 24 h photoperiod. ZT is zeitgeber time, with ZT=0 when light is on. Statistical analysis was performed using one-way ANOVA followed by Tukey test with *P<0,05; **P<0,01 and ***P<0,001 when compared indicated means with the corresponding maximal value in each group. The accession # for the sequences taken from the PubMed database are: CAT (Acc#: AH004967) and GPx (Acc#: AB004231). Arrows indicate the first translation codon, gray boxes represent exons, white circles are RAREsites, dashed circles RXREs, black ovals perfect E-box (CACGTG) sites and white ovals are E-box-like (CATATG, CATGTG or CACTTG) sites. Grey oval on rGPx promoter represents a RORE site. Negative (−) numbers indicate regulatory sites positions relative to the start of translation (+1). | 3,069,404 | 21239645 | 0 | 16 |
Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics Success rates for catheter ablation of persistent atrial fibrillation patients are currently low; however, there is a subset of patients for whom electrical isolation of the pulmonary veins alone is a successful treatment strategy. It is difficult to identify these patients because there are a multitude of factors affecting arrhythmia susceptibility and maintenance, and the individual contributions of these factors are difficult to determine clinically. We hypothesised that the combination of pulmonary vein (PV) electrophysiology and atrial body fibrosis determine driver location and effectiveness of pulmonary vein isolation (PVI). We used bilayer biatrial computer models based on patient geometries to investigate the effects of PV properties and atrial fibrosis on arrhythmia inducibility, maintenance mechanisms, and the outcome of PVI. Short PV action potential duration (APD) increased arrhythmia susceptibility, while longer PV APD was found to be protective. Arrhythmia inducibility increased with slower conduction velocity (CV) at the LA/PV junction, but not for cases with homogeneous CV changes or slower CV at the distal PV. Phase singularity (PS) density in the PV region for cases with PV fibrosis was increased. Arrhythmia dynamics depend on both PV properties and fibrosis distribution, varying from meandering rotors to PV reentry (in cases with baseline or long APD), to stable rotors at regions of high fibrosis density. Measurement of fibrosis and PV properties may indicate patient specific susceptibility to AF initiation and maintenance. PV PS density before PVI was higher for cases in which AF terminated or converted to | 3,069,405 | 44120062 | 0 | 16 |
a macroreentry; thus, high PV PS density may indicate likelihood of PVI success. Introduction Success rates for catheter ablation of persistent atrial fibrillation (AF) patients are currently low; however, there is a subset of patients for whom pulmonary vein isolation (PVI) alone is a successful treatment strategy [1]. PVI ablation may work by preventing triggered beats from entering the left atrial body, or by converting rotors or functional reentry around the left atrial/pulmonary vein (LA/PV) junction to anatomical reentry around a larger circuit, potentially converting AF to a simpler tachycardia [2]. It is difficult to predict whether PVI represents a sufficient treatment strategy for a given patient with persistent AF [1], and it is unclear what to do for the majority of patients for whom it is not effective. Patients with AF exhibit distinct properties in effective refractory period (ERP) and conduction velocity (CV) in the PVs. For example, paroxysmal AF patients have shorter ERP and longer conduction delays compared to control patients [3]. AF patients show a number of other differences to control patients: PVs are larger [4]; PV fibrosis is increased; and fiber direction may be more disorganised, particularly at the PV ostium [5]. There are also differences within patient groups; for example, patients for whom persistent AF is likely to terminate after PVI have a larger ERP gradient compared to those who require further ablation [1,3]. Electrical driver location changes as AF progresses; drivers (rotors or focal sources) are typically located close to the PVs in early AF, but are also located elsewhere | 3,069,406 | 44120062 | 0 | 16 |
in the atria with longer AF duration [6]. Atrial fibrosis is a major factor associated with AF and modifies conduction. However, there is conflicting evidence on the relationship between fibrosis distribution and driver location [7,8]. It is difficult to clinically separate the individual effects of these factors on arrhythmia susceptibility and maintenance. We hypothesise that the combination of PV properties and atrial body fibrosis determines driver location and, thus, the likely effectiveness of PVI. In this study, we tested this hypothesis by using computational modelling to gain mechanistic insight into the individual contribution of PV ERP, CV, fiber direction, fibrosis and anatomy on arrhythmia susceptibility and dynamics. We incorporated data on APD (action potential duration, as a surrogate for ERP) and CV for the PVs to determine mechanisms underlying arrhythmia susceptibility, by testing inducibility from PV ectopic beats. We also predicted driver location, and PVI outcome. Bilayer model All simulations were performed using the CARPentry simulator (available at https://carp. medunigraz.at/carputils/). We used a previously published bi-atrial bilayer model [9], which consists of resistively coupled endocardial and epicardial surfaces. This model incorporates detailed atrial structure and includes transmural heterogeneity at a similar computational cost to surface models. We chose to use a bilayer model rather than a volumetric model incorporating thickness for this study because of the large numbers of parameters investigated, which was feasible with the reduced computational cost of the bilayer model. As previously described, the bilayer model was constructed from computed tomography scans of a patient with paroxysmal AF, which were segmented and meshed | 3,069,407 | 44120062 | 0 | 16 |
to create a finite element mesh suitable for electrophysiology simulations. Fiber information was included in the model using a semi-automatic rule based method that matches histological descriptions of atrial fiber orientation [10]. The left atrium of the bilayer model consists of linearly coupled endocardial and epicardial layers, while the right atrium is an epicardial layer, with endocardial atrial structures including the pectinate muscles and crista terminalis. The left and right atrium of the model are electrically connected through three pathways: Bachmann's bundle, the coronary sinus and the fossa ovalis. Tissue conductivities were tuned to human activation mapping data from Lemery et al. [9,11]. The Courtemanche-Ramirez-Nattel human atrial ionic model was used with changes representing electrical remodelling during persistent AF [12], together with a doubling of sodium conductance to produce realistic action potential upstroke velocities [9], and a decrease in I K1 by 20% to match clinical restitution data [13]. Regional heterogeneity in repolarisation was included by modifying ionic conductances of the cellular model, as described in Bayer et al. [14], which follows Aslanidi et al. and Seemann et al. [15,16]. Parameters for the baseline PV model were taken from Krueger et al. [17]. The following PV properties were varied as shown in schematic Fig 1: APD, CV, fiber direction, the inclusion of fibrosis in the PVs and the atrial geometry. These are described in the following sections. Geometry To investigate the effects of PV length and diameter on arrhythmia inducibility and arrhythmia dynamics, bi-atrial bilayer meshes were constructed from MRI data for twelve patients. All patients | 3,069,408 | 44120062 | 0 | 16 |
gave written informed consent; this study is in accordance with the Declaration of Helsinki, and approved by the Institutional Ethics Committee at the University of Bordeaux. Patient-specific models with electrophysiological heterogeneity and fiber direction were constructed using our modelling pipeline, which uses a universal atrial coordinate system to map scalar and vector data from the original bilayer model to a new patient specific mesh. Late gadolinium enhancement MRI (average resolution 0.625mm x 0.625mm x 2.5mm) was performed using a 1.5T system (Avanto, Siemens Medical Solutions, Erlangen, Germany). These LGE-MRI data were manually segmented using the software MUSIC (Electrophysiology and Heart Modeling Institute, University of Bordeaux, Bordeaux France, and Inria, Sophia Antipolis, France, http://med.inria.fr). The resulting endocardial surfaces were meshed (using the Medical Imaging Registration Toolkit mcubes algorithm [18]) and cut to create open surfaces at the mitral valve, the four pulmonary veins, the tricuspid valve, and each of the superior vena cava, the inferior vena cava and the coronary sinus using ParaView software (Kitware, Clifton Park, NY, USA). The meshes were then remeshed using mmgtools meshing software (http://www.mmgtools.org/), with parameters chosen to produce meshes with an average edge length of 0.34mm to match the resolution of the previously published bilayer model [9]. Two atrial coordinates were defined for each of the LA and RA, which allow automatic transfer of atrial structures to the model, such as the pectinate muscles and Bachmann's bundle. These coordinates were also used to map fiber directions to the bilayer model. PV electrophysiology To investigate the effects of PV electrophysiology on arrhythmia | 3,069,409 | 44120062 | 0 | 16 |
inducibility and dynamics, we varied PV APD and CV by modifying the value of the inward rectifier current (I K1 ) conductance and tissue level conductivity respectively. I K1 conductance was chosen in this case to investigate macroscopic differences in APD [19], although several ionic conductances are known to change with AF [20]. Modifications were either applied homogeneously or following a ostial-distal gradient. This gradient was implemented by calculating geodesic distances from the rim of mesh nodes at the distal PV boundary to all nodes in the PV and from the rim of nodes at the LA/PV junction to all nodes in the PV. The ratio of these two distances was then used as a distance parameter from the LA/PV junction to the distal end of the PV (see Fig 1). I K1 conductance was multiplied by a value in the range 0.5-2.5, resulting in PV APDs in the clinical range of 100-190ms [3,21,22]. This rescaling was either a homogeneous change or followed a gradient along the PV length. Gradients of I K1 conductance varied from the baseline value at the LA/PV junction, to a maximum scaling factor at the distal boundary. PV APDs are reported at 90% repolarisation for a pacing cycle length of 1000ms. LA APD is 185ms, measured at a LA pacing cycle length of 200ms. To cover the clinically observed range of PV CVs, longitudinal and transverse tissue conductivities were divided by 1, 2, 3 or 5, resulting in CVs, measured along the PV axis, in the range: 0.28-0.67m/s [3,[21][22][23][24]. To model | 3,069,410 | 44120062 | 0 | 16 |
heterogeneous conduction slowing, conductivities were varied as a function of distance from the LA/PV junction, ranging from baseline at the junction to a maximum rescaling (minimum conductivity) at the distal boundary. The direction of this gradient was also reversed to model conduction slowing at the LA/PV junction [5]. Fibrosis modelling Motivated by the findings of Hocini et al. [5], interstitial fibrosis was modelled for the PVs with a density varying along the vein, increasing from the LA/PV junction to the distal boundary. This was implemented by randomly selecting edges of elements of the mesh with probability scaled by the distance parameter and the angle of the edge compared to the element fiber direction, where edges in the longitudinal fiber direction were four times more likely to be selected than those in the transverse direction, following our previous methodology [25]. To model microstructural discontinuities, no flux boundary conditions were applied along the connected edge networks, following Costa et al. [26]. An example of modelled PV interstitial fibrosis is shown in S1A Fig. For a subset of simulations, interstitial fibrosis was incorporated in the biatrial model based on late gadolinium enhancement (LGE)-MRI data, using our previously published methodology [25]. In brief, likelihood of interstitial fibrosis depended on both LGE intensity and the angle of the edge compared to the element fiber direction (see S1B Fig). LGE intensity distributions were either averaged over a population of patients [27], or for an individual patient. The averaged distributions were for patients with paroxysmal AF (averaged over 34 patients), or persistent AF | 3,069,411 | 44120062 | 0 | 16 |
(averaged over 26 patients). For patient-specific simulations, the model arrhythmia dynamics were compared to AF recordings from a commercially available non-invasive ECGi mapping technology (CardioInsight Technologies Inc., Cleveland, OH) for which phase mapping analysis was performed as previously described [28]. PV fiber direction PV fiber direction shows significant inter-patient variability. Endocardial and epicardial fiber direction in the four PVs was modified according to fiber arrangements described in the literature [5,29,30]. Six arrangements were considered, as follows: 1. circular arrangement on both the endocardium and epicardium; 2. spiralling arrangement on both the endocardium and epicardium; 3. circular arrangement on the endocardium, with longitudinal epicardial fibers; 4. fibers progress from longitudinal at the distal vein to circumferential at the ostium, with identical endocardial and epicardial fibers; 5. epicardial layer fibers as per case 4, with circumferential endocardial fibers; 6. as per case 4, but with a chaotic fiber arrangement at the LA/PV junction. These fiber distributions are shown in S2 Fig. Cases 4-6 were implemented by setting the fiber angle to be a function of the distance along the vein, measured from the LA/PV junction to the distal boundary, varying from circumferential at the junction to longitudinal at the distal end (representing a change of 90 degrees). The disorder in fiber direction at the LA/PV junction for case 6 was implemented by taking the fibers of case 4 and adding independent standard Gaussian distributions scaled by the distance from the distal boundary, resulting in the largest perturbations at the ostium. Pacing protocol to test inducibility Arrhythmia inducibility was | 3,069,412 | 44120062 | 0 | 16 |
tested by extrastimulus pacing from each of the four PVs individually using a clinically motivated protocol [31], to simulate the occurrence of PV ectopics. Simulations were performed for each of the PVs, to determine the effects of ectopic beat location on inducibility. Sinus rhythm was simulated by stimulating the sinoatrial node region of the model at a cycle length of 700ms throughout the simulation. Each PV was paced individually with five beats at a cycle length of 160ms, and coupling intervals between the first PV beat and a sinus rhythm beat in the range 200-500 ms. Thirty-two pacing protocols were applied for each model set up: eight coupling intervals (coupling interval = 200, 240, 280, 320, 360, 400, 440, 480ms), for each of the four PVs. Inducibility is reported as the proportion of cases resulting in reentry; termed the inducibility ratio. Pulmonary vein isolation The effects of PVI were determined for model set-ups that used the original bilayer geometry and in which the arrhythmia lasted for greater than two seconds. PVI was applied two seconds post AF initiation in each case by setting the tissue conductivity close to zero (0.001 S/m) in the regions shown in S3 Fig. Model phase singularity analysis For each case, ten seconds of arrhythmia data were analysed, starting from two seconds post AF initiation, to identify re-entrant waves and wavefront break-up using phase. The phase of the transmembrane voltage was calculated for each node of the mesh using the Hilbert transform, following subtraction of the mean [32]. Phase singularities (PSs) for | 3,069,413 | 44120062 | 0 | 16 |
the transmembrane potential data were identified by calculating the topological charge of each element in the mesh [33], and PS spatial density maps were calculated using previously published methods [14]. PS density maps were then partitioned into the LA body, PV regions, and the RA to assess where drivers were located in relation to the PVs (see S3 Fig). The PV region was defined as the areas enclosed by, and including, the PVI lines; the LA region was then the rest of the LA and left atrial appendage. The PV PS density ratio was then defined as the total PV PS count divided by the total model PS count over both atria. PV APD A difference in APD between the model LA and PVs was required for AF induction. Modelling the PVs using LA cellular properties resulted in non-inducibility, whereas, modelling the LA using PV cellular properties resulted in either non-inducibility or macroreentry. The effects of modifying PV APD homogeneously or following a gradient are shown in Table 1. Simulations in which PV APD was longer than LA APD were non-inducible (PV APD 191ms). As APD was decreased below the baseline value (181ms), inducibility initially increased and then fluctuated. Comparing cases with equal distal APD, arrhythmia inducibility was significantly higher for APD following a ostial-distal gradient than for homogeneous APD (p = 0.03 from McNemar's test). PS location was also affected by PV APD. PV PS density was low in cases of short APD, an example of which is shown in Fig 2 where reentry is | 3,069,414 | 44120062 | 0 | 16 |
no longer seen around the LA/PV junction in the case of short APD (120ms). This change was more noticeable for cases with homogeneous PV APD than for a gradient in APD; PV reentry was observed for the baseline case and a heterogeneous APD case, but not for a homogeneous decrease in APD. PV CV Arrhythmia inducibility decreased with homogeneous CV slowing (from 0.38 i.e. 12/32 at 0.67m/s to 0.03 i.e. 1/32 at 0.28m/s). In the baseline model, reentry occurs close to the LA/PV junction due to conduction block when the paced PV beat encounters a change in fiber direction at the base of the PVs, together with a longer LA APD compared to the PV APD. In this case, the wavefront encounters a region of refractory tissue due to the longer APD in the LA. However, when PV CV is slowed homogeneously, the wavefront takes longer to reach the LA tissue, giving the tissue enough time to recover, such that conduction block and reentry no longer occurs. Modifying conductivity following a gradient means that, unlike the homogeneous case, the time taken for the extrastimulus wavefront to reach the LA tissue is similar to the baseline case, so the LA tissue might still be refractory and conduction block might occur. In the case that conduction was slowest at the distal vein, the inducibility was similar to the baseline case (see Table 2, G A , inducibility is 0.38 at baseline and 0.34 for the cases with CV slowing). Cases with greatest conduction slowing at the LA/PV junction | 3,069,415 | 44120062 | 0 | 16 |
