bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis by metadynamics simulation of binding pathway of influenza virus M2 channel blockers
Authors: Sakai Yuri , Kawaguchi Atsushi , Nagata Kyosuke , Hirokawa Takatsugu 
Published: December 2017

ABSTRACTM2 protein of influenza A virus is a proton channel spanning the viral envelope. Activity of this proton channel is required for uncoating of viral particles and equilibrating the pH across the trans Golgi apparatus, which prevents conformational change in hemagglutinin. Amantadine, an anti‐influenza A virus drug, inhibits M2 proton channel activity by binding to the channel pore; however, most currently circulating influenza A viruses are amantadine‐resistant. The most prevalent resistant mutation is a substitution from Ser31 to Asn31 in M2. Further atomistic analysis of ligand‐M2 complexes is needed to provide new approaches for the design of novel M2 channel blockers. Here, the free energy profiles of the binding kinetics of M2 channel blockers were examined by well‐tempered metadynamics simulations and it was found that amantadine first binds to Asp24 of S31 M2 and forms a metastable conformation. In contrast, the free energy profiles of adamantyl bromothiophene dual inhibitor with either S31 M2 or N31 M2 are broad funnel‐shaped curves, suggesting that adamantyl bromothiophene does not form metastable complexes with M2. The trajectory of well‐tempered metadynamics simulations revealed that steric hindrance between adamantyl bromothiophene and S31 M2 interrupts formation of a metastable conformation at Asp24 and that a halogen bond between the bromine atom and N31 is responsible for pulling down the ligand to the channel pore of N31 M2 in the absence of a metastable state. Binding pathways of M2 channel blockers to M2 are here proposed on the basis of these findings; they may provide new approaches to designing further M2 channel blockers.
Avian Scavenging of Small‐Sized Pig Carcasses in Central Florida: Utilizing GIS to Analyze Site Variables Affecting Skeletal Dispersal
Authors: Schultz John J. , Mitchell Alexander T. 
Published: December 2017

AbstractScavengers can significantly alter a forensic scene and consume, modify, disarticulate, and disperse bodies on the ground surface. The research purpose was to examine vulture scavenging in central Florida, USA. Four small‐sized pig (Sus scrofa) carcasses were left on the ground surface of two microenvironments (shaded and open) at a secure site with game cameras. Dispersal data were mapped and analyzed using geographical information systems spatial analysis digital mapping tools. The primary avian scavengers recorded included black vultures (Coragyps atratus) and turkey vultures (Cathartes aura), as well as bald eagles (Haliaeetus leucocephalus). Carcass dispersal patterns were impacted by foliage density (grass height and concentrations of bushes and trees) and proximity to the perimeter fence. While the majority of skeletal elements were dispersed within 6 m of the carcass deposition locations, dispersion occurred over a greater distance in the wooded microenvironment. Overall, vulture behaviors deleteriously destroyed and changed the context of the scene, with black vultures having the greatest impact.
Fishy Odor and TMA Content Levels in Duck Egg Yolks
Authors: Li Xingzheng , Yuan Gongjiao , Chen Xia , Guo Yuying , Yang Ning , Pi Jinsong , Zhang Hao , Zheng Jiangxia 
Published: December 2017

AbstractThe differences between the trimethylamine (TMA) content levels in duck and chicken egg yolks under normal dietary conditions were compared. Moreover, the association between the polymorphisms of the duck FMO3 gene and TMA content levels in duck egg yolks was analyzed. Then, to detect the mutations associated with the fish‐flavor trait, duck populations were selected for a high‐choline diet experiment, which was followed by full‐length sequencing of the FMO3 exons. The results showed that the TMA content levels in duck eggs (3.60 μg/g) were significantly higher than those in chicken eggs (2.35 μg/g) under normal dietary conditions (P < 0.01). With regard to the high‐choline diet, the average TMA content levels in duck egg yolks (9.21 μg/g; P < 0.01) increased significantly. Furthermore, 5 SNPs reported in Ensembl database were detected in duck FMO3 exons. However, no mutation loci were found to be significantly associated with the TMA content levels in duck egg yolks. Besides, duck liver FMO3 mRNA expression levels were not associated with the TMA content levels. The results indicated that excessive TMA deposition in duck eggs is one of main factors causing the fishy odor in duck eggs, and the addition of choline in the ducks’ diets was responsible for inducing an increase in the TMA content levels in duck eggs.Practical ApplicationOur study can help to diminish the fishy taste in duck eggs by reducing the amount of supplemented choline. Furthermore, this study laid a solid foundation for revealing the genetic factors involved in the fishy odor in duck eggs.
Prevalence of knee osteoarthritis in a suburban, Srilankan, adult female population: a population‐based study
Authors: Prashansanie Hettihewa Akalanka , Gunawardena Nalika S. , Atukorala Inoshi , Hassan Fazliya , Lekamge Indra N. , Hunter David J. 
Published: December 2017

