julilili42/papers huggingface dataset:
Deep Learning-Based Superresolution Reconstruction for Upper Abdominal Magnetic Resonance Imaging
2021-02-27

Objectives The aim of this study was to investigate the impact of a deep learning-based superresolution reconstruction technique for T1-weighted volume-interpolated breath-hold examination (VIBE SR ) on image quality in comparison with standard VIBE images (VIBE SD ). Methods Between May and August 2020, a total of 46 patients with various abdominal pathologies underwent contrast-enhanced upper abdominal VIBE magnetic resonance imaging (MRI) at 1.5 T. After data acquisition, the precontrast and postcontrast T1-weighted VIBE raw data were processed by a deep learning-based prototype algorithm for deblurring and denoising the images as well as for enhancing their sharpness (VIBE SR ). In a randomized and blinded manner, 2 radiologists independently analyzed the image data sets using the unprocessed images VIBE SD as a standard reference. Outcome measures were as follows: overall image quality, anatomic clarity of organ borders, sharpness of vessels, artifacts, noise, and diagnostic confidence. All ratings were performed on an ordinal 4-point Likert scale. If the MRI examination encompassed a hepatic lesion, the maximum diameter of the largest hepatic lesion was quantified, and lesion sharpness and conspicuity were evaluated on an ordinal 4-point Likert scale. In addition, a post hoc regression analysis for lesion evaluation was computed. Finally, interrater/intrarater agreement was analyzed. Results The overall image quality, anatomic clarity of organ borders, and sharpness of vessels in both precontrast and postcontrast images were rated significantly higher in VIBE SR than in VIBE SD ( P &lt; 0.001). Similarly, diagnostic confidence was higher in VIBE SR than in VIBE SD ( P &lt; 0.001). Furthermore, VIBE SR images were rated to have significantly less noise and fewer artifacts in comparison with VIBE SD ( P &lt; 0.001). The interreader agreement was substantial with a Cohen κ of 0.72 for the precontrast analysis and a κ of 0.74 for the postcontrast analysis. A total of 28 hepatic lesions were analyzed. For both readers, lesion sharpness and conspicuity were rated significantly better in VIBE SR than in VIBE SD in both the precontrast and postcontrast data sets ( P &lt; 0.01), which was consistent with the post hoc regression analysis (for every 1-point increase in sharpness/conspicuity, the odds ratio revealed a positive relation with VIBE SR of 13-fold to 17-fold in comparison with VIBE SD ; P &lt; 0.001). In terms of lesion size, there was no significant difference between the precontrast VIBE SD and VIBE SR or between the postcontrast VIBE SD and VIBE SR for both readers. Similarly, there was an excellent interreader agreement regarding lesion size (intraclass correlation coefficient, &gt;0.9). Conclusions The data-driven superresolution reconstruction (VIBE SR ) is clinically feasible for precontrast and postcontrast upper abdominal VIBE MRI, providing improved image quality, diagnostic confidence, and lesion conspicuity compared with standard VIBE SD images.
Clinical Phenotype of PDE6B-Associated Retinitis Pigmentosa
2021-02-27

