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https://www.readbyqxmd.com/read/29156419/segmentation-of-the-hippocampus-by-transferring-algorithmic-knowledge-for-large-cohort-processing
#1
Benjamin Thyreau, Kazunori Sato, Hiroshi Fukuda, Yasuyuki Taki
The hippocampus is a particularly interesting target for neuroscience research studies due to its essential role within the human brain. In large human cohort studies, bilateral hippocampal structures are frequently identified and measured to gain insight into human behaviour or genomic variability in neuropsychiatric disorders of interest. Automatic segmentation is performed using various algorithms, with FreeSurfer being a popular option. In this manuscript, we present a method to segment the bilateral hippocampus using a deep-learned appearance model...
November 10, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/29155814/optimal-synaptic-signaling-connectome-for-locomotory-behavior-in-caenorhabditis-elegans-design-minimizing-energy-cost
#2
Franciszek Rakowski, Jan Karbowski
The detailed knowledge of C. elegans connectome for 3 decades has not contributed dramatically to our understanding of worm's behavior. One of main reasons for this situation has been the lack of data on the type of synaptic signaling between particular neurons in the worm's connectome. The aim of this study was to determine synaptic polarities for each connection in a small pre-motor circuit controlling locomotion. Even in this compact network of just 7 neurons the space of all possible patterns of connection types (excitation vs...
November 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29155671/capacity-development-through-the-us-president-s-malaria-initiative-supported-antimalarial-resistance-monitoring-in-africa-network
#3
Eric S Halsey, Meera Venkatesan, Mateusz M Plucinski, Eldin Talundzic, Naomi W Lucchi, Zhiyong Zhou, Celine I Mandara, Hawela Moonga, Busiku Hamainza, Abdoul Habib Beavogui, Simon Kariuki, Aaron M Samuels, Laura C Steinhardt, Don P Mathanga, Julie Gutman, Yves Eric Denon, Aline Uwimana, Ashenafi Assefa, Jimee Hwang, Ya Ping Shi, Pedro Rafael Dimbu, Ousmane Koita, Deus S Ishengoma, Daouda Ndiaye, Venkatachalam Udhayakumar
Antimalarial drug resistance is an evolving global health security threat to malaria control. Early detection of Plasmodium falciparum resistance through therapeutic efficacy studies and associated genetic analyses may facilitate timely implementation of intervention strategies. The US President's Malaria Initiative-supported Antimalarial Resistance Monitoring in Africa Network has assisted numerous laboratories in partner countries in acquiring the knowledge and capability to independently monitor for molecular markers of antimalarial drug resistance...
December 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29154799/integrative-omics-data-analyses-of-repeated-dose-toxicity-of-valproic-acid-in-vitro-reveal-new-mechanisms-of-steatosis-induction
#4
Simone G J van Breda, Sandra M H Claessen, Marcel van Herwijnen, Daniël H J Theunissen, Danyel G J Jennen, Theo M C M de Kok, Jos C S Kleinjans
Valproic acid (VPA) is a very potent anti-cancer and neuro-protective drug probably by its HCAC inhibiting properties, which may cause steatosis in the liver. The present study investigates the effect of repetitive VPA treatment of primary human hepatocytes (PHH) on whole genome gene expression-, DNA methylation-, and miRNA changes, using microarrays and integrated data analyses. PHH were exposed to a non-cytotoxic dose of VPA for 5days daily which induced lipid accumulation. Part of the PHH was left untreated for 3days for studying the persistence of 'omics' changes...
November 14, 2017: Toxicology
https://www.readbyqxmd.com/read/29154129/collective-behavior-of-place-and-non-place-neurons-in-the-hippocampal-network
#5
Leenoy Meshulam, Jeffrey L Gauthier, Carlos D Brody, David W Tank, William Bialek
Discussions of the hippocampus often focus on place cells, but many neurons are not place cells in any given environment. Here we describe the collective activity in such mixed populations, treating place and non-place cells on the same footing. We start with optical imaging experiments on CA1 in mice as they run along a virtual linear track and use maximum entropy methods to approximate the distribution of patterns of activity in the population, matching the correlations between pairs of cells but otherwise assuming as little structure as possible...
