bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Homeopathic Medicines on Intestinal Coccidia and Immune Response Cells in Spotted Rose Snapper (Lutjanus guttatus)
Authors: Rosero-García Antonia del Pilar , Mazón-Suástegui José Manuel , Dumas Silvie , Chávez-Sánchez María Cristina , Avilés-Quevedo Araceli , Rodríguez-Jaramillo Carmen 
Published: April 2019

Background Homeopathy has been widely applied in freshwater species but rarely in marine fish. Farm stress destabilises host–pathogen equilibrium, favouring parasites and disease. Coccidian endoparasites cause intestinal infections and cell degeneration.
Materials and Methods Naturally parasite-infested juvenile snapper Lutjanus guttatus (n = 430; weight 1.9 ± 0.01 g; length 4.9 ± 0.03 cm) specimens were distributed in group sizes of 43, in 10 fiberglass tanks (100 L) with aeration and continuous water change. Five groups in duplicate were assessed: Passival (PaV); Passival and Phosphoricum acid Similia (PaV–PhA); Passival and Silicea terra Similia (PaV–SiT); Endecto and Infecçoes (End–Inf) and a control (Ethanol) for 45 days. Feed was sprinkled with treatment (5% v/w) and dried to avoid ethanol side-effects. Statistical results were expressed as mean ± standard error of the mean.
Results Intestinal coccidia were recorded histopathologically, with the least incidence attained at T45 with End–Inf treatment (p < 0.001), coinciding with the highest lymphocyte (p = 0.015) count. Fish treated with PaV–PhA recorded a higher percentage of neutrophils (p = 0.015), and those treated with PaV–PhA, PaV–SiT and End–Inf revealed a decrease in lesions, degree of alteration and change in intestine and stomach tissues (p < 0.05). The number of mucous cells in gills was greater (p < 0.001) for End–Inf (43 ± 0.58), PaV–SiT (40 ± 2.89) and PaV–PhA (39 ± 3.46) as compared respectively with T0 and control (19 ± 0.58 and 28 ± 2.31). PaV and PaV–SiT increased carbohydrate reserves in liver (28.4 ± 1.39% and 22.4 ± 0.12%, respectively) compared with T0 and control (3.4 ± 0.32 and 5.6 ± 0.66%). The highest survival rate was 97.7 ± 0.16% in fish treated with PaV and End–Inf.
Conclusion Homeopathic treatments had a positive effect on fish health. Besides the accumulation of metabolic reserves in the liver, homeopathic treatment was associated with mucin increase in gills as well as raised production of lymphocytes and neutrophils in blood, which could act as macrophages against intestinal coccidia.
Climate models can correctly simulate the continuum of global-average temperature variability
Authors: Zhu Feng , Emile-Geay Julien , McKay Nicholas P. , Hakim Gregory J. , Khider Deborah , Ault Toby R. , Steig Eric J. , Dee Sylvia , Kirchner James W. 
Published: April 2019

SignificanceClimate models are foundational to formulations of climate policy and must successfully reproduce key features of the climate system. The temporal spectrum of observed global surface temperature is one such critical benchmark. This spectrum is known to obey scaling laws connecting astronomical forcings, from orbital to annual scales. We provide evidence that the current hierarchy of climate models is capable of reproducing the increase in variance in global-mean temperature at low frequencies. We suggest that successful climate predictions at decadal-to-centennial horizons hinge critically on the accuracy of initial and boundary conditions, particularly for the deep ocean state.
Causal inference accounts for heading perception in the presence of object motion
Authors: Dokka Kalpana , Park Hyeshin , Jansen Michael , DeAngelis Gregory C. , Angelaki Dora E. 
Published: April 2019

