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2.
RNA ; 28(4): 523-540, 2022 04.
Article in English | MEDLINE | ID: mdl-35082143

ABSTRACT

Alternative splicing transitions occur during organ development, and, in numerous diseases, splicing programs revert to fetal isoform expression. We previously found that extensive splicing changes occur during postnatal mouse heart development in genes encoding proteins involved in vesicle-mediated trafficking. However, the regulatory mechanisms of this splicing-trafficking network are unknown. Here, we found that membrane trafficking genes are alternatively spliced in a tissue-specific manner, with striated muscles exhibiting the highest levels of alternative exon inclusion. Treatment of differentiated muscle cells with chromatin-modifying drugs altered exon inclusion in muscle cells. Examination of several RNA-binding proteins revealed that the poly-pyrimidine tract binding protein 1 (PTBP1) and quaking regulate splicing of trafficking genes during myogenesis, and that removal of PTBP1 motifs prevented PTBP1 from binding its RNA target. These findings enhance our understanding of developmental splicing regulation of membrane trafficking proteins which might have implications for muscle disease pathogenesis.


Subject(s)
Alternative Splicing , Polypyrimidine Tract-Binding Protein , Animals , Exons , Heterogeneous-Nuclear Ribonucleoproteins/genetics , Heterogeneous-Nuclear Ribonucleoproteins/metabolism , Mice , Muscle Development/genetics , Polypyrimidine Tract-Binding Protein/genetics , Polypyrimidine Tract-Binding Protein/metabolism
3.
Pharmacoepidemiol Drug Saf ; 33(1): e5717, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37876360

ABSTRACT

PURPOSE: Real-world data (RWD) offers a valuable resource for generating population-level disease epidemiology metrics. We aimed to develop a well-tested and user-friendly R package to compute incidence rates and prevalence in data mapped to the observational medical outcomes partnership (OMOP) common data model (CDM). MATERIALS AND METHODS: We created IncidencePrevalence, an R package to support the analysis of population-level incidence rates and point- and period-prevalence in OMOP-formatted data. On top of unit testing, we assessed the face validity of the package. To do so, we calculated incidence rates of COVID-19 using RWD from Spain (SIDIAP) and the United Kingdom (CPRD Aurum), and replicated two previously published studies using data from the Netherlands (IPCI) and the United Kingdom (CPRD Gold). We compared the obtained results to those previously published, and measured execution times by running a benchmark analysis across databases. RESULTS: IncidencePrevalence achieved high agreement to previously published data in CPRD Gold and IPCI, and showed good performance across databases. For COVID-19, incidence calculated by the package was similar to public data after the first-wave of the pandemic. CONCLUSION: For data mapped to the OMOP CDM, the IncidencePrevalence R package can support descriptive epidemiological research. It enables reliable estimation of incidence and prevalence from large real-world data sets. It represents a simple, but extendable, analytical framework to generate estimates in a reproducible and timely manner.


Subject(s)
COVID-19 , Data Management , Humans , Incidence , Prevalence , Databases, Factual , COVID-19/epidemiology
4.
J Biomed Inform ; 134: 104162, 2022 10.
Article in English | MEDLINE | ID: mdl-36029954

ABSTRACT

The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) provides a unified model to integrate disparate real-world data (RWD) sources. An integral part of the OMOP CDM is the Standardized Vocabularies (henceforth referred to as the OMOP vocabulary), which enables organization and standardization of medical concepts across various clinical domains of the OMOP CDM. For concepts with the same meaning from different source vocabularies, one is designated as the standard concept, while the others are specified as non-standard or source concepts and mapped to the standard one. However, due to the heterogeneity of source vocabularies, there may exist mapping issues such as erroneous mappings and missing mappings in the OMOP vocabulary, which could affect the results of downstream analyses with RWD. In this paper, we focus on quality assurance of vaccine concept mappings in the OMOP vocabulary, which is necessary to accurately harness the power of RWD on vaccines. We introduce a semi-automated lexical approach to audit vaccine mappings in the OMOP vocabulary. We generated two types of vaccine-pairs: mapped and unmapped, where mapped vaccine-pairs are pairs of vaccine concepts with a "Maps to" relationship, while unmapped vaccine-pairs are those without a "Maps to" relationship. We represented each vaccine concept name as a set of words, and derived term-difference pairs (i.e., name differences) for mapped and unmapped vaccine-pairs. If the same term-difference pair can be obtained by both mapped and unmapped vaccine-pairs, then this is considered as a potential mapping inconsistency. Applying this approach to the vaccine mappings in OMOP, a total of 2087 potentially mapping inconsistencies were obtained. A randomly selected 200 samples were evaluated by domain experts to identify, validate, and categorize the inconsistencies. Experts identified 95 cases revealing valid mapping issues. The remaining 105 cases were found to be invalid due to the external and/or contextual information used in the mappings that were not reflected in the concept names of vaccines. This indicates that our semi-automated approach shows promise in identifying mapping inconsistencies among vaccine concepts in the OMOP vocabulary.


