Peptide Mediated In Vivo Tumor Targeting of Nanoparticles through Optimization in Single and Multilayer In Vitro Cell Models.
Optimizing the interface between nanoparticles (NPs) and the biological environment at various levels should be considered for improving delivery of NPs to the target tumor area. For NPs to be successfully delivered to cancer cells, NPs needs to be functionalized for circulation through the blood vessels. In this study, accumulation of Polyethylene Glycol (PEG) functionalized gold nanoparticles (GNPs) was first tested using in vitro monolayer cells and multilayer cell models prior to in vivo models. A diameter of 10 nm sized GNP was selected for this study for sufficient penetration through tumor tissue. The surfaces of the GNPs were modified with PEG molecules, to improve circulation time by reducing non-specific uptake by the reticuloendothelial system (RES) in animal models, and with a peptide containing integrin binding domain, RGD (arginyl-glycyl-aspartic acid), to improve internalization at the cellular level. A 10-12% accumulation of the injected GNP dose within the tumor was observed in vivo and the GNPs remained within the tumor tissue up to 72 h. This study suggests an in vitro platform for optimizing the accumulation of NP complexes in cells and tissue structures before testing them in animal models. Higher accumulation within the tumor in vivo upon surface modification is a promising outcome for future applications where GNPs can be used for drug delivery and radiation therapy.


Response of Streptococcus pyogenes to therapy with amoxicillin or amoxicillin-clavulanic acid in a mouse model of mixed infection caused by Staphylococcus aureus and Streptococcus pyogenes.
The response of Streptococcus pyogenes to amoxicillin or amoxicillin-clavulanic acid (Augmentin; Beecham Group) therapy of a mixed streptococcal-staphylococcal infection was studied in a surgical wound in mice. A superficial wound was produced on the backs of anesthetized mice, and a suture infected with S. pyogenes, Staphylococcus aureus, or a mixed inoculum of both organisms was inserted. Oral therapy was started 4 h after infection and continued for 3 days. Both amoxicillin and amoxicillin-clavulanic acid were effective in eliminating the streptococci from the pure wound infection. In contrast, amoxicillin failed to eliminate the streptococci from a mixed infection in which a beta-lactamase-producing strain of S. aureus was also present, wound counts reaching 10(7) streptococci per wound by 80 h, whereas amoxicillin-clavulanic acid reduced the count to less than 33 streptococci per wound by 24 h. Numbers of S. aureus were also reduced by amoxicillin-clavulanic acid therapy, controlling the infection, whereas amoxicillin was ineffective. Also of significance was the fact that successful therapy was achieved with blood and tissue concentrations of amoxicillin and clavulanic acid of the same order as those measured in humans. These results show that amoxicillin therapy failed to eliminate S. pyogenes from a wound infection in the presence of a beta-lactamase-producing strain of S. aureus and suggest the potential of amoxicillin-clavulanic acid in the treatment of mixed bacterial skin infections involving beta-lactamase-producing organisms.


Fatal Intoxication Involving 3-MeO-PCP: A Case Report and Validated Method.
We present in this case report a validated method for accurate quantitative analysis of 3-methoxy phencyclidine (3-MeO-PCP) to determine postmortem blood concentrations of this PCP analog. A 29-year-old male with a history of illicit drug use was found unresponsive in his bed with a bag of white powder next to him. Resuscitation efforts were unsuccessful and the individual was pronounced dead 9 minutes after arrival to the hospital. Initial ELISA screening suggested the presence of PCP in the decedent's blood. However, confirmatory testing revealed no detectable PCP. Instead, a large peak corresponding to a m/z 274.218 species with retention time similar to PCP was present on a LC-TOF-MS drug screen, suggesting a possible PCP analog. This mass corresponds specifically to a methoxy-PCP analog, several of which are available for purchase online. Standards for 3-MeO-PCP and 4-MeO-PCP were obtained and injected on the same instrument. Although the 3- and 4-MeO-PCP analogs have identical masses and retention times, they are still distinguishable through their mass spectra. The peak from the decedent's sample matched both the mass spectrum and the retention time of 3-MeO-PCP. A quantitative LC-MS-MS method was subsequently developed and validated for casework. Analysis using this method revealed a concentration of 139 ± 41 µg/L 3-MeO-PCP in the decedent's blood. Diphenhydramine (4.1 ± 0.7 mg/L), marijuana metabolite (presumptive positive, confirmation not performed) and a small amount of amphetamine (<0.10 mg/L) were also found in the decedent's blood. The cause of death was determined to be combined 3-MeO-PCP, diphenhydramine and amphetamine toxicity. The manner of death was certified as an accident.


Mechanochemical C-H bond activation: rapid and regioselective double cyclopalladation monitored by in situ Raman spectroscopy.
The first direct mechanochemical transition-metal-mediated activation of strong phenyl C-H bonds is reported. The mechanochemical procedure, resulting in cyclopalladated complexes, is quantitative and significantly faster than solution synthesis and allows highly regioselective activation of two C-H bonds by palladium(II) acetate in asymmetrically substituted azobenzene. Milling is monitored by in situ solid-state Raman spectroscopy which in combination with quantum-chemical calculations enabled characterization of involved reaction species, direct insight into the dynamics and reaction pathways, as well as the optimization of a milling process.


Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life.
Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data.


Distinct pathways of cell migration and antiapoptotic response to epithelial injury: structure-function analysis of human intestinal trefoil factor.
The trefoil peptide intestinal trefoil factor (ITF) plays a critical role in the protection of colonic mucosa and is essential to restitution after epithelial damage. These functional properties are accomplished through coordinated promotion of cell migration and inhibition of apoptosis. ITF contains a unique three-looped trefoil motif formed by intrachain disulfide bonds among six conserved cysteine residues, which is thought to contribute to its marked protease resistance. ITF also has a seventh cysteine residue, which permits homodimer formation. A series of cysteine-to-serine substitutions and a C-terminally truncated ITF were made by PCR site-directed mutagenesis. Any alteration of the trefoil motif or truncation resulted in loss of protease resistance. However, neither an intact trefoil domain nor dimerization was required to promote cell migration. This pro-restitution activity correlated with the ability of the ITF mutants to activate mitogen-activated protein (MAP) kinase independent of phosphorylation of the epidermal growth factor (EGF) receptor. In contrast, only intact ITF retained both phosphatidylinositol 3-kinase and the EGF receptor-dependent antiapoptotic effect in HCT116 and IEC-6 cells. The inability to block apoptosis correlated with a loss of trefoil peptide-induced transactivation of the EGF receptor or Akt kinase in HT-29 cells. In addition to defining structural requirements for the functional properties of ITF, these findings demonstrate that distinct intracellular signaling pathways mediate the effects of ITF on cell migration and apoptosis.


Quantifying faecal indicator organism hydrological transfer pathways and phases in agricultural catchments.
Faecal indicator organisms (FIOs) can impact on water quality and pose a health and environmental risk. The transfer of FIOs, such as Escherichia coli (E. coli), from land to water is driven by hydrological connectivity and may follow the same flowpaths as nutrients, from agricultural and human sources. This study investigated E. coli transfer in two catchment areas with high source and transport pressures. These pressures were: organic phosphorus (P) loading; human settlement; conduits and fissures in a grassland karst area; and clay rich and impermeable soils in a mixed arable area. The occurrence of E. coli and its transport pathways, along with the pathways of nutrients, were studied using a combination of targeted FIO sampling, during different hydrological phases and events, and high resolution nutrient analysis. The quick flow component in both catchments was found to be a more potent vector for E. coli, and was coincident with the total P flowpaths using a P Loadograph Recession Analysis (LRA). The karst grassland catchment was found to be a transport limited system and the mixed arable catchment a source limited system. Hence, despite the grassland catchment being a potentially higher FIO source, the E. coli loads leaving the catchment were low compared to the mixed arable catchment. E. coli load whole-event comparisons also indicated that the grassland karst transfers tended to be much lower on falling phases of runoff, while the arable catchment, over greywacke and mudstone geology, showed little change between the phases. Furthermore, the arable catchment showed asymptotic decline of sustained E. coli loads towards low flows, which may be indicative of chronic point sources. These results indicate the dominance of transport mechanisms over source mechanisms for mass E. coli loads and also chronic loads during low flow. These will be important considerations for risk assessment and mitigation.


Early and late components of EEG delay activity correlate differently with scene working memory performance.
Sustained and elevated activity during the working memory delay period has long been considered the primary neural correlate for maintaining information over short time intervals. This idea has recently been reinterpreted in light of findings generated from multiple neural recording modalities and levels of analysis. To further investigate the sustained or transient nature of activity, the temporal-spectral evolution (TSE) of delay period activity was examined in humans with high density EEG during performance of a Sternberg working memory paradigm with a relatively long six second delay and with novel scenes as stimuli. Multiple analyses were conducted using different trial window durations and different baseline periods for TSE computation. Sensor level analyses revealed transient rather than sustained activity during delay periods. Specifically, the consistent finding among the analyses was that high amplitude activity encompassing the theta range was found early in the first three seconds of the delay period. These increases in activity early in the delay period correlated positively with subsequent ability to distinguish new from old probe scenes. Source level signal estimation implicated a right parietal region of transient early delay activity that correlated positively with working memory ability. This pattern of results adds to recent evidence that transient rather than sustained delay period activity supports visual working memory performance. The findings are discussed in relation to synchronous and desynchronous intra- and inter-regional neural transmission, and choosing an optimal baseline for expressing temporal-spectral delay activity change.


[Thermal insulation of clothing for seated and standing postures].
The purpose of this study is to examine the effects of body posture on thermal insulation of clothing. Clothing ensembles including skirts were mainly investigated. A new thermal manikin was developed for this study. This manikin was able to change her body posture without increasing or decreasing her surface area. By changing posture from standing to seated, the total thermal insulation of clothing (It) was decreased by around 1.4%. The surface thermal resistance at nude (Ia) was increased by 8%. As a result, the basic thermal insulation of clothing (Icl) was decreased by 14%. The main reason for the decrease of basic thermal insulation (Icl) when the posture of thermal manikin changes from standing to seated was the increase of Ia at nude. The total thermal insulation of clothing for each body posture (Iti), when standing and seated, were compared. The parts affected by the changed posture were abdomen, hip and thighs, and especially under the skirt of 61cm length, the knees were most affected.


