Sakshat Labs: India's virtual proteomics initiative.
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ABSTRACT:
SUBMITTER: Ray S
PROVIDER: S-EPMC3393654 | biostudies-literature | 2012
REPOSITORIES: biostudies-literature
Publications
Sakshat Labs: India's virtual proteomics initiative.
Ray Sandipan S Koshy Nicole R NR Diwakar Shyam S Nair Bipin B Srivastava Sanjeeva S
PLoS biology 20120710 7
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Project description:The SARS CoV-2 pandemic forced many college courses to convert to remote instruction almost overnight in the middle of the spring 2020 teaching semester. This article presents two molecular biology labs formerly performed in person by students but converted into virtual labs. The virtual immunocytochemistry experiment teaches the specificity of antibody staining, principles of fluorescent microscopy, diversity of brain cell types and morphologies, and journal article Figure construction skills. The virtual Western blotting experiment teaches sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), the specificity of antibody binding, and graph creation and interpretation skills. Both virtual experiments use professionally-produced web-based videos of scientists conducting the lab procedures. Students must answer questions about the techniques and analyze real experimental data generated by past students to take a quiz and write a journal article-style lab report. At the whole-class level, student quiz and lab report scores from these virtual labs were not statistically different from those from the in-person versions of the same labs from a previous semester, using t tests with the Bonferroni correction. On the virtual Western blot quiz, students who did the virtual version actually scored higher than students who did the in-person version. These results were significant when the 2020 data were analyzed by within-student paired t tests for in-person labs done before COVID-19 versus those done virtually after dismissal for all-remote instruction. The students learned the laboratory concepts and data analysis skills just as well virtually as their predecessors had in person. However, the students trained virtually reported that they could not enter the lab and actually do Western blotting or fluorescent immunocytochemistry with their own hands without extensive additional training. These virtual experiments can be done with data included in the supplemental materials or can easily be adapted for any micrographs or Western blotting images available from previous lab experiments, or in the published literature. When COVID-19 or other public health emergencies necessitate remote instruction and we can't use the best practice of hands-on lab work, virtual labs can be the next best thing to being there.
| S-EPMC10653236 | biostudies-literature
Project description:We assessed the effectiveness of a quality improvement project to reduce routine labs in clinically stable patients, while also promoting sleep-friendly lab timing. The electronic health record was modified with an "Order Sleep" shortcut to facilitate sleep-friendly lab draws. A "4 AM Labs" column was added to electronic patient lists to signal which patients had early morning labs ordered. Among 7,045 patients over 50,951 total patient-days, on average we observed 26.3% fewer routine lab draws per patient-day per week postintervention (4.68 before vs 3.45 after; difference, 1.23; 95% CI, 0.82-1.63; P < .05). In interrupted time series analysis, the "Order Sleep" tool was associated with a significant increase in sleep-friendly lab orders per encounter per week on resident medicine services (intercept, 1.03; standard error (SE), 0.29; P < .001). The "4 AM Labs" column was associated with a significant increase in sleep-friendly lab orders per patient encounter per week on the hospitalist medical service (intercept, 1.17; SE, 0.50; P = .02). We demonstrate the success of an initiative to simultaneously reduce daily labs and improve sleep-friendly ordering.
| S-EPMC7518135 | biostudies-literature
Project description:IntroductionImmersive virtual reality (VR) based laboratory demonstrations have been gaining traction in STEM education as they can provide virtual hands-on experience. VR can also facilitate experiential and visual learning and enhanced retention. However, several optimizations of the implementation, in-depth analyses of advantages and trade-offs of the technology, and assessment of receptivity of modern techniques in STEM education are required to ensure better utilization of VR-based labs.MethodsIn this study, we developed VR-based demonstrations for a biomolecular engineering laboratory and assessed their effectiveness using surveys containing free responses and 5-point Likert scale-based questions. Insta360 Pro2 camera and Meta Quest 2 headsets were used in combination with an in-person lab. A cohort of 53 students watched the experimental demonstration on VR headsets in the lab after a brief lab overview in person and then performed the experiments in the lab.ResultsOnly 28.29% of students reported experiencing some form of discomfort after using the advanced VR equipment as opposed to 63.63% of students from the previous cohort. About 40% of the students reported that VR eliminated or reduced auditory and visual distractions from the environment, the length of the videos was appropriate, and they received enough information to understand the tasks.DiscussionThe traditional lab method was found to be more suitable for explaining background information and lab concepts while the VR was found to be suitable for demonstrating lab procedures and tasks. Analyzing open-ended questions revealed several factors and recommendations to overcome the potential challenges and pitfalls of integrating VR with traditional modes of learning. This study provides key insights to help optimize the implementation of immersive VR to effectively supplement in-person learning experiences.
| S-EPMC10985327 | biostudies-literature
Project description:The COVID-19 pandemic radically and without warning changed the laboratory learning environment for students and instructors. Students were faced with having to be receptive to new learning methods; instructors scrambled to devise innovative ways of providing a realistic lab experience for students. The demand for creative online teaching strategies and the expansion of gamified training platforms created an opportunity for the development of new and interactive lab experiences. Current online labs offer some elements of a "real" lab experience, but a system that incorporates all the tools needed to create a realistic, immersive lab environment has yet to be developed. This study examines using different gamification elements implemented in a PowerPoint-based platform. There was no cost associated with the virtual lab and it could be easily downloaded, increasing accessibility. In true gaming style, a student could "play" without restriction, without the limitations that accompany wet labs. Students were challenged with various scenarios throughout the lab, making choices and receiving feedback through the process. These features positively impacted student outcomes and improved engagement, as expressed in end-of-course evaluations. The implementation also stressed the need for further development of embedded assessments, competitive and interactive opportunities for students, and access to detailed learning analytics for instructors.
| S-EPMC8046662 | biostudies-literature
Project description:The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.
| S-EPMC3193076 | biostudies-literature
Project description:BackgroundPoor intrapartum care in India contributes to high maternal and newborn mortality. India's Labor Room Quality Improvement Initiative (LaQshya) launched in 2017, aims to improve intrapartum care by minimizing complications, enforcing protocols, and promoting respectful maternity care (RMC). However, limited studies pose a challenge to fully examine its potential to assess quality of maternal and newborn care. This study aims to bridge this knowledge gap and reviews LaQshya's ability to assess maternal and newborn care quality. Findings will guide modifications for enhancing LaQshya's effectiveness.MethodsWe reviewed LaQshya's ability to assess the quality of care through a two-step approach: a comprehensive descriptive analysis using document reviews to highlight program attributes, enablers, and challenges affecting LaQshya's quality assessment capability, and a comparison of its measurement parameters with the 352 quality measures outlined in the WHO Standards for Maternal and Newborn Care. Comparing LaQshya with WHO standards offers insights into how its measurement criteria align with global standards for assessing maternity and newborn care quality.ResultsLaQshya utilizes several proven catalysts to enhance and measure quality- institutional structures, empirical measures, external validation, certification, and performance incentives for high-quality care. The program also embodies contemporary methods like quality circles, rapid improvement cycles, ongoing facility training, and plan-do-check, and act (PDCA) strategies for sustained quality enhancement. Key drivers of LaQshya's assessment are- leadership, staff mentoring, digital infrastructure and stakeholder engagement from certified facilities. However, governance issues, understaffing, unclear directives, competency gaps, staff reluctance towards new quality improvement approaches inhibit the program, and its capacity to enhance quality of care. LaQshya addresses 76% of WHO's 352 quality measures for maternal and newborn care but lacks comprehensive assessment of crucial elements: harmful labor practices, mistreatment of mothers or newborns, childbirth support, and effective clinical leadership and supervision.ConclusionLaQshya is a powerful model for evaluating quality of care, surpassing other global assessment tools. To achieve its maximum potential, we suggest strengthening district governance structures and offering tailored training programs for RMC and other new quality processes. Furthermore, expanding its quality measurement metrics to effectively assess provider accountability, patient outcomes, rights, staff supervision, and health facility leadership will increase its ability to assess quality improvements.
| S-EPMC10993574 | biostudies-literature
Project description:BackgroundThe eHealth initiative of the Conference and Labs of the Evaluation Forum (CLEF) has aimed since 2012 to provide researchers working on health text analytics with annual workshops, shared development challenges and tasks, benchmark datasets, and software for processing and evaluation. In 2012, it ran as a scientific workshop with the aim of establishing an evaluation lab, and since 2013, this annual workshop has been supplemented with 3 or more preceding labs each year. An evaluation lab is an activity where the participating individuals or teams' goal is to solve the same problem, typically using the same dataset in a given time frame. The overall purpose of this initiative is to support patients, their next of kin, clinical staff, health scientists, and health care policy makers in accessing, understanding, using, and authoring health information in a multilingual setting. In the CLEF eHealth 2013 to 2017 installations, the aim was to address patient-centric text processing. From 2015, the scope was also extended to aid both patients' understanding and clinicians' authoring of various types of medical content. CLEF eHealth 2017 introduced a new pilot task on technology-assisted reviews (TARs) in empirical medicine in order to support health scientists and health care policymakers' information access.ObjectivesThis original research paper reports on the outcomes of the first 6 installations of CLEF eHealth from 2012 to 2017. The focus is on measuring and analyzing the scholarly influence by reviewing CLEF eHealth papers and their citations.MethodsA review and bibliometric study of the CLEF eHealth proceedings, working notes, and author-declared paper extensions were conducted. Citation content analysis was used for the publications and their citations collected from Google Scholar.ResultsAs many as 718 teams registered their interest in the tasks, leading to 130 teams submitting to the 15 tasks. A total of 184 papers using CLEF eHealth data generated 1299 citations, yielding a total scholarly citation influence of almost 963,000 citations for the 741 coauthors, and included authors from 33 countries across the world. Eight tasks produced statistically significant improvements (2, 3, and 3 times with P<.001, P=.009, and P=.04, respectively) in processing quality by at least 1 out of the top 3 methods.ConclusionsThese substantial participation numbers, large citation counts, and significant performance improvements encourage continuing to develop these technologies to address patient needs. Consequently, data and tools have been opened for future research and development, and the CLEF eHealth initiative continues to run new challenges.
| S-EPMC6086930 | biostudies-literature
Project description:IntroductionTrainees underrepresented in medicine (URiM) face additional challenges seeking community in predominantly white academic spaces, as they juggle the effects of institutional, interpersonal, and internalized racism while undergoing medical training. To offer support and a space to share these unique experiences, mentorship for URiM trainees is essential. However, URiM trainees have limited access to mentorship from URiM faculty. To address this gap, we developed a national virtual mentoring program that paired URiM trainees interested in emergency medicine (EM) with experienced mentors.MethodsWe describe the implementation of a virtual Diversity Mentoring Initiative (DMI) geared toward supporting URiM trainees interested in EM. The program development involved 1) partnering of national EM organizations to obtain funding; (2) identifying a comprehensive platform to facilitate participant communication, artificial intelligence-enabled matching, and ongoing data collection; 3) focusing on targeted recruitment of URiM trainees; and (4) fostering regular leadership meeting cadence to customize the platform and optimize the mentorship experience.ConclusionWe found that by using a virtual platform, the DMI enhanced the efficiency of mentor-mentee pairing, tailored matches based on participants' interests and the bandwidth of mentors, and successfully established cross-institutional connections to support the mentorship needs of URiM trainees.
| S-EPMC10393448 | biostudies-literature
Project description:GoalThe American Association of Colleges of Pharmacy (AACP) Leadership Development Special Interest Group (LD SIG) held a one-hour "Virtual Think Tank" (VTT) interactive session in 2020 for pharmacy educators interested in leadership development. The purpose of this study was to evaluate the quantitative and qualitative outcomes of this VTT.MethodsVTT attendees worked together in small groups created based on pre-selected common interest areas related to leadership development to create collaborative leadership initiative plans (CLIPs), which were ideas for new collaborative scholarly or programmatic initiatives.Principal findingsQuantitative outcomes of this VTT included statistically significant increases in positive perceptions toward the organization hosting the VTT regarding networking, scholarly collaboration, educational collaboration, and professional service opportunities, as well as significant improvements in attitudes regarding engagement with the sponsoring organization. Additionally, 18.4% of VTT attendees continued communicating with CLIP groups post-VTT and 13.2% of respondents indicated that they successfully implemented the CLIP ideas that were generated during the VTT. Qualitative outcomes included findings that the two most commonly encountered barriers were insufficient traction of the initial idea and lack of time (41.9% (n = 13) for both). Other barriers included lack of alignment with priorities at 12.9% (n = 4).Practical applicationsThis leadership VTT for pharmacy academicians led to development and implementation of important scholarly and programmatic outcomes, and fostered cross-institutional partnerships. Findings from this study evaluating a VTT provide a framework of expectations for other organizations seeking to implement a similar initiative.
| S-EPMC10839148 | biostudies-literature
Project description:As part of the Dystrophia Myotonica Biomarker Discovery Initiative (DMBDI) a dataset was obtained from 35 participants, including 31 Myotonic Dystrophy type 1 (DM1) cases and four unaffected controls. All DM1 cases in this research were heterozygous for the abnormally expanded CTG repeat. The mode of the length of the DM1 CTG expansion (Modal Allele Length, MAL) was determined by small-pool PCR of blood DNA for 35/36 patients. For this work we did not attempt to measure the repeat length from muscle, due to a very high degree of repeat instability in muscle cells, and associated difficulties in its experimental measurement. One patient refused blood donation. For each of the 35 blood-donating patients mRNA expression profiling of blood was performed using Affymetrix GeneChip™ Human Exon 1.0 ST microarray. For 28 of 36 patients a successful quadriceps muscle biopsy was obtained. The muscle tissue was mRNA profiled using the same type of microarray. In total, a complete set of samples (blood and muscle) was obtained for 27 of 36 patients; samples were given a disease staging score based on muscle impairment rating. mRNA profiling was carried out by the GeneLogic service lab (on a fee-for-service basis) using standard Affymetrix hybridisation protocol.
2019-05-31 | E-MTAB-7983 | biostudies-arrayexpress