bluuebunny/crossref_metadata_2025_split huggingface dataset:
GWAS-based Machine Learning for Prediction of Age-Related Macular Degeneration Risk
Authors: Yan Qi , Jiang Yale , Huang Heng , Swaroop Anand , Chew Emily Y. , Weeks Daniel E. , Chen Wei , Ding Ying 
Published: September 2019

ABSTRACTNumerous independent susceptibility variants have been identified for Age-related macular degeneration (AMD) by genome-wide association studies (GWAS). Since advanced AMD is currently incurable, an accurate prediction of a person’s AMD risk using genetic information is desirable for early diagnosis and clinical management. In this study, genotype data of 32,215 Caucasian individuals with age above 50 years from the International AMD Genomics Consortium in dbGAP were used to establish and validate prediction models for AMD risk using four different machine learning approaches: neural network, lasso regression, support vector machine, and random forest. A standard logistic regression model was also considered using a genetic risk score. To identify feature SNPs for AMD prediction models, we selected the genome-wide significant SNPs from GWAS. All methods achieved good performance for predicting normal controls versus advanced AMD cases (AUC=0.81∼0.82 in a separate test dataset) and normal controls versus any AMD (AUC=0.78∼0.79). By applying the state-of-art machine learning approaches on the large AMD GWAS data, the predictive models we established can provide an accurate estimation of an individual’s AMD risk profile across the person’s lifespan based on a comprehensive genetic information.
Heterogeneous genetic invasions of three insecticide resistance mutations in Indo-Pacific populations ofAedes aegypti(L.)
Authors: Endersby-Harshman Nancy M. , Schmidt Thomas L. , Chung Jessica , van Rooyen Anthony , Weeks Andrew R. , Hoffmann Ary A. 
Published: September 2019

AbstractNations throughout the Indo-Pacific region use pyrethroid insecticides to controlAedes aegypti, the mosquito vector of dengue, often without knowledge of pyrethroid resistance status of the pest or origin of resistance. Two mutations (V1016G + F1534C) in the sodium channel gene (Vssc) ofAe. aegyptimodify ion channel function and cause target-site resistance to pyrethroid insecticides, with a third mutation (S989P) having a potential additive effect. Of 27 possible genotypes involving these mutations, some allelic combinations are never seen while others predominate. Here, five allelic combinations common inAe. aegyptifrom the Indo-Pacific region are described and their geographical distributions investigated using genome-wide SNP markers. We tested the hypothesis that resistance allele combinations evolvedde novoin populations, versus the alternative that dispersal ofAe. aegyptibetween populations facilitated genetic invasions of allele combinations. We used latent factor mixed-models to detect SNPs throughout the genome that showed structuring in line with resistance allele combinations and compared variation at SNPs within theVsscgene with genome-wide variation. Mixed-models detected an array of SNPs linked to resistance allele combinations, all located within or in close proximity to theVsscgene. Variation at SNPs within theVsscgene was structured by resistance profile, while genome-wide SNPs were structured by population. These results demonstrate that alleles near to resistance mutations have been transferred between populations via linked selection. This indicates that genetic invasions have contributed to the widespread occurrence ofVsscallele combinations inAe. aegyptiin the Indo-Pacific region, pointing to undocumented mosquito invasions between countries.
Quorum sensing inBacillus subtilisslows down biofilm formation by enabling sporulation bet hedging
Authors: Spacapan Mihael , Danevčič Tjaša , Štefanic Polonca , Mandic-Mulec Ines 
Published: September 2019

