julilili42/papers huggingface dataset:
Deciphering the Variability of Stable Isotope (C, Cl) Fractionation of Tetrachloroethene Biotransformation by Desulfitobacterium strains Carrying Different Reductive Dehalogenases Enzymes
2019-12-27

Kinetic isotope effects have been used successfully to prove and characterize organic contaminant transformation on various scales including field and laboratory studies. For tetrachloroethene (PCE) biotransformation, however, causes for the substantial variability of reported isotope enrichment factors (ε) are still not deciphered (ε<sub>C</sub> = -0.4 to -19.0‰). Factors such as different reaction mechanisms and masking of isotope fractionation by either limited intracellular mass transfer or rate-limitations within the enzymatic multistep reaction are under discussion. This study evaluated the contribution of these factors to the magnitude of carbon and chlorine isotope fractionation of <i>Desulfitobacterium</i> strains harboring three different PCE-transforming enzymes (PCE-RdhA). Despite variable single element isotope fractionation (ε<sub>C</sub> = -5.0 to -19.7‰; ε<sub>Cl</sub> <i>=</i> -1.9 to -6.3‰), similar slopes of dual element isotope plots (Λ<sub>C/Cl</sub> values of 2.4 ± 0.1 to 3.6 ± 0.1) suggest a common reaction mechanism for different PCE-RdhAs. Cell envelope properties of the <i>Desulfitobacterium</i> strains allowed to exclude masking effects due to PCE mass transfer limitation. Our results thus revealed that different rate-limiting steps (e.g., substrate channel diffusion) in the enzymatic multistep reactions of individual PCE-RdhAs rather than different reaction mechanisms determine the extent of PCE isotope fractionation in the <i>Desulfitobacterium</i> genus.
AAPM recommendations on medical physics practices for ocular plaque brachytherapy: Report of task group 221
2019-12-28

The American Association of Physicists in Medicine (AAPM) formed Task Group 221 (TG‐221) to discuss a generalized commissioning process, quality management considerations, and clinical physics practice standards for ocular plaque brachytherapy. The purpose of this report is also, in part, to aid the clinician to implement recommendations of the AAPM TG‐129 report, which placed emphasis on dosimetric considerations for ocular brachytherapy applicators used in the Collaborative Ocular Melanoma Study (COMS). This report is intended to assist medical physicists in establishing a new ocular brachytherapy program and, for existing programs, in reviewing and updating clinical practices. The report scope includes photon‐ and beta‐emitting sources and source:applicator combinations. Dosimetric studies for photon and beta sources are reviewed to summarize the salient issues and provide references for additional study. The components of an ocular plaque brachytherapy quality management program are discussed, including radiation safety considerations, source calibration methodology, applicator commissioning, imaging quality assurance tests for treatment planning, treatment planning strategies, and treatment planning system commissioning. Finally, specific guidelines for commissioning an ocular plaque brachytherapy program, clinical physics practice standards in ocular plaque brachytherapy, and other areas reflecting the need for specialized treatment planning systems, measurement phantoms, and detectors (among other topics) to support the clinical practice of ocular brachytherapy are presented. Expected future advances and developments for ocular brachytherapy are discussed.
Current and emerging therapies for managing hyperphagia and obesity in Prader‐Willi syndrome: A narrative review
2019-12-30

Summary In early childhood, individuals with Prader‐Willi syndrome (PWS) experience excess weight gain and severe hyperphagia with food compulsivity, which often leads to early onset morbid obesity. Effective treatments for appetite suppression and weight control are currently unavailable for PWS. Our aim to further understand the pathogenesis of PWS led us to carry out a comprehensive search of the current and emerging therapies for managing hyperphagia and extreme weight gain in PWS. A literature search was performed using PubMed and the following keywords: “PWS” AND “therapy” OR “[drug name]”; reference lists, pharmaceutical websites, and the ClinicalTrials.gov registry were also reviewed. Articles presenting data from current standard treatments in PWS and also clinical trials of pharmacological agents in the pipeline were selected. Current standard treatments include dietary restriction/modifications, exercise, and growth hormone replacement, which appear to have limited efficacy for appetite and weight control in patients with PWS. The long‐term safety and effectiveness of bariatric surgery in PWS remains unknown. However, many promising pharmacotherapies are in development and, if approved, will bring much needed choices into the PWS pharmacological armamentarium. With the progress that is currently being made in our understanding of PWS, an effective treatment may not be far off.
Fe(III) Photoreduction Producing Feaq2+ in Oxic Freshwater Sediment
2019-12-30

