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https://www.readbyqxmd.com/read/28449114/neuro-symbolic-representation-learning-on-biological-knowledge-graphs
#1
Mona Alshahrani, Mohammed Asif Khan, Omar Maddouri, Akira R Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf
Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449079/small-non-coding-rna-and-cancer
#2
Giulia Romano, Dario Veneziano, Mario Acunzo, Carlo M Croce
The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of RNA transcribed but not translated into protein can be classified as housekeeping RNA (such as rRNA, tRNA) and regulatory RNA (such as miRNA, piRNA, lncRNA). Small non-coding RNAs, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated...
April 26, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28449068/development-of-a-novel-human-recellularized-endometrium-that-responds-to-a-28-day-hormone-treatment
#3
Susan A Olalekan, Joanna E Burdette, Spiro Getsios, Teresa K Woodruff, J Julie Kim
Three dimensional (3D) in vitro models have been established to study the physiology and pathophysiology of the endometrium. With emerging evidence that the native extracellular matrix (ECM) provides appropriate cues and growth factors essential for tissue homeostasis, we describe, a novel 3D endometrium in vitro model developed from decellularized human endometrial tissue repopulated with primary endometrial cells. Analysis of the decellularized endometrium using mass spectrometry analysis revealed an enrichment of cell adhesion molecules, cytoskeletal proteins and ECM proteins such as Collagen IV and Laminin...
April 25, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28448702/ketamine-for-depression-1-clinical-summary-of-issues-related-to-efficacy-adverse-effects-and-mechanism-of-action
#4
Chittaranjan Andrade
Ketamine is an anesthetic drug that is also used for off-label indications such as the mediation of analgesia and sedation in various settings. It is additionally recognized as an agent with antidepressant potential. For depression, it is most commonly administered as a slow intravenous infusion in subanesthetic doses (usually 0.5 mg/kg). As an antidepressant, is strikingly different from conventional antidepressant drugs in that it brings about rapid and marked attenuation of depressive symptoms even in patients with refractory depression...
April 2017: Journal of Clinical Psychiatry
https://www.readbyqxmd.com/read/28448381/higher-surgical-morbidity-for-ulcerative-colitis-patients-in-the-era-of-biologics
#5
Jonathan S Abelson, Fabrizio Michelassi, Jialin Mao, Art Sedrakyan, Heather Yeo
OBJECTIVE: To investigate differences in surgical approach and postoperative outcomes for patients with ulcerative colitis (UC) before and after the introduction of biologic therapy. BACKGROUND: Biologic use has dramatically increased since Food and Drug Administration approval of infliximab. Studies conflict as to the effect of these agents on surgical outcomes with some demonstrating worse surgical outcomes whereas others have found no difference. METHODS: We used an administrative, all-payer, all-age group database located in New York State...
April 26, 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28448195/design-characteristics-of-the-corrona-japan-rheumatoid-arthritis-registry
#6
Hisashi Yamanaka, Mitsumasa Kishimoto, Dimitrios A Pappas, Jeffrey D Greenberg, Joel M Kremer, Yoshiya Tanaka
OBJECTIVES: The primary objective is to prospectively study the comparative safety and effectiveness of older and newer classes of nonbiologic DMARDs (Disease-modifying antirheumatic drugs), biologic DMARDs and targeted synthetic therapies approved for rheumatoid arthritis (RA) in a real-world patient population in Japan. METHODS: Prospective, multicenter, noninterventional, observational study across geographic distribution of both private and public institutions for patients with RA who are newly prescribed one of the following medications: (1) methotrexate; (2) anti-TNF biologic DMARDs; (3) non-TNF biologic DMARDs; and (4) approved JAK inhibitors at the time of enrollment into the registry...
