bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins
Authors: Zhang Jian , Ghadermarzi Sina , Kurgan Lukasz 
Published: June 2020

Abstract

Motivation
There are over 30 sequence-based predictors of the protein-binding residues (PBRs). They use either structure-annotated or disorder-annotated training datasets, potentially creating a dichotomy where the structure-/disorder-specific models may not be able to cross-over to accurately predict the other type. Moreover, the structure-trained predictors were shown to substantially cross-predict PBRs among residues that interact with non-protein partners (nucleic acids and small ligands). We address these issues by performing first-of-its-kind comparative study of a representative collection of disorder- and structure-trained predictors using a comprehensive benchmark set with the structure- and disorder-derived annotations of PBRs (to analyze the cross-over) and the protein-, nucleic acid- and small ligand-binding proteins (to study the cross-predictions).

Results
Three predictors provide accurate results: SCRIBER, ANCHOR and disoRDPbind. Some of the structure-trained methods make accurate predictions on the structure-annotated proteins. Similarly, the disorder-trained predictors predict well on the disorder-annotated proteins. However, the considered predictors generally fail to cross-over, with the exception of SCRIBER. Our study also reveals that virtually all methods substantially cross-predict PBRs, except for SCRIBER for the structure-annotated proteins and disoRDPbind for the disorder-annotated proteins. We formulate a novel hybrid predictor, hybridPBRpred, that combines results produced by disoRDPbind and SCRIBER to accurately predict disorder- and structure-annotated PBRs. HybridPBRpred generates accurate results that cross-over structure- and disorder-annotated proteins and produces relatively low amount of cross-predictions, offering an accurate alternative to predict PBRs.

Availability and implementation
HybridPBRpred webserver, benchmark dataset and supplementary information are available at http://biomine.cs.vcu.edu/servers/hybridPBRpred/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Closure coefficients in scale-free complex networks
Authors: Stegehuis Clara 
Published: June 2020

Abstract
The formation of triangles in complex networks is an important network property that has received tremendous attention. The formation of triangles is often studied through the clustering coefficient. The closure coefficient or transitivity is another method to measure triadic closure. This statistic measures clustering from the head node of a triangle (instead of from the centre node, as in the often studied clustering coefficient). We perform a first exploratory analysis of the behaviour of the local closure coefficient in two random graph models that create simple networks with power-law degrees: the hidden-variable model and the hyperbolic random graph. We show that the closure coefficient behaves significantly different in these simple random graph models than in the previously studied multigraph models. We also relate the closure coefficient of high-degree vertices to the clustering coefficient and the average nearest neighbour degree.
Are Quality Metrics in Inflammatory Bowel Disease Rooted in Substantial Quality Evidence? A Systematic Review
Authors: Weissman Simcha , Goldowsky Alexander , Mehta Tej I , Sciarra Michael A , Feuerstein Joseph D 
Published: June 2020

Abstract

Background and Aims
Quality metrics were established to develop standards to help assess quality of care, yet variation in inflammatory bowel disease [IBD] clinical practice exists. We performed a systematic review to assess the overall quality of evidence cited in formulating IBD quality metrics.

Methods
A systematic search was performed on PubMed, MEDLINE, and EMBASE. All major national and international IBD societies were included. Quality metrics were assessed for evidence quality and categorised as category A [guideline based], category B [primarily retrospective and observational studies], or category C [expert opinion]. Quality metrics were examined for the type of metric, and the quality, measurability, review, existing conflicts of interest [COI], and patient participation of the metric. Statistical analysis was conducted in R.

Results
A total of 143 distinct, and an aggregate total of 217 quality metrics were included and analysed; 68%, 3.2%, and 28.6% of IBD quality metrics were based on low, moderate, and high quality of evidence, respectively. The proportion of high-quality evidence across societies was significantly different [p &lt;0.01]. Five organisations included patients in quality metric development, three reported external review, not all reported measurable outcomes or stated the presence of a COI. Finally, 43% of quality metrics were published more than 5 years ago.

