Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphometric, geographic, and territorial characterization of brain arterial trees

Morphometric information of the brain vascularization is valuable for a variety of clinical and scientific applications. In particular, this information is important when creating arterial tree models for imposing boundary conditions in numerical simulations of the brain hemodynamics. The purpose of this work is to provide quantitative descriptions of arterial branches, bifurcation patterns, shape, and geographical distribution of the arborization of the main cerebral arteries as well as estimations of the corresponding vascular territories. For this purpose, subject‐specific digital reconstructions of the brain vascular network created from 3T magnetic resonance angiography images of healthy volunteers are used to derive population‐averaged morphometric characteristics of the cerebral arterial trees. Copyright © 2014 John Wiley & Sons, Ltd.
Energy minimization in medical image analysis: Methodologies and applications

Energy minimization is of particular interest in medical image analysis. In the past two decades, a variety of optimization schemes have been developed. In this paper, we present a comprehensive survey of the state‐of‐the‐art optimization approaches. These algorithms are mainly classified into two categories: continuous method and discrete method. The former includes Newton–Raphson method, gradient descent method, conjugate gradient method, proximal gradient method, coordinate descent method, and genetic algorithm‐based method, while the latter covers graph cuts method, belief propagation method, tree‐reweighted message passing method, linear programming method, maximum margin learning method, simulated annealing method, and iterated conditional modes method. We also discuss the minimal surface method, primal‐dual method, and the multi‐objective optimization method. In addition, we review several comparative studies that evaluate the performance of different minimization techniques in terms of accuracy, efficiency, or complexity. These optimization techniques are widely used in many medical applications, for example, image segmentation, registration, reconstruction, motion tracking, and compressed sensing. We thus give an overview on those applications as well. Copyright © 2015 John Wiley & Sons, Ltd.
Global Longitudinal Pathway: Has Medical Education Curriculum Influenced Medical Students’ Skills and Attitudes Toward Culturally Diverse Populations?

Background: The Pathway represents a longitudinal program for medical students, consisting of both domestic and international experiences with poor populations. A previous study reported no significant attitudinal changes toward the medically indigent between Pathway and non-Pathway students. Purpose: The purpose of this study was to investigate and differentiate the skills and attitudes of Pathway and non-Pathway students in working with culturally diverse populations by conducting quantitative and qualitative analyses. Methods: Selected items from a cultural assessment were analyzed using independent t-tests and a proportional analysis using approximation of the binomial distribution. In addition, a qualitative assessment of non-Pathway and Pathway students was conducted. Results: A statistically significant difference was found at the end of Years 2, 3, and 4 regarding student confidence ratings, and qualitative results had similar findings. Conclusions: Clear and distinct differences between the two studied groups were found indicating the root of this increased confidence may have developed due to exposure to the Pathway program.
Effects of Peyton's Four-Step Approach on Objective Performance Measures in Technical Skills Training: A Controlled Trial

Background: Although skills-lab training is widely used for training undergraduates in technical procedures, the way in which clinical skills are to be used and instructed remains a matter of debate. Purpose: We conducted a randomized controlled trial to evaluate the learning outcome of two different instructional approaches in the context of acquiring procedural–technical skills. Methods: Volunteer 2nd- and 3rd-year medical students were randomly assigned to an intervention group receiving instruction according to Peyton's Four-Step Approach (IG; n = 17) or to a control group receiving standard instruction (CG; n = 17). Both groups were taught gastric-tube insertion using a manikin. Following each of the two forms of instruction, participants’ first independent gastric-tube insertions were video recorded and scored by two independent video assessors using binary checklists and global rating forms. The time required for each instructional approach and for the first independent performance of the skill was measured. Results: A total of 34 students agreed to participate in the trial. There were no statistically significant group differences with regard to age, sex, completed education in a medical profession, or completed medical clerkships. The groups did not differ in terms of correct stepwise performance of the procedure as assessed by a binary checklist (p < .802). However, ratings based on global rating scales assessing professionalism and accompanying patient-doctor communication proved significantly better in IG (both ps < .001). The length of the different instructional approaches did not differ significantly between the two groups (IG: 605 ± 65 s; CG: 572 ± 79 s; p < .122), but the time needed for the first independent performance of gastric-tube placement on the manikin was significantly shorter in IG (IG: 168 ± 30 s; CG: 242 ± 53 s; p < .001). Conclusions: Peyton's Four-Step Approach is superior to standard instruction with respect to professionalism and accompanying doctor–patient communication and leads to faster performance when trainees perform the learned skill for the first time.
Long-term Outcomes after Off-Pump or Conventional Coronary Artery Bypass Grafting within a Veteran Population

