bluuebunny/crossref_metadata_2025_split huggingface dataset:
MR1 recycling and blockade of endosomal trafficking reveal distinguishable antigen presentation pathways between Mycobacterium tuberculosis infection and exogenously delivered antigens
Authors: Karamooz Elham , Harriff Melanie J. , Narayanan Gitanjali A. , Worley Aneta , Lewinsohn David M. 
Published: March 2019

AbstractThe MHC-Ib molecule MR1 presents microbial metabolites to MR1-restricted T cells (MR1Ts). Given the ubiquitous expression of MR1 and the high prevalence of human MR1Ts, it is important to understand the mechanisms of MR1-dependent antigen presentation. Here, we show that MR1-dependent antigen presentation can be distinguished between intracellular Mycobacterium tuberculosis (Mtb) infection and exogenously added antigens. Although both Mtb infection and exogenously added antigens are presented by preformed MR1, only exogenously added antigens are capable of reusing MR1 that had been bound to the folic acid metabolite 6-formylpterin (6-FP). In addition, we identify an endosomal trafficking protein, Syntaxin 4, which is specifically involved in the presentation of exogenously delivered antigens but not Mtb-dependent antigen presentation. These data reveal there are multiple ways that MR1 can sample antigens and that MR1-mediated sampling of intracellular Mtb infection is distinguishable from the sampling of exogenously added antigens.
The influence of a year-round tillage and residue management model on soil N fractions in a wheat-maize cropping system in central China
Authors: Ye Xinxin , Ye Yin , Chai Rushan , Li Junli , Ma Chao , Li Hongying , Xiong Qizhong , Gao Hongjian 
Published: March 2019

AbstractTillage practice and residue management play important roles in N pool in soils. This study determined the impacts of tillage practice and residue management on crop yield. It also investigated the distribution, fractionation, and stratification of N at soil at depths ranging from 0 to 60 cm under wheat–maize cropping systems. Three treatments were established in 2009: no-tillage with straw removal for winter wheat and summer maize (NT), no-tillage with straw mulching for winter wheat and summer maize (NTS), no-tillage with straw mulching for summer maize and plow tillage with straw incorporation for winter wheat (NPTS). After 8 years, soil total nitrogen (TN) content in NTS was greater than in NT, but only in 0–10 cm layer. NPTS treatment increased TN content over NT and NTS in 10–20 cm layer by 18.0% and 13.9%, and by 16.8% and 18.1% in 20–30 cm layer, respectively. Particulate organic N, microbial biomass N and water-extractable organic N levels were the greatest in 0–10 cm layer under NTS treatment; and in 10–30 cm layer, the corresponding values were the highest under NPTS treatment. NPTS treatment could immobilize the mineral N in 10–30 cm layer, and reduced leaching losses into deeper soil layers (40–60 cm). Furthermore, total yield increased by 14.7% and 8.5% in NPTS treatment compared to NT and NTS treatments, respectively. These results indicate that NPTS is an effective and sustainable management practice, which will improve soil fertility, sustainable crop production, and environmental quality in low-productivity soils in central China.
Drug-loaded hyaluronic acid hydrogel as a sustained-release regimen with dual effects in early intervention of tendinopathy
Authors: Hsiao Ming-Yen , Lin An-Ci , Liao Wei-Hao , Wang Tyng-Guey , Hsu Chia-Hsien , Chen Wen-Shiang , Lin Feng-Huei 
Published: March 2019

AbstractResulting from accumulative microtrauma, impaired healing and oxidative stress, tendinopathy is a debilitating and relentlessly deteriorating disease that greatly affects daily function and quality of life. Current therapy usually provides symptomatic relief only. Sufferers undergo repetitive and protracted treatment courses that rarely alter the disease process. We aim to develop a sustained-release regimen with an intrinsic therapeutic effect in tendinopathy treatment, using oxidised hyaluronic acid/adipic acid dihydrazide hydrogel (HA hydrogel) as both the drug carrier and a mitigating agent of symptoms. We show that HA hydrogel can mitigate tendinopathy changes both in vitro (mechanically induced tendinopathy model) and in vivo (collagenase-induced tendinopathy model). A potent anti-oxidative (pigallocatechin gallate) incorporated into HA hydrogel conferred an additional protective effect in both models. The results indicate that when administered early, combined medications targeting different pathogenesis pathways can resolve tendinopathy. Although facilitating the healing process and mitigating oxidative stress are promising therapeutic strategies, the most effective regimen for tendinopathy treatment has to be determined yet. The established experimental model and drug carrier system provide a platform for exploring new therapeutics against this debilitating disease.
Correlating anisotropic mobility and intermolecular phonons in organic semiconductors to investigate transient localization
Authors: Bittle Emily G. , Biacchi Adam J. , Fredin Lisa A. , Herzing Andrew A. , Allison Thomas C. , Hight Walker Angela R. , Gundlach David J. 
Published: March 2019