Conclusions
Quality metrics are important to standardise practice. As more than two-thirds of the quality metrics in IBD are based on low-quality evidence, further studies are needed to improve the overall quality of evidence supporting the development of quality measures.
Consequences of Cryopreservation in Diverse Natural Isolates of Saccharomyces cerevisiae
Authors: Wing Kieslana M , Phillips Mark A , Baker Andrew R , Burke Molly K 
Published: June 2020

Abstract
Experimental evolution allows the observation of change over time as laboratory populations evolve in response to novel, controlled environments. Microbial evolution experiments take advantage of cryopreservation to archive experimental populations in glycerol media, creating a frozen, living “fossil” record. Prior research with Escherichia coli has shown that cryopreservation conditions can affect cell viability and that allele frequencies across the genome can change in response to a freeze–thaw event. We expand on these observations by characterizing fitness and genomic consequences of multiple freeze−thaw cycles in diploid yeast populations. Our study system is a highly recombinant Saccharomyces cerevisiae population (SGRP-4X) that harbors standing genetic variation that cryopreservation may threaten. We also investigate the four parental isogenic strains crossed to create the SGRP-4X. We measure cell viability over five consecutive freeze−thaw cycles; whereas we find that viability increases over time in the evolved recombinant populations, we observe no such viability improvements in the parental strains. We also collect genome-wide sequence data from experimental populations initially, after one freeze−thaw, and after five freeze−thaw cycles. In the recombinant evolved populations, we find a region of significant allele frequency change on chromosome 15 containing the ALR1 gene. In the parental strains, we find little evidence for new mutations. We conclude that cryopreserving yeast populations with standing genetic variation may have both phenotypic and genomic consequences, though the same cryopreservation practices may have only small impacts on populations with little or no initial variation.
Demographic Effects on Longitudinal Semantic Processing, Working Memory, and Cognitive Speed
Authors: Vonk Jet M J , Higby Eve , Nikolaev Alexandre , Cahana-Amitay Dalia , Spiro Avron , Albert Martin L , Obler Loraine K 
Published: June 2020

Abstract

Objectives
To better understand and compare effects of aging and education across domains of language and cognition, we investigated whether (a) these domains show different associations with age and education, (b) these domains show similar patterns of age-related change over time, and (c) education moderates the rate of decline in these domains.

Method
We analyzed data from 306 older adults aged 55–85 at baseline of whom 116 returned for follow-up 4–8 years later. An exploratory factor analysis identified domains of language and cognition across a range of tasks. A confirmatory factor analysis analyzed cross-sectional associations of age and education with these domains. Subsequently, mixed linear models analyzed longitudinal change as a function of age and moderation by education.

Results
We identified 2 language domains, that is, semantic control and semantic memory efficiency, and 2 cognitive domains, that is, working memory and cognitive speed. Older age negatively affected all domains except semantic memory efficiency, and higher education positively affected all domains except cognitive speed at baseline. In language domains, a steeper age-related decline was observed after age 73–74 compared to younger ages, while cognition declined linearly with age. Greater educational attainment did not protect the rate of decline over time in any domain.

Discussion
Separate domains show varying effects of age and education at baseline, language versus cognitive domains show dissimilar patterns of age-related change over time, and education does not moderate the rate of decline in these domains. These findings broaden our understanding of age effects on cognitive and language abilities by placing observed age differences in context.
AOAC-OMA/MicroVal Harmonized Validation of Peel PlateTM EB (Enterobacteriaceae Bacteria), First Action 2018.05
Authors: Salter Robert S , Durbin Gregory W , Martinez Denisse , Bird Patrick , Bastin Benjamin , Crowley Erin 
Published: June 2020

Abstract

Background
Peel PlateTM Enterobacteriaceae Bacteria (EB) is dried selective media on a 47 mm plastic plate that produces enzyme substrate colored colonies on rehydration and incubation for 24 h and up to 48 h at 37 ± 1°C.

