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Genetic architecture of host proteins involved in SARS-CoV-2 infection.
Pietzner M, Wheeler E, Carrasco-Zanini J, Raffler J, Kerrison ND, Oerton E, Auyeung VPW, Luan J, Finan C, Casas JP, Ostroff R, Williams SA, Kastenmüller G, Ralser M, Gamazon ER, Wareham NJ, Hingorani AD, Langenberg C
(2020) Nat Commun 11: 6397
MeSH Terms: ABO Blood-Group System, Aptamers, Peptide, Blood Coagulation, COVID-19, Drug Delivery Systems, Female, Gene Expression Regulation, Host-Derived Cellular Factors, Host-Pathogen Interactions, Humans, Internet, Male, Middle Aged, Proteins, Quantitative Trait Loci, SARS-CoV-2
Show Abstract · Added December 18, 2020
Understanding the genetic architecture of host proteins interacting with SARS-CoV-2 or mediating the maladaptive host response to COVID-19 can help to identify new or repurpose existing drugs targeting those proteins. We present a genetic discovery study of 179 such host proteins among 10,708 individuals using an aptamer-based technique. We identify 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links and evidence that putative viral interaction partners such as MARK3 affect immune response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and detailed interrogation of results is facilitated through an interactive webserver ( https://omicscience.org/apps/covidpgwas/ ).
0 Communities
1 Members
0 Resources
16 MeSH Terms
The Online Support Group as a Community: A Thematic Content Analysis of an Online Support Group for Idiopathic Subglottic Stenosis.
Haik D, Kashanchi K, Tajran S, Heilbronn C, Anderson C, Francis DO, Gelbard A, Verma SP
(2019) Ann Otol Rhinol Laryngol 128: 293-299
MeSH Terms: Access to Information, Disease Management, Emotions, Female, Global Health, Humans, Information Dissemination, Internet, Laryngostenosis, Male, Psychosocial Support Systems, Self-Help Groups
Show Abstract · Added July 30, 2020
OBJECTIVE: - Idiopathic subglottic stenosis (iSGS) is a rare disease with few local resources for individuals to use. With the explosive growth of online social networking, platforms such as Facebook possess compelling potential to facilitate user-driven sharing of health information and peer support. This study was performed to better understand the content shared in a busy online community for individuals with iSGS.
METHODS: - The largest online community (OC) for individuals with iSGS, Living With Idiopathic Subglottic Stenosis (LwiSGS), was examined. A thematic content analysis of the communications shared in February of 2018 was performed. A conventional qualitative analysis model was employed to analyze aggregated data. The data were then codified.
RESULTS: - Analysis demonstrated that communications primarily encompassed three major thematic elements: (1) information sharing; (2) emotional support, expression, and experience sharing; and (3) community building. Positively toned posts grossly overshadowed negatively toned posts by almost a factor of 3. A significant portion of group members requested information from their peers, suggesting a high level of trust toward the resources provided in this group, even those involving a surgical procedure or medication.
CONCLUSION: - LwiSGS is a forum for patients with a rare chronic condition to share informational resources, personal experiences, and emotional support, as well as a community with their peers. These data suggest that LwiSGS could be a powerful resource for individuals with iSGS to share information, personal experiences, or emotional support.
0 Communities
1 Members
0 Resources
MeSH Terms
A Web-Based Atlas Combining MRI and Histology of the Squirrel Monkey Brain.
Schilling KG, Gao Y, Christian M, Janve V, Stepniewska I, Landman BA, Anderson AW
(2019) Neuroinformatics 17: 131-145
MeSH Terms: Animals, Atlases as Topic, Brain, Diffusion Tensor Imaging, Internet, Male, Saimiri
Show Abstract · Added March 26, 2019
The squirrel monkey (Saimiri sciureus) is a commonly-used surrogate for humans in biomedical research. In the neuroimaging community, MRI and histological atlases serve as valuable resources for anatomical, physiological, and functional studies of the brain; however, no digital MRI/histology atlas is currently available for the squirrel monkey. This paper describes the construction of a web-based multi-modal atlas of the squirrel monkey brain. The MRI-derived information includes anatomical MRI contrast (i.e., T2-weighted and proton-density-weighted) and diffusion MRI metrics (i.e., fractional anisotropy and mean diffusivity) from data acquired both in vivo and ex vivo on a 9.4 Tesla scanner. The histological images include Nissl and myelin stains, co-registered to the corresponding MRI, allowing identification of cyto- and myelo-architecture. In addition, a bidirectional neuronal tracer, biotinylated dextran amine (BDA) was injected into the primary motor cortex, enabling highly specific identification of regions connected to the injection location. The atlas integrates the results of common image analysis methods including diffusion tensor imaging glyphs, labels of 57 white-matter tracts identified using DTI-tractography, and 18 cortical regions of interest identified from Nissl-revealed cyto-architecture. All data are presented in a common space, and all image types are accessible through a web-based atlas viewer, which allows visualization and interaction of user-selectable contrasts and varying resolutions. By providing an easy to use reference system of anatomical information, our web-accessible multi-contrast atlas forms a rich and convenient resource for comparisons of brain findings across subjects or modalities. The atlas is called the Combined Histology-MRI Integrated Atlas of the Squirrel Monkey (CHIASM). All images are accessible through our web-based viewer ( https://chiasm.vuse.vanderbilt.edu /), and data are available for download at ( https://www.nitrc.org/projects/smatlas/ ).