Pain and psychological well-being of older persons living in nursing homes: an exploratory study in planning patient-centred intervention.
This article is a report on a study to examine the pain situation, the use of oral analgesics and non-pharmacological strategies and the psychological well-being of older patients living in nursing homes; the relationships between pain and psychological well-being were also explored. Pain is common among older adults world-wide, and tends to be under-treated. Indeed, the high prevalence of pain may further hinder the fulfilment of psychological needs in a Maslow hierarchy of needs model. It was a quantitative cross-sectional study; older adults from six nursing homes were invited to join the study in 2007-2009, with a response rate of 100%. Pain was measured using the Geriatric Pain Assessment, happiness using the Subjective Happiness Scale, life satisfaction using the Life Satisfaction Index - A Form, loneliness using the Revised UCLA Loneliness Scale and depression was measured using the Geriatric Depression Scale. A convenience sample of 302 older patients (213 females and 89 males aged from 60 to 101, mean age of 84·99) joined the study. The majority of them had experienced pain in the previous 3 months, with a pain intensity of 4·51 on a 10-point scale. Pain sites were mainly the knee, back, shoulder and musculoskeletal areas. Only 50% of them took oral analgesics, and 70% used non-pharmacological measures for pain relief. The pain group reported significantly more loneliness and depression when compared with their no-pain counterparts. As the number of older patients increases, so does the need for alternative accommodation; thus, pain management education is urgently needed for staff and nursing home residents.


Childhood adiposity, adult adiposity, and cardiovascular risk factors.
Obesity in childhood is associated with increased cardiovascular risk. It is uncertain whether this risk is attenuated in persons who are overweight or obese as children but not obese as adults. We analyzed data from four prospective cohort studies that measured childhood and adult body-mass index (BMI, the weight in kilograms divided by the square of the height in meters). The mean length of follow-up was 23 years. To define high adiposity status, international age-specific and sex-specific BMI cutoff points for overweight and obesity were used for children, and a BMI cutoff point of 30 was used for adults. Data were available for 6328 subjects. Subjects with consistently high adiposity status from childhood to adulthood, as compared with persons who had a normal BMI as children and were nonobese as adults, had an increased risk of type 2 diabetes (relative risk, 5.4; 95% confidence interval [CI], 3.4 to 8.5), hypertension (relative risk, 2.7; 95% CI, 2.2 to 3.3), elevated low-density lipoprotein cholesterol levels (relative risk, 1.8; 95% CI, 1.4 to 2.3), reduced high-density lipoprotein cholesterol levels (relative risk, 2.1; 95% CI, 1.8 to 2.5), elevated triglyceride levels (relative risk, 3.0; 95% CI, 2.4 to 3.8), and carotid-artery atherosclerosis (increased intima-media thickness of the carotid artery) (relative risk, 1.7; 95% CI, 1.4 to 2.2) (P ≤ 0.002 for all comparisons). Persons who were overweight or obese during childhood but were nonobese as adults had risks of the outcomes that were similar to those of persons who had a normal BMI consistently from childhood to adulthood (P>0.20 for all comparisons). Overweight or obese children who were obese as adults had increased risks of type 2 diabetes, hypertension, dyslipidemia, and carotid-artery atherosclerosis. The risks of these outcomes among overweight or obese children who became nonobese by adulthood were similar to those among persons who were never obese. (Funded by the Academy of Finland and others.).


Involvement of alpha-2 adrenoceptors in the periaqueductal gray-induced inhibition of dorsal horn cell activity in rats.
The noradrenergic system is considered to be one of the major descending analgesia systems originating in the brainstem. The relationship between the periaqueductal gray (PAG) and the descending noradrenergic system is of great interest. A projection from the PAG to the locus ceruleus and parabrachial region has been reported. It is possible that electrical stimulation of the PAG activates spinally projecting collaterals of the noradrenergic cells in A5, the locus ceruleus, subceruleus and A7/Kölliker-Fuse nucleus. The current experiments were designed to study the role of alpha-2 adrenoceptors on spinal cord dorsal Horn cells in PAG-induced inhibition. A microdialysis fiber was introduced into the dorsal horn of the lumbar enlargement for drug administration. An electrode was placed in the vicinity of the microdialysis fiber for extracellular single-unit recording. Recordings were made from a total of 35 cells from 22 Sprague-Dawley rats (270-360 g). When the PAG was stimulated, responses to mechanical stimuli applied to the skin (brush, press and pinch) were inhibited. When an alpha-2 adrenoceptor agonist (clonidine) was administered, the background activity and the responses of the cell to brush, press and pinch stimuli were decreased. In contrast, administration of alpha-2 adrenoceptor antagonists (idazoxan or yohimbine) increased the responses of the cell to brush, press and pinch stimuli. The background activity was also increased by idazoxan. The PAG-induced inhibition of the response to mechanical stimuli was reduced by idazoxan and yohimbine. These results suggest an involvement of alpha-2 adrenoceptors in the mechanism of PAG-induced inhibition of dorsal horn cell activity.


Kin discrimination and outer membrane exchange in Myxococcus xanthus: A comparative analysis among natural isolates.
Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear. Using natural isolates from a centimetre-scale patch of soil, we analyse patterns of TraA diversity and ask whether relatedness at TraA is causally related to patterns of kin discrimination in the form of both colony-merger incompatibilities (CMIs) and interstrain antagonisms. A large proportion of TraA functional diversity documented among global isolates is predicted to be contained within this cm-scale population. We find evidence of balancing selection on the highly variable PA14-portion of TraA and extensive transfer of traA alleles across genomic backgrounds. CMIs are shown to be common among strains identical at TraA, suggesting that CMIs are not generally caused by TraA dissimilarity. Finally, it has been proposed that interstrain antagonisms might be caused by OME-mediated toxin transfer. However, we predict that most strain pairs previously shown to exhibit strong antagonisms are incapable of OME due to TraA dissimilarity. Overall, our results suggest that most documented patterns of kin discrimination in a natural population of M. xanthus are not causally related to the TraA sequences of interactants.


Global scenario of counterfeit antimalarials: A potential threat.
Malaria, a parasitic infectious disease causes approximately >1 million deaths annually worldwide. Treatment with effective antimalarials is one of the major strategies to combat malaria-related mortalities. However, there is a continuous threat of counterfeit antimalarials in the community. Counterfeit antimalarial drugs not only result in an economic loss but also decrease the efficacy of treatment resulting in the loss of faith in the health system and increases the the chances of drug resistance in the parasites. Counterfeit drugs hamper the intellectual property-based innovation paradigms as well. Awareness about these counterfeit drugs not only helps in avoiding drug resistance but may also enhance the drug therapeutic value. This review discusses the prevalence of counterfeit drugs in different geographic areas across the globe, the methods deployed for its detection and possible anticounterfeiting strategies. Literature search was conducted through PubMed, Google and International Pharmaceutical Abstracts using the terms 'counterfeit antimalarials', 'substandard', 'falsified', and 'drug resistance'. Free searches in other search engines included the terms 'antimalarial counterfeit drugs' and 'drug resistance'. Analysis of the literature survey indicated that majority of such studies were conducted in Southeast Asia and Africa region. The prevalence of substandard antimalarials was reported as high as 88.4% in Africa region and 53 % in Southeast Asia region. There is a need to follow a multifaceted approach to prevent the entry of falsified drugs with pre- and post-marketing surveillance. The samples need to be examined by regulatory bodies and strict legislation should be envisaged in order to maintain the quality of medicines.


Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S. cerevisiae.
Previous studies from this laboratory indicated that the product of the RSF1 gene of S. cerevisiae is present in both nucleus and mitochondria, and they suggested that Rsf1p acts as a transcriptional modulator. To investigate this latter question, we performed transcriptome profiling of an rsf1 mutant strain and its wild-type parent during a shift from glucose-based fermentative to glycerol-based respiratory growth to identify genes whose expression is regulated by Rsf1p. Loss of Rsf1p engendered a decrease in transcript levels from many genes encoding components of the electron transport chain and various other mitochondrially-localized products. The earlier studies further showed that rsf1 cells exhibit a growth defect on medium containing glycerol, but not ethanol, as sole carbon source. Importantly, transcriptome profiling of the rsf1 mutant during shift from glucose- to glycerol-based medium revealed that the product of this gene plays a major role in both orchestration of the transition to, and maintenance of, efficient growth on glycerol as sole carbon source. An increase in transcript levels from genes encoding products that function in the stress response, and an imbalance between expression of genes encoding glycerol anabolic and catabolic enzymes, was observed in the rsf1 mutant during steady-state growth on glycerol- but not ethanol-based medium; this suggests the presence of partially separate transcriptional regulatory systems for transition to respiratory growth on each of these two carbon sources. Genes whose expression is affected by loss of Rsf1p, which lacks a known DNA-binding motif, lack a common DNA sequence motif in their upstream regions. These and other data presented here strongly suggest that the transcriptional effects exerted by Rsf1p are mediated via interaction with other transcription factors.


rpfF mutants of Xanthomonas oryzae pv. oryzae are deficient for virulence and growth under low iron conditions.
Xanthomonas oryzae pv. oryzae causes bacterial leaf blight, a serious disease of rice. In the related bacterium Xanthomonas campestris pv. campestris, the rpfF gene is involved in production of a diffusible extracellular factor (DSF) that positively regulates synthesis of virulence-associated functions like extracellular polysaccharide (EPS) and extracellular enzymes. Transposon insertions in the rpfF homolog of X. oryzae pv. oryzae are deficient for virulence and production of a DSF but are proficient for EPS and extracellular enzyme production. The rpfF X. oryzae pv. oryzae mutants exhibit an unusual tetracycline susceptibility phenotype in which exogenous iron supplementation is required for phenotypic expression of a tetracycline resistance determinant that is encoded on an introduced plasmid. The rpfF X. oryzae pv. oryzae mutants also overproduce one or more siderophores and exhibit a growth deficiency under low iron conditions as well as in the presence of reducing agents that are expected to promote the conversion of Fe+3 to Fe+2. Exogenous iron supplementation promotes migration of rpfF X. oryzae pv. oryzae mutants in rice leaves. The results suggest that rpfF may be involved in controlling an iron-uptake system of X. oryzae pv. oryzae and that an inability to cope with the conditions of low iron availability in the host may be the reason for the virulence deficiency of the rpfF X. oryzae pv. oryzae mutants.


