Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Oxford University Press (OUP)  (12)
  • 1
    In: JAMIA Open, Oxford University Press (OUP), Vol. 2, No. 3 ( 2019-10-01), p. 353-359
    Abstract: To provide an open-source software package for determining temporal correlations between disease states using longitudinal electronic medical records (EMR). Materials and Methods We have developed an R-based package, Disease Correlation Network (DCN), which builds retrospective matched cohorts from longitudinal medical records to assess for significant temporal correlations between diseases using two independent methodologies: Cox proportional hazards regression and random forest survival analysis. This optimizable package has the potential to control for relevant confounding factors such as age, gender, and other demographic and medical characteristics. Output is presented as a DCN which may be analyzed using a JavaScript-based interactive visualization tool for users to explore statistically significant correlations between disease states of interest using graph-theory-based network topology. Results We have applied this package to a longitudinal dataset at Loyola University Chicago Medical Center with 654 084 distinct initial diagnoses of 51 conditions in 175 539 patients. Over 90% of disease correlations identified are supported by literature review. DCN is available for download at https://github.com/qunfengdong/DCN. Conclusions DCN allows screening of EMR data to identify potential relationships between chronic disease states. This data may then be used to formulate novel research hypotheses for further characterization of these relationships.
    Type of Medium: Online Resource
    ISSN: 2574-2531
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2940623-7
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  JAMIA Open Vol. 3, No. 4 ( 2021-02-15), p. 496-499
    In: JAMIA Open, Oxford University Press (OUP), Vol. 3, No. 4 ( 2021-02-15), p. 496-499
    Abstract: Accurate estimations of the seroprevalence of antibodies to severe acute respiratory syndrome coronavirus 2 need to properly consider the specificity and sensitivity of the antibody tests. In addition, prior knowledge of the extent of viral infection in a population may also be important for adjusting the estimation of seroprevalence. For this purpose, we have developed a Bayesian approach that can incorporate the variabilities of specificity and sensitivity of the antibody tests, as well as the prior probability distribution of seroprevalence. We have demonstrated the utility of our approach by applying it to a recently published large-scale dataset from the US CDC, with our results providing entire probability distributions of seroprevalence instead of single-point estimates. Our Bayesian code is freely available at https://github.com/qunfengdong/AntibodyTest.
    Type of Medium: Online Resource
    ISSN: 2574-2531
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2940623-7
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    In: Brain, Oxford University Press (OUP), Vol. 144, No. 2 ( 2021-03-03), p. 601-614
    Abstract: Oculopharyngodistal myopathy is a late-onset degenerative muscle disorder characterized by ptosis and weakness of the facial, pharyngeal, and distal limb muscles. A recent report suggested a non-coding trinucleotide repeat expansion in LRP12 to be associated with the disease. Here we report a genetic study in a Chinese cohort of 41 patients with the clinical diagnosis of oculopharyngodistal myopathy (21 cases from seven families and 20 sporadic cases). In a large family with 12 affected individuals, combined haplotype and linkage analysis revealed a maximum two-point logarithm of the odds (LOD) score of 3.3 in chromosomal region chr19p13.11-p13.2 and narrowed the candidate region to an interval of 4.5 Mb. Using a comprehensive strategy combining whole-exome sequencing, long-read sequencing, repeat-primed polymerase chain reaction and GC-rich polymerase chain reaction, we identified an abnormal CGG repeat expansion in the 5′ UTR of the GIPC1 gene that co-segregated with disease. Overall, the repeat expansion in GIPC1 was identified in 51.9% independent pedigrees (4/7 families and 10/20 sporadic cases), while the repeat expansion in LRP12 was only identified in one sporadic case (3.7%) in our cohort. The number of CGG repeats was & lt;30 in controls but & gt;60 in affected individuals. There was a slight correlation between repeat size and the age at onset. Both repeat expansion and retraction were observed during transmission but somatic instability was not evident. These results further support that non-coding CGG repeat expansion plays an essential role in the pathogenesis of oculopharyngodistal myopathy.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1474117-9
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  JAMIA Open Vol. 3, No. 2 ( 2020-07-01), p. 151-153
    In: JAMIA Open, Oxford University Press (OUP), Vol. 3, No. 2 ( 2020-07-01), p. 151-153
    Abstract: To develop a mathematical model to characterize age-specific case-fatality rates (CFR) of COVID-19. Based on 2 large-scale Chinese and Italian CFR data, a logistic model was derived to provide quantitative insight on the dynamics between CFR and age. We inferred that CFR increased faster in Italy than in China, as well as in females over males. In addition, while CFR increased with age, the rate of growth eventually slowed down, with a predicted theoretical upper limit for males (32%), females (21%), and the general population (23%). Our logistic model provided quantitative insight on the dynamics of CFR.
