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This study aimed to evaluate the effect of discrete passages of play on locomotor demands of international men's and women's rugby sevens matches and their relationship with winning or losing. Thirteen men's and thirteen women's international rugby sevens players wore 10 Hz Global Positioning Systems during twelve Tokyo Olympic games matches (966 observations; 507 for men, 459 for women). Discrete ball-in-play periods were categorised as: 'Single-phase defence', 'single-phase attack', 'multi-phase defence', 'multi-phase attack', 'multi-phase defence to attack', or 'multi-phase attack to defence'. Relative total distance, alongside high-speed (>5.0 m∙s-1), acceleration (>3 m∙s-2), and deceleration (>3 m∙s-2) distances were recorded for each passage. Separately for men and women, linear mixed models examined the effect of passage type and match outcome (win or loss) on locomotor demands, whilst controlling for opposition ranking. In men, relative total distance ranged from 137 m∙min-1 to 174 m∙min-1 for 'multi-phase defence to attack' and 'multi-phase attack', respectively. In women, 'multi-phase attack' elicited the lowest relative total distance (118 m∙min-1), whereas the greatest values (186 m∙min-1) were recorded for 'single-phase defence'. For men, there were significant interactions between match outcome and passage type for relative total (p

BackgroundLateral flow tests (LFTs) have been used to screen for SARS-CoV2 in Wales since January 2021. Between May and August 2021, adult care home staff policy was for biweekly Innova LFT and weekly Polymerase Chain Reaction (PCR) testing while asymptomatic. We estimated test performance of LFTs conducted in adult care home staff using PCR tests as a reference standard.MethodsTest results from surveillance data were matched by individual where both LFT and PCR were taken on the same day. We calculated sensitivity, specificity, positive and negative predictive values, and agreement using Matthew's correlation coefficient. Ct values of positive PCR results were compared by matched LFT result. Analysis was conducted using R v4.1.3.ResultsWe analysed 115,593 test pairs, 499 (0.43%) of which were PCR positive. Median age was 48 (IQR: 22) and 85.00% of the study population were female. Test result agreement was 99.59% (95%CI 99.55-99.63; MCC: 0.38, pConclusionsSpecificity and negative predictive value were high in an asymptomatic population of care home staff indicating this test is an effective tool for identifying cases of SARS-CoV-2 infection during periods of high prevalence where transmission is likely, due to the presence of high viral loads. Positive predictive value results are lower than existing literature yet should be considered in light of the asymptomatic study population and low prevalence (under 1%) at the time most of these tests were conducted. Performance improved at times of higher prevalence during the study. These results suggest that whilst lateral flow tests are effective for identifying SARS-COV-2 infections with high viral loads, they are not effective at identifying cases with a low viral load. When an LFT provides a negative result, false negatives should be considered and additional diagnostic tests performed.

Background Lateral flow tests (LFTs) have been used to screen for SARS-CoV2 in Wales since January 2021. Between May and August 2021, adult care home staff policy was for biweekly Innova LFT and weekly Polymerase Chain Reaction (PCR) testing while asymptomatic. We estimated test performance of LFTs conducted in adult care home staff using PCR tests as a reference standard. Methods Test results from surveillance data were matched by individual where both LFT and PCR were taken on the same day. We calculated sensitivity, specificity, positive and negative predictive values, and agreement using Matthew’s correlation coefficient. Ct values of positive PCR results were compared by matched LFT result. Analysis was conducted using R v4.1.3. Results We analysed 115,593 test pairs, 499 (0.43%) of which were PCR positive. Median age was 48 (IQR: 22) and 85.00% of the study population were female. Test result agreement was 99.59% (95%CI 99.55–99.63; MCC: 0.38, pConclusions Specificity and negative predictive value were high in an asymptomatic population of care home staff indicating this test is an effective tool for identifying cases of SARS-CoV-2 infection during periods of high prevalence where transmission is likely, due to the presence of high viral loads. Positive predictive value results are lower than existing literature yet should be considered in light of the asymptomatic study population and low prevalence (under 1%) at the time most of these tests were conducted. Performance improved at times of higher prevalence during the study. These results suggest that whilst lateral flow tests are effective for identifying SARS-COV-2 infections with high viral loads, they are not effective at identifying cases with a low viral load. When an LFT provides a negative result, false negatives should be considered and additional diagnostic tests performed.

Advancements in deep plasma proteomics are enabling high-resolution measurement of plasma proteoforms, which may reveal a rich source of novel biomarkers previously concealed by aggregated protein methods. Here, we analyze 188 plasma proteomes from non-small cell lung cancer subjects (NSCLC) and controls to identify NSCLC-associated protein isoforms by examining differentially abundant peptides as a proxy for isoform-specific exon usage. We find four proteins comprised of peptides with opposite patterns of abundance between cancer and control subjects. One of these proteins, BMP1, has known isoforms that can explain this differential pattern, for which the abundance of the NSCLC-associated isoform increases with stage of NSCLC progression. The presence of cancer and control-associated isoforms suggests differential regulation of BMP1 isoforms. The identified BMP1 isoforms have known functional differences, which may reveal insights into mechanisms impacting NSCLC disease progression.

Advancements in deep plasma proteomics are enabling high-resolution measurement of plasma proteoforms, which may reveal a rich source of novel biomarkers previously concealed by aggregated protein methods. Here, we analyze 188 plasma proteomes from non-small cell lung cancer subjects (NSCLC) and controls to identify NSCLC-associated protein isoforms by examining differentially abundant peptides as a proxy for isoform-specific exon usage. We find four proteins comprised of peptides with opposite patterns of abundance between cancer and control subjects. One of these proteins, BMP1, has known isoforms that can explain this differential pattern, for which the abundance of the NSCLC-associated isoform increases with stage of NSCLC progression. The presence of cancer and control-associated isoforms suggests differential regulation of BMP1 isoforms. The identified BMP1 isoforms have known functional differences, which may reveal insights into mechanisms impacting NSCLC disease progression.

The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiota to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat mass than germ-free (GF) or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure, and respiratory quotient using a novel isolator-housed metabolic cage system, which allows long-term measurements without contamination risk. This demonstrated that microbiota-released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and GF mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well integrated into appetite control. We also observed no significant difference in energy expenditure after normalization by lean mass between the different microbiota groups, suggesting that cumulative small differences in energy balance, or altered energy storage, must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: In GF mice, the respiratory exchange ratio (RER) was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly, the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied GF mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a GF-like drop in liver glycogen storage during the light phase and both liver and plasma metabolomes of OligoMM12 mice clustered closely with GF mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle and which are absent in the OligoMM12 consortium. A comparison of germ-free, gnotobiotic and fully-colonized mice reveals that microbiota-released calories are well compensated by food intake, but the metabolism of germ-free mice tends to burn less glucose and more fat throughout the circadian cycle. Model microbiota could rescue this respiratory substrate bias during the active/dark-phase of the circadian cycle but not during the light phase.

The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiota to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat mass than germ-free (GF) or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure, and respiratory quotient using a novel isolator-housed metabolic cage system, which allows long-term measurements without contamination risk. This demonstrated that microbiota-released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and GF mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well integrated into appetite control. We also observed no significant difference in energy expenditure after normalization by lean mass between the different microbiota groups, suggesting that cumulative small differences in energy balance, or altered energy storage, must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: In GF mice, the respiratory exchange ratio (RER) was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly, the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied GF mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a GF-like drop in liver glycogen storage during the light phase and both liver and plasma metabolomes of OligoMM12 mice clustered closely with GF mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle and which are absent in the OligoMM12 consortium.

Background Neurological COVID-19 disease has been reported widely, but published studies often lack information on neurological outcomes and prognostic risk factors. We aimed to describe the spectrum of neurological disease in hospitalised COVID-19 patients; characterise clinical outcomes; and investigate factors associated with a poor outcome. Methods We conducted an individual patient data (IPD) meta-analysis of hospitalised patients with neurological COVID-19 disease, using standard case definitions. We invited authors of studies from the first pandemic wave, plus clinicians in the Global COVID-Neuro Network with unpublished data, to contribute. We analysed features associated with poor outcome (moderate to severe disability or death, 3 to 6 on the modified Rankin Scale) using multivariable models. Results We included 83 studies (31 unpublished) providing IPD for 1979 patients with COVID-19 and acute new-onset neurological disease. Encephalopathy (978 [49%] patients) and cerebrovascular events (506 [26%]) were the most common diagnoses. Respiratory and systemic symptoms preceded neurological features in 93% of patients; one third developed neurological disease after hospital admission. A poor outcome was more common in patients with cerebrovascular events (76% [95% CI 67–82]), than encephalopathy (54% [42–65]). Intensive care use was high (38% [35–41]) overall, and also greater in the cerebrovascular patients. In the cerebrovascular, but not encephalopathic patients, risk factors for poor outcome included breathlessness on admission and elevated D-dimer. Overall, 30-day mortality was 30% [27–32]. The hazard of death was comparatively lower for patients in the WHO European region. Interpretation Neurological COVID-19 disease poses a considerable burden in terms of disease outcomes and use of hospital resources from prolonged intensive care and inpatient admission; preliminary data suggest these may differ according to WHO regions and country income levels. The different risk factors for encephalopathy and stroke suggest different disease mechanisms which may be amenable to intervention, especially in those who develop neurological symptoms after hospital admission.

BackgroundNeurological COVID-19 disease has been reported widely, but published studies often lack information on neurological outcomes and prognostic risk factors. We aimed to describe the spectrum of neurological disease in hospitalised COVID-19 patients; characterise clinical outcomes; and investigate factors associated with a poor outcome.MethodsWe conducted an individual patient data (IPD) meta-analysis of hospitalised patients with neurological COVID-19 disease, using standard case definitions. We invited authors of studies from the first pandemic wave, plus clinicians in the Global COVID-Neuro Network with unpublished data, to contribute. We analysed features associated with poor outcome (moderate to severe disability or death, 3 to 6 on the modified Rankin Scale) using multivariable models.ResultsWe included 83 studies (31 unpublished) providing IPD for 1979 patients with COVID-19 and acute new-onset neurological disease. Encephalopathy (978 [49%] patients) and cerebrovascular events (506 [26%]) were the most common diagnoses. Respiratory and systemic symptoms preceded neurological features in 93% of patients; one third developed neurological disease after hospital admission. A poor outcome was more common in patients with cerebrovascular events (76% [95% CI 67-82]), than encephalopathy (54% [42-65]). Intensive care use was high (38% [35-41]) overall, and also greater in the cerebrovascular patients. In the cerebrovascular, but not encephalopathic patients, risk factors for poor outcome included breathlessness on admission and elevated D-dimer. Overall, 30-day mortality was 30% [27-32]. The hazard of death was comparatively lower for patients in the WHO European region.InterpretationNeurological COVID-19 disease poses a considerable burden in terms of disease outcomes and use of hospital resources from prolonged intensive care and inpatient admission; preliminary data suggest these may differ according to WHO regions and country income levels. The different risk factors for encephalopathy and stroke suggest different disease mechanisms which may be amenable to intervention, especially in those who develop neurological symptoms after hospital admission.

BackgroundProtective effects of Bacillus Calmette-Guérin (BCG) vaccination and clofazimine and dapsone treatment against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been reported. Patients at risk for leprosy represent an interesting model for assessing the effects of these therapies on the occurrence and severity of coronavirus disease 2019 (COVID-19). We assessed the influence of leprosy-related variables in the occurrence and severity of COVID-19.Methodology/principal findingsWe performed a 14-month prospective real-world cohort study in which the main risk factor was 2 previous vaccinations with BCG and the main outcome was COVID-19 detection by reverse transcription polymerase chain reaction (RT-PCR). A Cox proportional hazards model was used. Among the 406 included patients, 113 were diagnosed with leprosy. During follow-up, 69 (16.99%) patients contracted COVID-19. Survival analysis showed that leprosy was associated with COVID-19 (pConclusions/significanceLeprosy patients are vulnerable to COVID-19 because they have more frequent contact with SARS-CoV-2-infected patients, possibly due to social and economic limitations. Our model showed that the use of corticosteroids, thalidomide, pentoxifylline, clofazimine, or dapsone or BCG vaccination did not affect the occurrence or severity of COVID-19.

Pseudomonas aeruginosa causes chronic airway infections, a major determinant of lung inflammation and damage in cystic fibrosis (CF). Loss-of-function lasR mutants commonly arise during chronic CF infections, are associated with accelerated lung function decline in CF patients and induce exaggerated neutrophilic inflammation in model systems. In this study, we investigated how lasR mutants modulate airway epithelial membrane bound ICAM-1 (mICAM-1), a surface adhesion molecule, and determined its impact on neutrophilic inflammation in vitro and in vivo. We demonstrated that LasR-deficient strains induce increased mICAM-1 levels in airway epithelial cells compared to wild-type strains, an effect attributable to the loss of mICAM-1 degradation by LasR-regulated proteases and associated with enhanced neutrophil adhesion. In a subacute airway infection model, we also observed that lasR mutant-infected mice displayed greater airway epithelial ICAM-1 expression and increased neutrophilic pulmonary inflammation. Our findings provide new insights into the intricate interplay between lasR mutants, LasR-regulated proteases and airway epithelial ICAM-1 expression, and reveal a new mechanism involved in the exaggerated inflammatory response induced by lasR mutants.

BackgroundAcute kidney injury (AKI) is an independent risk factor for mortality, which affects about 5% of hospitalized coronavirus disease-2019 (COVID-19) patients and up to 25-29% of severely ill COVID-19 patients. Lopinavir/ritonavir and hydroxychloroquine show in vitro activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have been used for the treatment of COVID-19. Both, lopinavir and hydroxychloroquine are metabolized by cytochrome P450 (CYP) 3A4. The impact of a triple therapy with lopinavir/ritonavir and hydroxychloroquine (triple therapy) on kidney function in COVID-19 is currently not known.MethodsWe retrospectively analyzed both non-ICU and ICU patients with COVID-19 receiving triple therapy for the incidence of AKI. Patients receiving standard therapy served as a control group. All patients were hospitalized at the University Hospital of Freiburg, Germany, between March and April 2020. A matched-pair analysis for the National Early Warning Score (NEWS) 2 was performed to control for the severity of illness among non-intensive care unit (ICU) patients.ResultsIn non-ICU patients, the incidence of AKI was markedly increased following triple therapy (78.6% vs. 21.4% in controls, p = 0.002), while a high incidence of AKI was observed in both groups of ICU patients (triple therapy: 80.0%, control group: 90.5%). ICU patients treated with triple therapy showed a trend towards more oliguric or anuric kidney injury. We also observed a linear correlation between the duration of the triple therapy and the maximum serum creatinine level (p = 0.004, R2 = 0.276, R = 0.597).ConclusionTriple therapy is associated with an increase in the incidence of AKI in non-ICU COVID-19 patients. The underlying mechanisms may comprise a CYP3A4 enzyme interaction, and may be relevant for any future therapy combining hydroxychloroquine with antiviral agents.