Significance
A moving observer faces an interpretational challenge when the visual scene contains independently moving objects. To correctly judge their direction of self-motion (heading), an observer must appropriately infer the causes of retinal image motion. We demonstrate that perception of object motion systematically influences heading judgments. When a moving object was erroneously perceived to be stationary in the world, heading judgments were significantly biased. On the contrary, when the object was correctly perceived to be moving, biases in heading estimates declined dramatically. Our results thus suggest that the brain makes inferences about sources of image motion using causal inference computations.
Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity
Authors: Stratford James P. , Edwards Conor L. A. , Ghanshyam Manjari J. , Malyshev Dmitry , Delise Marco A. , Hayashi Yoshikatsu , Asally Munehiro 
Published: April 2019

Significance
Transmembrane voltage in bacteria plays a central role both in electrical signaling and cell proliferation. However, whether proliferation state influences the response to electrical signals was unknown. Combining fluorescence time-lapse microscopy with a bespoke device and mathematical modeling, we show that proliferative and inhibited cells respond in opposite directions to an identical electrical signal. The response differentiation can be seen within a minute after stimulation. Therefore, our findings offer an approach for rapid detection of proliferative bacteria at the single-cell level.
Topic prominence in L2 acquisition
Authors: Gong Zhiqi 
Published: April 2019

AbstractThis study investigated the topic-prominent characteristics of the interlanguage development of native speakers of Chinese learning English as a foreign language (EFL). Two groups of Chinese EFL learners – an intermediate group and an advanced group – were recruited to complete two production tasks: a written Chinese-to-English translation task and an oral story-retelling task. The findings showed that Chinese EFL learners at each proficiency level transferred Chinese topic-prominent structures to their target language production at a varying degree. The topic-prominent constructions in the learners’ production, based on a hierarchy of difficulty, were placed on two slightly different Gradation Zones, one for written production and the other for oral production. Gradation Zones were a generalized reflection of how discourse and pragmatic relations in topic-prominent Chinese were gradually reanalyzed as syntactic relations with the development of learners’ English proficiency level. There was a tendency for topic-prominent features to decrease and subject-prominent features to increase as EFL learners’ proficiency level progressed. It was also argued that sources of these topic-prominent properties in interlanguage were an interaction of factors, including degree of markedness, perceptual saliency, second language (L2) input, and language production task type.
Optimal Facelift Vector and its Relation to Zygomaticus Major Orientation
Authors: Jacono Andrew A , Bryant Lucas M , Alemi A Sean 
Published: April 2019

Abstract

Background
The vector of superficial musculoaponeurotic system (SMAS) redraping in rhytidectomy is often described in relation to the zygomaticus major muscle (ZMM), so that suspension prevents distortion of the mimetic musculature and a “facelifted appearance.” There are no data describing the true orientation of this muscle in the midface.

Objectives
The aim of this study was to define the vector of the ZMM relative to the Frankfort horizontal plane.

Methods
One hundred patients underwent deep plane rhytidectomy. As part of this procedure the tissues overlying the ZMM are elevated, allowing muscle orientation to be measured as an angle relative to the Frankfort horizontal plane.

Results
Data for 200 hemifaces were aggregated. The average ZMM angle was 59° (standard deviation, 6°; range, 41–72°) relative to the Frankfort horizontal plane, and showed a statistically significant pattern of change with advancing age, becoming more acute with increasing age below the age of 60 years and more obtuse with age over 60 years.

Conclusions
The native vector of the ZMM varies significantly between rhytidectomy patients as demonstrated by the high variance in this cohort. Assumptions about its orientation should not be made in rhytidectomy techniques that do not identify its course. Standard vectors of SMAS redraping, such as superior-lateral, vertically oblique, and purely vertical, should be reconsidered and a customized vector implemented in each case. Aging affects the orientation of the muscle, which can potentially be explained by soft tissue and bony changes at its attachments. This furthers the variability of the SMAS vector in each individual case.

