bluuebunny/crossref_metadata_2025_split huggingface dataset:
OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates
Authors: Singh Param Priya , Isambert Hervé 
Published: October 2019

Abstract
All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
Authors: Palaniappan Krishnaveni , Chen I-Min A , Chu Ken , Ratner Anna , Seshadri Rekha , Kyrpides Nikos C , Ivanova Natalia N , Mouncey Nigel J 
Published: October 2019

Abstract
Microbial secondary metabolism is a reservoir of bioactive compounds of immense biotechnological and biomedical potential. The biosynthetic machinery responsible for the production of these secondary metabolites (SMs) (also called natural products) is often encoded by collocated groups of genes called biosynthetic gene clusters (BGCs). High-throughput genome sequencing of both isolates and metagenomic samples combined with the development of specialized computational workflows is enabling systematic identification of BGCs and the discovery of novel SMs. In order to advance exploration of microbial secondary metabolism and its diversity, we developed the largest publicly available database of predicted BGCs combined with experimentally verified BGCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc-public). Here we describe the first major content update of the IMG-ABC knowledgebase, since its initial release in 2015, refreshing the BGC prediction pipeline with the latest version of antiSMASH (v5) as well as presenting the data in the context of underlying environmental metadata sourced from GOLD (https://gold.jgi.doe.gov/). This update has greatly improved the quality and expanded the types of predicted BGCs compared to the previous version.
Unraveling allosteric landscapes of allosterome with ASD
Authors: Liu Xinyi , Lu Shaoyong , Song Kun , Shen Qiancheng , Ni Duan , Li Qian , He Xinheng , Zhang Hao , Wang Qi , Chen Yingyi , Li Xinyi , Wu Jing , Sheng Chunquan , Chen Guoqiang , Liu Yaqin , Lu Xuefeng , Zhang Jian 
Published: October 2019

Abstract
Allosteric regulation is one of the most direct and efficient ways to fine-tune protein function; it is induced by the binding of a ligand at an allosteric site that is topographically distinct from an orthosteric site. The Allosteric Database (ASD, available online at http://mdl.shsmu.edu.cn/ASD) was developed ten years ago to provide comprehensive information related to allosteric regulation. In recent years, allosteric regulation has received great attention in biological research, bioengineering, and drug discovery, leading to the emergence of entire allosteric landscapes as allosteromes. To facilitate research from the perspective of the allosterome, in ASD 2019, novel features were curated as follows: (i) >10 000 potential allosteric sites of human proteins were deposited for allosteric drug discovery; (ii) 7 human allosterome maps, including protease and ion channel maps, were built to reveal allosteric evolution within families; (iii) 1312 somatic missense mutations at allosteric sites were collected from patient samples from 33 cancer types and (iv) 1493 pharmacophores extracted from allosteric sites were provided for modulator screening. Over the past ten years, the ASD has become a central resource for studying allosteric regulation and will play more important roles in both target identification and allosteric drug discovery in the future.
New insights into protein–DNA binding specificity from hydrogen bond based comparative study
Authors: Lin Maoxuan , Guo Jun-tao 
Published: October 2019

AbstractKnowledge of protein–DNA binding specificity has important implications in understanding DNA metabolism, transcriptional regulation and developing therapeutic drugs. Previous studies demonstrated hydrogen bonds between amino acid side chains and DNA bases play major roles in specific protein–DNA interactions. In this paper, we investigated the roles of individual DNA strands and protein secondary structure types in specific protein–DNA recognition based on side chain-base hydrogen bonds. By comparing the contribution of each DNA strand to the overall binding specificity between DNA-binding proteins with different degrees of binding specificity, we found that highly specific DNA-binding proteins show balanced hydrogen bonding with each of the two DNA strands while multi-specific DNA binding proteins are generally biased towards one strand. Protein-base pair hydrogen bonds, in which both bases of a base pair are involved in forming hydrogen bonds with amino acid side chains, are more prevalent in the highly specific protein–DNA complexes than those in the multi-specific group. Amino acids involved in side chain-base hydrogen bonds favor strand and coil secondary structure types in highly specific DNA-binding proteins while multi-specific DNA-binding proteins prefer helices.
An independently validated survival nomogram for lower-grade glioma
Authors: Gittleman Haley , Sloan Andrew E , Barnholtz-Sloan Jill S 
Published: October 2019

Abstract

Background
Gliomas are the most common primary malignant brain tumor. Diffuse low-grade and intermediate-grade gliomas, which together compose the lower-grade gliomas (LGGs; World Health Organization [WHO] grades II and III), present a therapeutic challenge to physicians due to the heterogeneity of their clinical behavior. Nomograms are useful tools for individualized estimation of survival. This study aimed to develop and independently validate a survival nomogram for patients with newly diagnosed LGG.

