bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectro-astrometry of the pre-transitional star LkCa 15 does not reveal an accreting planet but extended Hα emission
Authors: Mendigutía I. , Oudmaijer R. D. , Schneider P. C. , Huélamo N. , Baines D. , Brittain S. D. , Aberasturi M. 
Published: October 2018

Context. The detection of forming planets in protoplanetary disks around young stars remains elusive, and state-of-the-art observational techniques provide somewhat ambiguous results. The pre-transitional T Tauri star LkCa 15 is an excellent example. It has been reported that it could host three planets; candidate planet b is in the process of formation, as inferred from its Hα emission. However, a more recent work casts doubts on the planetary nature of the previous detections.
Aims. We test the potential of spectro-astrometry in Hα as an alternative observational technique to detect forming planets around young stars, taking LkCa 15 as a reference case Methods. LkCa 15 was observed with the ISIS spectrograph at the 4.2 m William Herschel Telescope (WHT). The slit was oriented towards the last reported position of LkCa 15 b (parallel direction) and 90° from that (perpendicular). The photocenter and full width half maximum (FWHM) of the Gaussians fitting the spatial distribution at Hα and the adjacent continuum were measured. A wellknown binary (GU CMa) was used as a calibrator to test the spectro-astrometric performance of ISIS/WHT.
Results. A consistent spectro-astrometric signature is recovered for GU CMa. However, the photocenter shift predicted for LkCa 15 b is not detected, but the FWHM in Hα is broader than in the continuum for both slit positions. Our simulations show that the photocenter and FWHM observations cannot be explained simultaneously by an accreting planet, but the lack of photocenter shift alone could still be consistent with an emitting planet with contrast ≳5.5 mag in Hα or ≲6 mag in the adjacent continuum. In turn, both spectro-astrometric observations are naturally reproduced from a roughly symmetric Hα emitting region centered on the star and extent comparable to the orbit originally attributed to the planet at several au.
Conclusions. The extended Hα emission around LkCa 15 could be related to a variable disk wind, but additional multi-epoch data and detailed modeling are necessary to understand its physical nature. Optical spectro-astrometry carried out with mid-size telescopes is capable of probing small-scale structures in relatively faint young stars that are not easily accessible with state-of-the-art instrumentation mounted on larger telescopes. Therefore, spectro-astrometry in Hα is able to test the presence of accreting planets and can be used as a complementary technique to survey planet formation in circumstellar disks.
Comparison of Early Measurements of the Distraction Index, Norberg Angle on Distracted View and the Official Radiographic Evaluation of the Hips of 215 Dogs from Two Guide Dog Training Schools
Authors: Taroni Mathieu , Viguier Eric , Pillard Paul , Livet Véronique , Cachon Thibaut , Carozzo Claude , Genevois Jean-Pierre 
Published: October 2018

Objectives The main purpose of this article is to evaluate the correlation between the distraction index (DI) and Norberg angle values in distracted hips (distraction Norberg angle, DNA) at 4 months of age and the official hip score based on the Fédération Cynologique Internationale (FCI) grid at 12 months of age.
Methods For dogs (n = 215) from two guide dog training organizations, the DI and DNA were measured by a single expert on distraction radiographs performed at 4 months of age. The FCI score was determined by the same expert at 12 months of age on a standard hip-extended view.Statistical analysis included receiver operating characteristic curve analysis and concordance correlation coefficient calculation.
Results The mean DI was 0.48, the mean DNA was 86.5° and 59.5% of hips had an A FCI score. The concordance correlation coefficient of DI and DNA was 0.78. The DI threshold for D- and E-scored hips that was associated with the least misclassification was 0.58 (sensitivity [Se] = 0.6, specificity [Sp] = 0.82). The DNA threshold that was associated with the least misclassification was 85° (Se = 0.83, Sp = 0.68).
Clinical Significance DNA has a fair correlation with DI at 4 months and reflects hip passive laxity. D and E FCI scores at 12 months cannot be reliably predicted from the 4 months value of DI or DNA but 96% of hips with DI < 0.58 at 4 months had an A, B or C FCI score at 12 months of age. Similarly, 98% of hips with DNA > 85° at 4 months had an A, B or C FCI score at 12 months of age.
Genetic Depletion of Thromboxane A2/Thromboxane-Prostanoid Receptor Signalling Prevents Microvascular Dysfunction in Ischaemia/Reperfusion Injury
Authors: Chiang Chih-Yao , Chien Chen-Yen , Qiou Wei-Yin , Chang Christopher , Yu I-Shing , Chang Po-Yuan , Chien Chiang-Ting 
Published: October 2018

