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https://www.readbyqxmd.com/read/29667323/clades-a-classification-based-machine-learning-method-for-species-delimitation-from-population-genetic-data
#1
Jingwen Pei, Chong Chu, Xin Li, Bin Lu, Yufeng Wu
Species are considered to be the basic unit of ecological and evolutionary studies. Since multi-locus genomic data are increasingly available there has been considerable interests in the use of DNA sequence data to delimit species. In this paper, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667198/alcohol-availability-and-onset-and-recurrence-of-alcohol-use-disorder-examination-in-a-longitudinal-cohort-with-co-sibling-analysis
#2
Katherine J Karriker-Jaffe, Henrik Ohlsson, Kenneth S Kendler, Won Kim Cook, Kristina Sundquist
BACKGROUND: Recent reviews of associations of alcohol availability with alcohol outcomes suggest findings are highly inconsistent and highlight a lack of longitudinal and causal evidence. Effect modification (moderation or statistical interaction), which could contribute to the inconsistent picture in the existing literature, has not been systematically assessed. We examined associations of alcohol availability with onset and recurrence of alcohol use disorder (AUD) using multi-level, longitudinal population data from Sweden and test hypothesized effect modifiers to identify groups for whom increased alcohol availability may be particularly risky...
April 18, 2018: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29666327/association-analysis-of-multiple-traits-by-an-approach-of-combining-p-values
#3
Lili Chen, Yong Wang, Yajing Zhou
Increasing evidence shows that one variant can affect multiple traits, which is a widespread phenomenon in complex diseases. Joint analysis of multiple traits can increase statistical power of association analysis and uncover the underlying genetic mechanism. Although there are many statistical methods to analyse multiple traits, most of these methods are usually suitable for detecting common variants associated with multiple traits. However, because of low minor allele frequency of rare variant, these methods are not optimal for rare variant association analysis...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29665793/assessing-known-chronic-kidney-disease-associated-genetic-variants-in-saudi-arabian-populations
#4
Cyril Cyrus, Samir Al-Mueilo, Chittibabu Vatte, Shahanas Chathoth, Yun R Li, Hatem Qutub, Rudaynah Al Ali, Fahad Al-Muhanna, Matthew B Lanktree, Khaled Riyad Alkharsah, Abdullah Al-Rubaish, Brian Kim-Mozeleski, Brendan Keating, Amein Al Ali
BACKGROUND: Genome wide association studies of patients with European descent have identified common variants associated with risk of reduced estimated glomerular filtration rate (eGFR). A panel of eight variants were selected to evaluate their association and prevalence in a Saudi Arabian patient cohort with chronic kidney disease (CKD). METHODS: Eight genetic variants in four genes (SHROOM3, MYH9, SLC7A9, and CST3) were genotyped in 160 CKD patients and 189 ethnicity-matched healthy controls...
April 17, 2018: BMC Nephrology
https://www.readbyqxmd.com/read/29665771/evidence-for-late-pleistocene-origin-of-astyanax-mexicanus-cavefish
#5
Julien Fumey, Hélène Hinaux, Céline Noirot, Claude Thermes, Sylvie Rétaux, Didier Casane
BACKGROUND: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. RESULTS: We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages...
April 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29664734/potential-causes-of-asthma-in-the-united-arab-emirates-drawing-insights-from-the-arabian-gulf
#6
REVIEW
Sarah Dalibalta, Fatin Samara, Haya Qadri, Hibatallah Adouchana
There is considerable concern on the rise in the incidence of asthma worldwide with statistics in the United Arab Emirates (UAE) indicating that at least 13% of schoolchildren, particularly of Emirati descent, suffer from asthma. With its high rates of hospital admissions, negative socioeconomic impact and significant morbidity, this is a disease that requires optimal guidelines for control and awareness. In this article, we review the current knowledge of asthma in the UAE and draw on studies, especially from the surrounding region, to identify its contributing factors within this population...
April 17, 2018: Reviews on Environmental Health
https://www.readbyqxmd.com/read/29663709/soft-tissue-nasal-asymmetry-as-an-indicator-of-orofacial-cleft-predisposition
#7
Charles Zhang, Steven F Miller, Jasmien Roosenboom, George L Wehby, Lina M Moreno Uribe, Jacqueline T Hecht, Frederic W B Deleyiannis, Kaare Christensen, Mary L Marazita, Seth M Weinberg
The biological relatives of offspring with nonsyndromic orofacial clefts have been shown to exhibit distinctive facial features, including excess asymmetry, which are hypothesized to indicate the presence of genetic risk factors. The significance of excess soft tissue nasal asymmetry in at-risk relatives is unclear and was examined in the present study. Our sample included 164 unaffected parents from families with a history of orofacial clefting and 243 adult controls. Geometric morphometric methods were used to analyze the coordinates of 15 nasal landmarks collected from three-dimensional facial surface images...
