bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes
Authors: Rodrigue Nicolas , Latrille Thibault , Lartillot Nicolas 
Published: October 2020

Abstract
In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.
Mutation Rate Variability across Human Y-Chromosome Haplogroups
Authors: Ding Qiliang , Hu Ya , Koren Amnon , Clark Andrew G 
Published: October 2020

Abstract
A common assumption in dating patrilineal events using Y-chromosome sequencing data is that the Y-chromosome mutation rate is invariant across haplogroups. Previous studies revealed interhaplogroup heterogeneity in phylogenetic branch length. Whether this heterogeneity is caused by interhaplogroup mutation rate variation or nongenetic confounders remains unknown. Here, we analyzed whole-genome sequences from cultured cells derived from &gt;1,700 males. We confirmed the presence of branch length heterogeneity. We demonstrate that sex-chromosome mutations that appear within cell lines, which likely occurred somatically or in vitro (and are thus not influenced by nongenetic confounders) are informative for germline mutational processes. Using within-cell-line mutations, we computed a relative Y-chromosome somatic mutation rate, and uncovered substantial variation (up to 83.3%) in this proxy for germline mutation rate among haplogroups. This rate positively correlates with phylogenetic branch length, indicating that interhaplogroup mutation rate variation is a likely cause of branch length heterogeneity.
Genenames.org: the HGNC and VGNC resources in 2021
Authors: Tweedie Susan , Braschi Bryony , Gray Kristian , Jones Tamsin E M , Seal Ruth L , Yates Bethan , Bruford Elspeth A 
Published: October 2020

Abstract
The HUGO Gene Nomenclature Committee (HGNC) based at EMBL’s European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problematic symbols, we are working towards stabilizing symbols where possible; over 2000 symbols for disease associated genes are now marked as stable in our symbol reports. All of our data is available at the HGNC website https://www.genenames.org. The Vertebrate Gene Nomenclature Committee (VGNC) was established to assign standardized nomenclature in line with human for vertebrate species lacking their own nomenclature committee. In addition to the previous VGNC core species of chimpanzee, cow, horse and dog, we now name genes in cat, macaque and pig. Gene groups have been added to VGNC and currently include two complex families: olfactory receptors (ORs) and cytochrome P450s (CYPs). In collaboration with specialists we have also named CYPs in species beyond our core set. All VGNC data is available at https://vertebrate.genenames.org/. This article provides an overview of our online data and resources, focusing on updates over the last two years.
The Relationship Between Menthol Cigarette Use, Smoking Cessation, and Relapse: Findings From Waves 1 to 4 of the Population Assessment of Tobacco and Health Study
Authors: Mills Sarah D , Hao Yajing , Ribisl Kurt M , Wiesen Christopher A , Hassmiller Lich Kristen 
Published: October 2020

AbstractIntroductionSome, but not all, studies suggest that menthol cigarette smokers have more difficulty quitting than non-menthol cigarette smokers. Inconsistent findings may be a result of differences in smoker characteristics (eg, daily vs. non-daily smokers) across studies. This study examines the relationship between menthol cigarette use, cessation, and relapse in a longitudinal, nationally representative study of tobacco use in the United States.Aims and MethodsData come from four waves of the Population Assessment of Tobacco and Health Study. Waves 1–4 were conducted approximately annually from September 2013 to January 2018. Generalized estimating equation models were used to prospectively examine the relationship between menthol cigarette use, cessation, and relapse in non-daily and daily adult (18+) smokers. Cessation was defined as smokers who had not used cigarettes within the past 30 days at their subsequent assessment. Relapse was defined as cessation followed by past 30-day smoking in the next assessment.ResultsAmong daily smokers (n = 13 710), 4.0% and 5.3% of menthol and non-menthol smokers quit after 1 year, respectively. In an adjusted model, menthol smokers were less likely to quit compared with non-menthol smokers (odds ratio [OR] = 0.76 [0.63, 0.91]). When the sample was stratified by race/ethnicity, African American (OR = 0.47 [0.24, 0.91]) and White (OR = 0.78 [0.63, 0.97]) daily menthol users were less likely to have quit. Among non-daily smokers (n = 3608), there were no significant differences in quit rates. Among daily and non-daily former smokers, there were also no differences in relapse rates between menthol and non-menthol smokers.ConclusionsMenthol cigarette use is associated with lower odds of cessation.ImplicationsFindings from this study suggest that menthol cigarette use is associated with lower odds of cessation, but not relapse. Removing menthol cigarettes from the market may improve cessation rates.
Declines in Depressive Symptoms Among People who Inject Drugs Treated With Direct-Acting Antivirals While on Opioid Agonist Therapy
Authors: Pericot-Valverde Irene , Heo Moonseong , Niu Jiajing , Norton Brianna L , Akiyama Matthew J , Agyemang Linda , Litwin Alain H 
Published: October 2020

