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https://www.readbyqxmd.com/read/29158372/enhancing-next-generation-sequencing-guided-cancer-care-through-cognitive-computing
#1
Nirali M Patel, Vanessa V Michelini, Jeff M Snell, Saianand Balu, Alan P Hoyle, Joel S Parker, Michele C Hayward, David A Eberhard, Ashley H Salazar, Patrick McNeillie, Jia Xu, Claudia S Huettner, Takahiko Koyama, Filippo Utro, Kahn Rhrissorrakrai, Raquel Norel, Erhan Bilal, Ajay Royyuru, Laxmi Parida, H Shelton Earp, Juneko E Grilley-Olson, D Neil Hayes, Stephen J Harvey, Norman E Sharpless, William Y Kim
BACKGROUND: Using next-generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data to patients and caregivers. Specifically, providing current, accurate information on newly approved therapies and open clinical trials requires considerable manual curation performed mainly by human "molecular tumor boards" (MTBs). The purpose of this study was to determine the utility of cognitive computing as performed by Watson for Genomics (WfG) compared with a human MTB...
November 20, 2017: Oncologist
https://www.readbyqxmd.com/read/29158195/understanding-missing-proteins-a-functional-perspective
#2
REVIEW
Longjian Zhou, Limsoon Wong, Wilson Wen Bin Goh
A missing protein (MP) is an unconfirmed genetic sequence for which a protein product is not yet detected. Currently, MPs are tiered based on supporting evidence mainly in the form of protein existence (PE) classification. As we discuss here, this definition is overly restrictive because proteins go missing in day-to-day proteomics as a result of low abundance, lack of sequence specificity, splice variants, and so on. Thus, we propose a broader functional classification of MPs that complements PE classification, discuss major causes, and examine three corresponding solution tiers:...
November 17, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/29157568/providing-primary-care-using-an-interprofessional-collaborative-practice-model-what-clinicians-have-learned
#3
Cynthia S Selleck, Matthew Fifolt, Heidi Burkart, Jennifer Sandson Frank, William A Curry, Lisle S Hites
This article details a nurse-led, interprofessional collaborative practice (IPCP) model that was developed to provide primary care to a medically indigent population in Birmingham, Alabama. Funding to develop and implement this project came from a federal Nurse Education, Practice, Quality and Retention award to the University of Alabama at Birmingham (UAB) School of Nursing, with additional support coming from the UAB Hospital and Health System. The clinic is housed within a local community-based, non-profit organization and all services, including supplies and pharmaceuticals, are provided free of charge to this vulnerable population...
November 2017: Journal of Professional Nursing: Official Journal of the American Association of Colleges of Nursing
https://www.readbyqxmd.com/read/29155662/global-disease-detection-achievements-in-applied-public-health-research-capacity-building-and-public-health-diplomacy-2001-2016
#4
Carol Y Rao, Grace W Goryoka, Olga L Henao, Kevin R Clarke, Stephanie J Salyer, Joel M Montgomery
The Centers for Disease Control and Prevention has established 10 Global Disease Detection (GDD) Program regional centers around the world that serve as centers of excellence for public health research on emerging and reemerging infectious diseases. The core activities of the GDD Program focus on applied public health research, surveillance, laboratory, public health informatics, and technical capacity building. During 2015-2016, program staff conducted 205 discrete projects on a range of topics, including acute respiratory illnesses, health systems strengthening, infectious diseases at the human-animal interface, and emerging infectious diseases...
November 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29154853/standards-and-guidelines-for-validating-next-generation-sequencing-bioinformatics-pipelines-a-joint-recommendation-of-the-association-for-molecular-pathology-and-the-college-of-american-pathologists
#5
REVIEW
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding, Chen Wang, Alexis B Carter
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care...
November 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29154847/behavioural-informatics-for-improving-water-hygiene-practice-based-on-iot-environment
#6
Yang Fu, Wenyan Wu
The development of Internet of Things (IoT) and latest Information and Communication Technologies (ICT) have changed the nature of healthcare monitoring and health behaviour intervention in many applications. Water hygiene and water conservation behaviour intervention as important influence factors to human health are gaining much attentions for improving sustained sanitation practice. Based on face-to-face delivery, typical behaviour intervention method is costly and hardly to provide all day access to personalised intervention guidance and feedbacks...