Mental imagery and synaesthesia: Is synaesthesia from internally-generated stimuli possible?
Previous studies provide empirical support for the reported colour experience in grapheme-colour synaesthesia by measuring the synaesthetic experience from an externally presented grapheme. The current study explored the synaesthetic experience resulting from a visual mental image of a grapheme. Grapheme-colour synaesthetes (N=6) and matched controls (N=10 per synaesthete) completed a visual mental imagery task that involved visualising a letter and making a size-based decision about it. The background colour that the grapheme was visualised against was manipulated so that it was congruent or incongruent with the synaesthetic colour for the grapheme being visualised. Compared to matched controls, an effect of colour condition was found for four of the six synaesthetes, although importantly the direction of the effect varied between synaesthetes. In addition, a significant effect of group was found, as the synaesthetes were all faster than the matched controls at the imagery task, regardless of background colour. We conclude that there is some support for subjective reports of imagery-induced synaesthesia, but there are important individual differences. These findings are discussed in relation to both the visual imagery and synaesthesia literature.


Microbiota disbiosis is associated with colorectal cancer.
The dysbiosis of the human intestinal microbiota is linked to sporadic colorectal carcinoma (CRC). The present study was designed to investigate the gut microbiota distribution features in CRC patients. We performed pyrosequencing based analysis of the 16S rRNA gene V3 region to investigate microbiota of the cancerous tissue and adjacent non-cancerous normal tissue in proximal and distal CRC samples. The results revealed that the microbial structures of the CRC patients and healthy individuals differed significantly. Firmicutes and Fusobacteria were over-represented whereas Proteobacteria was under-represented in CRC patients. In addition, Lactococcus and Fusobacterium exhibited a relatively higher abundance while Pseudomonas and Escherichia-Shigella was reduced in cancerous tissues compared to adjacent non-cancerous tissues. Meanwhile, the overall microbial structures of proximal and distal colon cancerous tissues were similar; but certain potential pro-oncogenic pathogens were different. These results suggested that the mucosa-associated microbiota is dynamically associated with CRC, which may provide evidences for microbiota-associated diagnostic, prognostic, preventive, and therapeutic strategies for CRC.


Liver ubiquitome uncovers nutrient-stress-mediated trafficking and secretion of complement C3.
Adaptation to changes in nutrient availability is crucial for cells and organisms. Posttranslational modifications of signaling proteins are very dynamic and are therefore key to promptly respond to nutrient deprivation or overload. Herein we screened for ubiquitylation of proteins in the livers of fasted and refed mice using a comprehensive systemic proteomic approach. Among 1641 identified proteins, 117 were differentially ubiquitylated upon fasting or refeeding. Endoplasmic reticulum (ER) and secretory proteins were enriched in the livers of refed mice in part owing to an ER-stress-mediated response engaging retro-translocation and ubiquitylation of proteins from the ER. Complement C3, an innate immune factor, emerged as the most prominent ER-related hit of our screen. Accordingly, we found that secretion of C3 from the liver and primary hepatocytes as well as its dynamic trafficking are nutrient dependent. Finally, obese mice with a chronic nutrient overload show constitutive trafficking of C3 in the livers despite acute changes in nutrition, which goes in line with increased C3 levels and low-grade inflammation reported for obese patients. Our study thus suggests that nutrient sensing in the liver is coupled to release of C3 and potentially its metabolic and inflammatory functions.


Geographical Factors Affecting the Admission of Teenagers and Young Adults to Age-Specialist Inpatient Cancer Care in England.
Purpose: Little is known about the factors that influence the place of inpatient care for teenage and young adult (TYA) cancer patients. Recent guidelines have recommended centralization of care for this group to a small number of specialized centers. This study aimed to investigate the influence of geography and travel times on the likelihood of admission to an age-specialist center in England during cancer treatment for patients aged 15-24 at the time of diagnosis. Methods: Data for 6788 patients aged 15-24, diagnosed between 2001 and 2006 and treated as an inpatient in England between 2001 and 2009, were obtained from the National Cancer Data Repository. Eight TYA age-specialist centers were identified in England during this time period; road travel times to these centers were calculated using ArcGIS Network Analyst. Factors thought to affect the likelihood of admission, such as diagnostic group, gender, and age at diagnosis were modeled using logistic regression. Results: Overall, 66.9% of patients never received inpatient treatment at a TYA age-specialist center during the course of their treatment. Increasing travel time significantly reduced the likelihood of admission to a TYA age-specialist center after adjustment for case mix factors. Conclusion: Many TYA patients received little or no inpatient treatment at a TYA age-specialist center during their treatment. The variation between diagnostic groups suggests that factors other than distance to the closest center are affecting the likelihood of admission and demonstrates the potential need to consider improvements to the structured referral practice for this unique group of patients.


LIMIT CYCLES CAN REDUCE THE WIDTH OF THE HABITABLE ZONE.
The liquid water habitable zone (HZ) describes the orbital distance at which a terrestrial planet can maintain above-freezing conditions through regulation by the carbonate-silicate cycle. Recent calculations have suggested that planets in the outer regions of the HZ cannot maintain stable, warm climates, but rather should oscillate between long, globally glaciated states and shorter periods of climatic warmth. Such conditions, similar to "Snowball Earth" episodes experienced on Earth, would be inimical to the development of complex land life, including intelligent life. Here, we build on previous studies with an updated energy balance climate model to calculate this "limit cycle" region of the HZ where such cycling would occur. We argue that an abiotic Earth would have a greater CO2 partial pressure than today because plants and other biota help to enhance the storage of CO2 in soil. When we tune our abiotic model accordingly, we find that limit cycles can occur but that previous calculations have overestimated their importance. For G stars like the Sun, limit cycles occur only for planets with CO2 outgassing rates less than that on modern Earth. For K- and M-star planets, limit cycles should not occur; however, M-star planets may be inhospitable to life for other reasons. Planets orbiting late G-type and early K-type stars retain the greatest potential for maintaining warm, stable conditions. Our results suggest that host star type, planetary volcanic activity, and seafloor weathering are all important factors in determining whether planets will be prone to limit cycling.


What happens to functional mitral regurgitation after aortic valve replacement for aortic stenosis?
Patients with aortic stenosis (AS) treated with aortic valve replacement (AVR) may also present with associated functional mitral valve regurgitation (FMR). Whether to also address the mitral valve at the time of AVR remains unclear. This study was designed to determine the influence of MR on survival and its evolution over time. We retrospectively reviewed 74 patients with FMR who underwent isolated AVR between 1999 and 2006 at our institution. Inclusion criteria were surgery for AVR with severe AS (mean age, 69 years; N = 47; 64% women) and FMR (grade I, 80%; grade II, 19%; grade III, 1%). Echocardiography follow-up data were obtained by mail questionnaires sent to the referring cardiologists of all survivors. All parameters were analyzed with the Kaplan-Meier method and the sign test. The operative mortality rate was 2%, and 9 patients (12%) died during follow-up. The mean (SD) follow-up time was 48 ± 33 months, and follow-up 96% complete. The follow-up demonstrated a decrease of FMR by 2 degrees in 3 patients (4%), and 1 degree in 14 patients (19%); regurgitation remained unchanged in the majority of patients (n = 47; 63%). FMR worsened in 10 patients overall (14%), and new-onset atrial fibrillation was found in 24 patients (33%); however, the statistical analysis failed to demonstrate an impact of worsening FMR on survival. MR in patients with severe AS and FMR at the time of AVR does not appear to worsen significantly over time. Not dealing with the mitral valve at the time of AVR might be warranted for selected patients.


Diabetic Gastroparesis: Principles and Current Trends in Management.
This article is a comprehensive review of diabetic gastroparesis, defined as delayed or disordered gastric emptying, including basic principles and current trends in management. This review includes sections on anatomy and physiology, diagnosis and differential diagnosis as well as management and current guidelines for treatment of diabetic gastroparesis. Diabetic gastroparesis (DGp) is a component of autonomic neuropathy resulting from long-standing poorly controlled type 1 and type 2 diabetes. The diagnostic workup of DGp first excludes obstruction and other causes including medications that may mimic delayed/disordered gastric emptying. Targeting nutrition, hydration, symptomatic relief and glycemic control are mainstays of treatment for DGp. Additionally, optimal treatment of DGp includes good glycemic management, often involving customizing insulin delivery using basal-bolus insulin and technology, including sensor-augmented pumps and continuous glucose monitoring systems. Prokinetic medications may be helpful in DGp symptoms, although only limited number of medications is currently available in the USA. Selected medication-refractory patients with DGp may benefit from gastric neuromodulation, and some from surgical interventions including pyloric therapies that can also be done endoscopically. As is true of any of the diabetic complications, prevention of DGp by early and optimal glycemic control is more cost-effective.Funding: Hansa Medcell, India.


Cautery artifact understages urothelial cancer at initial transurethral resection of large bladder tumours.
We sought to determine how frequently cautery (thermal) artifact precludes an accurate determination of stage at initial transurethral resection of bladder tumour (TURBT) of large bladder tumours. We queried our institution's billing data to identify patients who underwent TURBT for large bladder tumours >5cm (CPT 52240) by two urologists at an academic centre from January 2009 through April 2013. Only patients who underwent initial-staging TURBT for urothelial cancer were included. Pathological reports were reviewed for stage, number of separate pathological specimens per TURBT, and presence of cautery artifact. Operative reports were reviewed for whether additional cold cup biopsies were taken of other suspicious areas of the bladder, resident involvement, and type of electrocautery. We identified 119 patients who underwent initial staging TURBT for large tumours. Cautery artifact interfered with accurate staging in 7/119 (6%) of cases. Of these, six patients underwent restaging TURBT, with 50% percent experiencing upstaging to T2 disease. Tumour size, tumour grade, whether additional cold cup biopsies were taken, number of separate pathological specimens sent, and resident involvement were not associated with cautery artifact (all p>0.05). Bipolar resection had a higher rate of cautery artifact 5/42 (12%), compared to monopolar resection 2/77 (2.6%) approaching significance (p=0.095). Cautery artifact may delay accurate staging at initial TURBT for large tumours by understaging up to 6% of patients.


