bluuebunny/crossref_metadata_2025_split huggingface dataset:
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance
Authors: Kaur Parwinder , Bayer Philipp E. , Milec Zbyněk , Vrána Jan , Yuan Yuxuan , Appels Rudi , Edwards David , Batley Jacqueline , Nichols Phillip , Erskine William , Doležel Jaroslav 
Published: January 2017

SummarySubterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1.1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano‐based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super‐scaffolds (43% of genome). Sequences longer than >1 Mb increased from 40 to 189 Mb giving 1.4‐fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re‐annotated using transcriptome atlas data to contain 31 272 protein‐coding genes capturing >96% of the gene content. Functional characterization and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24 893 Trifolium‐specific and 6325 subterranean‐clover‐specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro‐morphological traits, were fine‐mapped on the high‐density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker‐assisted breeding, comparative mapping and identification of tissue‐specific gene promoters for biotechnological improvement of forage legumes.
Vegetating Candidiasis: A Mimicker of Squamous Cell Carcinoma in Keratitis Ichthyosis Deafness Syndrome
Authors: Calderón‐Castrat Ximena , Vega‐Zuñiga Julio , Velásquez Felipe , Ballona Rosalía 
Published: January 2017

AbstractKeratitis ichthyosis deafness (KID) syndrome is a rare genodermatosis with a high risk of cutaneous malignancy and infections. Infections can induce pseudocarcinomatous epidermal hyperplasia, leading to erroneous diagnosis of squamous cell carcinoma. We present a pediatric case of KID syndrome with vegetating plantar and acral candidiasis and highlight the importance of correct biopsy technique and clinicopathologic correlation in appropriate management.
In situ immunopathological changes in cutaneous leishmaniasis due to Leishmania donovani
Authors: Manamperi N. H. , Oghumu S. , Pathirana N. , de Silva M. V. C. , Abeyewickreme W. , Satoskar A. R. , Karunaweera N. D. 
Published: January 2017

SummaryCutaneous leishmaniasis in Sri Lanka is a newly established parasitic disease caused by the usually visceralizing Leishmania donovani. Skin lesions manifest as non‐itchy, non‐tender papules, nodules or ulcers. In situ cytokine expression provides clues for immunopathogenesis of this localized form of disease. Skin biopsies from 58 patients were analyzed for histological appearance and in situ cytokine expression of T‐helper 1 (Th1) and T‐helper 2 (Th2) cytokines, namely interferon (IFN)‐γ, interleukin (IL)‐12A, tumor necrosis factor (TNF)‐α, IL‐4 and IL‐10 by real‐time RT‐PCR. Significant up‐regulation of the Th1 cytokine IFN‐γ and down‐regulation of the Th2 cytokine IL‐4 were seen in patients compared to healthy controls. Significantly elevated tissue expression of IFN‐γ and TNF‐α was seen in lesions that presented later than 6 months from the time of onset, while IL‐4 expression was more prominent in lesions that responded poorly to antimony therapy. A prominent Th1 response appears to support resolving of lesions, whereas a Th2‐biased milieu tends to favor poor responsiveness to antimony and delayed lesion healing in L. donovani infections in Sri Lanka.
The N2pc component reliably captures attentional bias in social anxiety
Authors: Reutter Mario , Hewig Johannes , Wieser Matthias J. , Osinsky Roman 
Published: January 2017

AbstractWe systematically compared different measures of attentional bias (i.e., reaction times, the N2pc component in the EEG, and explicit stimulus ratings) on their ability to reveal attentional engagement to threatening versus neutral facial stimuli in a Dot Probe Task and tested their relation to trait measures of general and social anxiety. We found that the N2pc component reflects a bias toward angry faces with excellent internal consistency. Similar results were obtained for explicit ratings. Reaction time (RT) differences, however, were not indicative of attentional biases and showed zero odd‐even reliability. We further found that both higher (i.e., more negative) N2pc amplitudes and earlier peak latencies were associated with more severe symptoms of social anxiety even when controlling for general trait anxiety. The explicit rating biases were also specifically associated with social anxiety. Conversely, the RT bias was not related to social anxiety levels but to general trait anxiety. This highlights the importance of valid and reliable outcome measures for interventions such as attentional bias modification protocols. Mutual exclusivity of different bias operationalizations is discussed.
Testosterone serum profile, semen characteristics and testicular biometry of Mangalarga Marchador stallions in a tropical environment
Authors: Waddington B , Penitente‐Filho JM , Neves JGS , Pinho RO , Chaya AY , Maitan PP , Silveira CO , Neves MG , Guimarães SEF , de Carvalho GR , Guimarães JD 
Published: January 2017