Objective Recently published data indicate that outcomes for off-pump coronary artery bypass grafting (OPCABG) may be inferior to conventional CABG (cCABG) within the Veteran population, but this has been only partly addressed within high-volume off-pump centers. Here, we seek to examine the long-term outcomes for these patients within the Veteran population at a single institution well experienced with OPCABG. Methods With the use of a preexisting in-house database, all patients who had undergone isolated CABG from 2000 to 2011 (n = 1125) were identified. From these data, 18 demographic and risk factors were compared and used to create a propensity score, which was used for matching between groups (OPCABG vs cCABG). The primary end point examined was death. Survival was analyzed using the Kaplan-Meier method and the log-rank test. Groups were compared using a Student t test or Fisher exact test, where appropriate. Results Unmatched OPCABG and cCABG groups were found to have significant differences in risk factors, with the OPCABG being a higher-risk population by ejection fraction, chronic obstructive pulmonary disease status, age, and renal function, among others (all P < 0.05). Kaplan-Meier analysis of the unmatched groups demonstrated an increased mortality rate within the higher-risk OPCABG group (P = 0.0002). With the use of propensity score matching, 337 OPCABG patients were then matched to 337 cCABG controls. Comparison of demographic and risk factors between these matched groups did not demonstrate any statistically significant difference. When Kaplan-Meier analysis was performed for the matched groups, there was no statistically significant difference in survival. In addition, in the matched data set, OPCABG patients had a shorter average length of stay (8.2 vs 9.7 days, P = 0.022), shorter operative time (205 vs 270 minutes, P < 0.001), and lower rate of bleeding complications (0.9% vs 3.6%, P = 0.032). Conclusions In this high-volume off-pump center, matched OPCABG survival is similar to cCABG. Although recent data indicate that OPCABG survival may be worse than that of cCABG within the entire Veteran population, in centers well experienced with OPCABG, this does not seem to hold true. In addition, the benefit of decreased length of stay and lower morbidity rates seems to be significant. Further study of the long-term outcomes of OPCABG in high-volume Veteran's centers is warranted.
A comprehensive pipeline for multi‐resolution modeling of the mitral valve: Validation, computational efficiency, and predictive capability

Multiple studies have demonstrated that the pathological geometries unique to each patient can affect the durability of mitral valve (MV) repairs. While computational modeling of the MV is a promising approach to improve the surgical outcomes, the complex MV geometry precludes use of simplified models. Moreover, the lack of complete in vivo geometric information presents significant challenges in the development of patient‐specific computational models. There is thus a need to determine the level of detail necessary for predictive MV models. To address this issue, we have developed a novel pipeline for building attribute‐rich computational models of MV with varying fidelity directly from the in vitro imaging data. The approach combines high‐resolution geometric information from loaded and unloaded states to achieve a high level of anatomic detail, followed by mapping and parametric embedding of tissue attributes to build a high‐resolution, attribute‐rich computational models. Subsequent lower resolution models were then developed and evaluated by comparing the displacements and surface strains to those extracted from the imaging data. We then identified the critical levels of fidelity for building predictive MV models in the dilated and repaired states. We demonstrated that a model with a feature size of about 5 mm and mesh size of about 1 mm was sufficient to predict the overall MV shape, stress, and strain distributions with high accuracy. However, we also noted that more detailed models were found to be needed to simulate microstructural events. We conclude that the developed pipeline enables sufficiently complex models for biomechanical simulations of MV in normal, dilated, repaired states.
Global catastrophizing vs catastrophizing subdomains: assessment and associations with patient functioning.

OBJECTIVE The primary objectives of the current study were to 1) confirm the three-factor model of the Pain Catastrophizing Scale (PCS) items in a Japanese sample and 2) identify the catastrophizing subdomain(s) most closely associated with measures of pain and functioning in a sample of individuals with chronic pain. DESIGN This was based on a cross-sectional observational study. SETTING This study was conducted in a university-based clinic. PATIENTS One hundred and sixty outpatients with chronic pain participated in this study. OUTCOME MEASURES Patients completed the PCS, the Brief Pain Inventory, and the Hospital Anxiety and Depression Scale; 30 patients completed the PCS again between 1 and 4 weeks later. RESULTS Confirmatory factor analysis supported a three-factor structure of the Japanese version of the PCS, and univariate and multivariate associations with validity criterion supported the validity of the measure. Catastrophic helplessness was shown to make a unique contribution to the prediction of pain intensity, pain interference and depression, and catastrophic magnification made a unique contribution to the prediction of anxiety. CONCLUSIONS The findings support the cross-cultural generalizability of the three-factor structure of the PCS and indicate that the PCS-assessed catastrophizing subdomains provide greater explanatory power than the PCS total score for understanding pain-related functioning.
Using the Tools and Resources of the RCSB Protein Data Bank

The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three‐dimensional structures of large biological molecules found in all three kingdoms of life. Atomic‐level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc.
In Vitro Dissection of Autophagy

Autophagy is an essential cellular process for bulk degradation of cytoplasmic components through the lysosome. Underlying this process is an intricate interaction between protein factors and the cell endomembrane system, leading to a gradual maturation of the autophagic membrane. This structure sequesters a portion of the cytoplasm by the formation of a double‐membrane compartment called the autophagosome. The autophagosome then delivers the cargo to the lysosome to complete degradation. The molecular mechanism accounting for the generation of the autophagic membrane is a longstanding question. Here, a cell‐free approach that has been established to understand the mechanism of early autophagic membrane generation is described. This system has provided insight into the membrane source of the autophagosome, the early protein‐membrane associations, and the membrane remodeling that generates the autophagosomal precursors. The cell‐free assay, in combination with other established approaches (e.g., cell imaging), will facilitate a deeper understanding of the mechanism of autophagy. © 2017 by John Wiley & Sons, Inc.
Overview of Methods and Strategies for Conducting Virtual Small Molecule Screening

Virtual screening (VS) in the context of drug discovery is the use of computational methods to discover novel ligands with a desired biological activity from within a larger collection of molecules. These techniques have been in use for many years, there is a wide range of methodologies available, and many successful applications have been reported in the literature. VS is often used as an alternative or a complement to High‐throughput screening (HTS) or other methods to identify ligands for target validation or medicinal chemistry projects. This unit does not present an exhaustive review of available methods, or document specific instructions on use of individual software packages. Rather, a general overview of the methods available are presented and general strategies are described for VS based on accepted practices and the authors’ experience as computational chemists in an industrial research laboratory. First, the most common methods available for VS are reviewed, categorized as either receptor‐ or ligand‐based. Subsequently, strategic considerations are presented for choosing a VS method, or a combination of methods, as well as the necessary steps to prepare, run, and analyze a VS campaign. © 2017 by John Wiley & Sons, Inc.
Diversity Efforts, Admissions, and National Rankings: Can We Align Priorities?

Background: Increasing student body diversity is a priority for national health education and professional organizations and for many medical schools. However, national rankings of medical schools, such as those published by U.S. News & World Report, place a heavy emphasis on grade point average (GPA) and Medical College Admissions Test (MCAT) scores, without considering student body diversity. These rankings affect organizational reputation and admissions outcomes, even though there is considerable controversy surrounding the predictive value of GPA and MCAT scores. Summary: Our aim in this article was to explore the relationship between standard admissions practices, which typically aim to attract students with the highest academic scores, and student body diversity. We examined how changes in GPA and MCAT scores over 5 years correlated with the percentage of enrolled students who are underrepresented in medicine. In a majority of medical schools in the United States from 2005 to 2009, average GPA and MCAT scores of applicants increased, whereas the percentage of enrolled students who are underrepresented in medicine decreased. Conclusions: Our findings suggest that efforts to increase the diversity of medical school student bodies may be complicated by a desire to maintain high average GPA and MCAT scores. We propose that U.S. News revise its ranking methodology by incorporating a new diversity score into its student selectivity score and by reducing the weight placed on GPA and MCAT scores.
Cheating in OSCEs: The Impact of Simulated Security Breaches on OSCE Performance

