bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Organic Syntactic Complexity Measure for the Chinese Language: The TC-Unit
Authors: Yu Qiaona 
Published: December 2019

AbstractLanguage complexity reveals the ability to use a wide and varied range of sophisticated structures and vocabulary. Although different languages compose complexity differently, complexity measures such as the T-unit have typically been based on clause subordination, which may underrepresent complexity and threaten the validity of studies. This study argues that an organic complexity measure should avoid the assumption of clause subordination and instead consider the typological features of the target language. Therefore, this study proposes the TC-unit in recognition of the topic chain as the underlying unit of Chinese complexity. It further validates TC-unit-based measures by investigating how accurately they predict proficiency group membership. Discriminant analyses of L1 and L2 Chinese speakers’ spoken (N = 115) and written (N = 116) output elicited from a designed timed online test, revealed that TC-unit-based measures classified proficiency group membership with high efficiency (61.2–75.7 per cent). Mean length of terminable TC-unit proved the most effective indicator of spoken Chinese syntactic complexity, while mean length of terminable TC-unit and single TC-units per terminable TC-unit in combination proved the most effective for written Chinese syntactic complexity.
Reproductive workers insufficiently signal their reproductive ability in a paper wasp
Authors: Tsuchida Koji , Saigo Takaharu , Asai Kazuyuki , Okamoto Tomoko , Ando Masaki , Ando Tetsu , Sasaki Ken , Yokoi Kakeru , Watanabe Dai , Sugime Yasuhiro , Miura Toru 
Published: December 2019

Abstract
Why workers forfeit direct reproduction is a crucial question in eusocial evolution. Worker reproduction provides an excellent opportunity to understand the mechanism of kin conflict resolution between the queen and workers. We evaluated behavioral and physiological differences among females in the paper wasp Polistes chinensis antennalis to examine why some workers reproduce under queenright conditions. Reproductive workers were old and foraged less early in the season; their cuticular hydrocarbon (CHC) profiles overlapped with those of queens but were significantly different. The distinct CHC profile of the eggs of the queen likely represented a cue for policing against those by workers. Juvenile hormone (JH) and dopamine seemed to be associated with gonadotropic function, and the JH level of reproductive workers was similar to that of the queen. The high JH level of reproductive workers likely facilitated their reproduction even under queenright conditions. Gene expression levels of the queen and reproductive workers differed only in vitellogenin. These results suggest that worker reproduction is facilitated by an increase in JH level; however, CHC is not a fertility-linked signal, but a queen-linked signal; consequently, reproductive workers without a queen-linked signal might be allowed to stay within the colony.
Aberrant DNA methylation and miRNAs in coronary artery diseases and stroke: a systematic review
Authors: Sharma Anu Radha , Shashikiran Umakanth , UK Abdul Razak , Shetty Ranjan , Satyamoorthy Kapaettu , Rai Padmalatha S 
Published: December 2019

Abstract
Coronary artery disease (CAD) and ischemic stroke are the two most predominant forms of cardiovascular diseases (CVDs) caused by genetic, epigenetic and environmental risk factors. Although studies on the impact of ‘epigenetics’ in CVDs is not new, its effects are increasingly being realized as a key regulatory determinant that may drive predisposition, pathophysiology and therapeutic outcome. The most widely studied epigenetic risk factors are regulated by DNA methylation and miRNA expression. To keep pace with growing developments and discoveries, a comprehensive review was performed using Pubmed, Science Direct and Scopus databases to highlight the role of DNA methylation and miRNAs in CAD and stroke subjects. Network analysis was performed using ClueGO software and miRTargetLink database. We identified 32 studies of DNA methylation on CAD and stroke, of which, 6 studies showed differences in global DNA methylation, 10 studies reported the genome-wide difference in DNA methylation and 16 studies demonstrated altered DNA methylation at 14 candidate loci. The network analysis showed positive regulation of nitric oxide biosynthetic process, homocysteine metabolic process and negative regulation of lipid storage. About, 155 miRNAs were associated with CAD, stroke and related phenotypes in 83 studies. Interestingly, mir-223 hypomethylation and altered expression were associated with cerebral infarction and stroke. The target prediction for 18 common miRNAs between CAD and stroke showed strong interaction with SP3 and SP1 genes. This systematic review addresses the present knowledge on DNA methylation and miRNAs in CAD and stroke, whose abnormal regulation has been implicated in etiology or progression of the diseases.
MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis
Authors: Randhawa Gurjit S , Hill Kathleen A , Kari Lila 
Published: December 2019

