Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of Emergency Medicine Residents’ Clinical Reasoning: Validation of a Script Concordance Test

Introduction A primary aim of residency training is to develop competence in clinical reasoning. However, there are few instruments that can accurately, reliably, and efficiently assess residents’ clinical decision-making ability. This study aimed to externally validate the script concordance test in emergency medicine (SCT-EM), an assessment tool designed for this purpose. Methods Using established methodology for the SCT-EM, we compared EM residents’ performance on the SCT-EM to an expert panel of emergency physicians at three urban academic centers. We performed adjusted pairwise t-tests to compare differences between all residents and attending physicians, as well as among resident postgraduate year (PGY) levels. We tested correlation between SCT-EM and Accreditation Council for Graduate Medical Education Milestone scores using Pearson’s correlation coefficients. Inter-item covariances for SCT items were calculated using Cronbach’s alpha statistic. Results The SCT-EM was administered to 68 residents and 13 attendings. There was a significant difference in mean scores among all groups (mean + standard deviation: PGY-1 59 + 7; PGY-2 62 + 6; PGY-3 60 + 8; PGY-4 61 + 8; 73 + 8 for attendings, p < 0.01). Post hoc pairwise comparisons demonstrated that significant difference in mean scores only occurred between each PGY level and the attendings (p < 0.01 for PGY-1 to PGY-4 vs attending group). Performance on the SCT-EM and EM Milestones was not significantly correlated (r = 0.12, p = 0.35). Internal reliability of the exam was determined using Cronbach’s alpha, which was 0.67 for all examinees, and 0.89 in the expert-only group. Conclusion The SCT-EM has limited utility in reliably assessing clinical reasoning among EM residents. Although the SCT-EM was able to differentiate clinical reasoning ability between residents and expert faculty, it did not between PGY levels, or correlate with Milestones scores. Furthermore, several limitations threaten the validity of the SCT-EM, suggesting further study is needed in more diverse settings.
Economic incentives to target species and fish size: prices and fine-scale product attributes in Norwegian fisheries

Frank Asche1*, Yanyou Chen2, and Martin D. Smith3 Department of Industrial Economics, University of Stavanger, Ullandhaug, 4036 Stavanger, Norway Department of Economics, Duke University, 213 Social Sciences Building, 419 Chapel Drive, Durham, NC, USA Nicholas School of the Environment and Department of Economics, Duke University, Box 90328, Durham, NC 27708, USA *Corresponding author: tel: +47 51 83 22 86; fax: +47 51 83 17 50; e-mail: frank.asche@uis.no
Linking Environmental Exposures to Molecular Pathogenesis in Non-Hodgkin Lymphoma Subtypes

Non-Hodgkin lymphoma comprises a heterogeneous group of hematologic malignancies, with about 60 subtypes that arise via various pathogenetic mechanisms. Although establishing etiology for specific NHL subtypes has been historically difficult given their relative rarity, environmental exposures have been repeatedly implicated as risk factors across many subtypes. Large-scale epidemiologic investigations have pinpointed chemical exposures in particular, but causality has not been established, and the exact biologic mechanisms underpinning these associations are unclear. Here we review chemical exposures that have been associated with development of NHL subtypes and discuss their biologic plausibility based on current research.
Recent advances in salt stress biology - a review

Soil salinity is one of the major abiotic stresses that adversely affects crop productivity and quality. Hence developing salt tolerant crops is essential for sustaining food production. Understanding of the molecular basis of salt stress signaling and tolerance mechanisms are essential for breeding and genetic engineering of salt tolerance in crop plants. The modern approaches being used to impart salt tolerance involves exploitation of natural genetic variations and/or the generation of transgenic plants. This review discusses the challenges and opportunities provided by recently developed molecular tools in the development of salt tolerant crops. Key words: Soil salinity, plasma membrane antiporter (AtSOS1), AtHKT1, vacuolar antiporter (AtNHX1), compatible solutes, reactive oxygen species (ROS), antioxidants.
Relevant functioning aspects and environmental factors for adults and seniors undergoing hemodialysis: A qualitative study