AbstractDeveloping a fundamental understanding of charge transport in organic semiconductors has been a decades-long challenge that hinders performance improvement. In particular, recent work suggests that organic semiconductors have unique charge–phonon interactions where phonons temporarily interrupt the band structure causing a transient localization of charge carriers. Despite growing evidence to support this mechanism, further understanding and control will depend on pinpointing the molecular motions that cause substantial change to the band structure. Here we combine experimental and theoretical techniques to demonstrate the phonon energies and associated molecular motions governing the charge–phonon interaction in single crystal tetracene. We investigate phonon properties using polarized Raman spectroscopy, transmission electron microscopy, and density functional theory, and correlate this with the anisotropic mobility. We find that specific phonons disrupt the band orbital in the high-mobility direction, evident in the discrepancy between measured and static calculations of the mobility anisotropy ratio in tetracene.
Freeway travel time estimation based on the general motors model: a genetic algorithm calibration framework
Authors: Yang Shu , Ou Jishun , Feng Yiheng , Wang Yuan 
Published: March 2019

Travel time estimation plays an important role in freeway performance assessment and reliability management. Conventional estimation methods based on speed information do not consider the level of congestion during modelling, leading to unreliable estimations under congested conditions. This study presents a freeway travel time estimation method based on the general motors (GM) model, where the concept ‘virtual vehicle’ was proposed to apply macroscopic traffic flow data to the microscopic GM model. First, a GM‐based travel time estimation (GMTTE) model was developed to estimate link travel time. Three sets of parameters , and were separately used under free‐flowing, congestion and transition conditions. Next, two corridor estimation models, namely GMTTE time‐slice‐based (GMTTE‐TSB) model and GMTTE continuous‐speed (GMTTE‐CS) model, were proposed. To calibrate the three parameters, a genetic algorithm framework was developed. The proposed method was calibrated and evaluated using traffic data collected from seven freeway segments in the greater St. Louis, Missouri region. Results show that (i) the GMTTE‐CS model outperformed the GMTTE‐TSB model; (ii) the optimal parameters of the GMTTE‐CS model under free‐flowing and congested conditions are and , respectively; (iii) the GMTTE‐CS model outperformed the instantaneous and time‐slice models under congested conditions, while showing similar accuracies with the two models under free‐flowing and status‐transition conditions; and (iv) the optimal time interval was found to be 9–10 min for free‐flowing conditions and 6–7 min for congested conditions.
Transit Lyman-α
signatures of terrestrial planets in the habitable zones of M dwarfs
Authors: Kislyakova K. G. , Holmström M. , Odert P. , Lammer H. , Erkaev N. V. , Khodachenko M. L. , Shaikhislamov I. F. , Dorfi E. , Güdel M. 
Published: March 2019

Aims. We modeled the transit signatures in the Lyman-alpha (Ly-α) line of a putative Earth-sized planet orbiting in the habitable zone (HZ) of the M dwarf GJ 436. We estimated the transit depth in the Ly-α line for an exo-Earth with three types of atmospheres: a hydrogen-dominated atmosphere, a nitrogen-dominated atmosphere, and a nitrogen-dominated atmosphere with an amount of hydrogen equal to that of the Earth. For all types of atmospheres, we calculated in-transit absorption they would produce in the stellar Ly-α line. We applied it to the out-of-transit Ly-α observations of GJ 436 obtained by the Hubble Space Telescope (HST) and compared the calculated in-transit absorption with observational uncertainties to determine if it would be detectable. To validate the model, we also used our method to simulate the deep absorption signature observed during the transit of GJ 436b and showed that our model is capable of reproducing the observations.
Methods. We used a direct simulation Monte Carlo (DSMC) code to model the planetary exospheres. The code includes several species and traces neutral particles and ions. It includes several ionization mechanisms, such as charge exchange with the stellar wind, photo- and electron impact ionization, and allows to trace particles collisions. At the lower boundary of the DSMC model we assumed an atmosphere density, temperature, and velocity obtained with a hydrodynamic model for the lower atmosphere.
Results. We showed that for a small rocky Earth-like planet orbiting in the HZ of GJ 436 only the hydrogen-dominated atmosphere is marginally detectable with the Space Telescope Imaging Spectrograph (STIS) on board the HST. Neither a pure nitrogen atmosphere nor a nitrogen-dominated atmosphere with an Earth-like hydrogen concentration in the upper atmosphere are detectable. We also showed that the Ly-α observations of GJ 436b can be reproduced reasonably well assuming a hydrogen-dominated atmosphere, both in the blue and red wings of the Ly-α line, which indicates that warm Neptune-like planets are a suitable target for Ly-α observations. Terrestrial planets, on the other hand, can be observed in the Ly-α line if they orbit very nearby stars, or if several observational visits are available.
Reclassification of Cepheids in the Gaia Data Release 2
Authors: Ripepi V. , Molinaro R. , Musella I. , Marconi M. , Leccia S. , Eyer L. 
Published: March 2019

