bluuebunny/crossref_metadata_2025_split huggingface dataset:
The quality of employment in the early labour market experience of young Europeans
Authors: Berloffa Gabriella , Matteazzi Eleonora , Şandor Alina , Villa Paola 
Published: March 2019

Abstract
This paper presents a new approach to evaluating individuals’ employment quality, considering the evolution of individuals’ employment conditions over a period of time, instead of the quality of jobs held at a point in time. In particular, we present a new definition of employment quality, based on four dimensions: employment security, income security, income success and occupational success. Using EU-SILC data, we analyse the early labour market experience of young adults and the extent to which the achievement of employment quality around five years after leaving education varies according to gender, education and labour market institutions. Our findings suggest that there is still a pressing need to enhance women’s chances of remaining continuously in employment and to move up in the labour income distribution. Stricter rules on the use of temporary contracts appear to improve youth employment prospects in general, whereas a more stringent regulation of individual dismissals seems to generate some difficulties for high-school and university graduates.
Sutured and sutureless repair of postinfarction left ventricular free-wall rupture: a systematic review
Authors: Matteucci Matteo , Fina Dario , Jiritano Federica , Blankesteijn W Matthijs , Raffa Giuseppe Maria , Kowalewski Mariusz , Beghi Cesare , Lorusso Roberto 
Published: March 2019

SummaryPostinfarction left ventricular free-wall rupture is a potentially catastrophic event. Emergency surgical intervention is almost invariably required, but the most appropriate surgical procedure remains controversial. A systematic review, from 1993 onwards, of all available reports in the literature about patients undergoing sutured or sutureless repair of postinfarction left ventricular free-wall rupture was performed. Twenty-five studies were selected, with a total of 209 patients analysed. Sutured repair was used in 55.5% of cases, and sutureless repair in the remaining cases. Postoperative in-hospital mortality was 13.8% in the sutured group, while it was 14% in the sutureless group. A trend towards a higher rate of in-hospital rerupture was observed in the sutureless technique. The most common cause of in-hospital mortality (44%) was low cardiac output syndrome. In conclusion, sutured and sutureless repair for postinfarction left ventricular free-wall rupture showed comparable in-hospital mortality. However, because of the limited number of patients and the variability of surgical strategies in each reported series, further studies are required to provide more consistent data and lines of evidence.
Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data
Authors: Gervin Kristina , Salas Lucas A. , Bakulski Kelly M. , van Zelm Menno C. , Koestler Devin C. , Wiencke John K. , Duijts Liesbeth , Moll Henriëtte A. , Kelsey Karl T. , Kobor Michael S. , Lyle Robert , Christensen Brock C. , Felix Janine , Jones Meaghan J. 
Published: March 2019

AbstractBackgroundUmbilical cord blood (UCB) is commonly used in epigenome-wide association studies of prenatal exposures. Accounting for cell type composition is critical in such studies as it reduces confounding due to the cell specificity of DNA methylation (DNAm). In the absence of cell sorting information, statistical methods can be applied to deconvolve heterogeneous cell mixtures. Among these methods, reference-based approaches leverage age appropriate cell-specific DNA-methylation profiles to estimate cellular composition. In UCB, four reference datasets comprising DNAm signatures profiled in purified cell populations have been published using the Illumina 450K and 850K EPIC arrays. These datasets are biologically and technically different, and currently there is no consensus on how to best apply them. Here, we systematically evaluate and compare these datasets and provide recommendations for reference-based UCB deconvolution.ResultsWe first evaluated the four reference datasets to ascertain both the purity of the samples and the potential cell cross-contamination. We filtered samples and combined datasets to obtain a joint UCB reference. We selected deconvolution libraries using two different approaches: automatic selection using the top differentially methylated probes from the functionpickCompProbesin minfi and a standardized library selected using the IDOL (Identifying Optimal Libraries) iterative algorithm. We compared the performance of each reference separately and in combination, using the two approaches for reference library selection, and validated the results in an independent cohort (Generation R Study, n=191) with matched FACS measured cell counts. Strict filtering and combination of the references significantly improved the accuracy and efficiency of cell type estimates. Ultimately, the IDOL library outperformed the library from the automatic selection method implemented inpickCompProbes.ConclusionThese results have important implications for epigenetic studies in UCB as implementing this method will optimally reduce confounding due to cellular heterogeneity. This work provides guidelines for future reference-based UCB deconvolution and establishes a framework for combining reference datasets in other tissues.
A high-throughput delayed fluorescence method reveals underlying differences in the control of circadian rhythms inTriticum aestivumandBrassica napus
Authors: Rees Hannah , Duncan Susan , Gould Peter , Wells Rachel , Greenwood Mark , Brabbs Thomas , Hall Anthony 
Published: March 2019

