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Molecular classification

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https://www.readbyqxmd.com/read/30103106/docking-and-qsar-analysis-of-tetracyclic-oxindole-derivatives-as-%C3%AE-glucosidase-inhibitors
#1
M Asadollahi-Baboli, S Dehnavi
The α-glucosidase inhibitors are considered as important agents in drug discovery against diabetes mellitus. Molecular docking and quantitative structure-activity relationship (QSAR) were performed based on a series of tetracyclic oxindole derivatives to elucidate key structural properties affecting inhibitory activity and support the design of new α-glucosidase inhibitors. The molecular docking results demonstrate that at least two hydrogen bonds between Thr681 and Arg676 residues and the oxygen atoms in amid groups have an important role in the optimum binding of inhibitors...
July 31, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/30102864/use-of-111-in-hexavalent-lactoside-for-liver-reserve-estimation-in-rodents-with-thioacetamide-induced-hepatic-fibrosis
#2
Mei-Hui Wang, Chuan-Yi Chien, Hung-Man Yu, Ping-Yen Wang, Wuu-Jyh Lin
Many biochemical tests detecting the presence of liver disease are not liver-specific and may be abnormal in non-hepatic conditions. Asialoglycoprotein receptor (ASGPR) is a hepatocyte-specific receptor for Gal/GalNAc-terminated glycopeptide or glycoprotein. The number of these receptors decreases in patients with chronic liver diseases. Here, we aimed to evaluate the use of 111 In-hexavalent lactoside, a known ASGPR imaging biomarker, as a more sensitive probe to detect small changes in liver reserve in animal models of chronic liver injury...
August 13, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/30102402/impulse-model-based-differential-expression-analysis-of-time-course-sequencing-data
#3
David S Fischer, Fabian J Theis, Nir Yosef
Temporal changes to the concentration of molecular species such as mRNA, which take place in response to various environmental cues, can often be modeled as simple continuous functions such as a single pulse (impulse) model. The simplicity of such functional representations can provide an improved performance on fundamental tasks such as noise reduction, imputation and differential expression analysis. However, temporal gene expression profiles are often studied with models that treat time as a categorical variable, neglecting the dependence between time points...
August 8, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30100533/ph-permeability-profiles-for-drug-substances-experimental-detection-comparison-with-human-intestinal-absorption-and-modelling
#4
Mare Oja, Uko Maran
The influence of pH on human intestinal absorption is frequently not considered in early drug discovery studies in the modelling and subsequent prediction of intestinal absorption for drug candidates. To bridge this gap, in this study, experimental membrane permeability data were measured for current and former drug substances with a parallel artificial membrane permeability assay (PAMPA) at different pH values (3, 5, 7.4 and 9). The presented data are in good agreement with human intestinal absorption, showing a clear influence of pH on the efficiency of intestinal absorption...
July 6, 2018: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/30100073/molecular-classification-of-breast-cancer
#5
REVIEW
Elena Provenzano, Gary A Ulaner, Suet-Feung Chin
Breast cancer is a heterogeneous disease, observed traditionally by morphology and protein expression but, more recently with the advent of modern molecular technologies, at the genomic and transcriptomic level. This review describes the association between the different molecular subtypes with the histologic subtypes of breast cancer alongside some of their major genomic characteristics and illustrates how these subtypes may affect the appearance of tumors on imaging studies. The authors aim to show how molecular stratification can be used to augment traditional methods to improve our understanding of breast cancers and their clinical management...
July 2018: PET Clinics
https://www.readbyqxmd.com/read/30098799/new-classification-of-tauopathies
#6
REVIEW
G U Höglinger, G Respondek, G G Kovacs
Tauopathies are a group of neurodegenerative diseases characterized by pathological intracellular deposits of the protein tau. Isoform composition, morphology and anatomical distribution of cellular tau-immunoreactivities are defining distinct tauopathies as molecular pathological disease entities. The clinical spectrum of tauopathies includes syndromes with primary motor symptoms and with primary cognitive dysfunction. The traditional syndrome-based classification is currently being complemented by a molecular-pathological classification...