PurposeThis study aimed to determine the survival outcome and prognostic factors of patients with nasopharyngeal cancer accessing treatment in Yogyakarta, Indonesia.MethodsData on 759 patients with NPC diagnosed from 2007 to 2016 at Dr Sardjito General Hospital were included. Potential prognostic variables included sociodemographic, clinicopathology and treatment parameters. Multivariable analyses were implemented using semi-parametric Cox proportional hazards modelling and fully parametric survival analysis.ResultsThe median time of observation was 14.39 months. In the whole cohort the median observed survival was 31.08 months. In the univariable analysis, age, education status, insurance type, BMI, ECOG index, stage and treatment strategy had an impact on overall survival (OS) (p values ConclusionsMedian OS for the cohort was low compared to those reported in both endemic and non-endemic regions. By combining the findings of multivariable analyses, we showed that age, education status, ECOG index, stage and first treatment modality were independent predictors for the OS.

Phenotype Prediction Scores (PPS) might be powerful tools to predict traits or the efficacy of treatments based on combinations of Single-Nucleotide Polymorphism (SNPs) in large samples. We developed a novel method to produce PPS models for small samples sizes. The set of SNPs is first filtered on those known to be relevant in biological pathways involved in a clinical condition, and then further filtered repeatedly in a survival strategy to select stabile positive/negative risk alleles. This method is applied on Female Sexual Interest/Arousal Disorder (FSIAD), for which two subtypes has been proposed: 1) a relatively insensitive excitatory system in the brain for sexual cues, and 2) a dysfunctional activation of brain mechanisms for sexual inhibition. A double-blind, randomized, placebo-controlled cross-over experiment was conducted on 129 women with FSIAD. The women received three different on-demand drug-combination treatments during 3 two-week periods: testosterone (0.5 mg) + sildenafil (50 mg), testosterone (0.5 mg) + buspirone (10 mg), or matching placebos. The resulted PPS were independently validated on patient-level and group-level. The AUC scores for T+S of the derivation set was 0.867 (95% CI = 0.796-0.939; p

What have been the causes and consequences of technological evolution in world history? In particular, what propels innovation and diffusion of military technologies, details of which are comparatively well preserved and which are often seen as drivers of broad socio-cultural processes? Here we analyze the evolution of key military technologies in a sample of pre-industrial societies world-wide covering almost 10,000 years of history using Seshat: Global History Databank. We empirically test previously speculative theories that proposed world population size, connectivity between geographical areas of innovation and adoption, and critical enabling technological advances, such as iron metallurgy and horse riding, as central drivers of military technological evolution. We find that all of these factors are strong predictors of change in military technology, whereas state-level factors such as polity population, territorial size, or governance sophistication play no major role. We discuss how our approach can be extended to explore technological change more generally, and how our results carry important ramifications for understanding major drivers of evolution of social complexity.

Peptide microarrays consisting of defined phosphorylation target sites are an effective approach for high throughput analysis of cellular kinase (kinome) activity. Kinome peptide arrays are highly customizable and do not require species-specific reagents to measure kinase activity, making them amenable for kinome analysis in any species. Our group developed software, Platform for Integrated, Intelligent Kinome Analysis (PIIKA), to enable more effective extraction of meaningful biological information from kinome peptide array data. A subsequent version, PIIKA2, unveiled new statistical tools and data visualization options. Here we introduce PIIKA 2.5 to provide two essential quality control metrics and a new background correction technique to increase the accuracy and consistency of kinome results. The first metric alerts users to improper spot size and informs them of the need to perform manual resizing to enhance the quality of the raw intensity data. The second metric uses inter-array comparisons to identify outlier arrays that sometimes emerge as a consequence of technical issues. In addition, a new background correction method, background scaling, can sharply reduce spatial biases within a single array in comparison to background subtraction alone. Collectively, the modifications of PIIKA 2.5 enable identification and correction of technical issues inherent to the technology and better facilitate the extraction of meaningful biological information. We show that these metrics demonstrably enhance kinome analysis by identifying low quality data and reducing batch effects, and ultimately improve clustering of treatment groups and enhance reproducibility. The web-based and stand-alone versions of PIIKA 2.5 are freely accessible at via http://saphire.usask.ca.

What have been the causes and consequences of technological evolution in world history? In particular, what propels innovation and diffusion of military technologies, details of which are comparatively well preserved and which are often seen as drivers of broad socio-cultural processes? Here we analyze the evolution of key military technologies in a sample of pre-industrial societies world-wide covering almost 10,000 years of history using Seshat: Global History Databank. We empirically test previously speculative theories that proposed world population size, connectivity between geographical areas of innovation and adoption, and critical enabling technological advances, such as iron metallurgy and horse riding, as central drivers of military technological evolution. We find that all of these factors are strong predictors of change in military technology, whereas state-level factors such as polity population, territorial size, or governance sophistication play no major role. We discuss how our approach can be extended to explore technological change more generally, and how our results carry important ramifications for understanding major drivers of evolution of social complexity.

We collect data on time preferences of a representative sample of the Hungarian adult population in a non-incentivized way and investigate how patience and present bias associate with important life outcomes in five domains: i) educational attainment, ii) unemployment, iii) income and wealth, iv) financial decisions and difficulties, and v) health. Based on the literature, we formulate the broad hypotheses that patience relates positively, while present bias associates negatively with positive outcomes in the domains under study. With the exception of unemployment, we document a consistent and often significant positive relationship between patience and the corresponding domain, with the strongest associations in educational attainment, wealth and financial decisions. We find that present bias associates significantly with saving decisions and financial difficulties.

AimsTo assess the impact of two different respiratory rates in hemodynamic, perfusion and ventilation parameters in a pediatric animal model of cardiac arrest (CA).MethodsAn experimental randomized controlled trial was carried out in 50 piglets under asphyxial CA. After ROSC, they were randomized into two groups: 20 and 30 respirations per minute (rpm). Hemodynamic, perfusion and ventilation parameters were measured 10 minutes after asphyxia, just before ROSC and at 5, 15, 30 and 60 minutes after ROSC. Independent medians test, Kruskal-Wallis test and χ2 test, were used to compare continuous and categorical variables, respectively. Spearman's Rho was used to assess correlation between continuous variables. A p-value ResultsArterial partial pressure of carbon dioxide (PaCO2) was significantly lower in the 30 rpm group after 15 minutes (41 vs. 54.5 mmHg, p ConclusionsThis animal model of asphyxial CA shows that a respiratory rate of 30 rpm is more effective to reach normoventilation than 20 rpm in piglets after ROSC. This ventilation strategy seems to be safe, as it does not cause hyperventilation and does not affect hemodynamics or cerebral tissue perfusion.

BackgroundAlongside a clinical and research setting, whole body magnetic resonance imaging (WB-MRI) is increasingly offered as a direct-to-consumer screening service. Data is needed on the clinical relevance of findings and associated psychological impact of such screening. Therefore, we conducted a prospective follow-up study to provide insight in the effectiveness and psychological impact of direct-to-consumer screening using both WB-MRI and cardiological examination.Methods and findingsThe study population consisted of 3603 voluntary, primarily middle-aged participants who underwent commercial WB-MRI and cardiological screening at one of 6 study clinics in Germany or the Netherlands between July 2014 and March 2016. MRI investigation consisted of directed scans of the brain, neck, abdomen and pelvis. Cardiovascular examination included pulmonary function, resting electrocardiogram, transthoracic echocardiogram and a bicycle exercise stress test. Findings were assessed by experienced radiologists and cardiologists. In addition, participants were inquired about several (psychological) domains, including the expectations and consequences of the screening procedure. Out of 3603 individuals, 402 (11.2%) demonstrated abnormal MRI (n = 381) and/or cardiological findings (n = 79) for which they were advised to undergo further consultation ConclusionsDirect-to-consumer screening using whole-body MRI and cardiological testing is feasible and effective for the detection of clinically relevant and treatable abnormalities. Psychological harm was not frequently reported in study participants.