November 15, 2017: Neuron
https://www.readbyqxmd.com/read/29153892/penalized-estimation-of-sparse-concentration-matrices-based-on-prior-knowledge-with-applications-to-placenta-elemental-data
#6
Jai Woo Lee, Tracy Punshon, Erika L Moen, Margaret R Karagas, Jiang Gui
Identifying patterns of association or dependency among high-dimensional biological datasets with sparse precision matrices remains a challenge. In this paper, we introduce a weighted sparse Gaussian graphical model that can incorporate prior knowledge to infer the structure of the network of trace element concentrations, including essential elements as well as toxic metals and metaloids measured in the human placentas. We present the weighted L1 penalized regularization procedure for estimating the sparse precision matrix in the setting of Gaussian graphical models...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153709/cytokines-in-the-pathogenesis-of-hemophilic-arthropathy
#7
REVIEW
Piotr Wojdasiewicz, Łukasz A Poniatowski, Paweł Nauman, Tomasz Mandat, Agnieszka Paradowska-Gorycka, Katarzyna Romanowska-Próchnicka, Dariusz Szukiewicz, Andrzej Kotela, Łukasz Kubaszewski, Ireneusz Kotela, Iwona Kurkowska-Jastrzębska, Robert Gasik
Hemophilic arthropathy (HA) is one of the most common and typical manifestation in the course of recurrent bleeding episodes in patients with hemophilia. Clinical and subclinical joint bleeding episodes gradually lead to irreversible changes manifesting themselves as pain, progressing ankylosis, marked limitation of the range of motion, muscle atrophy and osteoporosis commonly concomitant with joint deformity resulting from chronic proliferative synovitis and both cartilage and bone degeneration leading to the final functional impairment of the joint...
November 13, 2017: Cytokine & Growth Factor Reviews
https://www.readbyqxmd.com/read/29151801/formal-and-informal-concrete-support-and-discharge-disposition-among-women-in-substance-abuse-treatment-in-the-u-s
#8
MinKyoung Jun, Elizabeth M Tracy, Meeyoung O Min
The purpose of this study is to examine the relative contribution and the relationships between formal (treatment related members) • informal (family members) concrete support and discharge disposition. A total of 172 women interviewed upon intake in one of 3 counties funded substance abuse treatment programs in Cleveland, Ohio. Hierarchical logistic regression was performed to assess the impact of formal concrete support and informal concrete support on the likelihood of a discharge disposition of completed treatment...
2017: Chongsin Pogon Kwa Sahoe Saop
https://www.readbyqxmd.com/read/29150917/regulation-of-mesenchymal-stem-cell-differentiation-by-transforming-growth-factor-beta-superfamily
#9
Jelena Krstic, Drenka Trivanovic, Hristina Obradovic, Tamara Kukolj, Diana Bugarski, Juan F Santibanez
The ability to differentiate into cells of different lineage, such as muscle, bone, cartilage and fat, is the chief value of adult mesenchymal stem cells (MSCs) which can be used with the final aim to regenerate damaged tissue. Due to potential use, as well as importance in tissue development, a number of questions have been raised regarding the molecular mechanisms of MSC differentiation. As one of the crucial mediators in organism development, transforming growth factor beta (TGF-β) superfamily directs MSCs commitment in the selection of differentiation pathways...
November 16, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/29150417/using-facebook-to-recruit-young-australian-men-into-a-cross-sectional-human-papillomavirus-study
#10
Roopa Das, Dorothy A Machalek, Edmund G Molesworth, Suzanne M Garland
BACKGROUND: Young men can be difficult to engage in health research using traditional methods of recruitment. Social networking sites are increasingly being used to recruit participants into health research, due to their cost effectiveness, overall generalizability, and wide reach. OBJECTIVE: The aim of this study was to determine the feasibility of using Facebook to recruit young Australian men into a human papillomavirus (HPV) prevalence study. METHODS: We recruited male permanent residents of Australia, aged 18 to 35 years, into the HPV in Young Males (HYM) study through targeted advertising placed on Facebook...