AbstractIntroductionPrevalence of knee osteoarthritis (KOA) has not been assessed in Sri Lanka, since 2006. This study aimed to determine the prevalence of clinical KOA and radiographic KOA and to assess the severity of it, among adult females of a suburban setting in Sri Lanka.MethodsA cross‐sectional survey was conducted among a representative sample of 666 females aged 50 years or more resident in Pita Kotte Medical Officer of Health area. Four physiotherapy graduates applied American College of Rheumatology (ACR) criteria by performing the clinical assessment in the households. Participants with clinical knee osteoarthritis were referred for radiography to identify radiographic osteoarthritis and to assess severity. Age standardized prevalence of clinical KOA for Sri Lanka was estimated based on population statistics of 2001 Census.ResultsStudy included 666 adult females with a response rate of 99.4%. The mean age was 63.3 years (±9.29 years). A total of 134 were found to satisfy ACR criteria resulting in a crude prevalence of clinical KOA of 20.1% (95% CI 17.0%–23.2%). Estimated age standardized prevalence of clinical KOA for Sri Lanka was 21.8% (95% CI 21.7–21.9). Among those with clinical KOA 58.9% showed radiographic KOA and the prevalence of moderate/severe KOA among those with clinical KOA was 29.9%.Conclusion and RecommendationsPrevalence of clinical KOA among the adult females over 50 years was high with considerable proportion of them being moderate /severe KOA. These findings should be used to advice the health authorities regarding improving preventive and curative services for KOA.
Ultrasonographic detection of double contour sign and hyperechoic aggregates for diagnosis of gout: two sites examination is as good as six sites examination
Authors: Bhadu Danveer , Das Siddharth K. , Wakhlu Archana , Dhakad Urmila , Sharma Meha 
Published: December 2017

AbstractObjectiveTo compare ultrasound‐detected abnormalities, namely double contour sign (DCS) and hyperechoic aggregates (HAGs), at two sites (knee and first metatarsophalangeal [1st MTP] joints) versus six sites (knee joint, 1st MTP joint, radiocarpal joint, talar joint, patellar tendon and triceps tendon) in gout patients.MethodsForty‐seven clinically diagnosed gout patients and 50 subjects (serum uric acid < 7 mg/dL) as controls were included. DCS was looked for at three articular cartilage sites (first metatarsal, tibiotalar and femoral condyle), whereas HAGs were looked for at one joint site (radiocarpal joint) and two tendon sites (patellar tendon and triceps tendon). Ultrasound findings of both the groups were compared.ResultsSensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and positive likelihood ratio (LR) of two sites ultrasound findings for gout were 87.2%, 84%, 83.7%, 85.6% and 5.5 respectively. Similar sensitivity, specificity, PPV, NPV and positive LR were observed with six sites ultrasound findings. Among controls, 16% were found to have these abnormal ultrasound findings by both two sites and six sites examinations.ConclusionScreening of two sites (knee and 1st MTP) has similar sensitivity, specificity, PPV, NPV and positive LR as compared to six sites in diagnosing gout.
Sex, size and timing: Sampling design for reliable population genetics analyses using microsatellite data
Authors: Dubois Quentin , Lebigre Christophe , Schtickzelle Nicolas , Turlure Camille 
Published: December 2017

Abstract

Population genetics is used in a wide variety of fields such as ecology and biodiversity conservation. How estimated genetic characteristics of natural populations can be influenced by the sampling design has been a long‐standing concern. Multiple simulation and empirical studies illustrated the influence of both sample size and polymorphism of markers. However, our review of studies on butterfly population genetics indicates no consensus on sample size for the estimation of genetic diversity or differentiation. Furthermore, other aspects of sampling design (sex ratio and timing of sampling) were not addressed and their potential impact on genetic parameter estimates rarely explored.