Level of Evidence: 4
Continuous-state HMMs for modeling time-series single-cell RNA-Seq data
Authors: Lin Chieh , Bar-Joseph Ziv 
Published: April 2019

AbstractMotivationMethods for reconstructing developmental trajectories from time-series single-cell RNA-Seq (scRNA-Seq) data can be largely divided into two categories. The first, often referred to as pseudotime ordering methods are deterministic and rely on dimensionality reduction followed by an ordering step. The second learns a probabilistic branching model to represent the developmental process. While both types have been successful, each suffers from shortcomings that can impact their accuracy.ResultsWe developed a new method based on continuous-state HMMs (CSHMMs) for representing and modeling time-series scRNA-Seq data. We define the CSHMM model and provide efficient learning and inference algorithms which allow the method to determine both the structure of the branching process and the assignment of cells to these branches. Analyzing several developmental single-cell datasets, we show that the CSHMM method accurately infers branching topology and correctly and continuously assign cells to paths, improving upon prior methods proposed for this task. Analysis of genes based on the continuous cell assignment identifies known and novel markers for different cell types.Availability and implementationSoftware and Supporting website: www.andrew.cmu.edu/user/chiehl1/CSHMM/Supplementary informationSupplementary data are available at Bioinformatics online.
Dynamical important residue network (DIRN): network inference via conformational change
Authors: Li Quan , Luo Ray , Chen Hai-Feng 
Published: April 2019

Abstract

Motivation
Protein residue interaction network has emerged as a useful strategy to understand the complex relationship between protein structures and functions and how functions are regulated. In a residue interaction network, every residue is used to define a network node, adding noises in network post-analysis and increasing computational burden. In addition, dynamical information is often necessary in deciphering biological functions.

Results
We developed a robust and efficient protein residue interaction network method, termed dynamical important residue network, by combining both structural and dynamical information. A major departure from previous approaches is our attempt to identify important residues most important for functional regulation before a network is constructed, leading to a much simpler network with the important residues as its nodes. The important residues are identified by monitoring structural data from ensemble molecular dynamics simulations of proteins in different functional states. Our tests show that the new method performs well with overall higher sensitivity than existing approaches in identifying important residues and interactions in tested proteins, so it can be used in studies of protein functions to provide useful hypotheses in identifying key residues and interactions.

Supplementary information
Supplementary data are available at Bioinformatics online.
The lipid flippase subunit Cdc50 is required for antifungal drug resistance, endocytosis, hyphal development and virulence inCandida albicans
Authors: Xu Dayong , Zhang Xing , Zhang Biao , Zeng Xin , Mao Hongchen , Xu Haitao , Jiang Linghuo , Li Feng 
Published: April 2019

ABSTRACTCdc50 is the non-catalytic subunit of the flippase that establishes phospholipid asymmetry in membranes and functions in vesicle-mediated trafficking in Saccharomyces cerevisiae. Here, we have identified the homologous gene CaCDC50 that encodes a protein of 396 amino acids with two conserved transmembrane domains in Candidaalbicans. Deletion of CaCDC50 results in C. albicans cells becoming sensitive to the antifungal drugs azoles, terbinafine and caspofungin, as well as to the membrane-perturbing agent sodium dodecyl sulfate. We also show that CaCDC50 is involved in both endocytosis and vacuolar function. CaCDC50 confers tolerance to high concentrations of cations, although it is not required for osmolar response. Moreover, deletion of CaCDC50 leads to severe defects in hyphal development of C. albicans cells and highly attenuated virulence in the mouse model of systemic infection. Therefore, CaCDC50 regulates cellular responses to antifungal drugs, cell membrane stress, endocytosis, filamentation and virulence in the human fungal pathogen C. albicans.
Social media and e-learning use among European exercise science students
Authors: Rigamonti L , Dolci A , Galetta F , Stefanelli C , Hughes M , Bartsch M , Seidelmeier I , Bonaventura K , Back D A 
Published: April 2019