August 8, 2018: Revue Neurologique
https://www.readbyqxmd.com/read/30098726/the-genesis-of-the-neuroendocrine-tumors-concept-from-oberndorfer-to-2018
#7
REVIEW
Kjell Öberg
The concept of neuroendocrine tumors (NETs) began in the 1900s with Oberndorfer's description of carcinoid tumors, followed by specific cytotoxic agents and the identification of somatostatin. NETs diagnosis was confirmed by World Health Organization classification. Histopathology included immunohistochemistry with specific antibodies. Imaging was refined with molecular imaging. Somatostatin is the leading agent for controlling clinical symptoms related to hormone production. Increasing interest in these tumors, previously thought rare, led to increased incidence and prevalence...
September 2018: Endocrinology and Metabolism Clinics of North America
https://www.readbyqxmd.com/read/30097567/maximal-viral-information-recovery-from-sequence-data-using-virmap
#8
Nadim J Ajami, Matthew C Wong, Matthew C Ross, Richard E Lloyd, Joseph F Petrosino
Accurate classification of the human virome is critical to a full understanding of the role viruses play in health and disease. This implies the need for sensitive, specific, and practical pipelines that return precise outputs while still enabling case-specific post hoc analysis. Viral taxonomic characterization from metagenomic data suffers from high background noise and signal crosstalk that confounds current methods. Here we develop VirMAP that overcomes these limitations using techniques that merge nucleotide and protein information to taxonomically classify viral reconstructions independent of genome coverage or read overlap...
August 10, 2018: Nature Communications
https://www.readbyqxmd.com/read/30097523/wide-range-of-clinical-outcomes-in-patients-with-gliomatosis-cerebri-growth-pattern-a-clinical-radiographic-and-histopathologic-study
#9
K Ina Ly, Derek H Oakley, Alexander B Pine, Matthew P Frosch, Sy Han Chiou, Rebecca A Betensky, Stuart R Pomerantz, Fred H Hochberg, Tracy T Batchelor, Daniel P Cahill, Jorg Dietrich
BACKGROUND: The 2016 World Health Organization Classification of Central Nervous System Tumors categorizes gliomatosis cerebri growth pattern (GC) as a subgroup of diffuse infiltrating gliomas, defined by extent of brain involvement on magnetic resonance imaging (MRI). Clinical and radiographic features in GC patients are highly heterogeneous; however, prognosis has historically been considered poor. SUBJECTS, MATERIALS, AND METHODS: We performed a retrospective search for patients at our institution meeting radiographic criteria of primary, type I GC (defined as diffuse tumor infiltration without associated tumor mass and contrast enhancement on MRI) and analyzed their clinical, imaging, and histopathologic features...
August 10, 2018: Oncologist
https://www.readbyqxmd.com/read/30097488/non-invasive-detection-of-ctdna-reveals-intratumour-heterogeneity-and-is-associated-with-tumour-burden-in-gastrointestinal-stromal-tumour
#10
Heidi M Namløs, Kjetil Boye, Skyler J Mishkin, Tale Barøy, Susanne Lorenz, Bodil Bjerkehagen, Eva W Stratford, Else Munthe, Brian A Kudlow, Ola Myklebost, Leonardo A Meza-Zepeda
Molecular analysis of circulating tumour DNA (ctDNA) has a large potential for clinical application by capturing tumour-specific aberrations through non-invasive sampling. In gastrointestinal stromal tumour (GIST), analysis of KIT and PDGFRA mutations is important for therapeutic decisions, but the invasiveness of traditional biopsies limits the possibilities for repeated sampling. Using targeted next-generation sequencing, we have analysed circulating cell-free DNA from 50 GIST patients. Tumour-specific mutations were detected in 16 of 44 plasma samples (36%) from treatment-naïve patients and in 3 of 6 (50%) patients treated with tyrosine kinase inhibitors...
