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https://www.readbyqxmd.com/read/28812890/jaqpot-quattro-a-novel-computational-web-platform-for-modelling-and-analysis-in-nanoinformatics
#1
Charalampos Chomenidis, Georgios Drakakis, Georgia Tsiliki, Evangelia Anagnostopoulou, Angelos Valsamis, Philip Doganis, Pantelis Sopasakis, Haralambos Sarimveis
Engineered nanomaterials (ENMs) are increasingly infiltrating our lives due to their applications across multiple fields. However, ENM formulations may result in the modulation of pathways and mechanisms of toxic action that endanger human health and the environment. Alternative testing methods such as in silico approaches are becoming increasingly popular for assessing the safety of ENMs as they are cost- and time- effective. Additionally, computational approaches support the industrial safer-by-design challenge and the REACH legislation objective of reducing animal testing...
August 16, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28812672/rapid-and-direct-recoveries-of-predators-and-prey-through-synchronized-ecosystem-management
#2
Jameal F Samhouri, Adrian C Stier, Shannon M Hennessey, Mark Novak, Benjamin S Halpern, Phillip S Levin
One of the twenty-first century's greatest environmental challenges is to recover and restore species, habitats and ecosystems. The decision about how to initiate restoration is best-informed by an understanding of the linkages between ecosystem components and, given these linkages, an appreciation of the consequences of choosing to recover one ecosystem component before another. However, it remains difficult to predict how the sequence of species' recoveries within food webs influences the speed and trajectory of restoration, and what that means for human well-being...
March 1, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811580/%C3%AE-eta-2-glycoprotein-i-protects-mice-against-gram-negative-septicaemia-in-a-sexually-dimorphic-manner
#3
Fatima El-Assaad, Miao Qi, Alice Kizny Gordon, Jian Qi, Shangwen Dong, Freda Passam, James Crofton Weaver, Bill Giannakopoulos, Steven Anthony Krilis
The immune responses of males and females to bacterial infections display differences. The mechanisms that underlie this sexual dimorphism are multifactorial. Lipopolysaccharide (LPS) contributes to the pathogenesis of endotoxaemia. We have previously demonstrated that the plasma protein beta-2 glycoprotein-1 (β2GPI) reduces LPS-induced inflammation in male mice. In the present study using a more robust infection model of septicaemia the role of β2GPI is examined in both male and female wild type (WT) and β2GPI deficient (β2GPI(-/-)) mice challenged with Escherichia coli (E...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810905/omni-polya-a-method-and-tool-for-accurate-recognition-of-poly-a-signals-in-human-genomic-dna
#4
Arturo Magana-Mora, Manal Kalkatawi, Vladimir B Bajic
BACKGROUND: Polyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3'-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28809773/a-macaque-model-for-rectal-lymphogranuloma-venereum-and-non-lymphogranuloma-venereum-chlamydia-trachomatis-impact-on-rectal-simian-human-immunodeficiency-virus-acquisition
#5
Sundaram Ajay Vishwanathan, Rachael D Aubert, Monica R Morris, Chunxia Zhao, Christi Philips, George M Khalil, Frank Deyounks, Kristen Kelley, Jana M Ritter, C Y Chen, Ellen N Kersh, Janet M McNicholl
BACKGROUND: Sustained genital tract inflammation caused by sexually transmitted infections (STIs) is known to increase risk of vaginal human immunodeficiency virus (HIV) infections but, to our knowledge, there are no nonhuman primate studies that have evaluated its link to rectal HIV acquisition. METHODS: Rhesus macaques inoculated with Chlamydia trachomatis (CT) (serovars LGV-L2 and CT-E; n = 7) or saline (n = 7) received up to 20 rectal challenges twice a week of simian/HIV immunodeficiency virus (SHIVSF162p3)...
September 2017: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/28809709/a-new-method-for-automatic-sleep-stage-classification
#6
Junming Zhang, Yan Wu
Traditionally, automatic sleep stage classification is quite a challenging task because of the difficulty in translating open-textured standards to mathematical models and the limitations of handcrafted features. In this paper, a new system for automatic sleep stage classification is presented. Compared with existing sleep stage methods, our method can capture the sleep information hidden inside electroencephalography (EEG) signals and automatically extract features from raw data. To translate open sleep stage standards into machine rules recognized by computers, a new model named fast discriminative complex-valued convolutional neural network (FDCCNN) is proposed to extract features from raw EEG data and classify sleep stages...