April 27, 2017: Modern Rheumatology
https://www.readbyqxmd.com/read/28448116/quantitative-examination-of-the-active-targeting-effect%C3%AF-the-key-factor-for-maximal-tumor-accumulation-and-retention-of-short-circulated-biopolymeric-nanocarriers
#7
Jianquan Wang, Gee Young Lee, Qian Lu, Xianghong Peng, Jiangxiao Wu, Siyuan Wu, Brad A Kairdolf, Shuming Nie, Yiqing Wang, Lucas A Lane
Targeted and non-targeted biopolymeric nanoparticles with identical hydrodynamic sizes and surface charges were quantitatively examined in terms of the pharmacokinetic and biodistribution differences in detail. In adding cancer cell targeting folate molecules to the surface of the heparin nanocarriers, the amount of drug delivered to the tumor is doubled and tumor growth inhibition is significantly enhanced. The folate-targeted heparin particles offered similar therapeutic potentials compared to their synthetic long-circulating analogues, thus presenting a viable alternative for drug delivery vehicle construction using biological polymers which are easier for the body to eliminate...
April 27, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28448027/dry-powder-and-nebulized-aerosol-inhalation-of-pharmaceuticals-delivered-to-mice-using-a-nose-only-exposure-system
#8
Jonathan E Phillips, Xuxia Zhang, James A Johnston
Obstructive respiratory diseases like asthma and chronic obstructive pulmonary disease (COPD) are currently treated by inhaled anti-inflammatory and bronchodilator drugs. Despite the availability of multiple treatments, both diseases are growing public health concerns. The majority of asthma patients are well controlled on current inhaled therapies but a substantial number of patients with severe asthma are not. Asthma affects an estimated 300 million people worldwide and approximately 20 percent have a severe form of the disease...
April 6, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447543/human-egf-derived-direct-and-reverse-short-linear-motifs-conformational-dynamics-insight-into-the-receptor-binding-residues
#9
Nurbubu T Moldogazieva, Konstantin V Shaitan, Mikhail Yu Antonov, Innokenty M Mokhosoev, Olga V Levtsova, Аlexander A Terentiev
Short linear motifs (SLiMs) have been recognized to perform diverse functions in a variety of regulatory proteins through the involvement in protein-protein interactions, signal transduction, cell cycle regulation, protein secretion, etc. However, detailed molecular mechanisms underlying their functions including roles of definite amino acid residues remain obscure. In our previous studies, we demonstrated that conformational dynamics of amino acid residues in oligopeptides derived from regulatory proteins such as alpha-fetoprotein (AFP), carcino-embryonic antigen (CEA) and pregnancy specific β1-glycoproteins (PSGs) contributes greatly to their biological activities...
April 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28447487/tissue-engineered-vascular-grafts-current-state-of-the-field
#10
Chin Siang Ong, Xun Zhou, Chen Yu Huang, Takuma Fukunishi, Huaitao Zhang, Narutoshi Hibino
Conventional synthetic vascular grafts are limited by the inability to remodel, as well as issues of patency at smaller diameters. Tissue-engineered vascular grafts (TEVGs), constructed from biologically active cells and biodegradable scaffolds have the potential to overcome these limitations, and provide growth capacity and self-repair. Areas covered: This article outlines the TEVG design, biodegradable scaffolds, TEVG fabrication methods, cell seeding, drug delivery, strategies to reduce wait times, clinical trials, as well as a 5-year view with expert commentary...
April 27, 2017: Expert Review of Medical Devices
https://www.readbyqxmd.com/read/28447485/empirical-estimation-of-under-reporting-in-the-u-s-food-and-drug-administration-adverse-event-reporting-system-faers
#11
Yasser M Alatawi, Richard A Hansen
OBJECTIVE: To examine how closely reporting rates in the FDA Adverse Event Reporting System (FAERS) reflect expected rates of known adverse drug events (ADEs). METHODS: We selected three groups of drugs to reflect hypothesized variation in sensitivity to reporting, including statins, biologics, and narrow therapeutics index drugs (NTI). The numbers of ADEs in FAERS were divided by utilization estimates from ambulatory health care data (NAMCS/NHAMCS) to calculate a reported proportion...
