bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associating transcriptional regulation for rapid germination of rapeseed (Brassica napus L.) under low temperature stress through weighted gene co-expression network analysis
Authors: Luo Tao , Xian Mengzhu , Zhang Chen , Zhang Chunni , Hu Liyong , Xu Zhenghua 
Published: January 2019

AbstractSlow germination speed caused by low temperature stress intensifies the risk posed by adverse environmental factors, contributing to low germination rate and reduced production of rapeseed. The purpose of this study was to understand the transcriptional regulation mechanism for rapid germination of rapeseed. The results showed that seed components and size do not determine the seed germination speed. Different temporal transcriptomic profiles were generated under normal and low temperature conditions in genotypes with fast and slow germination speeds. Using weight gene co-expression network analysis, 37 823 genes were clustered into 15 modules with different expression patterns. There were 10 233 and 9111 differentially expressed genes found to follow persistent tendency of up- and down-regulation, respectively, which provided the conditions necessary for germination. Hub genes in the continuous up-regulation module were associated with phytohormone regulation, signal transduction, the pentose phosphate pathway, and lipolytic metabolism. Hub genes in the continuous down-regulation module were involved in ubiquitin-mediated proteolysis. Through pairwise comparisons, 1551 specific upregulated DEGs were identified for the fast germination speed genotype under low temperature stress. These DEGs were mainly enriched in RNA synthesis and degradation metabolisms, signal transduction, and defense systems. Transcription factors, including WRKY, bZIP, EFR, MYB, B3, DREB, NAC, and ERF, are associated with low temperature stress in the fast germination genotype. The aquaporin NIP5 and late embryogenesis abundant (LEA) protein genes contributed to the water uptake and transport under low temperature stress during seed germination. The ethylene/H2O2-mediated signal pathway plays an important role in cell wall loosening and embryo extension during germination. The ROS-scavenging system, including catalase, aldehyde dehydrogenase, and glutathione S-transferase, was also upregulated to alleviate ROS toxicity in the fast germinating genotype under low temperature stress. These findings should be useful for molecular assisted screening and breeding of fast germination speed genotypes for rapeseed.
Functional and morphological changes of the retinal vessels in Alzheimer’s disease and mild cognitive impairment
Authors: Querques Giuseppe , Borrelli Enrico , Sacconi Riccardo , De Vitis Luigi , Leocani Letizia , Santangelo Roberto , Magnani Giuseppe , Comi Giancarlo , Bandello Francesco 
Published: January 2019

AbstractImaging and histopathological studies have demonstrated that structural changes of the retina affect subjects with Alzheimer’s disease (AD) or mild cognitive impairment (MCI). The aim of this study was to quantitatively investigate the retinal vessels in these disorders, using dynamic vessel analyzer (DVA) and optical coherence tomography angiography (OCTA) analysis. Twelve subjects with AD, 12 subjects with MCI, and 32 gender- and age-matched controls were prospectively enrolled. Mean ± SD age was 72.9 ± 7.2 years in the AD group, 76.3 ± 6.9 years in the MCI group, and 71.6 ± 5.9 years in the control group (p = 0.104). In the DVA dynamic analysis, the arterial dilation was decreased in the AD group (0.77 ± 2.06%), in the comparison with the control group (3.53 ± 1.25%, p = 0.002). The reaction amplitude was decreased both in AD (0.21 ± 1.80%, <0.0001) and MCI (2.29 ± 1.81%, p = 0.048) subjects, compared with controls (3.86 ± 1.94%). OCTA variables did not differ among groups. In the Pearson correlation analysis, amyloid β level in the cerebrospinal fluid was directly correlated with the arterial dilation (R = 0.441, p = 0.040) and reaction amplitude (R = 0.580, p = 0.005). This study demonstrate that Alzheimer’s and MCI subjects are characterized by a significant impairment of the retinal neurovascular coupling. This impairment is inversely correlated with the level of amyloid β in the cerebrospinal fluid.
Predicting prolonged sick leave among trauma survivors
Authors: von Oelreich Erik , Eriksson Mikael , Brattström Olof , Discacciati Andrea , Strömmer Lovisa , Oldner Anders , Larsson Emma 
Published: January 2019

AbstractMany survivors after trauma suffer from long-term morbidity. The aim of this observational cohort study was to develop a prognostic prediction tool for early assessment of full-time sick leave one year after trauma. Potential predictors were assessed combining individuals from a trauma register with national health registers. Two models were developed using logistic regression and stepwise backward elimination. 4458 individuals were included out of which 488 were on sick leave full-time 12 months after the trauma. One comprehensive and one simplified model were developed including nine and seven predictors respectively. Both models showed excellent discrimination (AUC 0.81). The comprehensive model had very good calibration, and the simplified model good calibration. Prediction models can be used to assess post-trauma sick leave using injury-related variables as well as factors not related to the trauma per se. Among included variables, pre-injury sick leave was the single most important predictor for full-time sick leave one year after trauma. These models could facilitate a more efficient use of resources, targeting groups for follow-up interventions to improve outcome. External validation is necessary in order to evaluate generalizability.
Understanding phosphoinositides: rare, dynamic, and essential membrane phospholipids
Authors: Dickson Eamonn J. , Hille Bertil 
Published: January 2019

