bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting and quantifying natural selection at two linked loci from time series data of allele frequencies with forward-in-time simulations
Authors: He Zhangyi , Dai Xiaoyang , Beaumont Mark , Yu Feng 
Published: February 2019

AbstractRecent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such genomic time series data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modelling the sampled chromosomes that contain unknown alleles. Our approach is based on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for the selection coefficients is obtained by using the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our method can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We illustrate the utility of our approach on real data with an application to ancient DNA data associated with white spotting patterns in horses.
The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ
Authors: Wang Qi , Zhao Lanbo , Han Lu , Fu Guoxing , Tuo Xiaoqian , Ma Sijia , Li Qing , Wang Yiran , Liang Dongxin , Tang Miaomiao , Sun Chao , Wang Qing , Song Qing , Li Qiling 
Published: February 2019

AbstractThe female upper reproductive tract, including the uterus, fallopian tubes and ovaries, is believed to be a sterile environment. With the improvement of bacterial detection, the theory of the sterile female upper reproductive tract has been frequently challenged in recent years. However, thus far, no researchers have used ovaries as study targets. Six women who were diagnosed with ovarian cancer were included in the cancer group, and ten women who were diagnosed with a noncancerous ovarian condition (including three patients with uterine myoma and seven patients with uterine adenomyosis) were included in the control group. Immunohistochemistry staining using an antibacterial lipopolysaccharide (LPS) antibody was used to confirm the presence of bacteria in the ovarian tissues. In addition, 16S rRNA sequencing was used to compare the differences in the bacteria between ovarian cancer tissues and noncancerous ovarian tissues. BugBase and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to predict the functional composition of the bacteria. Bacterial LPS was present in ovarian cancer tissue and noncancerous ovarian tissue, which implied the presence of bacteria in ovarian tissue. When compared to the noncancerous ovarian bacteria at the phylum level, the cancerous ovarian bacteria were composed of increased Aquificae and Planctomycetes and decreased Crenarchaeota. When predicting metagenomes, gene functions associated with the potentially pathogenic and the oxidative stress-tolerant phenotype were enriched in the ovaries of the cancer group. Forty-six significantly different KEGG pathways existed in the ovarian bacteria of the cancer group compared to that of the control group. Different bacteria compositions were present in cancerous and noncancerous ovarian tissues.Author summaryAbdominal solid viscera have always been believed to be absolutely sterile. With the improvement of bacterial detection, this concept is being challenged. Researchers found some bacteria existed in endometrial diseases, the question of whether the ovaries are sterile is still unclear. Therefore, we assume that the bacteria in ovarian tissue are associated with ovarian cancer. When compared to the noncancerous ovarian bacteria at the phylum level, the cancerous ovarian bacteria were composed of increased Aquificae and Planctomycetes and decreased Crenarchaeota. When predicting metagenomes, gene functions associated with the potentially pathogenic and the oxidative stress-tolerant phenotype were enriched in the ovaries of the cancer group. Forty-six significantly different KEGG pathways existed in the ovarian bacteria of the cancer group compared to that of the control group. Different bacteria compositions were present in cancerous and noncancerous ovarian tissues.
Exploring HIV infection in a UK vulnerable prisoner population in response to newly identified cases
Authors: Perrett Stephanie E. , Waite Thomas D. 
Published: February 2019

Purpose
Prison populations are considered at elevated risk of blood borne virus (BBV) transmission. Between December 2015 and February 2016, four new cases of HIV infection were diagnosed across two male vulnerable prisoner (VP) custodial units in Wales, UK. Cases were identified through routine BBV testing. The paper aims to discuss these issues.

Design/methodology/approach
As a result of identifying four new HIV cases, targeted BBV testing across the VP units using dried blood spot testing for HIV, Hepatitis C (HCV) and Hepatitis B was undertaken.

Findings
A total of 617 men were offered testing, 256 (41 per cent) were tested. No further cases of HIV were identified. Eight men were identified as HCV antibody positive. There was no evidence to suggest the four original cases of HIV were linked.

Practical implications
Embedding universal BBV screening within prison health provision will ensure timely identification of cases. Further research is needed to better understand BBV transmission risks within subsets of the prison population such as the VP and sex offending groups.

