Miracle-dz/UniFAR-FTUs huggingface dataset:
Update of occurrence and hunting yield‐based data models for wild boar at European scale: new approach to handle the bioregion effect

The ENETWILD consortium updated in August 2019 suitability maps of wild boar occurrence and relative abundance based on hunting statistics, providing predictions at 10x10 km. External validation of this relative abundance model and a new downscaling on a 2x2 km grid was addressed in the ENETWILD report in January 2020. In this report, we update and incorporate additional data to provide new maps of wild boar suitability with a resolution of 2x2 km, obtained from a presence-only algorithm, and a new model based on hunting yield data for MS and neighbouring countries. Hunting yield-based modelling provides further novelties in two ways: new predictor variables and new (two) modelling approaches, i.e. smooth bioregion modelling and two-step independent bioregion modelling). Internal validations and comparisons among previous and new suitability and hunting yield models were also addressed, as well as external evaluation of the best new approach at European scale (at country level). The suitability map showed a good agreement with the expert-derived species range published by the International Union for Conservation of Nature. New models of relative abundance performed in general better than the previous one according to internal validations, concretely the two-step independent bioregion approach gives the best validation scores. This approach solved the abrupt changes in predictions between bioregion boundaries. As with the previous model, the external evaluation of the new model based on hunting yield presented certain over-prediction of the total hunting bags reported per country, although a high linearity between observed and predicted values was achieved. Previous and new hunting yield model predictions showed disagreements particularly in North and East regions, and other scattered areas in South and West, being areas in which the new model provides more reliable predictions. Hunting yield model outputs showed a relevant improvement in smoothing transitions between bioregions due to the flexibility provided by the new approach. Our analysis showed only partial agreement between suitability and relative abundance models, and reasons for these differences are discussed in this report. © European Food Safety Authority, 2020
Risk assessment in pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension

Background Current pulmonary hypertension treatment guidelines recommend use of a risk stratification model encompassing a range of parameters, allowing patients to be categorised as low, intermediate or high risk. Three abbreviated versions of this risk stratification model were previously evaluated in patients with pulmonary arterial hypertension (PAH) in the French, Swedish and COMPERA registries. Our objective was to investigate the three abbreviated risk stratification methods for patients with mostly prevalent PAH and chronic thromboembolic pulmonary hypertension (CTEPH), in patients from the PATENT-1/2 and CHEST-1/2 studies of riociguat. Methods Risk was assessed at baseline and at follow-up in PATENT-1 and CHEST-1. Survival and clinical worsening-free survival were assessed in patients in each risk group/strata. Results With all three methods, riociguat improved risk group/strata in patients with PAH after 12 weeks. The French non-invasive and Swedish/COMPERA methods discriminated prognosis for survival and clinical worsening-free survival at both baseline and follow-up. Furthermore, patients achieving one or more low-risk criteria or a low-risk stratum at follow-up had a significantly reduced risk of death and clinical worsening compared with patients achieving no low-risk criteria or an intermediate-risk stratum. Similar results were obtained in patients with inoperable or persistent/recurrent CTEPH. Conclusions This analysis confirms and extends the results of the registry analyses, supporting the value of goal-oriented treatment in PAH. Further assessment of these methods in patients with CTEPH is warranted. Riociguat improves risk group in patients with PAH and CTEPH according to three abbreviated versions of the ESC/ERS risk stratification model (results of a post hoc analysis) http://ow.ly/Herk30o8lKM
Irritability and Its Clinical Utility in Major Depressive Disorder: Prediction of Individual-Level Acute-Phase Outcomes Using Early Changes in Irritability and Depression Severity.

OBJECTIVE The authors evaluated improvement in irritability with antidepressant treatment and its prognostic utility in treatment-seeking adult outpatients with major depressive disorder. METHODS Mixed-model analyses were used to assess changes in irritability (as measured with the five-item irritability domain of the Concise Associated Symptom Tracking [CAST-IRR] scale) from baseline to week 4 after controlling for depression severity (as measured with the 16-item Quick Inventory of Depressive Symptomatology-Clinician Rated [QIDS-C]) in the Combining Medications to Enhance Depression Outcomes (CO-MED) trial (N=664). An interactive calculator for remission (QIDS-C score ≤5) and no meaningful benefit (<30% reduction in QIDS-C score from baseline) at week 8 was developed with logistic regression analyses in the CO-MED trial using participants with complete data (N=431) and independently replicated in the Suicide Assessment and Methodology Study (SAMS) (N=163). RESULTS In the CO-MED trial, irritability was significantly reduced (effect size=1.06) from baseline to week 4, and this reduction remained significant after adjusting for QIDS-C change (adjusted effect size=0.36). A one-standard-deviation greater reduction in CAST-IRR score from baseline to week 4 predicted a 1.73 times higher likelihood of remission and a 0.72 times lower likelihood of no meaningful benefit at week 8, independent of baseline QIDS-C and CAST-IRR scores and reduction in QIDS-C score from baseline to week 4. The model estimates for remission (area under the curve [AUC]=0.79) and no meaningful benefit (AUC=0.76) in the CO-MED trial were used to predict remission (AUC=0.80) and no meaningful benefit (AUC=0.84) in SAMS and to develop an interactive calculator. CONCLUSIONS Irritability is an important symptom domain of major depressive disorder that is not fully reflected in depressive symptom severity measures. Early reductions in irritability, when combined with changes in depressive symptom severity, provide a robust estimate of likelihood of remission or no meaningful benefit in outpatients with major depression.
Machine learning for patient risk stratification for acute respiratory distress syndrome

