Miracle-dz/UniFAR-FTUs huggingface dataset:
Postgraduate Selection in Medical Education: A Scoping Review of Current Priorities and Values

Purpose The process of screening and selecting trainees for postgraduate training has evolved significantly in recent years, yet remains a daunting task. Postgraduate training directors seek ways to feasibly and defensibly select candidates, which has resulted in an explosion of literature seeking to identify root causes for the problems observed in postgraduate selection and generate viable solutions. The authors therefore conducted a scoping review to analyze the problems and priorities presented within the postgraduate selection literature to explore practical implications and present a research agenda. Method Between May 2021 and February 2022, the authors searched PubMed, EMBASE, Web of Science, ERIC, and Google Scholar for English language literature published after 2000. Articles that described postgraduate selection were eligible for inclusion. 2,273 articles were ultimately eligible for inclusion. Thematic analysis was performed on a subset of 100 articles examining priorities and problems within postgraduate selection. Articles were sampled to ensure broad thematic and geographical variation across the breadth of articles that were eligible for inclusion. Results Five distinct perspectives or value statements were identified in the thematic analysis: (1) Using available metrics to predict performance in postgraduate training; (2) identifying the best applicants via competitive comparison; (3) seeking alignment between applicant and program in the selection process; (4) ensuring diversity, mitigation of bias, and equity in the selection process; and (5) optimizing the logistics or mechanics of the selection process. Conclusions This review provides insight into the framing and value statements authors use to describe postgraduate selection within the literature. The identified value statements provide a window into the assumptions and subsequent implications of viewing postgraduate selection through each of these lenses. Future research must consider the outcomes and consequences of the value statement chosen and the impact on current and future approaches to postgraduate selection.
Automated Patient Note Grading: Examining Scoring Reliability and Feasibility

Purpose Scoring postencounter patient notes (PNs) yields significant insights into student performance, but the resource intensity of scoring limits its use. Recent advances in natural language processing (NLP) and machine learning allow application of automated short answer grading (ASAG) for this task. This retrospective study evaluated psychometric characteristics and reliability of an ASAG system for PNs and factors contributing to implementation, including feasibility and case-specific phrase annotation required to tune the system for a new case. Method PNs from standardized patient (SP) cases within a graduation competency exam were used to train the ASAG system, applying a feed-forward neural networks algorithm for scoring. Using faculty phrase-level annotation, 10 PNs per case were required to tune the ASAG system. After tuning, ASAG item-level ratings for 20 notes were compared across ASAG-faculty (4 cases, 80 pairings) and ASAG-nonfaculty (2 cases, 40 pairings). Psychometric characteristics were examined using item analysis and Cronbach’s alpha. Inter-rater reliability (IRR) was examined using kappa. Results ASAG scores demonstrated sufficient variability in differentiating learner PN performance and high IRR between machine and human ratings. Across all items the ASAG-faculty scoring mean kappa was . 83 (SE ± .02). The ASAG-nonfaculty pairings kappa was . 83 (SE ± .02). The ASAG scoring demonstrated high item discrimination. Internal consistency reliability values at the case level ranged from a Cronbach’s alpha of . 65 to . 77. Faculty time cost to train and supervise nonfaculty raters for 4 cases was approximately $1,856. Faculty cost to tune the ASAG system was approximately $928. Conclusions NLP-based automated scoring of PNs demonstrated a high degree of reliability and psychometric confidence for use as learner feedback. The small number of phrase-level annotations required to tune the system to a new case enhances feasibility. ASAG-enabled PN scoring has broad implications for improving feedback in case-based learning contexts in medical education.
Shoreface behaviour and equilibrium