Abstract
Polyphosphoinositides (PPIs) are essential phospholipids located in the cytoplasmic leaflet of eukaryotic cell membranes. Despite contributing only a small fraction to the bulk of cellular phospholipids, they make remarkable contributions to practically all aspects of a cell's life and death. They do so by recruiting cytoplasmic proteins/effectors or by interacting with cytoplasmic domains of membrane proteins at the membrane–cytoplasm interface to organize and mold organelle identity. The present study summarizes aspects of our current understanding concerning the metabolism, manipulation, measurement, and intimate roles these lipids play in regulating membrane homeostasis and vital cell signaling reactions in health and disease.
Glutathione S-transferase gene polymorphisms and risk of nasal or colorectal polyposis
Authors: Zhang Yonglan , Zhang Haichao , Lin Peng , Zhang Guimin 
Published: January 2019

Abstract
We observed inconsistent conclusions regarding the genetic role of glutathione S-transferase gene polymorphisms, including glutathione S-transferase M1 (GSTM1), glutathione S-transferase T1 (GSTT1) present/null, and glutathione S-transferase pi (GSTP1) Ile105Val polymorphisms, in the susceptibility to nasal or colorectal polyposis (NP or CP). Thus, we aimed to perform a meta-analysis to comprehensively evaluate this association by applying Stata/SE software. After the heterogeneity assumption, Mantel–Haenszel statistics were used to obtain the odds ratio (OR), 95% confidence interval (95% CI) and P-value of the association test (PA). We obtained a total of 235 articles by searching online databases. After screening, ten eligible case–control studies were finally enrolled in our meta-analysis. For the meta-analysis of the GSTT1 gene under present versus null, we observed a decreased risk of NP [OR = 0.65; PA=0.018], but not CP. In addition, we did not detect any evident association between the GSTM1 present/null polymorphism and NP or CP risk. For the meta-analysis of the GSTP1 Ile105Val polymorphism, compared with controls, an increased risk of NP cases was detected under the models of Val versus Ile (OR = 1.36; PA=0.027), Ile/Val versus Ile/Ile (OR = 1.70; PA=0.011) and Ile/Val+Val/Val versus Ile/Ile (OR = 1.65; PA=0.010). In conclusion, the null genotype of the GSTT1 polymorphism may be linked to an increased susceptibility to NP, whereas the Ile/Val genotype of the GSTP1 Ile105Val polymorphism may be associated with a decreased risk of NP.
Neutral endopeptidase inhibitors blunt kidney fibrosis by reducing myofibroblast formation
Authors: Bijkerk Roel , Aleksinskaya Marina A. , Duijs Jacques M.G.J. , Veth Jennifer , Husen Bettina , Reiche Dania , Prehn Cornelia , Adamski Jerzy , Rabelink Ton J. , De Mey Jo G.R. , van Zonneveld Anton Jan 
Published: January 2019

Abstract
Kidney fibrosis is the common pathophysiological mechanism in end-stage renal disease characterized by excessive accumulation of myofibroblast-derived extracellular matrix. Natriuretic peptides have been demonstrated to have cyclic guanosine monophosphate (cGMP)-dependent anti-fibrotic properties likely due to interference with pro-fibrotic tissue growth factor β (TGF-β) signaling. However, in vivo, natriuretic peptides are rapidly degraded by neutral endopeptidases (NEP). In a unilateral ureteral obstruction (UUO) mouse model for kidney fibrosis we assessed the anti-fibrotic effects of SOL1, an orally active compound that inhibits NEP and endothelin-converting enzyme (ECE). Mice (n=10 per group) subjected to UUO were treated for 1 week with either solvent, NEP-/ECE-inhibitor SOL1 (two doses), reference NEP-inhibitor candoxatril or the angiotensin II receptor type 1 (AT1)-antagonist losartan. While NEP-inhibitors had no significant effect on blood pressure, they did increase urinary cGMP levels as well as endothelin-1 (ET-1) levels. Immunohistochemical staining revealed a marked decrease in renal collagen (∼55% reduction, P&lt;0.05) and α-smooth muscle actin (α-SMA; ∼40% reduction, P&lt;0.05). Moreover, the number of α-SMA positive cells in the kidneys of SOL1-treated groups inversely correlated with cGMP levels consistent with a NEP-dependent anti-fibrotic effect. To dissect the molecular mechanisms associated with the anti-fibrotic effects of NEP inhibition, we performed a ‘deep serial analysis of gene expression (Deep SAGE)’ transcriptome and targeted metabolomics analysis of total kidneys of all treatment groups. Pathway analyses linked increased cGMP and ET-1 levels with decreased nuclear receptor signaling (peroxisome proliferator-activated receptor [PPAR] and liver X receptor/retinoid X receptor [LXR/RXR] signaling) and actin cytoskeleton organization. Taken together, although our transcriptome and metabolome data indicate metabolic dysregulation, our data support the therapeutic potential of NEP inhibition in the treatment of kidney fibrosis via cGMP elevation and reduced myofibroblast formation.
A Comment on Test Validation: The Importance of the Clinical Perspective
Authors: Daub Olivia , Skarakis-Doyle Elizabeth , Bagatto Marlene P. , Johnson Andrew M. , Cardy Janis Oram 
Published: January 2019

