bluuebunny/crossref_metadata_2025_split huggingface dataset:
ViruSurf: an integrated database to investigate viral sequences
Authors: Canakoglu Arif , Pinoli Pietro , Bernasconi Anna , Alfonsi Tommaso , Melidis Damianos P , Ceri Stefano 
Published: September 2020

AbstractViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola and Dengue. The database is centered on sequences, described from their biological, technological and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.
Continuity Points Via Riesz Potentials for ℂ-Elliptic Operators
Authors: Diening Lars , Gmeineder Franz 
Published: September 2020

AbstractWe establish a Riesz potential criterion for Lebesgue continuity points of functions of bounded $\mathbb{A}$-variation, where $\mathbb{A}$ is a $\mathbb{C}$-elliptic differential operator of arbitrary order. This result generalizes a potential criterion that is known for full gradients to the case where full gradient estimates are not available by virtue of Ornstein’s non-inequality.
DEVELOPMENT OF 222RN IN AIR SECONDARY STANDARD IN THE SLOVAK REPUBLIC
Authors: Blahušiak Pavol , Krivošík Matej , Slučiak Jarmila , Javorník Andrej , Zálešáková Michaela , Chytil Miroslav , Müllerová Monika , Holý Karol 
Published: September 2020

Abstract
Slovak Institute of Metrology received in 2016 funding for realisation of a set up of a radon chamber with AlphaGUARD as a secondary standard of 222Rn in air as one part of the project. This secondary standard will serve to provide the traceability for laboratories that deal with 222Rn measurements in environmental samples. This project is a response to the European Union legislation and provides metrological support for the development and implementation of the national radon action plan, which the member states of the European Union are committed to fulfil in accordance with Council Directive 2013/59/Euratom. During development of the radon chamber, the determination of its basic technical parameters, such as the exact determination of the container volume and the area of the inner walls of the radon chamber, many tightness tests of the chamber, the definition of homogeneous radon atmosphere parameters and bilateral comparisons, were realised.
STUDY OF 222RN CONTINUOUS MONITORING TIME SERIES AND DOSE ASSESSMENT IN SIX EUROPEAN CAVES
Authors: Ambrosino F , Thinová L , Briestenský M , Sabbarese C 
Published: September 2020

Abstract
The present work aims to assess the effective doses from long-term continual radon monitoring in six European caves (Slovenia, Slovakia and the Czech Republic), including influencing environmental factors. Caves are important radiation protection subjects because of elevated radon activity concentration (~kBq/m3), mostly due to the low natural ventilation. The sources of radon gas are most often underground rock layers and clastic sediments. The radon activity concentrations show seasonal variations, for which the outside temperature is the main driving force. The human health impact due to the radon inhalation in monitored caves was estimated through the annual effective dose, using the methodology provided by the International Commission on Radiological Protection (ICRP Publication 137). The annual effective dose could reach several tens of mSv, depending on the working hours spent in the underground.
ANALYSIS OF TIME SERIES OF RADON ACTIVITY CONCENTRATION IN OUTDOOR AIR AND THEIR RECONSTRUCTION
Authors: Bulko Martin , Holý Karol , Müllerová Monika 
Published: September 2020

Abstract
222Rn (radon) is an ever-present radioactive component of the surface layer of the atmosphere. The knowledge of the shape of radon activity concentration (RAC) time series has several important applications in atmospheric studies. This study presents the results of RAC analysis according to Garzon et al. approach during the years 1991–2009, as well as attempts to reconstruct the shape of composite diurnal RAC cycles using either Garzon et al. original approach or other methods. From this study, it follows that in order to accurately reconstruct the mean diurnal RAC cycles for individual months in our locality (Central European region), the parameters have to be calibrated by local RAC and measured global solar radiation data. The original Garzon et al. approach underestimates the amplitude of mean diurnal RAC cycles during April–August by up to 10%, and overestimates the amplitude during September–March by up to 25%.
Sleep health, diseases, and pain syndromes: findings from an electronic health record biobank
Authors: Dashti Hassan S , Cade Brian E , Stutaite Gerda , Saxena Richa , Redline Susan , Karlson Elizabeth W 
Published: September 2020

Abstract

Study Objectives
Implementation of electronic health record biobanks has facilitated linkage between clinical and questionnaire data and enabled assessments of relationships between sleep health and diseases in phenome-wide association studies (PheWAS). In the Mass General Brigham Biobank, a large health system-based study, we aimed to systematically catalog associations between time in bed, sleep timing, and weekly variability with clinical phenotypes derived from ICD-9/10 codes.