MMP-9 deficiency shelters endothelial PECAM-1 expression and enhances regeneration of steatotic livers after ischemia and reperfusion injury.
Organ shortage has led to the use of steatotic livers in transplantation, despite their elevated susceptibility to ischemia/reperfusion injury (IRI). Matrix metalloproteinase-9 (MMP-9), an inducible gelatinase, is emerging as a central mediator of leukocyte traffic into inflamed tissues. However, its role in steatotic hepatic IRI has yet to be demonstrated. We examined the function of MMP-9 in mice fed with a high-fat diet (HFD), which developed approximately 50% hepatic steatosis, predominantly macrovesicular, prior to partial hepatic IRI. The inability of MMP-9(-/-) deficient steatotic mice to express MMP-9 significantly protected these mice from liver IRI. Compared to fatty controls, MMP-9(-/-) steatotic livers showed significantly reduced leukocyte infiltration, proinflammatory cytokine expression, and liver necrosis. Loss of MMP-9 activity preserved platelet endothelial cell adhesion molecule-1 (PECAM-1) expression, a modulator of vascular integrity at the endothelial cell-cell junctions in steatotic livers after IRI. Using in vitro approaches, we show that targeted inhibition of MMP-9 sheltered the extracellular portion of PECAM-1 from proteolytic processing, and disrupted leukocyte migration across this junctional molecule. Moreover, the evaluation of distinct parameters of regeneration, proliferating cell nuclear antigen (PCNA) and histone H3 phosphorylation (pH3), provided evidence that hepatocyte progression into S phase and mitosis was notably enhanced in MMP-9(-/-) steatotic livers after IRI. MMP-9 activity disrupts vascular integrity at least partially through a PECAM-1 dependent mechanism and interferes with regeneration of steatotic livers after IRI. Our novel findings establish MMP-9 as an important mediator of steatotic liver IRI.


Protein expression and genetic structure of the coral Porites lobata in an environmentally extreme Samoan back reef: does host genotype limit phenotypic plasticity?
The degree to which coral reef ecosystems will be impacted by global climate change depends on regional and local differences in corals' susceptibility and resilience to environmental stressors. Here, we present data from a reciprocal transplant experiment using the common reef building coral Porites lobata between a highly fluctuating back reef environment that reaches stressful daily extremes, and a more stable, neighbouring forereef. Protein biomarker analyses assessing physiological contributions to stress resistance showed evidence for both fixed and environmental influence on biomarker response. Fixed influences were strongest for ubiquitin-conjugated proteins with consistently higher levels found in back reef source colonies both pre and post-transplant when compared with their forereef conspecifics. Additionally, genetic comparisons of back reef and forereef populations revealed significant population structure of both the nuclear ribosomal and mitochondrial genomes of the coral host (F(ST) = 0.146 P < 0.0001, F(ST) = 0.335 P < 0.0001 for rDNA and mtDNA, respectively), whereas algal endosymbiont populations were genetically indistinguishable between the two sites. We propose that the genotype of the coral host may drive limitations to the physiological responses of these corals when faced with new environmental conditions. This result is important in understanding genotypic and environmental interactions in the coral algal symbiosis and how corals may respond to future environmental changes.


Urinary N-acetyl-beta-D-glucosaminidase changes in relation to age, sex, race, and diastolic and systolic blood pressure in a young adult biracial population. The Bogalusa Heart Study.
Increased urinary activity of N-acetyl-beta-D-glucosaminidase (NAG) has been reported in many clinical conditions, including essential hypertension. Since hypertension is increasingly recognized as beginning in childhood, we hypothesized that urinary NAG changes with increasing blood pressure may start early in life and may also be the evidence of the existence of early hypertensive disease. We analyzed the urinary NAG changes in 980 young adults, ages between 18 to 32, in relation to age, race, sex, and systolic and diastolic blood pressure. We observed that black women had the highest level of NAG, with or without adjustment for creatinine. With aging, urinary NAG significantly increased in men. As blood pressure increased, urinary NAG excretion appeared to increase, and this was more apparent in black women (P < .05). Significant correlations between NAG excretion and systolic (r = 0.12, P = .04) and diastolic (r = 0.18, P = .003) blood pressures existed in the oldest age group, 28 to 32 years old. These findings show that a significant association between urinary NAG and blood pressure exists in normal young adults and changes in urinary NAG may be evidence of early hypertensive disease.


Comprehensive use of cardiac computed tomography to guide left ventricular lead placement in cardiac resynchronization therapy.
Optimal lead positioning is an important determinant of cardiac resynchronization therapy (CRT) response. The purpose of this study was to evaluate cardiac computed tomography (CT) selection of the optimal epicardial vein for left ventricular (LV) lead placement by targeting regions of late mechanical activation and avoiding myocardial scar. Eighteen patients undergoing CRT upgrade with existing pacing systems underwent preimplant electrocardiogram-gated cardiac CT to assess wall thickness, hypoperfusion, late mechanical activation, and regions of myocardial scar by the derivation of the stretch quantifier for endocardial engraved zones (SQUEEZ) algorithm. Cardiac venous anatomy was mapped to individualized American Heart Association (AHA) bull's-eye plots to identify the optimal venous target and compared with acute hemodynamic response (AHR) in each coronary venous target using an LV pressure wire. Fifteen data sets were evaluable. CT-SQUEEZ-derived targets produced a similar mean AHR compared with the best achievable AHR (20.4% ± 13.7% vs 24.9% ± 11.1%; P = .36). SQUEEZ-derived guidance produced a positive AHR in 92% of target segments, and pacing in a CT-SQUEEZ target vein produced a greater clinical response rate vs nontarget segments (90% vs 60%). Preprocedural CT-SQUEEZ-derived target selection may be a valuable tool to predict the optimal venous site for LV lead placement in patients undergoing CRT upgrade.


Ultrafast transient absorption of eumelanin suspensions: the role of inverse Raman scattering.
An ultrafast investigation is carried out on synthetic eumelanin suspended either in water or in DMSO-methanol. Upon photoexcitation by visible femtosecond pulses, the transient absorption (TA) dynamics of the suspensions are probed in a broad visible spectral range, showing clear nonlinearities. The latter arise from pump-probe interactions that induce the inverse Raman scattering (IRS) effect. We show how eumelanin TA dynamics are modified in proximity of the solvent Stokes and anti-Stokes scattering peaks, demonstrating that IRS affects the sign of TA but not the relaxation times. We compare the results obtained in both suspensions, unveiling the role of the surrounding environment. Eventually, the intrinsic response of synthetic eumelanin to ultrafast photoexcitation is evaluated.


Decreased DGCR8 expression and miRNA dysregulation in individuals with 22q11.2 deletion syndrome.
Deletion of the 1.5-3 Mb region of chromosome 22 at locus 11.2 gives rise to the chromosome 22q11.2 deletion syndrome (22q11DS), also known as DiGeorge and Velocardiofacial Syndromes. It is the most common micro-deletion disorder in humans and one of the most common multiple malformation syndromes. The syndrome is characterized by a broad phenotype, whose characterization has expanded considerably within the last decade and includes many associated findings such as craniofacial anomalies (40%), conotruncal defects of the heart (CHD; 70-80%), hypocalcemia (20-60%), and a range of neurocognitive anomalies with high risk of schizophrenia, all with a broad phenotypic variability. These phenotypic features are believed to be the result of a change in the copy number or dosage of the genes located in the deleted region. Despite this relatively clear genetic etiology, very little is known about which genes modulate phenotypic variations in humans or if they are due to combinatorial effects of reduced dosage of multiple genes acting in concert. Here, we report on decreased expression levels of genes within the deletion region of chromosome 22, including DGCR8, in peripheral leukocytes derived from individuals with 22q11DS compared to healthy controls. Furthermore, we found dysregulated miRNA expression in individuals with 22q11DS, including miR-150, miR-194 and miR-185. We postulate this to be related to DGCR8 haploinsufficiency as DGCR8 regulates miRNA biogenesis. Importantly we demonstrate that the level of some miRNAs correlates with brain measures, CHD and thyroid abnormalities, suggesting that the dysregulated miRNAs may contribute to these phenotypes and/or represent relevant blood biomarkers of the disease in individuals with 22q11DS.


The effect of laparotomy on hydroxyl radicals, singlet oxygen and antioxidants measured by EPR method in the tails of rats.
The aim of the study was to demonstrate that direct measurement of hydroxyl radicals and singlet oxygen in the tail of living rats is possible. The basic level of hydroxyl radicals and singlet oxygen were measured and the effects of antioxidants on their levels were studied in the tail of living anaesthetized rats after acute postoperative pain. Laparotomy was performed as the source of acute abdominal pain. After closure of the abdominal cavity, the animals began to awaken within 30-60 minutes. They were left to recover for 2-3 hours; then they were reanesthetized and the effect of antioxidants was measured on the numbers of hydroxyl radicals and singlet oxygen via blood in the tail. The laparotomy was preformed under general anesthesia (Xylazin and Ketamin) using Wistar rats. After recovery and several hours of consciousness they were reanaesthetized and free radicals and singlet oxygen were measured. An antioxidant mixture (vitamins A, C, D and Selenium) was administered intramuscularly prior to the laparotomy. All measurements were done on the tail of anaesthetized animals. In this particular article, the effect of antioxidants is only reported for hydroxyl radicals. After laparotomy, which represented both somatic and visceral pain, hydroxyl radicals and singlet oxygen were increased. Antioxidant application prior to laparotomy decreased the numbers of hydroxyl radicals. Results are in agreement with our previous finding regarding the increase in hydroxyl free radicals and singlet oxygen following nociceptive stimulation, in this case a combination of both somatic and visceral pain. The administered antioxidants mitigated the increase. This is further confirmation that direct measurement of free radicals and singlet oxygen represents a very useful method for the biochemical evaluation of pain and nociception.