Objective Activation of thromboxane A2 synthase (TXAS)/thromboxane A2 (TXA2)/thromboxane prostanoid (TP) receptor leads to arterial constriction, platelet aggregation and vascular injury. We attempted to characterize the microvascular dysfunction in ischaemia/reperfusion injury using genetically modified TXAS−/−, TP−/− and TXAS−/−TP−/− mice.
Approach and Results The cardiac micro-circulation and electrocardiograms were evaluated from B6, TXAS−/−, TP−/− and TXAS−/−TP−/− mice in response to intravenous saline, endothelin-1, U46619 (a TXA2 agonist) and myocardial ischaemia/reperfusion injury. Cardiac function was investigated with myocardial permeability, the troponin I concentration and the infarct size. Myocardial TXAS, TP, endothelial nitric oxide (NO) synthase (eNOS), nicotinamide adenine dinucleotide phosphate oxidase 4 (NOx4), 4-hydroxynonenal, interleukin (IL)-1β, cell apoptosis, coronary effluent thromboxane B2 (TXB2) and superoxide anions (O2
−) and NO concentrations were measured. Mice mesenteric reactivity in response to various drugs was assessed by wire myography. In vivo fluorescent platelet adhesiveness to the mesenteric arterial endothelium after FeCl3 stimulation was examined. In B6 mice, ischaemia/reperfusion significantly increased levels of ST-segment elevation, myocardial TXAS, TP, NOx4, IL-1β, apoptosis, coronary endothelin-1, TXB2, O2
− release and the infarct size, with concomitant decreases in eNOS, NO concentrations and cardiac micro-circulation. These effects were remarkably depressed in TXAS−/−, TP−/− and TXAS−/−TP−/− mice. Aspirin treatment or depletion of the TXAS, TP or TXAS/TP gene significantly attenuated the exaggerated vascular reactivity by vasoconstrictors and vasodilators and efficiently reduced platelet adhesion to the mesenteric endothelium under FeCl3 stimulation.
Conclusion Inhibiting TXAS/TXA2/TP signalling confers microvascular protection against oxidative injury in both cardiac and mesenteric arteries.
Monocytes of Different Subsets in Complexes with Platelets in Patients with Myocardial Infarction
Authors: Loguinova Marina , Pinegina Natalia , Kogan Valeria , Vagida Murad , Arakelyan Anush , Shpektor Alexander , Margolis Leonid , Vasilieva Elena 
Published: October 2018

AbstractAcute myocardial infarction (AMI) is associated with activation of various cells, including platelets that form monocyte–platelet complexes (MPCs). Here, we analysed MPC in vivo and in vitro and investigated the abilities of different monocyte subclasses to form MPC, the characteristics of the cells involved in MPC formation and MPC changes in AMI. We identified MPC by co-staining for platelet antigen CD41a and monocyte antigens CD14 and CD16. Platelet activation was evaluated from expression of phosphatidylserine as revealed by annexin V. Our results confirm published data and provide new information regarding the patterns of MPC in AMI patients. We found that the patterns of platelet aggregation with monocytes were different in AMI patients and controls: (1) in AMI patients, MPC formed by intermediate monocytes carry more platelets whereas in healthy controls more platelets aggregated with classical monocytes; (2) the numbers of MPC in AMI patients, being already higher than in controls, were further increased if these patients suffered various in-hospital complications; (3) on the basis of the CD41a fluorescence of the antibody-stained MPC, some of the aggregates seem to consist of monocytes and platelet-derived extracellular vesicles (EVs); (4) aggregation of monocytes with platelet EV occurred in in vitro experiments; and (5) these experiments demonstrated that monocytes from AMI patients aggregate with both platelets and platelet EVs more efficiently than do monocytes from controls. MPC in AMI patients may play an important role in this pathology.
Visual Estimation of Force Applied During Simulated Deliveries Complicated by Shoulder Dystocia
Authors: Walters Margaret , Eubanks Allison , Weissbrod Elizabeth , Fischer John , Staat Barton , Deering Shad 
Published: October 2018