Purpose
The method validation compared quantification of EB to reference methods ISO 21528:2017 Parts 1 and 2.

Methods
Matrixes compared were whole milk, skim powdered milk, vanilla ice cream, butter, infant formulas (soy- and dairy-based), infant cereals ± probiotic, environmental sponge swab of stainless steel surface, and poultry carcass rinse with two different peptone buffers.

Results
In inclusivity and exclusivity studies, the method detected 54 of 54 EB strains and did not detect 30 of 30 non-EB strains. In matrix studies, the claimed foods were tested at three contamination levels using paired analysis between the reference and Peel Plate EB methods. Colony-forming units per gram or mL [CFU/g (mL)] were log10 transformed for statistical analysis. The candidate method and reference method were shown to be equivalent by the performance requirement of all 95% confidence intervals on mean difference falling between −0.5 and +0.5 log10 CFU/g (mL). An international collaborative study with dried infant formula spiked with Cronobacter sakazakii at log10 CFU/g (mL) 1.05, 2.31, and 3.21 levels, produced method differences −0.16, 0.15, and 0.18 log10 CFU/g (mL) with repeatabilities (r) = 0.33, 0.20, and 0.12 log10 CFU/g (mL) and reproducibilities (R) = 0.45, 0.26, and 0.18 log10 CFU/g (mL).

Conclusions
Based on these evaluations, the candidate method is considered equivalent to the reference methods at both the 24 h and 48 h incubation periods at 37 ± 1°C.

Highlights
Ready to use Enterobacteriaceae method equivalent to ISO-21528:2017 Parts 1 and 2; EB test colored colonies at 37°C for 24 h are equivalent at 48 h incubation; Singlet determined CFU/mL are statistically the same as duplicate average results; EB test validated for infant formula and dairy products including with probiotics; EB test for environmental surfaces and poultry carcass rinses using peptone buffers.
Flualprazolam Blood Concentrations in 197 Forensic Investigation Cases
Authors: Papsun Donna M , Krotulski Alex J , Homan Joseph , Temporal Keith D H , Logan Barry K 
Published: June 2020

Abstract
Flualprazolam is a designer benzodiazepine and novel psychoactive substance that is increasing in prevalence and appearing in forensic investigations. Flualprazolam was quantitatively confirmed in 197 blood samples from medicolegal death investigations and human performance cases reported between August 2019 and February 2020. Drug screening was performed using liquid chromatography–time-of-flight mass spectrometry and quantitative confirmation was performed using liquid chromatography–tandem mass spectrometry. A three-point standard addition protocol was implemented for quantitation in the absence of an available traditionally validated assay. In postmortem cases with quantitative results (n = 167), the mean (±standard deviation [SD]) flualprazolam concentration was 20 (±63) ng/mL, the median concentration was 8.2 ng/mL and the range of concentrations was 2.0–620 ng/mL. Four additional postmortem cases were reported positive (&lt;2.0 ng/mL). In drug impaired driving cases (n = 22), the mean (±SD) flualprazolam concentration was 22 (±18) ng/mL, the median concentration was 14 ng/mL and the range of concentrations was 4.4 to 68 ng/mL. The four remaining cases were of unknown circumstances. This report details the most extensive dataset of flualprazolam intoxication cases reported to date. There was significant overlap in concentrations of flualprazolam between postmortem and DUID cases. Flualprazolam was commonly (83% of the time) found in combination with opioids (e.g. fentanyl). Toxicologists should consider quantitative flualprazolam results in the context of case history, observations, and/or other toxicological findings. Addition of flualprazolam to the scope of drug testing should be considered by all laboratories.
The Other Side of Play: Fear and Frustration in the Design, Consumption and Use of Construction Sets
Authors: Yagou Artemis 
Published: June 2020