Abstract

Summary
Machine Learning with Digital Signal Processing and Graphical User Interface (MLDSP-GUI) is an open-source, alignment-free, ultrafast, computationally lightweight, and standalone software tool with an interactive GUI for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others.

Availability and implementation
MLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The dynamic of basal ganglia activity with a multiple covariance method: influences of Parkinson’s disease
Authors: Rodriguez-Sabate Clara , Morales Ingrid , Puertas-Avendaño Ricardo , Rodriguez Manuel 
Published: December 2019

Abstract
The closed-loop cortico-subcortical pathways of basal ganglia have been extensively used to describe the physiology of these centres and to justify the functional disorders of basal ganglia diseases. This approach justifies some experimental and clinical data but not others, and furthermore, it does not include a number of subcortical circuits that may produce a more complex basal ganglia dynamic than that expected for closed-loop linear networks. This work studied the functional connectivity of the main regions of the basal ganglia motor circuit with magnetic resonance imaging and a new method (functional profile method), which can analyse the multiple covariant activity of human basal ganglia. The functional profile method identified the most frequent covariant functional status (profiles) of the basal ganglia motor circuit, ordering them according to their relative frequency and identifying the most frequent successions between profiles (profile transitions). The functional profile method classified profiles as input profiles that accept the information coming from other networks, output profiles involved in the output of processed information to other networks and highly interconnected internal profiles that accept transitions from input profiles and send transitions to output profiles. Profile transitions showed a previously unobserved functional dynamic of human basal ganglia, suggesting that the basal ganglia motor circuit may work as a dynamic multiple covariance network. The number of internal profiles and internal transitions showed a striking decrease in patients with Parkinson’s disease, a fact not observed for input and output profiles. This suggests that basal ganglia of patients with Parkinson’s disease respond to requirements coming from other neuronal networks, but because the internal processing of information is drastically weakened, its response will be insufficient and perhaps also self-defeating. These marked effects were found in patients with few motor disorders, suggesting that the functional profile method may be an early procedure to detect the first stages of the Parkinson’s disease when the motor disorders are not very evident. The multiple covariance activity found presents a complementary point of view to the cortico-subcortical closed-loop model of basal ganglia. The functional profile method may be easily applied to other brain networks, and it may provide additional explanations for the clinical manifestations of other basal ganglia disorders.
Intestinal bacterial indicator phylotypes associate with impaired DNA double-stranded break sensors but augmented skeletal bone micro-structure
Authors: Maier Irene , Liu Jared , Ruegger Paul M , Deutschmann Julia , Patsch Janina M , Helbich Thomas H , Borneman James , Schiestl Robert H 
Published: December 2019