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7 MeSH Terms
A technology-based patient and family engagement consult service for the pediatric hospital setting.
Jackson GP, Robinson JR, Ingram E, Masterman M, Ivory C, Holloway D, Anders S, Cronin RM
(2018) J Am Med Inform Assoc 25: 167-174
MeSH Terms: Adolescent, Child, Child, Preschool, Consumer Health Informatics, Consumer Health Information, Family, Female, Hospitals, Pediatric, Humans, Infant, Infant, Newborn, Information Seeking Behavior, Information Technology, Internet, Male, Mobile Applications, Patient-Centered Care, Referral and Consultation, Retrospective Studies, Tennessee
Show Abstract · Added November 8, 2017
Objective - The Vanderbilt Children's Hospital launched an innovative Technology-Based Patient and Family Engagement Consult Service in 2014. This paper describes our initial experience with this service, characterizes health-related needs of families of hospitalized children, and details the technologies recommended to promote engagement and meet needs.
Materials and Methods - We retrospectively reviewed consult service documentation for patient characteristics, health-related needs, and consultation team recommendations. Needs were categorized using a consumer health needs taxonomy. Recommendations were classified by technology type.
Results - Twenty-two consultations were conducted with families of patients ranging in age from newborn to 15 years, most with new diagnoses or chronic illnesses. The consultation team identified 99 health-related needs (4.5 per consultation) and made 166 recommendations (7.5 per consultation, 1.7 per need). Need categories included 38 informational needs, 26 medical needs, 23 logistical needs, and 12 social needs. The most common recommendations were websites (50, 30%) and mobile applications (30, 18%). The most frequent recommendations by need category were websites for informational needs (39, 50%), mobile applications for medical needs (15, 40%), patient portals for logistical needs (12, 44%), and disease-specific support groups for social needs (19, 56%).
Discussion - Families of hospitalized pediatric patients have a variety of health-related needs, many of which could be addressed by technology recommendations from an engagement consult service.
Conclusion - This service is the first of its kind, offering a potentially generalizable and scalable approach to assessing health-related needs, meeting them with technologies, and promoting patient and family engagement in the inpatient setting.
© The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com
0 Communities
1 Members
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20 MeSH Terms
Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).
Moretti R, Lyskov S, Das R, Meiler J, Gray JJ
(2018) Protein Sci 27: 259-268
MeSH Terms: Internet, Molecular Docking Simulation, Peptides, Proteins, Software
Show Abstract · Added March 17, 2018
The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pK determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org.
© 2017 The Protein Society.
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5 MeSH Terms
Rheumatologists' perception of systemic lupus erythematosus quality indicators: significant interest and perceived barriers.
Casey C, Chung CP, Crofford LJ, Barnado A
(2017) Clin Rheumatol 36: 97-102
MeSH Terms: Adult, Attitude of Health Personnel, Cross-Sectional Studies, Female, Health Knowledge, Attitudes, Practice, Humans, Internet, Lupus Erythematosus, Systemic, Male, Middle Aged, Quality Improvement, Quality Indicators, Health Care, Rheumatologists, Rheumatology, Southeastern United States, Surveys and Questionnaires
Show Abstract · Added March 25, 2020
Differences in quality of care may contribute to health disparities in systemic lupus erythematosus (SLE). Studies show low physician adherence rates to the SLE quality indicators but do not assess physician perception of SLE quality indicators or quality improvement. Using a cross-sectional survey of rheumatologists in the southeastern USA, we assessed the perception and involvement of rheumatologists in quality improvement and the SLE quality indicators. Using electronic mail, an online survey of 32 questions was delivered to 568 rheumatologists. With a response rate of 19% (n = 106), the majority of participants were male, Caucasian, with over 20 years of experience, and seeing adult patients in an academic setting. Participants had a positive perception toward quality improvement (81%) with a majority responding that the SLE quality indicators would significantly impact quality of care (54%). While 66% of respondents were familiar with the SLE quality indicators, only 18% of respondents reported using them in everyday practice. The most commonly reported barrier to involvement in quality improvement and the SLE quality indicators was time. Rheumatologists had a positive perception of the SLE quality indicators and agreed that use of the quality indicators could improve quality of care in SLE; however, they identified time as a barrier to implementation. Future studies should investigate methods to increase use of the SLE quality indicators.
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MeSH Terms
FloWave.US: validated, open-source, and flexible software for ultrasound blood flow analysis.