Abstract

Background
Hepatitis C virus (HCV) frequently co-occurs with symptoms of depression, which are aggravated on interferon-based regimens. However, it is unknown whether HCV treatment with direct-acting antivirals (DAAs) has effects on depressive symptoms among people who inject drugs (PWID). In this study, we examined changes in depressive symptoms during and after HCV treatment among PWID on opioid agonist therapies (OATs).

Methods
Participants were 141 PWID who achieved sustained viral response after on-site HCV treatment at 3 OAT programs.
Depressive symptoms were assessed using the Beck Depression Inventory–II (BDI-II) at baseline, every 4 weeks during treatment, and 12 and 24 weeks after treatment completion. Current diagnosis of depression or other psychiatric diagnoses were obtained through chart review. Use of illicit drugs was measured by urine toxicology screening. Alcohol use was measured using the Addiction Severity Index–Lite.

Results
Of the 141 PWID infected with HCV, 24.1% had severe, 9.9% had moderate, 15.6% had mild, and 50.4% had minimal levels of depression as per BDI-II scores at baseline. HCV treatment was significantly associated with reductions in depressive symptoms that persisted long term, regardless of symptom severity (P &lt; .001) or presence of depression (P ≤ .01) or other psychiatric diagnoses (P ≤ .01) at baseline. Concurrent drug use (P ≤ .001) or hazardous alcohol drinking (P ≤ .001) did not interfere with reductions in depressive symptoms.

Conclusions
Depressive symptoms are highly prevalent among HCV-infected PWID. HCV treatment was associated with sustained reductions in depressive symptoms. HCV therapy with DAAs may have important implications for PWID that go beyond HCV cure.
Cutaneous Leishmaniasis: Case Series on Pregnancy Outcome
Authors: Bitton Yossi , Diav-Citrin Orna 
Published: October 2020

Abstract
We report the pregnancy outcomes of 6 women with cutaneous leishmaniasis; 5 of these women received topical antileishmenial therapy during gestation with paromomycin plus methylbenzethonium chloride combination ointment and/or sodium stibogluconate intralesional injections. No teratogenic effects were reported. Furthermore, no vertical transmission was observed.
Do generous parental leave policies help top female earners?
Authors: Corekcioglu Gozde , Francesconi Marco , Kunze Astrid 
Published: October 2020

Abstract
Generous government-mandated parental leave is generally viewed as an effective policy to support women’s careers around childbirth. But does it help women to reach top positions in the upper pay echelon of their firms? Using longitudinal employer–employee matched data for the entire Norwegian population, we address this question exploiting a series of reforms that expanded paid leave from 30 weeks in 1989 to 52 weeks in 1993. The representation of women in top positions has only moderately increased over time, and career profiles of female top earners within firms are significantly different from those of their male counterparts. The reforms did not affect, and possibly decreased, the probability for women to be at the top over their life cycle. We discuss some implications of this result to put into perspective the design of new family-friendly policy interventions.
Octaketide Synthase from Polygonum cuspidatum Implements Emodin Biosynthesis in Arabidopsis thaliana
Authors: Guo Yanwu , Nassar Sara , Ma Lanqing , Feng Guanping , Li Xing , Chen Mo , Chai Tuanyao , Abdel-Rahman Iman A M , Beuerle Till , Beerhues Ludger , Wang Hong , Liu Benye 
Published: October 2020