Background Shoulder dystocia occurs when the fetal head delivers, but the shoulder is lodged behind the pubic symphysis. Training for these emergency deliveries is not optimized, and litigation can occur around a shoulder dystocia delivery.
Objective Evaluate the ability of an outside observer to visually estimate the amount of traction applied to the fetal head during simulated deliveries complicated by shoulder dystocia.
Study Design Simulated deliveries with an objective measurement of traction were randomly organized for estimation of traction applied. Videos show providers applying a “normal” (75 N) and “excessive” (150 N) amount of force in both a “calm” and “stressed” delivery.
Results Fifty participants rated the amount of force applied. Observers estimated traction, on a scale from 1 to 5, higher in the 150-N deliveries as compared with 75-N deliveries (“calm” environment: 3.1 vs. 2.8, p < 0.001; and “stressed” environment: 3.2 vs. 2.8, p < 0.001). Only 15% of observers rated force “above average” or “excessive” in a “calm” environment, as opposed to 30% of observers in the “stressed” environment.
Conclusion Observers are not able to determine when “excessive force” is used and are twice as likely to overestimate the force applied to a fetal head when an average amount of force is used and the delivery environment is stressful.
Precis Observers are unable to determine when excessive traction is applied to the fetal head during simulated deliveries complicated by shoulder dystocia.
Metastatic growth instructed by neutrophil-derived transferrin
Authors: Liang Wei , Li Qin , Ferrara Napoleone 
Published: October 2018

SignificanceThe current study uncovers a mechanistic link between neutrophils and cancer metastasis. Transferrin, an iron-transporting protein, is expressed at mRNA and protein levels in mouse and human neutrophils and is mainly responsible for neutrophil-secreted mitogenic activity on tumor cells. GM-CSF, a cytokine largely produced by tumor cells in the metastatic microenvironment, selectively acts on neutrophils to enhance transferrin gene expression, through activation of the Jak/Stat5β pathway. Accordingly, deletion of the transferrin receptor (Tfr1) in tumor cells, blockade of GM-CSF, or inhibition of Jak kinases inhibited mouse tumor lung metastasis. Our findings raise the possibility that inhibiting GM-CSF or the Jak/Stat5b pathway may benefit patients with metastatic diseases and high local neutrophil infiltration.
Language alternation during L2 classroom discussion tasks
Authors: Tran Huong Quynh 
Published: October 2018

Abstract
Group-work discussion, as a speaking task without the teacher’s tight control of turn-taking, establishes a flexible speaking environment for language learners. However, our understanding of the micro-details of learners’ languages in use when they co-construct meaning to achieve task completion, especially in English as a Foreign Language (EFL) contexts, is still limited. This study investigates the language alternation practices of undergraduate university EFL students in a Vietnamese context as they participate in a group discussion task. The findings show that the students’ switch to Vietnamese is a backup resource to help them in word searches. The language alternation marks the transition between talk on language and talk on topic. This is also reflected in a transition in the sequence structure where the word search is contained in a side-sequence that momentarily disrupts the main or base sequence.
Non-nominative and depersonalized subjects in the Balkans
Authors: Friedman Victor A. , Joseph Brian D. 
Published: October 2018

Abstract
The languages of the Balkan sprachbund are surveyed here with regard to their constructions that show non-nominative subjects, typically in impersonal constructions. The issue of origins is considered, specifically as to whether these constructions represent inheritances from some earlier stage of the relevant languages or instead reflect the effects of contact. In the end, it is argued that a mix of areality, i.e. contact, and genealogy, i.e. inheritance, is needed to explain these constructions, with a nod required as well to typologically common patternings.
Accusative sickness?
Authors: Dewey-Findell Tonya Kim , Carey Stephen Mark 
Published: October 2018