(see Table 2, G B ) exhibit an increase in inducibility (from 0.38 to 0.53) when CV is decreased because of the discontinuity in conductivity at the junction. Fig 2 shows that reentry is seen around the LA/PV junction in cases with both baseline and slow CV, indicating that the presence of reentry at the LA/PV junction is independent of PV CV. PV fiber direction PV conduction properties are also affected by PV fiber direction. Modifications in fiber direction increased inducibility compared to the baseline fiber direction (baseline case: 0.38; modified fiber direction cases 1-6: 0.53-0.63). The highest inducibility occurred with circular fibers at the ostium (cases 1 and 4, 0.63), independent of fiber direction at the distal PV end. This inducibility was reduced if the epicardial fibers were not circular at the ostium (case 3, 0.56), or if fibers were spiralling (case 2, 0.56) instead of circular. PV properties plus fibrosis Next we investigated the interplay between PV properties and atrial fibrosis. LA fibrosis properties were varied to represent interstitial fibrosis in paroxysmal and persistent AF patients, incorporating average LGE-MRI distributions [27] into the model. These control, paroxysmal and persistent AF levels of fibrosis were then combined with PV properties varied as follows: baseline CV and APD (0.67m/s, 181ms), slow CV (0.51m/s), short APD (120ms), slow CV and short APD. PS distributions in Fig 2 show that reentry occurred around the LA/PV junction in Pulmonary vein electrophysiology, fibrosis and arrhythmia the case of baseline PV APD for control or paroxysmal levels of fibrosis, but not | 3,069,416 | 44120062 | 0 | 16 |
for shorter PV APD. Modifying PV CV did not affect whether LA/PV reentry is observed. Rotors were found to stabilise to regions of high fibrosis density in the persistent AF case. Models with PV fibrosis had a higher inducibility compared to the baseline case (0.47 vs. 0.38) and a higher PV PS density since reentry localised there. Fig 3 shows an example with moderate PV fibrosis (A) in which reentry changed from around the RIPV to the LIPV later in the simulation; adding a higher level of PV fibrosis resulted in a more stable reentry around the right PVs (B). Patient specific LA fibrosis vs PV properties The relationship between LA fibrosis and PV properties on driver location was investigated on an individual patient basis for four patients. For patients for whom rotors were located away from the PVs (Fig 4 LA1), increasing model fibrosis from low to high increased the model agreement with clinical PS density 2.3 ± 1.0 fold (comparing the sensitivity of identifying clinical regions of high PS density using model PS density between the two simulations). For other patients, lower levels of fibrosis were more appropriate (2.1 fold increase in agreement for lower fibrosis , Fig 4 LA2), and PV isolation converted fibrillation to macroreentry in the model. Anatomy Arrhythmia inducibility showed a large variation between patient geometries (0.16-0.47). Increasing PV area increased inducibility to a different degree for each vein: right superior PV (RSPV) inducibility was generally high (> 0.75 for all but one geometry) independent of PV Pulmonary vein isolation | 3,069,417 | 44120062 | 0 | 16 |
PVI outcome was assessed for cases with varied PV APD (both with a homogeneous change or following a gradient), with the inclusion of PV fibrosis and with varied PV fiber direction because these factors were found to affect the PV PS density ratio. PVI outcome was classified into three classes depending on the activity 1 second after PVI was applied in the model: termination, meaning there was no activity; macroreentry, meaning that there was a macroreentry around the LA/PV junctions; AF sustained by LA rotors, meaning there were drivers in the LA Pulmonary vein electrophysiology, fibrosis and arrhythmia Pulmonary vein electrophysiology, fibrosis and arrhythmia body. These classes accounted for different proportions of the outcomes: termination (27.3% of cases), macroreentry (39.4%), or AF sustained by LA rotors (33.3%). Calculating the PV PS density ratio before PVI for each of these classes shows that cases in which the arrhythmia either terminated or changed to a macroreentry are characterised by a statistically higher PV PS density ratio pre-PVI than cases sustained by LA rotors post-PVI (see Fig 6, t-test comparing termination and LA rotors shows they are significantly different, p<0.001; comparing macroreentry and LA rotors p = 0.01). High PV PS density ratio may indicate likelihood of PVI success. Main findings In this computational modelling study, we demonstrated that the PVs can play a large role in arrhythmia maintenance and initiation, beyond being simply sources of ectopic beats. We separated the effects of PV properties and atrial fibrosis on arrhythmia inducibility, maintenance mechanisms and the outcome of PVI, based | 3,069,418 | 44120062 | 0 | 16 |
on population or individual patient data. PV properties affect arrhythmia susceptibility from ectopic beats; short PV APD increased PV PS density ratio is higher for successful PVI cases. Simulation outcomes after PVI were classified as termination (no activity), macroreentry (a large reentry circuit around the LA/PV junctions), or AF sustained by LA rotors (drivers in the LA body). Box plots show PV PS density ratio pre-PVI. Termination PV PS density ratio is significantly higher than for LA rotors (p<0.001), and macroreentry PV PS density ratio is significantly higher than for LA rotors (p = 0.01). https://doi.org/10.1371/journal.pcbi.1006166.g006 Pulmonary vein electrophysiology, fibrosis and arrhythmia arrhythmia susceptibility, while longer PV APD was found to be protective. Arrhythmia inducibility increased with slower CV at the LA/PV junction, but not for cases with homogeneous CV changes or slower CV at the distal PV. The effectiveness of PVI is usually attributed to PV ectopy, but our study demonstrates that the PVs affect reentry in other ways and this may, in part, also account for success or failure of PVI. Both PV properties and fibrosis distribution affect arrhythmia dynamics, which varies from meandering rotors to PV reentry (in cases with baseline or long APD), and then to stable rotors at regions of high fibrosis density. PS density in the PV region was high for cases with PV fibrosis. The measurement of fibrosis and PV properties may indicate patient specific susceptibility to AF initiation and maintenance. PV PS density before PVI was higher in cases in which AF terminated or converted to a macroreentry; | 3,069,419 | 44120062 | 0 | 16 |
thus, high PV PS density may indicate likelihood of AF termination by PVI alone. PV APD PV repolarisation is heterogeneous in the PVs [23], and exhibits distinct properties in AF patients, with Rostock et al. reporting a greater decrease in PV ERP than LA ERP in patients with AF, termed AF begets AF in the PVs [21]. Jais et al. found that PV ERP is greater than LA ERP in AF patients, but this gradient is reversed in AF patients [3]. ERP measured at the distal PV is shorter than at the LA/PV junction during AF [5,22]. Motivated by these clinical and experimental studies, we modelled a decrease in PV APD, which was applied either homogeneously, or as a gradient of decreasing APD along the length of the PV, with the shortest APD at the distal PV rim. An initial decrease in APD increased inducibility (Table 1), which agrees with clinical findings of increased inducibility for AF patients. Applying this change following a gradient, as observed in previous studies, led to an increased inducibility compared to a homogeneous change in APD. Similar to Calvo et al. [34] we found that rotor location depends on PV APD (Fig 2). Thus PV APD affects PVI outcome in two ways; on the one hand, decreasing APD increases inducibility, emphasising the importance of PVI in the case of ectopic beats; on the other hand, PV PS density decreases for cases with short PV APD, and PVI was less likely to terminate AF. PV CV Multiple studies have measured conduction slowing | 3,069,420 | 44120062 | 0 | 16 |
in the PVs [3,5,[21][22][23][24]. We modelled changes in tissue conductivity either homogeneously, or as a function of distance along the PV. Simply decreasing conductivity and thus decreasing CV, decreased inducibility (Table 2). Kumagai et al. reported that conduction delay was longer for the distal to ostial direction [22]. We found that modifying conductivity following a gradient, with CV decreasing towards the LA/PV junction, resulted in an increase in inducibility in the model. This agrees with the clinical observations of Pascale et al. [1]. This suggests that PVI should be performed in cases in which CV decreases towards the LA/PV junction as these cases have high inducibility. Changes in CV may also be due to other factors, including gap junction remodelling, modified sodium conductance or changes in fiber direction [5,29]. PV fiber direction A variety of PV fiber patterns have been described in the literature and there is variability between patients. Interestingly, all of the PV fiber directions considered in our study showed an increased inducibility compared to the baseline model. Verheule et al. [29] documented circumferential strands that spiral around the lumen of the veins, motivating the arrangements for cases 1 and 4 in our study; Aslanidi et al. [15] reported that fibers run in a spiralling arrangement (case 2); Ho et al. [30] measured mainly circular or spiral bundles, with longitudinal bundles (cases 3 and 5); Hocini et al. [5] reported longitudinal fibers at the distal PV, with circumferential and a mixed chaotic fiber direction at the PV ostium (case 6). Using current imaging technologies, | 3,069,421 | 44120062 | 0 | 16 |
PV fiber direction cannot be reliably measured in vivo. In our study, fiber direction at the PV ostium was found to be more important than at the distal PV; the greatest inducibility was for cases with circular fibers at the ostium on both endocardial and epicardial surfaces, independent of fiber direction at the distal PV end. Similar to modelling studies by both Coleman [35] and Aslanidi [15], inducibility increased due to conduction block near the PVs. PV anatomy PVs may be larger in AF patients compared to controls [4,36], and this difference may vary between veins; Lin et al. found dilatation of the superior PVs in patients with focal AF originating from the PVs, but no difference in the dimensions of inferior PVs compared to control or to patients with focal AF from the superior vena cava or crista terminalis [37]. We found that inducibility increased with PV area for the LSPV, LIPV and RIPV, but not for the RSPV (see Fig 5). In addition, PV PS density ratio increased with total PV area, suggesting that PVI alone is more likely to be a successful treatment strategy in the case of larger veins. However, Den Uijl et al. found no relation between PV dimensions and the outcome of PVI [38]. Rotors were commonly found in areas of high surface curvature, including the LA/PV junction and left atrial appendage ostia, which agrees with findings of Tzortzis et al. [39]. However, there were differences in PS density between geometries, with varying importance of the LA/PV junction (Fig 5), | 3,069,422 | 44120062 | 0 | 16 |
demonstrating the importance of modelling the geometry of an individual patient. Atrial fibrosis Myocardial tissue within the PVs is significantly fibrotic, which may lead to slow conduction and reentry [5,30,40]. More fibrosis is found in the distal PV, with increased connective tissue deposition between myocardial cells [41]. We modelled interstitial PV fibrosis with increasing density distally, and found that the inclusion of PV fibrosis increased PS density in the PV region of the model due to increased reentry around the LA/PV junction and wave break in the areas of fibrosis. This, together with the results in Fig 6, suggests that PVI alone is more likely to be a successful in cases of high PV fibrosis. There are multiple methodologies for modelling atrial fibrosis [25,42,43], and the choice of method may affect this localisation. Population based distributions of atrial fibrosis were modelled for paroxysmal and persistent patients, together with varied PV properties. The presence of LA/PV reentry depends on both PV properties and the presence of fibrosis; reentry is seen at the LA/PV junction for cases with baseline PV APD, but not for short PV APD, and stabilised to areas of high fibrosis in persistent AF, for which LA/PV reentry no longer occurred. This suggests that rotor location depends on both fibrosis and PV properties. This finding may explain the clinical findings of Lim et al. in which drivers are primarily located in the PV region in early AF, but AF complexity increased with increased AF duration, and drivers are also located at sites away from the | 3,069,423 | 44120062 | 0 | 16 |
PVs [6]. During early AF, PV properties may be more important, while with increasing AF duration, there is increased atrial fibrosis in the atrial body that affects driver location. This suggests that in cases with increased atrial fibrosis in the atrial body, ablation in addition to PVI is likely to be required. Simulations of models with patient-specific atrial fibrosis together with varied PV properties performed in this study offer a proof of concept for using this approach in future studies. The level of atrial fibrosis and PV properties that gave the best fit of the model PS density to the clinical PS density varied between patients. Measurement of PV ERP and conduction properties using a lasso catheter before PVI could be used to tune the model properties, together with LGE-MRI or an electro-anatomic voltage map. Ablation strategies It is difficult to predict whether PVI alone is likely to be a successful treatment strategy for a patient with persistent AF [44]. This will depend on both the susceptibility to AF from ectopic beats, together with electrical driver location, and electrical size. Our study describes multiple factors that affect the susceptibility to AF from ectopic beats. Measurement of PV APD, PV CV and PV size will allow prediction of the susceptibility to AF from ectopic beats. Arrhythmia susceptibility increased in cases with short PV APD, slower CV at the LA/PV junction and larger veins, suggesting the importance of PVI in these cases. The likelihood that PVI terminates AF was also found to depend on driver location, assessed using | 3,069,424 | 44120062 | 0 | 16 |
PS density. Our simulation studies suggest that high PV PS density indicates likelihood of PVI success. Thus either measuring this clinically using non-invasive ECGi recordings, or running patient-specific simulations to estimate this value may suggest whether ablation in addition to PVI should be performed. In a recent clinical study, Navara et al. observed AF termination during ablation near the PVs, before complete isolation, in cases where rotational and focal activity were identified close to these ablation sites [45]. These data may support the PV PS density metric suggested in our study. Our simulations show that PV PS density depends on PV APD, the degree of PV fibrosis and to a lesser extent on PV fiber direction. To the best of the authors' knowledge, there are no previous studies on the relationship between fibrosis in the PVs, or PV fiber direction, and the success rate of PVI. Measuring atrial electrogram properties, including AF cycle length, before and after ablation may indicate changes in local tissue refractoriness [46]. PV APD can be estimated clinically by pacing to find the PV ERP; and PV fibrosis may be estimated using LGE-MRI, although this is challenging, as the tissue is thin. PV fiber direction data is not currently available clinically, which limits the predictive ability of the model. Areas of high PV PS density on ECGi need to be carefully interpreted in terms of expected accuracy of the inverse solution on the PVs and the incidence of false phase singularity detection [47]. In addition, multiple mechanisms may underlie areas of high | 3,069,425 | 44120062 | 0 | 16 |
PS density. Importantly, not all PSs sustain and drive AF, and represent suitable targets for ablation. Limitations Limitations to this study include that PV branching structures were not considered since PVs were trimmed at the highest level that results in a single PV rim at each distal PV. Mansour et al. found that just 56% of patients had four PVs with separate ostia [48], 29% of patients had an additional PV, and 17% a common PV trunk. Although some studies have reported differences in ERP between the endocardium and epicardium [23], we modelled the endocardium and epicardium ERP identically. Furthermore, we modelled changes in APD by modifying I K1 only and did not consider other ionic conductances or methods for parametrisation [20,49,50]. We used a bilayer model, rather than a volumetric model incorporating thickness, which will affect rotor drift [51]. In addition, we did not model changes in connexins [29] or cell morphology [52]. Furthermore, we modelled 2 seconds of activity following PVI in the model, where these ablation lesions were applied simultaneously rather than sequentially as in the clinic, and we did not model long term AF recurrence. Finally, we did not consider the case of AF sustained by focal beats; we either considered the inducibility due to PV ectopics, or maintenance due to reentry. Conclusion Our computational modelling study suggests that measurement of fibrosis and PV properties may indicate patient specific susceptibility to AF initiation and maintenance. In addition, high PV PS density pre-ablation indicates likelihood of PVI success in our simulations, motivating a | 3,069,426 | 44120062 | 0 | 16 |
retrospective clinical study into this metric. | 3,069,427 | 44120062 | 0 | 16 |
Understanding Tourists’ Preference for Mammal Species in Private Protected Areas: Is There a Case for Extralimital Species for Ecotourism? Private Protected Areas (PPAs) often use wildlife-based ecotourism as their primary means of generating business. Achieving tourist satisfaction has become a strong driving goal in the management of many PPAs, often at the expense of biodiversity. Many extralimitral species, those which historically did not occur in an area, are stocked in PPAs with the intention of increasing ecotourism attractions. Even though the ecological and economic costs of stocking these species are high, the social benefits are not understood and little information exists globally on the ecotourism role of extralimital species. This study assessed the value of stocking extralimital species using questionnaire-based surveys and observing tourists in Shamwari Private Game Reserve in the Eastern Cape Province of South Africa. No difference was found between indigenous and extralimital species with regards to the tourists’ weighted scoring system, average amount tourists were willing to pay, total viewing time, average viewing time or the likelihood of stopping to view species when encountered on game drives. During game drives a strong preference was found for the elephant (Loxodonta africana), lion (Panthera leo), leopard (Panthera pardus) and cheetah (Acynonix jubatus). With the exception of the cheetah, these species are all members of the “big five” and are indigenous. Species availability and visibility, however, may influence the amount of time tourists spend at an animal sighting. Our analysis suggests that certain extralimital species (typically larger and charismatic species) contribute to tourist satisfaction, while particularly | 3,069,428 | 14652077 | 0 | 16 |