Subject(s)
Vaccines , Vocabulary , Quality Improvement , Vocabulary, Controlled
5.
Phytopathology ; 112(2): 261-270, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34261341

ABSTRACT

Exotic diseases and pests of trees have caused continental-scale disturbances in forest ecosystems and industries, and their invasions are considered largely unpredictable. We tested the concept of preinvasion assessment of not yet invasive organisms, which enables empirical risk assessment of potential invasion and impact. Our example assesses fungi associated with Old World bark and ambrosia beetles and their potential to impact North American trees. We selected 55 Asian and European scolytine beetle species using host use, economic, and regulatory criteria. We isolated 111 of their most consistent fungal associates and tested their effect on four important southeastern American pine and oak species. Our test dataset found no highly virulent pathogens that should be classified as an imminent threat. Twenty-two fungal species were minor pathogens, which may require context-dependent response for their vectors at North American borders, while most of the tested fungi displayed no significant impact. Our results are significant in three ways; they ease the concerns over multiple overseas fungus vectors suspected of heightened potential risk, they provide a basis for the focus on the prevention of introduction and establishment of species that may be of consequence, and they demonstrate that preinvasion assessment, if scaled up, can support practical risk assessment of exotic pathogens.


Subject(s)
Coleoptera , Trees , Animals , Coleoptera/microbiology , Coleoptera/physiology , Ecosystem , Fungi/physiology , Plant Bark , Plant Diseases/microbiology , Trees/microbiology
6.
J Adv Nurs ; 78(2): 523-531, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34730841

ABSTRACT

AIM: To compare the satisfaction of patients managed by independent nurse prescribers with that of patients managed by nurses using PGDs with respect to experience of the consultation and information received about the medication. DESIGN: Survey. METHODS: Patients receiving medications from nurses in five urban sexual health services in the United Kingdom completed validated questionnaires immediately after the consultation, September 2015-August 2016. Scores of independent nurse prescribers and nurses using patient group directions were compared about consultation experience (5 items) Satisfaction with Information about Medicines (SIMS 16 items scale). RESULTS: Of 808 patients receiving medications, 393 (48.6%) received questionnaires and 380 were returned (independent nurse prescribers 180 of 198, 90.9%; patient group directions 173 of 195, 88.7%). Patients in both groups reported high levels of satisfaction. About the consultation experience, patients found nurses friendly/ approachable (>99%), instilling confidence and trust (>99%) and explaining reasons for medications clearly (97%). Satisfaction with medication information: Of 348 (92%) respondents completing SIMS, the overall mean score was 13.4 of maximum 16 (no difference between groups, t-test, p = .63). CONCLUSIONS: Patients were highly satisfied with nurse consultations and information around medications regardless of whether they were managed by independent nurse prescribers or nurses using patient group directions. IMPACT: Findings provide evidence in support of autonomous provision of medications by nurses in sexual health clinics.


