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https://www.readbyqxmd.com/read/28097074/resources-available-for-autism-research-in-the-big-data-era-a-systematic-review
#1
Reem Al-Jawahiri, Elizabeth Milne
Recently, there has been a move encouraged by many stakeholders towards generating big, open data in many areas of research. One area where big, open data is particularly valuable is in research relating to complex heterogeneous disorders such as Autism Spectrum Disorder (ASD). The inconsistencies of findings and the great heterogeneity of ASD necessitate the use of big and open data to tackle important challenges such as understanding and defining the heterogeneity and potential subtypes of ASD. To this end, a number of initiatives have been established that aim to develop big and/or open data resources for autism research...
2017: PeerJ
https://www.readbyqxmd.com/read/28080144/a-survey-of-the-current-situation-of-clinical-biobanks-in-china
#2
Haiyan Li, Mingyu Ni, Peng Wang, Xiaomin Wang
The development of biomedical research urgently needs the support of a large number of high-quality clinical biospecimens. Therefore, human biobanks at different levels have been established successively in China and other countries at a significantly increasing pace in recent years. To better understand the general current state of clinical biobanks in China, we surveyed 42 clinical biobanks based in hospitals and collected information involving their management systems, sharing mechanisms, quality control systems, and informational management systems using closed questionnaire methods...
January 12, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28075485/culturing-and-neuronal-differentiation-of-human-dental-pulp-stem-cells
#3
Sarita Goorha, Lawrence T Reiter
A major issue in studying human neurogenetic disorders, especially rare syndromes affecting the nervous system, is the ability to grow neuronal cultures that accurately represent these disorders for analysis. Although there has been some success in generating induced pluripotent stem (iPS) cells from both skin and blood, there are still limitations to the collection and production of iPS cells from these biospecimens. We have had significant success in collecting and growing human dental pulp stem (DPS) cells from exfoliated teeth sent to our laboratory by the parents of children with a variety of rare neurogenetic syndromes...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28072433/effects-of-superparamagnetic-nanoparticles-on-nucleation-and-crystal-growth-in-the-vitrified-vs55-during-warming
#4
Y Xu, H M Yu, Y Q Niu, S C Luo, X Cheng
:   BACKGROUND:Magnetic nanoparticles (mNPs), once excited by radiofrequency (RF) energy, could heat uniformly and rapidly the vitrified biospecimens. However, there are few studies about the impact of mNPs on crystallization kinetics of vitrified samples. OBJECTIVES: The present work aims to investigate the nucleation and crystal growth in the vitrification solution VS55 with mNPs. MATERIALS AND METHODS: Ferrotec EMG308 superparamagnetic nanoparticles (10 ± 2...
November 2016: Cryo Letters
https://www.readbyqxmd.com/read/28070115/proposal-for-a-prospective-registry-for-moyamoya-disease-in-japan
#5
Ken Kazumata, Masaki Ito, Haruto Uchino, Hiroshi Nishihara, Kiyohiro Houkin
The number of clinical research papers published worldwide on moyamoya disease (MMD) has increased recently. However, the majority of the literature comprises retrospective single-center studies collecting data on small numbers of patients. Several multi-center studies are ongoing in Japan; however, the current data are insufficient for comprehensively outlining the various characteristics of MMD. To enhance our knowledge on epidemiologic, vascular, and genetic aspects of MMD, a prospective multicenter registry will be established in Japan that will help to streamline clinical research as well as improve clinical treatments and long-term outcomes...
January 6, 2017: Neurologia Medico-chirurgica
https://www.readbyqxmd.com/read/28067089/metabolomic-applications-in-radiation-biodosimetry-exploring-radiation-effects-through-small-molecules
#6
Evan L Pannkuk, Albert J Fornace, Evagelia C Laiakis
PURPOSE: Exposure of the general population to ionizing radiation has increased in the past decades, primarily due to long distance travel and medical procedures. On the other hand, accidental exposures, nuclear accidents, and elevated threats of terrorism with the potential detonation of a radiological dispersal device or improvised nuclear device in a major city, all have led to increased needs for rapid biodosimetry and assessment of exposure to different radiation qualities and scenarios...
January 9, 2017: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/28060806/high-throughput-sequencing-of-extracellular-rna-from-human-plasma
#7
Kirsty M Danielson, Renee Rubio, Fieda Abderazzaq, Saumya Das, Yaoyu E Wang
The presence and relative stability of extracellular RNAs (exRNAs) in biofluids has led to an emerging recognition of their promise as 'liquid biopsies' for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs) using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids...
