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https://www.readbyqxmd.com/read/27933523/integrative-functional-genomics-for-systems-genetics-in-geneweaver-org
#1
Jason A Bubier, Michael A Langston, Erich J Baker, Elissa J Chesler
The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933501/toxicity-effect-of-graphene-oxide-on-growth-and-photosynthetic-pigment-of-the-marine-alga-picochlorum-sp-during-different-growth-stages
#2
Layla J Hazeem, Mohamed Bououdina, Etienne Dewailly, Christian Slomianny, Alexandre Barras, Yannick Coffinier, Sabine Szunerits, Rabah Boukherroub
Graphene oxide (GO), a recently discovered material, has been investigated for many applications in various fields. Thus, an immense awareness should be paid on the potential effects of the material on the environment as huge quantities of GO may get to the environment. Aquatic organisms, marine algae as an example, are exposed to such material when disposed to the environment. Accordingly, it is significant to assess the probable interactions of GO with algae in evaluating its possible environmental risks...
December 9, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27933461/factors-associated-with-hiv-testing-among-participants-from-substance-use-disorder-treatment-programs-in-the-us-a-machine-learning-approach
#3
Yue Pan, Hongmei Liu, Lisa R Metsch, Daniel J Feaster
HIV testing is the foundation for consolidated HIV treatment and prevention. In this study, we aim to discover the most relevant variables for predicting HIV testing uptake among substance users in substance use disorder treatment programs by applying random forest (RF), a robust multivariate statistical learning method. We also provide a descriptive introduction to this method for those who are unfamiliar with it. We used data from the National Institute on Drug Abuse Clinical Trials Network HIV testing and counseling study (CTN-0032)...
December 8, 2016: AIDS and Behavior
https://www.readbyqxmd.com/read/27933367/antipsychotic-inductors-of-brain-hypothermia-and-torpor-like-states-perspectives-of-application
#4
REVIEW
Yury S Tarahovsky, Irina S Fadeeva, Natalia P Komelina, Maxim O Khrenov, Nadezhda M Zakharova
Hypothermia and hypometabolism (hypometabothermia) normally observed during natural hibernation and torpor, allow animals to protect their body and brain against the damaging effects of adverse environment. A similar state of hypothermia can be achieved under artificial conditions through physical cooling or pharmacological effects directed at suppression of metabolism and the processes of thermoregulation. In these conditions called torpor-like states, the mammalian ability to recover from stroke, heart attack, and traumatic injuries greatly increases...
December 8, 2016: Psychopharmacology
https://www.readbyqxmd.com/read/27933273/prognostic-value-of-plasma-and-urine-glycosaminoglycan-scores-in-clear-cell-renal-cell-carcinoma
#5
Francesco Gatto, Marco Maruzzo, Cristina Magro, Umberto Basso, Jens Nielsen
BACKGROUND: The prognosis of metastatic clear cell renal cell carcinoma (ccRCC) vastly improved since the introduction of antiangiogenic-targeted therapy. However, it is still unclear which biological processes underlie ccRCC aggressiveness and affect prognosis. Here, we checked whether a recently discovered systems biomarker based on plasmatic or urinary measurements of glycosaminoglycans (GAGs) aggregated into diagnostic scores correlated with ccRCC prognosis. METHODS: Thirty-one patients with a diagnosis of ccRCC (23 metastatic) were prospectively enrolled, and their urine and plasma biomarker scores were correlated to progression-free survival (PFS) and overall survival (OS) as either a dichotomous ("Low" vs...
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27933262/software-project-management-tools-in-global-software-development-a-systematic-mapping-study
#6
Saad Yasser Chadli, Ali Idri, Joaquín Nicolás Ros, José Luis Fernández-Alemán, Juan M Carrillo de Gea, Ambrosio Toval
Global software development (GSD) which is a growing trend in the software industry is characterized by a highly distributed environment. Performing software project management (SPM) in such conditions implies the need to overcome new limitations resulting from cultural, temporal and geographic separation. The aim of this research is to discover and classify the various tools mentioned in literature that provide GSD project managers with support and to identify in what way they support group interaction. A systematic mapping study has been performed by means of automatic searches in five sources...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27933103/programmatic-conversion-of-crystal-structures-into-3d-printable-files-using-jmol
#7
Vincent F Scalfani, Antony J Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M Hanson, Jahred M Liddie, Jason E Bara
BACKGROUND: Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. RESULTS: A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27933000/in-depth-study-of-the-interaction-sensitivity-and-gating-modulation-by-pufas-on-k-channels-interaction-and-new-targets
#8
REVIEW
Cristina Moreno, Alicia de la Cruz, Carmen Valenzuela
Voltage gated potassium channels (KV) are membrane proteins that allow selective flow of K(+) ions in a voltage-dependent manner. These channels play an important role in several excitable cells as neurons, cardiomyocytes, and vascular smooth muscle. Over the last 20 years, it has been shown that omega-3 polyunsaturated fatty acids (PUFAs) enhance or decrease the activity of several cardiac KV channels. PUFAs-dependent modulation of potassium ion channels has been reported to be cardioprotective. However, the precise cellular mechanism underlying the cardiovascular benefits remained unclear in part because new PUFAs targets and signaling pathways continue being discovered...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27932956/hypothalamic-vasopressinergic-projections-innervate-central-amygdala-gabaergic-neurons-implications-for-anxiety-and-stress-coping
#9
Vito S Hernández, Oscar R Hernández, Miguel Perez de la Mora, María J Gómora, Kjell Fuxe, Lee E Eiden, Limei Zhang
The arginine-vasopressin (AVP)-containing hypothalamic magnocellular neurosecretory neurons (VPMNNs) are known for their role in hydro-electrolytic balance control via their projections to the neurohypophysis. Recently, projections from these same neurons to hippocampus, habenula and other brain regions in which vasopressin infusion modulates contingent social and emotionally-affected behaviors, have been reported. Here, we present evidence that VPMNN collaterals also project to the amygdaloid complex, and establish synaptic connections with neurons in central amygdala (CeA)...