AbstractBackgroundA robust circadian clock has been implicated in plant resilience, resource-use efficiency, competitive growth and yield. A huge number of physiological processes are under circadian control in plants including: responses to biotic and abiotic stresses; flowering time; plant metabolism; and mineral uptake. Understanding how the clock functions in crops such asTriticum aestivum(bread wheat) andBrassica napus(oilseed rape) therefore has great agricultural potential. Delayed fluorescence (DF) imaging has been shown to be applicable to a wide range of plant species and requires no genetic transformation. Although DF has been used to measure period length of both mutants and wild ecotypes ofArabidopsis, this assay has never been systematically optimised for crop plants. The physical size of bothB. napusandT. aestivumled us to develop a representative sampling strategy which enables high-throughput imaging of these crops.ResultsIn this study, we describe the plant-specific optimisation of DF imaging to obtain reliable circadian phenotypes with the robustness and reproducibility to detect diverging periods between cultivars of the same species. We find that the age of plant material, light regime and temperature conditions all significantly effect DF rhythms and describe the optimal conditions for measuring robust rhythms in each species. We also show that sections of leaf can be used to obtain period estimates with improved throughput for larger sample size experiments.ConclusionsWe present an optimized protocol for high-throughput phenotyping of circadian period specific to two economically valuable crop plants. Application of this method revealed significant differences between the periods of several widely grown elite cultivars. This method also identified intriguing differential responses of circadian rhythms inT. aestivumcompared toB. napus; specifically the dramatic change to rhythm robustness when plants were imaged under constant light versus constant darkness. This points towards diverging networks underling circadian control in these two species.
Genotype-free demultiplexing of pooled single-cell RNA-seq
Authors: Xu Jun , Falconer Caitlin , Nguyen Quan , Crawford Joanna , McKinnon Brett D. , Mortlock Sally , Pébay Alice , Hewitt Alex W. , Senabouth Anne , Andersen Stacey , Palpant Nathan , Chiu Han Sheng , Montgomery Grant W. , Powell Joseph , Coin Lachlan 
Published: March 2019

AbstractA variety of experimental and computational methods have been developed to demultiplex samples from pooled individuals in a single-cell RNA sequencing (scRNA-Seq) experiment which either require adding information (such as hashtag barcodes) or measuring information (such as genotypes) prior to pooling. We introduce scSplit which utilises genetic differences inferred from scRNA-Seq data alone to demultiplex pooled samples. scSplit also extracts a minimal set of high confidence presence/absence genotypes in each cluster which can be used to map clusters to original samples. Using a range of simulated, merged individual-sample as well as pooled multi-individual scRNA-Seq datasets, we show that scSplit is highly accurate and concordant with demuxlet predictions. Furthermore, scSplit predictions are highly consistent with the known truth in cell-hashing dataset. We also show that multiplexed-scRNA-Seq can be used to reduce batch effects caused by technical biases. scSplit is ideally suited to samples for which external genome-wide genotype data cannot be obtained (for example non-model organisms), or for which it is impossible to obtain unmixed samples directly, such as mixtures of genetically distinct tumour cells, or mixed infections. scSplit is available at: https://github.com/jon-xu/scSplit
Identification and characterization of putativeAeromonasspp. T3SS effectors
Authors: Rangel Luiz Thiberio , Marden Jeremiah , Colston Sophie , Setubal João Carlos , Graf Joerg , Gogarten J. Peter 
Published: March 2019

