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41. Database of Optimized Proteomic Quantitative Methods for Human Drug Disposition‐Related Proteins for Applications in Physiologically Based Pharmacokinetic Modeling (PubMed)

Database of Optimized Proteomic Quantitative Methods for Human Drug Disposition‐Related Proteins for Applications in Physiologically Based Pharmacokinetic Modeling The purpose of this study was to create an open access repository of validated liquid chromatography tandem mass spectrometry (LC-MS/MS) multiple reaction monitoring (MRM) methods for quantifying 284 important proteins associated with drug absorption, distribution, metabolism, and excretion (ADME). Various in silico (...) and experimental approaches were used to select surrogate peptides and optimize instrument parameters for LC-MS/MS quantification of the selected proteins. The final methods were uploaded to an online public database (QPrOmics; www.qpromics.uw.edu/qpromics/assay/), which provides essential information for facile method development in triple quadrupole mass spectrometry (MS) instruments. To validate the utility of the methods, the differential tissue expression of 107 key ADME proteins was characterized

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2017 CPT: pharmacometrics & systems pharmacology

42. EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network (PubMed)

EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network 28617437 2018 09 05 2018 11 13 2041-4889 8 6 2017 06 15 Cell death & disease Cell Death Dis EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network. e2872 10.1038/cddis.2017.267 Zhao Zhangxiang Z College of Bioinformatics Science and Technology, Department of Systems Biology, Harbin Medical University, Harbin 150086, China. Training Center for Students Innovation

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2017 Cell death & disease

43. Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database (PubMed)

Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis.We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA (...) ) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes.Four hundred and eighty-two differentially expressed genes (DEGs) were

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2017 Journal of thoracic disease

44. On the potential of preemptive genotyping towards preventing medication related adverse events: Results from the South Korean national health insurance database (PubMed)

On the potential of preemptive genotyping towards preventing medication related adverse events: Results from the South Korean national health insurance database 27873192 2017 10 26 2018 11 13 1179-1942 40 1 2017 01 Drug safety Drug Saf On the Potential of Preemptive Genotyping Towards Preventing Medication-Related Adverse Events: Results from the South Korean National Health Insurance Database. 1-2 10.1007/s40264-016-0476-z Schildcrout Jonathan S JS Department of Biostatistics, Vanderbilt (...) United States R01 GM105688 GM NIGMS NIH HHS United States Letter Research Support, N.I.H., Extramural Research Support, U.S. Gov't, P.H.S. Comment New Zealand Drug Saf 9002928 0114-5916 IM Drug Saf. 2017 Jan;40(1):65-80 27638658 Databases, Factual Genotype Humans National Health Programs Jonathan S. Schildcrout, Joshua C. Denny, and Dan M. Roden have no conflicts of interests directly relevant to the content of this commentary. 2016 11 23 6 0 2017 10 27 6 0 2016 11 23 6 0 ppublish 27873192 10.1007

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2017 Drug Safety

45. An OMOP CDM-Based Relational Database of Clinical Research Eligibility Criteria (PubMed)

An OMOP CDM-Based Relational Database of Clinical Research Eligibility Criteria Eligibility criteria are important for clinical research protocols or clinical practice guidelines for determining who qualify for studies and to whom clinical evidence is applicable, but the free-text format is not amenable for computational processing. In this paper, we described a practical method for transforming free-text clinical research eligibility criteria of Alzheimer's clinical trials into a structured (...) relational database compliant with standards for medical terminologies and clinical data models. We utilized a hybrid natural language processing system and a concept normalization tool to extract medical terms in clinical research eligibility criteria and represent them using the OMOP Common Data Model (CDM) v5. We created a database schema design to store syntactic relations to facilitate efficient cohort queries. We further discussed the potential of applying this method to trials on other diseases

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2017 Studies in health technology and informatics

46. Utilization of Osteoporosis-Related Health Services: Use of Data from the Korean National Health Insurance Database 2008–2012 (PubMed)

Utilization of Osteoporosis-Related Health Services: Use of Data from the Korean National Health Insurance Database 2008–2012 Osteoporosis and its related fractures are increasingly being recognized as major health problems because of the rapidly increasing elderly population. In this study, we investigated the annual trend of osteoporosis-related health services utilization.Participants aged over 50 years were identified from the Korean National Health Insurance Service database between 2008 (...) the Korea National Health and Nutrition Examination Survey from 2008 to 2010. Less than 60% of patients with osteoporosis were estimated to have utilized medical services because of osteoporosis. Drug treatment rates were 34.1%, 31.1%, and 33.5% in 2008, 2009, and 2010, respectively.This study demonstrated an increasing trend in the utilization of the osteoporosis-related health services from 2008 to 2012 in Korea. The proportion of newly diagnosed osteoporosis patients and the prevalence of access

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2017 Journal of Korean medical science

47. rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks (PubMed)

rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data (...) adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed

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2017 Nucleic acids research

48. Estimating the risk of severe hypoglycemic event related to glucose-lowering treatment among Italian patients with diabetes: the HYPOTHESIS database (PubMed)

