Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.
Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution.


From discourse to pathology: Automatic identification of Parkinson's disease patients via morphological measures across three languages.
Embodied cognition research on Parkinson's disease (PD) points to disruptions of frontostriatal language functions as sensitive targets for clinical assessment. However, no existing approach has been tested for crosslinguistic validity, let alone by combining naturalistic tasks with machine-learning tools. To address these issues, we conducted the first classifier-based examination of morphological processing (a core frontostriatal function) in spontaneous monologues from PD patients across three typologically different languages. The study comprised 330 participants, encompassing speakers of Spanish (61 patients, 57 matched controls), German (88 patients, 88 matched controls), and Czech (20 patients, 16 matched controls). All subjects described the activities they perform during a regular day, and their monologues were automatically coded via morphological tagging, a computerized method that labels each word with a part-of-speech tag (e.g., noun, verb) and specific morphological tags (e.g., person, gender, number, tense). The ensuing data were subjected to machine-learning analyses to assess whether differential morphological patterns could classify between patients and controls and reflect the former's degree of motor impairment. Results showed robust classification rates, with over 80% of patients being discriminated from controls in each language separately. Moreover, the most discriminative morphological features were associated with the patients' motor compromise (as indicated by Pearson r correlations between predicted and collected motor impairment scores that ranged from moderate to moderate-to-strong across languages). Taken together, our results suggest that morphological patterning, an embodied frontostriatal domain, may be distinctively affected in PD across languages and even under ecological testing conditions.


Effect of side chains on competing pathways for beta-scission reactions of peptide-backbone alkoxyl radicals.
High-level quantum chemistry calculations have been carried out to investigate beta-scission reactions of alkoxyl radicals located at the alpha-carbon of a peptide backbone. This type of alkoxyl radical may undergo three possible beta-scission reactions, namely C-C beta-scission of the backbone, C-N beta-scission of the backbone, and C-R beta-scission of the side chain. We find that the rates for the C-C beta-scission reactions are all very fast, with rate constants of the order 10(12) s(-1) that are essentially independent of the side chain. The C-N beta-scission reactions are all slow, with rate constants that range from 10(-0.7) to 10(-4.5) s(-1). The rates of the C-R beta-scission reactions depend on the side chain and range from moderately fast (10(7) s(-1)) to very fast (10(12) s(-1)). The rates of the C-R beta-scission reactions correlate well with the relative stabilities of the resultant side-chain product radicals (*R), as reflected in calculated radical stabilization energies (RSEs). The order of stabilities for the side-chain fragment radicals for the natural amino acids is found to be Ala < Glu < Gln approximately Leu approximately Met approximately Lys approximately Arg < Asp approximately Ile approximately Asn approximately Val < Ser approximately Thr approximately Cys < Phe approximately Tyr approximately His approximately Trp. We predict that for side-chain C-R beta-scission reactions to effectively compete with the backbone C-C beta-scission reactions, the side-chain fragment radicals would generally need an RSE greater than approximately 30 kJ mol(-1). Thus, the residues that may lead to competitive side-chain beta-scission reactions are Ser, Thr, Cys, Phe, Tyr, His, and Trp.


Archaeal diversity in Icelandic hot springs.
Whole-cell density gradient extractions from three solfataras (pH 2.5) ranging in temperature from 81 to 90 degrees C and one neutral hot spring (81 degrees C, pH 7) from the thermal active area of Hveragerethi (Iceland) were analysed for genetic diversity and local geographical variation of Archaea by analysis of amplified 16S rRNA genes. In addition to the three solfataras and the neutral hot spring, 10 soil samples in transects of the soil adjacent to the solfataras were analysed using terminal restriction fragment length polymorphism (t-RFLP). The sequence data from the clone libraries in combination with 14 t-RFLP profiles revealed a high abundance of clones clustering together with sequences from the nonthermophilic I.1b group of Crenarchaeota. The archaeal diversity in one solfatara was high; 26 different RFLP patterns were found using double digestion of the PCR products with restriction enzymes AluI and BsuRI. The sequenced clones from this solfatara belonged to Sulfolobales, Thermoproteales or were most closest related to sequences from uncultured Archaea. Sequences related to group I.1b were not found in the neutral hot spring or the hyperthermophilic solfatara (90 degrees C).


Subcortical Neuronal Correlates of Sleep in Neurodegenerative Diseases.
Sleep disturbance is common among patients with neurodegenerative diseases. Examining the subcortical neuronal correlates of sleep disturbances is important to understanding the early-stage sleep neurodegenerative phenomena. To examine the correlation between the number of important subcortical wake-promoting neurons and clinical sleep phenotypes in patients with Alzheimer disease (AD) or progressive supranuclear palsy (PSP). This longitudinal cohort study enrolled 33 patients with AD, 20 patients with PSP, and 32 healthy individuals from the Memory and Aging Center of the University of California, San Francisco, between August 22, 2008, and December 31, 2020. Participants received electroencephalographic and polysomnographic sleep assessments. Postmortem neuronal analyses of brainstem hypothalamic wake-promoting neurons were performed and were included in the clinicopathological correlation analysis. No eligible participants were excluded from the study. Electroencephalographic and polysomnographic assessment of sleep and postmortem immunohistological stereological analysis of 3 wake-promoting nuclei (noradrenergic locus coeruleus [LC], orexinergic lateral hypothalamic area [LHA], and histaminergic tuberomammillary nucleus [TMN]). Nocturnal sleep variables, including total sleep time, sleep maintenance, rapid eye movement (REM) latency, and time spent in REM sleep and stages 1, 2, and 3 of non-REM (NREM1, NREM2, and NREM3, respectively) sleep, and wake after sleep onset. Neurotransmitter, tau, and total neuronal counts of LC, LHA, and TMN. Among 19 patients included in the clinicopathological correlation analysis, the mean (SD) age at death was 70.53 (7.75) years; 10 patients (52.6%) were female; and all patients were White. After adjusting for primary diagnosis, age, sex, and time between sleep analyses and death, greater numbers of LHA and TMN neurons were correlated with decreased homeostatic sleep drive, as observed by less total sleep time (LHA: r = -0.63; P = .009; TMN: r = -0.62; P = .008), lower sleep maintenance (LHA: r = -0.85; P < .001; TMN: r = -0.78; P < .001), and greater percentage of wake after sleep onset (LHA: r = 0.85; P < .001; TMN: r = 0.78; P < .001). In addition, greater numbers of LHA and TMN neurons were correlated with less NREM2 sleep (LHA: r = -0.76; P < .001; TMN: r = -0.73; P < .001). A greater number of TMN neurons was also correlated with less REM sleep (r = -0.61; P = .01). A greater number of LC neurons was mainly correlated with less total sleep time (r = -0.68; P = .008) and greater REM latency (r = 0.71; P = .006). The AD-predominant group had significantly greater sleep drive, including higher total sleep time (mean [SD], 0.49 [1.18] vs -1.09 [1.37]; P = .03), higher sleep maintenance (mean [SD], 0.18 [1.22] vs -1.53 [1.78]; P = .02), and lower percentage of wake after sleep onset during sleep period time (mean [SD], -0.18 [1.20] vs 1.49 [1.72]; P = .02) than the PSP-predominant group based on unbiased k-means clustering and principal component analyses. In this cohort study, subcortical wake-promoting neurons were significantly correlated with sleep phenotypes in patients with AD and PSP, suggesting that the loss of wake-promoting neurons among patients with neurodegenerative conditions may disturb the control of sleep-wake homeostasis. These findings suggest that the subcortical system is a primary mechanism associated with sleep disturbances in the early stages of neurodegenerative diseases.


Two bactericidal targets for penicillin in pneumococci: autolysis-dependent and autolysis-independent killing mechanisms.
It has been assumed that penicillin (and also other cell wall inhibitors) kill pneumococci predominantly by triggering their major autolytic enzyme (an N-acetylmuramoyl-L-alanine amidase; referred to as amidase), resulting in massive cell wall degradation. Three types of experiments suggest that only part of this killing is due to cell lysis by amidase. (i) Suppression of penicillin-induced lysis by specific inhibitors of amidase protected pneumococci only marginally from killing in spite of prolonged exposure to concentrations of penicillin that were 10x, 20x, or 100x greater than the MIC. (ii) Mutants from which the amidase was completely eliminated by plasmid insertion or deletion (Lyt-) were still killed, albeit at a slower rate than the wild-type Lyt+ strains (3 to 4 log units instead of 4 to 5 log units per 6 h, i.e., about 1 log unit slower than the wild type; P less than 0.001). (iii) A new mutation (cid), which was not related to the amidase gene, further reduced killing of mutants lacking amidase to 1 log unit per 6 h (Lyt- Cid- phenotype). Reintroduction of the amidase gene into Lyt- Cid- cells partially restored penicillin-induced lysis but increased only slightly the rate of killing (from 1 log unit per 6 h in Lyt- Cid- cells to 2 log units per 6 h in Lyt+ Cid- cells). We conclude that penicillin kills pneumococci by two distinct mechanisms: one that involves the triggering of the amidase (about 1 log unit of killing per 6 h) and another, amidase-independent mechanism that is responsible for 3 to 4 log units of killing per 6 h. Triggering of the amidase activity in situ in growing bacteria was significantly reduced in Lyt+ Cid- cells, indicating that there is some regulatory interaction between the cid gene product and the amidase.


Diverging mental health after Brexit: Evidence from a longitudinal survey.
This study analyses the changes in mental health in the UK that occurred as a result of the 2016 referendum on UK membership of the EU (Brexit). Using the Household Longitudinal Study, we compare the levels of self-reported mental distress, mental functioning and life satisfaction be-fore and after the referendum. A linear fixed effects analysis revealed an overall decrease in mental health post-referendum with higher levels of mental distress, and a decline in the SF-12 Mental Component Summary score. Furthermore, the study does not find evidence of significant changes in overall life satisfaction in the two years after the referendum. Younger men, highly educated and Natives, especially those living in stronger "Remain areas", seem to be the groups most affected by the Brexit in terms of mental health. Overall, the results of this study suggest that the outcome of the referendum and the economic uncertainty that it brought impacted the mental health of voters in a negative and diverging way.