In this retrospective, longitudinal, observational cohort study, we investigated the phenotypic and genotypic features of retinitis pigmentosa associated with variants in the PDE6B gene. Patients underwent clinical examination and genetic testing at a single tertiary referral center, including best-corrected visual acuity (BCVA), kinetic visual field (VF), full-field electroretinography, full-field stimulus threshold, spectral domain optical coherence tomography, and fundus autofluorescence imaging. The genetic testing comprised candidate gene sequencing, inherited retinal disease gene panel sequencing, whole-genome sequencing, and testing for familial variants by Sanger sequencing. Twenty-four patients with mutations in PDE6B from 21 families were included in the study (mean age at the first visit: 32.1 ± 13.5 years). The majority of variants were putative splicing defects (8/23) and missense (7/23) mutations. Seventy-nine percent (38/48) of eyes had no visual acuity impairment at the first visit. Visual acuity impairment was mild in 4% (2/48), moderate in 13% (6/48), and severe in 4% (2/48). BCVA was symmetrical in the right and left eyes. The kinetic VF measurements were highly symmetrical in the right and left eyes, as was the horizontal ellipsoid zone (EZ) width. Regarding the genetic findings, 43% of the PDE6B variants found in our patients were novel. Thus, this study contributed substantially to the PDE6B mutation spectrum. The visual acuity impairment was mild in 83% of eyes, providing a window of opportunity for investigational new drugs. The EZ width was reduced in all patients and was highly symmetric between the eyes, making it a promising outcome measure. We expect these findings to have implications on the design of future PDE6B-related retinitis pigmentosa (RP) clinical trials.
Decision-Making Skills in Youth Basketball Players: Diagnostic and External Validation of a Video-Based Assessment
2021-02-27

Decision-making is a central skill of basketball players intending to excel individually and contribute to their teams’ success. The assessment of such skills is particularly challenging in complex team sports. To address this challenge, this study aimed to conceptualize a reliable and valid video-based decision-making assessment in youth basketball. The study sample comprised youth basketball players of the German U16 national team (n = 17; MAge = 16.01 ± 0.25 years) and students of a sports class (n = 17; MAge = 15.73 ± 0.35 years). Diagnostic validity was tested by determination of the performance levels according to response accuracy as well as response time in the assessment. External validity was examined by investigation of the correlation between the diagnostic results of the elite athletes and their real game performance data associated with passing skills. Logistic regression analysis revealed that the diagnostic results discriminate between performance levels (χ2(2) = 20.39, p &lt; 0.001, Nagelkerke’s R2 = 0.60). Multiple regression analysis demonstrated a positive relationship between the diagnostic results and assists (F(2,10) = 4.82, p &lt; 0.05; R2 = 0.49) as well as turnovers per game (F(2,10) = 5.23, p &lt; 0.05; R2 = 0.51). However, no relationship was detected regarding the assist-turnover ratio. Further, response time discriminated within the elite athletes’ performance data but not between performance levels while for response accuracy the opposite is the case. The results confirm the diagnostic and external validity of the assessment and indicate its applicability to investigate decision-making skills in youth basketball.
Outcomes of SARS‐CoV‐2 Infections in Patients with Neurodegenerative Diseases in the LEOSS Cohort
2021-02-27

The impact of preexisting neurodegenerative diseases on superimposed SARS-CoV-2 infections remains controversial. Here we examined the course and outcome of SARS-CoV-2 infections in patients affected by Parkinson's disease (PD) or dementia compared to matched controls without neurodegenerative diseases in the LEOSS (Lean European Open Survey on SARS-CoV-2-infected patients) cohort, a large-scale prospective multicenter cohort study...
The prognostic value of fat invasion and tumor expansion in the hilar veins in pT3a renal cell carcinoma
2021-02-27

Abstract Purpose The 7th TNM classification summarizes renal cell carcinoma (RCC) with perirenal (PFI) and/or sinus fat invasion (SFI) as well as hilar vein involvement (RVI) as pT3a tumors. In this study, we aimed to determine the prognostic value of fat invasion (FI) in the different compartments and RVI for medium-term cancer-specific-survival (CSS) in pT3a RCC. Materials and methods Patients with pT3a RCC were identified using an institutional database. All original pathological reports were reclassified according to the 7th TNM edition. The prognostic value of FI as well as divided into PFI, SFI, combined PFI + SFI, and RVI for CSS was assessed using univariate and multivariate Cox-regression analysis. Survival was estimated using the Kaplan–Meier method. Results Median follow-up in 184 pT3a tumors was 38 months. FI was detectable in 153 patients (32.7% PFI, 45.1% SFI, 22.2% PFI + SFI), 31 patients showed RVI alone. Combined PFI + SFI increased the risk of cancer-related death compared to PFI (HR 3.11, p &lt; 0.01), SFI (HR 1.84, p = 0.023) or sole RVI (HR 2.12, p = 0.025). In multivariate analysis, a combined PFI + SFI vs. PFI or SFI as the only compartment involved was confirmed as independent prognostic factor (HR 1.83, p = 0.029). Patients with FI and simultaneous RVI had significantly shorter CSS (HR 2.63, p &lt; 0.01). In an unweighted model, the difference between patients with combined PFI + SFI and RVI and those with PFI alone was highest (HR 4.01, p = 0.029). Conclusions These results underline the subdivision of pT3a RCC depending on the location of FI and RVI for patient stratification.
Low‐fat hypocaloric diet reduces neprilysin in overweight and obese human subjects
2021-02-27

