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https://www.readbyqxmd.com/read/29166735/-the-specific-cytotoxicities-of-chimeric-antigen-receptor-engineered-t-cells-on-different-lymphomas
#1
R Zhang, Q Deng, S N Sui, X Jin, M F Zhao
Objective: To investigate the specific cytotoxicities of the second and third generations of chimeric antigen receptor (CAR) -engineered T cells (CAR-T) on different lymphomas. Methods: CAR-Ts were prepared by lentivirus packaging and infection of T cells. CCK-8, ELISA and Lactate dehydrogenase cytotoxicity assay were applied to detect the proliferation capacity, the secretion level of inflammatory factor and the specific cytotoxicity. Flow cytometry assay showed the specific cytotoxicity and residual level of CAR-T in lymphomas of treated mice...
October 14, 2017: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/29165655/expression-atlas-gene-and-protein-expression-across-multiple-studies-and-organisms
#2
Irene Papatheodorou, Nuno A Fonseca, Maria Keays, Y Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew Geniza, Justin Preece, Pankaj Jaiswal, Andrew F Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaino, Alvis Brazma, Robert Petryszak
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165643/expanding-the-repertoire-of-dna-shape-features-for-genome-scale-studies-of-transcription-factor-binding
#3
Jinsen Li, Jared M Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs
Uncovering the mechanisms that affect the binding specificity of transcription factors (TFs) is critical for understanding the principles of gene regulation. Although sequence-based models have been used successfully to predict TF binding specificities, we found that including DNA shape information in these models improved their accuracy and interpretability. Previously, we developed a method for modeling DNA binding specificities based on DNA shape features extracted from Monte Carlo (MC) simulations. Prediction accuracies of our models, however, have not yet been compared to accuracies of models incorporating DNA shape information extracted from X-ray crystallography (XRC) data or Molecular Dynamics (MD) simulations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165330/prediction-of-mortality-in-patients-with-isolated-traumatic-subarachnoid-hemorrhage-using-a-decision-tree-classifier-a-retrospective-analysis-based-on-a-trauma-registry-system
#4
Cheng-Shyuan Rau, Shao-Chun Wu, Peng-Chen Chien, Pao-Jen Kuo, Yi-Chun Chen, Hsiao-Yun Hsieh, Ching-Hua Hsieh
Background: In contrast to patients with traumatic subarachnoid hemorrhage (tSAH) in the presence of other types of intracranial hemorrhage, the prognosis of patients with isolated tSAH is good. The incidence of mortality in these patients ranges from 0-2.5%. However, few data or predictive models are available for the identification of patients with a high mortality risk. In this study, we aimed to construct a model for mortality prediction using a decision tree (DT) algorithm, along with data obtained from a population-based trauma registry, in a Level 1 trauma center...
November 22, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29164570/von-willebrand-factor-and-adamts13-plasma-in-older-patients-with-high-cha2ds2-vasc-score-with-and-without-atrial-fibrillation
#5
F Zhang, X-C Yang, X-W Jia, X-H Tang, Z Wang, Z-Q Wang
OBJECTIVE: Ischemic stroke risk rises with the increasing cardiovascular risk factors in patients with and without AF. How atrial fibrillation (AF) incrementally contributes to the risk for ischemic stroke with increasing age and multiple cardiovascular risk factors is unclear. Von Willebrand factor (vWF) is a biomarker of endothelial dysfunction. PATIENTS AND METHODS: We suggested that in older patients with high CHA2DS2-VASc Score, the vWF and ADAMTS13 would be comparable between patients with and without AF...
November 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29162056/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies
#6
Rhys A Farrer
BACKGROUND: Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes. RESULTS: Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29161628/stigma-accounts-for-depression-in-patients-with-epilepsy
#7
Zerrin Yıldırım, Devrimsel Harika Ertem, Ayten Ceyhan Dirican, Sevim Baybaş
OBJECTIVE: Epilepsy is a chronic disease with an increased risk of stigmatization due to psychosocial consequences of the seizures. Intuitively, one may well conclude that stigmatization would lead to depression in patients with epilepsy as well as in other patient groups with increased risk of stigmatization. Indeed, there are a few studies in support of this intuition. In this study, we aimed to investigate the relationship between level of stigmatization and the severity of the depressive symptoms in our patients with epilepsy...
November 18, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/29157446/dynamic-visualization-of-multi-level-molecular-data-the-director-package-in-r
#8
Katherine Icay, Chengyu Liu, Sampsa Hautaniemi
BACKGROUND AND OBJECTIVE: High-throughput measurement technologies have triggered a rise in large-scale cancer studies containing multiple levels of molecular data. While there are a number of efficient methods to analyze individual data types, there are far less that enhance data interpretation after analysis. We present the R package Director, a dynamic visualization approach to linking and interrogating multiple levels of molecular data after analysis for clinically meaningful, actionable insights...