Objective To identify which functioning, personal and environmental factors are more relevant to adults in hemodialysis treatment. Materials and methods Data was collected by semi-structured interview, recorded, transcribed in full, verified and produced by Bardin Thematic content analysis. Two independent researchers identified the relevant themes and named the thematic categories found according to the coding of the International Classification of Functioning, Disability and Health (ICF). Results Six men and three women aged between 32–65 years were interviewed, with per capita family income between 1–2.9 minimum salaries and hemodialysis treatment time between 5 to 26 years. Fifty-seven ICF categories were listed: 17 Body Functions, 9 Body Structures, 21 Activities and Participation, and 10 Environmental Factors. Health, transportation and general social support services, systems and policies; doing housework; recreation and leisure; emotional functions, temperament and personality functions; energy and drive functions; sensation of pain; and structures of the cardiovascular system, lower extremity and musculoskeletal structures related to movement were the most reported aspects by the participants. Conclusion Patients’ need for physical/emotional support from their partners, friends and health professionals, including emotional and social support, with health policies, transportation and job maintenance, in order to increase their survival and quality of life.
Spectral Analysis and Mutual Information Estimation of Left and Right Intracardiac Electrograms during Ventricular Fibrillation

Ventricular fibrillation (VF) signals are characterized by highly volatile and erratic electrical impulses, the analysis of which is difficult given the complex behavior of the heart rhythms in the left (LV) and right ventricles (RV), as sometimes shown in intracardiac recorded Electrograms (EGM). However, there are few studies that analyze VF in humans according to the simultaneous behavior of heart signals in the two ventricles. The objective of this work was to perform a spectral and a non-linear analysis of the recordings of 22 patients with Congestive Heart Failure (CHF) and clinical indication for a cardiac resynchronization device, simultaneously obtained in LV and RV during induced VF in patients with a Biventricular Implantable Cardioverter Defibrillator (BICD) Contak Renewal IVTM (Boston Sci.). The Fourier Transform was used to identify the spectral content of the first six seconds of signals recorded in the RV and LV simultaneously. In addition, measurements that were based on Information Theory were scrutinized, including Entropy and Mutual Information. The results showed that in most patients the spectral envelopes of the EGM sources of RV and LV were complex, different, and with several frequency peaks. In addition, the Dominant Frequency (DF) in the LV was higher than in the RV, while the Organization Index (OI) had the opposite trend. The entropy measurements were more regular in the RV than in the LV, thus supporting the spectral findings. We can conclude that basic stochastic processing techniques should be scrutinized with caution and from basic to elaborated techniques, but they can provide us with useful information on the biosignals from both ventricles during VF.
Safety of Upper Pole Puncture in Percutaneous Nephrolithotomy with the Guidance of Ultrasonography versus Fluoroscopy: A Comparative Study

Introduction: The aim of this study was to compare the safety of ultrasonography-guided (UG) puncture and fluoroscopy-guided (FG) upper pole access (UPA) in percutaneous nephrolithotomy (PCNL). Methods: Consecutive patients with a solitary UPA were enrolled into the study from 2012 to 2020 and analyzed in a retrospective manner. In total, 177 patients were divided into 2 groups according to the method during the puncture phase of the access: FG (n = 105) and UG (n = 72). The UG and FG groups were compared in terms of complications (i.e., pleural injury and blood transfusion rate) and surgical outcomes. Results: Gender, side, grade of hydronephrosis, type of access (i.e., supracostal vs. subcostal), Guy’s stone score, age, stone diameter, skin-to-stone distance, and stone density were similar in the 2 groups (p > 0.05). Only in 25.9% of cases, UPA was done using a subcostal approach. The overall complication rates were similar between the groups (p > 0.178). For the UG and FG groups, the rate of pleural injury (8.5 vs. 4.1%) and the blood transfusion rate (8.5 vs. 2.8%) were also similar (p > 0.05). The fluoroscopy time and mean hemoglobin drop were significantly lower in the UG group than in the FG group (134.2 vs. 82.2 s, respectively, p = 0.001; 20.8 ± 9.8 vs. 16.8 ± 7.9 g/L, respectively, p = 0.001). Stone-free rate (SFR) was also similar in the FG and UG groups (77.1 vs. 75.0%, respectively, p = 0.742). Conclusion: While it is commonly expected that the complication rates are lower in UG puncture for UPA in PCNL than they are in FG puncture, the present study failed to show this difference. However, the radiation exposure time seemed to be lower in UG puncture than FG puncture and had a similar stone-free rate (SFR) for UPA in PCNL.
Editor’s Presentation: ‘Smoking habit and congenital heart defects in offspring’