Subject(s)
Nurse's Role , Patient Satisfaction , Drug Prescriptions , Humans , Referral and Consultation , Surveys and Questionnaires
7.
J Adv Nurs ; 78(1): 239-251, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34652029

ABSTRACT

BACKGROUND: Local services in the United Kingdom National Health Service enable autonomous provision of medication by nurses, supporting individual nurses to gain prescribing qualifications or by introducing local patient group directions. AIM: To compare nurse prescribing and patient group directions about clinic processes, patients' experiences, and costs from the perspectives of providers, nurses, and patients. DESIGN: Mixed methods, comparative case study in five urban sexual health services in the United Kingdom. METHODS: Data were collected from nurse prescribers, patient group direction users and their patients July 2015 to December 2016. Nurse questionnaires explored training (funding and methods). Nurses recorded consultation durations and support from other professionals in clinical diaries. Patient notes were reviewed to explore medication provision, appropriateness and safety; errors were judged by an expert panel. Patients completed satisfaction questionnaires about consultations and information about medications. RESULTS: Twenty-eight nurse prescribers and 67 patient group directions users took part; records of 1682 consultations were reviewed, with 1357 medications prescribed and 98.5% therapeutically appropriate. Most medication decisions were deemed safe (96.0% nurse prescribers, 98.7% patient group directions, Fisher's Exact Test p = .55). Errors were predominantly minor (55.6% nurse prescribers, 62.4% patient group directions) and related to documentation omissions (78.0%); no patients were harmed. Consultation durations and unplanned re-consultations were similar for both groups. Nurse prescribers sought assistance from colleagues less frequently (chi-squared = 46.748, df = 1, p < .001) but spent longer discussing cases. Nurse prescribing training required more resources from providers and nurses, compared with patient group directions. Nurse prescribers were on higher salary bands. Patient satisfaction was high in both groups (>96%). CONCLUSIONS: Nurse medication provision by both nurse prescribers and patient group direction users is safe and associated with high patient satisfaction; effects on clinic processes and costs are similar. Undertaking the prescribing qualification involves independent study but may bring longer-term career progression to nurses.


Subject(s)
Sexual Health , Ambulatory Care Facilities , Drug Prescriptions , Humans , Nurse's Role , Referral and Consultation , State Medicine
8.
FASEB J ; : fj201800413RR, 2018 Jun 19.
Article in English | MEDLINE | ID: mdl-29920218

ABSTRACT

The role of dyslipidemia in the development of retinal dysfunction remains poorly understood. Using an animal model of diet-induced obesity/pre-type 2 diabetes, we investigated molecular defects in the retina arising from consumption of a diet high in saturated fats and sugars ( i.e., a Western diet). We found that feeding mice a Western diet increased the abundance of retinal sphingolipids, attenuated protein kinase B (Akt) phosphorylation, enhanced JNK activation, and increased retinal cell death. When we used palmitate or C6-ceramide (Cer) to assess sphingolipid-mediated signaling in cultured murine and human cells, we observed similar effects on Akt, JNK, and cell death. Furthermore, both Western diet and C6-Cer exposure enhanced expression of the stress-response protein regulated in development and DNA damage response 1 (REDD1) and loss of REDD1 increased C6-Cer-induced JNK activation and cell death. Exogenous REDD1 expression repressed JNK-mediated phosphorylation in cultured cells. We found that thioredoxin-interacting protein (TXNIP) expression was elevated in REDD1-deficient cell lines and C6-Cer promoted TXNIP expression in both wild-type and REDD1-deficient cells. Likewise, TXNIP knockdown attenuated JNK activation and caspase 3 cleavage after either C6-Cer exposure or REDD1 deletion. The results support a model wherein Cer-induced REDD1 expression attenuates TXNIP-dependent JNK activation and retinal cell death.-Dai, W., Miller, W. P., Toro, A. L., Black, A. J., Dierschke, S. K., Feehan, R. P., Kimball, S. R., Dennis, M. D. Deletion of the stress-response protein REDD1 promotes ceramide-induced retinal cell death and JNK activation.