January 2018: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29157444/a-tool-to-visualize-and-analyze-perfusion-data-development-and-application-of-the-r-package-ctp
#9
Seth T Lirette, Andrew D Smith, Inmaculada B Aban
BACKGROUND AND OBJECTIVE: Computed tomography perfusion (CTP) is a widely used imaging modality especially in neuroimaging. Despite this, CTP is often prohibitive due to the dearth of free/open-source software. This could have wide-ranging implications for instruction and research. We have implemented an online-available CTP tool built and run completely within the R computing environment. METHODS: Called from within R, the user can select one of four different methods to construct a cerebral blood flow (CBF) map: (1) max-slope (2) singular value decomposition (3) block circulant singular value decomposition or (4) oscillation minimization singular value decomposition...
January 2018: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29157118/efficient-estimation-of-disease-odds-ratios-for-follow-up-genetic-association-studies
#10
Jiyuan Hu, Wei Zhang, Xinmin Li, Dongdong Pan, Qizhai Li
In the past decade, genome-wide association studies have identified thousands of susceptible variants associated with complex human diseases and traits. Conducting follow-up genetic association studies has become a standard approach to validate the findings of genome-wide association studies. One problem of high interest in genetic association studies is to accurately estimate the strength of the association, which is often quantified by odds ratios in case-control studies. However, estimating the association directly by follow-up studies is inefficient since this approach ignores information from the genome-wide association studies...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29155812/fluevidencesynthesis-an-r-package-for-evidence-synthesis-based-analysis-of-epidemiological-outbreaks
#11
Edwin van Leeuwen, Petra Klepac, Dominic Thorrington, Richard Pebody, Marc Baguelin
Public health related decisions often have to balance the cost of intervention strategies with the benefit of the reduction in disease burden. While the cost can often be inferred, forward modelling of the effect of different intervention options is complicated and disease specific. Here we introduce a package that is aimed to simplify this process. The package allows one to infer parameters using a Bayesian approach, perform forward modelling of the likely results of the proposed intervention and finally perform cost effectiveness analysis of the results...
November 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29155666/cdc-activities-for-improving-implementation-of-human-papillomavirus-vaccination-cervical-cancer-screening-and-surveillance-worldwide
#12
Virginia Senkomago, Denise Duran, Anagha Loharikar, Terri B Hyde, Lauri E Markowitz, Elizabeth R Unger, Mona Saraiya
Cervical cancer incidence and mortality rates are high, particularly in developing countries. Most cervical cancers can be prevented by human papillomavirus (HPV) vaccination, screening, and timely treatment. The US Centers for Disease Control and Prevention (CDC) provides global technical assistance for implementation and evaluation of HPV vaccination pilot projects and programs and laboratory-related HPV activities to assess HPV vaccines. CDC collaborates with global partners to develop global cervical cancer screening recommendations and manuals, implement screening, create standardized evaluation tools, and provide expertise to monitor outcomes...
December 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29154499/fuzzyid2-a-software-package-for-large-dataset-species-identification-via-barcoding-and-metabarcoding-using-hidden-markov-models-and-fuzzy-set-methods
#13
Z Y Shi, C Q Yang, M D Hao, X Y Wang, R D Ward, A B Zhang
Species identification through DNA barcoding or metabarcoding has become a key approach for biodiversity evaluation and ecological studies. However, the rapid accumulation of barcoding data has created some difficulties: for instance, global enquiries to a large reference library can take a very long time. We here devise a two-step searching strategy to speed identification procedures of such queries. This firstly uses a Hidden Markov Model (HMM) algorithm to narrow the searching scope to genus level, and then determines the corresponding species using minimum genetic distance...
November 20, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29154114/prevalence-and-predictors-of-phthalate-exposure-in-pregnant-women-in-charleston-sc
#14
Abby G Wenzel, John W Brock, Lori Cruze, Roger B Newman, Elizabeth R Unal, Bethany J Wolf, Stephen E Somerville, John R Kucklick
Phthalates are plasticizers commonly detected in human urine due to widespread exposure from PVC plastics, food packaging, and personal care products. Several phthalates are known antiandrogenic endocrine disruptors, which raises concern for prenatal exposure during critical windows of fetal development. While phthalate exposure is ubiquitous, certain demographics are subject to greater or lesser exposure. We sampled urine from 378 pregnant women during the second trimester of gestation living in Charleston, SC, and measured eight urinary phthalate metabolites as biomarkers of phthalate exposure: monobutyl phthalate (MBP), monobenzyl phthalate (MBzP), mono(2-ethylhexyl) phthalate (MEHP), mono(2-ethyl-5-oxohexyl) phthalate (MEOHP), mono(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP), monoethyl phthalate (MEP), monoisobutyl phthalate (MiBP), and monomethyl phthalate (MMP)...
