bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nine-Year Ethanol Intake Trajectories and Their Association With 15-Year Cognitive Decline Among Black and White Adults
Authors: Love Shelly-Ann M , North Kari E , Zeng Donglin , Petruski-Ivleva Natalia , Kucharska-Newton Anna , Palta Priya , Graff Mariaelisa , Loehr Laura , Jones Sarah B , Heiss Gerardo 
Published: January 2020

Abstract
Faster rates of age-related cognitive decline might result in early onset of cognitive impairment and dementia. The relationship between ethanol intake and cognitive decline, although studied extensively, remains poorly understood. Previous studies used single measurements of ethanol, and few were conducted in diverse populations. We assessed the association of 9-year trajectories of ethanol intake (1987–1998) with 15-year rate of decline in cognitive performance from mid- to late life (1996–2013) among 2,169 Black and 8,707 White participants of the US Atherosclerosis Risk in Communities study using multivariable linear regression models. We hypothesized that stable, low to moderate drinking would be associated with lesser 15-year cognitive decline, and stable, heavy drinking with greater 15-year cognitive decline. Stable, low to moderate drinking (for Blacks, adjusted mean difference (MD) = 0.03 (95% confidence interval (CI): −0.13, 0.19); for Whites, adjusted MD = 0.02 (95% CI: −0.05, 0.08)) and stable, heavy drinking (for Blacks, adjusted MD = 0.08 (95% CI: −0.34, 0.50); for Whites, adjusted MD = −0.03 (95% CI: −0.18, 0.11)) in midlife compared with stable never-drinking were not associated with 15-year decline in general cognitive function from mid- to late life. No association was observed for the stable former and “mostly” drinking trajectories with 15-year cognitive decline. Stable low, low to moderate, and stable heavy drinking in midlife are not associated with lesser and greater cognitive decline, respectively, from mid- to late life among Black and White adults.
Correlation of the Standardized Cosmesis and Health Nasal Outcomes Survey With Psychiatric Screening Tools
Authors: Spataro Emily A , Kandathil Cherian K , Saltychev Mikhail , Olds Cristen E , Most Sam P 
Published: January 2020

Abstract

Background
Identifying mental health disorders, including body dysmorphic disorder (BDD), is important prior to rhinoplasty surgery; however, these disorders are underdiagnosed, and screening tools are underutilized in clinical settings.

Objectives
The authors sought to evaluate the correlation of a rhinoplasty outcomes tool (Standardized Cosmesis and Health Nasal Outcomes Survey [SCHNOS]) with psychiatric screening tools.

Methods
Patients presenting for rhinoplasty consultation were prospectively enrolled and administered mental health instruments to assess depression (Patient Health Questionnaire-9), anxiety (Generalized Anxiety Disorder-7), and BDD (BDD Questionnaire-Aesthetic Surgery [BDDQ-AS]) as well as the SCHNOS rhinoplasty outcomes scale. Convergent validity of SCHNOS scores with these mental health instruments was assessed as well as calculation of an optimal SCHNOS-C score to screen for BDD.

Results
A total 76 patients were enrolled in the study. The average SCHNOS-O score (standard deviation) was 46.1 (34.0) and the average SCHNOS-C score was 61.1 (27.0). Five (7%) patients screened positive for depression, and 24 (32%) patients screened positive for mild, 5 (7%) for moderate, and 4 (5%) for severe anxiety. Twenty-four (32%) patients screened positive for BDD by BDDQ-AS scores. SCHNOS-O and SCHNOS-C did not correlate with Patient Health Questionnaire-9 or Generalized Anxiety Disorder-7 scores; SCHNOS-C did correlate with BDDQ-AS. A score of 73 or greater on SCHNOS-C maximized the sensitivity and specificity of also screening positive for BDD with BDDQ-AS. This score correlated with a sensitivity of 62.5%, specificity of 80.8%, and number needed to diagnose of 2.3, meaning for every 2 patients with a score of ≥73 on SCHNOS-C, 1 will have a positive BDDQ-AS score.

Conclusions
SCHNOS-C correlates with BDDQ-AS and may help screen rhinoplasty patients at higher risk for BDD.

