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https://www.readbyqxmd.com/read/29156837/meta-analysis-of-efficacy-and-adverse-events-of-erlotinib-based-targeted-therapies-for-advanced-metastatic-non-small-cell-lung-cancer
#1
Fei Li, Shu-Hua Zhang, Li-Min Pang
A network meta-analysis evaluating efficacy and adverse events of eight erlotinib-based therapies (erlotinib+placebo, erlotinib+tivantinib, erlotinib+celecoxib, erlotinib+onartuzumab, erlotinib+sunitinib, erlotinib+entinostat, erlotinib+sorafenib, and erlotinib+bevacizumab) for advanced/metastatic non-small-cell lung cancer (NSCLC) was performed. PubMed and Cochrane Library were reviewed, and ten randomized controlled trials were identified in which patients receiving at least one erlotinib-based therapy. Efficacy outcomes, including progression-free survival (PFS), overall survival (OS), overall response rate (ORR), disease control rate (DCR), and adverse outcomes were evaluated...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#2
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156680/vemurafenib-resistance-via-de-novo-rbm-genes-mutations-and-chromosome-5-aberrations-is-overcome-by-combined-therapy-with-palbociclib-in-thyroid-carcinoma-with-braf-v600e
#3
Zeus A Antonello, Nancy Hsu, Manoj Bhasin, Giovanni Roti, Mukta Joshi, Paul Van Hummelen, Emily Ye, Agnes S Lo, S Ananth Karumanchi, Christine R Bryke, Carmelo Nucera
Purpose: Papillary thyroid carcinoma (PTC) is the most frequent endocrine tumor. BRAF(V600E) represents the PTC hallmark and is targeted with selective inhibitors (e.g. vemurafenib). Although there have been promising results in clinical trials using these inhibitors, most patients develop resistance and progress. Tumor clonal diversity is proposed as one mechanism underlying drug resistance. Here we have investigated mechanisms of primary and secondary resistance to vemurafenib in BRAF(WT/V600E)-positive PTC patient-derived cells with P16(-/-) (CDKN2A(-/-))...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156542/computational-approaches-for-integrative-analysis-of-the-metabolome-and-microbiome
#4
REVIEW
Jasmine Chong, Jianguo Xia
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies...
November 18, 2017: Metabolites
https://www.readbyqxmd.com/read/29156541/effect-of-alumina-incorporation-on-the-surface-mineralization-and-degradation-of-a-bioactive-glass-cao-mgo-sio%C3%A2-na%C3%A2-o-p%C3%A2-o%C3%A2-caf%C3%A2-glycerol-paste
#5
Dilshat Tulyaganov, Khasan Abdukayumov, Olim Ruzimuradov, Mirabbos Hojamberdiev, Emanuel Ionescu, Ralf Riedel
This study investigates the dissolution behavior as well as the surface biomineralization in simulated body fluid (SBF) of a paste composed of glycerol (gly) and a bioactive glass in the system CaO-MgO-SiO₂-Na₂O-P₂O₅-CaF₂ (BG). The synthesis of the bioactive glass in an alumina crucible has been shown to significantly affect its bioactivity due to the incorporation of aluminum (ca. 1.3-1.4 wt %) into the glass network. Thus, the kinetics of the hydroxyapatite (HA) mineralization on the glass prepared in the alumina crucible was found to be slower than that reported for the same glass composition prepared in a Pt crucible...
November 18, 2017: Materials
https://www.readbyqxmd.com/read/29156215/gadolinium-perturbs-expression-of-skeletogenic-genes-calcium-uptake-and-larval-development-in-phylogenetically-distant-sea-urchin-species
#6
Chiara Martino, Caterina Costa, Maria Carmela Roccheri, Demian Koop, Rosaria Scudiero, Maria Byrne
Chelates of Gadolinium (Gd), a lanthanide metal, are employed as contrast agents for magnetic resonance imaging and are released into the aquatic environment where they are an emerging contaminant. We studied the effects of environmentally relevant Gd concentrations on the development of two phylogenetically and geographically distant sea urchin species: the Mediterranean Paracentrotus lividus and the Australian Heliocidaris tuberculata. We found a general delay of embryo development at 24h post-fertilization, and a strong inhibition of skeleton growth at 48h...
November 11, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/29156070/medical-crowdfunding-for-patients-undergoing-orthopedic-surgery
#7
Wesley M Durand, Joseph R Johnson, Adam E M Eltorai, Alan H Daniels
Crowdfunding for medical expenses is growing in popularity. Through several websites, patients create public campaign profiles to which donors can contribute. Research on medical crowdfunding is limited, and there have been no studies of crowdfunding in orthopedics. Active medical crowdfunding campaigns for orthopedic trauma, total joint arthroplasty, and spine surgery were queried from a crowdfunding website. The characteristics and outcomes of crowdfunding campaigns were abstracted and analyzed. For this study, 444 campaigns were analyzed, raising a total of $1,443,528...