AbstractIntestinal microbiota are considered a sensor for molecular pathways, which orchestrate energy balance, immune responses, and cell regeneration. We previously reported that microbiota restriction promoted higher levels of systemic radiation-induced genotoxicity, proliferative lymphocyte activation, and apoptotic polarization of metabolic pathways. Restricted intestinal microbiota (RM) that harbors increased abundance of Lactobacillus johnsonii (LBJ) has been investigated for bacterial communities that correlated radiation-induced genotoxicity. Indicator phylotypes were more abundant in RM mice and increased in prevalence after whole body irradiation in conventional microbiota (CM) mice, while none of the same ten most abundant phylotypes were different in abundance between CM mice before and after heavy ion irradiation. Muribaculum intestinale was detected highest in female small intestines in RM mice, which were lacking Ureaplasma felinum compared with males, and thus these bacteria could be contributing to the differential amounts of radiation-induced systemic genotoxicity between the CM and RM groups. Helicobacter rodentium and M.intestinale were found in colons in the radiation-resistant CM phenotype. While the expression of interferon-γ was elevated in the small intestine, and lower in blood in CM mice, high-linear energy transfer radiation reduced transforming growth factor-β with peripheral interleukin (IL)-17 in RM mice, particularly in females. We found that female RM mice showed improved micro-architectural bone structure and anti-inflammatory radiation response compared with CM mice at a delayed phase 6 weeks postexposure to particle radiation. However, microbiota restriction reduced inflammatory markers of tumor necrosis factor in marrow, when IL-17 was reduced by intraperitoneal injection of IL-17 neutralizing antibody.
WNT5a Regulates Epithelial Morphogenesis in the Developing Choroid Plexus
Authors: Langford Michael B , O’Leary Conor J , Veeraval Lenin , White Amanda , Lanoue Vanessa , Cooper Helen M 
Published: December 2019

AbstractThe choroid plexus (CP) is the predominant supplier of cerebral spinal fluid (CSF) and the site of the blood–CSF barrier and is thus essential for brain development and central nervous system homeostasis. Despite these crucial roles, our understanding of the molecular and cellular processes giving rise to the CPs within the ventricles of the mammalian brain is very rudimentary. Here, we identify WNT5a as an important regulator of CP development, where it acts as a pivotal factor driving CP epithelial morphogenesis in all ventricles. We show that WNT5a is essential for the establishment of a cohesive epithelium in the developing CP. We find that in its absence all CPs are substantially reduced in size and complexity and fail to expand into the ventricles. Severe defects were observed in the epithelial cytoarchitecture of all Wnt5a−/− CPs, exemplified by loss of apicobasally polarized morphology and detachment from the ventricular surface and/or basement membrane. We also present evidence that the WNT5a receptor, RYK, and the RHOA kinase, ROCK, are required for normal CP epithelial morphogenesis. Our study, therefore, reveals important insights into the molecular and cellular mechanisms governing CP development.
Value Neglect: A Critical Role for Ventromedial Frontal Lobe in Learning the Value of Spatial Locations
Authors: Pelletier Gabriel , Fellows Lesley K 
Published: December 2019

Abstract
Whether you are a gazelle bounding to the richest tract of grassland or a return customer heading to the freshest farm stand at a crowded market, the ability to learn the value of spatial locations is important in adaptive behavior. The ventromedial frontal lobe (VMF) is implicated in value-based decisions between objects and in flexibly learning to choose between objects based on feedback. However, it is unclear if this region plays a material-general role in reward learning. Here, we tested whether VMF is necessary for learning the value of spatial locations. People with VMF damage were compared with healthy participants and a control group with frontal damage sparing VMF in an incentivized spatial search task. Participants chose among spatial targets distributed among distractors, rewarded with an expected value that varied along the right-left axis of the screen. People with VMF damage showed a weaker tendency to reap reward in contralesional hemispace. In some individuals, this impairment could be dissociated from the ability to make value-based decisions between objects, assessed separately. This is the first evidence that the VMF is critically involved in reward-guided spatial search and offers a novel perspective on the relationships between value, spatial attention, and decision-making.
Smoking and outcomes following guided de-escalation of antiplatelet treatment in acute coronary syndrome patients: a substudy from the randomized TROPICAL-ACS trial
Authors: Orban Martin , Trenk Dietmar , Geisler Tobias , Rieber Johannes , Hadamitzky Martin , Gross Lisa , Orban Mathias , Kupka Danny , Baylacher Monika , Müller Susan , Huber Kurt , Koltowski Lukasz , Huczek Zenon , Heyn Jens , Jacobshagen Claudius , Aradi Dániel , Massberg Steffen , Sibbing Dirk , Hein Ralph ,   on behalf of the TROPICAL-ACS Investigators
Published: December 2019

