ICollections methodology: workflow, results and lessons learned.
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ABSTRACT:
SUBMITTER: Blagoderov V
PROVIDER: S-EPMC5665009 | biostudies-literature | 2017
REPOSITORIES: biostudies-literature
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<i>iCollections</i> methodology: workflow, results and lessons learned.
Blagoderov Vladimir V Penn Malcolm M Sadka Mike M Hine Adrian A Brooks Stephen S Siebert Darrell J DJ Sleep Chris C Cafferty Steve S Cane Elisa E Martin Geoff G Toloni Flavia F Wing Peter P Chainey John J Duffell Liz L Huxley Rob R Ledger Sophie S McLaughlin Caitlin C Mazzetta Gerardo G Perera Jasmin J Crowther Robyn R Douglas Lyndsey L Durant Joanna J Honey Martin M Huertas Blanca B Howard Theresa T Carter Victoria V Albuquerque Sara S Paterson Gordon G Kitching Ian J IJ
Biodiversity data journal 20170925 5
The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects - iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens represent ...[more]
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Project description:The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects - iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.
| S-EPMC5665004 | biostudies-literature
Project description:BackgroundWorkflow automation, which involves identifying sequences of tasks that can be streamlined by using technology and modern computing, offers opportunities to address the United States health care system's challenges with quality, safety, and efficiency. Other industries have successfully implemented workflow automation to address these concerns, and lessons learned from those experiences may inform its application in health care.ObjectiveOur aim was to identify and synthesize (1) current approaches in workflow automation across industries, (2) opportunities for applying workflow automation in health care, and (3) considerations for designing and implementing workflow automation that may be relevant to health care.MethodsWe conducted a targeted review of peer-reviewed and gray literature on automation approaches. We identified relevant databases and terms to conduct the searches across sources and reviewed abstracts to identify 123 relevant articles across 11 disciplines.ResultsWorkflow automation is used across industries such as finance, manufacturing, and travel to increase efficiency, productivity, and quality. We found automation ranged from low to full automation, and this variation was associated with task and technology characteristics. The level of automation is linked to how well a task is defined, whether a task is repetitive, the degree of human intervention and decision-making required, and the sophistication of available technology. We found that identifying automation goals and assessing whether those goals were reached was critical, and ongoing monitoring and improvement would help to ensure successful automation.ConclusionUse of workflow automation in other industries can inform automating health care workflows by considering the critical role of people, process, and technology in design, testing, implementation, use, and ongoing monitoring of automated workflows. Insights gained from other industries will inform an interdisciplinary effort by the Office of the National Coordinator for Health Information Technology to outline priorities for advancing health care workflow automation.
| S-EPMC8318703 | biostudies-literature
Project description:IntroductionNowadays, minimally invasive surgery in kidney transplantation is a reality thanks to robotic assistance. In this paper, we describe our experience, how we developed the robotic assisted Kidney transplantation (RAKT) technique, and analyze our results. Material and Methods. This is a retrospective study of all RAKTs performed at our center between July 2015 and March 2020. We describe the donor selection, surgical technique, and analyze the surgical results and complications. A comparison between the first 20 cases and the following ones is performed.ResultsDuring the aforementioned period, 82 living donor RAKTs were performed. The mean age was 47.4 ± 13.4 and 50 (61%) were male. Mean body mass index was 25 ± 4.7 and preemptive in 63.7% of cases. Right kidneys and multiple arteries were seen in 14.6% and 12.2%, respectively. Mean operative and rewarming time was 197 ± 42 and 47 ± 9.6 minutes, respectively. Five cases required conversion to open surgery because of abnormal kidney vascularization. Two patients required embolization for subcapsular and hypogastric artery bleeding without repercussion. Three kidneys were lost, two of them due to acute rejection and one because venous thrombosis. Late complications requiring surgery included one kidney artery stenosis, one ureteral stenosis, two lymphoceles, and three hernia repairs. We noticed a significant reduction in time between the first 20 cases and the following ones from 248.25 ± 38.1 to 189.75 ± 25.3 (p < 0.05). With a mean follow-up time of 1.8 years (SD 1.3), the mean creatinine was 1.52 (SD 0.7) and RAKT graft survival was 98%.ConclusionsThe robotic approach is an attractive, minimally invasive method for kidney transplantation, yielding good results. Further studies are needed to consider it a standard approach.
