Identifying core herbal treatments for children with asthma: implication from a chinese herbal medicine database in taiwan.

PubMed

Chen, Hsing-Yu; Lin, Yi-Hsuan; Thien, Peck-Foong; Chang, Shih-Chieh; Chen, Yu-Chun; Lo, Su-Shun; Yang, Sien-Hung; Chen, Jiun-Liang

2013-01-01

Asthma is one of the most common allergic respiratory diseases around the world and places great burden on medical payment. Chinese herbal medicine (CHM) is commonly used for Taiwanese children to control diseases. The aim of this study is to analyze the CHM prescriptions for asthmatic children by using a nationwide clinical database. The National Health Insurance Research Database (NHIRD) was used to perform this study. Medical records from 1997 to 2009 with diagnosis with asthma made for children aged 6 to 18 were included into the analysis. Association rule mining and social network analysis were used to analyze the prevalence of single CHM and its combinations. Ma-Xing-Gan-Shi-Tang (MXGST) was the most commonly used herbal formula (HF) (20.2% of all prescriptions), followed by Xiao-Qing-Long-Tang (13.1%) and Xing-Su-San (12.8%). Zhe Bei Mu is the most frequently used single herb (SH) (14.6%), followed by Xing Ren (10.7%). MXGST was commonly used with Zhe Bei Mu (3.5%) and other single herbs capable of dispelling phlegm. Besides, MXGST was the core formula to relieve asthma. Further studies about efficacy and drug safety are needed for the CHM commonly used for asthma based on the result of this study.

Molecular Biology and Prevention of Endometrial Cancer. Addendum

DTIC Science & Technology

2008-07-01

2) A subset of adenocarcinoma cases from the International DES Registry (IDESR) was analyzed for MSI 3) A case-control study of the CASH database... DES in- utero , for methylation and mutation of PTEN and MLH1 in order to determine if estrogen induces genetic alterations in these tumors...current trial within the “Gynecologic Disease Program”. Aim 2: To analyze vaginal and cervical adenocarcinomas , that have arisen in women exposed to

Assessment of research productivity of Arab countries in the field of infectious diseases using Web of Science database.

PubMed

Sweileh, Waleed M; Al-Jabi, Samah W; Abuzanat, Alaeddin; Sawalha, Ansam F; AbuTaha, Adham S; Ghanim, Mustafa A; Zyoud, Sa'ed H

2015-01-01

To meet the future challenges of infectious diseases and limit the spread of multidrug resistant microorganisms, a better understanding of published studies in the field of infectious diseases is needed. The objective of this study was to analyze the quantity and quality of research activity in the field of infectious diseases in Arab countries and compare it with that in non-Arab countries. Documents published in Arab countries within the research category of "infectious diseases" were extracted and analyzed using the Web of Science database. The data analyzed represent research productivity during the time interval between 1900 - 2012. Worldwide, the total number of documents published in the field of infectious diseases up to 2012 was 227,188. A total of 2,408 documents in the field of infectious diseases were published in Arab countries, which represents 1.06% of worldwide research output. Research output from Arab countries in the field of infectious diseases was low for decades. However, approximately a five-fold increase was observed in the past decade. Arab countries ranked 56(th) to 218(th) on the standard competition ranking (SCR) in worldwide publications in the field of infectious diseases. Egypt, with a total publication of 464 (19.27%) documents ranked first among Arab countries, while Kuwait University was the most productive institution with a total of 158 (6.56%) documents. Average citation per document published in Arab countries was 13.25 and the h-index was 64. Tuberculosis (230; 9.55%), malaria (223; 9.26%), and hepatitis (189; 7.8%) were the top three infectious diseases studied as according to the retrieved documents. The present data reveals that some Arab countries contribute significantly to the field of infectious diseases. However, Arab countries need to work harder to bridge the gap in this field. Compared with non-Arab countries in the Middle East, research output from Arab countries was high, but more efforts are needed to enhance the quality of this output. Future research in the field should be encouraged and correctly directed.

Phenotypic concordance in familial inflammatory bowel disease (IBD). Results of a nationwide IBD Spanish database.

PubMed

Cabré, Eduard; Mañosa, Míriam; García-Sánchez, Valle; Gutiérrez, Ana; Ricart, Elena; Esteve, Maria; Guardiola, Jordi; Aguas, Mariam; Merino, Olga; Ponferrada, Angel; Gisbert, Javier P; Garcia-Planella, Esther; Ceña, Gloria; Cabriada, José L; Montoro, Miguel; Domènech, Eugeni

2014-07-01

Disease outcome has been found to be poorer in familial inflammatory bowel disease (IBD) than in sporadic forms, but assessment of phenotypic concordance in familial IBD provided controversial results. We assessed the concordance for disease type and phenotypic features in IBD families. Patients with familial IBD were identified from the IBD Spanish database ENEIDA. Families in whom at least two members were in the database were selected for concordance analysis (κ index). Concordance for type of IBD [Crohn's disease (CD) vs. ulcerative colitis (UC)], as well as for disease extent, localization and behaviour, perianal disease, extraintestinal manifestations, and indicators of severe disease (i.e., need for immunosuppressors, biological agents, and surgery) for those pairs concordant for IBD type, were analyzed. 798 out of 11,905 IBD patients (7%) in ENEIDA had familial history of IBD. Complete data of 107 families (231 patients and 144 consanguineous pairs) were available for concordance analyses. The youngest members of the pairs were diagnosed with IBD at a significantly younger age (p<0.001) than the oldest ones. Seventy-six percent of pairs matched up for the IBD type (κ=0.58; 95%CI: 0.42-0.73, moderate concordance). There was no relevant concordance for any of the phenotypic items assessed in both diseases. Familial IBD is associated with diagnostic anticipation in younger individuals. Familial history does not allow predicting any phenotypic feature other than IBD type. Copyright © 2013 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

Prognostic factors for survival in patients with Ewing's sarcoma using the surveillance, epidemiology, and end results (SEER) program database.

PubMed

Duchman, Kyle R; Gao, Yubo; Miller, Benjamin J

2015-04-01

The current study aims to determine cause-specific survival in patients with Ewing's sarcoma while reporting clinical risk factors for survival. The Surveillance, Epidemiology, and End Results (SEER) Program database was used to identify patients with osseous Ewing's sarcoma from 1991 to 2010. Patient, tumor, and socioeconomic variables were analyzed to determine prognostic factors for survival. There were 1163 patients with Ewing's sarcoma identified in the SEER Program database. The 10-year cause-specific survival for patients with non-metastatic disease at diagnosis was 66.8% and 28.1% for patients with metastatic disease. Black patients demonstrated reduced survival at 10 years with an increased frequency of metastatic disease at diagnosis as compared to patients of other race, while Hispanic patients more frequently presented with tumor size>10cm. Univariate analysis revealed that metastatic disease at presentation, tumor size>10cm, axial tumor location, patient age≥20 years, black race, and male sex were associated with decreased cause-specific survival at 10 years. Metastatic disease at presentation, axial tumor location, tumor size>10cm, and age≥20 years remained significant in the multivariate analysis. Patients with Ewing's sarcoma have decreased cause-specific survival at 10 years when metastatic at presentation, axial tumor location, tumor size>10cm, and patient age≥20 years. Copyright © 2015 Elsevier Ltd. All rights reserved.

Increased incidence of peptic ulcer disease in central serous chorioretinopathy patients: a population-based retrospective cohort study.

PubMed

Chen, San-Ni; Lian, Iebin; Chen, Yi-Chiao; Ho, Jau-Der

2015-02-01

To investigate peptic ulcer disease and other possible risk factors in patients with central serous chorioretinopathy (CSR) using a population-based database. In this population-based retrospective cohort study, longitudinal data from the Taiwan National Health Insurance Research Database were analyzed. The study cohort comprised 835 patients with CSR and the control cohort comprised 4175 patients without CSR from January 2000 to December 2009. Conditional logistic regression was applied to examine the association of peptic ulcer disease and other possible risk factors for CSR, and stratified Cox regression models were applied to examine whether patients with CSR have an increased chance of peptic ulcer disease and hypertension development. The identifiable risk factors for CSR included peptic ulcer disease (adjusted odd ratio: 1.39, P = 0.001) and higher monthly income (adjusted odd ratio: 1.30, P = 0.006). Patients with CSR also had a significantly higher chance of developing peptic ulcer disease after the diagnosis of CSR (adjusted odd ratio: 1.43, P = 0.009). Peptic ulcer disease and higher monthly income are independent risk factors for CSR. Whereas, patients with CSR also had increased risk for peptic ulcer development.

The TREAT-NMD DMD Global Database: Analysis of More than 7,000 Duchenne Muscular Dystrophy Mutations

PubMed Central

Bladen, Catherine L; Salgado, David; Monges, Soledad; Foncuberta, Maria E; Kekou, Kyriaki; Kosma, Konstantina; Dawkins, Hugh; Lamont, Leanne; Roy, Anna J; Chamova, Teodora; Guergueltcheva, Velina; Chan, Sophelia; Korngut, Lawrence; Campbell, Craig; Dai, Yi; Wang, Jen; Barišić, Nina; Brabec, Petr; Lahdetie, Jaana; Walter, Maggie C; Schreiber-Katz, Olivia; Karcagi, Veronika; Garami, Marta; Viswanathan, Venkatarman; Bayat, Farhad; Buccella, Filippo; Kimura, En; Koeks, Zaïda; van den Bergen, Janneke C; Rodrigues, Miriam; Roxburgh, Richard; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Zimowski, Janusz; Santos, Rosário; Neagu, Elena; Artemieva, Svetlana; Rasic, Vedrana Milic; Vojinovic, Dina; Posada, Manuel; Bloetzer, Clemens; Jeannet, Pierre-Yves; Joncourt, Franziska; Díaz-Manera, Jordi; Gallardo, Eduard; Karaduman, A Ayşe; Topaloğlu, Haluk; El Sherif, Rasha; Stringer, Angela; Shatillo, Andriy V; Martin, Ann S; Peay, Holly L; Bellgard, Matthew I; Kirschner, Jan; Flanigan, Kevin M; Straub, Volker; Bushby, Kate; Verschuuren, Jan; Aartsma-Rus, Annemieke; Béroud, Christophe; Lochmüller, Hanns

2015-01-01

Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations). PMID:25604253

Employing image processing techniques for cancer detection using microarray images.

PubMed

Dehghan Khalilabad, Nastaran; Hassanpour, Hamid

2017-02-01

Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes. Finally, via the extracted data, cancerous cell is recognized. To evaluate the performance of the proposed system, microarray database is employed which includes Breast cancer, Myeloid Leukemia and Lymphomas from the Stanford Microarray Database. The results indicate that the proposed system is able to identify the type of cancer from the data set with an accuracy of 95.45%, 94.11%, and 100%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

A Bibliometric Assessment of Global Ice Bucket Challenge (Amyotrophic Lateral Sclerosis) Research.

PubMed

Ram, Shri

2016-10-01

This study is a quantitative and qualitative assessment of the global research trends on amyotrophic lateral sclerosis (ALS) (popularly known as Ice Bucket Challenge), through related literatures retrieved from SCOPUS multidisciplinary database for the period 1974-2013. This study is aimed at analyzing the literature on ALS in terms of document type, language, annual growth, productive country, journal, authors, subject, and most cited articles. The bibliographic data for this study was retrieved from the SCOPUS database using keywords 'amyotrophic lateral sclerosis', 'motor neurone disease', 'Charcot disease', 'Lou Gehrig's disease', 'Ice Bucket Challenge' available in title, abstract, and keyword fields of Scopus database from 1974 to 2013. The literature analysis included 21,750 articles during the period from 1974 to 2013 in different areas of ALS. USA was the most productive country in terms of literature produced, while Neurology was the most productive journal. An intensive awareness created by 'Ice Bucket Challenge' has attracted masses, and an intensive growth of literature is pertinent on ALS. The results of this study are expressed in terms of growth of literature, output of individual countries, and authors, and will be helpful in collaborative research in future.

Novel Nomogram That Predicts Aggressive Disease and Treatment Failure Among African-American Men with Prostate Cancer

DTIC Science & Technology

2014-10-01

and 55 AA men within the SCORE database. To date, 6 biomarkers have been analyzed including TMPRSS2-ERG, AMACR, PSMA , RB, c- Myc, and AR. We...analyzed so far including TMPRSS2-ERG, AMACR, PSMA , RB, c-Myc, and AR. In this cohort we observed statistically significant differences in marker...clinical practice. Not yet addressed Conclusion: Of the 20 biomarkers selected, six have been interrogated by IHC including TMPRSS2-ERG, AMACR, PSMA

Towards pathogenomics: a web-based resource for pathogenicity islands

PubMed Central

Yoon, Sung Ho; Park, Young-Kyu; Lee, Soohyun; Choi, Doil; Oh, Tae Kwang; Hur, Cheol-Goo; Kim, Jihyun F.

2007-01-01

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at . PMID:17090594

The Tip of the “Celiac Iceberg” in China: A Systematic Review and Meta-Analysis

PubMed Central

Yuan, Juanli; Gao, Jinyan; Li, Xin; Liu, Fahui; Wijmenga, Cisca; Chen, Hongbing; Gilissen, Luud J. W. J.

2013-01-01

Objective Until recently, celiac disease was considered to be rare in China. We aimed to estimate its true status. Methods By searching the MEDLINE database and four Chinese full-text databases (CNKI, CBM, VIP and WANFANG) (up to August 2012), as well as two HLA allele frequency net databases and the Chinese Statistics Yearbook databases, we systematically reviewed the literature on definite and suspected cases of celiac disease, the predisposing HLA allele frequencies, and on gluten exposure in China. Meta-analysis was performed by analyzing DQ2, DQ8 and DQB1*0201 gene frequencies and heterogeneity in populations from different geographic regions and ethnicities in China. Results At present, the number of reported celiac disease cases is extremely low in China. The frequencies of the HLA-DQ2.5 and HLA-DQ8 haplotypes were 3.4% (95% confidence interval 1.3–5.5%) and 2.1% (0.1–4.1%), respectively. HLA-DQ2 and HLA-DQ8 antigen frequencies were 18.4% (15.0–21.7%) and 8.0% (4.5–11.4%), respectively. The frequency of the DQB1*0201 allele was 10.5% (9.3–11.6%) and it was more common in the northern Chinese than in the southern Chinese populations. The chance of being exposed to gluten is rapidly increasing all over China nowadays. Conclusion The data on HLA haplotyping, in conjunction with increasing wheat consumption, strongly suggests that the occurrence of celiac disease is more common in China than currently reported. Coordinated measures by the Chinese government, medical and agricultural research institutions, and food industries, would be justified to create more awareness about celiac disease and to prevent it becoming a medical and societal burden. PMID:24324669

The BiolAD-DB system : an informatics system for clinical and genetic data.

PubMed

Nielsen, David A; Leidner, Marty; Haynes, Chad; Krauthammer, Michael; Kreek, Mary Jeanne

2007-01-01

The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password-protected BiolAD-DB SQL compliant server and database. BiolAD-DB tools further provide functionalities for generating customized reports and views. The BiolAD-DB system schema, client, and installation instructions are freely available at http://www.rockefeller.edu/biolad-db/.

Analysis of disease-associated objects at the Rat Genome Database

PubMed Central

Wang, Shur-Jen; Laulederkind, Stanley J. F.; Hayman, G. T.; Smith, Jennifer R.; Petri, Victoria; Lowry, Timothy F.; Nigam, Rajni; Dwinell, Melinda R.; Worthey, Elizabeth A.; Munzenmaier, Diane H.; Shimoyama, Mary; Jacob, Howard J.

2013-01-01

The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. In addition to organizing biological data from rats, the RGD team focuses on manual curation of gene–disease associations for rat, human and mouse. In this work, we have analyzed disease-associated strains, quantitative trait loci (QTL) and genes from rats. These disease objects form the basis for seven disease portals. Among disease portals, the cardiovascular disease and obesity/metabolic syndrome portals have the highest number of rat strains and QTL. These two portals share 398 rat QTL, and these shared QTL are highly concentrated on rat chromosomes 1 and 2. For disease-associated genes, we performed gene ontology (GO) enrichment analysis across portals using RatMine enrichment widgets. Fifteen GO terms, five from each GO aspect, were selected to profile enrichment patterns of each portal. Of the selected biological process (BP) terms, ‘regulation of programmed cell death’ was the top enriched term across all disease portals except in the obesity/metabolic syndrome portal where ‘lipid metabolic process’ was the most enriched term. ‘Cytosol’ and ‘nucleus’ were common cellular component (CC) annotations for disease genes, but only the cancer portal genes were highly enriched with ‘nucleus’ annotations. Similar enrichment patterns were observed in a parallel analysis using the DAVID functional annotation tool. The relationship between the preselected 15 GO terms and disease terms was examined reciprocally by retrieving rat genes annotated with these preselected terms. The individual GO term–annotated gene list showed enrichment in physiologically related diseases. For example, the ‘regulation of blood pressure’ genes were enriched with cardiovascular disease annotations, and the ‘lipid metabolic process’ genes with obesity annotations. Furthermore, we were able to enhance enrichment of neurological diseases by combining ‘G-protein coupled receptor binding’ annotated genes with ‘protein kinase binding’ annotated genes. Database URL: http://rgd.mcw.edu PMID:23794737

Management and Risk Reduction of Rheumatoid Arthritis in Individuals with Obstructive Sleep Apnea: A Nationwide Population-Based Study in Taiwan.

PubMed

Chen, Wei-Sheng; Chang, Yu-Sheng; Chang, Chi-Ching; Chang, Deh-Ming; Chen, Yi-Hsuan; Tsai, Chang-Youh; Chen, Jin-Hua

2016-10-01

To explore associations between obstructive sleep apnea (OSA) and autoimmune diseases and evaluate whether OSA management reduces the incidence of autoimmune diseases. This was a retrospective cohort study using nationwide database research. The data was from 105,846 adult patients in whom OSA was diagnosed and recorded in the Taiwan National Health Insurance Research Database between 2002 and 2011 were the patients were analyzed retrospectively. Patients with antecedent autoimmune diseases were excluded. A comparison cohort of 423,384 participants without OSA served as age- and sex-matched controls. Multivariable Cox regression analysis was performed on both cohorts to compute risk of autoimmune diseases during follow-up. Time-dependent OSA treatment effect was analyzed among patients with OSA. There were no interventions. Among patients with OSA, overall risk for incident autoimmune diseases was significantly higher than that in controls (adjusted hazard ratio [HR] = 1.95, 95% confidence interval [CI] = 1.66-2.27). Risk for individual autoimmune diseases, including rheumatoid arthritis (RA), Sjögren syndrome (SS), and Behçet disease, was significantly higher in patients with OSA than in controls (HRs [95% CI]: RA 1.33 [1.03-1.72, SS 3.45 [2.67-4.45] and Behçet disease 5.33 [2.45-12.66]). Increased risk for systemic lupus erythematosus (HR 1.00 [0.54-1.84]) and systemic sclerosis (HR 1.43 [0.51-3.96]) did not reach statistical significance. Patients with OSA receiving treatment had an overall reduced risk of RA and other autoimmune diseases (time-dependent HRs [95% CI]: 0.22 [0.05-0.94] and 0.51 [0.28-0.92], respectively). Patients with OSA are associated with higher risk for developing RA, SS, and Behçet disease. OSA management is associated with reduced risk of RA. © 2016 Associated Professional Sleep Societies, LLC.

Systemic inaccuracies in the National Surgical Quality Improvement Program database: Implications for accuracy and validity for neurosurgery outcomes research.

PubMed

Rolston, John D; Han, Seunggu J; Chang, Edward F

2017-03-01

The American College of Surgeons (ACS) National Surgical Quality Improvement Program (NSQIP) provides a rich database of North American surgical procedures and their complications. Yet no external source has validated the accuracy of the information within this database. Using records from the 2006 to 2013 NSQIP database, we used two methods to identify errors: (1) mismatches between the Current Procedural Terminology (CPT) code that was used to identify the surgical procedure, and the International Classification of Diseases (ICD-9) post-operative diagnosis: i.e., a diagnosis that is incompatible with a certain procedure. (2) Primary anesthetic and CPT code mismatching: i.e., anesthesia not indicated for a particular procedure. Analyzing data for movement disorders, epilepsy, and tumor resection, we found evidence of CPT code and postoperative diagnosis mismatches in 0.4-100% of cases, depending on the CPT code examined. When analyzing anesthetic data from brain tumor, epilepsy, trauma, and spine surgery, we found evidence of miscoded anesthesia in 0.1-0.8% of cases. National databases like NSQIP are an important tool for quality improvement. Yet all databases are subject to errors, and measures of internal consistency show that errors affect up to 100% of case records for certain procedures in NSQIP. Steps should be taken to improve data collection on the frontend of NSQIP, and also to ensure that future studies with NSQIP take steps to exclude erroneous cases from analysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Carbon dioxide balneotherapy and cardiovascular disease.

PubMed

Pagourelias, Efstathios D; Zorou, Paraskevi G; Tsaligopoulos, Miltiadis; Athyros, Vasilis G; Karagiannis, Asterios; Efthimiadis, Georgios K

2011-09-01

Carbon dioxide (CO(2)) balneotherapy is a kind of remedy with a wide spectrum of applications which have been used since the Middle Ages. However, its potential use as an adjuvant therapeutic option in patients with cardiovascular disease is not yet fully clarified. We performed a thorough review of MEDLINE Database, EMBASE, ISI WEB of Knowledge, COCHRANE database and sites funded by balneotherapy centers across Europe in order to recognize relevant studies and aggregate evidence supporting the use of CO(2) baths in various cardiovascular diseases. The three main effects of CO(2) hydrotherapy during whole body or partial immersion, including decline in core temperature, an increase in cutaneous blood flow, and an elevation of the score on thermal sensation, are analyzed on a pathophysiology basis. Additionally, the indications and contra-indications of the method are presented in an evidence-based way, while the need for new methodologically sufficient studies examining the use of CO(2) baths in other cardiovascular substrates is discussed.

Carbon dioxide balneotherapy and cardiovascular disease

NASA Astrophysics Data System (ADS)

Pagourelias, Efstathios D.; Zorou, Paraskevi G.; Tsaligopoulos, Miltiadis; Athyros, Vasilis G.; Karagiannis, Asterios; Efthimiadis, Georgios K.

2011-09-01

Carbon dioxide (CO2) balneotherapy is a kind of remedy with a wide spectrum of applications which have been used since the Middle Ages. However, its potential use as an adjuvant therapeutic option in patients with cardiovascular disease is not yet fully clarified. We performed a thorough review of MEDLINE Database, EMBASE, ISI WEB of Knowledge, COCHRANE database and sites funded by balneotherapy centers across Europe in order to recognize relevant studies and aggregate evidence supporting the use of CO2 baths in various cardiovascular diseases. The three main effects of CO2 hydrotherapy during whole body or partial immersion, including decline in core temperature, an increase in cutaneous blood flow, and an elevation of the score on thermal sensation, are analyzed on a pathophysiology basis. Additionally, the indications and contra-indications of the method are presented in an evidence-based way, while the need for new methodologically sufficient studies examining the use of CO2 baths in other cardiovascular substrates is discussed.

The Application and Future of Big Database Studies in Cardiology: A Single-Center Experience.

PubMed

Lee, Kuang-Tso; Hour, Ai-Ling; Shia, Ben-Chang; Chu, Pao-Hsien

2017-11-01

As medical research techniques and quality have improved, it is apparent that cardiovascular problems could be better resolved by more strict experiment design. In fact, substantial time and resources should be expended to fulfill the requirements of high quality studies. Many worthy ideas and hypotheses were unable to be verified or proven due to ethical or economic limitations. In recent years, new and various applications and uses of databases have received increasing attention. Important information regarding certain issues such as rare cardiovascular diseases, women's heart health, post-marketing analysis of different medications, or a combination of clinical and regional cardiac features could be obtained by the use of rigorous statistical methods. However, there are limitations that exist among all databases. One of the key essentials to creating and correctly addressing this research is through reliable processes of analyzing and interpreting these cardiologic databases.

Building an integrated neurodegenerative disease database at an academic health center.

PubMed

Xie, Sharon X; Baek, Young; Grossman, Murray; Arnold, Steven E; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M-Y; Trojanowski, John Q

2011-07-01

It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration. These comparative studies rely on powerful database tools to quickly generate data sets that match diverse and complementary criteria set by them. In this article, we present a novel integrated neurodegenerative disease (INDD) database, which was developed at the University of Pennsylvania (Penn) with the help of a consortium of Penn investigators. Because the work of these investigators are based on Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration, it allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used the Microsoft SQL server as a platform, with built-in "backwards" functionality to provide Access as a frontend client to interface with the database. We used PHP Hypertext Preprocessor to create the "frontend" web interface and then used a master lookup table to integrate individual neurodegenerative disease databases. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Using the INDD database, we compared the results of a biomarker study with those using an alternative approach by querying individual databases separately. We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies on several neurodegenerative diseases. Copyright © 2011 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

DDx: diagnostic assistance for the radiologist using PACS

NASA Astrophysics Data System (ADS)

Haynor, David R.

1993-09-01

A potentially valuable tool in medical imaging is the development, and integration with PACS, of systems which enhance the interpretive accuracy of the user -- his ability, given a set of findings (in the broad sense, including clinical information about the patient as well as characteristics of the lesion being analyzed), to assign the proper disease label, or diagnosis, to them. Such systems, which we call here interpretive tools (IT), contain a variety of types of information about diseases and their radiologic diagnosis. They can contain information about large numbers of diseases, including statistical information (incidence, characteristic anatomical locations, association with age and gender or with other diseases, probabilities of various findings given a disease), textual information (description of diseases, treatment, literature references, lists of other entities that might be confused with the disease of interest, additional diagnostic points that may not be represented, or even representable, within IT), and image-based information (typical and atypical examples for each entity and radiographic finding, examples of normal anatomy). These databases can be used both for teaching purposes and as a tool for improving interpretive accuracy [Swett, 1987]. This paper describes some of the requirements for these databases and then discusses early work on the implementation of DDx, an IT whose domain is neuroradiology.

Treatment Trends and Outcomes of Small-Cell Carcinoma of the Bladder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koay, Eugene J.; MD Anderson Cancer Center, Houston, Texas; Teh, Bin S., E-mail: bteh@tmh.org

2012-05-01

Purpose: Treatment for small-cell carcinoma of the bladder is largely guided by case reports, retrospective reviews, and small prospective trials. This study aimed to study outcomes using a large population-based database. Methods: The Surveillance, Epidemiology, and End Results-Medicare database (1991-2005) was used to analyze how different treatment combinations of specific bladder surgeries, chemotherapy, and radiation affected patient outcomes. Trends in the use of these combinations over time were also analyzed. Results: A total of 533 patients were retrieved from the database. A bladder-sparing approach involving transurethral resection of the bladder tumor (TURBT) combined with chemotherapy and radiation yielded no significantmore » difference in overall survival compared with patients undergoing at least a cystectomy (of whom over 90% received radical cystectomy) with chemotherapy (p > 0.05). The analysis of treatment trends indicated that these two general strategies for cure combined to account for fewer than 20% of patients. A majority of patients (54%) received TURBT as their only surgical treatment, and a subset analysis of these patients indicated that chemotherapy played a role in all stages of disease (p < 0.05) whereas radiation improved overall survival in regional-stage disease (p < 0.05). Conclusion: Relatively few patients with small-cell carcinoma of the bladder receive potentially curative therapies. Chemotherapy should be a major component of treatment. Cystectomy and bladder-sparing approaches represent two viable strategies and deserve further investigation to identify the patients who may benefit from organ preservation or not. In addition, the role of radiation in regional-stage disease should be investigated further, because it positively affects survival after TURBT.« less

Prevalence of physical inactivity in Iran: a systematic review.

PubMed

Fakhrzadeh, Hossein; Djalalinia, Shirin; Mirarefin, Mojdeh; Arefirad, Tahereh; Asayesh, Hamid; Safiri, Saeid; Samami, Elham; Mansourian, Morteza; Shamsizadeh, Morteza; Qorbani, Mostafa

2016-01-01

Introduction: Physical inactivity is one of the most important risk factors for chronic diseases, including cardiovascular disease, cancer, and stroke. We aim to conduct a systematic review of the prevalence of physical inactivity in Iran. Methods: We searched international databases; ISI, PubMed/Medline, Scopus, and national databases Irandoc, Barakat knowledge network system, and Scientific Information Database (SID). We collected data for outcome measures of prevalence of physical inactivity by sex, age, province, and year. Quality assessment and data extraction has been conducted independently by two independent research experts. There were no limitations for time and language. Results: We analyzed data for prevalence of physical inactivity in Iranian population. According to our search strategy we found 254 records; of them 185 were from international databases and the remaining 69 were obtained from national databases after refining the data, 34 articles that met eligible criteria remained for data extraction. From them respectively; 9, 20, 2 and 3 studies were at national, provincial, regional and local levels. The estimates for inactivity ranged from approximately 30% to almost 70% and had considerable variation between sexes and studied sub-groups. Conclusion: In Iran, most of studies reported high prevalence of physical inactivity. Our findings reveal a heterogeneity of reported values, often from differences in study design, measurement tools and methods, different target groups and sub-population sampling. These data do not provide the possibility of aggregation of data for a comprehensive inference.

Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease*

PubMed Central

Good, David M.; Zürbig, Petra; Argilés, Àngel; Bauer, Hartwig W.; Behrens, Georg; Coon, Joshua J.; Dakna, Mohammed; Decramer, Stéphane; Delles, Christian; Dominiczak, Anna F.; Ehrich, Jochen H. H.; Eitner, Frank; Fliser, Danilo; Frommberger, Moritz; Ganser, Arnold; Girolami, Mark A.; Golovko, Igor; Gwinner, Wilfried; Haubitz, Marion; Herget-Rosenthal, Stefan; Jankowski, Joachim; Jahn, Holger; Jerums, George; Julian, Bruce A.; Kellmann, Markus; Kliem, Volker; Kolch, Walter; Krolewski, Andrzej S.; Luppi, Mario; Massy, Ziad; Melter, Michael; Neusüss, Christian; Novak, Jan; Peter, Karlheinz; Rossing, Kasper; Rupprecht, Harald; Schanstra, Joost P.; Schiffer, Eric; Stolzenburg, Jens-Uwe; Tarnow, Lise; Theodorescu, Dan; Thongboonkerd, Visith; Vanholder, Raymond; Weissinger, Eva M.; Mischak, Harald; Schmitt-Kopplin, Philippe

2010-01-01

Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides. PMID:20616184

[Analysis of projects of infectious disease epidemiology sponsored by National Natural Science Foundation of China].

PubMed

Jian-Ming, Wang; Yan-Kai, Xia; Hui-Juan, Zhu; Feng, Chen; Hong-Bing, Shen

2016-05-10

To analyze the projects on the infectious disease epidemiology sponsored by the National Natural Science Foundation of China (NSFC), explore the hotspot and development trend, and offer a reference for researchers in this field. Based on the NSFC database, the projects on the infectious disease epidemiology (H2609) sponsored from 1987 to 2014 were analyzed. The changes of fund numbers, amounts and research fields were described. During the study period, NSFC sponsored 373 projects, including 228 general projects (61.1%), 78 youth projects (20.9%) and 67 other projects (18.0%). The average amount of the grant was 358.2 thousand Yuan (20 thousand-8 million). The main sponsored research fields were mechanisms of pathogen and immunity (36.2%) and population-based epidemiological studies (33.0%). The top three diseases were hepatitis, HIV/AIDS and tuberculosis. The amount of funding on researches of infectious disease epidemiology has increased continuously, which has played an important role in training scientific talents in the field of prevention and control of infectious diseases.

Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development.

PubMed

Sayers, Samantha; Ulysse, Guerlain; Xiang, Zuoshuang; He, Yongqun

2012-01-01

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format.

Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development

PubMed Central

Sayers, Samantha; Ulysse, Guerlain; Xiang, Zuoshuang; He, Yongqun

2012-01-01

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format. PMID:22505817

Study and analysis of the state of rare disease research in Shandong Province, China.

PubMed

Zhao, Heng; Cui, Yazhou; Zhou, Xiaoyan; Pang, Jingxiang; Zhang, Xiumei; Xu, Shuangqing; Han, Jinxiang

2012-11-01

As the world's most populous country, China has the world's largest number of rare disease groups in terms of prevalence. However, the country has no system of registering cases of most rare diseases, so there is very little documented information on the epidemiology of those diseases. The purpose of this study was to study the state of rare disease research and survey doctors in Shandong Province regarding their level of awareness of rare diseases. Types of rare diseases and numbers of cases were tallied and their geographical distribution over the decades was analyzed. Eight hundred and twenty-four doctors in tertiary hospitals and maternity and child care hospitals were surveyed by questionnaire. Data were descriptively analyzed and a map of disease distribution was created. Articles about rare diseases were retrieved from the Chinese Biomedical Literature Database to provide pertinent data. This study yielded 5,749 cases of 323 different types of rare diseases. The survey found that doctors lack awareness of research on rare diseases. An authoritative and information-rich platform for rare disease research is urgently needed. Key steps are to study epidemiological and statistical techniques and then obtain available data to provide a basis for the definition and regulation of rare diseases in China.

Study and analysis of the state of rare disease research in Shandong Province, China

PubMed Central

Zhao, Heng; Cui, Yazhou; Zhou, Xiaoyan; Pang, Jingxiang; Zhang, Xiumei; Xu, Shuangqing; Han, Jinxiang

2012-01-01

Summary As the world's most populous country, China has the world's largest number of rare disease groups in terms of prevalence. However, the country has no system of registering cases of most rare diseases, so there is very little documented information on the epidemiology of those diseases. The purpose of this study was to study the state of rare disease research and survey doctors in Shandong Province regarding their level of awareness of rare diseases. Types of rare diseases and numbers of cases were tallied and their geographical distribution over the decades was analyzed. Eight hundred and twenty-four doctors in tertiary hospitals and maternity and child care hospitals were surveyed by questionnaire. Data were descriptively analyzed and a map of disease distribution was created. Articles about rare diseases were retrieved from the Chinese Biomedical Literature Database to provide pertinent data. This study yielded 5,749 cases of 323 different types of rare diseases. The survey found that doctors lack awareness of research on rare diseases. An authoritative and information-rich platform for rare disease research is urgently needed. Key steps are to study epidemiological and statistical techniques and then obtain available data to provide a basis for the definition and regulation of rare diseases in China. PMID:25343091

A prototypic small molecule database for bronchoalveolar lavage-based metabolomics

NASA Astrophysics Data System (ADS)

Walmsley, Scott; Cruickshank-Quinn, Charmion; Quinn, Kevin; Zhang, Xing; Petrache, Irina; Bowler, Russell P.; Reisdorph, Richard; Reisdorph, Nichole

2018-04-01

The analysis of bronchoalveolar lavage fluid (BALF) using mass spectrometry-based metabolomics can provide insight into lung diseases, such as asthma. However, the important step of compound identification is hindered by the lack of a small molecule database that is specific for BALF. Here we describe prototypic, small molecule databases derived from human BALF samples (n=117). Human BALF was extracted into lipid and aqueous fractions and analyzed using liquid chromatography mass spectrometry. Following filtering to reduce contaminants and artifacts, the resulting BALF databases (BALF-DBs) contain 11,736 lipid and 658 aqueous compounds. Over 10% of these were found in 100% of samples. Testing the BALF-DBs using nested test sets produced a 99% match rate for lipids and 47% match rate for aqueous molecules. Searching an independent dataset resulted in 45% matching to the lipid BALF-DB compared to<25% when general databases are searched. The BALF-DBs are available for download from MetaboLights. Overall, the BALF-DBs can reduce false positives and improve confidence in compound identification compared to when general databases are used.

Medical cost, incidence rate, and treatment status of gastroesophageal reflux disease in Japan: analysis of claims data.

PubMed

Miwa, Hiroto; Takeshima, Tomomi; Iwasaki, Kosuke; Hiroi, Shinzo

2016-11-01

Published reports have shown the prevalence and incidence of gastroesophageal reflux disease (GERD) is increasing in Japan. The objective of this study is to examine change in GERD incidence, and to understand current patient demographics, medical costs, treatment status, and the suitability of current treatment based on analysis of an insurance claims database. An insurance claims database with data on ∼1.9 million company employees from January 2005 to May 2015 was used. Prevalence, demographics, and medical costs were analyzed by cross-sectional analysis, and incidence and treatment status were analyzed by longitudinal analysis among newly-diagnosed GERD patients. GERD prevalence in 2014 was 3.3% among 20-59 year-olds, accounting for 40,134 people in the database, and GERD incidence increased from 0.63% in 2009 to 0.98% in 2014. In 2014, mean medical cost per patient per month for GERD patients aged 20-59 was JPY 31,900 (USD 266 as of January 2016), which was ∼2.4-times the mean national healthcare cost. The most frequently prescribed drugs for newly-diagnosed GERD patients were proton pump inhibitors (PPIs). Although PPIs were prescribed more often in patients with more doctor visit months, over 20% of patients that made frequent doctor visits (19 or more visits during a 24 calendar months period) were prescribed PPIs during only 1 calendar month or not at all. The database included only reimbursable claims data and, therefore, did not cover over-the-counter drugs. The database also consisted of employee-based claims data, so included little data on people aged 60 years and older. Given the increasing incidence of GERD in Japan there is a need for up-to-date information on GERD incidence. This study suggests that some GERD patients may not be receiving appropriate treatment according to Japanese guidelines, which is needed to improve symptom control.

Microarray analysis to identify the similarities and differences of pathogenesis between aortic occlusive disease and abdominal aortic aneurysm.

PubMed

Wang, Guofu; Bi, Lechang; Wang, Gaofeng; Huang, Feilai; Lu, Mingjing; Zhu, Kai

2018-06-01

Objectives Expression profile of GSE57691 was analyzed to identify the similarities and differences between aortic occlusive disease and abdominal aortic aneurysm. Methods The expression profile of GSE57691 was downloaded from Gene Expression Omnibus database, including 20 small abdominal aortic aneurysm samples, 29 large abdominal aortic aneurysm samples, 9 aortic occlusive disease samples, and 10 control samples. Using the limma package in R, the differentially expressed genes were screened. Followed by enrichment analysis was performed for the differentially expressed genes using database for annotation, visualization, and integrated discovery online tool. Based on string online tool and Cytoscape software, protein-protein interaction network and module analyses were carried out. Moreover, integrated TF platform database and Cytoscape software were used for constructing transcriptional regulatory networks. Results As a result, 1757, 354, and 396 differentially expressed genes separately were identified in aortic occlusive disease, large abdominal aortic aneurysm, and small abdominal aortic aneurysm samples. UBB was significantly enriched in proteolysis related pathways with a high degree in three groups. SPARCL1 was another gene shared by these groups and regulated by NFIA, which had a high degree in transcriptional regulatory network. ACTB, a significant upregulated gene in abdominal aortic aneurysm samples, could be regulated by CLIC4, which was significantly enriched in cell motions. ACLY and NFIB were separately identified in aortic occlusive disease and small abdominal aortic aneurysm samples, and separately enriched in lipid metabolism and negative regulation of cell proliferation. Conclusions The downregulated UBB, NFIA, and SPARCL1 might play key roles in both aortic occlusive disease and abdominal aortic aneurysm, while the upregulated ACTB might only involve in abdominal aortic aneurysm. ACLY and NFIB were specifically involved in aortic occlusive disease and small abdominal aortic aneurysm separately.

Sinonasal fibrosarcoma: analysis of the Surveillance, Epidemiology, and End Results database.

PubMed

Patel, Tapan D; Carniol, Eric T; Vázquez, Alejandro; Baredes, Soly; Liu, James K; Eloy, Jean Anderson

2016-02-01

Primary fibrosarcoma of the sinonasal region is an infrequently occurring malignant neoplasm. Fibrosarcomas are most commonly found in the extremities, with only 1% of fibrosarcomas reported in the head and neck region. This study analyzes the demographic, clinicopathologic, and survival characteristics of sinonasal fibrosarcoma (SNFS). The Surveillance, Epidemiology, and End Results (SEER) database (1973 to 2012) was queried for SNFS cases. Data were analyzed with respect to various demographic and clinicopathologic factors. Survival was analyzed using the Kaplan-Meier model. Fifty-one cases of fibrosarcoma were identified in the sinonasal region. The mean age at diagnosis was 54.5 years and the mean survival was 119.7 months. There was no gender predilection with a male-to-female ratio of 1.04:1. The maxillary sinus was the most common site of involvement (54.9%), followed by the nasal cavity (23.5%). Five-year survival analysis revealed an overall survival rate of 71.7%, disease-specific survival rate of 77.8%, and relative survival (RS) rate of 78.8%. Disease-specific survival was better among those treated with surgery (with [76.2%] or without [87.5%] adjuvant radiotherapy) than those treated with primary radiotherapy alone (33.3%) (p = 0.0069). SNFS is a rare entity. This study represents the largest series of SNFS to date. The mainstay of treatment for this tumor is surgical resection with or without radiotherapy. © 2015 ARS-AAOA, LLC.

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

PubMed

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma.

Evaluation of personal digital assistant drug information databases for the managed care pharmacist.

PubMed

Lowry, Colleen M; Kostka-Rokosz, Maria D; McCloskey, William W

2003-01-01

Personal digital assistants (PDAs) are becoming a necessity for practicing pharmacists. They offer a time-saving and convenient way to obtain current drug information. Several software companies now offer general drug information databases for use on hand held computers. PDAs priced less than 200 US dollars often have limited memory capacity; therefore, the user must choose from a growing list of general drug information database options in order to maximize utility without exceeding memory capacity. This paper reviews the attributes of available general drug information software databases for the PDA. It provides information on the content, advantages, limitations, pricing, memory requirements, and accessibility of drug information software databases. Ten drug information databases were subjectively analyzed and evaluated based on information from the product.s Web site, vendor Web sites, and from our experience. Some of these databases have attractive auxiliary features such as kinetics calculators, disease references, drug-drug and drug-herb interaction tools, and clinical guidelines, which may make them more useful to the PDA user. Not all drug information databases are equal with regard to content, author credentials, frequency of updates, and memory requirements. The user must therefore evaluate databases for completeness, currency, and cost effectiveness before purchase. In addition, consideration should be given to the ease of use and flexibility of individual programs.

Mutation databases for inherited renal disease: are they complete, accurate, clinically relevant, and freely available?

PubMed

Savige, Judy; Dagher, Hayat; Povey, Sue

2014-07-01

This study examined whether gene-specific DNA variant databases for inherited diseases of the kidney fulfilled the Human Variome Project recommendations of being complete, accurate, clinically relevant and freely available. A recent review identified 60 inherited renal diseases caused by mutations in 132 genes. The disease name, MIM number, gene name, together with "mutation" or "database," were used to identify web-based databases. Fifty-nine diseases (98%) due to mutations in 128 genes had a variant database. Altogether there were 349 databases (a median of 3 per gene, range 0-6), but no gene had two databases with the same number of variants, and 165 (50%) databases included fewer than 10 variants. About half the databases (180, 54%) had been updated in the previous year. Few (77, 23%) were curated by "experts" but these included nine of the 11 with the most variants. Even fewer databases (41, 12%) included clinical features apart from the name of the associated disease. Most (223, 67%) could be accessed without charge, including those for 50 genes (40%) with the maximum number of variants. Future efforts should focus on encouraging experts to collaborate on a single database for each gene affected in inherited renal disease, including both unpublished variants, and clinical phenotypes. © 2014 WILEY PERIODICALS, INC.

Laparoscopy Improves Short-term Outcomes After Surgery for Diverticular Disease

PubMed Central

RUSS, ANDREW J.; OBMA, KARI L.; RAJAMANICKAM, VICTORIA; WAN, YIN; HEISE, CHARLES P.; FOLEY, EUGENE F.; HARMS, BRUCE; KENNEDY, GREGORY D.

2012-01-01

BACKGROUND & AIMS Observational studies and small randomized controlled trials have shown that the use of laparoscopy in colon resection for diverticular disease is feasible and results in fewer complications. We analyzed data from a large, prospectively maintained, multicenter database (National Surgical Quality Initiative Program) to determine whether the use of laparoscopy in the elective treatment of diverticular disease decreases rates of complications compared with open surgery, independent of preoperative comorbid factors. METHODS The analysis included data from 6970 patients who underwent elective surgeries for diverticular disease from 2005 to 2008. Patients with diverticular disease were identified by International Classification of Diseases, 9th revision codes and then categorized into open or laparoscopic groups based on Current Procedural Terminology codes. Preoperative, intraoperative, and postoperative data were analyzed to determine factors associated with increased risk for postoperative complications. RESULTS Data were analyzed from 3468 patients who underwent open surgery and 3502 patients who underwent laparoscopic procedures. After correcting for probability of morbidity, American Society of Anesthesiology class, and ostomy creation, overall complications (including superficial surgical site infections, deep incisional surgical site infections, sepsis, and septic shock) occurred with significantly lower incidence among patients who underwent laparoscopic procedures compared with those who received open operations. CONCLUSIONS The use of laparoscopy for treating diverticular disease, in the absence of absolute contraindications, results in fewer postoperative complications compared with open surgery. PMID:20193685

Hypothyroidism in Patients with Psoriasis or Rosacea: A Large Population Study.

PubMed

James, Sara M; Hill, Dane E; Feldman, Steven R

2016-10-15

Hypothyroidism is a common disease, and there may be a link between hypothyroidism and inflammatory skin disease. The purpose of this study is to assess whether hypothyroidism is more prevalent in psoriasis or rosacea patients. We utilized a large claims-based database to analyze rates of hypothyroidism in patients with psoriasis and rosacea compared to other patients with skin diseases. Participants were patients between 20-64 years of age with ICD-9 diagnosis codes for psoriasis, rosacea, and hypothyroidism. We found that rates of hypothyroidism in rosacea and psoriasis patients were similar to rates of hypothyroidism in those without rosacea or psoriasis.

Hypothyroidism in Patients with Psoriasis or Rosacea: A Large Population Study.

PubMed

James, Sara M; Hill, Dane E; Feldman, Steven R

2016-09-15

Hypothyroidism is a common disease, and there may be a link between hypothyroidism and inflammatory skin disease. The purpose of this study is to assess whether hypothyroidism is more prevalent in psoriasis or rosacea patients. We utilized a large claims-based database to analyze rates of hypothyroidism in patients with psoriasis and rosacea compared to other patients with skin diseases. Participants were patients between 20-64 years of age with ICD-9 diagnosis codes for psoriasis, rosacea, and hypothyroidism. We found that rates of hypothyroidism in rosacea and psoriasis patients were similar to rates of hypothyroidism in those without rosacea or psoriasis.

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

Xie, Sharon X.; Baek, Young; Grossman, Murray; Arnold, Steven E.; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M.-Y.; Trojanowski, John Q.

2010-01-01

Background It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies across several neurodegenerative diseases. PMID:21784346

Mining biological databases for candidate disease genes

NASA Astrophysics Data System (ADS)

Braun, Terry A.; Scheetz, Todd; Webster, Gregg L.; Casavant, Thomas L.

2001-07-01

The publicly-funded effort to sequence the complete nucleotide sequence of the human genome, the Human Genome Project (HGP), has currently produced more than 93% of the 3 billion nucleotides of the human genome into a preliminary `draft' format. In addition, several valuable sources of information have been developed as direct and indirect results of the HGP. These include the sequencing of model organisms (rat, mouse, fly, and others), gene discovery projects (ESTs and full-length), and new technologies such as expression analysis and resources (micro-arrays or gene chips). These resources are invaluable for the researchers identifying the functional genes of the genome that transcribe and translate into the transcriptome and proteome, both of which potentially contain orders of magnitude more complexity than the genome itself. Preliminary analyses of this data identified approximately 30,000 - 40,000 human `genes.' However, the bulk of the effort still remains -- to identify the functional and structural elements contained within the transcriptome and proteome, and to associate function in the transcriptome and proteome to genes. A fortuitous consequence of the HGP is the existence of hundreds of databases containing biological information that may contain relevant data pertaining to the identification of disease-causing genes. The task of mining these databases for information on candidate genes is a commercial application of enormous potential. We are developing a system to acquire and mine data from specific databases to aid our efforts to identify disease genes. A high speed cluster of Linux of workstations is used to analyze sequence and perform distributed sequence alignments as part of our data mining and processing. This system has been used to mine GeneMap99 sequences within specific genomic intervals to identify potential candidate disease genes associated with Bardet-Biedle Syndrome (BBS).

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

PubMed

Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

2016-06-01

MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources. © 2016 WILEY PERIODICALS, INC.

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

PubMed Central

Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T.; van Oven, Mannis; Wallace, Douglas C.; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F.; Attimonelli, Marcella; Zuchner, Stephan

2016-01-01

MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and disease. MSeqDR-LSDB is a locus specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar-compliant variant annotations. PhenoTips is used for phenotypic data submission on de-identified patients using human phenotype ontology terminology. Development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources. PMID:26919060

The relationship between RASSF1A promoter methylation and thyroid carcinoma: A meta-analysis of 14 articles and a bioinformatics of 2 databases (PRISMA).

PubMed

Niu, Heng; Yang, Jingyu; Yang, Kunxian; Huang, Yingze

2017-11-01

DNA promoter methylation can suppresses gene expression and shows an important role in the biological functions of Ras association domain family 1A (RASSF1A). Many studies have performed to elucidate the role of RASSF1A promoter methylation in thyroid carcinoma, while the results were conflicting and heterogeneous. Here, we analyzed the data of databases to determine the relationship between RASSF1A promoter methylation and thyroid carcinoma. We used the data from 14 cancer-normal studies and Gene Expression Omnibus (GEO) database to analyze RASSF1A promoter methylation in thyroid carcinoma susceptibility. The data from the Cancer Genome Atlas project (TCGA) database was used to analyze the relationship between RASSF1A promoter methylation and thyroid carcinoma susceptibility, clinical characteristics, prognosis. Odds ratios were estimated for thyroid carcinoma susceptibility and hazard ratios were estimated for thyroid carcinoma prognosis. The heterogeneity between studies of meta-analysis was explored using H, I values, and meta-regression. We adopted quality criteria to classify the studies of meta-analysis. Subgroup analyses were done for thyroid carcinoma susceptibility according to ethnicity, methods, and primers. Result of meta-analysis indicated that RASSF1A promoter methylation is associated with higher susceptibility to thyroid carcinoma with small heterogeneity. Similarly, the result from GEO database also showed that a significant association between RASSF1A gene promoter methylation and thyroid carcinoma susceptibility. For the results of TCGA database, we found that RASSF1A promoter methylation is associated with susceptibility and poor disease-free survival (DFS) of thyroid carcinoma. In addition, we also found a close association between RASSF1A promoter methylation and patient tumor stage and age, but not in patients of different genders. The methylation status of RASSF1A promoter is strongly associated with thyroid carcinoma susceptibility and DFS. The RASSF1A promoter methylation test can be applied in the clinical diagnosis of thyroid carcinoma.

[Infectious diseases among Brazilian preschool children attending daycare centers].

PubMed

Pedraza, Dixis Figueroa; Queiroz, Daiane de; Sales, Márcia Cristina

2014-02-01

The scope of this article is to analyze the prevalence and factors associated with the development of infectious diseases that affect children in daycare centers, namely respiratory infections, diarrheal disease and parasitic infections. Bibliographic research was conducted in the MEDLINE, LILACS and SciELO databases, and observational studies were included. 129 studies were identified, of which 21 were considered relevant to this study, namely two longitudinal and 19 cross-sectional studies. The systematization of the reviewed studies highlighted: i) the presence of intestinal parasites was the main outcome analyzed, followed by respiratory infections; ii) only one study investigated the occurrence of diarrheal disease; iii) the Giardia lamblia was the most prevalent parasitosis; iv) the variables that were most often associated with the development of intestinal parasitosis were child age, family income and maternal education; v) the attendance at daycare centers was a risk factor for intestinal parasites and respiratory infections. Respiratory and parasitic infections are major problems in institutionalized children in daycare centers. The reduction of such diseases involves a complex web of socio-economic, sanitation and daycare center infrastructure aspects.

Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense.

PubMed

Al-Obaidi, Jameel R; Mohd-Yusuf, Yusmin; Razali, Nurhanani; Jayapalan, Jaime Jacqueline; Tey, Chin-Chong; Md-Noh, Normahnani; Junit, Sarni Mat; Othman, Rofina Yasmin; Hashim, Onn Haji

2014-03-24

Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE). When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered.

Identification of Proteins of Altered Abundance in Oil Palm Infected with Ganoderma boninense

PubMed Central

Al-Obaidi, Jameel R.; Mohd-Yusuf, Yusmin; Razali, Nurhanani; Jayapalan, Jaime Jacqueline; Tey, Chin-Chong; Md-Noh, Normahnani; Junit, Sarni Mat; Othman, Rofina Yasmin; Hashim, Onn Haji

2014-01-01

Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE). When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered. PMID:24663087

[A novel compound heterozygous mutation in ABCA3 gene in a child with diffuse parenchymal lung disease].

PubMed

Bao, Y M; Liu, X L; Liu, X L; Chen, J H; Zheng, Y J

2017-11-02

Objective: To summarize the clinical characteristics of the diffuse parenchymal lung diseases in a child caused by a novel compound heterozygous ABCA3 mutation and explore the association between the phenotype and ABCA3 mutation. Method: The clinical material of a patient diagnosed with diffuse parenchymal lung disease with ABCA3 mutation in December 2016 in Shenzhen Children's Hospital was analyzed. The information about ABCA3 gene mutation updated before April, 2017 was searched and collected from the gene databases (including 1000Genomes, HGMD, EXAC) and the literatures (including Wanfang Chinese database and Pubmed). Result: The girl was one year and nine months old. She presented with chronic cough, tachypnea, cyanosis and failure to thrive since she was one year and three months old. Her condition gradually deteriorated after she was empirically treated. Physical examination showed malnutrition, tachypnea and clubbed-fingers. Her high resolution computed tomography (HRCT) revealed diffused ground-glass opacities, thickened interlobular septum, and multiple subpleural small air-filled lung cysts. The second generation sequencing study identified a novel compound heterozygous mutation (c.1755delC+c.2890G>A) in her ABCA3 gene, which derived respectively from her parents and has not been reported in the database and the literatures mentioned above. Conclusion: c.1755delC+c.2890G>A is a new kind of compound heterozygous mutation in ABCA3, which can cause children's diffuse parenchymal lung disease. Its phenotype is related to its genotype.

Methods for structuring scientific knowledge from many areas related to aging research.

PubMed

Zhavoronkov, Alex; Cantor, Charles R

2011-01-01

Aging and age-related disease represents a substantial quantity of current natural, social and behavioral science research efforts. Presently, no centralized system exists for tracking aging research projects across numerous research disciplines. The multidisciplinary nature of this research complicates the understanding of underlying project categories, the establishment of project relations, and the development of a unified project classification scheme. We have developed a highly visual database, the International Aging Research Portfolio (IARP), available at AgingPortfolio.org to address this issue. The database integrates information on research grants, peer-reviewed publications, and issued patent applications from multiple sources. Additionally, the database uses flexible project classification mechanisms and tools for analyzing project associations and trends. This system enables scientists to search the centralized project database, to classify and categorize aging projects, and to analyze the funding aspects across multiple research disciplines. The IARP is designed to provide improved allocation and prioritization of scarce research funding, to reduce project overlap and improve scientific collaboration thereby accelerating scientific and medical progress in a rapidly growing area of research. Grant applications often precede publications and some grants do not result in publications, thus, this system provides utility to investigate an earlier and broader view on research activity in many research disciplines. This project is a first attempt to provide a centralized database system for research grants and to categorize aging research projects into multiple subcategories utilizing both advanced machine algorithms and a hierarchical environment for scientific collaboration.

DGEM--a microarray gene expression database for primary human disease tissues.

PubMed

Xia, Yuni; Campen, Andrew; Rigsby, Dan; Guo, Ying; Feng, Xingdong; Su, Eric W; Palakal, Mathew; Li, Shuyu

2007-01-01

Gene expression patterns can reflect gene regulations in human tissues under normal or pathologic conditions. Gene expression profiling data from studies of primary human disease samples are particularly valuable since these studies often span many years in order to collect patient clinical information and achieve a large sample size. Disease-to-Gene Expression Mapper (DGEM) provides a beneficial community resource to access and analyze these data; it currently includes Affymetrix oligonucleotide array datasets for more than 40 human diseases and 1400 samples. The data are normalized to the same scale and stored in a relational database. A statistical-analysis pipeline was implemented to identify genes abnormally expressed in disease tissues or genes whose expressions are associated with clinical parameters such as cancer patient survival. Data-mining results can be queried through a web-based interface at http://dgem.dhcp.iupui.edu/. The query tool enables dynamic generation of graphs and tables that are further linked to major gene and pathway resources that connect the data to relevant biology, including Entrez Gene and Kyoto Encyclopedia of Genes and Genomes (KEGG). In summary, DGEM provides scientists and physicians a valuable tool to study disease mechanisms, to discover potential disease biomarkers for diagnosis and prognosis, and to identify novel gene targets for drug discovery. The source code is freely available for non-profit use, on request to the authors.

Interactome of the hepatitis C virus: Literature mining with ANDSystem.

PubMed

Saik, Olga V; Ivanisenko, Timofey V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2016-06-15

A study of the molecular genetics mechanisms of host-pathogen interactions is of paramount importance in developing drugs against viral diseases. Currently, the literature contains a huge amount of information that describes interactions between HCV and human proteins. In addition, there are many factual databases that contain experimentally verified data on HCV-host interactions. The sources of such data are the original data along with the data manually extracted from the literature. However, the manual analysis of scientific publications is time consuming and, because of this, databases created with such an approach often do not have complete information. One of the most promising methods to provide actualisation and completeness of information is text mining. Here, with the use of a previously developed method by the authors using ANDSystem, an automated extraction of information on the interactions between HCV and human proteins was conducted. As a data source for the text mining approach, PubMed abstracts and full text articles were used. Additionally, external factual databases were analyzed. On the basis of this analysis, a special version of ANDSystem, extended with the HCV interactome, was created. The HCV interactome contains information about the interactions between 969 human and 11 HCV proteins. Among the 969 proteins, 153 'new' proteins were found not previously referred to in any external databases of protein-protein interactions for HCV-host interactions. Thus, the extended ANDSystem possesses a more comprehensive detailing of HCV-host interactions versus other existing databases. It was interesting that HCV proteins more preferably interact with human proteins that were already involved in a large number of protein-protein interactions as well as those associated with many diseases. Among human proteins of the HCV interactome, there were a large number of proteins regulated by microRNAs. It turned out that the results obtained for protein-protein interactions and microRNA-regulation did not depend on how well the proteins were studied, while protein-disease interactions appeared to be dependent on the level of study. In particular, the mean number of diseases linked to well-studied proteins (proteins were considered well-studied if they were mentioned in 50 or more PubMed publications) from the HCV interactome was 20.8, significantly exceeding the mean number of associations with diseases (10.1) for the total set of well-studied human proteins present in ANDSystem. For proteins not highly poorly-studied investigated, proteins from the HCV interactome (each protein was referred to in less than 50 publications) distribution of the number of diseases associated with them had no statistically significant differences from the distribution of the number of diseases associated with poorly-studied proteins based on the total set of human proteins stored in ANDSystem. With this, the average number of associations with diseases for the HCV interactome and the total set of human proteins were 0.3 and 0.2, respectively. Thus, ANDSystem, extended with the HCV interactome, can be helpful in a wide range of issues related to analyzing HCV-host interactions in the search for anti-HCV drug targets. The demo version of the extended ANDSystem covered here containing only interactions between human proteins, genes, metabolites, diseases, miRNAs and molecular-genetic pathways, as well as interactions between human proteins/genes and HCV proteins, is freely available at the following web address: http://www-bionet.sscc.ru/psd/andhcv/. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Sys-BodyFluid: a systematical database for human body fluid proteome research

PubMed Central

Li, Su-Jun; Peng, Mao; Li, Hong; Liu, Bo-Shu; Wang, Chuan; Wu, Jia-Rui; Li, Yi-Xue; Zeng, Rong

2009-01-01

Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10 000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/. PMID:18978022

Sys-BodyFluid: a systematical database for human body fluid proteome research.

PubMed

Li, Su-Jun; Peng, Mao; Li, Hong; Liu, Bo-Shu; Wang, Chuan; Wu, Jia-Rui; Li, Yi-Xue; Zeng, Rong

2009-01-01

Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

PubMed Central

Wilbur, W. John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical–gene interactions, chemical–disease relationships and gene–disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein–protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. PMID:23160415

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

PubMed

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

Evolution of the Antidepressant Prescribing in Alzheimer's Disease and Related Disorders Between 2010 and 2014: Results from the French National Database on Alzheimer's Disease (BNA).

PubMed

David, Renaud; Manera, Valeria; Fabre, Roxane; Pradier, Christian; Robert, Philippe; Tifratene, Karim

2016-07-02

Safety warnings from health authorities are currently intended to limit the use of psychotropic agents in dementia-related conditions. Evidence concerning the use of antidepressants in dementia is, however, scarce and contradictory. To evaluate antidepressant use among individuals with Alzheimer's disease (AD) and related disorders in the French population between 2010 and 2014. Antidepressant prescriptions in individuals with AD, mixed dementia (MD), and vascular dementia (VaD) in the French National Alzheimer Database between 2010 and 2014 were analyzed (N = 199,544). Multivariate analysis showed an annual significant increase (p < 0.001) in the prescription rate of antidepressants from 26% (2010) to 31% (2014), and identified female gender, younger age, higher education, living in long-term facilities, more severe cognitive decline, and presence of vascular signs (VaD and MD) as associated factors for antidepressant prescribing. The annual increase of antidepressant prescribing among individuals with AD, MD, and VaD in French specialized settings may be partially related to the lack of current valuable medications for dementia-related behavioral symptoms.

ImmunemiR - A Database of Prioritized Immune miRNA Disease Associations and its Interactome.

PubMed

Prabahar, Archana; Natarajan, Jeyakumar

2017-01-01

MicroRNAs are the key regulators of gene expression and their abnormal expression in the immune system may be associated with several human diseases such as inflammation, cancer and autoimmune diseases. Elucidation of miRNA disease association through the interactome will deepen the understanding of its disease mechanisms. A specialized database for immune miRNAs is highly desirable to demonstrate the immune miRNA disease associations in the interactome. miRNAs specific to immune related diseases were retrieved from curated databases such as HMDD, miR2disease and PubMed literature based on MeSH classification of immune system diseases. The additional data such as miRNA target genes, genes coding protein-protein interaction information were compiled from related resources. Further, miRNAs were prioritized to specific immune diseases using random walk ranking algorithm. In total 245 immune miRNAs associated with 92 OMIM disease categories were identified from external databases. The resultant data were compiled as ImmunemiR, a database of prioritized immune miRNA disease associations. This database provides both text based annotation information and network visualization of its interactome. To our knowledge, ImmunemiR is the first available database to provide a comprehensive repository of human immune disease associated miRNAs with network visualization options of its target genes, protein-protein interactions (PPI) and its disease associations. It is freely available at http://www.biominingbu.org/immunemir/. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge.

PubMed

Ningthoujam, Sanjoy Singh; Talukdar, Anupam Das; Potsangbam, Kumar Singh; Choudhury, Manabendra Dutta

2012-05-07

Major research contributions in ethnopharmacology have generated vast amount of data associated with medicinal plants. Computerized databases facilitate data management and analysis making coherent information available to researchers, planners and other users. Web-based databases also facilitate knowledge transmission and feed the circle of information exchange between the ethnopharmacological studies and public audience. However, despite the development of many medicinal plant databases, a lack of uniformity is still discernible. Therefore, it calls for defining a common standard to achieve the common objectives of ethnopharmacology. The aim of the study is to review the diversity of approaches in storing ethnopharmacological information in databases and to provide some minimal standards for these databases. Survey for articles on medicinal plant databases was done on the Internet by using selective keywords. Grey literatures and printed materials were also searched for information. Listed resources were critically analyzed for their approaches in content type, focus area and software technology. Necessity for rapid incorporation of traditional knowledge by compiling primary data has been felt. While citation collection is common approach for information compilation, it could not fully assimilate local literatures which reflect traditional knowledge. Need for defining standards for systematic evaluation, checking quality and authenticity of the data is felt. Databases focussing on thematic areas, viz., traditional medicine system, regional aspect, disease and phytochemical information are analyzed. Issues pertaining to data standard, data linking and unique identification need to be addressed in addition to general issues like lack of update and sustainability. In the background of the present study, suggestions have been made on some minimum standards for development of medicinal plant database. In spite of variations in approaches, existence of many overlapping features indicates redundancy of resources and efforts. As the development of global data in a single database may not be possible in view of the culture-specific differences, efforts can be given to specific regional areas. Existing scenario calls for collaborative approach for defining a common standard in medicinal plant database for knowledge sharing and scientific advancement. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Prasugrel Use in Real Life: A Report From the Outpatient Setting in France.

PubMed

Sabouret, Pierre; Taiel-Sartral, Magali; Chartier, Florence; Akiki, Sabine; Cuisset, Thomas

2016-07-01

The objective of this study was to provide descriptive statistics on patterns of prasugrel usage in the outpatient setting in France. This retrospective study was conducted to describe treatment patterns for prasugrel in the outpatient setting in France using the Intercontinental Marketing Services (IMS) Disease Analyzer database, which collates electronic medical records updated by a nationally representative database of 1200 French general practitioners (GPs). Anonymous data were collected prospectively at each follow-up visit. The study population consisted of patients with ≥1 prescription for prasugrel in the outpatient setting from its launch date to 3 years post-launch. Patients were followed up from the date of the first prescription for prasugrel recorded in the database until they died, changed GP, or reached the end of the study, whichever came first. In France, the IMS Disease Analyzer included 1052 patients receiving ≥1 prescription of prasugrel from January 2010 until October 2012. Eighty-five percent of the population was male. The mean age was 58 years; 94.3% were age <75 years, and 95.0% weighed ≥60 kg. Of the total, 99.8% of patients were prescribed a daily maintenance dose of 10 mg, and 0.2% had a history of transient ischemic attack/stroke. Concomitant medications were antiplatelet agents (100%; aspirin, 93.7%), lipid-lowering agents (90.1%), β-blockers (83.7%), angiotensin-converting enzyme inhibitors (62.2%), and anti-ulcer medications (55.1%). The results reflect good usage of prasugrel by French GPs in the outpatient setting, with excellent implementation of the Prasugrel European Summary Product Characteristics. © 2016 Wiley Periodicals, Inc.

Non-invasive detection of the freezing of gait in Parkinson's disease using spectral and wavelet features.

PubMed

Nazarzadeh, Kimia; Arjunan, Sridhar P; Kumar, Dinesh K; Das, Debi Prasad

2016-08-01

In this study, we have analyzed the accelerometer data recorded during gait analysis of Parkinson disease patients for detecting freezing of gait (FOG) episodes. The proposed method filters the recordings for noise reduction of the leg movement changes and computes the wavelet coefficients to detect FOG events. Publicly available FOG database was used and the technique was evaluated using receiver operating characteristic (ROC) analysis. Results show a higher performance of the wavelet feature in discrimination of the FOG events from the background activity when compared with the existing technique.

Pathogen Research Databases

Science.gov Websites

Hepatitis C Virus (HCV) database project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The HCV database project started as a spin-off from the HIV database project. There are two databases for HCV, a sequence database

[Medical treatment of rheumatoid arthritis in 2014 : Current data from the German Collaborative Arthritis Centers].

PubMed

Albrecht, K; Huscher, D; Eidner, T; Kleinert, S; Späthling-Mestekemper, S; Bischoff, S; Zink, A

2017-02-01

Since the introduction of biologic treatment in rheumatoid arthritis (RA), disease activity and treatment modalities have changed substantially. The current provision and developments in recent years are analyzed with annual data from the National Database of the Collaborative Arthritis Centers in Germany. To analyze disease activity, diagnostics and treatment in RA patients in 2014 with regard to seropositivity and disease duration. Time trends from 2007-2014 are reported for disease activity (DAS28) distribution and biologic treatment. In 2014, a total of 8,084 RA patients were analyzed: 72 % were rheumatoid factor and/or ACPA positive, the mean age was 62 years and the mean disease duration 12 years. According to DAS28, 35.9 % were in remission, 19.2 % had low, 37.1 % moderate and 7.8 % high disease activity. An increase since 2007 was only observed in patients with a disease duration >2 years. Synthetic DMARDS were used for treatment in 78 %. Biologic treatment increased from 16 % (2007) to 27 % (2014). Especially those patients with a disease duration >5 years were treated more frequently with biologics. Seronegative patients had slightly less severe mean disease activity parameters. They were treated equally frequent with DMARDS but only half as often with biologics compared to seropositive patients. The use of biologics in RA patients has increased since 2007; however this was not observed in patients with short disease duration. Early intensive treatment adaption seems justified to improve disease activity in the large portion of patients who do not reach low disease activity under conventional DMARDs.

PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations

PubMed Central

Zhang, Chao; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan; Deng, Lian; Tian, Lei; Feng, Qidi

2018-01-01

Abstract There are a growing number of studies focusing on delineating genetic variations that are associated with complex human traits and diseases due to recent advances in next-generation sequencing technologies. However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variations within and among populations. The PGG.Population database documents 7122 genomes representing 356 global populations from 107 countries and provides essential information for researchers to understand human genomic diversity and genetic ancestry. These data and information can facilitate the design of research studies and the interpretation of results of both evolutionary and medical studies involving human populations. The database is carefully maintained and constantly updated when new data are available. We included miscellaneous functions and a user-friendly graphical interface for visualization of genomic diversity, population relationships (genetic affinity), ancestral makeup, footprints of natural selection, and population history etc. Moreover, PGG.Population provides a useful feature for users to analyze data and visualize results in a dynamic style via online illustration. The long-term ambition of the PGG.Population, together with the joint efforts from other researchers who contribute their data to our database, is to create a comprehensive depository of geographic and ethnic variation of human genome, as well as a platform bringing influence on future practitioners of medicine and clinical investigators. PGG.Population is available at https://www.pggpopulation.org. PMID:29112749

Analysis of vascular endothelial dysfunction genes and related pathways in obesity through systematic bioinformatics.

PubMed

Zhang, Hui; Wang, Jing; Sun, Ling; Xu, Qiuqin; Hou, Miao; Ding, Yueyue; Huang, Jie; Chen, Ye; Cao, Lei; Zhang, Jianmin; Qian, Weiguo; Lv, Haitao

2015-01-01

Obesity has become an increasingly serious health problem and popular research topic. It is associated with many diseases, especially cardiovascular disease (CVD)-related endothelial dysfunction. This study analyzed genes related to endothelial dysfunction and obesity and then summarized their most significant signaling pathways. Genes related to vascular endothelial dysfunction and obesity were extracted from a PubMed database, and analyzed by STRING, DAVID, and Gene-Go Meta-Core software. 142 genes associated with obesity were found to play a role in endothelial dysfunction in PubMed. A significant pathway (Angiotensin system maturation in protein folding and maturation) associated with obesity and endothelial dysfunction was explored. The genes and the pathway explored may play an important role in obesity. Further studies about preventing vascular endothelial dysfunction obesity should be conducted through targeting these loci and pathways.

Patient/family views on data sharing in rare diseases: study in the European LeukoTreat project

PubMed Central

Darquy, Sylviane; Moutel, Grégoire; Lapointe, Anne-Sophie; D'Audiffret, Diane; Champagnat, Julie; Guerroui, Samia; Vendeville, Marie-Louise; Boespflug-Tanguy, Odile; Duchange, Nathalie

2016-01-01

The purpose of this study was to explore patient and family views on the sharing of their medical data in the context of compiling a European leukodystrophies database. A survey questionnaire was delivered with help from referral centers and the European Leukodystrophies Association, and the questionnaires returned were both quantitatively and qualitatively analyzed. This study found that patients/families were strongly in favor of participating. Patients/families hold great hope and trust in the development of this type of research. They have a strong need for information and transparency on database governance, the conditions framing access to data, all research conducted, partnerships with the pharmaceutical industry, and they also need access to results. Our findings bring ethics-driven arguments for a process combining initial broad consent with ongoing information. On both, we propose key item-deliverables to database participants. PMID:26081642

Visibility graph analysis of heart rate time series and bio-marker of congestive heart failure

NASA Astrophysics Data System (ADS)

Bhaduri, Anirban; Bhaduri, Susmita; Ghosh, Dipak

2017-09-01

Study of RR interval time series for Congestive Heart Failure had been an area of study with different methods including non-linear methods. In this article the cardiac dynamics of heart beat are explored in the light of complex network analysis, viz. visibility graph method. Heart beat (RR Interval) time series data taken from Physionet database [46, 47] belonging to two groups of subjects, diseased (congestive heart failure) (29 in number) and normal (54 in number) are analyzed with the technique. The overall results show that a quantitative parameter can significantly differentiate between the diseased subjects and the normal subjects as well as different stages of the disease. Further, the data when split into periods of around 1 hour each and analyzed separately, also shows the same consistent differences. This quantitative parameter obtained using the visibility graph analysis thereby can be used as a potential bio-marker as well as a subsequent alarm generation mechanism for predicting the onset of Congestive Heart Failure.

Proteomic Analysis of Synovial Fluid Obtained From a Dog Diagnosed With Idiopathic Immune-Mediated Polyarthritis.

PubMed

Tan, Wei Miao; Lau, Seng Fong; Ajat, Mokrish; Mansor, Rozaihan; Abd Rani, Puteri Azaziah Megat; Rahmad, Norasfaliza Binti

2017-03-01

This case study is to report the proteins detected by proteomic analysis of synovial fluid from a dog diagnosed with idiopathic immune-mediated polyarthritis, and to compare it with healthy dogs. Synovial fluid was collected via arthrocentesis from a dog diagnosed with immune-mediated polyarthritis. Protein precipitation was performed on the synovial fluid, followed by isoelectric focusing and 2-dimensional gel electrophoresis. The spots on the 2-dimensional gels were analyzed using MALDI-TOF/MS. The results were then analyzed against the MASCOT database. The results from the proteomic analysis revealed an abundance of several types of immunoglobulins together with the presence of complement C4b-binding protein alpha chain. Actin and keratin were also among the proteins detected. Proteomic studies, facilitate a better understanding of the different levels of proteins expressed during disease activity. Potential disease biomarkers can aid in the diagnosis of disease, as well as help in monitoring treatment efficacy and providing prognosis for the patient. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis of direct medical and nonmedical costs for care of rheumatoid arthritis patients using the large cohort database, IORRA.