Methods
Data were obtained for newly diagnosed LGG patients from The Cancer Genome Atlas (TCGA) and the Ohio Brain Tumor Study (OBTS) with the following variables: tumor grade (II or III), age at diagnosis, sex, Karnofsky performance status (KPS), and molecular subtype (IDH mutant with 1p/19q codeletion [IDHmut-codel], IDH mutant without 1p/19q codeletion, and IDH wild-type). Survival was assessed using Cox proportional hazards regression, random survival forests, and recursive partitioning analysis, with adjustment for known prognostic factors. The models were developed using TCGA data and independently validated using the OBTS data. Models were internally validated using 10-fold cross-validation and externally validated with calibration curves.

Results
A final nomogram was validated for newly diagnosed LGG. Factors that increased the probability of survival included grade II tumor, younger age at diagnosis, having a high KPS, and the IDHmut-codel molecular subtype.

Conclusions
A nomogram that calculates individualized survival probabilities for patients with newly diagnosed LGG could be useful to health care providers for counseling patients regarding treatment decisions and optimizing therapeutic approaches. Free online software for implementing this nomogram is provided: https://hgittleman.shinyapps.io/LGG_Nomogram_H_Gittleman/.

Key Points
1. A survival nomogram for lower-grade glioma patients has been developed and externally validated.
2. Free online software for implementing this nomogram is provided allowing for ease of use by practicing health care providers.
The Kinetics of Our Discontent
Authors: Döşemeci Mehmet 
Published: October 2019

Abstract
Why do we think of social struggles as movements? What is in motion and where is it going? Has struggle been thought and practised otherwise? Not as movement but as disruption, arrest, stasis? If so, what are struggles trying to stop? Asking these questions pushes us to think about struggle kinetically: to analyse social struggle through the register of motion and its interruption. This article questions why we have come to understand the history of social struggle through the category of movement and the consequences and costs of this understanding for historical analysis. Against this association, it underscores how movement, as a practice and idea, was central to the establishment and legitimation of the capitalist economy and, using two case studies of labour and the New Left, examines how significant strands of these struggles sought freedom in the arrest of its coerced motion. Drawing from these examples, the final section discusses the usefulness of kinetic analysis for historical inquiry.
The Normative Significance of Cognitive Science Reconsidered
Authors: Locke Dustin 
Published: October 2019

Abstract
Josh Greene famously argued that his cognitive-scientific results undermine deontological moral theorizing. Greene is wrong about this: at best, his research has revealed that at least some characteristically deontological moral judgments are sensitive to factors that we deem morally irrelevant. This alone is not enough to undermine those judgments. However, cognitive science could someday tell us more: it could tell us that in forming those judgments, we treat certain factors as reasons to believe as we do. If we independently deem such factors to be morally irrelevant, such a result would undermine those judgments and any moral theorizing built upon them. This paper attempts to bring charity, clarity, and epistemological sophistication to Greene's argument and those like it.
Historic Lynching and Corporal Punishment in Contemporary Southern Schools
Authors: Ward Geoff , Petersen Nick , Kupchik Aaron , Pratt James 
Published: October 2019

AbstractThis study examines how corporal punishment in contemporary public schools, a disciplinary practice concentrated in southeastern U.S. states, relates to histories of lynching in the region. Using school-level data from the U.S. Department of Education, we examine these relationships in a series of multi-level regression models. After controlling for numerous school- and county-level factors, we find an increased likelihood of corporal punishment for all students in counties where greater numbers of lynchings occurred, and that lynching is particularly predictive of corporal punishment for black students. Consistent with prior research associating historic lynching with contemporary violence, these results suggest general and race-specific legacies for violent school discipline. We consider potential mechanisms linking histories of lynching with school corporal punishment, and implications for research and policy.
Association of Medicaid Expansion With Coverage and Access to Care for Pregnant Women
Authors: Clapp Mark A. , James Kaitlyn E. , Kaimal Anjali J. , Sommers Benjamin D. , Daw Jamie R. 
Published: October 2019

OBJECTIVE:
To identify the association of the Affordable Care Act's Medicaid expansion with payment for delivery, early access to prenatal care, preterm birth, and birth weights considered small for gestational age (SGA).