Background Existing prediction models for acute respiratory distress syndrome (ARDS) require manual chart abstraction and have only fair performance–limiting their suitability for driving clinical interventions. We sought to develop a machine learning approach for the prediction of ARDS that (a) leverages electronic health record (EHR) data, (b) is fully automated, and (c) can be applied at clinically relevant time points throughout a patient’s stay. Methods and Findings We trained a risk stratification model for ARDS using a cohort of 1,621 patients with moderate hypoxia from a single center in 2016, of which 51 patients developed ARDS. We tested the model in a temporally distinct cohort of 1,122 patients from 2017, of which 27 patients developed ARDS. Gold standard diagnosis of ARDS was made by intensive care trained physicians during retrospective chart review. We considered both linear and non-linear approaches to learning the model. The best model used L2-logistic regression with 984 features extracted from the EHR. For patients observed in the hospital at least six hours who then developed moderate hypoxia, the model achieved an area under the receiver operating characteristics curve (AUROC) of 0.81 (95% CI: 0.73–0.88). Selecting a threshold based on the 85th percentile of risk, the model had a sensitivity of 56% (95% CI: 35%, 74%), specificity of 86% (95% CI: 85%, 87%) and positive predictive value of 9% (95% CI: 5%, 14%), identifying a population at four times higher risk for ARDS than other patients with moderate hypoxia and 17 times the risk of hospitalized adults. Conclusions We developed an ARDS prediction model based on EHR data with good discriminative performance. Our results demonstrate the feasibility of a machine learning approach to risk stratifying patients for ARDS solely from data extracted automatically from the EHR.
Do Polish doctors suffer from occupational burnout syndrome? An attempt to find an answer - Pilot study.

INTRODUCTION AND OBJECTIVE A nationwide survey, carried out in Poland in 2013, showed that 42% of an examined group of doctors reported occupational burnout syndrome (OBS). The phenomenon of OBS among medical personnel shows a relationship with perceived stress scale (PSS) scores. The aim of the study was to estimate the prevalence of OBS in a group of Polish doctors, and the relationship with selected risk factors and personal resources. MATERIAL AND METHODS A cross-sectional study using quantitative methodology was used with the application of a questionnaire method and correlation design. Questionnaires were administered to 318 doctors (42 different specialties) working in medical facilities in Poland. All participants in the study completed two standardized questionnaires: Link Burnout Questionnaire (LBQ), Perceived Stress Scale (PSS), and responded to the questions on a proprietary questionnaire. ANOVA variance analysis and analysis of regression was performed. RESULTS The results of the measurement of four aspects of occupational burnout: psychophysical exhaustion (PE), commitment to relationships with patients (CP), effectiveness in performed work (EW), and existential expectations (EE), were in the medium and high levels range. Every second medical doctor who participated in the research declared a high degree of occupational burnout in each of the aspects of OBS. The high level of PSS scores, the large number of duties per month, the short work experience (years of employment) and the low number of holiday leaves, were the predictors of occupational burnout in the group of doctors taking part in the study. CONCLUSIONS The prevalence of the signs of OBS among Polish doctors is consistent with the results of research in other countries. Failures in the interventions taken to reduce stress seem to co-exist with the severity of signs of burnout.
Explanatory models of stroke in Ghana: perspectives of stroke survivors and their caregivers

ABSTRACT Objective: This study examines explanatory models (EMs) of stroke and its complications among people living with stroke, and their caregivers, in two urban poor communities in Accra (Ga Mashie) and Korle Bu Teaching Hospital (KBTH), Accra. Methods: Twenty-two stroke survivors and 29 caregivers were recruited from 2 urban poor communities in Accra and KBTH. Qualitative data were obtained using semi-structured interviews that lasted between 45 minutes and 2 hours. The interviews were audiotaped, transcribed and analysed thematically, informed by the concept of EMs of illness. Results: Participants referred to stroke as a sudden event and they expressed different emotional responses after the stroke onset. Stroke survivors and their caregivers attributed stroke with poor lifestyle practices, high blood pressure, unhealthy diet and dietary practices, supernatural causes, stress, family history, other chronic diseases, and delay in treatment of symptoms. While the stroke survivors associated stroke complications with physical disability and stigmatisation, the caregivers associated these with physical disability, behavioural and psychological changes, cognitive disability and death. These associations were mostly influenced by the biomedical model of stroke. Conclusion: The biomedical model of stroke is important for developing interventions that will be accepted by the stroke survivors and the caregivers. Nevertheless, sociocultural explanations of stroke need to be taken into consideration during delivery of medical information to the participants. This study proposes an integrated biopsychosociocultural approach for stroke intervention among the study participants.
Numerical predictions of hip joint and muscle forces during daily activities: A comparison of musculoskeletal models