Originality/value
Little is known about the prevalence of BBVs in vulnerable prison populations. The findings add to the knowledge available for practitioners in the field.
Case of coincident severe acne and psoriasis in AIDS patient successfully treated with antiretroviral therapy
Authors: Li Yu‐Ye , Dong Rong‐Jing , Cao Li‐Juan , Upadhyay Pratishtha , Kuang Yi‐Qun 
Published: February 2019

AbstractCutaneous disorders remain a major problem in HIV‐infected patients, even under antiretroviral therapy (ART). Patients at any stage of HIV/AIDS may suffer from skin lesions. Acnes and psoriasis are both common chronic and inflammatory skin diseases, and the treatment becomes more challenging and complex when combined with HIV infection. Whether the incidence and severity of acne and psoriasis are related to HIV infection is still controversial. Here, we report a rare case of an AIDS patient who developed severe acne along with psoriasis. The patient had initially received multiple systemic and topical antipsoriatic and anti‐acne treatments which failed. Ultimately, he achieved dramatic clinical improvement after initiation of ART for main treatment. An 8‐year follow up demonstrated that the patient has been free of symptoms of both psoriasis and acne till now.
Australian dietitians’ beliefs and attitudes towards weight loss counselling and health at every size counselling for larger‐bodied clients
Authors: Willer Fiona , Hannan‐Jones Mary , Strodl Esben 
Published: February 2019

AimResearch suggests that dietitians now employ weight‐neutral (WN) approaches (Health at Every Size (HAES), Intuitive Eating and non‐diet) as well as more traditional weight‐centric (WC) approaches (weight loss counselling) to address adult weight concerns. This study aimed to compare the knowledge of and attitudes towards WN practice compared with WC practice in Australian dietitians who work with larger‐bodied clients as delineated by practice approach.MethodsA cross‐sectional web‐based knowledge, attitudes and practices survey was conducted with Australian dietitians who counsel adults with a body mass index >25 kg/m2. Based on their responses, dietitians were categorised into WC (preferring weight loss counselling), WN (preferring HAES counselling) or mixed approach (MA). Between‐group comparisons were conducted using Pearson's chi‐squared tests for knowledge and practice and independent t‐tests for attitudes.ResultsOf the 317 respondents, 18.3% fulfilled the criteria for WN practitioners, 30.3% for WC practitioners and the remainder were classified as providing a MA. Weight‐neutral approaches were more positively regarded generally than WC approaches (84.5% vs 53.9%) as well as considered professionally responsible (86% vs 58.7%) and perceived as more helpful for clients (61.2% vs 35%). Knowledge of WN practice goals was poor with only 36.9% (n = 117) of the participants indicating correctly that this mode of treatment is incompatible with a weight loss goal.ConclusionsWeight‐neutral practice was considered acceptable by Australian dietetics professionals who counsel larger‐bodied people regardless of their personal practice preference although many displayed inaccurate knowledge of WN approaches.
Foodinformatics: Quantitative Structure‐Property Relationship Modeling of Volatile Organic Compounds in Peppers
Authors: Rojas Cristian , Duchowicz Pablo R. , Castro Eduardo A. 
Published: February 2019