Methods
Self-reported habitual bed and wake times were used to derive variables: short (&lt;7 hours) and long (≥9 hours) time in bed, sleep midpoint, social jetlag, and sleep debt. Logistic regression and Cox proportional hazards models were used to test cross-sectional and prospective associations, respectively, adjusted for age, gender, race/ethnicity, and employment status and further adjusted for body mass index.

Results
In cross-sectional analysis (n = 34,651), sleep variable associations were most notable for circulatory system, mental disorders, and endocrine/metabolic phenotypes. We observed the strongest associations for short time in bed with obesity, for long time in bed and sleep midpoint with major depressive disorder, for social jetlag with hypercholesterolemia, and for sleep debt with acne. In prospective analysis (n = 24,065), we observed short time in bed associations with higher incidence of acute pain and later sleep midpoint and higher sleep debt and social jetlag associations with higher incidence of major depressive disorder.

Conclusions
Our analysis reinforced that sleep health is a multidimensional construct, corroborated robust known findings from traditional cohort studies, and supported the application of PheWAS as a promising tool for advancing sleep research. Considering the exploratory nature of PheWAS, careful interrogation of novel findings is imperative.
Religion in the Age of Social Distancing: How COVID-19 Presents New Directions for Research
Authors: Baker Joseph O , Martí Gerardo , Braunstein Ruth , Whitehead Andrew L , Yukich Grace 
Published: September 2020

AbstractIn this brief note written during a global pandemic, we consider some of the important ways this historical moment is altering the religious landscape, aiming our investigative lens at how religious institutions, congregations, and individuals are affected by the social changes produced by COVID-19. This unprecedented time prompts scholars of religion to reflect on how to strategically approach the study of religion in the time of “social distancing,” as well as moving forward. Particularly important considerations include developing heuristic, innovative approaches for revealing ongoing changes to religion, as well as how religion continues to structure social life across a wide range of contexts, from the most intimate and personal to the most public and global. Although our note can only be indicative rather than exhaustive, we do suggest that the initial groundwork for reconsiderations might productively focus on several key analytical themes, including: Epidemiology, Ideology, Religious Practice, Religious Organizations and Institutions, as well as Epistemology and Methodology. In offering these considerations as a starting point, we remain aware (and hopeful) that inventive and unanticipated approaches will also emerge.
The Stockman’s Scorecard: quantitative evaluation of beef cattle stockmanship
Authors: Yost John K , Yates Jarred W , Davis Matt P , Wilson Matthew E 
Published: September 2020

AbstractAn animal’s action, or inaction, is the direct result of a stockman’s action or inaction. The Stockman’s Scorecard is a novel observation instrument that has been proven to be a valid and reliable tool to measure the quality of beef cattle stockmanship. Specific handler actions have been weighted based on their perceived negative relationship to cattle stress from handling. The purpose of this article is to 1) document the initial use of the scorecard in a beef cattle feedlot setting and 2) provide further support to its validity by establishing an association with other quantitative and qualitative means of evaluating stockmanship. The Scorecard was used at 39 beef feedlots in Texas between March 2018 and April 2019. Eighty-four stockman were observed, and the average score received was 84.5 (SD = 14.73, range = 20 to 100). The most frequent mistakes observed were as follows: fills crowd pen/tub over half full (n = 39), slow to remove pressure (n = 29), uses unnecessary noise (n = 25), stands in front and taps rear (n = 24), and fails to regulate animal flow through a pinch point (n = 22). A strong negative association (ρ = −0.51) was found between the points deducted from the Noise and Physical Contact theme of the Scorecard and the number of animals touched with an electric prod from the BQA Feedyard Assessment. Moderate negative associations were found between the Scorecard final score and the number of animals that vocalize in the chute prior to procedures (ρ = −0.31). Those stockmen that scored above average on the Scorecard were qualitatively observed to be calm and quiet while working with the cattle (Kappa = 0.44). The qualitative disposition of cattle had little effect on the final score of stockmen using the Scorecard (Kappa = 0.17). The use of the Scorecard in a feedlot setting has demonstrated that as stockman scores decrease, there is an increase in the number of negative actions toward cattle and a negative behavioral response of the cattle themselves. Establishment of an association between a stockman’s score using the Stockman’s Scorecard and the animal-based observations from the BQA Feedyard Assessment further strengthens the validity of the Stockman’s Scorecard as a tool to measure the quality of beef cattle stockmanship. The Scorecard has application as a tool to identify specific stockmanship deficiencies in order to target stockmanship training.
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation
Authors: Charre Caroline , Ginevra Christophe , Sabatier Marina , Regue Hadrien , Destras Grégory , Brun Solenne , Burfin Gwendolyne , Scholtes Caroline , Morfin Florence , Valette Martine , Lina Bruno , Bal Antonin , Josset Laurence 
Published: September 2020