The high rates of bat mortality caused by operating wind turbines is a concern for wind energy and wildlife stakeholders. One theory that explains the mortality is that bats are not only killed by impact trauma, but also by barotrauma that results from exposure to the pressure variations caused by rotating turbine blades. To date, no published research has calculated the pressure changes that bats may be exposed to when flying near wind turbines and then used these data to estimate the likelihood that turbines cause barotrauma in bats. To address this shortcoming, we performed computational fluid dynamics simulations of a wind turbine and analytical calculations of blade-tip vortices to estimate the characteristics of the sudden pressure changes bats may experience when flying near a utility-scale wind turbine. Because there are no data available that characterize the pressure changes that cause barotrauma in bats, we compared our results to changes in pressure levels that cause barotrauma and mortality in other mammals of similar size. This comparison shows that the magnitude of the low-pressures bats experience when flying near wind turbines is approximately 8 times smaller than the pressure that causes mortality in rats, the smallest mammal for which data are available. The magnitude of the high-pressures that bats may experience are approximately 80 times smaller than the exposure level that causes 50% mortality in mice, which have a body mass similar to several bat species that are killed by wind turbines. Further, our results show that for a bat to experience the largest possible magnitude of low- and high-pressures, they must take very specific and improbable flight paths that skim the surface of the blades. Even a small change in the flight path results in the bat being hit by the blade or experiencing a much smaller pressure change. Accordingly, if bats have a physiological response to rapid low- and high-pressure exposure that is similar to other mammals, we conclude that it is unlikely that barotrauma is responsible for a significant number of turbine-related bat fatalities, and that impact trauma is the likely cause of the majority of wind-turbine-related bat fatalities.

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes persistent arthritis in a subset of human patients. We report the isolation and functional characterization of monoclonal antibodies (mAbs) from two patients infected with CHIKV in the Dominican Republic. Single B cell sorting yielded a panel of 46 human mAbs of diverse germline lineages that targeted epitopes within the E1 or E2 glycoproteins. MAbs that recognized either E1 or E2 proteins exhibited neutralizing activity. Viral escape mutations localized the binding epitopes for two E1 mAbs to sites within domain I or the linker between domains I and III; and for two E2 mAbs between the β-connector region and the B-domain. Two of the E2-specific mAbs conferred protection in vivo in a stringent lethal challenge mouse model of CHIKV infection, whereas the E1 mAbs did not. These results provide insight into human antibody response to CHIKV and identify candidate mAbs for therapeutic intervention.

Atonal homolog 8 (Atoh8) is a transcription factor of the basic helix-loop-helix (bHLH) protein family, which is expressed in the cartilaginous elements of endochondral bones. To analyze its function during chondrogenesis we deleted Atoh8 in mice using a chondrocyte- (Atoh8flox/flox;Col2a1-Cre) and a germline- (Atoh8flox/flox;Prx1-Crefemale) specific Cre allele. In both strains, Atoh8 deletion leads to a reduced skeletal size of the axial and appendicular bones, but the stages of phenotypic manifestations differ. While we observed obviously shortened bones in Atoh8flox/flox;Col2a1-Cre mice only postnatally, the bones of Atoh8flox/flox;Prx1-Crefemale mice are characterized by a reduced bone length already at prenatal stages. Detailed histological and molecular investigations revealed reduced zones of proliferating and hypertrophic chondrocytes. In addition, Atoh8 deletion identified Atoh8 as a positive regulator of chondrocyte proliferation. As increased Atoh8 expression is found in the region of prehypertrophic chondrocytes where the expression of Ihh, a main regulator of chondrocyte proliferation and differentiation, is induced, we investigated a potential interaction of Atoh8 function and Ihh signaling. By activating Ihh signaling with Purmorphamine we demonstrate that Atoh8 regulates chondrocyte proliferation in parallel or downstream of Ihh signaling while it acts on the onset of hypertrophy upstream of Ihh likely by modulating Ihh expression levels.

The production of maple syrup is an important cultural and economic activity directly related to the climate of northeastern North America. As a result, there are signs that climate change could have negative impacts on maple syrup production in the next decades, particularly for regions located at the southern margins of the sugar maple (Acer saccharum Marsh.) range. The purpose of this survey study is to present the beliefs and opinions of maple syrup producers of Canada (N = 241) and the U.S. (N = 113) on climate change in general, its impacts on sugar maple health and maple syrup production, and potential adaptation measures. Using conditional inference classification trees, we examined how the socio-economic profile of respondents and the geographic location and size of respondents' sugar bushes shaped the responses of survey participants. While a majority (75%) of respondents are confident that the average temperature on Earth is increasing, less than half (46%) believe that climate change will have negative impacts on maple syrup yield in the next 30 years. Political view was a significant predictor of these results, with respondents at the right right and center-right of the political spectrum being less likely to believe in climate change and less likely to anticipate negative effects of climate change on maple syrup production. In addition, 77% of the participants indicated an interest in adopting adaptation strategies if those could increase maple syrup production. This interest was greater for respondents using vacuum tubing for sap collection than other collection methods. However, for many respondents (particularly in Canada), lack of information was identified as a constraint limiting adaptation to climate change.

The forest floor of boreal forest stores large amounts of organic C that may react to a warming climate and increased N deposition. It is therefore crucial to assess the impact of these factors on the temperature sensitivity of this C pool to help predict future soil CO2 emissions from boreal forest soils to the atmosphere. In this study, soil warming (+2-4°C) and canopy N addition (CNA; +0.30-0.35 kg·N·ha-1·yr-1) were replicated along a topographic gradient (upper, back and lower slope) in a boreal forest in Quebec, Canada. After nine years of treatment, the forest floor was collected in each plot, and its organic C composition was characterized through solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. Forest floor samples were incubated at four temperatures (16, 24, 32 and 40°C) and respiration rates (RR) measured to assess the temperature sensitivity of forest floor RR (Q10 = e10k) and basal RR (B). Both soil warming and CNA had no significant effect on forest floor chemistry (e.g., C, N, Ca and Mg content, amount of soil organic matter, pH, chemical functional groups). The NMR analyses did not show evidence of significant changes in the forest floor organic C quality. Nonetheless, a significant effect of soil warming on both the Q10 of RR and B was observed. On average, B was 72% lower and Q10 45% higher in the warmed, versus the control plots. This result implies that forest floor respiration will more strongly react to changes in soil temperature in a future warmer climate. CNA had no significant effect on the measured soil and respiration parameters, and no interaction effects with warming. In contrast, slope position had a significant effect on forest floor organic C quality. Upper slope plots had higher soil alkyl C:O-alkyl C ratios and lower B values than those in the lower slope, across all different treatments. This result likely resulted from a relative decrease in the labile C fraction in the upper slope, characterized by lower moisture levels. Our results point towards higher temperature sensitivity of RR under warmer conditions, accompanied by an overall down-regulation of RR at low temperatures (lower B). Since soil C quantity and quality were unaffected by the nine years of warming, the observed patterns could result from microbial adaptations to warming.