August 14, 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/28808275/screening-drug-target-interactions-with-positive-unlabeled-learning
#7
Lihong Peng, Wen Zhu, Bo Liao, Yu Duan, Min Chen, Yi Chen, Jialiang Yang
Identifying drug-target interaction (DTI) candidates is crucial for drug repositioning. However, usually only positive DTIs are deposited in known databases, which challenges computational methods to predict novel DTIs due to the lack of negative samples. To overcome this dilemma, researchers usually randomly select negative samples from unlabeled drug-target pairs, which introduces a lot of false-positives. In this study, a negative sample extraction method named NDTISE is first developed to screen strong negative DTI examples based on positive-unlabeled learning...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808080/characterization-of-the-human-thyroid-epigenome
#8
Celia Siu, Sam Michael Wiseman, Sitanshu Gakkhar, Alireza Heravi-Moussavi, Misha Bilenky, Annaick Carles, Thomas Sierocinski, Angela Tam, Eric Yang Zhao, Katayoon Kasaian, Richard A Moore, Andrew J Mungall, Blair Walker, Thomas Thomson, Marco A Marra, Martin Hirst, Steven Jones
The thyroid gland, necessary for normal human growth and development, functions as an essential regulator of metabolism by the production and secretion of appropriate levels of thyroid hormone. However, assessment of abnormal thyroid function may be challenging suggesting a more fundamental understanding of normal function is needed. One way to characterize normal gland function is to study the epigenome and resulting transcriptome within its constituent cells. This study generates the first published reference epigenomes for human thyroid from four individuals using ChIP-seq and RNA-seq...
August 14, 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/28807912/safety-and-efficacy-of-mhaa4549a-a-broadly-neutralizing-monoclonal-antibody-in-a-human-influenza-a-challenge-model-a-phase-2-randomized-trial
#9
Jacqueline M McBride, Jeremy J Lim, Tracy Burgess, Rong Deng, Michael A Derby, Mauricio Maia, Priscilla Horn, Omer Siddiqui, Daniel Sheinson, Haiyin Chen-Harris, Elizabeth M Newton, Dimitri Fillos, Denise Nazzal, Carrie M Rosenberger, Maikke B Ohlson, Rob Lambkin-Williams, Hosnieh Fathi, Jeffrey M Harris, Jorge A Tavel
BACKGROUND: MHAA4549A, a human monoclonal antibody targeting the hemagglutinin stalk region of influenza A virus (IAV), is being developed as a therapeutic for patients hospitalized with severe IAV infection. Safety and efficacy of MHAA4549A were assessed in a randomized, double-blind, placebo-controlled, dose-ranging study in a human IAV-challenge model. METHODS: One hundred healthy volunteers were inoculated with A/Wisconsin/67/2005 (H3N2) IAV and, 24-36 hours later, administered a single intravenous dose of either placebo, MHAA4549A (400, 1200, or 3600 mg) or a standard oral dose of oseltamivir...
August 14, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28807631/chitosan-hydrochloride-has-no-detrimental-effect-on-bladder-urothelial-cancer-cells
#10
Tanja Višnjar, Urška Dragin Jerman, Peter Veranič, Mateja Erdani Kreft
Bladder cancer is among the most common and aggressive human malignant carcinomas, thus targeting and removal of bladder cancer cells is still a challenge. Although it is well known that chitosan hydrochloride (CH-HCl) causes desquamation of normal urothelial cells, its effect on cancer urothelial cells has not been recognized yet. In this in vitro study, we analyzed the cytotoxicity of 0.05% CH-HCl on three urothelial models: two cancer urothelial models, i.e. invasive and papillary urothelial neoplasms, and a normal urothelial model...