Abstract

Aims
Prior analyses disclosed variations in antiplatelet drug response and clinical outcomes between smokers and non-smokers, thus the safety and efficacy of any dual antiplatelet therapy (DAPT) de-escalation strategy may differ in relation to smoking status. Hence, we assessed the impact of smoking on clinical outcomes and adenosine diphosphate-induced platelet aggregation following guided de-escalation of DAPT in invasively managed acute coronary syndrome (ACS) patients.

Methods and results
The multicentre TROPICAL-ACS trial randomized 2610 biomarker-positive ACS patients 1:1 to standard treatment with prasugrel for 12 months (control group) or a platelet function testing guided de-escalation of DAPT. Current smokers (n = 1182) showed comparable event rates between study groups [6.6% vs. 6.6%; hazard ratio (HR) 1.0, 95% confidence interval (CI) 0.64–1.56, P &gt; 0.99]. In non-smokers (n = 1428), a guided DAPT de-escalation was associated with a lower 1-year incidence of the primary endpoint [cardiovascular death, myocardial infarction, stroke, or bleeding ≥ Grade 2 according to Bleeding Academic Research Consortium (BARC) criteria] compared with control group patients (7.9% vs. 11.0%; HR 0.71, 95% CI 0.50–0.99, P = 0.048). This reduction was mainly driven by a lower rate of BARC ≥ Grade 2 bleedings (5.2% vs. 7.7%; HR 0.68, 95% CI 0.45–1.03, P = 0.066). There was no significant interaction of smoking status with treatment effects of guided DAPT de-escalation (Pint = 0.23). Adenosine diphosphate-induced platelet aggregation values were higher in current smokers [median 28 U, interquartile range (IQR: 20–40)] vs. non-smoker [median 24 U (16–25), P &lt; 0.0001] in the control group and in current smokers [median 42 U, IQR (27–68)] vs. non-smoker [median 37 U, IQR (25–55), P &lt; 0.001] in the monitoring group.

Conclusion
Guided DAPT de-escalation appears to be equally safe and effective in smokers and non-smokers. Regardless of smoking status and especially for those patients deemed unsuitable for 1 year of potent platelet inhibition this DAPT strategy might be used as an alternative antiplatelet treatment regimen.
Smallholder rice farmers’ post-harvest decisions: preferences and structural factors
Authors: Ruhinduka Remidius Denis , Alem Yonas , Eggert Håkan , Lybbert Travis 
Published: December 2019

Abstract
We study post-harvest decisions among Tanzanian rice farmers. Risk and time preference experiments are used to understand post-harvest decisions. In particular, we investigate storage and processing decisions, which according to our study can increase income by more than 50 per cent, but also introduce risk and time delays. Experimentally elicited risk and time preferences are statistically significant in explaining these post-harvest decisions. Impatient farmers are less likely to store paddy, and risk-averse farmers are less likely both to process and store paddy for future sales. Also, structural factors, such as milling costs, transportation costs and storage losses, influence the post-harvest choices.
Impact of weight on the efficacy and safety of direct-acting oral anticoagulants in patients with non-valvular atrial fibrillation: a meta-analysis
Authors: Malik Aaqib H , Yandrapalli Srikanth , Shetty Suchith , Aronow Wilbert S , Jain Diwakar , Frishman William H , Cooper Howard A , Panza Julio A ,   on behalf of MAGIC (Meta-analysis And oriGinal Investigations in Cardiology) Investigators
Published: December 2019

Abstract

Aims
This study sought to determine the impact of weight and body mass index (BMI) on the safety and efficacy of direct-acting oral anticoagulants (DOACs) compared with warfarin in patients with non-valvular atrial fibrillation.