Assessing the perception of key stakeholders within the forest sector is critical to evaluating their readiness to engage in adapting to climate change. Here, we report the results of the most comprehensive survey carried out in the Canadian forestry sector to date regarding perceptions of climate change. A total of 1158 individuals, representing a wide range of stakeholders across the five most important forestry provinces in Canada, were asked about climate change, its impact on forest ecosystems, and the suitability of current forest management for addressing future impacts. Overall, we found that respondents were more concerned about climate change than the general population. More than 90% of respondents agreed with the anthropogenic origins of climate change, and > 50% considered it a direct threat to their welfare. Political view was the main driver of general beliefs about the causes of climate change and its future consequences, while the province of origin proved to be the best predictor of perceived current impacts on forest ecosystems and its associated risks; and type of stakeholder was the main driver of perceived need for adaptation. Industrial stakeholders were the most skeptical about the anthropogenic cause(s) of climate change (18% disagreed with this statement, compared to an average of 8% in the other stakeholders), its impacts on forest ecosystems (28% for industry vs. 10% for other respondents), and the need for new management practices (18% vs. 7%). Although the degree of awareness and the willingness to implement adaptive practices were high even for the most skeptical groups, our study identified priority sectors or areas for action when designing awareness campaigns. We suggest that the design of a strategic framework for implementing climate adaptation within the Canadian forest sector should focus on the relationship between climate change and changes in disturbance regimes, and above all on the economic consequences of these changes, but it should also take into account the positions shown by each of the actors in each province.

Success in life is determined to a large extent by school performance so it is important to understand the effect of the factors that influence it. In this exploratory study, in addition to cognitive abilities, we attempt to link measures of preferences with outcomes of school performance. We measured in an incentivized way risk, time, social and competitive preferences and cognitive abilities of university students to look for associations between these measures and two important academic outcome measures: exam results and GPA. We find consistently that cognitive abilities (proxied by the Cognitive Reflection Test) are very well correlated with school performance. Regarding non-cognitive skills, we report suggestive evidence for many of our measured preferences. We used two alternative measures of time preference: patience and present bias. Present bias explains exam grades better, while patience explains GPA relatively better. Both measures of time preferences have a non-linear relation to school performance. Competitiveness matters, as students, who opt for a more competitive payment scheme in our experimental task have a higher average GPA. We observe also that risk-averse students perform a little better than more risk-tolerant students. That makes sense in case of multiple choice exams, because more risk-tolerant students may want to try to pass the exam less prepared, as the possibility of passing an exam just by chance is not zero. Finally, we have also detected that cooperative preferences-the amount of money offered in a public good game-associates strongly with GPA in a non-linear way. Students who offered around half of their possible amounts had significantly higher GPAs than those, who offered none or all their money.

Human cytomegalovirus (HCMV) is a widely distributed herpesvirus that causes significant morbidity in immunocompromised hosts. Inhibitors of viral DNA replication are available, but adverse effects limit their use. Alternative antiviral strategies may include inhibition of entry. We show that soluble derivatives of the platelet-derived growth factor receptor alpha (PDGFR-alpha), a putative receptor of HCMV, can inhibit HCMV infection of various cell types. A PDGFR-alpha-Fc fusion protein binds to and neutralizes cell-free virus particles at an EC50 of 10-30 ng/ml. Treatment of particles reduced both attachment to and fusion with cells. In line with the latter, PDGFR-alpha-Fc was also effective when applied postattachment. A peptide scan of the extracellular domain of PDGFR-alpha identified a 40mer peptide that inhibits infection at an EC50 of 1-2 nmol/ml. Both, peptide and fusion protein, were effective against various HCMV strains and are hence promising candidates for the development of novel anti-HCMV therapies.

Based on the hypothesis that HIV programs struggle to deliver health services that harmonize necessities of treatment and prevention, we described the outcomes of routinely provided HIV testing to partners of people living with HIV (PLWH) through a secondary analysis of routine data collected at a public hospital in Lima, Peru.Among PLWH enrolled in the study center's HIV program between 2005 and 2014, we identified index cases (IC): PLWH who reported a unique partner not previously enrolled. We grouped partners according to their HIV status as reported by IC and collected data on HIV testing, clinical characteristics and admissions. The main outcome was the frequency of HIV testing among partners with reported unknown/seronegative HIV status.Out of 1586 PLWH who reported a unique partner at enrollment, 171 had a previously enrolled partner, leaving 1415 (89%) IC. HIV status of the partner was reported as unknown in 571 (40%), seronegative in 325 (23%) and seropositive in 519 (37%). Out of 896 partners in the unknown/seronegative group, 72 (8%) had HIV testing, 42/72 (58%) tested within three months of IC enrollment. Among the 49/72 (68%) who tested positive for HIV, 33 (67%) were enrolled in the HIV program. The proportion in WHO clinical stage IV was lower in enrolled partners compared to IC (37% vs 9%, p = 0.04). Non-tested partners (824) were likely reachable by the hospital, as 297/824 (36%) of their IC were admitted in the study center at least once, 51/243 (21%) female IC had received pregnancy care at the study center, and 401/692 (64%) of IC on antiretroviral therapy had achieved viral suppression, implying frequent visits to the hospital for pill pick-up.In this setting, HIV testing of partners of PLWH was suboptimal, illustrating missed opportunities for HIV control. Integration of HIV strategies in primarily clinical-oriented services is a challenging need.

Increasing access to extensively replicated and broadly distributed tree-ring collections has led to a greater use of these large data sets to investigate climate forcing on tree growth. However, the number of chronologies added to large accessible databases is declining and few are updated, while chronologies are often sparsely distributed and are more representative of marginal growing environments. On the other hand, National Forest Inventories (NFI), although poorly replicated at the plot level as compared to classic dendrochronological sampling, contain a large amount of tree-ring data with high spatial density designed to be spatially representative of the forest cover. We propose an a posteriori approach to validating tree-ring measurements and dating, selecting individual tree-ring width time series, and building average chronologies at various spatial scales based on an extensive collection of ring width measurements of nearly 94,000 black spruce trees distributed over a wide area and collected as part of the NFI in the province of Quebec, Canada. Our results show that reliable signals may be derived at various spatial scales (from 37 to 583,000 km2) from NFI increment core samples. Signals from independently built chronologies are spatially coherent with each other and well-correlated with independent reference chronologies built at the stand level. We thus conclude that tree-ring data from NFIs provide an extraordinary opportunity to strengthen the spatial and temporal coverage of tree-ring data and to improve coordination with other contemporary measurements of forest growth to provide a better understanding of tree growth-climate relationships over broad spatial scales.

The community, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various generalized communities, i.e. assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalized communities.

Reversible phosphorylation of neuronal proteins plays an important role in the regulation of neurotransmitter release. Myosin phosphatase holoenzyme (MP) consists of a protein phosphatase-1 (PP1) catalytic subunit (PP1c) and a regulatory subunit, termed myosin phosphatase targeting subunit (MYPT1). The primary function of MP is to regulate the phosphorylation level of contractile proteins; however, recent studies have shown that MP is localized to neurons, and is also involved in the mediation of neuronal processes. Our goal was to investigate the effect of RhoA-activated kinase (ROK) and MP on the phosphorylation of one potential neuronal substrate, the synaptosomal-associated protein of 25 kDa (SNAP-25). SNAP-25 is a member of the SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) complex, along with synaptobrevin and syntaxin, and the primary role of SNAP25 is to mediate vesicle fusion. We showed that MYPT1 interacts with SNAP-25, as revealed by immunoprecipitation and surface plasmon resonance based binding studies. Mass spectrometry analysis and in vitro phosphorylation/dephosphorylation assays demonstrated that ROK phosphorylates, while MP dephosphorylates, SNAP-25 at Thr138. Silencing MYPT1 in B50 neuroblastoma cells increased phosphorylation of SNAP-25 at Thr138. Inhibition of PP1 with tautomycetin increased, whereas inhibition of ROK by H1152, decreased the phosphorylation of SNAP-25 at Thr138 in B50 cells, in cortical synaptosomes, and in brain slices. In response to the transduction of the MP inhibitor, kinase-enhanced PP1 inhibitor (KEPI), into synaptosomes, an increase in phosphorylation of SNAP-25 and a decrease in the extent of neurotransmitter release were detected. The interaction between SNAP-25 and syntaxin increased with decreasing phosphorylation of SNAP-25 at Thr138, upon inhibition of ROK. Our data suggest that ROK/MP play a crucial role in vesicle trafficking, fusion, and neurotransmitter release by oppositely regulating the phosphorylation of SNAP-25 at Thr138.