April 27, 2017: Expert Opinion on Drug Safety
https://www.readbyqxmd.com/read/28447382/quantitative-proteomic-analysis-of-ezh2-inhibition-in-acute-myeloid-leukemia-reveals-the-targets-and-pathways-that-precede-the-induction-of-cell-death
#12
Jarrod J Sandow, Giuseppe Infusini, Aliaksei Z Holik, Gabriela Brumatti, Tessa V Averink, Paul G Ekert, Andrew I Webb
PURPOSE: Chromosomal translocation of the Mixed Lineage Leukemia (MLL) locus generates fusion proteins that drive acute myeloid leukemia (AML) resulting in atypical histone methyltransferase activity and alterations in the epigenetic regulation of gene expression. Targeting histone regulators, such as Enhancer of Zeste Homologue 2 (EZH2), has shown promise in AML. Profiling differential protein expression following inhibition of epigenetic regulators in AML may help to identify novel targets for therapeutics...
April 26, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28447115/human-genetics-as-a-model-for-target-validation-finding-new-therapies-for-diabetes
#13
REVIEW
Soren K Thomsen, Anna L Gloyn
Type 2 diabetes is a global epidemic with major effects on healthcare expenditure and quality of life. Currently available treatments are inadequate for the prevention of comorbidities, yet progress towards new therapies remains slow. A major barrier is the insufficiency of traditional preclinical models for predicting drug efficacy and safety. Human genetics offers a complementary model to assess causal mechanisms for target validation. Genetic perturbations are 'experiments of nature' that provide a uniquely relevant window into the long-term effects of modulating specific targets...
April 26, 2017: Diabetologia
https://www.readbyqxmd.com/read/28446242/activity-of-distinct-growth-factor-receptor-network-components-in-breast-tumors-uncovers-two-biologically-relevant-subtypes
#14
Mumtahena Rahman, Shelley M MacNeil, David F Jenkins, Gajendra Shrestha, Sydney R Wyatt, Jasmine A McQuerry, Stephen R Piccolo, Laura M Heiser, Joe W Gray, W Evan Johnson, Andrea H Bild
BACKGROUND: The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components, or pathways, and the inability to study complex signaling networks in patient tumors. Here, pathway-specific genomic signatures were used to interrogate GFRN activity in breast tumors and the consequent phenotypic impact of GRFN activity patterns. METHODS: Novel pathway signatures were generated in human primary mammary epithelial cells by overexpressing key genes from GFRN pathways (HER2, IGF1R, AKT1, EGFR, KRAS (G12V), RAF1, BAD)...
April 26, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28446055/investigational-drugs-for-nasopharyngeal-carcinoma
#15
Brigette B Y Ma, Edwin P Hui, Anthony T C Chan
Nasopharyngeal carcinoma (NPC) is endemic to Southern China and Asia and is etiologically associated with the Epstein Barr virus (EBV). Whole exome and genome sequencing (WES, WGS) studies of NPC have reported several actionable therapeutic targets, and that the mutational load of NPC maybe comparable to that of squamous head and neck cancer. These unique biological characteristics have been exploited as potential targets and a wide range of investigational drugs are being investigated in clinical trials. Area covered: This review focused on the latest clinical development of the most promising classes of investigational agents in the treatment of advanced NPC...