1.2ABSTRACTThe ComQXPA quorum sensing (QS) system ofBacillus subtilis, a Gram-positive, industrially relevant, endospore forming bacterium, promotes surfactin production. This lipopeptide increases transcription of several genes involved in biofilm matrix synthesis via the Spo0A-P master regulator. We hypothesized that the inactivation of the QS system will therefore result in decreased rates of floating biofilm formation. We find that this is not the case and that the QS deficient mutant forms pellicles with a faster rate and produces more biofilm matrix components than the wild type. As Spo0A-P is the master regulator of sporulation initiation we hypothesized that the ComQXPA dependent signaling promotes sporulation and consequently slows the growth rate of the wild type strain. Indeed, our results confirm that cells with the inactive QS initiate endospore formation in biofilms later and more synchronously than the wild type, as evidenced by spore frequencies and the PspoIIQpromoter activity. We argue, that the QS system acts as a switch that promotes stochastic sporulation initiation and consequently bet hedging behavior. By committing a subpopulation of cells to sporulation early during growth, wild type population grows slower and produces thinner biofilms but also assures better survival under stressful conditions.1.1IMPORTANCEBacillus subtilisis widely employed model organism to study biofilm formation and sporulation in Gram-positive bacteria. The ComQXPA quorum sensing (QS) system indirectly increases the transcription of genes involved in biofilm matrix formation, which predicts a positive role of this QS in biofilm development Here we show that QS mutants actually form more matrix components per pellicle than the wild type and that their pellicles are thicker and form with a faster rate. We explain this, by showing that cells with an inactive QS exhibit a delay in sporulation entry, which is also more synchronous relative to the wild type. We argue, that the ComQXPA QS system acts as a switch that contributes to the stochastic sporulation initiation and though this path promotes bet hedging behavior. This finding is important in terms of “quorum quenching” strategies aiming to down modulate biofilm development through inhibition of QS signaling and underscores the richness of QS regulated phenotypic outcomes among bacterial species.
Predicting protein subcellular location using learned distributed representations from a protein-protein network
Authors: Pan Xiaoyong , Chen Lei , Liu Min , Huang Tao , Cai Yu-Dong 
Published: September 2019

AbstractFunctions of proteins are in general related to their subcellular locations. To identify the functions of a protein, we first need know where this protein is located. Interacting proteins tend to locate in the same subcellular location. Thus, it is imperative to take the protein-protein interactions into account for computational identification of protein subcellular locations.In this study, we present a deep learning-based method, node2loc, to predict protein subcellular location. node2loc first learns distributed representations of proteins in a protein-protein network using node2vec, which acquires representations from unlabeled data for downstream tasks. Then the learned representations are further fed into a recurrent neural network (RNN) to predict subcellular locations. Considering the severe class imbalance of different subcellular locations, Synthetic Minority Over-sampling Technique (SMOTE) is applied to artificially boost subcellular locations with few proteins.We construct a benchmark dataset with 16 subcellular locations and evaluate node2loc on this dataset. node2loc yields a Matthews correlation coefficient (MCC) value of 0.812, which outperforms other baseline methods. The results demonstrate that the learned presentations from a protein-protein network have strong discriminate ability for classifying protein subcellular locations and the RNN is a more powerful classifier than traditional machine learning models. node2loc is freely available athttps://github.com/xypan1232/node2loc.
Antagonistic Regulation of Circadian Output and Synaptic Development by the E3 Ubiquitin Ligase JETLAG and the DYSCHRONIC-SLOWPOKE Complex
Authors: Lamaze Angelique , Jepson James E.C , Akpoghiran Oghenerukevwe , Koh Kyunghee 
Published: September 2019

SummaryCircadian output genes act downstream of the clock to promote rhythmic changes in behavior and physiology, yet their molecular and cellular functions are not well understood. Here we characterize an interaction between regulators of circadian entrainment, output and synaptic development in Drosophila that influences clock-driven anticipatory increases in morning and evening activity. We previously showed the JETLAG (JET) E3 Ubiquitin ligase resets the clock upon light exposure, while the PDZ protein DYSCHRONIC (DYSC) regulates circadian locomotor output and synaptic development. Surprisingly, we find that JET and DYSC antagonistically regulate synaptic development at the larval neuromuscular junction, and reduced JET activity rescues arrhythmicity of dysc mutants. Consistent with our prior finding that DYSC regulates SLOWPOKE (SLO) potassium channel expression, jet mutations also rescue circadian and synaptic phenotypes in slo mutants. Collectively, our data suggest that JET, DYSC and SLO promote circadian output in part by regulating synaptic morphology.HighlightsLoss of DYSC differentially impacts morning and evening oscillatorsReduced JET activity rescues the dysc and slo arrhythmic phenotypeReduced JET activity causes synaptic defects at the larval NMJJET opposes DYSC and SLO function at the NMJ synapse
Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing
Authors: Chen Dafu , Du Yu , Fan Xiaoxue , Zhu Zhiwei , Jiang Haibin , Wang Jie , Fan Yuanchan , Chen Huazhi , Zhou Dingding , Xiong Cuiling , Zheng Yanzhen , Xu Xijian , Luo Qun , Guo Rui 
Published: September 2019