PubMed

Tanaka, Eiichi; Hoshi, Daisuke; Igarashi, Ataru; Inoue, Eisuke; Shidara, Kumi; Sugimoto, Naoki; Sato, Eri; Seto, Yohei; Nakajima, Ayako; Momohara, Shigeki; Taniguchi, Atsuo; Tsutani, Kiichiro; Yamanaka, Hisashi

2013-07-01

Our goal was to determine the annual direct medical and nonmedical costs for the care of patients with rheumatoid arthritis (RA) using data from a large cohort database in Japan. Direct medical costs [out of pocket to hospitals and pharmacies and for complementary and alternative medicine (CAM)] and nonmedical costs (caregiving, transportation, self-help devices, house modifications) were determined for RA patients who were participants in the Institute of Rheumatology, Rheumatoid Arthritis (IORRA) studies conducted in October 2007 and April 2008. Correlations between these costs and RA disease activity, disability level, and quality of life (QOL) were assessed. Data were analyzed from 5,204 and 5,265 RA patients in October 2007 and April 2008, respectively. The annual direct medical costs were JPY132,000 [out of pocket to hospital (US$1 = JPY90 in 2007)], JPY84,000 (out of pocket to pharmacy), and JPY146,000 (CAM). Annual direct nonmedical costs were JPY105,000 (caregiving), JPY22,000 (transportation), JPY30,000 (self-help devices), and JPY188,000 (house modifications). Based on the utilization rate for each cost component, the annual medical and nonmedical costs for each RA patient were JPY262,136 and JPY61,441, respectively. Costs increased with increasing RA disease activity and disability level or worsening quality of life (QOL). Based on the IORRA database, patients with RA bear heavy economic burdens that increase as the disease is exacerbated. The results also suggest that the increase in medical and nonmedical costs may be ameliorated by the proactive control of disease activity.

Downscaling climate information for local disease mapping.

PubMed

Bernardi, M; Gommes, R; Grieser, J

2006-06-01

The study of the impacts of climate on human health requires the interdisciplinary efforts of health professionals, climatologists, biologists, and social scientists to analyze the relationships among physical, biological, ecological, and social systems. As the disease dynamics respond to variations in regional and local climate, climate variability affects every region of the world and the diseases are not necessarily limited to specific regions, so that vectors may become endemic in other regions. Climate data at local level are thus essential to evaluate the dynamics of vector-borne disease through health-climate models and most of the times the climatological databases are not adequate. Climate data at high spatial resolution can be derived by statistical downscaling using historical observations but the method is limited by the availability of historical data at local level. Since the 90s', the statistical interpolation of climate data has been an important priority of the Agrometeorology Group of the Food and Agriculture Organization of the United Nations (FAO), as they are required for agricultural planning and operational activities at the local level. Since 1995, date of the first FAO spatial interpolation software for climate data, more advanced applications have been developed such as SEDI (Satellite Enhanced Data Interpolation) for the downscaling of climate data, LOCCLIM (Local Climate Estimator) and the NEW_LOCCLIM in collaboration with the Deutscher Wetterdienst (German Weather Service) to estimate climatic conditions at locations for which no observations are available. In parallel, an important effort has been made to improve the FAO climate database including at present more than 30,000 stations worldwide and expanding the database from developing countries coverage to global coverage.

[Waterborne diseases and basic sanitation in Colombia].

PubMed

Rodríguez Miranda, Juan P; García-Ubaque, César A; García-Ubaque, Juan C

2016-01-01

To analyze the relationship of sewerage coverage and wastewater treatment with waterborne disease behaviour. A descriptive retrospective study was conducted using secondary sources (document review and information available in databases) about basic sanitation coverage, treatment of domestic sewage in the country and the prevalence of waterborne diseases during the period 2008-2014. The country invested USD 1,100 million in the implementation of wastewater treatment systems from 2011 until the first half of 2013. However, the incidence of waterborne diseases, such as acute diarrheal disease, foodborne diseases and typhoid and paratyphoid fever did not decrease during the period 2008-2014; only hepatitis A registered a decrease. Investment in water supply and sewerage systems is relevant to improve health conditions of the population and to reduce the incidence and prevalence of various health conditions; however, it is necessary to address other aspects such as health education and social empowerment to address this problem more efficiently.

Mexican registry of pediatric cardiac surgery. First report.

PubMed

Cervantes-Salazar, Jorge; Calderón-Colmenero, Juan; Ramírez-Marroquín, Samuel; Palacios-Macedo, Alexis; Bolio Cerdán, Alejandro; Vizcaíno Alarcón, Alfredo; Curi-Curi, Pedro; de la Llata, Manuel; Erdmenger Orellana, Julio; González, Julieta; García Soriano, Federico; Calderón, Alejandro; Casillas, Luis; Villanueva, Filiberto; Sánchez Ramírez, Roberto; Osnaya, Héctor; Necoechea, Juan Carlos; Alva Espinoza, Carlos; Prado Villegas, Guillermo

Currently, there is a spreading worldwide tendency to characterize health issues and to propose alternative solutions via the creation of computerized databases. The aim of this study was to present the results in a computerized database of pediatric cardiac surgeries developed under the auspices of the Mexican Association of Specialists in Congenital Heart Diseases (Asociación Mexicana de Especialistas en Cardiopatías Congénitas A.C) and coordinated by the collegiate group of Pediatric Cardiology and Surgery as petitioned by the National Institutes of Health and High Specialty Hospitals Coordinating Commission. We analyzed all cases registered in the database during a 1-year observation period (August 1, 2011 to July 31, 2012) by all major Health Ministry-dependent institutes and hospitals offering surgical services related to pediatric cardiopathies to the non-insured population. Seven institutions participated voluntarily in completing the database. During the analyzed period, 943 surgeries in 880 patients with 7% reoperations (n=63) were registered. Thirty-eight percent of the surgeries were performed in children <1 year of age. The five most common cardiopathies were patent ductus arteriosus (n=96), ventricular septal defect (n=86), tetralogy of Fallot (n=72), atrial septal defect (n=68), and aortic coarctation (n=54). Ninety percent of surgeries were elective and extracorporeal circulation was used in 62% of surgeries. Global mortality rate was 7.5% with the following distribution in the RACHS-1 score categories: 1 (n=4, 2%), 2 (n=19, 6%), 3 (n=22, 8%), 4 (n=12, 19%), 5 (n=1, 25%), 6 (n=6, 44%), and non-classifiable (n=2, 9%). This analysis provides a representative view of the surgical practices in cardiovascular diseases in the pediatric population at the national non-insured population level. However, incorporating other health institutions to the national registry database will render a more accurate panorama of the national reality in surgical practices in the population <18 years of age. Copyright © 2014 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

GraphSAW: a web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data.

PubMed

Shoshi, Alban; Hoppe, Tobias; Kormeier, Benjamin; Ogultarhan, Venus; Hofestädt, Ralf

2015-02-28

Adverse drug reactions are one of the most common causes of death in industrialized Western countries. Nowadays, empirical data from clinical studies for the approval and monitoring of drugs and molecular databases is available. The integration of database information is a promising method for providing well-based knowledge to avoid adverse drug reactions. This paper presents our web-based decision support system GraphSAW which analyzes and evaluates drug interactions and side effects based on data from two commercial and two freely available molecular databases. The system is able to analyze single and combined drug-drug interactions, drug-molecule interactions as well as single and cumulative side effects. In addition, it allows exploring associative networks of drugs, molecules, metabolic pathways, and diseases in an intuitive way. The molecular medication analysis includes the capabilities of the upper features. A statistical evaluation of the integrated data and top 20 drugs concerning drug interactions and side effects is performed. The results of the data analysis give an overview of all theoretically possible drug interactions and side effects. The evaluation shows a mismatch between pharmaceutical and molecular databases. The concordance of drug interactions was about 12% and 9% of drug side effects. An application case with prescribed data of 11 patients is presented in order to demonstrate the functionality of the system under real conditions. For each patient at least two interactions occured in every medication and about 8% of total diseases were possibly induced by drug therapy. GraphSAW (http://tunicata.techfak.uni-bielefeld.de/graphsaw/) is meant to be a web-based system for health professionals and researchers. GraphSAW provides comprehensive drug-related knowledge and an improved medication analysis which may support efforts to reduce the risk of medication errors and numerous drastic side effects.

Coding accuracy for Parkinson's disease hospital admissions: implications for healthcare planning in the UK.

PubMed

Muzerengi, S; Rick, C; Begaj, I; Ives, N; Evison, F; Woolley, R L; Clarke, C E

2017-05-01

Hospital Episode Statistics data are used for healthcare planning and hospital reimbursements. Reliability of these data is dependent on the accuracy of individual hospitals reporting Secondary Uses Service (SUS) which includes hospitalisation. The number and coding accuracy for Parkinson's disease hospital admissions at a tertiary centre in Birmingham was assessed. Retrospective, routine-data-based study. A retrospective electronic database search for all Parkinson's disease patients admitted to the tertiary hospital over a 4-year period (2009-2013) was performed on the SUS database using International Classification of Disease codes, and on the local inpatient electronic prescription database, Prescription and Information Communications System, using medication prescriptions. Capture-recapture methods were used to estimate the number of patients and admissions missed by both databases. From the two databases, between July 2009 and June 2013, 1068 patients with Parkinson's disease accounted for 1999 admissions. During these admissions, the Parkinson's disease was coded as a primary or secondary diagnosis. Ninety-one percent of these admissions were recorded on the SUS database. Capture-recapture methods estimated that the number of Parkinson's disease patients admitted during this period was 1127 patients (95% confidence interval: 1107-1146). A supplementary search of both SUS and Prescription and Information Communications System was undertaken using the hospital numbers of these 1068 patients. This identified another 479 admissions. SUS database under-estimated Parkinson's disease admissions by 27% during the study period. The accuracy of disease coding is critical for healthcare policy planning and must be improved. If the under-reporting of Parkinson's disease admissions on the SUS database is repeated nationally, expenditure on Parkinson's disease admissions in England is under-estimated by approximately £61 million per year. Copyright © 2016 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Incorporation of spatial interactions in location networks to identify critical geo-referenced routes for assessing disease control measures on a large-scale campus.

PubMed

Wen, Tzai-Hung; Chin, Wei Chien Benny

2015-04-14

Respiratory diseases mainly spread through interpersonal contact. Class suspension is the most direct strategy to prevent the spread of disease through elementary or secondary schools by blocking the contact network. However, as university students usually attend courses in different buildings, the daily contact patterns on a university campus are complicated, and once disease clusters have occurred, suspending classes is far from an efficient strategy to control disease spread. The purpose of this study is to propose a methodological framework for generating campus location networks from a routine administration database, analyzing the community structure of the network, and identifying the critical links and nodes for blocking respiratory disease transmission. The data comes from the student enrollment records of a major comprehensive university in Taiwan. We combined the social network analysis and spatial interaction model to establish a geo-referenced community structure among the classroom buildings. We also identified the critical links among the communities that were acting as contact bridges and explored the changes in the location network after the sequential removal of the high-risk buildings. Instead of conducting a questionnaire survey, the study established a standard procedure for constructing a location network on a large-scale campus from a routine curriculum database. We also present how a location network structure at a campus could function to target the high-risk buildings as the bridges connecting communities for blocking disease transmission.

Comparison of the NCI open database with seven large chemical structural databases.

PubMed

Voigt, J H; Bienfait, B; Wang, S; Nicklaus, M C

2001-01-01

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

Development of Korean Rare Disease Knowledge Base

PubMed Central

Seo, Heewon; Kim, Dokyoon; Chae, Jong-Hee; Kang, Hee Gyung; Lim, Byung Chan; Cheong, Hae Il

2012-01-01

Objectives Rare disease research requires a broad range of disease-related information for the discovery of causes of genetic disorders that are maladies caused by abnormalities in genes or chromosomes. A rarity in cases makes it difficult for researchers to elucidate definite inception. This knowledge base will be a major resource not only for clinicians, but also for the general public, who are unable to find consistent information on rare diseases in a single location. Methods We design a compact database schema for faster querying; its structure is optimized to store heterogeneous data sources. Then, clinicians at Seoul National University Hospital (SNUH) review and revise those resources. Additionally, we integrated other sources to capture genomic resources and clinical trials in detail on the Korean Rare Disease Knowledge base (KRDK). Results As a result, we have developed a Web-based knowledge base, KRDK, suitable for study of Mendelian diseases that commonly occur among Koreans. This knowledge base is comprised of disease summary and review, causal gene list, laboratory and clinic directory, patient registry, and so on. Furthermore, database for analyzing and giving access to human biological information and the clinical trial management system are integrated on KRDK. Conclusions We expect that KRDK, the first rare disease knowledge base in Korea, may contribute to collaborative research and be a reliable reference for application to clinical trials. Additionally, this knowledge base is ready for querying of drug information so that visitors can search a list of rare diseases that is relative to specific drugs. Visitors can have access to KRDK via http://www.snubi.org/software/raredisease/. PMID:23346478

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

PubMed Central

Chowdhury, Saikat; Sarkar, Ram Rup

2015-01-01

Elucidating the complexities of cell signaling pathways is of immense importance to gain understanding about various biological phenomenon, such as dynamics of gene/protein expression regulation, cell fate determination, embryogenesis and disease progression. The successful completion of human genome project has also helped experimental and theoretical biologists to analyze various important pathways. To advance this study, during the past two decades, systematic collections of pathway data from experimental studies have been compiled and distributed freely by several databases, which also integrate various computational tools for further analysis. Despite significant advancements, there exist several drawbacks and challenges, such as pathway data heterogeneity, annotation, regular update and automated image reconstructions, which motivated us to perform a thorough review on popular and actively functioning 24 cell signaling databases. Based on two major characteristics, pathway information and technical details, freely accessible data from commercial and academic databases are examined to understand their evolution and enrichment. This review not only helps to identify some novel and useful features, which are not yet included in any of the databases but also highlights their current limitations and subsequently propose the reasonable solutions for future database development, which could be useful to the whole scientific community. PMID:25632107

Research Registries: A Tool to Advance Understanding of Rare Neuro-Ophthalmic Diseases

PubMed Central

Blankshain, Kimberly D; Moss, Heather E

2016-01-01

Background Medical research registries (MRR) are organized systems used to collect, store and analyze patient information. They are important tools for medical research with particular application to the study of rare diseases, including those seen in neuro-ophthalmic practice. Evidence Acquisition Evidence for this review was gathered from the writers’ experiences creating a comprehensive neuro-ophthalmology registry and review of the literature. Results MRR are typically observational and prospective databases of de-identified patient information. The structure is flexible and can accommodate a focus on specific diseases or treatments, surveillance of patient populations, physician quality improvement, or recruitment for future studies. They are particularly useful for the study of rare diseases. They can be integrated into the hierarchy of medical research at many levels provided their construction is well organized and they have several key characteristics including an easily manipulated database, comprehensive information on carefully selected patients and comply with human subjects regulations. MRR pertinent to neuro-ophthalmology include the UIC neuro-ophthalmology registry, Susac Syndrome Registry, Intracranial Hypertension Registry as well as larger scale patient outcome registries being developed by professional societies. Conclusion Medical research registries have a variety of forms and applications. With careful planning and clear goals, they are flexible and powerful research tools that can support multiple different study designs, and through this have the potential to advance understanding and care of neuro-ophthalmic diseases. PMID:27389624

Research Registries: A Tool to Advance Understanding of Rare Neuro-Ophthalmic Diseases.

PubMed

Blankshain, Kimberly D; Moss, Heather E

2016-09-01

Medical research registries (MRR) are organized systems used to collect, store, and analyze patient information. They are important tools for medical research with particular application to the study of rare diseases, including those seen in neuro-ophthalmic practice. Evidence for this review was gathered from the writers' experiences creating a comprehensive neuro-ophthalmology registry and review of the literature. MRR are typically observational and prospective databases of de-identified patient information. The structure is flexible and can accommodate a focus on specific diseases or treatments, surveillance of patient populations, physician quality improvement, or recruitment for future studies. They are particularly useful for the study of rare diseases. They can be integrated into the hierarchy of medical research at many levels provided their construction is well organized and they have several key characteristics including an easily manipulated database, comprehensive information on carefully selected patients, and comply with human subjects regulations. MRR pertinent to neuro-ophthalmology include the University of Illinois at Chicago neuro-ophthalmology registry, Susac Syndrome Registry, Intracranial Hypertension Registry, and larger-scale patient outcome registries being developed by professional societies. MRR have a variety of forms and applications. With careful planning and clear goals, they are flexible and powerful research tools that can support multiple different study designs, and this can provide the potential to advance understanding and care of neuro-ophthalmic diseases.

The Finnish disease heritage database (FinDis) update-a database for the genes mutated in the Finnish disease heritage brought to the next-generation sequencing era.

PubMed

Polvi, Anne; Linturi, Henna; Varilo, Teppo; Anttonen, Anna-Kaisa; Byrne, Myles; Fokkema, Ivo F A C; Almusa, Henrikki; Metzidis, Anthony; Avela, Kristiina; Aula, Pertti; Kestilä, Marjo; Muilu, Juha

2013-11-01

The Finnish Disease Heritage Database (FinDis) (http://findis.org) was originally published in 2004 as a centralized information resource for rare monogenic diseases enriched in the Finnish population. The FinDis database originally contained 405 causative variants for 30 diseases. At the time, the FinDis database was a comprehensive collection of data, but since 1994, a large amount of new information has emerged, making the necessity to update the database evident. We collected information and updated the database to contain genes and causative variants for 35 diseases, including six more genes and more than 1,400 additional disease-causing variants. Information for causative variants for each gene is collected under the LOVD 3.0 platform, enabling easy updating. The FinDis portal provides a centralized resource and user interface to link information on each disease and gene with variant data in the LOVD 3.0 platform. The software written to achieve this has been open-sourced and made available on GitHub (http://github.com/findis-db), allowing biomedical institutions in other countries to present their national data in a similar way, and to both contribute to, and benefit from, standardized variation data. The updated FinDis portal provides a unique resource to assist patient diagnosis, research, and the development of new cures. © 2013 WILEY PERIODICALS, INC.

Toward an open-access global database for mapping, control, and surveillance of neglected tropical diseases.

PubMed

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F L; Utzinger, Jürg; Kristensen, Thomas K; Vounatsou, Penelope

2011-12-01

After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and 'grey literature'), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay.

Analyses of Factors Affecting Endothelial Cell Density in an Eye Bank Corneal Donor Database.

PubMed

Kwon, Ji Won; Cho, Kyong Jin; Kim, Hong Kyu; Lee, Jimmy K; Gore, Patrick K; McCartney, Mitchell D; Chuck, Roy S

2016-09-01

To analyze the factors affecting central corneal endothelial cell density (ECD) in an eye bank corneal donor database. The Lion's Eye Institute corneal donor database consisting of 18,665 donors (34,234 corneas) aged 20 years or older was analyzed. In particular, differences in the ECD based on age, sex, race, prior ocular surgery, a history of systemic diseases, and smoking were investigated. Furthermore, risk factors for donor cell count inadequacy (defined here as ECD less than 2000/mm) were identified. ECD decreased with age. Regarding race, the average ECD of African American donors was higher than those of white or Hispanic donors. A history of diabetes mellitus (DM) and ocular surgery were associated with a lower ECD. Donor medical history of hypertension, glaucoma, depression, dementia, Parkinson disease, hyper- or hypothyroidism, or smoking did not seem to affect the ECD. The risk factors for donor cell count inadequacy, based on binary logistic regression analyses were advanced age [65-74 years yielded an odds ratio of 17.8; confidence interval (CI), 10.6-29.8; P < 0.001; and 75-99 years yielded an odds ratio of 24.6 (CI, 14.5-41.61; P < 0.001) when compared with 20-34 years], cataract surgery (odds ratio, 4.3; CI, 4.0-4.8; P < 0.001), and DM (odds ratio, 1.2; CI, 1.1-1.3; P = 0.001). Age, race, ocular surgery (cataract and refractive), and DM seem to significantly affect donor corneal ECD. Of these variables, age, a history of cataract surgery, and DM were found to be the greatest risk factors for inadequate donor cell density (less than 2000/mm).

Investigation of mutations in the HBB gene using the 1,000 genomes database.

PubMed

Carlice-Dos-Reis, Tânia; Viana, Jaime; Moreira, Fabiano Cordeiro; Cardoso, Greice de Lemos; Guerreiro, João; Santos, Sidney; Ribeiro-Dos-Santos, Ândrea

2017-01-01

Mutations in the HBB gene are responsible for several serious hemoglobinopathies, such as sickle cell anemia and β-thalassemia. Sickle cell anemia is one of the most common monogenic diseases worldwide. Due to its prevalence, diverse strategies have been developed for a better understanding of its molecular mechanisms. In silico analysis has been increasingly used to investigate the genotype-phenotype relationship of many diseases, and the sequences of healthy individuals deposited in the 1,000 Genomes database appear to be an excellent tool for such analysis. The objective of this study is to analyze the variations in the HBB gene in the 1,000 Genomes database, to describe the mutation frequencies in the different population groups, and to investigate the pattern of pathogenicity. The computational tool SNPEFF was used to align the data from 2,504 samples of the 1,000 Genomes database with the HG19 genome reference. The pathogenicity of each amino acid change was investigated using the databases CLINVAR, dbSNP and HbVar and five different predictors. Twenty different mutations were found in 209 healthy individuals. The African group had the highest number of individuals with mutations, and the European group had the lowest number. Thus, it is concluded that approximately 8.3% of phenotypically healthy individuals from the 1,000 Genomes database have some mutation in the HBB gene. The frequency of mutated genes was estimated at 0.042, so that the expected frequency of being homozygous or compound heterozygous for these variants in the next generation is approximately 0.002. In total, 193 subjects had a non-synonymous mutation, which 186 (7.4%) have a deleterious mutation. Considering that the 1,000 Genomes database is representative of the world's population, it can be estimated that fourteen out of every 10,000 individuals in the world will have a hemoglobinopathy in the next generation.

Analysis on composition rules of Chinese patent drugs treating pain-related diseases based on data mining method.

PubMed

Tang, Shi-Huan; Shen, Dan; Yang, Hong-Jun

2017-08-24

To analyze the composition rules of oral prescriptions in the treatment of headache, stomachache and dysmenorrhea recorded in National Standard for Chinese Patent Drugs (NSCPD) enacted by Ministry of Public Health of China and then make comparison between them to better understand pain treatment in different regions of human body. Constructed NSCPD database had been constructed in 2014. Prescriptions treating the three pain-related diseases were searched and screened from the database. Then data mining method such as association rules analysis and complex system entropy method integrated in the data mining software Traditional Chinese Medicine Inheritance Support System (TCMISS) were applied to process the data. Top 25 drugs with high frequency in the treatment of each disease were selected, and 51, 33 and 22 core combinations treating headache, stomachache and dysmenorrhea respectively were mined out as well. The composition rules of the oral prescriptions for treating headache, stomachache and dysmenorrhea recorded in NSCPD has been summarized. Although there were similarities between them, formula varied according to different locations of pain. It can serve as an evidence and reference for clinical treatment and new drug development.

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

Database for Parkinson Disease Mutations and Rare Variants

DTIC Science & Technology

2016-09-01

AWARD NUMBER: W81XWH-14-1-0097 TITLE: “ Database for Parkinson Disease Mutations and Rare Variants” PRINCIPAL INVESTIGATOR: JEFFERY M. VANCE...TO THE ABOVE ADDRESS. 1. REPORT DATE September 2016 2. REPORT TYPE FINAL 3. DATES COVERED 1 Jul 2014 – 30 Jun 2016 4. TITLE AND SUBTITLE Database ...For Parkinson Disease (PD) specifically, the variant databases currently available are incomplete, don’t assess impact and/or are not equipped to

Common hyperspectral image database design

NASA Astrophysics Data System (ADS)

Tian, Lixun; Liao, Ningfang; Chai, Ali

2009-11-01

This paper is to introduce Common hyperspectral image database with a demand-oriented Database design method (CHIDB), which comprehensively set ground-based spectra, standardized hyperspectral cube, spectral analysis together to meet some applications. The paper presents an integrated approach to retrieving spectral and spatial patterns from remotely sensed imagery using state-of-the-art data mining and advanced database technologies, some data mining ideas and functions were associated into CHIDB to make it more suitable to serve in agriculture, geological and environmental areas. A broad range of data from multiple regions of the electromagnetic spectrum is supported, including ultraviolet, visible, near-infrared, thermal infrared, and fluorescence. CHIDB is based on dotnet framework and designed by MVC architecture including five main functional modules: Data importer/exporter, Image/spectrum Viewer, Data Processor, Parameter Extractor, and On-line Analyzer. The original data were all stored in SQL server2008 for efficient search, query and update, and some advance Spectral image data Processing technology are used such as Parallel processing in C#; Finally an application case is presented in agricultural disease detecting area.

Syphilis in pregnancy and congenital syphilis in Amazonas State, Brazil: an evaluation using database linkage.

PubMed

Soeiro, Claudia Marques de Oliveira; Miranda, Angélica Espinosa; Saraceni, Valeria; Santos, Marcelo Cordeiro dos; Talhari, Sinesio; Ferreira, Luiz Carlos de Lima

2014-04-01

This study analyzes notification of syphilis in pregnancy and congenital syphilis in Amazo- nas State, Brazil, from 2007 to 2009 and verifies underreporting in databases in the National Information System on Diseases of Notification (SINAN) and the occurrence of perinatal deaths associated with congenital syphilis and not reported in the Mortality Information System (SIM). This was a cross-sectional study with probabilistic record linkage between the SINAN and SIM. There were 666 reports of syphilis in pregnant women, including 224 in 2007 (3.8/1,000), 244(4.5/1,000) in 2008, and 198(4.0/1,000) in 2009. The study found 486 cases of congenital syphilis, of which 153 in 2007 (2.1/1,000), 193 in 2008 (2.6/1,000), and 140 in 2009 (2.0/1,000). After linkage of the SINAN databases, 237 pregnant women (35.6%) had cases of congenital syphilis reported. The SIM recorded 4,905 perinatal deaths, of which 57.8% were stillbirths. Probabilistic record linkage between SIM and SINAN-Congenital Syphilis yielded 13 matched records. The use of SINAN and SIM may not reflect the total magnitude of syphilis, but provide the basis for monitoring and analyzing this health problem, with a view towards planning and management.

Risk of psychiatric and neurological diseases in patients with workplace mobbing experience in Germany: a retrospective database analysis.

PubMed

Kostev, Karel; Rex, Juliana; Waehlert, Lilia; Hog, Daniela; Heilmaier, Christina

2014-01-01

The number of mobbing experiences recorded has increased during recent years and it has now been established as global phenomenon among the working population. The goal of our study was to analyze the incidence of certain neurologic and psychiatric diseases as a consequence of mobbing as compared with a control group and to examine the possible influence of previous diseases that occurred within one year before the first mobbing documentation on the incidence of mobbing. We used a large database (IMS® Disease Analyzer, Germany) to collect data from general practitioners in Germany from 01/2003 until 12/2012. Based on age, gender, and health insurance, patients with experience of mobbing were matched with a control group of patients who had not reported workplace mobbing and who were being treated by the same physicians. At first, diseases that occurred within one year before the bullying experience took place ("index date") were noted and compared to a control group of similar composition in terms of gender, age, and health insurance. Subsequently, the prevalence of depression, anxiety, somatoform disorders, and sleep disorders following experiences of mobbing were determined. After adjustment to take into account the odds of bullying, the ratios of these diseases were assessed using a logistic regression model. The study population consisted of n=2,625 patients and n=2,625 controls, of which 33% were men. The number of cases of bullying documented rose continuously from 2003 to 2011 and remained high in 2012. Those who would later become victims of mobbing demonstrated a considerably higher prevalence of diseases in general - these diseases were not confined to the neurologic-psychiatric spectrum. Following experiences of bullying, depression, anxiety, somatoform disorders, and sleep disorders were significantly more prevalent than in the control group (for all, p<0.05). Similarly, odds ratios (OR) representing the risk of suffering from diseases were higher in affected patients, with the highest value (4.28) for depression and the lowest value for sleep disorders (OR=2.4). Those who will later become the victims of bullying are more prone to suffer from diseases in general, even before this experience of mobbing has occurred, which underlines the importance of supporting (chronically) ill patients to protect them against bullying. Sequelae of mobbing include, in particular, diseases from the neurologic-psychiatric spectrum.

Disbiome database: linking the microbiome to disease.

PubMed

Janssens, Yorick; Nielandt, Joachim; Bronselaer, Antoon; Debunne, Nathan; Verbeke, Frederick; Wynendaele, Evelien; Van Immerseel, Filip; Vandewynckel, Yves-Paul; De Tré, Guy; De Spiegeleer, Bart

2018-06-04

Recent research has provided fascinating indications and evidence that the host health is linked to its microbial inhabitants. Due to the development of high-throughput sequencing technologies, more and more data covering microbial composition changes in different disease types are emerging. However, this information is dispersed over a wide variety of medical and biomedical disciplines. Disbiome is a database which collects and presents published microbiota-disease information in a standardized way. The diseases are classified using the MedDRA classification system and the micro-organisms are linked to their NCBI and SILVA taxonomy. Finally, each study included in the Disbiome database is assessed for its reporting quality using a standardized questionnaire. Disbiome is the first database giving a clear, concise and up-to-date overview of microbial composition differences in diseases, together with the relevant information of the studies published. The strength of this database lies within the combination of the presence of references to other databases, which enables both specific and diverse search strategies within the Disbiome database, and the human annotation which ensures a simple and structured presentation of the available data.

Human Mitochondrial Protein Database

National Institute of Standards and Technology Data Gateway

SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

History and Medicine: ex voto as a tool for health and epidemiological surveillance.

PubMed

Nante, N; Azzolini, E; Troiano, G; Serafini, A; Gentile, A; Messina, G

2016-01-01

Ex voto is a donation for a divinity, a Saint or to Virgin Mary for a received mercy. From the analysis of an ex voto it's possible to obtain lots of information and therefore it can be used as a tool for health and epidemiological surveillance, to study morbidity in the past. The aim of this study was the creation of a database to rebuild epidemiological events and diseases, using ex voto as a source of health surveillance. We chose to study votive pictures using three types of sources: photographed alive, on-line archives, books and photographic collections. Ex voto have been saved in an Hard Disk, numbered and inserted in a database, then analyzed using Stata®. total of 6231 ex voto were collected and catalogued in our database. Ex voto referring to diseases are the most represented (41%), but they have decreased with the time. Road accidents (21.4%) have a constant increase, especially with the appearance of cars and motorcycles. Aggressions (5.45%) decrease constantly; warlike accidents (4.44%) had a peak in the period including both world wars; non professional accidents (10.60%) and accidents at work (3.79%) increase without peaks; maritime accidents (8.88%) have not uniform ups and downs during the time. The database let us rebuild epidemiological events of the past, which are not deductible from other sources. Our purpose is to expand in the space-time our source data in order to perform an interesting comparison between past and present.

PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations.

PubMed

Zhang, Chao; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan; Deng, Lian; Tian, Lei; Feng, Qidi; Xu, Shuhua

2018-01-04

There are a growing number of studies focusing on delineating genetic variations that are associated with complex human traits and diseases due to recent advances in next-generation sequencing technologies. However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variations within and among populations. The PGG.Population database documents 7122 genomes representing 356 global populations from 107 countries and provides essential information for researchers to understand human genomic diversity and genetic ancestry. These data and information can facilitate the design of research studies and the interpretation of results of both evolutionary and medical studies involving human populations. The database is carefully maintained and constantly updated when new data are available. We included miscellaneous functions and a user-friendly graphical interface for visualization of genomic diversity, population relationships (genetic affinity), ancestral makeup, footprints of natural selection, and population history etc. Moreover, PGG.Population provides a useful feature for users to analyze data and visualize results in a dynamic style via online illustration. The long-term ambition of the PGG.Population, together with the joint efforts from other researchers who contribute their data to our database, is to create a comprehensive depository of geographic and ethnic variation of human genome, as well as a platform bringing influence on future practitioners of medicine and clinical investigators. PGG.Population is available at https://www.pggpopulation.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The California Oak Disease and Arthropod (CODA) Database

Treesearch

Tedmund J. Swiecki; Elizabeth A. Bernhardt; Richard A. Arnold

1997-01-01

The California Oak Disease and Arthropod (CODA) host index database is a compilation of information on agents that colonize or feed on oaks in California. Agents in the database include plant-feeding insects and mites, nematodes, microorganisms, viruses, and abiotic disease agents. CODA contains summarized information on hosts, agents, information sources, and the...

Understanding Toxoplasmosis in the United States Through “Large Data” Analyses

PubMed Central

Lykins, Joseph; Wang, Kanix; Wheeler, Kelsey; Clouser, Fatima; Dixon, Ashtyn; El Bissati, Kamal; Zhou, Ying; Lyttle, Christopher; Rzhetsky, Andrey; McLeod, Rima

2016-01-01

Background. Toxoplasma gondii infection causes substantial morbidity and mortality in the United States, and infects approximately one-third of persons globally. Clinical manifestations vary. Seropositivity is associated with neurologic diseases and malignancies. There are few objective data concerning US incidence and distribution of toxoplasmosis. Methods. Truven Health MarketScan Database and International Classification of Diseases, Ninth Revision (ICD-9) codes, including treatment specific to toxoplasmosis, identified patients with this disease. Spatiotemporal distribution and patterns of disease manifestation were analyzed. Comorbidities between patients and matched controls were compared. Results. Between 2003 and 2012, 9260 patients had ICD-9 codes for toxoplasmosis. This database of patients with ICD-9 codes includes 15% of those in the United States, excluding patients with no or public insurance. Thus, assuming that demographics do not change incidence, the calculated total is 61 700 or 6856 patients per year. Disease was more prevalent in the South. Mean age at diagnosis was 37.5 ± 15.5 years; 2.4% were children aged 0–2 years, likely congenitally infected. Forty-one percent were male, and 73% of women were of reproductive age. Of identified patients, 38% had eye disease and 12% presented with other serious manifestations, including central nervous system and visceral organ damage. Toxoplasmosis was statistically associated with substantial comorbidities, including human immunodeficiency virus, autoimmune diseases, and neurologic diseases. Conclusions. Toxoplasmosis causes morbidity and mortality in the United States. Our analysis of private insurance records missed certain at-risk populations and revealed fewer cases of retinal disease than previously estimated, suggesting undercoding, underreporting, undertreating, or differing demographics of those with eye disease. Mandatory reporting of infection to health departments and gestational screening could improve care and facilitate detection of epidemics and, thereby, public health interventions. PMID:27353665

FCDD: A Database for Fruit Crops Diseases.

PubMed

Chauhan, Rupal; Jasrai, Yogesh; Pandya, Himanshu; Chaudhari, Suman; Samota, Chand Mal

2014-01-01

Fruit Crops Diseases Database (FCDD) requires a number of biotechnology and bioinformatics tools. The FCDD is a unique bioinformatics resource that compiles information about 162 details on fruit crops diseases, diseases type, its causal organism, images, symptoms and their control. The FCDD contains 171 phytochemicals from 25 fruits, their 2D images and their 20 possible sequences. This information has been manually extracted and manually verified from numerous sources, including other electronic databases, textbooks and scientific journals. FCDD is fully searchable and supports extensive text search. The main focus of the FCDD is on providing possible information of fruit crops diseases, which will help in discovery of potential drugs from one of the common bioresource-fruits. The database was developed using MySQL. The database interface is developed in PHP, HTML and JAVA. FCDD is freely available. http://www.fruitcropsdd.com/

Indian genetic disease database

PubMed Central

Pradhan, Sanchari; Sengupta, Mainak; Dutta, Anirban; Bhattacharyya, Kausik; Bag, Sumit K.; Dutta, Chitra; Ray, Kunal

2011-01-01

Indians, representing about one-sixth of the world population, consist of several thousands of endogamous groups with strong potential for excess of recessive diseases. However, no database is available on Indian population with comprehensive information on the diseases common in the country. To address this issue, we present Indian Genetic Disease Database (IGDD) release 1.0 (http://www.igdd.iicb.res.in)—an integrated and curated repository of growing number of mutation data on common genetic diseases afflicting the Indian populations. Currently the database covers 52 diseases with information on 5760 individuals carrying the mutant alleles of causal genes. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database is currently designed to work best with Internet Explorer 8 (optimal resolution 1440 × 900) and it can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers. Provisions have been made for deposition of new data and logistics for regular updation of the database. The IGDD web portal, planned to be made freely available, contains user-friendly interfaces and is expected to be highly useful to the geneticists, clinicians, biologists and patient support groups of various genetic diseases. PMID:21037256

Disease-free survival in patients with non-metastatic breast cancer.

PubMed

Diniz, Roberta Wolp; Guerra, Maximiliano Ribeiro; Cintra, Jane Rocha Duarte; Fayer, Vívian Assis; Teixeira, Maria Teresa Bustamante

2016-01-01

Breast cancer is the second most common malignancy in the world and the one with highest incidence in the female population; it is also a major cause of death from cancer among women. To analyze the disease-free survival (DFS) at 5 years and prognostic factors in women with non-metastatic invasive breast cancer treated at a referral center for cancer care located in a medium-sized city in the Southeast of Brazil. Patients diagnosed with the disease between 2003 and 2005 and identified through the institution's cancer hospital records were analyzed. The follow-up of cases was carried out through hospital records, and complemented by search in the database of the Mortality Information System (SIM) as well as telephone contact. The variables analyzed were distributed in the following blocks: socio-demographic data, tumor-related characteristics, and treatment-related characteristics. Survival functions were calculated using the Kaplan-Meier method and the prognostic factors were analyzed based on Cox proportional hazard model. The study showed a DFS at 5 years of 72% (95CI 67.6-75.9). The main variables independently associated with DFS were lymph node involvement, use of hormone therapy, and education level. This study reinforces the importance of early diagnosis for DFS, pointing to the role of social aspects in this regard. The relevance of this research in the country is also highlighted, given the scarcity of studies on DFS in the Brazilian population.

Tuberculosis screening prior to anti-tumor necrosis factor therapy among patients with immune-mediated inflammatory diseases in Japan: a longitudinal study using a large-scale health insurance claims database.

PubMed

Tomio, Jun; Yamana, Hayato; Matsui, Hiroki; Yamashita, Hiroyuki; Yoshiyama, Takashi; Yasunaga, Hideo

2017-11-01

Tuberculosis screening is recommended for patients with immune-mediated inflammatory diseases (IMIDs) prior to anti-tumor necrosis factor (TNF) therapy. However, adherence to the recommended practice is unknown in the current clinical setting in Japan. We used a large-scale health insurance claims database in Japan to conduct a longitudinal observational study. Of more than two million beneficiaries in the database between 2013 and 2014, we enrolled those with IMIDs aged 15-69 years who had initiated anti-TNF therapy. We defined tuberculosis screening primarily as tuberculin skin test and/or interferon-gamma release assay (TST/IGRA) within 2 months before commencing anti-TNF therapy. We analyzed the proportions of the patients who had undergone tuberculosis screening and the associations with primary disease, type of anti-TNF agent, methotrexate prescription prior to anti-TNF therapy, and treatment for latent tuberculosis infection (LTBI). Of 385 patients presumed to have initiated anti-TNF therapy, 252 (66%) had undergone tuberculosis screening by TST/IGRA (22% TST, 56% IGRA, and 12% both TST and IGRA), and 231 (60%) had undergone TST/IGRA and radiography. Patients with psoriasis tended to be more likely to undergo tuberculosis screening than those with other diseases; however, this association was not statistically significant. Treatment for LTBI was provided to 43 (11%) patients; 123 (32%) received neither TST/IGRA nor LTBI treatment. Tuberculosis screening was often not performed prior to anti-TNF therapy despite the guidelines' recommendations; thus, patients could be put at unnecessary risk of reactivation of tuberculosis. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Mutational screening in genes related with porto-pulmonary hypertension: An analysis of 6 cases.

PubMed

Pousada, Guillermo; Baloira, Adolfo; Valverde, Diana

2017-04-07

Portopulmonary hypertension (PPH) is a rare disease with a low incidence and without a clearly-identified genetic component. The aim of this work was to check genes and genetic modifiers related to pulmonary arterial hypertension in patients with PPH in order to clarify the molecular basis of the pathology. We selected a total of 6 patients with PPH and amplified the exonic regions and intronic flanking regions of the relevant genes and regions of interest of the genetic modifiers. Six patients diagnosed with PPH were analyzed and compared to 55 healthy individuals. Potentially-pathogenic mutations were identified in the analyzed genes of 5 patients. None of these mutations, which are highly conserved throughout evolution, were detected in the control patients nor different databases analyzed (1000 Genomes, ExAC and DECIPHER). After analyzing for genetic modifiers, we found different variations that could favor the onset of the disease. The genetic analysis carried out in this small cohort of patients with PPH revealed a large number of mutations, with the ENG gene showing the greatest mutational frequency. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

The Porphyromonas gingivalis/Host Interactome Shows Enrichment in GWASdb Genes Related to Alzheimer's Disease, Diabetes and Cardiovascular Diseases

PubMed Central

Carter, Chris J.; France, James; Crean, StJohn; Singhrao, Sim K.

2017-01-01

Periodontal disease is of established etiology in which polymicrobial synergistic ecology has become dysbiotic under the influence of Porphyromonas gingivalis. Following breakdown of the host's protective oral tissue barriers, P. gingivalis migrates to developing inflammatory pathologies that associate with Alzheimer's disease (AD). Periodontal disease is a risk factor for cardiovascular disorders (CVD), type II diabetes mellitus (T2DM), AD and other chronic diseases, whilst T2DM exacerbates periodontitis. This study analyzed the relationship between the P. gingivalis/host interactome and the genes identified in genome-wide association studies (GWAS) for the aforementioned conditions using data from GWASdb (P < 1E-03) and, in some cases, from the NCBI/EBI GWAS database (P < 1E-05). Gene expression data from periodontitis or P. gingivalis microarray was compared to microarray datasets from the AD hippocampus and/or from carotid artery plaques. The results demonstrated that the host genes of the P. gingivalis interactome were significantly enriched in genes deposited in GWASdb genes related to cognitive disorders, AD and dementia, and its co-morbid conditions T2DM, obesity, and CVD. The P. gingivalis/host interactome was also enriched in GWAS genes from the more stringent NCBI-EBI database for AD, atherosclerosis and T2DM. The misregulated genes in periodontitis tissue or P. gingivalis infected macrophages also matched those in the AD hippocampus or atherosclerotic plaques. Together, these data suggest important gene/environment interactions between P. gingivalis and susceptibility genes or gene expression changes in conditions where periodontal disease is a contributory factor. PMID:29311898

The Porphyromonas gingivalis/Host Interactome Shows Enrichment in GWASdb Genes Related to Alzheimer's Disease, Diabetes and Cardiovascular Diseases.

PubMed

Carter, Chris J; France, James; Crean, StJohn; Singhrao, Sim K

2017-01-01

Periodontal disease is of established etiology in which polymicrobial synergistic ecology has become dysbiotic under the influence of Porphyromonas gingivalis . Following breakdown of the host's protective oral tissue barriers, P. gingivalis migrates to developing inflammatory pathologies that associate with Alzheimer's disease (AD). Periodontal disease is a risk factor for cardiovascular disorders (CVD), type II diabetes mellitus (T2DM), AD and other chronic diseases, whilst T2DM exacerbates periodontitis. This study analyzed the relationship between the P. gingivalis /host interactome and the genes identified in genome-wide association studies (GWAS) for the aforementioned conditions using data from GWASdb ( P < 1E-03) and, in some cases, from the NCBI/EBI GWAS database ( P < 1E-05). Gene expression data from periodontitis or P. gingivalis microarray was compared to microarray datasets from the AD hippocampus and/or from carotid artery plaques. The results demonstrated that the host genes of the P. gingivalis interactome were significantly enriched in genes deposited in GWASdb genes related to cognitive disorders, AD and dementia, and its co-morbid conditions T2DM, obesity, and CVD. The P. gingivalis /host interactome was also enriched in GWAS genes from the more stringent NCBI-EBI database for AD, atherosclerosis and T2DM. The misregulated genes in periodontitis tissue or P. gingivalis infected macrophages also matched those in the AD hippocampus or atherosclerotic plaques. Together, these data suggest important gene/environment interactions between P. gingivalis and susceptibility genes or gene expression changes in conditions where periodontal disease is a contributory factor.

Evaluation of a National Call Center and a Local Alerts System for Detection of New Cases of Ebola Virus Disease - Guinea, 2014-2015.

PubMed

Lee, Christopher T; Bulterys, Marc; Martel, Lise D; Dahl, Benjamin A

2016-03-11

The epidemic of Ebola virus disease (Ebola) in West Africa began in Guinea in late 2013 (1), and on August 8, 2014, the World Health Organization (WHO) declared the epidemic a Public Health Emergency of International Concern (2). Guinea was declared Ebola-free on December 29, 2015, and is under a 90 day period of enhanced surveillance, following 3,351 confirmed and 453 probable cases of Ebola and 2,536 deaths (3). Passive surveillance for Ebola in Guinea has been conducted principally through the use of a telephone alert system. Community members and health facilities report deaths and suspected Ebola cases to local alert numbers operated by prefecture health departments or to a national toll-free call center. The national call center additionally functions as a source of public health information by responding to questions from the public about Ebola. To evaluate the sensitivity of the two systems and compare the sensitivity of the national call center with the local alerts system, the CDC country team performed probabilistic record linkage of the combined prefecture alerts database, as well as the national call center database, with the national viral hemorrhagic fever (VHF) database; the VHF database contains records of all known confirmed Ebola cases. Among 17,309 alert calls analyzed from the national call center, 71 were linked to 1,838 confirmed Ebola cases in the VHF database, yielding a sensitivity of 3.9%. The sensitivity of the national call center was highest in the capital city of Conakry (11.4%) and lower in other prefectures. In comparison, the local alerts system had a sensitivity of 51.1%. Local public health infrastructure plays an important role in surveillance in an epidemic setting.

GENEASE: Real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization.

PubMed

Ghandikota, Sudhir; Hershey, Gurjit K Khurana; Mersha, Tesfaye B

2018-03-24

Advances in high-throughput sequencing technologies have made it possible to generate multiple omics data at an unprecedented rate and scale. The accumulation of these omics data far outpaces the rate at which biologists can mine and generate new hypothesis to test experimentally. There is an urgent need to develop a myriad of powerful tools to efficiently and effectively search and filter these resources to address specific post-GWAS functional genomics questions. However, to date, these resources are scattered across several databases and often lack a unified portal for data annotation and analytics. In addition, existing tools to analyze and visualize these databases are highly fragmented, resulting researchers to access multiple applications and manual interventions for each gene or variant in an ad hoc fashion until all the questions are answered. In this study, we present GENEASE, a web-based one-stop bioinformatics tool designed to not only query and explore multi-omics and phenotype databases (e.g., GTEx, ClinVar, dbGaP, GWAS Catalog, ENCODE, Roadmap Epigenomics, KEGG, Reactome, Gene and Phenotype Ontology) in a single web interface but also to perform seamless post genome-wide association downstream functional and overlap analysis for non-coding regulatory variants. GENEASE accesses over 50 different databases in public domain including model organism-specific databases to facilitate gene/variant and disease exploration, enrichment and overlap analysis in real time. It is a user-friendly tool with point-and-click interface containing links for support information including user manual and examples. GENEASE can be accessed freely at http://research.cchmc.org/mershalab/genease_new/login.html. Tesfaye.Mersha@cchmc.org, Sudhir.Ghandikota@cchmc.org. Supplementary data are available at Bioinformatics online.

Are disease reservoirs special? Taxonomic and life history characteristics

PubMed Central

Burgess, Tristan L.; Eskew, Evan A.; Roth, Tara M.; Stephenson, Nicole; Foley, Janet E.

2017-01-01

Pathogens that spill over between species cause a significant human and animal health burden. Here, we describe characteristics of animal reservoirs that are required for pathogen spillover. We assembled and analyzed a database of 330 disease systems in which a pathogen spills over from a reservoir of one or more species. Three-quarters of reservoirs included wildlife, and 84% included mammals. Further, 65% of pathogens depended on a community of reservoir hosts, rather than a single species, for persistence. Among mammals, the most frequently identified reservoir hosts were rodents, artiodactyls, and carnivores. The distribution among orders of mammalian species identified as reservoirs did not differ from that expected by chance. Among disease systems with high priority pathogens and epidemic potential, we found birds, primates, and bats to be overrepresented. We also analyzed the life history traits of mammalian reservoir hosts and compared them to mammals as a whole. Reservoir species had faster life history characteristics than mammals overall, exhibiting traits associated with greater reproductive output rather than long-term survival. Thus, we find that in many respects, reservoirs of spillover pathogens are indeed special. The described patterns provide a useful resource for studying and managing emerging infectious diseases. PMID:28704402

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Wiegers, Thomas C.; King, Benjamin L.; Wiegers, Jolene; Grondin, Cynthia J.; Sciaky, Daniela; Johnson, Robin J.; Mattingly, Carolyn J.

2016-01-01

Strategies for discovering common molecular events among disparate diseases hold promise for improving understanding of disease etiology and expanding treatment options. One technique is to leverage curated datasets found in the public domain. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) manually curates chemical-gene, chemical-disease, and gene-disease interactions from the scientific literature. The use of official gene symbols in CTD interactions enables this information to be combined with the Gene Ontology (GO) file from NCBI Gene. By integrating these GO-gene annotations with CTD’s gene-disease dataset, we produce 753,000 inferences between 15,700 GO terms and 4,200 diseases, providing opportunities to explore presumptive molecular underpinnings of diseases and identify biological similarities. Through a variety of applications, we demonstrate the utility of this novel resource. As a proof-of-concept, we first analyze known repositioned drugs (e.g., raloxifene and sildenafil) and see that their target diseases have a greater degree of similarity when comparing GO terms vs. genes. Next, a computational analysis predicts seemingly non-intuitive diseases (e.g., stomach ulcers and atherosclerosis) as being similar to bipolar disorder, and these are validated in the literature as reported co-diseases. Additionally, we leverage other CTD content to develop testable hypotheses about thalidomide-gene networks to treat seemingly disparate diseases. Finally, we illustrate how CTD tools can rank a series of drugs as potential candidates for repositioning against B-cell chronic lymphocytic leukemia and predict cisplatin and the small molecule inhibitor JQ1 as lead compounds. The CTD dataset is freely available for users to navigate pathologies within the context of extensive biological processes, molecular functions, and cellular components conferred by GO. This inference set should aid researchers, bioinformaticists, and pharmaceutical drug makers in finding commonalities in disease mechanisms, which in turn could help identify new therapeutics, new indications for existing pharmaceuticals, potential disease comorbidities, and alerts for side effects. PMID:27171405

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database.

PubMed

Davis, Allan Peter; Wiegers, Thomas C; King, Benjamin L; Wiegers, Jolene; Grondin, Cynthia J; Sciaky, Daniela; Johnson, Robin J; Mattingly, Carolyn J

2016-01-01

Strategies for discovering common molecular events among disparate diseases hold promise for improving understanding of disease etiology and expanding treatment options. One technique is to leverage curated datasets found in the public domain. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) manually curates chemical-gene, chemical-disease, and gene-disease interactions from the scientific literature. The use of official gene symbols in CTD interactions enables this information to be combined with the Gene Ontology (GO) file from NCBI Gene. By integrating these GO-gene annotations with CTD's gene-disease dataset, we produce 753,000 inferences between 15,700 GO terms and 4,200 diseases, providing opportunities to explore presumptive molecular underpinnings of diseases and identify biological similarities. Through a variety of applications, we demonstrate the utility of this novel resource. As a proof-of-concept, we first analyze known repositioned drugs (e.g., raloxifene and sildenafil) and see that their target diseases have a greater degree of similarity when comparing GO terms vs. genes. Next, a computational analysis predicts seemingly non-intuitive diseases (e.g., stomach ulcers and atherosclerosis) as being similar to bipolar disorder, and these are validated in the literature as reported co-diseases. Additionally, we leverage other CTD content to develop testable hypotheses about thalidomide-gene networks to treat seemingly disparate diseases. Finally, we illustrate how CTD tools can rank a series of drugs as potential candidates for repositioning against B-cell chronic lymphocytic leukemia and predict cisplatin and the small molecule inhibitor JQ1 as lead compounds. The CTD dataset is freely available for users to navigate pathologies within the context of extensive biological processes, molecular functions, and cellular components conferred by GO. This inference set should aid researchers, bioinformaticists, and pharmaceutical drug makers in finding commonalities in disease mechanisms, which in turn could help identify new therapeutics, new indications for existing pharmaceuticals, potential disease comorbidities, and alerts for side effects.

Plus Disease in Retinopathy of Prematurity: Improving Diagnosis by Ranking Disease Severity and Using Quantitative Image Analysis.

PubMed

Kalpathy-Cramer, Jayashree; Campbell, J Peter; Erdogmus, Deniz; Tian, Peng; Kedarisetti, Dharanish; Moleta, Chace; Reynolds, James D; Hutcheson, Kelly; Shapiro, Michael J; Repka, Michael X; Ferrone, Philip; Drenser, Kimberly; Horowitz, Jason; Sonmez, Kemal; Swan, Ryan; Ostmo, Susan; Jonas, Karyn E; Chan, R V Paul; Chiang, Michael F

2016-11-01

To determine expert agreement on relative retinopathy of prematurity (ROP) disease severity and whether computer-based image analysis can model relative disease severity, and to propose consideration of a more continuous severity score for ROP. We developed 2 databases of clinical images of varying disease severity (100 images and 34 images) as part of the Imaging and Informatics in ROP (i-ROP) cohort study and recruited expert physician, nonexpert physician, and nonphysician graders to classify and perform pairwise comparisons on both databases. Six participating expert ROP clinician-scientists, each with a minimum of 10 years of clinical ROP experience and 5 ROP publications, and 5 image graders (3 physicians and 2 nonphysician graders) who analyzed images that were obtained during routine ROP screening in neonatal intensive care units. Images in both databases were ranked by average disease classification (classification ranking), by pairwise comparison using the Elo rating method (comparison ranking), and by correlation with the i-ROP computer-based image analysis system. Interexpert agreement (weighted κ statistic) compared with the correlation coefficient (CC) between experts on pairwise comparisons and correlation between expert rankings and computer-based image analysis modeling. There was variable interexpert agreement on diagnostic classification of disease (plus, preplus, or normal) among the 6 experts (mean weighted κ, 0.27; range, 0.06-0.63), but good correlation between experts on comparison ranking of disease severity (mean CC, 0.84; range, 0.74-0.93) on the set of 34 images. Comparison ranking provided a severity ranking that was in good agreement with ranking obtained by classification ranking (CC, 0.92). Comparison ranking on the larger dataset by both expert and nonexpert graders demonstrated good correlation (mean CC, 0.97; range, 0.95-0.98). The i-ROP system was able to model this continuous severity with good correlation (CC, 0.86). Experts diagnose plus disease on a continuum, with poor absolute agreement on classification but good relative agreement on disease severity. These results suggest that the use of pairwise rankings and a continuous severity score, such as that provided by the i-ROP system, may improve agreement on disease severity in the future. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Toward an Open-Access Global Database for Mapping, Control, and Surveillance of Neglected Tropical Diseases

PubMed Central

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F.; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F. L.; Utzinger, Jürg; Kristensen, Thomas K.; Vounatsou, Penelope

2011-01-01

Background After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. Methodology With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and ‘grey literature’), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. Principal Findings At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. Conclusions An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay. PMID:22180793

Quebec Trophoblastic Disease Registry: how to make an easy-to-use dynamic database.

PubMed

Sauthier, Philippe; Breguet, Magali; Rozenholc, Alexandre; Sauthier, Michaël

2015-05-01

To create an easy-to-use dynamic database designed specifically for the Quebec Trophoblastic Disease Registry (RMTQ). It is now well established that much of the success in managing trophoblastic diseases comes from the development of national and regional reference centers. Computerized databases allow the optimal use of data stored in these centers. We have created an electronic data registration system by producing a database using FileMaker Pro 12. It uses 11 external tables associated with a unique identification number for each patient. Each table allows specific data to be recorded, incorporating demographics, diagnosis, automated staging, laboratory values, pathological diagnosis, and imaging parameters. From January 1, 2009, to December 31, 2013, we used our database to register 311 patients with 380 diseases and have seen a 39.2% increase in registrations each year between 2009 and 2012. This database allows the automatic generation of semilogarithmic curves, which take into account β-hCG values as a function of time, complete with graphic markers for applied treatments (chemotherapy, radiotherapy, or surgery). It generates a summary sheet for a synthetic vision in real time. We have created, at a low cost, an easy-to-use database specific to trophoblastic diseases that dynamically integrates staging and monitoring. We propose a 10-step procedure for a successful trophoblastic database. It improves patient care, research, and education on trophoblastic diseases in Quebec and leads to an opportunity for collaboration on a national Canadian registry.

Vitamin D supplementation and disease activity in patients with immune-mediated rheumatic diseases: A systematic review and meta-analysis.

PubMed

Franco, André Silva; Freitas, Thiago Quadrante; Bernardo, Wanderley M; Pereira, Rosa Maria R

2017-06-01

Vitamin D serum levels and the presence and activity of rheumatic conditions have been associated. However, many studies are merely observational, and the existent randomized clinical trials were never systematically analyzed. Therefore, this study aims to provide a systematic review and meta-analysis of such a topic. MEDLINE, EMBASE, LILACS, COCHRANE, and CINAHL were explored to identify randomized trials that investigated clinical repercussions of vitamin D (or analogs) supplementation for at least 3 months in rheumatic diseases. Standardized clinical and/or laboratorial outcomes related to disease activity were analyzed according to each disease before and after supplementation. Database searches rendered 668 results; 9 were included-5 on rheumatoid arthritis, 3 on systemic lupus erythematosus, and 1 on systemic sclerosis. Seven of the studies were meta-analyzed. After vitamin D supplementation, rheumatoid arthritis recurrence decreased; however, not significantly (risk difference = -0.10, 95% CI = -0.21, 0.00, P = .05). No statistical significance was observed regarding visual analog scale (mean difference = 2.79, 95% CI = -1.87, 7.44, P = .24) and disease activity score28 (mean difference = -0.31, 95% CI = -0.86, 0.25, P = .28). Regarding systemic lupus erythematosus, anti-dsDNA positivity was significantly reduced (risk difference = -0.10, 95% CI = -0.18, -0.03; P = .005). Vitamin D supplementation reduced anti-dsDNA positivity on systemic lupus erythematosus and could possibly reduce rheumatoid arthritis recurrence, although novel randomized clinical trials are needed to confirm and extend the benefits of this hormone in immune-mediated rheumatic diseases.

KMeyeDB: a graphical database of mutations in genes that cause eye diseases.

PubMed

Kawamura, Takashi; Ohtsubo, Masafumi; Mitsuyama, Susumu; Ohno-Nakamura, Saho; Shimizu, Nobuyoshi; Minoshima, Shinsei

2010-06-01

KMeyeDB (http://mutview.dmb.med.keio.ac.jp/) is a database of human gene mutations that cause eye diseases. We have substantially enriched the amount of data in the database, which now contains information about the mutations of 167 human genes causing eye-related diseases including retinitis pigmentosa, cone-rod dystrophy, night blindness, Oguchi disease, Stargardt disease, macular degeneration, Leber congenital amaurosis, corneal dystrophy, cataract, glaucoma, retinoblastoma, Bardet-Biedl syndrome, and Usher syndrome. KMeyeDB is operated using the database software MutationView, which deals with various characters of mutations, gene structure, protein functional domains, and polymerase chain reaction (PCR) primers, as well as clinical data for each case. Users can access the database using an ordinary Internet browser with smooth user-interface, without user registration. The results are displayed on the graphical windows together with statistical calculations. All mutations and associated data have been collected from published articles. Careful data analysis with KMeyeDB revealed many interesting features regarding the mutations in 167 genes that cause 326 different types of eye diseases. Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene.

Using a Relational Database to Index Infectious Disease Information

PubMed Central

Brown, Jay A.

2010-01-01

Mapping medical knowledge into a relational database became possible with the availability of personal computers and user-friendly database software in the early 1990s. To create a database of medical knowledge, the domain expert works like a mapmaker to first outline the domain and then add the details, starting with the most prominent features. The resulting “intelligent database” can support the decisions of healthcare professionals. The intelligent database described in this article contains profiles of 275 infectious diseases. Users can query the database for all diseases matching one or more specific criteria (symptom, endemic region of the world, or epidemiological factor). Epidemiological factors include sources (patients, water, soil, or animals), routes of entry, and insect vectors. Medical and public health professionals could use such a database as a decision-support software tool. PMID:20623018

Primary Multimedia Objects and 'Educational Metadata' A Fundamental Dilemma for Developers of Multimedia Archives; Evaluation of Digital Library Impact and User Communities by Analysis of Usage Patterns; The KYVL Kentuckiana Digital Library Project: Background and Current Status; DPDx Collection.

ERIC Educational Resources Information Center

Shabajee, Paul; Bollen, Johan; Luce, Rick; Weig, Eric

2002-01-01

Includes four articles that discuss multimedia educational database systems and the use of metadata, including repurposing; the evaluation of digital library use that analyzes the retrieval habits of users; the Kentucky Virtual Library (KYVL) and digital collection project; and the collection of the Division of Parasitic Diseases, Centers for…

A Systematic Review of Techniques and Sources of Big Data in the Healthcare Sector.

PubMed

Alonso, Susel Góngora; de la Torre Díez, Isabel; Rodrigues, Joel J P C; Hamrioui, Sofiane; López-Coronado, Miguel

2017-10-14

The main objective of this paper is to present a review of existing researches in the literature, referring to Big Data sources and techniques in health sector and to identify which of these techniques are the most used in the prediction of chronic diseases. Academic databases and systems such as IEEE Xplore, Scopus, PubMed and Science Direct were searched, considering the date of publication from 2006 until the present time. Several search criteria were established as 'techniques' OR 'sources' AND 'Big Data' AND 'medicine' OR 'health', 'techniques' AND 'Big Data' AND 'chronic diseases', etc. Selecting the paper considered of interest regarding the description of the techniques and sources of Big Data in healthcare. It found a total of 110 articles on techniques and sources of Big Data on health from which only 32 have been identified as relevant work. Many of the articles show the platforms of Big Data, sources, databases used and identify the techniques most used in the prediction of chronic diseases. From the review of the analyzed research articles, it can be noticed that the sources and techniques of Big Data used in the health sector represent a relevant factor in terms of effectiveness, since it allows the application of predictive analysis techniques in tasks such as: identification of patients at risk of reentry or prevention of hospital or chronic diseases infections, obtaining predictive models of quality.

Pediatric Chest Pain-Low-Probability Referral: A Multi-Institutional Analysis From Standardized Clinical Assessment and Management Plans (SCAMPs®), the Pediatric Health Information Systems Database, and the National Ambulatory Medical Care Survey.

PubMed

Harahsheh, Ashraf S; O'Byrne, Michael L; Pastor, Bill; Graham, Dionne A; Fulton, David R

2017-11-01

We conducted a study to assess test characteristics of red-flag criteria for identifying cardiac disease causing chest pain and technical charges of low-probability referrals. Accuracy of red-flag criteria was ascertained through study of chest pain Standardized Clinical Assessment and Management Plans (SCAMPs®) data. Patients were divided into 2 groups: Group1 (concerning clinical elements) and Group2 (without). We compared incidence of cardiac disease causing chest pain between these 2 groups. Technical charges of Group 2 were analyzed using the Pediatric Health Information System database. Potential savings for the US population was estimated using National Ambulatory Medical Care Survey data. Fifty-two percent of subjects formed Group 1. Cardiac disease causing chest pain was identified in 8/1656 (0.48%). No heart disease was identified in patients in Group 2 ( P = .03). Applying red-flags in determining need for referral identified patients with cardiac disease causing chest pain with 100% sensitivity. Median technical charges for Group 2, over a 4-year period, were US2014$775 559. Eliminating cardiac testing of low-probability referrals would save US2014$3 775 182 in technical charges annually. Red-flag criteria were an effective screen for children with chest pain. Eliminating cardiac testing in children without red-flags for referral has significant technical charge savings.

Scale invariant texture descriptors for classifying celiac disease

PubMed Central

Hegenbart, Sebastian; Uhl, Andreas; Vécsei, Andreas; Wimmer, Georg

2013-01-01

Scale invariant texture recognition methods are applied for the computer assisted diagnosis of celiac disease. In particular, emphasis is given to techniques enhancing the scale invariance of multi-scale and multi-orientation wavelet transforms and methods based on fractal analysis. After fine-tuning to specific properties of our celiac disease imagery database, which consists of endoscopic images of the duodenum, some scale invariant (and often even viewpoint invariant) methods provide classification results improving the current state of the art. However, not each of the investigated scale invariant methods is applicable successfully to our dataset. Therefore, the scale invariance of the employed approaches is explicitly assessed and it is found that many of the analyzed methods are not as scale invariant as they theoretically should be. Results imply that scale invariance is not a key-feature required for successful classification of our celiac disease dataset. PMID:23481171

A bioinformatics analysis of Lamin-A regulatory network: a perspective on epigenetic involvement in Hutchinson-Gilford progeria syndrome.

PubMed

Arancio, Walter

2012-04-01

Hutchinson-Gilford progeria syndrome (HGPS) is a rare human genetic disease that leads to premature aging. HGPS is caused by mutation in the Lamin-A (LMNA) gene that leads, in affected young individuals, to the accumulation of the progerin protein, usually present only in aging differentiated cells. Bioinformatics analyses of the network of interactions of the LMNA gene and transcripts are presented. The LMNA gene network has been analyzed using the BioGRID database (http://thebiogrid.org/) and related analysis tools such as Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index) and GeneMANIA ( http://genemania.org/). The network of interaction of LMNA transcripts has been further analyzed following the competing endogenous (ceRNA) hypotheses (RNA cross-talk via microRNAs [miRNAs]) and using the miRWalk database and tools (www.ma.uni-heidelberg.de/apps/zmf/mirwalk/). These analyses suggest particular relevance of epigenetic modifiers (via acetylase complexes and specifically HTATIP histone acetylase) and adenosine triphosphate (ATP)-dependent chromatin remodelers (via pBAF, BAF, and SWI/SNF complexes).

Physicians’ influence on breast cancer patient compliance

PubMed Central

Kostev, Karel; Waehlert, Lilia; Jockwig, Achim; Jockwig, Barbara; Hadji, Peyman

2014-01-01

In recent years there have been major advances in the treatment of breast cancer. However, taking the prescribed medication for a sufficient period of time is crucial to the success of any therapy. Thus far, no database-based studies have been published in German-speaking countries empirically examining the influence of the physician on the compliance of patients. The aim of this study is to investigate, quantify, and critically discuss the effect treating physicians have on the compliance of their breast cancer patients. Patients with a confirmed breast cancer diagnosis who started therapy (tamoxifen or aromatase inhibitors) between January 2001 and December 2011 were selected from the representative IMS Disease Analyzer database and analyzed with regard to their compliance. Practices were grouped into two categories concerning the compliance of all treated patients. A regression model showed that a breast cancer patient who is treated in a practice with a trend toward poor compliance has a nearly 60% higher risk for treatment discontinuation than would be the case in a practice with good compliance. It shows how important it is to motivate physicians to strive toward good compliance rates. PMID:24454275

[A meta-analysis on the association between genetic polymorphisms of osteoprotegerin and cardiovascular disease].

PubMed

Xin, J Y; Cong, H L

2018-06-24

Objective: To explore the association between genetic polymorphisms of rs2073617T/C (950T/C) and rs2073618G/C(1181G/C) in the osteoprotegerin gene and cardiovascular disease with meta-analysis. Methods: A computer-based search for the study of relationship between genetic polymorphisms of rs2073617T/C and rs2073618G/C in the osteoprotegerin gene and cardiovascular disease were performed in electronic databases including China National Knowledge Infrastructure(CNKI), China Biomedical Literature Database, Wanfang Database, Chinese Journal Full-text Database, Embase, PubMed, and Cochrane Library, supplemented by manual search, from the beginning of library to February 28, 2017. The quality of the included studies were assessed by the Newcastle-Ottawa Scale (NOS) scoring system. Data were analyzed using STATA 12.0 software. Results: Eleven clinical case-control studies that enrolled 2 115 patients with cardiovascular disease and 1 467 healthy subjects were included.The results indicated that osteoprotegerin gene polymorphisms of rs2073617T/C and rs2073618G/C might be closely associated with the susceptibility to cardiovascular disease(rs2073617T/C allele model: OR= 0.79, 95% CI 0.73-0.87, P= 0.001;rs2073618G/C M allele and W allele: OR= 0.83, 95% CI 0.74-0.92, P= 0.001). The osteoprotegerin gene polymorphisms of rs2073617T/C and rs2073618G/C were significantly related to the incidence of coronary artery disease and acute coronary syndrome(coronary artery disease allele model: OR= 0.83, 95% CI 0.75-0.92, P= 0.001; acute coronary syndrome allele model: OR= 0.73, 95% CI 0.62-0.85, P< 0.001). However, there was no significant correlation between the genetic polymorphisms of these two sites and the lesion vessel number of coronary artery (rs2073617T/C allele model: OR= 1.00, 95% CI 0.81-1.24, P= 0.985;rs2073618G/C allele model: OR= 0.98, 95% CI 0.80-1.21, P= 0.626). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and polymerase chain reaction-ligase detection reaction(PCR-LDR) evidenced the association between osteoprotegerin gene polymorphisms and cardiovascular disease(allele model: OR= 0.79, 95% CI 0.72-0.86, P< 0.001), but no obvious relationship was found with fluorogenic quantitative detection and molecularprobe(allele model: OR= 0.86, 95% CI 0.65-1.12, P= 0.263). Conclusion: This meta-analysis indicates that the osteoprotegerin gene polymorphisms of rs2073617T/C and rs2073618G/C may be closely related to the increased risk of cardiovascular disease.

What have we learned in minimally invasive colorectal surgery from NSQIP and NIS large databases? A systematic review.

PubMed

Batista Rodríguez, Gabriela; Balla, Andrea; Corradetti, Santiago; Martinez, Carmen; Hernández, Pilar; Bollo, Jesús; Targarona, Eduard M

2018-06-01

"Big data" refers to large amount of dataset. Those large databases are useful in many areas, including healthcare. The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) and the National Inpatient Sample (NIS) are big databases that were developed in the USA in order to record surgical outcomes. The aim of the present systematic review is to evaluate the type and clinical impact of the information retrieved through NISQP and NIS big database articles focused on laparoscopic colorectal surgery. A systematic review was conducted using The Meta-Analysis Of Observational Studies in Epidemiology (MOOSE) guidelines. The research was carried out on PubMed database and revealed 350 published papers. Outcomes of articles in which laparoscopic colorectal surgery was the primary aim were analyzed. Fifty-five studies, published between 2007 and February 2017, were included. Articles included were categorized in groups according to the main topic as: outcomes related to surgical technique comparisons, morbidity and perioperatory results, specific disease-related outcomes, sociodemographic disparities, and academic training impact. NSQIP and NIS databases are just the tip of the iceberg for the potential application of Big Data technology and analysis in MIS. Information obtained through big data is useful and could be considered as external validation in those situations where a significant evidence-based medicine exists; also, those databases establish benchmarks to measure the quality of patient care. Data retrieved helps to inform decision-making and improve healthcare delivery.

Integration of Spatial and Social Network Analysis in Disease Transmission Studies.

PubMed

Emch, Michael; Root, Elisabeth D; Giebultowicz, Sophia; Ali, Mohammad; Perez-Heydrich, Carolina; Yunus, Mohammad

2012-01-01

This study presents a case study of how social network and spatial analytical methods can be used simultaneously for disease transmission modeling. The paper first reviews strategies employed in previous studies and then offers the example of transmission of two bacterial diarrheal diseases in rural Bangladesh. The goal is to understand how diseases vary socially above and beyond the effects of the local neighborhood context. Patterns of cholera and shigellosis incidence are analyzed in space and within kinship-based social networks in Matlab, Bangladesh. Data include a spatially referenced longitudinal demographic database which consists of approximately 200,000 people and laboratory-confirmed cholera and shigellosis cases from 1983 to 2003. Matrices are created of kinship ties between households using a complete network design and distance matrices are also created to model spatial relationships. Moran's I statistics are calculated to measure clustering within both social and spatial matrices. Combined spatial effects-spatial disturbance models are built to simultaneously analyze spatial and social effects while controlling for local environmental context. Results indicate that cholera and shigellosis always clusters in space and only sometimes within social networks. This suggests that the local environment is most important for understanding transmission of both diseases however kinship-based social networks also influence their transmission. Simultaneous spatial and social network analysis can help us better understand disease transmission and this study has offered several strategies on how.

Integration of Spatial and Social Network Analysis in Disease Transmission Studies

PubMed Central

Root, Elisabeth D; Giebultowicz, Sophia; Ali, Mohammad; Perez-Heydrich, Carolina; Yunus, Mohammad

2013-01-01

This study presents a case study of how social network and spatial analytical methods can be used simultaneously for disease transmission modeling. The paper first reviews strategies employed in previous studies and then offers the example of transmission of two bacterial diarrheal diseases in rural Bangladesh. The goal is to understand how diseases vary socially above and beyond the effects of the local neighborhood context. Patterns of cholera and shigellosis incidence are analyzed in space and within kinship-based social networks in Matlab, Bangladesh. Data include a spatially referenced longitudinal demographic database which consists of approximately 200,000 people and laboratory-confirmed cholera and shigellosis cases from 1983 to 2003. Matrices are created of kinship ties between households using a complete network design and distance matrices are also created to model spatial relationships. Moran's I statistics are calculated to measure clustering within both social and spatial matrices. Combined spatial effects-spatial disturbance models are built to simultaneously analyze spatial and social effects while controlling for local environmental context. Results indicate that cholera and shigellosis always clusters in space and only sometimes within social networks. This suggests that the local environment is most important for understanding transmission of both diseases however kinship-based social networks also influence their transmission. Simultaneous spatial and social network analysis can help us better understand disease transmission and this study has offered several strategies on how. PMID:24163443

Applying World Wide Web technology to the study of patients with rare diseases.

PubMed

de Groen, P C; Barry, J A; Schaller, W J

1998-07-15

Randomized, controlled trials of sporadic diseases are rarely conducted. Recent developments in communication technology, particularly the World Wide Web, allow efficient dissemination and exchange of information. However, software for the identification of patients with a rare disease and subsequent data entry and analysis in a secure Web database are currently not available. To study cholangiocarcinoma, a rare cancer of the bile ducts, we developed a computerized disease tracing system coupled with a database accessible on the Web. The tracing system scans computerized information systems on a daily basis and forwards demographic information on patients with bile duct abnormalities to an electronic mailbox. If informed consent is given, the patient's demographic and preexisting medical information available in medical database servers are electronically forwarded to a UNIX research database. Information from further patient-physician interactions and procedures is also entered into this database. The database is equipped with a Web user interface that allows data entry from various platforms (PC-compatible, Macintosh, and UNIX workstations) anywhere inside or outside our institution. To ensure patient confidentiality and data security, the database includes all security measures required for electronic medical records. The combination of a Web-based disease tracing system and a database has broad applications, particularly for the integration of clinical research within clinical practice and for the coordination of multicenter trials.

Sinonasal extramedullary plasmacytoma: a population-based incidence and survival analysis.