Abstract
Plant anthranoids are medicinally used for their purgative properties. Their scaffold was believed to be formed by octaketide synthase (OKS), a member of the superfamily of type III polyketide synthase (PKS) enzymes. Here, a cDNA encoding OKS of Polygonum cuspidatum was isolated using a homology-based cloning strategy. When produced in Escherichia coli, P. cuspidatum octaketide synthase (PcOKS) catalyzed the condensation of eight molecules of malonyl-CoA to yield a mixture of unphysiologically folded aromatic octaketides. However, when the ORF for PcOKS was expressed in Arabidopsis thaliana, the anthranoid emodin was detected in the roots of transgenic lines. No emodin was found in the roots of wild-type A. thaliana. This result indicated that OKS is the key enzyme of plant anthranoids biosynthesis. In addition, the root growth of the transgenic A. thaliana lines was inhibited to an extent that resembled the inhibitory effect of exogenous emodin on the root growth of wild-type A. thaliana. Immunochemical studies of P. cuspidatum plants detected PcOKS mainly in roots and rhizome, in which anthranoids accumulate. Co-incubation of E. coli - produced PcOKS and cell-free extract of wild-type A. thaliana roots did not form a new product, suggesting an alternative, physiological folding of PcOKS and its possible interaction with additional factors needed for anthranoids assembling in transgenic A. thaliana. Thus, transgenic A. thaliana plants producing PcOKS provide an interesting system for elucidating the route of plant anthranoid biosynthesis.
The Combination of Preoperative Pain, Conditioned Pain Modulation, and Pain Catastrophizing Predicts Postoperative Pain 12 Months After Total Knee Arthroplasty
Authors: Larsen Dennis Boye , Laursen Mogens , Edwards Robert R , Simonsen Ole , Arendt-Nielsen Lars , Petersen Kristian Kjær 
Published: October 2020

AbstractObjectivesApproximately 20% of knee osteoarthritis patients undergoing total knee arthroplasty (TKA) report chronic postoperative pain. Studies suggest that preoperative variables such as impaired descending pain control, catastrophizing, function, and neuropathic pain–like symptoms may predict postoperative pain 12 months after TKA, but the combined prediction value of these factors has not been tested. The current prospective cohort study aimed to combine preoperative risk factors to investigate the predictive value for postoperative pain 12 months after TKA.DesignProspective cohort with follow-up 12 months after surgery.PatientsA consecutive sample of 131 knee osteoarthritis patients undergoing TKA.MethodsPain intensity, Pain Catastrophizing Scale (PCS) scores, PainDETECT Questionnaire scores, conditioned pain modulation (CPM), and Oxford Knee Score (OKS) were obtained before and 12 months after TKA.ResultsTKA improved pain (P &lt; 0.001), PCS scores (P &lt; 0.001), PainDETECT Questionnaire scores (P &lt; 0.001), and OKSs (P &lt; 0.001). Preoperative pain correlated with preoperative PCS scores (r = 0.38, P &lt; 0.001), PainDETECT scores (r = 0.53, P &lt; 0.001), and OKSs (r = –0.25, P = 0.001). Preoperative PainDETECT scores were associated with preoperative PCS scores (r = 0.53, P &lt; 0.001) and OKSs (r = –0.25, P = 0.002). Higher postoperative pain was correlated with high preoperative pain (r = 0.424, P &lt; 0.001), PCS scores (r = 0.33, P &lt; 0.001), PainDETECT scores (r = 0.298, P = 0.001), and lower CPM (r = –0.18, P = 0.04). The combination of preoperative pain, PCS score, and CPM explained 20.5% of variance in follow-up pain. PCS scores had a significant effect on pain trajectory when accounting for patient variance (t = 14.41, P &lt; 0.0005).ConclusionThe combination of high preoperative clinical pain intensity, high levels of pain catastrophizing thoughts, and impaired CPM may predict long-term postoperative pain 12 months after surgery.
What is White Ignorance?
Authors: Martín Annette 
Published: October 2020