AbstractThe genetic determinants of bacterial pathogenicity are highly variable between species and strains. However, a factor that is commonly associated with virulent Gram-negative bacteria, including manyAeromonasspp., is the type 3 secretion system (T3SS), which is used to inject effector proteins into target eukaryotic cells. In this study, we developed a bioinformatics pipeline to identify T3SS effector proteins, applied this approach to the genomes of 105Aeromonasstrains isolated from environmental, mutualistic, or pathogenic contexts and evaluated the cytotoxicity of the identified effectors through their heterologous expression in yeast. The developed pipeline uses a two-step approach, where candidate families are initially selected using HMM profiles with minimal similarity scores against the Virulence Factors DataBase (VFDB), followed by strict comparisons against positive and negative control datasets, greatly reducing the number of false positives. Using our approach, we identified 21AeromonasT3SS likely effector groups, of which 8 represented known or characterized effectors, while the remaining 13 had not previously been described inAeromonas. We experimentally validated ourin silicofindings by assessing the cytotoxicity of representative effectors inSaccharomyces cerevisiaeBY4741, with 15 out of 21 assayed proteins eliciting a cytotoxic effect in yeast. The results of this study demonstrate the utility of our approach, combining a novelin silicosearch method within vivoexperimental validation, and will be useful in future research aimed at identifying and authenticating bacterial effector proteins from other genera.
Changes in the Physicochemical Properties and Microbial Communities of Rhizospheric Soil after Cassava/Peanut Intercropping
Authors: Tang Xiumei , Luo Saiyun , Huang Zhipeng , Wu Haining , Wang Jin , Shi Guoying , He Liangqiong , Xiong Faqian , Jiang Jing , Liu Jing , Liao Guojian , Tang Ronghua , He Longfei 
Published: March 2019

ABSTRACTCassava/peanut intercropping is a popular cultivation method in southern China and has the advantages of apparently increased yield and economic efficiency compared with monoculture, however, the ecological benefits of this method are poorly understood. This study aimed to investigate the effects of intercropping on the physicochemical properties and microbial community structures of soil. Field trials were performed to determine the effects of cassava/peanut intercropping on rhizospheric soil nutrient content, enzyme activities, microbial quantity and microbial community structure. The microbial community was characterized by 16S rRNA tag-based high-throughput sequencing on the Illumina MiSeq platform. Results showed that cassava/peanut intercropping could improve the physicochemical properties of rhizospheric soil by increasing the available nutrient content, pH, bacterial quantity, and some enzyme activities and by altering the microbial community structure. 16S rRNA gene sequencing demonstrated that the microbial community structure varied between the intercropping and monoculture systems. Nitrospirae, Verrucomicrobia and Gemmatimonadetes were more abundant in the intercropping system than in the monocultures. Redundancy analysis (RDA) revealed that the abundances ofDA101,PilimeliaandRamlibacterwere positively correlated with environmental parameters such as available nitrogen and pH, and these were dominant genera in the rhizospheric soil of the intercropped peanut plants.
Mortality among adults living with HIV treated for tuberculosis based on positive, negative, or no bacteriologic test results for tuberculosis: the IeDEA consortium
Authors: Humphrey John M , Mpofu Philani , Pettit April C. , Musick Beverly , Carter E. Jane , Messou Eugene , Marcy Olivier , Crabtree-Ramirez Brenda , Yotebieng Marcel , Anastos Kathryn , Sterling Timothy R. , Yiannoutsos Constantin , Diero Lameck , Wools-Kaloustian Kara ,   International Epidemiology Databases to Evaluate AIDS (IeDEA) Consortium
Published: March 2019