Level of Evidence: 2
The Protein Imager: a full-featured online molecular viewer interface with server-side HQ-rendering capabilities
Authors: Tomasello Gianluca , Armenia Ilaria , Molla Gianluca 
Published: January 2020

Abstract

Summary
Molecular viewers’ long learning curve is hindering researchers in approaching the field of structural biology for the first time. Herein, we present ‘The Protein Imager’, a lightweight, powerful and easy-to-use interface as a next-gen online molecular viewer. Furthermore, the interface is linked to an automated server-side rendering system able to generate publication-quality molecular illustrations. The Protein Imager interface has been designed for easy usage for beginners and experts in the field alike. The interface allows the preparation of very complex molecular views maintaining a high level of responsiveness even on mobile devices.

Availability and implementation
The Protein Imager interface is freely available online at https://3dproteinimaging.com/protein-imager.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nearest-neighbor Projected-Distance Regression (NPDR) for detecting network interactions with adjustments for multiple tests and confounding
Authors: Le Trang T , Dawkins Bryan A , McKinney Brett A 
Published: January 2020

Abstract

Summary
Machine learning feature selection methods are needed to detect complex interaction-network effects in complicated modeling scenarios in high-dimensional data, such as GWAS, gene expression, eQTL and structural/functional neuroimage studies for case–control or continuous outcomes. In addition, many machine learning methods have limited ability to address the issues of controlling false discoveries and adjusting for covariates. To address these challenges, we develop a new feature selection technique called Nearest-neighbor Projected-Distance Regression (NPDR) that calculates the importance of each predictor using generalized linear model regression of distances between nearest-neighbor pairs projected onto the predictor dimension. NPDR captures the underlying interaction structure of data using nearest-neighbors in high dimensions, handles both dichotomous and continuous outcomes and predictor data types, statistically corrects for covariates, and permits statistical inference and penalized regression. We use realistic simulations with interactions and other effects to show that NPDR has better precision-recall than standard Relief-based feature selection and random forest importance, with the additional benefit of covariate adjustment and multiple testing correction. Using RNA-Seq data from a study of major depressive disorder (MDD), we show that NPDR with covariate adjustment removes spurious associations due to confounding. We apply NPDR to eQTL data to identify potentially interacting variants that regulate transcripts associated with MDD and demonstrate NPDR’s utility for GWAS and continuous outcomes.

Availability and implementation
Available at: https://insilico.github.io/npdr/.

Supplementary information
Supplementary data are available at Bioinformatics online.
RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution
Authors: Ozadam Hakan , Geng Michael , Cenik Can 
Published: January 2020

Abstract

Summary
Ribosome occupancy measurements enable protein abundance estimation and infer mechanisms of translation. Recent studies have revealed that sequence read lengths in ribosome profiling data are highly variable and carry critical information. Consequently, data analyses require the computation and storage of multiple metrics for a wide range of ribosome footprint lengths. We developed a software ecosystem including a new efficient binary file format named ‘ribo’. Ribo files store all essential data grouped by ribosome footprint lengths. Users can assemble ribo files using our RiboFlow pipeline that processes raw ribosomal profiling sequencing data. RiboFlow is highly portable and customizable across a large number of computational environments with built-in capabilities for parallelization. We also developed interfaces for writing and reading ribo files in the R (RiboR) and Python (RiboPy) environments. Using RiboR and RiboPy, users can efficiently access ribosome profiling quality control metrics, generate essential plots and carry out analyses. Altogether, these components create a software ecosystem for researchers to study translation through ribosome profiling.

Availability and implementation
For a quickstart, please see https://ribosomeprofiling.github.io. Source code, installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling.