AbstractThe aim of this work was the foodinformatic (chemoinformatic) modeling of volatile organic compounds (VOCs) of different samples of peppers based on a quantitative structure‐property relationship (QSPR) for the retention indices of 273 identified compounds. The experimental retention indices were measured by means of comprehensive two‐dimensional gas chromatography combined with quadrupole‐mass spectrometry (GC × GC/qMS) using the BPX5 and BP20 column coupled system. All the VOCs were represented by means of both conformation‐independent molecular descriptors and molecular fingerprints calculated in the Dragon and PaDEL‐Descriptor software. The dataset was divided into training, validation and test sets of molecules according to the Balanced Subsets Method (BSM). Subsequently, the V‐WSP unsupervised variable reduction method was used to reduce the presence of multicollinearity, redundancy, and noise in the initial pool of 4,336 molecular descriptors and fingerprints. Using this method, a reduced pool of 1,664 was submitted to the supervised selection by means of the replacement method (RM) variable subset selection in order to define a four‐descriptor model. The quality of the model was measured by means of the coefficient of determination and the root‐mean‐square deviation in fitting ( and ), validation ( and ), and prediction ( and ). The negligible differences among the parameters in the three sets indicate a stable and predictive QSPR model. This quantitative structure‐activity relationship was developed keeping in mind the five principles defined by the Organization for Economic Co‐operation and Development (OECD) to make it applicable.Practical ApplicationThis predictive mathematical model developed from the retention indices of 273 volatile organic compounds (VOCs) detected in pepper samples could be useful for chromatographers working on the identification of other common VOCs in peppers or other foods by means of comprehensive two‐dimensional gas chromatography combined with quadrupole‐mass spectrometry (GC × GC/qMS) using a bi‐dimensional stationary phase coupled system (BPX5 and BP20).
Making use of the social network in conservation genomics: Integrating kinship and network analyses to understand connectivity
Authors: Carroll Emma L. , Gaggiotti Oscar E. 
Published: February 2019

AbstractInferring and quantifying recent barriers to connectivity is increasingly important for conservation and management in a world undergoing rapid environmental change. Traditional measures of genetic differentiation can take many generations to reflect a new barrier to connectivity. Although methods that use the linkage disequilibrium signal in mixed genetic samples are able to reflect recent levels of gene flow, they are not suitable for use in situations with low levels of genetic differentiation. Kinship‐based methods, those that assess the spatio‐temporal distribution of related individuals, have been used in this context, but a formal statistical framework for such approaches has been lacking. In this issue of Molecular Ecology Resources, Escoda, et al. adapt the assortativity coefficient, AC, to analyse the networks of kin relationships in the Pyrenean desman (Galemys pyrenaicus) across potential barriers to dispersal. Their modified AC quantifies the proportion of missing kin relationships across putative dispersal barriers with respect to the expected proportion if there was no barrier. This application highlights that AC can be used to test the null hypothesis that a putative barrier has no effect on gene flow, in which case AC is not significantly different from 0. The method represents a useful step forward in conservation genomics by developing and adapting tools to assess contemporary connectivity using genomic data.
Nuclear magnetic resonance‐based metabolomics reveals similar metabolomics profiles in undifferentiated peripheral spondyloarthritis and reactive arthritis
Authors: Ahmed Sakir , Dubey Durgesh , Chowdhury Abhra , Chaurasia Smriti , Guleria Anupam , Kumar Sandeep , Singh Rajeev , Kumar Dinesh , Misra Ramnath 
Published: February 2019

AbstractIntroductionAfter exclusion of reactive, psoriatic and enteritis‐associated arthritis, a group of “undifferentiated” peripheral spondyloarthritis (pSpA) remains. This group shares genetics, T‐cell repertoire, and cytokines with reactive arthritis (ReA). ReA is preceded by gut or urogenital infection. Otherwise the two may be similar. We know little of the metabolic pathways driving undifferentiated pSpA or ReA. Nuclear magnetic resonance (NMR)‐based metabolomics presents a hypothesis‐free approach to study and compare metabolic pathways driving undifferentiated pSpA and ReA.MethodsSerum and synovial fluid metabolomes of 19 ReA and 13 undifferentiated pSpA, and serum metabolome of 18 controls were profiled using 1H‐based NMR. Partial least square‐discriminant analysis (PLS‐DA) identified metabolites different in patients as compared to controls. Multivariate analysis confirmed these. Altered metabolic pathways were identified using metabolites set enrichment analysis (MSEA). The serum and synovial fluid metabolomes of ReA and undifferentiated pSpA were compared.ResultsTen serum metabolites of ReA/undifferentiated pSpA were different from those of controls. Six metabolites were different between serum and synovial fluid of these patients. MSEA identified five pathways different between patients and controls, and five pathways different between serum and synovial fluid of patients. PLS‐DA showed no difference between the metabolomes of serum or of synovial fluid between ReA and undifferentiated pSpA.DiscussionIdentified metabolic pathways may be explored further to understand the pathogenesis and to target therapeutics. The similar immuno‐metabolic pathways suggest similar pathogenesis of ReA and undifferentiated pSpA. Thus, they should be studied as a single disease entity.
Cyanophage MazG is a pyrophosphohydrolase but unable to hydrolyse magic spot nucleotides
Authors: Rihtman Branko , Bowman‐Grahl Sabine , Millard Andrew , Corrigan Rebecca M. , Clokie Martha R. J. , Scanlan David J. 
Published: February 2019