August 11, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28807602/neutralization-of-interferon-%C3%AE-reverts-clinical-and-laboratory-features-in-a-mouse-model-of-macrophage-activation-syndrome
#11
Giusi Prencipe, Ivan Caiello, Antonia Pascarella, Alexei A Grom, Claudia Bracaglia, Laurence Chatel, Walter G Ferlin, Emiliano Marasco, Raffaele Strippoli, Cristina de Min, Fabrizio De Benedetti
BACKGROUND: The pathogenesis of macrophage activation syndrome (MAS) is not clearly understood: a large body of evidence supports the involvement of mechanisms similar to those implicated in primary hemophagocytic lymphohistiocytosis. OBJECTIVE: To investigate the pathogenic role of interferon-γ (IFNγ) and the therapeutic efficacy of IFNγ neutralization in an animal model of macrophage activation syndrome. METHODS: We used a MAS model established in mice transgenic for human interleukin-6 (IL-6TG) challenged with LPS (MAS mice)...
August 11, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28807213/turkey-model-for-flexor-tendon-research-in%C3%A2-vitro-comparison-of-human-canine-turkey-and-chicken-tendons
#12
Assaf Kadar, Andrew R Thoreson, Ramona L Reisdorf, Peter C Amadio, Steven L Moran, Chunfeng Zhao
BACKGROUND: Flexor tendon injuries are one of the most common hand injuries and remain clinically challenging for functional restoration. Canine and chicken have been the most commonly used animal models for flexor tendon-related research but possess several disadvantages. The purpose of this study was to explore a potential turkey model for flexor tendon research. METHODS: The third digit from human cadaveric hands, canine forepaws, turkey foot, and chicken foot were used for this study...
August 2017: Journal of Surgical Research
https://www.readbyqxmd.com/read/28806493/olaparib-a-clinically-used-poly-adp-ribose-polymerase-inhibitor-protects-against-oxidant-induced-cardiac-myocyte-death-in-vitro-and-improves-cardiac-contractility-during-early-phase-after-heart-transplantation-in-a-rat-model-in-vivo
#13
Sevil Korkmaz-Icöz, Bartosz Szczesny, Michela Marcatti, Shiliang Li, Mihály Ruppert, Felix Lasitschka, Sivakkanan Loganathan, Csaba Szabo, Gábor Szabó
BACKGROUND AND PURPOSE: Olaparib, rucaparib and niraparib, potent inhibitors of poly(ADP-ribose) polymerase (PARP) have recently been approved for human use for oncological indications. Considering the previously demonstrated role of PARP in various forms of acute and chronic myocardial injury, we tested the effect of olaparib in in-vitro models of oxidative stress in cardiomyocytes, and in an in-vivo model of cardiac transplantation. EXPERIMENTAL APPROACH: H9c2-embryonic rat heart-derived myoblasts pretreated with vehicle or olaparib (10μM) were challenged with either hydrogen-peroxide (H2 O2 ) or with glucose-oxidase (GOx, which generates H2 O2 in the tissue culture medium)...
August 14, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28806483/mandate-for-the-nursing-profession-to-address-climate-change-through-nursing-education
#14
Jeanne Leffers, Ruth McDermott Levy, Patrice K Nicholas, Casey F Sweeney
PURPOSE: The adverse health effects from climate change demand action from the nursing profession. This article examines the calls to action, the status of climate change in nursing education, and challenges and recommendations for nursing education related to climate change and human health. ORGANIZING CONSTRUCT: Discussion paper. FINDINGS: The integration of climate change into nursing education is essential so that knowledge, skills, and insights critical for clinical practice in our climate-changing world are incorporated in curricula, practice, research, and policy...
August 14, 2017: Journal of Nursing Scholarship
https://www.readbyqxmd.com/read/28806419/effects-of-short-term-dry-immersion-on-bone-remodeling-markers-insulin-and-adipokines
#15
Marie-Thérèse Linossier, Liubov E Amirova, Mireille Thomas, Myriam Normand, Marie-Pierre Bareille, Guillemette Gauquelin-Koch, Arnaud Beck, Marie-Claude Costes-Salon, Christine Bonneau, Claude Gharib, Marc-Antoine Custaud, Laurence Vico
BACKGROUND: Dry immersion (DI), a ground-based model of microgravity previously used in Russia, has been recently implemented in France. The aim of this study was to analyze early events in a short-term DI model in which all conditions are met to investigate who is first challenged from osteo- or adipo-kines and to what extent they are associated to insulin-regulating hormones. METHODS: Twelve healthy men were submitted to a 3-day DI. Fasting blood was collected during pre-immersion phase for the determination of the baseline data collection (BDC), daily during DI (DI24h, DI48H and DI72h), then after recovery (R+3h and R+24h)...
