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https://www.readbyqxmd.com/read/29791923/inhaled-treprostinil-prodrug-lipid-nanoparticle-formulations-provide-long-acting-pulmonary-vasodilation
#1
Franziska G Leifer, Donna M Konicek, Kuan-Ju Chen, Adam J Plaunt, Dany Salvail, Charles E Laurent, Michel R Corboz, Zhili Li, Richard W Chapman, Walter R Perkins, Vladimir S Malinin
Treprostinil (TRE), a prostanoid analogue approved in the USA for the treatment of pulmonary arterial hypertension, requires continuous infusion or multiple dosing sessions per day for inhaled and oral routes of administration due to its short half-life. The inhaled drug is known to induce adverse systemic and local effects including headache, nausea, cough, and throat irritation which may be due at least in part to transiently high drug concentrations in the lungs and plasma immediately following administration [1]...
May 23, 2018: Drug Research
https://www.readbyqxmd.com/read/29790936/simextargid-a-comprehensive-package-for-real-time-lc-ms-data-acquisition-and-analysis
#2
William M B Edmands, Josie Hayes, Stephen M Rappaport
Summary: Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790906/bcseq-an-r-package-for-fast-sequence-mapping-in-high-throughput-shrna-and-crispr-screens
#3
Jiaxing Lin, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan, Jichun Xie, Kouros Owzar
Summary: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29788468/caviar-an-r-package-for-checking-displaying-and-processing-wood-formation-monitoring-data
#4
Cyrille B K Rathgeber, Philippe Santenoise, Henri E Cuny
In the last decade, the pervasive question of climate change impacts on forests has revived investigations on intra-annual dynamics of wood formation, involving disciplines such as plant ecology, tree physiology and dendrochronology. This resulted in the creation of many research groups working on this topic worldwide and a rapid increase in the number of studies and publications. Wood-formation-monitoring studies are generally based on a common conceptual model describing xylem cell formation as the succession of four differentiation phases (cell division, cell enlargement, cell wall thickening and mature cells)...
May 19, 2018: Tree Physiology
https://www.readbyqxmd.com/read/29786957/statistical-approaches-to-adjusting-weights-for-dependent-arms-in-network-meta-analysis
#5
Yu-Xuan Su, Yu-Kang Tu
Network meta-analysis compares multiple treatments in terms of their efficacy and harm by including evidence from randomized controlled trials. Most clinical trials use parallel design, where patients are randomly allocated to different treatments and receive only one treatment. However, some trials use within person designs such as split-body, split-mouth and cross-over designs, where each patient may receive more than one treatment. Data from treatment arms within these trials are no longer independent, so the correlations between dependent arms need to be accounted for within the statistical analyses...
May 22, 2018: Research Synthesis Methods
https://www.readbyqxmd.com/read/29785339/identification-of-potential-crucial-genes-and-pathways-associated-with-vein-graft-restenosis-based-on-gene-expression-analysis-in-experimental-rabbits
#6
Qiang Liu, Xiujie Yin, Mingzhu Li, Li Wan, Liqiao Liu, Xiang Zhong, Zhuoqi Liu, Qun Wang
Occlusive artery disease (CAD) is the leading cause of death worldwide. Bypass graft surgery remains the most prevalently performed treatment for occlusive arterial disease, and veins are the most frequently used conduits for surgical revascularization. However, the clinical efficacy of bypass graft surgery is highly affected by the long-term potency rates of vein grafts, and no optimal treatments are available for the prevention of vein graft restenosis (VGR) at present. Hence, there is an urgent need to improve our understanding of the molecular mechanisms involved in mediating VGR...
2018: PeerJ
https://www.readbyqxmd.com/read/29784576/normal-values-and-growth-related-changes-of-left-ventricular-volumes-stress-and-strain-in-healthy-children-measured-by-3-dimensional-echocardiography
#7
Joseph D Kuebler, Sunil Ghelani, David M Williams, Meena Nathan, Gerald Marx, Steven D Colan, David M Harrild
Normal pediatric values of three-dimensional (3D) left ventricular (LV) volumes and strain are not well established; moreover, no reports exist of the stress-strain relation and the heart rate-corrected velocity of circumferential fiber shortening (VCFc) based upon 3D imaging in children. Three-dimensional LV datasets were obtained in pediatric patients (≤18 years of age) with structurally normal hearts. Ventricular volumes and strain components (longitudinal, GLS; circumferential, GCS; and 3D strain, 3DS) were analyzed using a commercial 3D speckle-tracking analysis package...