9.
Sleep Breath ; 23(1): 243-250, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30032464

ABSTRACT

PURPOSE: Upper airway exercises for snoring treatment can be effective but difficult to administer and monitor. We hypothesized that a brief, relatively simple daily upper airway exercise regimen, administered by a smartphone application, would reduce snoring and encourage compliance. METHODS: Targeted vowel sounds causing tongue base movements were incorporated into a voice-controlled smartphone game application. Participants with habitual snoring, apnea hypopnea index (AHI) ≤ 14 events/h, and BMI ≤ 32 kg/m2 were randomly assigned to perform 15 min of daily gameplay (intervention group) or 5 s of daily voice recording (control group) and to audio record their snoring for 2 nights/week for up to 12 weeks. Sounds above 60 dB were extracted from recordings for snore classification with machine learning support vector machine classifiers. RESULTS: Sixteen patients (eight in each group) completed the protocol. Groups were similar at baseline in gender distribution (five males, three females), mean BMI (27.5 ± 3.8 vs 27.4 ± 3.8 kg/m2), neck circumference (15.1 ± 1.6 vs 14.7 ± 1.7 in.), Epworth Sleepiness Score (8 ± 3.5 vs 7 ± 4.0), and AHI (9.2 ± 4.0 vs 8.2 ± 3.2 events/h). At 8 weeks, the absolute change in snoring rate (> 60 dB/h) was greater for the intervention group than the control group (- 49.3 ± 55.3 vs - 6.23 ± 23.2; p = 0.037), a 22 and 5.6% reduction, respectively. All bed partners of participants in the intervention group reported reduced snoring volume and frequency, whereas no change was reported for the control group. CONCLUSIONS: Smartphone application-administered upper airway training reduces objective and subjective snoring measures and improves sleep quality. TRIAL REGISTRATION: ClinicalTrials.gov ; no.: NCT03264963; URL: www.clinicaltrials.gov.


Subject(s)
Delivery of Health Care/methods , Exercise Therapy/methods , Oropharynx/physiopathology , Smartphone , Snoring/rehabilitation , Therapy, Computer-Assisted/methods , Adult , Female , Follow-Up Studies , Humans , Male , Middle Aged , Patient Compliance , Polysomnography/methods , Snoring/classification , Snoring/physiopathology , Video Games
10.
BMC Public Health ; 19(1): 374, 2019 Apr 03.
Article in English | MEDLINE | ID: mdl-30943942

ABSTRACT

BACKGROUND: Accounting for nearly one-third of all deaths, cardiovascular disease is the leading cause of mortality and morbidity in the United States. Adverse health behaviors are major determinants of this high incidence of disease. Examining local food and physical activity environments and population characteristics in a poor, rural state may highlight underlying drivers of these behaviors. We aimed to identify demographic and environmental factors associated with both obesity and overall poor cardiovascular health (CVH) behaviors in Maine counties. METHODS: Our cross-sectional study analyzed 40,398 Behavioral Risk Factor Surveillance System (BRFSS) 2011-2014 respondents alongside county-level United States Department of Agriculture (USDA) Food Environment Atlas 2010-2012 measures of the built environment (i.e., density of restaurants, convenience stores, grocery stores, and fitness facilities; food store access; and county income). Poor CVH score was defined as exhibiting greater than 5 out of the 7 risk factors defined by the American Heart Association (current smoking, physical inactivity, obesity, poor diet, hypertension, diabetes, and high cholesterol). Multivariable logistic regression models described the contributions of built environment variables to obesity and overall poor CVH score after adjustment for demographic controls. RESULTS: Both demographic and environmental factors were associated with obesity and overall poor CVH. After adjustment for demographics (age, sex, personal income, and education), environmental characteristics most strongly associated with obesity included low full-service restaurant density (OR 1.34; 95% CI 1.24-1.45), low county median household income (OR 1.31; 95% CI 1.21-1.42) and high convenience store density (OR 1.21; 95% CI 1.12-1.32). The strongest predictors of overall poor CVH behaviors were low county median household income (OR 1.30; 95% CI 1.13-1.51), low full-service restaurant density (OR 1.38; 95% CI 1.19-1.59), and low fitness facility density (OR 1.27; 95% CI 1.11-1.46). CONCLUSIONS: In a rural state, both demographic and environmental factors predict overall poor CVH. These findings may help inform communities and policymakers of the impact of both social determinants of health and local environments on health outcomes.


Subject(s)
Cardiovascular Diseases/etiology , Diet , Environment , Exercise , Health Behavior , Obesity/etiology , Adolescent , Adult , Aged , Aged, 80 and over , Behavioral Risk Factor Surveillance System , Cardiovascular Diseases/epidemiology , Commerce , Cross-Sectional Studies , Fast Foods , Female , Humans , Income , Maine , Male , Middle Aged , Risk Factors , Rural Population , United States , Young Adult
11.
J Health Commun ; 23(5): 435-444, 2018.
Article in English | MEDLINE | ID: mdl-29648962