2016: Frontiers in Neural Circuits
https://www.readbyqxmd.com/read/27932950/amyloid-precursor-proteins-are-dynamically-trafficked-and-processed-during-neuronal-development
#10
Jenna M Ramaker, Robert S Cargill, Tracy L Swanson, Hanil Quirindongo, Marlène Cassar, Doris Kretzschmar, Philip F Copenhaver
Proteolytic processing of the Amyloid Precursor Protein (APP) produces beta-amyloid (Aβ) peptide fragments that accumulate in Alzheimer's Disease (AD), but APP may also regulate multiple aspects of neuronal development, albeit via mechanisms that are not well understood. APP is a member of a family of transmembrane glycoproteins expressed by all higher organisms, including two mammalian orthologs (APLP1 and APLP2) that have complicated investigations into the specific activities of APP. By comparison, insects express only a single APP-related protein (APP-Like, or APPL) that contains the same protein interaction domains identified in APP...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27932908/lifewatch-greece-data-services-discovering-biodiversity-data-using-semantic-web-technologies
#11
Nikos Minadakis, Yannis Marketakis, Martin Doerr, Chryssoula Bekiari, Panagiotis Papadakos, Alexandros Gougousis, Nicolas Bailly, Christos Arvanitidis
BACKGROUND: Biodiversity data is characterized by its cross-disciplinary character, the extremely broad range of data types and structures, and the variety of semantic concepts that it encompasses. Furthermore there is a plethora of different data sources providing resources for the same piece of information in a heterogeneous way. Even if we restrict our attention to Greek biodiversity domain, it is easy to see that biodiversity data remains unconnected and widely distributed among different sources...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27932899/sudden-cardiac-death-of-a-body-packer-due-to-cocaine-cardiotoxicity
#12
Parthasarathi Pramanik, Raghvendra Kumar Vidua
This article presents a case of sudden cardiac death due to the effects of cocaine concealed in the body of a male drug smuggler in his 40s, a so-called body packer. A total of 57 body packets filled with cocaine powder were discovered in his body cavities. The detailed autopsy examination, including histopathology and toxicology findings, is discussed with the aim of describing the mechanism of cocaine intoxication in the body packer and an analysis of cocaine-induced cardiotoxicity and sudden death.
2016: Clinical Medicine Insights. Pathology
https://www.readbyqxmd.com/read/27932867/clustering-algorithms-their-application-to-gene-expression-data
#13
REVIEW
Jelili Oyelade, Itunuoluwa Isewon, Funke Oladipupo, Olufemi Aromolaran, Efosa Uwoghiren, Faridah Ameh, Moses Achas, Ezekiel Adebiyi
Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27932854/predictors-of-ageing-related-decline-across-multiple-cognitive-functions
#14
Stuart J Ritchie, Elliot M Tucker-Drob, Simon R Cox, Janie Corley, Dominika Dykiert, Paul Redmond, Alison Pattie, Adele M Taylor, Ruth Sibbett, John M Starr, Ian J Deary
It is critical to discover why some people's cognitive abilities age better than others'. We applied multivariate growth curve models to data from a narrow-age cohort measured on a multi-domain IQ measure at age 11 years and a comprehensive battery of thirteen measures of visuospatial, memory, crystallized, and processing speed abilities at ages 70, 73, and 76 years (n = 1091 at age 70). We found that 48% of the variance in change in performance on the thirteen cognitive measures was shared across all measures, an additional 26% was specific to the four ability domains, and 26% was test-specific...