2017: PloS One
https://www.readbyqxmd.com/read/28806050/linking-high-throughput-screens-to-identify-moas-and-novel-inhibitors-of-mycobacterium-tuberculosis-dihydrofolate-reductase
#16
John P Santa Maria, Yumi Park, Lihu Yang, Nicholas Murgolo, Michael D Altman, Paul Zuck, Greg Adam, Chad Chamberlin, Peter Saradjian, Peter Dandliker, Helena I M Boshoff, Clifton E Barry, Charles Garlisi, David B Olsen, Katherine Young, Meir Glick, Elliott Nickbarg, Peter S Kutchukian
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for mechanism of action (MoA) and reveal actionable chemical matter. Here we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning is employed to identify chemical features with predicted efficacy targets for a given phenotypic screen...
August 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28805144/a-qm-protein-ligand-investigation-of-anti-psychotic-drugs-with-the-dopamine-d2-receptor-d2r
#17
Ramin Ekhteiari Salmas, Yusuf Serhat Is, Serdar Durdagi, Matthias Stein, Mine Yurtsever
The dopamine D2 Receptor (D2R) is a member of the G-Protein Coupled Receptor (GPCR) family and plays a critical role in neurotransmission activities in the human brain. Dysfunction in dopamine receptor signaling may lead to mental health illnesses such as schizophrenia and Parkinson's disease. D2R is the target protein of the commonly used anti-psychotic drugs such as risperidone, clozapine, aripiprazole, olanzapine, ziprasidone and quetiapine. Due to their significant side effects and nonselective profiles, the discovery of novel drugs has become a challenge for researchers working in this field...
August 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28805136/the-ovine-model-for-meniscus-tissue-engineering-considerations-of-anatomy-function-implantation-and-evaluation
#18
Andrzej Brzezinski, Salim A Ghodbane, Jay M Patel, Barbara A Perry, Charles J Gatt, Michael G Dunn
Meniscus injuries represent one of the most-common intra-articular knee injuries. The current treatment options include meniscectomy and allograft transplantation, both with poor long-term outcomes. Therefore, there is a need for regenerative techniques to restore meniscal function. In order to pre-clinically test scaffolds for meniscus replacement, large-animal models need to be established and standardized. This review establishes the anatomical and compositional similarities between the human and sheep menisci and provides guidance for implantation and evaluation of such devices...
August 12, 2017: Tissue Engineering. Part C, Methods
https://www.readbyqxmd.com/read/28803049/modeling-aging-in-hiv-infection-in-nonhuman-primates-to-address-an-emerging-challenge-of-the-post-art-era
#19
REVIEW
Tianyu He, Elizabeth Falwell, Egidio Brocca-Cofano, Ivona Pandrea
The advent of antiretroviral therapy (ART) has dramatically improved both quality and length of life for subjects infected with human immunodeficiency virus (HIV), delaying or preventing progression to acquired immunodeficiency syndrome (AIDS). However, the virus induces aging-related changes to the immune system which confound treatment. Additionally, the normal physiologic events that occur during aging lead to deficiencies in immunity which not only exacerbate HIV pathogenesis but also trigger a variety of comorbidities...
August 9, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28802833/new-pro-resolving-n-3-mediators-bridge-resolution-of-infectious-inflammation-to-tissue-regeneration
#20
REVIEW
Charles N Serhan, Nan Chiang, Jesmond Dalli
While protective, the acute inflammatory response when uncontrolled can lead to further tissue damage and chronic inflammation that is now widely recognized to play important roles in many commonly occurring diseases, such as cardiovascular disease, neurodegenerative diseases, metabolic syndrome, and many other diseases of significant public health concern. The ideal response to initial challenges of the host is complete resolution of the acute inflammatory response, which is now recognized to be a biosynthetically active process governed by specialized pro-resolving mediators (SPM)...
August 9, 2017: Molecular Aspects of Medicine
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