Using a large empirical dataset (with spatial and temporal replicates) collected on a butterfly species, Boloria aquilonaris, as well as simulated datasets reflecting (1) three scenarios of migration–genetic drift equilibrium and (2) one scenario of parameter stabilization after 100,000 generations, we quantified the impacts of three aspects of genetic sampling design (namely, sample size, sex ratio and timing of sampling) on the estimation of allele frequencies and its potential downstream impact on the estimation of genetic parameters.

With empirical data, we found that sample size and timing of sampling strongly affected the accuracy of allele frequencies and the downstream analyses, while sex ratio did not. Our results were consistent across spatial and temporal replicates. Also, with simulated data, we showed that the genetic sampling design had limited effect in systems where dispersal outweighs genetic drift, while it can have major consequences on our understanding of the genetic diversity and population differentiation in systems dominated by genetic drift (such as most study systems with conservation concerns).

We advocate for careful consideration of all aspects of the sampling design in population genetics studies, that is a sufficient number of samples, while ensuring similar sex ratio among sampling locations and collecting with timing appropriate to the question under study. This is particularly important when the study aims at species conservation.
Functional ecology and imperfect detection of species
Authors: Roth Tobias , Allan Eric , Pearman Peter B. , Amrhein Valentin 
Published: December 2017

Abstract

Functional traits are increasingly being used to understand the response of species to environmental change and their effects on ecosystem functioning. However, some ecologically important traits, such as plant height, influence the probability of species detection during field surveys. Imperfect detection of species could therefore bias measures of functional trait composition and diversity, leading to incorrect estimates of trait–environment relationships due to a process of “detection filtering.” The importance of detection filtering for functional ecological studies remains unknown.

We used hierarchical models that account for detection filtering to analyse data on 1,296 vascular plant species sampled in 362 1‐km2 plots, distributed along a 2,460‐m elevational gradient in Central Europe. We examined how detection filtering altered measures of functional diversity (multivariate functional richness and packing) and composition (community means of three traits). We also determined whether the strength of detection filtering varied over the gradient, to determine whether detection filtering biased trait–environment relationships.

Species detectability was correlated with all three functional traits tested in this study, meaning that short species with small seeds and high specific leaf area values were less likely to be detected. This suggests that imperfect detection has the potential to bias measures of functional composition. Generally, measures of functional composition were not strongly affected by detection filtering, but functional packing was underestimated when detection filtering was not accounted for. In addition to the traits, distributional characteristics were important; rare species and species occurring mainly at low elevations tended to have lower detection probabilities.

Overall, detection filtering did not strongly bias trait–environment relationships because the effects of the environment on functional composition and diversity were larger than the effects of detection.

Our results suggest that many measures of functional composition and diversity are robust to detection filtering, but some are likely biased. Functional ecologists should consider correcting for imperfect detection, and our approach provides a simple method to do so for a wide range of datasets.
Optimal survey designs for environmental DNA sampling
Authors: Lugg William H. , Griffiths Josh , van Rooyen Anthony R. , Weeks Andrew R. , Tingley Reid 
Published: December 2017

Abstract

Environmental DNA (eDNA) sampling is a promising tool for monitoring cryptic species. Numerous studies have demonstrated that eDNA sampling can achieve higher detection rates than traditional monitoring techniques, such as trapping; however, the consequences of that sensitivity for survey design requirements and resulting survey costs have not been investigated.

We demonstrate how site occupancy detection models and optimal survey design methods can be used to evaluate the cost‐efficiency of eDNA sampling vs. traditional survey methods. We apply these approaches to two datasets—one in which eDNA sampling and trapping were conducted simultaneously (paired dataset), and another in which sampling methods were independently deployed (unpaired dataset)—to assess the cost‐efficiency of eDNA sampling for detecting a freshwater mammal: the platypus Ornithorhynchus anatinus.