August 10, 2018: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/30096814/predicting-microrna-mediated-gene-regulation-between-human-and-viruses
#11
Xin Shu, Xinyuan Zang, Xiaoshuang Liu, Jie Yang, Jin Wang
MicroRNAs (miRNAs) mediate various biological processes by actively fine-tuning gene expression at the post-transcriptional level. With the identification of numerous human and viral miRNAs, growing evidence has indicated a common role of miRNAs in mediating the interactions between humans and viruses. However, there is only limited information about Cross-Kingdom miRNA target sites from studies. To facilitate an extensive investigation on the interplay among the gene regulatory networks of humans and viruses, we designed a prediction pipeline, mirTarP, that is suitable for miRNA target screening on the genome scale...
August 8, 2018: Cells
https://www.readbyqxmd.com/read/30096798/sonic-hedgehog-medulloblastoma-cancer-stem-cells-mirnome-and-transcriptome-highlight-novel-functional-networks
#12
Agnese Po, Luana Abballe, Claudia Sabato, Francesca Gianno, Martina Chiacchiarini, Giuseppina Catanzaro, Enrico De Smaele, Felice Giangaspero, Elisabetta Ferretti, Evelina Miele, Zein Mersini Besharat
Molecular classification has improved the knowledge of medulloblastoma (MB), the most common malignant brain tumour in children, however current treatments cause severe side effects in patients. Cancer stem cells (CSCs) have been described in MB and represent a sub population characterised by self-renewal and the ability to generate tumour cells, thus representing the reservoir of the tumour. To investigate molecular pathways that characterise this sub population, we isolated CSCs from Sonic Hedgehog Medulloblastoma (SHH MB) arisen in Patched 1 ( Ptch1 ) heterozygous mice, and performed miRNA- and mRNA-sequencing...
August 8, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/30096299/molecular-diversity-and-specializations-among-the-cells-of-the-adult-mouse-brain
#13
Arpiar Saunders, Evan Z Macosko, Alec Wysoker, Melissa Goldman, Fenna M Krienen, Heather de Rivera, Elizabeth Bien, Matthew Baum, Laura Bortolin, Shuyu Wang, Aleksandrina Goeva, James Nemesh, Nolan Kamitaki, Sara Brumbaugh, David Kulp, Steven A McCarroll
The mammalian brain is composed of diverse, specialized cell populations. To systematically ascertain and learn from these cellular specializations, we used Drop-seq to profile RNA expression in 690,000 individual cells sampled from 9 regions of the adult mouse brain. We identified 565 transcriptionally distinct groups of cells using computational approaches developed to distinguish biological from technical signals. Cross-region analysis of these 565 cell populations revealed features of brain organization, including a gene-expression module for synthesizing axonal and presynaptic components, patterns in the co-deployment of voltage-gated ion channels, functional distinctions among the cells of the vasculature and specialization of glutamatergic neurons across cortical regions...
August 9, 2018: Cell
https://www.readbyqxmd.com/read/30095247/organization-of-amino-acids-into-layered-supramolecular-secondary-structures
#14
Santu Bera, Sudipta Mondal, Sigal Rencus-Lazar, Ehud Gazit
The unique physiochemical properties and multiscale organization of layered materials draw the attention of researchers across a wide range of scientific disciplines. Layered structures are commonly found in diverse biological systems where they fulfill various functions. A prominent example of layered biological materials is the organization of proteins and polypeptides into the archetypal aggregated amyloidal structures. While the organization of proteins into amyloid structures was initially associated with various degenerative disorders, it was later revealed that proteins not related to any disease could also form identical layered assemblies...
August 10, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/30094880/analysis-of-factors-related-to-the-occurrence-of-important-drug-specific-postmarketing-safety-related-regulatory-actions-a-cohort-study-focused-on-first-in-class-drugs
#15
Junji Ikeda, Masayuki Kaneko, Mamoru Narukawa
PURPOSE: First-in-class (FIC) drugs with novel modes of action pose concerns regarding important postmarketing safety issues. The purpose of this study was to analyze the factors related to the occurrence of postmarketing safety-related regulatory actions (PSRAs) for drugs approved in the United States (US), with a focus on FIC drugs. METHODS: New molecular entities and new therapeutic biologics approved in the United States between 1 January 2003 and 31 December 2013 were included in the analysis...