Evolution of air breathing: oxygen homeostasis and the transitions from water to land and sky.
Life originated in anoxia, but many organisms came to depend upon oxygen for survival, independently evolving diverse respiratory systems for acquiring oxygen from the environment. Ambient oxygen tension (PO2) fluctuated through the ages in correlation with biodiversity and body size, enabling organisms to migrate from water to land and air and sometimes in the opposite direction. Habitat expansion compels the use of different gas exchangers, for example, skin, gills, tracheae, lungs, and their intermediate stages, that may coexist within the same species; coexistence may be temporally disjunct (e.g., larval gills vs. adult lungs) or simultaneous (e.g., skin, gills, and lungs in some salamanders). Disparate systems exhibit similar directions of adaptation: toward larger diffusion interfaces, thinner barriers, finer dynamic regulation, and reduced cost of breathing. Efficient respiratory gas exchange, coupled to downstream convective and diffusive resistances, comprise the "oxygen cascade"-step-down of PO2 that balances supply against toxicity. Here, we review the origin of oxygen homeostasis, a primal selection factor for all respiratory systems, which in turn function as gatekeepers of the cascade. Within an organism's lifespan, the respiratory apparatus adapts in various ways to upregulate oxygen uptake in hypoxia and restrict uptake in hyperoxia. In an evolutionary context, certain species also become adapted to environmental conditions or habitual organismic demands. We, therefore, survey the comparative anatomy and physiology of respiratory systems from invertebrates to vertebrates, water to air breathers, and terrestrial to aerial inhabitants. Through the evolutionary directions and variety of gas exchangers, their shared features and individual compromises may be appreciated.


Long-range-projecting GABAergic neurons modulate inhibition in hippocampus and entorhinal cortex.
The hippocampus and entorhinal cortex play a pivotal role in spatial learning and memory. The two forebrain regions are highly interconnected via excitatory pathways. Using optogenetic tools, we identified and characterized long-range γ-aminobutyric acid-releasing (GABAergic) neurons that provide a bidirectional hippocampal-entorhinal inhibitory connectivity and preferentially target GABAergic interneurons. Activation of long-range GABAergic axons enhances sub- and suprathreshold rhythmic theta activity of postsynaptic neurons in the target areas.


Construction of a leftover bath water model for microbial testing.
In this study, in order to construct a model of leftover bath water, we analyzed one hundred samples of used bath water samples which were provided by twenty-eight volunteer families. It appeared that the number of detected bacteria from such bath water was correlated closely with the number of bathers. Moreover, the pH, acidity, chemical oxygen demand (COD), ion, protein content of the leftover bath water were measured. The number of bathers had no connection with the pH, acidity, COD, and ion content of the leftover bath water. However, the protein content of the bath water correlated with the number of detected bacteria. Based on these results, the model of leftover bath water was constructed. Achromobacter xylosoxidans, Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa were incubated with the model bath water as indices of bath water contamination. The number of incubated viable cells in the model bath water increased with increasing concentrations of casamino acid. Consequently, it was suggested that varying the concentration of casamino acid based on family size or contamination would be necessary in the efficient use of the constructed model of leftover bath water for microbial testing.


Health-related quality of life in glomerular disease.
There is scant literature describing the effect of glomerular disease on health-related quality of life (HRQOL). The Cure Glomerulonephropathy study (CureGN) is an international longitudinal cohort study of children and adults with four primary glomerular diseases (minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, and IgA nephropathy). HRQOL is systematically assessed using items from the Patient-Reported Outcomes Measurement Informative System (PROMIS). We assessed the relationship between HRQOL and demographic and clinical variables in 478 children and 1115 adults at the time of enrollment into CureGN. Domains measured by PROMIS items included global assessments of health, mobility, anxiety, fatigue, and sleep impairment, as well as a derived composite measure incorporating all measured domains. Multivariable models were created that explained 7 to 32% of variance in HRQOL. Patient-reported edema consistently had the strongest and most robust association with each measured domain of HRQOL in multivariable analysis (adjusted β [95% CI] for composite PROMIS score in children, -5.2 [-7.1 to -3.4]; for composite PROMIS score in adults, -6.1 [-7.4 to -4.9]). Female sex, weight (particularly obesity), and estimated glomerular filtration rate were also associated with some, but not all, domains of HRQOL. Primary diagnosis, disease duration, and exposure to immunosuppression were not associated with HRQOL after adjustment. Sensitivity analyses and interaction testing demonstrated no significant association between disease duration or immunosuppression and any measured domain of HRQOL. Thus, patient-reported edema has a consistent negative association with HRQOL in patients with primary glomerular diseases, with substantially greater impact than other demographic and clinical variables.


Decreasing the minimum length criterion for an episode of hypomania: evaluation using self-reported data from patients with bipolar disorder.
Brief hypomania lasting less than 4 days may impair functioning and help to detect bipolarity. This study analyzed brief hypomania that occurred in patients with bipolar disorder who were diagnosed according to the DSM-IV criteria. Daily self-reported mood ratings were obtained from 393 patients (247 bipolar I and 146 bipolar II) for 6 months (75,284 days of data, mean 191.6 days). Episodes of hypomania were calculated using a 4, 3, 2, and single day length criterion. Brief hypomania occurred frequently. With a decrease in the minimum criterion from 4 days to 2 days, there were almost twice as many patients with an episode of hypomania (102 vs. 190), and more than twice as many episodes (305 vs. 863). Single days of hypomania were experienced by 271 (69%) of the sample. With a 2-day episode length, 33% of all hypomania remained outside of an episode. There was no significant difference in the percent of hypomanic days outside of an episode between patients with bipolar I and II disorders. There were no significant differences in the demographic characteristics of patients who met the 4-day minimum as compared with those who only experienced episodes of hypomania using a shortened length criterion. Decreasing the minimum length criterion for an episode of hypomania will cause a large increase in the number of patients who experience an episode and in the aggregate number of episodes, but will not distinguish subgroups within a sample who meet the DSM-IV criteria for bipolar disorder. Frequency may be an important dimensional aspect of brief hypomania. Clinicians should regularly probe for brief hypomania.


Discovery of LRE1 as a specific and allosteric inhibitor of soluble adenylyl cyclase.
The prototypical second messenger cAMP regulates a wide variety of physiological processes. It can simultaneously mediate diverse functions by acting locally in independently regulated microdomains. In mammalian cells, two types of adenylyl cyclase generate cAMP: G-protein-regulated transmembrane adenylyl cyclases and bicarbonate-, calcium- and ATP-regulated soluble adenylyl cyclase (sAC). Because each type of cyclase regulates distinct microdomains, methods to distinguish between them are needed to understand cAMP signaling. We developed a mass-spectrometry-based adenylyl cyclase assay, which we used to identify a new sAC-specific inhibitor, LRE1. LRE1 bound to the bicarbonate activator binding site and inhibited sAC via a unique allosteric mechanism. LRE1 prevented sAC-dependent processes in cellular and physiological systems, and it will facilitate exploration of the therapeutic potential of sAC inhibition.


Multicritical behavior in models with two competing order parameters.
We employ the nonperturbative functional renormalization group to study models with an O(N(1) ⊕O(N)(2)) symmetry. Here different fixed points exist in three dimensions, corresponding to bicritical and tetracritical behavior induced by the competition of two order parameters. We discuss the critical behavior of the symmetry-enhanced isotropic, the decoupled and the biconical fixed point, and analyze their stability in the N(1),N(2) plane. We study the fate of nontrivial fixed points during the transition from three to four dimensions, finding evidence for a triviality problem for coupled two-scalar models in high-energy physics. We also point out the possibility of noncanonical critical exponents at semi-Gaussian fixed points and show the emergence of Goldstone modes from discrete symmetries.


Simvastatin inhibits osteoclast differentiation by scavenging reactive oxygen species.
Osteoclasts, together with osteoblasts, control the amount of bone tissue and regulate bone remodeling. Osteoclast differentiation is an important factor related to the pathogenesis of bone-loss related diseases. Reactive oxygen species (ROS) acts as a signal mediator in osteoclast differentiation. Simvastatin, which inhibits 3-hydroxy-3-methylglutaryl coenzyme A, is a hypolipidemic drug which is known to affect bone metabolism and suppresses osteoclastogenesis induced by receptor activator of nuclear factor-κB ligand (RANKL). In this study, we analyzed whether simvastatin can inhibit RANKL-induced osteoclastogenesis through suppression of the subsequently formed ROS and investigated whether simvastatin can inhibit H2O2-induced signaling pathways in osteoclast differentiation. We found that simvastatin decreased expression of tartrate-resistant acid phosphatase (TRAP), a genetic marker of osteoclast differentiation, and inhibited intracellular ROS generation in RAW 264.7 cell lines. ROS generation activated NF-κB, protein kinases B (AKT), mitogen-activated protein kinases signaling pathways such as c-JUN N-terminal kinases, p38 MAP kinases as well as extracellular signal- regulated kinase. Simvastatin was found to suppress these H2O2-induced signaling pathways in osteoclastogenesis. Together, these results indicate that simvastatin acts as an osteoclastogenesis inhibitor through suppression of ROS-mediated signaling pathways. This indicates that simvastatin has potential usefulness for osteoporosis and pathological bone resorption.


