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Association mapping

Paula Ribeiro Prist, Maria Uriarte, Leandro Reverberi Tambosi, Amanda Prado, Renata Pardini, Paulo Sérgio D Andrea, Jean Paul Metzger
Hantavirus Pulmonary Syndrome (HPS) is a disease caused by Hantavirus, which are negative-sense RNA viruses in the family Bunyaviridae that are highly virulent to humans. Numerous factors modify risk of Hantavirus transmission and consequent HPS risk. Human-driven landscape change can foster transmission risk by increasing numbers of habitat generalist rodent species that serve as the principal reservoir host. Climate can also affect rodent population dynamics and Hantavirus survival, and a number of social factors can influence probability of HPS transmission to humans...
2016: PloS One
Luciano Rogério Braatz de Andrade, Roberto Fritsche Neto, Ítalo Stefanine Correia Granato, Gustavo César Sant'Ana, Pedro Patric Pinho Morais, Aluízio Borém
A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection...
2016: PloS One
Jing Jiang, You-Jin Zhao, Xin-Yu Hu, Ming-Ying Du, Zi-Qi Chen, Min Wu, Kai-Ming Li, Hong-Yan Zhu, Poornima Kumar, Qi-Yong Gong
BACKGROUND: Multiple meta-analyses of diffusion tensor imaging (DTI) studies have reported impaired white matter integrity in patients with major depressive disorder (MDD). However, owing to inclusion of medicated patients in these studies, it is difficult to conclude whether these reported alterations are associated with MDD or confounded by medication effects. A meta-analysis of DTI studies on medication-free (medication-naive and medication washout) patients with MDD would therefore be necessary to disentangle MDD-specific effects...
October 25, 2016: Journal of Psychiatry & Neuroscience: JPN
Alex I Wiesman, Elizabeth Heinrichs-Graham, Nathan M Coolidge, James E Gehringer, Max J Kurz, Tony W Wilson
Sensory gating (SG) is a phenomenon in which neuronal responses to subsequent similar stimuli are weaker, and is thought to be an important mechanism for preventing excessive environmental stimulation from overloading shared neural resources. Although gating has been demonstrated in multiple sensory systems, the neural dynamics and developmental trajectory underlying SG remain poorly understood. Herein, we adopt a data-driven approach to map the spectro-temporal amplitude and functional connectivity (FC) dynamics that support gating in the somatosensory system (somato-SG) in healthy children and adolescents using magnetoencephalography (MEG)...
October 25, 2016: Journal of Physiology
Shaobin Lin, Yi Zhou, Qun Fang, Jianzhu Wu, Zhiqiang Zhang, Yuanjun Ji, Yanmin Luo
The current study presents the cases of two unrelated patients with similar clinical features, including craniofacial anomalies, developmental delay/intellectual disability and cardiac malformations, that are consistent with chromosome 10q26 deletion syndrome. High‑resolution single‑nucleotide polymorphism analysis revealed that 10q26 terminal deletions were present in these two patients. The locations and sizes of the 10q26 deletions in these two patients were compared with the locations and sizes of 10q26 deletions in 30 patients recorded in the DECIPHER database and 18 patients characterized in previous studies through chromosomal microarray analysis...
October 19, 2016: Molecular Medicine Reports
Miguel Jesus Nunes Ramos, João Lucas Coito, Joana Fino, Jorge Cunha, Helena Silva, Patrícia Gomes de Almeida, Maria Manuela Ribeiro Costa, Sara Amâncio, Octávio S Paulo, Margarida Rocheta
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp...
October 24, 2016: Plant Molecular Biology
Alvin Z Yu, Stephen A Ramsey
We report an in silico method to screen for receptors or pathways that could be targeted to elicit beneficial transcriptional changes in a cellular model of a disease of interest. In our method, we integrate: (1) a dataset of transcriptome responses of a cell line to a panel of drugs; (2) two sets of genes for the disease; and (3) mappings between drugs and the receptors or pathways that they target. We carried out a gene set enrichment analysis (GSEA) test for each of the two gene sets against a list of genes ordered by fold-change in response to a drug in a relevant cell line (HL60), with the overall score for a drug being the difference of the two enrichment scores...