ABSTRACT

Communicating scientific uncertainty about public health threats is ethically desirable but challenging due to its tendency to promote avoidance of choice options with unknown probabilities-a phenomenon known as "ambiguity aversion." This study examined this phenomenon's potential magnitude, its responses to different communication strategies, and its mechanisms. In a factorial experiment, 2701 adult laypersons in Spain read one of three versions of a hypothetical newspaper article describing a pandemic vaccine-preventable disease (VPD), but varying in scientific uncertainty about VPD risk and vaccine effectiveness: No-Uncertainty, Uncertainty, and Normalized-Uncertainty (emphasizing its expected nature). Vaccination intentions were lower for the Uncertainty and Normalized-Uncertainty groups compared to the No-Uncertainty group, consistent with ambiguity aversion; Uncertainty and Normalized-Uncertainty groups did not differ. Ambiguity-averse responses were moderated by health literacy and mediated by perceptions of vaccine effectiveness, VPD likelihood, and VPD severity. Communicating scientific uncertainty about public health threats warrants caution and further research to elucidate its outcomes, mechanisms, and management.


Subject(s)
Communication , Health Knowledge, Attitudes, Practice , Health Literacy , Influenza, Human/prevention & control , Influenza, Human/psychology , Vaccination/psychology , Adolescent , Adult , Aged , Analysis of Variance , Female , Humans , Influenza A Virus, H7N3 Subtype , Influenza, Human/epidemiology , Male , Middle Aged , Pandemics , Random Allocation , Risk , Spain , Surveys and Questionnaires , Uncertainty , Vaccines/therapeutic use , Young Adult
12.
J Nutr ; 147(9): 1648-1657, 2017 09.
Article in English | MEDLINE | ID: mdl-28768832

ABSTRACT

Background: Fat-enriched diets produce metabolic changes in skeletal muscle, which in turn can mediate changes in gene regulation.Objective: We examined the high-fat-diet-induced changes in skeletal muscle gene expression by characterizing variations in pre-mRNA alternative splicing.Methods: Affymetrix Exon Array analysis was performed on the transcriptome of the gastrocnemius/plantaris complex of male obesity-prone Sprague-Dawley rats fed a 10% or 60% fat (lard) diet for 2 or 8 wk. The validation of exon array results was focused on troponin T (Tnnt3). Tnnt3 splice form analyses were extended in studies of rats fed 10% or 30% fat diets across 1- to 8-wk treatment periods and rats fed 10% or 45% fat diets with fat sources from lard or mono- or polyunsaturated fats for 2 wk. Nuclear magnetic resonance (NMR) was used to measure body composition.Results: Consumption of a 60% fat diet for 2 or 8 wk resulted in alternative splicing of 668 and 726 pre-mRNAs, respectively, compared with rats fed a 10% fat diet. Tnnt3 transcripts were alternatively spliced in rats fed a 60% fat diet for either 2 or 8 wk. The high-fat-diet-induced changes in Tnnt3 alternative splicing were observed in rats fed a 30% fat diet across 1- to 8-wk treatment periods. Moreover, this effect depended on fat type, because Tnnt3 alternative splicing occurred in response to 45% fat diets enriched with lard but not in response to diets enriched with mono- or polyunsaturated fatty acids. Fat mass (a proxy for obesity as measured by NMR) did not differ between groups in any study.Conclusions: Rat skeletal muscle responds to overconsumption of dietary fat by modifying gene expression through pre-mRNA alternative splicing. Variations in Tnnt3 alternative splicing occur independently of obesity and are dependent on dietary fat quantity and suggest a role for saturated fatty acids in the high-fat-diet-induced modifications in Tnnt3 alternative splicing.


Subject(s)
Alternative Splicing/drug effects , Diet, High-Fat , Dietary Fats/pharmacology , Fatty Acids/pharmacology , Muscle Proteins/genetics , Muscle, Skeletal/drug effects , RNA Precursors/metabolism , Adipose Tissue/metabolism , Animals , Dietary Fats/administration & dosage , Dietary Fats/metabolism , Fatty Acids/metabolism , Fatty Acids, Unsaturated/pharmacology , Male , Muscle Proteins/metabolism , Muscle, Skeletal/metabolism , Obesity/genetics , Obesity/metabolism , Rats, Sprague-Dawley , Transcriptome/drug effects , Troponin T/genetics , Troponin T/metabolism
13.
Nutr Cancer ; 67(6): 965-75, 2015.
Article in English | MEDLINE | ID: mdl-26226376