the smaller extralimital species add little to the game viewing experience, but add to the costs and risks of the PPAs. We recommend that extralimital species introductions for ecotourism purposes should be approached with caution with regards to the risks to the sustainability of PPAs. Introduction Protected Areas (PAs) have been established with the principle goals of conserving biodiversity [1].The conservation of biodiversity therefore relies on the sustainability of PAs which includes achieving financial security.Ecotourism has emerged as a major means of self-financing PAs [2], particularly in Private Protected Areas (PPAs) that often use wildlife-based ecotourism as their primary means of generating business [3].Achieving tourist satisfaction has therefore become a strong driving goal in the management of many PAs [4], often at the expense of biodiversity objectives. PPAs are largely driven to achieve successful game-viewing sightings [5].In South Africa high numbers of charismatic species are stocked in PPAs to enhance the wildlife experience [6].Many extralimital species, those which historically do not occur in an area, have been introduced into PPAs to increase the number of species available for viewing [7], [8], under the assumption that this would appeal to tourists [9]. Even though the social benefits are not well understood, the ecological and economic costs of introducing extralimital species have been documented [7], [10].In 2005, surveys indicated that the reintroduction of species into the Eastern Cape Province of South Africa cost between $97,500 and $1.8 million per PPA [8].These non-indigenous species can lead to hybridization, degradation of habitat, low survival rates and displacement of indigenous species | 3,069,429 | 14652077 | 0 | 16 |
[10], [7].The introduction of extralimital species diminishes biodiversity [11], [8], and may therefore threaten the ecological and economic sustainability of PPAs.This is of concern, especially in developing countries such as South Africa where the tourism economy is largely reliant on its biodiversity [12]. Ecotourism operators, however, are reluctant to remove these extralimital species, as they assume that this will have detrimental impact on ecotourism [10].Management decisions, however, are typically based on anecdotal sources and not empirical evidence [13].It is thus important to evaluate the role of extralimital species in PPAs to understand the implications of stocking these species with regards to ecotourism and conservation. It has been suggested that it is public preference that motivates the stocking of extralimital species [6], [10].We therefore hypothesize that tourists having a preference for viewing these species.Previous studies have investigated tourist preferences of wildlife [18], [19], [20].However, there is a general lack of data about tourists' preferences in terms of indigenous versus extralimital species.In this study we investigated the role that extralimital species play in ecotourism by analysing the value tourists place on viewing different mammal species.Understanding which species tourists focus on will determine whether preferences differ between species.The value placed on biodiversity in relation to human well-being is difficult to weigh [14], as biodiversity is not measurable through market value [15].The value can thus be classified as a 'use' value [16] which is associated with actual use, such as enjoyment from visiting a reserve [17]. We used ecotourism activities to measure this use value, which was expressed as the | 3,069,430 | 14652077 | 0 | 16 |
time spent by tourists viewing different species.If the hypothesis of the value of extralimital species is supported, we predict that more time would be spent viewing extralimital species than indigenous species, relative to species availability. Study Area and Species This study was conducted in Shamwari Private Game Reserve (between 33u209S; 26u019E and 33u329S; 26u109E) in the Eastern Cape, South Africa.Shamwari is approximately 25,000 ha in size and includes 3 of the 9 biomes found in South Africa [21] (figure 1).This reserve was used as a case study as it is recognised as an upmarket tourist destination [22].Many national and international tourists frequent Shamwari, with an average stay of 2-3 nights [22].Game viewing takes place through tourists being taken on an open game-viewing vehicle accompanied by an experienced guide, who also serves as the driver. Data Collection Questionnaires were used to measure the tourists' stated preference for mammal species stocked at Shamwari.The questionnaires were distributed in two different ways.Firstly, an online survey questionnaire was posted onto the Shamwari website (www.shamwari.com).This survey was posted in October 2011 and ran to January 2012.The same questionnaire was printed and given to the Shamwari guests upon arrival from October 2011 to January 2012.The first part of the questionnaire dealt with the socio-demographic information of the respondent, including country of origin, gender, age, highest educational qualification and occupation.The questionnaire then focused on the respondent's view of Shamwari, how they heard about the reserve, whether they had previously visited other reserves in South Africa, and motivations for choosing Shamwari.A list of the mammal | 3,069,431 | 14652077 | 0 | 16 |
species found in Shamwari was presented, and the respondent was asked to rank their top five species in order of preference from 1 (most preferred) to 5 (least preferred).A weighted average was derived from these data [24] using the following equation: Where a = 1 (most preferred species), and e = 5 (least preferred species).In the questionnaires the respondents were provided with a list of features suggesting possible motivations that attracted the respondent to their preferred species.The respondent indicated the importance of each feature using a ranking system where 1 = most important and 5 = not important at all.The respondent was asked whether, if the preferred animal was not available in Shamwari, but available at a reserve nearby, would they still visit Shamwari or would they have visited another reserve (see appendix). A willingness to pay approach (WTP), a contingent evaluation method [15], [16], was used to determine the value that tourists place on different large mammal species.This method is effective in making decisions and estimating monetary values for goods and services which normally don't have prices or where no market for them exists [16], [25], [26].The respondents were provided with a list of values and asked to select the amount they were willing to pay to see their preferred or favourite animal.A revealed preference method was not used, as we did not have the necessary data for that.In the opening statement of this question, respondents were informed that the study was carried out for academic purposes only.This was done to avoid possible bias, which | 3,069,432 | 14652077 | 0 | 16 |
would occur if the respondents believed their answers would influence pricing of the reserve.However, announcing a priori that the survey was an academic exercise may create 'hypothetical biases', an overestimation of WTP in contingent markets compared to actual payments [27], [28].The actual WTP values were therefore not analysed, but merely ranked to compare species.The questionnaire was pre-tested among tourists to ensure it was plausible and understandable.To test for significant differences in tourists' WTP values between indigenous and extralimital species, a two-tailed t-test was used [29].All statistical analyses were performed in Statistica 10 (Statsoft, Inc., USA), where significance was determined at the level p,0.05. Incorporating another scientific discipline into this study such as human ecology enables a better understanding of the motives behind the WTP values [30].We therefore conducted observational studies of tourists on game drives to analyse tourists' viewing preferences of mammal species to determine a relative measure of interest between indigenous and extralimital species.Observation studies give an accurate reflection of the tourist's experience in the ecotourism setting [31]. Field observations took place over a period of three months (October to December 2010) when tourists were accompanied on their morning and evening game drives.For all game drives the observer sat next to the guide.All questions directed at the guide as well as conversations among the tourists could be heard from this position.A Trimble JUNO TM SB handheld GIS receiver (PDA) was used to record the data at every viewing stop using the CyberTracker software (www.cybertracker.org).An animal viewing was only classified as such when the vehicle reached | 3,069,433 | 14652077 | 0 | 16 |
a full stop.This occurred to give tourists time to observe and photograph the animal.All species that were not stopped for within a viewing distance of 0.5 km were also noted, to determine the frequency of stopping in relation to the availability of species.The GPS coordinates at every animal sighting were recorded using the PDA, while a stop watch was used to record the duration of the stop.In order to avoid guide preference affecting tourist viewing, the guide was instructed to follow cues from the tourists as to how much time should be spent at each animal viewing event. The value that tourists place on different species was estimated as the duration of viewing time and frequency that each species was stopped for.The total time spent viewing indigenous and extralimital species were calculated, and a two-tailed t-test was used to test for a significant difference.The proportion of stopping to view a species when it was sighted, was classified as the likelihood of stopping to view a species.The relationship between the likelihood of stopping to view a species and the average time spent viewing the species was assessed using a linear model where likelihood was the dependent variable and average time spent viewing the independent variable.A general linear model was used to determine whether a difference was found in the likelihood of stopping to view indigenous versus extralimital species. The proportion of time spent viewing the animal indicated the level of interest in a particular species, and the proportion of viewing time in relation to time stopped for | 3,069,434 | 14652077 | 0 | 16 |
all species indicated interest in relation to other species.To eliminate the effect of diminishing returns from repetitive game drives, tourists were only accompanied on their first game drive when species were encountered for the first time on Shamwari.The number of times each species was encountered on all game drives represented the availability of species and the frequency of stopping at each encounter to view the animal was the usage of the species.Tourist preference was determined as the difference between the ranks of usage and availability to arrange the species in order of importance, known as the tourist importance rank [32].A Wilcoxon Matched Pairs Test was used to test for significant differences in the tourist importance rank between indigenous and extralimital species. The manager of Shamwari Game Reserve gave permission to conduct research on the reserve.The Nelson Mandela Metropolitan University Research Ethics Committee: Human issued a written waiver of the need of ethics approval for this research, as it fell within the stipulated ethical principles and guidelines for the protection of human subjects [33]. Results The response rate of the questionnaires was 45% (90 questionnaires returned).The majority of the respondents (88%) were international visitors, mostly from the United Kingdom.The respondents were mostly executive or managerial (31%), and 19% were retired.Almost 80% of the visitors to Shamwari had a tertiary qualification.Forty-two percent of the respondents had previously visited other reserves in South Africa, mostly frequenting National Parks.Thirty-five percent of these respondents had previously visited private reserves in South Africa, dominated by the international respondents (43%), in comparison to | 3,069,435 | 14652077 | 0 | 16 |
18% of South Africans.Forty percent of the respondents said that the most important criterion in selecting Shamwari was the variety of wildlife present, and that the availability of the ''big five'' species played an important role in their selection.More than half of the respondents (60%, n = 52) indicated that they would choose to visit a different reserve if their preferred species were not stocked at Shamwari.Of these respondents, few listed extralimital species such as the cheetah (8%, n = 7) or the giraffe (3%, n = 3) as their preferred animals to see. According to the weighted scoring system, the lion was ranked by the respondents as the most preferred large mammal, followed by leopard, elephant, black wildebeest and the cheetah (table 1).The black wildebeest and cheetah were the only extralimital species ranked within the top five preferred large mammal species, but no significant difference was found in the weighted scores between indigenous and extralimital species (t = 2.16, p = 0.30, df = 13) (table 1). No significant difference was found in the average amount tourists were willing to pay to view indigenous versus extralimital species (t = 1.07, p = 0.31, df = 12).The largest monetary value was attached to the big cats, firstly leopard, followed by cheetah and lion. During 243 hours of game drives (n = 80, 14,597 minutes), 80% of the time was spent driving and 20% of the time was spent viewing mammals.Of the viewing time 19% was spent observing elephants, followed by 16% on lions, and declining to | 3,069,436 | 14652077 | 0 | 16 |
0.1% for species such as caracal (Caracal caracal), mountain reedbuck (Redunca fulvorufula) and serval (Felis serval) (table 2, figure 2).No significant difference (t = 20.33,p = 0.74, df = 27) was found in total time spent viewing indigenous versus extralimital species.However the majority (61%) of the time was spent viewing indigenous species, where on average 114.9 min (6 SD 192.4) was spent viewing each species, compared to 39% that was spent viewing extralimital species (mean = 138.8min 6 SD 149.7) (figure 2). No significant difference was found between the average time spent viewing indigenous versus extralimital species (t = 0.58, p = 0.34, df = 27).However, when the total averages of each species were calculated, it was evident that more time (82.3 min) was spent viewing indigenous compared to extralimital species (33.6 min).Six indigenous species (lion, leopard, elephant, buffalo, black rhino and hippopotamus) and three extralimital species (cheetah, white rhino and giraffe) were viewed for longer than the average time calculated across all species (figure 3).For the members of the ''big five'' the likelihood of stopping to view these species was above 70% (figure 3).A significant relationship was found between the likelihood of stopping to view an animal and the average time spent viewing (F 1, 25 = 9.83, p,0.05,R 2 = 0.28) (figure 2).Nine species were always stopped for when they were sighted (figure 3).All of these, with the exception of the cheetah, are indigenous to Shamwari (figure 3).However, no significant relationship was found between the likelihood of stopping to view a species and whether | 3,069,437 | 14652077 | 0 | 16 |
the species was indigenous or not (Z = 1.45, p = 0.15, df = 25). Based on viewing-availability proportions, the five most important mammal species in terms of the Johnson's method [32] were the serval, nyala, mountain reedbuck and black-backed jackal (table 3).A significant difference was found in the ranking between indigenous and extralimital species (Z = 2.80, p,0.05, df = 22), where the proportion of viewing indigenous species in terms of availability was higher than extralimital species (table 3). Discussion We present a case study where we combine stated preference techniques with observational data to determine the ecotourism value of indigenous and extralimital species in PPAs.No significant difference was found between indigenous and extralimital species in the weighted scoring system, average amount tourists were WTP, viewing time or likelihood of stopping to view mammal species.This strongly suggests tourists do not have a specific preference for extralimital species in PPAs. Of the 10 extralimital species stocked at Shamwari, the cheetah was the only extralimital species that scored highly as one of the top animals to see in both the questionnaire and in the time spent viewing.Other studies also highlighted tourists' preference for cheetah [19], [20].This charismatic species is often ranked with the leopard, lion, rhino and elephant as the most popular species among tourists [18]. During game drives, tourists were mostly attracted to elephants, followed by the large carnivores, i.e. lion, leopard and cheetah.With the exception of the cheetah, these species are all members of the ''big five'' and are indigenous to Shamwari.Lion, leopard, cheetah and | 3,069,438 | 14652077 | 0 | 16 |
elephant also scored the highest in terms of the average amount of time spent at every animal viewing.This concurs with previous studies, where these charismatic species were highly ranked as tourist attractions [30], [20].In the Addo Elephant National Park (AENP), the majority of self-guided tourists listed elephants as an important reason for visiting the park [34].In Tanzania, the lions attracted the most vehicles during a game drive, and 29% of viewing time was spent with these large carnivores [19]. The type of species encountered on a game drive may influence the amount of time spent at the sighting, however there are other variables that may influence tourist preferences.During game drives, the rare species or species that were less frequently encountered such as the serval, buffalo and nyala played an important role in attracting tourists' attention.This is in accordance with previous studies where rare species were found to be more valuable than common species [35]. There is a difference between tourists' stated preferences in the questionnaires and their observed preferences as measured on game drives.In particular, a higher value was placed on viewing the indigenous black rhino in questionnaires, whereas on game drives, a larger proportion of time was devoted to viewing the white rhino.White rhino are usually found in open habitats [36], increasing their visibility, as opposed to the shyer black rhino.Species availability and visibility may thereby influence the time allocated to different species during game viewing.The same was found with giraffe, which were frequently encountered during game drives and a large amount of time was | 3,069,439 | 14652077 | 0 | 16 |