April 24, 2018: American Journal of Cardiology
https://www.readbyqxmd.com/read/29782266/-the-association-of-gene-polymorphisms-of-matrix-metalloproteinases-9-12-and-20-and-collagen-type-i-degradation-products-with-the-remodeling-of-the-left-ventricle-in-patients-with-acute-myocardial-infarction
#8
N A Sokolova, M S Danshova, A V Govorin, D N Zaytsev, Y N Smolyakov
OBJECTIVE: to study associations of polymorphism of the genes MMP9 rs17576, MMP12 rs2276109, MMP20 rs2245803, COL1A1 rs1800012, COL1A1 rs1107946 with remodeling of the left ventricle in patients with acute myocardial infarction. MATERIALS AND METHODS: We examined 84 patients with myocardial infarction (MI). Type of early postinfarction left ventricular (LV) remodeling was determined by echocardiography on the third day of the disease. Concentration of matrix metalloproteinases (MMP) was measured by enzyme immunoassay using commercial kits; content of C-terminal telopeptide of collagen type I degradation products (ICTP) was measured by chemiluminescent immunoassay...
March 2018: Kardiologiia
https://www.readbyqxmd.com/read/29780985/the-correlation-between-gelatin-macroscale-differences-and-nanoparticle-properties-providing-insight-into-biopolymer-variability
#9
André T Stevenson, Danny J Jankus, Max A Tarshis, Abby R Whittington
From therapeutic delivery to sustainable packaging, manipulation of biopolymers into nanostructures imparts biocompatibility to numerous materials with minimal environmental pollution during processing. While biopolymers are appealing natural based materials, the lack of nanoparticle (NP) physicochemical consistency has decreased their nanoscale translation into actual products. Insights regarding the macroscale and nanoscale property variation of gelatin, one of the most common biopolymers already utilized in its bulk form, are presented...
May 21, 2018: Nanoscale
https://www.readbyqxmd.com/read/29778507/factors-associated-with-outcomes-and-inpatient-90-day-cost-of-care-in-endometrial-cancer-patients-undergoing-hysterectomy-implications-for-bundled-care-payments
#10
Aimee Rolston, Ryan J Spencer, R Kevin Reynolds, Laurel W Rice, Shitanshu Uppal
OBJECTIVE: To investigate the association of obesity and other comorbidities as well as route of surgery with postoperative outcomes, as well as 30- and 90-day inpatient cost of care after hysterectomy for endometrial cancer. METHODS: From the 2013 National Readmission Database release, patients who underwent hysterectomy for endometrial cancer were included. Obesity was classified as non-obese (body mass index [BMI] < 35 kg/m2 ); class I/II obesity (BMI ≥ 35 but <40 kg/m2 and without obesity related medical condition qualifying it as morbid obesity), class III obesity (BMI ≥ 40 kg/m2 OR BMI ≥ 35 kg/m2 with an obesity-related medical condition)...
May 16, 2018: Gynecologic Oncology
https://www.readbyqxmd.com/read/29778470/genetic-diversity-of-thermoduric-spoilage-microorganisms-of-milk-from-brazilian-dairy-farms
#11
J C Ribeiro Júnior, R Tamanini, A L M de Oliveira, A A Alfieri, V Beloti
When correctly pasteurized, packaged, and stored, milk with low total bacterial counts (TBC) has a longer shelf life. Therefore, microorganisms that resist heat treatments are especially important in the deterioration of pasteurized milk and in its shelf life. The aim of this work was to quantify the thermoduric microorganisms after the pasteurization of refrigerated raw milk samples with low TBC and to identify the diversity of these isolates with proteolytic or lipolytic potential by RFLP analysis. Twenty samples of raw milk were collected in bulk milk tanks shortly after milking in different Brazilian dairy farms and pasteurized...
May 16, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29777750/post-a-framework-for-set-based-association-analysis-in-high-dimensional-data
#12
Xueyuan Cao, E Olusegun George, Mingjuan Wang, Dale B Armstrong, Cheng Cheng, Susana Raimondi, Jeffrey E Rubnitz, James R Downing, Mondira Kundu, Stanley B Pounds
Evaluating the differential expression of a set of genes belonging to a common biological process or ontology has proven to be a very useful tool for biological discovery. However, existing gene-set association methods are limited to applications that evaluate differential expression across k⩾2 treatment groups or biological categories. This limitation precludes researchers from most effectively evaluating the association with other phenotypes that may be more clinically meaningful, such as quantitative variables or censored survival time variables...