This thesis investigates shoreface behaviour relative to equilibrium over time scales of decades to millennia within a common sedimentary system in the U.S. Pacific Northwest. The study area encompasses the Columbia River littoral cell, a dynamic entity composed of four barrier/strandplain sub-cells (separated by estuary entrances) with regional morphologic gradients and variability. Within this system, contrasting modes of shoreface behaviour governed by different combinations of variables enabled comparative analysis. A number of complementary methods show that coastal evolution manifests over a range of temporal and spatial scales. Based on research within the study region, the concept of nested hierarchical scales is demonstrated, where the system of interest is evaluated within the framework of its environment and components. Two principal data sets-vibracores and historical shoreface profiles-are analyzed and interpreted within the context of previously collected seismic-reflection profiles and side-scan sonar images. Vibracore analysis-involving laboratory processing, logging, x-radiography, grain-size analysis, and radiocarbon dating-resolves shoreface change at centuria! to millennia! scale. Historical shoreface profile analysis uses data-processing techniques and algorithms to extract metrics that quantify change at decade to century scale. Mean trends are examined in light of factors governing equilibrium, as well as in response to two disequilibrium conditions: shallow shoreface shoals imposed by jetty construction, and coseismic subsidence. Historical shoreface profile change is quantified with respect to theoretical equilibrium, while the effect of rapid subsidence is explored using a behaviour-oriented shoreface model, calibrated by
Identification of a Protein Arginine Methyltransferase 7 (PRMT7)/Protein Arginine Methyltransferase 9 (PRMT9) Inhibitor

Less studied than the other protein arginine methyltransferase isoforms, PRMT7 and PRMT9 have recently been identified as important therapeutic targets. Yet, most of their biological roles and functions are still to be defined, as well as the structural requirements that could drive the identification of selective modulators of their activity. We recently described the structural requirements that led to the identification of potent and selective PRMT4 inhibitors spanning both the substrate and the cosubstrate pockets. The reanalysis of the data suggested a PRMT7 preferential binding for shorter derivatives and prompted us to extend these structural studies to PRMT9. Here, we report the identification of the first potent PRMT7/9 inhibitor and its binding mode to the two PRMT enzymes. Label-free quantification mass spectrometry confirmed significant inhibition of PRMT activity in cells. We also report the setup of an effective AlphaLISA assay to screen small molecule inhibitors of PRMT9.
Developmental Selection and the Perception of Mutation Bias

Abstract The notion that mutations are random relative to their fitness effects is central to the Neo-Darwinian view of evolution. However, a recent interpretation of the patterns of mutation accumulation in the genome of Arabidopsis thaliana has challenged this notion, arguing for the presence of a targeted DNA repair mechanism that causes a nonrandom association of mutation rates and fitness effects. Specifically, this mechanism was suggested to cause a reduction in the rates of mutations on essential genes, thus lowering the rates of deleterious mutations. Central to this argument were attempts to rule out selection at the population level. Here, we offer an alternative and parsimonious interpretation of the patterns of mutation accumulation previously attributed to mutation bias, showing how they can instead or additionally be caused by developmental selection, that is selection occurring at the cellular level during the development of a multicellular organism. Thus, the depletion of deleterious mutations in A. thaliana may indeed be the result of a selective process, rather than a bias in mutation. More broadly, our work highlights the importance of considering development in the interpretation of population-genetic analyses of multicellular organisms, and it emphasizes that efforts to identify mechanisms involved in mutational biases should explicitly account for developmental selection.
Novel applications of histopathological markers to distinguish prognostic subgroups in colorectal adenocarcinoma