Estimating the risk of severe hypoglycemic event related to glucose-lowering treatment among Italian patients with diabetes: the HYPOTHESIS database The primary objective of this study was to estimate 1) the annual risk of undergoing a severe hypoglycemic event in Italian patients with diabetes and 2) the risk of hospitalization following such event. From the HYPOTHESIS database, powered by 46 emergency departments covering a 12-million-odd population, data were extracted of 1,922 hypoglycemic (...) with that for subjects treated with OHA (p<0.02). Death occurs in 7% of hospitalized patients. Older age (p<0.0001) and comorbidities (p<0.0001) were risk factors for hypoglycemia-related hospitalization. Treatments with insulin alone (p<0.005) or in combination (p<0.049) were negatively associated with hospital admission. Severe hypoglycemic events associated with the use of oral glucose-lowering agents carry the highest risk of hospital treatment. As such, they are also likely to generate higher tangible

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2017 ClinicoEconomics and Outcomes Research: CEOR

49. Current Trends of Lung Cancer Surgery and Demographic and Social Factors Related to Changes in the Trends of Lung Cancer Surgery: An Analysis of the National Database from 2010 to 2014 (PubMed)

Current Trends of Lung Cancer Surgery and Demographic and Social Factors Related to Changes in the Trends of Lung Cancer Surgery: An Analysis of the National Database from 2010 to 2014 We investigated current trends in lung cancer surgery and identified demographic and social factors related to changes in these trends.We estimated the incidence of lung cancer surgery using a procedure code-based approach provided by the Health Insurance Review and Assessment Service (http://opendata.hira.or.kr

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2016 Cancer research and treatment : official journal of Korean Cancer Association

50. Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders (PubMed)

Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders Genetic skeletal disorders (GSD) involving the skeletal system arises through disturbances in the complex processes of skeletal development, growth and homeostasis and remain a diagnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decades, tremendous effort platforms have been made to explore the complex heterogeneity, and massive new genes (...) and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians. In this study, combined with Nosology and Classification of genetic skeletal disorders, we developed the first comprehensive and annotated genetic skeletal disorders database, named 'SkeletonGenetics', which contains information about all GSD-related knowledge including 8225 mutations in 357 genes, with detailed information

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2016 Database: The Journal of Biological Databases and Curation

51. DDRprot: a database of DNA damage response-related proteins (PubMed)

DDRprot: a database of DNA damage response-related proteins The DNA Damage Response (DDR) signalling network is an essential system that protects the genome's integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position (...) of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches

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2016 Database: The Journal of Biological Databases and Curation

52. 2016 update of the PRIDE database and its related tools (PubMed)

2016 update of the PRIDE database and its related tools 27683222 2018 03 28 1362-4962 44 22 2016 12 15 Nucleic acids research Nucleic Acids Res. 2016 update of the PRIDE database and its related tools. 11033 Vizcaíno Juan Antonio JA European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK juan@ebi.ac.uk. Csordas Attila A European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI

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2016 Nucleic acids research

53. Age-related patterns of vigorous-intensity physical activity in youth: The International Children's Accelerometry Database (PubMed)

Age-related patterns of vigorous-intensity physical activity in youth: The International Children's Accelerometry Database Physical activity declines during youth but most evidence reports on combined moderate and vigorous-intensity physical activity. We investigated how vigorous-intensity activity varies with age. Cross-sectional data from 24,025 participants (5.0-18.0 y; from 20 studies in 10 countries obtained 2008-2010) providing ≥ 1 day accelerometer data (International Children's (...) Accelerometry Database (ICAD)). Linear regression was used to investigate age-related patterns in vigorous-intensity activity; models included age (exposure), adjustments for monitor wear-time and study. Moderate-intensity activity was examined for comparison. Interactions were used to investigate whether the age/vigorous-activity association differed by sex, weight status, ethnicity, maternal education and region. A 6.9% (95% CI 6.2, 7.5) relative reduction in mean vigorous-intensity activity with every

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2016 Preventive medicine reports

54. Pathology report data extraction from relational database using R, with extraction from reports on melanoma of skin as an example (PubMed)

Pathology report data extraction from relational database using R, with extraction from reports on melanoma of skin as an example Different methods have been described for data extraction from pathology reports with varying degrees of success. Here a technique for directly extracting data from relational database is described.Our department uses synoptic reports modified from College of American Pathologists (CAP) Cancer Protocol Templates to report most of our cancer diagnoses. Choosing (...) for other pathology information systems that use relational database for data management.