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 resulted in a global pandemic with unprecedented consequences. The initial outbreak of COVID-19 in Wuhan spread rapidly, affecting other parts of China; within a few weeks, cases of COVID-19 were detected in several other countries and soon it became a global threat. The overarching need to reduce disease transmission has had an enormous impact on sports and uncertainties persist regarding exercise safety, resumption of sporting activity and how to manage infected athletes. Although regular moderate exercise has an abundance of beneficial effects beyond the cardiovascular system, including mental health and a boost to the immune system, several evidences showed that exhaustive and prolonged exercise negatively affects the immune system and increases susceptibility to infection. Clinical experience has taught us that COVID-19 may directly infect myocardial cells, leading to acute myocarditis with a severe impairment of cardiac muscle function, malignant ventricular arrhythmias and even death. However, a subclinical myocardial injury with a silent myocardial inflammation and potentially residual chronic scar with increased vulnerability to malignant ventricular arrhythmias could occur also in asymptomatic individuals. Given this lack of data on the incidence of cardiac injury in non-hospitalized individuals and the long-term cardiac effects of those exposed to COVID-19 it is mandatory that medical and sporting organizations develop strategies to ensure a safe return to training and competition for athletes. In this issue of the European Journal of Preventive Cardiology, Bhatia and colleagues utilize a ‘question and answer’ format to: (a) highlight the impact of COVID-19 on the heart, (b) stress the importance of regular physical activity and (c) provide guidance outlining the management of athletes and competitive sport during and beyond this pandemic. Investigations on the clinical utility of apolipoprotein B measurement
Beyond Thresholds: A Holistic Approach to Impact Assessment Is Needed to Enable Accurate Predictions of Environmental Risk from Oil Spills

The risk assessment for the environmental impact of oil spills in Australia is often conducted in part using a combination of spill mapping and toxicological thresholds derived from laboratory studies. While this process is useful in planning operational responses, such as where to position equipment stockpiles and whether to disperse oil, and can be used to identify areas near the spill site where impacts are likely to occur, it cannot accurately predict the environmental consequences of an oil spill or the ecosystem recovery times. Evidence of this disconnect between model predictions and observed impacts is the lack of a profound effect of the Deepwater Horizon wellhead blowout on recruitment to fisheries in the northern Gulf of Mexico, contrary to the predictions made in the Natural Resources Damage Assessment and despite the occurrence of impacts of the spill on marine mammals, marshes, and deep water ecosystems. The incongruity between predictions made with the current approach using threshold monitoring and impacts measured in the field results from some of the assumptions included in the oil spill models. The incorrect assumptions include that toxicity is acute, results from dissolved phase exposure, and would be readily reversible. The toxicity tests from which threshold models are derived use members of the ecosystem that are easily studied in the lab but may not represent the ecosystem as a whole. The test species are typically highly abundant plankton or planktonic life stages, and they have life histories that account for rapid changes in environmental conditions. As a consequence, these organisms recover quickly from an oil spill. The interdependence of ecosystem components, including the reliance of organisms on their microbiomes, is often overlooked. Additional research to assess these data gaps conducted using economically and ecologically relevant species, especially in Australia and other understudied areas of the world, and the use of population dynamic models, will improve the accuracy of environmental risk assessment for oil spills. Integr Environ Assess Manag 2020;16:813–830. © 2020 SETAC
Abiotic and biotic factors influencing nest‐site selection by Halictus rubicundus, a ground‐nesting halictine bee

