RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides open access to experimentally-determined three-dimensional (3D) structures of biomolecules. The RCSB PDB RCSB.org research-focused web portal is used annually by many millions of users around the world. They access biostructure information, run complex queries utilizing various search services (e.g., full-text, structural and chemical attribute, chemical, sequence, and structure similarity searches), and visualize macromolecules in 3D, all at no charge and with no limitations on data usage. Notwithstanding more than 24,000-fold growth of the PDB over the past five decades, experimentally-determined structures are only available for a small subset of the millions of proteins of known sequence. Recently developed machine learning software tools can predict 3D structures of proteins at accuracies comparable to lower-resolution experimental methods. The RCSB PDB now provides access to ∼1,000,000 Computed Structure Models (CSMs) of proteins coming from AlphaFold DB and the ModelArchive alongside ∼200,000 experimentally-determined PDB structures. Both CSMs and PDB structures are available on RCSB.org and via well-established RCSB PDB Data, Search, and 1D-Coordinates application programming interfaces (APIs). Simultaneous delivery of PDB data and CSMs provides users with access to complementary structural information across the human proteome and those of model organisms and selected pathogens. API enhancements are backwards-compatible and programmatic users can "opt in" to access CSMs with minimal effort. Herein, we describe modifications to RCSB PDB cyberinfrastructure required to support sixfold scaling of 3D biostructure data delivery and lay the groundwork for scaling to accommodate hundreds of millions of CSMs.

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

Predictors of performance of foreign-trained medical doctors in the registration examination of the Ghana medical and dental council: A 5-year analysis.

Introduction: Although the influx of foreign-trained medical doctors (FTMDs) can improve the doctor-to-patient ratio in Ghana, there is the need to ensure that the quality of training is maintained. We assessed the performance of FTMDs in registration examinations over a 5-year period. Methodology: Data were extracted from Ghana Medical and Dental Council (GMDC) records from 2015 to 2019. Chi-squared tests assessed the association between the selected characteristics and the final grades. A multivariate logistic regression analysis determined significant predictors of the failure. The data were analysed using the statistical software IBM SPSS (version 26). The significance level was set at P < 0.05. Results: Of the 1356 doctors, majority (63.1%) were male, 64.3% were aged 21-30 years and 95.5% were Ghanaian. In all, there were 41 countries of training with majority training in China (35.4%) and Ukraine (31.9%). More than half (58.5%) failed the examination. Country of training, number of years from qualification to time of registration examination and number of previous attempts were statistically significantly associated with success at the examination. The logistic regression analysis showed that those who failed were more likely to have trained in Belarus (odds ratio [OR] = 3.20, 95% confidence interval [CI]; 1.50-6.82), Ukraine (OR = 2.47, 95% CI; 1.55-3.92), China OR = 2.06, 95% CI; 1.30-3.26) and Russia (OR = 1.98, 95% CI; 1.21-3.23) and were 0.58 times likely to have trained in Cuba. Conclusion: The performance at the examination is low. The significant predictor of performance is country of training. The authors recommend that the GMDC provides counselling services for students who leave for medical training abroad.

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

Vocal pattern detection of depression among older adults.

Depression is a serious problem for many older adults but is too often undetected by the person, family or providers. Although vocal patterns have been successfully used to detect and predict depression in adults aged 18 to 65 years, no studies to date have included older adults. The study purpose was to determine whether vocal patterns associated with clinical depression in younger people also signify depression in older adults. An observational, repeated measures design was used to enroll 46 volunteer older adults who completed a semi-structured interview composed the 9-item Patient Health Questionnaire or PHQ-9 depression scale and selected speech measures. Recorded interviews were analysed by machine learning algorithms to evaluate whether vocal patterns may predict presence of depression in older adults. In this study, using the PHQ-9 and a supervised machine learning algorithm accurately predicted high and low depression scores between 86% and 92% of the time. Change in raw PHQ-9 scores between interview cycles was predicted within 1.17 points. These results provide strong and promising evidence that vocal patterns can be used effectively to detect clinical depression in adults who are 65 years and older.

Evaluation of Sleep Patterns and Self-Reported Academic Performance among Medical Students at the University of Ghana School of Medicine and Dentistry.

BACKGROUND: Sleep habits and problems play a vital role in determining sleep quality. We describe sleep habits and problems among medical students and assess their possible effect on self-reported academic performance. METHODS: We conducted a cross-sectional study among medical students at the University of Ghana during the 2014/2015 academic year. Data was collected using the Pittsburgh Sleep Quality Index (PSQI), a self-report questionnaire that assesses sleep quality over a 1-month time interval. RESULTS: 153 medical students were recruited comprising 83 (54.2%) females and 70 (45.8%) males with a mean age of 23.1 ± 2.4 years. The mean duration of night sleep was 5.7 ± 1.2 hours; 88 (57.5%) students had sleep latency of 10-30 minutes while 18 (11.8%) woke up nightly. 23 (15%) students experienced nightmares, 13 (8.5%) snored at night, and only one student reported coffee intake of 2-3 times daily. Sleep quality was poor in 86 (56.2%) and was significantly associated with sleep latency, morning tiredness, daytime sleepiness during lectures, academic performance, living conditions, leisure time, frequency of nocturnal awakenings, waking up due to noise, sleep walking, and nocturnal awakening to use washroom. There was also a significant positive relation between sleep quality and academic performance (X2 = 10.004 p = 0.019). CONCLUSION: Poor sleep quality and daytime dysfunction are widespread among medical students in Ghana. There was a significant positive relation between sleep quality and self-reported academic performance.

Episodic memory and the witness trump card.

We accept Mahr & Csibra's (M&C's) causal claim that episodic memory provides humans with the means for evaluating the veracity of reports about non-occurrent events. We reject their evolutionary argument that this is the proper function of episodic memory. We explore three intriguing implications of the causal claim, for cognitive neuropsychology, comparative psychology, and philosophy.

Test-retest and between-site reliability in a multicenter fMRI study.

In the present report, estimates of test-retest and between-site reliability of fMRI assessments were produced in the context of a multicenter fMRI reliability study (FBIRN Phase 1, www.nbirn.net). Five subjects were scanned on 10 MRI scanners on two occasions. The fMRI task was a simple block design sensorimotor task. The impulse response functions to the stimulation block were derived using an FIR-deconvolution analysis with FMRISTAT. Six functionally-derived ROIs covering the visual, auditory and motor cortices, created from a prior analysis, were used. Two dependent variables were compared: percent signal change and contrast-to-noise-ratio. Reliability was assessed with intraclass correlation coefficients derived from a variance components analysis. Test-retest reliability was high, but initially, between-site reliability was low, indicating a strong contribution from site and site-by-subject variance. However, a number of factors that can markedly improve between-site reliability were uncovered, including increasing the size of the ROIs, adjusting for smoothness differences, and inclusion of additional runs. By employing multiple steps, between-site reliability for 3T scanners was increased by 123%. Dropping one site at a time and assessing reliability can be a useful method of assessing the sensitivity of the results to particular sites. These findings should provide guidance toothers on the best practices for future multicenter studies.