spent at giraffe sightings, even though this species did not score highly as a popular species to see in the questionnaires.When located, however, a larger proportion of time was spent at black rhino sightings, compared to white rhino or giraffe, even though they were encountered less frequently during game drives. We therefore suggest that species type is not the only determining factor, but there may be other variables that influence tourists' preferences of large mammal species.The marketing of a reserve plays an important role in raising tourist expectations [37], [20].Tourists' preferences may also be influenced by their current knowledge of a species [15], [38].Studies have found that visitors better appreciate the reserve they are visiting when they are taught about the natural and cultural values of the PA [39].This suggests bringing more awareness to the indigenous species and educating tourists during game drives may increase tourist satisfaction in PPAs. Our findings do not unequivocally support or reject the hypothesis that tourists having a preference for viewing extralimital species, and we can conclude that some extralimital species have value for ecotourism, but others not.Revealingly, among the herbivores, it is the larger species (e.g.giraffe, white rhino) that add value, and the smaller species (e.g.impala, nyala) are of lesser interest.This is important, as these larger species will occur at lower densities by virtue of their body size, and are also easier to manage.This is because they are easier to locate to monitor and also remove if needed.In contrast, the small herbivores, and hence less interesting species, such as impala | 3,069,440 | 14652077 | 0 | 16 |
and nyala may occur at relatively higher densities, and are more difficult to manage, as they are less easy to locate for monitoring and management actions such as removal.Thus, there is some alignment between the desirability of introducing alien herbivores and the risks they present in terms of management of their impacts.This issue needs to be further explored. Without question, PAs are essential to the conservation of biodiversity [39] and PPAs play an important role in contributing to the PA estate.Stocking PPAs with high numbers of extralimital species however is not required to achieve tourist satisfaction.Certain extralimital species may contribute to the game viewing experience, however tourists do not have a specific preference for these species per se.Many other contributing factors play an important role in achieving tourist satisfaction.We thereby strongly recommend that management of PPAs should focus more on the principle goal of conserving biodiversity and rethink their current extralimital stocking rates. Figure 1 . Figure 1.The location of Shamwari Private Game Reserve, in the Eastern Cape Province of South Africa, and the different biome types and lodges.doi:10.1371/journal.pone.0088192.g001 Figure 2 . Figure 2. Proportion of total time spent viewing indigenous (black bars) and extralimital species (white bars) on game drives in Shamwari Private Game Reserve.doi:10.1371/journal.pone.0088192.g002 Figure 3 . Figure 3. Relationship between the likelihood of stopping to view a species and average time spent viewing indigenous species on game drives at Shamwari Private Game Reserve.Average of all species indicated by dashed horizontal (time) and vertical (likelihood) lines.doi:10.1371/journal.pone.0088192.g003 Table 1 . [24]most preferred large mammal species | 3,069,441 | 14652077 | 0 | 16 |
to see according to questionnaires issued to tourists at Shamwari Private Game Reserve, ranked according to weighted scores[24]. Table 2 . Total number of stops and total viewing time spent on each large mammal species in Shamwari Private Game Reserve, ranked according to viewing time. *Extralimital species, species which historically did not occur there and have been introduced to Shamwari.doi:10.1371/journal.pone.0088192.t002 Table 3 . [32]tive importance rank of species based on proportions of viewing and the availability of large mammal species in Shamwari Private Game Reserve, based on the Johnson Method[32].Extralimital species, species which historically did not occur on Shamwari and have been introduced there.doi:10.1371/journal.pone.0088192.t003 * | 3,069,442 | 14652077 | 0 | 16 |
Occurrence and Characteristics of the Extended-spectrum Beta-lactamase- producing Enterobacterale in a Hospital Setting A total of 239 non-repeated clinical isolates of the Enterobacterale family, including 202 (84.5%) Escherichia coli and Klebsiella pneumoniae 25 (12.3%) were collected. Identification and susceptibility tests were carried out on 60 (25.9%) ESBL phenotypes using biomérieux VITEK 2 compact system. Isolates showing ESBL positivity by the phenotypic method were all screened for blaTEM, blaCTX-M and blaSHV genes by PCR. INTRODUCTION Extended-Spectrum Beta-Lactamases (ESBLs) are rapidly evolving plasmid-mediated enzymes produced by certain bacteria that can hydrolyze extended-spectrum cephalosporin, thus making them effective against beta-lactam antibiotics [1,2]. ESBLs are found in gram-negative bacteria, especially in and the bla CTX-M gene that preferentially hydrolyze cefotaxime [4]. Other types of ESBLs genes include SHV, which is responsible for plasmid-mediated ampicillin resistance. The majority of the ESBLs are derivatives of TEM or SHV enzymes, which are most often found in the enterobacteria E. coli and K. pneumonia [5]. Because of the global spread of CTX-M enzyme, ESBL are the cause of increasing numbers of both nosocomial and community infections [6]. Rates of ESBL production among Enterobacterale range between 6-38.5% in the Kingdom of Saudi Arabia [7,8]. ESBL producing Enterobacterale in Saudi Arabia is dominated by E. coli where both hospital and community-based studies have shown that more than 70% harbored the gene blaCTM-X [9]. Detection of these genes in ESBL-producing bacteria by the most sensitive molecular methods can give valuable information about its epidemiology and help in the reasonable treatment of infections [10]. In Saudi Arabia, few | 3,069,443 | 221508247 | 0 | 16 |
studies have been performed to determine the prevalence of ESBL-producing Enterobacterale and little is known about their molecular characteristics. However, the few studies conducted on ESBL phenotypes isolated from clinical samples previously indicated a predominance of bla CTX -M-like genes [8,9,11,12]. Therefore, the aims of this study were to determine the prevalence of ESBL-producing Enterobacterale in a hospital setting from various clinical specimens taken from patients diagnosed with various infections and to detect the frequency of TEM, SHV, and CTX-M genes in an ever-changing prevalence and resistant pattern of ESBL-producing enterobacteria. Gram-negative (GN) cards and antibiotic susceptibility cards (AST) were used for the identification and the antibiotic sensitivity profile of the isolates, respectively. Antimicrobial susceptibility testing was performed using software version 06.01 and the AST-GN291 and AST-XN06 cards, according to the manufacturer's instructions. Susceptibility cards used included aminoglycosides (amikacin, gentamicin); aminopenicillins (ampicillin); cephalosporin (cefepime, ceftazidime, ceftriaxone, cefuroxime); carbapenems (imipenem); amoxicillin/clavulanate (augmentin); trimethoprim/sulfame-thoxazole (Bactrim); fluoroquinolone (ciprofloxacin); and piperacillintazobactam. Identification and susceptibility cards were inoculated and interpreted according to the manufacturer's instructions. The quality control strains tested with each run included the ESBL-producing strains E. coli ATCC 25922 and K. pneumoniae ATCC 700603 for the antimicrobial identification and susceptibility testing. MATERIALS AND METHODS Out of 239 non-repeated isolates, 62 were ESBL producers, which were further tested for the detection of ESBL genes in the PSMCHS Molecular Biology Laboratory. DNA was extracted using the method previously described [13]. The PCR mixture was made using QIAGEN Fast Cycling PCR Kit and the primers, which were designed and procured by the | 3,069,444 | 221508247 | 0 | 16 |
Eurofins Company (Eurofins Advantar Inc, San Diego USA). PCR was performed using CFX96 Touch™ Real-Time PCR Detection System (Bio-Rad Laboratories, Inc. USA). SHV, TEM, and CTX-M primers were used on all of the 62 ESBLproducing Enterobacterale isolates ( Table 1). The following PCR protocol was used for all primers as previously described [11]: initial denaturation (hot start) at 95°C for 5 minutes, followed by 30 cycles of denaturation, annealing, and extension at 92°C, 61°C, and 72°C, respectively, for 30 seconds each. The mixture was then incubated for final elongation at 72°C for 5 minutes. PCR products were then separated on 2% agarose electrophoresis gel and visualized using Syngene U Genius Gel Imaging System (Cambridge Scientific, Watertown, Massachusetts) for the presence of 403 bp, 293 bp, and 569 bp bands representing the TEM, SHV, and CTX-M primers, respectively. DISCUSSION Enterobacterale are among the most important causes of nosocomial and community-acquired infections. Infections caused by these microorganisms are mainly treated with betalactams and fluoroquinolones [6]. However, resistance to these compounds is being reported more frequently [14]. The current findings have detected a high occurrence of ESBLs (25.9%) among the Enterobacterale members isolated from various specimens. Previous studies have reported various ranges of ESBL prevalence of 10% to 36% [8, 15 -18]. ESBLproducing Enterobacterale prevalence varies greatly and has increased over time worldwide. The pooled estimated prevalence was the highest in the West Pacific (46%), followed by southeast Asia and Africa (22%), the Eastern Mediterranean (15%) and Northern Europe (4%) [19]. Factors associated with a higher risk of colonization | 3,069,445 | 221508247 | 0 | 16 |
were antibiotic use and international travel in the previous year [19]. In the present study, ESBL-producing Enterobacterale displayed an increasing rate of resistance for aminopenicillins (ampicillin), followed by piperacillin-tazobactam, cephalosporin groups (ceftriaxone, ceftazidime, cefepime, ciprofloxacin), and fluoroquinolone (ciprofloxacin). The study has shown that both E. coli and K. pneumoniae have developed a high rate of resistance to ampicillin, piperacillin-tazobactam, amoxicillin/clavulanic acid, the cephalosporin groups, ceftriaxone, ceftazidime, and fluoroquinolone (ciprofloxacin) (42.7%). Both the organisms showed a higher susceptibility to the carbapenems (imipenem) and the aminoglycosides (Amikacin). This resistance pattern has been observed in many other studies [8,9,12,15,17,18] and might probably be attributed to the extensive use of these antibiotics. Our study also included the molecular aspect of resistance through the identification of genes carried by these resistant isolates. The ESBL types detected in these isolates belonged to the CTX-M and TEM, while the SHV type was not detected alone in any of the tested isolates. The CTX-M genes are the most prevalent (35.5%) among the isolates of this study. This finding agrees with other studies conducted elsewhere in the Middle East and many parts of the world [7,20]. Among the different ESBL families, CTX-M has become the most prevalent worldwide, both in nosocomial and community-acquired infections [20]. The TEM class alone was the next frequent class of ESBLs (11.3%), but a higher percentage of harboring TEM also had CTX genes along with it (12.9%). Isolates were not found to harbor the SHV genes alone, whereas 12.9% had CTX-M also. Many different studies show that the distribution of | 3,069,446 | 221508247 | 0 | 16 |
ESBL genes is diverse. Some studies have shown a predominance of the TEM gene with less SHV and CTX-M [21]. In one study in Saudi Arabia, characterization of the resistance genes revealed the dominant presence of SHV, followed by TEM and CTX-M [22]. Other findings agree with ours, which indicated a predominance of CTX-M [9,23]. Earlier reports mentioned that the most prevalent type of ESBL genes is SHV, TEM, and CTX-M. During the past decade, TEM and SHV types were reported to be the most common types of b-lactamase genes, but recently, the CTX-M type has spread worldwide compared to TEM and SHV genotypes [24]. The most important finding in our study was the coexistence of different ESBLs. A number of the isolates had multiple genes, namely TEM and CTX-M; TEM, SHV, and CTX; and SHV and CTX-M in their genome suggesting the carriage of multiple plasmids. The co-existence of all three bla genes was observed in 32.5% of the ESBL isolates. Several studies reported the co-existence of various ESBL genes within the same isolates [5,24,31]. The co-existence of all the three bla genes observed in our study was similar to that previously described in Iran [21]. The findings in this study document the threat of ESBL among Enterobacterale especially the CTX-M class in our geographical region with the occurrence of these strains as etiological agents of infection in the hospital setting. The frequency of antibiotic usage and even the dosages and period of administration vary greatly from one country to another. This has led to | 3,069,447 | 221508247 | 0 | 16 |
large differentials in the emergence of resistant patterns. Therefore, it is essential to study and report trends in antimicrobial resistance on a regular basis. Our findings represent a preliminary study for follow-up work, establishing novel features concerning the potential of multiple plasmids. ETHICS APPROVAL AND CONSENT TO PARTICIPATE The ethical committee of Prince Sultan Military College of Health Science approved this study. HUMAN AND ANIMAL RIGHTS Not applicable. CONSENT FOR PUBLICATION Not applicable. AVAILABILITY OF DATA AND MATERIALS The authors confirm that the data supporting the findings of this research are available within the article. FUNDING None. CONFLICT OF INTEREST The authors declare no conflict of interest, financial or otherwise. | 3,069,448 | 221508247 | 0 | 16 |
Heterologous production of fungal natural products: Reconstitution of biosynthetic gene clusters in model host Aspergillus oryzae While exploring phytotoxic metabolites from phytopathogenic fungi in the 1970s, we became interested in biosynthetic enzymes that catalyze Diels–Alder reactions involving biosynthesis of several phytotoxins that we isolated. Target enzymes were successfully characterized, and this triggered the identification of various Diels–Alderases in a recent decade. Through our Diels–Alderase project in 1990s, we recognized a highly efficient expression system of various biosynthetic genes with Aspergillus oryzae as a host. With the development of tools such as genomic data and bioinformatics analysis to identify biosynthetic gene clusters for natural products, we developed a highly reliable methodology such as hot spot knock-in to elucidate the biosynthetic pathways of representative fungal metabolites including phytotoxic substances. This methodology allows total biosynthesis of natural products and genome mining using silent biosynthetic gene clusters to obtain novel bioactive metabolites. Further applications of this technology are discussed. Introduction Toxins produced by phytopathogenic microorganisms are one of the important causal factors in the development of many plant diseases. 1) In the 1970s, our laboratory isolated a number of phytotoxins from phytopathogenic microorganisms. One of the representative phytotoxins in our research program is coronatine isolated from a causal bacterium of chocolate spot disease Pseudomonas syringae (Fig. 1). 2) Recently, this toxin was rediscovered as an agonist of jasmonoyl-L-isoleucine, a genuine bioactive form of plant hormone jasmonic acid, and has played an important role in the recent progress of jasmonic acid research, as in the discovery of the coi1 mutant and | 3,069,449 | 226310123 | 0 | 16 |
the identification of the jasmonic acid receptor. 3) Although the actual role of phytotoxins is still difficult to uncover, elucidation of the function of phytotoxins is an important issue for understanding the defense response between plants and phytopathogenic microbes. During structural elucidations of phytotoxic metabolites produced by phytopathogenic fungi in our laboratory, we frequently encountered Diels-Alder-type adducts, such as betaenones, 4) solanapyrones, 5) pyrenocines, and pyrenochaetic acids 6) (Fig. 1). Our careful search in the literature showed that there are a number of putative natural [4 D 2] adducts in various types of natural products (NPs), including polyketides, terpenoids, phenylpropanoids, and alkaloids. 7)-9) These observations strongly indicated the involvement of the enzyme responsible for biochemically unusual Diels-Alder reactions, often named "Diels-Alderases (DAases)". Although considerable efforts have been made to identify the enzymatic Diels-Alder reaction, there has been no report on DAases thus far. By characterizing two important enzymes in DAase projects, we recognized the importance of a reliable expression system for studying the biosynthesis of fungal NPs. Such systems can enable us to achieve complete total NP biosynthesis and supply both sufficient amount of intermediates and NPs, and they can also be applied to the genome mining of novel NPs by expression of silent biosynthetic gene clusters (BGCs) on the fungal genome. I will also provide the details of our achievements in this topic. Discovery of DAases in fungal phytotoxin biosynthesis The Diels-Alder reaction is synthetically very useful and is one of the most widely used reactions in organic synthesis because it forms a six-membered ring | 3,069,450 | 226310123 | 0 | 16 |
from a 1,3-diene and a dienophile with high regioselectivity and stereoselectivity under mild conditions. In addition, the Diels-Alder reaction is a powerful tool for creating four chiral centers or quaternary stereogenic centers in organic synthesis and has been applied for the synthesis of complex pharmaceutical and biologically active compounds. The first target of DAase was a cyclization enzyme in the biosynthesis of phytotoxin solanapyrones A and D ( Fig. 2A). Initially, we confirmed that the solanapyrone producing fungus Alternaria solani transformed putative achiral linear precursors prosolanapyrones II and III into chiral solnapyrones. 10) In the crude enzyme from A. solani, we found enzymatic activity catalyzing the Diels-Alder reaction from prosolanapyrone II to solanapyrone A with excellent enantioselectivity (99% ee) and relatively high exoselectivity (6:1). 11) Subsequently, we reported the partial purification and properties of the enzyme, solanapyrone synthase (SPS), which is the first example of a DAase. 12) In addition, we observed that the SPS's cyclase activity is tightly correlated with oxidase activity. In parallel to the purification of the DAase, our genetic study using a heterologous expression of putative PKS genes in Aspergillus oryzae (AO) successfully confirmed the BGC of solanapyrone. 13) Our preliminary information led us to express flavin-dependent oxidase Sol5 among several modification enzyme genes in the cluster. Finally, we unveiled that the DAase SPS can oxidize prosolanapyrone II into aldehyde III and cyclized III into (!)-solanapyrones, proposing that the single enzyme catalyzes the oxidation from the alcohol II to the reactive aldehyde III, which is further converted into the adducts A and | 3,069,451 | 226310123 | 0 | 16 |