Context. Classical Cepheids are the most important primary indicators for the extragalactic distance scale. Establishing the precise zero points of their period-luminosity and period-Wesenheit (PL/PW) relations has profound consequences on the estimate of H0. Type II Cepheids are also important distance indicators and tracers of old stellar populations.
Aims. The recent Data Release 2 (DR2) of the Gaia spacecraft includes photometry and parallaxes for thousands of classical and Type II Cepheids. We seek to review the classification of Gaia DR2 Cepheids and to derive precise PL/PW for the Magellanic Clouds (MCs) and Galactic Cepheids.
Methods. We adopted information from the literature and the Gaia astrometry and photometry to assign DR2 Galactic Cepheids to the classical, anomalous, and Type II Cepheids classes.
Results. We reclassified the DR2 Galactic Cepheids and derived new precise PL/PW relations in the Gaia passbands for the MCs and Milky Way Cepheids. We investigated for the first time the dependence on metallicity of the PW relation for classical Cepheids in the Gaia bands, finding inconclusive results.
Conclusions. According to our analysis, the zero point of the Gaia DR2 parallaxes as estimated from classical and Type II Cepheids seems likely to be underestimated by ∼0.07 mas, which agrees with recent literature. The next Gaia data releases are expected to fix this zero point offset to allow eventually a determination of H0 to less than 1%.
Neuromuskuläre Erkrankungen und Schlaf
Authors: Spießhöfer Jens , Young Peter , Boentert Matthias 
Published: March 2019

ZusammenfassungViele neuromuskuläre Erkrankungen (NME) sind mit Begleitsymptomen verbunden, die den Schlaf und die Schlafqualität beeinträchtigen. Schlafstörungen können eine unspezifische Folge der Immobilisierung darstellen, aber besonders bei Erkrankungen des peripheren Nervensystems auch auf nächtliche Crampi oder ein Restless-legs-Syndrom zurückzuführen sein. Motoneuronerkrankungen, akute Immunneuropathien und viele Myopathien können im Verlauf mit einer relevanten Schwäche der Atemmuskulatur einhergehen, die sich initial als schlafbezogene Hypoventilation manifestiert und bis zur hyperkapnischen respiratorischen Insuffizienz voranschreiten kann. Zahlreiche Erkrankungen sind zudem mit einem erhöhten Risiko für eine obstruktive Schlafapnoe assoziiert. Schlafbezogene Symptome sind bei NME häufig und sollten gezielt erfragt werden, um eine geeignete Diagnostik und Therapie zu ermöglichen.
Alkoholintoxikation – ein psychiatrischer Notfall
Authors: Wetterling Tilman , Junghanns Klaus 
Published: March 2019

ZusammenfassungEine Alkoholintoxikation ist der häufigste Grund für eine psychiatrische Konsultation in Notfallambulanzen von Krankenhäusern. Viele der betroffenen Patienten verweigern eine adäquate Überwachung und Behandlung. In diesen Fällen muss dann der Dienstarzt entscheiden, ob eine Entlassung medizinisch vertretbar ist. Dabei muss insbesondere die Frage der Einwilligungsfähigkeit des Patienten geklärt werden. Das Risiko einer erheblichen unmittelbaren Eigengefährdung durch Unfälle, komplizierten Alkoholentzug oder Suizid und das Risiko der unmittelbaren Fremdgefährdung durch aggressives Verhalten gegenüber Dritten muss in der Entscheidung angemessen berücksichtigt werden. In dem Artikel werden die wesentlichen Punkte beim Notfall-Management von Alkoholintoxikierten erörtert und in Checklisten zusammengefasst.
Online-Selbstmanagement bei Depressionen – Die Beziehung von Dosis und Wirksamkeit im hausärztlichen Versorgungssetting
Authors: Löbner Margrit , Dorow Marie , Pabst Alexander , Stein Janine , Kersting Anette , Luppa Melanie , König Hans-Helmut , Riedel-Heller Steffi 
Published: March 2019