AbstractBackgroundIn resource-constrained settings, people living with HIV (PLWH) treated for tuberculosis (TB) despite negative bacteriologic tests have a higher mortality than those treated with positive tests. Many PLWH are treated without bacteriologic testing; their mortality compared to those with bacteriologic testing is uncertain.MethodsWe conducted an observational cohort study among PLWH ≥ 15 years of age who initiated TB treatment at clinical sites affiliated with four regions of the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium from 2012-2014: Caribbean, Central and South America, and Central, East, and West Africa. The primary exposure of interest was the TB bacteriologic test status at TB treatment initiation: positive, negative, or no test result. The hazard for death in the 12 months following TB treatment initiation was estimated using the Cox proportional hazard model, adjusted for patient- and site-level factors. Missing covariates were multiply imputed.ResultsAmong 2,091 PLWH included, the median age at TB treatment initiation was 36 years, 44% were female, 53% had CD4 counts ≤ 200 cells/mm3, and 52% were on antiretroviral treatment (ART). Compared to patients with positive bacteriologic tests, the adjusted hazard for death was higher among patients with no test results (HR 1.56, 95% CI 1.08-2.26) but not different than those with negative tests (HR 1.28, 95% CI 0.91-1.81). Older age was also associated with a higher hazard for death, while being on ART, having a higher CD4 count, West Africa region, and tertiary facility level were associated with lower hazards for death.ConclusionPLWH treated for TB with no bacteriologic test results were more likely to die than those treated with positive tests, underscoring the importance of TB bacteriologic diagnosis in resource-constrained settings. Research is needed to understand the causes of death among PLWH treated for TB in the absence of positive bacteriologic tests.
Direct inference of the distribution of fitness effects of spontaneous mutations inChlamydomonas reinhardtii
Authors: Böndel Katharina B. , Kraemer Susanne A. , Samuels Tobias S. , McClean Deirdre , Lachapelle Josianne , Ness Rob W. , Colegrave Nick , Keightley Peter D. 
Published: March 2019

AbstractSpontaneous mutations are the source of new genetic variation and are thus central to the evolutionary process. In molecular evolution and quantitative genetics, the nature of genetic variation depends critically on the distribution of fitness effects (DFE) of mutations. Spontaneous mutation accumulation (MA) experiments have been the principal approach for investigating the overall rate of occurrence and cumulative effect of mutations, but have not allowed the effects of individual mutations to be studied directly. Here, we crossed MA lines of the green algaChlamydomonas reinhardtiiwith its unmutated ancestral strain to create haploid recombinant lines, each carrying an average of 50% of the accumulated mutations in a variety of combinations. With the aid of the genome sequences of the MA lines, we inferred the genotypes of the mutations, assayed their growth rate as a measure of fitness, and inferred the DFE using a novel Bayesian mixture model that allows the effects of individual mutations to be estimated. We infer that the DFE is highly leptokurtic (L-shaped), and that a high proportion of mutations increase fitness in the laboratory environment. The inferred distribution of effects for deleterious mutations is consistent with a strong role for nearly neutral evolution. Specifically, such a distribution predicts that nucleotide variation and genetic variation for quantitative traits will be insensitive to change in the effective population size.
Capturing digital (in)equity in teaching and learning: a sociocritical approach
Authors: Collin Simon , Brotcorne Périne 
Published: March 2019

Purpose
The purpose of this paper is to present a sociocritical approach and describe how it is relevant to the study of digital equity in education.

Design/methodology/approach
The method is based on a synthesis of the literature regarding critical approaches to digital technology in education.

Findings
A sociocritical approach is an attempt to formulate a sociological perspective combined with a critical dimension. It provides a relevant theoretical basis for addressing digital (in)equity issues.

Originality/value
Little use has been made of critical theories in the study of digital technology in education. That may seem surprising insofar as the study of digital technology in education is related to other fields having a well-established critical tradition. The authors build on their work and tailor it to the case of digital technology in education.
The SNARE protein FolVam7 mediates intracellular trafficking to regulate conidiogenesis and pathogenicity in Fusarium oxysporum f. sp. lycopersici
Authors: Li Bing , Gao Ying , Mao Hui‐Ying , Borkovich Katherine A. , Ouyang Shou‐Qiang 
Published: March 2019

