bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Validation of an Analytical Method for Volatiles with Endogenous Production in Putrefaction and Submersion Situations
Authors: Pinto Mélanie , Eusébio Ermelinda , Monteiro Carla 
Published: October 2020

Abstract
A group of 16 volatile substances (ethyl acetate, 2-propanol, 1-propanol, methanol, acetone, ethanol, acetaldehyde, diethyl ether, methyl ethyl ketone, 1-butanol, 2-butanol, t-butanol, isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol and 1-pentanol) were qualitatively and quantitatively analyzed through a method developed for volatiles with endogenous production in putrefaction and submersion situations. The method was validated for blood, urine and vitreous humor, using a gas chromatograph (Varian 450-GC) with a flame ionization detector coupled to a headspace injector (HS-GC–FID). The vials were prepared by diluting 100 µL of the sample of interest in 1 mL of internal standard (acetonitrile 100 mg/L), using two capillary columns (VF-624ms and VF-5ms) with different polarities to ensure that all test compounds would be properly identified and undoubtedly distinguished from the rest. All volatiles were studied in a range of 50 to 2,000 mg/L in terms of selectivity/specificity, detection and quantification limits, linearity and calibration model, precision, accuracy, bias, robustness and stability according to the Scientific Working Group for Forensic Toxicology. Detection and quantification limits were between 1 to 8 mg/L and 4 to 24 mg/L, respectively, with coefficient of variation values under 10% in bias studies and in intermediate precision studies for most substances. The developed method was applied to real cases to test the method.
Giant otter diet differs between habitats and from fisheries offtake in a large Neotropical floodplain
Authors: Leuchtenberger Caroline , Rheingantz Marcelo L , Zucco Carlos A , Catella Agostinho C , Magnusson William E , Mourão Guilherme 
Published: October 2020

AbstractGiant otters Pteronura brasiliensis are semiaquatic mammals that mainly eat fish, the abundance of which is affected by seasonal flooding and habitat structure. The piscivorous habits of giant otters lead to negative human perception and conflicts with fisheries. We compared giant otter feeding habits between seasons and habitats in the Southern Pantanal, Brazil, by analyzing feces collected between September 2008 and June 2011.We investigated whether habitat and season affected P. brasiliensis diet composition and prey size. We calculated the frequency of occurrence, relative frequency, and overlap of fish species eaten by giant otters and caught by fishermen. The giant otters had a more diverse assemblage of fish prey than the offtake in the fisheries. We did not find strong seasonality in otter diets, but diet composition and prey size differed between rivers and lakes. The giant otter diet had higher overlap with the offtake of sport than with professional fishermen. Although the otters’ piscivorous diet often leads to negative perceptions by humans, the low overlap between otter diet and species taken in local fisheries suggests that otters have little effect on the commercial fishery. These results indicate that educational programs could be used to reduce perceived conflict between giant otters and fishermen.
Triple P for Parents of Children with Phenylketonuria: A Nonrandomized Trial
Authors: Mitchell Amy E , Morawska Alina , Kirby Grace , McGill James , Coman David , Inwood Anita 
Published: October 2020

