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https://www.readbyqxmd.com/read/28092796/global-open-data-management-in-metabolomics
#1
REVIEW
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28092721/use-of-maldi-tof-mass-spectrometry-in-the-battle-against-bacterial-infectious-diseases-recent-achievements-and-future-perspectives
#2
Vassilios Sandalakis, Ioannis Goniotakis, Iosif Vranakis, Dimosthenis Chochlakis, Anna Psaroulaki
Advancements in microbial identification occur increasingly faster as more laboratories explore, refine and extend the use of mass spectrometry in the field of microbiology. Areas covered: This review covers the latest knowledge found in the literature for quick identification of various classes of bacterial pathogens known to cause human infection by the use of MALDI-TOF MS technology. Except for identification of bacterial strains, more researchers try to "battle time" in favor of the patient. These novel approaches to identify bacteria directly from clinical samples and even determine antibiotic resistance are extensively revised and discussed...
January 16, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28092680/utilizing-somatic-mutation-data-from-numerous-studies-for-cancer-research-proof-of-concept-and-applications
#3
D Amar, S Izraeli, R Shamir
Large cancer projects measure somatic mutations in thousands of samples, gradually assembling a catalog of recurring mutations in cancer. Many methods analyze these data jointly with auxiliary information with the aim of identifying subtype-specific results. Here, we show that somatic gene mutations alone can reliably and specifically predict cancer subtypes. Interpretation of the classifiers provides useful insights for several biomedical applications. We analyze the COSMIC database, which collects somatic mutations from The Cancer Genome Atlas (TCGA) as well as from many smaller scale studies...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28092663/neural-regulation-of-immunity-molecular-mechanisms-and-clinical-translation
#4
REVIEW
Valentin A Pavlov, Kevin J Tracey
Studies bridging neuroscience and immunology have identified neural pathways that regulate immunity and inflammation. Recent research using methodological advances in molecular genetics has improved our understanding of the neural control of immunity. Here we outline mechanistic insights, focusing on translational relevance and conceptual developments. We also summarize findings from recent clinical studies of bioelectronic neuromodulation in inflammatory and autoimmune diseases.
January 16, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28092620/correlation-between-peripheral-blood-cell-transcriptomic-profile-and-clinical-parameters-of-chronic-mitral-valve-disease-in-dachshunds
#5
M Garncarz, M Hulanicka, H Maciejewski, M Parzeniecka-Jaworska, M Jank
Studies identifying specific pathologically expressed genes have been performed on diseased myocardial tissue samples, however less invasive studies on gene expression of peripheral blood mononucleated cells give promising results. This study assessed transcriptomic data that may be used to evaluate Dachshunds with chronic mitral valve disease. Dachshunds with different stages of heart disease were compared to a control, healthy group. Microarray data analysis revealed clusters of patients with similar expression profiles...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28092569/discovery-of-micrornas-and-transcription-factors-co-regulatory-modules-by-integrating-multiple-types-of-genomic-data
#6
Jiawei Luo, Gen Xiang, Chu Pan
It is well known that regulators known as microRNA (miRNA) and transcription factor (TF) have been found to play an important role in gene regulation. However, there are few researches of collaborative regulatory (co-regulatory) mechanism between miRNA and TF on system level (function level). Meanwhile, recent advances in high-throughput genomic technologies have enabled researchers to collect diverse large-scale genomic data, which can be used to study the co-regulatory mechanism between miRNA and TF. In this paper, we propose a novel method called SNCoNMF (Sparse Network regularized non-negative matrix factorization for Co-regulatory modules identification) which adopts multiple non-negative matrix factorization framework to identify co-regulatory modules including miRNAs, TFs and genes...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#7
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28092290/clinical-recommendations-of-cardiac-magnetic-resonance-part-ii-inflammatory-and-congenital-heart-disease-cardiomyopathies-and-cardiac-tumors-a-position-paper-of-the-working-group-applicazioni-della-risonanza-magnetica-of-the-italian-society-of-cardiology
#8
Gianluca Pontone, Gianluca Di Bella, Castelletti Silvia, Viviana Maestrini, Pierluigi Festa, Lamia Ait-Ali, Pier Giorgio Masci, Lorenzo Monti, Gabriella di Giovine, Manuel De Lazzari, Alberto Cipriani, Andrea I Guaricci, Santo Dellegrottaglie, Alessia Pepe, Martina Perazzolo Marra, Giovanni Donato Aquaro
The current document was developed by the working group on the 'application of cardiac magnetic resonance' of the Italian Society of Cardiology to provide a perspective on the current state of technical advances and clinical cardiac magnetic resonance applications and to inform cardiologists how to implement their clinical and diagnostic pathway with the introduction of this technique in the clinical practice. Appropriateness criteria were defined using a score system: score 1-3 = inappropriate (test is not generally acceptable and is not a reasonable approach for the indication), score 4-6 = uncertain (test may be generally acceptable and may be a reasonable approach for the indication but more research and/or patient information is needed to classify the indication definitively) and score 7-9 = appropriate (test is generally acceptable and is a reasonable approach for the indication)...