    Type of Medium: Online Resource
    ISSN: 2574-2531
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2940623-7
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2009
    In:  Bioinformatics Vol. 25, No. 7 ( 2009-04-01), p. 956-957
    In: Bioinformatics, Oxford University Press (OUP), Vol. 25, No. 7 ( 2009-04-01), p. 956-957
    Abstract: Summary: Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computation to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular biologists are often interested only in a small cluster of genes, catering to this need, we have developed a web-based software system that allows users to upload a list of genes, perform dynamic search against the genomes of their choices and interactively visualize the gene cluster conservation using a novel multi-genome browser. Our approach avoids expensive genome-wide pre-computing and allows users to dynamically change the search criteria to fit their genes of interest. Our system can be customized for any genome sequences. We have applied it to both prokaryotic and eukaryotic genomes to illustrate its usability. Availability: Our software is freely available at http://cgcv.cgb.indiana.edu/cgi-bin/index.cgi. Contact:  dongq@indiana.edu
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 1468345-3
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2009
    In:  Bioinformatics Vol. 25, No. 12 ( 2009-06-15), p. 1550-1551
    In: Bioinformatics, Oxford University Press (OUP), Vol. 25, No. 12 ( 2009-06-15), p. 1550-1551
    Abstract: Summary: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser and visualize the configured genomic features with the integrated GBrowse software. Availability: WebGBrowse is accessible via http://webgbrowse.cgb.indiana.edu/ and the system is also freely available for local installations. Contact:  dongq@indiana.edu
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 1468345-3
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Journal of the American Medical Informatics Association Vol. 28, No. 3 ( 2021-03-01), p. 472-476
    In: Journal of the American Medical Informatics Association, Oxford University Press (OUP), Vol. 28, No. 3 ( 2021-03-01), p. 472-476
    Abstract: Estimating the hospitalization risk for people with comorbidities infected by the SARS-CoV-2 virus is important for developing public health policies and guidance. Traditional biostatistical methods for risk estimations require: (i) the number of infected people who were not hospitalized, which may be severely undercounted since many infected people were not tested; (ii) comorbidity information for people not hospitalized, which may not always be readily available. We aim to overcome these limitations by developing a Bayesian approach to estimate the risk ratio of hospitalization for COVID-19 patients with comorbidities. Materials and Methods We derived a Bayesian approach to estimate the posterior distribution of the risk ratio using the observed frequency of comorbidities in COVID-19 patients in hospitals and the prevalence of comorbidities in the general population. We applied our approach to 2 large-scale datasets in the United States: 2491 patients in the COVID-NET, and 5700 patients in New York hospitals. Results Our results consistently indicated that cardiovascular diseases carried the highest hospitalization risk for COVID-19 patients, followed by diabetes, chronic respiratory disease, hypertension, and obesity, respectively. Discussion Our approach only needs (i) the number of hospitalized COVID-19 patients and their comorbidity information, which can be reliably obtained using hospital records, and (ii) the prevalence of the comorbidity of interest in the general population, which is regularly documented by public health agencies for common medical conditions. Conclusion We developed a novel Bayesian approach to estimate the hospitalization risk for people with comorbidities infected with the SARS-CoV-2 virus.
    Type of Medium: Online Resource
    ISSN: 1527-974X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2018371-9
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2012
    In:  Plant Physiology Vol. 159, No. 1 ( 2012-05-03), p. 299-310
    In: Plant Physiology, Oxford University Press (OUP), Vol. 159, No. 1 ( 2012-05-03), p. 299-310
    Abstract: Symbiotic nitrogen fixation occurs in nodules, specialized organs on the roots of legumes. Within nodules, host plant cells are infected with rhizobia that are encapsulated by a plant-derived membrane forming a novel organelle, the symbiosome. In Medicago truncatula, the symbiosome consists of the symbiosome membrane, a single rhizobium, and the soluble space between them, called the symbiosome space. The symbiosome space is enriched with plant-derived proteins, including the M. truncatula EARLY NODULIN8 (MtENOD8) protein. Here, we present evidence from green fluorescent protein (GFP) fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP). When ectopically expressed in nonnodulated root tissue, the MtENOD8 SP delivers GFP to the vacuole. During the course of nodulation, there is a nodule-specific redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates and subsequently to symbiosomes, with redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates preceding intracellular rhizobial infection. Experiments with M. truncatula mutants having defects in rhizobial infection and symbiosome development demonstrated that the MtNIP/LATD gene is required for redirection of the MtENOD8-SP-GFP from the vacuoles to punctate intermediates in nodules. Our evidence shows that MtENOD8 has evolved redundant targeting sequences for symbiosome targeting and that intracellular localization of ectopically expressed MtENOD8-SP-GFP is useful as a marker for monitoring the extent of development in mutant nodules.
    Type of Medium: Online Resource
    ISSN: 1532-2548
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2010
    In:  Bioinformatics Vol. 26, No. 8 ( 2010-04-15), p. 1122-1124
    In: Bioinformatics, Oxford University Press (OUP), Vol. 26, No. 8 ( 2010-04-15), p. 1122-1124
    Abstract: Summary: Ergatis is a flexible workflow management system for designing and executing complex bioinformatics pipelines. However, its complexity restricts its usage to only highly skilled bioinformaticians. We have developed a web-based prokaryotic genome annotation server, Integrative Services for Genomics Analysis (ISGA), which builds upon the Ergatis workflow system, integrates other dynamic analysis tools and provides intuitive web interfaces for biologists to customize and execute their own annotation pipelines. ISGA is designed to be installed at genomics core facilities and be used directly by biologists. Availability: ISGA is accessible at http://isga.cgb.indiana.edu/ and the system is also freely available for local installation. Contact:  qunfeng.dong@unt.edu Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2010
    detail.hit.zdb_id: 1468345-3
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2005
    In:  Plant Physiology Vol. 139, No. 2 ( 2005-10-01), p. 610-618
    In: Plant Physiology, Oxford University Press (OUP), Vol. 139, No. 2 ( 2005-10-01), p. 610-618
    Abstract: PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database.
    Type of Medium: Online Resource
    ISSN: 1532-2548 , 0032-0889
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2005
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages