Yoxas/statistical_literacy huggingface dataset:
Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.
Advances in single-cell biotechnology have increasingly revealed interactions of cells with their surroundings, suggesting a cellular society at the microscale. Similarities between cells and humans across multiple hierarchical levels have quantitative inference potential for reaching insights about phenotypic interactions that lead to morphological forms across multiple scales of cellular organization, namely cells, tissues and organs. Here, the functional and structural comparisons between how cells and individuals fundamentally socialize to give rise to the spatial organization are investigated. Integrative experimental cell interaction assays and computational predictive methods shape the understanding of societal perspective in the determination of the cellular interactions that create spatially coordinated forms in biological systems. Emerging quantifiable models from a simpler biological microworld such as bacterial interactions and single-cell organisms are explored, providing a route to model spatio-temporal patterning of morphological structures in humans. This analogical reasoning framework sheds light on structural patterning principles as a result of biological interactions across the cellular scale and up.
Advances in single-cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high-dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single-cell RNA sequencing (scRNA-seq) analysis, for high-dimensional flow cytometric data analysis. Based on a 20-marker antibody panel and analyses of T-cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high-dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8+ T-cell population defined as CD8+CD45RA+CD27+CD161+ T cell that was predominantly present in CB. We characterised its IFN-γ-producing and potential cytotoxic properties using flow cytometry experiments and scRNA-seq analysis from a published dataset. Collectively, we identified a unique human CB CD8+CD45RA+CD27+CD161+ T-cell subset and demonstrated that Seurat, a widely used package for scRNA-seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high-dimensional data using a single analytical pipeline and opens a novel avenue for data-driven investigation in clinical immunology.
Advances in technology and artificial intelligence (smart healthcare) open up a range of possibilities for precision intervention in the field of health sciences. The objectives of this study were to analyse the functionality of using supervised (prediction and classification) and unsupervised (clustering) machine learning techniques to analyse results related to the development of functional skills in patients at developmental ages of 0-6 years. We worked with a sample of 113 patients, of whom 49 were cared for in a specific centre for people with motor impairments (Group 1) and 64 were cared for in a specific early care programme for patients with different impairments (Group 2). The results indicated that in Group 1, chronological age predicted the development of functional skills at 85% and in Group 2 at 65%. The classification variable detected was functional development in the upper extremities. Two clusters were detected within each group that allowed us to determine the patterns of functional development in each patient with respect to functional skills. The use of smart healthcare resources has a promising future in the field of early care. However, data recording in web applications needs to be planned, and the automation of results through machine learning techniques is required.
Advances in technology are changing surgical education. Simulation provides an important adjunct to operative experience. This pedagogy has arguably become more important in light of the COVID-19 pandemic, with resultant reduction in operative exposure for trainees. Virtual reality (VR) simulators may provide significant contribution to experiential learning; however, much of the investigative focus to date has, correctly, been on establishing validity evidence for these constructs. The aim of this work was to perform a scoping review to assess the current status of VR simulation education to determine curricular development efforts for orthopedic residents. With a trained medical librarian, searches of PubMed, EMBASE, and Web of Science were conducted for all articles in the last 10 years (September 2011-September 2021). Controlled vocabulary Medical Subject Headings (MeSH) terms and natural language developed with subject matter experts describing virtual reality or VR simulation and orthopedic training were used. Two trained reviewers evaluated all abstracts for inclusion. Exclusion criteria were all articles that did not assess VR simulation education involving orthopedic residents. Data were extracted from the included full-text articles including: study design, type of participants, type of VR simulation, simulated orthopedic skill, type of educational event, learner assessment including Kirkpatrick's level, assessment of quality using the Medical Education Research Study Quality Instrument (MERSQI), and level of effectiveness (LoE). Initial search identified 1,394 articles, of which 61 were included in the final qualitative synthesis. The majority (54%) were published in 2019- 2021, 49% in Europe. The commonest VR simulator was ArthroS (23%) and the commonest simulated skill was knee arthroscopy (33%). The majority of studies (70%) focused on simulator validation. Twenty-three studies described an educational module or curriculum, and of the 21 (34%) educational modules, 43% were one-off events. Most modules (18/21, 86%) assessed learners at Kirkpatrick level 2. With regard to methodological quality, 44% of studies had MERSQI 11.5-15 and 89% of studies had LoE of 2. Two studies had LoE of 3. Current literature pertaining to VR training for orthopedic residents is focused on establishing validity and rarely forms part of a curriculum. Where the focus is education, the majority are discrete educational modules and do not teach a comprehensive amalgam of orthopedic skills. This suggests focus is needed to embed VR simulation training within formal curricula efforts guided by the work of Kern, and assess the efficacy of these against patient outcomes.
Adverse Childhood Experience (ACE) has detrimental impacts on neural development, especially hippocampal morphometry. Mindfulness-Based Interventions (MBI) has been shown to induce adaptive hippocampal changes especially at the subiculum. The present study aims to investigate the effects of MBI on subiculum volumes among ACE survivors, as well as the effects on episodic memory as a probe into hippocampal functionality. We analyzed anatomical MRI data and performance indices from an episodic memory task called the Mnemonic Similarity Task (MST) collected from a randomized controlled longitudinal study that compared an 8-week MBI (N = 20) to an active control condition of Stress Management Education (SME) (N = 19). FreeSurfer 6.0 was used for automated hippocampal subfield segmentation and volumetric estimation. Significant group differences were observed with the volumetric changes of the right whole hippocampus and right subiculum. Only the MBI group showed improved pattern separation capability from MST, which was associated with stress reduction and right subiculum volumetric changes. Modest sample size. MST task was performed outside of MRI. These findings suggest beneficial effects of MBI for hippocampal volumes and episodic memory, while highlighting the importance of the subiculum for MBI-induced neural and cognitive changes. The subiculum's known role in inhibitory control was interpreted as a potential mechanism for it to exhibit MBI-induced volumetric changes, which sheds light on the potential neural underpinnings of mindfulness meditation for reducing stress reactivity among ACE survivors.
Adverse Childhood Experiences (ACEs) are potentially traumatic events that occur before the age of 18. Researchers have examined the negative associations between adversity and adolescent and adult outcomes, such as education and physical health. However, research on ACEs, and their association with other outcomes in non-western contexts is sparse. The present study aims to increase our understanding of the prevalence of ACEs - and their association with educational aspirations - in low- and middle-income country contexts. We utilize data from the Family Migration and Early Life Outcomes (FAMELO) project, a multi-site survey project that collected data from families in historically high-migration contexts. ACEs and educational aspirations were measured in children aged 11 to17 years in Mexico (n = 853), Mozambique (n = 651), and Nepal (n = 1180). We use Poisson regressions to examine the prevalence of ACEs in multiple cultures, and then use multinomial logistic regressions to examine whether ACEs are associated with educational aspirations, as a practical application of the utility of the ACEs framework in cross-cultural contexts. Our results suggest that adolescents in Mozambique have a higher average number of ACEs (2.7) than adolescents in Mexico (1.4) and Nepal (1.3). Female adolescents reported fewer ACEs, while socioeconomic vulnerabilities (low-income and low parental education) were associated with higher exposure to ACEs, with differences by country. Lastly, ACEs were associated with lower educational aspirations in Mexico and Nepal. Our study attempted to heed the call of many scholars who have pushed for an expansion of research on ACEs in non-western, low- and middle-income country contexts.
Adverse drug events (ADEs) are associated with poor outcomes and increased costs but may be prevented with prediction tools. With the National Institute of Health All of Us (AoU) database, we employed machine learning (ML) to predict selective serotonin reuptake inhibitor (SSRI)-associated bleeding. The AoU program, beginning in 05/2018, continues to recruit ≥ 18 years old individuals across the United States. Participants completed surveys and consented to contribute electronic health record (EHR) for research. Using the EHR, we determined participants who were exposed to SSRIs (citalopram, escitalopram, fluoxetine, fluvoxamine, paroxetine, sertraline, vortioxetine). Features (n = 88) were selected with clinicians' input and comprised sociodemographic, lifestyle, comorbidities, and medication use information. We identified bleeding events with validated EHR algorithms and applied logistic regression, decision tree, random forest, and extreme gradient boost to predict bleeding during SSRI exposure. We assessed model performance with area under the receiver operating characteristic curve statistic (AUC) and defined clinically significant features as resulting in > 0.01 decline in AUC after removal from the model, in three of four ML models. There were 10,362 participants exposed to SSRIs, with 9.6% experiencing a bleeding event during SSRI exposure. For each SSRI, performance across all four ML models was relatively consistent. AUCs from the best models ranged 0.632-0.698. Clinically significant features included health literacy for escitalopram, and bleeding history and socioeconomic status for all SSRIs. We demonstrated feasibility of predicting ADEs using ML. Incorporating genomic features and drug interactions with deep learning models may improve ADE prediction.
Adverse health events within families can harm children's development, including their early literacy. Using data from a longitudinal Wisconsin birth cohort, we estimated the spillover effect of younger siblings' gestational ages on older siblings' kindergarten-level literacy. We sampled 20,014 sibling pairs born during 2007-2010 who took Phonological Awareness Literacy Screening-Kindergarten tests during 2012-2016. Exposures were gestational age (completed weeks), preterm birth (gestational age <37 weeks), and very preterm birth (gestational age <32 weeks). We used gain-score regression-a fixed effects strategy-to estimate spillover effect. A one-week increase in younger siblings' gestational age improved the older siblings' test score by 0.011 SD (95% confidence interval: 0.001, 0.021 SD). The estimated spillover effect was larger among siblings whose mothers reported having a high school diploma/equivalent only (0.024 SD; 95% CI: 0.004, 0.044 SD). The finding underscores the networked effects of one individual's early-life health shocks on their family members.
Advocacy is a critical component of pediatric training and practice. Pediatric resident advocacy experiences include skill development and real-world projects, but little is known about how pediatric residents participate in advocacy. Without this knowledge, educators run the risk of underpreparing residents for the full scope of advocacy work. This study sought to investigate how residents participate in advocacy by characterizing their projects using an evidence-informed conceptual framework and describing the unique lessons were learned by the residents. The authors used principles of thematic analysis to interrogate existing documents derived from pediatric residents from 2013 to 2021 at 1 institution. They purposefully sampled and deidentified project proposals and written reflections. Using a constant comparative method, they created codes. Codes, connections between codes, and findings were refined by discussion. Residents demonstrated 4 different types of advocacy: some residents participated in directed agency or activism and others focused on shared agency or activism. Residents reflected on different learning experiences; residents who participated in shared forms of advocacy learned skills such as "Partnering," "Evaluating," and "Planning." Residents who were involved in directed forms of advocacy shared lessons on "Leading," "Presenting," and "Intervening." Advocacy work also changed over time: in later projects (2016-2021) residents took ownership of the role of "advocate"; social and political climate was salient in reflections. Pediatric residents advocate through shared activism and agency and directed activism and agency. Educators should recognize, support, and supplement the experiences of residents as they participate in different types of advocacy.
Advocates and researchers have made many recommendations for forensic science improvement in the United States. These proposals are often motivated by wrongful convictions related to false or misleading forensic evidence. In many cases, the connection between the proposals and the actual experience of wrongful convictions has not been well defined. Further, recommendations may not have been realizable given the structure of the criminal justice system in the United States and the practical realities of forensic science laboratories. Finally, limited attempts have been made to assess recommendations over time to determine the progress of forensic science improvement and elucidate continuing gaps. Reports from the Department of Justice, the National Academy of Sciences, and the President's Council of Advisors on Science and Technology are assessed to determine the extent to which their recommendations have been implemented, whether the recommendations align with the actual experience of wrongful convictions, and how the American forensic science community has implemented forensic science improvement. The most successful proposals reflect a broad movement toward quality assurance, improved standards, and organizational improvement in the forensic sciences. Less successful proposals are associated with calls for large federal investments, difficulties in community-wide implementation, or uncertain linkage to foundations in science and practice. Significant progress has been made in the standardization of reporting and testimony, assessment of the foundational reliability of the disciplines, and DNA mixture interpretation. Significant gaps remain to improve medicolegal death investigation, governance, and the implementation of standards. Improved allocation and use of resources will be required to meet continuing challenges in capacity building, training, and proficiency testing, although past experience indicates that both federal and non-federal funding will be required to address these issues. Continued improvement is needed to address the issues associated with wrongful convictions, although forensic science leaders have demonstrated the ability to prioritize improvement initiatives.
Africa has one of the highest burdens of cervical cancer in the world. The unacceptably high incidence and mortality rates could be reduced through implementing a comprehensive approach to its prevention and control that includes screening, which however, is low in most low-and-middle-income countries. Hence, this systematic review aims at exploring factors that prevent women from utilising cervical cancer screening services in the region. A mixed method systematic review was conducted. A search was performed on PubMed (Medline), EMBASE, CINAHL (EBSCOHOST) and Scopus databases for articles published until May 2019 without time, language or study design limits. Two reviewers critically appraised the included studies independently using the standard quality assessment criteria for evaluating primary research papers. Results of the quantitative and mixed methods studies were transformed into qualitative data and synthesised using thematic analysis. From a potential 2 365 studies, 24 from 11 countries met the eligibility criteria and were selected; eight qualitative, 13 quantitative, and three that used the mixed-method approach. The primary barriers were identified as poor access to screening services, lack of awareness and knowledge on cervical cancer and screening, and socio-cultural influences. Service providers perceived lack of skills, screening equipment and supplies, and staff shortages as the major barriers to the provision of screening services. Barriers to cervical cancer screening in Africa are multifaceted and require a holistic approach that will address them concurrently at the health system, individual, interpersonal, community and structural levels. Political will complimented by stakeholder involvement is required in the development and implementation of strategies that will ensure acceptability, availability, accessibility, and affordability of screening to minimise barriers in accessing the service.
Africa presents a higher diabetic foot ulcer prevalence estimate of 7.2% against global figures of 6.3%. Engaging family members in self-care education interventions has been shown to be effective at preventing diabetes-related foot ulcers. This study culturally adapted and tested the feasibility and acceptability of an evidence-based footcare family intervention in Ghana. The initial phase of the study involved stakeholder engagement, comprising Patient Public Involvement activities and interviews with key informant nurses and people with diabetes (N = 15). In the second phase, adults at risk of diabetes-related foot ulcers and nominated caregivers (N = 50 dyads) participated in an individually randomised feasibility trial of the adapted intervention (N = 25) compared to usual care (N = 25). The study aimed to assess feasibility outcomes and to identify efficacy signals on clinical outcomes at 12 weeks post randomisation. Patient reported outcomes were foot care behaviour, foot self-care efficacy, diabetes knowledge and caregiver diabetes distress. Adjustments were made to the evidence-based intervention to reflect the literacy, information needs and preferences of stakeholders and to develop a context appropriate diabetic foot self-care intervention. A feasibility trial was then conducted which met all recruitment, retention, data quality and randomisation progression criteria. At 12 weeks post randomisation, efficacy signals favoured the intervention group on improved footcare behaviour, foot self-care efficacy, diabetes knowledge and reduced diabetes distress. Future implementation issues to consider include the staff resources needed to deliver the intervention, family members availability to attend in-person sessions and consideration of remote intervention delivery. A contextual family-oriented foot self-care education intervention is feasible, acceptable, and may improve knowledge and self-care with the potential to decrease diabetes-related complications. The education intervention is a strategic approach to improving diabetes care and prevention of foot disease, especially in settings with limited diabetes care resources. Future research will investigate the possibility of remote delivery to better meet patient and staff needs. Pan African Clinical Trials Registry (PACTR) - PACTR202201708421484: https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=19363 or pactr.samrc.ac.za/Search.aspx.