April 27, 2017: Expert Opinion on Investigational Drugs
https://www.readbyqxmd.com/read/28445958/repressing-cd147-is-a-novel-therapeutic-strategy-for-malignant-melanoma
#16
REVIEW
Xing Hu, Juan Su, Youyou Zhou, Xiaoyun Xie, Cong Peng, Zhimin Yuan, Xiang Chen
CD147/basigin, a transmembrane protein, is a member of the immunoglobulin super family. Accumulating evidence has revealed the role of CD147 in the development and progression of various cancers, including malignant melanoma (MM). MM is a malignancy of pigment-producing cells that causes the greatest number of skin cancer-related deaths worldwide. CD147 is overexpressed in MM and plays an important role in cell viability, apoptosis, proliferation, invasion, and metastasis, probably by mediating vascular endothelial growth factor (VEGF) production, glycolysis, and multi-drug resistance (MDR)...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445950/the-discovery-of-a-novel-compound-with-potent-antitumor-activity-virtual-screening-synthesis-biological-evaluation-and-preliminary-mechanism-study
#17
Yuanyuan Jin, Linhu Li, Zhaoyong Yang, Mingliang Liu, Huiyuan Guo, Weiyi Shen
Farnesyltransferase has been regarded as a promising drug target against cancer as it is critical for membrane association of several signal transduction proteins. In this study, a novel farnesyltransferase inhibitor (IMB-1406) was identified through virtual screening. It exhibits stronger potency (IC50s: 6.92-8.99 μM) than Sunitinib against all of the tested cancer cell lines. Preliminary studies on mechanism reveal that IMB-1406 induces apoptosis in HepG2 cells by arresting the cell cycle at the S phase, altering anti- and pro-apoptotic proteins leading to mitochondrial dysfunction and activation of caspase-3...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445704/development-of-standard-methods-for-zika-virus-propagation-titration-and-purification
#18
Sharton Vinicius Antunes Coelho, Rômulo Leão Silva Neris, Michelle Premazzi Papa, Laila Castro Schnellrath, Lana Monteiro Meuren, Diogo A Tschoeke, Luciana Leomil, Brunno Renato Farias Verçoza, Milene Miranda, Fabiano L Thompson, Andrea Thompson Da Poian, Thiago Moreno L Souza, Fabiana Avila Carneiro, Clarissa R Damaso, Iranaia Assunção-Miranda, Luciana Barros de Arruda
The emergence of Zika virus (ZIKV) infection has stimulated several research groups to study and collaborate to understand virus biology and pathogenesis. These efforts may assist with the development of antiviral drugs, vaccines and diagnostic tests, as well as to promote advancements in public health policies. Here, we aim to develop standard protocols for propagation, titration, and purification of Asian and Brazilian ZIKV strains, by systematically testing different cell types, kinetics, multiplicity of infection and centrifugation protocols...
April 23, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28445611/equivalence-of-complex-drug-products-advances-in-and-challenges-for-current-regulatory-frameworks
#19
Leonie Hussaarts, Stefan Mühlebach, Vinod P Shah, Scott McNeil, Gerrit Borchard, Beat Flühmann, Vera Weinstein, Sesha Neervannan, Elwyn Griffiths, Wenlei Jiang, Elena Wolff-Holz, Daan J A Crommelin, Jon S B de Vlieger
Biotechnology and nanotechnology provide a growing number of innovator-driven complex drug products and their copy versions. Biologics exemplify one category of complex drugs, but there are also nonbiological complex drug products, including many nanomedicines, such as iron-carbohydrate complexes, drug-carrying liposomes or emulsions, and glatiramoids. In this white paper, which stems from a 1-day conference at the New York Academy of Sciences, we discuss regulatory frameworks in use worldwide (e.g., the U...
April 26, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28445606/structural-and-biological-properties-of-thermosensitive-chitosan-graphene-hybrid-hydrogels-for-sustained-drug-delivery-applications
#20
Leyla Saeednia, Li Yao, Marcus Berndt, Kim Cluff, Ramazan Asmatulu
Chitosan has the ability to make injectable thermosensitive hydrogels which has been highly investigated for drug delivery applications. The addition of nanoparticles is one way to increase the mechanical strength of thermosensitive chitosan hydrogel and subsequently and control the burst release of drug. Graphene nanoparticles have shown unique mechanical, optical and electrical properties which can be exploited for biomedical applications, especially in drug delivery. This study, have focused on the mechanical properties of a thermosensitive and injectable hybrid chitosan hydrogel incorporated with graphene nanoparticles...
April 26, 2017: Journal of Biomedical Materials Research. Part A
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