bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective Evaluation of Health-Related Quality of Life in Patients Undergoing Anterolateral Craniofacial Resection with Orbital Exenteration
Authors: Mukoyama Nobuaki , Nishio Naoki , Kimura Hiroyuki , Kishi Shinichi , Tokura Tatsuya , Kimura Hiroki , Hiramatsu Mariko , Maruo Takashi , Tsuzuki Hidenori , Fujii Masazumi , Iwami Kenichiro , Takanari Keisuke , Kamei Yuzuru , Ozaki Norio , Sone Michihiko , Fujimoto Yasushi 
Published: July 2019

Objective This study was aimed to evaluate health-related quality of life in patients undergoing anterolateral craniofacial resection (AL-CFR) with orbital exenteration (OE) for malignant skull base tumors and to investigate the effects of early psychiatric intervention.Design Present study is a prospective, observational study.Setting The study took place at the hospital department.Participants Twenty-six consecutive patients were selected who underwent AL-CFR with OE at our hospital between 2005 and 2015.Main Outcome Measures Health-related quality of life was assessed preoperatively and 3, 6, 12, and 24 months after surgery using the Hospital Anxiety and Depression Scale (HADS) and medical outcomes study 8-items Short Form health survey (SF-8). In all cases, psychiatric intervention was organized by the consultation liaison psychiatry team preoperatively and postoperatively.Results Ten (38.0%) of the 26 patients died and 16 (62.0%) were alive and disease-free at the end of the study. The 3-year overall and disease-free survival rates were 64.9% and 53.3%, respectively. Twenty-one patients (80.8%) developed psychiatric complications after surgery and needed treatment with psychotropic medication. Before surgery, 28% of patients had HADS scores ≥8 for anxiety and 20% had scores ≥8 for depression. Seven of the eight items in the SF-8 were significantly lower than those for the general Japanese population. However, scores for all the SF-8 items gradually improved during postoperative follow-up, reaching approximately 50 points, which is the national standard value, at 2 years after surgery.Conclusions Craniofacial resection with OE was feasible and well tolerated in patients with malignant skull base tumors who received early psychiatric intervention to decrease the considerable psychological impact of this procedure.
Assembling multidomain protein structures through analogous global structural alignments
Authors: Zhou Xiaogen , Hu Jun , Zhang Chengxin , Zhang Guijun , Zhang Yang 
Published: July 2019

SignificanceMore than 80% of eukaryotic proteins and 67% of prokaryotic proteins contain multiple domains. Due to the technical difficulties in structural biology, however, 65.3% of solved proteins in the Protein Data Bank contain only single-domain structures. Similarly, most computational approaches are optimized for single-domain structure predictions. We propose a pipeline for assembling domain models into full-length structures with interdomain orientations constrained by an analogous structure alignment search. Large-scale benchmark tests showed an unprecedented ability of DEMO in modeling multidomain structures, with a success rate significantly beyond that of the state-of-the-art approaches built on linker modeling. This development helps bridge the significant gap between the increasingly improved ability of individual domain structure determination and the extremely high demands of community for multidomain structure models.
Rhetorical strategies in PhD conclusions of computer
science
Authors: Soler-Monreal Carmen 
Published: July 2019

Abstract
This study investigates the predominant moves and move patterns
used in the separate final conclusion chapters of 48 PhD theses of computer
science at a UK university. The focus is on the most salient connections of
steps in the review of the study (Move 1) with steps for the consolidation
of research space (Move 2). The most common combinations relate (1) a
summary of the thesis work to the product and the evaluation of the product, (2)
the purpose, thesis statement or hypothesis to the findings or results, (3) the
research questions to the methodology, product or claim, (4) a problem or need
to a specific methodology, a new product and/or a claim, and (5) a summary of
the work done in each thesis chapter to the findings and claims. Some findings
are specific of the field of computer science. The study has pedagogical
implications for courses of English for Academic Purposes (EAP).
El papel del oyente en la adquisición de la competencia
conversacional en ELE
Authors: Pascual Escagedo Consuelo 
Published: July 2019

Resumen
En este artículo, proponemos una secuencia didáctica dirigida a
estudiantes italianos de nivel C1 centrada en el papel del oyente activo en la
conversación. Los estudios llevados a cabo hasta hoy en el campo de la
Lingüística Aplicada a la enseñanza de lenguas extranjeras y siguiendo los
presupuestos del Análisis de la Conversación, coinciden en que los estilos
conversacionales varían según las lenguas y las culturas. De la revisión
bibliográfica realizada se desprende que se hace necesaria la enseñanza
explícita de diferentes mecanismos conversacionales. Por ello, hemos diseñado
una propuesta didáctica, dividida en cuatro fases (presentación, práctica
controlada, práctica libre y evaluación de las prácticas), que pretende fomentar
la adquisición/aprendizaje de la competencia conversacional atendiendo al papel
del oyente en la interacción, basada en el estudio de las funciones de los
turnos de apoyo verbales.
Trajectory analysis of few-cycle strong field ionization in two-color circularly polarized fields*
Authors: Huang Yan , Qin Chaochao , Zhang Yizhu , Wang Xincheng , Yan Tian-Min , Jiang Yuhai 
Published: July 2019

Abstract
Bichromatic circularly polarized fields provide a useful tool to probe the ionization dynamics. In this work, we compare the photoelectron momentum distribution in few-cycle bichromatic field of different helicities. The spectral features are analyzed with semiclassical trajectories derived from the strong field approximation. In particular, the interference fringes in momentum distribution are investigated by tracking the ionization time and tunneling exits of released photoelectrons. Different types of trajectories that contribute to the interference fringes are elucidated.
Influence of intraband motion on the interband excitation and high harmonic generation*
Authors: Zuo Rui-Xin , Song Xiao-Hong , Liu Xi-Wang , Yang Shi-Dong , Yang Wei-Feng 
Published: July 2019

Abstract
Tunnelling, acceleration, and collision of electrons are the basic events in the process of high harmonic generation (HHG) in strong-field interaction with atoms. However, the periodic array of atoms in semiconductor structure makes three steps become interatomic coherent process which leads to complicated carrier dynamics and two sources of high harmonic emission: interband polarization and intraband current. The difference of features of high harmonic generation between semiconductors and atoms is strongly linked to the unique presence of intraband motion which manifests itself a nontrivial role in intertwined two dynamics. Here, we review recent experimental and theoretical advances of understanding coupled interband and intraband mechanisms of HHG in semiconductors. Particularly we focus on the influence of intraband motion on the interband excitation, and on the subsequent HHG emission and attosecond pulse generation.
Dynamical properties of ultracold Bose atomic gases in one-dimensional optical lattices created by two schemes*
Authors: Zhu Jiang , Bian Cheng-Ling , Wang Hong-Chen 
Published: July 2019

Abstract
An optical lattice could be produced either by splitting an input light (splitting scheme) or by reflecting the input light by a mirror (retro-reflected scheme). We study quantum dynamical properties of an atomic Bose–Einstein condensate (BEC) in the two schemes. Adopting a mean field theory and neglecting collision interactions between atoms, we find that the momentum and spatial distributions of BEC are always symmetric in the splitting scheme which, however, are asymmetric in the retro-reflected scheme. The reason for this difference is due to the local field effect. Furthermore, we propose an effective method to avoid asymmetric diffraction.
Self-repair of the Lepidopteran Proboscis
Authors: Pometto Suellen F , Beard Charles E , Gerard Patrick D , Kornev Konstantin G , Adler Peter H 
Published: July 2019

AbstractSelf-repair in the animal world typically involves regeneration of body parts. We present an example featuring the proboscis of butterflies and moths, which after separation of the galeae, undergoes nonregenerative repair. We demonstrated the ability of representative species to completely reunite (repair) the proboscis after total separation of the two galeae, and we showed that the repaired proboscis can take up fluid. Movements of the proboscis during repair were similar to the initial proboscis assembly after emergence from the pupa. We tested the influence of labial palps, wing movements, coiling, and fluid immersion on self-repair. These factors showed no statistically significant influence on the ability to repair the proboscis, with the exception of wing movements in one species. We suggest that the major selection forces driving assembly and repair have been the need to insert the proboscis into restricted openings of floral tubes to obtain nectar and the need for a united, compactly coiled proboscis to reduce air resistance during flight.
Large Hind Wings Enhance Gliding Performance in Ground Effect in a Neotropical Butterfly (Lepidoptera: Nymphalidae)
Authors: Stylman Marc , Penz Carla M , DeVries Phil 
Published: July 2019

AbstractNeotropical butterflies in the nymphalid genera Pierella Herrich-Schäffer, 1865 (Lepidoptera, Nymphalidae) and Cithaerias Hübner, 1819 (Lepidoptera, Nymphalidae) are known to glide near ground level, and have a high forewing aspect ratio. The hind wings of Pierella are proportionately larger than those of Cithaerias, suggesting a potential role in gliding flight. We show that Pierella helvina (Hewitson, 1860) (Lepidoptera, Nymphalidae) is capable of gliding for longer periods of time than Cithaerias pireta (Stoll, 1780) (Lepidoptera, Nymphalidae) both in the field and a laboratory setting. Experimental reduction of hind wing area in P. helvina led to a decrease in male gliding performance, and an increase in female wing-beat frequency. We also found that escape velocity decreased in both sexes after hind wing area reduction, but the effect was strongest in females. Although the increased drag associated with large hind wings could be detrimental to gliding flight, the large hind wing area of P. helvina effectively enhances gliding performance in ground effect. This study is the first to investigate the role of hind wings on butterfly gliding performance.
Ultrastructural Characteristics of Gallbladder Epithelial Inclusions Mimicking Cystoisospora
Authors: Gopinath Arun , Mubeen Aysha , Baskovich Brett , Ginn Amber , Shukri Amal , Menes Manual , Kenneth Keyler , Makary Raafat , Herrera Guillermo A , Masood Shahla , Alkhasawneh Ahmad 
Published: July 2019

Abstract

Objectives
There is recently reported increased prevalence of Isospora organisms in cholecystectomy specimens from immunocompetent patients, especially in acalculous cholecystectomies. We performed an ultrastructural and molecular evaluation of these specimens.

Methods
From 28 gallbladders with intraepithelial inclusions, two specimens with diffuse involvement of the gallbladder epithelium were analyzed by electron microscopy. Polymerase chain reaction was performed on five samples for the ITS2 region of C belli and eukaryotic 18S region. The 18S products were sequenced by next-generation sequencing.

Results
Electron microscopic analysis showed cytoplasmic condensations leading to vacuole formation. In contrast with true C belli, there were no identifiable organelles or organization. None of these cases showed amplified products other than human on molecular analysis.

Conclusions
Electron microscopic analysis demonstrates that the inclusions are condensed cytoplasmic material and not true organisms.
Metabolome-Wide Association Study of the Relationship Between Habitual Physical Activity and Plasma Metabolite Levels
Authors: Ding Ming , Zeleznik Oana A , Guasch-Ferre Marta , Hu Jie , Lasky-Su Jessica , Lee I-Min , Jackson Rebecca D , Shadyab Aladdin H , LaMonte Michael J , Clish Clary , Eliassen A Heather , Sacks Frank , Willett Walter C , Hu Frank B , Rexrode Kathryn M , Kraft Peter 
Published: July 2019

Abstract
We identified plasma metabolites associated with habitual physical activity among 5,197 US participants from the Nurses’ Health Study (NHS), Nurses’ Health Study II (NHS II), and the Health Professionals Follow-up Study (HPFS). Physical activity was assessed every 2–4 years via self-report questionnaires. Blood was collected in the NHS in 1989–1990, in NHS II during 1996–1999, and in the HPFS during 1993–1995. Metabolic profiling was conducted by liquid chromatography–mass spectrometry. Our study included 337 known metabolites, with 256 of them classified as lipids. We corrected for multiple testing by controlling the tail probability of the proportion of false positives (TPPFP) and accounted for correlated tests using bootstrapping. Physical activity was significantly associated with 20 metabolites after correction for multiple testing (TPPFP < 0.05), and positive associations were found for most of the metabolites, including 2 amino acids (citrulline and glycine), 4 cholesteryl esters (C18:2, C18:1, C16:0, C18:3), 8 phosphocholines (PCs) (C36:4 PC-A, C34:3 PC plasmalogen, C36:3 PC plasmalogen, C34:2 PC plasmalogen, C36:2 PC) and lysophosphatidylcholines (C18:2, C20:5, C18:1), and 3 phosphatidylethanolamines (PEs) (C38:3 PE plasmalogen) and lysophosphatidylethanolamines (C18:2, C18:1). We independently replicated the 20 metabolites among 2,305 women in the Women’s Health Initiative using 1993 data, and half of the metabolites were replicated. Our study may help identify biomarkers of physical activity and provide insight into biological mechanisms underlying the beneficial effect of being physically active on cardiometabolic health.
The costs and benefits of decentralization and centralization of ant colonies
Authors: Burns Dominic D R , Pitchford Jon W , Parr Catherine L , Franks Daniel W , Robinson Elva J H 
Published: July 2019

Abstract
A challenge faced by individuals and groups of many species is determining how resources and activities should be spatially distributed: centralized or decentralized. This distribution problem is hard to understand due to the many costs and benefits of each strategy in different settings. Ant colonies are faced by this problem and demonstrate two solutions: 1) centralizing resources in a single nest (monodomy) and 2) decentralizing by spreading resources across many nests (polydomy). Despite the possibilities for using this system to study the centralization/decentralization problem, the trade-offs associated with using either polydomy or monodomy are poorly understood due to a lack of empirical data and cohesive theory. Here, we present a dynamic network model of a population of ant nests which is based on observations of a facultatively polydomous ant species (Formica lugubris). We use the model to test several key hypotheses for costs and benefits of polydomy and monodomy and show that decentralization is advantageous when resource acquisition costs are high, nest size is limited, resources are clustered, and there is a risk of nest destruction, but centralization prevails when resource availability fluctuates and nest size is limited. Our model explains the phylogenetic and ecological diversity of polydomous ants, demonstrates several trade-offs of decentralization and centralization, and provides testable predictions for empirical work on ants and in other systems.
Flexible polyandry in female flies is an adaptive response to infertile males
Authors: Sutter Andreas , Travers Laura M , Oku Keiko , L. Delaney Kynan , J. Store Stefan , Price Tom A R , Wedell Nina 
Published: July 2019

AbstractInfertility is common in nature despite its obvious cost to individual fitness. Rising global temperatures are predicted to decrease fertility, and male sterility is frequently used in attempts to regulate pest or disease vector populations. When males are infertile, females may mate with multiple males to ensure fertilization, and changes in female mating behavior in turn could intensify selection on male fertility. Fertility assurance is a potentially wide-spread explanation for polyandry, but whether and how it actually contributes to the evolution of polyandry is not clear. Moreover, whether a drop in male fertility would lead to a genetic increase in polyandry depends on whether females respond genetically or through behavioral plasticity to male infertility. Here, we experimentally manipulate male fertility through heat-exposure in Drosophila pseudoobscura, and test female discrimination against infertile males before and after mating. Using isogenic lines, we compare the roles of behaviorally plastic versus genetically fixed polyandry. We find that heat-exposed males are less active and attractive, and that females are more likely to remate after mating with these males. Remating rate increases with reduced reproductive output, indicating that females use current sperm storage threshold to make dynamic remating decisions. After remating with fertile males, females restore normal fecundity levels. Our results suggest that male infertility could explain the evolution of adaptively flexible polyandry, but is less likely to cause an increase in genetic polyandry.
Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity
Authors: Schneider Melanie , Pons Jean-Luc , Bourguet William , Labesse Gilles 
Published: July 2019

Abstract

Motivation
Nowadays, virtual screening (VS) plays a major role in the process of drug development. Nonetheless, an accurate estimation of binding affinities, which is crucial at all stages, is not trivial and may require target-specific fine-tuning. Furthermore, drug design also requires improved predictions for putative secondary targets among which is Estrogen Receptor alpha (ERα).

Results
VS based on combinations of Structure-Based VS (SBVS) and Ligand-Based VS (LBVS) is gaining momentum to improve VS performances. In this study, we propose an integrated approach using ligand docking on multiple structural ensembles to reflect receptor flexibility. Then, we investigate the impact of the two different types of features (structure-based and ligand molecular descriptors) on affinity predictions using a random forest algorithm. We find that ligand-based features have lower predictive power (rP = 0.69, R2 = 0.47) than structure-based features (rP = 0.78, R2 = 0.60). Their combination maintains high accuracy (rP = 0.73, R2 = 0.50) on the internal test set, but it shows superior robustness on external datasets. Further improvement and extending the training dataset to include xenobiotics, leads to a novel high-throughput affinity prediction method for ERα ligands (rP = 0.85, R2 = 0.71). The presented prediction tool is provided to the community as a dedicated satellite of the @TOME server in which one can upload a ligand dataset in mol2 format and get ligand docked and affinity predicted.

Availability and implementation
http://edmon.cbs.cnrs.fr.

Supplementary information
Supplementary data are available at Bioinformatics online.
BioNorm: deep learning-based event normalization for the curation of reaction databases
Authors: Lou Peiliang , Jimeno Yepes Antonio , Zhang Zai , Zheng Qinghua , Zhang Xiangrong , Li Chen 
Published: July 2019

Abstract

Motivation
A biochemical reaction, bio-event, depicts the relationships between participating entities. Current text mining research has been focusing on identifying bio-events from scientific literature. However, rare efforts have been dedicated to normalize bio-events extracted from scientific literature with the entries in the curated reaction databases, which could disambiguate the events and further support interconnecting events into biologically meaningful and complete networks.

Results
In this paper, we propose BioNorm, a novel method of normalizing bio-events extracted from scientific literature to entries in the bio-molecular reaction database, e.g. IntAct. BioNorm considers event normalization as a paraphrase identification problem. It represents an entry as a natural language statement by combining multiple types of information contained in it. Then, it predicts the semantic similarity between the natural language statement and the statements mentioning events in scientific literature using a long short-term memory recurrent neural network (LSTM). An event will be normalized to the entry if the two statements are paraphrase. To the best of our knowledge, this is the first attempt of event normalization in the biomedical text mining. The experiments have been conducted using the molecular interaction data from IntAct. The results demonstrate that the method could achieve F-score of 0.87 in normalizing event-containing statements.

Availability and implementation
The source code is available at the gitlab repository https://gitlab.com/BioAI/leen and BioASQvec Plus is available on figshare https://figshare.com/s/45896c31d10c3f6d857a.
Haplotype-aware graph indexes
Authors: Sirén Jouni , Garrison Erik , Novak Adam M , Paten Benedict , Durbin Richard 
Published: July 2019

Abstract

Motivation
The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes.

Results
We augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows–Wheeler transform. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.

Availability and implementation
Our software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt and https://github.com/jltsiren/gcsa2.

Supplementary information
Supplementary data are available at Bioinformatics online.