AbstractIn this paper, I identify a theoretical and political role for ‘white ignorance’, present three alternative accounts of white ignorance, and assess how well each fulfils this role. On the Willful Ignorance View, white ignorance refers to white individuals’ willful ignorance about racial injustice. On the Cognitivist View, white ignorance refers to ignorance resulting from social practices that distribute faulty cognitive resources. On the Structuralist View, white ignorance refers to ignorance that (1) results as part of a social process that systematically gives rise to racial injustice, and (2) is an active player in the process. I argue that, because of its greater power and flexibility, the Structuralist View better explains the patterns of ignorance that we observe, better illuminates the connection to white racial domination, and is overall better suited to the project of ameliorating racial injustice. As such, the Structuralist View should be preferred.
Multisystemic Increment of Cortical Thickness in Congenital Blind Children
Authors: Inuggi Alberto , Pichiecchio Anna , Ciacchini Benedetta , Signorini Sabrina , Morelli Federica , Gori Monica 
Published: October 2020

Abstract
It has been shown that the total or partial lack of visual experience is associated with a plastic reorganization at the brain level, more prominent in congenital blind. Cortical thickness (CT) studies, to date involving only adult subjects, showed that only congenital blind have a thicker cortex than age-matched sighted population while late blind do not. This was explained as a deviation from the physiological mechanism of initial neural growth followed by a pruning mechanism that, in congenital blind children, might be reduced by their visual deprivation, thus determining a thicker cortex. Since those studies involved only adults, it is unknown when these changes may appear and whether they are related to impairment degree. To address this question, we compared the CT among 28 children, from 2 to 12 years, with congenital visual impairments of different degree and an age-matched sighted population. Vertex-wise analysis showed that blind children, but not low vision one, had a thicker cortical surface in few clusters located in occipital, superior parietal, anterior-cingular, orbito-frontal, and mesial precentral regions. Our data suggest that the effect of visual impairment on determining thicker cortex is an early phenomenon, is multisystemic, and occurs only when blindness is almost complete.
Intrinsic Connectivity Changes Mediate the Beneficial Effect of Cardiovascular Exercise on Sustained Visual Attention
Authors: Lehmann Nico , Villringer Arno , Taubert Marco 
Published: October 2020

AbstractCardiovascular exercise (CE) is an evidence-based healthy lifestyle strategy. Yet, little is known about its effects on brain and cognition in young adults. Furthermore, evidence supporting a causal path linking CE to human cognitive performance via neuroplasticity is currently lacking. To understand the brain networks that mediate the CE–cognition relationship, we conducted a longitudinal, controlled trial with healthy human participants to compare the effects of a 2–week CE intervention against a non-CE control group on cognitive performance. Concomitantly, we used structural and functional magnetic resonance imaging to investigate the neural mechanisms mediating between CE and cognition. On the behavioral level, we found that CE improved sustained attention, but not processing speed or short-term memory. Using graph theoretical measures and statistical mediation analysis, we found that a localized increase in eigenvector centrality in the left middle frontal gyrus, probably reflecting changes within an attention-related network, conveyed the effect of CE on cognition. Finally, we found CE-induced changes in white matter microstructure that correlated with intrinsic connectivity changes (intermodal correlation). These results suggest that CE is a promising intervention strategy to improve sustained attention via brain plasticity in young, healthy adults.
Physical, chemical, and toxicological characterization of sulfated cellulose nanocrystals for food-related applications using in vivo and in vitro strategies
Authors: Ede James D , Ong Kimberly J , Mulenos Marina R , Pradhan Sahar , Gibb Matthew , Sayes Christie M , Shatkin Jo Anne 
Published: October 2020