PubMed

Patel, Tapan D; Vázquez, Alejandro; Choudhary, Moaz M; Kam, David; Baredes, Soly; Eloy, Jean Anderson

2015-09-01

Sinonasal extramedullary plasmacytoma (SN-EMP) is a rare plasma cell neoplasm. Published literature on this tumor largely consists of case reports and case-series with small sample sizes. This study analyzed population-based data on SN-EMP patients to understand demographic and clinical features as well as incidence and survival trends. The Surveillance, Epidemiology, and End Results (SEER) database was queried for SN-EMP and other head and neck EMP (HN-EMP) cases from 1973 to 2011. Cases were analyzed to determine patient demographics, initial treatment modality, and survival outcomes. Of 778 patients identified with EMP in the head and neck region, 367 patients had SN-EMP and 411 had other HN-EMP. There was a strong male predilection found, with a male-to-female ratio of 3.65:1 in the SN-EMP group and 1.87:1 in the other HN-EMP group. The majority of the patients presented with localized disease in both SN-EMP (84.4%) and other HN-EMP (81.0%) groups. The most common treatment modality reported in this database was surgery with adjuvant radiotherapy in both SN-EMP (46.3%) and other HN-EMP (38.9%) groups, followed by radiotherapy alone (SN-EMP: 40.7%; other HN-EMP: 34.2%). Five-year and 10-year disease-specific survival rates were comparable between SN-EMP (88.2% and 83.3%, respectively) and other HN-EMP (90.0% and 87.4%, respectively) (p = 0.6016 and p = 0.4015, respectively). This study analyzed the largest cohort of SN-EMP patients to date. There was no statistically significant survival advantage found for any 1 particular treatment modality over other treatment modalities in both SN-EMP and other HN-EMP. © 2015 ARS-AAOA, LLC.

Pathogen metadata platform: software for accessing and analyzing pathogen strain information.

PubMed

Chang, Wenling E; Peterson, Matthew W; Garay, Christopher D; Korves, Tonia

2016-09-15

Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and becoming a valuable resource not only for research but for biosurveillance and public health. However, current freely available tools for analyzing this data are geared towards bioinformaticians and/or do not provide summaries and visualizations needed to readily interpret results. We designed a platform to easily access and summarize data about pathogen samples. The software includes a PostgreSQL database that captures metadata useful for disease outbreak investigations, and scripts for downloading and parsing data from NCBI BioSample and BioProject into the database. The software provides a user interface to query metadata and obtain standardized results in an exportable, tab-delimited format. To visually summarize results, the user interface provides a 2D histogram for user-selected metadata types and mapping of geolocated entries. The software is built on the LabKey data platform, an open-source data management platform, which enables developers to add functionalities. We demonstrate the use of the software in querying for a pathogen serovar and for genome sequence identifiers. This software enables users to create a local database for pathogen metadata, populate it with data from NCBI, easily query the data, and obtain visual summaries. Some of the components, such as the database, are modular and can be incorporated into other data platforms. The source code is freely available for download at https://github.com/wchangmitre/bioattribution .

Mimvec: a deep learning approach for analyzing the human phenome.

PubMed

Gan, Mingxin; Li, Wenran; Zeng, Wanwen; Wang, Xiaojian; Jiang, Rui

2017-09-21

The human phenome has been widely used with a variety of genomic data sources in the inference of disease genes. However, most existing methods thus far derive phenotype similarity based on the analysis of biomedical databases by using the traditional term frequency-inverse document frequency (TF-IDF) formulation. This framework, though intuitive, not only ignores semantic relationships between words but also tends to produce high-dimensional vectors, and hence lacks the ability to precisely capture intrinsic semantic characteristics of biomedical documents. To overcome these limitations, we propose a framework called mimvec to analyze the human phenome by making use of the state-of-the-art deep learning technique in natural language processing. We converted 24,061 records in the Online Mendelian Inheritance in Man (OMIM) database to low-dimensional vectors using our method. We demonstrated that the vector presentation not only effectively enabled classification of phenotype records against gene ones, but also succeeded in discriminating diseases of different inheritance styles and different mechanisms. We further derived pairwise phenotype similarities between 7988 human inherited diseases using their vector presentations. With a joint analysis of this phenome with multiple genomic data, we showed that phenotype overlap indeed implied genotype overlap. We finally used the derived phenotype similarities with genomic data to prioritize candidate genes and demonstrated advantages of this method over existing ones. Our method is capable of not only capturing semantic relationships between words in biomedical records but also alleviating the dimensional disaster accompanying the traditional TF-IDF framework. With the approaching of precision medicine, there will be abundant electronic records of medicine and health awaiting for deep analysis, and we expect to see a wide spectrum of applications borrowing the idea of our method in the near future.

Genome-wide copy number variant analysis for congenital ventricular septal defects in Chinese Han population.

PubMed

An, Yu; Duan, Wenyuan; Huang, Guoying; Chen, Xiaoli; Li, Li; Nie, Chenxia; Hou, Jia; Gui, Yonghao; Wu, Yiming; Zhang, Feng; Shen, Yiping; Wu, Bailin; Wang, Hongyan

2016-01-08

Ventricular septal defects (VSDs) constitute the most prevalent congenital heart disease (CHD), occurs either in isolation (isolated VSD) or in combination with other cardiac defects (complex VSD). Copy number variation (CNV) has been highlighted as a possible contributing factor to the etiology of many congenital diseases. However, little is known concerning the involvement of CNVs in either isolated or complex VSDs. We analyzed 154 unrelated Chinese individuals with VSD by chromosomal microarray analysis. The subjects were recruited from four hospitals across China. Each case underwent clinical assessment to define the type of VSD, either isolated or complex VSD. CNVs detected were categorized into syndrom related CNVs, recurrent CNVs and rare CNVs. Genes encompassed by the CNVs were analyzed using enrichment and pathway analysis. Among 154 probands, we identified 29 rare CNVs in 26 VSD patients (16.9 %, 26/154) and 8 syndrome-related CNVs in 8 VSD patients (5.2 %, 8/154). 12 of the detected 29 rare CNVs (41.3 %) were recurrently reported in DECIPHER or ISCA database as associated with either VSD or general heart disease. Fifteen genes (5 %, 15/285) within CNVs were associated with a broad spectrum of complicated CHD. Among these15 genes, 7 genes were in "abnormal interventricular septum morphology" derived from the MGI (mouse genome informatics) database, and nine genes were associated with cardiovascular system development (GO:0072538).We also found that these VSD-related candidate genes are enriched in chromatin binding and transcription regulation, which are the biological processes underlying heart development. Our study demonstrates the potential clinical diagnostic utility of genomic imbalance profiling in VSD patients. Additionally, gene enrichment and pathway analysis helped us to implicate VSD related candidate genes.

A web based relational database management system for filariasis control

PubMed Central

Murty, Upadhyayula Suryanarayana; Kumar, Duvvuri Venkata Rama Satya; Sriram, Kumaraswamy; Rao, Kadiri Madhusudhan; Bhattacharyulu, Chakravarthula Hayageeva Narasimha Venakata; Praveen, Bhoopathi; Krishna, Amirapu Radha

2005-01-01

The present study describes a RDBMS (relational database management system) for the effective management of Filariasis, a vector borne disease. Filariasis infects 120 million people from 83 countries. The possible re-emergence of the disease and the complexity of existing control programs warrant the development of new strategies. A database containing comprehensive data associated with filariasis finds utility in disease control. We have developed a database containing information on the socio-economic status of patients, mosquito collection procedures, mosquito dissection data, filariasis survey report and mass blood data. The database can be searched using a user friendly web interface. Availability http://www.webfil.org (login and password can be obtained from the authors) PMID:17597846

RDIS: The Rabies Disease Information System.

PubMed

Dharmalingam, Baskeran; Jothi, Lydia

2015-01-01

Rabies is a deadly viral disease causing acute inflammation or encephalitis of the brain in human beings and other mammals. Therefore, it is of interest to collect information related to the disease from several sources including known literature databases for further analysis and interpretation. Hence, we describe the development of a database called the Rabies Disease Information System (RDIS) for this purpose. The online database describes the etiology, epidemiology, pathogenesis and pathology of the disease using diagrammatic representations. It provides information on several carriers of the rabies viruses like dog, bat, fox and civet, and their distributions around the world. Information related to the urban and sylvatic cycles of transmission of the virus is also made available. The database also contains information related to available diagnostic methods and vaccines for human and other animals. This information is of use to medical, veterinary and paramedical practitioners, students, researchers, pet owners, animal lovers, livestock handlers, travelers and many others. The database is available for free http://rabies.mscwbif.org/home.html.

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

PubMed

Hayman, G Thomas; Laulederkind, Stanley J F; Smith, Jennifer R; Wang, Shur-Jen; Petri, Victoria; Nigam, Rajni; Tutaj, Marek; De Pons, Jeff; Dwinell, Melinda R; Shimoyama, Mary

2016-01-01

The Rat Genome Database (RGD;http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its curation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets. To generate gene-disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the Comparative Toxicogenomics Database and adapted it for use by expanding this framework with the addition of over 1000 terms to create the RGD Disease Ontology (RDO). The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals. Two major disease areas are the focus of data acquisition and curation efforts each year, leading to the release of the related Disease Portals. Collaborative efforts to realize a more robust disease ontology are underway. Database URL:http://rgd.mcw.edu. © The Author(s) 2016. Published by Oxford University Press.

Interstitial lung disease induced by fluoxetine: Systematic review of literature and analysis of Vigiaccess, Eudravigilance and a national pharmacovigilance database.

PubMed

Deidda, Arianna; Pisanu, Claudia; Micheletto, Laura; Bocchetta, Alberto; Del Zompo, Maria; Stochino, Maria Erminia

2017-06-01

We investigated a pulmonary adverse drug reaction possibly induced by fluoxetine, the Interstitial Lung Disease, by performing a systematic review of published case reports on this subject, a review of the World Health Organization VigiAccess database, of the European EudraVigilance database and of a national Pharmacovigilance database (Italian Pharmacovigilance Network). The research found a total of seven cases linking fluoxetine to Interstitial Lung Disease in the literature. 36 cases of interstitial lung disease related to fluoxetine were retrieved from the VigiAccess database (updated to July 2016), and 36 reports were found in EudraVigilance database (updated to June 2016). In the Italian Pharmacovigilance database (updated to August 2016), we found only one case of Interstitial Lung Disease, codified as "pulmonary disease". Our investigation shows that fluoxetine might be considered as a possible cause of Interstitial Lung Disease. In particular, although here we do not discuss the assessment of benefits and harms of fluoxetine, since this antidepressant is widely used, our review suggests that fluoxetine-induced Interstitial Lung Disease should be considered in patients with dyspnea, associated or not with dry cough, who are treated with this drug. An early withdrawn of fluoxetine could be useful to obtain a complete remission of this adverse drug reaction and special attention should be particularly devoted to long-term therapy, and to female and elderly patients. Although the spontaneous reporting system is affected by important limitations, drug post- marketing surveillance represents an important tool to evaluate the real world effectiveness and safety of drugs. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Middle-Range Explanatory Theory of Self-Management Behavior for Collaborative Research and Practice.

PubMed

Blok, Amanda C

2017-04-01

To report an analysis of the concept of self-management behaviors. Self-management behaviors are typically associated with disease management, with frequent use by nurse researchers related to chronic illness management and by international health organizations for development of disease management interventions. A concept analysis was conducted within the context of Orem's self-care framework. Walker and Avant's eight-step concept analysis approach guided the analysis. Academic databases were searched for relevant literature including CIHAHL, Cochrane Databases of Systematic Reviews and Register of Controlled Trials, MEDLINE, PsycARTICLES and PsycINFO, and SocINDEX. Literature using the term "self-management behavior" and published between April 2001 and March 2015 was analyzed for attributes, antecedents, and consequences. A total of 189 journal articles were reviewed. Self-management behaviors are defined as proactive actions related to lifestyle, a problem, planning, collaborating, and mental support, as well as reactive actions related to a circumstantial change, to achieve a goal influenced by the antecedents of physical, psychological, socioeconomic, and cultural characteristics, as well as collaborative and received support. The theoretical definition and middle-range explanatory theory of self-management behaviors will guide future collaborative research and clinical practice for disease management. © 2016 Wiley Periodicals, Inc.

A longitudinal ecological study of seasonal influenza deaths in relation to climate conditions in the United States from 1999 through 2011.

PubMed

Geier, David A; Kern, Janet K; Geier, Mark R

2018-01-01

Introduction: Influenza is an acute respiratory disease with significant annual global morbidity/mortality. Influenza transmission occurs in distinct seasonal patterns suggesting an importance of climate conditions on disease pathogenesis. This hypothesis-testing study evaluated microenvironment conditions within different demographic/geographical groups on seasonal influenza deaths in the United States. Materials and methods: The United States Centers for Disease Control and Prevention (CDC) Wonder online computer interface was utilized to integrate and analyze potential correlations in data generated from 1999 through 2011 for climate conditions of mean daily sunlight (KJ/m 2 ), mean daily maximum air temperature ( o C), mean daily minimum air temperature ( o C), and mean daily precipitation (mm) from the North America Land Data Assimilation System (NLDAS) database and on influenza mortality (ICD-10 codes:J09, J10, or J11) from the Underlying Cause of Death database. Results and discussion: Significant inverse correlations between the climate conditions of temperature, sunlight, and precipitation and seasonal influenza death rate were observed. Similar effects were observed among males and females, but when the data were separated by race and urbanization status significant differences were observed. Conclusion: This study highlights key factors that can help shape public health policy to deal with seasonal influenza in the United States and beyond.

Lack of magnetic resonance imaging lesion activity as a treatment target in multiple sclerosis: An evaluation using electronically collected outcomes.

PubMed

Conway, Devon S; Thompson, Nicolas R; Cohen, Jeffrey A

2016-09-01

The appropriate treatment target in multiple sclerosis (MS) is unclear. Lack of magnetic resonance imaging (MRI) lesion activity, a component of the no evidence of disease activity concept, has been proposed as a treatment target in MS. We used our MS database to investigate whether aggressively pursuing MRI stability by changing disease modifying therapy (DMT) when MRI activity is observed leads to better clinical and imaging outcomes. The Knowledge Program (KP) is a database linked to our electronic medical record allowing capture of patient and clinician reported outcomes. Through KP query and chart review, we identified all relapsing-remitting MS patients visiting between 1 January 2008 and 31 December 2014 with active MRIs despite DMT. Propensity modeling based on demographic and disease characteristics was used to match DMT switchers to non-switchers. KP and MRI outcomes were compared 18 months after the active MRI using mixed-effects linear regression models. We identified 417 patients who met criteria for our analysis. After propensity matching, 78 switchers and 91 non-switchers were analyzed. There was no difference in clinical or radiologic outcomes between these groups at 18 months. We did not find a short-term benefit of changing DMT to pursue MRI stability. Copyright © 2016 Elsevier B.V. All rights reserved.

A Systems Biology-Based Investigation into the Pharmacological Mechanisms of Sheng-ma-bie-jia-tang Acting on Systemic Lupus Erythematosus by Multi-Level Data Integration.

PubMed

Huang, Lin; Lv, Qi; Liu, Fenfen; Shi, Tieliu; Wen, Chengping

2015-11-12

Sheng-ma-bie-jia-tang (SMBJT) is a Traditional Chinese Medicine (TCM) formula that is widely used for the treatment of Systemic Lupus Erythematosus (SLE) in China. However, molecular mechanism behind this formula remains unknown. Here, we systematically analyzed targets of the ingredients in SMBJT to evaluate its potential molecular mechanism. First, we collected 1,267 targets from our previously published database, the Traditional Chinese Medicine Integrated Database (TCMID). Next, we conducted gene ontology and pathway enrichment analyses for these targets and determined that they were enriched in metabolism (amino acids, fatty acids, etc.) and signaling pathways (chemokines, Toll-like receptors, adipocytokines, etc.). 96 targets, which are known SLE disease proteins, were identified as essential targets and the rest 1,171 targets were defined as common targets of this formula. The essential targets directly interacted with SLE disease proteins. Besides, some common targets also had essential connections to both key targets and SLE disease proteins in enriched signaling pathway, e.g. toll-like receptor signaling pathway. We also found distinct function of essential and common targets in immune system processes. This multi-level approach to deciphering the underlying mechanism of SMBJT treatment of SLE details a new perspective that will further our understanding of TCM formulas.

Patterns of lymph node sampling and the impact of lymph node density in favorable histology Wilms tumor: An analysis of the national cancer database.

PubMed

Saltzman, A F; Carrasco, A; Amini, A; Aldrink, J H; Dasgupta, R; Gow, K W; Glick, R D; Ehrlich, P F; Cost, N G

2018-04-01

There is controversy about the role of lymph node (LN) sampling or dissection in the management of favorable histology (FH) Wilms tumor (WT), specifically how it performed and how it may impact survival. The objective of this study was to analyze factors affecting LN sampling patterns and the impact of LN yield and density (number of positive LNs/LNs examined) on overall survival (OS) in patients with advanced-stage favorable histology Wilms tumor (FHWT). The National Cancer Database (NCDB) was queried for patients with FHWT during 2004-2013. Demographic, clinical and OS data were abstracted for those who underwent surgical resection. Poisson regression was performed to analyze how factors influenced LN yield. Patients with positive LNs had LN density calculated and were further analyzed. A total of 2340 patients met criteria, with a median age at diagnosis of 3 years (range 0-78 years). The median number of LNs examined was three (range 0-87). Lymph node yield was affected by age, race, insurance, tumor size, laterality, advanced stage, LN positivity, and institutional volume. A total of 390 (16.6%) patients had LN-positive disease. Median LN density for these LN-positive patients was 0.38 (range 0.02-1) (Summary Figure). Estimated 5-year OS was significantly improved for those with LN density ≤0.38 vs. >0.38 (94% vs. 84.6%, P = 0.012). In this population, on multivariate analysis, age and LN density were significant predictors of OS. It is difficult to compile large numbers of cases in rare diseases like WT, and fortunately a large administrative database such as the NCDB can serve as a great resource. However, administrative data come with inherent limitations such as missing data and inability to account for a variety of factors that may influence LN yield and/or OS (specimen designation, pathologist experience, surgeon experience/volume, institutional Children's Oncology Group (COG) association, etc.). In this specific disease, the American Joint Committee on Cancer staging (captured by the NCDB) is different than the COG WT staging system that is used clinically, and the NCDB does not capture oncologic outcomes beyond OS. In a review of the NCDB, various factors associated with LN yield and observed LN density were identified to be significantly associated with OS in patients with LN-positive FHWT. This reinforces the need for adequate LN sampling at the time of WT surgery, to maximize surgical disease control. It was proposed that LN density as a metric may allow for improved risk-stratification, and possibly allow for therapeutic reduction in a sub-set of patients with low LN density. Copyright © 2017 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

IRWRLDA: improved random walk with restart for lncRNA-disease association prediction.

PubMed

Chen, Xing; You, Zhu-Hong; Yan, Gui-Ying; Gong, Dun-Wei

2016-09-06

In recent years, accumulating evidences have shown that the dysregulations of lncRNAs are associated with a wide range of human diseases. It is necessary and feasible to analyze known lncRNA-disease associations, predict potential lncRNA-disease associations, and provide the most possible lncRNA-disease pairs for experimental validation. Considering the limitations of traditional Random Walk with Restart (RWR), the model of Improved Random Walk with Restart for LncRNA-Disease Association prediction (IRWRLDA) was developed to predict novel lncRNA-disease associations by integrating known lncRNA-disease associations, disease semantic similarity, and various lncRNA similarity measures. The novelty of IRWRLDA lies in the incorporation of lncRNA expression similarity and disease semantic similarity to set the initial probability vector of the RWR. Therefore, IRWRLDA could be applied to diseases without any known related lncRNAs. IRWRLDA significantly improved previous classical models with reliable AUCs of 0.7242 and 0.7872 in two known lncRNA-disease association datasets downloaded from the lncRNADisease database, respectively. Further case studies of colon cancer and leukemia were implemented for IRWRLDA and 60% of lncRNAs in the top 10 prediction lists have been confirmed by recent experimental reports.

A Brief Review of RNA–Protein Interaction Database Resources

PubMed Central

Yi, Ying; Zhao, Yue; Huang, Yan; Wang, Dong

2017-01-01

RNA–Protein interactions play critical roles in various biological processes. By collecting and analyzing the RNA–Protein interactions and binding sites from experiments and predictions, RNA–Protein interaction databases have become an essential resource for the exploration of the transcriptional and post-transcriptional regulatory network. Here, we briefly review several widely used RNA–Protein interaction database resources developed in recent years to provide a guide of these databases. The content and major functions in databases are presented. The brief description of database helps users to quickly choose the database containing information they interested. In short, these RNA–Protein interaction database resources are continually updated, but the current state shows the efforts to identify and analyze the large amount of RNA–Protein interactions. PMID:29657278

"Trust is not something you can reclaim easily": patenting in the field of direct-to-consumer genetic testing.

PubMed

Sterckx, Sigrid; Cockbain, Julian; Howard, Heidi; Huys, Isabelle; Borry, Pascal

2013-05-01

Recently, 23andMe announced that it had obtained its first patent, related to "polymorphisms associated with Parkinson's disease" (US-B-8187811). This announcement immediately sparked controversy in the community of 23andMe users and research participants, especially with regard to issues of transparency and trust. The purpose of this article was to analyze the patent portfolio of this prominent direct-to-consumer genetic testing company and discuss the potential ethical implications of patenting in this field for public participation in Web-based genetic research. We searched the publicly accessible patent database Espacenet as well as the commercially available database Micropatent for published patents and patent applications of 23andMe. Six patent families were identified for 23andMe. These included patent applications related to: genetic comparisons between grandparents and grandchildren, family inheritance, genome sharing, processing data from genotyping chips, gamete donor selection based on genetic calculations, finding relatives in a database, and polymorphisms associated with Parkinson disease. An important lesson to be drawn from this ongoing controversy seems to be that any (private or public) organization involved in research that relies on human participation, whether by providing information, body material, or both, needs to be transparent, not only about its research goals but also about its strategies and policies regarding commercialization.

Health Care Burden of Spinal Diseases in the Republic of Korea: Analysis of a Nationwide Database From 2012 Through 2016

PubMed Central

Lee, Chang-Hyun; Kim, Chi Heon; Kwon, Ji-Woong

2018-01-01

Objective This study aimed to determine the incidence and analyze trends related to spinal diseases based on a national database in the Republic of Korea (ROK) and to elucidate the healthcare burden that will serve as a useful resource for researchers, clinicians, and patients. Methods This study was a retrospective analysis of data obtained from Healthcare Bigdata Hub, the Korean Statistical Information Service, and Open Data Portal from 2012 through 2016. The main disease codes for spinal diseases (M40–M54) were used for identification of these conditions. Results The overall annual incidence rates for spinal disease in the ROK was median 15,877 (men, 13,181; women, 18,588) per 100,000 population, and sex ratio was 1:1.41 (p<0.01). The incidence rate and annual costs per patient increased by 7.6% and 14.7% over 5 years continuously, respectively. The age-adjusted incidence rate increased with age; the highest rates were 42.6% in the 75–79 years group. Patients older than 65 years old accounted for median 31.0% of number of patients and 40.1% of medical expenses over 5 years. Lumbar disc herniation (M51) and spinal stenosis (M48) might accounted for both the highest incidence and medical expenses in patients under the age of 60 and over 60 years, respectively. Conclusion The incidence and medical expenditures of spinal disease increased continuously. As the population of ROK in aging, the incidence and medical expenditures due to spondylosis and stenosis (M48) for the old are also increasing. The social burden of spinal diseases in elder patients needs to be prudently considered in health policy makers. PMID:29656624

Health Care Burden of Spinal Diseases in the Republic of Korea: Analysis of a Nationwide Database From 2012 Through 2016.

PubMed

Lee, Chang-Hyun; Chung, Chun Kee; Kim, Chi Heon; Kwon, Ji-Woong

2018-03-01

This study aimed to determine the incidence and analyze trends related to spinal diseases based on a national database in the Republic of Korea (ROK) and to elucidate the healthcare burden that will serve as a useful resource for researchers, clinicians, and patients. This study was a retrospective analysis of data obtained from Healthcare Bigdata Hub, the Korean Statistical Information Service, and Open Data Portal from 2012 through 2016. The main disease codes for spinal diseases (M40-M54) were used for identification of these conditions. The overall annual incidence rates for spinal disease in the ROK was median 15,877 (men, 13,181; women, 18,588) per 100,000 population, and sex ratio was 1:1.41 (p<0.01). The incidence rate and annual costs per patient increased by 7.6% and 14.7% over 5 years continuously, respectively. The age-adjusted incidence rate increased with age; the highest rates were 42.6% in the 75-79 years group. Patients older than 65 years old accounted for median 31.0% of number of patients and 40.1% of medical expenses over 5 years. Lumbar disc herniation (M51) and spinal stenosis (M48) might accounted for both the highest incidence and medical expenses in patients under the age of 60 and over 60 years, respectively. The incidence and medical expenditures of spinal disease increased continuously. As the population of ROK in aging, the incidence and medical expenditures due to spondylosis and stenosis (M48) for the old are also increasing. The social burden of spinal diseases in elder patients needs to be prudently considered in health policy makers.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

PubMed Central

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

Risk of psychiatric and neurological diseases in patients with workplace mobbing experience in Germany: a retrospective database analysis

PubMed Central

Kostev, Karel; Rex, Juliana; Waehlert, Lilia; Hog, Daniela; Heilmaier, Christina

2014-01-01

Introduction: The number of mobbing experiences recorded has increased during recent years and it has now been established as global phenomenon among the working population. The goal of our study was to analyze the incidence of certain neurologic and psychiatric diseases as a consequence of mobbing as compared with a control group and to examine the possible influence of previous diseases that occurred within one year before the first mobbing documentation on the incidence of mobbing. Material & methods: We used a large database (IMS® Disease Analyzer, Germany) to collect data from general practitioners in Germany from 01/2003 until 12/2012. Based on age, gender, and health insurance, patients with experience of mobbing were matched with a control group of patients who had not reported workplace mobbing and who were being treated by the same physicians. At first, diseases that occurred within one year before the bullying experience took place (“index date”) were noted and compared to a control group of similar composition in terms of gender, age, and health insurance. Subsequently, the prevalence of depression, anxiety, somatoform disorders, and sleep disorders following experiences of mobbing were determined. After adjustment to take into account the odds of bullying, the ratios of these diseases were assessed using a logistic regression model. Results: The study population consisted of n=2,625 patients and n=2,625 controls, of which 33% were men. The number of cases of bullying documented rose continuously from 2003 to 2011 and remained high in 2012. Those who would later become victims of mobbing demonstrated a considerably higher prevalence of diseases in general – these diseases were not confined to the neurologic-psychiatric spectrum. Following experiences of bullying, depression, anxiety, somatoform disorders, and sleep disorders were significantly more prevalent than in the control group (for all, p<0.05). Similarly, odds ratios (OR) representing the risk of suffering from diseases were higher in affected patients, with the highest value (4.28) for depression and the lowest value for sleep disorders (OR=2.4). Conclusion: Those who will later become the victims of bullying are more prone to suffer from diseases in general, even before this experience of mobbing has occurred, which underlines the importance of supporting (chronically) ill patients to protect them against bullying. Sequelae of mobbing include, in particular, diseases from the neurologic-psychiatric spectrum. PMID:24872810

Pyogenic Liver Abscess as Endemic Disease, Taiwan

PubMed Central

Tsai, Feng-Chiao; Huang, Yu-Tsung; Chang, Luan-Yin

2008-01-01

Pyogenic liver abscess has become a health problem in Taiwanese society. However, the extent of this problem has remained unclear because of the lack of a population-based study. We therefore performed a nationwide analysis of pyogenic liver abscess in Taiwan from 1996 through 2004. We analyzed 29,703 cases from the Taiwan National Health Insurance database and 506 cases from National Taiwan University Hospital. Our analysis showed that the annual incidence of pyogenic liver abscess increased steadily from 11.15/100,000 population in 1996 to 17.59/100,000 in 2004. Diabetes, malignancy, renal disease, and pneumonia were associated with a higher risk for the disease. By contrast, death due to pyogenic liver abscess decreased over time, although population-based abscess-related death increased slightly. Renal disease, malignancy, pneumonia, and heart disease correlated with higher death rates; Klebsiella pneumoniae infection and therapeutic procedures were related to lower death rates. Diabetes did not significantly change death rates for the 506 patients from the hospital. PMID:18826824

Using linked administrative and disease-specific databases to study end-of-life care on a population level.

PubMed

Maetens, Arno; De Schreye, Robrecht; Faes, Kristof; Houttekier, Dirk; Deliens, Luc; Gielen, Birgit; De Gendt, Cindy; Lusyne, Patrick; Annemans, Lieven; Cohen, Joachim

2016-10-18

The use of full-population databases is under-explored to study the use, quality and costs of end-of-life care. Using the case of Belgium, we explored: (1) which full-population databases provide valid information about end-of-life care, (2) what procedures are there to use these databases, and (3) what is needed to integrate separate databases. Technical and privacy-related aspects of linking and accessing Belgian administrative databases and disease registries were assessed in cooperation with the database administrators and privacy commission bodies. For all relevant databases, we followed procedures in cooperation with database administrators to link the databases and to access the data. We identified several databases as fitting for end-of-life care research in Belgium: the InterMutualistic Agency's national registry of health care claims data, the Belgian Cancer Registry including data on incidence of cancer, and databases administrated by Statistics Belgium including data from the death certificate database, the socio-economic survey and fiscal data. To obtain access to the data, approval was required from all database administrators, supervisory bodies and two separate national privacy bodies. Two Trusted Third Parties linked the databases via a deterministic matching procedure using multiple encrypted social security numbers. In this article we describe how various routinely collected population-level databases and disease registries can be accessed and linked to study patterns in the use, quality and costs of end-of-life care in the full population and in specific diagnostic groups.

IRIS: A database application system for diseases identification using FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Arshad, Ahmad Zulhilmi; Munajat, Yusof; Ibrahim, Raja Kamarulzaman Raja; Mahmood, Nasrul Humaimi

2015-05-01

Infrared information on diseases identification system (IRIS) is an application for diseases identification and analysis by using Fourier transform infrared (FTIR) spectroscopy. This is the preliminary step to gather information from the secondary data which was extracted from recognized various research and scientific paper, which are combined into a single database as in IRIS for our purpose of study. The importance of this database is to examine the fingerprint differences between normal and diseases cell or tissue. With the implementation of this application is it hopes that the diseases identification using FTIR spectroscopy would be more reliable and may assist either physicians, pathologists, or researchers to diagnose the certain type of disease efficiently.

Understanding Toxoplasmosis in the United States Through "Large Data" Analyses.

PubMed

Lykins, Joseph; Wang, Kanix; Wheeler, Kelsey; Clouser, Fatima; Dixon, Ashtyn; El Bissati, Kamal; Zhou, Ying; Lyttle, Christopher; Rzhetsky, Andrey; McLeod, Rima

2016-08-15

Toxoplasma gondii infection causes substantial morbidity and mortality in the United States, and infects approximately one-third of persons globally. Clinical manifestations vary. Seropositivity is associated with neurologic diseases and malignancies. There are few objective data concerning US incidence and distribution of toxoplasmosis. Truven Health MarketScan Database and International Classification of Diseases, Ninth Revision (ICD-9) codes, including treatment specific to toxoplasmosis, identified patients with this disease. Spatiotemporal distribution and patterns of disease manifestation were analyzed. Comorbidities between patients and matched controls were compared. Between 2003 and 2012, 9260 patients had ICD-9 codes for toxoplasmosis. This database of patients with ICD-9 codes includes 15% of those in the United States, excluding patients with no or public insurance. Thus, assuming that demographics do not change incidence, the calculated total is 61 700 or 6856 patients per year. Disease was more prevalent in the South. Mean age at diagnosis was 37.5 ± 15.5 years; 2.4% were children aged 0-2 years, likely congenitally infected. Forty-one percent were male, and 73% of women were of reproductive age. Of identified patients, 38% had eye disease and 12% presented with other serious manifestations, including central nervous system and visceral organ damage. Toxoplasmosis was statistically associated with substantial comorbidities, including human immunodeficiency virus, autoimmune diseases, and neurologic diseases. Toxoplasmosis causes morbidity and mortality in the United States. Our analysis of private insurance records missed certain at-risk populations and revealed fewer cases of retinal disease than previously estimated, suggesting undercoding, underreporting, undertreating, or differing demographics of those with eye disease. Mandatory reporting of infection to health departments and gestational screening could improve care and facilitate detection of epidemics and, thereby, public health interventions. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

PubMed

Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas; Petri, Victoria; Smith, Jennifer R; Tutaj, Marek; Nigam, Rajni; Dwinell, Melinda R; Shimoyama, Mary

2016-08-01

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality. Copyright © 2016 the American Physiological Society.

[Influence of selected endogenous and environmental factors on the course and complications of Grave's disease].

PubMed

Kurzynska, Anna; Przybylik-Mazurek, Elwira; Węgrzynowicz, Katarzyna; Morzywołek, Aleksandra; Wieczorek, Agata; Żarnowska, Maja; Hubalewska-Dydejczyk, Alicja

2014-01-01

Graves' disease (GD) is an autoimmune thyroid disease with complex and not fully established etiology. It occurs when environmental factors influence people genetically prone to this illness. The aim of this study was to determine the impact of selected factors (endogenous and environmental) on the course and complications of disease in patients with recurrent GD. Two hundred and four patients with relapsed GD, treated in the Clinical Department of Endocrinology in University Hospital in Cracow in years 2004-2006 and then in 2011 were retrospectively analyzed. Patients who agreed to participate in the study were sent questionnaire to complete. Demographic and clinical data were collected and entered into a database. Patient data included: gender, place of living, lifestyle (smoking), family history of autoimmune diseases, the course of the disease, its symptoms and the treatment strategy. Furthermore the medical documentation was analyzed. Descriptive statistical analyses were made. The study showed a significant difference in the frequency of appearance of ophthalmopathy between men and women (80% and 37.14%, respectively, p = 0.041), between smokers and nonsmokers (61.9% and 21.05%, respectively, p = 0.022) and between the age of patients with positive and negative family history of autoimmune diseases (37.6 years and 50.5 years respectively, p = 0.002). 1. Male gender is a risk factor for ophthalmopathy in GD. 2. Cigarette smoking affects the risk of Graves' ophthalmopathy. 3. A positive family history of thyroid diseases and/or autoimmune diseases promotes the development of GD at a younger age.

Global Distribution of Outbreaks of Water-Associated Infectious Diseases

PubMed Central

Yang, Kun; LeJeune, Jeffrey; Alsdorf, Doug; Lu, Bo; Shum, C. K.; Liang, Song

2012-01-01

Background Water plays an important role in the transmission of many infectious diseases, which pose a great burden on global public health. However, the global distribution of these water-associated infectious diseases and underlying factors remain largely unexplored. Methods and Findings Based on the Global Infectious Disease and Epidemiology Network (GIDEON), a global database including water-associated pathogens and diseases was developed. In this study, reported outbreak events associated with corresponding water-associated infectious diseases from 1991 to 2008 were extracted from the database. The location of each reported outbreak event was identified and geocoded into a GIS database. Also collected in the GIS database included geo-referenced socio-environmental information including population density (2000), annual accumulated temperature, surface water area, and average annual precipitation. Poisson models with Bayesian inference were developed to explore the association between these socio-environmental factors and distribution of the reported outbreak events. Based on model predictions a global relative risk map was generated. A total of 1,428 reported outbreak events were retrieved from the database. The analysis suggested that outbreaks of water-associated diseases are significantly correlated with socio-environmental factors. Population density is a significant risk factor for all categories of reported outbreaks of water-associated diseases; water-related diseases (e.g., vector-borne diseases) are associated with accumulated temperature; water-washed diseases (e.g., conjunctivitis) are inversely related to surface water area; both water-borne and water-related diseases are inversely related to average annual rainfall. Based on the model predictions, “hotspots” of risks for all categories of water-associated diseases were explored. Conclusions At the global scale, water-associated infectious diseases are significantly correlated with socio-environmental factors, impacting all regions which are affected disproportionately by different categories of water-associated infectious diseases. PMID:22348158

Long non-coding RNAs and complex diseases: from experimental results to computational models.

PubMed

Chen, Xing; Yan, Chenggang Clarence; Zhang, Xu; You, Zhu-Hong

2017-07-01

LncRNAs have attracted lots of attentions from researchers worldwide in recent decades. With the rapid advances in both experimental technology and computational prediction algorithm, thousands of lncRNA have been identified in eukaryotic organisms ranging from nematodes to humans in the past few years. More and more research evidences have indicated that lncRNAs are involved in almost the whole life cycle of cells through different mechanisms and play important roles in many critical biological processes. Therefore, it is not surprising that the mutations and dysregulations of lncRNAs would contribute to the development of various human complex diseases. In this review, we first made a brief introduction about the functions of lncRNAs, five important lncRNA-related diseases, five critical disease-related lncRNAs and some important publicly available lncRNA-related databases about sequence, expression, function, etc. Nowadays, only a limited number of lncRNAs have been experimentally reported to be related to human diseases. Therefore, analyzing available lncRNA-disease associations and predicting potential human lncRNA-disease associations have become important tasks of bioinformatics, which would benefit human complex diseases mechanism understanding at lncRNA level, disease biomarker detection and disease diagnosis, treatment, prognosis and prevention. Furthermore, we introduced some state-of-the-art computational models, which could be effectively used to identify disease-related lncRNAs on a large scale and select the most promising disease-related lncRNAs for experimental validation. We also analyzed the limitations of these models and discussed the future directions of developing computational models for lncRNA research. © The Author 2016. Published by Oxford University Press.

Hospital admissions for vitamin D related conditions and subsequent immune-mediated disease: record-linkage studies

PubMed Central

2013-01-01

Background Previous studies have suggested that there may be an association between vitamin D deficiency and the risk of developing immune-mediated diseases. Methods We analyzed a database of linked statistical records of hospital admissions and death registrations for the whole of England (from 1999 to 2011). Rate ratios for immune-mediated disease were determined, comparing vitamin D deficient cohorts (individuals admitted for vitamin D deficiency or markers of vitamin D deficiency) with comparison cohorts. Results After hospital admission for either vitamin D deficiency, osteomalacia or rickets, there were significantly elevated rates of Addison’s disease, ankylosing spondylitis, autoimmune hemolytic anemia, chronic active hepatitis, celiac disease, Crohn’s disease, diabetes mellitus, pemphigoid, pernicious anemia, primary biliary cirrhosis, rheumatoid arthritis, Sjogren’s syndrome, systemic lupus erythematosus, thyrotoxicosis, and significantly reduced risks for asthma and myxoedema. Conclusions This study shows that patients with vitamin D deficiency may have an increased risk of developing some immune-mediated diseases, although we cannot rule out reverse causality or confounding. Further study of these associations is warranted and these data may aid further public health studies. PMID:23885887

[Eperythrozoonosis complicated with hemophagocytic syndrome: report of four cases and review of literature].

PubMed

Li, J G; Zhang, D; Zhou, Z X; Li, S N; Kang, M; Lai, J M

2018-04-02

Objective: To analyze the clinical characteristics of eperythrozoonosis complicated with hemophagocytic syndrome (HPS) in 4 children. Methods: Four patients diagnosed with eperythrozoonosis complicated with HPS in the Children's Hospital Affiliated Capital Institute of Pediatrics during the period from June 2014 to July 2016 were enrolled. The clinical manifestations, laboratory examination data and therapeutic strategies were analyzed. A literature search (search terms included 'eperythrozoonosis' and 'hemophagocytic syndrome') was conducted using CNKI, Wanfang database, Chinese biomedical literature database and PubMed to include recently published studies (searched from the database establishment to January 2017). Results: Four patients were included in the study. One was boy and the other three were girls. The age range of the 4 patients was between 9 months and 17 years (9 months, 2 years and 17 years, 11 months respectively). All the patients presented with recurrent high fever. During the course of fever, 3 patients presented with rash, and 2 patients presented with joint pain and swelling, which mimicked systemic juvenile idiopathic arthritis. Only 1 patient had the contact history of infectious disease. All patients had normal or decreased white blood cell count ((0.80-13.12)×10 9 /L), suffered from varied degrees of anemia and showed the increased C reactive protein (13.0-84.7 mg/L) anderythrocyte sedimentation rate (13-72 mm/1 h). Examination of peripheral blood smears confirmed eperythrozoonosis. After fever continued about 1 month, all the 4 patients rapidly progressed. Among the 4 patients, 1 patient died for giving up further therapy, and the other 3 patients completely recovered after treatment, including azithromycin for the treatment of eperythrozoonosis, and high-dose intravenous methylprednisolone pulse therapy and human immunoglobulin for the treatment of HPS. For the disease not satisfactory, the hemophagocytic lymphohistiocytosis-2004 (HLH-2004) protocol is given. After the hospitalization of 1 to 2 months, the conditions improved and the children were discharged from hospital. Three patients were followed up for 8 months to 2 years, and their conditions were stable. In the PubMed database, no report was found. Nine cases of children with eperythrozoonosis were found in CNKI, Wanfang database and Chinese biomedical literature database, and 1 case was complicated with HPS. These findings, taken together our report, provided the data of 5 children with eperythrozoonosis complicated with HPS (4 cases were younger than 2 years old). A patient had contact history of infectious disease. Five patientss showed fever of unknown origin. All the patients had severe eperythrozoonosis, and 2 cases at younger age died. Conclusions: Children with eperythrozoonosis often present with the protracted fever of unknown origin, and clinical manifestations mimic those of juvenile idiopathic arthritis (systemic type). The patients with eperythrozoonosis of mild-to-moderate disease severity may have a good prognosis. Children with severe eperythrozoonosis, especially those HPS cases with early onset before 2 years old, may have high risk of mortality. Once the patient's condition aggravates in the course of fever, HPS should be highly suspected. For the patients with eperythrozoonosis complicated with HPS, early diagnosis and the combination of anti-infection with the treatment of HPS are crucial for a good prognosis. For the treatment of HPS, HLH-2004 protocol is recommended.

dbDSM: a manually curated database for deleterious synonymous mutations.

PubMed

Wen, Pengbo; Xiao, Peng; Xia, Junfeng

2016-06-15

Synonymous mutations (SMs), which changed the sequence of a gene without directly altering the amino acid sequence of the encoded protein, were thought to have no functional consequences for a long time. They are often assumed to be neutral in models of mutation and selection and were completely ignored in many studies. However, accumulating experimental evidence has demonstrated that these mutations exert their impact on gene functions via splicing accuracy, mRNA stability, translation fidelity, protein folding and expression, and some of these mutations are implicated in human diseases. To the best of our knowledge, there is still no database specially focusing on disease-related SMs. We have developed a new database called dbDSM (database of Deleterious Synonymous Mutation), a continually updated database that collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289 SMs and 443 human diseases from ClinVar, GRASP, GWAS Catalog, GWASdb, PolymiRTS database, PubMed database and Web of Knowledge. Additionally, we provided users a link to download all the data in the dbDSM and a link to submit novel data into the database. We hope dbDSM will be a useful resource for investigating the roles of SMs in human disease. dbDSM is freely available online at http://bioinfo.ahu.edu.cn:8080/dbDSM/index.jsp with all major browser supported. jfxia@ahu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Analysis of academic impact of publications from National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention based on SCIE database in recent five years].

PubMed

Zhen, Li; Bin, Zheng

2017-03-02

To describe the academic impact of publications from National Institute of Parasitic Diseases (NIPD), Chinese Center for Disease Control and Prevention, so as to give the quantity evidence for scientific research decision making. The SCIE papers of NIPD published from 2011-2015 were searched and statistically analyzed. The number of published papers, citation frequencies, h-index, and funding resources were analyzed. The academic impact of the institute was assessed according to these data. A total of 361 papers were published by NIPD, and the quantity increased year by year. The majority type is original articles. The total citations were 1 641 times, the average citation per paper was 5.19 and h-index was 17. The majority of these papers were published in foreign professional periodicals, whose impact factors were between 1.194 and 6.751. The major resources of NIPD were from China, and NIPD also had good collaborations with institutions in US and Switzerland. In China and Asia, NIPD led the research in the field of parasitology and tropical medicine. The quantity and quality of annual published papers of NIPD are on the rise. However, NIPD lagged behind the leading institutions in the world.

Genotator: a disease-agnostic tool for genetic annotation of disease.

PubMed

Wall, Dennis P; Pivovarov, Rimma; Tong, Mark; Jung, Jae-Yoon; Fusaro, Vincent A; DeLuca, Todd F; Tonellato, Peter J

2010-10-29

Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and organize this mounting sea of genetic data have emerged, but these resources differ dramatically in their disease coverage and genetic depth. With few exceptions, researchers must manually search a variety of sites to assemble a complete set of genetic evidence for a particular disease of interest, a process that is both time-consuming and error-prone. We designed a real-time aggregation tool that provides both comprehensive coverage and reliable gene-to-disease rankings for any disease. Our tool, called Genotator, automatically integrates data from 11 externally accessible clinical genetics resources and uses these data in a straightforward formula to rank genes in order of disease relevance. We tested the accuracy of coverage of Genotator in three separate diseases for which there exist specialty curated databases, Autism Spectrum Disorder, Parkinson's Disease, and Alzheimer Disease. Genotator is freely available at http://genotator.hms.harvard.edu. Genotator demonstrated that most of the 11 selected databases contain unique information about the genetic composition of disease, with 2514 genes found in only one of the 11 databases. These findings confirm that the integration of these databases provides a more complete picture than would be possible from any one database alone. Genotator successfully identified at least 75% of the top ranked genes for all three of our use cases, including a 90% concordance with the top 40 ranked candidates for Alzheimer Disease. As a meta-query engine, Genotator provides high coverage of both historical genetic research as well as recent advances in the genetic understanding of specific diseases. As such, Genotator provides a real-time aggregation of ranked data that remains current with the pace of research in the disease fields. Genotator's algorithm appropriately transforms query terms to match the input requirements of each targeted databases and accurately resolves named synonyms to ensure full coverage of the genetic results with official nomenclature. Genotator generates an excel-style output that is consistent across disease queries and readily importable to other applications.

Analysis of Outcomes After TKA: Do All Databases Produce Similar Findings?

PubMed

Bedard, Nicholas A; Pugely, Andrew J; McHugh, Michael; Lux, Nathan; Otero, Jesse E; Bozic, Kevin J; Gao, Yubo; Callaghan, John J

2018-01-01

Use of large clinical and administrative databases for orthopaedic research has increased exponentially. Each database represents unique patient populations and varies in their methodology of data acquisition, which makes it possible that similar research questions posed to different databases might result in answers that differ in important ways. (1) What are the differences in reported demographics, comorbidities, and complications for patients undergoing primary TKA among four databases commonly used in orthopaedic research? (2) How does the difference in reported complication rates vary depending on whether only inpatient data or 30-day postoperative data are analyzed? Patients who underwent primary TKA during 2010 to 2012 were identified within the National Surgical Quality Improvement Programs (NSQIP), the Nationwide Inpatient Sample (NIS), the Medicare Standard Analytic Files (MED), and the Humana Administrative Claims database (HAC). NSQIP is a clinical registry that captures both inpatient and outpatient events up to 30 days after surgery using clinical reviewers and strict definitions for each variable. The other databases are administrative claims databases with their comorbidity and adverse event data defined by diagnosis and procedure codes used for reimbursement. NIS is limited to inpatient data only, whereas HAC and MED also have outpatient data. The number of patients undergoing primary TKA from each database was 48,248 in HAC, 783,546 in MED, 393,050 in NIS, and 43,220 in NSQIP. NSQIP definitions for comorbidities and surgical complications were matched to corresponding International Classification of Diseases, 9 Revision/Current Procedural Terminology codes and these coding algorithms were used to query NIS, MED, and HAC. Age, sex, comorbidities, and inpatient versus 30-day postoperative complications were compared across the four databases. Given the large sample sizes, statistical significance was often detected for small, clinically unimportant differences; thus, the focus of comparisons was whether the difference reached an absolute difference of twofold to signify an important clinical difference. Although there was a higher proportion of males in NIS and NSQIP and patients in NIS were younger, the difference was slight and well below our predefined threshold for a clinically important difference. There was variation in the prevalence of comorbidities and rates of postoperative complications among databases. The prevalence of chronic obstructive pulmonary disease (COPD) and coagulopathy in HAC and MED was more than twice that in NIS and NSQIP (relative risk [RR] for COPD: MED versus NIS 3.1, MED versus NSQIP 4.5, HAC versus NIS 3.6, HAC versus NSQIP 5.3; RR for coagulopathy: MED versus NIS 3.9, MED versus NSQIP 3.1, HAC versus NIS 3.3, HAC versus NSQIP 2.7; p < 0.001 for all comparisons). NSQIP had more than twice the obesity as NIS (RR 0.35). Rates of stroke within 30 days of TKA had more than a twofold difference among all databases (p < 0.001). HAC had more than twice the rates of 30-day complications at all endpoints compared with NSQIP and more than twice the 30-day infections as MED. A comparison of inpatient and 30-day complications rates demonstrated more than twice the amount of wound infections and deep vein thromboses is captured when data are analyzed out to 30 days after TKA (p < 0.001 for all comparisons). When evaluating research utilizing large databases, one must pay particular attention to the type of database used (administrative claims, clinical registry, or other kinds of databases), time period included, definitions utilized for specific variables, and the population captured to ensure it is best suited for the specific research question. Furthermore, with the advent of bundled payments, policymakers must meticulously consider the data sources used to ensure the data analytics match historical sources. Level III, therapeutic study.

Emerging role of multimodality treatment in gall bladder cancer: Outcomes following 510 consecutive resections in a tertiary referral center.

PubMed

Patkar, Shraddha; Ostwal, Vikas; Ramaswamy, Anant; Engineer, Reena; Chopra, Supriya; Shetty, Nitin; Dusane, Rohit; Shrikhande, Shailesh V; Goel, Mahesh

2018-03-01

Gall bladder cancer (GBC) is a disease with high incidence in India. We analyzed the outcomes of patients with suspected GBC who underwent surgical exploration. Analysis of a prospectively maintained database of patients undergoing surgical exploration for clinic-radiologically suspected GBC from January 2010 to August 2015. Outcomes as well as factors influencing survival were analyzed. Five hundred and ten patients underwent surgery for suspected GBC. Of these 400 had histologically proven malignancy. Eighty patients were deemed inoperable. Radical cholecystectomy was performed in 153 patients, revision surgery for incidental GBC in 160 and port site excision in seven patients. A total of 112 received peri-operative chemotherapy or chemoradiation. Majority were stage III (36%, n = 144) and stage II (31.8% n = 127). At a median follow up of 28.4 months, the median overall survival (OS) was not yet reached. Median disease free survival (DFS) was 33.4 months. Lymph node involvement, stage of the disease and resection status were the main factors influencing outcomes (P = 0.0001). Surgery alone is curative only for early GBC (Stage I). Combination of surgery and peri-operative systemic therapy results in favorable outcomes even in stage II/III disease. Potentially, multimodality treatment may add meaningful survival for this disease with inherently aggressive tumor biology. © 2017 Wiley Periodicals, Inc.

Library of molecular associations: curating the complex molecular basis of liver diseases.

PubMed

Buchkremer, Stefan; Hendel, Jasmin; Krupp, Markus; Weinmann, Arndt; Schlamp, Kai; Maass, Thorsten; Staib, Frank; Galle, Peter R; Teufel, Andreas

2010-03-20

Systems biology approaches offer novel insights into the development of chronic liver diseases. Current genomic databases supporting systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations http://www.medicalgenomics.org/databases/loma/news, currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.

Concepts and data model for a co-operative neurovascular database.

PubMed

Mansmann, U; Taylor, W; Porter, P; Bernarding, J; Jäger, H R; Lasjaunias, P; Terbrugge, K; Meisel, J

2001-08-01

Problems of clinical management of neurovascular diseases are very complex. This is caused by the chronic character of the diseases, a long history of symptoms and diverse treatments. If patients are to benefit from treatment, then treatment decisions have to rely on reliable and accurate knowledge of the natural history of the disease and the various treatments. Recent developments in statistical methodology and experience from electronic patient records are used to establish an information infrastructure based on a centralized register. A protocol to collect data on neurovascular diseases with technical as well as logistical aspects of implementing a database for neurovascular diseases are described. The database is designed as a co-operative tool of audit and research available to co-operating centres. When a database is linked to a systematic patient follow-up, it can be used to study prognosis. Careful analysis of patient outcome is valuable for decision-making.

Comparative study on the National Renal Disease Registry in America, England and Iran.

PubMed

Ajami, Sima; Askarianzadeh, Mahdi; Saghaeiannejad-Isfahani, Sakineh; Mortazavi, Mojgan; Ehteshami, Asghar

2014-01-01

A disease registry is a database that includes information about people diagnosed with specific types of diseases. The registry collects information that can be used for capturing, managing, and organizing specific information for patients. The aim of this study was to identify and compare the National Renal Disease Registry (NRDR) in selected countries including the United States, United Kingdom, and Iran. Retrieval of data of the NRDR performed through scholars responsible in related agencies, including the Ministry of Health and Medical Education, and Renal Disease charity, and data registries in the United States, United Kingdom, and Iran. This research was an applied and descriptive, comparative study. The study population consisted of the National Renal Disease Registry of the selected countries including the United States, United Kingdom, and Iran, from which data were collected using forms that were designed according to the study objectives. Sources of data were researchers, scholars responsible in related agencies, including the Ministry of Health and Medical Education, and Renal Disease charity, data registries, articles, books, journals, databases, websites, and related documents. Data were gathered through phone, e-mail, study, observation, and interview. The researchers collected data for each country based on the study objectives and then put them in comparative tables. Data were analyzed by descriptive, comparative, and theoretical methods. There is no NRDR in Iran to report the short- and long-term results of renal disease. Most of the renal transplant teams report their own results as single-center experiences. America and Britain have pre-eminent national registry of renal disease, compared to other countries. The Iranian Society of Nephrology should be actively involved to create a National Renal Registry in Iran. The registry should have representatives from the universities, government, armed forces, and private sectors. Researchers proposed to design the Iran National Renal Registry according to the UK Renal Disease Registry model because of its prominent healthcare system.

The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

PubMed Central

Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce

2005-01-01

Background Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. Results We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. Conclusion The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. PMID:15850481

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.

PubMed

Ravikumar, Komandur Elayavilli; Wagholikar, Kavishwar B; Li, Dingcheng; Kocher, Jean-Pierre; Liu, Hongfang

2015-06-06

Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remains 'locked' in the unstructured text of biomedical publications. There is a substantial lag between the publication and the subsequent abstraction of such information into databases. Multiple text mining systems have been developed, but most of them focus on the sentence level association extraction with performance evaluation based on gold standard text annotations specifically prepared for text mining systems. We developed and evaluated a text mining system, MutD, which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database records. MutD achieves an F-measure of 64.3% for reconstructing protein mutation disease associations in curated database records. Discourse level analysis component of MutD contributed to a gain of more than 10% in F-measure when compared against the sentence level association extraction. Our error analysis indicates that 23 of the 64 precision errors are true associations that were not captured by database curators and 68 of the 113 recall errors are caused by the absence of associated disease entities in the abstract. After adjusting for the defects in the curated database, the revised F-measure of MutD in association detection reaches 81.5%. Our quantitative analysis reveals that MutD can effectively extract protein mutation disease associations when benchmarking based on curated database records. The analysis also demonstrates that incorporating discourse level analysis significantly improved the performance of extracting the protein-mutation-disease association. Future work includes the extension of MutD for full text articles.

Exploring Genetic, Genomic, and Phenotypic Data at the Rat Genome Database

PubMed Central

Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Lowry, Timothy F.; Nigam, Rajni; Petri, Victoria; Smith, Jennifer R.; Dwinell, Melinda R.; Jacob, Howard J.; Shimoyama, Mary

2013-01-01

The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat. PMID:23255149

Health coaching to improve healthy lifestyle behaviors: an integrative review.

PubMed

Olsen, Jeanette M; Nesbitt, Bonnie J

2010-01-01

Chronic diseases account for 70% of U.S. deaths. Health coaching may help patients adopt healthy lifestyle behaviors that prevent and control diseases. This integrative review analyzed health coaching studies for evidence of effectiveness and to identify key program features. Multiple electronic databases were utilized, yielding a final sample of 15 documents. The search was limited to peer-reviewed research articles published between 1999 and 2008. Studies were further analyzed if they (1) specifically cited coaching as a program intervention, and (2) applied the intervention to research. Articles describing various quantitative and qualitative methodologies were critically analyzed using a systematic method. Data were synthesized using a matrix format according to purpose, method, intervention, findings, critique, and quality rating. All 15 studies utilized nonprobability sampling, 7 (47%) with randomized intervention and control groups. Significant improvements in one or more of the behaviors of nutrition, physical activity, weight management, or medication adherence were identified in six (40%) of the studies. Common features of effective programs were goal setting (73%), motivational interviewing (27%), and collaboration with health care providers (20%). Health coaching studies with well-specified methodologies and more rigorous designs are needed to strengthen findings; however, this behavioral change intervention suggests promise.

Measuring disease prevalence: a comparison of musculoskeletal disease using four general practice consultation databases

PubMed Central

Jordan, Kelvin; Clarke, Alexandra M; Symmons, Deborah PM; Fleming, Douglas; Porcheret, Mark; Kadam, Umesh T; Croft, Peter

2007-01-01

Background Primary care consultation data are an important source of information on morbidity prevalence. It is not known how reliable such figures are. Aim To compare annual consultation prevalence estimates for musculoskeletal conditions derived from four general practice consultation databases. Design of study Retrospective study of general practice consultation records. Setting Three national general practice consultation databases: i) Fourth Morbidity Statistics from General Practice (MSGP4, 1991/92), ii) Royal College of General Practitioners Weekly Returns Service (RCGP WRS, 2001), and iii) General Practice Research Database (GPRD, 1991 and 2001); and one regional database (Consultations in Primary Care Archive, 2001). Method Age-sex standardised persons consulting annual prevalence rates for musculoskeletal conditions overall, rheumatoid arthritis, osteoarthritis and arthralgia were derived for patients aged 15 years and over. Results GPRD prevalence of any musculoskeletal condition, rheumatoid arthritis and osteoarthritis was lower than that of the other databases. This is likely to be due to GPs not needing to record every consultation made for a chronic condition. MSGP4 gave the highest prevalence for osteoarthritis but low prevalence of arthralgia which reflects encouragement for GPs to use diagnostic rather than symptom codes. Conclusion Considerable variation exists in consultation prevalence estimates for musculoskeletal conditions. Researchers and health service planners should be aware that estimates of disease occurrence based on consultation will be influenced by choice of database. This is likely to be true for other chronic diseases and where alternative symptom labels exist for a disease. RCGP WRS may give the most reliable prevalence figures for musculoskeletal and other chronic diseases. PMID:17244418

Osteoporosis and bone fractures in alcoholic liver disease: a meta-analysis.

PubMed

Bang, Chang Seok; Shin, In Soo; Lee, Sung Wha; Kim, Jin Bong; Baik, Gwang Ho; Suk, Ki Tae; Yoon, Jai Hoon; Kim, Yeon Soo; Kim, Dong Joon

2015-04-07

To evaluate the association between alcoholic liver disease (ALD) and bone fractures or osteoporosis. Non-randomized studies were identified from databases (PubMed, EMBASE, and the Cochrane Library). The search was conducted using Boolean operators and keywords, which included "alcoholic liver diseases", "osteoporosis", or "bone fractures". The prevalence of any fractures or osteoporosis, and bone mineral density (BMD) were extracted and analyzed using risk ratios and standardized mean difference (SMD). A random effects model was applied. In total, 15 studies were identified and analyzed. Overall, ALD demonstrated a RR of 1.944 (95%CI: 1.354-2.791) for the development of bone fractures. However, ALD showed a RR of 0.849 (95%CI: 0.523-1.380) for the development of osteoporosis. BMD was not significantly different between the ALD and control groups, although there was a trend toward lower BMD in patients with ALD (SMD in femur-BMD: -0.172, 95%CI: -0.453-0.110; SMD in spine-BMD: -0.169, 95%CI: -0.476-0.138). Sensitivity analyses showed consistent results. Current publications indicate significant associations between bone fractures and ALD, independent of BMD or the presence of osteoporosis.

Human Variome Project Quality Assessment Criteria for Variation Databases.

PubMed

Vihinen, Mauno; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard C P; Taschner, Peter

2016-06-01

Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. © 2016 WILEY PERIODICALS, INC.

The usefulness of administrative databases for identifying disease cohorts is increased with a multivariate model.

PubMed

van Walraven, Carl; Austin, Peter C; Manuel, Douglas; Knoll, Greg; Jennings, Allison; Forster, Alan J

2010-12-01

Administrative databases commonly use codes to indicate diagnoses. These codes alone are often inadequate to accurately identify patients with particular conditions. In this study, we determined whether we could quantify the probability that a person has a particular disease-in this case renal failure-using other routinely collected information available in an administrative data set. This would allow the accurate identification of a disease cohort in an administrative database. We determined whether patients in a randomly selected 100,000 hospitalizations had kidney disease (defined as two or more sequential serum creatinines or the single admission creatinine indicating a calculated glomerular filtration rate less than 60 mL/min/1.73 m²). The independent association of patient- and hospitalization-level variables with renal failure was measured using a multivariate logistic regression model in a random 50% sample of the patients. The model was validated in the remaining patients. Twenty thousand seven hundred thirteen patients had kidney disease (20.7%). A diagnostic code of kidney disease was strongly associated with kidney disease (relative risk: 34.4), but the accuracy of the code was poor (sensitivity: 37.9%; specificity: 98.9%). Twenty-nine patient- and hospitalization-level variables entered the kidney disease model. This model had excellent discrimination (c-statistic: 90.1%) and accurately predicted the probability of true renal failure. The probability threshold that maximized sensitivity and specificity for the identification of true kidney disease was 21.3% (sensitivity: 80.0%; specificity: 82.2%). Multiple variables available in administrative databases can be combined to quantify the probability that a person has a particular disease. This process permits accurate identification of a disease cohort in an administrative database. These methods may be extended to other diagnoses or procedures and could both facilitate and clarify the use of administrative databases for research and quality improvement. Copyright © 2010 Elsevier Inc. All rights reserved.

Applying data mining techniques to determine important parameters in chronic kidney disease and the relations of these parameters to each other.

PubMed

Tahmasebian, Shahram; Ghazisaeedi, Marjan; Langarizadeh, Mostafa; Mokhtaran, Mehrshad; Mahdavi-Mazdeh, Mitra; Javadian, Parisa

2017-01-01

Introduction: Chronic kidney disease (CKD) includes a wide range of pathophysiological processes which will be observed along with abnormal function of kidneys and progressive decrease in glomerular filtration rate (GFR). According to the definition decreasing GFR must have been present for at least three months. CKD will eventually result in end-stage kidney disease. In this process different factors play role and finding the relations between effective parameters in this regard can help to prevent or slow progression of this disease. There are always a lot of data being collected from the patients' medical records. This huge array of data can be considered a valuable source for analyzing, exploring and discovering information. Objectives: Using the data mining techniques, the present study tries to specify the effective parameters and also aims to determine their relations with each other in Iranian patients with CKD. Material and Methods: The study population includes 31996 patients with CKD. First, all of the data is registered in the database. Then data mining tools were used to find the hidden rules and relationships between parameters in collected data. Results: After data cleaning based on CRISP-DM (Cross Industry Standard Process for Data Mining) methodology and running mining algorithms on the data in the database the relationships between the effective parameters was specified. Conclusion: This study was done using the data mining method pertaining to the effective factors on patients with CKD.

Predictors of resource utilization in transsphenoidal surgery for Cushing disease.

PubMed

Little, Andrew S; Chapple, Kristina

2013-08-01

The short-term cost associated with subspecialized surgical care is an increasingly important metric and economic concern. This study sought to determine factors associated with hospital charges in patients undergoing transsphenoidal surgery for Cushing disease in an effort to identify the drivers of resource utilization. The authors analyzed the Nationwide Inpatient Sample (NIS) hospital discharge database from 2007 to 2009 to determine factors that influenced hospital charges in patients who had undergone transsphenoidal surgery for Cushing disease. The NIS discharge database approximates a 20% sample of all inpatient admissions to nonfederal US hospitals. A multistep regression model was developed that adjusted for patient demographics, acuity measures, comorbidities, hospital characteristics, and complications. In 116 hospitals, 454 transsphenoidal operations were performed. The mean hospital charge was $48,272 ± $32,060. A multivariate regression model suggested that the primary driver of resource utilization was length of stay (LOS), followed by surgeon volume, hospital characteristics, and postoperative complications. A 1% increase in LOS increased hospital charges by 0.60%. Patient charges were 13% lower when performed by high-volume surgeons compared with low-volume surgeons and 22% lower in large hospitals compared with small hospitals. Hospital charges were 12% lower in cases with no postoperative neurological complications. The proposed model accounted for 46% of hospital charge variance. This analysis of hospital charges in transsphenoidal surgery for Cushing disease suggested that LOS, hospital characteristics, surgeon volume, and postoperative complications are important predictors of resource utilization. These findings may suggest opportunities for improvement.

Applying data mining techniques to determine important parameters in chronic kidney disease and the relations of these parameters to each other

PubMed Central

Tahmasebian, Shahram; Ghazisaeedi, Marjan; Langarizadeh, Mostafa; Mokhtaran, Mehrshad; Mahdavi-Mazdeh, Mitra; Javadian, Parisa

2017-01-01

Introduction: Chronic kidney disease (CKD) includes a wide range of pathophysiological processes which will be observed along with abnormal function of kidneys and progressive decrease in glomerular filtration rate (GFR). According to the definition decreasing GFR must have been present for at least three months. CKD will eventually result in end-stage kidney disease. In this process different factors play role and finding the relations between effective parameters in this regard can help to prevent or slow progression of this disease. There are always a lot of data being collected from the patients’ medical records. This huge array of data can be considered a valuable source for analyzing, exploring and discovering information. Objectives: Using the data mining techniques, the present study tries to specify the effective parameters and also aims to determine their relations with each other in Iranian patients with CKD. Material and Methods: The study population includes 31996 patients with CKD. First, all of the data is registered in the database. Then data mining tools were used to find the hidden rules and relationships between parameters in collected data. Results: After data cleaning based on CRISP-DM (Cross Industry Standard Process for Data Mining) methodology and running mining algorithms on the data in the database the relationships between the effective parameters was specified. Conclusion: This study was done using the data mining method pertaining to the effective factors on patients with CKD. PMID:28497080

Clinical Research on Traditional Chinese Medicine compounds and their preparations for Amyotrophic Lateral Sclerosis.

PubMed

Zhu, Jiayi; Shen, Lan; Lin, Xiao; Hong, Yanlong; Feng, Yi

2017-12-01

Amyotrophic lateral sclerosis (ALS) is a chronic, fatal neurodegenerative disease which leads to progressive muscle atrophy and paralysis. In order to summarize the characteristics of Traditional Chinese Medicine compounds and their preparations in the prevention and treatment of ALS through analyzing the mechanism, action site, and symptoms according to effective clinical research. We searched ALS, motor neuron disease, chemical drugs, herbal medicine, Chinese medicine, Traditional Chinese Medicine (TCM), and various combinations of these terms in databases including the PudMed, Springer, Ovid, Google, China National Knowledge Infrastructure, and Wanfang databases. It was found that the chemical drugs almost had not sufficient evidence to show their effectiveness in the treatment of ALS, except RILUZOLE. According to the characteristics of clinical symptoms of ALS, Chinese medicine practitioners believe that this disease belongs to the category of "atrophic disease". In clinical research, many Chinese herbal formulas had good clinical efficacies in the treatment of ALS with multiple targets, multiple links, and few side effects. And four kinds of dialectical treatment had been developed based on Clinical data analysis and the use of dialectical therapy: Benefiting the kidney; Declaring the lungs; Enhancing the Qi; and Dredging the meridian. In this review, we provide an overview of chemical drugs and Traditional Chinese Medicine compound and its preparations in therapy of ALS as well as how they may contribute to the ALS pathogenesis, thereby offering some clues for further studies. Copyright © 2017. Published by Elsevier Masson SAS.

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases

PubMed Central

Xu, Yanjun; Yang, Haixiu; Wu, Tan; Dong, Qun; Sun, Zeguo; Shang, Desi; Li, Feng; Xu, Yingqi; Su, Fei; Liu, Siyao

2017-01-01

Abstract BioM2MetDisease is a manually curated database that aims to provide a comprehensive and experimentally supported resource of associations between metabolic diseases and various biomolecules. Recently, metabolic diseases such as diabetes have become one of the leading threats to people’s health. Metabolic disease associated with alterations of multiple types of biomolecules such as miRNAs and metabolites. An integrated and high-quality data source that collection of metabolic disease associated biomolecules is essential for exploring the underlying molecular mechanisms and discovering novel therapeutics. Here, we developed the BioM2MetDisease database, which currently documents 2681 entries of relationships between 1147 biomolecules (miRNAs, metabolites and small molecules/drugs) and 78 metabolic diseases across 14 species. Each entry includes biomolecule category, species, biomolecule name, disease name, dysregulation pattern, experimental technique, a brief description of metabolic disease-biomolecule relationships, the reference, additional annotation information etc. BioM2MetDisease provides a user-friendly interface to explore and retrieve all data conveniently. A submission page was also offered for researchers to submit new associations between biomolecules and metabolic diseases. BioM2MetDisease provides a comprehensive resource for studying biology molecules act in metabolic diseases, and it is helpful for understanding the molecular mechanisms and developing novel therapeutics for metabolic diseases. Database URL: http://www.bio-bigdata.com/BioM2MetDisease/ PMID:28605773

Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.

PubMed

Hakenberg, Jörg; Cheng, Wei-Yi; Thomas, Philippe; Wang, Ying-Chih; Uzilov, Andrew V; Chen, Rong

2016-01-08

Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort helps gain insights into polymorphic and disease-associated variants, a joint perspective can be more powerful in identifying polymorphisms, rare variants, disease-associations, genetic burden, somatic variants, and disease mechanisms. We have set up a Reference Variant Store (RVS) containing variants observed in a number of large-scale sequencing efforts, such as 1000 Genomes, ExAC, Scripps Wellderly, UK10K; various genotyping studies; and disease association databases. RVS holds extensive annotations pertaining to affected genes, functional impacts, disease associations, and population frequencies. RVS currently stores 400 million distinct variants observed in more than 80,000 human samples. RVS facilitates cross-study analysis to discover novel genetic risk factors, gene-disease associations, potential disease mechanisms, and actionable variants. Due to its large reference populations, RVS can also be employed for variant filtration and gene prioritization. A web interface to public datasets and annotations in RVS is available at https://rvs.u.hpc.mssm.edu/.

SpliceDisease database: linking RNA splicing and disease.

PubMed

Wang, Juan; Zhang, Jie; Li, Kaibo; Zhao, Wei; Cui, Qinghua

2012-01-01

RNA splicing is an important aspect of gene regulation in many organisms. Splicing of RNA is regulated by complicated mechanisms involving numerous RNA-binding proteins and the intricate network of interactions among them. Mutations in cis-acting splicing elements or its regulatory proteins have been shown to be involved in human diseases. Defects in pre-mRNA splicing process have emerged as a common disease-causing mechanism. Therefore, a database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, we manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference Pubmed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. We standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, we give direct links of the entry to the respective position/region in the genome browser. The users can freely browse, search and download the data in SpliceDisease at http://cmbi.bjmu.edu.cn/sdisease.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

Pregnancy Outcomes from the Branded Glatiramer Acetate Pregnancy Database.

PubMed

Sandberg-Wollheim, Magnhild; Neudorfer, Orit; Grinspan, Augusto; Weinstock-Guttman, Bianca; Haas, Judith; Izquierdo, Guillermo; Riley, Claire; Ross, Amy Perrin; Baruch, Peleg; Drillman, Talya; Coyle, Patricia K

2018-01-01

Appropriate counseling and treatment for women with multiple sclerosis (MS) who may become pregnant requires an understanding of the effects of exposure to disease-modifying therapies (DMTs) during pregnancy. Current reports and studies are limited in their usefulness, mostly by small sample size. Branded glatiramer acetate (GA) is a DMT approved for the treatment of relapsing forms of MS. For more than 2 decades, it has been shown to be efficacious and to have a favorable safety profile. The Teva Pharmaceutical Industries Ltd global pharmacovigilance database comprises data from more than 7000 pregnancies, during which women with MS were exposed to treatment with branded GA. We analyzed data from Teva's global pharmacovigilance database. Pregnancy outcomes for patients treated with branded GA were compared with reference rates of abnormal pregnancy outcomes reported in two large registries representing the general population. Pregnancies exposed to branded GA were not at higher risk for congenital anomalies than what is expected in the general population. These data provide evidence that branded GA exposure during pregnancy seems safe, without teratogenic effect.

Pregnancy Outcomes from the Branded Glatiramer Acetate Pregnancy Database

PubMed Central

Sandberg-Wollheim, Magnhild; Grinspan, Augusto; Weinstock-Guttman, Bianca; Haas, Judith; Izquierdo, Guillermo; Riley, Claire; Ross, Amy Perrin; Baruch, Peleg; Drillman, Talya; Coyle, Patricia K.

2018-01-01

Abstract Background: Appropriate counseling and treatment for women with multiple sclerosis (MS) who may become pregnant requires an understanding of the effects of exposure to disease-modifying therapies (DMTs) during pregnancy. Current reports and studies are limited in their usefulness, mostly by small sample size. Branded glatiramer acetate (GA) is a DMT approved for the treatment of relapsing forms of MS. For more than 2 decades, it has been shown to be efficacious and to have a favorable safety profile. The Teva Pharmaceutical Industries Ltd global pharmacovigilance database comprises data from more than 7000 pregnancies, during which women with MS were exposed to treatment with branded GA. Methods: We analyzed data from Teva's global pharmacovigilance database. Pregnancy outcomes for patients treated with branded GA were compared with reference rates of abnormal pregnancy outcomes reported in two large registries representing the general population. Results: Pregnancies exposed to branded GA were not at higher risk for congenital anomalies than what is expected in the general population. Conclusions: These data provide evidence that branded GA exposure during pregnancy seems safe, without teratogenic effect. PMID:29507538

A Method for Analyzing Commonalities in Clinical Trial Target Populations

PubMed Central

He, Zhe; Carini, Simona; Hao, Tianyong; Sim, Ida; Weng, Chunhua

2014-01-01

ClinicalTrials.gov presents great opportunities for analyzing commonalities in clinical trial target populations to facilitate knowledge reuse when designing eligibility criteria of future trials or to reveal potential systematic biases in selecting population subgroups for clinical research. Towards this goal, this paper presents a novel data resource for enabling such analyses. Our method includes two parts: (1) parsing and indexing eligibility criteria text; and (2) mining common eligibility features and attributes of common numeric features (e.g., A1c). We designed and built a database called “Commonalities in Target Populations of Clinical Trials” (COMPACT), which stores structured eligibility criteria and trial metadata in a readily computable format. We illustrate its use in an example analytic module called CONECT using COMPACT as the backend. Type 2 diabetes is used as an example to analyze commonalities in the target populations of 4,493 clinical trials on this disease. PMID:25954450

ELISA-BASE: An Integrated Bioinformatics Tool for Analyzing and Tracking ELISA Microarray Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Amanda M.; Collett, James L.; Seurynck-Servoss, Shannon L.

ELISA-BASE is an open-source database for capturing, organizing and analyzing protein enzyme-linked immunosorbent assay (ELISA) microarray data. ELISA-BASE is an extension of the BioArray Soft-ware Environment (BASE) database system, which was developed for DNA microarrays. In order to make BASE suitable for protein microarray experiments, we developed several plugins for importing and analyzing quantitative ELISA microarray data. Most notably, our Protein Microarray Analysis Tool (ProMAT) for processing quantita-tive ELISA data is now available as a plugin to the database.

