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https://www.readbyqxmd.com/read/29151019/bcrocsurface-an-r-package-for-correcting-verification-bias-in-estimation-of-the-roc-surface-and-its-volume-for-continuous-diagnostic-tests
#1
Khanh To Duc
BACKGROUND: Receiver operating characteristic (ROC) surface analysis is usually employed to assess the accuracy of a medical diagnostic test when there are three ordered disease status (e.g. non-diseased, intermediate, diseased). In practice, verification bias can occur due to missingness of the true disease status and can lead to a distorted conclusion on diagnostic accuracy. In such situations, bias-corrected inference tools are required. RESULTS: This paper introduce an R package, named bcROCsurface, which provides utility functions for verification bias-corrected ROC surface analysis...
November 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29145823/dbmdega-a-database-for-meta-analysis-of-differentially-expressed-genes-in-autism-spectrum-disorder
#2
Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng, Guangqin Fan
BACKGROUND: Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed. METHODS: Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples)...
November 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29134543/bayesian-inference-for-psychology-part-iii-parameter-estimation-in-nonstandard-models
#3
Dora Matzke, Udo Boehm, Joachim Vandekerckhove
We demonstrate the use of three popular Bayesian software packages that enable researchers to estimate parameters in a broad class of models that are commonly used in psychological research. We focus on WinBUGS, JAGS, and Stan, and show how they can be interfaced from R and MATLAB. We illustrate the use of the packages through two fully worked examples; the examples involve a simple univariate linear regression and fitting a multinomial processing tree model to data from a classic false-memory experiment. We conclude with a comparison of the strengths and weaknesses of the packages...
November 13, 2017: Psychonomic Bulletin & Review
https://www.readbyqxmd.com/read/29132999/radiologists-and-social-media-do-not-forget-about-facebook
#4
Rebecca L Seidel, Aryan Jalilvand, Jean Kunjummen, Lea Gilliland, Richard Duszak
PURPOSE: Facebook (Facebook, Inc, Menlo Park, California, USA) is the most popular social networking platform worldwide. Facebook groups are virtual communities of people who share a common interest. Breast Imaging Radiologists is a Facebook group for radiologists with an interest in breast imaging. The purpose of this study was to analyze the membership and activity of the Breast Imaging Radiologists Facebook group (BIRFG) for 2 years since its inception. METHODS: Using both the Grytics (www...
November 11, 2017: Journal of the American College of Radiology: JACR
https://www.readbyqxmd.com/read/29132408/using-semantics-for-representing-experimental-protocols
#5
Olga Giraldo, Alexander García, Federico López, Oscar Corcho
BACKGROUND: An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory...
November 13, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29125229/observational-review-of-paediatric-intraosseous-needle-placement-in-the-paediatric-emergency-department
#6
Elysha L Pifko, Amanda Price, Carrie Busch, Curren Smith, Yunyun Jiang, Joseph Dobson, Rachel Tuuri
AIM: Intraosseous (IO) access is a life-saving option during resuscitations in the paediatric emergency department (PED). This study aimed to compare success rates and time to placement for Manual IO versus EZ-IO needles in PED patients ≤8 and >8 kg. METHODS: This was a retrospective cross-sectional descriptive study of IO use in a single-centre tertiary PED from 2006 to 2014. Cases were identified through diagnosis codes for IO infusion, cardiopulmonary resuscitation and cardiac arrest and admissions to the intensive care unit...
November 10, 2017: Journal of Paediatrics and Child Health
https://www.readbyqxmd.com/read/29121073/diffslc-a-graph-centrality-method-to-detect-essential-proteins-of-a-protein-protein-interaction-network
#7
Divya Mistry, Roger P Wise, Julie A Dickerson
Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edges based on their importance to the network topology. These measures helped identify critical genes and proteins in biomolecular networks. The proposed centrality measure, DiffSLC, combines the number of interactions of a protein and the gene coexpression values of genes from which those proteins were translated, as a weighting factor to bias the identification of essential proteins in a protein interaction network...
2017: PloS One
https://www.readbyqxmd.com/read/29112383/ozone-formation-induced-by-the-impact-of-reactive-bromine-and-iodine-species-on-photochemistry-in-a-polluted-marine-environment
#8
Moshe Shechner, Eran Tas
Reactive iodine and bromine species (RIS and RBS, respectively) are known for altering atmospheric chemistry, causing sharp tropospheric ozone (O3) depletion in polar regions and significant O3 reduction in the marine boundary layer (MBL). Here we use measurement-based modelling to show that, unexpectedly, both RIS and RBS can lead to enhanced O3 formation in a polluted marine environment under volatile organic compound (VOC)-limited conditions associated with high nitrogen oxide (NOX = [NO] + [NO2]) concentrations...