ABSTRACT

Few studies have explored the effects of omega-3 polyunsaturated fatty acid (n-3 PUFA) supplementation on immune modulation in murine models of mammary carcinogenesis. HER-2/neu and PyMT mice were randomized to 2 dietary interventions: AIN-93G-based diet with 1) 11% of diet (per gram weight) as corn oil (CO) or 2) 10% of diet as menhaden fish oil plus 1% of diet as corn oil (FO). FO significantly reduced the incidence and multiplicity of tumors (P < 0.001) in HER-2/neu, but not PyMT mice. FO-fed mice had significantly larger splenocyte counts than CO-fed mice in both the HER-2/neu and PyMT models; and in both models this was comprised of an increase in most cell types, including Gr-1(+)/CD11b(+) cells. T cells from FO-fed HER-2/neu mice produced significantly more interleukin-2 (P = 0.004) and interferon-γ (P = 0.012) in response to in vitro stimulation with anti-CD3 (0.5 µg/ml). Lastly, FO-fed HER-2/neu mice had significantly more tumor immune infiltrates than CO-fed mice, including NK1.1(+), F4/80(+), and Gr-1(+)/CD11b(+) cells (P ≤ 0.05). Greater Th1 cytokine production and significantly more tumor immune infiltrates in FO-fed Her2/neu mice may account for the cancer prevention effect of fish oil in this model.


Subject(s)
Fish Oils/pharmacology , Neoplasms/prevention & control , T-Lymphocytes/drug effects , Animals , Cell Line, Tumor , Corn Oil/pharmacology , Disease Models, Animal , Fatty Acids, Omega-3/pharmacology , Female , Interferon-gamma/metabolism , Interleukin-2/metabolism , Mice , Mice, Transgenic , T-Lymphocytes/metabolism
14.
Appl Opt ; 54(24): 7252-7, 2015 Aug 20.
Article in English | MEDLINE | ID: mdl-26368760

ABSTRACT

We present a new design for spectral-domain optical coherence tomography that allows balanced detection using a single camera. The design uses polarization optics to encode the light in reference and sample arms. Two parallel and highly aligned spectra, which carry out-of-phase interference signals, in-phase common noise, and auto-interference terms, are focused on the camera, which performs the digital balanced detection for each wavelength. The optical system is characterized and tested for tissue imaging. Results demonstrate consistent signal gains in depth and suppression of DC and sample auto-interference. The design could be further amended for polarization-sensitive imaging and might demonstrate a market for manufacturing dual-line cameras with analog-balanced detection capability.


Subject(s)
Tomography, Optical Coherence/methods , Animals , Anisotropy , Equipment Design , Eye/anatomy & histology , Image Processing, Computer-Assisted , Interferometry/methods , Light , Optics and Photonics , Oscillometry/methods , Rats , Signal Processing, Computer-Assisted , Signal-To-Noise Ratio , Spectrophotometry/methods
15.
JAMIA Open ; 7(1): ooae017, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38425704

ABSTRACT

Background: The Observational Health Data Sciences and Informatics (OHDSI) community has emerged as a leader in observational research on real-world clinical data for promoting evidence for healthcare and decision-making. The community has seen rapid growth in publications, citations, and the number of authors. Components of its successful uptake have been attributed to an open science and collaborative culture for research and development. Investigating the adoption of OHDSI as a field of study provides an opportunity to understand how communities embrace new ideas, onboard new members, and enhance their impact. Objective: To track, study, and evaluate an open scientific community's growth and impact. Method: We present a modern architecture leveraging open application programming interfaces to capture publicly available data (PubMed, YouTube, and EHDEN) on open science activities (publication, teaching, and engagement). Results: Three interactive dashboard were implemented for each publicly available artifact (PubMed, YouTube, and EHDEN). Each dashboard provides longitudinal summary analysis and has a searchable table, which differs in the available features related to each public artifact. Conclusion: We discuss the insights enabled by our approach to monitor the growth and impact of the OHDSI community by capturing artifacts of learning, teaching, and creation. We share the implications for different users based on their functional needs. As other scientific networks adopt open-source frameworks, our framework serves as a model for tracking the growth of their community, driving the perception of their development, engaging their members, and attaining higher impact.