Iron(III) (Fe(III)) photoreduction plays an important role in Fe cycling and Fe(II) bioavailability in the upper ocean. Although well described for water columns, it is currently unknown to what extent light impacts the production of dissolved Fe(II) (Fe<sup>2+</sup>) in aquatic sediments. We performed high-resolution voltammetric microsensor measurements and demonstrated light-induced Fe<sup>2+</sup> release in freshwater sediments from Lake Constance. Fe<sup>2+</sup> concentrations increased up to 40 μM in the top 3 mm of the sediment during illumination in the visible range of light (400-700 nm), even in the presence of oxygen (100-280 μM). The Fe<sup>2+</sup> release was strongly dependent on the organic matter content of the sediment. A lack of photoreduced Fe<sup>2+</sup> was measured in sediments with concentrations of organic carbon <6 mg L<sup>-1</sup>. The simultaneous presence of sedimentary Fe(III) photoreduction besides microbial and abiotic Fe<sup>2+</sup> oxidation by oxygen suggests an active Fe redox cycling in the oxic and photic zone of aquatic sediments. Here, we provide evidence for a relevant contribution of Fe(III) photoreduction to the bio-geochemical Fe redox cycle in aquatic freshwater sediments.
Equal-time quark propagator in Coulomb gauge
2019-12-30

We investigate the equal-time (static) quark propagator in Coulomb gauge within the Hamiltonian approach to QCD. We use a non-Gaussian vacuum wave functional which includes the coupling of the quarks to the spatial gluons. The expectation value of the QCD Hamiltonian is expressed by the variational kernels of the vacuum wave functional by using the canonical recursive Dyson--Schwinger equations (CRDSEs) derived previously. Assuming the Gribov formula for the gluon energy we solve the CRDSE for the quark propagator in the bare-vertex approximation together with the variational equations of the quark sector. Within our approximation the quark propagator is fairly insensitive to the coupling to the spatial gluons and its infrared behaviour is exclusively determined by the strongly infrared diverging instantaneous colour Coulomb potential.
Efficient data management infrastructure for the integration of imaging and omics data in life science research
2019-12-30

Abstract As technical developments in omics and biomedical imaging drive the increase in quality, modality, and throughput of data generation in life sciences, the need for information systems capable of integrative, long-term storage and management of these heterogeneous digital assets is also increasing. Here, we propose an approach based on principles of Service Oriented Architecture design, to allow the integrated management and analysis of multi-omics and biomedical imaging data. The proposed architecture introduces an interoperable image management system, the OMERO server, into the backend of qPortal, a FAIR-compliant web-based platform for omics data management. The implementation of an integrated metadata model, the development of software components to enable the communication with the OMERO server, and an extension to the data management operations of established software, allows for FAIR management of heterogeneous omics and biomedical imaging data within an integrated system, which facilitates metadata queries from web-based scientific applications. The applicability of the proposed architecture is demonstrated in two prototypical use cases, a plant biology study using confocal scanning microscopy, and a clinical study on hepatocellular carcinoma, with data from a variety of medical imaging and omics modalities. We anticipate that FAIR data management systems for multi-modal data repositories will play a pivotal role in data-driven research, as the joint analysis of omics and imaging data becomes not only desirable but necessary to derive novel insights into biological processes. In particular for powerful machine learning applications where the availability of large datasets with high quality phenotypic annotations is a requirement.
Realistic collisional water transport during terrestrial planet formation
2019-12-31