2017: PloS One
https://www.readbyqxmd.com/read/28053876/rna-sequencing-of-archived-neonatal-dried-blood-spots
#8
Jonas Bybjerg-Grauholm, Christian Munch Hagen, Sok Kean Khoo, Maria Louise Johannesen, Christine Søholm Hansen, Marie Bækvad-Hansen, Michael Christiansen, David Michael Hougaard, Mads V Hollegaard
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of metabolism, hypothyroidism and other diseases. In Denmark, the Guthrie cards are stored at - 20 °C in the Danish Neonatal Screening Biobank and each sample is linked to elaborate social and medical registries. This provides a unique biospecimen repository to enable large population research at a perinatal level. Here, we demonstrate the feasibility to obtain gene expression data from DBS using next-generation RNA sequencing (RNA-seq)...
March 2017: Molecular Genetics and Metabolism Reports
https://www.readbyqxmd.com/read/28052061/integrated-genomic-characterization-of-oesophageal-carcinoma
#9
(no author information available yet)
Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas...
January 4, 2017: Nature
https://www.readbyqxmd.com/read/28050886/evaluation-of-cortisol-and-telomere-length-measurements-in-ethnically-diverse-women-with-breast-cancer-using-culturally-sensitive-methods
#10
Julio Ramirez, May Elmofty, Esperanza Castillo, Mindy DeRouen, Salma Shariff-Marco, Laura Allen, Scarlett Lin Gomez, Anna María Nápoles, Leticia Márquez-Magaña
The under-representation of ethnic minority participants, who are more likely to be socially disadvantaged in biomedical research, limits generalizability of results and reductions in health disparities. To facilitate investigations of how social disadvantage "gets under the skin," this pilot study evaluated low-intensity methods for collecting hair and saliva samples from multiethnic breast cancer survivors (N = 70) and analysis of biomarkers of chronic stress (cortisol levels) and biological age (telomere length)...
January 3, 2017: Journal of Community Genetics
https://www.readbyqxmd.com/read/28049410/tcga2bed-extracting-extending-integrating-and-querying-the-cancer-genome-atlas
#11
Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, Emanuel Weitschek
BACKGROUND: Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. RESULTS: We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28040692/prognostic-value-of-braf%C3%A2-and%C3%A2-kras%C3%A2-mutations-in-msi-and-mss-stage-iii-colon-cancer
#12
Julien Taieb, Karine Le Malicot, Qian Shi, Frédérique Penault Lorca, Olivier Bouché, Josep Tabernero, Enrico Mini, Richard M Goldberg, Gunnar Folprecht, Jean Luc Van Laethem, Daniel J Sargent, Steven R Alberts, Jean Francois Emile, Pierre Laurent Puig, Frank A Sinicrope
BACKGROUND: The prognostic value of BRAF and KRAS mutations within microsatellite-unstable (MSI) and microsatellite-stable (MSS) subgroups of resected colon carcinoma patients remains controversial. We examined this question in prospectively collected biospecimens from stage III colon cancer with separate analysis of MSI and MSS tumors from patients receiving adjuvant FOLFOX +/- cetuximab in two adjuvant therapy trials. METHODS: Three groups were defined: BRAF Mutant, KRAS Mutant, and double wild-type...
May 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28036235/biomarkers-for-uranium-risk-assessment-for-the-development-of-the-cure-concerted-uranium-research-in-europe-molecular-epidemiological-protocol
#13
Yann Guéguen, Laurence Roy, Sabine Hornhardt, Christophe Badie, Janet Hall, Sarah Baatout, Eileen Pernot, Ladislav Tomasek, Olivier Laurent, Teni Ebrahimian, Chrystelle Ibanez, Stephane Grison, Sylwia Kabacik, Dominique Laurier, Maria Gomolka
Despite substantial experimental and epidemiological research, there is limited knowledge of the uranium-induce health effects after chronic low-dose exposures in humans. Biological markers can objectively characterize pathological processes or environmental responses to uranium and confounding agents. The integration of such biological markers into a molecular epidemiological study would be a useful approach to improve and refine estimations of uranium-induced health risks. To initiate such a study, Concerted Uranium Research in Europe (CURE) was established, and involves biologists, epidemiologists and dosimetrists...
December 30, 2016: Radiation Research
https://www.readbyqxmd.com/read/28003258/the-ark-a-customizable-web-based-data-management-tool-for-health-and-medical-research
#14
Adrian Bickerstaffe, Thilina Ranaweera, Travis Endersby, Christopher Ellis, Sanjaya Maddumarachchi, George E Gooden, Paul White, Eric K Moses, Alex W Hewitt, John L Hopper
: The Ark is an open-source web-based tool that allows researchers to manage health and medical research data for humans and animals without specialized database skills or programming expertise. The system provides data management for core research information including demographic, phenotype, biospecimen and pedigree data, in addition to supporting typical investigator requirements such as tracking participant consent and correspondence, whilst also being able to generate custom data exports and reports...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27988499/the-effect-of-storage-temperature-fluctuations-on-the-stability-of-biochemical-analytes-in-blood-serum
#15
Helmuth Haslacher, Thomas Szekeres, Marlene Gerner, Elisabeth Ponweiser, Manuela Repl, Oswald F Wagner, Thomas Perkmann
BACKGROUND: Irreproducibility of scientific results constitutes an undesirably onerous economic burden and is in many cases caused by low-quality materials. Therefore, researchers are increasingly devoting their attention to the bioresources they use. In turn, those bioresources are required to validate their preanalytical processes in order to ensure best possible quality. The present study thus aimed to evaluate the impact of repeated temperature fluctuations, as they occur in most research biobanks due to repetitive opening and closing of freezer doors, on the stability of 26 biochemical analytes...