ContentsThis study was conducted to characterize the daily profile of testosterone secretion and its mean concentrations in the four seasons as well as to evaluate the semen characteristics and testicular biometry of Mangalarga Marchador stallions throughout the year in a tropical region. Three stallions were submitted to semen collections and evaluation of testicular biometry every 14 days along a year. Blood samples were collected once at the middle of each season, in a 20‐min interval during 24 hr in order to evaluate the testosterone secretion profiles among seasons. Testosterone concentrations along the day were higher at the beginning of the afternoon (from 12:00 to 15:00 hr), but a circadian secretion was not clearly observed. Mean testosterone concentrations did not differ among seasons (p > .05), but a pattern of secretion along the day showed variations with higher concentrations in the afternoon during the winter. Ejaculate volume was higher during summer; however, sperm motility decreased in summer and spring. Total sperm in ejaculate, sperm morphology and testicular biometry kept constant along the year showing no differences among the seasons. The results demonstrated that in a tropical region, reproductive aspects of stallions did not show a clearly defined seasonal variation, and months of autumn and winter were not unsuitable for reproduction of the males.
Dynamic contact strain measurement by time‐resolved stroboscopic energy dispersive synchrotron X‐ray diffraction
Authors: Mostafavi M. , Collins D. M. , Peel M. J. , Reinhard C. , Barhli S. M. , Mills R. , Marshall M. B. , Dwyer‐Joyce R. S. , Connolley T. 
Published: January 2017

AbstractRecent developments of synchrotron X‐ray sources and dedicated high‐energy beamlines are now enabling strain measurements from large volumes of industrially relevant metallic materials. Such capability is allowing the validation of novel and alternative nondestructive experimental methods of strain measurement or computational models of complex deformation processes. This study describes the first dynamic contact strain measurement of a ball bearing using stroboscopic energy dispersive X‐ray diffraction. The experiment probed the dynamic contact strain in the outer raceway of a test bearing. The inner raceway of the bearing was attached to a shaft rotating at 150 revolutions per minute, and the outer raceway, where the measurements were made, was fixed in a stationary bearing housing. A triggering system was used to synchronise the data acquisition of the energy dispersive X‐ray diffraction detector with the bearing rotation. Specifically, diffraction data were acquired, stroboscopically, from the material volume within the raceway, in a known location, when the ball was positioned directly below it. A total of 20 s of accumulated diffraction signal was recorded, acquiring 2 ms of data per revolution, providing diffraction patterns of sufficient quality for the dynamic contact strain to be measured. Macromechanical stress field was calculated from the micromechanical strains measured from five lattice planes. This allowed a comparison of the experimentally measured stress field and that of finite element simulations. Good agreement was observed between the finite element results and experimental measurements indicating the applicability of this novel dynamic strain measurement technique for tribological systems.
Label‐free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development
Authors: Szymanski Jedrzej , Levin Yishai , Savidor Alon , Breitel Dario , Chappell‐Maor Louise , Heinig Uwe , Töpfer Nadine , Aharoni Asaph 
Published: January 2017

SummaryCurrent innovations in mass‐spectrometry‐based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large‐scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages. The depth of our assay enabled identification of 61 differentially expressed transcription factors, including renowned ripening‐related regulators and elements of ethylene signaling. Significantly, we measured proteins involved in 83% of all predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were identified, including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns, which is most significant in light of the weak transcript‐protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique view of skin and flesh tissues in developing fruit. This study adds a new dimension to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post‐translational research in tomato and additional species, which is presently focused on transcription.
Calcium‐dependent protein kinase CPK28 targets the methionine adenosyltransferases for degradation by the 26S proteasome and affects ethylene biosynthesis and lignin deposition in Arabidopsis
Authors: Jin Yu , Ye Nenghui , Zhu Fuyuan , Li Haoxuan , Wang Juan , Jiang Liwen , Zhang Jianhua 
Published: January 2017