November 17, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/29149918/oxygen-transfer-in-moving-bed-biofilm-reactor-and-integrated-fixed-film-activated-sludge-processes
#11
(no author information available yet)
A demonstrated approach to design the, so-called, medium-bubble air diffusion network for oxygen transfer into the aerobic zone(s) of moving bed biofilm reactor (MBBR) and integrated fixed-film activated sludge (IFAS) processes is described in this paper. Operational full-scale biological water resource recovery systems treating municipal sewerage demonstrate that medium-bubble air diffusion networks designed using the method presented here provide reliable service. Further improvement is possible, however, as knowledge gaps prevent more rational process designs...
November 17, 2017: Water Environment Research: a Research Publication of the Water Environment Federation
https://www.readbyqxmd.com/read/29149859/medicinal-plants-used-by-women-in-mecca-urban-muslim-and-gendered-knowledge
#12
Afnan Alqethami, Julie A Hawkins, Irene Teixidor-Toneu
BACKGROUND: This study explores medicinal plant knowledge and use among Muslim women in the city of Mecca, Saudi Arabia. Ethnobotanical research in the region has focused on rural populations and male herbal healers in cities, and based on these few studies, it is suggested that medicinal plant knowledge may be eroding. Here, we document lay, female knowledge of medicinal plants in an urban centre, interpreting findings in the light of the growing field of urban ethnobotany and gendered knowledge and in an Islamic context...
November 17, 2017: Journal of Ethnobiology and Ethnomedicine
https://www.readbyqxmd.com/read/29149405/current-understanding-of-the-tctp-interactome
#13
Siting Li, Feng Ge
Evolutionarily conserved and pleiotropic, the translationally controlled tumor protein (TCTP) is a housekeeping protein present in eukaryotic organisms. It plays an important role in regulating many fundamental processes, such as cell proliferation, cell death, immune responses, and apoptosis. As a result of the pioneer work by Adam Telerman and Robert Amson, the critical role of TCTP in tumor reversion was revealed. Moreover, TCTP has emerged as a regulator of cell fate determination and a promising therapeutic target for cancers...
2017: Results and Problems in Cell Differentiation
https://www.readbyqxmd.com/read/29149350/a-data-fusion-pipeline-for-generating-and-enriching-adverse-outcome-pathway-descriptions
#14
Penny Nymark, Linda Rieswijk, Friederike Ehrhart, Nina Jeliazkova, Georgia Tsiliki, Haralambos Sarimveis, Chris T Evelo, Vesa Hongisto, Pekka Kohonen, Egon Willighagen, Roland C Grafström
Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven and informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development of non-animal based hazard and risk assessment methods. We devised a six-step workflow that integrated diverse types of toxicology data into a novel AOP scheme for pulmonary fibrosis. Mining of literature references and diverse data sources covering previous pathway descriptions and molecular results were coupled in a stepwise manner with informatics tools applications that enabled gene linkage and pathway identification in molecular interaction maps...
November 15, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29148114/on-the-character-and-production-of-active-participation-in-neuro-rehabilitation-an-actor-network-perspective
#15
Simon Horton, Kathryn Mares, Neil Coull, Fiona Poland
The importance of patients' active involvement in neuro-rehabilitation after acquired brain injury has been consistently emphasised in recent years. However, most approaches fail to show how 'active participation' is practically enacted, focusing on individualised explanations of patient choice and behaviours, or notions of inherent patient traits. Using actor-network theory (ANT) as a sensitising concept, we investigated neuro-rehabilitation practices, asking how participation is shaped through biological and socio-material specificities, how rights to knowledge and expertise are constructed, and how a body acclimatises and adjusts within an order of participation and transformation...