D by the intramolecular Diels-Alder reaction. 13) A similar bifunctional enzyme LovB giving decalin lovastatin was reported in 2000. 14) Later, the involvement of PKS LovB as a DAase was firmly established by an in vitro study. 15) For the study of intermolecular DAase, we chose an unusual conversion found in the biosynthesis of macrophomic acid. 16) The phytopathogenic fungus, Macrophoma commelinae has the ability to transform 2-pyrone into the corresponding benzoate analogue macrophomate as in the case of pyrenocine to pyrenochaetic acid (Fig. 2B). This complex transformation is catalyzed by a single enzyme, macrophomate synthase (MPS), with oxalacetate as a substrate for the C3-unit precursor. MPS is a Mg 2Ddependent enzyme with 339 amino acid residues (MW 36244 Da). 16) The catalytic mechanism of the whole pathway was investigated extensively, and it was shown that it proceeds through three separate steps: decarboxylation, two carbon-carbon bond formations, and decarboxylation with concomitant dehydration. 16) In the absence of 2-pyrone, MPS simply acts as a decarboxylase with high catalytic efficiency (Fig. 2B) Heterologous production of fungal natural products No. 9] aberrant adduct with pyrone and the observation that dehydration proceeds formally in an anti-sense, it was proposed that the higher-energy [4 D 2] adducts are transformed into either the rearranged product or benzoate analogue. The crystal structure of the MPS complexed with pyruvate and Mg 2D was determined. 17) In the catalytic cavity, a tight complex was observed between the two oxygen atoms of pyruvate enolate and Mg 2D , which is ligated with two amino acids residues | 3,069,452 | 226310123 | 0 | 16 |
of MPS. The proposed mechanism was further supported by this crystal structure. The rigorous discussion of this proposed mechanism was reviewed. 18) Other than SPS and MPS, we also studied several other natural [4 D 2] adducts such as PKS catalyzed [4 D 2] adducts betaenones, 19) nonenzymatic DA adducts didymellamide, 20) and macrocyclic DA adduct cytochalasin 21) (Fig. 3 Total biosynthesis of NPs using a versatile fungal host Through collaboration with our group, the Fujii and Ebizuka group successfully synthesized core skeletons of alternapyrone, 24) aslanipyrone, 25) and solanapyrones 13) by expression of HR-PKS genes obtained from the genomic DNAs of Alternaria solani. These pioneering works on functionally uncharacterized PKS genes that resulted in isolation of novel metabolites encouraged us to develop versatile tools for heterologous expression. 26), 27) Since 2010, in our group, the use of the AO expression system has been extended for the reconstitution of the biosynthetic machinery for fungal secondary metabolites. At that time, there were a few studies on the synthesis of biologically active NPs by expressing whole genes in the BGCs. For this purpose, multiple vectors are required to introduce all the biosynthetic genes in the clusters. To examine the expression of multiple NP biosynthetic genes, we selected an expression system using the quadruple-auxotrophic host AO NSAR1 (niaD ! , sC ! , "argB, adeA ! ) developed. 28) This host strain can accept multiple vectors such as pTAex3, pUNA, pUSA, and pAdeA, in addition to pPTRI17 with the pyrithiamine-resistant marker. Using this simple modification, we examined the heterologous | 3,069,453 | 226310123 | 0 | 16 |
production of phytotoxins, whose gene clusters we obtained ourselves. We successfully obtained diterpene aphidicolin 29),30) and polyketide solanapyrone 5),31) (9100 mg/kg, in solid medium) (Fig. 4). In addition, stepwise introduction of biosynthetic genes provided individual intermediates, thus clarifying each biochemical transformation. By further modification of the gene introduction using tandem transformation, we also succeeded in elucidating the early-stage biosynthesis of fungal indole diterpenes such as paxilline 32) and aflatrem 33) (Fig. 5). Heterologous production of fungal natural products No. 9] In the next stage, for the rapid reconstitution of the biosynthetic machinery in AO, we used the vectors pUARA2, pUSA2, pUNA2, and pAdeA2 carrying a tandemly arranged promoter/terminator set. Tandem transformation utilizing two plasmids with the same selectable marker is efficient, requiring the use of fewer vectors and allowing a rapid introduction of biosynthetic genes to obtain TFs. By applying this simple method, we completely elucidated the detailed biosynthetic pathway of fungal indole diterpenes such as shearinine, 34) lolitrem, 35) and especially penitrem 36) whose biosynthesis requires 17 genes, one of the largest number of genes in the fungal metabolite biosynthesis (Fig. 5). Initial diversification of indole terpenes is core construction, such as paspaline, by changing the chain length of the prenyl chain and various cyclization modes of epoxidized oligoprenyl chains. The second diversification is generated by two cytochrome P450 monooxygenase (P450)-catalyzed modifications (P: oxidative elimination of C30-methyl group and C10-oxidation; Q: allylic oxidation(s) at C13 and C7). 37) The final diversification is rather specific for indole terpene diprenylation coupled with various oxidative modifications. 37) A | 3,069,454 | 226310123 | 0 | 16 |
similar stepwise reconstitution strategy has been applied to synthesize fungal ribosomally generated peptides, 38) antifungal anhydrides, 39),40) and fungal polyketides. Furthermore, we recently unveiled the long-standing mystery in the biosynthesis of plant hormone abscisic acid in fungi, 41) which is significantly different from that in plants. Recently, fungal gene expression has become popular, especially in pathway elucidation of fungal metabolites. We believe that we have made significant contribution in this research field. Genome mining of novel NPs from silent BGCs To date, biologically active NPs have usually been found by suitable bioassay-guided screening. Recently, genome mining has become another attractive approach to discover novel NPs solely using gene sequences. By this approach, we can avoid duplicated isolation of known compounds whose Even obtaining microorganisms is not necessary when we use synthetic DNAs designed using the sequences from public databases. Recently, we and others succeeded in identifying a novel type of fungal di-/sesterterpenes, which are biosynthesized by a novel type of cyclopentane forming terpene synthases (CPF-TSs). 42) The preceding study of bifunctional TS (BFTS) with two catalytic domains of prenyltransferase GGPP synthase and diterpene synthase showed that two BFTS PaFS and PaPS generated unique molecular skeletons fusicoccin containing 8-membered ring and methyl phomopsenate multicyclic systems, respectively. Based on these results, we applied a genome mining approach with BFTS genes to find novel diterpenes. When we expressed a BFTS gene AcOS from A. clavatus using the AO expression system, the resultant TF did not give a diterpene but yielded a sesterterpene instead, which is identical to ophiobolin F, | 3,069,455 | 226310123 | 0 | 16 |
43) suggesting that the PT domain of BFTS can supply either C20-or C25-precursor GGPP/GFPP and the TS domain can produce either C20-or C25terpenes (Fig. 6A). Bioactive sesterterpenes are found throughout the tree of life, including in bacteria, plants, animals, and fungi, but remarkably, no sesterterpene-generating enzymes were known. This encouraged us to further explore novel sesterterpene synthases. Phylogenetic analysis of more than 100 BFTSs from the public database allowed us to categorize two clades: I and II. Assuming that the amino acid sequence was strongly correlated with the cyclization mechanism, we employed another genome for mining a clade I-BFTS gene NfSS from Neosartorya fischeri. In the extracts of AO-NfSS, we obtained a novel tetracyclic sesterterpene sesterfisherol (Fig. 6B). 44) Based on the common cyclization mechanism of di-/sesterterpenes putatively derived from type-A and type-B cyclizations, we proposed unified biogenesis for these CPF-TSs. Density functional theory calculations of the sesterfisherol formation revealed two alternative cyclization mechanisms (Paths a and b) that were thermodynamically and kinetically favorable. Actually, two metabolites were found, which were derived via both mechanisms (Fig. 6B). 42) To explore terpene synthases producing sesterfisherol-related sesterterpenes, we selected four clade I-BFTS genes from Bipolaris maydis and Phoma betae, which showed moderate identities (35%-38%) with NfSS. Applying the same strategy as for functional analysis of NfSS, we obtained four sesterterpenes, Bm1, Bm2, Bm3, and Pb1, whose structures were closely related with the carbocation intermediates in the cyclization giving sesterfisherol (Fig. 6B). 45) The structure of Bm2, including its absolute configuration, is the same as that of the tetracyclic | 3,069,456 | 226310123 | 0 | 16 |
carbocation, whereas the other three products are diastereomers of the bicyclic and tricyclic carbocations. This observation suggested that clade I CPF-TSs can generate various enantiomeric and diastereomeric cation intermediates that give rise to a diverse array of structural derivatives. This genome mining approach attracted several research groups, and nearly 20 CPF-TSs were characterized. 42) Heterologous expression of genes encoding modification enzymes led to the production of putative NPs. With the exception of the BGCs for fusicoccin (14 genes) 38) and brassicicene (> 10 genes), 46) BGCs of di-/sesterterpenes belonging to this class usually consist of fewer than 5 genes. To date, the function of these terpenoids remains unknown. Although some of them show strong phytotoxicity (ophiobolin) and antiviral/antiangiogenic activity (terpestacin 47) ), the remaining terpenes do not exhibit any obvious activities. However, the conidiation-inducing activity of conidiogenone 48) suggested that these terpenoids act as a signaling molecule in the fungi. Heterologous production of NPs from Basidiomycota fungi Mushroom-forming basidiomycete fungi are known to be prolific producers of structurally diverse, bioactive NPs. 49) However, despite their incredible potential for NP discovery, Basidiomycota fungi are a largely unexplored target for drug discovery compared with Ascomycota fungi. Unfortunately, Basidiomycota have very intron-rich genomes and genes that contain very small and unpredictable exons, and thus currently no reliable tool for automated intron prediction is available. The ability to directly express Basidiomycota biosynthetic genes from genomic DNA in a suitable fungal surrogate host would therefore greatly accelerate the functional characterization of NP pathways. After successful production of the widely used livestock | 3,069,457 | 226310123 | 0 | 16 |
antibiotic pleuromutilin in AO TF harboring cDNA gene from its producer mushroom, 50) we examined the heterologous expression of genomic DNAs. Preliminary expression of pleuromutilin genes gave the results that two genes ple3/4 for core construction were correctly spliced, and three intronrich P450 genes ple1/5/6 were mostly spliced in three . This suggested that we can produce the metabolites in AO using genomic DNA sequence by removing the remaining intron by PCR technique (Fig. 7). To establish the versatility of basidiomycete heterologous expression using AO, 30 sesquiterpene synthase genes were selected for characterization from two basidiomycete fungi: pleuromutilin producer Clitopilus pseudo-pinsitus and Stereum hirsutum. In the examination of unpredictable splicing of basidiomycete genes, we used the recently developed technique, a fungal clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system specifically optimized for AO, to ensure the expression of target genes. 49), 51) In addition, the STS genes were introduced (knocked-in) to the hot spot (HS) loci where target genes were integrated in the highly yielding TFs found in our previous studies. Sequence analysis of cDNAs recovered from the TFs revealed that 87% of total introns were correctly spliced, and nonspliced introns were simply skipped with no complicated missplicing. Following the removal of nonspliced introns in amplified cDNA, the fixed cDNAs were expressed by E. coli, which successfully yielded terpene products except a single TF. 49), 51) To confirm the versatility of the AO expression system, total biosynthesis of a typical Basidiomycota metabolite erinacine Q, a potential drug for Alzheimer's disease, was conducted. Before heterologous production, we | 3,069,458 | 226310123 | 0 | 16 |
prepared AO-transformants carrying the genomic DNA sequences of eriA-C, and eriH-L and confirmed their correct splicing (> 91%) in all genes. In this study, we faced the problem of detecting the activities of two P450 EriAC. These enzymes showed oxygenase activity in the coexpression of extra dehydrogenase EriH. In addition, expression of all required genes (eriEGACIJKLH ) resulted in the production of erinacine Q when we enhanced the supply of UDP-xylose by adding two plant genes AtUGD1 (UGD: UDP-D-glucose dehydrogenase) and AtUXS3 (UXS: UDP-D-glucuronic acid decarboxylase) to the TF (Fig. 7). The detailed function of SDR is currently unknown, but this phenomenon is likely mushroom-specific owing to the presence of EriH homologs in other basidiomycete terpene BGCs. 51) Overall, the complete elucidation of the erinacine biosynthetic pathway was achieved, and this study showed that heterologous production of mushroom NPs in AO is one of the promising methods. Conclusion and perspective Frequent occurrence of putative Diels-Alder adducts in phytotoxins from phytopathogenic fungi led us to study biosynthetic enzymes that catalyze Diels-Alder reactions involved in the biosynthesis of several phytotoxins that we isolated. The corresponding enzymes SPS and MPS were successfully characterized by our extensive chemical and biochemical analyses including X-ray crystallographic analysis. Our achievement triggered the identification of various Diels-Alderases in the last 10 years. A highly efficient expression system of various biosynthetic genes with AO as a host played a key role for identification of DAases (in the 1990s). With the advancement of DNA sequencing for accumulation of genomic data and tools for bioinformatics analysis to | 3,069,459 | 226310123 | 0 | 16 |
identify BGCs for NPs, we developed methods for multiple gene introduction and applied it to elucidation for the biosynthetic pathways of representative fungal NPs including phytotoxic substances. Eventually, we established the highly reliable methodology HS-knock-in to study biosynthesis of NPs from Basidiomycota fungi. Total biosynthesis and genome mining became accessible for genomic data-based heterologous production of biologically active metabolites. These technologies are now applied to isolate NPs that are produced transiently in a specific infection period by phytopathogenic fungi. Target NPs are usually unable to obtain a large amount and are therefore difficult to isolate because of conditional expression. However, the expression profile of the gene clusters may be sufficient information to fish out the target NPs if we apply the heterologous expression of silent gene clusters. For example, we successfully overexpressed biosynthetic genes to yield conidiogenone, 49) which is a conidation-inducing factor for the genus Penicillium. Conidiation is important for the pathogenicity of phytopathogens, and thus, understanding the cellular mechanism of conidiation is an urgent research topic in plant disease. Basically, enzymatic synthesis of biologically active NPs solely depends on the information about the DNA sequence of the gene. In the future, automated systems may generate TFs with plasmid-carrying genes derived from synthetic DNA. Once we establish these systems, we can use them to produce novel NPs by the TFs expressing whole genes of unidentified BGCs. Furthermore, the NPs thus obtained can be linked to the timing of individual BGC expressions under specific conditions of life cycle events. This information (where and when) may unveil | 3,069,460 | 226310123 | 0 | 16 |
the exact role of NPs in phytopathogenic fungi. | 3,069,461 | 226310123 | 0 | 16 |
High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or “Bio-GO-SHIP.” One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean. Measurement(s) DNA sequencing • temperature of water • concentration of phosphate in water • concentration of nitrogen atom in water Technology Type(s) Illumina sequencing • watercraft • continuous flow autoanalyzer Sample Characteristic - Organism marine metagenome Sample Characteristic - Environment ocean Sample Characteristic - Location global Measurement(s) DNA sequencing • temperature of water • concentration of phosphate in water • concentration of nitrogen atom in water Technology Type(s) Illumina sequencing • watercraft • continuous flow autoanalyzer Sample Characteristic - Organism marine metagenome Sample Characteristic - Environment ocean Sample Characteristic - Location global Machine-accessible metadata file describing the reported data: | 3,069,462 | 256838268 | 0 | 16 |
https://doi.org/10.6084/m9.figshare.13971122 www.nature.com/scientificdata www.nature.com/scientificdata/ comparison, systematic and sustained biological measurements of the microbial component of ocean ecosystems has lagged far behind. We present a dataset of 971 ocean surface water metagenomes collected at high spatio-temporal resolution in an effort to more mechanistically link marine microbial traits and biodiversity to both chemical and hydrodynamic ecosystem fluxes as a part of a novel Bio-GO-SHIP sampling program. Samples were collected in the Atlantic, Pacific, and Indian Ocean basins (Fig. 1, Table 1). This effort has been supported by GO-SHIP, SOCCOM, the Plymouth Marine Laboratory Atlantic Meridional Transect (PML AMT), and three National Science Foundation (NSF) Dimensions of Biodiversity funded cruises (AE1319, BVAL46, and NH1418) ( Table 2). Whereas the median distance between Tara Oceans sampling stations was 709 km and the median distance between bioGEOTRACES sampling stations was 191 km, the median distance between sampling stations in the current Bio-GO-SHIP dataset is 26.5 km (Fig. 2). In addition, the majority of Bio-GO-SHIP samples were collected every 4-6 hours, allowing for analysis of diel fluctuations in microbial composition and gene content 12 . We anticipate that our high-resolution sampling scheme will allow for a more detailed examination of the relationship between the broad range of geochemical parameters measured across the various cruises (Table 2) and microbial diversity and traits. Due to their rapid generation times and high diversity, microbial genomes integrate the impact of environmental change 13 and can be used as a 'biosensor' of subtle biogeochemical regimes that cannot be identified from physical parameters alone 12,[14][15][16] . Thus, the fields | 3,069,463 | 256838268 | 0 | 16 |