Genetic determination of plasma apolipoprotein AI in a population-based sample.
Apolipoprotein AI (apo AI) is the major protein of high-density lipoprotein (HDL). Using radioimmunoassay, we measured plasma apo AI levels in 1,880 individuals in 283 pedigrees randomly selected from the population with respect to disease status and risk factors for coronary artery disease. Apo AI levels were first adjusted for date of assay (6.8% of apo AI variation) and then adjusted for variability in age and body mass index (an additional 6.6%, 20.4%, and 23.0% of apo AI variations for males, females not using exogenous hormones, and females using exogenous hormones, respectively). A mixture of two normal distributions fit the adjusted data better than did a single normal distribution. Genetic and environmental models that could explain the mixture of normal distributions were investigated using complex segregation analysis. Heterogeneous etiologies for individual differences in adjusted apo AI levels were suggested by the data in the 283 pedigrees. In a subset of 126 pedigrees, there is evidence for the major effect of a nontransmitted environmental factor that explains the mixture of distributions as well as polygenic loci that influence apo AI levels within each distribution. The environmental factor and polygenic loci account for 32% and 65% of the adjusted variation, respectively. In the other 157 pedigrees there is strong support for a single locus with a major effect that accounts for 27% of the adjusted variation. The effect of the polygenic loci is not different from zero in these 157 pedigrees. This is the first study to present evidence for the segregation of a single unmeasured locus with a major effect on levels of apo AI in a population-based sample of pedigrees.


Ion mobility-mass spectrometry analysis of large protein complexes.
Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry.


Integrated omics-analysis reveals Wnt-mediated NAD+ metabolic reprogramming in cancer stem-like cells.
Abnormal tumor cell metabolism is a consequence of alterations in signaling pathways that provide critical selective advantage to cancer cells. However, a systematic characterization of the metabolic and signaling pathways altered in cancer stem-like cells (CSCs) is currently lacking. Using nuclear magnetic resonance and mass spectrometry, we profiled the whole-cell metabolites of a pair of parental (P-231) and stem-like cancer cells (S-231), and then integrated with whole transcriptome profiles. We identified elevated NAAD+ in S-231 along with a coordinated increased expression of genes in Wnt/calcium signaling pathway, reflecting the correlation between metabolic reprogramming and altered signaling pathways. The expression of CD38 and ALP, upstream NAAD+ regulatory enzymes, was oppositely regulated between P- and S-231; high CD38 strongly correlated with NAADP in P-231 while high ALP with NAAD+ levels in S-231. Antagonizing Wnt activity by dnTCF4 transfection reversed the levels of NAAD+ and ALP expression in S-231. Of note, elevated NAAD+ caused a decrease of cytosolic Ca2+ levels preventing calcium-induced apoptosis in nutrient-deprived conditions. Reprograming of NAD+ metabolic pathway instigated by Wnt signaling prevented cytosolic Ca2+ overload thereby inhibiting calcium-induced apoptosis in S-231. These results suggest that "oncometabolites" resulting from cross talk between the deranged core cancer signaling pathway and metabolic network provide a selective advantage to CSCs.


Olive oil's bitter principle reverses acquired autoresistance to trastuzumab (Herceptin) in HER2-overexpressing breast cancer cells.
A low incidence of breast cancer in the Mediterranean basin suggests that a high consumption of Extra Virgin Olive Oil (EVOO) might confer this benefit. While the anti-HER2 oncogene effects of the main omega-9 fatty acid present in EVOO triacylglycerols (i.e., oleic acid) have been recently described, the anti-breast cancer activities of EVOO non-glyceridic constituents--which consist of at least 30 phenolic compounds--remained to be evaluated. Semi-preparative HPLC was used to isolate EVOO polyphenols (i.e., tyrosol, hydroxytyrosol, oleuropein). Both the anti-proliferative and the pro-apoptotic effects of EVOO phenolics were evaluated by using MTT-based quantification of metabolically viable cells and ELISA-based detection of histone-associated DNA fragments, respectively. The nature of the interaction between oleuropein aglycone and the anti-HER2 monoclonal antibody trastuzumab (Herceptin) was mathematically evaluated by the dose-oriented isobologram technique. HER2-specific ELISAs were employed to quantitatively assess both the basal cleavage of the HER2 extracellular domain (ECD) and the expression level of total HER2. The activation status of HER2 was evaluated by immunoblotting procedures using a monoclonal antibody specifically recognizing the tyrosine phosphorylated (Phosphor-Tyr1248) form of HER2. Among EVOO polyphenols tested, oleuropein aglycone was the most potent EVOO phenolic in decreasing breast cancer cell viability. HER2 gene-amplified SKBR3 cells were ~5-times more sensitive to oleuropein aglycone than HER2-negative MCF-7 cells. Retroviral infection of the HER2 oncogene in MCF-7 cells resulted in a "SKBR3-assimilated" phenotype of hypersensitivity to oleuropein aglycone. An up to 50-fold increase in the efficacy of trastuzumab occurred in the presence of oleuropein aglycone. A preclinical model of acquired autoresistance to trastuzumab (SKBR3/Tzb100 cells) completely recovered trastuzumab sensitivity (> 1,000-fold sensitization) when co-cultured in the presence of oleuropein aglycone. Indeed, the nature of the interaction between oleuropein aglycone and trastuzumab was found to be strongly synergistic in Tzb-resistant SKBR3/Tzb100 cells. Mechanistically, oleuropein aglycone treatment significantly reduced HER2 ECD cleavage and subsequent HER2 auto-phosphorylation, while it dramatically enhanced Tzb-induced down-regulation of HER2 expression. Olive oil's bitter principle (i.e., oleuropein aglycone) is among the first examples of how selected nutrients from an EVOO-rich "Mediterranean diet" directly regulate HER2-driven breast cancer disease.


Postnatal changes in the expression of the trkA high-affinity NGF receptor in primary sensory neurons.
In development approximately 70-80% of dorsal root ganglion (DRG) cells are dependent on nerve growth factor (NGF) for their survival, while in the adult only some 40% of DRG cells express the high-affinity NGF receptor, trkA. This discrepancy suggests that trkA expression, and therefore neurotrophin sensitivity, may alter as the animal matures. We have tested this possibility by counting the number of L4/5 DRG neurons showing immunoreactivity for trkA in rats from the day of birth to postnatal day 14. We also examined changes in p75 and IB4 labelling. On the day of birth, 71% of DRG cells were found to express trkA. However, this percentage gradually fell with age and reached adult levels at postnatal day 14. The expression of p75 did not parallel that of trkA, remaining relatively constant at between 45 and 50% of cells from birth to postnatal day 14. Over the same period there was a marked increase in the proportion of cells which bind the lectin IB4 from 9 (day of birth) to 40% (day 14). Since in the adult the IB4 population consists of small cells which mostly do not express trkA, this finding suggests that the postnatal down-regulation of trkA occurs in this population. Consistent with this suggestion are the results of double labelling for trkA and IB4, which confirmed that at times intermediate between birth and postnatal day 14 there was a high degree of coexpression between these markers (which is absent in the adult). This result also suggests that the down-regulation of trkA is unlikely to be directly responsible for the emerging IB4 binding.


Evaluation of the molecular mechanisms of a palladium(II) saccharinate complex with terpyridine as an anticancer agent.
Metal-based compounds represent promising anticancer therapeutic agents. In this study, the mechanism of action of a novel metal-based drug, a palladium(II) (Pd) complex ([PdCl(terpy)](sac)·2H2O, terpy=2,2':6',2''-terpyridine and sac=saccharinate), was elucidated. The tested compound induced cytotoxicity in nine different human cancer cell lines that originated from various organs, suggesting a broad spectrum of activity. The IC50 values were significantly higher for noncancerous cells when compared with cancer cells. We found that cells treated with the Pd(II) complex exhibited increased caspase 3/7 activities and condensed/fragmented nuclei, as demonstrated by nuclear staining and DNA laddering. Morphological features, such as cellular shrinkage and blebbing, were also observed, indicating that apoptosis was the primary mechanism of cell death. Pd(II) treatment induced DNA double-stranded breaks both in vitro and in vivo, potentially accounting for the source of stress in these cells. Although caspase 3/7 activities were elevated after Pd(II) treatment, silencing or using inhibitors of caspase 3 did not block apoptosis. Other molecules that could potentially play a role in Pd(II)-induced apoptosis, such as p53 and Bax, were also tested using silencing technology. However, none of these proteins were essential for cell death, indicating either that these molecules do not participate in Pd(II)-induced apoptosis or that other pathways were activated in their absence. Hence, this new molecule might represent a promising anticancer agent that exhibits cytotoxicity in p53-mutant, Bax-mutant, and/or caspase 3-mutant cancer cells.


Association between Obesity and Physical Fitness, and Hemoglobin A1c Level and Metabolic Syndrome in Korean Adults.
The purpose of the current study was to investigate the association of obesity level, physical fitness level, hemoglobin A1c (HbA1c) level and metabolic syndrome (MetS) risk factors among Korean adults. A total of 557 adults (272 males and 285 females) who underwent medical check-up at local hospital were recruited. In addition to regular health check-up, cardiopulmonary fitness, muscular endurance were measured and their association were analyzed. The prevalence of MetS was 31.7% for males and 23.7% for females. Females with the higher muscular endurance had lower waist circumference, triglyceride level, and HbA1c level than those with the lower muscular endurance. Males with the higher level of cardiopulmonary fitness had lower diastolic blood pressure, lower high-sensitivity C-reactive protein level and higher high density lipoprotein cholesterol level than males with the lower level of cardiopulmonary fitness. Females with the higher level of cardiopulmonary fitness had lower body weight, body mass index, systolic blood pressure, and fasting blood glucose level than females with the lower level of cardiopulmonary fitness. Participants with the higher level of adiposity and the lower level of physical fitness were 5.26 times (95% confidence interval [CI], 2.19 to 12.62), 5.71 times (95% CI, 2.23 to 14.60) more likely to have MetS, respectively, in male and female compared to participants who were neither obese nor have the lower level of fitness. This study suggests that maintaining a healthy body weight as well as a certain level of fitness is important for the prevention of MetS.