November 2017: Sociology of Health & Illness
https://www.readbyqxmd.com/read/29147648/molecular-crosstalking-among-noncoding-rnas-a-new-network-layer-of-genome-regulation-in-cancer
#16
REVIEW
Marco Ragusa, Cristina Barbagallo, Duilia Brex, Angela Caponnetto, Matilde Cirnigliaro, Rosalia Battaglia, Davide Barbagallo, Cinzia Di Pietro, Michele Purrello
Over the past few years, noncoding RNAs (ncRNAs) have been extensively studied because of the significant biological roles that they play in regulation of cellular mechanisms. ncRNAs are associated to higher eukaryotes complexity; accordingly, their dysfunction results in pathological phenotypes, including cancer. To date, most research efforts have been mainly focused on how ncRNAs could modulate the expression of protein-coding genes in pathological phenotypes. However, recent evidence has shown the existence of an unexpected interplay among ncRNAs that strongly influences cancer development and progression...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29147122/use-of-lipid-lowering-medicinal-herbs-during-pregnancy-a-systematic-review-on-safety-and-dosage
#17
REVIEW
Hojjat Rouhi-Boroujeni, Esfandiar Heidarian, Hamid Rouhi-Boroujeni, Minasadat Khoddami, Mojgan Gharipour, Mahmoud Rafieian-Kopaei
BACKGROUND: Hyperlipidemia is one of the important diseases in pregnancy that causes fetal abnormalities during pregnancy and after the birth. Unfortunately, the usual anti-fat drugs are associated with high morbidity in fetus and due to people's inclination towards taking herbs, it is required to identify side effects of medicinal herbs in pregnancy. The aim of this study was to present hypolipidemic herbs that would not any complications for mother and fetus. METHODS: In this review article, the major electronic databases such as EBSCO, Central Register of Controlled Trials (CENTRAL), China Network Knowledge Infrastructure (CNKI), Cochrane, Google scholar, MEDLINE, SciVerse, Scopus, and Web of Science were searched using the key words "herbal" and "hyperlipidemia", "herbal" and "pregnancy" matched by MeSH from their respective inceptions till September, 2016...
May 2017: ARYA Atherosclerosis
https://www.readbyqxmd.com/read/29146547/a-gene-module-associated-with-dysregulated-tcr-signaling-pathways-in-cd4-t-cell-subsets-in-rheumatoid-arthritis
#18
Shuji Sumitomo, Yasuo Nagafuchi, Yumi Tsuchida, Haruka Tsuchiya, Mineto Ota, Kazuyoshi Ishigaki, Shinichiro Nakachi, Rika Kato, Keiichi Sakurai, Norio Hanata, Shoko Tateishi, Hiroko Kanda, Akari Suzuki, Yuta Kochi, Keishi Fujio, Kazuhiko Yamamoto
We analyzed the transcriptome of detailed CD4(+) T cell subsets including them after abatacept treatment, and examined the difference among CD4(+) T cell subsets and identified gene sets that are closely associated disease activity and abatacept treatment. Seven CD4(+) T cell subsets (naive, Th1, Th17, Th1/17, nonTh1/17, Tfh and Treg) were sorted from PBMCs taken from 10 RA patients and 10 healthy controls, and three RA patients donated samples before and 6 months after abatacept treatment. Paired-end RNA sequencing was performed using HiSeq 2500...
November 13, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29146076/short-term-effects-of-prescribed-burning-on-litterfall-biomass-in-mixed-stands-of-pinus-nigra-and-pinus-pinaster-and-pure-stands-of-pinus-nigra-in-the-cuenca-mountains-central-eastern-spain
#19
J Espinosa, J Madrigal, A C De La Cruz, M Guijarro, E Jimenez, C Hernando
Fire severity, defined as the magnitude of fire effects in an ecosystem, is a key factor to consider in planning management strategies for protecting forests against fire. Although prescribed burning has been used as a fuel reduction tool in forest ecosystems, it is quite limited in the Mediterranean region. Furthermore, little is known about how tree crowns are affected by prescribed underburning aimed at reducing fire severity in conifer stands. As part of an ongoing study to assess the effects of prescribed burning on the tree canopy, litterfall is currently being monitored in a network of experimental plots located in mixed (Pinus nigra and Pinus pinaster) and pure (P...
November 13, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29145615/iptmnet-an-integrated-resource-for-protein-post-translational-modification-network-discovery
#20
Hongzhan Huang, Cecilia N Arighi, Karen E Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K Vijay-Shanker, Cathy H Wu
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species...
November 14, 2017: Nucleic Acids Research
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