Purpose
The misuse of standardized assessments has been a long-standing concern in speech-language pathology and traditionally viewed as an issue of clinician competency and training. The purpose of this article is to consider the contribution of communication breakdowns between test developers and the end users to this issue.

Method
We considered the misuse of standardized assessments through the lens of the 2-communities theory, in which standardized tests are viewed as a product developed in 1 community (researchers/test developers) to be used by another community (frontline clinicians). Under this view, optimal test development involves a conversation to which both parties bring unique expertise and perspectives.

Results
Consideration of the interpretations that standardized tests are typically validated to support revealed a mismatch between these and the interpretations and decisions that speech-language pathologists typically need to make. Test development using classical test theory, which underpins many of the tests in our field, contributes to this mismatch. Application of item response theory could better equip clinicians with the psychometric evidence to support the interpretations they desire but is not commonly found in the standardized tests used by speech-language pathologists.

Conclusions
Advocacy and insistence on the consideration of clinical perspectives and decision making in the test validation process is a necessary part of our role. In improving the nature of the statistical evidence reported in standardized assessments, we can ensure these tools are appropriate to fulfill our professional obligations in a clinically feasible way.
The Subjective Experience of Inner Speech in Aphasia Is a Meaningful Reflection of Lexical Retrieval
Authors: Fama Mackenzie E. , Snider Sarah F. , Henderson Mary P. , Hayward William , Friedman Rhonda B. , Turkeltaub Peter E. 
Published: January 2019

Purpose
Individuals with aphasia often report that they feel able to say words in their heads, regardless of speech output ability. Here, we examine whether these subjective reports of successful “inner speech” (IS) are meaningful and test the hypothesis that they reflect lexical retrieval.

Method
Participants were 53 individuals with chronic aphasia. During silent picture naming, participants reported whether or not they could say the name of each item inside their heads. Using the same items, they also completed 3 picture-based tasks that required phonological retrieval and 3 matched auditory tasks that did not. We compared participants' performance on these tasks for items they reported being able to say internally versus those they reported being unable to say internally. Then, we examined the relationship of psycholinguistic word features to self-reported IS and spoken naming accuracy.

Results

Twenty-six participants reported successful IS on nearly all items, so they could not be included in the item-level analyses. These individuals performed correspondingly better than the remaining participants on tasks requiring phonological retrieval, but not on most other language measures. In the remaining group (
n
= 27), IS reports related item-wise to performance on tasks requiring phonological retrieval, but not to matched control tasks. Additionally, IS reports were related to 3 word characteristics associated with lexical retrieval, but not to articulatory complexity; spoken naming accuracy related to all 4 word characteristics. Six participants demonstrated evidence of unreliable IS reporting; compared with the group, they also detected fewer errors in their spoken responses and showed more severe language impairments overall.

Conclusions
Self-reported IS is meaningful in many individuals with aphasia and reflects lexical phonological retrieval. These findings have potential implications for treatment planning in aphasia and for our understanding of IS in the general population.
Massive star evolution: rotation, winds, and overshooting vectors in the mass-luminosity plane
Authors: Higgins Erin R. , Vink Jorick S. 
Published: January 2019