October 24, 2016: Interdisciplinary Sciences, Computational Life Sciences
P Goovaerts, Teresa Albuquerque, Margarida Antunes
This paper describes a multivariate geostatistical methodology to delineate areas of potential interest for future sedimentary gold exploration, with an application to an abandoned sedimentary gold mining region in Portugal. The main challenge was the existence of only a dozen gold measurements confined to the grounds of the old gold mines, which precluded the application of traditional interpolation techniques, such as cokriging. The analysis could, however, capitalize on 376 stream sediment samples that were analyzed for twenty two elements...
November 2016: Mathematical Geosciences
Santhilal Subhash, Per-Ola Andersson, Subazini Thankaswamy Kosalai, Chandrasekhar Kanduri, Meena Kanduri
BACKGROUND: Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status...
2016: Clinical Epigenetics
John D Hulleman, Joseph C Genereux, Annie Nguyen
Fibulin-3 (F3) is an important, disulfide-rich, extracellular matrix glycoprotein that has been associated with a number of diseases ranging from cancer to retinal degeneration. An Arg345Trp (R345W) mutation in F3 causes the rare, autosomal dominant macular dystrophy, Malattia Leventinese. The purpose of this study was to identify and validate novel intracellular interacting partners of wild-type (WT) and R345W F3 in retinal pigment epithelium cells. We used stable isotope labeling by amino acids in cell culture (SILAC) to generate 'heavy' and 'light' isotopically labeled ARPE-19 cell populations which were subsequently infected with adenovirus encoding for FLAG-tagged (FT) WT or R345W F3...
October 21, 2016: Experimental Eye Research
Erin L Rutherford, Laura Anne Lowery
Wolf-Hirschhorn syndrome (WHS) is a neurodevelopmental disorder characterized by mental retardation, craniofacial malformation, and defects in skeletal and heart development. The syndrome is associated with irregularities on the short arm of chromosome 4, including deletions of varying sizes and microduplications. Many of these genotypic aberrations in humans have been correlated with the classic WHS phenotype, and animal models have provided a context for mapping these genetic irregularities to specific phenotypes; however, there remains a significant knowledge gap concerning the cell biological mechanisms underlying these phenotypes...
October 21, 2016: Developmental Biology
Carola Vogel, Roman Rukwied, Lenka Stockinger, Marcus Schley, Martin Schmelz, Wolfgang Schleinzer, Christoph Konrad
: At-level and above-level hypersensitivity was assessed in patients with chronic complete thoracic spinal cord injury (SCI). Patients were classified by somatosensory mapping (brush, cold, pinprick) and assigned into two groups, i.e. patients i) with at-level hypersensitivity (SCIHs, n=8) and ii) without at-level hypersensitivity (SCINHs, n=7). Gender and age-matched healthy subjects served as controls. Quantitative sensory testing (QST), electrically- and histamine-induced pain and itch, laser Doppler imaging and laser-evoked potentials (LEP) were recorded at-level and above-level in SCI-patients...
October 21, 2016: Journal of Pain: Official Journal of the American Pain Society
Roberto Sanz-Requena, Luis Martí-Bonmatí, Rosario Pérez-Martínez, Gracián García-Martí
PURPOSE: The aim of this work is to establish normality and tumor tissue ranges for perfusion parameters from dynamic contrast-enhanced (DCE) MR of the peripheral prostate at 3T and to compare the diagnostic performance of quantitative and semi-quantitative parameters. MATERIALS AND METHODS: Thirty-six patients with prostate carcinomas (18 Gleason-6, 15 Gleason-7, and 3 Gleason-8) and 33 healthy subjects were included. Image analysis workflow comprised four steps: manual segmentation of whole prostate and lesions, series registration, voxelwise T1 mapping and calculation of pharmacokinetic and semi-quantitative parameters...
November 2016: European Journal of Radiology
Fakhriddin N Kushanov, Alan E Pepper, John Z Yu, Zabardast T Buriev, Shukhrat E Shermatov, Sukumar Saha, Mauricio Ulloa, Johnie N Jenkins, Abdusattor Abdukarimov, Ibrokhim Y Abdurakhmonov
BACKGROUND: Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs. RESULTS: Gossypium hirsutum and G...