August 10, 2018: Pharmacoepidemiology and Drug Safety
https://www.readbyqxmd.com/read/30094534/fragment-of-the-aspartyl-trna-synthetase-applicable-as-a-shared-classification-and-phylogenetic-marker-in-particular-representatives-of-the-order-lactobacillales
#16
Chahrazed Mekadim, Jiří Killer, Radko Pechar, Jakub Mrázek
The order Lactobacillales represents a morphologically, metabolically, and physiologically diverse group of bacteria. Lactic acid bacteria represent the core of this phylogenetic group. They are a part of epiphytic microflora, fermented dairy, meat, fruit and vegetable products, and the digestive tract of humans and animals. Despite the fact that these bacteria form a phenotypically and genotypically heterogeneous group, their phylogenetic relationship enables to propose a common genetic marker usable in classification, typing, and phylogeny...
August 9, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/30094339/molecular-karyotyping-in-children-and-adolescents-with-gender-dysphoria
#17
Ken C Pang, Debi Feldman, Ralph Oertel, Michelle Telfer
Purpose: The presence of a disorder of sexual development (DSD) acts as a diagnostic specifier for gender dysphoria (GD) under DSM-5, while the International Classification of Diseases (ICD)-10 specifically states that its equivalent diagnosis, gender identity disorder (GID), must not be the result of a chromosomal abnormality. For these reasons, routine karyotyping has been previously advocated in the clinical work-up of children and adolescents with suspected GD or GID. However, the utility of such testing remains unclear...
2018: Transgender Health
https://www.readbyqxmd.com/read/30092821/clonal-relatedness-in-tumour-pairs-of-breast-cancer-patients
#18
Jana Biermann, Toshima Z Parris, Szilárd Nemes, Anna Danielsson, Hanna Engqvist, Elisabeth Werner Rönnerman, Eva Forssell-Aronsson, Anikó Kovács, Per Karlsson, Khalil Helou
BACKGROUND: Molecular classification of tumour clonality is currently not evaluated in multiple invasive breast carcinomas, despite evidence suggesting common clonal origins. There is no consensus about which type of data (e.g. copy number, mutation, histology) and especially which statistical method is most suitable to distinguish clonal recurrences from independent primary tumours. METHODS: Thirty-seven invasive breast tumour pairs were stratified according to laterality and time interval between the diagnoses of the two tumours...
August 9, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/30092720/cancer-subtype-discovery-using-prognosis-enhanced-neural-network-classifier-in-multigenomic-data
#19
Prasanna Vasudevan, Thangamani Murugesan
OBJECTIVE: The main objective in studying large-scale cancer omics is to identify molecular mechanisms of cancer and discover novel biomedical targets. This work not only discovers the cancer subtypes in genome scale data by using clustering and classification but also measures their accuracy. METHODS: Initially, candidate cancer subtypes are recognized by max-flow/min-cut graph clustering. Finally, prognosis-enhanced neural network classifier is proposed for classification...
January 1, 2018: Technology in Cancer Research & Treatment
https://www.readbyqxmd.com/read/30090576/-in-silico-prediction-of-chemical-genotoxicity-using-machine-learning-methods-and-structural-alerts
#20
Defang Fan, Hongbin Yang, Fuxing Li, Lixia Sun, Peiwen Di, Weihua Li, Yun Tang, Guixia Liu
Genotoxicity tests can detect compounds that have an adverse effect on the process of heredity. The in vivo micronucleus assay, a genotoxicity test method, has been widely used to evaluate the presence and extent of chromosomal damage in human beings. Due to the high cost and laboriousness of experimental tests, computational approaches for predicting genotoxicity based on chemical structures and properties are recognized as an alternative. In this study, a dataset containing 641 diverse chemicals was collected and the molecules were represented by both fingerprints and molecular descriptors...
March 1, 2018: Toxicology Research
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