H3Africa and the African life sciences ecosystem: building sustainable innovation.
Interest in genomics research in African populations is experiencing exponential growth. This enthusiasm stems in part from the recognition that the genomic diversity of African populations is a window of opportunity for innovations in postgenomics medicine, ecology, and evolutionary biology. The recently launched H3Africa initiative, for example, captures the energy and momentum of this interest. This interdisciplinary socio-technical analysis highlights the challenges that have beset previous genomics research activities in Africa, and looking ahead, suggests constructive ways H3Africa and similar large scale science efforts could usefully chart a new era of genomics and life sciences research in Africa that is locally productive and globally competitive. As independent African scholars and social scientists, we propose that any serious global omics science effort, including H3Africa, aiming to build genomics research capacity and capability in Africa, needs to fund the establishment of biobanks and the genomic analyses platforms within Africa. Equally they need to prioritize community engagement and bioinformatics capability and the training of African scientists on these platforms. Historically, the financial, technological, and skills imbalance between Africa and developed countries has created exploitative frameworks of collaboration where African researchers have become merely facilitators of Western funded and conceived research agendas involving offshore expatriation of samples. Not surprisingly, very little funding was allocated to infrastructure and human capital development in the past. Moving forward, capacity building should materialize throughout the entire knowledge co-production trajectory: idea generation (e.g., brainstorming workshops for innovative hypotheses development by African scientists), data generation (e.g., genome sequencing), and high-throughput data analysis and contextualization. Additionally, building skills for political science scholarship that questions the unchecked assumptions of the innovation performers be they funders, scientists, and social scientists, would enable collective innovation that is truly sustainable, ethical, and robust.


Differences between males and females in rates of serotonin synthesis in human brain.
Rates of serotonin synthesis were measured in the human brain using positron emission tomography. The sensitivity of the method is indicated by the fact that measurements are possible even after a substantial lowering of synthesis induced by acute tryptophan depletion. Unlike serotonin levels in human brain, which vary greatly in different brain areas, rates of synthesis of the indolamine are rather uniform throughout the brain. The mean rate of synthesis in normal males was found to be 52% higher than in normal females; this marked difference may be a factor relevant to the lower incidence of major unipolar depression in males.


Labile haemoglobin as a glycaemic biomarker for patient-specific monitoring of diabetes: mathematical modelling approach.
Diabetes mellitus constitutes a major health problem and its clinical presentation and progression may vary considerably. A number of standardized diagnostic and monitoring tests are currently used for diabetes. They are based on measuring either plasma glucose, glycated haemoglobin or both. Their main goal is to assess the average blood glucose concentration. There are several sources of interference that can lead to discordances between measured plasma glucose and glycated haemoglobin levels. These include haemoglobinopathies, conditions associated with increased red blood cell turnover or the administration of some therapies, to name a few. Therefore, there is a need to provide new diagnostic tools for diabetes that employ clinically accessible biomarkers which, at the same time, can offer additional information allowing us to detect possible conflicting cases and to yield more reliable evaluations of the average blood glucose level concentration. We put forward a biomathematical model to describe the kinetics of two patient-specific glycaemic biomarkers to track the emergence and evolution of diabetes: glycated haemoglobin and its labile fraction. Our method incorporates erythrocyte age distribution and utilizes a large cohort of clinical data from blood tests to support its usefulness for diabetes monitoring.


Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection.
Human lung epithelial cells are likely among the first targets to encounter invading severe acute respiratory syndrome-associated coronavirus (SARS-CoV). Not only can these cells support the growth of SARS-CoV infection, but they are also capable of secreting inflammatory cytokines to initiate and, eventually, aggravate host innate inflammatory responses, causing detrimental immune-mediated pathology within the lungs. Thus, a comprehensive evaluation of the complex epithelial signaling to SARS-CoV is crucial for paving the way to better understand SARS pathogenesis. Based on microarray-based functional genomics, we report here the global gene response of 2B4 cells, a cloned bronchial epithelial cell line derived from Calu-3 cells. Specifically, we found a temporal and spatial activation of nuclear factor (NF)kappaB, activator protein (AP)-1, and interferon regulatory factor (IRF)-3/7 in infected 2B4 cells at 12-, 24-, and 48-hrs post infection (p.i.), resulting in the activation of many antiviral genes, including interferon (IFN)-beta, -lambdas, inflammatory mediators, and many IFN-stimulated genes (ISGs). We also showed, for the first time, that IFN-beta and IFN-lambdas were capable of exerting previously unrecognized, non-redundant, and complementary abilities to limit SARS-CoV replication, even though their expression could not be detected in infected 2B4 bronchial epithelial cells until 48 hrs p.i. Collectively, our results highlight the mechanics of the sequential events of antiviral signaling pathway/s triggered by SARS-CoV in bronchial epithelial cells and identify novel cellular targets for future studies, aiming at advancing strategies against SARS.


Creatine transporter deficiency impairs stress adaptation and brain energetics homeostasis.
The creatine transporter (CrT) maintains brain creatine (Cr) levels, but the effects of its deficiency on energetics adaptation under stress remain unclear. There are also no effective treatments for CrT deficiency, the second most common cause of X-linked intellectual disabilities. Herein, we examined the consequences of CrT deficiency in brain energetics and stress-adaptation responses plus the effects of intranasal Cr supplementation. We found that CrT-deficient (CrT-/y) mice harbored dendritic spine and synaptic dysgenesis. Nurtured newborn CrT-/y mice maintained baseline brain ATP levels, with a trend toward signaling imbalance between the p-AMPK/autophagy and mTOR pathways. Starvation elevated the signaling imbalance and reduced brain ATP levels in P3 CrT-/y mice. Similarly, CrT-/y neurons and P10 CrT-/y mice showed an imbalance between autophagy and mTOR signaling pathways and greater susceptibility to cerebral hypoxia-ischemia and ischemic insults. Notably, intranasal administration of Cr after cerebral ischemia increased the brain Cr/N-acetylaspartate ratio, partially averted the signaling imbalance, and reduced infarct size more potently than intraperitoneal Cr injection. These findings suggest important functions for CrT and Cr in preserving the homeostasis of brain energetics in stress conditions. Moreover, intranasal Cr supplementation may be an effective treatment for congenital CrT deficiency and acute brain injury.


Prevalence of Gastrointestinal Symptoms and Fecal Viral Shedding in Patients With Coronavirus Disease 2019: A Systematic Review and Meta-analysis.
Coronavirus disease 2019 (COVID-19) is a global pandemic and can involve the gastrointestinal (GI) tract, including symptoms like diarrhea and shedding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in feces. To provide a pooled estimate of GI symptoms, liver enzyme levels outside reference ranges, and fecal tests positive for SARS-CoV-2 among patients with COVID-19. An electronic literature search was performed for published (using MEDLINE/PubMed and Embase) and preprint (using bioRxiv and medRxiv) studies of interest conducted from November 1, 2019, to March 30, 2020. Search terms included "COVID-19," "SARS-Cov-2," and/or "novel coronavirus." Eligible studies were those including patients with SARS-CoV-2 infection who reported GI symptoms. Data on patients with GI symptoms (ie, diarrhea, nausea, or vomiting), liver enzyme level changes, and fecal shedding of virus were extracted. Quality of studies was examined using methodological index for nonrandomized studies. Pooled estimates (%) were reported with 95% CIs with level of heterogeneity (I2). Study and patient characteristics with pooled detection rates for diarrhea, nausea or vomiting, liver enzyme levels outside reference ranges, and SARS-CoV-2 positivity in feces tests were analyzed. Of 1484 records reviewed, 23 published and 6 preprint studies were included in the analysis, with a total of 4805 patients (mean [SD] age, 52.2 [14.8] years; 1598 [33.2%] women) with COVID-19. The pooled rates were 7.4% (95% CI, 4.3%-12.2%) of patients reporting diarrhea and 4.6% (95% CI, 2.6%-8.0%) of patients reporting nausea or vomiting. The pooled rate for aspartate aminotransferase levels outside reference ranges was 20% (95% CI, 15.3%-25.6%) of patients, and the pooled rate for alanine aminotransferase levels outside reference ranges was 14.6% (95% CI, 12.8%-16.6%) of patients. Fecal tests that were positive for SARS-CoV-2 were reported in 8 studies, and viral RNA shedding was detected in feces in 40.5% (95% CI, 27.4%-55.1%) of patients. There was high level of heterogeneity (I2 = 94%), but no statistically significant publication bias noted. These findings suggest that that 12% of patients with COVID-19 will manifest GI symptoms; however, SAR-CoV-2 shedding was observed in 40.5% of patients with confirmed SARS-CoV-2 infection. This highlights the need to better understand what measures are needed to prevent further spread of this highly contagious pathogen.


Biomechanical properties of concussions in high school football.
Sport concussion represents the majority of brain injuries occurring in the United States with 1.6–3.8 million cases annually. Understanding the biomechanical properties of this injury will support the development of better diagnostics and preventative techniques. We monitored all football related head impacts in 78 high school athletes (mean age = 16.7 yr) from 2005 to 2008 to better understand the biomechanical characteristics of concussive impacts. Using the Head Impact Telemetry System, a total of 54,247 impacts were recorded, and 13 concussive episodes were captured for analysis. A classification and regression tree analysis of impacts indicated that rotational acceleration (95582.3 rad·s−²), linear acceleration (996.1g), and impact location (front, top, and back) yielded the highest predictive value of concussion. These threshold values are nearly identical with those reported at the collegiate and professional level. If the Head Impact Telemetry System were implemented for medical use, sideline personnel can expect to diagnose one of every five athletes with a concussion when the impact exceeds these tolerance levels. Why all athletes did not sustain a concussion when the impacts generated variables in excess of our threshold criteria is not entirely clear, although individual differences between participants may play a role. A similar threshold to concussion in adolescent athletes compared with their collegiate and professional counterparts suggests an equal concussion risk at all levels of play.


First direct limits on lightly ionizing particles with electric charge less than e/6.
While the standard model of particle physics does not include free particles with fractional charge, experimental searches have not ruled out their existence. We report results from the Cryogenic Dark Matter Search (CDMS II) experiment that give the first direct-detection limits for cosmogenically produced relativistic particles with electric charge lower than e/6. A search for tracks in the six stacked detectors of each of two of the CDMS II towers finds no candidates, thereby excluding new parameter space for particles with electric charges between e/6 and e/200.