AbstractAscosphaera apis is a widespread fungal pathogen of honeybee larvae that results in chalkbrood disease, leading to heavy losses for the beekeeping industry in China and many other countries. This work was aimed at generating a full-length transcriptome of A. apis using PacBio single-molecule real-time (SMRT) sequencing. Here, more than 23.97 Gb of clean reads was generated from long-read sequencing of A. apis mecylia, including 464,043 circular consensus sequences (CCS) and 394,142 full-length non-chimeric (FLNC) reads. In total, we identified 174,095 high-confidence transcripts covering 5141 known genes with an average length of 2728 bp. We also discovered 2405 genic loci and 11,623 isoforms that have not been annotated yet within the current reference genome. Additionally, 16,049, 10,682, 4520 and 7253 of the discovered transcripts have annotations in the Non-redundant protein (Nr), Clusters of Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, 1205 long non-coding RNAs (lncRNAs) were identified, which have less exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percent, lower expression levels, and fewer alternative splicing (AS) evens, compared with protein-coding transcripts. A total of 253 members from 17 transcription factor (TF) families were identified from our transcript datasets. Finally, the expression of A. apis isoforms was validated using a molecular approach. Overall, this is the first report of a full-length transcriptome of entomogenous fungi including A. apis. Our data offer a comprehensive set of reference transcripts and hence contributes to improving the genome annotation and transcriptomic study of A. apis.
Straightforward clustering of single-cell RNA-Seq data with t-SNE and DBSCAN
Authors: Wagner Florian 
Published: September 2019

AbstractClustering of cells by cell type is arguably the most common and repetitive task encountered during the analysis of single-cell RNA-Seq data. However, as popular clustering methods operate largely independently of visualization techniques, the fine-tuning of clustering parameters can be unintuitive and time-consuming. Here, I propose Galapagos, a simple and effective clustering workflow based on t-SNE and DBSCAN that does not require a gene selection step. In practice, Galapagos only involves the fine-tuning of two parameters, which is straightforward, as clustering is performed directly on the t-SNE visualization results. Using peripheral blood mononuclear cells as a model tissue, I validate the effectiveness of Galapagos in different ways. First, I show that Galapagos generates clusters corresponding to all main cell types present. Then, I demonstrate that the t-SNE results are robust to parameter choices and initialization points. Next, I employ a simulation approach to show that clustering with Galapagos is accurate and robust to the high levels of technical noise present. Finally, to demonstrate Galapagos’ accuracy on real data, I compare clustering results to true cell type identities established using CITE-Seq data. In this context, I also provide an example of the primary limitation of Galapagos, namely the difficulty to resolve related cell types in cases where t-SNE fails to clearly separate the cells. Galapagos helps to make clustering scRNA-Seq data more intuitive and reproducible, and can be implemented in most programming languages with only a few lines of code.
Reconstructing species evolutionary trees using the numerical features of microRNA
Authors: Zhu Rongsheng , Xin Dawei , Zhang Zhanguo , Hu Zhenbang , Li Yang , Chen Qingshan 
Published: September 2019

AbstractResearch has revealed that some microRNAs show obvious lineage or species specificity, but others show highly conserved properties among species. Based on these properties, we aimed to reconstruct a species evolution tree using a new technique that refers to the numerical features of microRNA. First, we selected 132 microRNA numerical features that included base content, secondary structure matching state frequency, free energy features and information entropy features, and 32 species that included 22 animals, 9 plants and a representative virus group. Second, we found several significantly different numerical features among lineages or species by statistical analysis and confirmed that differences in each numerical feature were not identical. Third, we designed a comprehensive feature and confirmed that it showed obvious lineage and species specificity. Last, species trees were built using the comprehensive feature. The results showed that the reconstructed species tree was almost in keeping with the actual chronological order of species evolution. This indicated that our analysis was effective. Our research strategy offers a new route for investigating species evolution.
Discovery Function Labels Based On Numerical Features Of MicroRNA Found In Plant
Authors: Zhu Rongsheng , Liu Jinglu , Xin Dawei , Zhang Zhanguo , Hu Zhenbang , Li Yang , Chen Qingshan 
Published: September 2019