ABSTRACT Construct: Valid score interpretation is important for constructs in performance assessments such as objective structured clinical examinations (OSCEs). An OSCE is a type of performance assessment in which a series of standardized patients interact with the student or candidate who is scored by either the standardized patient or a physician examiner. Background: In high-stakes examinations, test security is an important issue. Students accessing unauthorized test materials can create an unfair advantage and lead to examination scores that do not reflect students' true ability level. The purpose of this study was to assess the impact of various simulated security breaches on OSCE scores. Approach: Seventy-six 3rd-year medical students participated in an 8-station OSCE and were randomized to either a control group or to 1 of 2 experimental conditions simulating test security breaches: station topic (i.e., providing a list of station topics prior to the examination) or egregious security breach (i.e., providing detailed content information prior to the examination). Overall total scores were compared for the 3 groups using both a one-way between-subjects analysis of variance and a repeated measure analysis of variance to compare the checklist, rating scales, and oral question subscores across the three conditions. Results: Overall total scores were highest for the egregious security breach condition (81.8%), followed by the station topic condition (73.6%), and they were lowest for the control group (67.4%). This trend was also found with checklist subscores only (79.1%, 64.9%, and 60.3%, respectively for the security breach, station topic, and control conditions). Rating scale subscores were higher for both the station topic and egregious security breach conditions compared to the control group (82.6%, 83.1%, and 77.6%, respectively). Oral question subscores were significantly higher for the egregious security breach condition (88.8%) followed by the station topic condition (64.3%), and they were the lowest for the control group (48.6%). Conclusions: This simulation of different OSCE security breaches demonstrated that student performance is greatly advantaged by having prior access to test materials. This has important implications for medical educators as they develop policies and procedures regarding the safeguarding and reuse of test content.
Actual measurements of body weight and height are essential: Most self-reported weights and heights are unreliable

W ith the increased prevalence of obesity-related health problems such as cardiovascular disease, type 2 diabetes, hypertension, and dyslipidemia, the need for accurate assessment of body weight, height, and body mass index (BMI; which is body weight in kilograms divided twice by height in meters) is a pressing issue. Self-reported weight and height may have contributed to the confusion about whether intentional weight loss would increase or decrease the mortality risk of the obese subjects. Ninety-seven overweight or obese women enrolled in a weight-reduction study underreported their weight and overreported their height, resulting in an underestimation of BMI by 1.14 kg/m, whereas 6% of subjects initially admitted for this study on the basis of self-reported weight and height had to be excluded because of errors. Misclassification of subjects’ weight or BMI category at the baseline can affect their treatment protocols in clinics, distort the subsequent analysis and interpretation of research data, and undermine the public’s confidence on scientific information if the data were published. We searched PubMed for studies that evaluated the validity of self-reported weights and heights. Forty-three publications on this subject published between 1981 and early August 2005 were reviewed. In each study, the subjects’ self-reported weights and heights were compared with the measured data and statistically analyzed by the respective author for validity. The self-reported weights, heights, and the BMIs (if reported) in each study were then classified into overestimated, underestimated, and appropriate (no statistical significance for the difference between self-reported and measured).
Optical Push by Geographical Slant Affects Postural Sway

This study shows that perceived geographical slant affects postural stability. In 2 experimental conditions participants stood on a force platform that measured center of pressure (COP) during quiet stance while looking at a rigid, flat ramp surface of varying geographical slants. Using an otherwise identical procedure, participants in the second condition also provided verbal estimates of the steepness of the surface in degrees. Several measures of postural stability offered converging evidence that COP sway gradually increased as geographical slant decreased to 0 (horizontal ground). Specifically, COP was sensitive to changes in surface slant. Both the range and the standard deviation of COP showed the same trend of increased variability with decreasing geographical slant angles in both conditions. The area of the ellipse covering COP sway (based on a principal components analysis) showed the same tendency: ellipse area got larger for smaller, more horizontal slants. Nonlinear fractal dynamics of COP sway, as measured by the Hurst exponent of COP, pointed in the same direction: more fractal patterns, known to be correlated with increased muscle activity and decline in postural stability, were measured for shallower surface slants. There were no effects of verbal estimates on any of the measures, suggesting that explicit awareness of slant does not bias postural stability above and beyond the effects of visual environment.
Review on Micro-Gas Analyzer Systems: Feasibility, Separations and Applications

ABSTRACT Over 30 years, portable systems for fast and reliable gas analysis are at the core of both academic and industrial research. Miniaturized systems can be helpful in several domains. The way to make it possible is to miniaturize the whole gas chromatograph. Micro-system conception by etching silicon channel is well known. The main objective is to obtain similar or superior efficiencies to those obtained from laboratory chromatographs. However, stationary phase coatings on silicon surface and micro-detector conception with a low limit of detection remain a challenge. Developments are still in progress to offer a large range of stationary phases and detectors to meet the needs of analytical scientists. This review covers the recent development of micro-gas analyzers. It focuses on injectors, stationary phases, column designs and detectors reported in the literature during the last three decades. A list of commercially available micro-systems and their performances will also be presented.