1. The nest‐site selection behaviour of the bee Halictus rubicundus (Christ) was examined both within and across sites in the U.K. Females utilized a range of edaphic and microclimatic conditions when choosing a site to excavate a nest. Factors with broad tolerances included slope and hardness; those with much narrower limits included aspect, soil humidity and soil particle composition.
Fosfat Kayası, Fosforik Asit ve Fosforlu Gübrelerdeki Toksik Ağır Metal (Cd, Pb, Ni, As) Konsantrasyonu

In this study, samples taken from phosphorous fertilizers, phosphoric acid and phosphate rocks used as raw materials for the production of phosphorous fertilizers were analyzed for their total Cd, Pb, Ni and As contents. The samples were obtained from a total of six fertilizer plants (five private and one state owned) which produce phosphorous fertilizers in Turkey. According to our results, maximum Cd, Pb, Ni and As concentrations of phosphate rocks imported from other countries were determined to be 358, 335, 386 ve 531 mg kg -1 P, respectively. Phosphate rocks were observed to contain the highest concentrations of Cd (358 mg/kg P) and As (531 mg/kg P) compared to other fertilizers. Samples from phosphoric acid, which has replaced phosphate rocks in the production of phosphorous fertilizers in recent years, were found to contain maximum Cd, Pb, Ni and As concentrations of 114, 11, 201 and 81 mg/L P, respectively. The metal contents of phosphoric acid and phosphate rocks showed variations depending on the exporter country. Toxic metal concentrations of fertilizers (TSP, DAP and compose) used in agricultural soils were compared with the current fertilizer metal standards of China and Japan. These results show that the Cd concentrations were above the Standard value of 8 mg/kg fertilizer in 10 of total of 14 fertilizers anayzed, and were close to this value in 2 fertilizers (7,5 mg/kg fertilizer). Pb concentration was about five times above the Standard value of 100 mg/kg fertilizer in 15:15:15 compose fertilizer (510 mg/kg fertilizer). As concentrations were found to be above the Standard value of 50 mg/kg fertilizer in 4 of total of 10 compose fertilizers analyzed. Finally, our results also indicate that the heavy metal concentrations of phosphorous fertilizers are heavily dependent on the heavy metal contents of raw materials (phosphoric acid or phosphate rocks) used in the production of phosphorous fertilizers.
Effects of exogenous methyl jasmonate and 2-isopentenyladenine on artemisinin production and gene expression in Artemisia annua

Artemisinin, produced in very low amounts in Artemisia annua L. plants, is one of the most effective drugs in treating malaria. In this study, the effect of exogenous applications of methyl jasmonate (MeJA) and 2-isopentenyladenine (2-iP) in artemisinin production and the main genes of its biosynthesis pathway within a 1-week time period were investigated. Both MeJA and 2-iP increased artemisinin content, but no correlation was found between gene expression and its content. In plants treated with 2-iP, despite increased gene expression following elicitor application, downregulation of gene expression was also observed, which might be attributed to the negative effects of rising artemisinin levels in gene expression. In plants treated with MeJA, the steady increase in artemisinin content was not explained by the few changes observed in gene expression, suggesting that some other mechanism may increase artemisinin. Our results indicate that the negative feedback mechanism of artemisinin is likely an obstacle for the selection of biotechnological strategies to increase artemisinin content. This may be overcome by studying the role of trichome in artemisinin production as a step toward achieving high yields of this valuable component.
Variation of selected genotoxic and epigenetic markers due to therapeutic exposure to PAHs and ultraviolet radiation.