AbstractObjectiveFamilies of children with phenylketonuria (PKU) report child emotional and behavioral problems, parenting stress, and parenting difficulties, which are associated with worse health-related quality of life. This study aimed to examine acceptability and feasibility of a brief, group-based parenting program (Healthy Living Triple P) for families of children with PKU.MethodsAn uncontrolled nonrandomized trial design was used. Families of children aged 2–12 years (N = 17) completed questionnaire measures assessing child behavior and impact of PKU on quality of life (primary outcomes), and parenting behavior, self-efficacy and stress, and children’s behavioral and emotional adjustment (secondary outcomes). Routinely collected blood phenylalanine (Phe) levels were obtained from the treating team. Parents selected two child behaviors as targets for change. The intervention comprised two, 2-hr group sessions delivered face-to-face or online. Assessment was repeated at 4-week postintervention (T2) and 4-month follow-up (T3).ResultsAttrition was low and parent satisfaction with the intervention (face-to-face and online) was high. All families achieved success with one or both child behavior goals, and 75% of families achieved 100% success with both behavior goals by T3; however, there was no change in health-related quality of life. There were moderate improvements in parent-reported ineffective parenting (total score, d = 0.87, 95% CI −1.01 to 2.75) and laxness (d = 0.59, 95% CI −1.27 to 2.46), but no effects on parenting stress or children’s adjustment. Phe levels improved by 6month post-intervention for children with elevated preintervention levels.ConclusionsResults support intervention acceptability and feasibility. A randomized controlled trial is warranted to establish intervention efficacy.
Nitric oxide affects seed oil accumulation and fatty acid composition through proteinS-nitrosation
Authors: Liu Jing , Zhu Xiao-Yi , Deng Lin-Bin , Liu Hong-Fang , Li Jun , Zhou Xue-Rong , Wang Han-Zhong , Hua Wei 
Published: October 2020

AbstractNitric oxide (NO) is a key signaling molecule regulating several plant developmental and stress responses. Here, we report that NO plays an important role in seed oil content and fatty acid composition. RNAi silencing of Arabidopsis S-nitrosoglutathione reductase 1 (GSNOR1) led to reduced seed oil content. In contrast, nitrate reductase double mutant nia1nia2 had increased seed oil content, compared with wild-type plants. Moreover, the concentrations of palmitic acid (C16:0), linoleic acid (C18:2), and linolenic acid (C18:3) were higher, whereas those of stearic acid (C18:0), oleic acid (C18:1), and arachidonic acid (C20:1) were lower, in seeds of GSNOR1 RNAi lines. Similar results were obtained with rapeseed embryos cultured in vitro with the NO donor sodium nitroprusside (SNP), and the NO inhibitor NG-Nitro-L-arginine Methyl Ester (L-NAME). Compared with non-treated embryos, the oil content decreased in SNP-treated embryos, and increased in L-NAME-treated embryos. Relative concentrations of C16:0, C18:2 and C18:3 were higher, whereas C18:1 concentration decreased in rapeseed embryos treated with SNP. Proteomics and transcriptome analysis revealed that three S-nitrosated proteins and some key genes involved in oil synthesis, were differentially regulated in SNP-treated embryos. Therefore, regulating NO content could be a novel approach to increasing seed oil content in cultivated oil crops.
How accurately can we detect the splashback radius of dark matter haloes and its correlation with accretion rate?
Authors: Xhakaj Enia , Diemer Benedikt , Leauthaud Alexie , Wasserman Asher , Huang Song , Luo Yifei , Adhikari Susmita , Singh Sukhdeep 
Published: October 2020

ABSTRACT
The splashback radius (Rsp) of dark matter haloes has recently been detected using weak gravitational lensing and cross-correlations with galaxies. However, different methods have been used to measure Rsp and to assess the significance of its detection. In this paper, we use simulations to study the precision and accuracy to which we can detect the splashback radius with 3D density, 3D subhalo, and weak lensing profiles. We study how well various methods and tracers recover Rsp by comparing it with the value measured directly from particle dynamics. We show that estimates of Rsp from density and subhalo profiles correspond to different percentiles of the underlying Rsp distribution of particle orbits. At low accretion rates, a second caustic appears and can bias results. Finally, we show that upcoming lensing surveys may be able to constrain the Rsp–Γdyn relation directly.
Deblending galaxies with variational autoencoders: A joint multiband, multi-instrument approach
Authors: Arcelin Bastien , Doux Cyrille , Aubourg Eric , Roucelle Cécile ,   (The LSST Dark Energy Science Collaboration)
Published: October 2020