Context. According to the latest theoretical and isotopic evidence, Earth’s water content originates mainly from today’s asteroid belt region, or at least from the same precursor material. This suggests that water was transported inwards to Earth, and to similar planets in their habitable zone, via (giant) collisions of planetary embryos and planetesimals during the chaotic final phase of planet formation. Aims. In current dynamical simulations water delivery to terrestrial planets is still studied almost exclusively by assuming oversimplified perfect merging, even though water and other volatiles are particularly prone to collisional transfer and loss. To close this gap we have developed a computational framework to model collisional water transport by direct combination of long-term N -body computations with dedicated 3D smooth particle hydrodynamics (SPH) collision simulations of differentiated, self-gravitating bodies for each event. Methods. Post-collision water inventories are traced self-consistently in the further dynamical evolution, in accretionary or erosive as well as hit-and-run encounters with two large surviving bodies, where besides collisional losses, water transfer between the encountering bodies has to be considered. This hybrid approach enables us for the first time to trace the full dynamical and collisional evolution of a system of approximately 200 bodies throughout the whole late-stage accretion phase (several hundred Myr). As a first application we choose a Solar System-like architecture with already formed giant planets on either circular or eccentric orbits and a debris disk spanning the whole terrestrial planet region (0.5–4 au). Results. Including realistic collision treatment leads to considerably different results than simple perfect merging, with lower mass planets and water inventories reduced regularly by a factor of two or more. Due to a combination of collisional losses and a considerably lengthened accretion phase, final water content, especially with giant planets on circular orbits, is strongly reduced to more Earth-like values, and closer to results with eccentric giant planets. Water delivery to potentially habitable planets is dominated by very few decisive collisions, mostly with embryo-sized or larger objects and only rarely with smaller bodies, at least if embryos have formed throughout the whole disk initially. The high frequency of hit-and-run collisions and the differences to predominantly accretionary encounters, such as generally low water (and mass) transfer efficiencies, are a crucial part of water delivery, and of system-wide evolution in general.
Performance of an Automated Workflow for Magnetic Resonance Imaging of the Prostate
2019-12-31

Objectives The aim of this study was to evaluate the performance of an automated workflow for multiparametric magnetic resonance imaging (mpMRI) of the prostate compared with a manual mpMRI workflow. Materials and Methods This retrospective study was approved by the local ethics committee. Two MR technicians scanned 2 healthy volunteers with a prototypical highly automated workflow (Siemens Healthineers GmbH, Erlangen, Germany) and with a manually adjusted scan protocol each. Thirty patients (mean age ± standard deviation, 68 ± 11 years; range, 41–93 years) with suspected prostate cancer underwent mpMRI on a 3 T MRI scanner. Fifteen patients were examined with the automated workflow and 15 patients with a conventional manual workflow. Two readers assessed image quality (contrast, zone distinction, organ margins, seminal vesicles, lymph nodes), organ coverage, orientation (T2w sequences), and artifacts (motion, susceptibility, noise) on a 5-point scale (1, poor; 5, excellent). Examination time and MR technicians' acceptance were compared between both groups. Interreader agreement was evaluated with Cohen's kappa (κ). Results The automated workflow proved consistent for sequence orientation and image quality in the intraindividual comparisons. There were no significant differences in examination time (automated vs manual; median 26 vs 28 minutes; interquartile range [IQR], 25–28 minutes each; P = 0.57), study volume coverage, artifacts, or scores for T2w sequence orientation (5 vs 4 each; P &gt; 0.3). Overall image quality was superior for automated MRI (4.6 vs 3.8; IQR, 3.9–4.8 vs 3.2–4.3; P = 0.002), especially concerning organ delineation and seminal vesicles ( P = 0.045 and P = 0.013). The acceptance score was higher for the manual workflow (median, 10 vs 8; IQR, 10 vs 7–10; P = 0.002). General interreader agreement was excellent (κ = 0.832; P &lt; 0.001). Conclusions The automated workflow for prostate MRI ensures accurate sequence orientation and maintains high image quality, whereas examination time remained unaffected compared with the manual procedure in our institution.
Acknowledgments
2019-12-31