The complex genetics of human insulin-like growth factor 2 are not reflected in public databases.

PubMed

Rotwein, Peter

2018-03-23

Recent advances in genetics present unique opportunities for enhancing knowledge about human physiology and disease susceptibility. Understanding this information at the individual gene level is challenging and requires extracting, collating, and interpreting data from a variety of public gene repositories. Here, I illustrate this challenge by analyzing the gene for human insulin-like growth factor 2 ( IGF2 ) through the lens of several databases. IGF2, a 67-amino acid secreted peptide, is essential for normal prenatal growth and is involved in other physiological and pathophysiological processes in humans. Surprisingly, none of the genetic databases accurately described or completely delineated human IGF2 gene structure or transcript expression, even though all relevant information could be found in the published literature. Although IGF2 shares multiple features with the mouse Igf2 gene, it has several unique properties, including transcription from five promoters. Both genes undergo parental imprinting, with IGF2 / Igf2 being expressed primarily from the paternal chromosome and the adjacent H19 gene from the maternal chromosome. Unlike mouse Igf2 , whose expression declines after birth, human IGF2 remains active throughout life. This characteristic has been attributed to a unique human gene promoter that escapes imprinting, but as shown here, it involves several different promoters with distinct tissue-specific expression patterns. Because new testable hypotheses could lead to critical insights into IGF2 actions in human physiology and disease, it is incumbent that our fundamental understanding is accurate. Similar challenges affecting knowledge of other human genes should promote attempts to critically evaluate, interpret, and correct human genetic data in publicly available databases. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

[Phenotypic and genotypic spectra of patients with glucose-6-phosphate dehydrogenase deficiency gene known pathogenic variants: a single-center study].

PubMed

Chen, X; Yang, L; Wang, H J; Wu, B B; Lu, Y L; Dong, X R; Zhou, W H

2018-05-02

Objective: To analyze the hotspots of known pathogenic disease-causing variants of glucose-6-phosphate dehydrogenase (G6PD) and the phenotype spectrum of neonatal patients with known pathogenic disease-causing variants of G6PD. Methods: The known pathogenic disease-causing variants of G6PD were collected from Human Gene Mutation Database. Screening was performed for these variants among the 7 966 cases (2 357 neonatal, 5 609 non-neonatal) in the database of sequencing at Molecular Diagnosis Center, Children's Hospital of Fudan University. All these samples were from patients suspected with genetic disorder. The database contained Whole Exon Sequencing data and Clinical Exon Sequencing data. We screened out the patients with known pathogenic disease-causing variants of G6PD, analyzed the hotspot of G6PD and the phenotype spectrum of neonatal patients with known pathogenic disease-causing variants of G6PD. Results: (1) Among the next generation sequencing data of the 7 966 samples, 86 samples (1.1%) were detected as positive for the known pathogenic disease-causing variants of G6PD (positive samples set). In the positive sample set, 51 patients (33 males, 18 females) were newborn babies. Forty-three patients (26 males, 17 females) had the enzyme activity data of G6PD. (2) Among the 86 samples, Arg463His, Arg459Leu, Leu342Phe, Val291Met were the leading 4 disease-causing variants found in 72 samples (84%). (3) Male neonatal patients with the same variants had the statistically significant differences in enzyme activity: among 13 patients with Arg463His, enzyme activity of 9 patients was ranked as grade Ⅲ, 1 case ranked as Ⅳ, 3 cases had no activity data;among 10 patients with Arg459Leu, enzyme activity of 4 patients was ranked as Ⅱ, 4 cases ranked as Ⅲ, 2 cases had no activity data;among 2 patients with His32Arg, enzyme activity of one patient was ranked as Ⅱ, another was Ⅲ. Male neonatal patients with the same mutation and enzyme activity also had the statistically significant differences in phenotype spectrum: among 9 patients with Arg463His and level Ⅲ enzyme activity, 6 presented hyperbilirubinemia, 2 met the criteria for exchange transfusion therapy, 2 showed hemolysis;among 4 patients with Arg459Leu and level Ⅱ enzyme activity, 3 presented hyperbilirubinemia;among 4 patients with Arg459Leu and level Ⅲ enzyme activity, 2 presented hyperbilirubinemia, 1 met the standard of exchange transfusion therapy;among 3 patients with Val291Met and level Ⅲ enzyme activity, 1 presented hyperbilirubinemia. Conclusions: Arg463His, Arg459Leu, Leu342Phe, Val291Met were the hotspots variants for the G6PD. Patients with the same G6PD variants and sex present different phenotype, patients with the same G6PD variants, sex and enzyme activity also present different phenotype .

Utility of combinations of biomarkers, cognitive markers, and risk factors to predict conversion from mild cognitive impairment to Alzheimer disease in patients in the Alzheimer's disease neuroimaging initiative.

PubMed

Gomar, Jesus J; Bobes-Bascaran, Maria T; Conejero-Goldberg, Concepcion; Davies, Peter; Goldberg, Terry E

2011-09-01

Biomarkers have become increasingly important in understanding neurodegenerative processes associated with Alzheimer disease. Markers include regional brain volumes, cerebrospinal fluid measures of pathological Aβ1-42 and total tau, cognitive measures, and individual risk factors. To determine the discriminative utility of different classes of biomarkers and cognitive markers by examining their ability to predict a change in diagnostic status from mild cognitive impairment to Alzheimer disease. Longitudinal study. We analyzed the Alzheimer's Disease Neuroimaging Initiative database to study patients with mild cognitive impairment who converted to Alzheimer disease (n = 116) and those who did not convert (n = 204) within a 2-year period. We determined the predictive utility of 25 variables from all classes of markers, biomarkers, and risk factors in a series of logistic regression models and effect size analyses. The Alzheimer's Disease Neuroimaging Initiative public database. Primary outcome measures were odds ratios, pseudo- R(2)s, and effect sizes. In comprehensive stepwise logistic regression models that thus included variables from all classes of markers, the following baseline variables predicted conversion within a 2-year period: 2 measures of delayed verbal memory and middle temporal lobe cortical thickness. In an effect size analysis that examined rates of decline, change scores for biomarkers were modest for 2 years, but a change in an everyday functional activities measure (Functional Assessment Questionnaire) was considerably larger. Decline in scores on the Functional Assessment Questionnaire and Trail Making Test, part B, accounted for approximately 50% of the predictive variance in conversion from mild cognitive impairment to Alzheimer disease. Cognitive markers at baseline were more robust predictors of conversion than most biomarkers. Longitudinal analyses suggested that conversion appeared to be driven less by changes in the neurobiologic trajectory of the disease than by a sharp decline in functional ability and, to a lesser extent, by declines in executive function.

[Utility of axial images in an early Alzheimer disease diagnosis support system (VSRAD)].

PubMed

Goto, Masami; Aoki, Shigeki; Abe, Osamu; Masumoto, Tomohiko; Watanabe, Yasushi; Satake, Yoshiroh; Nishida, Katsuji; Ino, Kenji; Yano, Keiichi; Iida, Kyohhito; Mima, Kazuo; Ohtomo, Kuni

2006-09-20

In recent years, voxel-based morphometry (VBM) has become a popular tool for the early diagnosis of Alzheimer disease. The Voxel-Based Specific Regional Analysis System for Alzheimer's Disease (VSRAD), a VBM system that uses MRI, has been reported to be clinically useful. The able-bodied person database (DB) of VSRAD, which employs sagittal plane imaging, is not suitable for analysis by axial plane imaging. However, axial plane imaging is useful for avoiding motion artifacts from the eyeball. Therefore, we created an able-bodied person DB by axial plane imaging and examined its utility. We also analyzed groups of able-bodied persons and persons with dementia by axial plane imaging and reviewed the validity. After using the DB of axial plane imaging, the Z-score of the intrahippocampal region improved by 8 in 13 instances. In all brains, the Z-score improved by 13 in all instances.

Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews.

PubMed

Fan, Jung-Wei; Lussier, Yves A

2017-01-01

Dietary supplements remain a relatively underexplored source for drug repurposing. A systematic approach to soliciting responses from a large consumer population is desirable to speed up innovation. We tested a workflow that mines unexpected benefits of dietary supplements from massive consumer reviews. A (non-exhaustive) list of regular expressions was used to screen over 2 million reviews on health and personal care products. The matched reviews were manually analyzed, and one supplement-disease pair was linked to biological databases for enriching the hypothesized association. The regular expressions found 169 candidate reviews, of which 45.6% described unexpected benefits of certain dietary supplements. The manual analysis showed some of the supplement-disease associations to be novel or in agreement with evidence published later in the literature. The hypothesis enrichment was able to identify meaningful function similarity between the supplement and the disease. The results demonstrated value of the workflow in identifying candidates for supplement repurposing.

Genetic discovery in Xylella fastidiosa through sequence analysis of selected randomly amplified polymorphic DNAs.

PubMed

Chen, Jianchi; Civerolo, Edwin L; Jarret, Robert L; Van Sluys, Marie-Anne; de Oliveira, Mariana C

2005-02-01

Xylella fastidiosa causes many important plant diseases including Pierce's disease (PD) in grape and almond leaf scorch disease (ALSD). DNA-based methodologies, such as randomly amplified polymorphic DNA (RAPD) analysis, have been playing key roles in genetic information collection of the bacterium. This study further analyzed the nucleotide sequences of selected RAPDs from X. fastidiosa strains in conjunction with the available genome sequence databases and unveiled several previously unknown novel genetic traits. These include a sequence highly similar to those in the phage family of Podoviridae. Genome comparisons among X. fastidiosa strains suggested that the "phage" is currently active. Two other RAPDs were also related to horizontal gene transfer: one was part of a broadly distributed cryptic plasmid and the other was associated with conjugal transfer. One RAPD inferred a genomic rearrangement event among X. fastidiosa PD strains and another identified a single nucleotide polymorphism of evolutionary value.

Listeria, Then and Now: A Call to Reevaluate Patient Teaching Based on Analysis of US Federal Databases, 1998-2016.

PubMed

Simon, Katya; Simon, Valentina; Rosenzweig, Rachel; Barroso, Rebeca; Gillmor-Kahn, Mickey

2018-05-01

Listeria monocytogenes is a foodborne pathogen capable of crossing the placental-fetal barrier; infection with the bacterium causes listeriosis. An exposed fetus may suffer blindness, neurological damage including meningitis, or even death. The adverse consequences of listeriosis place the infection on the federally reportable disease list. Primary prevention relies on women avoiding 6 categories of foods most likely to be contaminated with L monocytogenes, as indicated in guidelines developed by the Centers for Disease Control and Prevention (CDC), adapted by the American College of Obstetricians and Gynecologists (ACOG) in 2014, and reaffirmed without changes by ACOG in 2016. This report contains a critical evaluation of United States listeriosis prevention guidelines. Between 1998 and 2016, there were 876 identified listeriosis events documented in the illness and recall databases maintained by the CDC, Food and Drug Administration (FDA), and United States Department of Agriculture - Food Safety and Inspection Service (USDA-FSIS). Each contaminated food was manually compared to the existing listeriosis avoidance guidelines, placing each event within or outside the guidelines. Trends were analyzed over time. Database analysis demonstrates that prior to the year 2000, abiding by the current guidelines would have prevented all reported listeriosis cases. However, in 2015 and 2016, only 5% of confirmed L monocytogenes infections originated from the 6 food groups listed in the CDC and ACOG guidelines. Similar trends emerged for food processing plant recalls (USDA-FSIS database) and grocery store recalls (FDA database). The total number of listeriosis illnesses in the United States doubled from 2007 to 2014. A gradual shift in detection of L monocytogenes contamination in ready-to-eat meals, frozen foods, and ready-to-eat salads has occurred. Another emerging culprit is pasteurized dairy products. Revision of listeriosis avoidance guidelines by a consensus-seeking, multidisciplinary task force, is needed. © 2018 by the American College of Nurse-Midwives.

Charting a Path to Location Intelligence for STD Control.

PubMed

Gerber, Todd M; Du, Ping; Armstrong-Brown, Janelle; McNutt, Louise-Anne; Coles, F Bruce

2009-01-01

This article describes the New York State Department of Health's GeoDatabase project, which developed new methods and techniques for designing and building a geocoding and mapping data repository for sexually transmitted disease (STD) control. The GeoDatabase development was supported through the Centers for Disease Control and Prevention's Outcome Assessment through Systems of Integrated Surveillance workgroup. The design and operation of the GeoDatabase relied upon commercial-off-the-shelf tools that other public health programs may also use for disease-control systems. This article provides a blueprint of the structure and software used to build the GeoDatabase and integrate location data from multiple data sources into the everyday activities of STD control programs.

Risk of venous thrombosis in users of hormonal contraceptives in German gynaecological practices: a patient database analysis.

PubMed

Ziller, M; Ziller, V; Haas, G; Rex, J; Kostev, K

2014-02-01

Recent studies showed differences in the risk of venous thrombosis between different combined hormonal contraceptives. Database studies comprising large cohorts can add relevant aspects from daily clinical practice. The purpose of this study was to evaluate different progestogen in combination with ethinylestradiol on the risk of venous thrombosis in Germany. Computerized data from 68,168 contraceptive users in gynecological practices throughout Germany (Disease Analyzer Database) were analyzed. The adjusted odds ratios for risk of thrombosis were estimated in users of different oral contraceptive (OC) formulations relative to users of levonorgestrel-containing preparations. In total, 38 (0.06 %) of the 68,168 contraceptive users had a recorded diagnosis of thrombosis within 365 days after the initial prescription. The adjusted risk was 1.95 for desogestrel (95 % CI 0.52-7.29), 2.97 for dienogest (95 % CI 0.96-9.24), 1.57 for drospirenone (95 % CI 0.46-5.38), 2.54 for chlormadinone (95 % CI 0.72-9.04), and 3.24 for norgestimate (95 % CI 0.59-17.75) compared to levonorgestrel. None of those findings reached statistical significance. The maximum absolute increase versus levonorgestrel was 6 cases per 10,000 women (n.s.). The study shows the low incidence rates of thrombosis in OC users. Since there is no significant difference, this study does not confirm an increased risk but shows only a tendency for this risk of third- and fourth-generation OC versus levonorgestrel-containing products.

In silico strategies for the selection of chelating compounds with potential application in metal-promoted neurodegenerative diseases

NASA Astrophysics Data System (ADS)

Rodríguez-Rodríguez, Cristina; Rimola, Albert; Alí-Torres, Jorge; Sodupe, Mariona; González-Duarte, Pilar

2011-01-01

The development of new strategies to find commercial molecules with promising biochemical features is a main target in the field of biomedicine chemistry. In this work we present an in silico-based protocol that allows identifying commercial compounds with suitable metal coordinating and pharmacokinetic properties to act as metal-ion chelators in metal-promoted neurodegenerative diseases (MpND). Selection of the chelating ligands is done by combining quantum chemical calculations with the search of commercial compounds on different databases via virtual screening. Starting from different designed molecular frameworks, which mainly constitute the binding site, the virtual screening on databases facilitates the identification of different commercial molecules that enclose such scaffolds and, by imposing a set of chemical and pharmacokinetic filters, obey some drug-like requirements mandatory to deal with MpND. The quantum mechanical calculations are useful to gauge the chelating properties of the selected candidate molecules by determining the structure of metal complexes and evaluating their stability constants. With the proposed strategy, commercial compounds containing N and S donor atoms in the binding sites and capable to cross the BBB have been identified and their chelating properties analyzed.

Oral lichen planus in childhood: a case series.

PubMed

Cascone, Marco; Celentano, Antonio; Adamo, Daniela; Leuci, Stefania; Ruoppo, Elvira; Mignogna, Michele D

2017-06-01

Although the exact incidence of pediatric oral lichen planus (OLP) is unknown, the oral mucosa seems to be less commonly involved, and the clinical presentation is often atypical. The aim of the study is to present a case series of OLP in childhood. From our database, we retrospectively selected and analyzed the clinical data of OLP patients under the age of 18 where the diagnosis had been confirmed by histopathological analysis. The case series from our database shows eight patients, four males and four females. The mean (±SD) age at the time of diagnosis of the disease was 13.5 (±2.73) years, ranging in age from 9 to 17. Clinically, a reticular pattern was present in six patients (75%), and the tongue was the most commonly involved oral site (six cases, 75%). We also report the first case of OLP in a 9-year-old girl affected by autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. We report the largest case series of pediatric OLP published in literature thus far. Differences in the disease between adults and pediatric patients have been detected, but further investigation and a larger case series are needed to establish any detailed differences in clinical outcomes. © 2017 The International Society of Dermatology.

Idiopathic sudden sensorineural hearing loss and acute low-tone sensorineural hearing loss: a comparison of the results of a nationwide epidemiological survey in Japan.

PubMed

Yoshida, Tadao; Sone, Michihiko; Kitoh, Ryosuke; Nishio, Shin-Ya; Ogawa, Kaoru; Kanzaki, Sho; Hato, Naohito; Fukuda, Satoshi; Hara, Akira; Ikezono, Tetsuo; Ishikawa, Kotaro; Iwasaki, Satoshi; Kaga, Kimitaka; Kakehata, Seiji; Matsubara, Atsushi; Matsunaga, Tatsuo; Murata, Takaaki; Naito, Yasushi; Nakagawa, Takashi; Nishizaki, Kazunori; Noguchi, Yoshihiro; Sano, Hajime; Sato, Hiroaki; Suzuki, Mikio; Shojaku, Hideo; Takahashi, Haruo; Takeda, Hidehiko; Tono, Testuya; Yamashita, Hiroshi; Yamasoba, Tatsuya; Usami, Shin-Ichi

2017-01-01

The aim of this study was to investigate the differences between idiopathic sudden sensorineural hearing loss (SSNHL), and acute low-tone sensorineural hearing loss (ALHL) using the results of a nationwide survey database in Japan and to analyze the variables associated with their clinical features and the severity of hearing impairment, treatment, and prognosis. Participants were patients registered between April 2014 and March 2016 in a multicenter epidemiological survey database involving 30 university hospitals and medical centers across Japan. Statistical analysis was performed to clarify the factors associated with their clinical characteristics and the severity of hearing impairment, treatment, and prognosis. Idiopathic SSNHL and ALHL differed significantly in terms of male-to-female ratio, age distribution, and time from onset to start of treatment. The treatment methods and hearing prognosis also differed markedly between the two diseases. A majority (92%) of idiopathic SSNHL patients were administered some type of corticosteroid, while half of the ALHL patients received corticosteroids and a diuretic agent. The results suggested that idiopathic SSNHL and ALHL belonged to different categories of inner ear disease.

A double closed loop to enhance the quality of life of Parkinson's Disease patients: REMPARK system.

PubMed

Samà, Albert; Pérez-López, Carlos; Rodríguez-Martín, Daniel; Moreno-Aróstegui, J Manuel; Rovira, Jordi; Ahlrichs, Claas; Castro, Rui; Cevada, João; Graça, Ricardo; Guimarães, Vânia; Pina, Bernardo; Counihan, Timothy; Lewy, Hadas; Annicchiarico, Roberta; Bayés, Angels; Rodríguez-Molinero, Alejandro; Cabestany, Joan

2014-01-01

This paper presents REMPARK system, a novel approach to deal with Parkinson's Disease (PD). REMPARK system comprises two closed loops of actuation onto PD. The first loop consists in a wearable system that, based on a belt-worn movement sensor, detects movement alterations that activate an auditory cueing system controlled by a smartphone in order to improve patient's gait. The belt-worn sensor analyzes patient's movement through real-time learning algorithms that were developed on the basis of a database previously collected from 93 PD patients. The second loop consists in disease management based on the data collected during long periods and that enables neurologists to tailor medication of their PD patients and follow the disease evolution. REMPARK system is going to be tested in 40 PD patients in Spain, Ireland, Italy and Israel. This paper describes the approach followed to obtain this system, its components, functionalities and trials in which the system will be validated.

Is Human-induced Pluripotent Stem Cell the Best Optimal?

PubMed

Wang, Feng; Kong, Jie; Cui, Yi-Yao; Liu, Peng; Wen, Jian-Yan

2018-04-05

Since the advent of induced pluripotent stem cell (iPSC) technology a decade ago, enormous progress has been made in stem cell biology and regenerative medicine. Human iPSCs have been widely used for disease modeling, drug discovery, and cell therapy development. In this review, we discuss the progress in applications of iPSC technology that are particularly relevant to drug discovery and regenerative medicine, and consider the remaining challenges and the emerging opportunities in the field. Articles in this review were searched from PubMed database from January 2014 to December 2017. Original articles about iPSCs and cardiovascular diseases were included and analyzed. iPSC holds great promises for human disease modeling, drug discovery, and stem cell-based therapy, and this potential is only beginning to be realized. However, several important issues remain to be addressed. The recent availability of human cardiomyocytes derived from iPSCs opens new opportunities to build in vitro models of cardiac disease, screening for new drugs and patient-specific cardiac therapy.

The Cost of Psoriasis and Psoriatic Arthritis in 5 European Countries: A Systematic Review.

PubMed

Burgos-Pol, R; Martínez-Sesmero, J M; Ventura-Cerdá, J M; Elías, I; Caloto, M T; Casado, M Á

2016-09-01

While the introduction of biologics has improved the quality of life of patients with psoriasis and psoriatic arthritis, it may have increased the economic burden of these diseases. To perform a systematic review of studies on the costs associated with managing and treating psoriasis and psoriatic arthritis in 5 European countries: Germany, Spain, France, Italy, and the United Kingdom. We undertook a systematic review of the literature (up to May 2015) using the MEDLINE and EMBASE databases. The methodological quality of the studies identified was evaluated using the Consolidated Health Economic Evaluation Reporting Standards checklist. We considered both direct costs (medical and nonmedical) and indirect costs, adjusted for country-specific inflation and converted to international dollars using purchasing power parity exchange rates for 2015 ($US PPP). The search retrieved 775 studies; 68.3% analyzed psoriasis and 31.7% analyzed psoriatic arthritis. The total annual cost per patient ranged from US $2,077 to US $13,132 PPP for psoriasis and from US $10,924 to US $17,050 PPP for psoriatic arthritis. Direct costs were the largest component of total expenditure in both diseases. The severity of these diseases was associated with higher costs. The introduction of biologics led to a 3-fold to 5-fold increase in direct costs, and consequently to an increase in total costs. We have analyzed the economic burden of psoriasis and psoriatic arthritis and shown that costs increase with the treatment and management of more severe disease and the use of biologics. Copyright © 2016 AEDV. Publicado por Elsevier España, S.L.U. All rights reserved.

The MicroRNA Interaction Network of Lipid Diseases

PubMed Central

Kandhro, Abdul H.; Shoombuatong, Watshara; Nantasenamat, Chanin; Prachayasittikul, Virapong; Nuchnoi, Pornlada

2017-01-01

Background: Dyslipidemia is one of the major forms of lipid disorder, characterized by increased triglycerides (TGs), increased low-density lipoprotein-cholesterol (LDL-C), and decreased high-density lipoprotein-cholesterol (HDL-C) levels in blood. Recently, MicroRNAs (miRNAs) have been reported to involve in various biological processes; their potential usage being a biomarkers and in diagnosis of various diseases. Computational approaches including text mining have been used recently to analyze abstracts from the public databases to observe the relationships/associations between the biological molecules, miRNAs, and disease phenotypes. Materials and Methods: In the present study, significance of text mined extracted pair associations (miRNA-lipid disease) were estimated by one-sided Fisher's exact test. The top 20 significant miRNA-disease associations were visualized on Cytoscape. The CyTargetLinker plug-in tool on Cytoscape was used to extend the network and predicts new miRNA target genes. The Biological Networks Gene Ontology (BiNGO) plug-in tool on Cytoscape was used to retrieve gene ontology (GO) annotations for the targeted genes. Results: We retrieved 227 miRNA-lipid disease associations including 148 miRNAs. The top 20 significant miRNAs analysis on CyTargetLinker provides defined, predicted and validated gene targets, further targeted genes analyzed by BiNGO showed targeted genes were significantly associated with lipid, cholesterol, apolipoprotein, and fatty acids GO terms. Conclusion: We are the first to provide a reliable miRNA-lipid disease association network based on text mining. This could help future experimental studies that aim to validate predicted gene targets. PMID:29018475

A Review and Framework for Categorizing Current Research and Development in Health Related Geographical Information Systems (GIS) Studies.

PubMed

Lyseen, A K; Nøhr, C; Sørensen, E M; Gudes, O; Geraghty, E M; Shaw, N T; Bivona-Tellez, C

2014-08-15

The application of GIS in health science has increased over the last decade and new innovative application areas have emerged. This study reviews the literature and builds a framework to provide a conceptual overview of the domain, and to promote strategic planning for further research of GIS in health. The framework is based on literature from the library databases Scopus and Web of Science. The articles were identified based on keywords and initially selected for further study based on titles and abstracts. A grounded theory-inspired method was applied to categorize the selected articles in main focus areas. Subsequent frequency analysis was performed on the identified articles in areas of infectious and non-infectious diseases and continent of origin. A total of 865 articles were included. Four conceptual domains within GIS in health sciences comprise the framework: spatial analysis of disease, spatial analysis of health service planning, public health, health technologies and tools. Frequency analysis by disease status and location show that malaria and schistosomiasis are the most commonly analyzed infectious diseases where cancer and asthma are the most frequently analyzed non-infectious diseases. Across categories, articles from North America predominate, and in the category of spatial analysis of diseases an equal number of studies concern Asia. Spatial analysis of diseases and health service planning are well-established research areas. The development of future technologies and new application areas for GIS and data-gathering technologies such as GPS, smartphones, remote sensing etc. will be nudging the research in GIS and health.

A Review and Framework for Categorizing Current Research and Development in Health Related Geographical Information Systems (GIS) Studies

PubMed Central

Nøhr, C.; Sørensen, E. M.; Gudes, O.; Geraghty, E. M.; Shaw, N. T.; Bivona-Tellez, C.

2014-01-01

Summary Objectives The application of GIS in health science has increased over the last decade and new innovative application areas have emerged. This study reviews the literature and builds a framework to provide a conceptual overview of the domain, and to promote strategic planning for further research of GIS in health. Method The framework is based on literature from the library databases Scopus and Web of Science. The articles were identified based on keywords and initially selected for further study based on titles and abstracts. A grounded theory-inspired method was applied to categorize the selected articles in main focus areas. Subsequent frequency analysis was performed on the identified articles in areas of infectious and non-infectious diseases and continent of origin. Results A total of 865 articles were included. Four conceptual domains within GIS in health sciences comprise the framework: spatial analysis of disease, spatial analysis of health service planning, public health, health technologies and tools. Frequency analysis by disease status and location show that malaria and schistosomiasis are the most commonly analyzed infectious diseases where cancer and asthma are the most frequently analyzed non-infectious diseases. Across categories, articles from North America predominate, and in the category of spatial analysis of diseases an equal number of studies concern Asia. Conclusion Spatial analysis of diseases and health service planning are well-established research areas. The development of future technologies and new application areas for GIS and data-gathering technologies such as GPS, smartphones, remote sensing etc. will be nudging the research in GIS and health. PMID:25123730

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis.

PubMed

Van Doorslaer, Koenraad; Tan, Qina; Xirasagar, Sandhya; Bandaru, Sandya; Gopalan, Vivek; Mohamoud, Yasmin; Huyen, Yentram; McBride, Alison A

2013-01-01

The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information. From a design perspective, the PaVE adopts an Open Source software approach and stresses the integration and reuse of existing tools. Reference PV genome sequences have been extracted from publicly available databases and reannotated using a custom-created tool. To date, the PaVE contains 241 annotated PV genomes, 2245 genes and regions, 2004 protein sequences and 47 protein structures, which users can explore, analyze or download. The PaVE provides scientists with the data and tools needed to accelerate scientific progress for the study and treatment of diseases caused by PVs.

Study of Porphyromonas gingivalis in periodontal diseases: A systematic review and meta-analysis.

PubMed

Rafiei, Mohammad; Kiani, Faezeh; Sayehmiri, Fatemeh; Sayehmiri, Kourosh; Sheikhi, Abdolkarim; Zamanian Azodi, Mona

2017-01-01

Background : The mouth cavity hosts various types of anaerobic bacteria including Porphyromonas gingivalis , which causes periodontal inflammatory diseases. P. gingivalis is a gram-negative oral anaerobe and is considered as a main etiological factor in periodontal diseases. Several studies have reported a relationship between P. gingivalis in individuals with periodontal diseases and a critical role of this bacterium in the pathogenesis of periodontal diseases. The present study aimed at estimating this probability using a meta-analysis. Methods : We searched several databases including PubMed, Scopus, Google Scholar, and Web of Science to identify case-control studies addressing the relationship between P. gingivalis with periodontal diseases. A total of 49 reports published from different countries from 1993 to 2014 were included in this study. I² (heterogeneity index) statistics were calculated to examine heterogeneity. Data were analyzed using STATA Version 11. Results : After a detailed analysis of the selected articles, 49 case-control studies with 5924 individuals fulfilled the inclusion criteria for the meta-analysis. The healthy controls included 2600 healthy individuals with a Mean±SD age of 36.56±7.45 years. The periodontal diseases group included 3356 patients with a mean age of 43.62±8.35 years. There was a statistically significant difference between P. gingivalis in periodontal patients and healthy controls; 9.24 (95% CI: 5.78 to 14.77; P = 0.000). In the other word, there was a significant relationship between the presence of P. gingivalis and periodontal diseases. Conclusion : Analyzing the results of the present study, we found a strong association between the presence of P. gingivalis and periodontal diseases. This result suggests that another research is needed to further assess this subject.

A novel database of bio-effects from non-ionizing radiation.

PubMed

Leach, Victor; Weller, Steven; Redmayne, Mary

2018-06-06

A significant amount of electromagnetic field/electromagnetic radiation (EMF/EMR) research is available that examines biological and disease associated endpoints. The quantity, variety and changing parameters in the available research can be challenging when undertaking a literature review, meta-analysis, preparing a study design, building reference lists or comparing findings between relevant scientific papers. The Oceania Radiofrequency Scientific Advisory Association (ORSAA) has created a comprehensive, non-biased, multi-categorized, searchable database of papers on non-ionizing EMF/EMR to help address these challenges. It is regularly added to, freely accessible online and designed to allow data to be easily retrieved, sorted and analyzed. This paper demonstrates the content and search flexibility of the ORSAA database. Demonstration searches are presented by Effect/No Effect; frequency-band/s; in vitro; in vivo; biological effects; study type; and funding source. As of the 15th September 2017, the clear majority of 2653 papers captured in the database examine outcomes in the 300 MHz-3 GHz range. There are 3 times more biological "Effect" than "No Effect" papers; nearly a third of papers provide no funding statement; industry-funded studies more often than not find "No Effect", while institutional funding commonly reveal "Effects". Country of origin where the study is conducted/funded also appears to have a dramatic influence on the likely result outcome.

The LISS--a public database of common imaging signs of lung diseases for computer-aided detection and diagnosis research and medical education.

PubMed

Han, Guanghui; Liu, Xiabi; Han, Feifei; Santika, I Nyoman Tenaya; Zhao, Yanfeng; Zhao, Xinming; Zhou, Chunwu

2015-02-01

Lung computed tomography (CT) imaging signs play important roles in the diagnosis of lung diseases. In this paper, we review the significance of CT imaging signs in disease diagnosis and determine the inclusion criterion of CT scans and CT imaging signs of our database. We develop the software of abnormal regions annotation and design the storage scheme of CT images and annotation data. Then, we present a publicly available database of lung CT imaging signs, called LISS for short, which contains 271 CT scans and 677 abnormal regions in them. The 677 abnormal regions are divided into nine categories of common CT imaging signs of lung disease (CISLs). The ground truth of these CISLs regions and the corresponding categories are provided. Furthermore, to make the database publicly available, all private data in CT scans are eliminated or replaced with provisioned values. The main characteristic of our LISS database is that it is developed from a new perspective of CT imaging signs of lung diseases instead of commonly considered lung nodules. Thus, it is promising to apply to computer-aided detection and diagnosis research and medical education.

Hyaline membrane disease is underreported in a linked birth-infant death certificate database.

PubMed Central

Hamvas, A; Kwong, P; DeBaun, M; Schramm, W; Cole, F S

1998-01-01

OBJECTIVE: This study compared the Missouri State Department of Health linked birth-infant death certificate database and medical records with respect to recording hyaline membrane disease in very low-birth-weight infants. METHODS: We reviewed the records for all 976 infants weighing 500 to 1500 g who were born to St. Louis, Mo, residents in 1989, 1991, and 1992. RESULTS: Eighteen percent of the birth certificates and 54% of the medical records documented hyaline membrane disease, resulting in 34% sensitivity and 99% specificity. CONCLUSIONS: The Missouri State Department of Health birth-infant death certificate database underestimates the incidence of hyaline membrane disease, which suggest that national statistics for the disease are also underestimated. PMID:9736884

Data base management system for lymphatic filariasis--a neglected tropical disease.

PubMed

Upadhyayula, Suryanaryana Murty; Mutheneni, Srinivasa Rao; Kadiri, Madhusudhan Rao; Kumaraswamy, Sriram; Nelaturu, Sarat Chandra Babu

2012-01-01

Researchers working in the area of Public Health are being confronted with large volumes of data on various aspects of entomology and epidemiology. To obtain the relevant information out of these data requires particular database management system. In this paper, we have described about the usages of our developed database on lymphatic filariasis. This database application is developed using Model View Controller (MVC) architecture, with MySQL as database and a web based interface. We have collected and incorporated the data on filariasis in the database from Karimnagar, Chittoor, East and West Godavari districts of Andhra Pradesh, India. The importance of this database is to store the collected data, retrieve the information and produce various combinational reports on filarial aspects which in turn will help the public health officials to understand the burden of disease in a particular locality. This information is likely to have an imperative role on decision making for effective control of filarial disease and integrated vector management operations.

Omics databases on kidney disease: where they can be found and how to benefit from them.

PubMed

Papadopoulos, Theofilos; Krochmal, Magdalena; Cisek, Katryna; Fernandes, Marco; Husi, Holger; Stevens, Robert; Bascands, Jean-Loup; Schanstra, Joost P; Klein, Julie

2016-06-01

In the recent decades, the evolution of omics technologies has led to advances in all biological fields, creating a demand for effective storage, management and exchange of rapidly generated data and research discoveries. To address this need, the development of databases of experimental outputs has become a common part of scientific practice in order to serve as knowledge sources and data-sharing platforms, providing information about genes, transcripts, proteins or metabolites. In this review, we present omics databases available currently, with a special focus on their application in kidney research and possibly in clinical practice. Databases are divided into two categories: general databases with a broad information scope and kidney-specific databases distinctively concentrated on kidney pathologies. In research, databases can be used as a rich source of information about pathophysiological mechanisms and molecular targets. In the future, databases will support clinicians with their decisions, providing better and faster diagnoses and setting the direction towards more preventive, personalized medicine. We also provide a test case demonstrating the potential of biological databases in comparing multi-omics datasets and generating new hypotheses to answer a critical and common diagnostic problem in nephrology practice. In the future, employment of databases combined with data integration and data mining should provide powerful insights into unlocking the mysteries of kidney disease, leading to a potential impact on pharmacological intervention and therapeutic disease management.

National Databases for Neurosurgical Outcomes Research: Options, Strengths, and Limitations.

PubMed

Karhade, Aditya V; Larsen, Alexandra M G; Cote, David J; Dubois, Heloise M; Smith, Timothy R

2017-08-05

Quality improvement, value-based care delivery, and personalized patient care depend on robust clinical, financial, and demographic data streams of neurosurgical outcomes. The neurosurgical literature lacks a comprehensive review of large national databases. To assess the strengths and limitations of various resources for outcomes research in neurosurgery. A review of the literature was conducted to identify surgical outcomes studies using national data sets. The databases were assessed for the availability of patient demographics and clinical variables, longitudinal follow-up of patients, strengths, and limitations. The number of unique patients contained within each data set ranged from thousands (Quality Outcomes Database [QOD]) to hundreds of millions (MarketScan). Databases with both clinical and financial data included PearlDiver, Premier Healthcare Database, Vizient Clinical Data Base and Resource Manager, and the National Inpatient Sample. Outcomes collected by databases included patient-reported outcomes (QOD); 30-day morbidity, readmissions, and reoperations (National Surgical Quality Improvement Program); and disease incidence and disease-specific survival (Surveillance, Epidemiology, and End Results-Medicare). The strengths of large databases included large numbers of rare pathologies and multi-institutional nationally representative sampling; the limitations of these databases included variable data veracity, variable data completeness, and missing disease-specific variables. The improvement of existing large national databases and the establishment of new registries will be crucial to the future of neurosurgical outcomes research. Copyright © 2017 by the Congress of Neurological Surgeons

The Perioperative Use of Dexmedetomidine in Pediatric Patients with Congenital Heart Disease: An Analysis from the Congenital Cardiac Anesthesia Society-Society of Thoracic Surgeons Congenital Heart Disease Database.

PubMed

Schwartz, Lawrence I; Twite, Mark; Gulack, Brian; Hill, Kevin; Kim, Sunghee; Vener, David F

2016-09-01

Dexmedetomidine is a selective α-2 receptor agonist with a sedative and cardiopulmonary profile that makes it an attractive anesthetic for pediatric patients with congenital heart disease (CHD). Although several smaller, single-center studies suggest that dexmedetomidine use is gaining traction in the perioperative setting in children with CHD, there are limited multicenter data, with little understanding of the variation in use across age ranges, procedural complexity, and centers. The aim of this study was to use the Congenital Cardiac Anesthesia Society-Society of Thoracic Surgeons (CCAS-STS) registry to describe patient- and center-level variability in the use of dexmedetomidine in the perioperative setting in children with heart disease. To describe the use of dexmedetomidine in patients for CHD surgery, we analyzed all index cardiopulmonary bypass operations entered in the CCAS-STS database from 2010 to 2013. Patient and operative characteristics were compared between those who received intraoperative dexmedetomidine and those who did not. Selective outcomes associated with dexmedetomidine use were also described. Of the 12,142 operations studied, 3600 (29.6%) received perioperative dexmedetomidine (DEX) and 8542 did not receive the drug (NoDEX). Patient characteristics were different between the 2 groups with the DEX group generally exhibiting both lower patient and procedural risk factors. Patients who received dexmedetomidine were more likely to have a lower level of Society of Thoracic Surgeons mortality complexity than patient who did not receive it. Consistent with their overall lower risk profile, children in the DEX group also demonstrated improved outcomes compared with patients who did not receive dexmedetomidine. We described the growing use of dexmedetomidine in children anesthetized for surgical repair of CHD. Dexmedetomidine appears to be preferentially given to older and larger children who are undergoing less complex CHD surgery. We believe that the data provided in this study are the largest investigating the use of an anesthetic drug in CHD patients. It is also the first analysis of the anesthesia data in the CCAS-STS Congenital Heart Disease database.

HEDD: Human Enhancer Disease Database

PubMed Central

Wang, Zhen; Zhang, Quanwei; Zhang, Wen; Lin, Jhih-Rong; Cai, Ying; Mitra, Joydeep

2018-01-01

Abstract Enhancers, as specialized genomic cis-regulatory elements, activate transcription of their target genes and play an important role in pathogenesis of many human complex diseases. Despite recent systematic identification of them in the human genome, currently there is an urgent need for comprehensive annotation databases of human enhancers with a focus on their disease connections. In response, we built the Human Enhancer Disease Database (HEDD) to facilitate studies of enhancers and their potential roles in human complex diseases. HEDD currently provides comprehensive genomic information for ∼2.8 million human enhancers identified by ENCODE, FANTOM5 and RoadMap with disease association scores based on enhancer–gene and gene–disease connections. It also provides Web-based analytical tools to visualize enhancer networks and score enhancers given a set of selected genes in a specific gene network. HEDD is freely accessible at http://zdzlab.einstein.yu.edu/1/hedd.php. PMID:29077884

Infectious diseases and global warming: Tracking disease incidence rates globally

DOE Office of Scientific and Technical Information (OSTI.GOV)

Low, N.C.

1995-09-01

Given the increasing importance of impact of global warming on public health, there is no global database system to monitor infectious disease and disease in general, and to which global data of climate change and environmental factors, such as temperature, greenhouse gases, and human activities, e.g., coastal development, deforestation, can be calibrated, investigated and correlated. The author proposes the diseases incidence rates be adopted as the basic global measure of morbidity of infectious diseases. The importance of a correctly chosen measure of morbidity of disease is presented. The importance of choosing disease incidence rates as the measure of morbidity andmore » the mathematical foundation of which are discussed. The author further proposes the establishment of a global database system to track the incidence rates of infectious diseases. Only such a global system can be used to calibrate and correlate other globally tracked climatic, greenhouse gases and environmental data. The infrastructure and data sources for building such a global database is discussed.« less

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

PubMed

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

Systemic sclerosis: a world wide global analysis.

PubMed

Coral-Alvarado, Paola; Pardo, Aryce L; Castaño-Rodriguez, Natalia; Rojas-Villarraga, Adriana; Anaya, Juan-Manuel

2009-07-01

The objective of this study was to analyze epidemiological tendencies of systemic sclerosis (SSc) around the world in order to identify possible local variations in the presentation and occurrence of the disease. A systematic review of the literature was performed through electronic databases using the keywords "Systemic Sclerosis" and "Clinical Characteristics." Out of a total of 167 articles, 41 were included in the analysis. Significant differences in the mean age at the time of diagnosis, subsets of SSc, clinical characteristics, and presence of antibodies were found between different regions of the word. Because variations in both additive and nonadditive genetic factors and the environmental variance are specific to the investigated population, ethnicity and geography are important characteristics to be considered in the study of SSc and other autoimmune diseases.

Is Khat (Catha edulis) chewing a risk factor for periodontal diseases? A systematic review.

PubMed

Kalakonda, Butchibabu; Al-Maweri, Sadeq-Ali; Al-Shamiri, Hashem-Motahir; Ijaz, Anum; Gamal, Shukri; Dhaifullah, Esam

2017-10-01

Khat (Catha edulis) chewing is a highly prevalent habit in the Arabian Peninsula and East Africa, and has recently spread to Western countries. The association between khat chewing and oral mucosal lesions is well documented in the literature. However, there is no concrete evidence on the association between khat chewing and periodontal disease. The purpose of this systematic review was to analyze the influence of khat chewing on periodontal health. A literature search of PubMed, Scopus and Web of Sciences databases was carried out to identify relevant articles published from 1990 to May 2017. The inclusion criteria were all clinical studies that assessed the relationship between khat chewing and periodontal disease. The search yielded 122 articles, of which 10 were included in this systematic review. Most of the studies exhibited a positive correlation between khat chewing and periodontal disease. Altogether, the analysis of the current evidence reveals that khat chewing is destructive to the periodontium and enhances the risk of periodontal disease progression. However, due to variability of studies, more longitudinal case-controlled studies are highly warranted to establish a causal relation between khat chewing and periodontal disease. Key words: Khat chewing, periodontal health, periodontal disease, risk factor.

Supervised Clustering Based on DPClusO: Prediction of Plant-Disease Relations Using Jamu Formulas of KNApSAcK Database

PubMed Central

Husnawati, Husnawati; Afendi, Farit Mochamad; Darusman, Latifah K.; Altaf-Ul-Amin, Md.; Sato, Tetsuo; Ono, Naoaki; Sugiura, Tadao; Kanaya, Shigehiko

2014-01-01

Indonesia has the largest medicinal plant species in the world and these plants are used as Jamu medicines. Jamu medicines are popular traditional medicines from Indonesia and we need to systemize the formulation of Jamu and develop basic scientific principles of Jamu to meet the requirement of Indonesian Healthcare System. We propose a new approach to predict the relation between plant and disease using network analysis and supervised clustering. At the preliminary step, we assigned 3138 Jamu formulas to 116 diseases of International Classification of Diseases (ver. 10) which belong to 18 classes of disease from National Center for Biotechnology Information. The correlation measures between Jamu pairs were determined based on their ingredient similarity. Networks are constructed and analyzed by selecting highly correlated Jamu pairs. Clusters were then generated by using the network clustering algorithm DPClusO. By using matching score of a cluster, the dominant disease and high frequency plant associated to the cluster are determined. The plant to disease relations predicted by our method were evaluated in the context of previously published results and were found to produce around 90% successful predictions. PMID:24804251

A survey on computer aided diagnosis for ocular diseases

PubMed Central

2014-01-01

Background Computer Aided Diagnosis (CAD), which can automate the detection process for ocular diseases, has attracted extensive attention from clinicians and researchers alike. It not only alleviates the burden on the clinicians by providing objective opinion with valuable insights, but also offers early detection and easy access for patients. Method We review ocular CAD methodologies for various data types. For each data type, we investigate the databases and the algorithms to detect different ocular diseases. Their advantages and shortcomings are analyzed and discussed. Result We have studied three types of data (i.e., clinical, genetic and imaging) that have been commonly used in existing methods for CAD. The recent developments in methods used in CAD of ocular diseases (such as Diabetic Retinopathy, Glaucoma, Age-related Macular Degeneration and Pathological Myopia) are investigated and summarized comprehensively. Conclusion While CAD for ocular diseases has shown considerable progress over the past years, the clinical importance of fully automatic CAD systems which are able to embed clinical knowledge and integrate heterogeneous data sources still show great potential for future breakthrough. PMID:25175552

[Prescription rules of preparations containing Crataegi Fructus in Chinese patent drug].

PubMed

Geng, Ya; Ma, Yue-Xiang; Xu, Hai-Yu; Li, Jun-Fang; Tang, Shi-Huan; Yang, Hong-Jun

2016-08-01

To analyze the prescription rules of preparations containing Crataegi Fructus in the drug standards of the People's Republic of China Ministry of Public Health-Chinese Patent Drug(hereinafter referred to as Chinese patent drug), and provide some references for clinical application and the research and development of new medicines. Based on TCMISS(V2.5), the prescriptions containing Crataegi Fructus in Chinese patent drug were collected to build the database; association rules, frequency statistics and other data mining methods were used to analyze the disease syndrome, common drug compatibility and prescription rules. There were a total of 308 prescriptions containing Crataegi Fructus, involving 499 kinds of Chinese medicines, 34 commonly used drug combinations, and mainly for 18 kinds of diseases. Drug combination analysis was done with "Crataegi Fructus-Citri Reticulatae Pericarpium" and "Crataegi Fructus-Poria" as the high-frequency herb pairs and with "stagnation" and "diarrhea" as the high-frequency diseases. The results indicated that the Crataegi Fructus in different herb pairs had a roughly same function, and its therapy effect was different in different diseases. The prescriptions containing Crataegi Fructus in Chinese patent drug had the effect of digestion, and they were widely used in clinical application, often used together with spleen-strengthening medicines to achieve different treatment effects; the prescription rules reflected the prescription characteristics of Crataegi Fructus for different diseases, providing a basis for its clinically scientific application and the research and development of new medicines. Copyright© by the Chinese Pharmaceutical Association.

A systematic approach to analyze the social determinants of cardiovascular disease.

PubMed

Martínez-García, Mireya; Salinas-Ortega, Magaly; Estrada-Arriaga, Iván; Hernández-Lemus, Enrique; García-Herrera, Rodrigo; Vallejo, Maite

2018-01-01

Cardiovascular diseases are the leading cause of human mortality worldwide. Among the many factors associated with the etiology, incidence, and evolution of such diseases; social and environmental issues constitute an important and often overlooked component. Understanding to a greater extent the scope to which such social determinants of cardiovascular diseases (SDCVD) occur as well as the connections among them would be useful for public health policy making. Here, we will explore the historical trends and associations among the main SDCVD in the published literature. Our aim will be finding meaningful relations among those that will help us to have an integrated view on this complex phenomenon by providing historical context and a relational framework. To uncover such relations, we used a data mining approach to the current literature, followed by network analysis of the interrelationships discovered. To this end, we systematically mined the PubMed/MEDLINE database for references of published studies on the subject, as outlined by the World Health Organization's framework on social determinants of health. The analyzed structured corpus consisted in circa 1190 articles categorized by means of the Medical Subheadings (MeSH) content-descriptor. The use of data analytics techniques allowed us to find a number of non-trivial connections among SDCVDs. Such relations may be relevant to get a deeper understanding of the social and environmental issues associated with cardiovascular disease and are often overlooked by traditional literature survey approaches, such as systematic reviews and meta-analyses.

A systematic approach to analyze the social determinants of cardiovascular disease

PubMed Central

Martínez-García, Mireya; Salinas-Ortega, Magaly; Estrada-Arriaga, Iván; Hernández-Lemus, Enrique; García-Herrera, Rodrigo

2018-01-01

Cardiovascular diseases are the leading cause of human mortality worldwide. Among the many factors associated with the etiology, incidence, and evolution of such diseases; social and environmental issues constitute an important and often overlooked component. Understanding to a greater extent the scope to which such social determinants of cardiovascular diseases (SDCVD) occur as well as the connections among them would be useful for public health policy making. Here, we will explore the historical trends and associations among the main SDCVD in the published literature. Our aim will be finding meaningful relations among those that will help us to have an integrated view on this complex phenomenon by providing historical context and a relational framework. To uncover such relations, we used a data mining approach to the current literature, followed by network analysis of the interrelationships discovered. To this end, we systematically mined the PubMed/MEDLINE database for references of published studies on the subject, as outlined by the World Health Organization’s framework on social determinants of health. The analyzed structured corpus consisted in circa 1190 articles categorized by means of the Medical Subheadings (MeSH) content-descriptor. The use of data analytics techniques allowed us to find a number of non-trivial connections among SDCVDs. Such relations may be relevant to get a deeper understanding of the social and environmental issues associated with cardiovascular disease and are often overlooked by traditional literature survey approaches, such as systematic reviews and meta-analyses. PMID:29370200

Software support for Huntingtons disease research.

PubMed

Conneally, P M; Gersting, J M; Gray, J M; Beidleman, K; Wexler, N S; Smith, C L

1991-01-01

Huntingtons disease (HD) is a hereditary disorder involving the central nervous system. Its effects are devastating, to the affected person as well as his family. The Department of Medical and Molecular Genetics at Indiana University (IU) plays an integral part in Huntingtons research by providing computerized repositories of HD family information for researchers and families. The National Huntingtons Disease Research Roster, founded in 1979 at IU, and the Huntingtons Disease in Venezuela Project database contain information that has proven to be invaluable in the worldwide field of HD research. This paper addresses the types of information stored in each database, the pedigree database program (MEGADATS) used to manage the data, and significant findings that have resulted from access to the data.

On exploration of medical database of Crohn's disease

NASA Astrophysics Data System (ADS)

Manerowska, Anna; Dadalski, Maciej; Socha, Piotr; Mulawka, Jan

2010-09-01

The primary objective of this article is to find a new, more effective method of diagnosis of Crohn's disease. Having created the database on this disease we wanted to find the most suitable classification models. We used the algorithms with their implementations stored in R environment. Having carried out the investigations we have reached results interesting for clinical practice.

e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations.

PubMed

Karim, Sajjad; NourEldin, Hend Fakhri; Abusamra, Heba; Salem, Nada; Alhathli, Elham; Dudley, Joel; Sanderford, Max; Scheinfeldt, Laura B; Chaudhary, Adeel G; Al-Qahtani, Mohammed H; Kumar, Sudhir

2016-10-17

Genome-wide association studies (GWAS) have become a mainstay of biological research concerned with discovering genetic variation linked to phenotypic traits and diseases. Both discrete and continuous traits can be analyzed in GWAS to discover associations between single nucleotide polymorphisms (SNPs) and traits of interest. Associations are typically determined by estimating the significance of the statistical relationship between genetic loci and the given trait. However, the prioritization of bona fide, reproducible genetic associations from GWAS results remains a central challenge in identifying genomic loci underlying common complex diseases. Evolutionary-aware meta-analysis of the growing GWAS literature is one way to address this challenge and to advance from association to causation in the discovery of genotype-phenotype relationships. We have created an evolutionary GWAS resource to enable in-depth query and exploration of published GWAS results. This resource uses the publically available GWAS results annotated in the GRASP2 database. The GRASP2 database includes results from 2082 studies, 177 broad phenotype categories, and ~8.87 million SNP-phenotype associations. For each SNP in e-GRASP, we present information from the GRASP2 database for convenience as well as evolutionary information (e.g., rate and timespan). Users can, therefore, identify not only SNPs with highly significant phenotype-association P-values, but also SNPs that are highly replicated and/or occur at evolutionarily conserved sites that are likely to be functionally important. Additionally, we provide an evolutionary-adjusted SNP association ranking (E-rank) that uses cross-species evolutionary conservation scores and population allele frequencies to transform P-values in an effort to enhance the discovery of SNPs with a greater probability of biologically meaningful disease associations. By adding an evolutionary dimension to the GWAS results available in the GRASP2 database, our e-GRASP resource will enable a more effective exploration of SNPs not only by the statistical significance of trait associations, but also by the number of studies in which associations have been replicated, and the evolutionary context of the associated mutations. Therefore, e-GRASP will be a valuable resource for aiding researchers in the identification of bona fide, reproducible genetic associations from GWAS results. This resource is freely available at http://www.mypeg.info/egrasp .

Cross-Border Use of Food Databases: Equivalence of US and Australian Databases for Macronutrients

PubMed Central

Summer, Suzanne S.; Ollberding, Nicholas J.; Guy, Trish; Setchell, Kenneth D. R.; Brown, Nadine; Kalkwarf, Heidi J.

2013-01-01

When estimating dietary intake across multiple countries, the lack of a single comprehensive dietary database may lead researchers to modify one database to analyze intakes for all participants. This approach may yield results different from those using the country-specific database and introduce measurement error. We examined whether nutrient intakes of Australians calculated with a modified US database would be similar to those calculated with an Australian database. We analyzed 3-day food records of 68 Australian adults using the US-based Nutrition Data System for Research, modified to reflect food items consumed in Australia. Modification entailed identifying a substitute food whose energy and macronutrient content were within 10% of the Australian food or by adding a new food to the database. Paired Wilcoxon signed rank tests were used to compare differences in nutrient intakes estimated by both databases, and Pearson and intraclass correlation coefficients measured degree of association and agreement between intake estimates for individuals. Median intakes of energy, carbohydrate, protein, and fiber differed by <5% at the group level. Larger discrepancies were seen for fat (11%; P<0.0001) and most micronutrients. Despite strong correlations, nutrient intakes differed by >10% for an appreciable percentage of participants (35% for energy to 69% for total fat). Adding country-specific food items to an existing database resulted in similar overall macronutrient intake estimates but was insufficient for estimating individual intakes. When analyzing nutrient intakes in multinational studies, greater standardization and modification of databases may be required to more accurately estimate intake of individuals. PMID:23871108

Multi-categorical deep learning neural network to classify retinal images: A pilot study employing small database.

PubMed

Choi, Joon Yul; Yoo, Tae Keun; Seo, Jeong Gi; Kwak, Jiyong; Um, Terry Taewoong; Rim, Tyler Hyungtaek

2017-01-01

Deep learning emerges as a powerful tool for analyzing medical images. Retinal disease detection by using computer-aided diagnosis from fundus image has emerged as a new method. We applied deep learning convolutional neural network by using MatConvNet for an automated detection of multiple retinal diseases with fundus photographs involved in STructured Analysis of the REtina (STARE) database. Dataset was built by expanding data on 10 categories, including normal retina and nine retinal diseases. The optimal outcomes were acquired by using a random forest transfer learning based on VGG-19 architecture. The classification results depended greatly on the number of categories. As the number of categories increased, the performance of deep learning models was diminished. When all 10 categories were included, we obtained results with an accuracy of 30.5%, relative classifier information (RCI) of 0.052, and Cohen's kappa of 0.224. Considering three integrated normal, background diabetic retinopathy, and dry age-related macular degeneration, the multi-categorical classifier showed accuracy of 72.8%, 0.283 RCI, and 0.577 kappa. In addition, several ensemble classifiers enhanced the multi-categorical classification performance. The transfer learning incorporated with ensemble classifier of clustering and voting approach presented the best performance with accuracy of 36.7%, 0.053 RCI, and 0.225 kappa in the 10 retinal diseases classification problem. First, due to the small size of datasets, the deep learning techniques in this study were ineffective to be applied in clinics where numerous patients suffering from various types of retinal disorders visit for diagnosis and treatment. Second, we found that the transfer learning incorporated with ensemble classifiers can improve the classification performance in order to detect multi-categorical retinal diseases. Further studies should confirm the effectiveness of algorithms with large datasets obtained from hospitals.

TCMSP: a database of systems pharmacology for drug discovery from herbal medicines.

PubMed

Ru, Jinlong; Li, Peng; Wang, Jinan; Zhou, Wei; Li, Bohui; Huang, Chao; Li, Pidong; Guo, Zihu; Tao, Weiyang; Yang, Yinfeng; Xu, Xue; Li, Yan; Wang, Yonghua; Yang, Ling

2014-01-01

Modern medicine often clashes with traditional medicine such as Chinese herbal medicine because of the little understanding of the underlying mechanisms of action of the herbs. In an effort to promote integration of both sides and to accelerate the drug discovery from herbal medicines, an efficient systems pharmacology platform that represents ideal information convergence of pharmacochemistry, ADME properties, drug-likeness, drug targets, associated diseases and interaction networks, are urgently needed. The traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) was built based on the framework of systems pharmacology for herbal medicines. It consists of all the 499 Chinese herbs registered in the Chinese pharmacopoeia with 29,384 ingredients, 3,311 targets and 837 associated diseases. Twelve important ADME-related properties like human oral bioavailability, half-life, drug-likeness, Caco-2 permeability, blood-brain barrier and Lipinski's rule of five are provided for drug screening and evaluation. TCMSP also provides drug targets and diseases of each active compound, which can automatically establish the compound-target and target-disease networks that let users view and analyze the drug action mechanisms. It is designed to fuel the development of herbal medicines and to promote integration of modern medicine and traditional medicine for drug discovery and development. The particular strengths of TCMSP are the composition of the large number of herbal entries, and the ability to identify drug-target networks and drug-disease networks, which will help revealing the mechanisms of action of Chinese herbs, uncovering the nature of TCM theory and developing new herb-oriented drugs. TCMSP is freely available at http://sm.nwsuaf.edu.cn/lsp/tcmsp.php.

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

PubMed Central

Johnson, Robin J.; Lay, Jean M.; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J.

2013-01-01

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. PMID:23613709

Missed Diagnosis of Cardiovascular Disease in Outpatient General Medicine: Insights from Malpractice Claims Data.

PubMed

Quinn, Gene R; Ranum, Darrell; Song, Ellen; Linets, Margarita; Keohane, Carol; Riah, Heather; Greenberg, Penny

2017-10-01

Diagnostic errors are an underrecognized source of patient harm, and cardiovascular disease can be challenging to diagnose in the ambulatory setting. Although malpractice data can inform diagnostic error reduction efforts, no studies have examined outpatient cardiovascular malpractice cases in depth. A study was conducted to examine the characteristics of outpatient cardiovascular malpractice cases brought against general medicine practitioners. Some 3,407 closed malpractice claims were analyzed in outpatient general medicine from CRICO Strategies' Comparative Benchmarking System database-the largest detailed database of paid and unpaid malpractice in the world-and multivariate models were created to determine the factors that predicted case outcomes. Among the 153 patients in cardiovascular malpractice cases for whom patient comorbidities were coded, the majority (63%) had at least one traditional cardiac risk factor, such as diabetes, tobacco use, or previous cardiovascular disease. Cardiovascular malpractice cases were more likely to involve an allegation of error in diagnosis (75% vs. 47%, p <0.0001), have high clinical severity (86% vs. 49%, p <0.0001) and result in death (75% vs. 27%, p <0.0001), as compared to noncardiovascular cases. Initial diagnoses of nonspecific chest pain and mimics of cardiovascular pain (for example, esophageal disease) were common and independently increased the likelihood of a claim resulting in a payment (p <0.01). Cardiovascular malpractice cases against outpatient general medicine physicians mostly occur in patients with conventional risk factors for coronary artery disease and are often diagnosed with common mimics of cardiovascular pain. These findings suggest that these patients may be high-yield targets for preventing diagnostic errors in the ambulatory setting. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Clinical Prediction Models for Cardiovascular Disease: Tufts Predictive Analytics and Comparative Effectiveness Clinical Prediction Model Database.

PubMed

Wessler, Benjamin S; Lai Yh, Lana; Kramer, Whitney; Cangelosi, Michael; Raman, Gowri; Lutz, Jennifer S; Kent, David M

2015-07-01

Clinical prediction models (CPMs) estimate the probability of clinical outcomes and hold the potential to improve decision making and individualize care. For patients with cardiovascular disease, there are numerous CPMs available although the extent of this literature is not well described. We conducted a systematic review for articles containing CPMs for cardiovascular disease published between January 1990 and May 2012. Cardiovascular disease includes coronary heart disease, heart failure, arrhythmias, stroke, venous thromboembolism, and peripheral vascular disease. We created a novel database and characterized CPMs based on the stage of development, population under study, performance, covariates, and predicted outcomes. There are 796 models included in this database. The number of CPMs published each year is increasing steadily over time. Seven hundred seventeen (90%) are de novo CPMs, 21 (3%) are CPM recalibrations, and 58 (7%) are CPM adaptations. This database contains CPMs for 31 index conditions, including 215 CPMs for patients with coronary artery disease, 168 CPMs for population samples, and 79 models for patients with heart failure. There are 77 distinct index/outcome pairings. Of the de novo models in this database, 450 (63%) report a c-statistic and 259 (36%) report some information on calibration. There is an abundance of CPMs available for a wide assortment of cardiovascular disease conditions, with substantial redundancy in the literature. The comparative performance of these models, the consistency of effects and risk estimates across models and the actual and potential clinical impact of this body of literature is poorly understood. © 2015 American Heart Association, Inc.

Background and Data Configuration Process of a Nationwide Population-Based Study Using the Korean National Health Insurance System

PubMed Central

Song, Sun Ok; Jung, Chang Hee; Song, Young Duk; Park, Cheol-Young; Kwon, Hyuk-Sang; Cha, Bong Soo; Park, Joong-Yeol; Lee, Ki-Up

2014-01-01

Background The National Health Insurance Service (NHIS) recently signed an agreement to provide limited open access to the databases within the Korean Diabetes Association for the benefit of Korean subjects with diabetes. Here, we present the history, structure, contents, and way to use data procurement in the Korean National Health Insurance (NHI) system for the benefit of Korean researchers. Methods The NHIS in Korea is a single-payer program and is mandatory for all residents in Korea. The three main healthcare programs of the NHI, Medical Aid, and long-term care insurance (LTCI) provide 100% coverage for the Korean population. The NHIS in Korea has adopted a fee-for-service system to pay health providers. Researchers can obtain health information from the four databases of the insured that contain data on health insurance claims, health check-ups and LTCI. Results Metabolic disease as chronic disease is increasing with aging society. NHIS data is based on mandatory, serial population data, so, this might show the time course of disease and predict some disease progress, and also be used in primary and secondary prevention of disease after data mining. Conclusion The NHIS database represents the entire Korean population and can be used as a population-based database. The integrated information technology of the NHIS database makes it a world-leading population-based epidemiology and disease research platform. PMID:25349827

Background and data configuration process of a nationwide population-based study using the korean national health insurance system.

PubMed

Song, Sun Ok; Jung, Chang Hee; Song, Young Duk; Park, Cheol-Young; Kwon, Hyuk-Sang; Cha, Bong Soo; Park, Joong-Yeol; Lee, Ki-Up; Ko, Kyung Soo; Lee, Byung-Wan

2014-10-01

The National Health Insurance Service (NHIS) recently signed an agreement to provide limited open access to the databases within the Korean Diabetes Association for the benefit of Korean subjects with diabetes. Here, we present the history, structure, contents, and way to use data procurement in the Korean National Health Insurance (NHI) system for the benefit of Korean researchers. The NHIS in Korea is a single-payer program and is mandatory for all residents in Korea. The three main healthcare programs of the NHI, Medical Aid, and long-term care insurance (LTCI) provide 100% coverage for the Korean population. The NHIS in Korea has adopted a fee-for-service system to pay health providers. Researchers can obtain health information from the four databases of the insured that contain data on health insurance claims, health check-ups and LTCI. Metabolic disease as chronic disease is increasing with aging society. NHIS data is based on mandatory, serial population data, so, this might show the time course of disease and predict some disease progress, and also be used in primary and secondary prevention of disease after data mining. The NHIS database represents the entire Korean population and can be used as a population-based database. The integrated information technology of the NHIS database makes it a world-leading population-based epidemiology and disease research platform.

Prescription patterns of traditional Chinese medicine for peptic ulcer disease in Taiwan: A nationwide population-based study.

PubMed

Huang, Chin-Ying; Lai, Wan-Yu; Sun, Mao-Feng; Lin, Che-Chen; Chen, Bor-Chyuan; Lin, Hung-Jen; Chang, Ching-Mao; Yang, Chung-Hsien; Huang, Kuo-Chin; Yen, Hung-Rong

2015-12-24

Peptic ulcer disease is a common digestive disease. There is a lack of large-scale survey on the use of traditional Chinese medicine (TCM) for the treatment of peptic ulcer disease. This study aimed to investigate the utilization of TCM for the treatment of peptic ulcer disease in Taiwan. We analyzed a random sample comprised of one million individuals with newly diagnosed peptic ulcer disease between 2001 and 2010 from the National Health Insurance Research Database in Taiwan. Demographic characteristics and TCM usage, including Chinese herbal formulas and the single herbs prescribed for patients with peptic ulcer disease, were analyzed. A total of 96,624 newly diagnosed subjects with peptic ulcer disease were included. 14,983 (15.5%) patients were TCM users. People residing in highly urbanized areas, younger people and female (compared with male) were more likely to use TCM. With regard to the comorbidities, TCM users had a lower prevalence of coronary artery disease, chronic obstructive lung disease, diabetes mellitus and liver cirrhosis and stroke. The average time between onset of peptic ulcer disease and the first visit to a TCM clinic was 4.7 months. Majority of the patients (n=14,449; 96.4%) received only Chinese herbal remedies. The most frequently prescribed Chinese herbal formula and single herb was Ban-Xia-Xie-Xin-Tang (Pinelliae Decoction to Drain the Epigastrium) and Hai-Piao-Xiao (Os Sepiae), respectively. The core pattern analysis showed that combination of Ban-Xia-Xie-Xin-Tang, Hai-Piao-Xiao (Os Sepiae), Yan-Hu-Suo (Rhizoma Corydalis), Bei-Mu (Bulbus Fritillariae Thunbergii) and Chuan-Lian-Zi (Fructus Toosendan) was most frequently used for peptic ulcer disease. Our study identified the core prescription patterns of TCM for patients with peptic ulcer disease in Taiwan. Further basic and clinical studies are necessary to elucidate the efficacy and mechanisms. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases

PubMed Central

Buza, Teresia M.; Jack, Sherman W.; Kirunda, Halid; Khaitsa, Margaret L.; Lawrence, Mark L.; Pruett, Stephen; Peterson, Daniel G.

2015-01-01

There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides more plausible arguments to achieve better understanding of infectious and zoonotic diseases. We have developed a model for interlinking annotations of these diseases. These diseases are of particular interest because of the threats they pose to animal health, human health and global health security. We demonstrated the application of this model using brucellosis, an infectious and zoonotic disease. Preliminary annotations were deposited into VetBioBase database (http://vetbiobase.igbb.msstate.edu). This database is associated with user-friendly tools to facilitate searching, retrieving and downloading of disease-related information. Database URL: http://vetbiobase.igbb.msstate.edu PMID:26581408

Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database

PubMed Central

2012-01-01

Background Huntington’s disease (HD) is a fatal progressive neurodegenerative disorder caused by the expansion of the polyglutamine repeat region in the huntingtin gene. Although the disease is triggered by the mutation of a single gene, intensive research has linked numerous other genes to its pathogenesis. To obtain a systematic overview of these genes, which may serve as therapeutic targets, CHDI Foundation has recently established the HD Research Crossroads database. With currently over 800 cataloged genes, this web-based resource constitutes the most extensive curation of genes relevant to HD. It provides us with an unprecedented opportunity to survey molecular mechanisms involved in HD in a holistic manner. Methods To gain a synoptic view of therapeutic targets for HD, we have carried out a variety of bioinformatical and statistical analyses to scrutinize the functional association of genes curated in the HD Research Crossroads database. In particular, enrichment analyses were performed with respect to Gene Ontology categories, KEGG signaling pathways, and Pfam protein families. For selected processes, we also analyzed differential expression, using published microarray data. Additionally, we generated a candidate set of novel genetic modifiers of HD by combining information from the HD Research Crossroads database with previous genome-wide linkage studies. Results Our analyses led to a comprehensive identification of molecular mechanisms associated with HD. Remarkably, we not only recovered processes and pathways, which have frequently been linked to HD (such as cytotoxicity, apoptosis, and calcium signaling), but also found strong indications for other potentially disease-relevant mechanisms that have been less intensively studied in the context of HD (such as the cell cycle and RNA splicing, as well as Wnt and ErbB signaling). For follow-up studies, we provide a regularly updated compendium of molecular mechanism, that are associated with HD, at http://hdtt.sysbiolab.eu Additionally, we derived a candidate set of 24 novel genetic modifiers, including histone deacetylase 3 (HDAC3), metabotropic glutamate receptor 1 (GRM1), CDK5 regulatory subunit 2 (CDK5R2), and coactivator 1ß of the peroxisome proliferator-activated receptor gamma (PPARGC1B). Conclusions The results of our study give us an intriguing picture of the molecular complexity of HD. Our analyses can be seen as a first step towards a comprehensive list of biological processes, molecular functions, and pathways involved in HD, and may provide a basis for the development of more holistic disease models and new therapeutics. PMID:22741533

Descriptive epidemiology of children hospitalized for inflammatory bowel disease in Japan: Inpatient database analysis.

PubMed

Takeuchi, Masato; Tomomasa, Takeshi; Yasunaga, Hideo; Horiguchi, Hiromasa; Fushimi, Kiyohide

2015-06-01

Inflammatory bowel disease (IBD) - Crohn's disease (CD) and ulcerative colitis (UC) - are chronic inflammatory disorders of the intestine. Patients with IBD are at risk of hospitalization for disease exacerbation or IBD-associated complications. In the pediatric population, however, there are limited data on IBD hospitalizations. We therefore investigated the descriptive epidemiology of hospitalizations relevant to pediatric IBD. The national inpatient claims database in Japan was searched for children (≤ 18 years old) with a diagnosis of IBD. The study period was 2007-2010. Data on demographic characteristics and descriptive statistics of the hospital course were extracted and analyzed. A total of 3559 admissions of 2175 patients met the definition of pediatric IBD: there were 1999 admissions for CD and 1560 admissions for UC. Internists were responsible for patient care in 56.6% of admissions, followed by pediatricians (27.5%). Of 3559 admissions, unscheduled hospitalizations accounted for 79.7%, and 7.6% of hospitalizations were attributable to complications of IBD, including intestinal, extraintestinal and other manifestations. The median age at first admission was 16 years (IQR, 13-17 years), in both the CD and UC groups. Compared with UC patients, CD patients had a higher number of hospitalizations (P < 0.001), but hospital stay was shorter (median: 6 vs 16 days, P < 0.001). There were seven fatal cases of IBD, accounting for 0.32% in the present series, and sepsis was the cause in five. This study provides a description of pediatric inpatients with IBD and their hospital course in Japan. © 2014 Japan Pediatric Society.

A web-based relational database for monitoring and analyzing mosquito population dynamics.

PubMed

Sucaet, Yves; Van Hemert, John; Tucker, Brad; Bartholomay, Lyric

2008-07-01

Mosquito population dynamics have been monitored on an annual basis in the state of Iowa since 1969. The primary goal of this project was to integrate light trap data from these efforts into a centralized back-end database and interactive website that is available through the internet at http://iowa-mosquito.ent.iastate.edu. For comparative purposes, all data were categorized according to the week of the year and normalized according to the number of traps running. Users can readily view current, weekly mosquito abundance compared with data from previous years. Additional interactive capabilities facilitate analyses of the data based on mosquito species, distribution, or a time frame of interest. All data can be viewed in graphical and tabular format and can be downloaded to a comma separated value (CSV) file for import into a spreadsheet or more specialized statistical software package. Having this long-term dataset in a centralized database/website is useful for informing mosquito and mosquito-borne disease control and for exploring the ecology of the species represented therein. In addition to mosquito population dynamics, this database is available as a standardized platform that could be modified and applied to a multitude of projects that involve repeated collection of observational data. The development and implementation of this tool provides capacity for the user to mine data from standard spreadsheets into a relational database and then view and query the data in an interactive website.

Polyamines in foods: development of a food database

PubMed Central

Ali, Mohamed Atiya; Poortvliet, Eric; Strömberg, Roger; Yngve, Agneta

2011-01-01

Background Knowing the levels of polyamines (putrescine, spermidine, and spermine) in different foods is of interest due to the association of these bioactive nutrients to health and diseases. There is a lack of relevant information on their contents in foods. Objective To develop a food polyamine database from published data by which polyamine intake and food contribution to this intake can be estimated, and to determine the levels of polyamines in Swedish dairy products. Design Extensive literature search and laboratory analysis of selected Swedish dairy products. Polyamine contents in foods were collected using an extensive literature search of databases. Polyamines in different types of Swedish dairy products (milk with different fat percentages, yogurt, cheeses, and sour milk) were determined using high performance liquid chromatography (HPLC) equipped with a UV detector. Results Fruits and cheese were the highest sources of putrescine, while vegetables and meat products were found to be rich in spermidine and spermine, respectively. The content of polyamines in cheese varied considerably between studies. In analyzed Swedish dairy products, matured cheese had the highest total polyamine contents with values of 52.3, 1.2, and 2.6 mg/kg for putrescine, spermidine, and spermine, respectively. Low fat milk had higher putrescine and spermidine, 1.2 and 1.0 mg/kg, respectively, than the other types of milk. Conclusions The database aids other researchers in their quest for information regarding polyamine intake from foods. Connecting the polyamine contents in food with the Swedish Food Database allows for estimation of polyamine contents per portion. PMID:21249159

DEXTER: Disease-Expression Relation Extraction from Text.

PubMed

Gupta, Samir; Dingerdissen, Hayley; Ross, Karen E; Hu, Yu; Wu, Cathy H; Mazumder, Raja; Vijay-Shanker, K

2018-01-01

Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research, and diagnostics and prognostics of diseases. There are currently several high-quality databases that capture gene expression information, obtained mostly from large-scale studies, such as microarray and next-generation sequencing technologies, in the context of disease. The scientific literature is another rich source of information on gene expression-disease relationships that not only have been captured from large-scale studies but have also been observed in thousands of small-scale studies. Expression information obtained from literature through manual curation can extend expression databases. While many of the existing databases include information from literature, they are limited by the time-consuming nature of manual curation and have difficulty keeping up with the explosion of publications in the biomedical field. In this work, we describe an automated text-mining tool, Disease-Expression Relation Extraction from Text (DEXTER) to extract information from literature on gene and microRNA expression in the context of disease. One of the motivations in developing DEXTER was to extend the BioXpress database, a cancer-focused gene expression database that includes data derived from large-scale experiments and manual curation of publications. The literature-based portion of BioXpress lags behind significantly compared to expression information obtained from large-scale studies and can benefit from our text-mined results. We have conducted two different evaluations to measure the accuracy of our text-mining tool and achieved average F-scores of 88.51 and 81.81% for the two evaluations, respectively. Also, to demonstrate the ability to extract rich expression information in different disease-related scenarios, we used DEXTER to extract information on differential expression information for 2024 genes in lung cancer, 115 glycosyltransferases in 62 cancers and 826 microRNA in 171 cancers. All extractions using DEXTER are integrated in the literature-based portion of BioXpress.Database URL: http://biotm.cis.udel.edu/DEXTER.