Abstract Objective To explore the novel applications of histological factors by stratifying the prognostic markers of the overall CRC patients in subgroups. Materials and methods A total of 17 histopathological and molecular factors were retrospectively collected and systematically analyzed for the prediction of CRC prognosis in the overall and stratified subgroups by using the Kaplan-Meier curve analysis as well as the Cox regression test. The χ2 test was used to analyze the correlation of the prognostic markers with other factors. Results The histopathological markers including the lymph node metastasis (LNM), perineural/venous invasion (PVI), TNM stage, the local recurrence or distant metastasis after surgery (R/M) and the molecular markers Ki-67 expression as well as KRAS mutation were identified to be the independent prognostic biomarkers in the overall CRC. The differential prognosis of LNM was found to be significant in age, tumor site, histological classification (histo_classification), cell differentiation, and KRAS/NRAS/BRAF (KNB) mutation stratified subgroups. The PVI was discovered to differently predict survival for patients in age, histo_classification, differentiation, and R/M stratified subgroups. Same as LNM and PVI, TNM was also found to demonstrate differential prognosis in age, tumor site, histo_classification, differentiation, R/M status and KRAS/KNB mutation stratified subgroups. More importantly, R/M was firstly identified not to be terrible for patients in age, histo_classification, LNM, TNM, Ki-67, and KRAS/KNB stratified subgroups. Besides, KRAS mutation was innovatively found to show differential prognosis in age, differentiation, and LNM stratified subgroups. Conclusions The stratification analyses of prognostic markers in CRC patients indicate novel applications of the above histopathological and molecular markers in clinic and the findings provide new insights into future investigations of precision pathology.
Strategic use of tobacco treatment specialists as an innovation for tobacco cessation health systems change within health care organizations

Background Tobacco screening interventions have demonstrated effectiveness at improving population health, yet many people who want to quit using tobacco lack access to professional assistance. One way to address this gap is to train members of the clinical team as tobacco treatment specialists (TTSs). Purpose The purpose of this study was to understand how TTSs have been used across a variety of health care organizations implementing health systems change for tobacco treatment and examine the sustainability of TTSs as a health systems change innovation for tobacco cessation. Methodology This study used qualitative interviews (n = 25) to identify themes related to implementing TTSs as a health systems change innovation and examined these themes within the constructs of the theory of innovation implementation. Results Insights about implementing TTSs as an innovation primarily aligned with four theoretical constructs: implementation policies and practices, implementation climate, innovation-values fit, and implementation effectiveness. Specific themes were perceived to facilitate the sustainability of TTSs including team-based TTS efforts, widespread awareness of TTS roles, leadership buy-in, and recognized value of TTS services. Barriers to sustainability included inadequate resources (e.g., time and staff), lack of tracking outcomes, inappropriate referrals, and lack of reimbursement. Practice Implications Health care organizations planning to implement health systems change for tobacco cessation can encourage committed use of TTSs as an innovation by considering the insights provided in this study. These primarily related to five overarching implementation considerations: staff selection and training, tracking and dissemination of impacts, adequate resources, referrals and workflow, and billing and reimbursement.
PTSD Symptom dynamics after the great east japan earthquake: mapping the temporal structure using Dynamic Time Warping

ABSTRACT Background: After the Great East Japan Earthquake [GEJE], approximately 70,000 Japan Ground Self Defense Force [JGSDF] personnel were deployed, risking Post-Traumatic Stress Disorder [PTSD]. The network approach to psychopathology suggests that symptoms may cause and exacerbate each other, resulting in the emergence and maintenance of disorders, including PTSD. It is therefore important to further explore the temporal interplay between symptoms. Most studies assessing the factor structure of the Impact of Event Scale-Revised [IES-R] have used cross-sectional designs. In this study, the structure of the IES-R was re-evaluated while incorporating the temporal interplay between symptoms. Methods: Using Dynamic Time Warping [DTW] the distances between PTSD symptoms on the IES-R were modelled in 1120 JGSDF personnel. Highly correlated symptoms were clustered at the group level using Distatis three-way principal component analyses of the distance matrices. The resulting clusters were compared to the original three subscales of the IES-R using a Confirmatory Factor Analysis (CFA). Results: The DTW analysis yielded four symptom clusters: Intrusion (five items), Hyperarousal (six items), Avoidance (six items), and Dissociation (five items). CFA yielded better fit estimates for this four-factor solution (RMSEA = 0.084, CFI = 0.918, TLI = 0.906), compared to the original three subscales of the IES-R (RMSEA = 0.103, CFI = 0.873, TLI = 0.858). Conclusions: DTW offers a new method of modelling the temporal relationships between symptoms. It yielded four IES-R symptom clusters, which may facilitate understanding of PTSD as a complex dynamic system. HIGHLIGHTS Personnel from the Japan Ground Self-Defense Force responded to the aftermath of the 2011 Great East Japan Earthquake, putting them at increased risk of developing symptoms of Post-Traumatic Stress Disorder. In recent years, psychological research has focused increasingly on methods to map the ways in which symptoms of psychopathology cause and exacerbate each other. The Dynamic Time Warping algorithm seems to be an appropriate and useful tool to analyse the interaction between post-traumatic stress symptoms over time, especially if these are not instantaneous or linear. This can improve our understanding of psychopathology and help move towards personalized medicine.
PSASL: Pixel-Level and Superpixel-Level Aware Subspace Learning for Hyperspectral Image Classification