Context. Massive star evolution is dominated by various physical effects, including mass loss, overshooting, and rotation, but the prescriptions of their effects are poorly constrained and even affect our understanding of the main sequence.
Aims. We aim to constrain massive star evolution models using the unique test-bed eclipsing binary HD 166734 with new grids of MESA stellar evolution models, adopting calibrated prescriptions of overshooting, mass loss, and rotation.
Methods. We introduce a novel tool, called the mass-luminosity plane or M−L plane, as an equivalent to the traditional HR diagram, utilising it to reproduce the test-bed binary HD 166734 with newly calibrated MESA stellar evolution models for single stars.
Results. We can only reproduce the Galactic binary system with an enhanced amount of core overshooting (αov = 0.5), mass loss, and rotational mixing. We can utilise the gradient in the M−L plane to constrain the amount of mass loss to 0.5–1.5 times the standard prescription test-bed, and we can exclude extreme reduction or multiplication factors. The extent of the vectors in the M−L plane leads us to conclude that the amount of core overshooting is larger than is normally adopted in contemporary massive star evolution models. We furthermore conclude that rotational mixing is mandatory to obtain the correct nitrogen abundance ratios between the primary and secondary components (3:1) in our test-bed binary system.
Conclusions. Our calibrated grid of models, alongside our new M−L plane approach, present the possibility of a widened main sequence due to an increased demand for core overshooting. The increased amount of core overshooting is not only needed to explain the extended main sequence, but the enhanced overshooting is also needed to explain the location of the upper-luminosity limit of the red supergiants. Finally, the increased amount of core overshooting has – via the compactness parameter – implications for supernova explodability.
An XMM-Newton look at the strongly variable radio-weak BL Lac Fermi J1544–0639
Authors: Ursini F. , Bassani L. , Panessa F. , Pian E. , Bruni G. , Bazzano A. , Masetti N. , Sokolovsky K. , Ubertini P. 
Published: January 2019

Context. Fermi J1544–0639/ASASSN-17gs/AT2017egv was identified as a gamma-ray/optical transient on May 15, 2017. Subsequent multiwavelength observations suggest that this source may belong to the new class of radio-weak BL Lacs.
Aims. We studied the X-ray spectral properties and short-term variability of Fermi J1544–0639 to constrain the X-ray continuum emission mechanism of this peculiar source.
Methods. We present the analysis of an XMM-Newton observation, 56 ks in length, performed on February 21, 2018.
Results. The source exhibits strong X-ray variability, both in flux and spectral shape, on timescales of ∼10 ks, with a harder-when-brighter behaviour typical of BL Lacs. The X-ray spectrum is nicely described by a variable broken power law, with a break energy of around 2.7 keV consistent with radiative cooling due to Comptonization of broad-line region photons. We find evidence for a “soft excess”, nicely described by a blackbody with a temperature of ∼0.2 keV, consistent with being produced by bulk Comptonization along the jet.
Intermittent plasticity in individual grains: A study using high energy x-ray diffraction
Authors: Chatterjee K. , Beaudoin A. J. , Pagan D. C. , Shade P. A. , Philipp H. T. , Tate M. W. , Gruner S. M. , Kenesei P. , Park J.-S. 
Published: January 2019

Abstract
Long-standing evidence suggests that plasticity in metals may proceed in an intermittent fashion. While the documentation of intermittency in plastically deforming materials has been achieved in several experimental settings, efforts to draw connections from dislocation motion and structure development to stress relaxation have been limited, especially in the bulk of deforming polycrystals. This work uses high energy x-ray diffraction measurements to build these links by characterizing plastic deformation events inside individual deforming grains in both the titanium alloy, Ti-7Al, and the magnesium alloy, AZ31. This analysis is performed by combining macroscopic stress relaxation data, complete grain stress states found using far-field high energy diffraction microscopy, and rapid x-ray diffraction spot measurements made using a Mixed-Mode Pixel Array Detector. Changes in the dislocation content within the deforming grains are monitored using the evolution of the full 3-D shapes of the diffraction spot intensity distributions in reciprocal space. The results for the Ti-7Al alloy show the presence of large stress fluctuations in contrast to AZ31, which shows a lesser degree of intermittent plastic flow.
Measuring the difficulty of text translation
Authors: Liu Yanmei , Zheng Binghan , Zhou Hao 
Published: January 2019

AbstractThis paper explores the impact of text complexity on translators’ subjective perception of translation difficulty and on their cognitive load. Twenty-six MA translation students from a UK university were asked to translate three English texts with different complexity into Chinese. Their eye movements were recorded by an eye-tracker, and their cognitive load was self-assessed with a Likert scale before translation and NASA-TLX scales after translation. The results show that: (i) the intrinsic complexity measured by readability, word frequency and non-literalness was in line with the results received from informants’ subjective assessment of translation difficulty; (ii) moderate and positive correlations existed between most items in the self-assessments and the indicator (fixation and saccade durations) obtained by the eye-tracking measurements; and (iii) the informants’ cognitive load as indicated by fixation and saccade durations (but not for pupil size) increased significantly in two of the three texts along with the increase in source text complexity.
Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae)
Authors: Freitas Elyse S , Datta-Roy Aniruddha , Karanth Praveen , Grismer L Lee , Siler Cameron D 
Published: January 2019

AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.