November 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29149350/a-data-fusion-pipeline-for-generating-and-enriching-adverse-outcome-pathway-descriptions
#7
Penny Nymark, Linda Rieswijk, Friederike Ehrhart, Nina Jeliazkova, Georgia Tsiliki, Haralambos Sarimveis, Chris T Evelo, Vesa Hongisto, Pekka Kohonen, Egon Willighagen, Roland C Grafström
Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven and informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development of non-animal based hazard and risk assessment methods. We devised a six-step workflow that integrated diverse types of toxicology data into a novel AOP scheme for pulmonary fibrosis. Mining of literature references and diverse data sources covering previous pathway descriptions and molecular results were coupled in a stepwise manner with informatics tools applications that enabled gene linkage and pathway identification in molecular interaction maps...
November 15, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29143395/a-novel-classification-scheme-to-decline-the-mortality-rate-among-women-due-to-breast-tumor
#8
Bushra Mughal, Muhammad Sharif, Nazeer Muhammad, Tanzila Saba
Early screening of skeptical masses or breast carcinomas in mammograms is supposed to decline the mortality rate among women. This amount can be decreased more on development of the computer-aided diagnosis with reduction of false suppositions in medical informatics. Our aim is to provide a robust tumor detection system for accurate classification of breast masses using normal, abnormal, benign, or malignant classes. The breast carcinomas are classified on the basis of observed classes. This is highly dependent on feature extraction process...
November 16, 2017: Microscopy Research and Technique
https://www.readbyqxmd.com/read/29141839/patient-health-record-systems-scope-and-functionalities-literature-review-and-future-directions
#9
REVIEW
Lina Bouayad, Anna Ialynytchev, Balaji Padmanabhan
BACKGROUND: A new generation of user-centric information systems is emerging in health care as patient health record (PHR) systems. These systems create a platform supporting the new vision of health services that empowers patients and enables patient-provider communication, with the goal of improving health outcomes and reducing costs. This evolution has generated new sets of data and capabilities, providing opportunities and challenges at the user, system, and industry levels. OBJECTIVE: The objective of our study was to assess PHR data types and functionalities through a review of the literature to inform the health care informatics community, and to provide recommendations for PHR design, research, and practice...
November 15, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/29141338/-spatial-and-temporal-clustering-characteristics-of-typhoid-and-paratyphoid-fever-and-its-change-pattern-in-3-provinces-in-southwestern-china-2001-2012
#10
L X Wang, B Yang, M Y Yan, Y Q Tang, Z C Liu, R Q Wang, S Li, L Ma, B Kan
Objective: To analyze the spatial and temporal clustering characteristics of typhoid and paratyphoid fever and its change pattern in Yunnan, Guizhou and Guangxi provinces in southwestern China in recent years. Methods: The incidence data of typhoid and paratyphoid fever cases at county level in 3 provinces during 2001-2012 were collected from China Information System for Diseases Control and Prevention and analyzed by the methods of descriptive epidemiology and geographic informatics. And the map showing the spatial and temporal clustering characters of typhoid and paratyphoid fever cases in three provinces was drawn...
November 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/29136101/identification-of-topological-features-in-renal-tumor-microenvironment-associated-with-patient-survival
#11
Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani, Qianjin Feng, Kun Huang
Motivation: As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However traditional qualitative and/or semi-quantitative parameters obtained by pathologist's visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29132635/need-of-informatics-in-designing-interoperable-clinical-registries
#12
Majid Rastegar-Mojarad, Sunghwan Sohn, Liwei Wang, Feichen Shen, Troy C Bleeker, William A Cliby, Hongfang Liu
Clinical registries are designed to collect information relating to a particular condition for research or quality improvement. Intuitively, informatics in the area of data management and extraction plays a central role in clinical registries. Due to various reasons such as lack of informatics awareness or expertise, there may be little informatics involvement in designing clinical registries. In this paper, we studied a clinical registry from two critical perspectives, data quality and interoperability, where informatics can play a role...
December 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29132622/know-thy-ehealth-user-development-of-biopsychosocial-personas-from-a-study-of-older-adults-with-heart-failure
#13
Richard J Holden, Anand Kulanthaivel, Saptarshi Purkayastha, Kathryn M Goggins, Sunil Kripalani
BACKGROUND: Personas are a canonical user-centered design method increasingly used in health informatics research. Personas-empirically-derived user archetypes-can be used by eHealth designers to gain a robust understanding of their target end users such as patients. OBJECTIVE: To develop biopsychosocial personas of older patients with heart failure using quantitative analysis of survey data. METHOD: Data were collected using standardized surveys and medical record abstraction from 32 older adults with heart failure recently hospitalized for acute heart failure exacerbation...