Abstract
With the rise of digital technologies, electronic learning and communication tools are becoming a firm part of academia to promote knowledge of health sciences. This study sought to analyse the attitude of students regarding social media and digital learning for study purposes in sport and exercise science. A survey was carried out with a questionnaire (20 main items) in six sport science faculties, equally spread across Germany (G), Italy (I) and the United Kingdom (UK) between February and October 2017. The focus areas were students’ usage of social media (Facebook, Google+, Instagram, LinkedIn, Skype, Twitter, WhatsApp, YouTube) for academic purposes and their use of e-learning. Data were analysed by quantitative and qualitative methods. 229 students participated in the study (G: 68, I: 121, UK: 40). While YouTube was mostly used for receiving knowledge, WhatsApp and Facebook showed additional preferences for peer contacts for learning purposes and knowledge discussions. Preferred online data sources were PubMed (77%), free access journals (67%), YouTube (66%) and Wikipedia (63%). Often used digital learning materials were own universities’ PowerPoints (77%), scripts (59%) and scientific articles (53%). However, some preferences showed national differences. The evaluated participants showed an overall high use of social media and e-learning tools for their studies. Students would like more digital learning sources made available to them by their institutions. However, some differences in preferences of digital learning or communication tools may exist and this should be considered for international approaches to promote health knowledge among students.
A study of deep learning approaches for medication and adverse drug event extraction from clinical text
Authors: Wei Qiang , Ji Zongcheng , Li Zhiheng , Du Jingcheng , Wang Jingqi , Xu Jun , Xiang Yang , Tiryaki Firat , Wu Stephen , Zhang Yaoyun , Tao Cui , Xu Hua 
Published: April 2019

AbstractObjectiveThis article presents our approaches to extraction of medications and associated adverse drug events (ADEs) from clinical documents, which is the second track of the 2018 National NLP Clinical Challenges (n2c2) shared task.Materials and MethodsThe clinical corpus used in this study was from the MIMIC-III database and the organizers annotated 303 documents for training and 202 for testing. Our system consists of 2 components: a named entity recognition (NER) and a relation classification (RC) component. For each component, we implemented deep learning-based approaches (eg, BI-LSTM-CRF) and compared them with traditional machine learning approaches, namely, conditional random fields for NER and support vector machines for RC, respectively. In addition, we developed a deep learning-based joint model that recognizes ADEs and their relations to medications in 1 step using a sequence labeling approach. To further improve the performance, we also investigated different ensemble approaches to generating optimal performance by combining outputs from multiple approaches.ResultsOur best-performing systems achieved F1 scores of 93.45% for NER, 96.30% for RC, and 89.05% for end-to-end evaluation, which ranked #2, #1, and #1 among all participants, respectively. Additional evaluations show that the deep learning-based approaches did outperform traditional machine learning algorithms in both NER and RC. The joint model that simultaneously recognizes ADEs and their relations to medications also achieved the best performance on RC, indicating its promise for relation extraction.ConclusionIn this study, we developed deep learning approaches for extracting medications and their attributes such as ADEs, and demonstrated its superior performance compared with traditional machine learning algorithms, indicating its uses in broader NER and RC tasks in the medical domain.
Significant influence of lignin on axial elastic modulus of poplar wood at low microfibril angles under wet conditions
Authors: Özparpucu Merve , Gierlinger Notburga , Cesarino Igor , Burgert Ingo , Boerjan Wout , Rüggeberg Markus 
Published: April 2019

Abstract
Wood is extensively used as a construction material. Despite increasing knowledge of its mechanical properties, the contribution of the cell-wall matrix polymers to wood mechanics is still not well understood. Previous studies have shown that axial stiffness correlates with lignin content only for cellulose microfibril angles larger than around 20°, while no influence is found for smaller angles. Here, by analysing the wood of poplar with reduced lignin content due to down-regulation of CAFFEOYL SHIKIMATE ESTERASE, we show that lignin content also influences axial stiffness at smaller angles. Micro-tensile tests of the xylem revealed that axial stiffness was strongly reduced in the low-lignin transgenic lines. Strikingly, microfibril angles were around 15° for both wild-type and transgenic poplars, suggesting that cellulose orientation is not responsible for the observed changes in mechanical behavior. Multiple linear regression analysis showed that the decrease in stiffness was almost completely related to the variation in both density and lignin content. We suggest that the influence of lignin content on axial stiffness may gradually increase as a function of the microfibril angle. Our results may help in building up comprehensive models of the cell wall that can unravel the individual roles of the matrix polymers.
Transcript and metabolite changes during the early phase of abscisic acid-mediated induction of crassulacean acid metabolism in Talinum triangulare
Authors: Maleckova Eva , Brilhaus Dominik , Wrobel Thomas J , Weber Andreas P M 
Published: April 2019