Zusammenfassung
Ziel der Studie Auf dem Gebiet der internetbasierten kognitiven Verhaltenstherapie wurde der Dosis-Wirksamkeits-Effekt von Online-Selbstmanagementprogrammen bislang unzureichend untersucht. Das Ziel der Studie war es, die Wirksamkeit einer Online-Intervention für verschiedene Nutzungsintensitätsgruppen (NIGs) hinsichtlich der depressiven Symptomatik zu überprüfen.
Methodik Die Untersuchung wurde im Rahmen der cluster-randomisierten kontrollierten @ktiv-Studie durchgeführt. Hausarztpatienten (n = 647) mit leichten bis mittelschweren depressiven Erkrankungen aus 112 Praxen wurden rekrutiert und in eine Interventionsgruppe (IG: moodgym + treatment as usual, TAU) oder Kontrollgruppe (KG: TAU) eingeteilt. Alle Patienten wurden schriftlich zu drei Messzeitpunkten befragt (zur Baseline, nach 6 Wochen und nach 6 Monaten). Zur Untersuchung des Dosis-Wirksamkeits-Effekts wurde das Beck-Depressions-Inventar II (BDI-II) nach 6 Monaten herangezogen. Um Unterschiede im BDI-II zwischen verschiedenen NIGs der IG im Vergleich zur KG zu schätzen, wurden lineare gemischte Regressionsmodelle verwendet.
Ergebnisse Über alle NIGs der IG hinweg zeigte sich eine signifikant stärkere Verbesserung der depressiven Symptomatik im Vergleich zur KG. Am größten war die Symptomreduktion bei Viel-Nutzern (-5,77; p < 0,01) sowie Langzeit-Nutzern (-7,22; p < 0,01) des Programms.
Schlussfolgerung Die Ergebnisse legen einen Dosis-Wirksamkeits-Effekt der Online-Intervention nahe. Hausarztpatienten mit leichten bis mittelgradigen depressiven Symptomen scheinen stärker von dem Programm zu profitieren, je intensiver sie es nutzen.
Modelling the Acceleration and Deceleration Profile of Elite-level Soccer Players
Authors: Newans Timothy , Bellinger Phillip , Dodd Karl , Minahan Clare 
Published: March 2019

AbstractThe ability to change velocity rapidly is a key element of field-based sports. This study quantified the acceleration and deceleration profiles of soccer players during match play. Global positioning system measures were collected from 20 male soccer players competing in the Australian Hyundai A-League during 58 matches. Match data were organized into ten 9 min periods (i. e., P1: 0–9 min) and the time spent at moderate (1–2 m·s−2) and high (>2 m·s−2) acceleration and deceleration thresholds were quantified. Additionally, a novel deceleration: acceleration ratio was quantified to identify the transient nature of deceleration activity. Linear mixed models were used to model the acceleration and deceleration profiles. All acceleration and deceleration metrics displayed negative logarithmic curves within each half. There was no change in the ratio of high deceleration: acceleration; however, a significant increase in the ratio of moderate deceleration:acceleration was evident. Using negative logarithmic curves to illustrate the acceleration and deceleration decay provides a novel methodological approach to quantify the high-intensity actions during match play. A decrease in the time spent decelerating throughout a match may be attributed to a lack of opportunity. Practitioners can use the coefficients, intercepts, and deceleration: acceleration ratios to monitor a player’s deceleration profile in match play.
Highlights of the mini‐symposium on extracellular vesicles in inter‐organismal communication, held in Munich, Germany, August 2018
Authors: Bielska E. , Birch P.R.J. , Buck A.H. , Abreu‐Goodger C. , Innes R.W. , Jin H. , Pfaffl M.W. , Robatzek S. , Regev‐Rudzki N. , Tisserant C. , Wang S. , Weiberg A. 
Published: March 2019