December 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29132619/a-statistical-analysis-based-recommender-model-for-heart-disease-patients
#14
Anam Mustaqeem, Syed Muhammad Anwar, Abdul Rashid Khan, Muhammad Majid
OBJECTIVES: An intelligent information technology based system could have a positive impact on the life-style of patients suffering from chronic diseases by providing useful health recommendations. In this paper, we have proposed a hybrid model that provides disease prediction and medical recommendations to cardiac patients. The first part aims at implementing a prediction model, that can identify the disease of a patient and classify it into one of the four output classes i.e., non-cardiac chest pain, silent ischemia, angina, and myocardial infarction...
December 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29129497/frailty-and-clinical-outcomes-in-advanced-heart-failure-patients-undergoing-left-ventricular-assist-device-implantation-a-systematic-review-and-meta-analysis
#15
Gary Tse, Mengqi Gong, Sunny Hei Wong, William K K Wu, George Bazoukis, Konstantinos Lampropoulos, Wing Tak Wong, Yunlong Xia, Martin C S Wong, Tong Liu, Jean Woo
BACKGROUND: Frailty has been identified as a risk factor for adverse clinical outcomes after cardiac intervention or surgery. However, whether it increases the risk of adverse outcomes in patients undergoing left ventricular assist device (LVAD) therapy has been controversial. Therefore, we conducted a systematic review and meta-analysis of the frailty measures and clinical outcomes of length of stay and mortality in this setting. METHODS: PubMed and Embase were searched until September 11, 2017, for studies evaluating the association between frailty and clinical outcomes in advanced heart failure patients undergoing LVAD implantation...
November 9, 2017: Journal of the American Medical Directors Association
https://www.readbyqxmd.com/read/29127041/logical-comparison-over-rdf-resources-in-bio-informatics
#16
S Colucci, F M Donini, E Di Sciascio
Comparison of resources is a frequent task in different bio-informatics applications, including drug-target interaction, drug repositioning and mechanism of action understanding, among others. This paper proposes a general method for the logical comparison of resources modeled in Resource Description Framework and shows its distinguishing features with reference to the comparison of drugs. In particular, the method returns a description of the commonalities between resources, rather than a numerical value estimating their similarity and/or relatedness...
November 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29126751/shift-to-community-onset-clostridium-difficile-infection-in-the-national-veterans-health-administration-2003-2014
#17
Kelly R Reveles, Mary Jo V Pugh, Kenneth A Lawson, Eric M Mortensen, Jim M Koeller, Jacqueline R Argamany, Christopher R Frei
BACKGROUND: Clostridium difficile infection (CDI) occurs frequently in inpatient settings; however, community-onset cases have been reported more frequently in recent years. This study evaluated hospital-onset and community-onset CDI in the national Veterans Health Administration (VHA) population over a 12-year period. METHODS: This was a retrospective cohort study of all adult VHA beneficiaries with CDI between October 1, 2002, and September 30, 2014. Data were obtained from the Veterans Affairs Informatics and Computing Infrastructure...
November 7, 2017: American Journal of Infection Control
https://www.readbyqxmd.com/read/29126216/pager-2-0-an-update-to-the-pathway-annotated-list-and-gene-signature-electronic-repository-for-human-network-biology
#18
Zongliang Yue, Qi Zheng, Michael T Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y Chen
Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126148/consensus-coding-sequence-ccds-database-a-standardized-set-of-human-and-mouse-protein-coding-regions-supported-by-expert-curation
#19
Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox, Claire Davidson, Tamara Goldfarb, Jose M Gonzalez, Toby Hunt, John Jackson, Vinita Joardar, Mike P Kay, Vamsi K Kodali, Fergal J Martin, Monica McAndrews, Kelly M McGarvey, Michael Murphy, Bhanu Rajput, Sanjida H Rangwala, Lillian D Riddick, Ruth L Seal, Marie-Marthe Suner, David Webb, Sophia Zhu, Bronwen L Aken, Elspeth A Bruford, Carol J Bult, Adam Frankish, Terence Murphy, Kim D Pruitt
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID)...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29125897/image-analysis-of-neural-stem-cell-division-patterns-in-the-zebrafish-brain
#20
Valerio Lupperger, Felix Buggenthin, Prisca Chapouton, Carsten Marr
Proliferating stem cells in the adult body are the source of constant regeneration. In the brain, neural stem cells (NSCs) divide to maintain the stem cell population and generate neural progenitor cells that eventually replenish mature neurons and glial cells. How much spatial coordination of NSC division and differentiation is present in a functional brain is an open question. To quantify the patterns of stem cell divisions, one has to (i) identify the pool of NSCs that have the ability to divide, (ii) determine NSCs that divide within a given time window, and (iii) analyze the degree of spatial coordination...
November 10, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
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