AbstractCrassulacean acid metabolism (CAM) has evolved as a water-saving strategy, and its engineering into crops offers an opportunity to improve their water use efficiency. This requires a comprehensive understanding of the regulation of the CAM pathway. Here, we use the facultative CAM species Talinum triangulare as a model in which CAM can be induced rapidly by exogenous abscisic acid. RNA sequencing and metabolite measurements were employed to analyse the changes underlying CAM induction and identify potential CAM regulators. Non-negative matrix factorization followed by k-means clustering identified an early CAM-specific cluster and a late one, which was specific for the early light phase. Enrichment analysis revealed abscisic acid metabolism, WRKY-regulated transcription, sugar and nutrient transport, and protein degradation in these clusters. Activation of the CAM pathway was supported by up-regulation of phosphoenolpyruvate carboxylase, cytosolic and chloroplastic malic enzymes, and several transport proteins, as well as by increased end-of-night titratable acidity and malate accumulation. The transcription factors HSFA2, NF-YA9, and JMJ27 were identified as candidate regulators of CAM induction. With this study we promote the model species T. triangulare, in which CAM can be induced in a controlled way, enabling further deciphering of CAM regulation.
Shearing-box simulations of MRI-driven turbulence in weakly collisional accretion discs
Authors: Kempski Philipp , Quataert Eliot , Squire Jonathan , Kunz Matthew W 
Published: April 2019

ABSTRACT
We present a systematic shearing-box investigation of magnetorotational instability (MRI)-driven turbulence in a weakly collisional plasma by including the effects of an anisotropic pressure stress, i.e. anisotropic (Braginskii) viscosity. We constrain the pressure anisotropy (Δp) to lie within the stability bounds that would be otherwise imposed by kinetic microinstabilities. We explore a broad region of parameter space by considering different Reynolds numbers and magnetic-field configurations, including net vertical flux, net toroidal-vertical flux, and zero net flux. Remarkably, we find that the level of turbulence and angular-momentum transport are not greatly affected by large anisotropic viscosities: the Maxwell and Reynolds stresses do not differ much from the MHD result. Angular-momentum transport in Braginskii MHD still depends strongly on isotropic dissipation, e.g. the isotropic magnetic Prandtl number, even when the anisotropic viscosity is orders of magnitude larger than the isotropic diffusivities. Braginskii viscosity nevertheless changes the flow structure, rearranging the turbulence to largely counter the parallel rate of strain from the background shear. We also show that the volume-averaged pressure anisotropy and anisotropic viscous transport decrease with increasing isotropic Reynolds number (Re); e.g. in simulations with net vertical field, the ratio of anisotropic to Maxwell stress (αA/αM) decreases from ∼0.5 to ∼0.1 as we move from Re ∼ 103 to Re ∼ 104, while 〈4$\pi$Δp/B2〉 → 0. Anisotropic transport may thus become negligible at high Re. Anisotropic viscosity nevertheless becomes the dominant source of heating at large Re, accounting for ${\gtrsim } 50 {{\ \rm per\ cent}}$ of the plasma heating. We conclude by briefly discussing the implications of our results for radiatively inefficient accretion flows on to black holes.
SEanalysis: a web tool for super-enhancer associated regulatory analysis
Authors: Qian Feng-Cui , Li Xue-Cang , Guo Jin-Cheng , Zhao Jian-Mei , Li Yan-Yu , Tang Zhi-Dong , Zhou Li-Wei , Zhang Jian , Bai Xue-Feng , Jiang Yong , Pan Qi , Wang Qiu-Yu , Li En-Min , Li Chun-Quan , Xu Li-Yan , Lin De-Chen 
Published: April 2019

Abstract
Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.