April 16, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29662471/maize-endophytic-bacterial-diversity-as-affected-by-soil-cultivation-history
#8
David Correa-Galeote, Eulogio J Bedmar, Gregorio J Arone
The bacterial endophytic communities residing within roots of maize ( Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29662324/clinical-and-molecular-genetic-features-of-hb-h-and-ae-bart-s-diseases-in-central-thai-children
#9
Chanchai Traivaree, Boonchai Boonyawat, Chalinee Monsereenusorn, Piya Rujkijyanont, Apichat Photia
Background: α-Thalassemia, one of the major thalassemia types in Thailand, is caused by either deletion or non-deletional mutation of one or both α-globin genes. Inactivation of three α-globin genes causes hemoglobin H (Hb H) disease, and the combination of Hb H disease with heterozygous hemoglobin E (Hb E) results in AE Bart's disease. Objective: This study aimed to characterize the clinical and hematological manifestations of 76 pediatric patients with Hb H and AE Bart's diseases treated at Phramongkutklao Hospital, a tertiary care center for thalassemia patients in central Thailand...
2018: Application of Clinical Genetics
https://www.readbyqxmd.com/read/29661871/the-genetic-polymorphism-ugt1a4-3-is-associated-with-low-posaconazole-plasma-concentrations-in-hematological-malignancy-patients-receiving-the-oral-suspension
#10
Hyeon Jeong Suh, Seo Hyun Yoon, Kyung-Sang Yu, Joo-Youn Cho, Sang-In Park, Eunyoung Lee, Jeong-Ok Lee, Youngil Koh, Kyoung-Ho Song, Pyoeng Gyun Choe, Eu Suk Kim, Soo-Mee Bang, Hong Bin Kim, Inho Kim, Nam Joong Kim, Sang Hoon Song, Wan Beom Park, Myoung-Don Oh
The metabolism of posaconazole is mediated mainly by uridine 5' -diphospho-glucuronosyltransferase (UGT) enzymes, especially the UGT1A4. The aim of this study was to investigate the effects of genetic polymorphisms on the posaconazole plasma concentration (PPC). This prospective study was conducted from September 2014 to August 2016. We enrolled patients with acute myeloid leukemia or myelodysplastic syndrome treated with posaconazole oral suspension (200 mg) three times daily for fungal prophylaxis. The multi-drug resistance gene 1 3435C>T and 2677G>T/A variations, and UGT1A4*3 were examined by direct sequencing of DNA from peripheral whole blood samples...
April 16, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29661148/identification-of-missing-variants-by-combining-multiple-analytic-pipelines
#11
Yingxue Ren, Joseph S Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P Sinnwell, Shannon K McDonnell, Joanna M Biernacka, Minerva M Carrasquillo, Owen A Ross, Nilüfer Ertekin-Taner, Rosa Rademakers, Matthew Hudson, Liudmila Sergeevna Mainzer, Yan W Asmann
BACKGROUND: After decades of identifying risk factors using array-based genome-wide association studies (GWAS), genetic research of complex diseases has shifted to sequencing-based rare variants discovery. This requires large sample sizes for statistical power and has brought up questions about whether the current variant calling practices are adequate for large cohorts. It is well-known that there are discrepancies between variants called by different pipelines, and that using a single pipeline always misses true variants exclusively identifiable by other pipelines...
April 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29660412/mycoplasma-hominis-shows-strain-dependent-increase-of-resistance-to-selected-antibiotics-after-symbiosis-with-trichomonas-vaginalis
#12
Ursula Fürnkranz, Julia Walochnik, Birgit Henrich
OBJECTIVES: Mycoplasma hominis, a genetically heterogeneous, cell-wall less bacterium, is able to live in symbiosis with the protozoan parasite Trichomonas vaginalis. While impacts of this symbiosis on T. vaginalis have been investigated to a certain extent, less light has been shed on the influence on M. hominis. METHODS: In an in vitro minimal inhibitory concentration (MIC) study the antibiotic susceptibility of three clinical M. hominis isolates, V475, AKH136 and MhSS10, to clindamycin, moxifloxacin, ciprofloxacin and gentamicin was investigated in dependence on symbiosis with T...
April 13, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29660239/the-population-genetic-test-tajima-s-d-identifies-genes-encoding-pathogen-associated-molecular-patterns-and-other-virulence-related-genes-in-ralstonia-solanacearum
#13
Noam Eckshtain-Levi, Alexandra J Weisberg, Boris A Vinatzer
Detection of pathogen-associated molecular patterns (PAMPs) by plant pattern receptors (PRRs) is an essential part of plant immunity. Until recently, elf18, an epitope of elongation factor tu (EF-Tu), was the sole confirmed PAMP of Ralstonia solanacearum, the causal agent of bacterial wilt disease, limiting our understanding of R. solanacearum - plant interactions. Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to avoid recognition by plant PRRs...