Musculoskeletal loading plays an important role in pre-clinical evaluations of hip implants, in particular, bone ingrowth and bone remodelling. Joint force estimation using musculoskeletal models evolved as a viable alternative to in vivo measurement owing to the development of computational resources. This study investigated the efficiencies of four eminent open-source musculoskeletal models in order to determine the model that predicts the most accurate values of hip joint reaction and muscle forces during daily activities. Seven daily living activities of slow walking, normal walking, fast walking, sitting down, standing up, stair down and stair up were simulated in OpenSim using inverse dynamics method. Model predictions of joint kinematics, kinetics and muscle activation patterns were compared with published results. The estimated values of hip joint reaction force were found to corroborate well with in vivo measurements for each activity. Although the estimated values of hip joint reaction force were within a satisfactory range, overestimation of hip joint reaction force (75% BW of measured value) was observed during the late stance phase of walking cycles for all the models. In case of stair up, stair down, standing up and sitting down activities, the error in estimated values of hip joint reaction force were within ~20% BW of the measured value. Based on the results of our study, the London Lower Extremity Model predicted the most accurate value of hip joint reaction force and therefore can be used for applied musculoskeletal loading conditions for numerical investigations on hip implants.
Draft Genome Sequence of an Enterococcus faecalis Strain (24FS) That Was Isolated from Healthy Infant Feces and Exhibits High Antibacterial Activity, Multiple-Antibiotic Resistance, and Multiple Virulence Factors

Enterococcus faecalis 24FS is a bacteriocin-producing, multiply antibiotic-resistant, and potentially virulent bacterium isolated from healthy infant feces. The draft 2.9-Mb genome sequence revealed 2,968 protein-encoding genes; 11 antibiotic resistance, 8 virulence, and 3 bacteriocin genes; and 2 plasmids, 4 prophages, 30 insertion sequence (IS) elements, 1 transposon, and 1 integron. ABSTRACT Enterococcus faecalis 24FS is a bacteriocin-producing, multiply antibiotic-resistant, and potentially virulent bacterium isolated from healthy infant feces. The draft 2.9-Mb genome sequence revealed 2,968 protein-encoding genes; 11 antibiotic resistance, 8 virulence, and 3 bacteriocin genes; and 2 plasmids, 4 prophages, 30 insertion sequence (IS) elements, 1 transposon, and 1 integron.
CytoProcessorTM: A New Cervical Cancer Screening System for Remote Diagnosis

Background: Current automated cervical cytology screening systems still heavily depend on manipulation of glass slides. We developed a new system called CytoProcessorTM (DATEXIM, Caen, France), which increases sensitivity and takes advantage of virtual slide technology to simplify the workflow and save worker time. We used an approach based on artificial intelligence to identify abnormal cells among the tens of thousands in a cervical preparation. Objectives: We set out to compare the diagnostic sensitivity and specificity of CytoProcessorTM and the ThinPrep Imaging System (HOLOGIC, Marlborough, MA, USA). Methods: A representative population of 1,352 cases was selected from the routine workflow in a private laboratory. Diagnoses were established using the ThinPrep Imaging System and CytoProcessorTM. All discordances were resolved by a consensus committee. Results: Compared to the ThinPrep Imaging System, CytoProcessorTM significantly improves diagnostic sensitivity without compromising specificity. The sensitivity of detection of “atypical squamous cells of undetermined significance (ASC-US) and more severe” and “low-grade squamous intraepithelial lesion and more severe” was significantly higher using CytoProcessorTM. Considering that cases with a truth diagnosis of ASC-US or more severe required clinical follow-up, 1.5% of the cases (21/1,360) would have been missed if the CytoProcessorTM diagnosis had been used for clinical decision-making. In contrast, 4% of the cases (54/1,360) were missed when the ThinPrep Imaging System diagnosis was used for clinical decision-making. There were 2.6 times fewer false negatives using CytoProcessorTM. The CytoProcessorTM workflow was 1.5 times faster in terms of worker time. Conclusions: CytoProcessorTM is the first of a new generation of automated screening systems, demonstrating improved sensitivity and yielding significant gains in processing time. In addition, the fully digital nature of slide presentation in CytoProcessorTM allows the remote diagnosis of Papanicolaou tests for the first time.
PENGARUH DIVIDEND PAYOUT RATIO, FIRM SIZE, DAN LEVERAGE TERHADAP VOLATILITAS HARGA SAHAM (Studi pada Perusahaan Indeks LQ-45 yang Terdaftar di Bursa Efek Indonesia Periode 2016-2018)