Conditional probabilities of platypus eDNA being captured in a single water sample (paired dataset: 0.838, unpaired: 0.879), and detected in a single water sample by qPCR (paired: 0.892, unpaired: 0.858), were higher than the conditional probability of detecting a platypus with a single trapping visit (paired: 0.470, unpaired: 0.219).

eDNA sampling was more cost‐efficient than trapping, regardless of whether the management objective was to (1) minimize the survey budget needed to achieve a particular asymptotic variance of the occupancy estimator, or (2) minimize the survey budget needed to detect a change in occupancy over time.

Site occupancy detection models coupled with optimal survey design methods provide a powerful means with which to compare the sensitivity and cost‐efficiency of eDNA sampling vs. traditional sampling methods.
Young plasma reverses age‐dependent alterations in hepatic function through the restoration of autophagy
Authors: Liu Anding , Guo Enshuang , Yang Jiankun , Yang Yan , Liu Shenpei , Jiang Xiaojing , Hu Qi , Dirsch Olaf , Dahmen Uta , Zhang Cuntai , Gewirtz David A , Fang Haoshu 
Published: December 2017

SummaryRecent studies showing the therapeutic effect of young blood on aging‐associated deterioration of organs point to young blood as the solution for clinical problems related to old age. Given that defective autophagy has been implicated in aging and aging‐associated organ injuries, this study was designed to determine the effect of young blood on aging‐induced alterations in hepatic function and underlying mechanisms, with a focus on autophagy. Aged rats (22 months) were treated with pooled plasma (1 ml, intravenously) collected from young (3 months) or aged rats three times per week for 4 weeks, and 3‐methyladenine or wortmannin was used to inhibit young blood‐induced autophagy. Aging was associated with elevated levels of alanine transaminase and aspartate aminotransferase, lipofuscin accumulation, steatosis, fibrosis, and defective liver regeneration after partial hepatectomy, which were significantly attenuated by young plasma injections. Young plasma could also restore aging‐impaired autophagy activity. Inhibition of the young plasma‐restored autophagic activity abrogated the beneficial effect of young plasma against hepatic injury with aging. In vitro, young serum could protect old hepatocytes from senescence, and the antisenescence effect of young serum was abrogated by 3‐methyladenine, wortmannin, or small interfering RNA to autophagy‐related protein 7. Collectively, our data indicate that young plasma could ameliorate age‐dependent alterations in hepatic function partially via the restoration of autophagy.
Autophagy controls mesenchymal stem cell properties and senescence during bone aging
Authors: Ma Yang , Qi Meng , An Ying , Zhang Liqiang , Yang Rui , Doro Daniel H , Liu Wenjia , Jin Yan 
Published: December 2017

SummaryBone marrow‐derived mesenchymal stem cells (BMMSCs) exhibit degenerative changes, including imbalanced differentiation and reduced proliferation during aging, that contribute to age‐related bone loss. We demonstrate here that autophagy is significantly reduced in aged BMMSCs compared with young BMMSCs. The autophagy inhibitor 3‐methyladenine (3‐MA) could turn young BMMSCs into a relatively aged state by reducing their osteogenic differentiation and proliferation capacity and enhancing their adipogenic differentiation capacity. Accordingly, the autophagy activator rapamycin could restore the biological properties of aged BMMSCs by increasing osteogenic differentiation and proliferation capacity and decreasing adipogenic differentiation capacity. Possible underlying mechanisms were explored, and the analysis revealed that autophagy could affect reactive oxygen species and p53 levels, thus regulating biological properties of BMMSCs. In an in vivo study, we found that activation of autophagy restored bone loss in aged mice. In conclusion, our results suggest that autophagy plays a pivotal role in the aging of BMMSCs, and activation of autophagy could partially reverse this aging and may represent a potential therapeutic avenue to clinically treat age‐related bone loss.
Systematic review of aged care interventions for older prisoners
Authors: Stevens Bruce A , Shaw Rhonda , Bewert Peter , Salt Mavis , Alexander Rebecca , Loo Gee Brendan 
Published: December 2017