Brain and behavioral correlates of action semantic deficits in autism.
Action-perception circuits containing neurons in the motor system have been proposed as the building blocks of higher cognition; accordingly, motor dysfunction should entail cognitive deficits. Autism spectrum conditions (ASC) are marked by motor impairments but the implications of such motor dysfunction for higher cognition remain unclear. We here used word reading and semantic judgment tasks to investigate action-related motor cognition and its corresponding fMRI brain activation in high-functioning adults with ASC. These participants exhibited hypoactivity of motor cortex in language processing relative to typically developing controls. Crucially, we also found a deficit in semantic processing of action-related words, which, intriguingly, significantly correlated with this underactivation of motor cortex to these items. Furthermore, the word-induced hypoactivity in the motor system also predicted the severity of ASC as expressed by the number of autistic symptoms measured by the Autism-Spectrum Quotient (Baron-Cohen etal., 2001). These significant correlations between word-induced activation of the motor system and a newly discovered semantic deficit in a condition known to be characterized by motor impairments, along with the correlation of such activation with general autistic traits, confirm critical predictions of causal theories linking cognitive and semantic deficits in ASC, in part, to dysfunctional action-perception circuits and resultant reduction of motor system activation.


Significant Impact of Coffee Consumption on MR-Based Measures of Cardiac Function in a Population-Based Cohort Study without Manifest Cardiovascular Disease.
Subclinical effects of coffee consumption (CC) with regard to metabolic, cardiac, and neurological complications were evaluated using a whole-body magnetic resonance imaging (MRI) protocol. A blended approach was used to estimate habitual CC in a population-based study cohort without a history of cardiovascular disease. Associations of CC with MRI markers of gray matter volume, white matter hyperintensities, cerebral microhemorrhages, total and visceral adipose tissue (VAT), hepatic proton density fat fraction, early/late diastolic filling rate, end-diastolic/-systolic and stroke volume, ejection fraction, peak ejection rate, and myocardial mass were evaluated by linear regression. In our analysis with 132 women and 168 men, CC was positively associated with MR-based cardiac function parameters including late diastolic filling rate, stroke volume (p < 0.01 each), and ejection fraction (p < 0.05) when adjusting for age, sex, smoking, hypertension, diabetes, Low-density lipoprotein (LDL), triglycerides, cholesterol, and alcohol consumption. CC was inversely associated with VAT independent of demographic variables and cardiovascular risk factors (p < 0.05), but this association did not remain significant after additional adjustment for alcohol consumption. CC was not significantly associated with potential neurodegeneration. We found a significant positive and independent association between CC and MRI-based systolic and diastolic cardiac function. CC was also inversely associated with VAT but not independent of alcohol consumption.


Search for new phenomena in tt events with large missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV with the ATLAS detector.
A search for new phenomena in tt events with large missing transverse momentum in proton-proton collisions at a center-of-mass energy of 7 TeV is presented. The measurement is based on 1.04 fb(-1) of data collected with the ATLAS detector at the LHC. Contributions to this final state may arise from a number of standard model extensions. The results are interpreted in terms of a model where new top-quark partners are pair produced and each decay to an on-shell top (or antitop) quark and a long-lived undetected neutral particle. The data are found to be consistent with standard model expectations. A limit at 95% confidence level is set excluding a cross section times branching ratio of 1.1 pb for a top-partner mass of 420 GeV and a neutral particle mass less than 10 GeV. In a model of exotic fourth generation quarks, top-partner masses are excluded up to 420 GeV and neutral particle masses up to 140 GeV.


Scattering theory derivation of a 3D acoustic cloaking shell.
Through acoustic scattering theory we derive the mass density and bulk modulus of a spherical shell that can eliminate scattering from an arbitrary object in the interior of the shell--in other words, a 3D acoustic cloaking shell. Calculations confirm that the pressure and velocity fields are smoothly bent and excluded from the central region as for previously reported electromagnetic cloaking shells. The shell requires an anisotropic mass density with principal axes in the spherical coordinate directions and a radially dependent bulk modulus. The existence of this 3D cloaking shell indicates that such reflectionless solutions may also exist for other wave systems that are not isomorphic with electromagnetics.


Endothelial C3a receptor mediates vascular inflammation and blood-brain barrier permeability during aging.
Dysfunction of immune and vascular systems has been implicated in aging and Alzheimer disease; however, their interrelatedness remains poorly understood. The complement pathway is a well-established regulator of innate immunity in the brain. Here, we report robust age-dependent increases in vascular inflammation, peripheral lymphocyte infiltration, and blood-brain barrier (BBB) permeability. These phenotypes were subdued by global inactivation and by endothelial cell-specific ablation of C3ar1. Using an in vitro model of the BBB, we identified intracellular Ca2+ as a downstream effector of C3a/C3aR signaling and a functional mediator of vascular endothelial cadherin junction and barrier integrity. Endothelial C3ar1 inactivation also dampened microglia reactivity and improved hippocampal and cortical volumes in the aging brain, demonstrating a crosstalk between brain vasculature dysfunction and immune cell activation and neurodegeneration. Further, prominent C3aR-dependent vascular inflammation was also observed in a tau-transgenic mouse model. Our studies suggest that heightened C3a/C3aR signaling through endothelial cells promotes vascular inflammation and BBB dysfunction and contributes to overall neuroinflammation in aging and neurodegenerative disease.


Propagation constants of resonant waves on homogeneous, isotropic slab waveguides.
A general graphical study of the complex valued propagation constants, defining the various types of TE waves that are resonant on optical thin-film (slab) waveguides, is presented. The dielectric constants of both the slab and its surroundings are allowed to take on all possible complex values. The corresponding waves are classified into two general types: surface waves, with conductive losses only; and leaky waves, with both conductive and radiative losses.


Sleep deprivation directly following eyeblink-conditioning impairs memory consolidation.
The relation between sleep and different forms of memory formation continues to be a relevant topic in our daily life. Sleep has been found to affect cerebellum-dependent procedural memory formation, but it remains to be elucidated to what extent the level of sleep deprivation directly after motor training also influences our ability to store and retrieve memories. Here, we studied the effect of disturbed sleep in mice during two different time-windows, one covering the first four hours following eyeblink conditioning (EBC) and another window following the next period of four hours. Compared to control mice with sleep ad libitum, the percentage of conditioned responses and their amplitude were impaired when mice were deprived of sleep directly after conditioning. This impairment was still significant when the learned EBC responses were extinguished and later reacquired. However, consolidation of eyeblink responses was not affected when mice were deprived later than four hours after acquisition, not even when tested during a different day-night cycle for control. Moreover, mice that slept longer directly following EBC showed a tendency for more conditioned responses. Our data indicate that consolidation of motor memories can benefit from sleep directly following memory formation.


Conditional knockout of Mn-SOD targeted to type IIB skeletal muscle fibers increases oxidative stress and is sufficient to alter aerobic exercise capacity.
In vitro studies of isolated skeletal muscle have shown that oxidative stress is limiting with respect to contractile function. Mitochondria are a potential source of muscle function-limiting oxidants. To test the hypothesis that skeletal muscle-specific mitochondrial oxidative stress is sufficient to limit muscle function, we bred mice expressing Cre recombinase driven by the promoter for the inhibitory subunit of troponin (TnIFast-iCre) with mice containing a floxed Sod2 (Sod2(fl/fl)) allele. Mn-SOD activity was reduced by 82% in glycolytic (mainly type II) muscle fiber homogenates from young TnIFastCreSod2(fl/fl) mice. Furthermore, Mn-SOD content was reduced by 70% only in type IIB muscle fibers. Aconitase activity was decreased by 56%, which suggests an increase in mitochondrial matrix superoxide. Mitochondrial superoxide release was elevated more than twofold by mitochondria isolated from glycolytic skeletal muscle in TnIFastCreSod2(fl/fl) mice. In contrast, the rate of mitochondrial H(2)O(2) production was reduced by 33%, and only during respiration with complex II substrate. F(2)-isoprostanes were increased by 36% in tibialis anterior muscles isolated from TnIFastCreSod2(fl/fl) mice. Elevated glycolytic muscle-specific mitochondrial oxidative stress and damage in TnIFastCreSod2(fl/fl) mice were associated with a decreased ability of the extensor digitorum longus and gastrocnemius muscles to produce contractile force as a function of time, whereas force production by the soleus muscle was unaffected. TnIFastCreSod2(fl/fl) mice ran 55% less distance on a treadmill than wild-type mice. Collectively, these data suggest that elevated mitochondrial oxidative stress and damage in glycolytic muscle fibers are sufficient to reduce contractile muscle function and aerobic exercise capacity.


Envisioning a social-health information exchange as a platform to support a patient-centered medical neighborhood: a feasibility study.
Social determinants directly contribute to poorer health, and coordination between healthcare and community-based resources is pivotal to addressing these needs. However, our healthcare system remains poorly equipped to address social determinants of health. The potential of health information technology to bridge this gap across the delivery of healthcare and social services remains unrealized. We conducted in-depth, in-person interviews with 50 healthcare and social service providers to determine the feasibility of a social-health information exchange (S-HIE) in an urban safety-net setting in Dallas County, Texas. After completion of interviews, we conducted a town hall meeting to identify desired functionalities for a S-HIE. We conducted thematic analysis of interview responses using the constant comparative method to explore perceptions about current communication and coordination across sectors, and barriers and enablers to S-HIE implementation. We sought participant confirmation of findings and conducted a forced-rank vote during the town hall to prioritize potential S-HIE functionalities. We found that healthcare and social service providers perceived a need for improved information sharing, communication, and care coordination across sectors and were enthusiastic about the potential of a S-HIE, but shared many technical, legal, and ethical concerns around cross-sector information sharing. Desired technical S-HIE functionalities encompassed fairly simple transactional operations such as the ability to view basic demographic information, visit and referral data, and medical history from both healthcare and social service settings. A S-HIE is an innovative and feasible approach to enabling better linkages between healthcare and social service providers. However, to develop S-HIEs in communities across the country, policy interventions are needed to standardize regulatory requirements, to foster increased IT capability and uptake among social service agencies, and to align healthcare and social service priorities to enable dissemination and broader adoption of this and similar IT initiatives.