Intravenous Artesunate Reduces Parasite Clearance Time, Duration of Intensive Care, and Hospital Treatment in Patients With Severe Malaria in Europe: The TropNet Severe Malaria Study.

PubMed

Kurth, Florian; Develoux, Michel; Mechain, Matthieu; Clerinx, Jan; Antinori, Spinello; Gjørup, Ida E; Gascon, Joaquím; Mørch, Kristine; Nicastri, Emanuele; Ramharter, Michael; Bartoloni, Alessandro; Visser, Leo; Rolling, Thierry; Zanger, Philipp; Calleri, Guido; Salas-Coronas, Joaquín; Nielsen, Henrik; Just-Nübling, Gudrun; Neumayr, Andreas; Hachfeld, Anna; Schmid, Matthias L; Antonini, Pietro; Pongratz, Peter; Kern, Peter; Saraiva da Cunha, José; Soriano-Arandes, Antoni; Schunk, Mirjam; Suttorp, Norbert; Hatz, Christoph; Zoller, Thomas

2015-11-01

Intravenous artesunate improves survival in severe malaria, but clinical trial data from nonendemic countries are scarce. The TropNet severe malaria database was analyzed to compare outcomes of artesunate vs quinine treatment. Artesunate reduced parasite clearance time and duration of intensive care unit and hospital treatment in European patients with imported severe malaria. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

DNetDB: The human disease network database based on dysfunctional regulation mechanism.

PubMed

Yang, Jing; Wu, Su-Juan; Yang, Shao-You; Peng, Jia-Wei; Wang, Shi-Nuo; Wang, Fu-Yan; Song, Yu-Xing; Qi, Ting; Li, Yi-Xue; Li, Yuan-Yuan

2016-05-21

Disease similarity study provides new insights into disease taxonomy, pathogenesis, which plays a guiding role in diagnosis and treatment. The early studies were limited to estimate disease similarities based on clinical manifestations, disease-related genes, medical vocabulary concepts or registry data, which were inevitably biased to well-studied diseases and offered small chance of discovering novel findings in disease relationships. In other words, genome-scale expression data give us another angle to address this problem since simultaneous measurement of the expression of thousands of genes allows for the exploration of gene transcriptional regulation, which is believed to be crucial to biological functions. Although differential expression analysis based methods have the potential to explore new disease relationships, it is difficult to unravel the upstream dysregulation mechanisms of diseases. We therefore estimated disease similarities based on gene expression data by using differential coexpression analysis, a recently emerging method, which has been proved to be more potential to capture dysfunctional regulation mechanisms than differential expression analysis. A total of 1,326 disease relationships among 108 diseases were identified, and the relevant information constituted the human disease network database (DNetDB). Benefiting from the use of differential coexpression analysis, the potential common dysfunctional regulation mechanisms shared by disease pairs (i.e. disease relationships) were extracted and presented. Statistical indicators, common disease-related genes and drugs shared by disease pairs were also included in DNetDB. In total, 1,326 disease relationships among 108 diseases, 5,598 pathways, 7,357 disease-related genes and 342 disease drugs are recorded in DNetDB, among which 3,762 genes and 148 drugs are shared by at least two diseases. DNetDB is the first database focusing on disease similarity from the viewpoint of gene regulation mechanism. It provides an easy-to-use web interface to search and browse the disease relationships and thus helps to systematically investigate etiology and pathogenesis, perform drug repositioning, and design novel therapeutic interventions.Database URL: http://app.scbit.org/DNetDB/ #.

Metastatic Neuroblastoma Confined to Distant Lymph Nodes (stage 4N) Predicts Outcome in Patients With Stage 4 Disease: A Study From the International Neuroblastoma Risk Group Database

PubMed Central

Morgenstern, Daniel A.; London, Wendy B.; Stephens, Derek; Volchenboum, Samuel L.; Hero, Barbara; Di Cataldo, Andrea; Nakagawara, Akira; Shimada, Hiroyuki; Ambros, Peter F.; Matthay, Katherine K.; Cohn, Susan L.; Pearson, Andrew D.J.; Irwin, Meredith S.

2014-01-01

Purpose The presence of distant metastases is one of the most powerful predictors of outcome in patients with neuroblastoma. However, the pattern of metastatic spread is not incorporated into current risk stratification systems. Small case series have suggested that patients with neuroblastoma who have metastatic disease limited to distant lymph nodes (4N disease) may have improved outcomes. Patients and Methods We analyzed retrospective data from the International Neuroblastoma Risk Group database for patients diagnosed from 1990 to 2002. 4N patients were compared with the remaining stage 4 patients (non-4N), excluding those with missing metastatic site data. Results In all, 2,250 International Neuroblastoma Staging System stage 4 patients with complete data were identified, of whom 146 (6.5%) had 4N disease. For 4N patients, event-free survival (EFS; 5-year, 77% ± 4%) and overall survival (OS; 5-year, 85% ± 3%) were significantly better than EFS (5-year, 35% ± 1%) and OS (5-year, 42% ± 1%) for non-4N stage 4 patients (P < .001). 4N patients were more likely to be younger (P < .001) and have tumors with favorable characteristics, including absence of MYCN amplification (89% v 69%; P < .001). In a multivariable analysis, 4N disease remained a significant predictor of outcome (hazard ratio for non-4N v 4N: 3.40 for EFS and 3.69 for OS). Within subgroups defined by age at diagnosis and tumor MYCN status, 4N disease was significantly associated with improved outcomes. Conclusion 4N represents a subgroup with better outcome than that of other patients with metastatic disease. These findings suggest that the biology and treatment response of 4N tumors differ from other stage 4 tumors, and less intensive therapy should be considered for this cohort. Future exploration of biologic factors determining the pattern of metastatic spread is warranted. PMID:24663047

Relational databases: a transparent framework for encouraging biology students to think informatically.

PubMed

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills.

Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically

PubMed Central

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills. PMID:15592597

Development of USDA's expanded flavonoid database: A Tool for Epidemiological Research

USDA-ARS?s Scientific Manuscript database

The scientific community continues to be interested in potential links between flavonoid intakes and beneficial health effects associated with certain chronic diseases such as cardiovascular diseases, some cancers and type 2 diabetes. Three separate flavonoid databases (Flavonoids (5 subclasses: fl...

WormQTLHD—a web database for linking human disease to natural variation data in C. elegans

PubMed Central

van der Velde, K. Joeri; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, L. Basten; Kammenga, Jan E.; Jansen, Ritsert C.; Swertz, Morris A.; Li, Yang

2014-01-01

Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism—Caenorhabditis elegans—has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTLHD (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene–disease associations in man. WormQTLHD, available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene–disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench. PMID:24217915

WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.

PubMed

van der Velde, K Joeri; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, L Basten; Kammenga, Jan E; Jansen, Ritsert C; Swertz, Morris A; Li, Yang

2014-01-01

Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism-Caenorhabditis elegans-has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTL(HD) (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene-disease associations in man. WormQTL(HD), available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene-disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench.

Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

USDA-ARS?s Scientific Manuscript database

Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database...

Software support for Huntingtons disease research.

PubMed Central

Conneally, P. M.; Gersting, J. M.; Gray, J. M.; Beidleman, K.; Wexler, N. S.; Smith, C. L.

1991-01-01

Huntingtons disease (HD) is a hereditary disorder involving the central nervous system. Its effects are devastating, to the affected person as well as his family. The Department of Medical and Molecular Genetics at Indiana University (IU) plays an integral part in Huntingtons research by providing computerized repositories of HD family information for researchers and families. The National Huntingtons Disease Research Roster, founded in 1979 at IU, and the Huntingtons Disease in Venezuela Project database contain information that has proven to be invaluable in the worldwide field of HD research. This paper addresses the types of information stored in each database, the pedigree database program (MEGADATS) used to manage the data, and significant findings that have resulted from access to the data. PMID:1839672

Biological age as a health index for mortality and major age-related disease incidence in Koreans: National Health Insurance Service – Health screening 11-year follow-up study

PubMed Central

Kang, Young Gon; Suh, Eunkyung; Lee, Jae-woo; Kim, Dong Wook; Cho, Kyung Hee; Bae, Chul-Young

2018-01-01

Purpose A comprehensive health index is needed to measure an individual’s overall health and aging status and predict the risk of death and age-related disease incidence, and evaluate the effect of a health management program. The purpose of this study is to demonstrate the validity of estimated biological age (BA) in relation to all-cause mortality and age-related disease incidence based on National Sample Cohort database. Patients and methods This study was based on National Sample Cohort database of the National Health Insurance Service – Eligibility database and the National Health Insurance Service – Medical and Health Examination database of the year 2002 through 2013. BA model was developed based on the National Health Insurance Service – National Sample Cohort (NHIS – NSC) database and Cox proportional hazard analysis was done for mortality and major age-related disease incidence. Results For every 1 year increase of the calculated BA and chronological age difference, the hazard ratio for mortality significantly increased by 1.6% (1.5% in men and 2.0% in women) and also for hypertension, diabetes mellitus, heart disease, stroke, and cancer incidence by 2.5%, 4.2%, 1.3%, 1.6%, and 0.4%, respectively (p<0.001). Conclusion Estimated BA by the developed BA model based on NHIS – NSC database is expected to be used not only as an index for assessing health and aging status and predicting mortality and major age-related disease incidence, but can also be applied to various health care fields. PMID:29593385

Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

NASA Astrophysics Data System (ADS)

Hasan, Nor'Aishah; Rafii, Mohd Y.; Rahim, Harun A.; Ali, Nusaibah Syd; Mazlan, Norida; Abdullah, Shamsiah

2016-02-01

Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberang Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.

Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, Nor’Aishah, E-mail: aishahnh@ns.uitm.edu.my; Rafii, Mohd Y., E-mail: mrafii@upm.edu.my; Department of Crop Science, Universiti Putra Malaysia

2016-02-01

Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberangmore » Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.« less

Determining Chronic Disease Prevalence in Local Populations Using Emergency Department Surveillance

PubMed Central

Long, Judith A.; Wall, Stephen P.; Carr, Brendan G.; Satchell, Samantha N.; Braithwaite, R. Scott; Elbel, Brian

2015-01-01

Objectives. We sought to improve public health surveillance by using a geographic analysis of emergency department (ED) visits to determine local chronic disease prevalence. Methods. Using an all-payer administrative database, we determined the proportion of unique ED patients with diabetes, hypertension, or asthma. We compared these rates to those determined by the New York City Community Health Survey. For diabetes prevalence, we also analyzed the fidelity of longitudinal estimates using logistic regression and determined disease burden within census tracts using geocoded addresses. Results. We identified 4.4 million unique New York City adults visiting an ED between 2009 and 2012. When we compared our emergency sample to survey data, rates of neighborhood diabetes, hypertension, and asthma prevalence were similar (correlation coefficient = 0.86, 0.88, and 0.77, respectively). In addition, our method demonstrated less year-to-year scatter and identified significant variation of disease burden within neighborhoods among census tracts. Conclusions. Our method for determining chronic disease prevalence correlates with a validated health survey and may have higher reliability over time and greater granularity at a local level. Our findings can improve public health surveillance by identifying local variation of disease prevalence. PMID:26180983

Determining Chronic Disease Prevalence in Local Populations Using Emergency Department Surveillance.

PubMed

Lee, David C; Long, Judith A; Wall, Stephen P; Carr, Brendan G; Satchell, Samantha N; Braithwaite, R Scott; Elbel, Brian

2015-09-01

We sought to improve public health surveillance by using a geographic analysis of emergency department (ED) visits to determine local chronic disease prevalence. Using an all-payer administrative database, we determined the proportion of unique ED patients with diabetes, hypertension, or asthma. We compared these rates to those determined by the New York City Community Health Survey. For diabetes prevalence, we also analyzed the fidelity of longitudinal estimates using logistic regression and determined disease burden within census tracts using geocoded addresses. We identified 4.4 million unique New York City adults visiting an ED between 2009 and 2012. When we compared our emergency sample to survey data, rates of neighborhood diabetes, hypertension, and asthma prevalence were similar (correlation coefficient = 0.86, 0.88, and 0.77, respectively). In addition, our method demonstrated less year-to-year scatter and identified significant variation of disease burden within neighborhoods among census tracts. Our method for determining chronic disease prevalence correlates with a validated health survey and may have higher reliability over time and greater granularity at a local level. Our findings can improve public health surveillance by identifying local variation of disease prevalence.

Health Information-Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease.

PubMed

Pesälä, Samuli; Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-11-06

People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician's Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs' queries, and what causes possible differences in behavior. The aim of our study was to evaluate how the general public's and HCPs' information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public's information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician's Databases, were used. We compared the general public's article openings on Lyme disease from Health Library to HCPs' article openings on Lyme disease from Physician's Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Both databases, Health Library and Physician's Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Lyme disease-related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public's article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public's access to Health Library. ©Samuli Pesälä, Mikko J Virtanen, Jussi Sane, Pekka Mustonen, Minna Kaila, Otto Helve. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.11.2017.

WOVOdat - An online, growing library of worldwide volcanic unrest

NASA Astrophysics Data System (ADS)

Newhall, C. G.; Costa, F.; Ratdomopurbo, A.; Venezky, D. Y.; Widiwijayanti, C.; Win, Nang Thin Zar; Tan, K.; Fajiculay, E.

2017-10-01

The World Organization of Volcano Observatories (WOVO), with major support from the Earth Observatory of Singapore, is developing a web-accessible database of seismic, geodetic, gas, hydrologic, and other unrest from volcanoes around the world. This database, WOVOdat, is intended for reference during volcanic crises, comparative studies, basic research on pre-eruption processes, teaching, and outreach. Data are already processed to have physical meaning, e.g. earthquake hypocenters rather than voltages or arrival times, and are historical rather than real-time, ranging in age from a few days to several decades. Data from > 900 episodes of unrest covering > 75 volcanoes are already accessible. Users can visualize and compare changes from one episode of unrest or from one volcano to the next. As the database grows more complete, users will be able to analyze patterns of unrest in the same way that epidemiologists study the spatial and temporal patterns and associations among diseases. WOVOdat was opened for station and data visualization in August 2013, and now includes utilities for data downloads and Boolean searches. Many more data sets are being added, as well as utilities interfacing to new applications, e.g., the construction of event trees. For more details, please see www.wovodat.org.

TISSUES 2.0: an integrative web resource on mammalian tissue expression

PubMed Central

Palasca, Oana; Santos, Alberto; Stolte, Christian; Gorodkin, Jan; Jensen, Lars Juhl

2018-01-01

Abstract Physiological and molecular similarities between organisms make it possible to translate findings from simpler experimental systems—model organisms—into more complex ones, such as human. This translation facilitates the understanding of biological processes under normal or disease conditions. Researchers aiming to identify the similarities and differences between organisms at the molecular level need resources collecting multi-organism tissue expression data. We have developed a database of gene–tissue associations in human, mouse, rat and pig by integrating multiple sources of evidence: transcriptomics covering all four species and proteomics (human only), manually curated and mined from the scientific literature. Through a scoring scheme, these associations are made comparable across all sources of evidence and across organisms. Furthermore, the scoring produces a confidence score assigned to each of the associations. The TISSUES database (version 2.0) is publicly accessible through a user-friendly web interface and as part of the STRING app for Cytoscape. In addition, we analyzed the agreement between datasets, across and within organisms, and identified that the agreement is mainly affected by the quality of the datasets rather than by the technologies used or organisms compared. Database URL: http://tissues.jensenlab.org/ PMID:29617745

Current status of registry of vaccine clinical trials conducted by Korean investigators in ClinicalTrials.gov, database of US National Institutes of Health.

PubMed

Cho, Jahyang; Kim, Bo Bae; Bae, Chong-Woo; Cha, Sung-Ho

2013-01-01

PubMed is not only includes international medical journals but also has a registration site for the ongoing clinical trials, such as ClinicalTrials.gov, under the supervision of US National Institutes of Health. We analyzed current status of vaccine clinical trials conducted by Korean investigators in database of ClinicalTrial.gov. As of October 2012, there are total of 72 trials found on registry of vaccine clinical trials conducted by Korean investigators in database of ClinicalTrial.gov. These trials were analyzed and classified by conditions of vaccine clinical trials, biologicals or drugs used in vaccine clinical trials, status of proceeding research, and list of sponsor and collaborators. Total 72 trials of vaccine clinical trials conducted by Korean investigators are classified by groups of infection (64 trials), cancer (4 trials), and others (4 trials). Infections group shown are as follows: poliomyelitis, pertussis, diphtheria, tetanus, and Haemophilus influenzae type b (10), influenza (9), human papillomavirus infection (8), pneumococcal vaccine (6), herpes zoster (4), smallpox (4), hepatitis B (4), etc. One trial of each in lung cancer, breast cancer, prostate cancer, and colorectal cancer are shown in cancer group. One trial of each in Crohn's disease, ulcerative colitis, renal failure, and rheumatoid arthritis are shown in other group. Vaccine clinical trials conducted by Korean investigators in ClinicalTrial.gov reflects the current status of Korean research on vaccine clinical trials at the international level and can indicate research progress. It is hoped that this aids the development of future vaccine clinical trials in Korea.

Economic evaluation of manual therapy for musculoskeletal diseases: a protocol for a systematic review and narrative synthesis of evidence.

PubMed

Kim, Chang-Gon; Mun, Su-Jeong; Kim, Ka-Na; Shin, Byung-Cheul; Kim, Nam-Kwen; Lee, Dong-Hyo; Lee, Jung-Han

2016-05-13

Manual therapy is the non-surgical conservative management of musculoskeletal disorders using the practitioner's hands on the patient's body for diagnosing and treating disease. The aim of this study is to systematically review trial-based economic evaluations of manual therapy relative to other interventions used for the management of musculoskeletal diseases. Randomised clinical trials (RCTs) on the economic evaluation of manual therapy for musculoskeletal diseases will be included in the review. The following databases will be searched from their inception: Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Econlit, Mantis, Index to Chiropractic Literature, Science Citation Index, Social Science Citation Index, Allied and Complementary Medicine Database (AMED), Cochrane Database of Systematic Reviews (CDSR), National Health Service Database of Abstracts of Reviews of Effects (NHS DARE), National Health Service Health Technology Assessment Database (NHS HTA), National Health Service Economic Evaluation Database (NHS EED), CENTRAL, five Korean medical databases (Oriental Medicine Advanced Searching Integrated System (OASIS), Research Information Service System (RISS), DBPIA, Korean Traditional Knowledge Portal (KTKP) and KoreaMed) and three Chinese databases (China National Knowledge Infrastructure (CNKI), VIP and Wanfang). The evidence for the cost-effectiveness, cost-utility and cost-benefit of manual therapy for musculoskeletal diseases will be assessed as the primary outcome. Health-related quality of life and adverse effects will be assessed as secondary outcomes. We will critically appraise the included studies using the Cochrane risk of bias tool and the Drummond checklist. Results will be summarised using Slavin's qualitative best-evidence synthesis approach. The results of the study will be disseminated via a peer-reviewed journal and/or conference presentations. PROSPERO CRD42015026757. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

A comprehensive global genotype-phenotype database for rare diseases.

PubMed

Trujillano, Daniel; Oprea, Gabriela-Elena; Schmitz, Yvonne; Bertoli-Avella, Aida M; Abou Jamra, Rami; Rolfs, Arndt

2017-01-01

The ability to discover genetic variants in a patient runs far ahead of the ability to interpret them. Databases with accurate descriptions of the causal relationship between the variants and the phenotype are valuable since these are critical tools in clinical genetic diagnostics. Here, we introduce a comprehensive and global genotype-phenotype database focusing on rare diseases. This database (CentoMD ® ) is a browser-based tool that enables access to a comprehensive, independently curated system utilizing stringent high-quality criteria and a quickly growing repository of genetic and human phenotype ontology (HPO)-based clinical information. Its main goals are to aid the evaluation of genetic variants, to enhance the validity of the genetic analytical workflow, to increase the quality of genetic diagnoses, and to improve evaluation of treatment options for patients with hereditary diseases. The database software correlates clinical information from consented patients and probands of different geographical backgrounds with a large dataset of genetic variants and, when available, biomarker information. An automated follow-up tool is incorporated that informs all users whenever a variant classification has changed. These unique features fully embedded in a CLIA/CAP-accredited quality management system allow appropriate data quality and enhanced patient safety. More than 100,000 genetically screened individuals are documented in the database, resulting in more than 470 million variant detections. Approximately, 57% of the clinically relevant and uncertain variants in the database are novel. Notably, 3% of the genetic variants identified and previously reported in the literature as being associated with a particular rare disease were reclassified, based on internal evidence, as clinically irrelevant. The database offers a comprehensive summary of the clinical validity and causality of detected gene variants with their associated phenotypes, and is a valuable tool for identifying new disease genes through the correlation of novel genetic variants with specific, well-defined phenotypes.

Validation of chronic obstructive pulmonary disease (COPD) diagnoses in healthcare databases: a systematic review protocol.

PubMed

Rimland, Joseph M; Abraha, Iosief; Luchetta, Maria Laura; Cozzolino, Francesco; Orso, Massimiliano; Cherubini, Antonio; Dell'Aquila, Giuseppina; Chiatti, Carlos; Ambrosio, Giuseppe; Montedori, Alessandro

2016-06-01

Healthcare databases are useful sources to investigate the epidemiology of chronic obstructive pulmonary disease (COPD), to assess longitudinal outcomes in patients with COPD, and to develop disease management strategies. However, in order to constitute a reliable source for research, healthcare databases need to be validated. The aim of this protocol is to perform the first systematic review of studies reporting the validation of codes related to COPD diagnoses in healthcare databases. MEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched using appropriate search strategies. Studies that evaluated the validity of COPD codes (such as the International Classification of Diseases 9th Revision and 10th Revision system; the Real codes system or the International Classification of Primary Care) in healthcare databases will be included. Inclusion criteria will be: (1) the presence of a reference standard case definition for COPD; (2) the presence of at least one test measure (eg, sensitivity, positive predictive values, etc); and (3) the use of a healthcare database (including administrative claims databases, electronic healthcare databases or COPD registries) as a data source. Pairs of reviewers will independently abstract data using standardised forms and will assess quality using a checklist based on the Standards for Reporting of Diagnostic accuracy (STARD) criteria. This systematic review protocol has been produced in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) 2015 statement. Ethics approval is not required. Results of this study will be submitted to a peer-reviewed journal for publication. The results from this systematic review will be used for outcome research on COPD and will serve as a guide to identify appropriate case definitions of COPD, and reference standards, for researchers involved in validating healthcare databases. CRD42015029204. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Incidence, disease phenotype at diagnosis, and early disease course in inflammatory bowel diseases in Western Hungary, 2002-2006.

PubMed

Lakatos, Laszlo; Kiss, Lajos S; David, Gyula; Pandur, Tunde; Erdelyi, Zsuzsanna; Mester, Gabor; Balogh, Mihaly; Szipocs, Istvan; Molnar, Csaba; Komaromi, Erzsebet; Lakatos, Peter Laszlo

2011-12-01

Recent trends indicate a change in the epidemiology of inflammatory bowel diseases (IBD), with previously low incidence areas now reporting a progressive rise in the incidence. Our aim was to analyze the incidence and disease phenotype at diagnosis in IBD in the population-based Veszprem Province database, which included incident patients diagnosed between January 1, 2002 and December 31, 2006. Data of 393 incident patients were analyzed (ulcerative colitis [UC]: 220, age-at-diagnosis: 40.5 years; Crohn's disease [CD]: 163, age-at-diagnosis: 32.5 years; and indeterminate colitis [IC]: 10). Both hospital and outpatient records were collected and comprehensively reviewed. Adjusted mean incidence rates were 8.9/10(5) person-years for CD and 11.9/10(5) person-years in UC. Peak onset age in both CD and UC patients was 21-30 years old. Location at diagnosis in UC was proctitis in 26.8%, left-sided colitis in 50.9%, and pancolitis in 22.3%. The probability of proximal extension and colectomy after 5 years was 12.7% and 2.8%. The disease location in CD was ileal in 20.2%, colonic in 35.6%, ileocolonic in 44.2%, and upper gastrointestinal in four patients. Behavior at diagnosis was stenosing/penetrating in 35.6% and perianal in 11.1%. Patients with colonic disease were older at diagnosis compared to patients with ileal or ileocolonic disease. In a Kaplan-Meier analysis, probability of surgical resection was 9.8%, 18.5%, and 21.3% after 1, 3, and 5 years of disease duration, respectively. The incidence of IBD in Veszprem Province in the last decade was high, equal to that in high-incidence areas in Western European countries. Early disease course is milder compared to data reported in the literature. Copyright © 2011 Crohn's & Colitis Foundation of America, Inc.

Including the Group Quarters Population in the US Synthesized Population Database

PubMed Central

Chasteen, Bernadette M.; Wheaton, William D.; Cooley, Philip C.; Ganapathi, Laxminarayana; Wagener, Diane K.

2011-01-01

In 2005, RTI International researchers developed methods to generate synthesized population data on US households for the US Synthesized Population Database. These data are used in agent-based modeling, which simulates large-scale social networks to test how changes in the behaviors of individuals affect the overall network. Group quarters are residences where individuals live in close proximity and interact frequently. Although the Synthesized Population Database represents the population living in households, data for the nation’s group quarters residents are not easily quantified because of US Census Bureau reporting methods designed to protect individuals’ privacy. Including group quarters population data can be an important factor in agent-based modeling because the number of residents and the frequency of their interactions are variables that directly affect modeling results. Particularly with infectious disease modeling, the increased frequency of agent interaction may increase the probability of infectious disease transmission between individuals and the probability of disease outbreaks. This report reviews our methods to synthesize data on group quarters residents to match US Census Bureau data. Our goal in developing the Group Quarters Population Database was to enable its use with RTI’s US Synthesized Population Database in the Modeling of Infectious Diseases Agent Study. PMID:21841972

The European Narcolepsy Network (EU-NN) database.

PubMed

Khatami, Ramin; Luca, Gianina; Baumann, Christian R; Bassetti, Claudio L; Bruni, Oliviero; Canellas, Francesca; Dauvilliers, Yves; Del Rio-Villegas, Rafael; Feketeova, Eva; Ferri, Raffaele; Geisler, Peter; Högl, Birgit; Jennum, Poul; Kornum, Birgitte R; Lecendreux, Michel; Martins-da-Silva, Antonio; Mathis, Johannes; Mayer, Geert; Paiva, Teresa; Partinen, Markku; Peraita-Adrados, Rosa; Plazzi, Guiseppe; Santamaria, Joan; Sonka, Karel; Riha, Renata; Tafti, Mehdi; Wierzbicka, Aleksandra; Young, Peter; Lammers, Gert Jan; Overeem, Sebastiaan

2016-06-01

Narcolepsy with cataplexy is a rare disease with an estimated prevalence of 0.02% in European populations. Narcolepsy shares many features of rare disorders, in particular the lack of awareness of the disease with serious consequences for healthcare supply. Similar to other rare diseases, only a few European countries have registered narcolepsy cases in databases of the International Classification of Diseases or in registries of the European health authorities. A promising approach to identify disease-specific adverse health effects and needs in healthcare delivery in the field of rare diseases is to establish a distributed expert network. A first and important step is to create a database that allows collection, storage and dissemination of data on narcolepsy in a comprehensive and systematic way. Here, the first prospective web-based European narcolepsy database hosted by the European Narcolepsy Network is introduced. The database structure, standardization of data acquisition and quality control procedures are described, and an overview provided of the first 1079 patients from 18 European specialized centres. Due to its standardization this continuously increasing data pool is most promising to provide a better insight into many unsolved aspects of narcolepsy and related disorders, including clear phenotype characterization of subtypes of narcolepsy, more precise epidemiological data and knowledge on the natural history of narcolepsy, expectations about treatment effects, identification of post-marketing medication side-effects, and will contribute to improve clinical trial designs and provide facilities to further develop phase III trials. © 2016 European Sleep Research Society.

FIREMON Database

Treesearch

John F. Caratti

2006-01-01

The FIREMON database software allows users to enter data, store, analyze, and summarize plot data, photos, and related documents. The FIREMON database software consists of a Java application and a Microsoft® Access database. The Java application provides the user interface with FIREMON data through data entry forms, data summary reports, and other data management tools...

Database constraints applied to metabolic pathway reconstruction tools.

PubMed

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Invasive candidiasis and oral manifestations in premature newborns.

PubMed

Tinoco-Araujo, José Endrigo; Araújo, Diana Ferreira Gadelha; Barbosa, Patrícia Gomes; Santos, Paulo Sérgio da Silva; Medeiros, Ana Myriam Costa de

2013-01-01

To investigate prevalence of invasive candidiasis in a Neonatal Intensive Care Unit and to evaluate oral diseases and Candida spp. colonization in low birth weight preterm newborns. A descriptive epidemiological study performed in two stages. First, prevalence of candidiasis was analyzed in a database of 295 preterm patients admitted to hospital for over 10 days and birth weight less than 2,000g. In the second stage, oral changes and Candida spp. colonization were assessed in 65 patients weighing less than 2,000g, up to 4 week-old, hospitalized for over 10 days and presenting oral abnormalities compatible with fungal lesions. Swab samples were collected in the mouth to identify fungi. Prevalence of candidiasis was 5.4% in the database analyzed. It correlated with prolonged hospital length of stay (p<0.001), in average, 31 days, and 85% risk of developing infection in the first 25 days. It correlated with low birth weight (p<0.001), with mean of 1,140g. The most frequent alterations were white soft plaques, detachable, in oral mucosa and tongue. Intense oral colonization by Candida spp was observed (80%). The frequency of invasive candidiasis was low and correlated with low birth weight and prolonged hospital stay. The most common oral changes were white plaques compatible with pseudomembranous candidiasis and colonization by Candida spp. was above average.

Sex differences in acupuncture effectiveness in animal models of Parkinson's disease: a systematic review.

PubMed

Lee, Sook-Hyun; van den Noort, Maurits; Bosch, Peggy; Lim, Sabina

2016-11-03

Many animal experimental studies have been performed to investigate the efficacy of acupuncture in Parkinson's disease (PD). Sex differences are a major issue in all diseases including PD. However, to our knowledge, there have been no reviews investigating sex differences on the effectiveness of acupuncture treatment for animal PD models. The current study aimed to summarize and analyze past studies in order to evaluate these possible differences. Each of 7 databases (MEDLINE, EMBASE, the Cochrane Library, 3 Korean medical databases, and the China National Knowledge Infrastructure) was searched from its inception through March 2015 without language restrictions. We included studies of the use of acupuncture treatment in animal models of PD. A total of 810 potentially relevant articles were identified, 57 of which met our inclusion criteria. C57/BL6 mice were used most frequently (42 %) in animal PD models. Most of the studies were carried out using only male animals (67 %); only 1 study (2 %) was performed using solely females. The further 31 % of the studies used a male/female mix or did not specify the sex. The results of our review suggest that acupuncture is an effective treatment for animal PD models, but there is insufficient evidence to determine whether sex differences exist. Future studies of acupuncture treatment for PD should use female animal models because they reflect the physiological characteristics of both males and females to fully evaluate the effect and the safety of the treatment for each sex.

Psychotropics in different causes of itch: systematic review with controlled studies*

PubMed Central

Brasileiro, Lízie Emanuelle Eulalio; Barreto, Dayanna Patrícia de Carvalho; Nunes, Emerson Arcoverde

2016-01-01

Among the wide range of symptoms neglected or resistant to conventional treatments in clinical practice, itch is emerging gradually as a theme to be studied. Itch complaints and the negative effects in the quality of life are observed in several medical fields. Although the partially obscure pathophysiology, some researchers decided to check and test the use of psychotropic drugs in resistant itch to conventional topical treatments and antihistamines. The objective of this study was to evaluate scientific evidence in psychotropic use in the treatment of itch of various causes. This is a systematic review of scientific literature. The following databases were used: PubMed, Web of Science, Scopus and Scielo. Randomized controlled trials that should focus on treatment with psychotropic drugs of pruritus of various causes were the inclusion criteria. All articles were analyzed by the authors, and the consensus was reached in cases of disagreement. Fifteen articles were included after analysis and selection in databases, with the majority of clinical trials focusing on psychopharmacological treatment of itch on account of chronic kidney disease. Clinical trials with psychotropic drugs mostly indicated significant improvement in the itching. In most trials of chronic kidney disease as basal disease for itch, greater effectiveness was observed with the use of psychotropic drugs compared with placebo or other antipruritic. However, the small amount of controlled trials conducted precludes the generalization that psychiatric drugs are effective for itch of various causes. PMID:28099602

Burden of herpes simplex virus encephalitis in the United States.

PubMed

Modi, S; Mahajan, Abhimanyu; Dharaiya, D; Varelas, P; Mitsias, P

2017-06-01

Herpes simplex virus encephalitis (HSVE) is a disease of public health concern, but its burden on the healthcare of United States has not been adequately assessed recently. We aimed to define the incidence, complications and outcomes of HSVE in the recent decade by analyzing data from a nationally representative database. Healthcare Cost and Utilization Project databases were utilized to identify patients with primary discharge diagnosis of HSVE. Annual hospitalization rate was estimated and several preselected inpatient complications were identified. Regression analyses were used to identify mortality predictors. Key epidemiological factors were compared with those from other countries. Total 4871 patients of HSVE were included in our study. The annual hospitalization rate was 10.3 ± 2.2 cases/million in neonates, 2.4 ± 0.3 cases/million in children and 6.4 ± 0.4 cases/million in adults. Median age was 57 years and male:female incidence ratio was 1:1. Rates of some central nervous system complications were seizures (38.4%), status epilepticus (5.5%), acute respiratory failure (20.1%), ischemic stroke (5.6%) and intracranial hemorrhage (2.7%), all of which were significantly associated with mortality. In-hospital mortality in neonates, children and adults were 6.9, 1.2 and 7.7%, respectively. HSVE still remains a potentially lethal infectious disease with high morbidity and mortality. Most recent epidemiological data in this study may help understanding this public health disease, and the patient outcome data may have prognostic significance.

Data Auditor: Analyzing Data Quality Using Pattern Tableaux

NASA Astrophysics Data System (ADS)

Srivastava, Divesh

Monitoring databases maintain configuration and measurement tables about computer systems, such as networks and computing clusters, and serve important business functions, such as troubleshooting customer problems, analyzing equipment failures, planning system upgrades, etc. These databases are prone to many data quality issues: configuration tables may be incorrect due to data entry errors, while measurement tables may be affected by incorrect, missing, duplicate and delayed polls. We describe Data Auditor, a tool for analyzing data quality and exploring data semantics of monitoring databases. Given a user-supplied constraint, such as a boolean predicate expected to be satisfied by every tuple, a functional dependency, or an inclusion dependency, Data Auditor computes "pattern tableaux", which are concise summaries of subsets of the data that satisfy or fail the constraint. We discuss the architecture of Data Auditor, including the supported types of constraints and the tableau generation mechanism. We also show the utility of our approach on an operational network monitoring database.

Protocol for developing a Database of Zoonotic disease Research in India (DoZooRI).

PubMed

Chatterjee, Pranab; Bhaumik, Soumyadeep; Chauhan, Abhimanyu Singh; Kakkar, Manish

2017-12-10

Zoonotic and emerging infectious diseases (EIDs) represent a public health threat that has been acknowledged only recently although they have been on the rise for the past several decades. On an average, every year since the Second World War, one pathogen has emerged or re-emerged on a global scale. Low/middle-income countries such as India bear a significant burden of zoonotic and EIDs. We propose that the creation of a database of published, peer-reviewed research will open up avenues for evidence-based policymaking for targeted prevention and control of zoonoses. A large-scale systematic mapping of the published peer-reviewed research conducted in India will be undertaken. All published research will be included in the database, without any prejudice for quality screening, to broaden the scope of included studies. Structured search strategies will be developed for priority zoonotic diseases (leptospirosis, rabies, anthrax, brucellosis, cysticercosis, salmonellosis, bovine tuberculosis, Japanese encephalitis and rickettsial infections), and multiple databases will be searched for studies conducted in India. The database will be managed and hosted on a cloud-based platform called Rayyan. Individual studies will be tagged based on key preidentified parameters (disease, study design, study type, location, randomisation status and interventions, host involvement and others, as applicable). The database will incorporate already published studies, obviating the need for additional ethical clearances. The database will be made available online, and in collaboration with multisectoral teams, domains of enquiries will be identified and subsequent research questions will be raised. The database will be queried for these and resulting evidence will be analysed and published in peer-reviewed journals. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Clinical effectiveness and safety of leflunomide in inflammatory arthritis: a report from the RAPPORT database with supporting patient survey.

PubMed

Schultz, Morgan; Keeling, Stephanie O; Katz, Steven J; Maksymowych, Walter P; Eurich, Dean T; Hall, Jill J

2017-07-01

Leflunomide is indicated for the treatment of adults with rheumatoid arthritis, yet is underutilized. Given the cost of biologic therapy, understanding real-life effectiveness, safety, and sustainability of leflunomide, particularly in patients who have failed methotrexate, would be of value. The primary objective was to assess the proportion of patients achieving clinically meaningful benefit following an adequate trial of leflunomide. A retrospective analysis of a cohort supplemented with patient self-reported data using a standardized questionnaire. Data were analyzed using descriptive statistics, with a database multivariate logistic regression analysis to determine predictors of leflunomide response. Of the cohort available (N = 2591), 1671 patients with confirmed leflunomide use were included in the retrospective analysis, of whom 249 were incident users. Low disease activity (DAS-28 < 3.2) was achieved or maintained by 20% of incident users, with 19% achieving a clinical response (DAS-28 decrease ≥1.2) at 3 months. Adverse effects (AE) were reported by 29% of incident users and after 1 year, 45% remained on leflunomide. Achievement of "minimal or no joint symptoms" was reported by 34% in the 661 analyzable survey responses (39% response rate). AE were reported by 55%, with nuisance (hair loss, nausea, stomach pain) AE and diarrhea being most common. Leflunomide was discontinued by 67% of responders within 1 year. An important proportion of patients, the majority of whom had previously failed methotrexate, achieved disease response with leflunomide with a low risk of serious adverse effects, suggesting that a trial of leflunomide may be a reasonable and cost-effective strategy prior to biologic therapy.

Exploring Site-Specific N-Glycosylation Microheterogeneity of Haptoglobin using Glycopeptide CID Tandem Mass Spectra and Glycan Database Search

PubMed Central

Chandler, Kevin Brown; Pompach, Petr; Goldman, Radoslav

2013-01-01

Glycosylation is a common protein modification with a significant role in many vital cellular processes and human diseases, making the characterization of protein-attached glycan structures important for understanding cell biology and disease processes. Direct analysis of protein N-glycosylation by tandem mass spectrometry of glycopeptides promises site-specific elucidation of N-glycan microheterogeneity, something which detached N-glycan and de-glycosylated peptide analyses cannot provide. However, successful implementation of direct N-glycopeptide analysis by tandem mass spectrometry remains a challenge. In this work, we consider algorithmic techniques for the analysis of LC-MS/MS data acquired from glycopeptide-enriched fractions of enzymatic digests of purified proteins. We implement a computational strategy which takes advantage of the properties of CID fragmentation spectra of N-glycopeptides, matching the MS/MS spectra to peptide-glycan pairs from protein sequences and glycan structure databases. Significantly, we also propose a novel false-discovery-rate estimation technique to estimate and manage the number of false identifications. We use a human glycoprotein standard, haptoglobin, digested with trypsin and GluC, enriched for glycopeptides using HILIC chromatography, and analyzed by LC-MS/MS to demonstrate our algorithmic strategy and evaluate its performance. Our software, GlycoPeptideSearch (GPS), assigned glycopeptide identifications to 246 of the spectra at false-discovery-rate 5.58%, identifying 42 distinct haptoglobin peptide-glycan pairs at each of the four haptoglobin N-linked glycosylation sites. We further demonstrate the effectiveness of this approach by analyzing plasma-derived haptoglobin, identifying 136 N-linked glycopeptide spectra at false-discovery-rate 0.4%, representing 15 distinct glycopeptides on at least three of the four N-linked glycosylation sites. The software, GlycoPeptideSearch, is available for download from http://edwardslab.bmcb.georgetown.edu/GPS. PMID:23829323

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.

PubMed

Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin; Senger, Philipp

2015-01-01

Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer's disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html. © The Author(s) 2015. Published by Oxford University Press.

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

PubMed Central

Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin

2015-01-01

Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article’s supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer’s disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html PMID:26475471

Digestive system-related pathophysiological symptoms of Sasang typology: Systematic review.

PubMed

Lee, Mi Suk; Sohn, Kyungwoo; Kim, Yun Hee; Hwang, Min-Woo; Kwon, Young Kyu; Bae, Na Young; Chae, Han

2013-06-01

The purpose of this study was to review clinical studies on digestive system-related pathophysiological symptoms of each Sasang type to obtain the generalizable typespecific clinical features, which are important for the diagnosis of the Sasang type and subsequent disease treatment. Sasang typology and digestive system symptom-related keywords were used to search through eight domestic and foreign databases up to March 2012. The results were organized and analyzed based on four categories [digestive function, appetite, eating pattern, and body mass index (BMI)] to elucidate type-specific symptoms. Sasang type-specific digestive system-related symptoms were identified by reviewing 30 related articles that were gathered by searching through the databases. The Tae-Eum (TE) type had the highest digestive functions and the So-Eum (SE) type had the lowest. The TE type appeared to have larger volume with fast eating speed compared with the SE type and individuals in the TE category preferred fatty or salty food, which is responsible for the high occurrence rates of organic digestive diseases such as gastritis. Moreover, BMI was higher in the TE type and lower in the SE type. We systematically reviewed previously published clinical reports on digestive functions, which can be used to meet the objective of Sasang-type differentiation and pathophysiological pattern identification.

A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

PubMed

Kogi, M; Fukushige, S; Lefevre, C; Hadano, S; Ikeda, J E

1997-06-01

In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

PATRIC, the bacterial bioinformatics database and analysis resource.

PubMed

Wattam, Alice R; Abraham, David; Dalay, Oral; Disz, Terry L; Driscoll, Timothy; Gabbard, Joseph L; Gillespie, Joseph J; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K; Olson, Robert; Overbeek, Ross; Pusch, Gordon D; Shukla, Maulik; Schulman, Julie; Stevens, Rick L; Sullivan, Daniel E; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J C; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W

2014-01-01

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

PATRIC, the bacterial bioinformatics database and analysis resource

PubMed Central

Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J.C.; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W.

2014-01-01

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue. PMID:24225323

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.

PubMed

Buza, Teresia M; Jack, Sherman W; Kirunda, Halid; Khaitsa, Margaret L; Lawrence, Mark L; Pruett, Stephen; Peterson, Daniel G

2015-01-01

There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides more plausible arguments to achieve better understanding of infectious and zoonotic diseases. We have developed a model for interlinking annotations of these diseases. These diseases are of particular interest because of the threats they pose to animal health, human health and global health security. We demonstrated the application of this model using brucellosis, an infectious and zoonotic disease. Preliminary annotations were deposited into VetBioBase database (http://vetbiobase.igbb.msstate.edu). This database is associated with user-friendly tools to facilitate searching, retrieving and downloading of disease-related information. Database URL: http://vetbiobase.igbb.msstate.edu. © The Author(s) 2015. Published by Oxford University Press.

Development, Use, and Impact of a Global Laboratory Database During the 2014 Ebola Outbreak in West Africa.

PubMed

Durski, Kara N; Singaravelu, Shalini; Teo, Junxiong; Naidoo, Dhamari; Bawo, Luke; Jambai, Amara; Keita, Sakoba; Yahaya, Ali Ahmed; Muraguri, Beatrice; Ahounou, Brice; Katawera, Victoria; Kuti-George, Fredson; Nebie, Yacouba; Kohar, T Henry; Hardy, Patrick Jowlehpah; Djingarey, Mamoudou Harouna; Kargbo, David; Mahmoud, Nuha; Assefa, Yewondwossen; Condell, Orla; N'Faly, Magassouba; Van Gurp, Leon; Lamanu, Margaret; Ryan, Julia; Diallo, Boubacar; Daffae, Foday; Jackson, Dikena; Malik, Fayyaz Ahmed; Raftery, Philomena; Formenty, Pierre

2017-06-15

The international impact, rapid widespread transmission, and reporting delays during the 2014 Ebola outbreak in West Africa highlighted the need for a global, centralized database to inform outbreak response. The World Health Organization and Emerging and Dangerous Pathogens Laboratory Network addressed this need by supporting the development of a global laboratory database. Specimens were collected in the affected countries from patients and dead bodies meeting the case definitions for Ebola virus disease. Test results were entered in nationally standardized spreadsheets and consolidated onto a central server. From March 2014 through August 2016, 256343 specimens tested for Ebola virus disease were captured in the database. Thirty-one specimen types were collected, and a variety of diagnostic tests were performed. Regular analysis of data described the functionality of laboratory and response systems, positivity rates, and the geographic distribution of specimens. With data standardization and end user buy-in, the collection and analysis of large amounts of data with multiple stakeholders and collaborators across various user-access levels was made possible and contributed to outbreak response needs. The usefulness and value of a multifunctional global laboratory database is far reaching, with uses including virtual biobanking, disease forecasting, and adaption to other disease outbreaks. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

DRUMS: a human disease related unique gene mutation search engine.

PubMed

Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

2011-10-01

With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

The World Database for Pediatric and Congenital Heart Surgery: The Dawn of a New Era of Global Communication and Quality Improvement in Congenital Heart Disease.

PubMed

St Louis, James D; Kurosawa, Hiromi; Jonas, Richard A; Sandoval, Nestor; Cervantes, Jorge; Tchervenkov, Christo I; Jacobs, Jeffery P; Sakamoto, Kisaburo; Stellin, Giovanni; Kirklin, James K

2017-09-01

The World Society for Pediatric and Congenital Heart Surgery was founded with the mission to "promote the highest quality comprehensive cardiac care to all patients with congenital heart disease, from the fetus to the adult, regardless of the patient's economic means, with an emphasis on excellence in teaching, research, and community service." Early on, the Society's members realized that a crucial step in meeting this goal was to establish a global database that would collect vital information, allowing cardiac surgical centers worldwide to benchmark their outcomes and improve the quality of congenital heart disease care. With tireless efforts from all corners of the globe and utilizing the vast experience and invaluable input of multiple international experts, such a platform of global information exchange was created: The World Database for Pediatric and Congenital Heart Disease went live on January 1, 2017. This database has been thoughtfully designed to produce meaningful performance and quality analyses of surgical outcomes extending beyond immediate hospital survival, allowing capture of important morbidities and mortalities for up to 1 year postoperatively. In order to advance the societal mission, this quality improvement program is available free of charge to WSPCHS members. In establishing the World Database, the Society has taken an essential step to further the process of global improvement in care for children with congenital heart disease.

Health Information–Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease

PubMed Central

Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-01-01

Background People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician’s Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs’ queries, and what causes possible differences in behavior. Objective The aim of our study was to evaluate how the general public’s and HCPs’ information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public’s information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Methods Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician’s Databases, were used. We compared the general public’s article openings on Lyme disease from Health Library to HCPs’ article openings on Lyme disease from Physician’s Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Results Both databases, Health Library and Physician’s Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Conclusions Lyme disease–related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public’s article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public’s access to Health Library. PMID:29109071

Development of an Integrated Biospecimen Database among the Regional Biobanks in Korea.

PubMed

Park, Hyun Sang; Cho, Hune; Kim, Hwa Sun

2016-04-01

This study developed an integrated database for 15 regional biobanks that provides large quantities of high-quality bio-data to researchers to be used for the prevention of disease, for the development of personalized medicines, and in genetics studies. We collected raw data, managed independently by 15 regional biobanks, for database modeling and analyzed and defined the metadata of the items. We also built a three-step (high, middle, and low) classification system for classifying the item concepts based on the metadata. To generate clear meanings of the items, clinical items were defined using the Systematized Nomenclature of Medicine Clinical Terms, and specimen items were defined using the Logical Observation Identifiers Names and Codes. To optimize database performance, we set up a multi-column index based on the classification system and the international standard code. As a result of subdividing 7,197,252 raw data items collected, we refined the metadata into 1,796 clinical items and 1,792 specimen items. The classification system consists of 15 high, 163 middle, and 3,588 low class items. International standard codes were linked to 69.9% of the clinical items and 71.7% of the specimen items. The database consists of 18 tables based on a table from MySQL Server 5.6. As a result of the performance evaluation, the multi-column index shortened query time by as much as nine times. The database developed was based on an international standard terminology system, providing an infrastructure that can integrate the 7,197,252 raw data items managed by the 15 regional biobanks. In particular, it resolved the inevitable interoperability issues in the exchange of information among the biobanks, and provided a solution to the synonym problem, which arises when the same concept is expressed in a variety of ways.

Nonmotor Symptoms in Parkinson Disease: A Descriptive Review on Social Cognition Ability.

PubMed

Palmeri, Rosanna; Lo Buono, Viviana; Corallo, Francesco; Foti, Maria; Di Lorenzo, Giuseppe; Bramanti, Placido; Marino, Silvia

2017-03-01

Parkinson disease (PD) is a neurodegenerative disorder characterized by motor and nonmotor symptoms. Nonmotor symptoms include cognitive deficits and impairment in emotions recognition ability associated with loss of dopaminergic neurons in the substantia nigra and with alteration in frontostriatal circuits. In this review, we analyzed the studies on social cognition ability in patients with PD. We searched on PubMed and Web of Science databases and screening references of included studied and review articles for additional citations. From initial 260 articles, only 18 met search criteria. A total of 496 patients were compared with 514 health controls, through 16 different tests that assessed some subcomponents of social cognition, such as theory of mind, decision-making, and emotional face recognition. Studies on cognitive function in patients with PD have focused on executive function. Patients with PD showed impairment in social cognition from the earliest stages of disease. This ability seems to not be significantly associated with other cognitive functions.

Use of information on disease diagnoses from databases for animal health economic, welfare and food safety purposes: strengths and limitations of recordings.

PubMed

Houe, Hans; Gardner, Ian Andrew; Nielsen, Liza Rosenbaum

2011-01-01

Many animal health, welfare and food safety databases include data on clinical and test-based disease diagnoses. However, the circumstances and constraints for establishing the diagnoses vary considerably among databases. Therefore results based on different databases are difficult to compare and compilation of data in order to perform meta-analysis is almost impossible. Nevertheless, diagnostic information collected either routinely or in research projects is valuable in cross comparisons between databases, but there is a need for improved transparency and documentation of the data and the performance characteristics of tests used to establish diagnoses. The objective of this paper is to outline the circumstances and constraints for recording of disease diagnoses in different types of databases, and to discuss these in the context of disease diagnoses when using them for additional purposes, including research. Finally some limitations and recommendations for use of data and for recording of diagnostic information in the future are given. It is concluded that many research questions have such a specific objective that investigators need to collect their own data. However, there are also examples, where a minimal amount of extra information or continued validation could make sufficient improvement of secondary data to be used for other purposes. Regardless, researchers should always carefully evaluate the opportunities and constraints when they decide to use secondary data. If the data in the existing databases are not sufficiently valid, researchers may have to collect their own data, but improved recording of diagnostic data may improve the usefulness of secondary diagnostic data in the future.

Incidence of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis: A Nationwide Population-Based Study Using National Health Insurance Database in Korea.

PubMed

Yang, Min-Suk; Lee, Jin Yong; Kim, Jayeun; Kim, Gun-Woo; Kim, Byung-Keun; Kim, Ju-Young; Park, Heung-Woo; Cho, Sang-Heon; Min, Kyung-Up; Kang, Hye-Ryun

2016-01-01

Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are life-threatening diseases; however, it is hard to estimate their incidence due to the rarity of these diseases. We evaluated the incidence of SJS and TEN using a nationwide administrative database. We used a national medical insurance review system (Health Insurance Review and Assessment) database which contained the claim data of the entire nation from 2009 to 2013 to estimate the accurate incidence of SJS and TEN in Korea. The diagnostic codes of L511 (SJS) or L512 (TEN) from the International Classification of Diseases-10th revision were used to define the target study population. We also retrospectively followed up a 2011 SJS and TEN cohort for 24 months in order to assess the in-hospital mortality, related complications and total claims cost due to SJS and TEN. A total of 1,167 (938 SJS and 229 TEN) cases were newly diagnosed from 2010 to 2013. The age- and sex-standardized annual incidences estimated in this study were 3.96 to 5.03 in SJS and 0.94 to 1.45 in TEN per million. There was no significant change in annual incidence throughout the study periods. When analyzed by 10-year age groups, the annual incidence was the lowest in group 20-29 years and the highest in group 70 for both SJS and TEN. Based on the 2011 cohort analysis, the in-hospital mortality were 5.7 and 15.1% for SJS and TEN, respectively. The mortality increased with age, particularly, after 40 years of age. Among the complications related with SJS or TEN, ocular sequelae was the most common (43.1 and 43.4% of SJS and TEN patients, respectively) followed by urethral sequelae (5.7 and 9.4% of SJS and TEN patients, respectively). Overall, our data suggest that SJS, and TEN are infrequent but constantly arise throughout the years.

Stage Presentation, Care Patterns, and Treatment Outcomes for Squamous Cell Carcinoma of the Penis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burt, Lindsay M.; Shrieve, Dennis C.; Tward, Jonathan D., E-mail: Jonathan.Tward@hci.utah.edu

Purpose: Penile squamous cell carcinoma (SCC) is a rare entity, with few published series on outcomes. We evaluated the stage distributions and outcomes for surgery and radiation therapy in a U.S. population database. Methods and Materials: Subjects with SCC of the penis were identified using the National Cancer Institute Surveillance, Epidemiology and End Results (SEER) Program database between 1988 and 2006. Descriptive statistics were performed, and cause-specific survival (CSS) was estimated using Kaplan-Meier analysis. Comparisons of treatment modalities were analyzed using multivariate Cox regression. Subjects were staged using American Joint Committee on Cancer, sixth edition, criteria. Results: There were 2458more » subjects identified. The median age was 66.8 years (range, 17-102 years). Grade 2 disease was present in 94.5% of cases. T1, T2, T3, T4, and Tx disease was present in 64.8%, 17.1%, 9.5%, 2.1%, and 6.5% of cases, respectively. N0, N1, N2, N3, and Nx disease was noted in 61.6%, 6.9%, 4.0%, 3.7%, and 23.8% of cases, respectively. M1 disease was noted in 2.5% of subjects. Individuals of white ethnicity accounted for 85.1% of cases. Lymphadenectomy was performed in 16.7% of cases. The CSS for all patients at 5 and 10 years was 80.8% and 78.6%. By multivariable analysis grades 2 and 3 disease, T3 stage, and positive lymph nodes were adverse prognostic factors for CSS. Conclusion: SCC of the penis often presents as early-stage T1, N0, M0, grade 1, or grade 2 disease. The majority of patients identified were treated with surgery, and only a small fraction of patients received radiation therapy alone or as adjuvant therapy.« less

Valganciclovir Use Among Commercially and Medicaid-insured Infants With Congenital CMV Infection in the United States, 2009-2015.

PubMed

Leung, Jessica; Dollard, Sheila C; Grosse, Scott D; Chung, Winnie; Do, ThuyQuynh; Patel, Manisha; Lanzieri, Tatiana M

2018-03-01

The aim of this study was to assess the clinical characteristics and trends in valganciclovir use among infants diagnosed with congenital cytomegalovirus (CMV) disease in the United States. We analyzed data from medical claims dated 2009-2015 from the Truven Health MarketScan ® Commercial Claims and Encounters and Medicaid databases. We identified infants with a live birth code in the first claim who were continuously enrolled for at least 45 days. Among infants diagnosed with congenital CMV disease, identified by an ICD-9-CM or ICD-10-CM code for congenital CMV infection or CMV disease within 45 days of birth, we assessed data from claims containing codes for any CMV-associated clinical condition within the same period, and data from claims for hearing loss and/or valganciclovir within the first 180 days of life. In the commercial and Medicaid databases, we identified 257 (2.5/10,000) and 445 (3.3/10,000) infants, respectively, diagnosed with congenital CMV disease, among whom 135 (53%) and 282 (63%) had ≥1 CMV-associated condition, 30 (12%) and 32 (7%) had hearing loss, and 41 (16%) and 78 (18%) had a claim for valganciclovir. Among infants with congenital CMV disease who had a claim for valganciclovir, 37 (90%) among commercially insured infants and 68 (87%) among Medicaid-insured infants had ≥1 CMV-associated condition and/or hearing loss. From 2009 to 2015, the percentages with a claim for valganciclovir increased from 0% to 29% among commercially insured infants and from 4% to 37% among Medicaid-insured infants (P < 0.0001). During 2009-2015, there was a strong upward trend in valganciclovir claims among insured infants who were diagnosed with congenital CMV disease, the majority of whom had CMV-associated conditions and/or hearing loss. Published by Elsevier Inc.

Adjuvant radiation for salivary gland malignancies is associated with improved survival: A National Cancer Database analysis.

PubMed

Bakst, Richard L; Su, William; Ozbek, Umut; Knoll, Miriam A; Miles, Brett A; Gupta, Vishal; Rhome, Ryan

2017-01-01

There are no randomized data to support the use of postoperative radiation for salivary gland malignancies. This study uses the National Cancer Database (NCDB) to describe the epidemiology of salivary gland cancer patients and to investigate whether treatment with adjuvant radiation improves overall survival. A total of 8243 patients diagnosed with a major salivary gland cancer were identified from the NCDB. All patients received primary surgical resection of their malignancy. Patients were risk-stratified by adverse features, and overall survival rates were determined. Patients were considered high risk if they had extracapsular extension and/or positive margin after resection. Patients were considered intermediate risk if they did not meet the criteria for high risk but had pT3-T4 disease, pN+ disease, lymphovascular space invasion, adenoid cystic histology, or grade 2-3 disease. Patients who did not meet criteria for high or intermediate risk were considered low risk. Overall patient demographics, disease characteristics, treatment factors, and outcomes were summarized with descriptive statistics and analyzed with STATA. Median follow-up in this cohort was 42.4 months, with the median age of 58 years. Patients in the high-risk group had greater survival (hazard ratio [HR], 0.76; P = .002; 95% confidence interval [CI], 0.64-0.91) if they received adjuvant radiation therapy. In contrast, patients in the intermediate- (HR, 1.01; P = .904; 95% CI, 0.85-1.20) and low-risk groups (HR, 0.85; P  = .427; 95% CI, 0.57-1.26) did not experience a survival benefit with adjuvant radiation therapy. This large analysis compared survival outcomes between observation and adjuvant radiation alone in risk-stratified patients after resection of major salivary glands using a national database. The use of adjuvant radiation for high-risk major salivary gland cancers appears to offer a survival benefit. Although an overall survival benefit was not seen in low- and intermediate-risk salivary gland cancers, this study could not address impact on local control because of the limitations of the NCDB.

Association Between Psychotropic and Cardiovascular Iatrogenic Alerts and Risk of Hospitalizations in Elderly People Treated for Dementia: A Self-Controlled Case Series Study Based on the Matching of 2 French Health Insurance Databases.

PubMed

Zerah, Lorene; Boddaert, Jacques; Leperre-Desplanques, Armelle; Bonnet-Zamponi, Dominique; Verny, Marc; Deligne, Jean; Boelle, Pierre-Yves

2017-06-01

Elderly people are at risk of repeated hospitalizations, some of which may be drug related and preventable. In 2011, a group of French healthcare experts selected 5 iatrogenic alerts (IAs), based on criteria identified in a literature search and from their professional experience, to assess the appropriateness of medication in elderly patients. Our objective was to examine the association between hospitalizations and IAs in elderly patients treated for Alzheimer disease who are particularly sensitive to adverse drug events. A 2-year (January 1, 2011, to December 31, 2012) longitudinal national database study, with a study design similar to self-controlled case series, was performed to analyze data on drug prescriptions and hospitalization. IAs were defined as (1) long half-life benzodiazepine; (2) antipsychotic drugs in patients with Alzheimer disease; (3) co-prescription of 3 or more psychotropic drugs; (4) co-prescription of 2 or more diuretics; and (5) co-prescription of 4 or more antihypertensive drugs. Data were obtained by matching of 2 French National Health Insurance Databases. France. All affiliates, aged ≥75 years, receiving treatment for Alzheimer disease, alive on January 1, 2011 were included. We calculated the relative increase in the number of hospitalizations in patients with IAs. The analysis was performed over four 6-month periods. A total of 10,754 patients were included. During the periods with IAs, hospitalization rates increased by 0.36/year compared with 0.23/year in the periods without for the same patient, and the number of hospitalizations doubled [proportional fold change = 1.9, 95% confidence interval (1.8, 2.1)]. We estimated that 22% [95% confidence interval (20%, 23%)] of all hospitalizations were associated with IAs, 80% of which were due to psychotropic IAs. The IAs could be used as a simple and clinically relevant tool by prescribing physicians to assess the appropriateness of the prescription in elderly patients treated for Alzheimer disease. Copyright © 2017 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

Language and communication non-pharmacological interventions in patients with Alzheimer's disease: a systematic review. Communication intervention in Alzheimer

PubMed Central

Morello, Aline Nunes da Cruz; Lima, Tatiane Machado; Brandão, Lenisa

2017-01-01

ABSTRACT Alzheimer's disease considerably compromises communication skills. Language changes become more prominent as the disease progresses. Deterioration of language and cognition reduces the ability of holding conversations, which has a negative impact on social interaction. OBJECTIVE: To conduct a systematic review of the literature for articles reporting interventions focused on the language and communication of people with Alzheimer's disease (AD) without use of medication. METHODS: We performed a search using the keywords Alzheimer's disease, language, communication, cognition, cognitive intervention, rehabilitation and therapy, and their corresponding Portuguese and Spanish terms, on the SciELO, LILACS, PubMed and PsychINFO databases. We analyzed intervention studies published from 1993 to 2016 that involved stimulation of language skills and/or communication with pre-and post-intervention quantitative results, and whose samples included at least 50% with a diagnosis of probable AD. Studies were analyzed and classified into four levels of evidence, according to the criteria described in the literature. RESULTS: Twenty-eight articles were included. The majority of the designs had medium-to-low scientific evidence. Most interventions showed benefits for at least one language or communicative skill. Eight types of interventions emerged from the analysis of the studies. Further research with higher levels of evidence is recommended in the investigation of interventions focused on language and communication skills of patients with dementia. CONCLUSION: Studies with high levels of evidence on the topic investigated are only being conducted on a small scale. Two intervention techniques seem potentially effective: lexical-semantic approaches and interventions that work with different cognitive skills (including language). PMID:29213519

Use of complementary and alternative medicine by patients with lysosomal storage diseases.

PubMed

Balwani, Manisha; Fuerstman, Laura; Desnick, Robert J; Buckley, Brian; McGovern, Margaret M

2009-10-01

To evaluate the extent of complementary and alternative medicine use and perceived effectiveness in patients with lysosomal storage diseases. A 26-item survey was distributed to 495 patients with type 1 Gaucher, Fabry, and type B Niemann-Pick diseases who were seen at the Lysosomal Storage Disease Program at the Mount Sinai School of Medicine. Survey responses were entered into an access database and analyzed using descriptive statistics. Surveys were completed by 167 respondents with an overall response rate of 34%. Complementary and alternative medicines were used by 45% of patients with type 1 Gaucher disease, 41% of patients with Fabry disease, and 47% of patients with type B Niemann-Pick for symptoms related to their disease. Complementary and alternative medicines were used most frequently by adult females (55%), in patients who reported having one or more invasive procedures due to their disease, patients who use one or more conventional medical therapies, or those with depression and/or anxiety. Overall perceived effectiveness of complementary and alternative medicine supplements was low; however, complementary and alternative medicine therapies were perceived as effective. Complementary and alternative medicines are commonly used among patients with lysosomal storage diseases. Assessment of the effectiveness of these approaches in the lysosomal storage diseases is needed, and physicians should be aware of complementary and alternative medicine therapies used by patients to evaluate safety and possible drug interactions.

Deep insight into the Ganoderma lucidum by comprehensive analysis of its transcriptome.

PubMed

Yu, Guo-Jun; Wang, Man; Huang, Jie; Yin, Ya-Lin; Chen, Yi-Jie; Jiang, Shuai; Jin, Yan-Xia; Lan, Xian-Qing; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

2012-01-01

Ganoderma lucidum is a basidiomycete white rot fungus and is of medicinal importance in China, Japan and other countries in the Asiatic region. To date, much research has been performed in identifying the medicinal ingredients in Ganoderma lucidum. Despite its important therapeutic effects in disease, little is known about Ganoderma lucidum at the genomic level. In order to gain a molecular understanding of this fungus, we utilized Illumina high-throughput technology to sequence and analyze the transcriptome of Ganoderma lucidum. We obtained 6,439,690 and 6,416,670 high-quality reads from the mycelium and fruiting body of Ganoderma lucidum, and these were assembled to form 18,892 and 27,408 unigenes, respectively. A similarity search was performed against the NCBI non-redundant nucleotide database and a customized database composed of five fungal genomes. 11,098 and 8, 775 unigenes were matched to the NCBI non-redundant nucleotide database and our customized database, respectively. All unigenes were subjected to annotation by Gene Ontology, Eukaryotic Orthologous Group terms and Kyoto Encyclopedia of Genes and Genomes. Differentially expressed genes from the Ganoderma lucidum mycelium and fruiting body stage were analyzed, resulting in the identification of 13 unigenes which are involved in the terpenoid backbone biosynthesis pathway. Quantitative real-time PCR was used to confirm the expression levels of these unigenes. Ganoderma lucidum was also studied for wood degrading activity and a total of 22 putative FOLymes (fungal oxidative lignin enzymes) and 120 CAZymes (carbohydrate-active enzymes) were predicted from our Ganoderma lucidum transcriptome. Our study provides comprehensive gene expression information on Ganoderma lucidum at the transcriptional level, which will form the foundation for functional genomics studies in this fungus. The use of Illumina sequencing technology has made de novo transcriptome assembly and gene expression analysis possible in species that lack full genome information.

Deep Insight into the Ganoderma lucidum by Comprehensive Analysis of Its Transcriptome

PubMed Central

Yu, Guo-Jun; Wang, Man; Huang, Jie; Yin, Ya-Lin; Chen, Yi-Jie; Jiang, Shuai; Jin, Yan-Xia; Lan, Xian-Qing; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

2012-01-01

Background Ganoderma lucidum is a basidiomycete white rot fungus and is of medicinal importance in China, Japan and other countries in the Asiatic region. To date, much research has been performed in identifying the medicinal ingredients in Ganoderma lucidum. Despite its important therapeutic effects in disease, little is known about Ganoderma lucidum at the genomic level. In order to gain a molecular understanding of this fungus, we utilized Illumina high-throughput technology to sequence and analyze the transcriptome of Ganoderma lucidum. Methodology/Principal Findings We obtained 6,439,690 and 6,416,670 high-quality reads from the mycelium and fruiting body of Ganoderma lucidum, and these were assembled to form 18,892 and 27,408 unigenes, respectively. A similarity search was performed against the NCBI non-redundant nucleotide database and a customized database composed of five fungal genomes. 11,098 and 8, 775 unigenes were matched to the NCBI non-redundant nucleotide database and our customized database, respectively. All unigenes were subjected to annotation by Gene Ontology, Eukaryotic Orthologous Group terms and Kyoto Encyclopedia of Genes and Genomes. Differentially expressed genes from the Ganoderma lucidum mycelium and fruiting body stage were analyzed, resulting in the identification of 13 unigenes which are involved in the terpenoid backbone biosynthesis pathway. Quantitative real-time PCR was used to confirm the expression levels of these unigenes. Ganoderma lucidum was also studied for wood degrading activity and a total of 22 putative FOLymes (fungal oxidative lignin enzymes) and 120 CAZymes (carbohydrate-active enzymes) were predicted from our Ganoderma lucidum transcriptome. Conclusions Our study provides comprehensive gene expression information on Ganoderma lucidum at the transcriptional level, which will form the foundation for functional genomics studies in this fungus. The use of Illumina sequencing technology has made de novo transcriptome assembly and gene expression analysis possible in species that lack full genome information. PMID:22952861

Methodological reviews of economic evaluations in health care: what do they target?

PubMed

Hutter, Maria-Florencia; Rodríguez-Ibeas, Roberto; Antonanzas, Fernando

2014-11-01

An increasing number of published studies of economic evaluations of health technologies have been reviewed and summarized with different purposes, among them to facilitate decision-making processes. These reviews have covered different aspects of economic evaluations, using a variety of methodological approaches. The aim of this study is to analyze the methodological characteristics of the reviews of economic evaluations in health care, published during the period 1990-2010, to identify their main features and the potential missing elements. This may help to develop a common procedure for elaborating these kinds of reviews. We performed systematic searches in electronic databases (Scopus, Medline and PubMed) of methodological reviews published in English, period 1990-2010. We selected the articles whose main purpose was to review and assess the methodology applied in the economic evaluation studies. We classified the data according to the study objectives, period of the review, number of reviewed studies, methodological and non-methodological items assessed, medical specialty, type of disease and technology, databases used for the review and their main conclusions. We performed a descriptive statistical analysis and checked how generalizability issues were considered in the reviews. We identified 76 methodological reviews, 42 published in the period 1990-2001 and 34 during 2002-2010. The items assessed most frequently (by 70% of the reviews) were perspective, type of economic study, uncertainty and discounting. The reviews also described the type of intervention and disease, funding sources, country in which the evaluation took place, type of journal and author's characteristics. Regarding the intertemporal comparison, higher frequencies were found in the second period for two key methodological items: the source of effectiveness data and the models used in the studies. However, the generalizability issues that apparently are creating a growing interest in the economic evaluation literature did not receive as much attention in the reviews of the second period. The remaining items showed similar frequencies in both periods. Increasingly more reviews of economic evaluation studies aim to analyze the application of methodological principles, and offer summaries of papers classified by either diseases or health technologies. These reviews are useful for finding literature trends, aims of studies and possible deficiencies in the implementation of methods of specific health interventions. As no significant methodological improvement was clearly detected in the two periods analyzed, it would be convenient to pay more attention to the methodological aspects of the reviews.

The Association Between Extreme Precipitation and Waterborne Disease Outbreaks in the United States, 1948–1994

PubMed Central

Curriero, Frank C.; Patz, Jonathan A.; Rose, Joan B.; Lele, Subhash

2001-01-01

Objectives. Rainfall and runoff have been implicated in site-specific waterborne disease outbreaks. Because upward trends in heavy precipitation in the United States are projected to increase with climate change, this study sought to quantify the relationship between precipitation and disease outbreaks. Methods. The US Environmental Protection Agency waterborne disease database, totaling 548 reported outbreaks from 1948 through 1994, and precipitation data of the National Climatic Data Center were used to analyze the relationship between precipitation and waterborne diseases. Analyses were at the watershed level, stratified by groundwater and surface water contamination and controlled for effects due to season and hydrologic region. A Monte Carlo version of the Fisher exact test was used to test for statistical significance. Results. Fifty-one percent of waterborne disease outbreaks were preceded by precipitation events above the 90th percentile (P = .002), and 68% by events above the 80th percentile (P = .001). Outbreaks due to surface water contamination showed the strongest association with extreme precipitation during the month of the outbreak; a 2-month lag applied to groundwater contamination events. Conclusions. The statistically significant association found between rainfall and disease in the United States is important for water managers, public health officials, and risk assessors of future climate change. PMID:11499103

Themes in the literature related to cardiovascular disease risk reduction.

PubMed

Cohen, Shannon Munro; Kataoka-Yahiro, Merle

2009-01-01

This article aimed to identify themes in the literature related to patient-healthcare provider beliefs, barriers to adherence, and interventions pertaining to cardiovascular disease risk reduction. Twenty quantitative and qualitative primary research studies including 2 meta-analyses published between 1995 and 2008 were analyzed for themes and practice implications to synthesize existing research on cardiovascular disease risk reduction. Databases searched included EBSCO, CINAHL, MEDLINE, ScienceDirect, HealthSource, and PsychLit using the search terms patient- provider adherence, adherence and shared decision making, adherence and decision support, patient- provider goal setting, and cardiovascular disease risk reduction. The emergent themes found in this literature review included (1) complex medication regimens; (2) risk perception, quality of life, and competing priorities; (3) motivation for change; (4) provider clinical inertia; and (5) goal setting, feedback, and reminders. Studies reporting the highest rates of adherence to cardiovascular disease risk reduction recommendations incorporated patient-provider goal setting and decision support, self-management techniques, and personalized printed communication. Goal setting in cardiovascular disease risk reduction is a relatively unexplored area and is an important component of shared decision making and adherence to cardiovascular disease health recommendations. The following review will address the 5 themes identified in more detail and provide a basis for improved clinical practice.

Trends of Do-Not-Resuscitate consent and hospice care utilization among noncancer decedents in a tertiary hospital in Taiwan between 2010 and 2014

PubMed Central

Chang, Hsiao-Ting; Lin, Ming-Hwai; Chen, Chun-Ku; Chou, Pesus; Chen, Tzeng-Ji; Hwang, Shinn-Jang

2016-01-01

Abstract Do-Not-Resuscitate (DNR) and hospice care are not only applied to cancer patients but also to patients with noncancer progressive illness. However, the trends of DNR consent and hospice utilization are not well explored for noncancer patients. This study aimed to explore the trends of DNR consent and hospice care utilization among noncancer decedents in a tertiary hospital in Taiwan. We analyzed the Death and Hospice Palliative Care Database from the Taipei Veterans General Hospital in Taiwan. The Death and Hospice Palliative Care Database contains information including patient sex, major diagnosis, admission date, date of death, age at death, department at discharge, status of DNR consent, and status of hospice care of patients who died in the Taipei Veterans General Hospital. Data on patients aged 20 years old or more who died of major terminal noncancer diseases, including brain diseases, amyotrophic lateral sclerosis, dementia, chronic obstructive pulmonary disease (COPD) and other lung diseases, heart failure, chronic liver diseases and cirrhosis, and renal failure between 2010 and 2014 were extracted for analysis. A total of 1416 patients aged 20 years or more died of major noncancer diseases in Taipei Veterans General Hospital during the study period. The most common diagnosis was brain diseases, amyotrophic lateral sclerosis, and dementias (n = 510, 36%) followed by chronic obstructive pulmonary disease and other lung diseases (n = 322, 22.7%). Among these noncancer decedents, 1045 (73.8%) had DNR consents, while 134 (9.5%) received hospice care. Patients diagnosed with renal failure had the highest percentage of DNR consent (80%), followed by chronic liver diseases and cirrhosis (77.7%). Patients diagnosed with chronic liver diseases and cirrhosis had the highest percentage of hospice utilization (17.4%), followed by renal failure (15.8%). The percentages of DNR consent and hospice utilization were significantly different across different disease diagnosis, hospitalization department, and year of death. There were increased trends of DNR consent in patients with major noncancer diagnoses, and increased hospice care utilization in patients diagnosed with lung diseases and renal failure from 2010 to 2014. However, the hospice care utilization could be improved. Further study to evaluate factors associated hospice care to improve the utilization is suggested. PMID:27861375

Trends of Do-Not-Resuscitate consent and hospice care utilization among noncancer decedents in a tertiary hospital in Taiwan between 2010 and 2014: A Hospital-based observational study.