Abstract Aims Neprilysin (NEP), a zinc metallopeptidase, degrades a variety of bioactive peptides including natriuretic peptides terminating their biological action on arterial blood pressure and natriuresis. Pharmacological inhibition of NEP reduces mortality in patients with heart failure with reduced ejection fraction. Physiological interventions reducing NEP levels are unknown in humans. Because obesity leads to increased NEP levels and increases the risk for heart failure, we hypothesized that weight loss reduces NEP concentrations in plasma and tissue. Methods and results We randomized overweight to obese human subjects to a low‐fat or low‐carbohydrate hypocaloric 6 month weight loss intervention. Soluble NEP was determined in plasma, and NEP mRNA was analysed from subcutaneous adipose tissue before and after diet. Low‐fat diet‐induced weight loss reduced soluble NEP levels from 0.83 ± 0.18 to 0.72 ± 0.18 μg/L ( P = 0.038), while subcutaneous adipose tissue NEP mRNA expression was reduced by both dietary interventions [21% ( P = 0.0057) by low‐fat diet and 16% ( P = 0.048) by low‐carbohydrate diet]. We also analysed the polymorphisms of the gene coding for NEP, rs9827586 and rs701109, known to be associated with plasma NEP levels. For both single‐nucleotide polymorphisms, minor allele carriers (A/A) had higher baseline plasma NEP levels (rs9827586: β = 0.53 ± 0.23, P &lt; 0.0001; rs701109: β = 0.43 ± 0.22, P = 0.0016), and minor allele carriers of rs9827586 responded to weight loss with a larger NEP reduction (rs9827586: P = 0.0048). Conclusions Our study identifies weight loss via a hypocaloric low‐fat diet as the first physiological intervention in humans to reduce NEP in plasma and adipose tissue. Specific single‐nucleotide polymorphisms further contribute to the decrease. Our findings may help to explain the beneficial effect of weight loss on cardiac function in patients with heart failure.
Attacking Key Performance Indicators in Soccer: Current Practice and Perceptions from the Elite to Youth Academy Level
2021-02-28

Key Performance Indicators (KPIs) are used to evaluate the offensive success of a soccer team (e.g. penalty box entries) or player (e.g. pass completion rate). However, knowledge transfer from research to applied practice is understudied. The current study queried practitioners (n = 145, mean ± SD age: 36 ± 9 years) from 42 countries across different roles and levels of competition (National Team Federation to Youth Academy levels) on various forms of data collection, including an explicit assessment of twelve attacking KPIs. 64.3% of practitioners use data tools and applications weekly (predominately) to gather KPIs during matches. 83% of practitioners use event data compared to only 52% of practitioners using positional data, with a preference for shooting related KPIs. Differences in the use and value of metrics derived from positional tracking data (including Ball Possession Metrics) were evident between job role and level of competition. These findings demonstrate that practitioners implement KPIs and gather tactical information in a variety of ways with a preference for simpler metrics related to shots. The low perceived value of newer KPIs afforded by positional data could be explained by low buy-in, a lack of education across practitioners, or insufficient translation of findings by experts towards practice.
Vertebrate species knowledge: an important skill is threatened by extinction
2021-02-28