of microbial ecology and oceanography would benefit from coordinated, high resolution measurements of marine 'omics products (i.e., metagenomes, metatranscriptomes, metaproteomes, etc.). This dataset provides an important example of the benefits of a high spatial and temporal resolution sampling regime. In addition, our data highlights the need for increased sampling of marine metagenomes in the Central and Western Pacific Ocean (Fig. 1), areas above 50°N and 50°S (Fig. 2), and below the euphotic zone. We hope and expect that these challenges will be addressed by the scientific community in the coming decade. 60˚S A total of 971 metagenomic libraries from 932 locations were prepared using Illumina-specific Nextera DNA transposase adapters and a Tagment To quality control tagmentation products, dimers that were less than 150 nucleotides long were removed using a buffered solution (1 M NaCl, 1 mM EDTA, 10 mM Tris-HCl, 44.4 M PEG-8000, 0.055% Tween-20 final concentration) of Sera-mag SpeedBeads (ThermoFisher, Waltham, MA). Metagenomic libraries were quantified using a Qubit dsDNA HS Assay kit (ThermoFisher, Waltham, MA) and a Synergy 2 Microplate Reader (BioTek, Winooski, VT). Libraries were then pooled at equimolar concentrations. Pooled library concentration was verified using a KAPA qPCR platform (Roche, Basel, Switzerland). Finally, dimer removal as well as read size distribution were checked using a 2100 Bioanalyzer high sensitivity DNA trace (Agilent, Santa Clara, CA). 54 samples were sequenced on two Illumina HiSeq 4000 lanes using 150 bp paired-end chemistry with 300 cycles (Illumina, San Diego, CA). A total of 666 samples were sequenced on three Illumina NovaSeq S4 flowcells and an | 3,069,464 | 256838268 | 0 | 16 |
additional 251 samples were sequenced on a combination of S1 and SP flowcells using 150 bp paired-end chemistry with 300 cycles. The sequencing strategy produced a total of 2.42 × 10 10 reads, or 3.65 × 10 12 bp. The Table 2. Publicly available metadata variables collected on Bio-GO-SHIP cruises. These data may be updated as additional samples or stations are processed by the principal investigators of each dataset. Another 48 metadata variables not listed here were collected aboard the GO-SHIP, PML AMT, and NSF cruises and may be available upon request from CCDHO, BODC, or SOCCOM. *C13.5 is a partial occupation of the A13.5 GO-SHIP line that was aborted due to COVID-19. Thus, CTD casts corresponding to DNA collection were only performed at 8 stations. www.nature.com/scientificdata www.nature.com/scientificdata/ median number of bases per sample was 3.41 billion (range: 61,400,000-21.4 billion). Prior to read trimming and quality filtering, 74% of all forward and reverse reads had an average quality score ≥Q25 (Table 1). The sequencing cost per bp in US dollars was $8.2 × 10 −9 . Data Records The majority of the samples here were collected under the auspices of the international GO-SHIP program and the national programs that contribute to it [21][22][23][24] . Links to publicly available metadata variables collected via CTD cast are provided in Table 2 All sequencing products associated with the Bio-GO-SHIP program can be found under BioProject ID PRJNA656268 hosted by the National Center for Biotechnology Information Sequence Read Archive (SRA) 30 . SRA accession numbers associated with each metagenome file | 3,069,465 | 256838268 | 0 | 16 |
are provided in Supplementary Table 1. technical Validation To ensure that no contamination of metagenomes occurred, negative controls were used. To ensure optimum paired-end short read sequencing, a 2100 Bioanalyzer high sensitivity DNA trace (Agilent, Santa Clara, CA) was used for each library to confirm that ~90% of the sequence fragments were above 200 bp and below 600 bp in length (Table 3). A Qubit (ThermoFisher, Waltham, MA) and a KAPA qPCR platform (Roche, Basel, Switzerland) were used to ensure that all pooled libraries were submitted for sequencing at a concentration > 15 nM. Table 3. Sequencing run breakdown of Bio-GO-SHIP metagenomes including technical validation statistics. *Run 1 was concentrated via SpeedVac to 15 nM and bead size-selected such that 90% of fragments were between 200-600 bp by the UC Davis Genome Center DNA Technologies Core prior to sequencing. Final values for this run are not available. | 3,069,466 | 256838268 | 0 | 16 |
Using Computational Methods to Understand the Past in The Present Cultural heritage is a wide concept; an expression of the ways of living developed by community and passed on from generation to generation (ICOMOS 2002). In this paper I examine the idea that “archaeological heritage” is the information we can extract from material evidence from the past with use of scientific analysis. As prehistoric stones and ancient potsherds do not speak for themselves, the transformation of archaeological material into scientific data and into explanatory knowledge is the most challenging aspect of modern archaeological methodology. New techniques based on artificial intelligence, virtual reality and reverse engineering are needed to approach cultural heritage in a explicitly functional way. The challenge is to demonstrate how we may put our knowledge of the past to beneficial use in helping people to understand where the present came from and shaping their way into some future. Short Communication Archaeological heritage should not be reduced to a series of objects presented in museums or depicted as pictures in books. It should be converted into knowledge that needs to be acquired, processed and transferred. This knowledge will provide information about our past that is basic for understanding our present and to produce our future in a rational way. Archaeological observables are something to be explained, and not something that merely documents the past. Archaeologists' intention should be to study social events, that is to say, the material consequences of social actions performed sometime in the past, some of which are perceivable in the present | 3,069,467 | 113405418 | 0 | 16 |
and are recognized as cultural assets due to its relevance for understanding modern identities. Therefore, preserved material evidence about the past (objects, buildings and landscapes) should be linked to our scientific knowledge of social history in an interactive way. My assumption is that the "function" of the object in the past is a sign of what people could be made with it there and then. What is seen here and now but was produced/ used there and then becomes a sign of its own historical signifier. And as sign, it is involved in paradigmatic relations (substitutions) as well as syntactic combinations. The paradigmatic order is the order of historical possibilities, offering substituting items for the signification and places them at the disposal of the action, in a given state of semiotic values. On the other hand, the syntactic order is that of the irreversible sequences, fixing the order of the cognitive actions-historical explanation-which must be carried out to achieve a certain goal, in a certain space-time context. The starting point in this paradigm shift is that we are not referring to "monuments" or "reliques" but to past objects and buildings having historically resulted from the articulation between human intention and the physics of materiality. The knowledge of the way artefacts, buildings and landscapes were created and used in the past should reflect the causal interactions that someone had or could potentially have had with needs, goals and products in the course of using such elements. That means that material entities preserved from the past and recognized | 3,069,468 | 113405418 | 0 | 16 |
as cultural assets in the present should be explained by the particular causal structure in which they are supposed to have been participated. To achive those goals we should focus on processes, rather than on static visual/non-visual components. This constant interaction between task and object, between what ancient people could do in the past and what we know today about what they wanted to do then can be defined as the archaeological (historical)-explanation cycle. What is the role of computer technology in solving those problems? Current computer technology is part of the problem, although it should be part of the solution. Virtual archaeology, for instance, has developed as an independent branch of archaeology; in the last decade the availability of powerful hardware and software tools has accustomed the public to a formal perfection in computer graphics, while the quality of Abstract Cultural heritage is a wide concept; an expression of the ways of living developed by community and passed on from generation to generation (ICOMOS 2002). In this paper I examine the idea that "archaeological heritage" is the information we can extract from material evidence from the past with use of scientific analysis. As prehistoric stones and ancient potsherds do not speak for themselves, the transformation of archaeological material into scientific data and into explanatory knowledge is the most challenging aspect of modern archaeological methodology. New techniques based on artificial intelligence, virtual reality and reverse engineering are needed to approach cultural heritage in a explicitly functional way. The challenge is to demonstrate how we may put | 3,069,469 | 113405418 | 0 | 16 |
our knowledge of the past to beneficial use in helping people to understand where the present came from and shaping their way into some future. the digital products is improving day by day thanks to rapid technological development. This process has led, on the one hand, to some very impressive results, but on the other, it has meant that the message in the cultural communication of archaeology is often conditioned by a mainstream and superficial idea of antiquity. The lack of interest of many archaeologist, and the needs to make fast profit of current investments have resulted in a proliferation of products in which there is no guarantee of quality or reliability of content. Nevertheless, investigating historical heritage through computer methods and artificial intelligence approaches can provide new insights into the complex dynamics of human past. The goal should be to unveil production, construction and building processes through time, by rendering public and accessible, the reasoning form their builders in the past. This is a real example of a Reverse Engineering approach to the study of ancient remains, which can be defined by the process of extracting missing knowledge from the past, by going backwards through its development cycle and analyzing its structure, function and operation. Through reverse engineering and computer simulation mechanisms, it is possible to advance from a physical-to-digital stage to an explanation stage, by simulating the ancient artefacts' and building' functions and inferring possible inherent working and/or use processes. In this way, we may analyze and evaluate potentialities, constraints, quality, robustness and effectiveness, | 3,069,470 | 113405418 | 0 | 16 |
by controlling the flow of information and vulnerabilities of a hypothetical model. In other words, computer technologies should help us in discovering what cannot be seen (social causes) in terms of what is actually seen (material effects) and we know for certain that it was produced sometime in the past. This explanatory process can be divided into three very general categories, and the idea is to program computers to perform them "out of the mind of the researcher". If a task implies obtaining information about the empirical characteristics of an archaeological site or some archaeological material and producing a representation useful for other tasks (description, representation, analysis, explanation), then it falls in the SENSE category. If the task is based on processing information (either from primary data or some previous theoretical knowledge about the material evidences of social action) about how to generate descriptions "automatically", representations, analysis, and explanations, this is an instance of cognitive planning behavior. Finally, and most importantly, cognitive tasks producing explanations fall into the ACT category. It is necessary to insist in the fact that I view scientific reasoning as a form of behavior, and then we need to consider that computer programs may act. Obviously, I am speaking about epistemic actions. Expressed in its most basic terms, the epistemic action to be performed may be understood in terms of predicting which explanations should be generated in face of determined evidence. In that sense, explanations are for the computer a form of acting. Explanation is not an explanatory structure, nor something that | 3,069,471 | 113405418 | 0 | 16 |
explains, but a process of providing understanding. Explanation is something that people do, mechanically, with the help of a machine, and not an eternal property of sets of sentences. The main argument presented in this paper is that archaeological reasoning can be formalized in terms of information-processing machines, which transform inputs into outputs. These mechanisms are usually called automata. Simply stated, an automaton is a discrete processing mechanism, characterized by internal states. Computers provide a perfect example of a physical system in which output is related to input in a far more complicated way that could ever be expressed as a stimulus-response pattern. Programmed appropriately, they can respond selectively and conditionally to well-defined (and in some cases, even not-so-well-defined) categories. The problem an "automated archaeologist" must solve can be defined in formal terms as the transformation of any incoming sensory vector into an appropriate conceptual vector, which should be consistent with a hypothetical causal model of the input vector. That is, given a description of archaeologically observable features and a set of already known mechanisms corresponding to hypothetical social activities, actions, and/or behavior models known to the automatic archaeologist, it should assign correct causal explanations to the material consequences of social actions. Here lies the basis of an "automatic" approach to archaeology, or if you want, a "mechanically" driven way of reasoning about the past. I am speaking about storing and retrieving abstract mathematical or logical descriptions implemented in a computer program, which takes the geometrical, spatial and material perperties of the current observation at the | 3,069,472 | 113405418 | 0 | 16 |
archaeological site as input and which returns an explanatory structure as output. Essentially, the idea is to set up appropriate, well-conditioned, tight feedback loops between input and output, with the actual and past observations as the medium for the loop. We can say then that an automated archaeologist "perceives" some reality because it is able to recognize input information according to previously learnt categories. The goal of explanation is to perform relevant associations between input and output correctly, in the sense that the recognition reflects a meaningful property of the world in terms of what has been already learnt of its formation process through previous experiments or controlled observations, and which is independent of the particular data that is being interpreted. First, a visual sub-system has classified the percept as being a member of one of a large number of results from known causal processes according to visible properties, such as its shape, size, color, and location, and relations between them. Second, this identification allows access to a large body of stored information about this type of object, including its function and various forms of expectations about its future behaviors. This two-step schema has the advantage that any functional property can be associated with any object, because the relation between the visual characteristics of an object and Global Journal of Archaeology & Anthropology the information stored about its function, history, and use can be purely arbitrary, owing to its mediation by the process of categorization. This procedure seems to ask for an organized "library" of internal | 3,069,473 | 113405418 | 0 | 16 |
representations of various prototypical perceptual situations, situations to which the results of perceptions are associated. Explanatory understanding consists then in the apprehension of the problematic case as an instance of a general type. Such a representation would allow the machine to anticipate aspects of the case so far unperceived, and to deploy practical techniques appropriate to the case at hand. Consequently, automated understanding can be understood as the generator of a set of descriptions of the actual physical world that might be sufficient (perhaps in concert with other contextual information) to identify instances of social actions performed in the past, according to what the robot knows about them from the laboratory experiments, computer simulations or ethnoarchaeological analogies. Clearly, nothing is gained if we merely assume that x occurs, because y occurred (where x refer to archaeological observables, and y to different acts, events or processes that happened somewhere and somewhen). Such descriptive mechanisms, even if true, are not explanations but are themselves something to be explained. Statistical regularities don't explain, but require explanation by appeal to the activities of individual entities and collections of entities. Studies offering models for the detection of event-related properties typically fail to distinguish between description and explanation. Archaeologists should intend to build historical explanations in terms of the description of some hypothetical mechanism connecting different temporal states on the same reality. The idea is to discover changes in the temporal and spatial trajectory of some properties of an entity, which appear to be causally linked to changes in properties of another | 3,069,474 | 113405418 | 0 | 16 |