PubMed

Chang, Hsiao-Ting; Lin, Ming-Hwai; Chen, Chun-Ku; Chou, Pesus; Chen, Tzeng-Ji; Hwang, Shinn-Jang

2016-11-01

Do-Not-Resuscitate (DNR) and hospice care are not only applied to cancer patients but also to patients with noncancer progressive illness. However, the trends of DNR consent and hospice utilization are not well explored for noncancer patients. This study aimed to explore the trends of DNR consent and hospice care utilization among noncancer decedents in a tertiary hospital in Taiwan. We analyzed the Death and Hospice Palliative Care Database from the Taipei Veterans General Hospital in Taiwan. The Death and Hospice Palliative Care Database contains information including patient sex, major diagnosis, admission date, date of death, age at death, department at discharge, status of DNR consent, and status of hospice care of patients who died in the Taipei Veterans General Hospital. Data on patients aged 20 years old or more who died of major terminal noncancer diseases, including brain diseases, amyotrophic lateral sclerosis, dementia, chronic obstructive pulmonary disease (COPD) and other lung diseases, heart failure, chronic liver diseases and cirrhosis, and renal failure between 2010 and 2014 were extracted for analysis. A total of 1416 patients aged 20 years or more died of major noncancer diseases in Taipei Veterans General Hospital during the study period. The most common diagnosis was brain diseases, amyotrophic lateral sclerosis, and dementias (n = 510, 36%) followed by chronic obstructive pulmonary disease and other lung diseases (n = 322, 22.7%). Among these noncancer decedents, 1045 (73.8%) had DNR consents, while 134 (9.5%) received hospice care. Patients diagnosed with renal failure had the highest percentage of DNR consent (80%), followed by chronic liver diseases and cirrhosis (77.7%). Patients diagnosed with chronic liver diseases and cirrhosis had the highest percentage of hospice utilization (17.4%), followed by renal failure (15.8%). The percentages of DNR consent and hospice utilization were significantly different across different disease diagnosis, hospitalization department, and year of death. There were increased trends of DNR consent in patients with major noncancer diagnoses, and increased hospice care utilization in patients diagnosed with lung diseases and renal failure from 2010 to 2014. However, the hospice care utilization could be improved. Further study to evaluate factors associated hospice care to improve the utilization is suggested.

Disease burden of herpes zoster in Korea.

PubMed

Choi, Won Suk; Noh, Ji Yun; Huh, Joong Yeon; Jo, Yu Mi; Lee, Jacob; Song, Joon Young; Kim, Woo Joo; Cheong, Hee Jin

2010-04-01

The occurrence of herpes zoster can deteriorate the quality of life considerably, resulting in high disease burden. While Korea is assumed to have high disease burden of herpes zoster, there has been no researches analyzing this. We performed this study to investigate the disease burden of herpes zoster in the Korean population as a whole. We used the database of the Health Insurance Review & Assessment Service of Korea and analyzed the data of patients who had herpes zoster as a principal diagnosis during the period from 2003 to 2007. We investigated the annual prevalence, rate of clinical visits, rate of hospitalization, and the pattern of medical services use. The socioeconomic burden of herpes zoster was calculated by a conversion into cost. Rates of clinic visits and hospitalizations due to herpes zoster during the 5-year period from 2003 to 2007 were 7.93-12.54 per 1000 population and 0.22-0.32 per 1000 population, respectively. Prevalence rates according to age increased sharply after 50 years and reached a peak at 70 years. The total socioeconomic cost of herpes zoster was $75.9-143.8 million per year, increasing every year by 14-20%. There is a heavy socioeconomic burden due to herpes zoster in Korea and indicate that appropriate policies need to be established to reduce this burden. Additional researches are also necessary to assess the safety, efficacy and cost-effectiveness of a herpes zoster vaccine in the Korean population. Copyright 2010 Elsevier B.V. All rights reserved.

Drug-Associated Acute Kidney Injury Identified in the United States Food and Drug Administration Adverse Event Reporting System Database.

PubMed

Welch, Hanna K; Kellum, John A; Kane-Gill, Sandra L

2018-06-08

Acute kidney injury (AKI) is a common condition associated with both short-term and long-term consequences including dialysis, chronic kidney disease, and mortality. Although the United States Food and Drug Administration Adverse Event Reporting System (FAERS) database is a powerful tool to examine drug-associated events, to our knowledge, no study has analyzed this database to identify the most common drugs reported with AKI. The objective of this study was to analyze AKI reports and associated medications in the FAERS database. Retrospective pharmacovigilance disproportionality analysis. FAERS database. We queried the FAERS database for reports of AKI from 2004 quarter 1 through 2015 quarter 3. Extracted drugs were assessed using published references and categorized as known, possible, or new potential nephrotoxins. The reporting odds ratio (ROR), a measure of reporting disproportionality, was calculated for the 20 most frequently reported drugs in each category. We retrieved 7,241,385 adverse event reports, of which 193,996 (2.7%) included a report of AKI. Of the AKI reports, 16.5% were known nephrotoxins, 18.6% were possible nephrotoxins, and 64.8% were new potential nephrotoxins. Among the most commonly reported drugs, those with the highest AKI ROR were aprotinin (7,614 reports; ROR 115.70, 95% confidence interval [CI] 110.63-121.01), sodium phosphate (1,687 reports; ROR 55.81, 95% CI 51.78-60.17), furosemide (1,743 reports; ROR 12.61, 95% CI 11.94-13.32), vancomycin (1,270 reports, ROR 12.19, 95% CI 11.45-12.99), and metformin (4,701 reports; ROR 10.65, 95% CI 10.31-11.00). The combined RORs for the 20 most frequently reported drugs with each nephrotoxin classification were 3.71 (95% CI 3.66-3.76) for known nephrotoxins, 2.09 (95% CI 2.06-2.12) for possible nephrotoxins, and 1.55 (95% CI 1.53-1.57) for new potential nephrotoxins. AKI was a common reason for adverse event reporting in the FAERS. Most AKI reports were generated for medications not recognized as nephrotoxic according to our classification system. This report provides data on medications needing further research to determine the risk of AKI with these new potential nephrotoxins. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A comparison of the surgical mortality due to colorectal perforation at different hospitals with data from 10,090 cases in the Japanese National Clinical Database.

PubMed

Ohki, Takeshi; Yamamoto, Masakazu; Miyata, Hiroaki; Sato, Yasuto; Saida, Yoshihisa; Morimoto, Tsuyoshi; Konno, Hiroyuki; Seto, Yasuyuki; Hirata, Koichi

2017-01-01

Colorectal perforation has a high rate of mortality. We compared the incidence and fatality rates of colorectal perforation among different hospitals in Japan using data from the nationwide surgical database.Patients were registered in the National Clinical Database (NCD) between January 1st, 2011 and December 31st, 2013. Patients with colorectal perforation were identified from surgery records by examining if acute diffuse peritonitis (ADP) and diseases associated with a high probability of colorectal perforation were noted. The primary outcome measures included the 30-day postsurgery mortality and surgical mortality of colorectal perforation. We analyzed differences in the observed-to-expected mortality (O/E) ratio between the two groups of hospitals, that is, specialized and non-specialized, using the logistic regression analysis forward selection method.There were 10,090 cases of disease-induced colorectal perforation during the study period. The annual average postoperative fatality rate was 11.36%. There were 3884 patients in the specialized hospital group and 6206 in the non-specialized hospital group. The O/E ratio (0.9106) was significantly lower in the specialized hospital group than in the non-specialized hospital group (1.0704). The experience level of hospitals in treating cases of colorectal perforation negatively correlated with the O/E ratio.We conducted the first study investigating differences among hospitals with respect to their fatality rate of colorectal perforation on the basis of data from a nationwide database. Our data suggest that patients with colorectal perforation should choose to be treated at a specialized hospital or a hospital that treats five or more cases of colorectal perforation per year. The results of this study indicate that specialized hospitals may provide higher quality medical care, which in turn proves that government policy on healthcare is effective at improving the medical system in Japan.

FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

PubMed Central

Naithani, Sushma; Partipilo, Christina M.; Raja, Rajani; Elser, Justin L.; Jaiswal, Pankaj

2016-01-01

FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition of new pathways, enzymes, reactions, compounds, and small molecules in the database. To date, FragariaCyc comprises 66 super-pathways, 488 unique pathways, 2348 metabolic reactions, 3507 enzymes, and 2134 compounds. In addition to searching and browsing FragariaCyc, researchers can compare pathways across various plant metabolic networks and analyze their data using Omics Viewer tool. We view FragariaCyc as a resource for the community of researchers working with strawberry and related fruit crops. It can help understanding the regulation of overall metabolism of strawberry plant during development and in response to diseases and abiotic stresses. FragariaCyc is available online at http://pathways.cgrb.oregonstate.edu. PMID:26973684

The design and implementation of the immune epitope database and analysis resource

PubMed Central

Peters, Bjoern; Sidney, John; Bourne, Phil; Bui, Huynh-Hoa; Buus, Soeren; Doh, Grace; Fleri, Ward; Kronenberg, Mitch; Kubo, Ralph; Lund, Ole; Nemazee, David; Ponomarenko, Julia V.; Sathiamurthy, Muthu; Schoenberger, Stephen P.; Stewart, Scott; Surko, Pamela; Way, Scott; Wilson, Steve; Sette, Alessandro

2016-01-01

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, “The Immune Epitope Database and Analysis Resource.” We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide. PMID:15895191

Risk of colorectal cancer and small bowel adenocarcinoma in Crohn's disease: a population-based study from western Hungary 1977-2008.

PubMed

Lakatos, Peter Laszlo; David, Gyula; Pandur, Tunde; Erdelyi, Zsuzsanna; Mester, Gabor; Balogh, Mihaly; Szipocs, Istvan; Molnar, Csaba; Komaromi, Erzsebet; Kiss, Lajos S; Lakatos, Laszlo

2011-04-01

Limited data are available on the incidence and predictors of colorectal (CRC) and small bowel adenocarcinoma (SBA) in patients with Crohn's disease (CD) from population-based cohorts. Since data are completely missing from Eastern Europe, our aim was to analyze the incidence and risk factors of CD associated CRC and SBA in the population-based, Veszprem province database, which included incident patients diagnosed between January 1, 1977 and December 31, 2008. The data of 506 incident CD patients were analyzed (age-at-diagnosis: 31.5, SD: 13.8 years). Both hospital and outpatient records were collected and comprehensively reviewed. CRC was diagnosed in five patients (5/5758 person-year-duration) during follow-up, while no patients developed SBA in this cohort. Standardized incidence ratio (SIR) of CRC was not increased overall with five cases observed vs. 5.02 expected (SIR: 0.99, 95% CI: 0.41-2.39); however, there was a tendency for increased incidence in males (five cases observed vs. 2.56 expected; SIR: 1.95, 95% CI: 0.81-4.70). Age at onset of CD (p<0.001), male gender (p=0.022) and stenosing disease behavior at diagnosis (p<0.001) but not disease location were identified as risk factors for developing CRC in univariate analysis and Kaplan-Meier analysis. The cumulative risk for developing CRC after a disease duration of 20 years was 1.1% (95% CI: 0.6-1.7%). The incidence of CRC and SBA was not increased in this population-based CD cohort. Age at onset of CD, male gender and stenosing disease behavior at diagnosis were identified as risk factors of CRC. Copyright © 2010 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

PedAM: a database for Pediatric Disease Annotation and Medicine.

PubMed

Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Li, Xin; Liang, Yunxiang; Guo, Dongming; Tai, Jun; Chen, Geng; Jin, Yaqiong; Liu, Zhimei; Ni, Xin; Shi, Tieliu

2018-01-04

There is a significant number of children around the world suffering from the consequence of the misdiagnosis and ineffective treatment for various diseases. To facilitate the precision medicine in pediatrics, a database namely the Pediatric Disease Annotations & Medicines (PedAM) has been built to standardize and classify pediatric diseases. The PedAM integrates both biomedical resources and clinical data from Electronic Medical Records to support the development of computational tools, by which enables robust data analysis and integration. It also uses disease-manifestation (D-M) integrated from existing biomedical ontologies as prior knowledge to automatically recognize text-mined, D-M-specific syntactic patterns from 774 514 full-text articles and 8 848 796 abstracts in MEDLINE. Additionally, disease connections based on phenotypes or genes can be visualized on the web page of PedAM. Currently, the PedAM contains standardized 8528 pediatric disease terms (4542 unique disease concepts and 3986 synonyms) with eight annotation fields for each disease, including definition synonyms, gene, symptom, cross-reference (Xref), human phenotypes and its corresponding phenotypes in the mouse. The database PedAM is freely accessible at http://www.unimd.org/pedam/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Epidemiology of radical prostatectomy for localized prostate cancer in the era of prostate-specific antigen: an overview of the Department of Defense Center for Prostate Disease Research national database.

PubMed

Moul, Judd W; Wu, Hongyu; Sun, Leon; McLeod, David G; Amling, Christopher; Lance, Raymond; Kusuda, Leo; Donahue, Timothy; Foley, John; Chung, Andrew; Sexton, Wade; Soderdahl, Douglas; Rich, Norman M

2002-08-01

Because of public awareness and screening, the incidence of clinically localized prostate cancer has increased dramatically in the last 15 years. The Department of Defense Center for Prostate Disease Research (CPDR) was established by the US Congress in 1991 to study prostate cancer in the US military health care system. A key component of CPDR is a multicenter prospective and retrospective prostate research database that collects comprehensive standardized data on all consenting patients. To verify and document changes in the epidemiology of men electing radical prostatectomy (RP) as primary treatment for their localized prostate cancer, we undertook an analysis of such cases when the PSA screening test became widely available and used. The CPDR database consists of standardized data collection forms for each episode of care completed prospectively, and in some cases, retrospectively, on men with prostate cancer and those undergoing a prostate biopsy for presumed cancer at participating medical centers. In July 2001, a query of all RPs performed between January 1, 1991, and December 31, 2000, was conducted, revealing 3681 cases for analysis from 9 hospital sites. These cases were analyzed over time (calendar year), and changes in the characteristics of the patients, disease severity, and surgical results were compared. There was a significant shift to younger men undergoing RP with the median age declining to 62.3 years old by 2000, and more than 40% of the men were less than 60 years old. There was an increase in African-Americans undergoing RP and a large increase in clinical stage T1 disease candidates of both races representing 56.5% of men by 2000. There was a large increase in patients having pretreatment PSA levels between 4 and 10 ng/mL (59.2% by 2000). Retropubic approach was predominant (over 80%) and was associated with a much lower blood loss by 2000 (approximately 800 mL). There was an increase in use of nerve-sparing procedures, and operative time declined significantly to a median of 3.5 hours by 2000. Finally, there was a marked surgical stage migration with a higher proportion of men with organ-confined disease and negative surgical margins; by 2000, 63.4% had pT2 disease. The early outcomes improved with a 1-year disease-free survival in excess of 93%. RP is being performed more commonly on younger men with earlier stage disease in the PSA era. The operation is now performed more rapidly with less blood loss, and the surgical pathology outcome end points and early disease-free survival are improved. These results portend well for improved long-term outcomes of surgical therapy.

Web server to identify similarity of amino acid motifs to compounds (SAAMCO).

PubMed

Casey, Fergal P; Davey, Norman E; Baran, Ivan; Varekova, Radka Svobodova; Shields, Denis C

2008-07-01

Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth, and signaling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which protein-protein interactions derive substantial affinity from short linear peptide sequences, or motifs, we can develop search algorithms for peptidomimetic compounds that resemble the short peptide's structure but are not compromised by poor pharmacological properties. SAAMCO is a Web service ( http://bioware.ucd.ie/ approximately saamco) that facilitates the screening of motifs with known structures against bioactive compound databases. It is built on an algorithm that defines compound similarity based on the presence of appropriate amino acid side chain fragments and a favorable Root Mean Squared Deviation (RMSD) between compound and motif structure. The methodology is efficient as the available compound databases are preprocessed and fast regular expression searches filter potential matches before time-intensive 3D superposition is performed. The required input information is minimal, and the compound databases have been selected to maximize the availability of information on biological activity. "Hits" are accompanied with a visualization window and links to source database entries. Motif matching can be defined on partial or full similarity which will increase or reduce respectively the number of potential mimetic compounds. The Web server provides the functionality for rapid screening of known or putative interaction motifs against prepared compound libraries using a novel search algorithm. The tabulated results can be analyzed by linking to appropriate databases and by visualization.

Hypothyroidism is associated with all-cause mortality in a national cohort of chronic haemodialysis patients.

PubMed

Lin, Hsuan-Jen; Lin, Chung-Chih; Lin, Hsuan Ming; Chen, Hsuan-Ju; Lin, Che-Chen; Chang, Chiz-Tzung; Chou, Che-Yi; Huang, Chiu-Ching

2018-06-01

The prevalence of hypothyroidism is high in haemodialysis (HD) patients and hypothyroidism increases all-cause mortality in HD patients. Comorbidities are common in HD patients and are associated with both mortality and hypothyroidism. The aim of the study is to explore the effect of the interactions of comorbidities and hypothyroidism on all-cause mortality in HD patients. Patients with hypothyroidism (ICD-9-CM 244.0, 244.1, and 244.9) and matched patients without hypothyroidism in the Registry for Catastrophic Illness Patient Database of Taiwan Health Insurance from 2000 to 2010 were analyzed. The association of hypothyroidism and risk of all-cause mortality was analyzed using Cox proportional hazard regression. Nine hundred and eight HD patients with hypothyroidism and 3632 sex-, age-, gender- matched HD patients without hypothyroidism were analyzed. Hypothyroidism was associated with increased all-cause mortality with an adjusted hazard ratio of 1.22 [95% confidence interval (CI): 1.10-1.36, P < 0.001]. TRT may decrease mortality associated with hypothyroidism (P < 0.001). There was a significant interaction (P = 0.04) between diabetes and hypothyroidism. There was no significant interaction found in hypothyroidism and the following comorbidities: hyperlipidaemia, hypertension, chronic obstructive pulmonary disease, coronary artery disease, stroke, peripheral arterial disease, asthma, congestive heart failure and cancer. Hypothyroidism is associated with increased all-cause mortality in chronic HD patients. The interaction of hypothyroidism and diabetes, but not other common comorbidities in HD patients, has an effect on mortality risks. © 2017 Asian Pacific Society of Nephrology.

A cross-species analysis method to analyze animal models' similarity to human's disease state

PubMed Central

2012-01-01

Background Animal models are indispensable tools in studying the cause of human diseases and searching for the treatments. The scientific value of an animal model depends on the accurate mimicry of human diseases. The primary goal of the current study was to develop a cross-species method by using the animal models' expression data to evaluate the similarity to human diseases' and assess drug molecules' efficiency in drug research. Therefore, we hoped to reveal that it is feasible and useful to compare gene expression profiles across species in the studies of pathology, toxicology, drug repositioning, and drug action mechanism. Results We developed a cross-species analysis method to analyze animal models' similarity to human diseases and effectiveness in drug research by utilizing the existing animal gene expression data in the public database, and mined some meaningful information to help drug research, such as potential drug candidates, possible drug repositioning, side effects and analysis in pharmacology. New animal models could be evaluated by our method before they are used in drug discovery. We applied the method to several cases of known animal model expression profiles and obtained some useful information to help drug research. We found that trichostatin A and some other HDACs could have very similar response across cell lines and species at gene expression level. Mouse hypoxia model could accurately mimic the human hypoxia, while mouse diabetes drug model might have some limitation. The transgenic mouse of Alzheimer was a useful model and we deeply analyzed the biological mechanisms of some drugs in this case. In addition, all the cases could provide some ideas for drug discovery and drug repositioning. Conclusions We developed a new cross-species gene expression module comparison method to use animal models' expression data to analyse the effectiveness of animal models in drug research. Moreover, through data integration, our method could be applied for drug research, such as potential drug candidates, possible drug repositioning, side effects and information about pharmacology. PMID:23282076

A cross-species analysis method to analyze animal models' similarity to human's disease state.

PubMed

Yu, Shuhao; Zheng, Lulu; Li, Yun; Li, Chunyan; Ma, Chenchen; Li, Yixue; Li, Xuan; Hao, Pei

2012-01-01

Animal models are indispensable tools in studying the cause of human diseases and searching for the treatments. The scientific value of an animal model depends on the accurate mimicry of human diseases. The primary goal of the current study was to develop a cross-species method by using the animal models' expression data to evaluate the similarity to human diseases' and assess drug molecules' efficiency in drug research. Therefore, we hoped to reveal that it is feasible and useful to compare gene expression profiles across species in the studies of pathology, toxicology, drug repositioning, and drug action mechanism. We developed a cross-species analysis method to analyze animal models' similarity to human diseases and effectiveness in drug research by utilizing the existing animal gene expression data in the public database, and mined some meaningful information to help drug research, such as potential drug candidates, possible drug repositioning, side effects and analysis in pharmacology. New animal models could be evaluated by our method before they are used in drug discovery. We applied the method to several cases of known animal model expression profiles and obtained some useful information to help drug research. We found that trichostatin A and some other HDACs could have very similar response across cell lines and species at gene expression level. Mouse hypoxia model could accurately mimic the human hypoxia, while mouse diabetes drug model might have some limitation. The transgenic mouse of Alzheimer was a useful model and we deeply analyzed the biological mechanisms of some drugs in this case. In addition, all the cases could provide some ideas for drug discovery and drug repositioning. We developed a new cross-species gene expression module comparison method to use animal models' expression data to analyse the effectiveness of animal models in drug research. Moreover, through data integration, our method could be applied for drug research, such as potential drug candidates, possible drug repositioning, side effects and information about pharmacology.

Hypertension-Induced Cerebral Small Vessel Disease Leading to Cognitive Impairment.

PubMed

Liu, Yang; Dong, Yan-Hong; Lyu, Pei-Yuan; Chen, Wei-Hong; Li, Rui

2018-03-05

Alzheimer's disease and vascular dementia are responsible for more than 80% of dementia cases. These two conditions share common risk factors including hypertension. Cerebral small vessel disease (CSVD) is strongly associated with both hypertension and cognitive impairment. In this review, we identify the pathophysiological changes in CSVD that are caused by hypertension and further explore the relationship between CSVD and cognitive impairment. We searched and scanned the PubMed database for recently published literatures up to December 2017. We used the keywords of "hypertension", "cerebral small vessel disease", "white matter lesions", "enlarged perivascular spaces", "lacunar infarcts", "cerebral microbleeds", and "cognitive impairment" in the database of PubMed. Articles were obtained and reviewed to analyze the hypertension-induced pathophysiological changes that occur in CSVD and the correlation between CSVD and cognitive impairment. In recent years, studies have demonstrated that hypertension-related changes (e.g., small vascular lesions, inflammatory reactions, hypoperfusion, oxidative stress, damage to autoregulatory processes and the blood-brain barrier, and cerebral amyloid angiopathy) can occur over time in cerebral small vessels, potentially leading to lower cognitive function when blood pressure (BP) control is poor or lacking. Both isolated and co-occurrent CSVD can lead to cognitive deterioration, and this effect may be attributable to a dysfunction in either the cholinergic system or the functionality of cortical and subcortical tracts. We explore the currently available evidence about the hypertensive vasculopathy and inflammatory changes that occur in CSVD. Both are vital prognostic indicators of the development of cognitive impairment. Future studies should be performed to validate the relationship between BP levels and CSVD progression and between the numbers, volumes, and anatomical locations of CSVD and cognitive impairment.

Etiologies and predictors of 30-day readmissions in patients undergoing percutaneous mechanical circulatory support-assisted percutaneous coronary intervention in the United States: Insights from the Nationwide Readmissions Database.

PubMed

Bavishi, Chirag; Lemor, Alejandro; Trivedi, Vrinda; Chatterjee, Saurav; Moreno, Pedro; Lasala, John; Aronow, Herbert D; Dawn Abbott, J

2018-04-01

Patients undergoing percutaneous mechanical circulatory support (pMCS)-assisted percutaneous coronary intervention (PCI) represent a high-risk group vulnerable to complications and readmissions. Thirty-day readmissions after pMCS-assisted PCI are common among patients with comorbidities and account for a significant amount of healthcare spending. Patients undergoing PCI and pMCS (Impella, TandemHeart, or intra-aortic balloon pump) for any indication between January 1, 2012, and November 30, 2014, were selected from the Nationwide Readmissions Database. Patients were identified using appropriate ICD-9-CM codes. Clinical risk factors and complications were analyzed for association with 30-day readmission. Our analysis included 29 247 patients, of which 4535 (15.5%) were readmitted within 30 days. On multivariate analysis, age ≥ 65 years, female sex, hypertension, diabetes, chronic lung disease, heart failure, prior implantable cardioverter-defibrillator, liver disease, end-stage renal disease, and length of stay ≥5 days during index hospitalization were independent predictors of 30-day readmission. Cardiac etiologies accounted for ~60% of readmissions, of which systolic or diastolic heart failure (22%), stable coronary artery disease (11.1%), acute coronary syndromes (8.9%), and nonspecific chest pain (4.0%) were the most common causes. In noncardiac causes, sepsis/septic shock (4.6%), hypotension/syncope (3.2%), gastrointestinal bleed (3.1%), and acute kidney injury (2.6%) were among the most common causes of 30-day readmissions. Mean length of stay and cost of readmissions was 4 days and $16 191, respectively. Thirty-day readmissions after pMCS-assisted PCI are common and are predominantly associated with increased burden of comorbidities. Reducing readmissions for common cardiac etiologies could save substantial healthcare costs. © 2018 Wiley Periodicals, Inc.

Features and outcomes of hospitalized Thai patients with pyogenic arthritis: analysis from the nationwide hospital database.

PubMed

Mahakkanukrauh, Ajanee; Thavornpitak, Yupa; Foocharoen, Chingching; Suwannaroj, Siraphop; Nanagara, Ratanavadee

2013-08-01

Pyogenic arthritis (PA) is still a problematic arthritic disease that requires hospitalization. To study the epidemiological characteristics and predictors of treatment outcomes for Thai patients hospitalized with PA. The nationwide hospital database from the 2010 fiscal year was analyzed. Patients 18 years of age onward, who had primary diagnosis of pyogenic arthritis, were included in this study. There were a total of 6242 PA admissions during 2010. It was ranked third among hospitalized musculoskeletal patients after osteoarthritis (OA) and gouty arthritis. The estimated prevalence of PA was 13.5 per 100 000 adult population. Geographic distributions of PA was related to the population density of each region; however it seemed more frequent in the northern and northeastern regions of Thailand. The prevalence increased with age, 3.6 and 43.6 per 100 000 in young adults and the elderly, respectively. Among the 2877 co-morbidities coded, diabetes was the most common, followed by crystal-induced arthritis, existing other foci of infections (urinary tract infection, skin and soft tissue infections and pneumonia) and pre-existing chronic joint diseases (OA,rheumatoid arthritis), respectively. Overall hospital mortality rate was 2.6%. Poorer outcomes were found among patients with chronic liver disease and other existing foci of infections. The prevalence of hospitalized PA is still modest in Thailand, showing the highest prevalence in the advanced age group. Diabetes was the most commonly co-morbidity found; however, poorer outcomes were noted among patients with chronic liver disease and existing multiple sites of infections. © 2013 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

PubMed Central

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

[Genetic mutation databases: stakes and perspectives for orphan genetic diseases].

PubMed

Humbertclaude, V; Tuffery-Giraud, S; Bareil, C; Thèze, C; Paulet, D; Desmet, F-O; Hamroun, D; Baux, D; Girardet, A; Collod-Béroud, G; Khau Van Kien, P; Roux, A-F; des Georges, M; Béroud, C; Claustres, M

2010-10-01

New technologies, which constantly become available for mutation detection and gene analysis, have contributed to an exponential rate of discovery of disease genes and variation in the human genome. The task of collecting and documenting this enormous amount of data in genetic databases represents a major challenge for the future of biological and medical science. The Locus Specific Databases (LSDBs) are so far the most efficient mutation databases. This review presents the main types of databases available for the analysis of mutations responsible for genetic disorders, as well as open perspectives for new therapeutic research or challenges for future medicine. Accurate and exhaustive collection of variations in human genomes will be crucial for research and personalized delivery of healthcare. Copyright © 2009 Elsevier Masson SAS. All rights reserved.

Toward a mtDNA locus-specific mutation database using the LOVD platform.

PubMed

Elson, Joanna L; Sweeney, Mary G; Procaccio, Vincent; Yarham, John W; Salas, Antonio; Kong, Qing-Peng; van der Westhuizen, Francois H; Pitceathly, Robert D S; Thorburn, David R; Lott, Marie T; Wallace, Douglas C; Taylor, Robert W; McFarland, Robert

2012-09-01

The Human Variome Project (HVP) is a global effort to collect and curate all human genetic variation affecting health. Mutations of mitochondrial DNA (mtDNA) are an important cause of neurogenetic disease in humans; however, identification of the pathogenic mutations responsible can be problematic. In this article, we provide explanations as to why and suggest how such difficulties might be overcome. We put forward a case in support of a new Locus Specific Mutation Database (LSDB) implemented using the Leiden Open-source Variation Database (LOVD) system that will not only list primary mutations, but also present the evidence supporting their role in disease. Critically, we feel that this new database should have the capacity to store information on the observed phenotypes alongside the genetic variation, thereby facilitating our understanding of the complex and variable presentation of mtDNA disease. LOVD supports fast queries of both seen and hidden data and allows storage of sequence variants from high-throughput sequence analysis. The LOVD platform will allow construction of a secure mtDNA database; one that can fully utilize currently available data, as well as that being generated by high-throughput sequencing, to link genotype with phenotype enhancing our understanding of mitochondrial disease, with a view to providing better prognostic information. © 2012 Wiley Periodicals, Inc.

Toward a mtDNA Locus-Specific Mutation Database Using the LOVD Platform

PubMed Central

Elson, Joanna L.; Sweeney, Mary G.; Procaccio, Vincent; Yarham, John W.; Salas, Antonio; Kong, Qing-Peng; van der Westhuizen, Francois H.; Pitceathly, Robert D.S.; Thorburn, David R.; Lott, Marie T.; Wallace, Douglas C.; Taylor, Robert W.; McFarland, Robert

2015-01-01

The Human Variome Project (HVP) is a global effort to collect and curate all human genetic variation affecting health. Mutations of mitochondrial DNA (mtDNA) are an important cause of neurogenetic disease in humans; however, identification of the pathogenic mutations responsible can be problematic. In this article, we provide explanations as to why and suggest how such difficulties might be overcome. We put forward a case in support of a new Locus Specific Mutation Database (LSDB) implemented using the Leiden Open-source Variation Database (LOVD) system that will not only list primary mutations, but also present the evidence supporting their role in disease. Critically, we feel that this new database should have the capacity to store information on the observed phenotypes alongside the genetic variation, thereby facilitating our understanding of the complex and variable presentation of mtDNA disease. LOVD supports fast queries of both seen and hidden data and allows storage of sequence variants from high-throughput sequence analysis. The LOVD platform will allow construction of a secure mtDNA database; one that can fully utilize currently available data, as well as that being generated by high-throughput sequencing, to link genotype with phenotype enhancing our understanding of mitochondrial disease, with a view to providing better prognostic information. PMID:22581690

Tennis Shoe Town. Marketing & Cooperative Education Database Application Unit. Database Applications for Marketing Operations and Selling Units.

ERIC Educational Resources Information Center

Forrest, Melanie D.

This curriculum guide is intended for Missouri teachers teaching a course in database applications for high school students enrolled in marketing and cooperative education. The curriculum presented includes learning activities in which students are taught to analyze database tables containing the types of data typically encountered by employees…

Relational Databases: A Transparent Framework for Encouraging Biology Students to Think Informatically

ERIC Educational Resources Information Center

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a…

Development and validation of an administrative case definition for inflammatory bowel diseases

PubMed Central

Rezaie, Ali; Quan, Hude; Fedorak, Richard N; Panaccione, Remo; Hilsden, Robert J

2012-01-01

BACKGROUND: A population-based database of inflammatory bowel disease (IBD) patients is invaluable to explore and monitor the epidemiology and outcome of the disease. In this context, an accurate and validated population-based case definition for IBD becomes critical for researchers and health care providers. METHODS: IBD and non-IBD individuals were identified through an endoscopy database in a western Canadian health region (Calgary Health Region, Calgary, Alberta). Subsequently, using a novel algorithm, a series of case definitions were developed to capture IBD cases in the administrative databases. In the second stage of the study, the criteria were validated in the Capital Health Region (Edmonton, Alberta). RESULTS: A total of 150 IBD case definitions were developed using 1399 IBD patients and 15,439 controls in the development phase. In the validation phase, 318,382 endoscopic procedures were searched and 5201 IBD patients were identified. After consideration of sensitivity, specificity and temporal stability of each validated case definition, a diagnosis of IBD was assigned to individuals who experienced at least two hospitalizations or had four physician claims, or two medical contacts in the Ambulatory Care Classification System database with an IBD diagnostic code within a two-year period (specificity 99.8%; sensitivity 83.4%; positive predictive value 97.4%; negative predictive value 98.5%). An alternative case definition was developed for regions without access to the Ambulatory Care Classification System database. A novel scoring system was developed that detected Crohn disease and ulcerative colitis patients with a specificity of >99% and a sensitivity of 99.1% and 86.3%, respectively. CONCLUSION: Through a robust methodology, a reproducible set of criteria to capture IBD patients through administrative databases was developed. The methodology may be used to develop similar administrative definitions for chronic diseases. PMID:23061064

Integrating genome-wide association study summaries and element-gene interaction datasets identified multiple associations between elements and complex diseases.

PubMed

He, Awen; Wang, Wenyu; Prakash, N Tejo; Tinkov, Alexey A; Skalny, Anatoly V; Wen, Yan; Hao, Jingcan; Guo, Xiong; Zhang, Feng

2018-03-01

Chemical elements are closely related to human health. Extensive genomic profile data of complex diseases offer us a good opportunity to systemically investigate the relationships between elements and complex diseases/traits. In this study, we applied gene set enrichment analysis (GSEA) approach to detect the associations between elements and complex diseases/traits though integrating element-gene interaction datasets and genome-wide association study (GWAS) data of complex diseases/traits. To illustrate the performance of GSEA, the element-gene interaction datasets of 24 elements were extracted from the comparative toxicogenomics database (CTD). GWAS summary datasets of 24 complex diseases or traits were downloaded from the dbGaP or GEFOS websites. We observed significant associations between 7 elements and 13 complex diseases or traits (all false discovery rate (FDR) < 0.05), including reported relationships such as aluminum vs. Alzheimer's disease (FDR = 0.042), calcium vs. bone mineral density (FDR = 0.031), magnesium vs. systemic lupus erythematosus (FDR = 0.012) as well as novel associations, such as nickel vs. hypertriglyceridemia (FDR = 0.002) and bipolar disorder (FDR = 0.027). Our study results are consistent with previous biological studies, supporting the good performance of GSEA. Our analyzing results based on GSEA framework provide novel clues for discovering causal relationships between elements and complex diseases. © 2017 WILEY PERIODICALS, INC.

Database integration of protocol-specific neurological imaging datasets

PubMed Central

Pacurar, Emil E.; Sethi, Sean K.; Habib, Charbel; Laze, Marius O.; Martis-Laze, Rachel; Haacke, E. Mark

2016-01-01

For many years now, Magnetic Resonance Innovations (MR Innovations), a magnetic resonance imaging (MRI) software development, technology, and research company, has been aggregating a multitude of MRI data from different scanning sites through its collaborations and research contracts. The majority of the data has adhered to neuroimaging protocols developed by our group which has helped ensure its quality and consistency. The protocols involved include the study of: traumatic brain injury, extracranial venous imaging for multiple sclerosis and Parkinson's disease, and stroke. The database has proven invaluable in helping to establish disease biomarkers, validate findings across multiple data sets, develop and refine signal processing algorithms, and establish both public and private research collaborations. Myriad Masters and PhD dissertations have been possible thanks to the availability of this database. As an example of a project that cuts across diseases, we have used the data and specialized software to develop new guidelines for detecting cerebral microbleeds. Ultimately, the database has been vital in our ability to provide tools and information for researchers and radiologists in diagnosing their patients, and we encourage collaborations and welcome sharing of similar data in this database. PMID:25959660

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases.

PubMed

Xu, Yanjun; Yang, Haixiu; Wu, Tan; Dong, Qun; Sun, Zeguo; Shang, Desi; Li, Feng; Xu, Yingqi; Su, Fei; Liu, Siyao; Zhang, Yunpeng; Li, Xia

2017-01-01

BioM2MetDisease is a manually curated database that aims to provide a comprehensive and experimentally supported resource of associations between metabolic diseases and various biomolecules. Recently, metabolic diseases such as diabetes have become one of the leading threats to people’s health. Metabolic disease associated with alterations of multiple types of biomolecules such as miRNAs and metabolites. An integrated and high-quality data source that collection of metabolic disease associated biomolecules is essential for exploring the underlying molecular mechanisms and discovering novel therapeutics. Here, we developed the BioM2MetDisease database, which currently documents 2681 entries of relationships between 1147 biomolecules (miRNAs, metabolites and small molecules/drugs) and 78 metabolic diseases across 14 species. Each entry includes biomolecule category, species, biomolecule name, disease name, dysregulation pattern, experimental technique, a brief description of metabolic disease-biomolecule relationships, the reference, additional annotation information etc. BioM2MetDisease provides a user-friendly interface to explore and retrieve all data conveniently. A submission page was also offered for researchers to submit new associations between biomolecules and metabolic diseases. BioM2MetDisease provides a comprehensive resource for studying biology molecules act in metabolic diseases, and it is helpful for understanding the molecular mechanisms and developing novel therapeutics for metabolic diseases. http://www.bio-bigdata.com/BioM2MetDisease/. © The Author(s) 2017. Published by Oxford University Press.

Effect of restricted protein diet supplemented with keto analogues in end-stage renal disease: a systematic review and meta-analysis.

PubMed

Jiang, Zheng; Tang, Yi; Yang, Lichuan; Mi, Xuhua; Qin, Wei

2018-04-01

To evaluate the efficacy and safety of the restricted protein diet supplemented with keto analogues when applied in end-stage renal disease (ESRD). The Cochrane Library, PubMed, Embase, CBM and CENTRAL databases were searched and reviewed up to January 2017. Clinical trials were analyzed using RevMan 5.3 software. Five randomized controlled trials were selected and included in this study according to our inclusion and exclusion criteria. Changes in serum albumin, PTH, triglyceride, cholesterol, calcium, phosphorus, hemoglobin, Kt/v and CRP before and after treatment were analyzed. Meta-analysis results indicated that, compared with normal protein diet, low-protein diet (LPD) supplemented with keto analogues (sLPD) could improve serum albumin (P < 0.00001), hyperparathyroidism (P < 0.00001) and hyperphosphatemia (P = 0.008). No differences in triglyceride, cholesterol, hemoglobin, Kt/v and CRP were observed between different protein intake groups. Restricted protein diet supplemented with keto analogues (sLPD) may improve nutritional status and prevent hyperparathyroidism in ESRD patients. The current data were mainly obtained from short-term, single-center trails with small sample sizes and limited nutritional status indexes, indicating a need for further study.

Osteoporosis and bone fractures in alcoholic liver disease: A meta-analysis

PubMed Central

Bang, Chang Seok; Shin, In Soo; Lee, Sung Wha; Kim, Jin Bong; Baik, Gwang Ho; Suk, Ki Tae; Yoon, Jai Hoon; Kim, Yeon Soo; Kim, Dong Joon

2015-01-01

AIM: To evaluate the association between alcoholic liver disease (ALD) and bone fractures or osteoporosis. METHODS: Non-randomized studies were identified from databases (PubMed, EMBASE, and the Cochrane Library). The search was conducted using Boolean operators and keywords, which included “alcoholic liver diseases”, “osteoporosis”, or “bone fractures”. The prevalence of any fractures or osteoporosis, and bone mineral density (BMD) were extracted and analyzed using risk ratios and standardized mean difference (SMD). A random effects model was applied. RESULTS: In total, 15 studies were identified and analyzed. Overall, ALD demonstrated a RR of 1.944 (95%CI: 1.354-2.791) for the development of bone fractures. However, ALD showed a RR of 0.849 (95%CI: 0.523-1.380) for the development of osteoporosis. BMD was not significantly different between the ALD and control groups, although there was a trend toward lower BMD in patients with ALD (SMD in femur-BMD: -0.172, 95%CI: -0.453-0.110; SMD in spine-BMD: -0.169, 95%CI: -0.476-0.138). Sensitivity analyses showed consistent results. CONCLUSION: Current publications indicate significant associations between bone fractures and ALD, independent of BMD or the presence of osteoporosis. PMID:25852292

An informatics approach to analyzing the incidentalome.

PubMed

Berg, Jonathan S; Adams, Michael; Nassar, Nassib; Bizon, Chris; Lee, Kristy; Schmitt, Charles P; Wilhelmsen, Kirk C; Evans, James P

2013-01-01

Next-generation sequencing has transformed genetic research and is poised to revolutionize clinical diagnosis. However, the vast amount of data and inevitable discovery of incidental findings require novel analytic approaches. We therefore implemented for the first time a strategy that utilizes an a priori structured framework and a conservative threshold for selecting clinically relevant incidental findings. We categorized 2,016 genes linked with Mendelian diseases into "bins" based on clinical utility and validity, and used a computational algorithm to analyze 80 whole-genome sequences in order to explore the use of such an approach in a simulated real-world setting. The algorithm effectively reduced the number of variants requiring human review and identified incidental variants with likely clinical relevance. Incorporation of the Human Gene Mutation Database improved the yield for missense mutations but also revealed that a substantial proportion of purported disease-causing mutations were misleading. This approach is adaptable to any clinically relevant bin structure, scalable to the demands of a clinical laboratory workflow, and flexible with respect to advances in genomics. We anticipate that application of this strategy will facilitate pretest informed consent, laboratory analysis, and posttest return of results in a clinical context.

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.

PubMed

Aguilera-Mendoza, Longendri; Marrero-Ponce, Yovani; Tellez-Ibarra, Roberto; Llorente-Quesada, Monica T; Salgado, Jesús; Barigye, Stephen J; Liu, Jun

2015-08-01

The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

How Have States Used Executive Orders to Address Public Health?

PubMed

Gakh, Maxim; Callahan, Karen; Goodie, Aaliyah; Rutkow, Lainie

2018-06-07

Gubernatorial executive orders (GEOs) are important, yet poorly understood, public health tools. We analyzed health-related GEOs nationwide using a modified legal mapping approach. We searched Westlaw's Netscan Executive Orders database for orders issued between 2008 and 2014. Search terms were generated from the Healthy People 2020 Leading Health Indicators (LHIs). GEOs were screened with data abstracted and analyzed on the basis of LHIs, states, years, and characteristics identified in previous literature. We found differences in GEOs issued per LHI. Of the 303 unique orders, they ranged from 32 to 53 issued per year and 0 to 45 issued per state. Most GEOs managed governmental public health functions, required collaboration, and mandated studying problems. Fewer directly addressed health equity, chronic disease, and resource deployment. Gubernatorial authority and political and institutional factors appear relevant to GEO issuance. GEOs offer means to institute public health policies and should be considered by public health professionals.

[Xerostomia: clinic, etiology, diagnosis and treatment].

PubMed

Guobis, Zygimantas; Baseviciene, Nomeda; Paipaliene, Pajauta; Sabalys, Gintautas; Kubilius, Ricardas

2006-01-01

The aim of this article is to review the problem of xerostomia considering its clinical, etiological, diagnostic and treatment features, basing on the today's tutorials and scientific articles found in databases on the Internet. Recent epidemiologic data on the prevalence of xerostomia in different countries are introduced. There are analyzed the main aspects of clinical manifestations of xerostomia, according to the different etiology analyzed. The most common etiological factors causing xerostomia, especially the main three of them: radiation therapy, Sjögren's syndrome, and drugs, are pointed out. The most popular and accepted clinical and laboratory assays for measuring and evaluating the function of salivary glands are represented. Attention is paid to xerostomia as substantiation of the separate diagnosis and its role in diagnosing other diseases. The concept of possible treatment modalities and prognosis are discussed. The main and most common problems concerning xerostomia are revealed.

[Matematical modeling of antibiotic resistance: perspectives from a meta-analysys].

PubMed

Fresnadillo-Martínez, M J; García-Sánchez, E; García-Merino, E; Martín-Del-Rey, A; Rodríguez-Encinas, A; Rodríguez-Sánchez, G; García-Sánchez, J E

2012-09-01

The antibiotic resistance is one of the greatest challenges of the international health community. The study of antibiotic resistance must be a multidisciplinary task and, in this sense, the main goal of this work is to analyze the role that Mathematical Modeling can play in this scenario. A qualitative and cuantitative analysis of the works published in the scientific literature is done by means of a search in the most important databases: MEDLINE, SCOPUS and ISI Web of Science. Consequently, there are few papers related to our topic but the existing works have been published in high-quality and impact international journals. Moreover, we can state that mathematical models are a very important and useful tool to analyze and study both the treatments protocols for resistance prevention and the assesment of control strategies in hospital environtment, or the prediction of the evolution of diseases due to resistant strains.

aCGH-MAS: Analysis of aCGH by means of Multiagent System

PubMed Central

Benito, Rocío; Bajo, Javier; Rodríguez, Ana Eugenia; Abáigar, María

2015-01-01

There are currently different techniques, such as CGH arrays, to study genetic variations in patients. CGH arrays analyze gains and losses in different regions in the chromosome. Regions with gains or losses in pathologies are important for selecting relevant genes or CNVs (copy-number variations) associated with the variations detected within chromosomes. Information corresponding to mutations, genes, proteins, variations, CNVs, and diseases can be found in different databases and it would be of interest to incorporate information of different sources to extract relevant information. This work proposes a multiagent system to manage the information of aCGH arrays, with the aim of providing an intuitive and extensible system to analyze and interpret the results. The agent roles integrate statistical techniques to select relevant variations and visualization techniques for the interpretation of the final results and to extract relevant information from different sources of information by applying a CBR system. PMID:25874203

Human Disease Insight: An integrated knowledge-based platform for disease-gene-drug information.

PubMed

Tasleem, Munazzah; Ishrat, Romana; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

2016-01-01

The scope of the Human Disease Insight (HDI) database is not limited to researchers or physicians as it also provides basic information to non-professionals and creates disease awareness, thereby reducing the chances of patient suffering due to ignorance. HDI is a knowledge-based resource providing information on human diseases to both scientists and the general public. Here, our mission is to provide a comprehensive human disease database containing most of the available useful information, with extensive cross-referencing. HDI is a knowledge management system that acts as a central hub to access information about human diseases and associated drugs and genes. In addition, HDI contains well-classified bioinformatics tools with helpful descriptions. These integrated bioinformatics tools enable researchers to annotate disease-specific genes and perform protein analysis, search for biomarkers and identify potential vaccine candidates. Eventually, these tools will facilitate the analysis of disease-associated data. The HDI provides two types of search capabilities and includes provisions for downloading, uploading and searching disease/gene/drug-related information. The logistical design of the HDI allows for regular updating. The database is designed to work best with Mozilla Firefox and Google Chrome and is freely accessible at http://humandiseaseinsight.com. Copyright © 2015 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

E-Learning for Rare Diseases: An Example Using Fabry Disease.

PubMed

Cimmaruta, Chiara; Liguori, Ludovica; Monticelli, Maria; Andreotti, Giuseppina; Citro, Valentina

2017-09-24

Rare diseases represent a challenge for physicians because patients are rarely seen, and they can manifest with symptoms similar to those of common diseases. In this work, genetic confirmation of diagnosis is derived from DNA sequencing. We present a tutorial for the molecular analysis of a rare disease using Fabry disease as an example. An exonic sequence derived from a hypothetical male patient was matched against human reference data using a genome browser. The missense mutation was identified by running BlastX, and information on the affected protein was retrieved from the database UniProt. The pathogenic nature of the mutation was assessed with PolyPhen-2. Disease-specific databases were used to assess whether the missense mutation led to a severe phenotype, and whether pharmacological therapy was an option. An inexpensive bioinformatics approach is presented to get the reader acquainted with the diagnosis of Fabry disease. The reader is introduced to the field of pharmacological chaperones, a therapeutic approach that can be applied only to certain Fabry genotypes. The principle underlying the analysis of exome sequencing can be explained in simple terms using web applications and databases which facilitate diagnosis and therapeutic choices.

Extraction, integration and analysis of alternative splicing and protein structure distributed information

PubMed Central

D'Antonio, Matteo; Masseroli, Marco

2009-01-01

Background Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structures. This suggests possible correlations between alternative splicing and protein structure. In order to support the investigation of such relationships, we have developed the Alternative Splicing and Protein Structure Scrutinizer (PASS), a Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank. Primary data from these databases have been integrated and analyzed using the Protein Identifier Cross-Reference, BLAST, CLUSTALW and FeatureMap3D software tools. Results A database has been developed to store the considered primary data and the results from their analysis; a system of Perl scripts has been implemented to automatically create and update the database and analyze the integrated data; a Web interface has been implemented to make the analyses easily accessible; a database has been created to manage user accesses to the PASS Web application and store user's data and searches. Conclusion PASS automatically integrates data from the Alternative Splicing Database with protein structure data from the Protein Data Bank. Additionally, it comprehensively analyzes the integrated data with publicly available well-known bioinformatics tools in order to generate structural information of isoform pairs. Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different functions. PMID:19828075

Gastroesophageal reflux, dental erosion, and halitosis in epidemiological surveys: a systematic review.

PubMed

Marsicano, Juliane A; de Moura-Grec, Patrícia G; Bonato, Rafaela C S; Sales-Peres, Matheus de Carvalho; Sales-Peres, Arsenio; Sales-Peres, Sílvia Helena de Carvalho

2013-02-01

In published studies, it has been suggested that dental wear is associated with gastroesophageal reflux disease (GERD). This systematic review was carried out to evaluate the association of GERD, dental erosion, and halitosis and to compare the indices adopted in epidemiological surveys. The Medline database (until October, 2011) was searched systematically to identify studies evaluating the prevalence of oral alterations, such as dental erosion and halitosis, in patients with GERD symptoms. Two reviewers analyzed all reports and the selected studies were evaluated according to the quality of evidence, using the validated Newcastle-Ottawa Quality Assessment Scale. Full-text copies of a total of 32 publications were obtained in duplicate. Sixteen publications were identified among the citations in the Bibliographic lists of studies that fulfilled the exclusion/inclusion criteria and quality of evidence. The relationship between dental erosion and GERD patients was significant in only seven studies. According to three studies, halitosis could be one of several extraesophageal symptoms or manifestations in GERD patients. In one study, it was found that the mucosa of GERD patients was significantly more acidic in comparison with that of the control group. This systematic review showed that there is a relationship between GERD and oral diseases (dental erosion and halitosis). The epidemiological surveys used different indices to analyze GERD and dental erosion. Further research could investigate the best method for assessing the two diseases.

Salivary proteomics of healthy dogs: An in depth catalog

PubMed Central

Furrow, Eva; Souza, Clarissa P.; Granick, Jennifer L.; de Jong, Ebbing P.; Griffin, Timothy J.; Wang, Xiong

2018-01-01

Objective To provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups. Methods 36 healthy dogs without evidence of periodontal disease representing four breed phylogeny groups, based upon single nucleotide polymorphism haplotypes (ancient, herding/sighthound, and two miscellaneous groups). Saliva collected from dogs was pooled by phylogeny group and analyzed using nanoscale liquid chromatography-tandem mass spectrometry. Resulting tandem mass spectra were compared to databases for identification of endogenous peptides and inferred proteins. Results 2,491 proteins and endogenous peptides were found in the saliva of healthy dogs with no periodontal disease. All dog phylogeny groups’ saliva was rich in proteins and peptides with antimicrobial functions. The ancient breeds group was distinct in that it contained unique proteins and was missing many proteins and peptides present in the other groups. Conclusions and clinical relevance Using a sophisticated nanoscale liquid chromatography-tandem mass spectrometry, we were able to identify 10-fold more salivary proteins than previously reported in dogs. Seven of the top 10 most abundant proteins or peptides serve immune functions and many more with various antimicrobial mechanisms were found. This is the most comprehensive analysis of healthy canine saliva to date, and will provide the groundwork for future studies analyzing salivary proteins and endogenous peptides in disease states. PMID:29329347

Salivary proteomics of healthy dogs: An in depth catalog.

PubMed

Torres, Sheila M F; Furrow, Eva; Souza, Clarissa P; Granick, Jennifer L; de Jong, Ebbing P; Griffin, Timothy J; Wang, Xiong

2018-01-01

To provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups. 36 healthy dogs without evidence of periodontal disease representing four breed phylogeny groups, based upon single nucleotide polymorphism haplotypes (ancient, herding/sighthound, and two miscellaneous groups). Saliva collected from dogs was pooled by phylogeny group and analyzed using nanoscale liquid chromatography-tandem mass spectrometry. Resulting tandem mass spectra were compared to databases for identification of endogenous peptides and inferred proteins. 2,491 proteins and endogenous peptides were found in the saliva of healthy dogs with no periodontal disease. All dog phylogeny groups' saliva was rich in proteins and peptides with antimicrobial functions. The ancient breeds group was distinct in that it contained unique proteins and was missing many proteins and peptides present in the other groups. Using a sophisticated nanoscale liquid chromatography-tandem mass spectrometry, we were able to identify 10-fold more salivary proteins than previously reported in dogs. Seven of the top 10 most abundant proteins or peptides serve immune functions and many more with various antimicrobial mechanisms were found. This is the most comprehensive analysis of healthy canine saliva to date, and will provide the groundwork for future studies analyzing salivary proteins and endogenous peptides in disease states.

Is 123I-metaiodobenzylguanidine heart-to-mediastinum ratio dependent on age? From Japanese Society of Nuclear Medicine normal database.

PubMed

Nakajima, Kenichi; Okuda, Koichi; Matsuo, Shinro; Wakabayashi, Hiroshi; Kinuya, Seigo

2018-04-01

Heart-to-mediastinum ratios (HMRs) of 123 I-metaiodobenzylguanidine (MIBG) have usually been applied to prognostic evaluations of heart failure and Lewy body disease. However, whether these ratios depend on patient age has not yet been clarified using normal databases. We analyzed 62 patients (average age 57 ± 19 years, male 45%) derived from a normal database of the Japanese Society of Nuclear Medicine working group. The HMR was calculated from early (15 min) and delayed (3-4 h) anterior planar 123 I-MIBG images. All HMRs were standardized to medium-energy general purpose (MEGP) collimator equivalent conditions using conversion coefficients for the collimator types. Washout rates (WR) were also calculated, and we analyzed whether early and late HMR, and WR are associated with age. Before standardization of HMR to MEGP collimator conditions, HMR and age did not significantly correlate. However, late HMR significantly correlated with age after standardization: late HMR = - 0.0071 × age + 3.69 (r 2  = 0.078, p = 0.028), indicating that a 14-year increase in age corresponded to a decrease in HMR of 0.1. Whereas the lower limit (2.5% quantile) of late HMR was 2.3 for all patients, it was 2.5 and 2.0 for those aged ≤ 63 and > 63 years, respectively. Early HMR tended to be lower in subjects with the higher age (p = 0.076), whereas WR was not affected by age. While late HMR was slightly decreased in elderly patients, the lower limit of 2.2-2.3 can still be used to determine both early and late HMR.

The Innate Immune Database (IIDB)

PubMed Central

Korb, Martin; Rust, Aistair G; Thorsson, Vesteinn; Battail, Christophe; Li, Bin; Hwang, Daehee; Kennedy, Kathleen A; Roach, Jared C; Rosenberger, Carrie M; Gilchrist, Mark; Zak, Daniel; Johnson, Carrie; Marzolf, Bruz; Aderem, Alan; Shmulevich, Ilya; Bolouri, Hamid

2008-01-01

Background As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site . Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens. Description We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser. Conclusion We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at . PMID:18321385

PrionScan: an online database of predicted prion domains in complete proteomes.

PubMed

Espinosa Angarica, Vladimir; Angulo, Alfonso; Giner, Arturo; Losilla, Guillermo; Ventura, Salvador; Sancho, Javier

2014-02-05

Prions are a particular type of amyloids related to a large variety of important processes in cells, but also responsible for serious diseases in mammals and humans. The number of experimentally characterized prions is still low and corresponds to a handful of examples in microorganisms and mammals. Prion aggregation is mediated by specific protein domains with a remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. These compositional features have been used to predict new prion proteins in the genomes of different organisms. Despite these efforts, there are only a few available data sources containing prion predictions at a genomic scale. Here we present PrionScan, a new database of predicted prion-like domains in complete proteomes. We have previously developed a predictive methodology to identify and score prionogenic stretches in protein sequences. In the present work, we exploit this approach to scan all the protein sequences in public databases and compile a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. PrionScan can be used in two different ways: database query and analysis of protein sequences submitted by the users. In the first mode, simple queries allow to retrieve a detailed description of the properties of a defined protein. Queries can also be combined to generate more complex and specific searching patterns. In the second mode, users can submit and analyze their own sequences. It is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, allowing researches performing cross-species prion biology studies. Our database might also be useful for guiding experimentalists in the identification of new candidates for further experimental characterization.

SAMMD: Staphylococcus aureus microarray meta-database.

PubMed

Nagarajan, Vijayaraj; Elasri, Mohamed O

2007-10-02

Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL). SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes.

SAMMD: Staphylococcus aureus Microarray Meta-Database

PubMed Central

Nagarajan, Vijayaraj; Elasri, Mohamed O

2007-01-01

Background Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. Description SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL). Conclusion SAMMD is hosted and available at . Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes. PMID:17910768

[Exploring pharmacological principle of Artemisia carvifolia with textmining technology].

PubMed

Zhao, Yu-Ping; Wang, Hui; Yang, Guang; Qiu, Zhi-Dong; Qu, Xiao-Bo; Zhang, Xiao-Bo

2016-08-01

To explore the pharmacological principle of Artemisia carvifolia,the text mining technique was used. All the references of A. carvifolia were collected from PubMed database, and then the rules of the main ingredient,relative diseases, organs, tissues, proteins and metabolites were analyzed. Finally, a network was set up. Then it was found that the main ingredients included sesquiterpenoids,flavonoids,and volatileoils.The diseases such as malaria, cerebral malaria, falciparum malaria, visceral leishmaniasis and systemic lupus erythematosus were often treated with A. carvifolia. In association in organ were the liver, skin, trachea,lungs,and spleen.Correlations with tissues were mainly including macrophages, T lymphocytes, blood vessels, epithelial cells.The protein was correlation with it involved CYP450, PI3K, TNF-α, AASDPPT, DNA polymerase and so on. Comprehensive and systematic treatment principle of A. carvifolia was obtained by text mining, which was helpful in clinical application. Copyright© by the Chinese Pharmaceutical Association.

Comparison of genetic characteristics of canine papillomaviruses in Turkey.

PubMed

Oğuzoğlu, Tuba Çiğdem; Timurkan, Mehmet Özkan; Koç, Bahattin Taylan; Alkan, Feray

2017-11-01

Papillomavirus (PV) infections often cause benign and malignant skin neoplasia in dogs. To date, twenty types of canine papillomaviruses (CPVs) have been described worldwide. A detailed molecular characterization of CPVs in Turkey is lacking. In the present study, oral and mucosal lesions from 13 dogs with suspected CPV infection from the Mediterranean and central Anatolian regions of Turkey were analyzed. The partial gene sequences of the L1, E6, and E7 regions were compared with those of CPV types in the GenBank database. The results showed that CPV-1 infection was the dominant type of canine papillomatosis in Turkey. In addition, there was no statistically significant association between the frequency of the disease and the age or gender of the dog (p>0.05). However, all the dogs were pedigree breeds, suggesting that the disease may be more prevalent among pure-bred dogs than mixed breeds. Copyright © 2017 Elsevier B.V. All rights reserved.

Organizing, exploring, and analyzing antibody sequence data: the case for relational-database managers.

PubMed

Owens, John

2009-01-01

Technological advances in the acquisition of DNA and protein sequence information and the resulting onrush of data can quickly overwhelm the scientist unprepared for the volume of information that must be evaluated and carefully dissected to discover its significance. Few laboratories have the luxury of dedicated personnel to organize, analyze, or consistently record a mix of arriving sequence data. A methodology based on a modern relational-database manager is presented that is both a natural storage vessel for antibody sequence information and a conduit for organizing and exploring sequence data and accompanying annotation text. The expertise necessary to implement such a plan is equal to that required by electronic word processors or spreadsheet applications. Antibody sequence projects maintained as independent databases are selectively unified by the relational-database manager into larger database families that contribute to local analyses, reports, interactive HTML pages, or exported to facilities dedicated to sophisticated sequence analysis techniques. Database files are transposable among current versions of Microsoft, Macintosh, and UNIX operating systems.

LiverAtlas: a unique integrated knowledge database for systems-level research of liver and hepatic disease.

PubMed

Zhang, Yanqiong; Yang, Chunyuan; Wang, Shaochuang; Chen, Tao; Li, Mansheng; Wang, Xue; Li, Dongsheng; Wang, Kang; Ma, Jie; Wu, Songfeng; Zhang, Xueli; Zhu, Yunping; Wu, Jinsheng; He, Fuchu

2013-09-01

A large amount of liver-related physiological and pathological data exist in publicly available biological and bibliographic databases, which are usually far from comprehensive or integrated. Data collection, integration and mining processes pose a great challenge to scientific researchers and clinicians interested in the liver. To address these problems, we constructed LiverAtlas (http://liveratlas.hupo.org.cn), a comprehensive resource of biomedical knowledge related to the liver and various hepatic diseases by incorporating 53 databases. In the present version, LiverAtlas covers data on liver-related genomics, transcriptomics, proteomics, metabolomics and hepatic diseases. Additionally, LiverAtlas provides a wealth of manually curated information, relevant literature citations and cross-references to other databases. Importantly, an expert-confirmed Human Liver Disease Ontology, including relevant information for 227 types of hepatic disease, has been constructed and is used to annotate LiverAtlas data. Furthermore, we have demonstrated two examples of applying LiverAtlas data to identify candidate markers for hepatocellular carcinoma (HCC) at the systems level and to develop a systems biology-based classifier by combining the differential gene expression with topological features of human protein interaction networks to enhance the ability of HCC differential diagnosis. LiverAtlas is the most comprehensive liver and hepatic disease resource, which helps biologists and clinicians to analyse their data at the systems level and will contribute much to the biomarker discovery and diagnostic performance enhancement for liver diseases. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Locus-Specific Mutation Databases for Neurodegenerative Brain Diseases

PubMed Central

Cruts, Marc; Theuns, Jessie; Van Broeckhoven, Christine

2012-01-01

The Alzheimer disease and frontotemporal dementia (AD&FTLD) and Parkinson disease (PD) Mutation Databases make available curated information of sequence variations in genes causing Mendelian forms of the most common neurodegenerative brain disease AD, frontotemporal lobar degeneration (FTLD), and PD. They are established resources for clinical geneticists, neurologists, and researchers in need of comprehensive, referenced genetic, epidemiologic, clinical, neuropathological, and/or cell biological information of specific gene mutations in these diseases. In addition, the aggregate analysis of all information available in the databases provides unique opportunities to extract mutation characteristics and genotype–phenotype correlations, which would be otherwise unnoticed and unexplored. Such analyses revealed that 61.4% of mutations are private to one single family, while only 5.7% of mutations occur in 10 or more families. The five mutations with most frequent independent observations occur in 21% of AD, 43% of FTLD, and 48% of PD families recorded in the Mutation Databases, respectively. Although these figures are inevitably biased by a publishing policy favoring novel mutations, they probably also reflect the occurrence of multiple rare and few relatively common mutations in the inherited forms of these diseases. Finally, with the exception of the PD genes PARK2 and PINK1, all other genes are associated with more than one clinical diagnosis or characteristics thereof. Hum Mutat 33:1340–1344, 2012. © 2012 Wiley Periodicals, Inc. PMID:22581678

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

Relational-database model for improving quality assurance and process control in a composite manufacturing environment

NASA Astrophysics Data System (ADS)

Gentry, Jeffery D.

2000-05-01

A relational database is a powerful tool for collecting and analyzing the vast amounts of inner-related data associated with the manufacture of composite materials. A relational database contains many individual database tables that store data that are related in some fashion. Manufacturing process variables as well as quality assurance measurements can be collected and stored in database tables indexed according to lot numbers, part type or individual serial numbers. Relationships between manufacturing process and product quality can then be correlated over a wide range of product types and process variations. This paper presents details on how relational databases are used to collect, store, and analyze process variables and quality assurance data associated with the manufacture of advanced composite materials. Important considerations are covered including how the various types of data are organized and how relationships between the data are defined. Employing relational database techniques to establish correlative relationships between process variables and quality assurance measurements is then explored. Finally, the benefits of database techniques such as data warehousing, data mining and web based client/server architectures are discussed in the context of composite material manufacturing.

MCAW-DB: A glycan profile database capturing the ambiguity of glycan recognition patterns.

PubMed

Hosoda, Masae; Takahashi, Yushi; Shiota, Masaaki; Shinmachi, Daisuke; Inomoto, Renji; Higashimoto, Shinichi; Aoki-Kinoshita, Kiyoko F

2018-05-11

Glycan-binding protein (GBP) interaction experiments, such as glycan microarrays, are often used to understand glycan recognition patterns. However, oftentimes the interpretation of glycan array experimental data makes it difficult to identify discrete GBP binding patterns due to their ambiguity. It is known that lectins, for example, are non-specific in their binding affinities; the same lectin can bind to different monosaccharides or even different glycan structures. In bioinformatics, several tools to mine the data generated from these sorts of experiments have been developed. These tools take a library of predefined motifs, which are commonly-found glycan patterns such as sialyl-Lewis X, and attempt to identify the motif(s) that are specific to the GBP being analyzed. In our previous work, as opposed to using predefined motifs, we developed the Multiple Carbohydrate Alignment with Weights (MCAW) tool to visualize the state of the glycans being recognized by the GBP under analysis. We previously reported on the effectiveness of our tool and algorithm by analyzing several glycan array datasets from the Consortium of Functional Glycomics (CFG). In this work, we report on our analysis of 1081 data sets which we collected from the CFG, the results of which we have made publicly and freely available as a database called MCAW-DB. We introduce this database, its usage and describe several analysis results. We show how MCAW-DB can be used to analyze glycan-binding patterns of GBPs amidst their ambiguity. For example, the visualization of glycan-binding patterns in MCAW-DB show how they correlate with the concentrations of the samples used in the array experiments. Using MCAW-DB, the patterns of glycans found to bind to various GBP-glycan binding proteins are visualized, indicating the binding "environment" of the glycans. Thus, the ambiguity of glycan recognition is numerically represented, along with the patterns of monosaccharides surrounding the binding region. The profiles in MCAW-DB could potentially be used as predictors of affinity of unknown or novel glycans to particular GBPs by comparing how well they match the existing profiles for those GBPs. Moreover, as the glycan profiles of diseased tissues become available, glycan alignments could also be used to identify glycan biomarkers unique to that tissue. Databases of these alignments may be of great use for drug discovery. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Vitamin D and Graves' disease: a meta-analysis update.

PubMed

Xu, Mei-Yan; Cao, Bing; Yin, Jian; Wang, Dong-Fang; Chen, Kai-Li; Lu, Qing-Bin

2015-05-21

The association between vitamin D levels and Graves' disease is not well studied. This update review aims to further analyze the relationship in order to provide an actual view of estimating the risk. We searched for the publications on vitamin D and Graves' disease in English or Chinese on PubMed, EMBASE, Chinese National Knowledge Infrastructure, China Biology Medical and Wanfang databases. The standardized mean difference (SMD) and 95% confidence interval (CI) were calculated for the vitamin D levels. Pooled odds ratio (OR) and 95% CI were calculated for vitamin D deficiency. We also performed sensitivity analysis and meta-regression. Combining effect sizes from 26 studies for Graves' disease as an outcome found a pooled effect of SMD = -0.77 (95% CI: -1.12, -0.42; p < 0.001) favoring the low vitamin D level by the random effect analysis. The meta-regression found assay method had the definite influence on heterogeneity (p = 0.048). The patients with Graves' disease were more likely to be deficient in vitamin D compared to the controls (OR = 2.24, 95% CI: 1.31, 3.81) with a high heterogeneity (I2 = 84.1%, p < 0.001). We further confirmed that low vitamin D status may increase the risk of Graves' disease.

Vitamin D and Graves’ Disease: A Meta-Analysis Update

PubMed Central

Xu, Mei-Yan; Cao, Bing; Yin, Jian; Wang, Dong-Fang; Chen, Kai-Li; Lu, Qing-Bin

2015-01-01

The association between vitamin D levels and Graves’ disease is not well studied. This update review aims to further analyze the relationship in order to provide an actual view of estimating the risk. We searched for the publications on vitamin D and Graves’ disease in English or Chinese on PubMed, EMBASE, Chinese National Knowledge Infrastructure, China Biology Medical and Wanfang databases. The standardized mean difference (SMD) and 95% confidence interval (CI) were calculated for the vitamin D levels. Pooled odds ratio (OR) and 95% CI were calculated for vitamin D deficiency. We also performed sensitivity analysis and meta-regression. Combining effect sizes from 26 studies for Graves’ disease as an outcome found a pooled effect of SMD = −0.77 (95% CI: −1.12, −0.42; p < 0.001) favoring the low vitamin D level by the random effect analysis. The meta-regression found assay method had the definite influence on heterogeneity (p = 0.048). The patients with Graves’ disease were more likely to be deficient in vitamin D compared to the controls (OR = 2.24, 95% CI: 1.31, 3.81) with a high heterogeneity (I2 = 84.1%, p < 0.001). We further confirmed that low vitamin D status may increase the risk of Graves’ disease. PMID:26007334

Subject-specific longitudinal shape analysis by coupling spatiotemporal shape modeling with medial analysis

NASA Astrophysics Data System (ADS)

Hong, Sungmin; Fishbaugh, James; Rezanejad, Morteza; Siddiqi, Kaleem; Johnson, Hans; Paulsen, Jane; Kim, Eun Young; Gerig, Guido

2017-02-01

Modeling subject-specific shape change is one of the most important challenges in longitudinal shape analysis of disease progression. Whereas anatomical change over time can be a function of normal aging, anatomy can also be impacted by disease related degeneration. Anatomical shape change may also be affected by structural changes from neighboring shapes, which may cause non-linear variations in pose. In this paper, we propose a framework to analyze disease related shape changes by coupling extrinsic modeling of the ambient anatomical space via spatiotemporal deformations with intrinsic shape properties from medial surface analysis. We compare intrinsic shape properties of a subject-specific shape trajectory to a normative 4D shape atlas representing normal aging to isolate shape changes related to disease. The spatiotemporal shape modeling establishes inter/intra subject anatomical correspondence, which in turn enables comparisons between subjects and the 4D shape atlas, and also quantitative analysis of disease related shape change. The medial surface analysis captures intrinsic shape properties related to local patterns of deformation. The proposed framework jointly models extrinsic longitudinal shape changes in the ambient anatomical space, as well as intrinsic shape properties to give localized measurements of degeneration. Six high risk subjects and six controls are randomly sampled from a Huntington's disease image database for qualitative and quantitative comparison.

Hepatosplenic T-cell lymphoma in patients receiving TNF-α inhibitor therapy: expanding the groups at risk.

PubMed

Parakkal, Deepak; Sifuentes, Humberto; Semer, Rumi; Ehrenpreis, Eli Daniel

2011-11-01

Hepatosplenic T-cell lymphoma (HSTCL) is a rare, lethal disease generally seen in young male patients with inflammatory bowel disease. The study of biologic and immunomodulator naive patients in Crohn's disease (SONIC), advocates combining infliximab with an immunomodulator in moderate-to-severe Crohn's disease. Unfortunately, combined immunosuppression increases risk for HSTCL. We herein review all cases of HSTCL reported to the Food and Drug Administration (FDA) in patients receiving TNF-α inhibitors. Individual reports from the FDA Adverse Event Reporting System database for lymphomas from the biological agents - infliximab, adalimumab, certolizumab, natalizumab, and etanercept were downloaded and analyzed with Microsoft Access. Full reports for all identified HSTCL cases were obtained from the FDA. Twenty-five cases of HSTCL were identified. Twenty-two (88%) patients had inflammatory bowel disease and three had rheumatoid arthritis. Four cases (16%) were in women and four patients were above 65 years of age. Twenty-four cases (96%) also received an immunomodulator (azathioprine, 6-mercaptopurine, or methotrexate). Two patients received adalimumab alone. HSTCL is no longer restricted to the previously identified risk group of young male patients, but can also occur in patients with rheumatoid arthritis, females and older adults receiving TNF-α inhibitors and immunomodulators. Improved disease outcomes using combination therapy should be tempered by the risk of developing HSTCL.

Socio-Cultural Aspects of Chagas Disease: A Systematic Review of Qualitative Research

PubMed Central

Ventura-Garcia, Laia; Roura, Maria; Pell, Christopher; Posada, Elisabeth; Gascón, Joaquim; Aldasoro, Edelweis; Muñoz, Jose; Pool, Robert

2013-01-01

Background Globally, more than 10 million people are infected with Trypanosoma cruzi, which causes about 20 000 annual deaths. Although Chagas disease is endemic to certain regions of Latin America, migratory flows have enabled its expansion into areas where it was previously unknown. Economic, social and cultural factors play a significant role in its presence and perpetuation. This systematic review aims to provide a comprehensive overview of qualitative research on Chagas disease, both in endemic and non-endemic countries. Methodology/Principal Findings Searches were carried out in ten databases, and the bibliographies of retrieved studies were examined. Data from thirty-three identified studies were extracted, and findings were analyzed and synthesized along key themes. Themes identified for endemic countries included: socio-structural determinants of Chagas disease; health practices; biomedical conceptions of Chagas disease; patient's experience; and institutional strategies adopted. Concerning non-endemic countries, identified issues related to access to health services and health seeking. Conclusions The emergence and perpetuation of Chagas disease depends largely on socio-cultural aspects influencing health. As most interventions do not address the clinical, environmental, social and cultural aspects jointly, an explicitly multidimensional approach, incorporating the experiences of those affected is a potential tool for the development of long-term successful programs. Further research is needed to evaluate this approach. PMID:24069473

The impact of network medicine in gastroenterology and hepatology.