The performance of hyperspectral image (HSI) classification relies on the pixel information obtained from hundreds of contiguous and narrow spectral bands. Existing approaches, however, are limited to exploit an appropriate latent subspace for data representation within the pixel-level or superpixel-level. To utilize spectral information and spatial correlation among pixels in HSI and avoid the “salt-and-pepper” problem generated in the pixel-based HSI classification, a novel pixel-level and superpixel-level aware subspace learning method called PSASL is developed. The PSASL constructs the subspace learning framework based on the reconstruction independent component analysis algorithm. The spectral–spatial graph regularization and label space regularization are developed as the pixel-level constraints. To avoid the “salt-and-pepper” problem generated in the pixel-based classification methods, superpixel-level constraints are introduced for integrating the data representations defined in the subspace and class probabilities of the pixels in the same superpixel. The subspace learning and the pixel-level regularization are combined with the superpixel-level regularization to form a unified objective function. The solution to the objective function is efficiently achieved by employing a customized iterative algorithm, and it converges very fast. A discriminative data representation and a universal multiclass classifier are learned simultaneously. We test the PSASL on three widely used HSI data sets. Experimental results demonstrate the superior performance of our method over many recently proposed methods in HSI classification.
The paralogs' enigma of germ-cell specific genes dispensable for fertility: the case of 19 oogenesin genes

Abstract Gene knockout experiments have shown that many genes are dispensable for a given biological function. In this review, we make an assessment of male and female germ cell-specific genes dispensable for the function of reproduction in mice, the inactivation of which does not affect fertility. In particular, we describe the deletion of a 1 Mb block containing nineteen paralogous genes of the oogenesin/Pramel family specifically expressed in female and/or male germ cells, which has no consequences in both sexes. We discuss this notion of dispensability and the experiments that need to be carried out to definitively conclude that a gene is dispensable for a function.
Lipofection with Lipofectamine™ 2000 in a heparin‐free growth medium results in high transfection efficiency in chicken primordial germ cells

Primordial germ cells (PGCs) that can differentiate into gametes are used to produce genome‐edited chickens. However, the transfection efficiency into PGCs is low in chickens; therefore, the yield efficiency of PGCs modified via genome editing is problematic. In this study, we improved transfection efficiency and achieved highly efficient genome editing in chicken PGCs. For transfection, we used lipofection, which is convenient for gene transfer. Chicken PGC cultures require adding heparin to support growth; however, heparin significantly reduces lipofection efficiency (p < 0.01). Heparin‐induced lipofection efficiency was restored by adding protamine. Based on these results, we optimized gene transfer into chicken PGCs. Lipofectamine 2000 and our PGC medium were the most efficient transfection reagent and medium, respectively. Finally, based on established conditions, we compared the gene knock‐out efficiencies of ovomucoid, a major egg allergen, and gene knock‐in efficiencies at the ACTB locus. These results indicate that optimized lipofection is useful for CRISPR/Cas9‐mediated knock‐out and knock‐in. Our findings may contribute to the generation of genome‐edited chickens and stimulate research in various applications involving them.
University of Huddersfield Repository Monte-Carlo Planning for Pathfinding in Real-Time Strategy Games

