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https://www.readbyqxmd.com/read/29353371/a-systematic-assessment-of-google-search-queries-and-readability-of-online-gynecologic-oncology-patient-education-materials
#1
Alexandra Martin, J Ryan Stewart, Jeremy Gaskins, Erin Medlin
The Internet is a major source of health information for gynecologic cancer patients. In this study, we systematically explore common Google search terms related to gynecologic cancer and calculate readability of top resulting websites. We used Google AdWords Keyword Planner to generate a list of commonly searched keywords related to gynecologic oncology, which were sorted into five groups (cervical cancer, ovarian cancer, uterine cancer, vulvar cancer, vaginal cancer) using five patient education websites from sgo...
January 20, 2018: Journal of Cancer Education: the Official Journal of the American Association for Cancer Education
https://www.readbyqxmd.com/read/29347830/an-omic-biomarker-detection-algorithm-trivote-and-its-application-in-methylomic-biomarker-detection
#2
Cheng Xu, Jiamei Liu, Weifeng Yang, Yayun Shu, Zhipeng Wei, Weiwei Zheng, Xin Feng, Fengfeng Zhou
AIM: Transcriptomic and methylomic patterns represent two major OMIC data sources impacted by both inheritable genetic information and environmental factors, and have been widely used as disease diagnosis and prognosis biomarkers. MATERIALS & METHODS: Modern transcriptomic and methylomic profiling technologies detect the status of tens of thousands or even millions of probing residues in the human genome, and introduce a major computational challenge for the existing feature selection algorithms...
January 19, 2018: Epigenomics
https://www.readbyqxmd.com/read/29344887/phosphoproteomics-based-profiling-of-kinase-activities-in-cancer-cells
#3
Jakob Wirbel, Pedro Cutillas, Julio Saez-Rodriguez
Cellular signaling, predominantly mediated by phosphorylation through protein kinases, is found to be deregulated in most cancers. Accordingly, protein kinases have been subject to intense investigations in cancer research, to understand their role in oncogenesis and to discover new therapeutic targets. Despite great advances, an understanding of kinase dysfunction in cancer is far from complete.A powerful tool to investigate phosphorylation is mass-spectrometry (MS)-based phosphoproteomics, which enables the identification of thousands of phosphorylated peptides in a single experiment...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29343101/macon-a-web-tool-for-computing-dna-methylation-data-obtained-by-the-illumina-infinium-human-dna-methylation-beadarray
#4
Naoko Iida, Yoshihiro Okuda, Osamu Ogasawara, Satoshi Yamashita, Hideyuki Takeshima, Toshikazu Ushijima
AIM: Bioinformatics analysis for Illumina Infinium Human DNA methylation BeadArray is essential, but still remains difficult task for many experimental researchers. We here aimed to develop a browser-accessible bioinformatics tool for analyzing the BeadArray data. MATERIALS & METHODS: The tool was established as an analytical pipeline using R, Perl and Python programming languages. RESULTS: We introduced a method that groups neighboring probes into a genomic block, which facilitated efficient identification of densely methylated/unmethylated regions...
January 18, 2018: Epigenomics
https://www.readbyqxmd.com/read/29342271/melodi-mining-enriched-literature-objects-to-derive-intermediates
#5
Benjamin Elsworth, Karen Dawe, Emma E Vincent, Ryan Langdon, Brigid M Lynch, Richard M Martin, Caroline Relton, Julian P T Higgins, Tom R Gaunt
Background: The scientific literature contains a wealth of information from different fields on potential disease mechanisms. However, identifying and prioritizing mechanisms for further analytical evaluation presents enormous challenges in terms of the quantity and diversity of published research. The application of data mining approaches to the literature offers the potential to identify and prioritize mechanisms for more focused and detailed analysis. Methods: Here we present MELODI, a literature mining platform that can identify mechanistic pathways between any two biomedical concepts...
January 12, 2018: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29342169/interactions-between-the-invasive-burmese-python-python-bivittatus-kuhl-and-the-local-mosquito-community-in-florida-usa
#6
Lawrence E Reeves, Kenneth L Krysko, Michael L Avery, Jennifer L Gillett-Kaufman, Akito Y Kawahara, C Roxanne Connelly, Phillip E Kaufman
The Burmese python, Python bivittatus Kuhl, is a well-established invasive species in the greater Everglades ecosystem of southern Florida, USA. Most research on its ecological impacts focuses on its role as a predator and its trophic interactions with native vertebrate species, particularly mammals. Beyond predation, there is little known about the ecological interactions between P. bivittatus and native faunal communities. It is likely that established populations of P. bivittatus in southern Florida serve as hosts for native mosquito communities...