16.
Stud Health Technol Inform ; 310: 966-970, 2024 Jan 25.
Article in English | MEDLINE | ID: mdl-38269952

ABSTRACT

The Health-Analytics Data to Evidence Suite (HADES) is an open-source software collection developed by Observational Health Data Sciences and Informatics (OHDSI). It executes directly against healthcare data such as electronic health records and administrative claims, that have been converted to the Observational Medical Outcomes Partnership (OMOP) Common Data Model. Using advanced analytics, HADES performs characterization, population-level causal effect estimation, and patient-level prediction, potentially across a federated data network, allowing patient-level data to remain locally while only aggregated statistics are shared. Designed to run across a wide array of technical environments, including different operating systems and database platforms, HADES uses continuous integration with a large set of unit tests to maintain reliability. HADES implements OHDSI best practices, and is used in almost all published OHDSI studies, including some that have directly informed regulatory decisions.


Subject(s)
Data Science , Electronic Health Records , Humans , Databases, Factual , Reproducibility of Results , Software , Observational Studies as Topic
17.
Fungal Genet Biol ; 56: 147-57, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23608321

ABSTRACT

Ambrosia beetle fungiculture represents one of the most ecologically and evolutionarily successful symbioses, as evidenced by the 11 independent origins and 3500 species of ambrosia beetles. Here we document the evolution of a clade within Fusarium associated with ambrosia beetles in the genus Euwallacea (Coleoptera: Scolytinae). Ambrosia Fusarium Clade (AFC) symbionts are unusual in that some are plant pathogens that cause significant damage in naïve natural and cultivated ecosystems, and currently threaten avocado production in the United States, Israel and Australia. Most AFC fusaria produce unusual clavate macroconidia that serve as a putative food source for their insect mutualists. AFC symbionts were abundant in the heads of four Euwallacea spp., which suggests that they are transported within and from the natal gallery in mandibular mycangia. In a four-locus phylogenetic analysis, the AFC was resolved in a strongly supported monophyletic group within the previously described Clade 3 of the Fusarium solani species complex (FSSC). Divergence-time estimates place the origin of the AFC in the early Miocene ∼21.2 Mya, which coincides with the hypothesized adaptive radiation of the Xyleborini. Two strongly supported clades within the AFC (Clades A and B) were identified that include nine species lineages associated with ambrosia beetles, eight with Euwallacea spp. and one reportedly with Xyleborus ferrugineus, and two lineages with no known beetle association. More derived lineages within the AFC showed fixation of the clavate (club-shaped) macroconidial trait, while basal lineages showed a mix of clavate and more typical fusiform macroconidia. AFC lineages consisted mostly of genetically identical individuals associated with specific insect hosts in defined geographic locations, with at least three interspecific hybridization events inferred based on discordant placement in individual gene genealogies and detection of recombinant loci. Overall, these data are consistent with a strong evolutionary trend toward obligate symbiosis coupled with secondary contact and interspecific hybridization.


Subject(s)
Fusarium/classification , Fusarium/isolation & purification , Genetic Variation , Persea/parasitology , Symbiosis , Weevils/microbiology , Animal Structures/microbiology , Animals , Cluster Analysis , DNA, Fungal/chemistry , DNA, Fungal/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , DNA, Ribosomal Spacer/chemistry , DNA, Ribosomal Spacer/genetics , Fusarium/genetics , Fusarium/physiology , Genes, rRNA , Molecular Sequence Data , Peptide Elongation Factor 1/genetics , Phylogeny , RNA Polymerase II/genetics , RNA, Fungal/genetics , RNA, Ribosomal/genetics , Sequence Analysis, DNA , Weevils/growth & development
18.
Appl Opt ; 52(29): 7165-70, 2013 Oct 10.
Article in English | MEDLINE | ID: mdl-24217734

ABSTRACT

We describe a method for differential phase measurement of Faraday rotation from multiple depth locations simultaneously. A polarization-maintaining fiber-based spectral-domain interferometer that utilizes a low-coherent light source and a single camera is developed. Light decorrelated by the orthogonal channels of the fiber is launched on a sample as two oppositely polarized circular states. These states reflect from sample surfaces and interfere with the corresponding states of the reference arm. A custom spectrometer, which is designed to simplify camera alignment, separates the orthogonal channels and records the interference-related oscillations on both spectra. Inverse Fourier transform of the spectral oscillations in k-space yields complex depth profiles, whose amplitudes and phase difference are related to reflectivity and Faraday rotation within the sample, respectively. Information along a full depth profile is produced at the camera speed without performing an axial scan for a multisurface sample. System sensitivity for the Faraday rotation measurement is 0.86 min of arc. Verdet constants of clear liquids and turbid media are measured at 687 nm.