SummarySoluble N‐ethylmaleimide‐sensitive factor attachment protein receptors (SNAREs) are conserved in fungi, plants and animals. The Vam7 gene encodes a v‐SNARE protein that involved in vesicle trafficking in fungi. Here, we identified and characterized the function of FolVam7, a homologue of the yeast SNARE protein Vam7p in Fusarium oxysporum f. sp. lycopersici (Fol), a fungal pathogen of tomato. FolVam7 contains SNARE and PX (Phox homology) domains that are indispensable for normal localization and function of FolVam7. Targeted gene deletion showed that FolVam7‐mediated vesicle trafficking is important for vegetative growth, asexual development, conidial morphology and plant infection. Further cytological examinations revealed that FolVam7 is localized to vesicles and vacuole membranes in the hyphae stage. Moreover, the ΔFolvam7 mutant is insensitive to salt and osmotic stresses and hypersensitive to cell wall stressors. Taken together, our results suggested that FolVam7‐mediated vesicle trafficking promotes vegetative growth, conidiogenesis and pathogenicity of Fol.
The p53/miRNAs/Ccna2 pathway serves as a novel regulator of cellular senescence: Complement of the canonical p53/p21 pathway
Authors: Xu Shun , Wu Weijia , Huang Haijiao , Huang Ruxiao , Xie Luoyijun , Su Ailing , Liu Shuang , Zheng Ruinian , Yuan Yuan , Zheng Hui‐ling , Sun Xuerong , Xiong Xing‐dong , Liu Xinguang 
Published: March 2019

AbstractAging is a multifactorial process characterized by the progressive deterioration of physiological functions. Among the multiple molecular mechanisms, microRNAs (miRNAs) have increasingly been implicated in the regulation of Aging process. However, the contribution of miRNAs to physiological Aging and the underlying mechanisms remain elusive. We herein performed high‐throughput analysis using miRNA and mRNA microarray in the physiological Aging mouse, attempted to deepen into the understanding of the effects of miRNAs on Aging process at the “network” level. The data showed that various p53 responsive miRNAs, including miR‐124, miR‐34a and miR‐29a/b/c, were up‐regulated in Aging mouse compared with that in Young mouse. Further investigation unraveled that similar as miR‐34a and miR‐29, miR‐124 significantly promoted cellular senescence. As expected, mRNA microarray and gene co‐expression network analysis unveiled that the most down‐regulated mRNAs were enriched in the regulatory pathways of cell proliferation. Fascinatingly, among these down‐regulated mRNAs, Ccna2 stood out as a common target of several p53 responsive miRNAs (miR‐124 and miR‐29), which functioned as the antagonist of p21 in cell cycle regulation. Silencing of Ccna2 remarkably triggered the cellular senescence, while Ccna2 overexpression delayed cellular senescence and significantly reversed the senescence‐induction effect of miR‐124 and miR‐29. Moreover, these p53 responsive miRNAs were significantly up‐regulated during the senescence process of p21‐deficient cells; overexpression of p53 responsive miRNAs or knockdown of Ccna2 evidently accelerated the cellular senescence in the absence of p21. Taken together, our data suggested that the p53/miRNAs/Ccna2 pathway might serve as a novel senescence modulator independent of p53/p21 pathway.
Impaired decision making following escalation of cocaine self‐administration predicts vulnerability to relapse in rats
Authors: Cocker Paul John , Rotge Jean‐Yves , Daniel Marie‐Laure , Belin‐Rauscent Aude , Belin David 
Published: March 2019

AbstractImpairments in cost‐benefit decision making represent a cardinal feature of drug addiction. However, whether these alterations predate drug exposure, thereby contributing to facilitating loss of control over drug intake, or alternatively arise as a result of drug use and subsequently confer vulnerability to relapse has yet to be determined. Male Sprague‐Dawley rats were trained to self‐administer (SA) cocaine during 19 daily long‐access (12‐h) sessions; conditions reliably shown to promote escalation. One week after cocaine SA, rats underwent an extinction/relapse test immediately followed by conditioned stimuli–, stress‐, and drug‐primed reinstatement challenges. The influence of escalated cocaine intake on decision making was measured over time by four test sessions of a rodent analogue of the Iowa Gambling Task (rGT), once prior to cocaine exposure and then 1 day, 1 week, and 1 month after the last SA session. Substantial individual variability was observed in the influence of escalated cocaine SA on decision‐making performance. A subset of rats displayed pronounced deficits, while others showed unaffected or even improved performance on the rat Gambling Task (rGT) 24 hours after the last SA session. When challenged with a relapse test after 1 week of forced abstinence, animals that showed impaired decision making following SA displayed an increased propensity to respond for cocaine under extinction. These data suggest that decision‐making deficits in individuals with drug addiction are not antecedent to—but arise as a consequence of—drug exposure. Moreover, these data indicate that susceptibility to the deleterious effects of drugs on decision making confers vulnerability toward relapse.