2018: PloS One
https://www.readbyqxmd.com/read/29340970/ultrahigh-temporal-resolution-of-visual-presentation-using-gaming-monitors-and-g-sync
#7
Christian H Poth, Rebecca M Foerster, Christian Behler, Ulrich Schwanecke, Werner X Schneider, Mario Botsch
Vision unfolds as an intricate pattern of information processing over time. Studying vision and visual cognition therefore requires precise manipulations of the timing of visual stimulus presentation. Although standard computer display technologies offer great accuracy and precision of visual presentation, their temporal resolution is limited. This limitation stems from the fact that the presentation of rendered stimuli has to wait until the next refresh of the computer screen. We present a novel method for presenting visual stimuli with ultrahigh temporal resolution (<1 ms) on newly available gaming monitors...
January 16, 2018: Behavior Research Methods
https://www.readbyqxmd.com/read/29340616/pychimera-use-ucsf-chimera-modules-in-any-python-2-7-project
#8
Jaime Rodríguez-Guerra Pedregal, Jean-Didier Maréchal
Motivation: UCSF Chimera (Pettersen et al., 2004) is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C ++ core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera's arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX (Goddard et al...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29340210/treetime-maximum-likelihood-phylodynamic-analysis
#9
Pavel Sagulenko, Vadim Puller, Richard A Neher
Mutations that accumulate in the genome of cells or viruses can be used to infer their evolutionary history. In the case of rapidly evolving organisms, genomes can reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. As the number of genome sequences available for different pathogens has increased dramatically over the last years, phylodynamic analysis with traditional methods becomes challenging as these methods scale poorly with growing datasets...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29337991/hasappy-a-tool-for-candidate-identification-in-pooled-forward-genetic-screens-of-haploid-mammalian-cells
#10
Giulio Di Minin, Andreas Postlmayr, Anton Wutz
Haploid cells are increasingly used for screening of complex pathways in animal genomes. Hemizygous mutations introduced through viral insertional mutagenesis can be directly selected for phenotypic changes. Here we present HaSAPPy a tool for analysing sequencing datasets of screens using insertional mutations in large pools of haploid cells. Candidate gene prediction is implemented through identification of enrichment of insertional mutations after selection by simultaneously evaluating several parameters...
January 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29335872/disruptor-of-telomeric-silencing-1-like-dot1l-disclosing-a-new-class-of-non-nucleoside-inhibitors-by-means-of-ligand-based-and-structure-based-approaches
#11
Manuela Sabatino, Dante Rotili, Alexandros Patsilinakos, Mariantonietta Forgione, Daniela Tomaselli, Fréderic Alby, Paola B Arimondo, Antonello Mai, Rino Ragno
Chemical inhibition of chromatin-mediated signaling involved proteins is an established strategy to drive expression networks and alter disease progression. Protein methyltransferases are among the most studied proteins in epigenetics and, in particular, disruptor of telomeric silencing 1-like (DOT1L) lysine methyltransferase plays a key role in MLL-rearranged acute leukemia Selective inhibition of DOT1L is an established attractive strategy to breakdown aberrant H3K79 methylation and thus overexpression of leukemia genes, and leukemogenesis...
January 15, 2018: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29331233/a-biophysical-modelling-platform-of-the-cochlear-nucleus-and-other-auditory-circuits-from-channels-to-networks
#12
Paul B Manis, Luke Campagnola
Models of the auditory brainstem have been an invaluable tool for testing hypotheses about auditory information processing and for highlighting the most important gaps in the experimental literature. Due to the complexity of the auditory brainstem, and indeed most brain circuits, the dynamic behavior of the system may be difficult to predict without a detailed, biologically realistic computational model. Despite the sensitivity of models to their exact construction and parameters, most prior models of the cochlear nucleus have incorporated only a small subset of the known biological properties...
December 28, 2017: Hearing Research
https://www.readbyqxmd.com/read/29329683/respiratory-disease-in-ball-pythons-python-regius-experimentally-infected-with-ball-python-nidovirus
#13
Laura L Hoon-Hanks, Marylee L Layton, Robert J Ossiboff, John S L Parker, Edward J Dubovi, Mark D Stenglein
Circumstantial evidence has linked a new group of nidoviruses with respiratory disease in pythons, lizards, and cattle. We conducted experimental infections in ball pythons (Python regius) to test the hypothesis that ball python nidovirus (BPNV) infection results in respiratory disease. Three ball pythons were inoculated orally and intratracheally with cell culture isolated BPNV and two were sham inoculated. Antemortem choanal, oroesophageal, and cloacal swabs and postmortem tissues of infected snakes were positive for viral RNA, protein, and infectious virus by qRT-PCR, immunohistochemistry, western blot and virus isolation...