January 13, 2017: Journal of Cardiovascular Medicine
https://www.readbyqxmd.com/read/28092280/challenges-and-opportunities-to-enhance-global-drug-development-in-neonates
#9
Alexandra M Smith, Jonathan M Davis
PURPOSE OF REVIEW: This study reviews the history of neonatal drug development, recent legislative efforts designed to facilitate the study of therapeutic agents in neonates, and future steps necessary to advance drug development. RECENT FINDINGS: Although many federal regulations have been introduced over the past 15 years to encourage pediatric and neonatal drug development, the majority of medications that are used in the Neonatal Intensive Care Unit are not approved by the Food and Drug Administration (FDA) for use in neonates...
January 13, 2017: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/28092123/complex-hollow-nanostructures-synthesis-and-energy-related-applications
#10
REVIEW
Le Yu, Han Hu, Hao Bin Wu, Xiong Wen David Lou
Hollow nanostructures offer promising potential for advanced energy storage and conversion applications. In the past decade, considerable research efforts have been devoted to the design and synthesis of hollow nanostructures with high complexity by manipulating their geometric morphology, chemical composition, and building block and interior architecture to boost their electrochemical performance, fulfilling the increasing global demand for renewable and sustainable energy sources. In this Review, we present a comprehensive overview of the synthesis and energy-related applications of complex hollow nanostructures...
January 16, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28092053/sh2-domain-based-fret-biosensor-for-measuring-bcr-abl-activity-in-living-cml-cells
#11
Mari Fujioka, Yumi Asano, Shigeyuki Nakada, Yusuke Ohba
Fluorescent proteins (FPs) displaying distinct spectra have shed their light on a wide range of biological functions. Moreover, sophisticated biosensors engineered to contain single or multiple FPs, including Förster resonance energy transfer (FRET)-based biosensors, spatiotemporally reveal the molecular mechanisms underlying a variety of pathophysiological processes. However, their usefulness for applied life sciences has yet to be fully explored. Recently, our research group has begun to expand the potential of FPs from basic biological research to the clinic...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091625/mplex-a-method-for-simultaneous-pathogen-inactivation-and-extraction-of-samples-for-multi-omics-profiling
#12
Kristin E Burnum-Johnson, Jennifer E Kyle, Amie J Eisfeld, Cameron P Casey, Kelly G Stratton, Juan F Gonzalez, Fabien Habyarimana, Nicholas M Negretti, Amy C Sims, Sadhana Chauhan, Larissa B Thackray, Peter J Halfmann, Kevin B Walters, Young-Mo Kim, Erika M Zink, Carrie D Nicora, Karl K Weitz, Bobbie-Jo M Webb-Robertson, Ernesto S Nakayasu, Brian Ahmer, Michael E Konkel, Vladimir Motin, Ralph S Baric, Michael S Diamond, Yoshihiro Kawaoka, Katrina M Waters, Richard D Smith, Thomas O Metz
The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements...
January 16, 2017: Analyst
https://www.readbyqxmd.com/read/28091566/efficient-generation-of-hpsc-derived-midbrain-dopaminergic-neurons-in-a-fully-defined-scalable-3d-biomaterial-platform
#13
Maroof M Adil, Gonçalo M C Rodrigues, Rishikesh U Kulkarni, Antara T Rao, Nicole E Chernavsky, Evan W Miller, David V Schaffer
Pluripotent stem cells (PSCs) have major potential as an unlimited source of functional cells for many biomedical applications; however, the development of cell manufacturing systems to enable this promise faces many challenges. For example, there have been major recent advances in the generation of midbrain dopaminergic (mDA) neurons from stem cells for Parkinson's Disease (PD) therapy; however, production of these cells typically involves undefined components and difficult to scale 2D culture formats. Here, we used a fully defined, 3D, thermoresponsive biomaterial platform to rapidly generate large numbers of action-potential firing mDA neurons after 25 days of differentiation (~40% tyrosine hydroxylase (TH) positive, maturing into 25% cells exhibiting mDA neuron-like spiking behavior)...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091415/advances-of-coagulation-factor-xiii
#14
REVIEW
Da-Yu Shi, Shu-Jie Wang
OBJECTIVE: To provide a comprehensive literature review on roles of coagulation factor XIII (FXIII) in coagulation, wound healing, neoplasm, bone metabolism, and pregnancy. DATA SOURCES: All articles in PubMed with key words "Coagulation factor XIII", "wound", "leukemia", "tumor", "bone," and "pregnancy" with published date from 2001 to 2016 were included in the study. Frequently cited publications before 2000 were also included. STUDY SELECTION: We reviewed the role of FXIII in biologic processes as documented in clinical, animal, and in vitro studies...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28091414/acute-myeloid-leukemia-advancements-in-diagnosis-and-treatment
#15
REVIEW
Meng-Ge Yu, Hu-Yong Zheng
OBJECTIVE: Leukemia is the most common pediatric malignancy and a major cause of morbidity and mortality in children. Among all subtypes, a lack of consensus exists regarding the diagnosis and treatment of acute myeloid leukemia (AML). Patient survival rates have remained modest for the past three decades in AML. Recently, targeted therapy has emerged as a promising treatment. DATA SOURCES: We searched the PubMed database for recently published research papers on diagnostic development, target therapy, and other novel therapies of AML...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28090750/professionals-views-on-mental-health-service-users-education-challenges-and-support
#16
I Nieminen, M Kaunonen
: WHAT IS KNOWN ON THE SUBJECT?: Mental health service users (MHSUs) may experience disruptions in their education. However, education has been shown to have a positive influence on their recovery, potentially offering them broader employment opportunities. The literature suggests that providing support for MHSUs in their educational efforts may be beneficial and is wished for by the service users themselves. However, there is a lack of mental health professionals' views on the topic in the setting of a community mental health centre...