Abstract
Play is typically considered to be a highly pleasurable and stress-free activity; nevertheless, there is a strong but neglected connection between toy design and the fear of a technological future. The production and promotion of technology-inspired toys for middle-class children in the late nineteenth and early twentieth centuries reflected both the great fascination of adults with new technology and their anxiety about its impact. Different types of technical toys were meant not only as playthings, but also as tools for coming to terms with a changing social and technological milieu. For children themselves, playing with construction sets could be a source not only of pleasure, but also of frustration. This essay discusses a range of negative emotions related to construction toys and offers insights into this hitherto under-researched aspect of play. We argue that toys of a technical nature offered a small-scale and safe environment for testing out practices and mentalities related to the tensions and contradictions of modernity.
Significance of para-aortic lymph node evaluation in patients with FIGO IIIC1 cervical cancer
Authors: Cho Won Kyung , Kim Yeon Joo , Kim Hakyoung , Kim Young Seok , Park Won 
Published: June 2020

Abstract

Objective
This study investigated the effect of para-aortic lymph node sampling or dissection in recently revised International Federation of Gynecology and Obstetrics IIIC1p cervical cancer treated with primary surgery and adjuvant radiation therapy with concurrent chemotherapy.

Methods
We retrospectively reviewed the records of 343 patients with early-stage cervical cancer and pathologically proven pelvic lymph node metastasis following curative surgery from 2001 to 2014. No patient had imaging evidence of para-aortic lymph node involvement, and all patients received adjuvant concurrent chemotherapy with or without concurrent chemotherapy. We investigated the significance of para-aortic lymph node sampling or dissection on disease-free survival and overall survival.

Results
After median follow-up of 58.3 months, 5-year disease-free survival and overall survival in all patients were 69.9 and 80.2%, respectively. Disease-free survival and overall survival did not differ between the para-aortic lymph node dissection group and the No para-aortic lymph node dissection group (P = 0.700 and P = 0.605). However, patients with para-aortic lymph node-positive disease had poorer disease-free survival and overall survival compared with those with para-aortic lymph node-negative disease (P &lt; 0.001 and P &lt; 0.001).

Conclusions
This study found no survival benefit of para-aortic lymph node evaluation among patients with International Federation of Gynecology and Obstetrics IIIC1p cervical cancer who were clinically para-aortic lymph node-negative. Although para-aortic lymph node metastasis is a poor prognosticator, the benefit of para-aortic lymph node dissection in terms of survival needs further investigation.
Paeonol alleviates dextran sodium sulfate induced colitis involving Candida albicans-associated dysbiosis
Authors: Ge Yuzhu , Pan Min , Zhang Chuanfeng , Wang Changzhong , Ma Kelong , Yan Guiming , Wang Tianming , Wu Daqiang , Shao Jing 
Published: June 2020

Abstract

Inflammatory bowel disease (IBD), which consists of ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammatory disorder of the gastrointestinal tract. Occurrence and development of UC have been associated with multiple potential causative factors, which include fungal dysbiosis. Growing evidence reveals that Candida albicans-associated dysbiosis is correlated with clinical deterioration in UC. Paeonol (PAE) is a commonly used traditional medicine with multiple reported properties including effective alleviation of UC. In this study, a murine UC model was established by colonizing mice with additional C. albicans via gavage prior to dextran sodium sulfate (DSS) administration. Effects of PAE treatment were also assessed at initiation and in preestablished C. albicans-associated colitis. The results showed that C. albicans supplementation could aggravate disease activity index (DAI), compromise mucosal integrity, exacerbate fecal and tissue fungal burdens, increase serum β-glucan and anti-Saccharomyces cerevisiae antibody (ASCA) levels, promote serum and colonic tissue pro-inflammatory cytokine secretion (tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, and IL-8) and decrease the anti-inflammatory cytokine IL-10 level. It also stimulated Dectin-1, TLR2 and TLR4 as well as expression of their downstream effector NF-κB in colonic tissue. After PAE treatment, the adverse impacts of C. albicans on colitis were relieved, via decreased receptor-associated local and systemic inflammation. Our study suggests that PAE should be a candidate for treatment of fungal dysbiosis-associated UC and may act through the Dectin-1/NF-κB pathway in collaboration with TLR2 and TLR4.