The study is aimed at analyzing the influence of Dividend Payout Ratio, Firm Size and, Leverage on Stock Price Volatility. The population in this study are companies listed in the LQ-45 Index on the Indonesia Stock Exchange for the period of 2016-2018. The data used are secondary data from Bloomberg and the Indonesia Stock Exchange Financial Reports that are published. Total companies that meet the criteria are 22 companies. The analysis technique used is linear regression analysis with the SPSS application program. The results showed that partially Leverage had a significant negative effect on Stock Price Volatility. Other variables, namely Dividend Payout Ratio and Firm Size do not significantly influence the Stock Price Volatility. Stimulously, Dividend Payout Ratio, Firm Size and Leverage have a significant effect on Stock Price Volatility. And based on the results of multiple analyzes, leverage is a variable that has a dominant influence on stock price volatility as indicated by the value of the beta coefficient (β) that is -0.040.
Arabidopsis and Chlamydomonas phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin–Benson cycle

Significance In chloroplasts, five enzymes of the Calvin–Benson (CB) cycle are regulated by thioredoxins (TRXs). These enzymes have all been structurally characterized, with the notable exception of phosphoribulokinase (PRK). Here, we determined the crystal structure of chloroplast PRK from two model photosynthetic organisms. Regulatory cysteines appear distant from each other and are linked by a long loop that is present only in plant-type PRKs and allows disulfide-bond formation and subsequent conformational rearrangements. Structural comparisons with ancient PRKs indicate that the presence of flexible regions close to regulatory cysteines is a unique feature that is shared by TRX-dependent CB cycle enzymes, suggesting that the evolution of the PRK structure has resulted in a global increase in protein flexibility for photosynthetic eukaryotes. In land plants and algae, the Calvin–Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga Chlamydomonas reinhardtii (CrPRK) and the land plant Arabidopsis thaliana (AtPRK). PRK is an elongated homodimer characterized by a large central β-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 Å apart and connected by a flexible region exclusive to photosynthetic eukaryotes—the clamp loop—which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both AtPRK and CrPRK have a strongly reduced dimer interface and an increased number of random-coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes.
Histone 2B monoubiquitination complex integrates transcript elongation with RNA processing at circadian clock and flowering regulators

Significance In eukaryotes, the genomic DNA is organized in chromatin that consists of nucleosomal units formed by histone proteins. The accessibility of genes for RNA polymerase II transcription by the dynamic modification of histone tails during the transcript elongation phase is emerging as an important regulatory mechanism. Here, we show that RNA-binding proteins, together with the conserved HISTONE MONOUBIQUITINATION1–HISTONE MONOUBIQUITINATION2 complex that mediates histone H2B monoubiquitination at the circadian clock, and flowering time-regulatory genes during transcript elongation are required for the processing of their pre-mRNA and antisense RNA, respectively. HISTONE MONOUBIQUITINATION1 (HUB1) and its paralog HUB2 act in a conserved heterotetrameric complex in the chromatin-mediated transcriptional modulation of developmental programs, such as flowering time, dormancy, and the circadian clock. The KHD1 and SPEN3 proteins were identified as interactors of the HUB1 and HUB2 proteins with in vitro RNA-binding activity. Mutants in SPEN3 and KHD1 had reduced rosette and leaf areas. Strikingly, in spen3 mutants, the flowering time was slightly, but significantly, delayed, as opposed to the early flowering time in the hub1-4 mutant. The mutant phenotypes in biomass and flowering time suggested a deregulation of their respective regulatory genes CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and FLOWERING LOCUS C (FLC) that are known targets of the HUB1-mediated histone H2B monoubiquitination (H2Bub). Indeed, in the spen3-1 and hub1-4 mutants, the circadian clock period was shortened as observed by luciferase reporter assays, the levels of the CCA1α and CCA1β splice forms were altered, and the CCA1 expression and H2Bub levels were reduced. In the spen3-1 mutant, the delay in flowering time was correlated with an enhanced FLC expression, possibly due to an increased distal versus proximal ratio of its antisense COOLAIR transcript. Together with transcriptomic and double-mutant analyses, our data revealed that the HUB1 interaction with SPEN3 links H2Bub during transcript elongation with pre-mRNA processing at CCA1. Furthermore, the presence of an intact HUB1 at the FLC is required for SPEN3 function in the formation of the FLC-derived antisense COOLAIR transcripts.