Abstract
Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (&gt;99%) for high viral loads samples (n = 8), with mNGS and RVOP producing the most complete genomes. For mid viral loads (Ct 20–25), amplicon-based enrichment methods led to genome coverage &gt;99 per cent for all samples while 1/8 sample sequenced with RVOP and 2/8 samples sequenced with mNGS had a genome coverage below 99 per cent. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34nt-deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a loss of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer-annealing or probe-hybridizing regions and would require further validation using unbiased metagenomic sequencing.
Evolutionary systematics of the viviparous gastropod Sermyla (Gastropoda: Cerithioidea: Thiaridae), with the description of a new species
Authors: Lentge-Maaß Nora , Neiber Marco T , Gimnich France , Glaubrecht Matthias 
Published: September 2020

Abstract
While most Cerithioidea are marine, some occur in brackish and freshwater habitats. Many members are systematically problematic due to variability or homoplasy in conchological characters, which has led to taxonomic redundancy, but also because of discrepancies between phylogenetic trees and morphologically distinguishable units as revealed in recent molecular genetic studies. We have chosen an evolutionary systematic approach and combine analyses of shell biometry and geometric morphometrics with the analyses of reproductive traits and molecular genetics based on mtDNA and AFLP markers in order to resolve the relationships among species of the genus Sermyla. We describe a new species from Sulawesi, Sermyla kupaensis sp. nov., which is characterized by a distinct reproductive strategy. This unique reproductive strategy corresponds with its distinct molecular genetic signal. However, it is not possible to distinguish S. kupaensis from S. riquetii based on shell morphology alone. We also provide data on the population structure of the endemic Australian species Sermyla carbonata, for which we found a drainage-based population structure. Overall, we present a new concept of the relationships among the species within the genus Sermyla based on morphological and genetic data.
Intraoperative axial patellar imaging: a new technique
Authors: Lapin Harrison , Bidwell Richard , Williams Kevin , Thier Zachary , Locke Mark 
Published: September 2020

Background:
The medial patellofemoral ligament (MPFL) functions by providing patellar stability and preventing lateral displacement of the patella. Surgical fixation is commonly recommended for MPFL tears in the form of MPFL reconstruction via anatomic techniques. Intraoperative fluoroscopy is critical for identifying anatomical landmarks during surgery. Using the C-arm, both anteroposterior and lateral views are routinely obtained, leaving the surgeon blinded to the angle of approaching the patella. Thus, our team saw a need to develop a method to capture an axial-type view of the patella using available intraoperative imaging technology.

Technique:
After guide-pin insertion, fluoroscopy is positioned for an anteroposterior view. The knee is hyperflexed while externally rotating the tibia and ankle. The patient’s ankle is slightly below the edge of the operating table, causing the tibia to rotate out of view of the radiograph. The C-arm is angled cephalad, approximately 20 to 30 degrees with the C-arm lowered, the operating table is raised until the knee almost touches the C-arm. The angle of tibial rotation and knee flexion is adjusted to obtain a view that closely resembles is the Merchant view. Our axial patellofemoral fluoroscopic technique augments traditional anteroposterior and lateral views by providing increased accuracy of patellar fixation in relation to the patellofemoral joint.

Discussion:
As MPFL reconstruction and repair procedures become more common, there will be a desire to improve upon the technique and approach to the procedure. Anatomic positioning of the graft is the most important prognostic factor in determining success of the operation. To decrease complications, such as patellar fracture, accuracy of patellar fixation placement is paramount, and any measure to ensure proper graft placement should be utilized.

Conclusions:
Our technique established more precise guide-pin placement for the patellar tunnel. It also reduced time spent evaluating patellar fixation via additional orthogonal imaging. This could be associated with better outcomes and avoidance of common complications such as patellar fracture attributed to violation of the anterior cortex.