January 9, 2018: Virology
https://www.readbyqxmd.com/read/29329398/lenup-learning-nucleosome-positioning-from-dna-sequences-with-improved-convolutional-neural-networks
#14
Juhua Zhang, Wenbo Peng, Lei Wang
Motivation: Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy profiles and computational tools to the analysis on these data, the complex language of eukaryotic Nucleosome positioning remains incompletely understood. Results: Here, we address this challenge using an approach based on a state-of-the-art machine learning method...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29326411/-semantic-network-analysis-of-online-news-and-social-media-text-related-to-comprehensive-nursing-care-service
#15
Minji Kim, Mona Choi, Yoosik Youm
PURPOSE: As comprehensive nursing care service has gradually expanded, it has become necessary to explore the various opinions about it. The purpose of this study is to explore the large amount of text data regarding comprehensive nursing care service extracted from online news and social media by applying a semantic network analysis. METHODS: The web pages of the Korean Nurses Association (KNA) News, major daily newspapers, and Twitter were crawled by searching the keyword 'comprehensive nursing care service' using Python...
December 2017: Journal of Korean Academy of Nursing
https://www.readbyqxmd.com/read/29317384/identifying-opinion-leaders-to-promote-organ-donation-on-social-media-network-study
#16
Jingyuan Shi, Charles T Salmon
BACKGROUND: In the recent years, social networking sites (SNSs, also called social media) have been adopted in organ donation campaigns, and recruiting opinion leaders for such campaigns has been found effective in promoting behavioral changes. OBJECTIVE: The aim of this paper was to focus on the dissemination of organ donation tweets on Weibo, the Chinese equivalent of Twitter, and to examine the opinion leadership in the retweet network of popular organ donation messages using social network analysis...
January 9, 2018: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/29316487/available-sight-distance-on-existing-highways-meeting-stopping-sight-distance-requirements-of-an-aging-population
#17
Suliman A Gargoum, Mostafa H Tawfeek, Karim El-Basyouny, James C Koch
An important element of highway design is ensuring that the available sight distance (ASD) on a highway meets driver needs. For instance, if the ASD at any point on a highway is less than the distance required to come to a complete stop after seeing a hazard (i.e. Stopping Sight Distance (SSD)), the driver will not be able to stop in time to avoid a collision. SSD is function of a number of variables which vary depending on the driver, the vehicle driven and surface conditions; examples of such variables include a driver's perception reaction time or PRT (i...
January 6, 2018: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/29313469/reptiles-and-amphibians-as-potential-reservoir-hosts-of-chikungunya-virus
#18
Angela M Bosco-Lauth, Airn E Hartwig, Richard A Bowen
Chikungunya virus is an emerging arbovirus of significant human-health concern. Little is known about its sylvatic cycle, including whether ectothermic vertebrates are permissive to infection. In this study, individuals from ten species of reptiles and amphibians were inoculated with chikungunya virus and samples of blood were tested to characterize viremia and seroconversion. Viremia was not detected in cane toads, house geckos, or American alligators, but most of the green iguanas, red-eared sliders, ball and Burmese pythons, leopard frogs, Texas toads, and garter snakes developed viremia...
January 8, 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29303497/a-chiral-diamine-practical-implications-of-a-three-stereoisomer-cocrystallization
#19
Brian S Dolinar, Kerim Samedov, Andrew G P Maloney, Robert West, Victor N Khrustalev, Ilia A Guzei
A brief comparison of seven straightforward methods for molecular crystal-volume estimation revealed that their precisions are comparable. A chiral diamine, N2,N3-bis[2,6-bis(propan-2-yl)phenyl]butane-2,3-diamine, C28H44N2, has been used to illustrate the application of the methods. Three stereoisomers of the diamine cocrystallize in the centrosymmetric space group P21/c with Z' = 1.5. The molecules occupying general positions are RR and SS, whereas that residing on an inversion center is meso. This is one of only ten examples of three stereoisomers with two asymmetric atoms cocrystallizing together reported to the Cambridge Structural Database (CSD)...
January 1, 2018: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/29300846/chopstitch-exon-annotation-and-splice-graph-construction-using-transcriptome-assembly-and-whole-genome-sequencing-data
#20
Hamza Khan, Hamid Mohamadi, Benjamin P Vandervalk, Rene L Warren, Justin Chu, Inanc Birol
Motivation: Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques, when the species and closely related species lack high quality reference resources. For certain applications such as de novo annotation, information on putative exons and alternative splicing may be desirable. Results: Here we present ChopStitch, a new method for finding putative exons de novo and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data...
December 29, 2017: Bioinformatics
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