SummaryBacteriophage possess a variety of auxiliary metabolic genes of bacterial origin. These proteins enable them to maximize infection efficiency, subverting bacterial metabolic processes for the purpose of viral genome replication and synthesis of the next generation of virion progeny. Here, we examined the enzymatic activity of a cyanophage MazG protein – a putative pyrophosphohydrolase previously implicated in regulation of the stringent response via reducing levels of the central alarmone molecule (p)ppGpp. We demonstrate, however, that the purified viral MazG shows no binding or hydrolysis activity against (p)ppGpp. Instead, dGTP and dCTP appear to be the preferred substrates of this protein, consistent with a role preferentially hydrolysing deoxyribonucleotides from the high GC content host Synechococcus genome. This showcases a new example of the fine‐tuned nature of viral metabolic processes.
Clinical and computed tomography characteristics of non‐small cell lung cancer with ALK gene rearrangement: Comparison with EGFR mutation and ALK/EGFR‐negative lung cancer
Authors: Mori Mio , Hayashi Hideyuki , Fukuda Minoru , Honda Sumihisa , Kitazaki Takeshi , Shigematsu Kazuto , Matsuyama Naohiro , Otsubo Mayumi , Nagayasu Takeshi , Hashisako Mikiko , Tabata Kazuhiro , Uetani Masataka , Ashizawa Kazuto 
Published: February 2019

BackgroundThe study was conducted to evaluate the clinical and computed tomography (CT) findings of non‐small cell lung cancer (NSCLC) patients to distinguish between ALK gene rearrangement, EGFR mutation, and non‐ALK/EGFR (no genetic abnormalities).MethodsWe enrolled 201 patients with primary NSCLC who had undergone molecular testing for both ALK gene rearrangement and EGFR mutation. The clinical features and CT findings of the main lesion and associated pulmonary abnormalities were investigated.ResultsFemale gender (P = 0.0043 vs. non‐ALK/EGFR), young age (P = 0.0156 vs. EGFR), and a light or never smoking history (P = 0.0039 vs. non‐ALK/EGFR) were significant clinical characteristics of NSCLC with ALK gene rearrangement. The significant CT characteristics compared to NSCLC with EGFR mutation were a large mass (P = 0.0155), solid mass (P = 0.0048), and no air bronchogram (P = 0.0148). A central location (P = 0.0322) and lymphadenopathy (P = 0.0353) were also more frequently observed. Coexisting emphysema was significantly less frequent in NSCLC patients with ALK gene rearrangement (P = 0.0135) than non‐ALK/EGFR.ConclusionsNSCLC with ALK gene rearrangement was more likely to develop in younger women with a light or never smoking history. The characteristic CT findings of NSCLC with ALK gene rearrangement were a large solid mass, less air bronchogram, a central location, and lymphadenopathy.
JNK modifies neuronal metabolism to promote proteostasis and longevity
Authors: Wang Lifen , Davis Sonnet S. , Borch Jensen Martin , Rodriguez‐Fernandez Imilce A. , Apaydin Cagsar , Juhasz Gabor , Gibson Bradford W. , Schilling Birgit , Ramanathan Arvind , Ghaemmaghami Sina , Jasper Heinrich 
Published: February 2019