Areas of global importance for conserving terrestrial biodiversity, carbon and water.
To meet the ambitious objectives of biodiversity and climate conventions, the international community requires clarity on how these objectives can be operationalized spatially and how multiple targets can be pursued concurrently. To support goal setting and the implementation of international strategies and action plans, spatial guidance is needed to identify which land areas have the potential to generate the greatest synergies between conserving biodiversity and nature's contributions to people. Here we present results from a joint optimization that minimizes the number of threatened species, maximizes carbon retention and water quality regulation, and ranks terrestrial conservation priorities globally. We found that selecting the top-ranked 30% and 50% of terrestrial land area would conserve respectively 60.7% and 85.3% of the estimated total carbon stock and 66% and 89.8% of all clean water, in addition to meeting conservation targets for 57.9% and 79% of all species considered. Our data and prioritization further suggest that adequately conserving all species considered (vertebrates and plants) would require giving conservation attention to ~70% of the terrestrial land surface. If priority was given to biodiversity only, managing 30% of optimally located land area for conservation may be sufficient to meet conservation targets for 81.3% of the terrestrial plant and vertebrate species considered. Our results provide a global assessment of where land could be optimally managed for conservation. We discuss how such a spatial prioritization framework can support the implementation of the biodiversity and climate conventions.


Smoking abstinence and depressive symptoms modulate the executive control system during emotional information processing.
Smoking abstinence disrupts affective and cognitive processes. In this study, functional magnetic resonance imaging (fMRI) was used to investigate the effects of smoking abstinence on emotional information processing. Smokers (n = 17) and non-smokers (n = 18) underwent fMRI while performing an emotional distractor oddball task in which rare targets were presented following negative and neutral task-irrelevant distractors. Smokers completed two sessions: once following 24-hour abstinence and once while satiated. The abstinent versus satiated states were compared by evaluating responses to distractor images and to targets following each distractor valence within frontal executive and limbic brain regions. Regression analyses were done to investigate whether self-reported negative affect influences brain response to images and targets. Exploratory regression analyses examined relations between baseline depressive symptoms and smoking state on brain function. Smoking state affected response to target detection in the right inferior frontal gyrus (IFG). During satiety, activation was greater in response to targets following negative versus neutral distractors; following abstinence, the reverse was observed. Withdrawal-related negative affect was associated with right insula activation to negative images. Finally, depression symptoms were associated with abstinence-induced hypoactive response to negative emotional distractors and task-relevant targets following negative distractors in frontal brain regions. Neural processes related to novelty detection/attention in the right IFG may be disrupted by smoking abstinence and negative stimuli. Reactivity to emotional stimuli and the interfering effects on cognition are moderated by the magnitude of smoking state-dependent negative affect and baseline depressive symptoms.


Estimating low-density lipoprotein cholesterol by the Friedewald equation is adequate for classifying patients on the basis of nationally recommended cutpoints.
We compared low-density lipoprotein cholesterol (LDL) values obtained by the Friedewald formula--i.e., total cholesterol minus high-density lipoprotein (HDL) cholesterol minus very-low-density lipoprotein (VLDL) cholesterol (estimated as triglyceride divided by 5)--with those obtained by lipoprotein fractionation, using 4736 specimens. When triglycerides were less than 2.0 g/L, greater than 90% of estimated LDL cholesterol values were acceptable, within +/- 10% of measured values. At triglyceride concentrations of 2.0-4.0 g/L and 4.0-6.0 g/L, only 72% and 39%, respectively, of the estimates were acceptable. LDL values derived from an alternative formula, estimating VLDL as triglycerides divided by 6, were even less accurate. Nevertheless, the use of estimated LDL for risk classification based on the National Cholesterol Education Program Adult Treatment Panel cutpoints of 1.30 and 1.60 g/L was considered acceptable. At triglyceride concentrations less than or equal to 5.0 g/L, 88% of classifications based on estimated LDL (using triglycerides divided by 5) were concordant with those by measured LDL. Eleven percent of classifications were shifted across one cutpoint, evenly distributed between high and low. Fewer than 1% of classifications, all with Type III hyperlipoproteinemia, were misclassified two cutpoints high. Refinements in the estimation model did not substantially improve LDL estimation or concordance of risk classification.


Orthographic distinctiveness and semantic elaboration provide separate contributions to memory.
Orthographic distinctiveness and semantic elaboration both enhance memory. The present behavioral and functional magnetic resonance imaging (fMRI) studies examined the relationship between the influences of orthographic distinctiveness and semantic elaboration on memory, and explored whether they make independent contributions. As is typical for manipulations of processing levels, words studied during semantic encoding were better remembered than words studied during nonsemantic encoding. Notably, orthographically distinct words were better recalled and received more remember responses on recognition memory tests than orthographically common words regardless of encoding task, suggesting that orthographic distinctiveness has an additive effect to that of semantic elaboration on memory. In the fMRI study, orthographic distinctiveness and semantic elaboration engaged separate networks of brain regions. Semantic elaboration modulated activity in left inferior prefrontal and lateral temporal regions. In contrast, orthographic distinctiveness modulated activity in distinct bilateral inferior prefrontal, extrastriate, and parietal regions. Orthographic distinctiveness and semantic elaboration appear to have separate behavioral and functional-anatomic contributions to memory.


Enhanced transcription of the Arabidopsis disease resistance genes RPW8.1 and RPW8.2 via a salicylic acid-dependent amplification circuit is required for hypersensitive cell death.
The Arabidopsis disease resistance (R) genes RPW8.1 and RPW8.2 couple the recognition of powdery mildew pathogens of this plant with the subsequent induction of a localized necrosis, or hypersensitive response (HR). The HR restricts the spread of the infection and renders the plant resistant. One-third of Arabidopsis plants transformed with a genomic fragment containing RPW8.1 and RPW8.2 developed spontaneous HR-like lesions (SHL) in the absence of pathogens. We demonstrate that SHL occurs in transgenic lines that contain multiple copies of the transgene and express RPW8.1 and RPW8.2 at high levels. SHL is associated with salicylic acid (SA) accumulation, and at the site of the lesion, there is increased expression of RPW8.1, increased production of H(2)O(2), and increased expression of pathogenesis-related genes. These lesions are physiologically similar to the pathogen-induced HR mediated by RPW8.1 and RPW8.2. Significantly, environmental conditions that suppress SHL suppress the transcription of RPW8.1 and RPW8.2 and also suppress resistance to powdery mildews, even in transgenic lines containing RPW8.1 and RPW8.2 that normally do not express SHL. Furthermore, treatment with SA increases the transcription of RPW8.1 and RPW8.2, induces SHL, and enhances resistance to powdery mildews. We conclude that HR requires the transcription of RPW8.1 and RPW8.2, which is regulated independently of the pathogen by SA-dependent feedback amplification.


Seasonal and regional short-term effects of fine particles on hospital admissions in 202 US counties, 1999-2005.
The authors investigated whether short-term effects of fine particulate matter with an aerodynamic diameter < or =2.5 microm (PM(2.5)) on risk of cardiovascular and respiratory hospitalizations among the elderly varied by region and season in 202 US counties for 1999-2005. They fit 3 types of time-series models to provide evidence for 1) consistent particulate matter effects across the year, 2) different particulate matter effects by season, and 3) smoothly varying particulate matter effects throughout the year. The authors found statistically significant evidence of seasonal and regional variation in estimates of particulate matter effect. Respiratory disease effect estimates were highest in winter, with a 1.05% (95% posterior interval: 0.29, 1.82) increase in hospitalizations per 10-microg/m(3) increase in same-day PM(2.5). Cardiovascular diseases estimates were also highest in winter, with a 1.49% (95% confidence interval: 1.09, 1.89) increase in hospitalizations per 10-microg/m(3) increase in same-day PM(2.5), with associations also observed in other seasons. The strongest evidence of a relation between PM(2.5) and hospitalizations was in the Northeast for both respiratory and cardiovascular diseases. Heterogeneity of PM(2.5) effects on hospitalizations may reflect seasonal and regional differences in emissions and in particles' chemical constituents. Results can help guide development of hypotheses and further epidemiologic studies on potential heterogeneity in the toxicity of constituents of the particulate matter mixture.


Compressed vessels bias red blood cell partitioning at bifurcations in a hematocrit-dependent manner: Implications in tumor blood flow.
The tumor microenvironment is abnormal and associated with tumor tissue hypoxia, immunosuppression, and poor response to treatment. One important abnormality present in tumors is vessel compression. Vessel decompression has been shown to increase survival rates in animal models via enhanced and more homogeneous oxygenation. However, our knowledge of the biophysical mechanisms linking tumor decompression to improved tumor oxygenation is limited. In this study, we propose a computational model to investigate the impact of vessel compression on red blood cell (RBC) dynamics in tumor vascular networks. Our results demonstrate that vessel compression can alter RBC partitioning at bifurcations in a hematocrit-dependent and flow rate-independent manner. We identify RBC focusing due to cross-streamline migration as the mechanism responsible and characterize the spatiotemporal recovery dynamics controlling downstream partitioning. Based on this knowledge, we formulate a reduced-order model that will help future research to elucidate how these effects propagate at a whole vascular network level. These findings contribute to the mechanistic understanding of hemodilution in tumor vascular networks and oxygen homogenization following pharmacological solid tumor decompression.