Level of Evidence:
Level V.
Tuberous Sclerosis Complex Secondary to the Presence of Fetal Cardiac Rhabdomyoma: A Case Report and Literature Review
Authors: Li Hui-Fan , Wang Dong , Li Jun-Qi , Zhang Li , Zhang Xu , Qi Hong-Bo , Li Jun-Nan 
Published: September 2020

Abstract
Fetal cardiac rhabdomyoma is associated with tuberous sclerosis complex (TSC) which is an autosomal dominant hereditary neurocutaneous disease with an incidence of approximately 1 in 5 000 to 10 000 live birth. It is caused by mutations in the TSC1 or TSC2 gene, de novo mutations accounting for approximately 80% of TSC cases, which can involve multiple organs and systems such as the heart, brain, kidney, lung, skin, and so on. Cardiac rhabdomyoma is the most common fetal heart tumor, accounting for about 60% of cases. It is closely related to TSC and may be the only manifestation of TSC which occurs during pregnancy. This study retrospectively analyzed the clinical data of a neonate with TSC diagnosed with fetal cardiac rhabdomyomas and confirmed by amniocentesis prenatal diagnosis as gene testing TSC1 gene positively. The parents had no such mutation. However, due to the influence of the sudden coronavirus disease 2019 (COVID-19) epidemic, the TSC genetic test report was not obtained until 38 weeks of pregnancy. Multiple hypo-pigmented spots (diameter >5 mm) were found immediately after birth. The characteristic cardiac feature of TSC is a rhabdomyoma and the diagnosis of TSC is based upon genetic testing and multiple ultrasound examinations or magnetic resonance imaging. Most patients with TSC have epilepsy, and one-half or more have cognitive deficits and learning disabilities. So rigorous follow-up will continue for the case we reported.
Successful Antenatal Diagnosis and Management of a Rare Case of Congenital Fetal Choledochal Cyst
Authors: Lata Indu , Mandelia Ankur , Mandal Kausik 
Published: September 2020

Abstract
Choledochal cysts is a rare congenital cystic dilatation of common biliary duct. The most common prenatal diagnosed form type- I (85%-90%), consists of fusiform dilation of the common bile duct. There is communication between the bile duct and the cyst. In antenatal period diagnosis may be made by the presence of a cyst in the upper right side of the fetal abdomen on ultrasound. To differentiate it with other cystic lesions prenatal ultrasonography (USG), three-dimensional USG and magnetic resonance imaging may be helpful. By early diagnosis and prompt removal of cyst in postnatal period long term complications like development of biliary cirrhosis, portal hypertension, calculi formation or adenocarcinoma can be avoided in later life. The operative mortality is about 10%. We are reporting a case of antenatal diagnosis type I congenital choledochal cysts at 21 weeks, its follow up and successful postnatal management.
Placenta Accreta Spectrum: Conservative Management and Its Impact on Future Fertility
Authors: Abbas Riwa A. , Nassar Anwar H. 
Published: September 2020

Abstract
Placenta accreta spectrum is a complication of pregnancy, which poses a great risk on maternal health. Historically, hysterectomy was the modality of treatment of such condition, but an approach towards a more conservative management has been in the light recently. This includes several methods with varying rates of success and complications. Expectant management is effective in up to 78%–80% of the cases. The extirpative method is associated with a high risk of postpartum hemorrhage. The success of the one-step conservative procedure depends on the degree of placental invasion, and the triple-P procedure appears to be successful but requires and interdisciplinary approach. Adjuvant treatment options can be tailored according to individual cases, and these include methotrexate injection, uterine devascularization and hysteroscopic resection of retained placental tissues. Follow up after conservative management is crucial to detect complications early, and it can be done by ultrasound, Doppler examination, and trending β human chorionic gonadotropin levels. Conservative management of placenta accreta spectrum can preserve future fertility but should only be done in hospitals with enough experience as it carries a high risk of maternal complications. In the future, more research should be directed to achieve clear guidelines regarding this topic.
Effectiveness of a Modular Cognitive-Behavioral Skills Curriculum in High-Risk Justice-Involved Youth
Authors: Marques Luana , Youn Soo Jeong , Zepeda E. David , Chablani-Medley Anisha , Bartuska Anna D. , Baldwin Molly , Shtasel Derri L. 
Published: September 2020

Abstract
The aim of this study was to evaluate the effectiveness of a flexible modular cognitive-behavioral theory (CBT) skills curriculum delivered by paraprofessionals in a community organization targeting high-risk justice-involved youth. Programmatic data were collected from 980 high-risk young men (M
age, 21.12; SD, 2.30), and Cox proportional hazards regression was used. The results showed that compared with young men with no CBT encounters, those with one or more CBT encounters had a 66% (hazard ratio [HR], 0.34; 95% confidence interval [CI], 0.28–0.42; p < 0.001) lower risk of unenrolling from programming, 65% (HR, 1.65; 95% CI, 1.29–2.12; p < 0.001) higher risk of obtaining a job, and no difference in risk of engaging in new criminal activity while enrolled in programming (HR, 0.99; 95% CI, 0.78–1.25; p = 0.918), despite higher risk factors. Training paraprofessionals to deliver CBT skills to high-risk populations is effective and has scalability potential.