[This corrects the article DOI: 10.1371/journal.pone.0177046.].

VEGFA is an angiogenic factor secreted by tumors, in particular those with VEGFA amplification, as well as by macrophages and lymphocytes in the tumor microenvironment. Here we sought to define the presence of M1/M2 macrophages, PD-1-positive lymphocytes and PD-L1 tumoral and stromal expression in colorectal cancers harboring VEGFA amplification or chromosome 6 polysomy. 38 CRCs of which 13 harbored VEGFA amplification, 6 with Chr6 polysomy and 19 with neutral VEGFA copy number were assessed by immunohistochemistry for CD68 (marker for M1/M2 macrophages), CD163 (M2 macrophages), programmed death 1(PD-1)- tumor infiltrating and stromal lymphocytes as well as tumoral and stromal PD-1 ligand (PD-L1) expression. CRCs with VEGFA amplification or Chr6 polysomy were associated with decreased M1/M2 macrophages, reduced PD-1-expressing lymphocyte infiltration, as well as reduced stromal expression of PD-L1 at the tumor front. Compared to intermediate-grade CRCs, high-grade CRCs were associated with increased M1/M2 macrophages and increased tumoral expression of PD-L1. Our results suggest that VEGFA amplification or Chr6 polysomy is associated with an altered tumor immune microenvironment.

Specific selection pressures often lead to specifically mutated genomes. The open source software SeqFeatR has been developed to identify associations between mutation patterns in biological sequences and specific selection pressures ("features"). For instance, SeqFeatR has been used to discover in viral protein sequences new T cell epitopes for hosts of given HLA types. SeqFeatR supports frequentist and Bayesian methods for the discovery of statistical sequence-feature associations. Moreover, it offers novel ways to visualize results of the statistical analyses and to relate them to further properties. In this article we demonstrate various functions of SeqFeatR with real data. The most frequently used set of functions is also provided by a web server. SeqFeatR is implemented as R package and freely available from the R archive CRAN (http://cran.r-project.org/web/packages/SeqFeatR/index.html). The package includes a tutorial vignette. The software is distributed under the GNU General Public License (version 3 or later). The web server URL is https://seqfeatr.zmb.uni-due.de.

We aimed to determine the prognostic significance of pretreatment plasma fibrinigen in patients with oral and oropharyngeal squamous cell carcinoma (OOSCC).A cohort of 183 patients with locally advanced OOSCC receiving preoperative chemoradiotherapy was retrospectively examined. Using ROC curve analysis, a pretreatment plasma fibrinogen cutoff value of 447mg/dL was determined. The primary endpoints were overall survival and recurrence-free survival. A secondary endpoint was to determine whether pretreatment plasma fibrinogen could predict treatment response to neoadjuvant chemoradiotherapy. Cox regression models and Kaplan-Meier curves were used for survival analyses.Seventy-one patients had an elevated pretreatment plasma fibrinogen (fibrinogen >447mg/dL). Patients with high fibrinogen showed significantly higher pathologic stages after neoadjuvant treatment than those with low fibrinogen (p = 0.037). In univariate analysis, elevated fibrinogen was associated with poor overall survival (p = 0.005) and recurrence-free survival (p = 0.008) Multivariate analysis revealed that elevated fibrinogen remained an independent risk factor for death (hazard ratio 1.78, 95% CI 1.09-2.90, p = 0.021) and relapse (hazard ratio 1.78, 95% CI 1.11-2.86, p = 0.016).Elevated pretreatment plasma fibrinogen is associated with lack of response to neoadjuvant chemoradiotherapy and reduced OS and RFS in patients with OOSCC. Thus, plasma fibrinogen may emerge as a novel prognostic indicator and a potential therapeutic target in OOSCC.

Harlequin Ichthyosis is a severe skin disease caused by mutations in the human gene encoding ABCA12. Here, we characterize a novel mutation in intron 29 of the mouse Abca12 gene that leads to the loss of a 5' splice donor site and truncation of the Abca12 RNA transcript. Homozygous mutants of this smooth skin or smsk allele die perinatally with shiny translucent skin, typical of animal models of Harlequin Ichthyosis. Characterization of smsk mutant skin showed that the delivery of glucosylceramides and CORNEODESMOSIN was defective, while ultrastructural analysis revealed abnormal lamellar bodies and the absence of lipid lamellae in smsk epidermis. Unexpectedly, mutant stratum corneum remained intact when subjected to harsh chemical dissociation procedures. Moreover, both KALLIKREIN 5 and -7 were drastically decreased, with retention of desmoplakin in mutant SC. In cultured wild type keratinocytes, both KALLIKREIN 5 and -7 colocalized with ceramide metabolites following calcium-induced differentiation. Reducing the intracellular levels of glucosylceramide with a glucosylceramide synthase inhibitor resulted in decreased secretion of KALLIKREIN proteases by wild type keratinocytes, but not by smsk mutant keratinocytes. Together, these findings suggest an essential role for ABCA12 in transferring not only lipids, which are required for the formation of multilamellar structures in the stratum corneum, but also proteolytic enzymes that are required for normal desquamation. Smsk mutant mice recapitulate many of the pathological features of HI and can be used to explore novel topical therapies against a potentially lethal and debilitating neonatal disease.

Using data obtained from 4004 participants across eight countries (Canada, India, Japan, Korea, Poland, Slovakia, Uganda, and the U.S.), the factorial reliability, validity and structural/measurement invariance of a 30-item version of Expressions of Spirituality Inventory (ESI-R) was evaluated. The ESI-R measures a five factor model of spirituality developed through the conjoint factor analysis of several extant measures of spiritual constructs. Exploratory factor analyses of pooled data provided evidence that the five ESI-R factors are reliable. Confirmatory analyses comparing four and five factor models revealed that the five dimensional model demonstrates superior goodness-of-fit with all cultural samples and suggest that the ESI-R may be viewed as structurally invariant. Measurement invariance, however, was not supported as manifested in significant differences in item and dimension scores and in significantly poorer fit when factor loadings were constrained to equality across all samples. Exploratory analyses with a second adjective measure of spirituality using American, Indian, and Ugandan samples identified three replicable factors which correlated with ESI-R dimensions in a manner supportive of convergent validity. The paper concludes with a discussion of the meaning of the findings and directions needed for future research.