In this work, we explore two Monte-Carlo planning approaches: Upper Confidence Tree (UCT) and Rapidly-exploring Random Tree (RRT). These Monte-Carlo planning approaches are applied in a real-time strategy game for solving the path finding problem. The planners are evaluated using a grid-based representation of our game world. The results show that the UCT planner solves the path planning problem with significantly less search effort than the RRT planner. The game playing performance of each planner is evaluated using the mean, maximum and minimum scores in the test games. With respect to the mean scores, the RRT planner shows better performance than the UCT planner. The RRT planner achieves more maximum scores than the UCT planner in the test games.
Inhibition of 6-Phosphogluconate Dehydrogenase Reverses Epirubicin Resistance Through Metabolic Reprograming in Triple-Negative Breast Cancer Cells

At present, chemotherapy is the most effective strategy for treating triple-negative breast cancer (TNBC), but its efficacy was limited by the development of chemo-resistance. The exact mechanism of chemoresistance still remains unclear. This study aims to examine whether 6-phosphogluconate dehydrogenase (6PGD), a key enzyme in the oxidative pentose phosphate pathway (PPP), could promote the resistance of TNBC cells to epirubicin. A TNBC epirubicin-resistant cell line was developed by increasing concentration and the effectiveness was tested. The expression and knockdown efficiency of 6PGD were further validated by performing quantitative real-time PCR (qPCR) and Western blot. The effects of 6PGD on parental and drug-resistant TNBC cell lines were verified based on proliferation and apoptosis experiments. Finally, nicotinamide adenine dinucleotide phosphate (NADPH) and lactate quantitative experiments were performed to examine the mechanism of 6PGD in promoting drug resistance. Epirubicin-resistant cancer cells exhibited a higher level of 6PGD in contrast to epirubicin-sensitive cells. In addition, 6PGD inhibited by genetic and pharmacological approaches significantly suppressed the growth and survival of both epirubicin-sensitive and epirubicin-resisteant TNBC cells. It should be noted that 6PGD inhibition sensitized epirubicin-resistant TNBC cells to epirubicin treatment. Moreover, it was also found that the levels of NADPH and lactate increased in epirubicin-resistant TNBC cells but decreased in response to 6PGD inhibition. The present results indicated that 6PGD inhibition disrupted metabolic reprogramming in epirubicin-resistant TNBC cells. Our work demonstrated that 6PGD inhibition reversed the resistance of TNBC cells to epirubicin, providing an alternative therapeutic choice to tackle the challenge of epirubicin resistance in TNBC treatment.
Sustained selective attention to chromatic information enhances visuocortical gain at the population level

Prior work in selective attention research has shown that colour‐selective attention enhances neural activity in visuocortical areas sensitive to the attended colour while suppressing activity in areas sensitive to ignored colours. However, it is currently unclear whether this effect is limited to attending to specific colour hues or extends to chromatic information more broadly. To investigate this question, we used steady‐state visual evoked potentials (ssVEPs) frequency tagging to quantify participants' visuocortical responses to specific elements embedded in arrays of flickering, randomly moving mid‐complex patterns. Participants were instructed to attend to either coloured or greyscale patterns while ignoring the others. We found that attending to either coloured or greyscale patterns produced robust increases in ssVEP amplitudes both compared to ignored stimuli and to baseline. There was however no evidence of suppressed responses to ignored patterns. These findings demonstrate that attentional selection based on the presence or absence of chromatic information prompts selectively enhanced visuocortical processing but this selective amplification is not accompanied by suppression of unattended stimuli. Findings are consistent with theoretical notions that predict strong competition between specific exemplars within a given feature dimension, such as red or green, but weak competition between broadly defined stimulus categories, such as chromatic versus non‐chromatic.