November 2016: Intelligence
https://www.readbyqxmd.com/read/27932660/identification-of-beak-and-feather-disease-virus-in-an-unusual-novel-host-merops-ornatus-using-nested-pcr
#15
Subir Sarker, Shubhagata Das, Karla Helbig, Shane R Raidal
The complete genome sequence of beak and feather disease virus (BFDV) was discovered from a rainbow bee-eater (Merops ornatus), a species of Coraciiformes The genome consisted of 1,996 bp encoding two major bidirectional transcribed open reading frames. This is the first evidence of BFDV infection and complete genome characterization for this novel host species.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27932481/modeling-monogenic-human-nephrotic-syndrome-in-the-drosophila-garland-cell-nephrocyte
#16
Tobias Hermle, Daniela A Braun, Martin Helmstädter, Tobias B Huber, Friedhelm Hildebrandt
Steroid-resistant nephrotic syndrome is characterized by podocyte dysfunction. Drosophila garland cell nephrocytes are podocyte-like cells and thus provide a potential in vivo model in which to study the pathogenesis of nephrotic syndrome. However, relevant pathomechanisms of nephrotic syndrome have not been studied in nephrocytes. Here, we discovered that two Drosophila slit diaphragm proteins, orthologs of the human genes encoding nephrin and nephrin-like protein 1, colocalize within a fingerprint-like staining pattern that correlates with ultrastructural morphology...
December 8, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27932461/structural-characterization-and-ligand-inhibitor-identification-provide-functional-insights-into-the-mycobacterium-tuberculosis-cytochrome-p450-cyp126a1
#17
Jude T Chenge, Duyet Van Le, Shalini Swami, Kirsty J McLean, Madeline E Kavanagh, Anthony G Coyne, Stephen E J Rigby, Myles R Cheesman, Hazel M Girvan, Colin W Levy, Bernd Rupp, Jens P von Kries, Chris Abell, David Leys, Andrew W Munro
The Mycobacterium tuberculosis (Mtb) H37Rv genome encodes 20 cytochromes P450, including P450s crucial to infection and bacterial viability. Many Mtb P450s remain uncharacterized, suggesting their further analysis may provide new insights into Mtb metabolic processes and new targets for drug discovery. CYP126A1 is representative of a P450 family widely distributed in mycobacteria and other bacteria. Here we explore the biochemical and structural properties of CYP126A1, including its interactions with new chemical ligands...
December 8, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27932245/knockdown-of-trem-1-suppresses-il-1%C3%AE-induced-chondrocyte-injury-via-inhibiting-the-nf-%C3%AE%C2%BAb-pathway
#18
Jianfei Tang, Qirong Dong
Triggering receptor expressed on myeloid cells 1 (TREM-1) is a recently discovered molecule that modulates inflammatory responses. This study aimed to investigate the specific function of TREM-1 in chondrocytes and its association with the pathophysiology of osteoarthritis (OA). We observed upregulation of TREM-1 in OA cartilage compared to normal tissues. Knockdown of TREM-1 suppressed interleukin 1 beta (IL-1β)-induced extracellular matrix (ECM) metabolic imbalance, pro-inflammatory cytokine production, decrease in cell viability and apoptosis...
December 5, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27932211/a-novel-class-of-somatic-mutations-in-blood-detected-preferentially-in-cd8-cells
#19
Miko Valori, Lilja Jansson, Anna Kiviharju, Pekka Ellonen, Hanna Rajala, Shady Adnan Awad, Satu Mustjoki, Pentti J Tienari
Somatic mutations have a central role in cancer but their role in other diseases such as autoimmune disorders is poorly understood. Earlier work has provided indirect evidence of rare somatic mutations in autoreactive T-lymphocytes in multiple sclerosis (MS) patients but such mutations have not been identified thus far. We analysed somatic mutations in blood in 16 patients with relapsing MS and 4 with other neurological autoimmune disease. To facilitate the detection of somatic mutations CD4+, CD8+, CD19+ and CD4-/CD8-/CD19- cell subpopulations were separated...
December 5, 2016: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/27931571/incidence-of-diabetes-mellitus-after-kidney-transplantation-in-slovakia-multicentric-prospective-analysis
#20
L Dedinská, T Baltesová, Ĺ Beňa, M Čellár, P Galajda, M Chrastina, A Jurčina, L Kováčiková, L Laca, E Lacková, S Lauková Valachová, J Miklušica, J Rosenberger, M Sersenová, P Skalová, Z Žilinská, M Mokáň
BACKGROUND: The incidence rate of post-transplant diabetes mellitus (PTDM) after kidney transplantation (KT) is 5% to 40%. The objective of this analysis was to identify the risk factors of PTDM after KT in the Slovak Republic (SR). METHODS: In the group of 133 patients/non-diabetics, we identified the risk factors of PTDM in the monitored period of 12 months from transplantation. RESULTS: The incidence of PTDM in the SR in 2014 was 38.3%...
December 2016: Transplantation Proceedings
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