BackgroundPerinatal undernutrition may lead to important metabolic adaptations in adult life, short stature being the most visible. The present study aimed to evaluate the association between stature and total energy expenditure of low-income women.MethodWomen aged 19-45 years from low-income communities in Maceió-AL were recruited. A sample of 67 volunteers was selected and divided into either short stature (≤ 152.4 cm; n = 34) or non-short stature (≥ 158.7 cm; n = 33) group. Data on socioeconomic status, anthropometric variables, and hormonal profiles was collected. Total energy expenditure and body composition were assessed by the doubly labeled water technique with multiple points over 14 days. In addition, physical activity levels were measured with triaxial accelerometers and dietary intake data were collected using three 24-hour food records.ResultsThe mean subject age was 30.94 years. Women of short stature had lower body weight and lean body mass compared to non-short women, but there were no differences in thyroid hormone concentrations or daily energy intake between the two groups. Short-stature women showed lower total energy expenditure (P = 0.01) and a significantly higher physical activity level (P = 0.01) compared to non-short women. However, the difference in total energy expenditure was no longer significant after statistical adjustment for age, lean body mass, and triiodothyronine concentrations.ConclusionWomen with short stature present the same energy intake, but lower total energy expenditure than non-short women, even with a higher physical activity level, which suggests that they are more prone to weight gain.

ObjectivesWe analysed the impact of different parameters on genotypic tropism testing related to clinical outcome prediction in 108 patients on maraviroc (MVC) treatment.Methods87 RNA and 60 DNA samples were used. The viral tropism was predicted using the geno2pheno[coreceptor] and T-CUP tools with FPR cut-offs ranging from 1%-20%. Additionally, 27 RNA and 28 DNA samples were analysed in triplicate, 43 samples with the ESTA assay and 45 with next-generation sequencing. The influence of the genotypic susceptibility score (GSS) and 16 MVC-resistance mutations on clinical outcome was also studied.ResultsConcordance between single-amplification testing compared to ESTA and to NGS was in the order of 80%. Concordance with NGS was higher at lower FPR cut-offs. Detection of baseline R5 viruses in RNA and DNA samples by all methods significantly correlated with treatment success, even with FPR cut-offs of 3.75%-7.5%. Triple amplification did not improve the prediction value but reduced the number of patients eligible for MVC. No influence of the GSS or MVC-resistance mutations but adherence to treatment, on the clinical outcome was detected.ConclusionsProviral DNA is valid to select candidates for MVC treatment. FPR cut-offs of 5%-7.5% and single amplification from RNA or DNA would assure a safe administration of MVC without excluding many patients who could benefit from this drug. In addition, the new prediction system T-CUP produced reliable results.

Multivariate biomarkers that can predict the effectiveness of targeted therapy in individual patients are highly desired. Previous biomarker discovery studies have largely focused on the identification of single biomarker signatures, aimed at maximizing prediction accuracy. Here, we present a different approach that identifies multiple biomarkers by simultaneously optimizing their predictive power, number of features, and proximity to the drug target in a protein-protein interaction network. To this end, we incorporated NSGA-II, a fast and elitist multi-objective optimization algorithm that is based on the principle of Pareto optimality, into the biomarker discovery workflow. The method was applied to quantitative phosphoproteome data of 19 non-small cell lung cancer (NSCLC) cell lines from a previous biomarker study. The algorithm successfully identified a total of 77 candidate biomarker signatures predicting response to treatment with dasatinib. Through filtering and similarity clustering, this set was trimmed to four final biomarker signatures, which then were validated on an independent set of breast cancer cell lines. All four candidates reached the same good prediction accuracy (83%) as the originally published biomarker. Although the newly discovered signatures were diverse in their composition and in their size, the central protein of the originally published signature - integrin β4 (ITGB4) - was also present in all four Pareto signatures, confirming its pivotal role in predicting dasatinib response in NSCLC cell lines. In summary, the method presented here allows for a robust and simultaneous identification of multiple multivariate biomarkers that are optimized for prediction performance, size, and relevance.

Brown adipose tissue (BAT) thermogenesis is an emerging target for prevention and treatment of obesity. Mitochondria are the heat generators of BAT. Yet, there is no noninvasive means to image the temporal dynamics of the mitochondrial activity in BAT in vivo. Here, we report a technology for quantitative monitoring of principal kinetic components of BAT adaptive thermogenesis in the living animal, using the PET imaging voltage sensor 18F-fluorobenzyltriphenylphosphonium (18F-FBnTP). 18F-FBnTP targets the mitochondrial membrane potential (ΔΨm)--the voltage analog of heat produced by mitochondria. Dynamic 18F-FBnTP PET imaging of rat's BAT was acquired just before and during localized skin cooling or systemic pharmacologic stimulation, with and without administration of propranolol. At ambient temperature, 18F-FBnTP demonstrated rapid uptake and prolonged steady-state retention in BAT. Conversely, cold-induced mitochondrial uncoupling resulted in an immediate washout of 18F-FBnTP from BAT, which was blocked by propranolol. Specific variables of BAT evoked activity were identified and quantified, including response latency, magnitude and kinetics. Cold stimulation resulted in partial washout of 18F-FBnTP (39.1%±14.4% of basal activity). The bulk of 18F-FBnTP washout response occurred within the first minutes of the cold stimulation, while colonic temperature remained nearly intact. Drop of colonic temperature to shivering zone did not have an additive effect. The ß3-adrenergic agonist CL-316,243 elicited 18F-FBnTP washout from BAT of kinetics similar to those caused by cold stimulation. Thus, monitoring ΔΨm in vivo using 18F-FBnTP PET provides insights into the kinetic physiology of BAT. 18F-FBnTP PET depicts BAT as a highly sensitive and rapidly responsive organ, emitting heat in short burst during the first minutes of stimulation, and preceding change in core temperature. 18F-FBnTP PET provides a novel set of quantitative metrics highly important for identifying novel therapeutic targets at the mitochondrial level, for developing means to maximize BAT mass and activity, and assessing intervention efficacy.

Diabetes peer support, where one person with diabetes helps guide and support others, has been proposed as a way to improve diabetes management. We have tested whether different diabetes peer support strategies can improve metabolic and/or psychological outcomes.People with type 2 diabetes (n = 1,299) were invited to participate as either 'peer' or 'peer support facilitator' (PSF) in a 2x2 factorial randomised cluster controlled trial across rural communities (130 clusters) in England. Peer support was delivered over 8-12 months by trained PSFs, supported by monthly meetings with a diabetes educator. Primary end point was HbA1c. Secondary outcomes included quality of life, diabetes distress, blood pressure, waist, total cholesterol and weight. Outcome assessors and investigators were masked to arm allocation. Main factors were 1:1 or group intervention. Analysis was by intention-to-treat adjusting for baseline.The 4 arms were well matched (Group n = 330, 1:1(individual) n = 325, combined n = 322, control n = 322); 1035 (79·7%) completed the mid-point postal questionnaire and 1064 (81·9%) had a final HbA1c. A limitation was that although 92.6% PSFs and peers were in telephone contact, only 61.4% of intervention participants attended a face to face session. Mean baseline HbA1c was 57 mmol/mol (7·4%), with no significant change across arms. Follow up systolic blood pressure was 2·3 mm Hg (0.6 to 4.0) lower among those allocated group peer-support and 3·0 mm Hg (1.1 to 5.0) lower if the group support was attended at least once. There was no impact on other outcomes by intention to treat or significant differences between arms in self-reported adherence or medication.Group diabetes peer support over 8-12 months was associated with a small improvement in blood pressure but no other significant outcomes. Long term benefits should be investigated.ISRCTN.com ISRCTN6696362166963621.

