Application of a bioinformatics training delivery method for reaching dispersed and distant trainees.
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ABSTRACT:
SUBMITTER: Hall CR
PROVIDER: S-EPMC7971692 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Demand for training life scientists in bioinformatics skills led to the development of a train-the-trainer collaboration between the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-the-trainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors.
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Project description:Gaps in data collection systems, as well as challenges associated with gathering data from rare and dispersed populations, render current health surveillance systems inadequate to identify and monitor efforts to reduce health disparities. Using sexual and gender minorities we investigated the utility of using a large nonprobability online panel to conduct rapid population assessments of such populations using brief surveys. Surveys of the Google Android Panel (four assessing sexual orientation and one assessing gender identity and sex assigned at birth) were conducted resulting in invitation of 53,739 application users (37,505 of whom viewed the invitation) to generate a total of 34,759 who completed screening questions indicating their sexual orientation, or gender identity and sex at birth. Where possible we make comparisons to similar data from two population-based surveys (NHIS and NESARC). We found that 99.4% to 100.0% of respondents across our Google Android panel samples completed the screening questions and 97.8% to 99.2% of those that consented to participate in our surveys indicated they were "OK" with the content of surveys that assessed sexual orientation and sex/gender. In our Google Android panel samples there was a higher percentage of sexual minority respondents than in either NHIS or NESARC with 7.4% of men and 12.4% of women reporting gay, lesbian or bisexual identities. The proportion sexual minority was 2.8 to 5.6 times higher in the Google Android panel samples than was found in the 2012 NHIS sample, for men and women, respectively. The percentage of "transgender" identified individuals in the Google sample was 0.7%, which is similar to 0.5% transgender identified through the Massachusetts BRFSS, and using a transgender status item we found that 2.0% of the overall sample fit could be classified as transgender. The Google samples sometimes more closely approximated national averages for ethnicity and race than NHIS.
| S-EPMC4671660 | biostudies-literature
Project description:Core surgical training programmes are associated with a high risk of burnout. This study aimed to assess the influence of a novel enhanced stress-resilience training (ESRT) course delivered at the start of core surgical training in a single UK statutory education body. All newly appointed core surgical trainees (CSTs) were invited to participate in a 5-week ESRT course teaching mindfulness-based exercises to develop tools to deal with stress at work and burnout. The primary aim was to assess the feasibility of this course; secondary outcomes were to assess degree of burnout measured using Maslach Burnout Inventory (MBI) scoring. Of 43 boot camp attendees, 38 trainees completed questionnaires, with 24 choosing to participate in ESRT (63.2 per cent; male 13, female 11, median age 28 years). Qualitative data reflected challenges delivering ESRT because of arduous and inflexible clinical on-call rotas, time pressures related to academic curriculum demands and the concurrent COVID-19 pandemic (10 of 24 drop-out). Despite these challenges, 22 (91.7 per cent) considered the course valuable and there was unanimous support for programme development. Of the 14 trainees who completed the ESRT course, nine (64.3 per cent) continued to use the techniques in daily clinical work. Burnout was identified in 23 trainees (60.5 per cent) with no evident difference in baseline MBI scores between participants (median 4 (range 0-11) versus 5 (1-11), P = 0.770). High stress states were significantly less likely, and mindfulness significantly higher in the intervention group (P < 0.010); MBI scores were comparable before and after ESRT in the intervention cohort (P = 0.630, median 4 (range 0-11) versus 4 (1-10)). Despite arduous emergency COVID rotas ESRT was feasible and, combined with protected time for trainees to engage, deserves further research to determine medium-term efficacy.
| S-EPMC8320339 | biostudies-literature
Project description:MotivationMany bioinformatics resources are provided as 'web services', with large databases and analysis software stored on a central server, and clients interacting with them using the hypertext transport protocol (HTTP). While some provide only a visual HTML interface, requiring a web browser to use them, many provide programmatic access using a web application programming interface (API) which returns XML, JSON or plain text that computer programs can interpret more easily. This allows access to be automated. Initially, many bioinformatics APIs used the 'simple object access protocol' (SOAP) and, more recently, representational state transfer (REST).ResultsGraphQL is a novel, increasingly prevalent alternative to REST and SOAP that represents the available data in the form of a graph to which any conceivable query can be submitted, and which is seeing increasing adoption in industry. Here, we review the principles of GraphQL, outline its particular suitability to the delivery of bioinformatics resources and describe its implementation in our ZincBind resource.Availability and implementationhttps://api.zincbind.net.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
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Project description:Over the past 20 years, a series of reports written by groups of senior researchers and administrators have recommended changes to improve the training environments for graduate students and postdoctoral researchers in the United States. However, academic institutions and departments have largely failed to implement these recommendations, which has exacerbated the problems faced by these trainees. Here, based on input from trainees at different career stages, we outline seven practical changes that academic institutions and departments can make to improve their training environments.