ABSTRACTAll living organisms secrete molecules for intercellular communication. Recent research has revealed that extracellular vesicles (EVs) play an important role in inter‐organismal cell‐to‐cell communication by transporting diverse messenger molecules, including RNA, DNA, lipids and proteins. These discoveries have raised fundamental questions regarding EV biology. How are EVs biosynthesized and loaded with messenger/cargo molecules? How are EVs secreted into the extracellular matrix? What are the EV uptake mechanisms of recipient cells? As EVs are produced by all kind of organisms, from unicellular bacteria and protists, filamentous fungi and oomycetes, to complex multicellular life forms such as plants and animals, basic research in diverse model systems is urgently needed to shed light on the multifaceted biology of EVs and their role in inter‐organismal communications. To help catalyse progress in this emerging field, a mini‐symposium was held in Munich, Germany in August 2018. This report highlights recent progress and major questions being pursued across a very diverse group of model systems, all united by the question of how EVs contribute to inter‐organismal communication.
Enhanced flood risk with 1.5 °C global warming in the Ganges–Brahmaputra–Meghna basin
Authors: Uhe P F , Mitchell D M , Bates P D , Sampson C C , Smith A M , Islam A S 
Published: March 2019

Abstract
Flood hazard is a global problem, but regions such as south Asia, where people’s livelihoods are highly dependent on water resources, can be affected disproportionally. The 2017 monsoon flooding in the Ganges–Brahmaputra–Meghna (GBM) basin, with record river levels observed, resulted in ∼1200 deaths, and dramatic loss of crops and infrastructure. The recent Paris Agreement called for research into impacts avoided by stabilizing climate at 1.5 °C over 2 °C global warming above pre-industrial conditions. Climate model scenarios representing these warming levels were combined with a high-resolution flood hazard model over the GBM region. The simulations of 1.5 °C and 2 °C warming indicate an increase in extreme precipitation and corresponding flood hazard over the GBM basin compared to the current climate. So, for example, even with global warming limited to 1.5 °C, for extreme precipitation events such as the south Asian crisis in 2017 there is a detectable increase in the likelihood in flooding. The additional ∼0.6 °C warming needed to take us from current climate to 1.5 °C highlights the changed flood risk even with low levels of warming.
maTE: discovering expressed interactions between microRNAs and their targets
Authors: Yousef Malik , Abdallah Loai , Allmer Jens 
Published: March 2019

Abstract

Motivation
Disease is often manifested via changes in transcript and protein abundance. MicroRNAs (miRNAs) are instrumental in regulating protein abundance and may measurably influence transcript levels. miRNAs often target more than one mRNA (for humans, the average is three), and mRNAs are often targeted by more than one miRNA (for the genes considered in this study, the average is also three). Therefore, it is difficult to determine the miRNAs that may cause the observed differential gene expression. We present a novel approach, maTE, which is based on machine learning, that integrates information about miRNA target genes with gene expression data. maTE depends on the availability of a sufficient amount of patient and control samples. The samples are used to train classifiers to accurately classify the samples on a per miRNA basis. Multiple high scoring miRNAs are used to build a final classifier to improve separation.

Results
The aim of the study is to find a set of miRNAs causing the regulation of their target genes that best explains the difference between groups (e.g. cancer versus control). maTE provides a list of significant groups of genes where each group is targeted by a specific miRNA. For the datasets used in this study, maTE generally achieves an accuracy well above 80%. Also, the results show that when the accuracy is much lower (e.g. ∼50%), the set of miRNAs provided is likely not causative of the difference in expression. This new approach of integrating miRNA regulation with expression data yields powerful results and is independent of external labels and training data. Thereby, this approach allows new avenues for exploring miRNA regulation and may enable the development of miRNA-based biomarkers and drugs.

Availability and implementation
The KNIME workflow, implementing maTE, is available at Bioinformatics online.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Diffusion of Detriment: Tracking Displacement Using a City-Wide Mixed Methods Approach
Authors: Hodgkinson Tarah , Saville Gregory , Andresen Martin A 
Published: March 2019

AbstractCrime reduction strategies are often faced with the criticism of crime displacement. Conversely, criminologists find that reductions in crime in one area have a ‘diffusion of benefits’ to surrounding areas. However, these findings are limited due to a lack of extensive longitudinal data and qualitative data that provide context. We examine a natural experiment in displacement: the removal of a convergence setting in which calls for service immediately declined. However, other areas emerged as problematic and, in some places, crime increased dramatically. Using a qualitatively informed trajectory analysis, we examine whether the removal of a convergence setting results in displacement across the entire city. We discuss the implications for opportunity theories and prevention strategies.