Acknowled gmentsThis book began to take shape in the summer of 1998.At the time, I was immersed in research for a project on the relevance of slavery for the formulation of late Roman Christian notions of leadership: that is, for the role of the bishop.Gregory of Nazianzus's second oration soon emerged as a central source, and I was already working on a number of papers devoted to it when Martin Nettesheim suggested I write instead a short little book on Gregory.Over a decade later, this short little book has accumulated an enormous debt of gratitude from friends, students, and colleagues.During a year spent at the Shelby Cullom Davis Center for Historical Studies at Princeton in 2000-2001, I formulated a first draft of what have become the first six chapters.It was an enormously fruitful and enjoyable time, for which I thank Anthony Grafton and Kenneth Mills.
Computer Vision for Autonomous Vehicles: Problems, Datasets and State of the Art
2020-01-01

Recent years have witnessed enormous progress in AI-related fields such as computer vision, machine learning, and autonomous vehicles. As with any rapidly growing field, it becomes increasingly difficult to stay up-to-date or enter the field as a beginner. While several survey papers on particular sub-problems have appeared, no comprehensive survey on problems, datasets, and methods in computer vision for autonomous vehicles has been published. This monograph attempts to narrow this gap by providing a survey on the state-of-the-art datasets and techniques. Our survey includes both the historically most relevant literature as well as the current state of the art on several specific topics, including recognition, reconstruction, motion estimation, tracking, scene understanding, and end-to-end learning for autonomous driving. Towards this goal, we analyze the performance of the state of the art on several challenging benchmarking datasets, including KITTI, MOT, and Cityscapes. Besides, we discuss open problems and current research challenges. To ease accessibility and accommodate missing references, we also provide a website that allows navigating topics as well as methods and provides additional information.
SemEval-2020 Task 12: Multilingual Offensive Language Identification in Social Media (OffensEval 2020)
2020-01-01

We present the results and main findings of SemEval-2020 Task 12 on Multilingual Offensive Language Identification in Social Media (OffensEval 2020). The task involves three subtasks corresponding to the hierarchical taxonomy of the OLID schema (Zampieri et al., 2019a) from OffensEval 2019. The task featured five languages: English, Arabic, Danish, Greek, and Turkish for Subtask A. In addition, English also featured Subtasks B and C. OffensEval 2020 was one of the most popular tasks at SemEval-2020 attracting a large number of participants across all subtasks and also across all languages. A total of 528 teams signed up to participate in the task, 145 teams submitted systems during the evaluation period, and 70 submitted system description papers.
Trihalomethanes in Drinking Water and Bladder Cancer Burden in the European Union
2020-01-01

Efforts have been made to reduce THM levels in the European Union. However, assuming a causal association, current levels in certain countries still could lead to a considerable burden of bladder cancer that could potentially be avoided by optimizing water treatment, disinfection, and distribution practices, among other possible measures. https://doi.org/10.1289/EHP4495.
Passengers' destinations from China: low risk of Novel Coronavirus (2019-nCoV) transmission into Africa and South America
2020-01-01

Abstract Novel Coronavirus (2019-nCoV [SARS-COV-2]) was detected in humans during the last week of December 2019 at Wuhan city in China, and caused 24 554 cases in 27 countries and territories as of 5 February 2020. The objective of this study was to estimate the risk of transmission of 2019-nCoV through human passenger air flight from four major cities of China (Wuhan, Beijing, Shanghai and Guangzhou) to the passengers' destination countries. We extracted the weekly simulated passengers' end destination data for the period of 1–31 January 2020 from FLIRT, an online air travel dataset that uses information from 800 airlines to show the direct flight and passengers' end destination. We estimated a risk index of 2019-nCoV transmission based on the number of travellers to destination countries, weighted by the number of confirmed cases of the departed city reported by the World Health Organization (WHO). We ranked each country based on the risk index in four quantiles (4 th quantile being the highest risk and 1 st quantile being the lowest risk). During the period, 388 287 passengers were destined for 1297 airports in 168 countries or territories across the world. The risk index of 2019-nCoV among the countries had a very high correlation with the WHO-reported confirmed cases (0.97). According to our risk score classification, of the countries that reported at least one Coronavirus-infected pneumonia (COVID-19) case as of 5 February 2020, 24 countries were in the 4 th quantile of the risk index, two in the 3 rd quantile, one in the 2 nd quantile and none in the 1 st quantile. Outside China, countries with a higher risk of 2019-nCoV transmission are Thailand, Cambodia, Malaysia, Canada and the USA, all of which reported at least one case. In pan-Europe, UK, France, Russia, Germany and Italy; in North America, USA and Canada; in Oceania, Australia had high risk, all of them reported at least one case. In Africa and South America, the risk of transmission is very low with Ethiopia, South Africa, Egypt, Mauritius and Brazil showing a similar risk of transmission compared to the risk of any of the countries where at least one case is detected. The risk of transmission on 31 January 2020 was very high in neighbouring Asian countries, followed by Europe (UK, France, Russia and Germany), Oceania (Australia) and North America (USA and Canada). Increased public health response including early case recognition, isolation of identified case, contract tracing and targeted airport screening, public awareness and vigilance of health workers will help mitigate the force of further spread to naïve countries.
The Global Health Security index and Joint External Evaluation score for health preparedness are not correlated with countries' COVID-19 detection response time and mortality outcome
2020-01-01