November 20, 2017: Orthopedics
https://www.readbyqxmd.com/read/29156009/discovering-cancer-vulnerabilities-using-high-throughput-micro-rna-screening
#8
Iva Nikolic, Benjamin Elsworth, Eoin Dodson, Sunny Z Wu, Cathryn M Gould, Pieter Mestdagh, Glenn M Marshall, Lisa G Horvath, Kaylene J Simpson, Alexander Swarbrick
Micro-RNAs (miRNAs) are potent regulators of gene expression and cellular phenotype. Each miRNA has the potential to target hundreds of transcripts within the cell thus controlling fundamental cellular processes such as survival and proliferation. Here, we exploit this important feature of miRNA networks to discover vulnerabilities in cancer phenotype, and map miRNA-target relationships across different cancer types. More specifically, we report the results of a functional genomics screen of 1280 miRNA mimics and inhibitors in eight cancer cell lines, and its presentation in a sophisticated interactive data portal...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155983/meox1-accelerates-myocardial-hypertrophic-decompensation-through-gata4
#9
Dan Lu, Jizheng Wang, Jing Li, Feifei Guan, Xu Zhang, Wei Dong, Ning Liu, Shan Gao, Lianfeng Zhang
Aims: Pathological hypertrophy is the result of gene network regulation, which ultimately leads to adverse cardiac remodelling and heart failure (HF), and is accompanied by the reactivation of a 'foetal gene programme'. The Mesenchyme homeobox 1 (Meox1) gene is one of the foetal programme genes. Meox1 may play a role in embryonic development, but its regulation of pathological hypertrophy is not known. Therefore, this study investigated the effect of Meox1 on pathological hypertrophy, including familial and pressure overload-induced hypertrophy, and its potential mechanism of action...
November 16, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/29155944/molecular-interaction-search-tool-mist-an-integrated-resource-for-mining-gene-and-protein-interaction-data
#10
Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie E Mohr, Norbert Perrimon
Model organism and human databases are rich with information about genetic and physical interactions. These data can be used to interpret and guide the analysis of results from new studies and develop new hypotheses. Here, we report the development of the Molecular Interaction Search Tool (MIST; http://fgrtools.hms.harvard.edu/MIST/). The MIST database integrates biological interaction data from yeast, nematode, fly, zebrafish, frog, rat and mouse model systems, as well as human. For individual or short gene lists, the MIST user interface can be used to identify interacting partners based on protein-protein and genetic interaction (GI) data from the species of interest as well as inferred interactions, known as interologs, and to view a corresponding network...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155928/modeling-positional-effects-of-regulatory-sequences-with-spline-transformations-increases-prediction-accuracy-of-deep-neural-networks
#11
Žiga Avsec, Mohammadamin Barekatain, Jun Cheng, Julien Gagneur
Motivation: Regulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries, or polyadenylation site. Deep learning has become the approach of choice for modeling regulatory sequences because of its strength to learn complex sequence features. However, modeling relative distances to genomic landmarks in deep neural networks has not been addressed. Results: Here we developed spline transformation, a neural network module based on splines to flexibly and robustly model distances...
November 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29155820/mass-spectrometry-based-quantification-of-the-cellular-response-to-ultraviolet-radiation-in-hela-cells
#12
Hong Xu, Xuanyi Chen, Nanjiao Ying, Meixia Wang, Xiaoli Xu, Rongyi Shi, Yuejin Hua
Ultraviolet (UV) irradiation is a common form of DNA damage that can cause pyrimidine dimers between DNA, which can cause gene mutations, even double-strand breaks and threaten genome stability. If DNA repair systems default their roles at this stage, the organism can be damaged and result in disease, especially cancer. To better understand the cellular response to this form of damage, we applied highly sensitive mass spectrometry to perform comparative proteomics of phosphorylation in HeLa cells. A total of 4367 phosphorylation sites in 2100 proteins were identified, many of which had not been reported previously...
2017: PloS One
https://www.readbyqxmd.com/read/29155816/liposomal-amphotericin-b-in-travelers-with-cutaneous-and-muco-cutaneous-leishmaniasis-not-a-panacea
#13
Romain Guery, Benoit Henry, Guillaume Martin-Blondel, Claire Rouzaud, Florence Cordoliani, Gundel Harms, Jean-Pierre Gangneux, Françoise Foulet, Emmanuelle Bourrat, Michel Baccard, Gloria Morizot, Paul-Henri Consigny, Antoine Berry, Johannes Blum, Olivier Lortholary, Pierre Buffet
BACKGROUND: Complex cutaneous and muco-cutaneous leishmaniasis (CL and MCL) often requires systemic therapy. Liposomal amphotericin B (L-AmB) has a strong potential for a solid clinical benefit in this indication. METHODS: We conducted a retrospective analysis of data from a French centralized referral treatment program and from the "LeishMan" European consortium database. All patients with parasitologically proven CL or MCL who received at least one dose of L-AmB were included...