ABSTRACT
Blending of galaxies has a major contribution in the systematic error budget of weak-lensing studies, affecting photometric and shape measurements, particularly for ground-based, deep, photometric galaxy surveys, such as the Rubin Observatory Legacy Survey of Space and Time (LSST). Existing deblenders mostly rely on analytic modelling of galaxy profiles and suffer from the lack of flexible yet accurate models. We propose to use generative models based on deep neural networks, namely variational autoencoders (VAE), to learn probabilistic models directly from data. We train a VAE on images of centred, isolated galaxies, which we reuse, as a prior, in a second VAE-like neural network in charge of deblending galaxies. We train our networks on simulated images including six LSST bandpass filters and the visible and near-infrared bands of the Euclid satellite, as our method naturally generalizes to multiple bands and can incorporate data from multiple instruments. We obtain median reconstruction errors on ellipticities and r-band magnitude between ±0.01 and ±0.05, respectively, in most cases, and ellipticity multiplicative bias of 1.6 per cent for blended objects in the optimal configuration. We also study the impact of decentring and prove the method to be robust. This method only requires the approximate centre of each target galaxy, but no assumptions about the number of surrounding objects, pointing to an iterative detection/deblending procedure we leave for future work. Finally, we discuss future challenges about training on real data and obtain encouraging results when applying transfer learning.
Pfam: The protein families database in 2021
Authors: Mistry Jaina , Chuguransky Sara , Williams Lowri , Qureshi Matloob , Salazar Gustavo A , Sonnhammer Erik L L , Tosatto Silvio C E , Paladin Lisanna , Raj Shriya , Richardson Lorna J , Finn Robert D , Bateman Alex 
Published: October 2020

Abstract
The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been made to existing entries. To facilitate research on COVID-19, we have revised the Pfam entries that cover the SARS-CoV-2 proteome, and built new entries for regions that were not covered by Pfam. We have reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family. The new Pfam-B is based on a clustering by the MMseqs2 software. We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families. Pfam is freely available for browsing and download at http://pfam.xfam.org/.
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
Authors:   RNAcentral Consortium, Sweeney Blake A , Petrov Anton I , Ribas Carlos E , Finn Robert D , Bateman Alex , Szymanski Maciej , Karlowski Wojciech M , Seemann Stefan E , Gorodkin Jan , Cannone Jamie J , Gutell Robin R , Kay Simon , Marygold Steven , dos Santos Gil , Frankish Adam , Mudge Jonathan M , Barshir Ruth , Fishilevich Simon , Chan Patricia P , Lowe Todd M , Seal Ruth , Bruford Elspeth , Panni Simona , Porras Pablo , Karagkouni Dimitra , Hatzigeorgiou Artemis G , Ma Lina , Zhang Zhang , Volders Pieter-Jan , Mestdagh Pieter , Griffiths-Jones Sam , Fromm Bastian , Peterson Kevin J , Kalvari Ioanna , Nawrocki Eric P , Petrov Anton S , Weng Shuai , Bouchard-Bourelle Philia , Scott Michelle , Lui Lauren M , Hoksza David , Lovering Ruth C , Kramarz Barbara , Mani Prita , Ramachandran Sridhar , Weinberg Zasha 
Published: October 2020

Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and &gt;18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for &gt;13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.
Determinants of correlated expression of transcription factors and their target genes
Authors: Zaborowski Adam B , Walther Dirk 
Published: October 2020

AbstractWhile transcription factors (TFs) are known to regulate the expression of their target genes (TGs), only a weak correlation of expression between TFs and their TGs has generally been observed. As lack of correlation could be caused by additional layers of regulation, the overall correlation distribution may hide the presence of a subset of regulatory TF–TG pairs with tight expression coupling. Using reported regulatory pairs in the plant Arabidopsis thaliana along with comprehensive gene expression information and testing a wide array of molecular features, we aimed to discern the molecular determinants of high expression correlation of TFs and their TGs. TF-family assignment, stress-response process involvement, short genomic distances of the TF-binding sites to the transcription start site of their TGs, few required protein-protein-interaction connections to establish physical interactions between the TF and polymerase-II, unambiguous TF-binding motifs, increased numbers of miRNA target-sites in TF-mRNAs, and a young evolutionary age of TGs were found particularly indicative of high TF–TG correlation. The modulating roles of post-transcriptional, post-translational processes, and epigenetic factors have been characterized as well. Our study reveals that regulatory pairs with high expression coupling are associated with specific molecular determinants.
Benchmarking and integrating genome-wide CRISPR off-target detection and prediction
Authors: Yan Jifang , Xue Dongyu , Chuai Guohui , Gao Yuli , Zhang Gongchen , Liu Qi 
Published: October 2020