Supplementary information
Supplementary data are available at Bioinformatics online.
Differentiation of developmental plasticity as a major cause of morphological evolution in stag beetles (Coleoptera: Lucanidae)
Authors: Kawano Kazuo 
Published: January 2020

AbstractStag beetles show great developmental plasticity (DP) in their external morphology. In intraspecific evolution, DP functions as a stabilizer for morphological change, whereas interspecifically, the evolution of external morphology is primarily a process of differentiation in DP. Greater DP in external morphology has evolved as a species trait through selection for survival in conditions that vary stochastically, rather than a long-term unidirectional trend in conditions. All the interspecific transitions towards larger size, multimodal morphology and adaptive expansion are preceded by an increase in DP. Here, differentiation of DP is more a cause, rather than a result, of species-level evolution. This contrasts with the differentiation of other important traits, such as the morphology of the genitalia, which follow the conventional known process of small effects accumulating to larger effects from an intraspecific stage to an interspecific stage, in which DP plays no significant role. The DP of external morphology, as an emergent property of species, provides the means by which they can survive and subsequently evolve to be better adapted to novel conditions. This contrasting mode of evolution through differentiation of DP should play a crucial role in species survival and the maintenance of biodiversity in the Anthropocene.
Influence of mass on tarsus shape variation: a morphometrical investigation among Rhinocerotidae (Mammalia: Perissodactyla)
Authors: Etienne Cyril , Mallet Christophe , Cornette Raphaël , Houssaye Alexandra 
Published: January 2020

AbstractMany tetrapod lineages show extreme increases in body mass in their evolutionary history, associated with important osteological changes. The ankle joint, essential for foot movement, is assumed to be particularly affected in this regard. We investigated the morphological adaptations of the astragalus and the calcaneus in Rhinocerotidae, and analysed them in light of a comparative analysis with other Perissodactyla. We performed 3D geometric morphometrics and correlated shape with centroid size of the bone and body mass of the species. Our results show that mass has an influence on bone shape in Rhinocerotidae and in Perissodactyla, but this is not as strong as expected. In heavy animals the astragalus has a flatter trochlea, orientated more proximally, associated with a more upright posture of the limb. The calcaneus is more robust, possibly to sustain the greater tension force exerted by the muscles during plantarflexion. Both bones show wider articular facets, providing greater cohesion and better dissipation of the loading forces. The body plan of the animals also has an influence. Short-legged Teleoceratina have a flatter astragalus than the other rhinocerotids. Paraceratherium has a thinner calcaneus than expected. This study clarifies adaptations to high body weight among Rhinocerotidae and calls for similar investigations in other groups with massive forms.
Ecophylogeography of the disjunct South American xerophytic tree species Prosopis chilensis (Fabaceae)
Authors: Aguilar Dana Lucía , Acosta María Cristina , Baranzelli Matías Cristian , Sérsic Alicia Noemí , Delatorre-Herrera Jose , Verga Anibal , Cosacov Andrea 
Published: January 2020

AbstractThe intraspecific evolutionary history of South American xerophytic plant species has been poorly explored. The tree species Prosopis chilensis has a disjunct distribution in four South American regions: southern Peru, southern Bolivia, central–western Argentina and central Chile. Here, we combined phylogeographical (based on chloroplast and nuclear markers), morphological and climatic data to evaluate the relative contribution of historical demo-stochastic and adaptive processes in differentiating the disjunct areas of distribution. The results obtained with the two molecular markers revealed two closely related phylogroups (Northern and Southern, predominating in Bolivian Chaco and in Argentine Chaco/Monte, respectively), which would have diverged at ~5 Mya, probably associated with transgression of the Paranaense Sea. Bolivia and Argentina have a larger number of exclusive haplotypes/alleles and higher molecular diversity than Chile, suggesting a long-lasting in situ persistence in the former and a relatively recent colonization in the latter, from the Bolivian and Argentinian lineages. The two main lineages differ in morphology and climatic niche, revealing two significant, independent evolutionary units within P. chilensis promoted by local adaptation and geographical isolation.
Applying intersectionality to partnerships between women’s organizations and the criminal justice system in relation to domestic violence
Authors: Day Aviah Sarah , Gill Aisha K 
Published: January 2020