November 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29155775/mapping-genome-wide-accessible-chromatin-in-primary-human-t-lymphocytes-by-atac-seq
#14
Ivana Grbesa, Miriam Tannenbaum, Avital Sarusi-Portuguez, Michal Schwartz, Ofir Hakim
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs...
November 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155751/dissection-and-immunofluorescent-staining-of-mushroom-body-and-photoreceptor-neurons-in-adult-drosophila-melanogaster-brains
#15
Seth M Kelly, Alexandra Elchert, Michael Kahl
Nervous system development involves a sequential series of events that are coordinated by several signaling pathways and regulatory networks. Many of the proteins involved in these pathways are evolutionarily conserved between mammals and other eukaryotes, such as the fruit fly Drosophila melanogaster, suggesting that similar organizing principles exist during the development of these organisms. Importantly, Drosophila has been used extensively to identify cellular and molecular mechanisms regulating processes that are required in mammals including neurogenesis, differentiation, axonal guidance, and synaptogenesis...
November 6, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155609/using-neural-networks-to-predict-hfacs-unsafe-acts-from-the-pre-conditions-of-unsafe-acts
#16
Don Harris, Wen-Chin Li
HFACS (Human Factors Analysis and Classification System) is based upon Reason's (1990; 1997) organizational model of human error which suggests that there is a 'one to many' mapping of condition tokens (HFACS level 2 psychological precursors) to unsafe act tokens (HFACS level 1 error and violations). Using accident data derived from 523 military aircraft accidents, the relationship between HFACS level 2 pre-conditions and level 1 unsafe acts was modelled using an artificial Neural Network (NN). This allowed an empirical model to be developed congruent with the underlying theory of HFACS...
November 18, 2017: Ergonomics
https://www.readbyqxmd.com/read/29155562/quantification-of-nanomaterial-nanomedicine-trafficking-in-vivo
#17
Liming Wang, Liang Yan, Jing Liu, Chunying Chen, Yuliang Zhao
Absorption, distribution, metabolism and excretion (ADME) of nanomaterials (NMs) or nanomedicines (NMs), are fundamental biological processes that dominate their nanomedical functions or nanotoxicities. Mostly, NMs exist in biological systems as a form of nanoparticles (NPs). However, to determine the composition, spatial distribution, and states of existence of NMs/NPs in vivo, upon entry into the body, as well as to monitor the dynamic changes of these information over time remain a challenge for the current analytical methodology due to their limited efficiently in characterizing interactions between these complex(nano)-complex(bio) systems...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29155504/cervical-funneling-or-intra-amniotic-debris-and-preterm-birth-among-nulliparous-women-with-a-midtrimester-cervical-length-less-than-30-mm
#18
George R Saade, Elizabeth A Thom, William A Grobman, Jay D Iams, Brian M Mercer, Uma M Reddy, Alan T N Tita, Dwight J Rouse, Yoram Sorokin, Ronald J Wapner, Kenneth J Leveno, Sean C Blackwell, M Sean Esplin, Jorge E Tolosa, John M Thorp, Steve N Caritis, J Peter VanDorsten
OBJECTIVE: To evaluate whether the presence of cervical funneling or intra-amniotic debris identified in the second trimester is associated with higher rates of preterm birth (PTB) in asymptomatic nulliparous women with a midtrimester cervical length (CL) less than 30 mm (i.e., less than the 10(th) percentile). METHODS: A secondary cohort analysis of a multicenter trial of women between 16 and 22 weeks with a singleton gestation and a CL less than 30 mm by transvaginal ultrasound randomized to either 17-alpha hydroxyprogesterone caproate or placebo...
November 20, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/29155333/ima-identifying-disease-related-genes-using-mesh-terms-and-association-rules
#19
Jeongwoo Kim, Changbae Bang, Hyeonseo Hwang, Doyoung Kim, Chihyun Park, Sanghyun Park
Genes play an important role in several diseases. Hence, in biology, identifying relationships between diseases and genes is important for the analysis of diseases, because mutated or dysregulated genes play an important role in pathogenesis. Here, we propose a method to identify disease-related genes using MeSH terms and association rules. We identified genes by analyzing the MeSH terms and extracted information on gene-gene interactions based on association rules. By integrating the extracted interactions, we constructed gene-gene networks and identified disease-related genes...
November 15, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29155263/identification-and-characterisation-of-the-epididymal-proteins-in-the-lizard-eutropis-carinata-reptilia-squamata-schneider-1801
#20
R Medini, M Bhagya, S Samson
Lizards are seasonal breeders. Cyclic reproductive nature makes lizard as a useful model for the study of the reproductively active protein secretions in the epididymis. During breeding season, the epididymides of the lizard secret proteins that mixes with the spermatozoa and create a favourable environment for sperm maturation. In this spectrum, the aim of this study is to identify and characterize proteins which are present in the lumen of the epididymis of the lizard, E. carinata during the active phase of reproduction...
November 16, 2017: General and Comparative Endocrinology
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