SummaryS‐adenosylmethionine (AdoMet) is synthesized by methionine adenosyltransferase (MAT), and plays an essential role in ethylene biosynthesis and other methylation reactions. Despite increasing knowledge of MAT regulation at transcriptional levels, how MAT is post‐translationally regulated remains unknown in plant cells. Phosphorylation is an important post‐translational modification for regulating the activity of enzymes, protein function and signaling transduction. Using molecular and biochemical approaches, we have identified the phosphorylation of MAT proteins by calcium‐dependent protein kinase (CPK28). Phenotypically, both MAT2‐overexpressing transgenic plants and cpk28 mutants display short hypocotyls and ectopic lignifications. Their shortened hypocotyl phenotypes are caused by ethylene overproduction and rescued by ethylene biosynthesis inhibitor aminoethoxyvinylglycine treatment. Genetic evidence reveals that MAT2 mutation restores the phenotype of ectopic lignification in CPK28‐deficient plants. We find that total MAT proteins and AdoMet are increased in cpk28 mutants, but decreased in CPK28‐overexpressing seedlings. We also find that MATs in OE::CPK28 are degraded through the 26S proteasome pathway. Our work suggests that CPK28 targets MATs (MAT1, MAT2 and MAT3) for degradation by the 26S proteasome pathway, and thus affects ethylene biosynthesis and lignin deposition in Arabidopsis.
Assessment of tuber coxae bone biopsy in the standing horse
Authors: Mitchell Colin F. , Richbourg Heather A. , Goupil Brad A. , Gillett Ashley N. , McNulty Margaret A. 
Published: January 2017

AbstractObjectiveTo describe a biopsy technique in standing horses with minimal morbidity that consistently provides a substantial bone biopsy with intact, undamaged architecture.Study DesignExperimental, prospective study.AnimalsTen Thoroughbred horses.MethodsBiopsies were obtained from the tuber coxae of 10 sedated, standing horses using an oscillating saw. Bilateral biopsies, separated by 60 days, were evaluated with micro‐computed tomography (microCT). The first biopsy was prepared for decalcified histology; the second for undecalcified histology. Both biopsies were evaluated qualitatively for histologic quality.ResultsThe biopsy technique did not result in any significant complications, was well tolerated and all biopsies were of good histologic quality.ConclusionCortical and trabecular bone biopsies can be successfully collected from the tuber coxa using a simple technique that creates minimal morbidity and allows sequential samples to be collected. The biopsies were larger than those described previously, provided adequate bone for multiple histologic sections, and had intact, undamaged architecture on examination with microCT and light microscopy.
Barreras geográficas de acceso a los servicios de salud oral en el departamento de Nariño, Colombia
Authors: Caicedo-Rosero Ángela Viviana , Estrada-Montoya John Harold 
Published: January 2017

<p>Estudio de corte trasversal cuyo objetivo fue identificar presencia de barreras geográficas de acceso a salud y elaborar un inventario de prestadores de salud oral del departamento de Nariño, con información de 64 municipios. <em>Metodología: </em>se desarrolló un sistema de medida de distancia y tiempo, identificando el tiempo de viaje que toma el desplazamiento de un municipio hasta la capital en diferentes medios de transporte. Como determinante de barrera de acceso: tiempo de viaje mayor a cuatro horas y distancia mayor a 25 km. <em>Resultados: </em>se identificaron 305 prestadores públicos, 1062 privados; en salud oral 670 prestadores. Nariño cuenta con primer nivel de atención en todos los municipios, segundo en cuatro y tercero en Pasto. De los 64 municipios tres no tienen barrera de acceso. <em>Conclusiones: </em>el tiempo de viaje y el medio de transporte son determinantes de barrera de acceso a salud, especialmente en las áreas del Pacífico de Nariño. </p>
Resilience Analysis Framework for Interconnected Critical
Infrastructures
Authors: Liu X. , Ferrario E. , Zio E. 
Published: January 2017

Abstract
To investigate the resilience of interconnected critical infrastructures (CIs), a framework combining dynamic modeling and resilience analysis is proposed. Resilience is defined in this work as the capacity of a system to absorb the impacts of perturbations and recover quickly from disruptive states. It is seen as a property of the system, which depends on a number of design, operation, and control parameters. Within this framework, we introduce the concept of resilience regions in the parameters space: as long as the parameters values remain inside these regions during operation, the system visits only recoverable states or, in other words, it maintains nominal operation or recovers quickly to it. Based on this concept, we perform a resilience analysis of two interconnected critical infrastructures, a gas network and an electric power system. The analysis is performed by numerical calculation of the resilience conditions in terms of design, operation, and control parameters values for given failure scenarios. To render computationally feasible analysis, we resort to an abstract representation of the system dynamics by a linear model of switching dynamics. Although the high-level modeling adopted may suffer from predictive accuracy, the proposed framework can still provide valuable insights in the analysis of system resilience and its dependence on the design, operation, and control parameters under different failure scenarios, which can be valuable to inform the decision making process of CIs operators and other stakeholders.
Benefit of Distributed Security Queuing for Reducing Risks Associated
With Improvised Explosive Device Attacks in Airport Terminals
Authors: Grant Matthew J. , Stewart Mark G. 
Published: January 2017