AbstractThe challenges facing domestic violence (DV) survivors has become the subject of a growing body of intersectional analysis; this paper presents a new intersectional framework for analysing DV policy and practice. Examining a partnership between women’s sector organizations and the criminal justice system in London, using interviews with professionals from the bodies, the paper offers an intersectional analysis of the implications, positive and negative, for both policy and practice. The complex interplay between women’s sector organizations and the criminal justice system demonstrate how the intersections of gender, class, ‘race’ and immigration status affect the way DV survivors are able to access and benefit from support, concluding that, to operate more effectively, DV support must consider all forms of oppression and violence affecting the lives of all their users.
Judicial Activism of Provincial Courts in China: Medical Negligence Law as a Case Study
Authors: Ding Chunyan 
Published: January 2020

Abstract
By presenting a case study of local judicial activism in medical negligence law reform in recent China, this article examines the active engagement of Chinese provincial courts in bottom-up reform of national laws. Contrary to conventional wisdom that law-making is the least important function of local courts, it finds that provincial courts in China, like the Supreme People’s Court, are actively engaging in law-making, which is an essential part of their functions. It also reveals that the national judiciary is more susceptible to political pressure while the provincial judiciary tends to be less vulnerable to political pressure and more responsive to populist pressure when exercising its law-making power. Therefore, provincial courts may be in a better position to reform national laws in response to urgent social needs, in contrast to the Supreme People’s Court, which encounters political obstacles in pursing top-down law reform. By exploring the dynamic national–local judiciary relationship in the law-making landscape, this article argues that judicial activism of provincial courts in national law reform opens an alternative channel through which populist views can effectively move up to become part of national laws despite China being a non-democratic country.
Rememorying Slavery: Intergenerational Memory and Trauma in Toni Morrison’s Beloved (1987) and Conceição Evaristo’s Ponciá Vicêncio (2003)
Authors: de Souza Sutter Luana 
Published: January 2020

AbstractThis paper looks at parallels in the articulation of memory and trauma between Toni Morrison’s Beloved and the more recent publication Ponciá Vicêncio, written in 2003 by the Afro-Brazilian writer Conceição Evaristo. It examines the novels’ illustration of slavery trauma and the creative investment of descendants of slaves in re-presenting traumatic family history. With this concern, it proposes a comparative reading of Beloved and Ponciá Vicêncio, focusing, first, on their representations of the embodiment of trauma; second, on their respective concepts of rememory and memory-thoughts – or pensamentos-lembranças; and third, on the descendants’ engagement with the revision of narratives of family past, through the characters Denver and Ponciá.
Do ground-glass opacity-dominant features have prognostic significance in node-negative adenocarcinomas with invasive components of similar sizes?
Authors: Han Sung Joon , Jeon Jae Hyun , Jung Woohyun , Seong Yong Won , Cho Sukki , Kim Kwhanmien , Jheon Sanghoon 
Published: January 2020

Abstract

OBJECTIVES
The purpose of this study was to analyse the prognostic significance of the dominant features of ground-glass opacities (GGOs) in part-solid node-negative adenocarcinomas with invasive components of similar sizes.

METHODS
From 2004 to 2017, a total of 544 patients with a diagnosis of part-solid pathological node-negative adenocarcinoma with an invasive component &lt;20 mm in size were selected. The enrolled patients were categorized into 2 groups: a GGO-dominant [50% &lt; GGO (%) &lt; 100%, n = 245] group (group 1) and a solid-dominant [0% &lt; GGO (%) ≤ 50%, n = 299] group (group 2). To analyse the prognostic significance of GGO-dominant features, propensity score matching incorporating variables such as age, sex, preoperative pulmonary function, operation methods and size of the solid component was performed.

RESULTS
Propensity score matching produced 92 patients in each group for the prognostic analysis. The mean size of the solid part was 8.8 mm in the GGO-dominant group and 9.0 mm in the solid-dominant group (P = 0.34); the mean size of the total lesion was 22.2 mm in the GGO-dominant group and 14.9 mm in the solid-dominant group (P &lt; 0.001). The 5-year overall survival rates were 96.7% in group 1 and 96.2% in group 2 (P = 0.52), and the 5-year disease-free survival rates were 96.7% in group 1 and 94.3% in group 2 (P = 0.48).