METHODS:
A difference-in-difference design was used to assess changes in outcomes before and after Medicaid expansion in expansion states, using nonexpansion states as a control group. We used national birth certificate data from 2009 to 2017. Difference-in-difference linear probability models were used to assess the effects of the policy implementation, adjusting for demographics, month of birth, state, year, and county-level unemployment rates. Standard errors were clustered at the state level. Two prespecified subgroup analyses were performed of nulliparous women and women with no more than a high school diploma.

RESULTS:
The study sample included 8,701,889 women from 15 expansion states and 9,509,994 from 11 nonexpansion states. In the adjusted analysis, the percentage of Medicaid-covered deliveries increased by 2.3 absolute percentage points (95% CI 0.2–4.4, P=.04) in expansion states compared with nonexpansion states. There were no significant changes in the proportion of women who were uninsured, as there was a relative decrease in the percentage of deliveries covered by private insurance (−2.8 percentage points [95% CI −4.9 to −0.8, P=.01]). There were also no significant differences in the rate of women initiating prenatal care in the first trimester, preterm birth rates, or rates of low birth weight after the Medicaid expansion. Findings were similar in both subgroups.

CONCLUSION:
Medicaid expansion was associated with increased Medicaid coverage for childbirth in expansion states; similar gains in private coverage were seen in nonexpansion states. There were no associations with changes in early access to prenatal care, preterm birth, or SGA birth weights.
Development and Validation of a Machine Learning Algorithm for Predicting Response to Anticholinergic Medications for Overactive Bladder Syndrome
Authors: Sheyn David , Ju Mingxuan , Zhang Sixiao , Anyaeche Caleb , Hijaz Adonis , Mangel Jeffrey , Mahajan Sangeeta , Conroy Britt , El-Nashar Sherif , Ray Soumya 
Published: October 2019

OBJECTIVE:
To develop and externally validate a prediction model for anticholinergic response in patients with overactive bladder (OAB).

METHODS:
A machine learning model to predict the likelihood of anticholinergic treatment failure was constructed using a retrospective data set (n=559) of female patients with OAB who were treated with anticholinergic medications between January 2010 and December 2017. Treatment failure was defined as less than 50% improvement in frequency, urgency, incontinence episodes, and nocturia, and the patient's subjective impression of symptomatic relief. Patients were stratified by age (younger than 40 years, 40–60 years, and older than 60 years), and number of previously failed medications. K-fold stratified cross-validation was performed on each stratum using machine learning algorithms. Of these, the random forest model was the most accurate. This model was refined using internal cross validation within each stratum. The area under the curve (AUC) was calculated for each stratum and used to identify the optimal operating points for prediction of treatment failure. The random forest model was then externally validated using a prospectively collected data set (n=82) of women treated with anticholinergic medications at a different clinical site between January 2018 and December 2018.

RESULTS:
The global accuracy of the final model was 80.3% (95% CI 79.1–81.3), and the AUC was 0.77 (95% CI 0.74–0.79). Using the external validation data set, the model's sensitivity and specificity was 80.4% (95% CI 66.5–89.7%) and 77.4% (95% CI 58.6–89.7%), respectively. The model performed best in women aged younger than 40 years (AUC 0.84, 95% CI 0.81–0.84) and worst in women aged older than 60 years who had previously failed medication (AUC 0.71, 95% CI 0.67–0.75).

CONCLUSION:
Our externally validated machine learning prediction model can predict anticholinergic treatment failure during the standard 3-month treatment trial period with greater than 80% accuracy. The model can be accessed at https://oabweb.herokuapp.com/app/pre/.
Association Between Stillbirth at 23 Weeks of Gestation or Greater and Severe Maternal Morbidity
Authors: Lewkowitz Adam K. , Rosenbloom Joshua I. , López Julia D. , Keller Matt , Macones George A. , Olsen Margaret A. , Cahill Alison G. 
Published: October 2019

OBJECTIVE:
To estimate whether stillbirth at 23 weeks of gestation or more is associated with increased risk of severe maternal morbidity compared with live birth, when stratified by maternal comorbidities.

METHODS:
This retrospective cohort study used International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM) diagnosis and procedure codes within the Healthcare Cost and Utilization Project's Florida State Inpatient Database. The first delivery of female Florida residents aged 13–54 years old from 2005 to 2014 was included. The exposure was an ICD-9-CM code of stillbirth at 23 weeks of gestation or more; the control was an ICD-9-CM code of singleton live birth. Deliveries were stratified by the presence of 1 or more conditions within a well-validated maternal morbidity composite using ICD-9-CM codes during delivery hospitalization. The primary outcome was an ICD-9-CM diagnosis or procedure code during delivery hospitalization of any indices within the Centers for Disease Control and Prevention's severe maternal morbidity composite. Multivariable analyses adjusted for maternal sociodemographic factors and delivery mode to compare outcomes after stillbirth with live-birth delivery.