Lay Summary
Candida albicans is believed to be an important stimulator in ulcerative colitice (UC) development. Suppressing the growth of intestinal C. albicans can be contributory to the amelioration of UC. Paeonol (PAE) is a commonly used traditional medicine with multiple biological functions. In this study, we observed that PAE could alleviate symptoms in mice UC model accompanying with burden reduction of C. albicans. Therefore, we suppose that PAE can be a candidate in the treatment of C. albicans-associated UC.
The TESS light curve of AI Phoenicis
Authors: Maxted P F L , Gaulme Patrick , Graczyk D , Hełminiak K G , Johnston C , Orosz Jerome A , Prša Andrej , Southworth John , Torres Guillermo , Davies Guy R , Ball Warrick , Chaplin William J 
Published: June 2020

ABSTRACT
Accurate masses and radii for normal stars derived from observations of detached eclipsing binary stars are of fundamental importance for testing stellar models and may be useful for calibrating free parameters in these model if the masses and radii are sufficiently precise and accurate. We aim to measure precise masses and radii for the stars in the bright eclipsing binary AI Phe, and to quantify the level of systematic error in these estimates. We use several different methods to model the Transiting Exoplanet Survey Satellite (TESS) light curve of AI Phe combined with spectroscopic orbits from multiple sources to estimate precisely the stellar masses and radii together with robust error estimates. We find that the agreement between different methods for the light-curve analysis is very good but some methods underestimate the errors on the model parameters. The semi-amplitudes of the spectroscopic orbits derived from spectra obtained with modern échelle spectrographs are consistent to within 0.1 per cent. The masses of the stars in AI Phe are $M_1 = 1.1938 \pm 0.0008\, \rm M_{\odot }$ and $M_2 = 1.2438 \pm 0.0008\, \rm M_{\odot }$, and the radii are $R_1 = 1.8050 \pm 0.0022\, \rm R_{\odot }$ and $R_2 = 2.9332 \pm 0.0023\, \rm R_{\odot }$. We conclude that it is possible to measure accurate masses and radii for stars in bright eclipsing binary stars to a precision of 0.2 per cent or better using photometry from TESS and spectroscopy obtained with modern échelle spectrographs. We provide recommendations for publishing masses and radii of eclipsing binary stars at this level of precision.
BRITE-Constellation photometry of π5 Orionis, an ellipsoidal SPB variable
Authors: Jerzykiewicz M , Pigulski A , Handler G , Moffat A F J , Popowicz A , Wade G A , Zwintz K , Pablo H 
Published: June 2020

ABSTRACT
Results of an analysis of the BRITE-Constellation photometry of the SB1 system and ellipsoidal variable π5 Ori (B2 III) are presented. In addition to the orbital light-variation, which can be represented as a five-term Fourier cosine series with the frequencies forb, 2forb, 3forb, 4forb, and 6forb, where forb is the system’s orbital frequency, the star shows five low-amplitude but highly significant sinusoidal variations with frequencies fi (i = 2, .., 5, 7) in the range from 0.16 to 0.92 d−1. With an accuracy better than 1σ, the latter frequencies obey the following relations: f2 − f4 = 2forb, f7 − f3 = 2forb, f5 = f3 − f4 = f7 − f2. We interpret the first two relations as evidence that two high-order ℓ = 1, m = 0 gravity modes are self-excited in the system’s tidally distorted primary component. The star is thus an ellipsoidal SPB variable. The last relations arise from the existence of the first-order differential combination term between the two modes. Fundamental parameters, derived from photometric data in the literature and the Hipparcos parallax, indicate that the primary component is close to the terminal stages of its main-sequence (MS) evolution. Extensive Wilson–Devinney modelling leads to the conclusion that best fits of the theoretical to observed light curves are obtained for the effective temperature and mass consistent with the primary’s position in the HR diagram and suggests that the secondary is in an early MS evolutionary stage.