Microbiological diversity and prevalence of spoilage and pathogenic bacteria in commercial fermented alcoholic beverages (beer, fruit wine, refined rice wine, and yakju).
The present study examined 469 commercially available fermented alcoholic beverages (FABs), including beer (draft, microbrewed, and pasteurized), fruit wine (grape and others), refined rice wine, and yakju (raw and pasteurized). Samples were screened for Escherichia coli and eight foodborne pathogens (Bacillus cereus, Campylobacter jejuni, Clostridium perfringens, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., Staphylococcus aureus, and Yersinia enterocolitica), and the aerobic plate count, lactic acid bacteria, acetic acid bacteria, fungi, and total coliforms were also enumerated. Microbrewed beer contained the highest number of microorganisms (average aerobic plate count, 3.5; lactic acid bacteria, 2.1; acetic acid bacteria, 2.0; and fungi, 3.6 log CFU/ml), followed by draft beer and yakju (P < 0.05), whereas the other FABs contained , 25 CFU/25 ml microorganisms. Unexpectedly, neither microbial diversity nor microbial count correlated with the alcohol content (4.7 to 14.1%) or pH (3.4 to 4.2) of the product. Despite the harsh conditions, coliforms (detected in 23.8% of microbrewed beer samples) and B. cereus (detected in all FABs) were present in some products. B. cereus was detected most frequently in microbrewed beer (54.8% of samples) and nonpasteurized yakju (50.0%), followed by pasteurized yakju (28.8%), refined rice wine (25.0%), other fruit wines (12.3%), grape wine (8.6%), draft beer (5.6%), and pasteurized beer (2.2%) (P < 0.05). The finding that spore-forming B. cereus and coliform bacteria can survive the harsh conditions present in alcoholic beverages should be taken into account (alongside traditional quality indicators such as the presence of lactic acid-producing bacteria, acetic acid-producing bacteria, or both) when developing manufacturing systems and methods to prolong the shelf life of high-quality FAB products. New strategic quality management plans for various FABs are needed.


Δ9-THC Disrupts Gamma (γ)-Band Neural Oscillations in Humans.
Gamma (γ)-band oscillations play a key role in perception, associative learning, and conscious awareness and have been shown to be disrupted by cannabinoids in animal studies. The goal of this study was to determine whether cannabinoids disrupt γ-oscillations in humans and whether these effects relate to their psychosis-relevant behavioral effects. The acute, dose-related effects of Δ-9-tetrahydrocannabinol (Δ(9)-THC) on the auditory steady-state response (ASSR) were studied in humans (n=20) who completed 3 test days during which they received intravenous Δ(9)-THC (placebo, 0.015, and 0.03 mg/kg) in a double-blind, randomized, crossover, and counterbalanced design. Electroencephalography (EEG) was recorded while subjects listened to auditory click trains presented at 20, 30, and 40 Hz. Psychosis-relevant effects were measured with the Positive and Negative Syndrome scale (PANSS). Δ(9)-THC (0.03 mg/kg) reduced intertrial coherence (ITC) in the 40 Hz condition compared with 0.015 mg/kg and placebo. No significant effects were detected for 30 and 20 Hz stimulation. Furthermore, there was a negative correlation between 40 Hz ITC and PANSS subscales and total scores under the influence of Δ(9)-THC. Δ(9)-THC (0.03 mg/kg) reduced evoked power during 40 Hz stimulation at a trend level. Recent users of cannabis showed blunted Δ(9)-THC effects on ITC and evoked power. We show for the first time in humans that cannabinoids disrupt γ-band neural oscillations. Furthermore, there is a relationship between disruption of γ-band neural oscillations and psychosis-relevant phenomena induced by cannabinoids. These findings add to a growing literature suggesting some overlap between the acute effects of cannabinoids and the behavioral and psychophysiological alterations observed in psychotic disorders.


Global transcriptional response to interferon is a determinant of HCV treatment outcome and is modified by race.
Interferon (IFN)-alpha-based therapy for chronic hepatitis C is effective in fewer than 50% of all treated patients, with a substantially lower response rate in black patients. The goal of this study was to investigate the underlying host transcriptional response associated with interferon treatment outcomes. We collected peripheral blood mononuclear cells from chronic hepatitis C patients before initiation of IFN-alpha therapy and incubated the cells with or without IFN-alpha for 6 hours, followed by microarray assay to identify IFN-induced gene transcription. The microarray datasets were analyzed statistically according to the patients' race and virological responses to subsequent IFN-alpha treatment. The global induction of IFN-stimulated genes (ISGs) was significantly greater in sustained virological responders compared with nonresponders and in white patients compared with black patients. In addition, a significantly greater global induction of ISGs was observed in sustained virological responders compared with nonresponders within the group of white patients. The level of IFN-induced signal transducer and activator of transcription (STAT) 1 activation, a key component of the Janus kinase (JAK)-STAT signaling pathway, correlated with the global induction of ISGs and was significantly higher in white patients than in black patients. In conclusion, both treatment outcome and race are associated with different transcriptional responses to IFN-alpha. Because this difference is evident in the global induction of ISGs rather than a selective effect on a subset of such genes, key factors affecting the outcome of IFN-alpha therapy are likely to act at the JAK-STAT pathway that controls transcription of downstream ISGs.


Negative Mood States or Dysfunctional Cognitions: Their Independent and Interactional Effects in Influencing Severity of Gambling Among Chinese Problem Gamblers in Hong Kong.
Gambling-related cognitions and negative psychological states have been proposed as major factors in the initiation and maintenance of problem gambling (PG). While there are a substantial number of studies supporting the role of cognitive dysfunctions in the initiation and maintenance of PG, very few empirical studies have explored the specific role of negative psychological states in influencing PG behaviours. In addition, very few studies have examined the interaction effects of cognitive dysfunctions and negative psychological states in exerting influence on PG behaviours. Therefore, the present study aims to examine the main and interaction effects of gambling-related cognitions and psychological states on the gambling severity among a group of problem gamblers in Hong Kong. A cross-sectional research design was adopted. A purposive sample of 177 problem gamblers who sought treatment from a social service organization in Hong Kong completed a battery of standardised questionnaires. While gambling-related cognitions were found to exert significant effects on gambling severity, negative psychological states (i.e. stress) significantly moderated the relationship between gambling cognitions and gambling severity. In essence, those participants who reported a higher level of stress had more stable and serious gambling problems than those who reported a lower level of stress irrespective of the level of gambling-related cognitions. The findings of the moderating role of negative emotions in the relationship between cognitive distortions and severity of gambling provide insight towards developing an integrated intervention model which includes both cognitive-behavioural and emotion regulation strategies in helping people with PG.


Robust document image binarization technique for degraded document images.
Segmentation of text from badly degraded document images is a very challenging task due to the high inter/intra-variation between the document background and the foreground text of different document images. In this paper, we propose a novel document image binarization technique that addresses these issues by using adaptive image contrast. The adaptive image contrast is a combination of the local image contrast and the local image gradient that is tolerant to text and background variation caused by different types of document degradations. In the proposed technique, an adaptive contrast map is first constructed for an input degraded document image. The contrast map is then binarized and combined with Canny's edge map to identify the text stroke edge pixels. The document text is further segmented by a local threshold that is estimated based on the intensities of detected text stroke edge pixels within a local window. The proposed method is simple, robust, and involves minimum parameter tuning. It has been tested on three public datasets that are used in the recent document image binarization contest (DIBCO) 2009 & 2011 and handwritten-DIBCO 2010 and achieves accuracies of 93.5%, 87.8%, and 92.03%, respectively, that are significantly higher than or close to that of the best-performing methods reported in the three contests. Experiments on the Bickley diary dataset that consists of several challenging bad quality document images also show the superior performance of our proposed method, compared with other techniques.


Asymmetric total synthesis of paecilomycin C through intramolecular nucleophilic ring opening of an epoxide.
The convergent total synthesis of naturally occurring paecilomycin C is described here for the first time. Asymmetric Brown allylation, E-selective cross metathesis, and a biomimetic carboxylate assisted intramolecular nucleophilic ring opening of an epoxide were employed to access the enantiopure γ-lactone framework of the natural product. Late stage E-selective Julia-Kocienski olefination was then employed to furnish the natural product in an efficient way.


Clinical phenotypes of Italian and Spanish patients with α1-antitrypsin deficiency.
With the aim of providing better clinical characterisation of patients with α1-antitrypsin deficiency (AATD), we analysed the data of adult patients with severe AATD enrolled in the Spanish and Italian national registries. We assessed 745 subjects, 416 of whom were enrolled in the Spanish registry and 329 in the Italian registry. 57.2% were male and 64.9% were smokers or former smokers with a mean±sd age of 49.9±13.8 years. Most (81.2%) were index cases, mainly having the PI*ZZ genotype (73.4%), and the mean±sd diagnostic delay was 9.0±12.1 years. Patients with chronic bronchitis were younger, had better preserved lung function and lower tobacco consumption. Overlap patients (chronic obstructive pulmonary disease with asthma) were mainly females, more frequently never-smokers and received respiratory medications more often. 48% of emphysema, 27.5% of chronic bronchitis and 44.8% of overlap subjects were receiving augmentation therapy. Compared with PI*ZZ patients (n=547), the PI*SZ (n=124) subjects were older at diagnosis and had more preserved lung function, despite a higher mean smoking consumption. Early diagnosis of AATD is still an unmet need. Augmentation therapy is administered to similar proportions of patients with different clinical phenotypes. PI*ZZ patients in both registries had more severe respiratory disease than those with PI*SZ, despite lower smoking levels.


Liproxstatin-1 protects the mouse myocardium against ischemia/reperfusion injury by decreasing VDAC1 levels and restoring GPX4 levels.
Ferroptosis is a distinct iron-dependent mechanism of regulated cell death recognized in cancer and ischemia/reperfusion (I/R) injury of different organs. It has been reported that molecules such as liproxstatin-1 (Lip-1) inhibit ferroptosis and promote cell survival however, the mechanisms underlying this action are not clearly understood. We investigated the role and mechanism of Lip-1 in reducing cell death in the ischemic myocardium. Using an I/R model of isolated perfused mice hearts in which Lip-1 was given at the onset of reperfusion, we found that Lip-1 protects the heart by reducing myocardial infarct sizes and maintaining mitochondrial structural integrity and function. Further investigation revealed that Lip-1-induced cardioprotection is mediated by a reduction of VDAC1 levels and oligomerization, but not VDAC2/3. Lip-1 treatment also decreased mitochondrial reactive oxygen species production and rescued the reduction of the antioxidant GPX4 caused by I/R stress. Meanwhile, mitochondrial Ca2+ retention capacity needed to induce mitochondrial permeability transition pore opening did not change with Lip-1 treatment. Thus, we report that Lip-1 induces cardioprotective effects against I/R injury by reducing VDAC1 levels and restoring GPX4 levels.