Coolbaugh CL, Bush EC, Caskey CF, Damon BM, Towse TF
(2016) J Appl Physiol (1985) 121: 849-857
MeSH Terms: Algorithms, Arteries, Blood Flow Velocity, Humans, Image Interpretation, Computer-Assisted, Internet, Phantoms, Imaging, Reproducibility of Results, Sensitivity and Specificity, Software, Ultrasonography
Show Abstract · Added January 19, 2017
Automated software improves the accuracy and reliability of blood velocity, vessel diameter, blood flow, and shear rate ultrasound measurements, but existing software offers limited flexibility to customize and validate analyses. We developed FloWave.US-open-source software to automate ultrasound blood flow analysis-and demonstrated the validity of its blood velocity (aggregate relative error, 4.32%) and vessel diameter (0.31%) measures with a skeletal muscle ultrasound flow phantom. Compared with a commercial, manual analysis software program, FloWave.US produced equivalent in vivo cardiac cycle time-averaged mean (TAMean) velocities at rest and following a 10-s muscle contraction (mean bias <1 pixel for both conditions). Automated analysis of ultrasound blood flow data was 9.8 times faster than the manual method. Finally, a case study of a lower extremity muscle contraction experiment highlighted the ability of FloWave.US to measure small fluctuations in TAMean velocity, vessel diameter, and mean blood flow at specific time points in the cardiac cycle. In summary, the collective features of our newly designed software-accuracy, reliability, reduced processing time, cost-effectiveness, and flexibility-offer advantages over existing proprietary options. Further, public distribution of FloWave.US allows researchers to easily access and customize code to adapt ultrasound blood flow analysis to a variety of vascular physiology applications.
Copyright © 2016 the American Physiological Society.
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11 MeSH Terms
Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.
Bender BJ, Cisneros A, Duran AM, Finn JA, Fu D, Lokits AD, Mueller BK, Sangha AK, Sauer MF, Sevy AM, Sliwoski G, Sheehan JH, DiMaio F, Meiler J, Moretti R
(2016) Biochemistry 55: 4748-63
MeSH Terms: Algorithms, Computational Biology, Internet, Models, Molecular, Protein Binding, Protein Conformation, Protein Folding, Protein Interaction Mapping, Proteins, RNA, Software, User-Computer Interface
Show Abstract · Added April 8, 2017
Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K. W., et al. (2010) Biochemistry 49, 2987-2998]. The overwhelming positive response to this publication we received motivates us to here share the next iteration of these tutorials that feature de novo folding, comparative modeling, loop construction, protein docking, small molecule docking, and protein design. This updated and expanded set of tutorials is needed, as since 2010 Rosetta has been fully redesigned into an object-oriented protein modeling program Rosetta3. Notable improvements include a substantially improved energy function, an XML-like language termed "RosettaScripts" for flexibly specifying modeling task, new analysis tools, the addition of the TopologyBroker to control conformational sampling, and support for multiple templates in comparative modeling. Rosetta's ability to model systems with symmetric proteins, membrane proteins, noncanonical amino acids, and RNA has also been greatly expanded and improved.
1 Communities
2 Members
0 Resources
12 MeSH Terms
Review of information technology for surgical patient care.
Robinson JR, Huth H, Jackson GP
(2016) J Surg Res 203: 121-39
MeSH Terms: Consumer Health Information, Electronic Health Records, Humans, Internet, Medical Order Entry Systems, Patient Acceptance of Health Care, Perioperative Care
Show Abstract · Added January 16, 2017
BACKGROUND - Electronic health records (EHRs), computerized provider order entry (CPOE), and patient portals have experienced increased adoption by health care systems. The objective of this study was to review evidence regarding the impact of such health information technologies (HIT) on surgical practice.
MATERIALS AND METHODS - A search of Medline, EMBASE, CINAHL, and the Cochrane Library was performed to identify data-driven, nonsurvey studies about the effects of HIT on surgical care. Domain experts were queried for relevant articles. Two authors independently reviewed abstracts for inclusion criteria and analyzed full text of eligible articles.
RESULTS - A total of 2890 citations were identified. Of them, 32 observational studies and two randomized controlled trials met eligibility criteria. EHR or CPOE improved appropriate antibiotic administration for surgical procedures in 13 comparative observational studies. Five comparative observational studies indicated that electronically generated operative notes had increased accuracy, completeness, and availability in the medical record. The Internet as an information resource about surgical procedures was generally inadequate. Surgical patients and providers demonstrated rapid adoption of patient portals, with increasing proportions of online versus inperson outpatient surgical encounters.
CONCLUSIONS - The overall quality of evidence about the effects of HIT in surgical practice was low. Current data suggest an improvement in appropriate perioperative antibiotic administration and accuracy of operative reports from CPOE and EHR applications. Online consumer health educational resources and patient portals are popular among patients and families, but their impact has not been studied well in surgical populations. With increasing adoption of HIT, further research is needed to optimize the efficacy of such tools in surgical care.
Copyright © 2016 Elsevier Inc. All rights reserved.
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7 MeSH Terms
Data publication with the structural biology data grid supports live analysis.
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P
(2016) Nat Commun 7: 10882
MeSH Terms: Crystallography, X-Ray, Databases, Genetic, Internet, Macromolecular Substances, Publications, Software
Show Abstract · Added April 7, 2017
Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.
1 Communities
2 Members
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6 MeSH Terms