Production of autoimmune gastric hyperplasia in mice by the transfer of spleen cells from thymectomized donors.
Previous work showed that mice that had been thymectomized at 3 days of age tended, in later life, to develop a hyperplastic autoimmune gastritis and were also hypersusceptible to sarcogenesis by low dosages of 3-methylcholanthrene. In the present work, it was found that the hyperplastic autoimmune gastritis could be transferred with great efficiency with spleen cells obtained from 3-mo-old donors that had been thymectomized at 3 days of age, but which had not, at the time of transfer, themselves developed overt disease. The recipients were 1-mo-old syngeneic mice that had been made receptive by thymectomy during the first day of life, a procedure that does not, of itself, cause autoimmune disease. The high efficiency of the transfer suggests that, during the transfer process, effector cells may have been differentially favored as compared with the suppressor cells that, in normal animals, supposedly prevent autoimmunity. The practicality of the transfer technique should permit an investigation of the cellular basis of the autoimmunity and the associated increased susceptibility to low-dose hydrocarbon sarcogenesis.


Generation of non-diffractive Bessel beams by inward cylindrical traveling wave aperture distributions.
The focusing capabilities of an inward cylindrical traveling wave aperture distribution and the non-diffractive behaviour of its radiated field are analyzed. The wave dynamics of the infinite aperture radiated field is clearly unveiled by means of closed form expressions, based on incomplete Hankel functions, and their ray interpretation. The non-diffractive behaviour is also confirmed for finite apertures up to a defined limited range. A radial waveguide made by metallic gratings over a ground plane and fed by a coaxial feed is used to validate numerically the analytical results. The proposed system and accurate analysis of non-diffractive Bessel beams launched by inward waves opens new opportunities for planar, low profile beam generators at microwaves, Terahertz and optics.


Optimal population codes for space: grid cells outperform place cells.
Rodents use two distinct neuronal coordinate systems to estimate their position: place fields in the hippocampus and grid fields in the entorhinal cortex. Whereas place cells spike at only one particular spatial location, grid cells fire at multiple sites that correspond to the points of an imaginary hexagonal lattice. We study how to best construct place and grid codes, taking the probabilistic nature of neural spiking into account. Which spatial encoding properties of individual neurons confer the highest resolution when decoding the animal's position from the neuronal population response? A priori, estimating a spatial position from a grid code could be ambiguous, as regular periodic lattices possess translational symmetry. The solution to this problem requires lattices for grid cells with different spacings; the spatial resolution crucially depends on choosing the right ratios of these spacings across the population. We compute the expected error in estimating the position in both the asymptotic limit, using Fisher information, and for low spike counts, using maximum likelihood estimation. Achieving high spatial resolution and covering a large range of space in a grid code leads to a trade-off: the best grid code for spatial resolution is built of nested modules with different spatial periods, one inside the other, whereas maximizing the spatial range requires distinct spatial periods that are pairwisely incommensurate. Optimizing the spatial resolution predicts two grid cell properties that have been experimentally observed. First, short lattice spacings should outnumber long lattice spacings. Second, the grid code should be self-similar across different lattice spacings, so that the grid field always covers a fixed fraction of the lattice period. If these conditions are satisfied and the spatial "tuning curves" for each neuron span the same range of firing rates, then the resolution of the grid code easily exceeds that of the best possible place code with the same number of neurons.


Does the colonization of new biogeographic regions influence the diversification and accumulation of clade richness among the Corvides (Aves: Passeriformes)?
Regional variation in clade richness can be vast, reflecting differences in the dynamics of historical dispersal and diversification among lineages. Although it has been proposed that dispersal into new biogeographic regions may facilitate diversification, to date there has been limited assessment of the importance of this process in the generation, and maintenance, of broad-scale biodiversity gradients. To address this issue, we analytically derive biogeographic regions for a global radiation of passerine birds (the Corvides, c. 790 species) that are highly variable in the geographic and taxonomic distribution of species. Subsequently, we determine rates of historical dispersal between regions, the dynamics of diversification following regional colonization, and spatial variation in the distribution of species that differ in their rates of lineage diversification. The results of these analyses reveal spatiotemporal differences in the build-up of lineages across regions. The number of regions occupied and the rate of transition between regions both predict family richness well, indicating that the accumulation of high clade richness is associated with repeated expansion into new geographic areas. However, only the largest family (the Corvidae) had significantly heightened rates of both speciation and regional transition, implying that repeated regional colonization is not a general mechanism promoting lineage diversification among the Corvides.


Discontinuity induced angular distribution of photon plasmon coupling.
Metal-dielectric transitions are important structures that can display a host of optical characteristics including excitation of plasmons. Metal-dielectric discontinuities can furthermore support plasmon excitation without a severe condition on the incident angle of the exciting photons. Using a semi-infinite thin gold film, we study surface plasmon (SP) excitation and the associated electromagnetic near-field distribution by recording the resulting plasmon interference patterns. In particular, we measure interference periods involving SPs at the scanable metal/air interface and the buried metal/glass one. Supported by optical near-field simulations and experiments, we demonstrate that the metal/glass surface plasmon is observable over a wide range of incident angles encompassing values above and below the critical incident angle. As a result, it is shown that scanning near-field microscopy can provide quantitative evaluation of the real part of the buried surface plasmon wavevector.


Pathogenic and saprophytic Leptospira species in water and soils from selected urban sites in peninsular Malaysia.
Leptospira species were studied in water and soils from selected urban sites in Malaysia. A total of 151 water (n=121) and soil (n=30) samples were collected from 12 recreational lakes and wet markets. All samples were filtered and inoculated into semi-solid Ellinghausen and McCullough modified by Johnson and Harris (EMJH) media supplemented with additional 5-fluorouracil. The cultures were then incubated at 30°C and observed under a dark field microscope with intervals of 10 days. A PCR assay targeting the rrs gene was used to confirm the genus Leptospira among the isolates. Subsequently, the pathogenic status of the isolates was determined using primer sets G1/G2 and Sapro1/Sapro2, which target the secY and rrs genes, respectively. The isolates were identified at serogroup level using the microscopic agglutination test (MAT) while their genetic diversity was assessed by pulsed field gel electrophoresis (PFGE). Based on dark field microscopy, 23.1% (28/121) water and 23.3% (7/30) soil cultures were positive for Leptospira spp. Of the 35 positive cultures, only 8 were pure and confirmed as Leptospira genus by PCR assay. Two out of 8 isolates were confirmed as pathogenic, 5 were saprophytic and one was intermediate. These 8 isolates were negative for the 25 reference hyperimmune rabbit sera tested in the MAT. PFGE showed that all 8 of these environmental Leptospira spp. were genetically diverse. In conclusion, the presence of pathogenic Leptospira spp. in the urban Malaysian environment may indicate and highlight the importance of water screening, especially in recreational lakes, in order to minimize any chance of Leptospira infection.


Virulence properties of motile aeromonads isolated from farmed frogs Rana tigerina and R. rugulosa.
Virulence factors were compared in Aeromonas species isolated from clinically normal and septicaemic farmed frogs from Thailand. Haemolysin activities against frog erythrocytes were significantly different within the collection of aeromonads. Groups of high haemolytic activity (unspeciated Aeromonas, Au), moderate haemolytic activity (A. hydrophila), and low haemolytic activity (A. veronii biovar sobria, A. veronii biovar veronii, A. caviae, A. schubertii) were noted. DNA colony hybridisation studies revealed that Au isolates possessed a haemolysin gene (ASH1) which was not present in any of the other Thai aeromonads or type strains tested. Elastinolytic activity was demonstrated in 90% of the Au isolates, 60% of the A. hydrophila isolates and in none of the other motile aeromonads. The cytotoxic activity of the Aeromonas isolates varied according to the source of cells used in the assays. Cells from rainbow trout were extremely sensitive to Au toxins but less so to toxins produced by other species. In contrast mammalian cells showed very little sensitivity to Au toxins but were more sensitive to toxins produced by A. hydrophila. Selection of suitable assay substrates is therefore important.


Dynamical characterization of a cellulose acetate polysaccharide.
This work brings together dynamical and structural information at a molecular level for cellulose acetate being an original contribution to the general description of polysaccharide properties. In particular, it allowed reinterpreting the secondary relaxation mechanisms that are still controversial in the literature; a compilation of data provided by different authors is provided. Detailed dynamical information is provided by dielectric relaxation spectroscopy (DRS) (10(-1)-10(6) Hz) for cellulose acetate (CA) in the sub-T(g) region below ambient temperature; results were compared with cellulose acetate structured as an asymmetric membrane (CAmb). In samples with low water content, two secondary relaxation processes between 173 and 298 K were identified by DRS, associated with localized mobility. The process located at the lowest temperatures (process I) has a different mobility in CA relative to CAmb. The identical crystalline/amorphous state of both materials allowed rationalizing the distinct behavior in terms of polymeric arrangement and ability for water uptake. The looser structure of the CA relative to CAmb as confirmed by FTIR, TGA, and DSC analysis makes more sites accessible to water molecules, resulting in a higher water retention in CA (2.73% w/w) relative to CAmb (1.60% w/w) and an increased molecular mobility in the former due to a plasticizing effect. In both materials, process I is significantly influenced by hydration, shifting to higher frequencies and lower temperatures upon water uptake. This process seems to be associated with mobility occurring within the monomeric unit, which embraces the two anhydroglucose rings connected by the glycosidic linkage and the polar groups directly attached to it. It should involve a very limited length scale, as suggested by its location, far below the glass transition, and the tau(infinity) value with a low entropic effect. The relaxation process that emerges later, process II, is similar for both samples being much less influenced by water but experiencing a slight antiplasticizing effect shifting to lower frequencies and higher temperatures upon hydration. It should involve side group motions, strongly coupled to the mobility of the anhydroglucose rings, which become hindered probably due to establishment of H-bonds with water molecules. The plasticizing/antiplasticizing effect is being discussed only on the basis of the frequency position of the relaxation peak. Processes I and II merge into a broad relaxation (gamma(dry)) upon water removal in both CA and CAmb, however evolving slower in the former with drying, due to a more disordered structure of CA that allows water to interact with more internal sites in the polymer. At higher temperatures (T > or = 353 K), a process emerges in the high frequency side of the dynamic alpha-relaxation which is compatible with a beta(JG)-relaxation. The structured specimen CAmb provided an additional way to probe the morphological changes undergone by the material when annealed to temperatures higher than 353 K, originating an increase in the dielectric response. This effect can be associated with a skin densification and partial collapse of the membrane porous network, as observed by SEM.