May 16, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#13
Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto, Jan Baumbach
BACKGROUND: Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. RESULTS: We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29774217/effective-network-size-predicted-from-simulations-of-pathogen-outbreaks-through-social-networks-provides-a-novel-measure-of-structure-standardized-group-size
#14
Collin M McCabe, Charles L Nunn
The transmission of infectious disease through a population is often modeled assuming that interactions occur randomly in groups, with all individuals potentially interacting with all other individuals at an equal rate. However, it is well known that pairs of individuals vary in their degree of contact. Here, we propose a measure to account for such heterogeneity: effective network size (ENS), which refers to the size of a maximally complete network (i.e., unstructured, where all individuals interact with all others equally) that corresponds to the outbreak characteristics of a given heterogeneous, structured network...
2018: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29771934/multilevel-analysis-of-dendroclimatic-series-with-the-r-package-biodry
#15
Wilson Lara, Stella Bogino, Felipe Bravo
The R-package BIOdry allows to model and compare fluctuations of Tree-ring Width (TRW) and climate, or dendroclimatic fluctuations, while accounting for source variability. The package eases multilevel modeling and multivariate comparison in dendroclimatic analysis using the nlme and ecodist packages, respectively. For implementing such libraries, the in-package algorithms transform the dendroclimatic fluctuations into Multilevel Dendroclimatic Data Series and maintain categorical variables and time units in the outputs...
2018: PloS One
https://www.readbyqxmd.com/read/29771738/prediction-of-transfer-among-multiple-states-of-blood-pressure-based-on-markov-model-an-18-year-cohort-study
#16
Yunfeng Wang, Zhimin Ma, Chaonan Xu, ZiKun Wang, Xinghua Yang
OBJECTIVE: This study aimed to identify the rules of transition between normotension, prehypertension and hypertension states and to establish a prediction model for the incidence of prehypertension and hypertension. METHODS: Data from the China Health and Nutrition Survey from 1991 to 2009 were used as training data to develop the model. Data of the year 2011 were used for model validation. The multistate Markov model was developed using the msm package in R software...
May 15, 2018: Journal of Hypertension
https://www.readbyqxmd.com/read/29771531/exosomes-as-a-drug-delivery-system-in-cancer-therapy-potential-and-challenges
#17
Golam Kibria, Erika Kathryn Ramos, David R Gius, Yong Wan, Huiping Liu
Exosomes play a pivotal role in mediating intercellular communications and package delivery. They have recently been discovered to serve as diagnostic biomarkers as well as a possible drug delivery vehicle based on their nanometer size range and capability to transfer biological materials to recipient cells. Their unique biocompatibility, high stability, preferred tumor homing, and adjustable targeting efficiency can make exosomes an attractive and potentially effective tool of drug delivery in cancer therapy...
May 17, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29771422/has-mir-196a-2-is-up-regulated-and-acts-as-an-independent-unfavorable-prognostic-factor-in-thyroid-carcinoma
#18
Y-T Fu, D-Q Zhang, L Zhou, S-J Li, H Sun, X-L Liu, H-B Zheng
OBJECTIVE: To identify the role of hsa-miR-196a-2 in thyroid cancer by bioinformatics analysis. MATERIALS AND METHODS: The expression profiles of thyroid cancer was download from TCGA. The dysregulated microRNAs were obtained by edger R package. Then, the prognostic data were analyzed by K-M plot. The difference between different groups was analyzed by the t-test. At last, the biological processes of has-miR-196a-2 were obtained with GSEA. RESULTS: In this study, we found that has-miR-196a-2 was upregulated in thyroid carcinoma by analyzing the TCGA database, which was inversely proportional to the prognosis of patients with thyroid carcinoma...
May 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29771315/palimpsest-an-r-package-for-studying-mutational-and-structural-variant-signatures-along-clonal-evolution-in-cancer
#19
Jayendra Shinde, Quentin Bayard, Sandrine Imbeaud, Théo Z Hirsch, Feng Liu, Victor Renault, Jessica Zucman-Rossi, Eric Letouzé
Summary: Cancer genomes are altered by various mutational processes and, like palimpsests, bear the signatures of these different processes. The Palimpsest R package provides a complete workflow for the characterization and visualization of mutational signatures and their evolution along tumor development. The package covers a wide range of functions for extracting both base substitution and structural variant signatures, inferring the clonality of each alteration and analyzing the evolution of mutational processes between early clonal and late subclonal events...
May 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29771280/identification-and-characterization-of-moonlighting-long-non-coding-rnas-based-on-rna-and-protein-interactome
#20
Lixin Cheng, Kwong-Sak Leung
Motivation: Moonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a novel methodology, MoonFinder, for the identification of moonlighting lncRNAs...
May 16, 2018: Bioinformatics
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