November 7, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29111167/heme-oxygenase-1-protects-bone-marrow-mesenchymal-stem-cells-from-iron-overload-through-decreasing-reactive-oxygen-species-and-promoting-il-10-generation
#9
Zheng Y Yu, Dan Ma, Zheng C He, Ping Liu, Jun Huang, Qin Fang, Jiang Y Zhao, Ji S Wang
Iron overload (IO) caused by frequent blood transfusion in hematological diseases has become a major concern. In this study, up-regulation of heme oxygenase-1 (HO-1), a protector against oxidative stress, was observed in bone marrow mesenchymal stem cells (BMMSCs) at the early stage of IO and had favorable prognosis in an IO mouse model. Given that the protective role of HO-1 in IO damage of BMMSCs was still unknown, the mechanism was explored in vitro and in vivo. BMMSCs were transfected with HO-1/siHO-1 in vitro, and the mouse model was established to further evaluate the effect of HO-1 on IO in vivo...
October 28, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/29108572/a-cost-effective-assay-for-antioxidant-using-simple-cotton-thread-combining-paper-based-device-with-mobile-phone-detection
#10
Suphasinee Sateanchok, Sunanta Wangkarn, Chalermpong Saenjum, Kate Grudpan
A cost-effective assay for antioxidant using simple cotton thread combining paper based device with mobile phone detection has been investigated. Standard and sample solutions flow along a bunch of cotton thread treated with sodium hydroxide via microfluidic behaviors without external pumping. The analyte solution reacts with the reagents that have been immobilized on the paper strip fixed at the end of the cotton bunch. The developed platforms were used for the assays of total phenolic content and antioxidant capacity by employing Folin-Ciocalteu and 2, 2-diphenyl-1-picryhydrazyl (DPPH) respectively...
January 15, 2018: Talanta
https://www.readbyqxmd.com/read/29103755/a-failure-type-specific-risk-prediction-tool-for-selection-of-head-and-neck-cancer-patients-for-experimental-treatments
#11
Katrin Håkansson, Jacob H Rasmussen, Gregers B Rasmussen, Jeppe Friborg, Thomas A Gerds, Barbara Malene Fischer, Flemming L Andersen, Søren M Bentzen, Lena Specht, Ivan R Vogelius
OBJECTIVES: The objective of this work was to develop a tool for decision support, providing simultaneous predictions of the risk of loco-regional failure (LRF) and distant metastasis (DM) after definitive treatment for head-and-neck squamous cell carcinoma (HNSCC). MATERIALS AND METHODS: Retrospective data for 560HNSCC patients were used to generate a multi-endpoint model, combining three cause-specific Cox models (LRF, DM and death with no evidence of disease (death NED))...
November 2017: Oral Oncology
https://www.readbyqxmd.com/read/29100252/guidelines-regarding-%C3%A2-16-of-the-german-transplantation-act-initial-experiences-with-structured-reporting
#12
Daniel Pinto Dos Santos, Gordon Arnhold, Peter Mildenberger, Christoph Düber, Roman Kloeckner
Purpose To transfer the report sheet from the guidelines regarding the German Transplantation Act to a standards-compliant report template and to evaluate it in the clinical routine. Materials and Methods The template was developed using the freely available software brackets.io. It was implemented in the clinical routine using a reporting platform developed in-house. Interfaces to the department RIS and PACS allowed for integration into the usual reporting workflow. The evaluation period was 70 days. Results Developing the template for implementation of the guidelines was possible without any difficulties...
November 3, 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/29095980/pedigreejs-a-web-based-graphical-pedigree-editor
#13
Tim Carver, Alex P Cunningham, Chantal Babb de Villiers, Andrew Lee, Simon Hartley, Marc Tischkowitz, Fiona M Walter, Douglas F Easton, Antonis C Antoniou
Motivation: The collection, management and visualisation of clinical pedigree (family history) data is a core activity in clinical genetics centres. However, clinical pedigree datasets can be difficult to manage, as they are time consuming to capture, and can be difficult to build, manipulate and visualise graphically. Several standalone graphical pedigree editors and drawing applications exist but there are no freely available lightweight graphical pedigree editors that can be easily configured and incorporated into web applications...