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2016 Journal of pathology informatics

55. Study to Validate Coded Medical Terms Used to Identify Opioid-Related Overdose in Databases Used for PMR Study 1B

Study to Validate Coded Medical Terms Used to Identify Opioid-Related Overdose in Databases Used for PMR Study 1B Study to Validate Coded Medical Terms Used to Identify Opioid-Related Overdose in Databases Used for PMR Study 1B - Full Text View - ClinicalTrials.gov Hide glossary Glossary Study record managers: refer to the if submitting registration or results information. Search for terms x × Study Record Detail Saved Studies Save this study Warning You have reached the maximum number of saved (...) studies (100). Please remove one or more studies before adding more. Study to Validate Coded Medical Terms Used to Identify Opioid-Related Overdose in Databases Used for PMR Study 1B The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Read our for details. ClinicalTrials.gov Identifier: NCT02667197 Recruitment Status : Active, not recruiting First Posted

2016 Clinical Trials

56. The effect of marital status on breast cancer-related outcomes in women under 65: A SEER database analysis. (PubMed)

The effect of marital status on breast cancer-related outcomes in women under 65: A SEER database analysis. Marital status is strongly associated with improved health and longevity. Being married has been shown to be positively associated with survival in patients with multiple different types of malignancy; however, little is known about the relationship between marital status and breast cancer in younger women. The purpose of this study is to investigate the effect of marital status (...) on diagnosis, and survival of women under the age of 65 with breast cancer.The SEER 18 regions database was used to identify women between the ages of 25-64 diagnosed with invasive breast cancer in the years 2004-2009. Logistic regression was used to predict later stage diagnosis by marital status and Cox proportional hazards models were used to compare breast cancer-related and all-cause survival by marital status classification. Models were stratified by AJCC stage.After adjusting for age, race, and ER

2016 Breast

57. The psychological impact of symptoms related to esophagogastric cancer resection presenting in primary care: A national linked database study. (PubMed)

The psychological impact of symptoms related to esophagogastric cancer resection presenting in primary care: A national linked database study. The objective was to evaluate incidence, risk factors and impact of postoperative symptoms following esophagogastric cancer resection in primary care.Patients undergoing esophagogastrectomy for cancer from 1998 to 2010 with linked records in Clinical Practice Research Datalink, Hospital Episodes Statistics and Office of National Statistics databases were (...) of postoperative depression/anxiety included younger age (OR = 0.97 95%CI 0.96-0.99), complications (OR = 2.40 95%CI 1.51-3.83), psychiatric history (OR = 6.73 95%CI 4.25-10.64) and postoperative symptoms (OR = 1.78 95%CI 1.17-2.71).Over 40% of patients had symptoms related to esophagogastric cancer resection recorded in primary care, and were associated with an increase in postoperative depression and anxiety.Copyright © 2016 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society

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2016 European Journal of Surgical Oncology

58. YIA 01-03 OUTCOME-DRIVEN REFERENCE FRAME FOR SELF-MEASURED HOME BLOOD PRESSURE VARIABILITY: INTERNATIONAL DATABASE OF HOME BLOOD PRESSURE IN RELATION TO CARDIOVASCULAR OUTCOME (IDHOCO). (PubMed)

YIA 01-03 OUTCOME-DRIVEN REFERENCE FRAME FOR SELF-MEASURED HOME BLOOD PRESSURE VARIABILITY: INTERNATIONAL DATABASE OF HOME BLOOD PRESSURE IN RELATION TO CARDIOVASCULAR OUTCOME (IDHOCO).

2016 Journal of Hypertension

59. Assessing the Real World Effect of Laparoscopic Bariatric Surgery on the Management of Obesity-Related Comorbidities - A Retrospective Matched Cohort Study using a U.S. Claims Database. (PubMed)

Assessing the Real World Effect of Laparoscopic Bariatric Surgery on the Management of Obesity-Related Comorbidities - A Retrospective Matched Cohort Study using a U.S. Claims Database. To evaluate the real-world effect of laparoscopic bariatric surgery, comprising adjustable gastric banding (LAGB), laparoscopic Roux-en-Y gastric bypass (LRYGB) and laparoscopic sleeve gastrectomy (LSG), on the management of obesity-related comorbidities.Patients who underwent laparoscopic bariatric surgeries (...) between 2006 and 2013 were identified from the Optum Clinformatics administrative claims database. Those surgical patients were matched to medically managed patients (controls) on selected patient characteristics. Comorbidity management was assessed every 6 months up to 5 years after the surgery or an assigned index date for control subjects (follow-up), by evaluating the number of medication classes used to treat type 2 diabetes, hypertension and dyslipidaemia, as well as by evaluating

2016 obesity & metabolism

60. Gender differences in a reference database of age-related femoral neck geometric parameters for Chinese population and their association with femoral neck fractures. (PubMed)

Gender differences in a reference database of age-related femoral neck geometric parameters for Chinese population and their association with femoral neck fractures. Femoral neck geometric parameters (FNGPs) are closely related to the strength of the femoral neck and the risk of fragility fractures. No reference database is available for FNGPs for Chinese population, and gender-related differences in FNGPs as well as their association with the risk of femoral neck fractures are unknown (...) . This investigation aimed to set up reference databases for FNGPs, understand gender-related differences in FNGPs, and examine the association between FNGPs and the risk of osteoporotic fractures of the femoral neck. This study included 5268 females and 2156 males (aged 15-91years) from Chinese population. A total of 384 patients (282 females and 102 males) had sustained femoral neck fractures; 384 age- and sex-matched individuals without any fractures served as controls. Femoral neck DXA images were used

2016 Bone

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