Vertebrate species knowledge, a key factor for conserving biodiversity, is a compulsory part of school curricula. This study evaluated the vertebrate species knowledge of sixth-grade German grammar school pupils (aged 11–13) to investigate the influence of socio-demographic factors (gender, size of hometown, mother tongue), personal expectations (favourite school subject, performance in biology, expected test results) and possibilities to do nature observations (favourite playing area, number of excursions to nature) on identification skills. In addition, the study examined whether schoolchildren's taxonomic knowledge changed over the years. In a species identification test, participants (N = 984) scored an average of 14.18 ± 3.82 out of 25 points. The results showed that their species knowledge was significantly influenced by their personal expectations on test performance, the school, favourite playing area, mother tongue and gender. Hometown size, the number of excursions to nature, favourite school subject and performance in biology did not significantly affect children's species knowledge. Mammals had the highest identification rates, whereas birds and reptiles were rather unknown. These results were compared with a similar dataset in 2006 indicating a 15% loss in pupils' species knowledge within the last decade. A change in the curriculum as a reason for this decline in taxonomic knowledge is discussed.
Cardiometabolic risk factors associated with brain age and accelerate brain ageing
2021-02-28

Abstract The structure and integrity of the ageing brain is interchangeably linked to physical health, and cardiometabolic risk factors (CMRs) are associated with dementia and other brain disorders. In this mixed cross-sectional and longitudinal study (interval mean and standard deviation = 19.7 ± 0.5 months), including 1062 datasets from 790 healthy individuals (mean (range) age = 46.7 (18-94) years, 54% women), we investigated CMRs and health indicators including anthropometric measures, lifestyle factors, and blood biomarkers in relation to brain structure using MRI-based morphometry and diffusion tensor imaging (DTI). We performed tissue specific brain age prediction using machine learning and performed Bayesian multilevel modelling to assess changes in each CMR over time, their respective association with brain age gap (BAG), and their interaction effects with time and age on the tissue-specific BAGs. The results showed credible associations between DTI-based BAG and blood levels of phosphate and mean cell volume (MCV), and between T1-based BAG and systolic blood pressure, smoking, pulse, and C-reactive protein (CRP), indicating older-appearing brains in people with higher cardiometabolic risk (smoking, higher blood pressure and pulse, low-grade inflammation). Longitudinal evidence supported interactions between both BAGs and waist-to-hip ratio (WHR), and between DTI-based BAG and systolic blood pressure and smoking, indicating accelerated ageing in people with higher cardiometabolic risk (smoking, higher blood pressure, and WHR). The results demonstrate that cardiometabolic risk factors are associated with brain ageing. While randomised controlled trials are needed to establish causality, our results indicate that public health initiatives and treatment strategies targeting modifiable cardiometabolic risk factors may also improve risk trajectories and delay brain ageing.
Lifestyle Intervention Improves Prothrombotic Coagulation Profile in Individuals at High Risk for Type 2 Diabetes
2021-02-28

Abstract Context Patients with obesity and insulin resistance are at higher risk for arterial and venous thrombosis due to a prothrombotic state. Objective The present study addressed whether this is reversible by lifestyle intervention and elucidated potential underlying associations. Methods A total of 100 individuals with impaired glucose tolerance or impaired fasting plasma glucose participated in a 1-year lifestyle intervention, including precise metabolic phenotyping and MRS-based determination of liver fat content as well as a comprehensive analysis of coagulation parameters before and after this intervention. Results During the lifestyle intervention, significant reductions in coagulation factor activities (II, VII, VIII, IX, XI, and XII) were observed. Accordingly, prothrombin time (PT%) and activated partial thromboplastin time (aPTT) were slightly decreased and prolonged, respectively. Moreover, plasminogen activator inhibitor-1 (PAI-1), von Willebrand factor (vWF), and also protein C and protein S decreased. Fibrinogen, antithrombin, D-dimer, and FXIII remained unchanged. Searching for potential regulators, especially weight loss, but also liver fat reduction, improved insulin sensitivity, and decreased low-grade inflammation were linked to favorable changes in hemostasis parameters. Independent of weight loss, liver fat reduction (FII, protein C, protein S, PAI-1, vWF), improved insulin sensitivity (protein S, PAI-1), and reduced low-grade inflammation (PT%, aPTT, FVIII/IX/XI/XII, vWF) were identified as single potential regulators. Conclusion Lifestyle intervention is able to improve a prothrombotic state in individuals at high risk for type 2 diabetes. Besides body weight, liver fat content, insulin sensitivity, and systemic low-grade inflammation are potential mechanisms for improvements in hemostasis and could represent future therapeutic targets.
Apoptotic Blocks in Primary Non-Hodgkin B Cell Lymphomas Identified by BH3 Profiling
2021-02-28