Neutrophil extracellular traps are pathogenic in primary graft dysfunction after lung transplantation.
Primary graft dysfunction (PGD) causes early mortality after lung transplantation and may contribute to late graft failure. No effective treatments exist. The pathogenesis of PGD is unclear, although both neutrophils and activated platelets have been implicated. We hypothesized that neutrophil extracellular traps (NETs) contribute to lung injury in PGD in a platelet-dependent manner. To study NETs in experimental models of PGD and in lung transplant patients. Two experimental murine PGD models were studied: hilar clamp and orthotopic lung transplantation after prolonged cold ischemia (OLT-PCI). NETs were assessed by immunofluorescence microscopy and ELISA. Platelet activation was inhibited with aspirin, and NETs were disrupted with DNaseI. NETs were also measured in bronchoalveolar lavage fluid and plasma from lung transplant patients with and without PGD. NETs were increased after either hilar clamp or OLT-PCI compared with surgical control subjects. Activation and intrapulmonary accumulation of platelets were increased in OLT-PCI, and platelet inhibition reduced NETs and lung injury, and improved oxygenation. Disruption of NETs by intrabronchial administration of DNaseI also reduced lung injury and improved oxygenation. In bronchoalveolar lavage fluid from human lung transplant recipients, NETs were more abundant in patients with PGD. NETs accumulate in the lung in both experimental and clinical PGD. In experimental PGD, NET formation is platelet-dependent, and disruption of NETs with DNaseI reduces lung injury. These data are the first description of a pathogenic role for NETs in solid organ transplantation and suggest that NETs are a promising therapeutic target in PGD.


Gyrase B inhibitor impairs HIV-1 replication by targeting Hsp90 and the capsid protein.
Chemical genetics is an emerging approach to investigate the biology of host-pathogen interactions. We screened several inhibitors of ATP-dependent DNA motors and detected the gyrase B inhibitor coumermycin A1 (C-A1) as a potent antiretroviral. C-A1 inhibited HIV-1 integration and gene expression from acutely infected cell, but the two activities mapped to distinct targets. Target discovery identified Hsp90 as the C-A1 target affecting viral gene expression. Chromatin immunoprecipitation revealed that Hsp90 associates with the viral promoter and may directly regulate gene expression. Molecular docking suggested that C-A1 binds to two novel pockets at the C terminal domain of Hsp90. C-A1 inhibited Hsp90 dimer formation, suggesting that it impairs viral gene expression by preventing Hsp90 dimerization at the C terminus. The inhibition of HIV-1 integration imposed by C-A1 was independent of Hsp90 and mapped to the capsid protein, and a point mutation at residue 105 made the virus resistant to this block. HIV-1 susceptibility to the integration block mediated by C-A1 was influenced by cyclophilin A. Our chemical genetic approach revealed an unexpected function of capsid in HIV-1 integration and provided evidence for a role of Hsp90 in regulating gene expression in mammalian cells. Both activities were amenable to inhibition by small molecules and represent novel antiretroviral drug targets.


COVID-19 Prevention and Control Measures in Workplace Settings: A Rapid Review and Meta-Analysis.
Workplaces can be high-risk environments for SARS-CoV-2 outbreaks and subsequent community transmission. Identifying, understanding, and implementing effective workplace SARS-CoV-2 infection prevention and control (IPC) measures is critical to protect workers, their families, and communities. A rapid review and meta-analysis were conducted to synthesize evidence assessing the effectiveness of COVID-19 IPC measures implemented in global workplace settings through April 2021. Medline, Embase, PubMed, and Cochrane Library were searched for studies that quantitatively assessed the effectiveness of workplace COVID-19 IPC measures. The included studies comprised varying empirical designs and occupational settings. Measures of interest included surveillance measures, outbreak investigations, environmental adjustments, personal protective equipment (PPE), changes in work arrangements, and worker education. Sixty-one studies from healthcare, nursing home, meatpacking, manufacturing, and office settings were included, accounting for ~280,000 employees based in Europe, Asia, and North America. Meta-analyses showed that combined IPC measures resulted in lower employee COVID-19 positivity rates (0.2% positivity; 95% CI 0-0.4%) than single measures such as asymptomatic PCR testing (1.7%; 95% CI 0.9-2.9%) and universal masking (24%; 95% CI 3.4-55.5%). Modelling studies showed that combinations of (i) timely and widespread contact tracing and case isolation, (ii) facilitating smaller worker cohorts, and (iii) effective use of PPE can reduce workplace transmission. Comprehensive COVID-19 IPC measures incorporating swift contact tracing and case isolation, PPE, and facility zoning can effectively prevent workplace outbreaks. Masking alone should not be considered sufficient protection from SARS-CoV-2 outbreaks in the workplace.


Glaucoma progression detection using nonlocal Markov random field prior.
Glaucoma is neurodegenerative disease characterized by distinctive changes in the optic nerve head and visual field. Without treatment, glaucoma can lead to permanent blindness. Therefore, monitoring glaucoma progression is important to detect uncontrolled disease and the possible need for therapy advancement. In this context, three-dimensional (3-D) spectral domain optical coherence tomography (SD-OCT) has been commonly used in the diagnosis and management of glaucoma patients. We present a new framework for detection of glaucoma progression using 3-D SD-OCT images. In contrast to previous works that use the retinal nerve fiber layer thickness measurement provided by commercially available instruments, we consider the whole 3-D volume for change detection. To account for the spatial voxel dependency, we propose the use of the Markov random field (MRF) model as a prior for the change detection map. In order to improve the robustness of the proposed approach, a nonlocal strategy was adopted to define the MRF energy function. To accommodate the presence of false-positive detection, we used a fuzzy logic approach to classify a 3-D SD-OCT image into a "non-progressing" or "progressing" glaucoma class. We compared the diagnostic performance of the proposed framework to the existing methods of progression detection.


Macronutrients Imbalance and Micronutrient Deficiencies among Healthy Saudi Physicians in Al Madina, Saudi Arabia.
Diet and nutrition are important factors in the promotion and maintenance of good health. Physicians are involved in medical nutrition therapy of their patients; however, little is known on how physicians are personally adherent to good nutrition. The aim of the study was to assess the nutritional practices of Saudi physicians. This is a pilot study that included 48 healthy Saudi physicians, of both genders, randomly selected from King Fahad Hospital, Madina, Saudi Arabia from June 2013 to December 2013. Self-reported dietary intake over 24 h was assessed. The adequacy of nutrient intake was evaluated by comparing the physicians' intake to the dietary reference intakes (DRI). The mean age of physicians was 41.6 ± 10 years, weight was 78 ± 20.2 kg, and body mass index was 27.76 ± 5.37 kg/m2. They reported adequate daily consumption of food energy with high intake of carbohydrate (178.5 ± 46.4%) of DRI and high fat and protein intake from animal sources with low fiber intake (34.9 ± 25.1%) of DRI. Daily intakes for most of the micronutrients were lower than recommended with the exception of phosphorus, Vitamin E, and Vitamin B12 with no significant difference between males and females, except for lower intake of iron and Vitamin D by females. Vitamin D was the most severe deficient vitamin; 46.1 ± 53.9% of DRI. Nutritional practices of the sampled group of Saudi Physicians were not optimal. They have a high prevalence of micronutrients deficiencies. In addition, they tend to consume less fiber, more carbohydrate, and food from animal sources. Actions are needed to control nutrition status in Saudi Arabia, including the adoption of healthy eating pattern early in life, extensive nutrition and health education, and intervention strategies.


Persistence in soil of Miscanthus biochar in laboratory and field conditions.
Evaluating biochars for their persistence in soil under field conditions is an important step towards their implementation for carbon sequestration. Current evaluations might be biased because the vast majority of studies are short-term laboratory incubations of biochars produced in laboratory-scale pyrolyzers. Here our objective was to investigate the stability of a biochar produced with a medium-scale pyrolyzer, first through laboratory characterization and stability tests and then through field experiment. We also aimed at relating properties of this medium-scale biochar to that of a laboratory-made biochar with the same feedstock. Biochars were made of Miscanthus biomass for isotopic C-tracing purposes and produced at temperatures between 600 and 700°C. The aromaticity and degree of condensation of aromatic rings of the medium-scale biochar was high, as was its resistance to chemical oxidation. In a 90-day laboratory incubation, cumulative mineralization was 0.1% for the medium-scale biochar vs. 45% for the Miscanthus feedstock, pointing to the absence of labile C pool in the biochar. These stability results were very close to those obtained for biochar produced at laboratory-scale, suggesting that upscaling from laboratory to medium-scale pyrolyzers had little effect on biochar stability. In the field, the medium-scale biochar applied at up to 25 t C ha-1 decomposed at an estimated 0.8% per year. In conclusion, our biochar scored high on stability indices in the laboratory and displayed a mean residence time > 100 years in the field, which is the threshold for permanent removal in C sequestration projects.


Home-based nursing: an endless journey.
The aim of this study was to explore metaphors for discovering values and norms held by nurses in home-based nursing care. Ten interviews were analysed and interpreted in accordance with a metaphor analytical method. In the analysis, metaphoric linguistic expressions and two entailments emerged, grounded in the conceptual metaphor 'home-based nursing care is an endless journey', which were created in a cross-domain mapping between the two conceptual domains of home-based nursing care and travel. The metaphor exposed home-based nursing care as being in constant motion, thereby requiring nurses to adjust to circumstances that demand ethical maturity. The study focuses on the importance of developing further theories supporting nurses' expressions of their experiences of everyday ethical issues.