February 2017: Journal of Psychiatric and Mental Health Nursing
https://www.readbyqxmd.com/read/28090716/does-item-overlap-render-measured-relationships-between-pain-and-challenging-behaviour-trivial-results-from-a-multicentre-cross-sectional-study-in-13-german-nursing-homes
#17
Patrick Kutschar, Zsuzsa Bauer, Irmela Gnass, Jürgen Osterbrink
Several studies suggest that pain is a trigger for challenging behaviour in older adults with cognitive impairment. However, such measured relationships might be confounded due to item overlap as instruments share similar or identical items. The purpose of this study was to examine whether the frequently observed association between pain and challenging behaviour might be traced back to item overlap. This multicentre cross-sectional study was conducted in 13 nursing homes and examined pain (measure: Pain Assessment in Advanced Dementia Scale) and challenging behaviour (measure: Cohen-Mansfield Agitation Inventory) in 150 residents with severe cognitive impairment...
January 16, 2017: Nursing Inquiry
https://www.readbyqxmd.com/read/28090703/differentiation-of-islet-progenitors-regulated-by-nicotinamide-into-transcriptome-verified-%C3%AE-cells-that-ameliorate-diabetes
#18
Fang-Xu Jiang, Kevin Li, Michael Archer, Munish Mehta, Emma Jamieson, Adrian Charles, Jan E Dickinson, Masahito Matsumoto, Grant Morahan
Developmental stage-specific differentiation of stem or progenitor cells into safe and functional cells is of fundamental importance in regenerative medicine, including β-cell replacement. However, the differentiation of islet progenitor cells (IPCs) into insulin-secreting β cells remains elusive. Here, we report that the multi-functional molecule nicotinamide (NIC) is a specific differentiation regulator of mouse IPCs. The differentiated cells regulated by NIC exhibited many characteristics of adult β cells, including ameliorating preclinical diabetes and a highly comparable transcriptome profile...
January 16, 2017: Stem Cells
https://www.readbyqxmd.com/read/28090513/an-update-and-review-of-cell-based-wound-dressings-and-their-integration-into-clinical-practice
#19
REVIEW
Austin Pourmoussa, Daniel J Gardner, Maxwell B Johnson, Alex K Wong
Chronic wounds affect over 4 million individuals and pose a significant burden to the US healthcare system. Diabetes, venous stasis, radiation or paralysis are common risk factors for chronic wounds. Unfortunately, the current standard of care (SOC) has a high relapse rate and these wounds continue to adversely affect patients' quality of life. Fortunately, advances in tissue engineering have allowed for the development of cell-based wound dressings that promote wound healing by improving cell migration and differentiation...
December 2016: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28090431/a-role-for-3d-printing-in-kidney-on-a-chip-platforms
#20
Ryan D Sochol, Navin R Gupta, Joseph V Bonventre
The advancement of "kidney-on-a-chip" platforms - submillimeter-scale fluidic systems designed to recapitulate renal functions in vitro - directly impacts a wide range of biomedical fields, including drug screening, cell and tissue engineering, toxicity testing, and disease modelling. To fabricate kidney-on-a-chip technologies, researchers have primarily adapted traditional micromachining techniques that are rooted in the integrated circuit industry; hence the term, "chip." A significant challenge, however, is that such methods are inherently monolithic, which limits one's ability to accurately recreate the geometric and architectural complexity of the kidney in vivo...
March 2016: Current Transplantation Reports
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