December 19, 2016: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/27929677/assessing-researcher-needs-for-a-virtual-biobank
#16
Jenna van Draanen, Pamela Davidson, Helene Bour-Jordan, LeeAnna Bowman-Carpio, David Boyle, Steve Dubinett, Brian Gardner, Jachael Gardner, Courtney McFall, Dan Mercola, Terry Nakazono, Stephanie Soares, Hubert Stoppler, Margaret Tempero, Scott Vandenberg, Yu-Jui Yvonne Wan, Sarah Dry
INTRODUCTION: Biosamples and associated clinical data accelerate translational and clinical research discoveries. A lack of high quality biosamples both stalls projects and limits research advances. In this study, we targeted a wide audience of University of California (UC) biobanking stakeholders who were either involved with the collection or the utilization of biosamples to assess the scope of their biobanking activities and their interest in virtual biobanking or cooperating in the formation of the UC-wide biorepository...
December 8, 2016: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/27929525/the-precision-medicine-initiative-s-all-of-us-research-program-an-agenda-for-research-on-its-ethical-legal-and-social-issues
#17
REVIEW
Pamela L Sankar, Lisa S Parker
The Precision Medicine Initiative (PMI) is an innovative approach to developing a new model of health care that takes into account individual differences in people's genes, environments, and lifestyles. A cornerstone of the initiative is the PMI All of Us Research Program (formerly known as PMI-Cohort Program) which will create a cohort of 1 million volunteers who will contribute their health data and biospecimens to a centralized national database to support precision medicine research. The PMI All of US Research Program is the largest longitudinal study in the history of the United States...
December 8, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27926908/community-perceptions-of-biobanking-participation-a-qualitative-study-among-mexican-americans-in-three-texas-cities
#18
Natalia I Heredia, Sarah Krasny, Larkin L Strong, Laura Von Hatten, Lynne Nguyen, Belinda M Reininger, Lorna H McNeill, María E Fernández
BACKGROUND: Most biospecimens in the US are collected from non-Hispanic Whites, limiting the generalizability of findings. There is a need to increase participation in biobanking among ethnic and racial minorities. The purpose of this study was to use qualitative methods to identify factors that may influence Mexican-American individuals' willingness to participate in biobanking. METHODS: We conducted 15 focus groups in three Texas cities with Mexican-American individuals, in both Spanish and English...
December 8, 2016: Public Health Genomics
https://www.readbyqxmd.com/read/27925796/a-severe-asthma-disease-signature-from-gene-expression-profiling-of-peripheral-blood-from-u-biopred-cohorts
#19
Jeannette Bigler, Michael Boedigheimer, James P R Schofield, Paul J Skipp, Julie Corfield, Anthony Rowe, Ana R Sousa, Martin Timour, Lori Twehues, Xuguang Hu, Graham Roberts, Andrew A Welcher, Wen Yu, Kian F Chung, Ian M Adcock, Peter J Sterk, Ratko Djukanović
RATIONALE: Stratification of asthma at the molecular level, especially using accessible biospecimens, could greatly enable patient selection for targeted therapy. OBJECTIVES: To determine the value of blood to identify transcriptional differences between clinically defined asthmatic and non-asthmatic groups, identify potential patient subgroups based on gene expression, and explore biological pathways associated with identified differences. METHODS: Transcriptomics profiles were generated by microarray analysis of blood from 610 asthmatic and control participants in U-BIOPRED...
December 7, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27924041/exposome-explorer-a-manually-curated-database-on-biomarkers-of-exposure-to-dietary-and-environmental-factors
#20
Vanessa Neveu, Alice Moussy, Héloïse Rouaix, Roland Wedekind, Allison Pon, Craig Knox, David S Wishart, Augustin Scalbert
Exposome-Explorer (http://exposome-explorer.iarc.fr) is the first database dedicated to biomarkers of exposure to environmental risk factors. It contains detailed information on the nature of biomarkers, their concentrations in various human biospecimens, the study population where measured and the analytical techniques used for measurement. It also contains correlations with external exposure measurements and data on biological reproducibility over time. The data in Exposome-Explorer was manually collected from peer-reviewed publications and organized to make it easily accessible through a web interface for in-depth analyses...
January 4, 2017: Nucleic Acids Research
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