entity. That is to say, social actions cannot be understood without a frame of reference created by the corresponding social motivation or intention. An automated archaeologist may understand archaeological observables in terms of a priori affordances: relationships between observed properties and the inferred properties/ abilities of people having generated those properties. The affordances of any archaeological evidence become obvious in its use and/or formation process. Both involve establishing and exploiting constraints (between the user/producer and the material evidence of his/her action, the user/producer and the natural environment, and the material evidence and the natural environment). Physical affordances, closely related to constraints, are mutual relationships that involve both the agent and the material elements she/he manipulates (and the environment he/she operates). The implementation of such causal affordances or potentialities inside a machine to explain what it "sees, is usually called computer "simulation" of a causal process [1][2][3][4][5]. By running such a "virtual world" archaeologists can test the accomplishment a tool or a building had in the past to effectively fulfill a specific action or task, which has been formally described and parameterized; that is to say, whether the object or building was used in a certain way and to satisfy a specific goal. Such an approach can be characterized as "understanding by building". It is is based upon the general assumption that theory building would be better served by synthesis (simulation) than analysis (logics). Here, the problem-to-be-solved is translated into a design issue: How can we design an artificial archaeologist so that it will exhibit the desired | 3,069,475 | 113405418 | 0 | 16 |
epistemic behaviors? I have tried to give some posible answers to this question in my book Computational Intelligence in Archaeology [6]. For this sort of cognitive task to work, a virtual world, that is, the computer simulation of observed things in a reconstructed environment, should be defined in terms of precipitating conditions generating an increase in the probability of occurrence of an effect, and not in terms of a single linear mechanism. The visual attributes observed at the archaeological record cannot be shown to follow from some general law that, given certain initial conditions at time t0, will inevitably produce the thing or event that the intelligent machine is trying to explain at time t1. Nevertheless, the automated archaeologist can suggest that those effects seem to have a different degree of probability in some circumstances than in others. The automated archaeologist will study the non-linearity of the observed instances of causeeffect relationships, and will try to make emphasis on the cases that deviates from what was hypothetically predicted (simulated). What is assumed is that the past is not necessary like the present, and not any action performed here and now should produce the same consequences of an action performed there and then. The key of this approach lies in the study of the intrinsic variability of a causal process in experimental or ethnoarchaeological circumstances. In other words, the starting point of the explanation of the archaeological record by means of computer simulation is not the reproduction of one particular object but the investigation of the mathematically | 3,069,476 | 113405418 | 0 | 16 |
possible development of specific classes of model systems. As these pure systems usually generate a lot more different paths of development than are known from real human history, we should limit these possibilities by introducing known historical constraints from previous knolwedge. The key question is then why these constraints appeared in reality. This particular procedure was aptly described by Bateson with the concept of "cybernetic explanation" [7]. The suggestion that scientific reasoning might simply consist in a sequence of inputoutput or perception-action associations has been suggested, among others, by Howard Margolies (1987), Paul Thagard [8] and Paul Churchland [9,10]. The core idea seems to be that scientific reasoning does not involve any introspection into the process of thinking, but rather is itself a process of pattern recognition. Models should be specified a priori; the adaptation or learning is achieved by estimating model parameters from Global Journal of Archaeology & Anthropology the available data. A priori models account for any deterministic variability, whereas deviations from the model are random and statistically independent for different subsets. Explanation represents an expected, deterministic aspect of the data, although the deterministic uncertainties can be implemented in terms of unknown model parameters [11,12]. In any case, archaeological explanations should not be considered as semantic abstractions or verbal labels but opportunities some explanatory context affords. Interpreting the shape, texture, materiality and spatio-temporal location of some archaeologically observed items must be grounded in an understanding of both the social and natural events that have influenced the presence/absence, alteration, and displacement (relative to it as | 3,069,477 | 113405418 | 0 | 16 |
a primary site of production, use or discard) of its individual components and of the assemblage as a whole. In other words, the a priori contents of the problem-solver are not concepts, but a kind of "pre-concepts" having dynamic, adaptive nature. They are a bridge between the mind and the experience. Concepts-as-potentialities belong to the a priori content of the mind, whereas concepts-as-actualities come immediately close to the world of experience. Artificial intellence, virtual reality and reverse engineering help us to define how ancient objects, buildings and landscapes were shaped and used in the past, even if we do not have access to any written description by any contemporaneous witness, starting from the identification of the choices made (among the many possible) in an hypothetical reconstruction of the production process (the cause). In this way we can investigate scientifically and explain to wider audiences the effects of social actions considering alternative explanatory scenarios, where the parameters of possible behaviors can be changed and tested. | 3,069,478 | 113405418 | 0 | 16 |
The Second Data Release of the Beijing-Arizona Sky Survey This paper presents the second data release (DR2) of the Beijing-Arizona Sky Survey (BASS). BASS is an imaging survey of about 5400 deg$^2$ in $g$ and $r$ bands using the 2.3 m Bok telescope. DR2 includes the observations as of July 2017 obtained by BASS and Mayall $z$-band Legacy Survey (MzLS). This is our first time to include the MzLS data covering the same area as BASS. BASS and MzLS have respectively completed about 72% and 76% of their observations. The two surveys will be served for the spectroscopic targeting of the upcoming Dark Energy Spectroscopic Instrument. Both BASS and MzLS data are reduced by the same pipeline. We have updated the basic data reduction and photometric methods in DR2. In particular, source detections are performed on stacked images, and photometric measurements are co-added from single-epoch images based on these sources. The median 5$\sigma$ depths with corrections of the Galactic extinction are 24.05, 23.61, and 23.10 mag for $g$, $r$, and $z$ bands, respectively. The DR2 data products include stacked images, co-added catalogs, and single-epoch images and catalogs. The BASS website (http://batc.bao.ac.cn/BASS/) provides detailed information and links to download the data. Introduction Large-scale spectroscopic surveys over the past 20 years have revolutionized our view of the universe from the structure of the Milk Way and galaxy evolution to large-scale structure and dark energy (Colless et al. 2001;York et al. 2000;Scoville et al. 2007;Sánchez et al. 2012;Zhao et al. 2012;Newman et al. 2013;Liske et al. 2015). The Sloan | 3,069,479 | 119462399 | 0 | 16 |
Digital Sky Survey (SDSS; York et al. 2000) began with spectroscopy on the brightest targets in its imaging data. SDSS has since performed spectroscopy on progressively deeper targets, with SDSS-III/BOSS and SDSS-IV/eBOSS pushing to the faint limits of that imaging for the measurement of baryonic acoustic oscillations (Dawson et al. 2013(Dawson et al. , 2016. Deeper wide-field imaging data is required prior to the era of the Large Synoptic Survey Telescope (LSST; LSST Science Collaboration et al. 2009) to select targets for upcoming wide-field spectroscopic surveys, such as the Dark Energy Spectroscopic Instrument (DESI; DESI Collaboration et al. 2016) and Subaru Prime Focus Spectrograph (PFS; Takada et al. 2014). DESI is a next-generation dark energy experiment that will accurately measure the expansion rate and structure growth of the universe. It will obtain spectroscopic redshifts of about 34 million galaxies and quasars, which is one magnitude more than those of the SDSS (DESI Collaboration et al. 2016). In addition to cosmology, the DESI project will play an important role in shaping our understanding of the Milky Way and galaxy evolution by observing stars and low-redshift galaxies during bright time. The spectroscopic target selection for DESI will be based on three optical bands (g, r, and z) and two nearinfrared bands (W 1 and W 2). The optical imaging surveys include three components: the Beijing-Arizona Sky Survey (BASS; Zou et al. 2017b), the Dark Energy Camera Legacy Survey (DECaLS; Blum et al. 2016), and the Mayall z-band Legacy Survey (MzLS; Silva et al. 2016). DECaLS covers a 9000 | 3,069,480 | 119462399 | 0 | 16 |
deg 2 equatorial footprint using the Dark Energy Camera (DECam) on the 4 m Blanco telescope at CTIO. BASS and MzLS, using the Bok and Mayall Telescopes, respectively, on Kitt Peak, are covering an adjacent 5000 deg 2 footprint in the north Galactic cap. All three optical surveys share a similar observing strategy. Dynamic exposure time calculators (ETCs) ensure their imaging depths will satisfy the requirement of the DESI spectroscopic target selection. The near-infrared images at wavelengths of 3.6 µm (W 1) and 4.5 µm (W 2) make use of the full-sky data from the W ide-f ield Inf rared Survey Explorer mission (WISE; Wright et al. 2010) and the N EOW ISE-Reactivation data (Mainzer et al. 2014), coadded to their full depth (Meisner, Lang & Schlegel 2017, 2018. BASS is a g− and r-band imaging survey that uses the wide-field 90Prime camera mounted on the 2.3 m Bok telescope (Williams et al. 2004). The observation started in 2015. It mainly covered gray and dark nights from January to July of each year. BASS had its early data and first data releases (DR1) in 2015 December and 2017 January (Zou et al. 2017a). DR1 only includes BASS data taken before 2016 July. By 2017 July, BASS has completed about 72% of the whole survey area. The MzLS covers the same area as BASS and have finished more than 76% of its observations by 2017 July. In this paper, we present the second BASS data release (DR2), which includes both BASS and MzLS data taken as of | 3,069,481 | 119462399 | 0 | 16 |
2017 July. This paper describes the details of BASS DR2. The paper is organized as follows. Section 2 presents basic information on the BASS and MzLS surveys and their observation status. Section 3 updates BASS data reduction. The source detection and photometry are described in Section 4. Section 5 presents the data quality and provides comparisons with other photometric surveys. Section 6 describes data access and provides guidelines for users. Section 7 is the summary. Table 1 gives a summary of both the BASS and MzLS surveys. BASS uses the Bok telescope to image the northern part of the North Galactic cap with the optical g and r bands. The telescope is located on Kitt Peak near Tucson, Arizona. It is a 2.3 m telescope operated by Steward Observatory of University of Arizona. A wide-field camera, 90Prime, is mounted at the prime focus. It is composed of four 4k × 4k blue-sensitive CCDs, providing a feild of view (FoV) of 1 • .08×1 • .03. The CCD pixel scale is about 0 ′′ .454. There are gaps between the CCDs and the filling factor is about 94%. Telescope and instruments MzLS uses the 4 m Mayall Telescope at Kitt Peak to image nearly the same area as BASS with the z band. The telescope is located at the highest peak of the mountain, close to the Bok telescope. Its mirror diameter is about 4 m and its clear aperture diameter is about 3.8 m. The survey uses the Mosaic-3 imager deployed at the prime focus. It | 3,069,482 | 119462399 | 0 | 16 |
is a new wide-field imaging camera In order to achieve homogeneous spectroscopic target selections for DESI, photometric systems of the imaging surveys should be as similar as possible. The DECaLS uses the DECam system, which is also used for the Dark Energy Survey (The Dark Energy Survey Collaboration 2005). The BASS g band is the existing SDSS g filter. It is very close to the DECam g band. The BASS r filter is newly purchased by the Lawrence Berkeley National Laboratory, which is almost the same as the DECam r band. The MzLS uses a newly purchased DECam z-band filter. Figure 1 shows the filter responses of these three filters. The response is the total throughput, including CCD quantum efficiency, filter transmission, and atmospheric extinction at the zenith, aluminum reflectivity of the prime mirror, and throughput of the optical corrector at the prime focus. The effective wavelengths for the BASS g and r and MzLS z bands are 4789, 6404, and 1 https://www.noao.edu/kpno/mosaic/manual/ 9210Å, respectively (see Table 2 for detailed filter parameters). For comparison, DECam filter responses are also plotted in Figure 1 and related parameters are presented in Table 2. The Galactic extinction coefficients are k g =3.214, k r =2.165, and k z =1.211, which are adopted from the DECaLS webpage 2 . Survey status All DESI imaging surveys have similar observing strategies. Each survey tiles the sky in three passes or exposures. These three passes are dithered to fill CCD gaps. This is also benificial for detecting variable objects and allows zero-point determination | 3,069,483 | 119462399 | 0 | 16 |
with ubercalibration (Zou et al. 2017b). Pass 1 is observed in both photometric and good seeing conditions. Pass 2 is observed in either photometric or good seeing conditions. Pass 3 is observed in any other usable conditions. The seeing thresholds for BASS and MzLS are 1 ′′ .7 and 1 ′′ .3, respectively. Normally, g-band observation occur on dark nights, r-band observations occur on dark or gray nights, and z band observations occur on gray and bright nights. The ETC can adjust the exposure time for each pass in real time according to sky brightness, seeing, atmospheric transparency, and Galactic extinction. In this way, both surveys can maintain uniform imaging depths for different passes. BASS began its observation in 2015 January. The survey was awarded 55, 89, and 92 nights in the spring of 2015, 2016, and 2017, respectively. Since 2015, a number of updates have been implemented, such as instrument control software, telescope flexure maps, and observing tools, which greatly improved the pointing accuracy of the telescope, camera focusing, and observing efficiency. It was discovered that data taken in 2015 suffered from defective electronics in the read-out system, so these data were much noisier. Those electronics were replaced in 2015 September. The MzLS began regular observations in 2016 February. The imaging data suffered from variable crosstalk and pattern noise, which must specially treated. The MzLS has completed its scheduled with about 250 total observations. Figure 2 presents the observation progress as of 2017 July. Some test regions (< 100 deg 2 ) located at Cosmic | 3,069,484 | 119462399 | 0 | 16 |
Evolution Survey (COS-MOS) and SDSS Stripe 82 fields are not shown in this figure. The BASS has completed about 72% of its scheduled observations, while the MzLS has completed about 76%. With typical observational conditions, BASS is expected to finish all observations in 2018, with an additional 100 nights. The MzLS completed the remaining observations before the Mayall telescope was shut down in 2018 February. Image processing The BASS and MzLS raw data are processed using the same pipeline. The basic corrections of overscan, bias, flat, and crosstalk effect are almost the same as those in BASS DR1. We make minor modifications when dealing with BASS data taken in 2015. The read-out mode was different in 2015. Bias frames were taken sequentially without flushing. Consequently, only the first bias frame can be used for bias subtraction. In addition, gain, readout noise, and crosstalk coefficients for each amplifier are calculated after the camera was remounted every summer. The identification of cosmic rays is also different in DR2. A Laplacian algorithm 3 originating from van Dokkum (2001) was used to detect cosmic rays. The crosstalk effect in MzLS data is much more serious than that in BASS data. The maximum intra-CCD crosstalk coefficient in MzLS reaches up to 5.2%, while for BASS it is only about 0.3%. There is also serious pattern noise in MzLS caused by the electromagnetic interference during CCD reading out, which is demonstrated in the left panel of Figure 3. We apply a low-pass filter to reconstruct the noise pattern. First, a 5-order low-pass | 3,069,485 | 119462399 | 0 | 16 |
Butterworth digital filter is designed by using the "butter" program in a Python package of SciPy 4 . Then, the low-pass filter is applied to the source-removed z-band image and a smoothed pattern is constructed as shown in the middle panel of Figure 3. Finally, the pattern is subtracted from the original image as shown in the right panel of this figure. Astrometry The Software for Calibrating AstroMetry and Photometry (SCAMP; Bertin 2006) is used for calculating astrometric solutions. In DR1, the SDSS and Two Micron All Sky Survey (2MASS; Skrutskie et al. 2006) pointsource catalogs were used as the reference catalogs. However, the Gaia (Gaia Collaboration et al. 2016) catalog is adopted in DR2. The first data release of Gaia (hereafter Gaia DR1; Gaia Collaboration et al. 2016) was published in 2016 September. It provides accurate astrometric measurements for objects in the G band down to 20.5 mag over the entire sky. There are some images (about 1.5%) with faulty astrometry due to sparse sources in Gaia cat- alogs, the 2MASS catalog is used to derive astrometric solutions for these. Figure 4 gives a comparison of the astrometric accuracy when using different reference catalogs. The astrometric accuracy is much improved when using the Gaia DR1 catalog as the reference. The median errors in R. A. and decl. are both about 28 mas. By contrast, if the SDSS catalog is used, the median errors in R. A. and decl. are about 93 mas. Zero-point calculation As in DR1, the DR2 still uses Pan-STARRS1 data (hereafter PS1; | 3,069,486 | 119462399 | 0 | 16 |
Chambers et al. 2016) to derive photometric solutions. A large aperture diameter of 26 pixels is used for counting source fluxes. The aperture is equivalent to about 11 ′′ .9 for BASS and 6 ′′ .8 for MzLS (i.e. about 7 times the seeing FWHM). Point sources with S/N larger than 10 are selected and then matched to the PS1 catalogs with a cross-matching radius of 2 ′′ . The PS1 magnitudes are transformed to the BASS and MzLS photometric systems using the following equations: These color terms are valid for stars with 0.4 < g − i < 2.7. The constant terms are kept to ensure no systematic offsets between BASS/MzLS and PS1. The zero-point of a CCD image is calculated as the error-weighted difference between instrumental aperture magnitudes and transformed PS1 PSF magnitudes with outliers removed. In addition to the zero-point obtained with the external catalogs discussed above, we can also calculate an internal zero-point by using objects located in overlaps of different exposures. We have three passes for each field. Each pass has sufficiently large position offsets. For a specified image, an internal zero-point offset is calculated by comparing magnitudes of common objects in adjacent images. This offset is derived iteratively until its change is less than 0.001. We require that there are at least 50 stars to calculate the offset and the maximum number of iterations is 20. Normally, the computations for most images are converged after 10 steps. Figure 5 shows the distributions of the zero-point offsets for different filters. The | 3,069,487 | 119462399 | 0 | 16 |