PubMed

Baffy, György

2013-10-01

In the footsteps of groundbreaking achievements made by biomedical research, another scientific revolution is unfolding. Systems biology draws from the chaos and complexity theory and applies computational models to predict emerging behavior of the interactions between genes, gene products, and environmental factors. Adaptation of systems biology to translational and clinical sciences has been termed network medicine, and is likely to change the way we think about preventing, predicting, diagnosing, and treating complex human diseases. Network medicine finds gene-disease associations by analyzing the unparalleled digital information discovered and created by high-throughput technologies (dubbed as "omics" science) and links genetic variance to clinical disease phenotypes through intermediate organizational levels of life such as the epigenome, transcriptome, proteome, and metabolome. Supported by large reference databases, unprecedented data storage capacity, and innovative computational analysis, network medicine is poised to find links between conditions that were thought to be distinct, uncover shared disease mechanisms and key drivers of the pathogenesis, predict individual disease outcomes and trajectories, identify novel therapeutic applications, and help avoid off-target and undesirable drug effects. Recent advances indicate that these perspectives are increasingly within our reach for understanding and managing complex diseases of the digestive system. Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.

The association between glucose levels and hospital outcomes in patients with acute exacerbations of chronic obstructive pulmonary disease

PubMed Central

Islam, Ebtesam A.; Limsuwat, Chok; Nantsupawat, Teerapat; Berdine, Gilbert G.; Nugent, Kenneth M.

2015-01-01

BACKGROUND: Corticosteroids used for chronic obstructive pulmonary disease (COPD) exacerbations can cause hyperglycemia in hospitalized patients, and hyperglycemia may be associated with increased mortality, length of stay (LOS), and re-admissions in these patients. MATERIALS AND METHODS: We did three retrospective studies using charts from July 2008 through June 2009, January 2006 through December 2010, and October 2010 through March 2011. We collected demographic and clinical information, laboratory results, radiographic results, and information on LOS, mortality, and re-admission. RESULTS: Glucose levels did not predict outcomes in any of the studied cohorts, after adjustment for covariates in multivariable analysis. The first database included 30 patients admitted to non-intensive care unit (ICU) hospital beds. Six of 20 non-diabetic patients had peak glucoses above 200 mg/dl. Nine of the ten diabetic patients had peak glucoses above 200 mg/dl. The maximum daily corticosteroid dose had no apparent effect on the glucose levels. The second database included 217 patients admitted to ICUs. The initial blood glucose was higher in patients who died than those who survived using bivariate analysis (P = 0.015; odds ratio, OR, 1.01) but not in multivariable analysis. Multivariable logistic regression analysis also demonstrated that glucose levels did not affect LOS. The third database analyzing COPD re-admission rates included 81 patients; the peak glucose levels were not associated with re-admission. CONCLUSIONS: Our data demonstrate that COPD patients treated with corticosteroids developed significant hyperglycemia, but the increase in blood glucose levels did not correlate with the maximum dose of corticosteroids. Blood glucose levels were not associated with mortality, LOS, or re-admission rates. PMID:25829959

The impact of bacteremia on the outcome of bone infections.

PubMed

Roger, P-M; Cua, E; Courjon, J; Landraud, L; Carles, M; Bernard, E

2014-08-01

We have used a medical database to analyze our activity since 2005. We observed a frequent association between bone and joint infection (BI) and bacteremia. Our aim was to characterize patients with BI and bacteremia, and focus on the outcome. Our database includes the prospective recording of 28 characteristics of all hospitalized patients, including diagnosis, comorbid conditions, microbiological data, therapy, and outcome. We selected patients presenting with BI in this database, from July 2005 to December 2012. Fever before blood culture was retrospectively documented from the patient's chart. Chronic BI was defined as a disease lasting more than 1 month. An unfavorable outcome was defined by the need for intensive care or death. Six hundred and thirty-two patients presented with BI and 125 with bacteremia (19.8%). We used a stepwise logistic regression analysis and determined that bacteremia was associated with vertebral osteomyelitis, OR, 3.97, P<0.001; alcohol abuse, OR, 2.51, P=0.010; fever, OR, 2.43, P<0.001; neurological and/or psychiatric diseases, OR, 2.41, P ≤ 0.001; and Staphylococcus aureus infection, OR, 2.32, P<0.001. The outcome was unfavorable in 23 cases (3.6%), associated with bacteremia, OR, 8.00, P<0.001, age> 60 years, OR, 4.78, P=0.018, and S. aureus infection, OR, 3.96, P=0.010. No single comorbid condition was significantly associated with an unfavorable outcome. Bacteremia occurred in nearly 20% of the patients presenting with BI, and was associated with identifiable comorbid conditions; it was the main risk factor for an unfavorable outcome. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Nutritional impact of inflammatory bowel diseases on children and adolescents☆

PubMed Central

dos Santos, Gilton Marques; Silva, Luciana Rodrigues; Santana, Genoile Oliveira

2014-01-01

OBJECTIVE: To perform a sistematiy review of the literature about the nutritional impact of inflammatory bowel diseases in children and adolescents. DATA SOURCES: A systematic review was performed using PubMed/MEDLINE, LILACS and SciELO databases, with inclusion of articles in Portuguese and in English with original data, that analyzed nutritional aspects of inflammatory bowel diseases in children and adolescents. The initial search used the terms "inflammatory bowel diseases" and "children" or "adolescents" and "nutritional evaluation" or "nutrition deficiency". The selection of studies was initially performed by reading the titles and abstracts. Review studies and those withouth data for pediatric patients were excluded. Subsequently, the full reading of the articles considered relevant was performed. RESULTS: 237 studies were identified, and 12 of them were selected according to the inclusion criteria. None of them was performed in South America. During the analysis of the studies, it was observed that nutritional characteristics of patients with inflammatory bowel disease may be altered; the main reports were related to malnutrition, growth stunting, delayed puberty and vitamin D deficiency. CONCLUSION: There are nutritional consequences of inflammatory bowel diseases in children and adolescents, mainly growth stunting, slower pubertal development, underweight and vitamin deficiencies. Nutritional impairments were more significant in patients with Crohn's disease; overweight and obesity were more common in patients with ulcerative rectocolitis. A detailed nutritional assessment should be performed periodically in children and adolescents with inflammatory bowel disease. PMID:25511006

Brazilian Guidelines for transcranial doppler in children and adolescents with sickle cell disease

PubMed Central

Lobo, Clarisse Lopes de Castro; Cançado, Rodolfo Delfini; Leite, Ana Claudia Celestino Bezerra; dos Anjos, Ana Claudia Mendonça; Pinto, Ana Cristina Silva; Matta, Andre Palma da Cunha; Silva, Célia Maria; Silva, Gisele Sampaio; Friedrisch, João Ricardo; Braga, Josefina Aparecida Pellegrini; Lange, Marcos Christiano; Figueiredo, Maria Stella; Rugani, Marília Álvares; Veloso, Orlando; Moura, Patrícia Gomes; Cortez, Paulo Ivo; Adams, Robert; Gualandro, Sandra Fátima Menosi; de Castilho, Shirley Lopes; Thomé, Ursula; Zetola, Viviane Flumignan

2011-01-01

Background Sickle cell disease is the most common monogenic hereditary disease in Brazil. Although strokes are one of the main causes of morbidity and mortality in these patients, the use of transcranial Doppler to identify children at risk is not universally used. Objective To develop Brazilian guidelines for the use of transcranial Doppler in sickle cell disease children and adolescents, so that related health policies can be expanded, and thus contribute to reduce morbidity and mortality. Methods The guidelines were formulated in a consensus meeting of experts in transcranial Doppler and sickle cell disease. The issues discussed were previously formulated and scientific articles in databases (MEDLINE, SciELO and Cochrane) were carefully analyzed. The consensus for each question was obtained by a vote of experts on the specific theme. Results Recommendations were made, including indications for the use of transcranial Doppler according to the sickle cell disease genotype and patients age; the necessary conditions to perform the exam and its periodicity depending on exam results; the criteria for the indication of blood transfusions and iron chelation therapy; the indication of hydroxyurea; and the therapeutic approach in cases of conditional transcranial Doppler. Conclusion The Brazilian guidelines on the use of transcranial doppler in sickle cell disease patients may reduce the risk of strokes, and thus reduce the morbidity and mortality and improve the quality of life of sickle cell disease patients. PMID:23284243

The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases.

PubMed

Yang, Haixiu; Shang, Desi; Xu, Yanjun; Zhang, Chunlong; Feng, Li; Sun, Zeguo; Shi, Xinrui; Zhang, Yunpeng; Han, Junwei; Su, Fei; Li, Chunquan; Li, Xia

2017-07-27

Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.

Matrix metalloproteinase-8 levels in periodontal disease patients: A systematic review.

PubMed

de Morais, E F; Pinheiro, J C; Leite, R B; Santos, P P A; Barboza, C A G; Freitas, R A

2018-04-01

Periodontal disease is characterized as a disorder of the oral microbiota resulting in an immune response which, in turn, leads to the destruction of periodontal tissue. Matrix metalloproteinase-8 (MMP-8) has been reported as the major metalloproteinase involved in periodontal disease, being present at high levels in gingival crevicular fluid and salivary fluid (SF). The aim of this systematic review was to evaluate the scientific literature regarding the expression of MMP-8 in gingival crevicular fluid and SF in patients with periodontal disease, analyzing its validity as a possible biomarker in the diagnosis of periodontal disease. A systematic review of the literature was performed using the PubMed/Medline, CENTRAL and Science Direct databases. Studies concerning the use of MMP-8 in the diagnosis of periodontal disease that evaluated its effectiveness as a biomarker for periodontal disease were selected. The search strategy provided a total of 6483 studies. After selection, six articles met all the inclusion criteria and were included in the present systematic review. The studies demonstrated significantly higher concentrations of MMP-8 in patients with periodontal disease compared with controls, as well as in patients presenting more advanced stages of periodontal disease. The findings on higher MMP-8 concentrations in patients with periodontal disease compared with controls imply the potential adjunctive use of MMP-8 in the diagnosis of periodontal disease. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Typical cerebral metabolic patterns in neurodegenerative brain diseases.

PubMed

Teune, Laura K; Bartels, Anna L; de Jong, Bauke M; Willemsen, Antoon T M; Eshuis, Silvia A; de Vries, Jeroen J; van Oostrom, Joost C H; Leenders, Klaus L

2010-10-30

The differential diagnosis of neurodegenerative brain diseases on clinical grounds is difficult, especially at an early disease stage. Several studies have found specific regional differences of brain metabolism applying [(18)F]-fluoro-deoxyglucose positron emission tomography (FDG-PET), suggesting that this method can assist in early differential diagnosis of neurodegenerative brain diseases.We have studied patients who had an FDG-PET scan on clinical grounds at an early disease stage and included those with a retrospectively confirmed diagnosis according to strictly defined clinical research criteria. Ninety-six patients could be included of which 20 patients with Parkinson's disease (PD), 21 multiple system atrophy (MSA), 17 progressive supranuclear palsy (PSP), 10 corticobasal degeneration (CBD), 6 dementia with Lewy bodies (DLB), 15 Alzheimer's disease (AD), and 7 frontotemporal dementia (FTD). FDG PET images of each patient group were analyzed and compared to18 healthy controls using Statistical Parametric Mapping (SPM5).Disease-specific patterns of relatively decreased metabolic activity were found in PD (contralateral parietooccipital and frontal regions), MSA (bilateral putamen and cerebellar hemispheres), PSP (prefrontal cortex and caudate nucleus, thalamus, and mesencephalon), CBD (contralateral cortical regions), DLB (occipital and parietotemporal regions), AD (parietotemporal regions), and FTD (frontotemporal regions).The integrated method addressing a spectrum of various neurodegenerative brain diseases provided means to discriminate patient groups also at early disease stages. Clinical follow-up enabled appropriate patient inclusion. This implies that an early diagnosis in individual patients can be made by comparing each subject's metabolic findings with a complete database of specific disease related patterns.

Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer

PubMed Central

Lee, Ji-Hyun; You, Sungyong; Hyeon, Do Young; Kang, Byeongsoo; Kim, Hyerim; Park, Kyoung Mii; Han, Byungwoo; Hwang, Daehee; Kim, Sunghoon

2015-01-01

Mammalian cells have cytoplasmic and mitochondrial aminoacyl-tRNA synthetases (ARSs) that catalyze aminoacylation of tRNAs during protein synthesis. Despite their housekeeping functions in protein synthesis, recently, ARSs and ARS-interacting multifunctional proteins (AIMPs) have been shown to play important roles in disease pathogenesis through their interactions with disease-related molecules. However, there are lacks of data resources and analytical tools that can be used to examine disease associations of ARS/AIMPs. Here, we developed an Integrated Database for ARSs (IDA), a resource database including cancer genomic/proteomic and interaction data of ARS/AIMPs. IDA includes mRNA expression, somatic mutation, copy number variation and phosphorylation data of ARS/AIMPs and their interacting proteins in various cancers. IDA further includes an array of analytical tools for exploration of disease association of ARS/AIMPs, identification of disease-associated ARS/AIMP interactors and reconstruction of ARS-dependent disease-perturbed network models. Therefore, IDA provides both comprehensive data resources and analytical tools for understanding potential roles of ARS/AIMPs in cancers. Database URL: http://ida.biocon.re.kr/, http://ars.biocon.re.kr/ PMID:25824651

Computer-Assisted Classification Patterns in Autoimmune Diagnostics: The AIDA Project

PubMed Central

Benammar Elgaaied, Amel; Cascio, Donato; Bruno, Salvatore; Ciaccio, Maria Cristina; Cipolla, Marco; Fauci, Alessandro; Morgante, Rossella; Taormina, Vincenzo; Gorgi, Yousr; Marrakchi Triki, Raja; Ben Ahmed, Melika; Louzir, Hechmi; Yalaoui, Sadok; Imene, Sfar; Issaoui, Yassine; Abidi, Ahmed; Ammar, Myriam; Bedhiafi, Walid; Ben Fraj, Oussama; Bouhaha, Rym; Hamdi, Khouloud; Soumaya, Koudhi; Neili, Bilel; Asma, Gati; Lucchese, Mariano; Catanzaro, Maria; Barbara, Vincenza; Brusca, Ignazio; Fregapane, Maria; Amato, Gaetano; Friscia, Giuseppe; Neila, Trai; Turkia, Souayeh; Youssra, Haouami; Rekik, Raja; Bouokez, Hayet; Vasile Simone, Maria; Fauci, Francesco; Raso, Giuseppe

2016-01-01

Antinuclear antibodies (ANAs) are significant biomarkers in the diagnosis of autoimmune diseases in humans, done by mean of Indirect ImmunoFluorescence (IIF) method, and performed by analyzing patterns and fluorescence intensity. This paper introduces the AIDA Project (autoimmunity: diagnosis assisted by computer) developed in the framework of an Italy-Tunisia cross-border cooperation and its preliminary results. A database of interpreted IIF images is being collected through the exchange of images and double reporting and a Gold Standard database, containing around 1000 double reported images, has been settled. The Gold Standard database is used for optimization of a CAD (Computer Aided Detection) solution and for the assessment of its added value, in order to be applied along with an Immunologist as a second Reader in detection of autoantibodies. This CAD system is able to identify on IIF images the fluorescence intensity and the fluorescence pattern. Preliminary results show that CAD, used as second Reader, appeared to perform better than Junior Immunologists and hence may significantly improve their efficacy; compared with two Junior Immunologists, the CAD system showed higher Intensity Accuracy (85,5% versus 66,0% and 66,0%), higher Patterns Accuracy (79,3% versus 48,0% and 66,2%), and higher Mean Class Accuracy (79,4% versus 56,7% and 64.2%). PMID:27042658

Relation of pregnancy and neonatal factors to subsequent development of childhood epilepsy: a population-based cohort study.

PubMed

Whitehead, Elizabeth; Dodds, Linda; Joseph, K S; Gordon, Kevin E; Wood, Ellen; Allen, Alexander C; Camfield, Peter; Dooley, Joseph M

2006-04-01

We examined the effect of pregnancy and neonatal factors on the subsequent development of childhood epilepsy in a population-based cohort study. Children born between January 1986 and December 2000 in Nova Scotia, Canada were followed up to December 2001. Data on pregnancy and neonatal events and on diagnoses of childhood epilepsy were obtained through record linkage of 2 population-based databases: the Nova Scotia Atlee Perinatal Database and the Canadian Epilepsy Database and Registry. Factors analyzed included events during the prenatal, labor and delivery, and neonatal time periods. Cox proportional hazards regression models were used to estimate relative risks and 95% confidence intervals. There were 648 new cases of epilepsy diagnosed among 124,207 live births, for an overall rate of 63 per 100,000 person-years. Incidence rates were highest among children <1 year of age. In adjusted analyses, factors significantly associated with an increased risk of epilepsy included eclampsia, neonatal seizures, central nervous system (CNS) anomalies, placental abruption, major non-CNS anomalies, neonatal metabolic disorders, neonatal CNS diseases, previous low birth weight infant, infection in pregnancy, small for gestational age, unmarried, and not breastfeeding infant at the time of discharge from hospital. Our study supports the concept that prenatal factors contribute to the occurrence of subsequent childhood epilepsy.

Prospects for the therapeutic application of sulfated polysaccharides of brown algae in diseases of the cardiovascular system: review.

PubMed

Zaporozhets, Tatyana; Besednova, Natalia

2016-12-01

Fucoidans are water-soluble, highly sulfated, branched homo- and hetero-polysaccharides derived from the fibrillar cell walls and intercellular spaces of brown seaweeds of the class Phaeophyceae. Fucoidans possess mimetic properties of the natural ligands of protein receptors and regulate functions of biological systems via key signaling molecules. The aim of this review was to collect and combine all available scientific literature about the potential use of the fucoidans for diseases of cardiovascular system. The review has been compiled using references from major databases such as Web of Science, PubMed, Scopus, Elsevier, Springer and Google Scholar (up to September 2015). After obtaining all reports from database (a total number is about 580), the papers were carefully analyzed in order to find data related to the topic of this review (129 references). An exhaustive survey of literature revealed that fucoidans possess a broad spectrum of biological activity, including anti-coagulant, hypolipidemic, anti-thrombotic, anti-inflammatory, immunomodulatory, anti-tumor, anti-adhesive and anti-hypertensive properties. Numerous investigations of fucoidans in diseases of the cardiovascular system mainly focus on pleiotropic anti-inflammatory effects. Fucoidans also possess pro-angiogenic and pro-vasculogenic properties. A great number of investigations in the past years have demonstrated that fucoidans has great potential for in-depth investigation of their effects on cardiovascular system. Through this review, the authors hope to attract the attention of researchers to use fucoidan as mimetic of natural ligand receptor protein with the view of developing new formulations with an improved therapeutic value.

Multiple SNPs in Intron 41 of Thyroglobulin Gene Are Associated with Autoimmune Thyroid Disease in the Japanese Population

PubMed Central

Ban, Yoshiyuki; Tozaki, Teruaki; Taniyama, Matsuo; Skrabanek, Luce; Nakano, Yasuko; Ban, Yoshio; Hirano, Tsutomu

2012-01-01

Background The etiology of the autoimmune thyroid diseases (AITDs), Graves' disease (GD) and Hashimoto's thyroiditis (HT), is largely unknown. However, genetic susceptibility is believed to play a major role. Two whole genome scans from Japan and from the US identified a locus on chromosome 8q24 that showed evidence for linkage with AITD and HT. Recent studies have demonstrated an association between thyroglobulin (Tg) polymorphisms and AITD in Caucasians, suggesting that Tg is a susceptibility gene on 8q24. Objectives The objective of the study was to refine Tg association with AITD, by analyzing a panel of 25 SNPs across an extended 260 kb region of the Tg. Methods We studied 458 Japanese AITD patients (287 GD and 171 HT patients) and 221 matched Japanese control subjects in association studies. Case-control association studies were performed using 25 Tg single nucleotide polymorphisms (SNPs) chosen from a database of the Single Nucleotide Polymorphism Database (dbSNP). Haplotype analysis was undertaken using the computer program SNPAlyze version 7.0. Principal Findings and Conclusions In total, 5 SNPs revealed association with GD (P<0.05), with the strongest SNP associations at rs2256366 (P = 0.002) and rs2687836 (P = 0.0077), both located in intron 41 of the Tg gene. Because of the strong LD between these two strongest associated variants, we performed the haplotype analysis, and identified a major protective haplotype for GD (P = 0.001).These results suggested that the Tg gene is involved in susceptibility for GD and AITD in the Japanese. PMID:22662162

Enigma of urethral pain syndrome: why are there so many ascribed etiologies and therapeutic approaches?

PubMed

Phillip, Harris; Okewole, Idris; Chilaka, Victor

2014-06-01

Urethral pain syndrome has had several sobriquets, which have led to much confusion over the existence of this pathological condition and the useful options in the care of the afflicted patient. Our aim was to explore the proposed etiologies of this syndrome, and to provide a critical analysis of each proposed etiology and present a balanced argument on the plausibility of the proposed etiology and therapeutic approaches. We carried out an English language electronic search in the following databases: Medline, Embase, Amed, Cinahl, Pubmed, Cochrane Library, Trip Database and SUMSearch using the following search terms: urethral syndrome, urethral diseases, urethra, urologic diseases etiology/etiology, presentation, treatment, outcome, therapeutics and treatment from 1951 to 2011. In excess of 200 articles were recovered. With the clearly defined objectives of analyzing the proposed etiologies and therapeutic regimes, two author(s) (HP and IO) perused the abstracts of all the recovered articles, selecting those that addressed the etiologies and therapeutic approaches to treating the urethral pain syndrome. The number of articles was reduced to 25. The full text of all 25 articles were retrieved and reviewed. Through the present article, we hope to elucidate the most probable etiology of this condition whilst simultaneously, advance a logical explanation for the apparent success in the treatment of this condition using a range of different therapeutic modalities. We have carried out a narrative review, which we hope will reduce some of the confusion around this clinical entity by combining the known facts about the disease. © 2014 The Japanese Urological Association.

Trends in Radical Prostatectomy Risk Group Distribution in a European Multicenter Analysis of 28 572 Patients: Towards Tailored Treatment.

PubMed

van den Bergh, Roderick; Gandaglia, Giorgio; Tilki, Derya; Borgmann, Hendrik; Ost, Piet; Surcel, Christian; Valerio, Massimo; Sooriakumaran, Prasanna; Salomon, Laurent; Briganti, Alberto; Graefen, Markus; van der Poel, Henk; de la Taille, Alexandre; Montorsi, Francesco; Ploussard, Guillaume

2017-08-08

Active surveillance (AS) has been increasingly proposed as the preferential initial management strategy for low-risk prostate cancer (PC), while in high-risk PC the indication for surgery has widened. To evaluate the development of risk group distribution of patients undergoing radical prostatectomy (RP). Retrospective database review of combined RP databases (2000-2015) of four large European centers (Créteil, Paris; San Rafaele, Milan; Martini Klinik, Hamburg; NKI, AvL, Amsterdam). Clinical and pathological characteristics per year of surgery. Eligibility for AS was defined according to Prostate Cancer Research International Active Surveillance criteria: cT≤2c, cN0/X, cM0/X, PSA ≤10ng/ml, prostate-specific antigen density <0.2ng/ml/ml, one to two positive biopsies, and Gleason score ≤6, high-risk disease as: cT≥3, c N1, cM1, PSA >20ng/ml, and/or Gleason ≥8. In total, 28572 patients had complete clinical and 24790 complete pathological data available. The absolute number of RPs increased: 401, 975, 2344, and 2504 in 2000, 2005, 2010, and 2015, respectively. The proportion of cases considered suitable for AS decreased: 31%, 32%, 18%, and 5%, while the cases considered high risk increased: 10%, 8%, 16%, and 30%. The percentage of patients having only localized Gleason 6 disease after RP decreased: 46%, 34%, 14%, and 8% for all patients (p<0.01), as well as for AS-suitable patients: 70%, 54%, 41%, and 38% (p<0.01). Comparisons between centers were outside the scope of this article. Developments in diagnostics may have impacted on results. This European analysis confirmed the risk profile of patients undergoing RP shifting away of the most favorable disease spectrum. Patients with PC clinically considered suitable for AS and men having only localized Gleason 6 disease pathologically comprised a decreasing share of all RP performed. High-risk disease comprised an increasing share of all RPs. The databases of four large European centers of prostate cancer surgery were analyzed. In recent years, the risk profile of patients shifted away of low-risk cancer, while high-risk cancer comprised a larger part of cases. This confirms the introduction of active surveillance for low-risk prostate cancer and increase in potentially curative options for high-risk disease. Copyright © 2017 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

PubMed Central

2013-01-01

Background A large-scale, highly accurate, machine-understandable drug-disease treatment relationship knowledge base is important for computational approaches to drug repurposing. The large body of published biomedical research articles and clinical case reports available on MEDLINE is a rich source of FDA-approved drug-disease indication as well as drug-repurposing knowledge that is crucial for applying FDA-approved drugs for new diseases. However, much of this information is buried in free text and not captured in any existing databases. The goal of this study is to extract a large number of accurate drug-disease treatment pairs from published literature. Results In this study, we developed a simple but highly accurate pattern-learning approach to extract treatment-specific drug-disease pairs from 20 million biomedical abstracts available on MEDLINE. We extracted a total of 34,305 unique drug-disease treatment pairs, the majority of which are not included in existing structured databases. Our algorithm achieved a precision of 0.904 and a recall of 0.131 in extracting all pairs, and a precision of 0.904 and a recall of 0.842 in extracting frequent pairs. In addition, we have shown that the extracted pairs strongly correlate with both drug target genes and therapeutic classes, therefore may have high potential in drug discovery. Conclusions We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. PMID:23742147

Clinically Unsuspected Prion Disease Among Patients With Dementia Diagnoses in an Alzheimer's Disease Database.

PubMed

Maddox, Ryan A; Blase, J L; Mercaldo, N D; Harvey, A R; Schonberger, L B; Kukull, W A; Belay, E D

2015-12-01

Brain tissue analysis is necessary to confirm prion diseases. Clinically unsuspected cases may be identified through neuropathologic testing. National Alzheimer's Coordinating Center (NACC) Minimum and Neuropathologic Data Set for 1984 to 2005 were reviewed. Eligible patients had dementia, underwent autopsy, had available neuropathologic data, belonged to a currently funded Alzheimer's Disease Center (ADC), and were coded as having an Alzheimer's disease clinical diagnosis or a nonprion disease etiology. For the eligible patients with neuropathology indicating prion disease, further clinical information, collected from the reporting ADC, determined whether prion disease was considered before autopsy. Of 6000 eligible patients in the NACC database, 7 (0.12%) were clinically unsuspected but autopsy-confirmed prion disease cases. The proportion of patients with dementia with clinically unrecognized but autopsy-confirmed prion disease was small. Besides confirming clinically suspected cases, neuropathology is useful to identify unsuspected clinically atypical cases of prion disease. © The Author(s) 2015.

Multi-categorical deep learning neural network to classify retinal images: A pilot study employing small database

PubMed Central

Seo, Jeong Gi; Kwak, Jiyong; Um, Terry Taewoong; Rim, Tyler Hyungtaek

2017-01-01

Deep learning emerges as a powerful tool for analyzing medical images. Retinal disease detection by using computer-aided diagnosis from fundus image has emerged as a new method. We applied deep learning convolutional neural network by using MatConvNet for an automated detection of multiple retinal diseases with fundus photographs involved in STructured Analysis of the REtina (STARE) database. Dataset was built by expanding data on 10 categories, including normal retina and nine retinal diseases. The optimal outcomes were acquired by using a random forest transfer learning based on VGG-19 architecture. The classification results depended greatly on the number of categories. As the number of categories increased, the performance of deep learning models was diminished. When all 10 categories were included, we obtained results with an accuracy of 30.5%, relative classifier information (RCI) of 0.052, and Cohen’s kappa of 0.224. Considering three integrated normal, background diabetic retinopathy, and dry age-related macular degeneration, the multi-categorical classifier showed accuracy of 72.8%, 0.283 RCI, and 0.577 kappa. In addition, several ensemble classifiers enhanced the multi-categorical classification performance. The transfer learning incorporated with ensemble classifier of clustering and voting approach presented the best performance with accuracy of 36.7%, 0.053 RCI, and 0.225 kappa in the 10 retinal diseases classification problem. First, due to the small size of datasets, the deep learning techniques in this study were ineffective to be applied in clinics where numerous patients suffering from various types of retinal disorders visit for diagnosis and treatment. Second, we found that the transfer learning incorporated with ensemble classifiers can improve the classification performance in order to detect multi-categorical retinal diseases. Further studies should confirm the effectiveness of algorithms with large datasets obtained from hospitals. PMID:29095872

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications

PubMed Central

Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Sarkadi, Balázs

2015-01-01

Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics. Database URL: http://rbcc.hegelab.org PMID:26078478

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database.

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful AOP-DB user interface in...

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful user interface in the for...

Invasive candidiasis and oral manifestations in premature newborns

PubMed Central

Tinoco-Araujo, José Endrigo; Araújo, Diana Ferreira Gadelha; Barbosa, Patrícia Gomes; Santos, Paulo Sérgio da Silva; de Medeiros, Ana Myriam Costa

2013-01-01

ABSTRACT Objective: To investigate prevalence of invasive candidiasis in a Neonatal Intensive Care Unit and to evaluate oral diseases and Candida spp. colonization in low birth weight preterm newborns. Methods: A descriptive epidemiological study performed in two stages. First, prevalence of candidiasis was analyzed in a database of 295 preterm patients admitted to hospital for over 10 days and birth weight less than 2,000g. In the second stage, oral changes and Candida spp. colonization were assessed in 65 patients weighing less than 2,000g, up to 4 week-old, hospitalized for over 10 days and presenting oral abnormalities compatible with fungal lesions. Swab samples were collected in the mouth to identify fungi. Results: Prevalence of candidiasis was 5.4% in the database analyzed. It correlated with prolonged hospital length of stay (p<0.001), in average, 31 days, and 85% risk of developing infection in the first 25 days. It correlated with low birth weight (p<0.001), with mean of 1,140g. The most frequent alterations were white soft plaques, detachable, in oral mucosa and tongue. Intense oral colonization by Candida spp was observed (80%). Conclusions: The frequency of invasive candidiasis was low and correlated with low birth weight and prolonged hospital stay. The most common oral changes were white plaques compatible with pseudomembranous candidiasis and colonization by Candida spp. was above average. PMID:23579747

HerDing: herb recommendation system to treat diseases using genes and chemicals

PubMed Central

Choi, Wonjun; Choi, Chan-Hun; Kim, Young Ran; Kim, Seon-Jong; Na, Chang-Su; Lee, Hyunju

2016-01-01

In recent years, herbs have been researched for new drug candidates because they have a long empirical history of treating diseases and are relatively free from side effects. Studies to scientifically prove the medical efficacy of herbs for target diseases often spend a considerable amount of time and effort in choosing candidate herbs and in performing experiments to measure changes of marker genes when treating herbs. A computational approach to recommend herbs for treating diseases might be helpful to promote efficiency in the early stage of such studies. Although several databases related to traditional Chinese medicine have been already developed, there is no specialized Web tool yet recommending herbs to treat diseases based on disease-related genes. Therefore, we developed a novel search engine, HerDing, focused on retrieving candidate herb-related information with user search terms (a list of genes, a disease name, a chemical name or an herb name). HerDing was built by integrating public databases and by applying a text-mining method. The HerDing website is free and open to all users, and there is no login requirement. Database URL: http://combio.gist.ac.kr/herding PMID:26980517

HerDing: herb recommendation system to treat diseases using genes and chemicals.

PubMed

Choi, Wonjun; Choi, Chan-Hun; Kim, Young Ran; Kim, Seon-Jong; Na, Chang-Su; Lee, Hyunju

2016-01-01

In recent years, herbs have been researched for new drug candidates because they have a long empirical history of treating diseases and are relatively free from side effects. Studies to scientifically prove the medical efficacy of herbs for target diseases often spend a considerable amount of time and effort in choosing candidate herbs and in performing experiments to measure changes of marker genes when treating herbs. A computational approach to recommend herbs for treating diseases might be helpful to promote efficiency in the early stage of such studies. Although several databases related to traditional Chinese medicine have been already developed, there is no specialized Web tool yet recommending herbs to treat diseases based on disease-related genes. Therefore, we developed a novel search engine, HerDing, focused on retrieving candidate herb-related information with user search terms (a list of genes, a disease name, a chemical name or an herb name). HerDing was built by integrating public databases and by applying a text-mining method. The HerDing website is free and open to all users, and there is no login requirement. Database URL: http://combio.gist.ac.kr/herding. © The Author(s) 2016. Published by Oxford University Press.

The Degradome database: expanding roles of mammalian proteases in life and disease

PubMed Central

Pérez-Silva, José G.; Español, Yaiza; Velasco, Gloria; Quesada, Víctor

2016-01-01

Since the definition of the degradome as the complete repertoire of proteases in a given organism, the combined effort of numerous laboratories has greatly expanded our knowledge of its roles in biology and pathology. Once the genomic sequences of several important model organisms were made available, we presented the Degradome database containing the curated sets of known protease genes in human, chimpanzee, mouse and rat. Here, we describe the updated Degradome database, featuring 81 new protease genes and 7 new protease families. Notably, in this short time span, the number of known hereditary diseases caused by mutations in protease genes has increased from 77 to 119. This increase reflects the growing interest on the roles of the degradome in multiple diseases, including cancer and ageing. Finally, we have leveraged the widespread adoption of new webtools to provide interactive graphic views that show information about proteases in the global context of the degradome. The Degradome database can be accessed through its web interface at http://degradome.uniovi.es. PMID:26553809

HEROD: a human ethnic and regional specific omics database.

PubMed

Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

2017-10-15

Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Gene expression patterns associated with neurological disease in human HIV infection

PubMed Central

Repunte-Canonigo, Vez; Masliah, Eliezer; Lefebvre, Celine

2017-01-01

The pathogenesis and nosology of HIV-associated neurological disease (HAND) remain incompletely understood. Here, to provide new insight into the molecular events leading to neurocognitive impairments (NCI) in HIV infection, we analyzed pathway dysregulations in gene expression profiles of HIV-infected patients with or without NCI and HIV encephalitis (HIVE) and control subjects. The Gene Set Enrichment Analysis (GSEA) algorithm was used for pathway analyses in conjunction with the Molecular Signatures Database collection of canonical pathways (MSigDb). We analyzed pathway dysregulations in gene expression profiles of patients from the National NeuroAIDS Tissue Consortium (NNTC), which consists of samples from 3 different brain regions, including white matter, basal ganglia and frontal cortex of HIV-infected and control patients. While HIVE is characterized by widespread, uncontrolled inflammation and tissue damage, substantial gene expression evidence of induction of interferon (IFN), cytokines and tissue injury is apparent in all brain regions studied, even in the absence of NCI. Various degrees of white matter changes were present in all HIV-infected subjects and were the primary manifestation in patients with NCI in the absence of HIVE. In particular, NCI in patients without HIVE in the NNTC sample is associated with white matter expression of chemokines, cytokines and β-defensins, without significant activation of IFN. Altogether, the results identified distinct pathways differentially regulated over the course of neurological disease in HIV infection and provide a new perspective on the dynamics of pathogenic processes in the course of HIV neurological disease in humans. These results also demonstrate the power of the systems biology analyses and indicate that the establishment of larger human gene expression profile datasets will have the potential to provide novel mechanistic insight into the pathogenesis of neurological disease in HIV infection and identify better therapeutic targets for NCI. PMID:28445538

Single-Port Video-Assisted Thoracoscopic Major Lung Resections: Experience with 150 Consecutive Cases.

PubMed

Ng, Calvin S H; Kim, Hyun Koo; Wong, Randolph H L; Yim, Anthony P C; Mok, Tony S K; Choi, Young Ho

2016-06-01

Background Video-assisted thoracic surgery (VATS) for major lung resection has undergone major changes from three or four-port approach to the recently possible single-port VATS approach. Outcomes following single-port VATS major lung resection are analyzed to determine safety and efficacy. Methods A prospective database of 150 consecutive patients who underwent single-port VATS major lung resection between March 2012 and January 2014 was reviewed. Patient demographics, perioperative parameters, histopathology, and outcomes up to follow-up of 2 years were analyzed by descriptive and Kaplan-Meier survival statistics. Results Single-port VATS major lung resection was successfully performed in 142 patients (conversion rate 5.3%) for both malignant and benign diseases of the lung. Overall, 130 patients (87%) had nonsmall-cell lung carcinoma (NSCLC), 9 (6%) had other types of primary lung cancer, and the remaining for secondary malignancies and benign diseases. Among the 130 patients with NSCLC, 93 (71.5%) were stage I, 28 were stage II (21.5%), and 9 (7%) were stage III or greater. There was no intraoperative or 30-day mortality. However, one perioperative death occurred on day 49, and another on day 60 postoperatively due to infective causes. The overall 2-year mortality rate for all patients was 3%. The disease-free survival rate for subgroups, stage I NSCLC, and stage II or greater NSCLC were 96 and 83%, respectively. Conclusions Single-port VATS major lung resection for malignant and benign lung diseases is associated with low perioperative morbidity and mortality. Disease-free survival rates for NSCLC are acceptable and comparable with conventional VATS. Georg Thieme Verlag KG Stuttgart · New York.

Protein-driven inference of miRNA–disease associations

PubMed Central

Mørk, Søren; Pletscher-Frankild, Sune; Palleja Caro, Albert; Gorodkin, Jan; Jensen, Lars Juhl

2014-01-01

Motivation: MicroRNAs (miRNAs) are a highly abundant class of non-coding RNA genes involved in cellular regulation and thus also diseases. Despite miRNAs being important disease factors, miRNA–disease associations remain low in number and of variable reliability. Furthermore, existing databases and prediction methods do not explicitly facilitate forming hypotheses about the possible molecular causes of the association, thereby making the path to experimental follow-up longer. Results: Here we present miRPD in which miRNA–Protein–Disease associations are explicitly inferred. Besides linking miRNAs to diseases, it directly suggests the underlying proteins involved, which can be used to form hypotheses that can be experimentally tested. The inference of miRNAs and diseases is made by coupling known and predicted miRNA–protein associations with protein–disease associations text mined from the literature. We present scoring schemes that allow us to rank miRNA–disease associations inferred from both curated and predicted miRNA targets by reliability and thereby to create high- and medium-confidence sets of associations. Analyzing these, we find statistically significant enrichment for proteins involved in pathways related to cancer and type I diabetes mellitus, suggesting either a literature bias or a genuine biological trend. We show by example how the associations can be used to extract proteins for disease hypothesis. Availability and implementation: All datasets, software and a searchable Web site are available at http://mirpd.jensenlab.org. Contact: lars.juhl.jensen@cpr.ku.dk or gorodkin@rth.dk PMID:24273243

Functional integration of automated system databases by means of artificial intelligence

NASA Astrophysics Data System (ADS)

Dubovoi, Volodymyr M.; Nikitenko, Olena D.; Kalimoldayev, Maksat; Kotyra, Andrzej; Gromaszek, Konrad; Iskakova, Aigul

2017-08-01

The paper presents approaches for functional integration of automated system databases by means of artificial intelligence. The peculiarities of turning to account the database in the systems with the usage of a fuzzy implementation of functions were analyzed. Requirements for the normalization of such databases were defined. The question of data equivalence in conditions of uncertainty and collisions in the presence of the databases functional integration is considered and the model to reveal their possible occurrence is devised. The paper also presents evaluation method of standardization of integrated database normalization.

Risk factors and prognosis in T-cell posttransplantation lymphoproliferative diseases: reevaluation of 163 cases.

PubMed

Tiede, Christina; Maecker-Kolhoff, Britta; Klein, Christoph; Kreipe, Hans; Hussein, Kais

2013-02-15

Posttransplantation lymphoproliferative diseases (PTLD) are mainly Epstein-Barr virus (EBV)-associated disorders of B-cell origin. Due to the rarity of monomorphic T-cell PTLD (T-PTLD), knowledge about pathogenesis, risk factors, therapy, and prognosis relies predominantly on case reports and small series. Therefore, we aimed to provide an overview and a retrospective analysis of this rare PTLD subtype. We analyzed all available articles on T-PTLD in the PubMed database as well as in our own databases (Institute of Pathology/Department of Paediatric Haematology and Oncology, Hannover Medical School) from 1988 to 2010. Reevaluated parameters were gender, age, transplanted organ, immunosuppressant regimen, time between transplantation and T-PTLD manifestation, T-PTLD subtype, virus positivity, localization, therapy, and follow-up. A total of 163 cases were evaluated. We found that hematopoietic stem cell transplantation was associated with early-onset T-PTLD, whereas late onset occurred after immunosuppression with steroids and azathioprine without administration of calcineurin inhibitors. The major independent favorable prognostic factors were T-PTLD of the large granular lymphocytic leukemia subtype, young age, and a combination of radiotherapy/radiochemotherapy and reduced immunosuppression, whereas the hepatosplenic T-cell lymphoma subtype and cases with involvement of bone marrow, the central nervous system, or graft had an adverse prognosis. T-PTLD is a heterogeneous group of different aberrant T-cell proliferations and represents a significant complication following transplantation, showing a uniformly poor prognosis.

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

PubMed Central

Culhane, Aedín C.; Schröder, Markus S.; Sultana, Razvan; Picard, Shaita C.; Martinelli, Enzo N.; Kelly, Caroline; Haibe-Kains, Benjamin; Kapushesky, Misha; St Pierre, Anne-Alyssa; Flahive, William; Picard, Kermshlise C.; Gusenleitner, Daniel; Papenhausen, Gerald; O'Connor, Niall; Correll, Mick; Quackenbush, John

2012-01-01

GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from 575 to 3515 gene signatures, which were collected and transcribed from 1604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. We have made substantial upgrades to the GeneSigDB website to improve accessibility and usability, including adding a tag cloud browse function, facetted navigation and a ‘basket’ feature to store genes or gene signatures of interest. Users can analyze GeneSigDB gene signatures, or upload their own gene list, to identify gene signatures with significant gene overlap and results can be viewed on a dynamic editable heatmap that can be downloaded as a publication quality image. All data in GeneSigDB can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB is available from http://www.genesigdb.org. PMID:22110038

In silico analysis of cacao (Theobroma cacao L.) genes that involved in pathogen and disease responses

NASA Astrophysics Data System (ADS)

Agung, Muhammad Budi; Budiarsa, I. Made; Suwastika, I. Nengah

2017-02-01

Cocoa bean is one of the main commodities from Indonesia for the world, which still have problem regarding yield degradation due to pathogens and disease attack. Developing robust cacao plant that genetically resistant to pathogen and disease attack is an ideal solution in over taking on this problem. The aim of this study was to identify Theobroma cacao genes on database of cacao genome that homolog to response genes of pathogen and disease attack in other plant, through in silico analysis. Basic information survey and gene identification were performed in GenBank and The Arabidopsis Information Resource database. The In silico analysis contains protein BLAST, homology test of each gene's protein candidates, and identification of homologue gene in Cacao Genome Database using data source "Theobroma cacao cv. Matina 1-6 v1.1" genome. Identification found that Thecc1EG011959t1 (EDS1), Thecc1EG006803t1 (EDS5), Thecc1EG013842t1 (ICS1), and Thecc1EG015614t1 (BG_PPAP) gene of Cacao Genome Database were Theobroma cacao genes that homolog to plant's resistance genes which highly possible to have similar functions of each gene's homologue gene.

Herpes zoster surveillance using electronic databases in the Valencian Community (Spain)

PubMed Central

2013-01-01

Background Epidemiologic data of Herpes Zoster (HZ) disease in Spain are scarce. The objective of this study was to assess the epidemiology of HZ in the Valencian Community (Spain), using outpatient and hospital electronic health databases. Methods Data from 2007 to 2010 was collected from computerized health databases of a population of around 5 million inhabitants. Diagnoses were recorded by physicians using the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM). A sample of medical records under different criteria was reviewed by a general practitioner, to assess the reliability of codification. Results The average annual incidence of HZ was 4.60 per 1000 persons-year (PY) for all ages (95% CI: 4.57-4.63), is more frequent in women [5.32/1000PY (95% CI: 5.28-5.37)] and is strongly age-related, with a peak incidence at 70-79 years. A total of 7.16/1000 cases of HZ required hospitalization. Conclusions Electronic health database used in the Valencian Community is a reliable electronic surveillance tool for HZ disease and will be useful to define trends in disease burden before and after HZ vaccine introduction. PMID:24094135

Thailand mutation and variation database (ThaiMUT).

PubMed

Ruangrit, Uttapong; Srikummool, Metawee; Assawamakin, Anunchai; Ngamphiw, Chumpol; Chuechote, Suparat; Thaiprasarnsup, Vilasinee; Agavatpanitch, Gallissara; Pasomsab, Ekawat; Yenchitsomanus, Pa-Thai; Mahasirimongkol, Surakameth; Chantratita, Wasun; Palittapongarnpim, Prasit; Uyyanonvara, Bunyarit; Limwongse, Chanin; Tongsima, Sissades

2008-08-01

With the completion of the human genome project, novel sequencing and genotyping technologies had been utilized to detect mutations. Such mutations have continually been produced at exponential rate by researchers in various communities. Based on the population's mutation spectra, occurrences of Mendelian diseases are different across ethnic groups. A proportion of Mendelian diseases can be observed in some countries at higher rates than others. Recognizing the importance of mutation effects in Thailand, we established a National and Ethnic Mutation Database (NEMDB) for Thai people. This database, named Thailand Mutation and Variation database (ThaiMUT), offers a web-based access to genetic mutation and variation information in Thai population. This NEMDB initiative is an important informatics tool for both research and clinical purposes to retrieve and deposit human variation data. The mutation data cataloged in ThaiMUT database were derived from journal articles available in PubMed and local publications. In addition to collected mutation data, ThaiMUT also records genetic polymorphisms located in drug related genes. ThaiMUT could then provide useful information for clinical mutation screening services for Mendelian diseases and pharmacogenomic researches. ThaiMUT can be publicly accessed from http://gi.biotec.or.th/thaimut.

The effective use of newspaper information in corporations (2) Centered around corporate and managemant information

NASA Astrophysics Data System (ADS)

Kamio, Tatsuo

A newspaper article is a fragmentary record of fact. For information activities in corporations it is fundamental to gather newspaper articles related to the object thema as many as possible, integrate them, analyze them, and then, create new intelligence based on them. Here in databases become effective measures. It seems essential to construct searching strategy with high recall of necessary information and understand the databases in detail when we use newspaper article databases. The cases that newspaper databases are useful for business are represented by (1) research and analysis for problem solving, (2) gathering of knowledge, and confirmation of the facts, and (3) constant observation of facts without missing any change in there. Particularly for case (1) various methods are tried for analyzing the tendency.

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

Genetic variants of the DNA repair genes from Exome Aggregation Consortium (EXAC) database: significance in cancer.

PubMed

Das, Raima; Ghosh, Sankar Kumar

2017-04-01

DNA repair pathway is a primary defense system that eliminates wide varieties of DNA damage. Any deficiencies in them are likely to cause the chromosomal instability that leads to cell malfunctioning and tumorigenesis. Genetic polymorphisms in DNA repair genes have demonstrated a significant association with cancer risk. Our study attempts to give a glimpse of the overall scenario of the germline polymorphisms in the DNA repair genes by taking into account of the Exome Aggregation Consortium (ExAC) database as well as the Human Gene Mutation Database (HGMD) for evaluating the disease link, particularly in cancer. It has been found that ExAC DNA repair dataset (which consists of 228 DNA repair genes) comprises 30.4% missense, 12.5% dbSNP reported and 3.2% ClinVar significant variants. 27% of all the missense variants has the deleterious SIFT score of 0.00 and 6% variants carrying the most damaging Polyphen-2 score of 1.00, thus affecting the protein structure and function. However, as per HGMD, only a fraction (1.2%) of ExAC DNA repair variants was found to be cancer-related, indicating remaining variants reported in both the databases to be further analyzed. This, in turn, may provide an increased spectrum of the reported cancer linked variants in the DNA repair genes present in ExAC database. Moreover, further in silico functional assay of the identified vital cancer-associated variants, which is essential to get their actual biological significance, may shed some lights in the field of targeted drug development in near future. Copyright © 2017. Published by Elsevier B.V.

Administrative Databases Can Yield False Conclusions-An Example of Obesity in Total Joint Arthroplasty.

PubMed

George, Jaiben; Newman, Jared M; Ramanathan, Deepak; Klika, Alison K; Higuera, Carlos A; Barsoum, Wael K

2017-09-01

Research using large administrative databases has substantially increased in recent years. Accuracy with which comorbidities are represented in these databases has been questioned. The purpose of this study was to evaluate the extent of errors in obesity coding and its impact on arthroplasty research. Eighteen thousand thirty primary total knee arthroplasties (TKAs) and 10,475 total hip arthroplasties (THAs) performed at a single healthcare system from 2004-2014 were included. Patients were classified as obese or nonobese using 2 methods: (1) body mass index (BMI) ≥30 kg/m 2 and (2) international classification of disease, 9th edition codes. Length of stay, operative time, and 90-day complications were collected. Effect of obesity on various outcomes was analyzed separately for both BMI- and coding-based obesity. From 2004 to 2014, the prevalence of BMI-based obesity increased from 54% to 63% and 40% to 45% in TKA and THA, respectively. The prevalence of coding-based obesity increased from 15% to 28% and 8% to 17% in TKA and THA, respectively. Coding overestimated the growth of obesity in TKA and THA by 5.6 and 8.4 times, respectively. When obesity was defined by coding, obesity was falsely shown to be a significant risk factor for deep vein thrombosis (TKA), pulmonary embolism (THA), and longer hospital stay (TKA and THA). The growth in obesity observed in administrative databases may be an artifact because of improvements in coding over the years. Obesity defined by coding can overestimate the actual effect of obesity on complications after arthroplasty. Therefore, studies using large databases should be interpreted with caution, especially when variables prone to coding errors are involved. Copyright © 2017 Elsevier Inc. All rights reserved.

[Analysis of ophthalmic projects granted by National Natural Science Foundation].

PubMed

Shao, Jing-Jing; Mo, Xiao-Fen; Pan, Zhi-Qiang; Gan, De-Kang; Xu, Yan-Ying

2008-09-01

To understand the status of basic research work in the field of ophthalmology by analyzing the projects funded by the National Natural Science Foundation of China (NSFC) from the year of 1986 to 2007, and offer as a reference to the ophthalmologists and researchers. NSFC supported ophthalmology projects in the 22 year's period were collected from the database of NSFC. The field of funded projects, the research team and their achievements were analyzed. There were 228 applicants from 47 home institutions were funded in the field of ophthalmology during the past 22 years, 323 projects funded with 66.74 million Yuan in total, in which 165 projects were fulfilled before the end of 2006. The applied and funded projects mainly focus on six different kinds of research area related to retinal diseases, corneal diseases, glaucoma, optic nerve diseases, myopia and cataract, and 70% of them were basic research in nature. As a brief achievement of 165 fulfilled projects, more than 610 papers were published in domestic journals, over 140 papers were published in Science Citation Index journals, more than 600 people were trained, and over 20 scientific awards were obtained. The number of funded projects and achievement of fulfilled projects in the discipline of ophthalmology gradually increased over the past two decades, the research fields were concentrated in certain diseases. NSFC has played an important role in promoting the development of ophthalmology research and bringing up specialists in China. However, clinical research, continuously research, transforming from basic research to clinic applications and multidisciplinary cross studies should be strengthened.

Quality of Life of patients with chronic kidney disease in Iran: Systematic Review and Meta-analysis

PubMed Central

Ghiasi, Bahareh; Sarokhani, Diana; Dehkordi, Ali Hasanpour; Sayehmiri, Kourosh; Heidari, Mohammad Hossein

2018-01-01

Introduction: Renal diseases are among the major health problems around the world that cause major changes in patients’ lifestyle and affect their quality of lives. The aim of this study was to evaluate the quality of life of patients with chronic kidney disease (CKD) in Iran through a meta-analysis. Materials and Methods: This study was conducted using authentic Persian and English keywords in the national and international databases including IranMedex, SID, Magiran, IranDoc, Medlib, Science Direct, Pubmed, Scopus, Cochrane, Embase, Web of Science, and Medline. The data were analyzed using meta-analysis (random effects model). Heterogeneity of studies was assessed using I2 index. In this study, SF-36: 36-Item Short Form health-related quality of life (HRQOL), kidney disease quality of life-SF (KDQOL-SF), KDQOL and KDQOL-SFTM questionnaires were used. Data were analyzed using STATA Version 11 software. Results: A total of 17200 individuals participated in 45 reviewed studies, and the mean score of CKD patients’ quality of life was estimated by SF-36 (60.31), HRQOL (60.51), and KDQOL-SF (50.37) questionnaires. In addition, meta-regression showed that the mean score of CKD patients’ quality of life did not significantly decrease during the past years. Conclusion: The mean score of quality of life of patients with CKD was lower in different dimensions in comparison with that of normal people. Therefore, interventional measures should be taken to improve the quality of life of these patients in all dimensions. PMID:29440817

Is early limited surgery associated with a more benign disease course in Crohn’s disease?

PubMed Central

Golovics, Petra Anna; Lakatos, Laszlo; Nagy, Attila; Pandur, Tunde; Szita, Istvan; Balogh, Mihaly; Molnar, Csaba; Komaromi, Erzsebet; Lovasz, Barbara Dorottya; Mandel, Michael; Veres, Gabor; Kiss, Lajos S; Vegh, Zsuzsanna; Lakatos, Peter Laszlo

2013-01-01

AIM: To analyze the difference in disease course and need for surgery in patients with Crohn’s disease (CD). METHODS: Data of 506 patients with incident CD were analyzed (age at diagnosis: 31.5 ± 13.8 years). Both hospital and outpatient records were collected prospectively with a complete clinical follow-up and comprehensively reviewed in the population-based Veszprem province database, which includes incident CD patients diagnosed between January 1, 1977 and December 31, 2008. Follow-up data were collected until December 31, 2009. All patients included had at least 1 year of follow-up available. Patients with indeterminate colitis at diagnosis were excluded from the analysis. RESULTS: Overall, 73 patients (14.4%) required resective surgery within 1 year of diagnosis. Steroid exposure and need for biological therapy were lower in patients with early limited surgery (P < 0.001 and P = 0.09). In addition, surgery rates during follow-up in patients with and without early surgery differed significantly after matching on propensity scores (P < 0.001, HR = 0.23). The need for reoperation was also lower in patients with early limited resective surgery (P = 0.038, HR = 0.42) in a Kaplan-Meier and multivariate Cox regression (P = 0.04) analysis. However, this advantage was not observed after matching on propensity scores (PLogrank = 0.656, PBreslow = 0.498). CONCLUSION: Long-term surgery rates and overall exposure to steroids and biological agents were lower in patients with early limited resective surgery, but reoperation rates did not differ. PMID:24282358

Assessment of text documentation accompanying uncoded diagnoses in computerized health insurance claims in Japan.

PubMed

Tanihara, Shinichi

2015-01-01

Uncoded diagnoses in health insurance claims (HICs) may introduce bias into Japanese health statistics dependent on computerized HICs. This study's aim was to identify the causes and characteristics of uncoded diagnoses. Uncoded diagnoses from computerized HICs (outpatient, inpatient, and the diagnosis procedure-combination per-diem payment system [DPC/PDPS]) submitted to the National Health Insurance Organization of Kumamoto Prefecture in May 2010 were analyzed. The text documentation accompanying the uncoded diagnoses was used to classify diagnoses in accordance with the International Classification of Diseases-10 (ICD-10). The text documentation was also classified into four categories using the standard descriptions of diagnoses defined in the master files of the computerized HIC system: 1) standard descriptions of diagnoses, 2) standard descriptions with a modifier, 3) non-standard descriptions of diagnoses, and 4) unclassifiable text documentation. Using these classifications, the proportions of uncoded diagnoses by ICD-10 disease category were calculated. Of the uncoded diagnoses analyzed (n = 363 753), non-standard descriptions of diagnoses for outpatient, inpatient, and DPC/PDPS HICs comprised 12.1%, 14.6%, and 1.0% of uncoded diagnoses, respectively. The proportion of uncoded diagnoses with standard descriptions with a modifier for Diseases of the eye and adnexa was significantly higher than the overall proportion of uncoded diagnoses among every HIC type. The pattern of uncoded diagnoses differed by HIC type and disease category. Evaluating the proportion of uncoded diagnoses in all medical facilities and developing effective coding methods for diagnoses with modifiers, prefixes, and suffixes should reduce number of uncoded diagnoses in computerized HICs and improve the quality of HIC databases.

Changes in chronic disease management among community health centers (CHCs) in China: Has health reform improved CHC ability?

PubMed

Wang, Zhaoxin; Shi, Jianwei; Wu, Zhigui; Xie, Huiling; Yu, Yifan; Li, Ping; Liu, Rui; Jing, Limei

2017-07-01

Since the 1980s, China has been criticized for its mode of chronic disease management (CDM) that passively provides treatment in secondary and tertiary hospitals but lacks active prevention in community health centers (CHCs). Since there are few systematic evaluations of the CHCs' methods for CDM, this study aimed to analyze their abilities. On the macroperspective, we searched the literature in China's largest and most authoritative databases and the official websites of health departments. Literature was used to analyze the government's efforts in improving CHCs' abilities to perform CDM. At the microlevel, we examined the CHCs' longitudinal data after the New Health Reform in 2009, including financial investment, facilities, professional capacities, and the conducted CDM activities. A policy analysis showed that there was an increasing tendency towards government efforts in developing CDM, and the peak appeared in 2009. By evaluating the reform at CHCs, we found that there was an obvious increase in fiscal and public health subsidies, large-scale equipment, general practitioners, and public health physicians. The benefited vulnerable population in this area also rose significantly. However, rural centers were inferior in their CDM abilities compared with urban ones, and the referral system is still not effective in China. This study showed that CHCs are increasingly valued in managing chronic diseases, especially after the New Health Reform in 2009. However, we still need to improve collaborative management for chronic diseases in the community and strengthen the abilities of CHCs, especially in rural areas. Copyright © 2017 John Wiley & Sons, Ltd.

Inborn errors of metabolism and the human interactome: a systems medicine approach.

PubMed

Woidy, Mathias; Muntau, Ania C; Gersting, Søren W

2018-02-05

The group of inborn errors of metabolism (IEM) displays a marked heterogeneity and IEM can affect virtually all functions and organs of the human organism; however, IEM share that their associated proteins function in metabolism. Most proteins carry out cellular functions by interacting with other proteins, and thus are organized in biological networks. Therefore, diseases are rarely the consequence of single gene mutations but of the perturbations caused in the related cellular network. Systematic approaches that integrate multi-omics and database information into biological networks have successfully expanded our knowledge of complex disorders but network-based strategies have been rarely applied to study IEM. We analyzed IEM on a proteome scale and found that IEM-associated proteins are organized as a network of linked modules within the human interactome of protein interactions, the IEM interactome. Certain IEM disease groups formed self-contained disease modules, which were highly interlinked. On the other hand, we observed disease modules consisting of proteins from many different disease groups in the IEM interactome. Moreover, we explored the overlap between IEM and non-IEM disease genes and applied network medicine approaches to investigate shared biological pathways, clinical signs and symptoms, and links to drug targets. The provided resources may help to elucidate the molecular mechanisms underlying new IEM, to uncover the significance of disease-associated mutations, to identify new biomarkers, and to develop novel therapeutic strategies.

[Systematic review and evidence mapping of empirical studies on health status and medical care among refugees and asylum seekers in Germany (1990-2014)].

PubMed

Bozorgmehr, Kayvan; Mohsenpour, Amir; Saure, Daniel; Stock, Christian; Loerbroks, Adrian; Joos, Stefanie; Schneider, Christine

2016-05-01

Owing to a lack of routine statistics on the health status and medical care of asylum seekers, empirical studies play a major role in the mapping of these aspects. The aim of this review is to provide a comprehensive overview of the research landscape in this area, synthesizing knowledge from empirical studies and identifying evidence gaps. A three-tiered search strategy included searching for empirical studies in national/international databases and on the internet, screening reference lists, and contacting experts. Studies meeting predefined inclusion criteria were thematically organized and described in a narrative synthesis. The searches generated 1,190 hits; 52 articles met the inclusion criteria. Of these, 41 were quantitative studies (78.9 %), 10 qualitative (19.2 %), and 1 was a review (1.9 %). A total of 30 primary articles (58.9 %) analyzed mental health aspects, followed by infectious diseases (n = 12, 23.5 %). Qualitative studies, mainly ethnographies and case studies, explored mental health and social determinants of health, providing evidence for the impact of living conditions on health and medical care. Few studies analyzed chronic diseases (n = 3) or childhood illnesses (n = 6). No studies analyzed the health needs or medical care of asylum-seeking women during pregnancy and child birth. In 62.7 % of the primary studies, a single sampling point was used to recruit asylum seekers. Nationwide external validity was given in two quantitative studies. The priority research areas identified are chronic diseases and childhood and maternal health. The divergency and heterogeneity of the studies hamper a comprehensive and comparable acquisition of knowledgeand emphasize the  need for collaborative research to close the existing evidence gaps.

Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS.

PubMed

Sana, Theodore R; Roark, Joseph C; Li, Xiangdong; Waddell, Keith; Fischer, Steven M

2008-09-01

In an effort to simplify and streamline compound identification from metabolomics data generated by liquid chromatography time-of-flight mass spectrometry, we have created software for constructing Personalized Metabolite Databases with content from over 15,000 compounds pulled from the public METLIN database (http://metlin.scripps.edu/). Moreover, we have added extra functionalities to the database that (a) permit the addition of user-defined retention times as an orthogonal searchable parameter to complement accurate mass data; and (b) allow interfacing to separate software, a Molecular Formula Generator (MFG), that facilitates reliable interpretation of any database matches from the accurate mass spectral data. To test the utility of this identification strategy, we added retention times to a subset of masses in this database, representing a mixture of 78 synthetic urine standards. The synthetic mixture was analyzed and screened against this METLIN urine database, resulting in 46 accurate mass and retention time matches. Human urine samples were subsequently analyzed under the same analytical conditions and screened against this database. A total of 1387 ions were detected in human urine; 16 of these ions matched both accurate mass and retention time parameters for the 78 urine standards in the database. Another 374 had only an accurate mass match to the database, with 163 of those masses also having the highest MFG score. Furthermore, MFG calculated a formula for a further 849 ions that had no match to the database. Taken together, these results suggest that the METLIN Personal Metabolite database and MFG software offer a robust strategy for confirming the formula of database matches. In the event of no database match, it also suggests possible formulas that may be helpful in interpreting the experimental results.

The research of network database security technology based on web service

NASA Astrophysics Data System (ADS)

Meng, Fanxing; Wen, Xiumei; Gao, Liting; Pang, Hui; Wang, Qinglin

2013-03-01

Database technology is one of the most widely applied computer technologies, its security is becoming more and more important. This paper introduced the database security, network database security level, studies the security technology of the network database, analyzes emphatically sub-key encryption algorithm, applies this algorithm into the campus-one-card system successfully. The realization process of the encryption algorithm is discussed, this method is widely used as reference in many fields, particularly in management information system security and e-commerce.

High-Content Movement Analysis as a Diagnostic Tool in C. elegans

NASA Astrophysics Data System (ADS)

Winter, Peter; Lancichinetti, Andrea; Krevitt, Leah; Amaral, Luis; Morimoto, Rick

2013-03-01

Many neurodegenerative diseases manifest themselves through a loss of motor control and give us information about the underlying disease. This loss of coordination is observed in humans and in the model organisms used to study neurodegeneration. In Caenorhabditis elegans, there is an extensive genetic library of strains that lack functional neuronal signaling pathways and expressing proteins associated with neurodegenerative diseases. While most of these strains have decrease motility or cause paralysis, relatively few have been screened to look for more subtle changes in motor control such as stiffness, twitching, or other changes in behavior. we use high-resolution position and posture data to automatically analyze the movement of worms from different genetic backgrounds and characterize 14 movement characteristics. By creating a quantitative mapping between the movement characterization and an online database of gene annotation, gene expression, and anatomy, we aim to predict a likely set of cellular and molecular disruptions. This work provides a proof of concept for the use of detailed movement analysis to uncover novel disruptions in certain motor control processes. Knowledge of the molecular origin of these disruptions provided by our understanding of C. elegans genetics and physiology could lead to new diagnostic and therapeutic targets for neurodegenerative disease.

Effects of Non-Pharmacological Treatments on Quality of Life in Parkinson's Disease: A Review

PubMed Central

Ahn, Sangwoo; Chen, Yan; Bredow, Tim; Cheung1, Corjena; Yu, Fang

2017-01-01

Parkinson's disease is a neurodegenerative chronic condition with a declining trajectory and lack of a cure, making quality of life an important aspect of care. The purpose of this literature review was to analyze the state-of-the-science on the effects of non-pharmacological treatments on quality of life in person's with Parkinson's disease. Literature search was conducted using keywords in electronic databases up to September 1, 2016 and cross-searching the references of identified articles. Of the 259 articles generated, 26 met the eligibility criteria and were included in this review. The majority of studies (77%) were Level I evidence and 23% Level II evidence. The levels of study quality were: strong (50%), moderate (15%), and weak (35%). The interventions varied across studies with 15 studies evaluating a similar intervention. About 58% of the studies showed that the interventions improved quality of life. In conclusion, a variety of non-pharmacological interventions have been increasingly studied for their effects on quality of life in Parkinson's disease, showing initial promising results. However, most interventions were only examined by a limited number of studies and the minimal and optimal intervention doses needed for improving quality of life are yet unknown. PMID:28932811

Safety profile of methotrexate in inflammatory bowel disease.

PubMed

Gabbani, Tommaso; Deiana, Simona; Lunardi, Sarah; Manetti, Natalia; Annese, Vito

2016-10-01

Methotrexate, which was initially developed in 1948 for the treatment of leukemia, is known to be an immunomodulatory and anti-inflammatory drug. It has been widely used for over 60 years as both a low and high-dose therapy in chronic inflammatory diseases. The aim of this review was to analyze and summarize the available data specifically on the safety of this drug in the management of inflammatory bowel diseases. A structured search of articles was conducted using the PubMed database up to April 2016. All articles in English with isolated or combined keywords were included according to their relevance to the aims of this study. Numerous of studies have established the efficacy of parenteral methotrexate in the management of steroid-dependent and steroid-resistant Crohn's disease, either for inducing or maintaining remission. However, its efficacy in ulcerative colitis has not been properly investigated. Additionally, methotrexate has been shown to reduce the effect of immunization with anti-TNF agents when combined. The drug has potential advantages over thiopurines such as its weekly administration, a possible shorter time of action, low cost, decreased risk for malignancy and overall a comparable safety profile.

MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis.

PubMed

Flandrois, Jean-Pierre; Lina, Gérard; Dumitrescu, Oana

2014-04-14

Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the basis of the treatment, and the emergence and spread of multidrug and extensively drug-resistant mutant strains raise significant challenges. As these bacteria grow very slowly, drug resistance mutations are currently detected using molecular biology techniques. Resistance mutations are identified by sequencing the resistance-linked genes followed by a comparison with the literature data. The only online database is the TB Drug Resistance Mutation database (TBDReaM database); however, it requires mutation detection before use, and its interrogation is complex due to its loose syntax and grammar. The MUBII-TB-DB database is a simple, highly structured text-based database that contains a set of Mycobacterium tuberculosis mutations (DNA and proteins) occurring at seven loci: rpoB, pncA, katG; mabA(fabG1)-inhA, gyrA, gyrB, and rrs. Resistance mutation data were extracted after the systematic review of MEDLINE referenced publications before March 2013. MUBII analyzes the query sequence obtained by PCR-sequencing using two parallel strategies: i) a BLAST search against a set of previously reconstructed mutated sequences and ii) the alignment of the query sequences (DNA and its protein translation) with the wild-type sequences. The post-treatment includes the extraction of the aligned sequences together with their descriptors (position and nature of mutations). The whole procedure is performed using the internet. The results are graphs (alignments) and text (description of the mutation, therapeutic significance). The system is quick and easy to use, even for technicians without bioinformatics training. MUBII-TB-DB is a structured database of the mutations occurring at seven loci of major therapeutic value in tuberculosis management. Moreover, the system provides interpretation of the mutations in biological and therapeutic terms and can evolve by the addition of newly described mutations. Its goal is to provide easy and comprehensive access through a client-server model over the Web to an up-to-date database of mutations that lead to the resistance of M. tuberculosis to antibiotics.

Linking white matter and deep gray matter alterations in premanifest Huntington disease.

PubMed

Faria, Andreia V; Ratnanather, J Tilak; Tward, Daniel J; Lee, David Soobin; van den Noort, Frieda; Wu, Dan; Brown, Timothy; Johnson, Hans; Paulsen, Jane S; Ross, Christopher A; Younes, Laurent; Miller, Michael I

2016-01-01

Huntington disease (HD) is a fatal progressive neurodegenerative disorder for which only symptomatic treatment is available. A better understanding of the pathology, and identification of biomarkers will facilitate the development of disease-modifying treatments. HD is potentially a good model of a neurodegenerative disease for development of biomarkers because it is an autosomal-dominant disease with complete penetrance, caused by a single gene mutation, in which the neurodegenerative process can be assessed many years before onset of signs and symptoms of manifest disease. Previous MRI studies have detected abnormalities in gray and white matter starting in premanifest stages. However, the understanding of how these abnormalities are related, both in time and space, is still incomplete. In this study, we combined deep gray matter shape diffeomorphometry and white matter DTI analysis in order to provide a better mapping of pathology in the deep gray matter and subcortical white matter in premanifest HD. We used 296 MRI scans from the PREDICT-HD database. Atrophy in the deep gray matter, thalamus, hippocampus, and nucleus accumbens was analyzed by surface based morphometry, and while white matter abnormalities were analyzed in (i) regions of interest surrounding these structures, using (ii) tractography-based analysis, and using (iii) whole brain atlas-based analysis. We detected atrophy in the deep gray matter, particularly in putamen, from early premanifest stages. The atrophy was greater both in extent and effect size in cases with longer exposure to the effects of the CAG expansion mutation (as assessed by greater CAP-scores), and preceded detectible abnormalities in the white matter. Near the predicted onset of manifest HD, the MD increase was widespread, with highest indices in the deep and posterior white matter. This type of in-vivo macroscopic mapping of HD brain abnormalities can potentially indicate when and where therapeutics could be targeted to delay the onset or slow the disease progression.

Validity of peptic ulcer disease and upper gastrointestinal bleeding diagnoses in administrative databases: a systematic review protocol.

PubMed

Montedori, Alessandro; Abraha, Iosief; Chiatti, Carlos; Cozzolino, Francesco; Orso, Massimiliano; Luchetta, Maria Laura; Rimland, Joseph M; Ambrosio, Giuseppe

2016-09-15

Administrative healthcare databases are useful to investigate the epidemiology, health outcomes, quality indicators and healthcare utilisation concerning peptic ulcers and gastrointestinal bleeding, but the databases need to be validated in order to be a reliable source for research. The aim of this protocol is to perform the first systematic review of studies reporting the validation of International Classification of Diseases, 9th Revision and 10th version (ICD-9 and ICD-10) codes for peptic ulcer and upper gastrointestinal bleeding diagnoses. MEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched, using appropriate search strategies. We will include validation studies that used administrative data to identify peptic ulcer disease and upper gastrointestinal bleeding diagnoses or studies that evaluated the validity of peptic ulcer and upper gastrointestinal bleeding codes in administrative data. The following inclusion criteria will be used: (a) the presence of a reference standard case definition for the diseases of interest; (b) the presence of at least one test measure (eg, sensitivity, etc) and (c) the use of an administrative database as a source of data. Pairs of reviewers will independently abstract data using standardised forms and will evaluate quality using the checklist of the Standards for Reporting of Diagnostic Accuracy (STARD) criteria. This systematic review protocol has been produced in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocol (PRISMA-P) 2015 statement. Ethics approval is not required given that this is a protocol for a systematic review. We will submit results of this study to a peer-reviewed journal for publication. The results will serve as a guide for researchers validating administrative healthcare databases to determine appropriate case definitions for peptic ulcer disease and upper gastrointestinal bleeding, as well as to perform outcome research using administrative healthcare databases of these conditions. CRD42015029216. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

A database for coconut crop improvement.

PubMed

Rajagopal, Velamoor; Manimekalai, Ramaswamy; Devakumar, Krishnamurthy; Rajesh; Karun, Anitha; Niral, Vittal; Gopal, Murali; Aziz, Shamina; Gunasekaran, Marimuthu; Kumar, Mundappurathe Ramesh; Chandrasekar, Arumugam

2005-12-08

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. http://www.bioinfcpcri.org.

Utilization of a multimedia PACS workstation for surgical planning of epilepsy

NASA Astrophysics Data System (ADS)

Soo Hoo, Kent; Wong, Stephen T.; Hawkins, Randall A.; Knowlton, Robert C.; Laxer, Kenneth D.; Rowley, Howard A.

1997-05-01

Surgical treatment of temporal lobe epilepsy requires the localization of the epileptogenic zone for surgical resection. Currently, clinicians utilize electroencephalography, various neuroimaging modalities, and psychological tests together to determine the location of this zone. We investigate how a multimedia neuroimaging workstation built on top of the UCSF Picture Archiving and Communication System can be used to aid surgical planning of epilepsy and related brain diseases. This usage demonstrates the ability of the workstation to retrieve image and textural data from PACS and other image sources, register multimodality images, visualize and render 3D data sets, analyze images, generate new image and text data from the analysis, and organize all data in a relational database management system.

Survey of Natural Language Processing Techniques in Bioinformatics.

PubMed

Zeng, Zhiqiang; Shi, Hua; Wu, Yun; Hong, Zhiling

2015-01-01

Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases. For example, protein-protein interactions and gene-disease relationship can be mined from PubMed. Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA. Finally, numerous methods and applications, as well as their contributions to bioinformatics, are discussed for future use by text mining and natural language processing researchers.

Glaucoma correlates with increased risk of Parkinson's disease in the elderly: a national-based cohort study in Taiwan.

PubMed

Lai, Shih-Wei; Lin, Cheng-Li; Liao, Kuan-Fu

2017-08-01

Very little is known about the association between glaucoma and Parkinson's disease in the elderly. The objective of this study was to determine whether glaucoma is associated with Parkinson's disease in older people in Taiwan. A retrospective cohort study was conducted to analyze the Taiwan National Health Insurance Program database from 2000 to 2010. We included 4330 subjects aged 65 years or older with newly diagnosed glaucoma as the glaucoma group, and 17,000 randomly selected subjects without a glaucoma diagnosis as the non-glaucoma group. Both groups were matched for sex, age, other comorbidities, and index year of glaucoma diagnosis. The incidence of Parkinson's disease at the end of 2011 was measured. A multivariable Cox proportional hazard regression model was used to measure the hazard ratio and 95% confidence intervals for Parkinson's disease associated with glaucoma. The overall incidence of Parkinson's disease was 1.28-fold higher in the glaucoma group than that in the non-glaucoma group (7.73 vs. 6.02 per 1000 person-years; 95% confidence interval 1.18, 1.40). After controlling for potential confounding factors, the adjusted hazard ratio of Parkinson's disease was 1.23 for the glaucoma group (95% confidence interval 1.05, 1.46), compared with the non-glaucoma group. Older people with glaucoma correlate with a small but statistically significant increase in the risk for Parkinson's disease. Whether glaucoma may be a non-motor feature of Parkinson's disease in older people requires further research to confirm.