Abstract Global Health Security Index (GHSI) and Joint External Evaluation (JEE) are two well-known health security and related capability indices. We hypothesised that countries with higher GHSI or JEE scores would have detected their first COVID-19 case earlier, and would experience lower mortality outcome compared to countries with lower scores. We evaluated the effectiveness of GHSI and JEE in predicting countries' COVID-19 detection response times and mortality outcome (deaths/million). We used two different outcomes for the evaluation: (i) detection response time, the duration of time to the first confirmed case detection (from 31st December 2019 to 20th February 2020 when every country's first case was linked to travel from China) and (ii) mortality outcome (deaths/million) until 11th March and 1st July 2020, respectively. We interpreted the detection response time alongside previously published relative risk of the importation of COVID-19 cases from China. We performed multiple linear regression and negative binomial regression analysis to evaluate how these indices predicted the actual outcome. The two indices, GHSI and JEE were strongly correlated ( r = 0.82), indicating a good agreement between them. However, both GHSI ( r = 0.31) and JEE ( r = 0.37) had a poor correlation with countries' COVID-19–related mortality outcome. Higher risk of importation of COVID-19 from China for a given country was negatively correlated with the time taken to detect the first case in that country (adjusted R 2 = 0.63–0.66), while the GHSI and JEE had minimal predictive value. In the negative binomial regression model, countries' mortality outcome was strongly predicted by the percentage of the population aged 65 and above (incidence rate ratio (IRR): 1.10 (95% confidence interval (CI): 1.01–1.21) while overall GHSI score (IRR: 1.01 (95% CI: 0.98–1.01)) and JEE (IRR: 0.99 (95% CI: 0.96–1.02)) were not significant predictors. GHSI and JEE had lower predictive value for detection response time and mortality outcome due to COVID-19. We suggest introduction of a population healthiness parameter, to address demographic and comorbidity vulnerabilities, and reappraisal of the ranking system and methods used to obtain the index based on experience gained from this pandemic.
Community movement and COVID-19: a global study using Google's Community Mobility Reports
2020-01-01

Abstract Google's ‘Community Mobility Reports’ (CMR) detail changes in activity and mobility occurring in response to COVID-19. They thus offer the unique opportunity to examine the relationship between mobility and disease incidence. The objective was to examine whether an association between COVID-19-confirmed case numbers and levels of mobility was apparent, and if so then to examine whether such data enhance disease modelling and prediction. CMR data for countries worldwide were cross-correlated with corresponding COVID-19-confirmed case numbers. Models were fitted to explain case numbers of each country's epidemic. Models using numerical date, contemporaneous and distributed lag CMR data were contrasted using Bayesian Information Criteria. Noticeable were negative correlations between CMR data and case incidence for prominent industrialised countries of Western Europe and the North Americas. Continent-wide examination found a negative correlation for all continents with the exception of South America. When modelling, CMR-expanded models proved superior to the model without CMR. The predictions made with the distributed lag model significantly outperformed all other models. The observed relationship between CMR data and case incidence, and its ability to enhance model quality and prediction suggests data related to community mobility could prove of use in future COVID-19 modelling.