AbstractSystematic evaluation of genome-wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) off-target profiles is a fundamental step for the successful application of the CRISPR system to clinical therapies. Many experimental techniques and in silico tools have been proposed for detecting and predicting genome-wide CRISPR off-target profiles. These techniques and tools, however, have not been systematically benchmarked. A comprehensive benchmark study and an integrated strategy that takes advantage of the currently available tools to improve predictions of genome-wide CRISPR off-target profiles are needed. We focused on the specificity of the traditional CRISPR SpCas9 system for gene knockout. First, we benchmarked 10 available genome-wide off-target cleavage site (OTS) detection techniques with the published OTS detection datasets. Second, taking the datasets generated from OTS detection techniques as the benchmark datasets, we benchmarked 17 available in silico genome-wide OTS prediction tools to evaluate their genome-wide CRISPR off-target prediction performances. Finally, we present the first one-stop integrated Genome-Wide Off-target cleavage Search platform (iGWOS) that was specifically designed for the optimal genome-wide OTS prediction by integrating the available OTS prediction algorithms with an AdaBoost ensemble framework.
DescribePROT: database of amino acid-level protein structure and function predictions
Authors: Zhao Bi , Katuwawala Akila , Oldfield Christopher J , Dunker A Keith , Faraggi Eshel , Gsponer Jörg , Kloczkowski Andrzej , Malhis Nawar , Mirdita Milot , Obradovic Zoran , Söding Johannes , Steinegger Martin , Zhou Yaoqi , Kurgan Lukasz 
Published: October 2020

AbstractWe present DescribePROT, the database of predicted amino acid-level descriptors of structure and function of proteins. DescribePROT delivers a comprehensive collection of 13 complementary descriptors predicted using 10 popular and accurate algorithms for 83 complete proteomes that cover key model organisms. The current version includes 7.8 billion predictions for close to 600 million amino acids in 1.4 million proteins. The descriptors encompass sequence conservation, position specific scoring matrix, secondary structure, solvent accessibility, intrinsic disorder, disordered linkers, signal peptides, MoRFs and interactions with proteins, DNA and RNAs. Users can search DescribePROT by the amino acid sequence and the UniProt accession number and entry name. The pre-computed results are made available instantaneously. The predictions can be accesses via an interactive graphical interface that allows simultaneous analysis of multiple descriptors and can be also downloaded in structured formats at the protein, proteome and whole database scale. The putative annotations included by DescriPROT are useful for a broad range of studies, including: investigations of protein function, applied projects focusing on therapeutics and diseases, and in the development of predictors for other protein sequence descriptors. Future releases will expand the coverage of DescribePROT. DescribePROT can be accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.
Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging
Authors: Liu Lei , Hyeon Changbong 
Published: October 2020

AbstractThe accessibility of target gene, a factor critical for gene regulation, is controlled by epigenetic fine-tuning of chromatin organization. While there are multiple experimental techniques to study change of chromatin architecture with its epigenetic state, measurements from them are not always complementary. A qualitative discrepancy is noted between recent super-resolution imaging studies, particularly on Polycomb-group protein repressed domains in Drosophila cell. One of the studies shows that Polycomb-repressed domains are more compact than inactive domains and are segregated from neighboring active domains, whereas Hi-C and chromatin accessibility assay as well as the other super-resolution imaging studies paint a different picture. To examine this issue in detail, we analyzed Hi-C libraries of Drosophila chromosomes as well as distance constraints from one of the imaging studies, and modeled different epigenetic domains by employing a polymer-based approach. According to our chromosome models, both Polycomb-repressed and inactive domains are featured with a similar degree of intra-domain packaging and significant intermixing with adjacent active domains. The epigenetic domains explicitly visualized by our polymer model call for extra attention to the discrepancy of the super-resolution imaging with other measurements, although its precise physicochemical origin still remains to be elucidated.
The Cigarette Smoking Initiation and Continuation in Adolescents Undergoing a Long-Term Behavioral Intervention
Authors: Masihay-Akbar Hasti , Amiri Parisa , Cheraghi Leila , Momenan Amir Abbas , Azizi Fereidoun 
Published: October 2020