CONCLUSIONS
Although the total sizes of the GGO-dominant lesions were larger than those of the solid-dominant lesions, the prognosis of patients with GGO-dominant lesions was not significantly different from that of patients with solid-dominant lesions in node-negative adenocarcinomas with a similar invasive component size &lt;20 mm.
Cognitive Sociology, Social Cognition and Coping with Racial Discrimination in International Law
Authors: Hirsch Moshe 
Published: January 2020

Abstract
Cognitive science is the interdisciplinary study of mental processes involved in the acquisition, classification, organization and interpretation of knowledge in the human environment as well as the decision taken on the appropriate action based upon it. The point of departure is that people do not directly sense information; cognitive processes mediate between sensory input from the environment and behaviour. These cognitive processes are influenced by neurological, psychological, socio-cultural and other factors. In recent years, there has been growing scholarly interest in the study of cognitive sociology, focusing on the interactions between culture and cognition. This stream in sociological literature draws upon and complements cognitive psychological literature. The prohibition on discrimination constitutes one of the fundamental rules in international human rights law, but studies reveal that racial discrimination is pervasive and persistent in many states. Non-compliance with this international legal rule is significantly related to cognitive processes through which people acquire and interpret incoming information about other people. Racial groups are socially constructed and deeply ingrained socio-cognitive biases feed and reproduce racially discriminatory behaviour. These biased mental processes, however, are not inevitable and may change over time. Effective struggle against racial discrimination requires that international legal mechanisms also address the socio-cognitive infrastructure that facilitates and sustains racial discrimination. Consequently, this study also discusses some international legal strategies aimed at mitigating cognitive biases and enhancing compliance with treaties prohibiting racial discrimination.
Variation in the microbiome of the spider mite Tetranychus truncatus with sex, instar and endosymbiont infection
Authors: Zhu Yu-Xi , Song Zhang-Rong , Huo Shi-Mei , Yang Kun , Hong Xiao-Yue 
Published: January 2020

ABSTRACTMost arthropod-associated bacterial communities play a crucial role in host functional traits, whose structure could be dominated by endosymbionts. The spider mite Tetranychus truncatus is a notorious agricultural pest harboring various endosymbionts, yet the effects of endosymbionts on spider mite microbiota remain largely unknown. Here, using deep sequencing of the 16S rRNA gene, we characterized the microbiota of male and female T. truncatus with different endosymbionts (Wolbachia and Spiroplasma) across different developmental stages. Although the spider mite microbiota composition varied across the different developmental stages, Proteobacteria were the most dominant bacteria harbored in all samples. Positive relationships among related operational taxonomic units dominated the significant coassociation networks among bacteria. Moreover, the spider mites coinfected with Wolbachia and Spiroplasma had a significantly higher daily fecundity and juvenile survival rate than the singly infected or uninfected spider mites. The possible function of spider-mite associated bacteria was discussed. Our results highlight the dynamics of spider mite microbiotas across different life stages, and the potential role of endosymbionts in shaping the microbiota of spider mites and improving host fitness.
Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life
Authors: O'Hara Eóin , Kenny David A , McGovern Emily , Byrne Colin J , McCabe Matthew S , Guan Le Luo , Waters Sinéad M 
Published: January 2020

ABSTRACTManipulation of the rumen microorganisms during early life has emerged as a promising strategy for persistent improvement of nutrient utilisation and lowering of enteric methanogenesis. However, limited understanding of the dynamics of rumen microbial colonisation has prevented the identification of the optimum timeframe for such interventions. The present study used DNA amplicon sequencing of the 16S rRNA gene to assess bacterial and archaeal dynamics in the rumen digesta of beef calves raised on two farms from birth through to post-weaning. The colonisation patterns of both communities were influenced by age (P &lt; 0.05) and farm of origin (P &lt; 0.05). The bacterial community exhibited an age-wise progression during the first month of life which appeared to be partly related to diet, and settled by day 21, indicating that this may mark the boundary of a timeframe for intervention. The archaeal community appeared less sensitive to age/diet than bacteria in the first month of life but was more sensitive to farm environment. These data show that ruminal microbial composition during early life is driven by calf age, diet and local environment, and provide important fundamental information concerning the ontogeny of the rumen microbiota from birth.