To determine causes of apoptotic resistance, we analyzed 124 primary B cell NHL samples using BH3 profiling, a technique that measures the mitochondrial permeabilization upon exposure to synthetic BH3 peptides. Our cohort included samples from chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), high-grade B cell lymphoma with translocations in MYC and BCL2 (HGBL-DH), mantle cell lymphoma (MCL) and marginal zone lymphoma (MZL). While a large number of our samples displayed appropriate responses to apoptosis-inducing peptides, pro-apoptotic functional defects, implicating BAX, BAK, BIM or BID, were seen in 32.4% of high-grade NHLs (12/37) and in 3.4% of low-grade NHLs (3/87, p &lt; 0.0001). The inhibition of single anti-apoptotic proteins induced apoptosis in only a few samples, however, the dual inhibition of BCL2 and MCL1 was effective in 83% of samples, indicating MCL1 was the most common cause of lack of response to the BCL2 inhibitor, venetoclax. We then profiled Toledo and OCI-Ly8 high-grade lymphoma cell lines to determine which drugs could reduce MCL1 expression and potentiate venetoclax responses. Doxorubicin and vincristine decreased levels of MCL1 and increased venetoclax-induced apoptosis (all p &lt; 0.05). Overall, in primary NHLs expressing BCL2 that have no defects in pro-apoptotic signaling, a poor response to venetoclax is primarily due to the presence of MCL1, which may be overcome by combining venetoclax with doxorubicin and vincristine-based chemotherapy or with other anti-microtubule inhibitors.
Social Lives of Monumental Walls: Hunting along the Upper Tigris
2021-02-28

On the left bank of the Tigris in northern Iraq, in an area today partially flooded by the Mosul Dam reservoir, lies an enigmatic monumental enclosure known in the literature as the “Tigris Wall.” Before its partial submersion under the waters of the modern lake, the large L-shaped embankment, about 4 × 4 km long, enclosed an area of ca. 1600 ha, overlooking the Tigris and its alluvial plain. By means of a holistic strategy that includes different levels of analysis (remote sensing, pedestrian and UAV photogrammetric surveys, excavation, and settlement pattern analysis), this paper addresses the structure, its context, and its environment. Relying on the results of this multi-disciplinary approach, we present an updated and detailed discussion of the structure’s possible functions and interpretations. Parallels from northern Mesopotamia and neighboring regions are used to suggest that the Tigris Wall may be the first archaeologically known hunting park in the region, probably dating to the Late Sasanian or Early Islamic epoch.
Spatial alanine metabolism determines local growth dynamics ofEscherichia colicolonies
2021-02-28

Abstract Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
Environmental Implications and Chalcolithic Ornamental Use of Marine Barnacle Shells Present in the Tholos of ‘La Pastora’ (Valencina de la Concepción, Sevilla, Spain)
2021-02-28

Trabajo científico sobre unas cuentas de collar halladas en el monumento prehistórico del tholos de La Pastora. Estas cuentas son conchas de una especie de Balanus (Chthamalus montagui), siendo la primera vez que se documenta este uso en este tipo de organismos litorales. En el trabajo se extraen conclusiones paleoambientales, del medio del que se extranjeron y cronológicas absolutas del uso del tholos.