Abstract
Brussels Airport ceased operations for 12 days after a coordinated improvised explosive device (IED) attack by suicide bombers in March 2016, demonstrating that critical transport hubs can be disrupted for significant durations by terrorists. Designers of critical infrastructure need to consider countermeasures to such attacks, reducing a target's attractiveness and improving opportunities for business continuity. This can be achieved by considering the cost–benefit of potential countermeasures during the design phase for infrastructure. This paper uses a probabilistic risk assessment (PRA) model for IED attack to assess the costs and benefits of using distributed security queuing at airport terminals. Our results demonstrate that the use of distributed security queuing will offer casualty reductions when used in preference to centralized security queuing. However, when considering the cost–benefit of introducing distributed security queuing, on the basis of a single small to medium IED attack, it is likely that implementing this countermeasure would not be deemed cost-effective from a purely financial perspective, particularly when the threat likelihood is very low.
Seismic Reliability Assessment of a Concrete Water Tank Based on the
Bayesian Updating of the Finite Element Model
Authors: Marsili Francesca , Croce Pietro , Friedman Noemi , Formichi Paolo , Landi Filippo 
Published: January 2017

Abstract
Failure or malfunction of complex engineered networks involves relevant social and economic aspects, so that their maintenance is of primary importance. In assessing the reliability of such networks, it should be duly considered that they are a whole made of different parts, and that some of these individual parts or structures are often crucial to assure the proper operation of the entire network. Moreover, each of these structures can be considered a complex system by itself: structural reliability theory should be thus combined with advanced numerical analysis tools in order to obtain realistic estimates of the probability of failure. Accurate estimations are especially required in seismic zones, aiming to efficiently plan future interventions. This paper presents a method for the reliability assessment of a critical element of engineered networks. The method is discussed with special reference to a relevant case study: a concrete water tank, which is a key component of a water supply system. Special attention is devoted to the reliability assessment of the tank under seismic loads, based on a structural identification approach. The calibration of the finite element model (FEM) of the structure is carried out on probabilistic basis, applying the Bayes theorem and response surface methods. The proposed approach allows to significantly speed up the structural identification process, leading to sounder estimate of the input parameters. Finally, the seismic fragility curves of the structure are developed according to the relevant limit states, demonstrating that information regarding the global structural behavior and local checks can be effectively combined in structural reliability assessments.
Whole-Body Pose Estimation in Physical Rider–Bicycle Interactions
With a Monocular Camera and Wearable Gyroscopes
Authors: Lu Xiang , Yu Kaiyan , Zhang Yizhai , Yi Jingang , Liu Jingtai , Zhao Qijie 
Published: January 2017

Abstract
Pose estimation of human–machine interactions such as bicycling plays an important role to understand and study human motor skills. In this paper, we report the development of a human whole-body pose estimation scheme with application to rider–bicycle interactions. The pose estimation scheme is built on the fusion of measurements of a monocular camera on the bicycle and a set of small wearable gyroscopes attached to the rider's upper- and lower-limbs and the trunk. A single feature point is collocated with each wearable gyroscope and also on the body segment link where the gyroscope is not attached. An extended Kalman filter (EKF) is designed to fuse the visual-inertial measurements to obtain the drift-free whole-body poses. The pose estimation design also incorporates a set of constraints from human anatomy and the physical rider–bicycle interactions. The performance of the estimation design is validated through ten subject riding experiments. The results illustrate that the maximum errors for all joint angle estimations by the proposed scheme are within 3 degs. The pose estimation scheme can be further extended and used in other types of physical human–machine interactions.
Annual Dynamics of Shortwave Radiation as Consequence of Smoothing of Previously Plowed and Harrowed Soils in Poland
Authors: Cierniewski Jerzy , Królewicz Sławomir , Kaźmierowski Cezary 
Published: January 2017

AbstractSmoothing a rough, deeply plowed soil increases its albedo, which determines a lower amount of shortwave radiation absorbed by its surface layer. That surface emits less longwave radiation, leading to a reduction in its temperature, which in turn can affect the climate, influencing the energy transfer between soil, vegetation, and the atmosphere. This paper presents a multistage procedure for estimating the annual dynamics of shortwave radiation reflected from bare soils as a consequence of smoothing the previously plowed and disk-harrowed fields in Poland. This procedure takes into account the spatial diversity of soil units and their properties within bare soil surfaces (extracted from Landsat 8 images), analyzed using digital maps of land use and soils as well as soil datasets stored in soil databases. One minimum and two peaks were found in the annual distribution of the radiation amount reflected from the soils only when smoothing the data. Expressing this reflected radiation as a fraction of the daily energy reaching the studied areas with clear-skies, it was predicted that those spring and summer peaks can reach about 2.2%–2.3% and 1%, respectively, of the incident shortwave radiation for soils that had been plowed and disk harrowed.