AbstractAging is associated with a progressive loss of tissue and metabolic homeostasis. This loss can be delayed by single‐gene perturbations, increasing lifespan. How such perturbations affect metabolic and proteostatic networks to extend lifespan remains unclear. Here, we address this question by comprehensively characterizing age‐related changes in protein turnover rates in the Drosophila brain, as well as changes in the neuronal metabolome, transcriptome, and carbon flux in long‐lived animals with elevated Jun‐N‐terminal Kinase signaling. We find that these animals exhibit a delayed age‐related decline in protein turnover rates, as well as decreased steady‐state neuronal glucose‐6‐phosphate levels and elevated carbon flux into the pentose phosphate pathway due to the induction of glucose‐6‐phosphate dehydrogenase (G6PD). Over‐expressing G6PD in neurons is sufficient to phenocopy these metabolic and proteostatic changes, as well as extend lifespan. Our study identifies a link between metabolic changes and improved proteostasis in neurons that contributes to the lifespan extension in long‐lived mutants.
Cerebellar alterations in cannabis users: A systematic review
Authors: Blithikioti Chrysanthi , Miquel Laia , Batalla Albert , Rubio Belen , Maffei Giovanni , Herreros Ivan , Gual Antoni , Verschure Paul , Balcells‐Oliveró Mercedes 
Published: February 2019

AbstractCannabis is the most used illicit substance in the world. As many countries are moving towards decriminalization, it is crucial to determine whether and how cannabis use affects human brain and behavior. The role of the cerebellum in cognition, emotion, learning, and addiction is increasingly recognized. Because of its high density in CB1 receptors, it is expected to be highly affected by cannabis use. The aim of this systematic review is to investigate how cannabis use affects cerebellar structure and function, as well as cerebellar‐dependent behavioral tasks. Three databases were searched for peer‐reviewed literature published until March 2018. We included studies that focused on cannabis effects on cerebellar structure, function, or cerebellar‐dependent behavioral tasks. A total of 348 unique records were screened, and 40 studies were included in the qualitative synthesis. The most consistent findings include (1) increases in cerebellar gray matter volume after chronic cannabis use, (2) alteration of cerebellar resting state activity after acute or chronic use, and (3) deficits in memory, decision making, and associative learning. Age of onset and higher exposure to cannabis use were frequently associated with increased cannabis‐induced alterations. Chronic cannabis use is associated with alterations in cerebellar structure and function, as well as with deficits in behavioral paradigms that involve the cerebellum (eg, eyeblink conditioning, memory, and decision making). Future studies should consider tobacco as confounding factor and use standardized methods for assessing cannabis use. Paradigms exploring the functional activity of the cerebellum may prove useful as monitoring tools of cannabis‐induced impairment.
Fetus morphology changes by second‐trimester ultrasound in pregnant women drinking alcohol
Authors: Ferraguti Giampiero , Merlino Lucia , Battagliese Gemma , Piccioni Maria Grazia , Barbaro Greta , Carito Valentina , Messina Marisa Patrizia , Scalese Bruna , Coriale Giovanna , Fiore Marco , Ceccanti Mauro 
Published: February 2019

AbstractFetal alcohol spectrum disorders (FASDs) are a group of negative conditions occurring in children exposed to alcohol during gestation. The early discovery of FASD is crucial for mother and infant follow‐ups. In this study, we investigated in pregnant women the association between urine ethylglucuronide (EtG—a biomarker of alcohol drinking) and indicators of the physical characteristics of FASD by prenatal ultrasound in the second trimester of gestation. We also correlated these data with the AUDIT‐C, T‐ACE/TACER‐3, TWEAK, and food habit diary, screening questionnaires used to disclose alcohol drinking during pregnancy. Forty‐four pregnant women were randomly enrolled and examined for ultrasound investigation during the second trimester of gestation. Urine samples were provided by pregnant women immediately after the routine interviews. EtG determinations were performed with a cutoff established at 100 ng/mL, a value indicating occasional alcohol drinking. Fifteen of the enrolled pregnant women overcame the EtG cutoff (34.09%). Analysis of variance (ANOVA) revealed that the fetuses of the positive EtG pregnant women had significantly longer interorbital distance and also significantly increased frontothalamic distance (P's < 0.02). Quite interestingly, no direct correlation was found between EtG data and both food diary and AUDIT‐C. However, a significant correlation was observed between urinary EtG and T‐ACE (r = 0.375; P = 0.012) and between urinary EtG and TWEAK (r = 0.512; P < 0.001) and a concordance with all questionnaire for EtG values higher than 500 ng/mL. This study provides clinical evidence that the diagnosis of maternal alcohol consumption during pregnancy by urine EtG may disclose FASD‐related damage in the fetus.