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Project description:The study aimed to determine whether four weeks of motor imagery training (MIT) of goal-directed reaching (reaching to grasp task) would affect the cortical activity during motor imagery of reaching (MIR) and grasping (MIG) in the same way. We examined cortical activity regarding event-related potentials (ERPs) in healthy young participants. Our study also evaluated the subjective vividness of the imagery. Furthermore, we aimed to determine the relationship between the subjective assessment of motor imagery (MI) ability to reach and grasp and the cortical activity during those tasks before and after training to understand the underlying neuroplasticity mechanisms. Twenty-seven volunteers participated in MIT of goal-directed reaching and two measurement sessions before and after MIT. During the sessions 128-channel electroencephalography (EEG) was recorded during MIR and MIG. Also, participants assessed the vividness of the MI tasks using a visual analog scale (VAS). The vividness of imagination improved significantly (P < .05) after MIT. A repeated measures ANOVA showed that the task (MIR/MIG) and the location of electrodes had a significant effect on the ERP's amplitude (P < .05). The interaction between the task, location, and session (before/after MIT) also had a significant effect on the ERP's amplitude (P < .05). Finally, the location of electrodes and the interaction between location and session had a significant effect on the ERP's latency (P < .05). We found that MIT influenced the EEG signal associated with reaching differently than grasping. The effect was more pronounced for MIR than for MIG. Correlation analysis showed that changes in the assessed parameters due to MIT reduced the relationship between the subjective evaluation of imagining and the EEG signal. This finding means that the subjective evaluation of imagining cannot be a simple, functional insight into the bioelectrical activity of the cerebral cortex expressed by the ERPs in mental training. The changes we noted in ERPs after MIT may benefit the use of non-invasive EEG in the brain-computer interface (BCI) context.Trial registration: NCT04048083.
| S-EPMC9633838 | biostudies-literature
Project description:Neuroimaging has gained widespread use in neuropsychological research and practice. However, there are neither established guidelines on how neuropsychologists might become competent researchers or consumers of neuroimaging data, nor any published studies describing the state of neuroimaging training among neuropsychologists. We report the results of two online surveys, one of 13 expert neuropsychologist-neuroimagers whose responses informed the formulation of a second, larger survey to neuropsychologists-at-large that were a random selection of a third of the members of the International Neuropsychological Society and American Academy of Clinical Neuropsychology. A total of 237 doctoral-level neuropsychologists, or 15.3% of potential participants, provided complete responses. Most respondents (69.2%) received training in neuroimaging, mostly at the post-doctoral level, largely through independent study, clinical conferences, instruction by clinical supervisors, and individualized mentoring, on topics such as neuroimaging modalities in neurology, neuroanatomy, and the appropriate information to glean from neuroradiology reports. Of the remaining respondents who did not receive training in neuroimaging, 64.4% indicated that such training would be very or extremely beneficial to one's career as a neuropsychologist. Both neuropsychologist-neuroimagers and neuropsychologists-at-large provided specific recommendations for training. Findings from this initial effort will guide trainees who seek to develop competence in neuroimaging, and inform future formulations of neuropsychological training.
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Project description:Many biomedical PhD trainees lack exposure to business principles, which limits their competitiveness and effectiveness in academic and industry careers. To fill this training gap, we developed Business and Management Principles for Scientists, a semester-long program that combined didactic exposure to business fundamentals with practical team-based projects aimed at solving real business problems encountered by institutional shared--resource core facilities. The program also included a retreat featuring presentations by and networking with local life science entrepreneurs and final team presentations to expert judges. Quantitative and qualitative metrics were used to evaluate the program's impact on trainees. A pretest-posttest approach was used to assess trainees' baseline knowledge and mastery of module concepts, and each individual's pretest and posttest responses were compared. The mean score improved by more than 17 percentage points. Trainees also took an online survey to provide feedback about the module. Nearly all participants agreed or strongly agreed that the module was a valuable use of their time and will help guide their career decisions and that project work helped drive home module concepts. More than 75% of trainees reported discussing the module with their research advisors, and all of these participants reported supportive or neutral responses. Collectively, the trainee feedback about the module, improvement in test scores, and trainee perception of advisor support suggest that this short module is an effective method of providing scientists with efficient and meaningful exposure to business concepts.
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Project description:The single pellet reaching task is commonly used in rodents to assess the acquisition of fine motor skill and recovery of function following nervous system injury. Although this task is useful for gauging skilled forelimb use in rodents, the process of training animals is labor intensive and variable across studies and labs. To address these limitations, we developed a single pellet reaching paradigm for training and testing group housed mice within their home cage. Mice enter a training compartment attached to the outside of the cage and retrieve millet seeds presented on a motorized pedestal that can be individually positioned to present seeds to either forelimb. To identify optimal training parameters, we compared task participation and success rates between groups of animals that were presented seeds at two different heights (floor vs mouth height) and at different intervals (fixed-time vs trial-based). The mouth height/fixed interval presentation style was most effective at promoting reaching behavior as all mice reached for seeds within 5 d. Using this paradigm, we assessed stroke-induced deficits in home-cage reaching. Following three weeks of baseline training, reaching success rate was ∼40%, with most trials performed during the dark cycle. A forelimb motor cortex stroke significantly decreased interaction with presented seeds within the first 2 d and impaired reaching success rates for the first 7 d. Our data demonstrate that group-housed mice can be efficiently trained on a single pellet reaching task in the home cage and that this assay is sensitive to stroke induced motor impairments.
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Project description:The authors propose a new training method for artificial neural networks (ANNs) in two-class classification tasks such as classifying breast lesions on a mammogram as malignant or benign.Whereas the conventional binary training method uses binary training target values based on the diagnostic truth of a lesion being malignant or benign, the authors use multiple training target values based on more detailed histological diagnosis that presumably are related to the posterior probability of a lesion being malignant. The authors performed Monte Carlo simulation studies in which training target values were assigned based on posterior probability, and they also performed a mammography study in which training target values were assigned according to histological subtypes.These studies showed that the multitarget training method produced less variability in the ANN outputs than the binary training method. The simulation studies also showed that except for when the number of training cases was extremely large, the multitarget training method produced improved overall classification performance over the binary training method.Therefore, the multitarget ANN training method is potentially useful for ANN applications in computer-aided diagnosis of breast cancer.
| S-EPMC3543375 | biostudies-other