Systematic review of electronic surveillance of infectious diseases with emphasis on antimicrobial resistance surveillance in resource-limited settings.

PubMed

Rattanaumpawan, Pinyo; Boonyasiri, Adhiratha; Vong, Sirenda; Thamlikitkul, Visanu

2018-02-01

Electronic surveillance of infectious diseases involves rapidly collecting, collating, and analyzing vast amounts of data from interrelated multiple databases. Although many developed countries have invested in electronic surveillance for infectious diseases, the system still presents a challenge for resource-limited health care settings. We conducted a systematic review by performing a comprehensive literature search on MEDLINE (January 2000-December 2015) to identify studies relevant to electronic surveillance of infectious diseases. Study characteristics and results were extracted and systematically reviewed by 3 infectious disease physicians. A total of 110 studies were included. Most surveillance systems were developed and implemented in high-income countries; less than one-quarter were conducted in low-or middle-income countries. Information technologies can be used to facilitate the process of obtaining laboratory, clinical, and pharmacologic data for the surveillance of infectious diseases, including antimicrobial resistance (AMR) infections. These novel systems require greater resources; however, we found that using electronic surveillance systems could result in shorter times to detect targeted infectious diseases and improvement of data collection. This study highlights a lack of resources in areas where an effective, rapid surveillance system is most needed. The availability of information technology for the electronic surveillance of infectious diseases, including AMR infections, will facilitate the prevention and containment of such emerging infectious diseases. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Computer-Based Image Analysis for Plus Disease Diagnosis in Retinopathy of Prematurity

PubMed Central

Wittenberg, Leah A.; Jonsson, Nina J.; Chan, RV Paul; Chiang, Michael F.

2014-01-01

Presence of plus disease in retinopathy of prematurity (ROP) is an important criterion for identifying treatment-requiring ROP. Plus disease is defined by a standard published photograph selected over 20 years ago by expert consensus. However, diagnosis of plus disease has been shown to be subjective and qualitative. Computer-based image analysis, using quantitative methods, has potential to improve the objectivity of plus disease diagnosis. The objective was to review the published literature involving computer-based image analysis for ROP diagnosis. The PubMed and Cochrane library databases were searched for the keywords “retinopathy of prematurity” AND “image analysis” AND/OR “plus disease.” Reference lists of retrieved articles were searched to identify additional relevant studies. All relevant English-language studies were reviewed. There are four main computer-based systems, ROPtool (AU ROC curve, plus tortuosity 0.95, plus dilation 0.87), RISA (AU ROC curve, arteriolar TI 0.71, venular diameter 0.82), Vessel Map (AU ROC curve, arteriolar dilation 0.75, venular dilation 0.96), and CAIAR (AU ROC curve, arteriole tortuosity 0.92, venular dilation 0.91), attempting to objectively analyze vessel tortuosity and dilation in plus disease in ROP. Some of them show promise for identification of plus disease using quantitative methods. This has potential to improve the diagnosis of plus disease, and may contribute to the management of ROP using both traditional binocular indirect ophthalmoscopy and image-based telemedicine approaches. PMID:21366159

An epidemiological modeling and data integration framework.

PubMed

Pfeifer, B; Wurz, M; Hanser, F; Seger, M; Netzer, M; Osl, M; Modre-Osprian, R; Schreier, G; Baumgartner, C

2010-01-01

In this work, a cellular automaton software package for simulating different infectious diseases, storing the simulation results in a data warehouse system and analyzing the obtained results to generate prediction models as well as contingency plans, is proposed. The Brisbane H3N2 flu virus, which has been spreading during the winter season 2009, was used for simulation in the federal state of Tyrol, Austria. The simulation-modeling framework consists of an underlying cellular automaton. The cellular automaton model is parameterized by known disease parameters and geographical as well as demographical conditions are included for simulating the spreading. The data generated by simulation are stored in the back room of the data warehouse using the Talend Open Studio software package, and subsequent statistical and data mining tasks are performed using the tool, termed Knowledge Discovery in Database Designer (KD3). The obtained simulation results were used for generating prediction models for all nine federal states of Austria. The proposed framework provides a powerful and easy to handle interface for parameterizing and simulating different infectious diseases in order to generate prediction models and improve contingency plans for future events.

Comparison of Informal Care Time and Costs in Different Age-Related Dementias: A Review

PubMed Central

Costa, Nadège; Ferlicoq, Laura; Derumeaux-Burel, Hélène; Rapp, Thomas; Garnault, Valérie; Gillette-Guyonnet, Sophie; Andrieu, Sandrine; Vellas, Bruno; Lamure, Michel; Grand, Alain; Molinier, Laurent

2013-01-01

Objectives. Age-related dementia is a progressive degenerative brain syndrome whose prevalence increases with age. Dementias cause a substantial burden on society and on families who provide informal care. This study aims to review the relevant papers to compare informal care time and costs in different dementias. Methods. A bibliographic search was performed on an international medical literature database (MEDLINE). All studies which assessed the social economic burden of different dementias were selected. Informal care time and costs were analyzed in three care settings by disease stages. Results. 21 studies met our criteria. Mean informal care time was 55.73 h per week for Alzheimer disease and 15.8 h per week for Parkinson disease (P = 0.0076), and the associated mean annual informal costs were $17,492 versus $3,284, respectively (P = 0.0393). Conclusion. There is a lack of data about informal care time and costs among other dementias than AD or PD. Globally, AD is the most costly in terms of informal care costs than PD, $17,492 versus $3,284, respectively. PMID:23509789

A novel quantification-driven proteomic strategy identifies an endogenous peptide of pleiotrophin as a new biomarker of Alzheimer's disease.

PubMed

Skillbäck, Tobias; Mattsson, Niklas; Hansson, Karl; Mirgorodskaya, Ekaterina; Dahlén, Rahil; van der Flier, Wiesje; Scheltens, Philip; Duits, Floor; Hansson, Oskar; Teunissen, Charlotte; Blennow, Kaj; Zetterberg, Henrik; Gobom, Johan

2017-10-17

We present a new, quantification-driven proteomic approach to identifying biomarkers. In contrast to the identification-driven approach, limited in scope to peptides that are identified by database searching in the first step, all MS data are considered to select biomarker candidates. The endopeptidome of cerebrospinal fluid from 40 Alzheimer's disease (AD) patients, 40 subjects with mild cognitive impairment, and 40 controls with subjective cognitive decline was analyzed using multiplex isobaric labeling. Spectral clustering was used to match MS/MS spectra. The top biomarker candidate cluster (215% higher in AD compared to controls, area under ROC curve = 0.96) was identified as a fragment of pleiotrophin located near the protein's C-terminus. Analysis of another cohort (n = 60 over four clinical groups) verified that the biomarker was increased in AD patients while no change in controls, Parkinson's disease or progressive supranuclear palsy was observed. The identification of the novel biomarker pleiotrophin 151-166 demonstrates that our quantification-driven proteomic approach is a promising method for biomarker discovery, which may be universally applicable in clinical proteomics.

Administrative database code accuracy did not vary notably with changes in disease prevalence.

PubMed

van Walraven, Carl; English, Shane; Austin, Peter C

2016-11-01

Previous mathematical analyses of diagnostic tests based on the categorization of a continuous measure have found that test sensitivity and specificity varies significantly by disease prevalence. This study determined if the accuracy of diagnostic codes varied by disease prevalence. We used data from two previous studies in which the true status of renal disease and primary subarachnoid hemorrhage, respectively, had been determined. In multiple stratified random samples from the two previous studies having varying disease prevalence, we measured the accuracy of diagnostic codes for each disease using sensitivity, specificity, and positive and negative predictive value. Diagnostic code sensitivity and specificity did not change notably within clinically sensible disease prevalence. In contrast, positive and negative predictive values changed significantly with disease prevalence. Disease prevalence had no important influence on the sensitivity and specificity of diagnostic codes in administrative databases. Copyright © 2016 Elsevier Inc. All rights reserved.

Choosing a Database for Social Work: A Comparison of Social Work Abstracts and Social Service Abstracts

ERIC Educational Resources Information Center

Flatley, Robert K.; Lilla, Rick; Widner, Jack

2007-01-01

This study compared Social Work Abstracts and Social Services Abstracts databases in terms of indexing, journal coverage, and searches. The authors interviewed editors, analyzed journal coverage, and compared searches. It was determined that the databases complement one another more than compete. The authors conclude with some considerations.

Bridging the Qualitative/Quantitative Software Divide

PubMed Central

Annechino, Rachelle; Antin, Tamar M. J.; Lee, Juliet P.

2011-01-01

To compare and combine qualitative and quantitative data collected from respondents in a mixed methods study, the research team developed a relational database to merge survey responses stored and analyzed in SPSS and semistructured interview responses stored and analyzed in the qualitative software package ATLAS.ti. The process of developing the database, as well as practical considerations for researchers who may wish to use similar methods, are explored. PMID:22003318

Alignment of systematic reviews published in the Cochrane Database of Systematic Reviews and the Database of Abstracts and Reviews of Effectiveness with global burden-of-disease data: a bibliographic analysis.

PubMed

Yoong, Sze Lin; Hall, Alix; Williams, Christopher M; Skelton, Eliza; Oldmeadow, Christopher; Wiggers, John; Karimkhani, Chante; Boyers, Lindsay N; Dellavalle, Robert P; Hilton, John; Wolfenden, Luke

2015-07-01

Systematic reviews of high-quality evidence are used to inform policy and practice. To improve community health, the production of such reviews should align with burden of disease. This study aims to assess if the volume of research output from systematic reviews proportionally aligns with burden of disease assessed using percentages of mortality and disability-adjusted life years (DALYs). A cross-sectional audit of reviews published between January 2012 and August 2013 in the Cochrane Database of Systematic Reviews (CDSR) and Database of Abstracts of Reviews of Effects (DARE) was undertaken. Percentages of mortality and DALYs were obtained from the 2010 Global Burden of Disease study. Standardised residual differences (SRD) based on percentages of mortality and DALYs were calculated, where conditions with SRD of more than or less than three were considered overstudied or understudied, respectively. 1029 reviews from CDSR and 1928 reviews from DARE were examined. There was a significant correlation between percentage DALYs and systematic reviews published in CDSR and DARE databases (CDSR: r=0.68, p=0.001; DARE: r=0.60, p<0.001). There was no significant correlation between percentage mortality and number of systematic reviews published in either database (CDSR: r=0.34, p=0.14; DARE: r=0.22, p=0.34). Relative to percentage of mortality, mental and behavioural disorders, musculoskeletal conditions and other non-communicable diseases were overstudied. Maternal disorders were overstudied relative to percentages of mortality and DALYs in CDSR. The focus of systematic reviews is moderately correlated with DALYs. A number of conditions may be overstudied relative to percentage of mortality particularly in the context of health and medical reviews. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Establishment of Kawasaki disease database based on metadata standard.

PubMed

Park, Yu Rang; Kim, Jae-Jung; Yoon, Young Jo; Yoon, Young-Kwang; Koo, Ha Yeong; Hong, Young Mi; Jang, Gi Young; Shin, Soo-Yong; Lee, Jong-Keuk

2016-07-01

Kawasaki disease (KD) is a rare disease that occurs predominantly in infants and young children. To identify KD susceptibility genes and to develop a diagnostic test, a specific therapy, or prevention method, collecting KD patients' clinical and genomic data is one of the major issues. For this purpose, Kawasaki Disease Database (KDD) was developed based on the efforts of Korean Kawasaki Disease Genetics Consortium (KKDGC). KDD is a collection of 1292 clinical data and genomic samples of 1283 patients from 13 KKDGC-participating hospitals. Each sample contains the relevant clinical data, genomic DNA and plasma samples isolated from patients' blood, omics data and KD-associated genotype data. Clinical data was collected and saved using the common data elements based on the ISO/IEC 11179 metadata standard. Two genome-wide association study data of total 482 samples and whole exome sequencing data of 12 samples were also collected. In addition, KDD includes the rare cases of KD (16 cases with family history, 46 cases with recurrence, 119 cases with intravenous immunoglobulin non-responsiveness, and 52 cases with coronary artery aneurysm). As the first public database for KD, KDD can significantly facilitate KD studies. All data in KDD can be searchable and downloadable. KDD was implemented in PHP, MySQL and Apache, with all major browsers supported.Database URL: http://www.kawasakidisease.kr. © The Author(s) 2016. Published by Oxford University Press.

In silico profiling for secondary metabolites from Lepidium meyenii (maca) by the pharmacophore and ligand-shape-based joint approach.

PubMed

Yi, Fan; Tan, Xiao-Lei; Yan, Xin; Liu, Hai-Bo

2016-01-01

Lepidium meyenii Walpers (maca) is an herb known as a traditional nutritional supplement and widely used in Peru, North America, and Europe to enhance human fertility and treat osteoporosis. The secondary metabolites of maca, namely, maca alkaloids, macaenes, and macamides, are bioactive compounds, but their targets are undefined. The pharmacophore-based PharmaDB targets database screening joint the ligand shape similarity-based WEGA validation approach is proposed to predict the targets of these unique constituents and was performed using Discovery Studio 4.5 and PharmaDB. A compounds-targets-diseases network was established using Cytoscape 3.2. These suitable targets and their genes were calculated and analyzed using ingenuity pathway analysis and GeneMANIA. Certain targets were identified in osteoporosis (8 targets), prostate cancer (9 targets), and kidney diseases (11 targets). This was the first study to identify the targets of these bioactive compounds in maca for cardiovascular diseases (29 targets). The compound with the most targets (46) was an amide alkaloid (MA-24). In silico target fishing identified maca's traditional effects on treatment and prevention of osteoporosis, prostate cancer, and kidney diseases, and its potential function of treating cardiovascular diseases, as the most important of this herb's possible activities.

Huntington's Disease Research Roster Support with a Microcomputer Database Management System

PubMed Central

Gersting, J. M.; Conneally, P. M.; Beidelman, K.

1983-01-01

This paper chronicles the MEGADATS (Medical Genetics Acquisition and DAta Transfer System) database development effort in collecting, storing, retrieving, and plotting human family pedigrees. The newest system, MEGADATS-3M, is detailed. Emphasis is on the microcomputer version of MEGADATS-3M and its use to support the Huntington's Disease research roster project. Examples of data input and pedigree plotting are included.

DDMGD: the database of text-mined associations between genes methylated in diseases from different species.

PubMed

Bin Raies, Arwa; Mansour, Hicham; Incitti, Roberto; Bajic, Vladimir B

2015-01-01

Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD's scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

IIKmTA: Inter and Intra Kingdom miRNA-Target Analyzer.

PubMed

Mal, Chittabrata; Aftabuddin, Md; Kundu, Sudip

2018-03-16

Growing evidences suggest that microRNAs (miRNAs) can efficiently regulate gene expression at intracellular and extracellular levels. It has been previously reported that plant/food-derived miRNAs are highly enriched in human serum or serum from phytophagous animals, and they are responsible for regulating mammalian gene expression. Thus, miRNAs could function as active signaling molecules, which carry information across distinct species or even kingdoms. However, the mode of miRNA shuttling among various organisms is still a mystery to unravel. The intra and inter kingdom miRNA transfer has boosted up the hypothesis about the potential impact of plant or animal miRNAs on each other. To our knowledge, the software for analyzing cross-kingdom miRNA-targets is lacking. We have developed a web-tool "IIKmTA: Inter and Intra Kingdom miRNA-Target Analyzer" utilizing a database; the data of which have been collected from another web server. Here, user can analyze the targeting potential of (i) plant miRNAs on animal UTRs (Untranslated regions), and vice versa (i.e., inter kingdom), (ii) plant miRNAs on plant UTRs and animal miRNAs on animal UTRs (i.e., intra kingdom). Further, user can analyze (i) miRNAs to targets, (ii) targets to miRNAs, and (iii) miRNA sets targeting sets of targets. For a wide variety of animal and plant species, IIKmTA can identify the miRNA binding sites in the probable target UTRs. Moreover, GC% and AU% of miRNAs will be calculated. All the results can be saved as .csv file. Recent researches identified miRNAs in plants and human secretions and their role in regulating the human genes. Such findings indicate the therapeutic role of secretory miRNAs of such plants which exhibits medicinal value and in near future many diseases may be treated by consumption of these plant miRNAs through food. Using our newly developed database and analyzing tool, one can easily determine the different relationships between miRNAs and their targets across kingdoms. IIKmTA is freely available at http://www.bioinformatics.org/iikmta/ .

The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

PubMed Central

Howe, Douglas G.; Bradford, Yvonne M.; Eagle, Anne; Fashena, David; Frazer, Ken; Kalita, Patrick; Mani, Prita; Martin, Ryan; Moxon, Sierra Taylor; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; Toro, Sabrina; Van Slyke, Ceri; Westerfield, Monte

2017-01-01

The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model organisms, zebrafish are superbly suited for rapid generation of sequence-targeted mutant lines, characterization of phenotypes including gene expression patterns, and generation of human disease models. The recent rapid adoption of zebrafish as human disease models is making management of these data particularly important to both the research and clinical communities. Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, ‘Fish’ records in the ZFIN database, support for gene expression phenotypes, models of human disease, mutation details at the DNA, RNA and protein levels, and updates to the ZFIN single box search. PMID:27899582

Central Colorado Assessment Project (CCAP)-Geochemical data for rock, sediment, soil, and concentrate sample media

USGS Publications Warehouse

Granitto, Matthew; DeWitt, Ed H.; Klein, Terry L.

2010-01-01

This database was initiated, designed, and populated to collect and integrate geochemical data from central Colorado in order to facilitate geologic mapping, petrologic studies, mineral resource assessment, definition of geochemical baseline values and statistics, environmental impact assessment, and medical geology. The Microsoft Access database serves as a geochemical data warehouse in support of the Central Colorado Assessment Project (CCAP) and contains data tables describing historical and new quantitative and qualitative geochemical analyses determined by 70 analytical laboratory and field methods for 47,478 rock, sediment, soil, and heavy-mineral concentrate samples. Most samples were collected by U.S. Geological Survey (USGS) personnel and analyzed either in the analytical laboratories of the USGS or by contract with commercial analytical laboratories. These data represent analyses of samples collected as part of various USGS programs and projects. In addition, geochemical data from 7,470 sediment and soil samples collected and analyzed under the Atomic Energy Commission National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) program (henceforth called NURE) have been included in this database. In addition to data from 2,377 samples collected and analyzed under CCAP, this dataset includes archived geochemical data originally entered into the in-house Rock Analysis Storage System (RASS) database (used by the USGS from the mid-1960s through the late 1980s) and the in-house PLUTO database (used by the USGS from the mid-1970s through the mid-1990s). All of these data are maintained in the Oracle-based National Geochemical Database (NGDB). Retrievals from the NGDB and from the NURE database were used to generate most of this dataset. In addition, USGS data that have been excluded previously from the NGDB because the data predate earliest USGS geochemical databases, or were once excluded for programmatic reasons, have been included in the CCAP Geochemical Database and are planned to be added to the NGDB.

Variability in Standard Outcomes of Posterior Lumbar Fusion Determined by National Databases.

PubMed

Joseph, Jacob R; Smith, Brandon W; Park, Paul

2017-01-01

National databases are used with increasing frequency in spine surgery literature to evaluate patient outcomes. The differences between individual databases in relationship to outcomes of lumbar fusion are not known. We evaluated the variability in standard outcomes of posterior lumbar fusion between the University HealthSystem Consortium (UHC) database and the Healthcare Cost and Utilization Project National Inpatient Sample (NIS). NIS and UHC databases were queried for all posterior lumbar fusions (International Classification of Diseases, Ninth Revision code 81.07) performed in 2012. Patient demographics, comorbidities (including obesity), length of stay (LOS), in-hospital mortality, and complications such as urinary tract infection, deep venous thrombosis, pulmonary embolism, myocardial infarction, durotomy, and surgical site infection were collected using specific International Classification of Diseases, Ninth Revision codes. Analysis included 21,470 patients from the NIS database and 14,898 patients from the UHC database. Demographic data were not significantly different between databases. Obesity was more prevalent in UHC (P = 0.001). Mean LOS was 3.8 days in NIS and 4.55 in UHC (P < 0.0001). Complications were significantly higher in UHC, including urinary tract infection, deep venous thrombosis, pulmonary embolism, myocardial infarction, surgical site infection, and durotomy. In-hospital mortality was similar between databases. NIS and UHC databases had similar demographic patient populations undergoing posterior lumbar fusion. However, the UHC database reported significantly higher complication rate and longer LOS. This difference may reflect academic institutions treating higher-risk patients; however, a definitive reason for the variability between databases is unknown. The inability to precisely determine the basis of the variability between databases highlights the limitations of using administrative databases for spinal outcome analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

On pump versus off pump coronary artery bypass grafting in patients with end-stage renal disease and coronary artery disease - A nation-wide, propensity score matched database analyses.

PubMed

Chen, Jien-Jiun; Lin, Lian-Yu; Yang, Yao-Hsu; Hwang, Juey-Jen; Chen, Pau-Chung; Lin, Jiunn-Lee; Chi, Nai-Hsin

2017-01-15

The usage of on or off cardiopulmonary bypass in patients with coronary artery disease receiving coronary artery bypass grafting (CABG) surgery had been debated and had not yet been investigated thoroughly in patients with end-stage renal disease (ESRD). We aimed to study cardiovascular outcomes and total mortality in these patients by using our National Health Insurance (NHI) database. By using our NHI ESRD claim database, we searched ESRD patients aged more than 18years, who received CABG and divided them into on pump and off pump groups. Baseline characteristics and underlying comorbidities were identified from the database. Propensity score (PS) method was used to match all the potential confounders between patients. Outcomes including mortality, myocardial infarction, stroke and repeat revascularization within 30days, 1year and whole follow-up period were also obtained. A total of 134,410 ESRD patients were identified in the database. We included 341 patients and 543 patients who received off pump and on pump CABG respectively. The hazard ratios of different outcomes at 30days, 1year and a median of 745days after CABG did not show significant different between on, or off pump groups before and after PS match. ESRD patients with CAD undergoing either on pump or off pump CABG surgery showed similar outcomes in 30days, 1year and whole follow-up period. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions

PubMed Central

Das, Sankha Subhra; Saha, Pritam

2018-01-01

Abstract MicroRNAs (miRNAs) are well-known as key regulators of diverse biological pathways. A series of experimental evidences have shown that abnormal miRNA expression profiles are responsible for various pathophysiological conditions by modulating genes in disease associated pathways. In spite of the rapid increase in research data confirming such associations, scientists still do not have access to a consolidated database offering these miRNA-pathway association details for critical diseases. We have developed miRwayDB, a database providing comprehensive information of experimentally validated miRNA-pathway associations in various pathophysiological conditions utilizing data collected from published literature. To the best of our knowledge, it is the first database that provides information about experimentally validated miRNA mediated pathway dysregulation as seen specifically in critical human diseases and hence indicative of a cause-and-effect relationship in most cases. The current version of miRwayDB collects an exhaustive list of miRNA-pathway association entries for 76 critical disease conditions by reviewing 663 published articles. Each database entry contains complete information on the name of the pathophysiological condition, associated miRNA(s), experimental sample type(s), regulation pattern (up/down) of miRNA, pathway association(s), targeted member of dysregulated pathway(s) and a brief description. In addition, miRwayDB provides miRNA, gene and pathway score to evaluate the role of a miRNA regulated pathways in various pathophysiological conditions. The database can also be used for other biomedical approaches such as validation of computational analysis, integrated analysis and prediction of computational model. It also offers a submission page to submit novel data from recently published studies. We believe that miRwayDB will be a useful tool for miRNA research community. Database URL: http://www.mirway.iitkgp.ac.in PMID:29688364

MIRO and IRbase: IT Tools for the Epidemiological Monitoring of Insecticide Resistance in Mosquito Disease Vectors

PubMed Central

Dialynas, Emmanuel; Topalis, Pantelis; Vontas, John; Louis, Christos

2009-01-01

Background Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more efficiently when assisted by IT (Information Technology) tools, ranging from modern integrated databases to GIS (Geographic Information System). Here we describe an application ontology that we developed de novo, and a specially designed database that, based on this ontology, can be used for the purpose of controlling mosquitoes and, thus, the diseases that they transmit. Methodology/Principal Findings The ontology, named MIRO for Mosquito Insecticide Resistance Ontology, developed using the OBO-Edit software, describes all pertinent aspects of insecticide resistance, including specific methodology and mode of action. MIRO, then, forms the basis for the design and development of a dedicated database, IRbase, constructed using open source software, which can be used to retrieve data on mosquito populations in a temporally and spatially separate way, as well as to map the output using a Google Earth interface. The dependency of the database on the MIRO allows for a rational and efficient hierarchical search possibility. Conclusions/Significance The fact that the MIRO complies with the rules set forward by the OBO (Open Biomedical Ontologies) Foundry introduces cross-referencing with other biomedical ontologies and, thus, both MIRO and IRbase are suitable as parts of future comprehensive surveillance tools and decision support systems that will be used for the control of vector-borne diseases. MIRO is downloadable from and IRbase is accessible at VectorBase, the NIAID-sponsored open access database for arthropod vectors of disease. PMID:19547750

Impact of CHA2DS2VASc Score on Candidacy for Anticoagulation in Patients With Atrial Fibrillation: A Multi-payer Analysis.

PubMed

Patel, Aarti A; Nelson, Winnie W; Schein, Jeff

2016-10-01

The purpose of this study is to report on the effect of using CHA 2 DS 2 VASc (congestive heart failure, hypertension, age ≥75 years [doubled], type 1 or type 2 diabetes mellitus, stroke or transient ischemic attack or thromboembolism [doubled], vascular disease [prior myocardial infarction, peripheral artery disease, or aortic plaque], age 65-75 years, sex category [female]) rather than CHADS 2 (congestive heart failure, hypertension, age ≥75 years, diabetes mellitus, and prior stroke) to determine candidacy for anticoagulant prophylaxis in insured patients with atrial fibrillation (AF). Six administrative claims databases that included medical and pharmacy claims for patients aged ≥18 years with a new or existing diagnosis of AF and patient outcomes assessed for 1 year after diagnosis were analyzed. Retrospective health plan data analyses were performed using a software tool (Anticoagulant Quality Improvement Analyzer). Study measures included stroke risk (identified by CHADS 2 and CHA 2 DS 2 VASc scores), bleeding risk (identified by the Anticoagulation and Risk Factors in Atrial Fibrillation score), and anticoagulant use. A total of 115,906 patients with AF (range of mean ages among the 6 databases, 56-79 years) met the inclusion criteria. All ranges reported represent the minimum and maximum values among the 6 databases. Using the CHA 2 DS 2 VASc compared with the CHADS 2 index to assess stroke risk resulted in a 23% to 32% increase in patients considered potential candidates for anticoagulant prophylaxis. This translated to a 38% to 114% increase in the number of ostensibly undertreated patients. Among patients with high stroke and low bleeding risk, 18% to 28% more patients were considered potential candidates for anticoagulation treatment using CHA 2 DS 2 VASc compared with CHADS 2 , or a 57% to 151% increase in the number of undertreated patients. Use of the CHA 2 DS 2 VASc score to determine the risk of stroke increased the number of AF patients for whom oral anticoagulation would be recommended. Additional research is needed to determine whether this paradigm shift to greater use of oral anticoagulants improves patient outcomes. Copyright © 2016 Elsevier HS Journals, Inc. All rights reserved.

Mapping the literature of nursing: 1996–2000

PubMed Central

Allen, Margaret (Peg); Jacobs, Susan Kaplan; Levy, June R.

2006-01-01

Introduction: This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. Method: Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. Results: Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals. Discussion: Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. Conclusion: For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered. PMID:16636714

Mapping the literature of nursing: 1996-2000.

PubMed

Allen, Margaret Peg; Jacobs, Susan Kaplan; Levy, June R

2006-04-01

This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals. Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered.

Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis.

PubMed

Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

2004-02-25

Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups.

Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis

PubMed Central

Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

2004-01-01

Background Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. Results To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. Conclusion A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups. PMID:15113403

Can different primary care databases produce comparable estimates of burden of disease: results of a study exploring venous leg ulceration.

PubMed

Petherick, Emily S; Pickett, Kate E; Cullum, Nicky A

2015-08-01

Primary care databases from the UK have been widely used to produce evidence on the epidemiology and health service usage of a wide range of conditions. To date there have been few evaluations of the comparability of estimates between different sources of these data. To estimate the comparability of two widely used primary care databases, the Health Improvement Network Database (THIN) and the General Practice Research Database (GPRD) using venous leg ulceration as an exemplar condition. Cross prospective cohort comparison. GPRD and the THIN databases using data from 1998 to 2006. A data set was extracted from both databases containing all cases of persons aged 20 years or greater with a database diagnosis of venous leg ulceration recorded in the databases for the period 1998-2006. Annual rates of incidence and prevalence of venous leg ulceration were calculated within each database and standardized to the European standard population and compared using standardized rate ratios. Comparable estimates of venous leg ulcer incidence from the GPRD and THIN databases could be obtained using data from 2000 to 2006 and of prevalence using data from 2001 to 2006. Recent data collected by these two databases are more likely to produce comparable results of the burden venous leg ulceration. These results require confirmation in other disease areas to enable researchers to have confidence in the comparability of findings from these two widely used primary care research resources. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Naval Ship Database: Database Design, Implementation, and Schema

DTIC Science & Technology

2013-09-01

incoming data. The solution allows database users to store and analyze data collected by navy ships in the Royal Canadian Navy ( RCN ). The data...understanding RCN jargon and common practices on a typical RCN vessel. This experience led to the development of several error detection methods to...data to be stored in the database. Mr. Massel has also collected data pertaining to day to day activities on RCN vessels that has been imported into

Pressure Injuries in Inpatient Care Facilities in the Czech Republic: Analysis of a National Electronic Database.

PubMed

Pokorná, Andrea; Benešová, Klára; Jarkovský, Jirˇí; Mužík, Jan; Beeckman, Dimitri

The purpose of this study was to analyze pressure injury (PI) occurrence upon admission and at any time during the hospital course inpatients care facilities in the Czech Republic. Secondary aims were to evaluate demographic and clinical data of patients with PI and the impact of a PI on length of stay (LOS) in the hospital. Retrospective, cross-sectional analysis. The sample comprised data of hospitalized patients entered into the National Register of Hospitalized Patients (NRHOSP) database of the Czech Republic between 2007 and 2014 with a diagnosis L89 (pressure ulcer of unspecified site based on the International Classification of Diseases, Tenth Revision, ICD-10). Electronic records of 17,762,854 hospitalizations were reviewed. Data from the NRHOSP from all acute and non-acute care hospitals in the Czech Republic were analyzed. Specifically, we analyzed patients admitted to acute and non-acute care facilities with a primary or secondary diagnosis of PI. The NRHOSP database included 17,762,854 cases, of which 46,224 cases (33,342 cases in acute care hospitals; 12,882 in non-acute care hospitals) had the L89 diagnosis (0.3%). The mean age of patients admitted with a PI was 73.8 ± 15.3 years (mean ± SD), and their average LOS was 33.2 ± 76.9 days. The mean LOS of patients hospitalized with L89 code as a primary diagnosis (n = 6877) was significantly longer compared to those patients for whom L89 code was a secondary diagnosis (25.8 vs 20.2 days, P < .001) in acute care facilities. In contrast, we found no difference in the mean LOS for patients hospitalized in non-acute care facility (58.7 days vs 65.1 days; P = .146) with ICD code L89. Pressure injuries were associated with significant LOS in both acute and non-acute care settings in the Czech Republic. Despite the valuable insights we obtained from the analysis of NRHOSP data, we advocate creation of a more valid and reliable electronic reporting system that enables policy makers to evaluate the quality and safety concerning PI and its impact on patients and the healthcare system.

Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

PubMed

Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

2011-12-01

The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

Infectious Disease Information Collection System at the Scene of Disaster Relief Based on a Personal Digital Assistant.

PubMed

Li, Ya-Pin; Gao, Hong-Wei; Fan, Hao-Jun; Wei, Wei; Xu, Bo; Dong, Wen-Long; Li, Qing-Feng; Song, Wen-Jing; Hou, Shi-Ke

2017-12-01

The objective of this study was to build a database to collect infectious disease information at the scene of a disaster through the use of 128 epidemiological questionnaires and 47 types of options, with rapid acquisition of information regarding infectious disease and rapid questionnaire customization at the scene of disaster relief by use of a personal digital assistant (PDA). SQL Server 2005 (Microsoft Corp, Redmond, WA) was used to create the option database for the infectious disease investigation, to develop a client application for the PDA, and to deploy the application on the server side. The users accessed the server for data collection and questionnaire customization with the PDA. A database with a set of comprehensive options was created and an application system was developed for the Android operating system (Google Inc, Mountain View, CA). On this basis, an infectious disease information collection system was built for use at the scene of disaster relief. The creation of an infectious disease information collection system and rapid questionnaire customization through the use of a PDA was achieved. This system integrated computer technology and mobile communication technology to develop an infectious disease information collection system and to allow for rapid questionnaire customization at the scene of disaster relief. (Disaster Med Public Health Preparedness. 2017;11:668-673).

Psychiatric comorbidities in patients with systemic lupus erythematosus: a systematic review of the last 10 years.

PubMed

Asano, Nadja Maria Jorge; Coriolano, Maria das Graças Wanderley de Sales; Asano, Breno Jorge; Lins, Otávio Gomes

2013-01-01

To analyze the frequency of psychiatric comorbidities in patients with systemic lupus erythematosus (SLE) using the systematic review method. A systematic literature search was performed between April and July 2011 in the following databases: BIREME, PubMed and CAPES thesis database. This search prioritized studies published over the last ten years (2001-2011), involving the presence of psychiatric comorbidities in patients with SLE. Out of 314 articles published in scientific journals (PubMed) and 29 (BIREME), previously identified ones, 13 articles on psychiatric disorders and SLE were selected so they could be submitted to the systematic review methodological approach. The articles indicated high frequency of psychiatric comorbidities, especially mood and anxiety disorders. There is no consensus between the disease activity and psychiatric disorders. Patients with active SLE showed a higher risk of developing mood disorders than patients with inactive SLE. Patients with SLE had a higher suicide risk than the general population. More thorough studies to evaluate the psychological and genetic role, specific and non-specific autoimmune inflammatory mechanisms in mood and anxiety disorders are needed.

Total antioxidant capacity of spices, dried fruits, nuts, pulses, cereals and sweets consumed in Italy assessed by three different in vitro assays.

PubMed

Pellegrini, Nicoletta; Serafini, Mauro; Salvatore, Sara; Del Rio, Daniele; Bianchi, Marta; Brighenti, Furio

2006-11-01

With the aim to expand the Italian total antioxidant capacity (TAC) database, the TAC values of 11 spices, 5 dried fruits, 7 sweets, 18 cereal products, 5 pulses, and 6 nuts were determined using three different assays and considering the contribution of bound antioxidant compounds in fiber-rich foods (i. e. cereals, legumes, and nuts). Among spices, saffron displayed the highest antioxidant capacity, whereas among dried fruits, prune exhibited the highest value. The TAC values of all the chocolates analyzed were far higher than the other sweet extracts measured. Among cereal products, whole meal buckwheat and wheat bran had the greatest TAC. Among pulses and nuts, broad bean, lentil and walnuts had the highest antioxidant capacity, whereas chickpeas, pine nuts and peanuts were less effective. The contribution of bound phytochemicals to the overall TAC was relevant in cereals as well as in nuts and pulses. The complete TAC database could be utilized to properly investigate the role of dietary antioxidants in disease prevention.

A database for coconut crop improvement

PubMed Central

Rajagopal, Velamoor; Manimekalai, Ramaswamy; Devakumar, Krishnamurthy; Rajesh; Karun, Anitha; Niral, Vittal; Gopal, Murali; Aziz, Shamina; Gunasekaran, Marimuthu; Kumar, Mundappurathe Ramesh; Chandrasekar, Arumugam

2005-01-01

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. Availability http://www.bioinfcpcri.org PMID:17597858

[Quality of water for human consumption and its association with morbimortality in Colombia, 2008-2012].

PubMed

Guzmán, Blanca Lisseth; Nava, Gerardo; Díaz, Paula

2015-08-01

The quality of water for human consumption has been correlated with the occurrence of different diseases. Studying the relationship between these parameters would allow determining the impact of water quality on human health, and to direct preventative measures and promote environmental health. To analyze the quality of water intended for human consumption and its association with morbimortality in Colombia, 2008-2012. The database for surveillance of water quality was analyzed by means of descriptive statistics of the principal indicators (total coliforms, Escherichia coli , turbidity, color, pH, free residual chlorine and water quality risk index). The results were correlated with infant mortality and morbidity due to acute diarrheal diseases, foodborne diseases and hepatitis A. A risk map was prepared to identify those municipalities with the highest risk of water contamination and infant mortality. A high percentage of municipalities did not conform to existing standards for water potability values. Problems were identified that were related to presence of E. coli and total coliforms, as well as absence of free residual chlorine, a situation that was exacerbated in rural areas. Water quality showed a high correlation with infant mortality, highlighting its importance for children's health. Water quality was found to have an important impact on infant mortality. Improving water quality in Colombia will require policies that strengthen water supply systems in this country. Strengthening of environmental health surveillance programs is essential to guide actions aimed at improving water quality and exert a positive impact on health.

Spectrum of De Novo Cancers and Predictors in Liver Transplantation: Analysis of the Scientific Registry of Transplant Recipients Database.

PubMed

Zhou, Jie; Hu, Zhenhua; Zhang, Qijun; Li, Zhiwei; Xiang, Jie; Yan, Sheng; Wu, Jian; Zhang, Min; Zheng, Shusen

2016-01-01

De novo malignancies occur after liver transplantation because of immunosuppression and improved long-term survival. But the spectrums and associated risk factors remain unclear. To describe the overall pattern of de novo cancers in liver transplant recipients. Data from Scientific Registry of Transplant Recipients from October 1987 to December 2009 were analyzed. The spectrum of de novo cancer was analyzed and logistic-regression was used to identify predictors of do novo malignancies. Among 89,036 liver transplant recipients, 6,834 recipients developed 9,717 post-transplant malignancies. We focused on non-skin malignancies. A total of 3,845 recipients suffered from 4,854 de novo non-skin malignancies, including 1,098 de novo hematological malignancies, 38 donor-related cases, and 3,718 de novo solid-organ malignancies. Liver transplant recipients had more than 11 times elevated cancer risk compared with the general population. The long-term overall survival was better for recipients without de novo cancer. Multivariate analysis indicated that HCV, alcoholic liver disease, autoimmune liver disease, nonalcoholic steatohepatitis, re-transplantation, combined transplantation, hepatocellular carcinoma, immunosuppression regime of cellcept, cyclosporine, sirolimus, steroids and tacrolimus were independent predictors for the development of solid malignancies after liver transplantation. De novo cancer risk was elevated in liver transplant recipients. Multiple factors including age, gender, underlying liver disease and immunosuppression were associated with the development of de novo cancer. This is useful in guiding recipient selection as well as post-transplant surveillance and prevention.

New database facilitates characterization of flavonoid intake, sources, and positive associations with diet quality among U.S. adults

USDA-ARS?s Scientific Manuscript database

Epidemiologic studies show inverse associations between flavonoid intake and chronic disease risk. However, a lack of comprehensive databases of the flavonoid content of foods has hindered efforts to fully characterize population intake. Using a newly released database of flavonoid values, we soug...

A searchable database for the genome of Phomopsis longicolla (isolate MSPL 10-6).

PubMed

Darwish, Omar; Li, Shuxian; May, Zane; Matthews, Benjamin; Alkharouf, Nadim W

2016-01-01

Phomopsis longicolla (syn. Diaporthe longicolla) is an important seed-borne fungal pathogen that primarily causes Phomopsis seed decay (PSD) in most soybean production areas worldwide. This disease severely decreases soybean seed quality by reducing seed viability and oil quality, altering seed composition, and increasing frequencies of moldy and/or split beans. To facilitate investigation of the genetic base of fungal virulence factors and understand the mechanism of disease development, we designed and developed a database for P. longicolla isolate MSPL 10-6 that contains information about the genome assemblies (contigs), gene models, gene descriptions and GO functional ontologies. A web-based front end to the database was built using ASP.NET, which allows researchers to search and mine the genome of this important fungus. This database represents the first reported genome database for a seed borne fungal pathogen in the Diaporthe- Phomopsis complex. The database will also be a valuable resource for research and agricultural communities. It will aid in the development of new control strategies for this pathogen. http://bioinformatics.towson.edu/Phomopsis_longicolla/HomePage.aspx.

A searchable database for the genome of Phomopsis longicolla (isolate MSPL 10-6)

PubMed Central

May, Zane; Matthews, Benjamin; Alkharouf, Nadim W.

2016-01-01

Phomopsis longicolla (syn. Diaporthe longicolla) is an important seed-borne fungal pathogen that primarily causes Phomopsis seed decay (PSD) in most soybean production areas worldwide. This disease severely decreases soybean seed quality by reducing seed viability and oil quality, altering seed composition, and increasing frequencies of moldy and/or split beans. To facilitate investigation of the genetic base of fungal virulence factors and understand the mechanism of disease development, we designed and developed a database for P. longicolla isolate MSPL 10-6 that contains information about the genome assemblies (contigs), gene models, gene descriptions and GO functional ontologies. A web-based front end to the database was built using ASP.NET, which allows researchers to search and mine the genome of this important fungus. This database represents the first reported genome database for a seed borne fungal pathogen in the Diaporthe– Phomopsis complex. The database will also be a valuable resource for research and agricultural communities. It will aid in the development of new control strategies for this pathogen. Availability: http://bioinformatics.towson.edu/Phomopsis_longicolla/HomePage.aspx PMID:28197060

The Identification of People with Disabilities in National Databases: A Failure to Communicate. Technical Report 6.

ERIC Educational Resources Information Center

McGrew, Kevin; And Others

This research analyzes similarities and differences in how students with disabilities are identified in national databases, through examination of 19 national data collection programs in the U.S. Departments of Education, Commerce, Justice, and Health and Human Services, as well as databases from the National Science Foundation. The study found…

Teaching Database Modeling and Design: Areas of Confusion and Helpful Hints

ERIC Educational Resources Information Center

Philip, George C.

2007-01-01

This paper identifies several areas of database modeling and design that have been problematic for students and even are likely to confuse faculty. Major contributing factors are the lack of clarity and inaccuracies that persist in the presentation of some basic database concepts in textbooks. The paper analyzes the problems and discusses ways to…

[Nutritional impact of inflammatory bowel diseases on children and adolescents].

PubMed

dos Santos, Gilton Marques; Silva, Luciana Rodrigues; Santana, Genoile Oliveira

2014-12-01

To perform a systematic review of the literature about the nutritional impact of inflammatory bowel diseases in children and adolescents. A systematic review was performed using PubMed/MEDLINE, LILACS and SciELo databases, with inclusion of articles in Portuguese and in English with original data, that analyzed nutritional aspects of inflammatory bowel diseases in children and adolescents. The initial search used the terms "inflammatory bowel diseases" and "children" or "adolescents" and "nutritional evaluation" or "nutrition deficiency". The selection of studies was initially performed by reading the titles and abstracts. Review studies and those without data for pediatric patients were excluded. Subsequently, the full reading of the articles considered relevant was performed. 237 studies were identified, and 12 of them were selected according to the inclusion criteria. None of them was performed in South America. During the analysis of the studies, it was observed that nutritional characteristics of patients with inflammatory bowel disease may be altered; the main reports were related to malnutrition, growth stunting, delayed puberty and vitamin D deficiency. There are nutritional consequences of inflammatory bowel diseases in children and adolescents, mainly growth stunting, slower pubertal development, underweight and vitamin deficiencies. Nutritional impairments were more significant in patients with Crohn's disease; overweight and obesity were more common in patients with ulcerative rectocolitis. A detailed nutritional assessment should be performed periodically in children and adolescents with inflammatory bowel disease. Copyright © 2014 Associação de Pediatria de São Paulo. Publicado por Elsevier Editora Ltda. All rights reserved.

NIH disease funding levels and burden of disease.

PubMed

Gillum, Leslie A; Gouveia, Christopher; Dorsey, E Ray; Pletcher, Mark; Mathers, Colin D; McCulloch, Charles E; Johnston, S Claiborne

2011-02-24

An analysis of NIH funding in 1996 found that the strongest predictor of funding, disability-adjusted life-years (DALYs), explained only 39% of the variance in funding. In 1998, Congress requested that the Institute of Medicine (IOM) evaluate priority-setting criteria for NIH funding; the IOM recommended greater consideration of disease burden. We examined whether the association between current burden and funding has changed since that time. We analyzed public data on 2006 NIH funding for 29 common conditions. Measures of US disease burden in 2004 were obtained from the World Health Organization's Global Burden of Disease study and national databases. We assessed the relationship between disease burden and NIH funding dollars in univariate and multivariable log-linear models that evaluated all measures of disease burden. Sensitivity analyses examined associations with future US burden, current and future measures of world disease burden, and a newly standardized NIH accounting method. In univariate and multivariable analyses, disease-specific NIH funding levels increased with burden of disease measured in DALYs (p = 0.001), which accounted for 33% of funding level variation. No other factor predicted funding in multivariable models. Conditions receiving the most funding greater than expected based on disease burden were AIDS ($2474 M), diabetes mellitus ($390 M), and perinatal conditions ($297 M). Depression ($719 M), injuries ($691 M), and chronic obstructive pulmonary disease ($613 M) were the most underfunded. Results were similar using estimates of future US burden, current and future world disease burden, and alternate NIH accounting methods. Current levels of NIH disease-specific research funding correlate modestly with US disease burden, and correlation has not improved in the last decade.

Development of a database of health insurance claims: standardization of disease classifications and anonymous record linkage.

PubMed

Kimura, Shinya; Sato, Toshihiko; Ikeda, Shunya; Noda, Mitsuhiko; Nakayama, Takeo

2010-01-01

Health insurance claims (ie, receipts) record patient health care treatments and expenses and, although created for the health care payment system, are potentially useful for research. Combining different types of receipts generated for the same patient would dramatically increase the utility of these receipts. However, technical problems, including standardization of disease names and classifications, and anonymous linkage of individual receipts, must be addressed. In collaboration with health insurance societies, all information from receipts (inpatient, outpatient, and pharmacy) was collected. To standardize disease names and classifications, we developed a computer-aided post-entry standardization method using a disease name dictionary based on International Classification of Diseases (ICD)-10 classifications. We also developed an anonymous linkage system by using an encryption code generated from a combination of hash values and stream ciphers. Using different sets of the original data (data set 1: insurance certificate number, name, and sex; data set 2: insurance certificate number, date of birth, and relationship status), we compared the percentage of successful record matches obtained by using data set 1 to generate key codes with the percentage obtained when both data sets were used. The dictionary's automatic conversion of disease names successfully standardized 98.1% of approximately 2 million new receipts entered into the database. The percentage of anonymous matches was higher for the combined data sets (98.0%) than for data set 1 (88.5%). The use of standardized disease classifications and anonymous record linkage substantially contributed to the construction of a large, chronologically organized database of receipts. This database is expected to aid in epidemiologic and health services research using receipt information.

HoPaCI-DB: host-Pseudomonas and Coxiella interaction database

PubMed Central

Bleves, Sophie; Dunger, Irmtraud; Walter, Mathias C.; Frangoulidis, Dimitrios; Kastenmüller, Gabi; Voulhoux, Romé; Ruepp, Andreas

2014-01-01

Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The host-Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database (http://mips.helmholtz-muenchen.de/HoPaCI/) of host–pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii. The resource provides structured information on 3585 experimentally validated interactions between molecules, bioprocesses and cellular structures extracted from the scientific literature. Systematic annotation and interactive graphical representation of disease networks make HoPaCI-DB a versatile knowledge base for biologists and network biology approaches. PMID:24137008

Impact of Antiinflammatory Treatment on the Onset of Uveitis in Juvenile Idiopathic Arthritis: Longitudinal Analysis From a Nationwide Pediatric Rheumatology Database.

PubMed

Tappeiner, Christoph; Schenck, Sandra; Niewerth, Martina; Heiligenhaus, Arnd; Minden, Kirsten; Klotsche, Jens

2016-01-01

Based on a nationwide database, this study analyzed the influence of methotrexate (MTX), tumor necrosis factor (TNF) inhibitors, and a combination of the 2 medications on uveitis occurrence in juvenile idiopathic arthritis (JIA) patients. Data from the National Paediatric Rheumatological Database in Germany were used in this study. Between 2002 and 2013, data from JIA patients were annually documented at the participating pediatric rheumatologic sites. Patients with a JIA disease duration of <12 months at initial documentation and ≥2 years of followup were included in this study. The impact of antiinflammatory treatment on the occurrence of uveitis was evaluated by discrete-time survival analysis. A total of 3,512 JIA patients (mean ± SD age 8.3 ± 4.8 years, 65.7% female, 53.2% antinuclear antibody positive, and mean ± SD age at arthritis onset 7.8 ± 4.8 years) fulfilled the inclusion criteria. Mean ± SD total followup time was 3.6 ± 2.4 years. Uveitis developed in a total of 180 patients (5.1%) within 1 year after arthritis onset. Uveitis onset after the first year was observed in another 251 patients (7.1%). Disease-modifying antirheumatic drug (DMARD) treatment in the year before uveitis onset significantly reduced the risk for uveitis as follows: MTX: hazard ratio (HR) 0.63, P = 0.022; TNF inhibitors: HR 0.56, P < 0.001; and a combination of the 2 medications: HR 0.10, P < 0.001. Patients treated with MTX within the first year of JIA had an even a lower uveitis risk (HR 0.29, P < 0.001). The use of DMARDs in JIA patients significantly reduced the risk for uveitis onset. Early MTX use within the first year of disease and the combination of MTX with a TNF inhibitor had the highest protective effect. © 2016 The Authors. Arthritis Care & Research published by Wiley Periodicals, Inc. on behalf of the American College of Rheumatology.

Effect of restricted protein diet supplemented with keto analogues in chronic kidney disease: a systematic review and meta-analysis.

PubMed

Jiang, Zheng; Zhang, Xiaoyan; Yang, Lichuan; Li, Zi; Qin, Wei

2016-03-01

To evaluate the efficacy and safety of the restricted protein diet (low or very low protein diet) supplemented with keto analogues in the treatment of chronic kidney disease (CKD). The Cochrane library, PubMed, Embase, CBM and CENTRAL databases were searched and reviewed up to April 2015. Clinical trials were analyzed using RevMan 5.3 software. Seven random control trials, one cross-over trial and one non-randomized concurrent control trial were selected and included in this study according to our inclusion and exclusion criteria. The changes of eGFR, BUN, Scr, albumin, PTH, triglyceride, cholesterol, calcium, phosphorus and nutrition indexes (BMI, lean body mass and mid-arm muscular circumference) before and after treatment were analyzed. The meta-analysis results indicated that, comparing with normal protein diet, low protein diet (LPD) or very low protein diet (vLPD) supplemented with keto analogues (s(v)LPD) could significantly prevent the deterioration of eGFR (P < 0.001), hyperparathyroidism (P = 0.04), hypertension (P < 0.01) and hyperphosphatemia (P < 0.001). No differences in BUN, Scr, Albumin, triglyceride, cholesterol, hemoglobin, calcium and nutrition indexes were observed between different protein intake groups. Restricted protein diet supplemented with keto analogues (s(v)LPD) could delay the progression of CKD effectively without causing malnutrition.

Essential medicines availability is still suboptimal in many countries: a scoping review.

PubMed

Mahmić-Kaknjo, Mersiha; Jeličić-Kadić, Antonia; Utrobičić, Ana; Chan, Kit; Bero, Lisa; Marušić, Ana

2018-06-01

To identify uses of WHO Model list of essential medicines (EMs) and summarize studies examining EM and national EM lists (NEMLs). In this scoping review, we searched PubMed, Scopus, WHO website and WHO Regional Databases for studies on NEMLs, reimbursement medicines lists, and WHO EML, with no date or language restrictions. Three thousand one hundred forty-four retrieved documents were independently screened by two reviewers; 100 full-text documents were analyzed; 37 contained data suitable for quantitative and qualitative analysis on EMs availability (11 documents), medicines for specific diseases (13 documents), and comparison of WHO EML and NEMLs (13 documents). From the latter, two documents analyzed the relevance of evidence from Cochrane systematic reviews for medicines that were on NEMLs but not on the WHO EML. EMs availability is still suboptimal in low-income countries. Availability of children formulations and EMs for specific diseases such as chronic, cancer, pain, and reproductive health is suboptimal even in middle-income countries. WHO EML can be used as a basic set of medicines for different settings. More evidence is needed into how NEMLs can contribute to better availability of children formulations, pain, and cancer medicines in developing countries. Copyright © 2018 Elsevier Inc. All rights reserved.

Factors Affecting the Length of Stay in the Intensive Care Unit: Our Clinical Experience

PubMed Central

Sengul Samanci, Nilay; Akkoc, İbrahim; Yucetas, Esma; Cebeci, Egemen; Ozturk, Savas

2018-01-01

Background and Aim Long hospital days in intensive care unit (ICU) due to life-threatening diseases are increasing in the world. The primary goal in ICU is to decrease length of stay in order to improve the quality of medical care and reduce cost. The aim of our study is to identify and categorize the factors associated with prolonged stays in ICU. Materials and Method We retrospectively analyzed 3925 patients. We obtained the patients' demographic, clinical, diagnostic, and physiologic variables; mortality; lengths of stay by examining the intensive care unit database records. Results The mean age of the study was 61.6 ± 18.9 years. The average length of stay in intensive care unit was 10.2 ± 25.2 days. The most common cause of hospitalization was because of multiple diseases (19.5%). The length of stay was positively correlated with urea, creatinine, and sodium. It was negatively correlated with uric acid and hematocrit levels. Length of stay was significantly higher in patients not operated on than in patients operated on (p < 0.001). Conclusion Our study showed a significantly increased length of stay in patients with cardiovascular system diseases, multiple diseases, nervous system diseases, and cerebrovascular diseases. Moreover we showed that when urea, creatinine, and sodium values increase, in parallel the length of stay increases. PMID:29750174

Innovative measures to combat rare diseases in China: The national rare diseases registry system, larger-scale clinical cohort studies, and studies in combination with precision medicine research.

PubMed

Song, Peipei; He, Jiangjiang; Li, Fen; Jin, Chunlin

2017-02-01

China is facing the great challenge of treating the world's largest rare disease population, an estimated 16 million patients with rare diseases. One effort offering promise has been a pilot national project that was launched in 2013 and that focused on 20 representative rare diseases. Another government-supported special research program on rare diseases - the "Rare Diseases Clinical Cohort Study" - was launched in December 2016. According to the plan for this research project, the unified National Rare Diseases Registry System of China will be established as of 2020, and a large-scale cohort study will be conducted from 2016 to 2020. The project plans to develop 109 technical standards, to establish and improve 2 national databases of rare diseases - a multi-center clinical database and a biological sample library, and to conduct studies on more than 50,000 registered cases of 50 different rare diseases. More importantly, this study will be combined with the concept of precision medicine. Chinese population-specific basic information on rare diseases, clinical information, and genomic information will be integrated to create a comprehensive predictive model with a follow-up database system and a model to evaluate prognosis. This will provide the evidence for accurate classification, diagnosis, treatment, and estimation of prognosis for rare diseases in China. Numerous challenges including data standardization, protecting patient privacy, big data processing, and interpretation of genetic information still need to be overcome, but research prospects offer great promise.

An online database for IHN virus in Pacific Salmonid fish: MEAP-IHNV

USGS Publications Warehouse

Kurath, Gael

2012-01-01

The MEAP-IHNV database provides access to detailed data for anyone interested in IHNV molecular epidemiology, such as fish health professionals, fish culture facility managers, and academic researchers. The flexible search capabilities enable the user to generate various output formats, including tables and maps, which should assist users in developing and testing hypotheses about how IHNV moves across landscapes and changes over time. The MEAP-IHNV database is available online at http://gis.nacse.org/ihnv/ (fig. 1). The database contains records that provide background information and genetic sequencing data for more than 1,000 individual field isolates of the fish virus Infectious hematopoietic necrosis virus (IHNV), and is updated approximately annually. It focuses on IHNV isolates collected throughout western North America from 1966 to the present. The database also includes a small number of IHNV isolates from Eastern Russia. By engaging the expertise of the broader community of colleagues interested in IHNV, our goal is to enhance the overall understanding of IHNV epidemiology, including defining sources of disease outbreaks and viral emergence events, identifying virus traffic patterns and potential reservoirs, and understanding how human management of salmonid fish culture affects disease. Ultimately, this knowledge can be used to develop new strategies to reduce the effect of IHN disease in cultured and wild fish.

Semi-Automated Annotation of Biobank Data Using Standard Medical Terminologies in a Graph Database.

PubMed

Hofer, Philipp; Neururer, Sabrina; Goebel, Georg

2016-01-01

Data describing biobank resources frequently contains unstructured free-text information or insufficient coding standards. (Bio-) medical ontologies like Orphanet Rare Diseases Ontology (ORDO) or the Human Disease Ontology (DOID) provide a high number of concepts, synonyms and entity relationship properties. Such standard terminologies increase quality and granularity of input data by adding comprehensive semantic background knowledge from validated entity relationships. Moreover, cross-references between terminology concepts facilitate data integration across databases using different coding standards. In order to encourage the use of standard terminologies, our aim is to identify and link relevant concepts with free-text diagnosis inputs within a biobank registry. Relevant concepts are selected automatically by lexical matching and SPARQL queries against a RDF triplestore. To ensure correctness of annotations, proposed concepts have to be confirmed by medical data administration experts before they are entered into the registry database. Relevant (bio-) medical terminologies describing diseases and phenotypes were identified and stored in a graph database which was tied to a local biobank registry. Concept recommendations during data input trigger a structured description of medical data and facilitate data linkage between heterogeneous systems.

Diet History Questionnaire: Development of the DHQ Nutrient Database

Cancer.gov

The nutrient and food group database, created for analyzing the DHQ, is based on national dietary intake data from the 1994-96 US Department of Agriculture's Continuing Survey of Food Intake by Individuals (CSFII).

How Artificial Intelligence Can Improve Our Understanding of the Genes Associated with Endometriosis: Natural Language Processing of the PubMed Database

PubMed Central

Mashiach, R.; Cohen, S.; Kedem, A.; Baron, A.; Zajicek, M.; Feldman, I.; Seidman, D.; Soriano, D.

2018-01-01

Endometriosis is a disease characterized by the development of endometrial tissue outside the uterus, but its cause remains largely unknown. Numerous genes have been studied and proposed to help explain its pathogenesis. However, the large number of these candidate genes has made functional validation through experimental methodologies nearly impossible. Computational methods could provide a useful alternative for prioritizing those most likely to be susceptibility genes. Using artificial intelligence applied to text mining, this study analyzed the genes involved in the pathogenesis, development, and progression of endometriosis. The data extraction by text mining of the endometriosis-related genes in the PubMed database was based on natural language processing, and the data were filtered to remove false positives. Using data from the text mining and gene network information as input for the web-based tool, 15,207 endometriosis-related genes were ranked according to their score in the database. Characterization of the filtered gene set through gene ontology, pathway, and network analysis provided information about the numerous mechanisms hypothesized to be responsible for the establishment of ectopic endometrial tissue, as well as the migration, implantation, survival, and proliferation of ectopic endometrial cells. Finally, the human genome was scanned through various databases using filtered genes as a seed to determine novel genes that might also be involved in the pathogenesis of endometriosis but which have not yet been characterized. These genes could be promising candidates to serve as useful diagnostic biomarkers and therapeutic targets in the management of endometriosis. PMID:29750165

How Artificial Intelligence Can Improve Our Understanding of the Genes Associated with Endometriosis: Natural Language Processing of the PubMed Database.

PubMed

Bouaziz, J; Mashiach, R; Cohen, S; Kedem, A; Baron, A; Zajicek, M; Feldman, I; Seidman, D; Soriano, D

2018-01-01

Endometriosis is a disease characterized by the development of endometrial tissue outside the uterus, but its cause remains largely unknown. Numerous genes have been studied and proposed to help explain its pathogenesis. However, the large number of these candidate genes has made functional validation through experimental methodologies nearly impossible. Computational methods could provide a useful alternative for prioritizing those most likely to be susceptibility genes. Using artificial intelligence applied to text mining, this study analyzed the genes involved in the pathogenesis, development, and progression of endometriosis. The data extraction by text mining of the endometriosis-related genes in the PubMed database was based on natural language processing, and the data were filtered to remove false positives. Using data from the text mining and gene network information as input for the web-based tool, 15,207 endometriosis-related genes were ranked according to their score in the database. Characterization of the filtered gene set through gene ontology, pathway, and network analysis provided information about the numerous mechanisms hypothesized to be responsible for the establishment of ectopic endometrial tissue, as well as the migration, implantation, survival, and proliferation of ectopic endometrial cells. Finally, the human genome was scanned through various databases using filtered genes as a seed to determine novel genes that might also be involved in the pathogenesis of endometriosis but which have not yet been characterized. These genes could be promising candidates to serve as useful diagnostic biomarkers and therapeutic targets in the management of endometriosis.

Care plan program reduces the number of visits for challenging psychiatric patients in the ED.

PubMed

Abello, Arthur; Brieger, Ben; Dear, Kim; King, Ben; Ziebell, Chris; Ahmed, Atheer; Milling, Truman J

2012-09-01

A small number of patients representing a significant demand on emergency department (ED) services present regularly for a variety of reasons, including psychiatric or behavioral complaints and lack of access to other services. A care plan program was created as a database of ED high users and patients of concern, as identified by ED staff and approved by program administrators to improve care and mitigate ED strain. A list of medical record numbers was assembled by searching the care plan program database for adult patients initially enrolled between the dates of November 1, 2006, and October 21, 2007. Inclusion criteria were the occurrence of a psychiatric International Classification Diseases, Ninth Revision, code in their medical record and a care plan level implying a serious psychiatric disorder causing harmful behavior. Additional data about these patients were acquired using an indigent care tracking database and electronic medical records. Variables collected from these sources were analyzed for changes before and after program enrollment. Of 501 patients in the database in the period studied, 48 patients fulfilled the criteria for the cohort. There was a significant reduction in the number of visits to the ED from the year before program enrollment to the year after enrollment (8.9, before; 5.9, after; P < .05). There was also an increase in psychiatric hospital visits (2%, before; 25%, after; P < .05). An alert program that identifies challenging ED patients with psychiatric conditions and creates a care plan appears to reduce visits and lead to more appropriate use of other resources. Copyright © 2012 Elsevier Inc. All rights reserved.

Big Data Research in Neurosurgery: A Critical Look at this Popular New Study Design.

PubMed

Oravec, Chesney S; Motiwala, Mustafa; Reed, Kevin; Kondziolka, Douglas; Barker, Fred G; Michael, L Madison; Klimo, Paul

2018-05-01

The use of "big data" in neurosurgical research has become increasingly popular. However, using this type of data comes with limitations. This study aimed to shed light on this new approach to clinical research. We compiled a list of commonly used databases that were not specifically created to study neurosurgical procedures, conditions, or diseases. Three North American journals were manually searched for articles published since 2000 utilizing these and other non-neurosurgery-specific databases. A number of data points per article were collected, tallied, and analyzed.A total of 324 articles were identified since 2000 with an exponential increase since 2011 (257/324, 79%). The Journal of Neurosurgery Publishing Group published the greatest total number (n = 200). The National Inpatient Sample was the most commonly used database (n = 136). The average study size was 114 841 subjects (range, 30-4 146 777). The most prevalent topics were vascular (n = 77) and neuro-oncology (n = 66). When categorizing study objective (recognizing that many papers reported more than 1 type of study objective), "Outcomes" was the most common (n = 154). The top 10 institutions by primary or senior author accounted for 45%-50% of all publications. Harvard Medical School was the top institution, using this research technique with 59 representations (31 by primary author and 28 by senior).The increasing use of data from non-neurosurgery-specific databases presents a unique challenge to the interpretation and application of the study conclusions. The limitations of these studies must be more strongly considered in designing and interpreting these studies.

NCCDPHP PUBLICATION DATABASE

EPA Science Inventory

This database provides bibliographic citations and abstracts of publications produced by the CDC's National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) including journal articles, monographs, book chapters, reports, policy documents, and fact sheets. Full...

Pathological Outcome following Radical Prostatectomy in Men with Prostate Specific Antigen Greater than 10 ng/ml and Histologically Favorable Risk Prostate Cancer.

PubMed

Yu, Jiwoong; Kwon, Young Suk; Kim, Sinae; Han, Christopher Sejong; Farber, Nicholas; Kim, Jongmyung; Byun, Seok Soo; Kim, Wun-Jae; Jeon, Seong Soo; Kim, Isaac Yi

2016-05-01

Active surveillance is now the treatment of choice in men with low risk prostate cancer. Although there is no consensus on which patients are eligible for active surveillance, prostate specific antigen above 10 ng/ml is generally excluded. In an attempt to determine the validity of using a prostate specific antigen cutoff of 10 ng/ml to counsel men considering active surveillance we analyzed a multi-institution database to determine the pathological outcome in men with prostate specific antigen greater than 10 ng/ml but histologically favorable risk prostate cancer. We queried a prospectively maintained database of men with histologically favorable risk prostate cancer who underwent radical prostatectomy between 2003 and 2015. The cohort was categorized into 3 groups based on prostate specific antigen level, including low-less than 10 ng/ml, intermediate-10 or greater to less than 20 and high-20 or greater. Associations of prostate specific antigen group with adverse pathological and oncologic outcomes were analyzed. Of 2,125 patients 1,327 were categorized with histologically favorable risk disease. However on multivariate analyses the rates of up staging and upgrading were similar between the intermediate and low prostate specific antigen groups. In contrast compared to the intermediate prostate specific antigen group the high group had higher incidences of up staging (p = 0.02) and upgrading to 4 + 3 or greater disease (p = 0.046). Biochemical recurrence-free survival rates revealed no pairwise intergroup differences except between the low and high groups. Patients with preoperatively elevated prostate specific antigen between 10 and less than 20 ng/ml who otherwise had histologically favorable risk prostate cancer were not at higher risk for adverse pathological outcomes than men with prostate specific antigen less than 10 ng/ml. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Reconstruction of a Functional Human Gene Network, with an Application for Prioritizing Positional Candidate Genes

PubMed Central

Franke, Lude; Bakel, Harm van; Fokkens, Like; de Jong, Edwin D.; Egmont-Petersen, Michael; Wijmenga, Cisca

2006-01-01

Most common genetic disorders have a complex inheritance and may result from variants in many genes, each contributing only weak effects to the disease. Pinpointing these disease genes within the myriad of susceptibility loci identified in linkage studies is difficult because these loci may contain hundreds of genes. However, in any disorder, most of the disease genes will be involved in only a few different molecular pathways. If we know something about the relationships between the genes, we can assess whether some genes (which may reside in different loci) functionally interact with each other, indicating a joint basis for the disease etiology. There are various repositories of information on pathway relationships. To consolidate this information, we developed a functional human gene network that integrates information on genes and the functional relationships between genes, based on data from the Kyoto Encyclopedia of Genes and Genomes, the Biomolecular Interaction Network Database, Reactome, the Human Protein Reference Database, the Gene Ontology database, predicted protein-protein interactions, human yeast two-hybrid interactions, and microarray coexpressions. We applied this network to interrelate positional candidate genes from different disease loci and then tested 96 heritable disorders for which the Online Mendelian Inheritance in Man database reported at least three disease genes. Artificial susceptibility loci, each containing 100 genes, were constructed around each disease gene, and we used the network to rank these genes on the basis of their functional interactions. By following up the top five genes per artificial locus, we were able to detect at least one known disease gene in 54% of the loci studied, representing a 2.8-fold increase over random selection. This suggests that our method can significantly reduce the cost and effort of pinpointing true disease genes in analyses of disorders for which numerous loci have been reported but for which most of the genes are unknown. PMID:16685651

Microarray analysis reveals key genes and pathways in Tetralogy of Fallot

PubMed Central

He, Yue-E; Qiu, Hui-Xian; Jiang, Jian-Bing; Wu, Rong-Zhou; Xiang, Ru-Lian; Zhang, Yuan-Hai

2017-01-01

The aim of the present study was to identify key genes that may be involved in the pathogenesis of Tetralogy of Fallot (TOF) using bioinformatics methods. The GSE26125 microarray dataset, which includes cardiovascular tissue samples derived from 16 children with TOF and five healthy age-matched control infants, was downloaded from the Gene Expression Omnibus database. Differential expression analysis was performed between TOF and control samples to identify differentially expressed genes (DEGs) using Student's t-test, and the R/limma package, with a log2 fold-change of >2 and a false discovery rate of <0.01 set as thresholds. The biological functions of DEGs were analyzed using the ToppGene database. The ReactomeFIViz application was used to construct functional interaction (FI) networks, and the genes in each module were subjected to pathway enrichment analysis. The iRegulon plugin was used to identify transcription factors predicted to regulate the DEGs in the FI network, and the gene-transcription factor pairs were then visualized using Cytoscape software. A total of 878 DEGs were identified, including 848 upregulated genes and 30 downregulated genes. The gene FI network contained seven function modules, which were all comprised of upregulated genes. Genes enriched in Module 1 were enriched in the following three neurological disorder-associated signaling pathways: Parkinson's disease, Alzheimer's disease and Huntington's disease. Genes in Modules 0, 3 and 5 were dominantly enriched in pathways associated with ribosomes and protein translation. The Xbox binding protein 1 transcription factor was demonstrated to be involved in the regulation of genes encoding the subunits of cytoplasmic and mitochondrial ribosomes, as well as genes involved in neurodegenerative disorders. Therefore, dysfunction of genes involved in signaling pathways associated with neurodegenerative disorders, ribosome function and protein translation may contribute to the pathogenesis of TOF. PMID:28713939

Laryngeal adenoid cystic carcinoma: A population-based perspective.

PubMed

Dubal, Pariket M; Svider, Peter F; Folbe, Adam J; Lin, Ho-Sheng; Park, Richard C; Baredes, Soly; Eloy, Jean Anderson

2015-11-01

Adenoid cystic carcinoma (ACC) occurs infrequently in the larynx. Consequently, no large samples describing its clinical behavior are available in the literature. Our objective was to use a nationally representative population-based resource to evaluate clinical behavior, patient demographics, and outcomes among patients diagnosed with laryngeal ACC (LACC). Retrospective database analysis. The National Cancer Institute's Surveillance, Epidemiology, and End Results database was analyzed for patients diagnosed with LACC between 1973 and 2011. Patient demographics, incidence, treatment, and survival between LACC and other laryngeal malignancies were compared. Of 69 LACC patients, 63.8% were female, 78.2% Caucasian, and the median age was 54 years. LACC patients were much more likely to have subglottic lesions (44.9%) than individuals with other malignancies (1.6%). The incidence of LACC was 0.005/100,000 individuals. The majority of patients with LACC harbored T4 lesions at initial diagnosis, although 87.9% had N0 disease, and only 6.1% had distant metastasis at diagnosis. Disease-specific survival (DSS) was greater at 1 year for LACC compared to other laryngeal malignancies, but not at 5 or 10 years. Five-year DSS was greater for LACC patients who underwent surgery versus those who did not undergo surgery. This analysis notes that LACC has a low incidence with no significant change in incidence over the study period. Compared to other laryngeal malignancies, LACC has a female preponderance, is much more common in the subglottis, presents at a younger age, and more often presents with T4 disease. Surgery was noted to confer a survival advantage in LACC. 4. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

Single-site Versus Multiport Robotic Hysterectomy in Benign Gynecologic Diseases: A Retrospective Evaluation of Surgical Outcomes and Cost Analysis.

PubMed

Bogliolo, Stefano; Ferrero, Simone; Cassani, Chiara; Musacchi, Valentina; Zanellini, Francesca; Dominoni, Mattia; Spinillo, Arsenio; Gardella, Barbara

2016-01-01

To compare the surgical outcomes and costs of robotic-assisted hysterectomy with the single-site (RSSH) or multiport approach (RH). A retrospective analysis of a prospectively collected database (Canadian Task Force classification II1). A university hospital. Consecutive women who underwent robotic-assisted total laparoscopic hysterectomy and bilateral salpingo-oophorectomy for the treatment of benign gynecologic diseases. Data on surgical approach, surgical outcomes, and costs were collected in a prospective database and retrospectively analyzed. The total operative time, console time, docking time, estimated blood loss, conversion rate, and surgical complications rate were compared between the 2 study groups. Cost analysis was performed. One hundred four patients underwent total robotic-assisted hysterectomy and bilateral salpingo-oophorectomy (45 RSSH and 59 RH). There was no significant difference in the indications for surgery and in the characteristics of the patients between the 2 study groups. There was no significant difference between the single-site and multiport approach in console time, surgical complication rate, conversion rate, and postoperative pain. The docking time was lower in the RH group (p = .0001). The estimated blood loss and length of hospitalization were lower in the RSSH group (p = .0008 and p = .009, respectively). The cost analysis showed significant differences in favor of RSSH. RSSH should be preferred to RH when hysterectomy is performed for benign disease because it could be at least as equally effective and safe with a potential cost reduction. However, because of the high cost and absence of clear advantages, the robotic approach should be considered only for selected patients. Copyright © 2016 AAGL. Published by Elsevier Inc. All rights reserved.

Clinical trials involving positron emission tomography and prostate cancer: an analysis of the ClinicalTrials.gov database.

PubMed

Cihoric, Nikola; Vlaskou Badra, Eugenia; Tsikkinis, Alexandros; Prasad, Vikas; Kroeze, Stephanie; Igrutinovic, Ivan; Jeremic, Branislav; Beck, Marcus; Zschaeck, Sebastian; Wust, Peter; Ghadjar, Pirus

2018-06-18

The goal of this study is to evaluate the status and future perspectives of clinical trials on positron emission tomography in prostate cancer for diagnostic or therapeutic as well as for surveillance purposes. The www.ClinicalTrials.gov database was searched on the 20th of January 2017 for all trials containing terms describing "prostate cancer" (prostate, prostatic, malignant, malignancy, cancer, tumor) and "positron emission tomography". In total 167 trials were identified. Trials that included diseases other than PCa were excluded (n = 27; 16%). Furthermore, we excluded trials (n = 4, 2%) withdrawn prior to first patient enrollment. The remaining trials (n = 137, 82%) were selected for further manual classification analysis. One hundred thirty-seven trials were detected and analyzed. Majority of trials were in "active" recruitment status (n = 46, 34%) followed by trials that had been "completed" - (n = 34, 25%) and trials with "closed recruitment but active follow-up" (n = 23, 17%). Phase 1 and 2 comprised 46% of the complete trial portfolio. Locally confined disease was of major interest (n = 46, 34%), followed by metastatic disease - not otherwise specified (n = 43, 13%). Evaluation of PET was the primary goal of the trial in 114 (83%) cases. Most of the trials evaluated only one agent (n = 122, 89%). Choline and PSMA represented two major groups (total 50%) and they were equally distributed across trial portfolio with 25% (n = 34) each. PSMA trials showed the highest average annual growth rate of 56%. The trials were conducted in 17 countries. The scientific community is showing a strong and ever-growing interest in the field and we expect that in the coming years, more phase III trials will be initiated ultimately delivering the required Level 1 evidence.