Maple syrup production is an important economic activity in north-eastern North-America. The beginning and length of the production season is linked to daily variation in temperature. There are increasing concerns about the potential impact of climatic change on this industry. Here, we used weekly data of syrup yield for the 1999-2011 period from 121 maple stands in 11 regions of Québec (Canada) to predict how the period of production may be impacted by climate warming. The date at which the production begins is highly variable between years with an average range of 36 days among the regions. However, the average start date for a given region, which ranged from Julian day 65 to 83, was highly predictable (r2 = 0.88) using the average temperature from January to April (TJ-A). A logistic model predicting the weekly presence or absence of production was also developed. Using the inputs of 77 future climate scenarios issued from global models, projections of future production timing were made based on average TJ-A and on the logistic model. The projections of both approaches were in very good agreement and suggest that the sap season will be displaced to occur 15-19 days earlier on average in the 2080-2100 period. The data also show that the displacement in time will not be accompanied by a greater between years variability in the beginning of the season. However, in the southern part of Québec, very short periods of syrup production due to unfavourable conditions in the spring will occur more frequently in the future although their absolute frequencies will remain low.

High throughput sequencing (HTSeq) of small ribosomal subunit amplicons has the potential for a comprehensive characterization of microbial community compositions, down to rare species. However, the error-prone nature of the multi-step experimental process requires that the resulting raw sequences are subjected to quality control procedures. These procedures often involve an abundance cutoff for rare sequences or clustering of sequences, both of which limit genetic resolution. Here we propose a simple experimental protocol that retains the high genetic resolution granted by HTSeq methods while effectively removing many low abundance sequences that are likely due to PCR and sequencing errors. According to this protocol, we split samples and submit both halves to independent PCR and sequencing runs. The resulting sequence data is graphically and quantitatively characterized by the discordance between the two experimental branches, allowing for a quick identification of problematic samples. Further, we discard sequences that are not found in both branches ("AmpliconDuo filter"). We show that the majority of sequences removed in this way, mostly low abundance but also some higher abundance sequences, show features expected from random modifications of true sequences as introduced by PCR and sequencing errors. On the other hand, the filter retains many low abundance sequences observed in both branches and thus provides a more reliable census of the rare biosphere. We find that the AmpliconDuo filter increases biological resolution as it increases apparent community similarity between biologically similar communities, while it does not affect apparent community similarities between biologically dissimilar communities. The filter does not distort overall apparent community compositions. Finally, we quantitatively explain the effect of the AmpliconDuo filter by a simple mathematical model.

Type 2 diabetes (T2D) occurs when there is insufficient insulin release to control blood glucose, due to insulin resistance and impaired β-cell function. The GPR39 receptor is expressed in metabolic tissues including pancreatic β-cells and has been proposed as a T2D target. Specifically, GPR39 agonists might improve β-cell function leading to more adequate and sustained insulin release and glucose control. The present study aimed to test the hypothesis that GPR39 agonism would improve glucose stimulated insulin secretion in vivo. A high throughput screen, followed by a medicinal chemistry program, identified three novel potent Zn2+ modulated GPR39 agonists. These agonists were evaluated in acute rodent glucose tolerance tests. The results showed a lack of glucose lowering and insulinotropic effects not only in lean mice, but also in diet-induced obese (DIO) mice and Zucker fatty rats. It is concluded that Zn2+ modulated GPR39 agonists do not acutely stimulate insulin release in rodents.

Sonic Hedgehog (Shh) is a representative of the evolutionary closely related class of Hedgehog proteins that have essential signaling functions in animal development. The N-terminal domain (ShhN) is also assigned to the group of LAS proteins (LAS = Lysostaphin type enzymes, D-Ala-D-Ala metalloproteases, Sonic Hedgehog), of which all members harbor a structurally well-defined Zn2+ center; however, it is remarkable that ShhN so far is the only LAS member without proven peptidase activity. Another unique feature of ShhN in the LAS group is a double-Ca2+ center close to the zinc. We have studied the effect of these calcium ions on ShhN structure, dynamics, and interactions. We find that the presence of calcium has a marked impact on ShhN properties, with the two calcium ions having different effects. The more strongly bound calcium ion significantly stabilizes the overall structure. Surprisingly, the binding of the second calcium ion switches the putative catalytic center from a state similar to LAS enzymes to a state that probably is catalytically inactive. We describe in detail the mechanics of the switch, including the effect on substrate co-ordinating residues and on the putative catalytic water molecule. The properties of the putative substrate binding site suggest that ShhN could degrade other ShhN molecules, e.g. by cleavage at highly conserved glycines in ShhN. To test experimentally the stability of ShhN against autodegradation, we compare two ShhN mutants in vitro: (1) a ShhN mutant unable to bind calcium but with putative catalytic center intact, and thus, according to our hypothesis, a constitutively active peptidase, and (2) a mutant carrying additionally mutation E177A, i.e., with the putative catalytically active residue knocked out. The in vitro results are consistent with ShhN being a cannibalistic zinc-peptidase. These experiments also reveal that the peptidase activity depends on pH.

With the introduction of omics-technologies such as transcriptomics and proteomics, numerous methods for the reliable identification of significantly regulated features (genes, proteins, etc.) have been developed. Experimental practice requires these tests to successfully deal with conditions such as small numbers of replicates, missing values, non-normally distributed expression levels, and non-identical distributions of features. With the MeanRank test we aimed at developing a test that performs robustly under these conditions, while favorably scaling with the number of replicates. The test proposed here is a global one-sample location test, which is based on the mean ranks across replicates, and internally estimates and controls the false discovery rate. Furthermore, missing data is accounted for without the need of imputation. In extensive simulations comparing MeanRank to other frequently used methods, we found that it performs well with small and large numbers of replicates, feature dependent variance between replicates, and variable regulation across features on simulation data and a recent two-color microarray spike-in dataset. The tests were then used to identify significant changes in the phosphoproteomes of cancer cells induced by the kinase inhibitors erlotinib and 3-MB-PP1 in two independently published mass spectrometry-based studies. MeanRank outperformed the other global rank-based methods applied in this study. Compared to the popular Significance Analysis of Microarrays and Linear Models for Microarray methods, MeanRank performed similar or better. Furthermore, MeanRank exhibits more consistent behavior regarding the degree of regulation and is robust against the choice of preprocessing methods. MeanRank does not require any imputation of missing values, is easy to understand, and yields results that are easy to interpret. The software implementing the algorithm is freely available for academic and commercial use.

Lying is a common occurrence in social interactions, but what predicts whether an individual will tell a lie? While previous studies have focused on personality factors, here we asked whether lying tendencies might be transmitted through social networks. Using an international sample of 1,687 socially connected pairs, we investigated whether lying tendencies were related in socially connected individuals, and tested two moderators of observed relationships. Participants recruited through a massive open online course reported how likely they would be to engage in specific lies; a friend or relative responded to the same scenarios independently. We classified lies according to their beneficiary (antisocial vs. prosocial lies), and their directness (lies of commission vs. omission), resulting in four unique lying categories. Regression analyses showed that antisocial commission, antisocial omission, and prosocial commission lying tendencies were all uniquely related in connected pairs, even when the analyses were limited to pairs that were not biologically related. For antisocial lies of commission, these relationships were strongest, and were moderated by amount of time spent together. Randomly paired individuals from the same countries were also related in their antisocial commission lying tendencies, signifying country-level norms. Our results indicate that a person's lying tendencies can be predicted by the lying tendencies of his or her friends and family members.

In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR) by quantitative trait locus (QTL) analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools. One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68 × 10(-3)). We confirmed that the genotype of mouse Chromosome 12 is an important determinant of lung responsiveness using a Chromosome 12 substitution strain. Mice with an A/J Chromosome 12 on a C57BL/6J background have an AHR phenotype similar to hyperresponsive strains A/J and BcA86. Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype. Overall, through QTL analysis of a recombinant congenic strain, microarray analysis and coding variant analysis we identified Chromosome 12 and three potential candidate genes to be in linkage with airway responsiveness.