AbstractIntroductionTargeting adolescents’ smoking reduces its burden on health systems. We investigated the effects of the first multidisciplinary community-based lifestyle intervention in the Eastern Mediterranean region, on smoking initiation, continuation, and risk of current smoking in Iranian adolescents.MethodsThe current analyses were conducted on 945 nonsmoker adolescents (12–18 years) who participated in Phase II of Tehran Lipid and Glucose Study (TLGS) and were examined four times in 12 years. The lifestyle intervention including school-based and public programs was implemented, focusing on all components of healthy lifestyle. Using a two-step cluster analysis, families were classified as high and low risk, based on parental risk factors of adolescents’ smoking. Participants who failed to complete all the follow-ups (n = 99) and those with missing smoking data were excluded. Subsequently, 872 adolescents (538 control, 334 intervention) were included in the Cox model on smoking initiation, and 674 adolescents (414 control, 260 intervention) were included in the logistic regression on smoking status.ResultsMean age of adolescents was 15.08 ± 1.94 years at baseline. The hazard of the smoking initiation was significantly lower in the intervention (hazard ratio = 0.71, 95% confidence interval: 0.51–0.99; p = .044) compared with control group. At the end of the fourth follow-up, intervention reduced the odds of current cigarette smoking by 29%. Within the intervention group, the high-risk cluster was at a 35% lower risk of initiating smoking and had 37% lower odds of becoming a current smoker. However, the intervention could not make a difference in preventing those who initiated smoking from maintaining it during the follow-ups.ConclusionsOur results demonstrate that lifestyle modification programs targeting at-risk populations could reduce risk of smoking initiation and current smoking in adolescents in long term.ImplicationsExperiencing cigarette smoking at the critical period of adolescence could result in adulthood habitual smoking. Therefore, identifying adolescents who are more at risk of smoking initiation and implementing targeted interventions are of great importance in public health. Our findings highlight the long-term effectiveness of a multidisciplinary community-based behavioral intervention on forming smoking behaviors in adolescents. The current intervention was successful in reducing smoking uptake in adolescents living in high-risk families.
Fear of Pain Across the Adult Life Span
Authors: Wright Casey D , McNeil Daniel W 
Published: October 2020

AbstractBackgroundPain continues to be an important public health concern, especially given the opioid crisis in industrialized countries. It is important to understand the association between emotions such as fear and anxiety and the experience of pain as both a physiological and affective experience. Fear or anxiety about pain is in fact a well-known predictor of and close associate of pain. Nociception and pain history differ depending on age, yet little empirical evidence exists on how fear of pain varies over the life span. The purpose of this study was to provide a cross-sectional examination of the relations between age and fear of pain across the adult life span.MethodsUsing cross-sectional data from 4,122 participants who completed the Fear of Pain Questionnaire-9, structural equation modeling and regression techniques were used to examine the association between fear of pain and age.ResultsA positive linear association was discovered between age and fear of severe or minor pain, and a negative association was discovered between age and fear of medical or dental pain. Quadratic and cubic relations were also significant for fear of severe pain, fear of medical and dental pain, and overall fear of pain, but not for fear of minor pain.ConclusionsUnique trajectories for different components of pain-related fear exist across the adult life span and may be affected by increased exposure to medical and dental experiences over time and by the awareness of a greater likelihood of experiencing pain later in the life span.