RESULTS:
Nine thousand five hundred twenty-three women who delivered stillborn fetuses and 1,353,044 with liveborn neonates were included. Among 6,590 stillbirths and 935,913 live births without maternal comorbidities, severe maternal morbidity was significantly more common during stillbirth delivery (n=345 [5.2%]), corresponding to a seven-fold increased risk compared with live birth (n=8,318 [0.9]; adjusted odds ratio [aOR] 7.05 [95% CI 6.27–7.93]). Among 2,933 stillbirths and 417,131 live births with maternal comorbidities, severe maternal morbidity was significantly more common during stillbirth delivery (n=390 [13.3%]): the risk was more than six-fold higher comparatively (n=11,122 [2.7%]; aOR 6.21 [95% CI 5.54–6.96]). Most maternal comorbidities were individually associated with higher risk of severe maternal morbidity during stillbirth compared with live-birth delivery.

CONCLUSION:
Though severe maternal morbidity is overall uncommon, delivering a stillborn fetus 23 weeks of gestation or greater is associated with increased likelihood of severe maternal morbidity, particularly among women with comorbidities, suggesting health care providers must be vigilant about severe maternal morbidity during stillbirth delivery.
Cognitive Profiles and Autism Symptoms in Comorbid Down Syndrome and Autism Spectrum Disorder
Authors: Hamner Taralee , Hepburn Susan , Zhang Fengqing , Fidler Deborah , Robinson Rosenberg Cordelia , Robins Diana L. , Lee Nancy R. 
Published: October 2019

ABSTRACT:Objective:The prevalence of comorbid autism spectrum disorder (ASD) in children with Down syndrome (DS) is estimated to be around 16%. This study aims to fill gaps in the literature by describing developmental and behavioral phenotypes in this group relative to those with DS or ASD in isolation.Methods:Participants included 173 children (Mage= 73 months) with ASD, DS, or DS + ASD. Two 3 × 2 repeated-measures analyses of variance were completed with between-subject factors of the diagnostic group (DS, ASD, and DS + ASD) and within-subject factors of cognitive performance (verbal and nonverbal developmental quotient [DQ]) or ASD symptoms (social affect [SA] and restricted and repetitive behaviors [RRBs]).Results:Significant group-by-scale interactions were found, and pairwise comparisons revealed that for verbal DQ, DS + ASD < DS, ASD, whereas for nonverbal DQ, DS + ASD < DS < ASD. For SA, DS < DS + ASD < ASD, whereas for RRB, DS, DS + ASD < ASD.Conclusion:Findings suggest greater cognitive impairment in DS + ASD on both verbal and nonverbal measures. Despite these significant cognitive challenges, ASD symptoms appeared less severe in DS + ASD relative to peers with ASD in isolation, although SA symptoms were elevated over DS-only. This unique DS + ASD presentation has important implications for early identification and intervention. Given previous research suggesting relative social strengths in DS and less severe ASD symptoms documented in this study, future research may benefit from investigating different aspects of SA (i.e., components related to reciprocal social interaction vs. social communication) in those with DS + ASD to more clearly delineate the social phenotype in this group and potentially inform intervention efforts.
Translucent and Ultrasonographic Studies of the Inferior Labial Artery for Improvement of Filler Injection Techniques
Authors: Tansatit Tanvaa , Phumyoo Thirawass , MCCabe Hannah , Jitaree Benrita 
Published: October 2019

Background:
Lower lip augmentation by filler injection is an aesthetic procedure essential for achieving a feminine look and to enhance attractiveness. Complications as a result of injury to the inferior labial artery can result in undesirable outcomes.

Methods:
The translucent technique was used to study the origin of the inferior labial artery in 11 cadavers. Ultrasonography of the inferior labial artery was also performed in 20 volunteers, which provided supplemental data to this study, in relation to establishing recommendations for filler injection.

Results:
Five different types of inferior labial artery were described. These types were found in various combination patterns. Types 2, 4, and 5 are more vulnerable to arterial injury during filler injection. Ultrasonography revealed a depth of 6 mm and an arterial position at the vermillion border as the dangerous injection plane.

Conclusion:
The origins and courses of the inferior labial artery are classified into 5 types. These types are often found in combination with each other in different faces, resulting in large anatomical variation between people. Types of combination influence severity of lower lip necrosis when arterial injury occurs. The physician should be aware of these anatomical variations during aesthetic treatments and reconstructive procedures to avoid the dangers of accidental arterial injury.