October 24, 2016: BMC Genetics
Sushmita Das, Rakesh Mandal, Vidya Nand Rabidas, Neena Verma, Krishna Pandey, Ashok Kumar Ghosh, Sreekant Kesari, Ashish Kumar, Bidyut Purkait, Chandra Sekhar Lal, Pradeep Das
BACKGROUND: Visceral leishmaniasis (VL), with the squeal of Post-kala-azar dermal leishmaniasis (PKDL), is a global threat for health. Studies have shown sodium stibogluconate (SSG) resistance in VL patients with chronic arsenic exposure. Here, we assessed the association between arsenic exposure and risk of developing PKDL in treated VL patients. METHODS: In this retrospective study, PKDL patients (n = 139), earlier treated with SSG or any other drug during VL, were selected from the study cohort...
October 2016: PLoS Neglected Tropical Diseases
Elisabeth Salzer, Deniz Cagdas, Miroslav Hons, Emily M Mace, Wojciech Garncarz, Özlem Yüce Petronczki, René Platzer, Laurène Pfajfer, Ivan Bilic, Sol A Ban, Katharina L Willmann, Malini Mukherjee, Verena Supper, Hsiang Ting Hsu, Pinaki P Banerjee, Papiya Sinha, Fabienne McClanahan, Gerhard J Zlabinger, Winfried F Pickl, John G Gribben, Hannes Stockinger, Keiryn L Bennett, Johannes B Huppa, Loïc Dupré, Özden Sanal, Ulrich Jäger, Michael Sixt, Ilhan Tezcan, Jordan S Orange, Kaan Boztug
RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1...
October 24, 2016: Nature Immunology
Cristian Axenie, Christoph Richter, Jörg Conradt
Biological and technical systems operate in a rich multimodal environment. Due to the diversity of incoming sensory streams a system perceives and the variety of motor capabilities a system exhibits there is no single representation and no singular unambiguous interpretation of such a complex scene. In this work we propose a novel sensory processing architecture, inspired by the distributed macro-architecture of the mammalian cortex. The underlying computation is performed by a network of computational maps, each representing a different sensory quantity...
October 20, 2016: Sensors
Jean-Louis Vincent, Marc Leone
Distributive shock is associated with decreased systemic vascular resistance and altered oxygen extraction. Septic shock is the most frequent form of distributive shock. In shock states, duration of hypotension is associated with poor outcomes. The speed at which treatment to restore adequate perfusion pressure is initiated is, therefore, important to improve survival. Areas covered: This review presents an overview of the literature related to the management of vasopressor-dependent distributive shock, and in particular the relationship between arterial pressure and organ perfusion and function...
October 24, 2016: Expert Review of Anti-infective Therapy
Orso Pusterla, Grzegorz Bauman, Mark O Wielpütz, Sylvia Nyilas, Philipp Latzin, Claus P Heussel, Oliver Bieri
PURPOSE: To introduce a reproducible, nonenhanced 1H MRI method for rapid in vivo functional assessment of the whole lung at 1.5 Tesla (T). METHODS: At different respiratory volumes, the pulmonary signal of ultra-fast steady-state free precession (ufSSFP) follows an adapted sponge model, characterized by a respiratory index α. From the model, α reflects local ventilation-related information, is virtually independent from the lung density and thus from the inspiratory phase and breathing amplitude...
October 23, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Stephanie A Korenic, Sarah J Nisonger, Benjamin W Krause, S Andrea Wijtenburg, L Elliot Hong, Laura M Rowland
Fast mapping (FM), a process that promotes the expeditious incidental learning of information, is thought to support rapid vocabulary acquisition in young children through extra-medial temporal lobe (MTL) regions. A recent study suggested that patients with MTL damage resulting in profound amnesia were able to learn novel word-image associations using an FM paradigm. The present study investigated whether FM would be an effective strategy to promote learning for individuals with schizophrenia, a severe mental illness associated with compromised MTL functionality...
June 2016: Schizophrenia Research. Cognition
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