October 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29093505/coherence-transformations-in-single-qubit-systems
#14
Hai-Long Shi, Xiao-Hui Wang, Si-Yuan Liu, Wen-Li Yang, Zhan-Ying Yang, Heng Fan
We investigate the single qubit transformations under several typical coherence-free operations, such as, incoherent operation (IO), strictly incoherent operation (SIO), physically incoherent operation (PIO), and coherence-preserving operation (CPO). Quantitative connection has been built between IO and SIO in single qubit systems. Moreover, these coherence-free operations have a clear hierarchical relationship in single qubit systems: CPO ⊂ PIO ⊂ SIO=IO. A new and explicit proof for the necessary and sufficient condition of single qubit transformation via IO or SIO has been provided, which indicates that SIO with only two Kraus operators are enough to realize this transformation...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29093221/experience-dependent-mushroom-body-plasticity-in-butterflies-consequences-of-search-complexity-and-host-range
#15
Laura J A van Dijk, Niklas Janz, Alexander Schäpers, Gabriella Gamberale-Stille, Mikael A Carlsson
An ovipositing insect experiences many sensory challenges during her search for a suitable host plant. These sensory challenges become exceedingly pronounced when host range increases, as larger varieties of sensory inputs have to be perceived and processed in the brain. Neural capacities can be exceeded upon information overload, inflicting costs on oviposition accuracy. One presumed generalist strategy to diminish information overload is the acquisition of a focused search during its lifetime based on experiences within the current environment, a strategy opposed to a more genetically determined focus expected to be seen in relative specialists...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29092952/timer-a-web-server-for-comprehensive-analysis-of-tumor-infiltrating-immune-cells
#16
Taiwen Li, Jingyu Fan, Binbin Wang, Nicole Traugh, Qianming Chen, Jun S Liu, Bo Li, X Shirley Liu
Recent clinical successes of cancer immunotherapy necessitate the investigation of the interaction between malignant cells and the host immune system. However, elucidation of complex tumor-immune interactions presents major computational and experimental challenges. Here, we present Tumor Immune Estimation Resource (TIMER; cistrome.shinyapps.io/timer) to comprehensively investigate molecular characterization of tumor-immune interactions. Levels of six tumor-infiltrating immune subsets are precalculated for 10,897 tumors from 32 cancer types...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29092951/computational-radiomics-system-to-decode-the-radiographic-phenotype
#17
Joost J M van Griethuysen, Andriy Fedorov, Chintan Parmar, Ahmed Hosny, Nicole Aucoin, Vivek Narayan, Regina G H Beets-Tan, Jean-Christophe Fillion-Robin, Steve Pieper, Hugo J W L Aerts
Radiomics aims to quantify phenotypic characteristics on medical imaging through the use of automated algorithms. Radiomic artificial intelligence (AI) technology, either based on engineered hard-coded algorithms or deep learning methods, can be used to develop noninvasive imaging-based biomarkers. However, lack of standardized algorithm definitions and image processing severely hampers reproducibility and comparability of results. To address this issue, we developed PyRadiomics, a flexible open-source platform capable of extracting a large panel of engineered features from medical images...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29091996/visualization-portal-for-genetic-variation-vizgvar-a-tool-for-interactive-visualization-of-snps-and-somatic-mutations-in-exons-genes-and-protein-domains
#18
Antonio Solano Román, Verónica Alfaro, Carlos Cruz, Allan Orozco Solano
Motivation: VizGVar was designed to meet the growing need of the research community for improved genomic and proteomic data viewers that benefit from better information visualization. Results: We implemented a new information architecture and applied user centered design principles to provide a new improved way of visualizing genetic information and protein data related to human disease. VizGVar connects the entire database of Ensembl protein motifs, domains, genes and exons with annotated SNPs and somatic variations from PharmGKB and COSMIC...
October 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29082436/adolescent-young-adults-aya-with-cancer-seeking-integrative-oncology-consultations-demographics-characteristics-and-self-reported-outcomes
#19
Gabriel Lopez, Wenli Liu, Kevin Madden, Bryan Fellman, Yisheng Li, Eduardo Bruera
PURPOSE: Integrative Oncology (IO) consultations offer cancer patients counseling regarding complementary integrative medicine (CIM). We explored the CIM interests and symptom burden of AYA cancer patients presenting for an IO consultation. METHODS: Patients referred for an IO physician consultation at an academic medical center from September 1, 2009 to December 31, 2013 completed an assessment on presentation: MYCaW, ESAS (10 symptoms, 0-10, 10 worst possible), CIM use survey, and SF-12 QOL survey...
October 29, 2017: Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer
https://www.readbyqxmd.com/read/29082119/relationships-between-radiation-clouds-and-convection-during-dynamo
#20
Paul E Ciesielski, Richard H Johnson, Xianan Jiang, Yunyan Zhang, Shaocheng Xie
The relationships between radiation, clouds, and convection on an intraseasonal time scale are examined with data taken during the Dynamics of the Madden-Julian Oscillation (MJO) field campaign. Specifically, column-net, as well as vertical profiles of radiative heating rates, computed over Gan Island in the central Indian Ocean (IO) are used along with an objective analysis of large-scale fields to examine three MJO events that occurred during the 3 month period (October to December 2011) over this region...
March 16, 2017: Journal of Geophysical Research. Atmospheres: JGR
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