Identification of behaviour in freely moving dogs (Canis familiaris) using inertial sensors.
Monitoring and describing the physical movements and body postures of animals is one of the most fundamental tasks of ethology. The more precise the observations are the more sophisticated the interpretations can be about the biology of a certain individual or species. Animal-borne data loggers have recently contributed much to the collection of motion-data from individuals, however, the problem of translating these measurements to distinct behavioural categories to create an ethogram is not overcome yet. The objective of the present study was to develop a "behaviour tracker": a system composed of a multiple sensor data-logger device (with a tri-axial accelerometer and a tri-axial gyroscope) and a supervised learning algorithm as means of automated identification of the behaviour of freely moving dogs. We collected parallel sensor measurements and video recordings of each of our subjects (Belgian Malinois, N=12; Labrador Retrievers, N=12) that were guided through a predetermined series of standard activities. Seven behavioural categories (lay, sit, stand, walk, trot, gallop, canter) were pre-defined and each video recording was tagged accordingly. Evaluation of the measurements was performed by support vector machine (SVM) classification. During the analysis we used different combinations of independent measurements for training and validation (belonging to the same or different individuals or using different training data size) to determine the robustness of the application. We reached an overall accuracy of above 90% perfect identification of all the defined seven categories of behaviour when both training and validation data belonged to the same individual, and over 80% perfect recognition rate using a generalized training data set of multiple subjects. Our results indicate that the present method provides a good model for an easily applicable, fast, automatic behaviour classification system that can be trained with arbitrary motion patterns and potentially be applied to a wide range of species and situations.


Extensive cross-contamination of specimens with Mycobacterium tuberculosis in a reference laboratory.
A striking increase in the numbers of cultures positive for Mycobacterium tuberculosis was noticed in a mycobacterial reference laboratory in Campinas, Sao Paulo State, Brazil, in May 1995. A contaminated bronchoscope was the suspected cause of the increase. All 91 M. tuberculosis isolates grown from samples from patients between 8 May and 18 July 1995 were characterized by spoligotyping and IS6110 fingerprinting. Sixty-one of the 91 isolates had identical spoligotype patterns, and the pattern was arbitrarily designated S36. The 61 specimens containing these isolates had been processed and cultured in a 21-day period ending on 1 June 1995, but only 1 sample was smear positive for acid-fast bacilli. The patient from whom this sample was obtained was considered to be the index case patient and had a 4+ smear-positive lymph node aspirate that had been sent to the laboratory on 10 May. Virtually all organisms with spoligotype S36 had the same IS6110 fingerprint pattern. Extensive review of the patients' charts and investigation of laboratory procedures revealed that cross-contamination of specimens had occurred. Because the same strain was grown from all types of specimens, the bronchoscope was ruled out as the outbreak source. The most likely source of contamination was a multiple-use reagent used for specimen processing. The organism was cultured from two of the solutions 3 weeks after mock contamination. This investigation strongly supports the idea that M. tuberculosis grown from smear-negative specimens should be analyzed by rapid and reliable strain differentiation techniques, such as spoligotyping, to help rule out laboratory contamination.


The effects of nicotine in the neonatal quinpirole rodent model of psychosis: Neural plasticity mechanisms and nicotinic receptor changes.
Neonatal quinpirole (NQ) treatment to rats increases dopamine D2 receptor sensitivity persistent throughout the animal's lifetime. In Experiment 1, we analyzed the role of α7 and α4β2 nicotinic receptors (nAChRs) in nicotine behavioral sensitization and on the brain-derived neurotrophic factor (BDNF) response to nicotine in NQ- and neonatally saline (NS)-treated rats. In Experiment 2, we analyzed changes in α7 and α4β2 nAChR density in the nucleus accumbens (NAcc) and dorsal striatum in NQ and NS animals sensitized to nicotine. Male and female Sprague-Dawley rats were neonatally treated with quinpirole (1mg/kg) or saline from postnatal days (P)1-21. Animals were given ip injections of either saline or nicotine (0.5mg/kg free base) every second day from P33 to P49 and tested on behavioral sensitization. Before each injection, animals were ip administered the α7 nAChR antagonist methyllycaconitine (MLA; 2 or 4mg/kg) or the α4β2 nAChR antagonist dihydro beta erythroidine (DhβE; 1 or 3mg/kg). Results revealed NQ enhanced nicotine sensitization that was blocked by DhβE. MLA blocked the enhanced nicotine sensitization in NQ animals, but did not block nicotine sensitization. NQ enhanced the NAcc BDNF response to nicotine which was blocked by both antagonists. In Experiment 2, NQ enhanced nicotine sensitization and enhanced α4β2, but not α7, nAChR upregulation in the NAcc. These results suggest a relationship between accumbal BDNF and α4β2 nAChRs and their role in the behavioral response to nicotine in the NQ model which has relevance to schizophrenia, a behavioral disorder with high rates of tobacco smoking.


A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2.
The DNA-binding protein MeCP2 is reported to bind methylated cytosine in CG and CA motifs in genomic DNA, but it was recently proposed that arrays of tandemly repeated CA containing either methylated or hydroxymethylated cytosine are the primary targets for MeCP2 binding and function. Here we investigated the predictions of this hypothesis using a range of published datasets. We failed to detect enrichment of cytosine modification at genomic CA repeat arrays in mouse brain regions and found no evidence for preferential MeCP2 binding at CA repeats. Moreover, we did not observe a correlation between the CA repeat density near genes and their degree of transcriptional deregulation when MeCP2 was absent. Our results do not provide support for the hypothesis that CA repeats are key mediators of MeCP2 function. Instead, we found that CA repeats are subject to CAC methylation to a degree that is typical of the surrounding genome and contribute modestly to MeCP2-mediated modulation of gene expression in accordance with their content of this canonical target motif.


Costs of encephalization: the energy trade-off hypothesis tested on birds.
Costs and benefits of encephalization are a major topic of debate in the study of primate and human evolution. Comparative studies provide an opportunity to test the validity of a hypothesis as a general principle, rather than it being a special case in primate or hominid evolution. If a population evolves a larger brain, the metabolic costs of doing so must be paid for by either an increased energy turnover (direct metabolic constraint) or by a trade-off with other energetically expensive costs of body maintenance, locomotion, or reproduction, here referred to as the energy trade-off hypothesis, an extension of the influential Expensive Tissue Hypothesis of Aiello and Wheeler (1995, Curr. Anthropol. 36, 199-221). In the present paper, we tested these hypotheses on birds using raw species values, family means, and independent contrasts analysis to account for phylogenetic influences. First, we tested whether basal metabolic rates are correlated with brain mass or any other variable of interest. This not being the case, we examined various trade-offs between brain mass and the mass of other expensive tissues such as gut mass, which is approximated by gut length or diet quality. Only weak support was found for this original Expensive Tissue Hypothesis in birds. However, other energy allocations such as locomotor mode and reproductive strategy may also be reduced to shunt energy to an enlarged brain. We found a significantly negative correlation between brain mass and pectoral muscle mass, which averages 18% of body mass in birds and is indicative of their relative costs of flight. Reproductive costs, on the other hand, are positively correlated with brain mass in birds. An increase in brain mass may allow birds to devote more energy to reproduction, although not through an increase in their own energy budget as in mammals, but through direct provisioning of their offspring. The trade-off between locomotor costs and brain mass in birds lets us conclude that an analogous effect could have played a role in the evolution of a larger brain in human evolution.


Cervical cancer data and data systems in limited-resource settings: Challenges and opportunities.
Appropriate collection and use of health information is critical to the planning, scaling up, and improvement of cervical cancer programs. The health information systems implementation landscape is unique to each country; however, systems serving cervical cancer programs in low-resource settings share characteristics that present common challenges. In response, many programs have taken innovative approaches to generating the quality information needed for decision making. Recent advances in health information technology also provide feasible solutions to challenges. This article draws from the experiences of the authors and from current literature to describe outstanding challenges and promising practices in the implementation of cervical cancer data systems, and to make recommendations for next steps. Recommendations include engaging all stakeholders-including providers, program managers, implementing partners, and donors-in promoting national, district, and community information systems; building on existing systems and processes, as well as introducing new technologies; and evolving data collection and data systems as programs advance.


Highly attenuated modified vaccinia virus Ankara (MVA) as an effective recombinant vector: a murine tumor model.
Modified vaccinia virus Ankara (MVA), a highly attenuated strain of vaccinia virus (VV) that is unable to replicate in most mammalian cells, was evaluated as an expression vector for a model tumor associated antigen (TAA) and as a potential anti-cancer vaccine. We employed an experimental murine model in which an adenocarcinoma tumor line, CT26.CL25, was stably transfected with a model TAA, beta-galactosidase (beta-gal). Mice injected intramuscularly with a recombinant MVA (rMVA) expressing beta-gal (MVA-LZ), were protected from a lethal intravenous (i.v.) challenge with CT26.CL25. In addition, splenocytes from mice primed with MVA-LZ were therapeutically effective upon adoptive transfer to mice bearing pulmonary metastases of the CT26.CL25 tumor established 3 days earlier. Most importantly, i.v. inoculation with MVA-LZ resulted in significantly prolonged survival of mice bearing three day old pulmonary metastases. This prolonged survival compared favorably to mice treated with a replication competent recombinant VV expressing beta-gal. These findings indicate that rMVA is an efficacious alternative to the more commonly used replication competent VV for the development of new recombinant anti-cancer vaccines.


Pseudomonas aeruginosa cystic fibrosis isolates of similar RAPD genotype exhibit diversity in biofilm forming ability in vitro.
Pseudomonas aeruginosa is considered to grow in a biofilm in cystic fibrosis (CF) chronic lung infections. Bacterial cell motility is one of the main factors that have been connected with P. aeruginosa adherence to both biotic and abiotic surfaces. In this investigation, we employed molecular and microscopic methods to determine the presence or absence of motility in P. aeruginosa CF isolates, and statistically correlated this with their biofilm forming ability in vitro. Our investigations revealed a wide diversity in the production, architecture and control of biofilm formation. Of 96 isolates, 49% possessed swimming motility, 27% twitching and 52% swarming motility, while 47% were non-motile. Microtitre plate assays for biofilm formation showed a range of biofilm formation ability from biofilm deficient phenotypes to those that formed very thick biofilms. A comparison of the motility and adherence properties of individual strains demonstrated that the presence of swimming and twitching motility positively affected biofilm biomass. Crucially, however, motility was not an absolute requirement for biofilm formation, as 30 non-motile isolates actually formed thick biofilms, and three motile isolates that had both flagella and type IV pili attached only weakly. In addition, CLSM analysis showed that biofilm-forming strains of P. aeruginosa were in fact capable of entrapping non-biofilm forming strains, such that these 'non-biofilm forming' cells could be observed as part of the mature biofilm architecture. Clinical isolates that do not produce biofilms in the laboratory must have the ability to survive in the patient lung. We propose that a synergy exists between isolates in vivo, which allows "non biofilm-forming" isolates to be incorporated into the biofilm. Therefore, there is the potential for strains that are apparently non-biofilm forming in vitro to participate in biofilm-mediated pathogenesis in the CF lung.