November 8, 2017: Chemosphere
https://www.readbyqxmd.com/read/29154046/simulation-of-guided-wave-ultrasound-propagation-in-composite-laminates-benchmark-comparisons-of-numerical-codes-and-experiment
#15
Cara A C Leckey, Kevin R Wheeler, Vasyl N Hafiychuk, Halyna Hafiychuk, Doğan A Timuçin
Ultrasonic wave methods constitute the leading physical mechanism for nondestructive evaluation (NDE) and structural health monitoring (SHM) of solid composite materials, such as carbon fiber reinforced polymer (CFRP) laminates. Computational models of ultrasonic wave excitation, propagation, and scattering in CFRP composites can be extremely valuable in designing practicable NDE and SHM hardware, software, and methodologies that accomplish the desired accuracy, reliability, efficiency, and coverage. The development and application of ultrasonic simulation approaches for composite materials is an active area of research in the field of NDE...
November 4, 2017: Ultrasonics
https://www.readbyqxmd.com/read/29153470/impact-of-a-pharmacist-driven-care-package-on-staphylococcus-aureus-bacteremia-management-in-a-large-community-healthcare-network-a-propensity-score-matched-quasi-experimental-study
#16
Jordan R Smith, Jeremy J Frens, Cynthia B Snider, Kimberly C Claeys
OBJECTIVES: Staphylococcus aureus bacteremia (SAB) is an important cause of morbidity and mortality. Suboptimal treatment has been associated with poor patient outcomes. Our antimicrobial stewardship program (ASP) evaluated SAB management based on predefined performance measures both prior to and after instituting a "care package" intervention led by clinical pharmacists and infectious diseases physicians. The primary outcome included a 4-point "optimal care score" (OCS) consisting of targeted antibiotic therapy within 24hours, repeating blood cultures, antibiotic duration assessment, and appropriate duration of therapy...
October 7, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29153179/a-100-year-review-a-century-of-dairy-processing-advancements-pasteurization-cleaning-and-sanitation-and-sanitary-equipment-design
#17
S A Rankin, R L Bradley, G Miller, K B Mildenhall
Over the past century, advancements within the mainstream dairy foods processing industry have acted in complement with other dairy-affiliated industries to produce a human food that has few rivals with regard to safety, nutrition, and sustainability. These advancements, such as milk pasteurization, may appear commonplace in the context of a modern dairy processing plant, but some consideration of how these advancements came into being serve as a basis for considering what advancements will come to bear on the next century of processing advancements...
December 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29153152/a-100-year-review-milestones-in-the-development-of-frozen-desserts
#18
R W Hartel, S A Rankin, R L Bradley
Ice cream has come a long way since the first snow cone was made. Innovations in a variety of areas over the past century have led to the development of highly sophisticated, automated manufacturing plants that churn out pint after pint of ice cream. Significant advances in fields such as mechanical refrigeration, chilling and freezing technologies, cleaning and sanitation, packaging, and ingredient functionality have shaped the industry. Advances in our understanding of the science of ice cream, particularly related to understanding the complex structures that need to be controlled to create a desirable product, have also enhanced product quality and shelf stability...
December 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29152921/proximity-to-pediatric-cardiac-surgical-care-among-adolescents-with-congenital-heart-defects-in-11-new-york-counties
#19
Kristin M Sommerhalter, Tabassum Z Insaf, Tugba Akkaya-Hocagil, Claire E McGarry, Sherry L Farr, Karrie F Downing, George K Lui, Ali N Zaidi, Alissa R Van Zutphen
BACKGROUND: Many individuals with congenital heart defects (CHDs) discontinue cardiac care in adolescence, putting them at risk of adverse health outcomes. Because geographic barriers may contribute to cessation of care, we sought to characterize geographic access to comprehensive cardiac care among adolescents with CHDs. METHODS: Using a population-based, 11-county surveillance system of CHDs in New York, we characterized proximity to the nearest pediatric cardiac surgical care center among adolescents aged 11 to 19 years with CHDs...
November 1, 2017: Birth defects research
https://www.readbyqxmd.com/read/29152649/identification-of-key-genes-in-glioma-cpg-island-methylator-phenotype-via-network-analysis-of-gene-expression-data
#20
Lijuan Bo, Bo Wei, Zhanfeng Wang, Daliang Kong, Zheng Gao, Zhuang Miao
Gene expression data were analysed using bioinformatic tools to demonstrate molecular mechanisms underlying the glioma CpG island methylator phenotype (CIMP). A gene expression data set (accession no. GSE30336) was downloaded from Gene Expression Omnibus, including 36 CIMP+ and 16 CIMP- glioma samples. Differential analysis was performed for CIMP+ vs. CIMP‑ samples using the limma package in R. Functional enrichment analysis was subsequently conducted for differentially expressed genes (DEGs) using Database for Annotation, Visualization and Integration Discovery...
October 19, 2017: Molecular Medicine Reports
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