Abstract
Germanic languages that retain case marking and oblique subjects may undergo a change in argument structure over time. Nominative Sickness in Germanic has been demonstrated by Eythórsson (2002) and Barðdal (2009, 2011) for verbal arguments in which obliques are replaced with the nominative. Additionally, formerly accusative subjects become dative, a process widely referred to as Dative Sickness or Dative Substitution in the international literature. Dative Sickness is found across the development of several Germanic Languages (Barðdal 2011; Dunn et al. 2017). However, a change in case marking from a dative subject to an accusative subject is not well attested. The following examination explores instances in which Dative Subject Constructions in Old High German experience Accusative Sickness in Middle High German. That is, they start occurring with an accusative argument instead of the earlier, historically correct, dative.
Active and passive tough-infinitives
Authors: Haumann Dagmar 
Published: October 2018

Abstract
This paper probes into the determinants of the long-term grammatical variation of active and passive tough-infinitives, as well as into the factors that ultimately led to the decline of passive tough-infinitives. It is argued that, throughout their coexistence, the active and the passive tough-infinitive are functionally equivalent and that the demise of the passive tough-infinitive is a concomitant of the extensive and rapid spread of the passive infinitive governed by be expressing deontic modality. It is further argued that, due to the surface similarity of the passive infinitive governed by be and the passive tough-infinitive, deontic modality percolates into the passive tough-infinitive, which expresses dispositional modality. Thus, the obsolescence of the passive tough-infinitive is driven by a clash in modality.
Central auditory processing findings in a group of cognitively impaired individuals
Authors: Ghannoum Mohamed Tarek , Shalaby Amany Ahmed , Farghaly Marwa , Hamdy Mona , Hamdy Hussein Sherif 
Published: October 2018

Introduction:
Prevalence of central auditory processing disorders (CAPD) increases with age. Central auditory dysfunction is also more prevalent in older people with mild memory impairment compared with cognitively normal older people. These findings suggest that CAPD could be a marker of subtle cognitive dysfunction. A logical question is whether tests of CAPD have a potential role in evaluation of possible cognitive decline in elderly people with hearing complaints. This question has direct clinical relevance because tests for CAPD are widely available, easy to administer in a short time.

Methods:
Fifty-one patient having cognitive impairment (diagnosed according Diagnostic and Statistical Manual of Mental disorders, fifth edition 2013 (DSM-V) comprise the study group. The control group includes twenty age and gender matched individuals. A detailed neuropsychological assessment of both groups with tests from various cognitive domains (Visuospatial functions, executive function, short-term memory and verbal episodic memory). Behavioural central auditory tests included the Arabic versions of speech in noise test (SPIN) and/or synthetic sentence identification (SSI) test according to education of patient, the dichotic digits test (DDT), The auditory fusion test (AFT) and auditory memory tests.

Results:
There was a statistically significant difference between both groups in the behavioural central auditory tests.

Conclusions:
The relation of some measures of auditory processing to deficits in cognitive function might enable the early identification of cognitive decline with such measures in the older population. Aging can contribute to changes in central auditory processing (CAP) in the elderly especially in Speech understanding in background noise, Dichotic listening and Temporal Processing.
Green architecture concept in Chinese region at Clan Jetties area, Penang Malaysia
Authors: Nur’aini R D , Windarta  , Firdaus F , Makinudin I 
Published: October 2018

Abstract
Penang is part of Malaysia’s territory where there is an area recognized by UNESCO as the world heritage, George Town. As a center of the conservation area, it is a port that became the center of commerce during the colonial period. It makes the city inhabited by multi ethnics from different parts of the world, such as Malay ethnic, Chinese ethnic, and Indian ethnic. This multi ethnic settlement becomes the main attraction to be made as the research material. This study aims to find the concept of green architecture of clan jetties area, describe the use of natural materials in its buildings and residences and explain the utility system on the region. This research uses qualitative method with analysis approach using general-specific method. Based on the research we conducted with the method of observation and direct observation of the research object, it can be concluded that clan jetties is a special settlement for Chinese ethnic who are migrants. The residential location is along the coastline adjacent to the Weld Quay harbor. The settlement is divided into 7 areas based on family or clan; Ong Jetty, Lim Jetty, Chew Jetty, Tan Jetty, Lee Jetty, New Jetty and Yeoh Jetty. Each clan has a similar pattern of settlement that extends to the sea with one main road and the side of the road is occupied by the houses of the citizens. The utility system of the area is broadly divided according to the utility of clean water for sewage and fire, lighting, and fire-fighting utilities. Each clan is already equipped with the utility. The main material used for building houses is wood. The placement of vegetation for greening using a flower pot is either placed at the bottom or hung on top.
PrecursorFinder: a customized biosynthetic precursor explorer
Authors: Yuan Le , Tian Yu , Ding Shaozhen , Liu Yanfang , Chen Fu , Zhang Tong , Tu Weizhong , Chen Junni , Hu Qian-Nan 
Published: October 2018