Abstract
Cellulose nanocrystals (CNCs) are a next-generation cellulose product with many unique properties including applications in the food industry as a food additive, food coating, and in food-contact packaging material. While CNC is anticipated to be safe due to its similarity to the many forms of cellulose currently used as food additives, special consideration is given to it as it is the first manufactured form of cellulose that is nanoscale in both length and width. A proactive approach to safety has been adopted by manufacturers to demonstrate CNC safety toward responsible commercialization. As part of the safety demonstration, in vivo and in vitro testing strategies were commissioned side-by-side with conventional cellulose, which has been safely used in food for decades. Testing included a 90-day rodent feeding study as well as additional physical, chemical, and biological studies in vitro that follow European Food Safety Authority (EFSA) guidance to demonstrate the safe use of novel food ingredients. The strategy includes assessment of neat materials side-by-side with simulated digestion, mimicking conditions that occur along the gastrointestinal tract as well as intracellularly. An intestinal co-culture model examined any potential toxicological effects from exposure to either pristine or digested forms of CNC including cytotoxicity, metabolic activity, membrane permeability, oxidative stress, and proinflammatory responses. None of the studies demonstrated any toxicity via oral or simulated oral exposure. These studies demonstrate that CNC produced by InnoTech Alberta is similarly safe by ingestion as conventional cellulose with a no-observed-adverse-effect level of 2085.3 (males) and 2682.8 (females) mg/kg/day.
Acetaminophen Modulates the Expression of Steroidogenesis-Associated Genes and Estradiol Levels in Human Placental JEG-3 Cells
Authors: Addo Kezia A , Palakodety Niharika , Fry Rebecca C 
Published: October 2020

Abstract
Acetaminophen is the only medication recommended for pain and fever management during pregnancy. However, studies have reported an association between in utero acetaminophen and neurocognitive disorders later in life. Additionally, acetaminophen has been shown to have endocrine disrupting properties altering hormones critical for normal fetal development. As the placenta is an endocrine organ that produces hormones for fetal development, any attempts to elucidate the mechanism underlying in utero acetaminophen and birth outcomes must also focus on the placenta. The present study set out to examine the effect of acetaminophen on mRNA expression, protein expression, and hormone synthesis in placental JEG-3 cells. The analysis focused on genes involved in steroidogenesis and acetaminophen metabolism as well those with known roles as nuclear receptors and transporters. The results highlight that at high concentrations, acetaminophen reduced the gene expression of aromatase (CYP19A1) and type 1 3β-hydroxysteroid dehydrogenase (HSD3B1), and increased the expression of 17β-hydroxysteroid dehydrogenase (HSD17B1). Additionally, acetaminophen at high concentrations also reduced the protein expression of aromatase (CYP19A1). These effects were accompanied by a significant dose-dependent decrease in estradiol secretion. Estradiol plays an important role in the development of reproductive organs and the brain of the developing fetus. This study highlights the potential for acetaminophen to interfere with hormone regulation during pregnancy and underscores the need for additional studies aimed at understanding the endocrine disruption activity of acetaminophen during fetal development.
Predictors of Functional Dependence After COVID-19
Authors: Leigh Alexandra E. , McCall Jonathan , Burke Rebecca V. , Rome Robin , Raines Amanda M. 
Published: October 2020

Objective
The aim of this study was to examine the impact of demographics, preexisting medical conditions, and in-hospital complications of COVID-19 infection on functional status at discharge.

Design and Participants
A retrospective chart review was conducted on 119 patients hospitalized for COVID-19 infection between March 1, 2020, and April 20, 2020. Demographics, preexisting medical conditions, and newly diagnosed COVID-19 complications were collected from electronic medical records and entered in a deidentified database.

Main Outcome
The primary outcome was functional status at discharge, as measured by independence in activities of daily living.

Results
Older age, respiratory failure, cardiac conditions, and thromboembolic complications all made a statistically significant contribution to functional dependence at discharge, with thromboembolic complications evincing the strongest association (odds ratio, 25.58).

Conclusion and Relevance
New diagnosis of thrombosis during COVID-19 hospitalization, a measure of COVID-19 disease severity, was the factor most associated with dependence in activities of daily living at discharge. Interestingly, preexisting conditions including hypertension, severe obesity, lung disease, and diabetes did not correlate with dependent functional status at discharge.