Methods and results
A systematic literature search was employed in PubMed, Embase, and Cochrane clinical trials with no language or date restrictions. Randomized trials or their substudies were assessed for relevant outcome data for efficacy that included stroke or systemic embolization (SSE), and safety including major bleeding and all-cause mortality. Binary outcome data and odds ratios from the relevant articles were used to calculate the pooled relative risk. For SSE, the data from the four Phase III trials showed that DOACs are better or similarly effective with low BMI 0.73 (0.56–0.97), normal BMI 0.72 (0.58–0.91), overweight 0.87 (0.76–0.99), and obese 0.87 (0.76–1.00). The risk of major bleeding was also better or similar with DOACs in all BMI subgroups with low BMI 0.62 (0.37–1.05), normal BMI 0.72 (0.58–0.90), overweight 0.83 (0.71–0.96), and obese 0.91 (0.81–1.03). There was no impact on mortality in all the subgroups. In a meta-regression analysis, the effect size advantage of DOACs compared with warfarin in terms of safety and efficacy gradually attenuated with increasing weight.

Conclusion
Our findings suggest that a weight-based dosage adjustment may be necessary to achieve optimal benefits of DOACs for thromboembolic prevention in these patients with non-valvular atrial fibrillation. Further dedicated trials are needed to confirm these findings. PROSPERO 2019 CRD42019140693. Available from: https://www.crd.york.ac.uk/prospero/display_record.php? ID=CRD42019140693.
Ecology and physiology of halophilic microorganisms – Thematic issue based on papers presented at Halophiles 2019 – 12th International Conference on Halophilic Microorganisms, Cluj-Napoca, Romania, 24–28 June, 2019
Authors: Banciu Horia L , Enache Mădălin , Rodriguez Rafael Montalvo , Oren Aharon , Ventosa Antonio 
Published: December 2019

ABSTRACT
In June 2019, the 12th International Conference on Halophilic Microorganisms – Halophiles 2019, was held in Cluj-Napoca, Romania. This thematic issue of FEMS Microbiology Letters contains papers based on lectures and posters presented at the conference. We here provide a short overview of past research on hypersaline environments in Romania and the microorganisms inhabiting them, and briefly present the papers published in this thematic issue.
The Roles of Body Composition and Specific Strength in the Relationship Between Race and Physical Performance in Older Adults
Authors: Chiles Shaffer Nancy , Simonsick Eleanor M , Thorpe Roland J , Studenski Stephanie A 
Published: December 2019

Abstract

Background
Socioeconomics may explain black–white differences in physical performance; few studies examine racial differences among socioeconomically similar groups. Performance is also affected by body composition and specific strength, which differ by race. We assessed whether racial differences in physical performance exist among older adults with high education and similar income and whether body composition and specific strength attenuate observed differences.

Methods
Cross-sectional analysis of 536 men (18% black) and 576 women (28% black) aged more than 60 years from the Baltimore Longitudinal Study of Aging. Body composition was evaluated using dual-energy x-ray absorptiometry. Specific strength was assessed by quadricep peak torque divided by height-normalized thigh cross-sectional area and grip strength divided by body mass index-normalized appendicular lean mass. Physical performance was assessed using usual gait speed and fast 400 m walk time. Sex-stratified linear regression models, adjusted for age, height, education, and recent income, determined whether body composition or specific strength attenuated associations between race and physical performance.

Results
Blacks were younger, with higher weight and appendicular lean mass. Black women had higher percent fat and specific strength. In both sexes, blacks had poorer physical performance after adjustment for socioeconomic factors. In women, neither body composition nor specific strength altered the association with gait speed. In men, neither body composition nor specific strength attenuated racial differences in either performance measure.

Conclusions
Poorer physical performance among black compared to white older adults persists among persons with high education and similar income and cannot generally be attributed to differences in body composition or specific strength.