April 16, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29659925/tobacco-smoking-associated-alterations-in-the-immune-microenvironment-of-squamous-cell-carcinomas
#14
Alexis Desrichard, Fengshen Kuo, Diego Chowell, Ken-Wing Lee, Nadeem Riaz, Richard J Wong, Timothy A Chan, Luc G T Morris
Background: Tobacco smoking creates DNA damage, inducing mutations and potentially altering the tumor immune microenvironment. These types of genetic and immune microenvironment alterations are critical factors known to affect tumor response to immunotherapy. Here we analyze the association between the mutational signature of tobacco smoking, tumor mutational load, and metrics of immune activity in squamous cell carcinomas arising in the head and neck and lung. Methods: Using RNA and DNA sequencing data from The Cancer Genome Atlas head and neck (HNSC; n = 287) and lung (LUSC; n = 130) squamous cell carcinoma data sets and two independent gene expression data sets (HNSC, n = 136; LUSC, n = 75), we examined associations between the mutational smoking signature, mutation count, immune cell infiltration, cytolytic activity, and interferon-γ signaling...
April 11, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29659698/molecular-subtyping-of-cancer-current-status-and-moving-toward-clinical-applications
#15
Lan Zhao, Victor H F Lee, Michael K Ng, Hong Yan, Maarten F Bijlsma
Cancer is a collection of genetic diseases, with large phenotypic differences and genetic heterogeneity between different types of cancers and even within the same cancer type. Recent advances in genome-wide profiling provide an opportunity to investigate global molecular changes during the development and progression of cancer. Meanwhile, numerous statistical and machine learning algorithms have been designed for the processing and interpretation of high-throughput molecular data. Molecular subtyping studies have allowed the allocation of cancer into homogeneous groups that are considered to harbor similar molecular and clinical characteristics...
April 12, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29658841/genetic-structure-of-zymoseptoria-tritici-in-northern-france-at-region-field-plant-and-leaf-layer-scales
#16
Ali Siah, Myriam Bomble, Benoit Tisserant, Thierry Cadalen, Maxime Holvoet, Jean-Louis Hilbert, Patrice Halama, Philippe Lucien Reignault
Population genetic structure of the worldwide-distributed wheat pathogen Zymoseptoria tritici has been extensively studied at large geographical scales, but to a much less extent at small or local spatial scales. A total of 627 single-conidial fungal isolates were sampled from several locations in northern France (Hauts-de-France Region) to assess fungal genetic structure at region, field, plant and leaf layer scales, using highly polymorphic microsatellite markers and mating type idiomorphs. Important and overall similar levels of both gene and genotype diversities (gene diversity values ≥ 0...
April 16, 2018: Phytopathology
https://www.readbyqxmd.com/read/29658407/c-mix-a-high-dimensional-mixture-model-for-censored-durations-with-applications-to-genetic-data
#17
Simon Bussy, Agathe Guilloux, Stéphane Gaïffas, Anne-Sophie Jannot
We introduce a supervised learning mixture model for censored durations (C-mix) to simultaneously detect subgroups of patients with different prognosis and order them based on their risk. Our method is applicable in a high-dimensional setting, i.e. with a large number of biomedical covariates. Indeed, we penalize the negative log-likelihood by the Elastic-Net, which leads to a sparse parameterization of the model and automatically pinpoints the relevant covariates for the survival prediction. Inference is achieved using an efficient Quasi-Newton Expectation Maximization algorithm, for which we provide convergence properties...
January 1, 2018: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29658380/genetic-diversity-and-population-genetic-structure-of-the-only-population-of-aoluguya-reindeer-rangifer-tarandus-in-china
#18
Yan Ju, Huamiao Liu, Min Rong, Ranran Zhang, Yimeng Dong, Yongna Zhou, Xiumei Xing
Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time...
April 16, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29656243/different-permeabilization-patterns-of-splenocytes-and-thymocytes-to-combination-of-pulsed-electric-and-magnetic-field-treatments
#19
Vitalij Novickij, Auksė Zinkevičienė, Justinas Valiulis, Jurgita Švedienė, Algimantas Paškevičius, Eglė Lastauskienė, Svetlana Markovskaja, Jurij Novickij, Irutė Girkontaitė
Genetic manipulation of T cells is frequently inefficient, however, when combined with physical methods (i.e. electroporation) a promising alliance with immunotherapy can be formed. This study presents new data on permeabilization of murine thymocytes and splenocytes as a T cell model using pulsed electric (PEF) and electromagnetic field (EMF). The 300ns, 500ns, 2μs and 100μs pulse bursts in a broad range of PEF 0-8kV/cm were applied separately and in combination with 3.3T, 0.2kV/cm EMF pulses. The permeabilization efficiency was evaluated using fluorescent dye (YO-PRO-1) and flow cytometry...
April 10, 2018: Bioelectrochemistry
https://www.readbyqxmd.com/read/29655398/adult-empathy-possible-gender-differences-in-gene-environment-architecture-for-cognitive-and-emotional-components-in-a-large-italian-twin-sample
#20
Virgilia Toccaceli, Corrado Fagnani, Nancy Eisenberg, Guido Alessandri, Augusto Vitale, Maria Antonietta Stazi
Empathy plays a central role in prosocial behavior and human cooperation. Very few twin researchers have investigated innate and environmental effects in adult empathy, and twin research on gender differences in these effects is sparse. The goal of this study was to examine innate and environmental influences on three components of an empathy scale frequently used with adults - the expression of cognitive (CE), emotional (EE), and social skills (SS) empathy - and to explore gender differences in the influences...
April 15, 2018: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
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