| S-EPMC7484686 | biostudies-literature
Project description:Pharmacogenomic (PGx) evidence for selective serotonin reuptake inhibitors (SSRIs) continues to evolve. For sites offering testing, maintaining up-to-date interpretations and implementing new clinical decision support (CDS) driven by existing results creates practical and technical challenges. Vanderbilt University Medical Center initiated panel testing in 2010, added CYP2D6 testing in 2017, and released CDS for SSRIs in 2020. We systematically reinterpreted historic CYP2C19 and CYP2D6 genotypes to update phenotypes to current nomenclature and to launch provider CDS and patient-oriented content for SSRIs. Chart review was conducted to identify and recontact providers caring for patients with current SSRI therapy and new actionable recommendations. A total of 15,619 patients' PGx results were reprocessed. Of the non-deceased patients reprocessed, 21% (n = 3278) resulted in CYP2C19*1/*17 reinterpretations. Among 289 patients with an actionable recommendation and SSRI medication prescription, 31.8% (n = 92) did not necessitate contact of a clinician, while 43.2% (n = 125) resulted in clinician contacted, and for 25% (n = 72) no appropriate clinician was able to be identified. Maintenance of up-to-date interpretations and recommendations for PGx results over the lifetime of a patient requires continuous effort. Reprocessing is a key strategy for maintenance and expansion of PGx content to be periodically considered and implemented.
| S-EPMC8617828 | biostudies-literature
Project description:PURPOSE:In genomics, the return of negative screening results for rare, medically actionable conditions in large unselected populations with low prior risk of disease is novel and may involve important and nuanced concerns for communicating their meaning. Recruitment may result in self-selection because of participants' personal or family history, changing the characteristics of the screened population and interpretation of both positive and negative findings; prior motivations may also affect responses to results. METHODS:Using data from GeneScreen, an exploratory adult screening project that targets 17 genes related to 11 medically actionable conditions, we address four questions: (1) Do participants self-select based on actual or perceived risk for one of the conditions? (2) Do participants understand negative results? (3) What are their psychosocial responses? (4) Are negative results related to changes in reported health-related behaviors? RESULTS:We found disproportionate enrollment of individuals at elevated prior risk for conditions being screened, and a need to improve communication about the nature of screening and meaning of negative screening results. Participants expressed no decision regret and did not report intention to change health-related behaviors. CONCLUSION:This study illuminates critical challenges to overcome if genomic screening is to benefit the general population.
| S-EPMC6281871 | biostudies-literature
Project description:ObjectiveMaternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement.MethodsA convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR.ResultsThirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism).ConclusionsUnderstanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.
| S-EPMC6721610 | biostudies-literature
Project description:Introduction. The Helping Babies Breathe (HBB) curriculum is an established, effective method to combat neonatal mortality. The COVID-19 pandemic has disrupted in-person HBB training sessions worldwide, portending deficits in the dissemination of this important intervention. Methods. A pilot study to compare in-person versus virtual HBB training among US-based pediatric and family medicine residents. Two HBB master trainers condensed the curriculum into an abbreviated course that was offered to 14 learners in-person (n = 6) and virtually via Zoom (n = 8). A standardized 10-item survey was administered before and after the session to measure reported self-efficacy of critical elements of HBB. Difference of difference analysis was performed to detect differences in post vs pre-training results among the 2 groups using STATA MP 15. Results. All learners showed improvement in preparedness, assessment, and skills subcomponents of self-efficacy with no notable differences based on the type of learning medium. At baseline, in-person learners had a 7-point higher self-efficacy score (69.7) in comparison to virtual learners (62.8; P = .26). After training, the confidence score improved significantly; by 14.3 units for in-person learners (P = .01) and 12.9 for virtual learners (P = .04). There was no statistically significant difference in improvement between the 2 groups (P = .67). Furthermore, all learners passed the post-training knowledge assessment. Discussion. Virtual learning of HBB may be an alternative option in the setting of resource and travel limitations. Future work needs to assess possible differences in attainment of assessment skills and retention of the HBB curriculum among virtual learners.