BACKGROUND Goeckerman therapy (GT) of psoriasis involves dermal application of crude coal tar containing polycyclic aromatic hydrocarbons (PAHs) and exposure to ultraviolet radiation (UVR). Little is known about GT influence on DNA epigenetics. OBJECTIVE The study aim was to discover epigenetic mechanisms altered by the exposure related to the GT of psoriasis. METHODS Observed group of patients with plaque psoriasis (n = 23) was treated by GT with 3 % CCT. Before and after GT, we analyzed the levels of benzo[a]pyrene-7,8-diol-9,10-epoxide-DNA adducts (BPDE-DNA), p53 protein in serum, 5-methylcytosine (5-mC, global DNA methylation), and methylation in selected CpG sites of p53 gene. RESULTS We found a significant increase in the levels of BPDE-DNA (p < 0.01) and serum levels of p53 protein (p < 0.01) after GT, and an insignificant decrease in the percentage of 5-mC in peripheral blood DNA. Methylation of p53 CpG sites was affected neither by psoriasis nor by GT. The study confirmed good effectiveness of GT (significantly reduced psoriasis area and severity index; p < 0.001). CONCLUSION Our findings indicate that there is a significantly increased genotoxic hazard related to the exposure of PAHs and UV radiation after GT of psoriasis. However, global DNA methylation and p53 gene methylation evade the effect of GT, as they remained unchanged (Tab. 4, Fig. 3, Ref. 50).
A hybrid cyt c maturation system enhances the bioelectrical performance of engineered Escherichia coli by improving the rate-limiting step

Bioelectronic devices can use electron flux to enable communication between biotic components and abiotic electrodes. We have modified Escherichia coli to electrically interact with electrodes by expressing the cytochrome c from Shewanella oneidensis MR-1. However, we observe inefficient electrical performance, which we hypothesize is due to the limited compatibility of the E. coli cytochrome c maturation (Ccm) systems with MR-1 cytochrome c. Here we test whether the bioelectronic performance of E. coli can be improved by constructing hybrid Ccm systems containing protein domains from both E. coli and S. oneidensis MR-1. The hybrid CcmH increased cytochrome c expression by increasing the abundance of CymA 60%, while only slightly changing the abundance of the other cytochromes c. Electrochemical measurements showed that the overall current from the hybrid ccm strain increased 121% relative to the wildtype ccm strain, with an electron flux per cell of 12.3 ± 0.3 fA·cell-1. Additionally, the hybrid ccm strain doubled its electrical response with the addition of exogenous flavin, and quantitative analysis of this demonstrates CymA is the rate-limiting step in this electron conduit. These results demonstrate that this hybrid Ccm system can enhance the bioelectrical performance of the cyt c expressing E. coli, allowing the construction of more efficient bioelectronic devices.
Refinement of pairwise potentials via logistic regression to score protein‐protein interactions

Protein‐protein interactions (PPIs) are ubiquitous and functionally of great importance in biological systems. Hence, the accurate prediction of PPIs by protein‐protein docking and scoring tools is highly desirable in order to characterize their structure and biological function. Ab initio docking protocols are divided into the sampling of docking poses to produce at least one near‐native structure, and then to evaluate the vast candidate structures by scoring. Concurrent development in both sampling and scoring is crucial for the deployment of protein‐protein docking software. In the present work, we apply a machine learning model on pairwise potentials to refine the task of protein quaternary structure native structure detection among decoys. A decoy set was featurized using the Knowledge and Empirical Combined Scoring Algorithm 2 (KECSA2) pairwise potential. The highly unbalanced decoy set was then balanced using a comparison concept between native and decoy structures. The resultant comparison descriptors were used to train a logistic regression (LR) classifier. The LR model yielded the optimal performance for native detection among decoys compared with conventional scoring functions, while exhibiting lesser performance for the detection of low root mean square deviation decoy structures. Its deployment on an independent benchmark set confirms that the scoring function performs competitively relative to other scoring functions. The scripts used are available at https://github.com/TanemuraKiyoto/PPI-native-detection-via-LR.
Ketoreductase activity for reduction of substituted-β-tetralones utilizing aqueous-organic systems and β-cyclodextrin derivatives

Abstract Ketoreductases (KREDs) were employed for enantioselective reduction of 7-hydroxy-2-tetralone 1a and adduct 7-methoxy-2-tetralonbisulfite 2a to their corresponding (S)-/(R)-alcohols. In addition, the effect of additives such as organic solvents and β-cyclodextrin derivatives on the enzyme reductions was investigated. The changes in enzyme activity as a function of additives were correlated to structural alterations of the KREDs using circular dichroism and fluorescence spectrophotometric measurements. The effects of both the organic solvents and β-cyclodextrin derivatives on substrate solubility and equilibrium binding constants (log K) of β-cyclodextrin-substrate complexes were determined.