ObjectiveThe care of older prisoners is a growing problem. This review examined aged care interventions in prisons.MethodsA systematic review was conducted following preferred reporting items for systematic reviews and meta‐analyses guidelines. A total of 1186 abstracts were screened for inclusion. Quantitative and qualitative studies were included.ResultsTwo quantitative studies and five qualitative studies examined aged care interventions (n = 7). An intervention involving physical health activities was not effective in reducing distress compared to a control, and an intervention of psychosocial, physical and spiritual health activities for veterans was not effective when compared to a comparison group. Qualitative analysis generated themes that apply to best practices: addressing older prisoners’ needs, identifying barriers for older prisoners and staff, considering the prison culture, program delivery and cultivating older prisoners and staff attitudes.ConclusionThis review found no significant interventions in prisons. However, the qualitative findings showed evidence of best practice.
A rare ANOS1 variant in siblings with Kallmann syndrome identified by whole exome sequencing
Authors: Lopategui D. M. , Griswold A. J. , Arora H. , Clavijo R. I. , Tekin M. , Ramasamy R. 
Published: December 2017

SummaryKallmann syndrome is a rare genetic condition causing congenital hypogonadotropic hypogonadism. It presents with delayed puberty, anosmia, and infertility. Here, we set out to identify a causative DNA variant for Kallmann syndrome in two affected brothers of Hispanic ancestry. The male siblings presented with a clinical diagnosis of Kallmann syndrome (anosmia, delayed puberty, azoospermia, and undetectable luteinizing hormone and follicle stimulating hormone levels). Genetic variations were investigated by whole exome sequencing. Potentially pathogenic variants were filtered and prioritized followed by validation by Sanger sequencing in the two brothers and their mother. A pathogenic variant was identified in the ANOS1 gene on the X chromosome: c.1267C>T; both brothers were hemizygous, and their mother was heterozygous for the variant. The variant is a single nucleotide change that introduces a stop codon in exon 9 (p.R423*), likely producing a truncated variant of the protein. This variant has only been reported twice in the literature, in the setting of finding genetic causes for other conditions. This result supports the clinical value of whole exome sequencing for identification of genetic pathogenic variants. Genetic diagnosis is the essential first step for genetic counseling, preimplantation diagnosis, and research for a potential treatment.
Parents with overweight children two and five years of age did not perceive them as weighing too much
Authors: Berggren Sara , Roswall Josefine , Alm Bernt , Bergman Stefan , Dahlgren Jovanna , Almquist‐Tangen Gerd 
Published: December 2017

AbstractAimThis study examined whether the parents of children who were overweight at two and five years of age perceived their children as being too heavy and related the findings to sociodemographic factors.MethodsThe data collection included parental questionnaires and anthropometric data from a longitudinal birth cohort of 2666 children born in the south‐west region of Sweden in 2007–2008.ResultsWe found that 14.9 and 11.8% of the children were considered overweight or obese at the age of two and five, but 96.4 and 87.1% of their parents perceived their weight to be just about right at these ages. The difference was statistically significant (p < 0.001). Parents who were overweight themselves and had a low educational level were associated with a higher probability of misperception: at two years of age, the odds ratio was 2.75 (95% confidence interval 1.80–4.21), and at the age of five, it was 1.92 (1.24–2.97).ConclusionMost parents did not perceive that their overweight children weighed too much, but their judgement improved as the child got older. Parents who were overweight or had a low educational level were more likely to misperceive their child's weight. Health Care professionals need to be aware of this gap in perception.
Challenges for Low‐Income Children in an Era of Increasing Income Inequality
Authors: Odgers Candice L. , Adler Nancy E. 
Published: December 2017

AbstractChildren growing up in poverty are at heightened risk for poor health. Researchers have identified some mechanisms responsible for this association but we know less about how children are affected by growing up in communities, schools, and countries with varying levels of income inequality. In this article, we summarize what is known about the association between children's well‐being and income inequality, and outline three challenges that increasing levels of income inequality may pose to children from low‐income families. We also discuss implications for research and policy.