Subject(s)
Interferometry/instrumentation , Nephelometry and Turbidimetry/instrumentation , Refractometry/instrumentation , Spectrum Analysis/instrumentation , Equipment Design , Equipment Failure Analysis , Light , Phase Transition , Rotation , Scattering, Radiation
19.
J Adv Nurs ; 69(3): 535-45, 2013 Mar.
Article in English | MEDLINE | ID: mdl-22551089

ABSTRACT

AIM: This article is a report of a study to explore the application and safety of non-medical prescribing in an accident and emergency and sexual health department. Background. Since 1 May 2006 non-medical prescribers in the UK have had prescribing powers comparable with doctors. Evidence suggests that nurses give safe, competent, autonomous care packages in their scope of practice but despite the perceived benefits there is limited evidence detailing how it is specifically applied in practice. DESIGN: Cross-sectional comparative design. METHODS: The study explored non-medical prescribing in accident and emergency and sexual health retrospectively reviewing 764 nurse prescribers' case notes. For intra-department comparison 490 case notes from those who could not prescribe were included. Patient attendances from 1 July 2009-30 June 2010 were randomly sampled. Prescribing frequency, range of medications and diagnoses, independent episode completion, and prescribing safety was recorded. RESULTS/FINDINGS: Over 53·5% (n = 409) of prescribers' patients required medication, with 99·8% (n = 568) being clinically appropriate. Analgesia was most commonly prescribed in accident and emergency (31%, n = 85) and antibiotics in sexual health (55%, n = 162). Intra-department comparison of independent episode completion had statistically significant results using the chi-square test in sexual health, but not in accident and emergency. The use of patient group directions in accident and emergency explains this difference. Safe prescribing practice was evident in 99·4% of cases, with a lack of documentation (n = 2) and a contraindicated prescription (n = 1) identified. CONCLUSION: Nurses having access to medication facilitate safe, appropriate, and independent prescribing practice. Further research is advised in this area.


Subject(s)
Drug Prescriptions/nursing , Emergency Medical Services/organization & administration , Nurse Practitioners , Practice Patterns, Nurses'/statistics & numerical data , Primary Health Care/organization & administration , Adolescent , Adult , Aged , Aged, 80 and over , Cross-Sectional Studies , Drug Prescriptions/statistics & numerical data , Female , Humans , London , Male , Middle Aged , Nurse's Role , Professional Autonomy , Reproductive Health , Retrospective Studies , Young Adult
20.
Appl Opt ; 51(14): 2713-21, 2012 May 10.
Article in English | MEDLINE | ID: mdl-22614494

ABSTRACT

Myocardial infarction, caused by a major blockage of a coronary artery, creates a border zone (BZ) between perfused and nonperfused tissue, which is believed to be the origin of fatal cardiac arrhythmias. We used a combination of optical clearing and polarization-sensitive optical coherence tomography to visualize a three-dimensional organization of the BZ in isolated rabbit hearts (n=5) at the microscopic level with a high spatial resolution. We found that the BZ has a complex three-dimensional structure with nonperfused areas penetrating into perfused tissue with finger-like projections. These "fingers" may play an important role in the initiation and maintenance of ventricular arrhythmias.


Subject(s)
Myocardial Infarction/pathology , Tomography, Optical Coherence/methods , Animals , Arrhythmias, Cardiac/etiology , Arrhythmias, Cardiac/pathology , Arrhythmias, Cardiac/physiopathology , Electrophysiological Phenomena , Imaging, Three-Dimensional , In Vitro Techniques , Myocardial Infarction/complications , Myocardial Infarction/physiopathology , Myocardium/pathology , Optical Phenomena , Rabbits
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