| S-EPMC8172947 | biostudies-literature
Project description:Since its start in 1998, Software Carpentry has evolved from a week-long training course at the US national laboratories into a worldwide volunteer effort to improve researchers' computing skills. This paper explains what we have learned along the way, the challenges we now face, and our plans for the future.
| S-EPMC3976103 | biostudies-literature
Project description:BackgroundSustained, routine care is vital to the health of people with HIV (PWH) and decreasing transmission of HIV. We evaluated whether the identification of PWH at-risk of falling out of care and prompts for outreach were effective in retaining PWH in care in the United States.MethodsIn this cluster randomized controlled trial, 20 AIDS Healthcare Foundation Healthcare Centers (HCCs) were randomized to the intervention (n = 10) or control (n = 10) arm; all maintained existing retention efforts. The intervention included daily automated flags in CHORUS™, a mobile app and web-based reporting solution utilizing electronic health record data, that identified PWH at-risk of falling out of care to clinic staff. Among flagged PWH, the association between the intervention and visits after a flag was assessed using logistic regression models fit with generalized estimating equations (independent correlation structure) to account for clustering. To adjust for differences between HCCs, models included geographic region, number of PWH at HCC, and proportions of PWH who self-identified as Hispanic or had the Ryan White Program as a payer.ResultsOf 15,875 PWH in care, 56% were flagged; 76% (intervention) and 75% (control) resulted in a visit, of which 76% were within 2 months of the flag. In adjusted analyses, flags had higher odds of being followed by a visit (odds ratio [OR]: 1.08, 95% confidence interval [CI]: 0.97, 1.21) or a visit within 2 months (OR: 1.07, 95% CI: 0.97, 1.17) at intervention than control HCCs. Among at-risk PWH with viral loads at baseline and study end, the proportion with < 50 copies/mL increased in both study arms, but more so at intervention (65% to 74%) than control (62% to 67%) HCCs.ConclusionDespite challenges of the COVID-19 pandemic, adding an intervention to existing retention efforts, and the reality that behavior change takes time, PWH flagged as at-risk of falling out of care were marginally more likely to return for care at intervention than control HCCs and a greater proportion achieved undetectability. Sustained use of the retention module in CHORUS™ has the potential to streamline retention efforts, retain more PWH in care, and ultimately decrease transmission of HIV.Trial registrationThe study was first registered at Clinical Trials.gov (NCT04147832, https://clinicaltrials.gov/show/NCT04147832 ) on 01/11/2019.
| S-EPMC9685944 | biostudies-literature
Project description:To determine trends in either frog distribution or abundance in the State of Louisiana, we reviewed and analyzed frog call data from the Louisiana Amphibian Monitoring Program (LAMP). The data were collected between 1997 and 2017 using North American Amphibian Monitoring Program protocols. Louisiana was divided into three survey regions for administration and analysis: the Florida Parishes, and 2 areas west of the Florida parishes called North and South. Fifty-four routes were surveyed with over 12,792 stops and 1,066 hours of observation. Observers heard 26 species of the 31 species reported to be in Louisiana. Three of the species not heard were natives with ranges that did not overlap with survey routes. The other two species were introduced species, the Rio Grande Chirping Frog (Eleutherodactylus cystignathoides) and the Cuban Treefrog (Osteopilus septentrionalis). Both seem to be limited to urban areas with little to no route coverage. The 15 most commonly occurring species were examined in detail using the percentage of stops at which they observed along a given survey and their call indices. Most species exhibited a multimodal, concave, or convex pattern of abundance over a 15-year period. Among LAMP survey regions, none of the species had synchronous population trends. Only one group of species, winter callers, regularly co-occur. Based on the species lists, the North region could be seen as a subset of the South. However, based on relative abundance, the North was more similar to Florida parishes for both the winter and summer survey runs. Our analyses demonstrate that long-term monitoring (10 years or more) may be necessary to determine population and occupancy trends, and that frog species may have different local demographic patterns across large geographic areas.
| S-EPMC8483421 | biostudies-literature