Leptospirosis in Hawaii, 1974-1998: epidemiologic analysis of 353 laboratory-confirmed cases.
The epidemiologic characterization of leptospirosis in the United States has been limited by difficulties associated with both case detection and confirmation. In addition, leptospirosis was eliminated from the list of National Notifiable Diseases in 1995. From 1974 until the cessation of national surveillance, Hawaii consistently had the highest reported annual incidence rate in the United States. From 1974 through 1998, 752 leptospirosis cases were reported in the State of Hawaii. Of these, 353 had exposures within the state and were laboratory confirmed. The mean annual incidence rate was 1.29 per 100,000. Cases were predominately male. Rates were highest in rural areas. Occupational exposures diminished over time while recreational exposures increased. This series represents the first large U.S. leptospirosis surveillance report since 1979. With leptospirosis recently being identified as a re-emerging zoonosis, continued national surveillance and case reporting should be reconsidered.


Differences in Blood Pressure in Infants After General Anesthesia Compared to Awake Regional Anesthesia (GAS Study-A Prospective Randomized Trial).
The General Anesthesia compared to Spinal anesthesia (GAS) study is a prospective randomized, controlled, multisite, trial designed to assess the influence of general anesthesia (GA) on neurodevelopment at 5 years of age. A secondary aim obtained from the blood pressure data of the GAS trial is to compare rates of intraoperative hypotension after anesthesia and to identify risk factors for intraoperative hypotension. A total of 722 infants ≤60 weeks postmenstrual age undergoing inguinal herniorrhaphy were randomized to either bupivacaine regional anesthesia (RA) or sevoflurane GA. Exclusion criteria included risk factors for adverse neurodevelopmental outcome and infants born at <26 weeks of gestation. Moderate hypotension was defined as mean arterial pressure measurement of <35 mm Hg. Any hypotension was defined as mean arterial pressure of <45 mm Hg. Epochs were defined as 5-minute measurement periods. The primary outcome was any measured hypotension <35 mm Hg from start of anesthesia to leaving the operating room. This analysis is reported primarily as intention to treat (ITT) and secondarily as per protocol. The relative risk of GA compared with RA predicting any measured hypotension of <35 mm Hg from the start of anesthesia to leaving the operating room was 2.8 (confidence interval [CI], 2.0-4.1; P < .001) by ITT analysis and 4.5 (CI, 2.7-7.4, P < .001) as per protocol analysis. In the GA group, 87% and 49%, and in the RA group, 41% and 16%, exhibited any or moderate hypotension by ITT, respectively. In multivariable modeling, group assignment (GA versus RA), weight at the time of surgery, and minimal intraoperative temperature were risk factors for hypotension. Interventions for hypotension occurred more commonly in the GA group compared with the RA group (relative risk, 2.8, 95% CI, 1.7-4.4 by ITT). RA reduces the incidence of hypotension and the chance of intervention to treat it compared with sevoflurane anesthesia in young infants undergoing inguinal hernia repair.


Personal receptor repertoires: olfaction as a model.
Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individuals. To this end, we focused on the complete inventory of human olfactory receptor coding regions as a model for personal receptor repertoires. By performing data-mining from public and private sources we scored genetic variations in 413 intact OR loci, for which one or more individuals had an intact open reading frame. Using 1000 Genomes Project haplotypes, we identified a total of 4069 full-length polypeptide variants encoded by these OR loci, average of ~10 per locus, constituting a lower limit for the effective human OR repertoire. Each individual is found to harbor as many as 600 OR allelic variants, ~50% higher than the locus count. Because OR neuronal expression is allelically excluded, this has direct effect on smell perception diversity of the species. We further identified 244 OR segregating pseudogenes (SPGs), loci showing both intact and pseudogene forms in the population, twenty-six of which are annotatively "resurrected" from a pseudogene status in the reference genome. Using a custom SNP microarray we validated 150 SPGs in a cohort of 468 individuals, with every individual genome averaging 36 disrupted sequence variations, 15 in homozygote form. Finally, we generated a multi-source compendium of 63 OR loci harboring deletion Copy Number Variations (CNVs). Our combined data suggest that 271 of the 413 intact OR loci (66%) are affected by nonfunctional SNPs/indels and/or CNVs. These results portray a case of unusually high genetic diversity, and suggest that individual humans have a highly personalized inventory of functional olfactory receptors, a conclusion that might apply to other receptor multigene families.


Beyond pairwise strategy updating in the prisoner's dilemma game.
In spatial games players typically alter their strategy by imitating the most successful or one randomly selected neighbor. Since a single neighbor is taken as reference, the information stemming from other neighbors is neglected, which begets the consideration of alternative, possibly more realistic approaches. Here we show that strategy changes inspired not only by the performance of individual neighbors but rather by entire neighborhoods introduce a qualitatively different evolutionary dynamics that is able to support the stable existence of very small cooperative clusters. This leads to phase diagrams that differ significantly from those obtained by means of pairwise strategy updating. In particular, the survivability of cooperators is possible even by high temptations to defect and over a much wider uncertainty range. We support the simulation results by means of pair approximations and analysis of spatial patterns, which jointly highlight the importance of local information for the resolution of social dilemmas.


Constant-sum paired comparisons for eliciting stated preferences: a tutorial.
There is growing recognition of the importance of formally including public preferences and values in societal decision-making processes. Constant-sum paired comparison (CSPC), sometimes known as a 'budget pie' task, is a stated preference method than can be used to elicit and measure these preferences and values. It requires respondents to allocate resources between two alternatives, and the relative allocation of this resource is assumed to reflect the importance or priority that respondents attach to the attribute levels in each alternative. CSPC is useful in addressing questions over preferences for the distribution of resources, and allows for an explicit linkage of budget constraints, opportunity costs, outcomes and group characteristics. A key property of CSPC is the ability to allocate some resources to the less preferred alternative, forcing respondents to reflect on the relative value of both alternatives, and possibly giving it an advantage in contexts such as healthcare where respondents may find it ethically difficult or objectionable to make all-or-nothing allocations. This tutorial will outline the theory underlying CSPC, and will work through a detailed example of administering and interpreting a CSPC elicitation, including defining attributes and levels, constructing experimental design, task presentation, and analysis and interpretation.


A Geometric Approach to Joint 2D Region-Based Segmentation and 3D Pose Estimation Using a 3D Shape Prior.
In this work, we present an approach to jointly segment a rigid object in a two-dimensional (2D) image and estimate its three-dimensional (3D) pose, using the knowledge of a 3D model. We naturally couple the two processes together into a shape optimization problem and minimize a unique energy functional through a variational approach. Our methodology differs from the standard monocular 3D pose estimation algorithms since it does not rely on local image features. Instead, we use global image statistics to drive the pose estimation process. This confers a satisfying level of robustness to noise and initialization for our algorithm and bypasses the need to establish correspondences between image and object features. Moreover, our methodology possesses the typical qualities of region-based active contour techniques with shape priors, such as robustness to occlusions or missing information, without the need to evolve an infinite dimensional curve. Another novelty of the proposed contribution is to use a unique 3D model surface of the object, instead of learning a large collection of 2D shapes to accommodate the diverse aspects that a 3D object can take when imaged by a camera. Experimental results on both synthetic and real images are provided, which highlight the robust performance of the technique in challenging tracking and segmentation applications.


A novel composite two-stage urethroplasty for complex penile strictures: A multicenter experience.
Complex penile strictures are usually repaired using a two-stage urethroplasty. Buccal mucosal graft (BMG) placed in the first stage can have a significant contraction rate, which may require a subsequent revision surgery. We describe a composite two-stage penile urethroplasty using BMG for patients of complex penile strictures who have some salvageable urethral plate. Within a multi-institutional cohort, 82 patients underwent a two-stage urethroplasty for complex stricture of the penile urethra. Of these 42 patients who underwent our composite two-stage penile urethroplasty using BMG implanted at the second-stage were included. Patients with genital lichen sclerosus or incomplete clinical records were excluded from this study. The primary outcome of the study was to evaluate stricture-free success rate. Of total 42, 4 patients were lost to follow-up. 42% of stricture etiology was failed hypospadias repair. Mean stricture length was 4.5 cm (range 3-8 cm). Seventeen (44.7%) patients had undergone the previous urethroplasty. At a median follow-up of 44 months, of 38 patients, 34 (89.5%) were successful, and 4 (10.5%) had a recurrence. No patient required revision surgery before the second-stage and required redo buccal graft harvesting for subsequent urethroplasty. The composite two-stage technique in repairing complex penile urethral strictures is a valid and reproducible surgical treatment for complex penile stricture and it may reduce the rate of contraction of the transplanted BMG.


Sonic hedgehog expression in corticofugal projection neurons directs cortical microcircuit formation.
The precise connectivity of inputs and outputs is critical for cerebral cortex function; however, the cellular mechanisms that establish these connections are poorly understood. Here, we show that the secreted molecule Sonic Hedgehog (Shh) is involved in synapse formation of a specific cortical circuit. Shh is expressed in layer V corticofugal projection neurons and the Shh receptor, Brother of CDO (Boc), is expressed in local and callosal projection neurons of layer II/III that synapse onto the subcortical projection neurons. Layer V neurons of mice lacking functional Shh exhibit decreased synapses. Conversely, the loss of functional Boc leads to a reduction in the strength of synaptic connections onto layer Vb, but not layer II/III, pyramidal neurons. These results demonstrate that Shh is expressed in postsynaptic target cells while Boc is expressed in a complementary population of presynaptic input neurons, and they function to guide the formation of cortical microcircuitry.