dispersions are 0.005, 0.008 and 0.01 for g, r, and z bands, respectively. Figure 6 gives an example of the performance of zero-point correction in one specially selected g-band image. This image is out of the PS1 coverage, so we use the Fourth US Naval Observatory CCD Astrograph Catalog to calculate a crude external zero-point. The histograms in this figure show the distributions of magnitude differences of common objects in multiple exposures before and after zero-point corrections are applied. We can see that after applying the corrections, both offset and scatter decrease. In practice, the internal zero point is used in DR2 only if the number of common stars are larger than 100 and its RMS error is less than 0.1. Otherwise the external zero-point is used. Photometry There are significant changes in source detection and photometry between DR1 and DR2. In DR1, the source detection and corresponding photometry are performed on single-epoch images. However, we detect sources in stacked images in order to improve the detection efficiency in DR2. The DR2 photometry occurs in singleepoch images based on the positions of those sources. Image stacking and source detection As described in Zou et al. (2017a), the full sky is equally divided into 96,775 blocks. These blocks are evenly spaced in decl.. Each block has an area of 0 • .681×0.681 deg 2 , equal to an image size of 5400 × 5400 with a pixel scale of 0 ′′ .454. There are overlaps of 0 • .02 in both R.A. and decl. between adjacent blocks. | 3,069,488 | 119462399 | 0 | 16 |
The stacked image is generated with a simple tangent-plane projection around the block center. We create four stacked images: three images for the g, r, and z bands and one composite from these three stacks. The composite image is combined from g, r, and z-band stacked images with flux scales of 0.65, 1.0, and 1.5, respectively, which makes the g − r and r − z colors of F/G type stars close to zero. These flux scales are also used for generating color pictures. For a specified band and block, we collect single-epoch images that are connected to the block. These images are resampled and reprojected by Swarp 5 and then combined by median to form a stacked image and corresponding weight image (Bertin et al. 2002). The sky background map for each single-exposure image is estimated by using a mesh with a grid size of 410 pixels and masking large objects from the Third Reference Catalog of bright galaxies (RC3) and New General Catalog (NGC). The flux of each single-epoch image is scaled to make the stack image have a photometric zero-point of 30 (i.e. magnitude is calculated as m = −2.5log 10 F + 30). The single-epoch images used for stacking should satisfy the following conditions: (a) exposure time > 30 s; (b) seeing < 3 ′′ .5 for BASS and < 2 ′′ .5 for MzLS; (c) zero-point RMS error < 0.2; (d) number of stars used for calculating the zero-point > 50; (e) astrometric RMS error in both R.A. and decl. < | 3,069,489 | 119462399 | 0 | 16 |
0 ′′ .5; (f) 5σ depths are at most 1.5 mag shallower than the required one; (g) sky ADU < 15,000 for BASS and < 25,000 for MzLS; (h) transparency > 0.5. Here the transparency is related to the level of atmospheric extinction. It is defined as 10 0.4(zp0−zp) , where zp is the zero-point of an image corrected with airmass and zp 0 is the typical zenith zero point on clear nights. Figure 7 gives examples of a g-band stacked image, its weight map, and corresponding color image composed of three-band stacked images. Source detections are performed first on the composite image and then separately on g-, r-, and z-band stacked images by SExtractor (Bertin & Arnouts 1996). Objects are kept only if they are detected at least twice in those four images. In this way, a majority of fake sources with brightnesses close to the detecting threshold in each stacked image can be filtered out. Table 3 lists some key configuration parameters that significantly im- pact our detection and deblending. We chose a relative small threshold, minimum number of connected pixels, and convolution kernel so as to detect as many objects as possible for a single band. In addition, the minimum contrast parameter of "DEBLEND MINCONST" is set to 0.001, which is determined as a compromise. A higher value will lead to more fragments of a large object and more fake sources within this object, while a lower value will give fewer fragments. Figure 8 shows Kron elliptical apertures (see Section 4.2.3) of final | 3,069,490 | 119462399 | 0 | 16 |
detected sources on composite images. From the left and middle panels of this figure, we can see that the deblending algorithm is suitable for small and medium-sized galaxies (typical size of about 1 arcmin). For larger extended galaxies, the deblending method may not be appropriate due to bright foreground stars and substructures hesitated in these galaxies. We also notice that there are still some fake sources surrounding large bright stars or galaxies that are detected due to large noise fluctuation. As checked with external deep catalogs from COSMOS and DEEP2 6 , about 8% of objects might be spurious. Most of these objects are located around bright stars and large galaxies. A few of them are probably CCD artifacts such as cosmic rays (especially in the z band), which are not well identified by the imaging pipeline or not effectively removed due to a lack of enough exposure numbers. Methods of photometry We have developed a new Python-based package for photometry (H. Zou et al. in preparation). It can be used for more general purposes, but at present it is just applied to BASS DR2. The current code can make accurate measurements of circular aperture, elliptical aperture, and PSF magnitudes at specific positions. However, model measurements with galaxy profiles, such as deVauculeurs, exponential profiles, and composite profiles, are still in development. We describe a few key features below. Segmentation and shape measurements Different kinds of magnitude measurements are performed on a single-epoch image for objects detected on stacked images. These objects are first projected onto the | 3,069,491 | 119462399 | 0 | 16 |
image. A watershed segmentation algorithm 7 is then adopted to separate signal pixels belonging to each object. The signal pixels are identified with a detecting threshold at 1σ above the sky background after the image is smoothed with a Gaussian kernel of σ = 1.5 pixels. The global sky background and its RMS map are calculated in mesh grids. Based on the segmentation of each object, we calculate the centroid, shape parameters, and refined center using a Gaussian-kernel window. The shape parameters describe the shape of an object as an ellipse, including semi-major (A) and semi-minor (B) axis lengths and position angle (PA). They are also called as 1σ elliptical parameters. Circular aperture photometry We adopt 12 apertures for circular aperture photometry with radii ranging from 3 to 40 pixels. These aperture sizes are the same as those used in the South Galactic Cap u-band Sky Survey, which utilized the Bok telescope and the 90Prime camera to perform a u-band imaging survey (Zou et al. 2015(Zou et al. , 2016Zhou et al. 2016). Table 4 shows the aperture radii in both pixels and arcseconds. Isophotal and Kron elliptical aperture photometry Isophotal magnitudes are derived by simply integrating pixel fluxes within segments. For better magnitude measurements of galaxies, we estimate an appropriate elliptical aperture for each object. The elliptical aperture should enclose most flux. We use the "Kron aperture", which was introduced in Kron (1980). The Kron aperture size is described by the Kron radius. This radius is determined in a similar way as in SExtractor. First, | 3,069,492 | 119462399 | 0 | 16 |
a characteristic radius r 1 is calculated as the first-order moment within an large ellipse, whose size is 6 times the 1σ ellipse: r 1 = rF (r) F (r) , where r is the elliptical distance of a pixel to the center and F (r) is the corresponding flux in this pixel. We set the Kron radius r k to be 2.5r 1 . The Kron aperture magnitudes are measured by integrating the fluxes of pixels within the Kron ellipse. The major and minor axis lengths of the Kron ellipse are computed as r k √ e and r k √ e , respectively, where e is the elongation. To avoid extremely small and large apertures, we set lower and upper limits of the Kron radius to be 3r 0 and 10r 0 , where r 0 = √ AB. It is shown that more than 94% of the light for galaxies is located in the Kron ellipse, al-most independent of their magnitudes. For both circular and Kron aperture photometry, special handling is done for objects contaminated by nearby sources in order to improve the photometric accuracy. In the aperture, the pixels occupied by nearby objects are filled by mirroring the opposite pixels relative to the object center. In addition, each pixel is divided into 5×5 sub-pixels to more accurately count the fluxes of pixels at the boundary of the aperture. PSF photometry PSF magnitudes are measured with the PSF model derived by PSFEx (Bertin 2011). PSFEx models the PSF as a linear combination of | 3,069,493 | 119462399 | 0 | 16 |
basis vectors. The pixel basis and automatic sampling step are selected in this software. We use a third-degree polynomial to model the positiondependent variation of the PSF. The PSF size is 45×45 for both BASS and MzLS, which is about 12 times the seeing FWHM. Table 5 lists some key input parameters in PSFEx. When fitting with the PSF model using our code, the pixels belonging to the segment of each object are used. If objects are not isolated, i.e. their segments are connected to each other, they are fitted simultaneously. We use k-means clustering to iteratively group objects. First, two groups are generated by the k-means clustering algorithm. Then the members in each group are divided into two subgroups using the same algorithm. All groups are divided in this way until the number of members in each group is not larger than three. Finally, all groups are ranked by their brightest members, and the PSF magnitudes in each group are measured simultaneously. Co-adding measurements Based on the detections on stacked images, we perform circular aperture, isophotal, Kron elliptical aperture, and PSF flux measurements on single-epoch images. As described in our DR1 paper (Zou et al. 2017a), the coordinates of objects are corrected with astrometric residuals, which mainly origin from poor charge transfer efficiencies of detectors. The amount of corrections is about a few percent of an arcsecond. All magnitudes are aperturecorrected with growth curves produced by circular aperture photometry. In addition, magnitudes are corrected with photometric residuals, which are mainly caused by the focal distortion, | 3,069,494 | 119462399 | 0 | 16 |
improper flat-fielding, and scattered light. These astrometric and photometric residuals are obtained by comparing the coordinates and magnitudes with those in the Gaia DR1 and PS1 catalogs, respectively. The parameters measured in single-epoch images are merged to generate co-added catalogs. For each object, we take weighted averages of the refined centers, shape parameters, and fluxes (equivalently magnitudes). Here, the weight is the inverse variance (w = 1 σ 2 ). Thus, the errors of these averages come from errors of single-epoch measurements, which are computed as 1 √ Σwi , where w i is the weight. We also calculate the parameter standard error, which is rms of multiple parameter measurements divided by the square root of the number of measurements. The standard error including all possible error sources is a more realistic error estimation. Particularly, a large magnitude standard error for a variable star indicates light variation. The effective seeing and sky background, number of exposures, and average, minimum, and maximum of the Julian day when observations were taken, are recorded in the catalogs. Data quality of single-epoch images The ETC ensures our imaging depths to meet the requirements, although the observing strategy entails different passes being observed under different weather conditions. Table 6 presents median observational and imaging parameters for different filters. The z-band seeing is the best. The depth is estimated as the median PSF magnitude at the error of about 0.21 mag (5σ). The single-epoch depths are 23.3, 23.1, and 22.6 mag for the g, r, and z bands, respectively. We also have | 3,069,495 | 119462399 | 0 | 16 |
checked that the depths for different passes of the same filter are quite similar owing to the ETC. Co-added Depths The depth requirements for DESI are 23.91, 23.47, and 22.60 mag for the g, r, and z bands, respectively, which are defined by 5σ extended sources with a correction of Galactic extinction and converted to our photometric systems with color terms as shown in Equation (4). The Galactic reddening map comes from Schlegel et al. (1998). We estimate the 5σ depths by using co-added PSF magnitude errors. Figure 9 shows the depth distributions of all blocks with exposure numbers equal to 3. They are so-called "full depth," with three complete passes. The g-band distribution has a fatter tail at the bright end. Because of this we include the data taken in 2015. These data were shallower due to the imperfect ETC and problematic due to bad A/D converters. The low bits of ADU integers were lost. This seriously affects the photometry of faint sources. This issue mostly affects the g-band images. Some of the affected areas have been re-observed in recent years and will be totally covered in future observations. Table 7 lists the median depths and fractions of objects for different exposure numbers. The median 5σ depths for the g, r, and z bands are 24.05, 23.61, and 23.10 mag, respectively. Most of the area covered by the g band has more than 3 exposures due to duplicate observations from 2015. Figure 10 shows the number counts of objects in the g, r and z | 3,069,496 | 119462399 | 0 | 16 |
bands in the regions of DEEP2 fields. The Kron magnitude is adopted here, which is a good brightness measurement for both stars and galaxies. The photometric data were taken with the CFH12K camera on the 3.6 m Canada-France-Hawaii Telescope and cover about 5 deg 2 over the sky, with completeness limits of B = 25.25, R = 24.75, and I = 24.25 mag (Coil et al. 2004). We overplot the R-band number count in Figure 10 after the R-band magnitude is converted to BASS r using a color term based on B − R. In general, the BASS and MzLS completeness limits reach or exceed the nominal DESI depths and the r-band magnitude distribution matches well with the DEEP2 R-band distribution. About 2% of objects have BASS r-band exposure numbers less than 3, so corresponding magnitude limits are about 0.3-0.6 mag shallower. This causes a slightly lower number count at r ∼ 22. In addition, different photometric systems and photometric methods between BASS and DEEP2 might also affect the discrepancy of the magnitude distribution. The co-added depths are 1.5-2.5 mag deeper than the SDSS imaging. For a visual comparison, we demonstrate the imaging data around a group of galaxies from both BASS/MzLS and SDSS in Figure 11. There are many more fainter objects that can be seen in BASS/MzLS images. The SDSS z-band is much shallower, leading to a much noisier background. Photometric comparisons The DECaLS has released its DR5 in 2017 June. Its typical depths with three exposures are 24.7, 23.6 and 22.8 mag for | 3,069,497 | 119462399 | 0 | 16 |
the g, r, and z bands, respectively. The g-band and r-band depths are a little deeper than those of BASS DR2, while the z band is somewhat shallower. There are some overlaps between DECaLS and BASS observations. These two surveys almost cover the whole SDSS footprint, but they are 1.5-2.5 mag deeper. We show some photometric comparisons of the three surveys with the data in the overlapping area. Figure 12 shows the magnitude difference as function of magnitude for point sources, which are randomly selected based on the morphological type in DECaLS DR5. The DECaLS and SDSS data are both transformed to the BASS/MzLS photometric systems using different color terms. The photometric scatters of point sources brighter than 20 mag between DECaLS and BASS are about half of those between SDSS and BASS. We also compare the color-color diagrams of three surveys with the same dataset (r < 23 mag), as shown in the upper panels of Figure 13. The color distributions of g − r at r − z ∼ 1.6 and r − z at g − r ∼ 0.7 are also shown in the middle and bottom panels of Figure 13. The standard deviations of the color distributions are annotated in each panel. From these plots, we can see that BASS DR2 is as good as DECaLS DR5, and it is obviously better than the SDSS data. 6. Data Access and Guidelines for DR2 Data Access Information about the surveys, such as the telescopes, instruments, and observations, can be retrieved on the public | 3,069,498 | 119462399 | 0 | 16 |
data release website 8 . The data cover the observations between 2015 January and 2017 July. There are 297,367 calibrated single-epoch CCD images. Those images with zero-point calibrations have corresponding catalogs. There are 13,419 blocks in total that have stacked images. For each block, there are three stacked images for the g, r, and z bands and one co-added catalog. The summary files for single-epoch images and blocks can be 10 · · · · · · · · · found on the webpage 9 . Figure 14 shows the sky coverage of the DR2 catalogs. In addition to the regular survey area as shown in a green envelope, there are some test regions (e.g. COSMOS and Stripe 82) and scattered regions with observations shared with BASS by other ob-9 http://batc.bao.ac.cn/BASS/doku.php?id=datarelease:dr2: home#data_access servers. Access to DR2 data is provided by the Chinese Virtual Observatory. Select data can be acquired from the following links. The sky viewer is based on Aladin HiPS 10 . 6.2. A few guidelines for using the data description on the wiki page 12 . The single-epoch images with the column "imq" = 1 are used for generating stacked images and co-added catalogs. There are several columns, as shown in Table 8, that denote astrometry qualities and zero-point. The "astr ref" have two options: GAIA-DR1 and 2MASS. Usually, the astrometric accuracy obtained from using 2MASS as the reference catalog is worse than that using the Gaia catalog. The internal and external zero-points are combined as "zp", which is used in our photometry. The | 3,069,499 | 119462399 | 0 | 16 |
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