Infection with Edwardsiella tarda causes hypertrophy of liver cells in the Japanese flounder Paralichthys olivaceus.
To study the direct cause of liver enlargement in the Japanese flounder Paralichthys olivaceus infected with Edwardsiella tarda, the fish were challenged with E. tarda and reared without feeding. The liver of fish exposed to the bacteria was markedly enlarged compared to that of the controls while no severe histopathological change appeared in the organ during the experiments. No notable difference was observed in the crude fat, glycogen, and water content of the liver between challenged and control fish. The size of liver cells and nuclei of the challenged fish was apparently larger than that of the controls. Analysis of crude DNA in the liver suggested that the number of liver cells of starved control fish significantly decreased during the experiment while that of the challenged fish was maintained at a level of the initial control. RNA/DNA ratio of the liver of challenged fish clearly increased while it decreased in the control fish during the experiment. These observations suggest that liver enlargement of flounder infected with E. tarda, at least in the early stage of infection, is not a result of any readily observable histopathological changes and that E. tarda infection causes hypertrophy of the cells, as well as preventing decrease in liver cell number.


Influence of autoclavation on the efficacy of extracted tooth roots used for vertical alveolar ridge augmentation.
To assess the influence of autoclavation on the efficacy of extracted tooth roots (TR) used for vertical alveolar ridge augmentation and two-stage osseointegration. Maxillary premolars were randomly assigned to either autoclavation (TR-A) or were left untreated (TR-C) and used as block grafts for vertical alveolar ridge augmentation in both lower quadrants (n = 4 beagle dogs). At 12 weeks, titanium implants were inserted and left to heal for 3 weeks. Histological analyses considered vertical bone gain (BD-BC), augmented area (AA) and bone-to-implant contact (BIC) at vestibular (v) and oral (o) aspects. Both TR-C and TR-A (exposures n = 3) grafts were associated with a replacement resorption and marked vertical bone gain. Median BD-BC (TR-C: 1.45 [v] to 1.62 mm [o] versus TR-A: 0.97 [v] to 1.79 mm [o]) and AA (TR-C: 0.64 [v] to 2.36 mm2 [o] versus TR-A: 0.22 [v] to 2.36 mm2 [o]) values were comparable in both groups. V BIC (TR-C: 49.32 [v] to 52.97% [o] versus TR-A: 25.34 [v] to 46.11% [o]) values were significantly higher in the TR-C group. Both TR-C and TR-A grafts equally supported vertical alveolar ridge augmentation; however, osseointegration was partially facilitated in the TR-C group.


From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data.
The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at different stages during the processing pipeline, such as assembly of paired-end reads, chimera removal, correction of sequencing errors, and clustering of those sequences into Operational Taxonomic Units (OTUs). Individual algorithms grappling with each of those challenges have been combined into various bioinformatics pipelines, such as mothur, QIIME, LotuS, and USEARCH. Using a set of well-described bacterial mock communities, state-of-the-art pipelines for Illumina MiSeq amplicon sequencing data are benchmarked at the level of the amount of sequences retained, computational cost, error rate, and quality of the OTUs. In addition, a new pipeline called OCToPUS is introduced, which is making an optimal combination of different algorithms. Huge variability is observed between the different pipelines in respect to the monitored performance parameters, where in general the amount of retained reads is found to be inversely proportional to the quality of the reads. By contrast, OCToPUS achieves the lowest error rate, minimum number of spurious OTUs, and the closest correspondence to the existing community, while retaining the uppermost amount of reads when compared to other pipelines. The newly introduced pipeline translates Illumina MiSeq amplicon sequencing data into high-quality and reliable OTUs, with improved performance and accuracy compared to the currently existing pipelines.


Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins.
One of the biggest limitations in the study and engineering of anaerobic Clostridium organisms is the lack of strong fluorescent reporters capable of strong and real-time fluorescence. Recently, we developed a strong fluorescent reporter system for Clostridium organisms based on the FAST protein. Here, we report the development of two new strong fluorescent reporter systems for Clostridium organisms based on the HaloTag and SNAP-tag proteins, which produce strong fluorescent signals when covalently bound to fluorogenic ligands. These new fluorescent reporters are orthogonal to the FAST ligands and to each other, allowing for simultaneous labeling and visualization. We used HaloTag and SNAP-tag to label the strictly anaerobic organisms Clostridium acetobutylicum and Clostridium ljungdahlii We have also identified a new strong promoter for protein expression in C. acetobutylicum, based on the phosphotransacetylase gene (pta) from C. ljungdahlii Furthermore, the HaloTag and the SNAP-tag, in combination with the previously described FAST system, were successfully used to measure cell populations in bacterial mixed cultures and showed the simultaneous orthogonal labeling of HaloTag and SNAP-tag together with the FAST protein reporter. Finally, we show the expression of recombinant fusion protein of FAST and the ZapA division protein (from C. acetobutylicum) in C. ljungdahlii. The availability of multiple strong fluorescent reporters is a major addition to the genetic toolkit of Clostridium and other anaerobes that will lead to better understanding of these unique organisms.IMPORTANCE Up to this point, assays and methods involving fluorescent reporter proteins were unavailable or limited in Clostridium organisms and other strict anaerobes. Green fluorescent protein (GFP), mCherry, and flavin-binding proteins (and their derivatives) have been used only in a few clostridia with limited success and yielded low fluorescence compared to aerobic microbial systems. Recently, we reported a new strong fluorescent reporter system based on the FAST protein as a first step in expanding the fluorescence-based reporters for Clostridium and other anaerobic microbial platforms. Additional strong orthogonal fluorescent proteins, with distinct emission spectra are needed to allow for (i) multispecies tracking within the growing field of microbial cocultures and microbiomes, (ii) protein localization and tracking in anaerobes, and (iii) identification and development of natural and synthetic promoters, ribosome-binding sites (RBS), and terminators for optimal protein expression in anaerobes. Here, we present two new strong fluorescent reporter systems based on the HaloTag and SNAP-tag proteins.


Systematic characterization of nuclear proteome during apoptosis: a quantitative proteomic study by differential extraction and stable isotope labeling.
Identification and characterization of the nuclear proteome is important for detailed understanding of multiple signaling events in eukaryotic cells. Toward this goal, we extensively characterized the nuclear proteome of human T leukemia cells by sequential extraction of nuclear proteins with different physicochemical properties using three buffer conditions. This large scale proteomic study also tested the feasibility and technical challenges associated with stable isotope labeling by amino acids in cell culture (SILAC) to uncover quantitative changes during apoptosis. Analyzing proteins from three nuclear fractions extracted from naive and apoptotic cells generated 780,530 MS/MS spectra that were used for database searching using the SEQUEST algorithm. This analysis resulted in the identification and quantification of 1,174 putative nuclear proteins. A number of known nuclear proteins involved in apoptosis as well as novel proteins not known to be part of the nuclear apoptotic machinery were identified and quantified. Consistent with SILAC-based quantifications, immunofluorescence staining of nucleus, mitochondria, and some associated proteins from both organelles revealed a dynamic recruitment of mitochondria into nuclear invaginations during apoptosis.


Hepatitis B and C among adolescents at an STD clinic on the US-Mexico border.
Risky sexual behavior and drug use are factors associated with acquisition of hepatitis B and C. This cross-sectional study investigated hepatitis B and C among 296 adolescents at a sexually transmitted disease clinic in El Paso, Texas, between April 1, 1997, and February 1, 1998. Questionnaires, medical record abstraction, and serum antibody tests provided data on demographics, risk factors, and seroprevalence status. Only 15% of participants always used condoms, 23% had a previous sexually transmitted disease, 46% had more than 1 sexual partner in the last 6 months, and 7% used intravenous drugs. Results showed low seroprevalence of hepatitis B (4.1%) and hepatitis C (3.1%). No significant risk factors were associated with hepatitis B seroprevalence. In contrast, male gender, speaking Spanish, not attending school, having more than 1 sexual partner, and injection drug use were all associated with hepatitis C. Hepatitis B and C seroprevalence rates among high-risk adolescents are lower in El Paso than in other similar US populations, presenting an ideal climate for prevention programs.


The Influence of Vestibular Schwannoma Tumor Volume and Growth on Hearing Loss.
To ascertain the relationship among vestibular schwannoma (VS) tumor volume, growth, and hearing loss. Retrospective cohort study. Single tertiary center. Adults with observed VS and serviceable hearing at diagnosis were included. The primary outcome was the development of nonserviceable hearing as estimated using the Kaplan-Meier method. Associations of tumor volume with baseline hearing were assessed using Spearman rank correlation coefficients. Associations of volume and growth with the development of nonserviceable hearing over time were assessed using Cox proportional hazards models and summarized with hazard ratios (HRs). Of 230 patients with VS and serviceable hearing at diagnosis, 213 had serial volumetric tumor data for analysis. Larger tumor volume at diagnosis was associated with increased pure-tone average (PTA) (P < .001) and decreased word recognition score (WRS) (P = .014). Estimated rates of maintaining serviceable hearing at 6 and 10 years following diagnosis were 67% and 49%, respectively. Larger initial tumor volume was associated with development of nonserviceable hearing in a univariable setting (HR for 1-cm3 increase: 1.36, P = .040) but not after adjusting for PTA and WRS. Tumor growth was not significantly associated with time to nonserviceable hearing (HR, 1.57; P = .14), although estimated rates of maintaining serviceable hearing during observation were poorer in the group that experienced growth. Larger initial VS tumor volume was associated with poorer hearing at baseline. Larger initial tumor volume was also associated with the development of nonserviceable hearing during observation in a univariable setting; however, this association was not statistically significant after adjusting for baseline hearing status.