Abstract

Summary
Synthetic biology has a great potential to produce high value pharmaceuticals, commodities or bulk chemicals. However, many biosynthetic target molecules have no defined or predicted biosynthetic pathways. Biosynthetic precursors are crucial to create biosynthetic pathways. Thus computer-assisted tools for precursor identification are urgently needed to develop novel metabolic pathways. To this end, we present PrecursorFinder, a computational tool that explores biosynthetic precursors for the query target molecules using chemical structure, similarity as well as MCS (maximum common substructure). This platform comprises more than 60 000 compounds biosynthesized for being promising precursors, which are extracted from &gt;500 000 scientific literatures and manually curated by more than 100 people over the past 8 years. The PrecursorFinder could speed up the process of biosynthesis research and make synthetic biology or metabolic engineering more efficient.

Availability and implementation
PrecursorFinder is available at: http://www.rxnfinder.org/precursorfinder/.

Supplementary information
Supplementary data are available at Bioinformatics online.
A novel approach for drug response prediction in cancer cell lines via network representation learning
Authors: Yang Jianghong , Li Ao , Li Yongqiang , Guo Xiangqian , Wang Minghui 
Published: October 2018

Abstract

Motivation
Prediction of cancer patient’s response to therapeutic agent is important for personalized treatment. Because experimental verification of reactions between large cohort of patients and drugs is time-intensive, expensive and impractical, preclinical prediction model based on large-scale pharmacogenomic of cancer cell line is highly expected. However, most of the existing computational studies are primarily based on genomic profiles of cancer cell lines while ignoring relationships among genes and failing to capture functional similarity of cell lines.

Results
In this study, we present a novel approach named NRL2DRP, which integrates protein–protein interactions and captures similarity of cell lines’ functional contexts, to predict drug responses. Through integrating genomic aberrations and drug responses information with protein–protein interactions, we construct a large response-related network, where the neighborhood structure of cell line provides a functional context to its therapeutic responses. Representation vectors of cell lines are extracted through network representation learning method, which could preserve vertices’ neighborhood similarity and serve as features to build predictor for drug responses. The predictive performance of NRL2DRP is verified by cross-validation on GDSC dataset and methods comparison, where NRL2DRP achieves AUC &gt; 79% for half drugs and outperforms previous methods. The validity of NRL2DRP is also supported by its effectiveness on uncovering accurate novel relationships between cell lines and drugs. Lots of newly predicted drug responses are confirmed by reported experimental evidences.

Availability and implementation
The code and documentation are available on https://github.com/USTC-HIlab/NRL2DRP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nonparametric regression with adaptive truncation via a convex hierarchical penalty
Authors: Haris Asad , Shojaie Ali , Simon Noah 
Published: October 2018

SUMMARYWe consider the problem of nonparametric regression with a potentially large number of covariates. We propose a convex, penalized estimation framework that is particularly well suited to high-dimensional sparse additive models and combines the appealing features of finite basis representation and smoothing penalties. In the case of additive models, a finite basis representation provides a parsimonious representation for fitted functions but is not adaptive when component functions possess different levels of complexity. In contrast, a smoothing spline-type penalty on the component functions is adaptive but does not provide a parsimonious representation. Our proposal simultaneously achieves parsimony and adaptivity in a computationally efficient way. We demonstrate these properties through empirical studies and show that our estimator converges at the minimax rate for functions within a hierarchical class. We further establish minimax rates for a large class of sparse additive models. We also develop an efficient algorithm that scales similarly to the lasso with the number of covariates and sample size.