AbstractMicroRNAs(miRNAs),are a class of small endogenous non-coding RNAs that play Important post-transcriptional regulation role by degrading targeted mRNAs or repressing mRNA translation. We screened 84 miRNAs belonging to 21 conserved family from 4014 miRNAs in miRBase database which distributed in 47 plant species. Of the predicted 274 target genes,42 GO terms were found in the Gene Ontology. With the 135 numerical features which extracted by perl program, the difference significantly result of ANOVA (P<0.001) and multiple comparison show that the function labels G…,GC content and Helix in biological process, cellular component and biological function, respectively. Our result have suggested a potential connection between numerical features of miRNAs and the function of target genes of miRNAs.
The promoters and the barriers for organizational culture change in a Finnish construction company
Authors: Teräväinen Ville Juhani , Junnonen Juha-Matti 
Published: September 2019

Purpose
The construction industry has struggled with efficiency issues for decades. Organizational culture is identified as one of the biggest hindrances for the enhancement of efficiency in a highly labor-intensive sector such as construction. Based on recent academic studies, Finnish construction industry professionals would embrace clan and adhocracy culture features to achieve a better level of construction efficiency. The purpose of this paper is to investigate the promoters and the barriers for making the desired culture change happen in the case company.

Design/methodology/approach
The paper presents a semi-structured theme interview case study, including 12 in-depth interviews. The interviews were recorded, and later, transcribed into text, which forms the empirical data of this paper.

Findings
The Finnish construction industry must adopt a holistic approach to enhance its prevailing level of efficiency through the culture change. Basic learning and knowledge management processes seem to be missing from the industry and organizational levels. Better knowledge management in the case company would be the first step to start fixing this problem.

Research limitations/implications
Because of the nature of a case study, the research results can be generalized only with caution in the Finnish construction industry. Generalizing the findings in another country would require further studies in a different cultural environment, e.g. in another European country.

Practical implications
The paper includes implications for the development of the organizational culture on the Finnish construction industry level and on an organizational level.

Originality/value
The found influencers are discussed through Engeström’s activity model for the first time in the construction culture context.
Liberal gender equality and social difference: an institutional ethnography
Authors: Reddy Raghunandan 
Published: September 2019

PurposeThe purpose of this paper is to examine the workplace experiences of women employees during maternity and post-maternity periods to reveal the institutional order that coordinated the social relations and shaped their experiences through local and extra-local texts.Design/methodology/approachThe institutional ethnography research framework allowed for mapping of workplace experiences of women employees during their maternity and post-maternity periods in their local context, connecting them to the invisible extra-local social relations.FindingsThe research study explored the disjuncture between the gender diversity initiatives that aimed at the inclusion of women employees and the workplace experiences of women employees in terms of work disengagement and work role degradation, including career discontinuity.Practical implicationsThe gender diversity and inclusion initiatives of an organization need to examine the local and extra-local institutional texts that govern their context and coordinate social relations, such that there is no inconsistency between the intentions, implementation and outcomes.Social implicationsThe state needs to revisit the maternity benefit act to provide additional measures to protect the career continuity of women, who choose maternity at some point in their work lives.Originality/valueThe paper explored the institutional order that influences the career continuity of women employees during maternity and post-maternity periods using institutional ethnography research framework in an information technology services organization in India. No such research study has even been attempted.
Improving the forming quality of fused filament fabrication parts by applied vibration
Authors: Jiang Shijie , Siyajeu Yannick , Shi Yinfang , Zhu Shengbo , Li He 
Published: September 2019

Purpose
The purpose of this study is to investigate the efficiency of applied vibration in improving the forming quality (mechanical property and dynamics characteristics) of fused filament fabrication (FFF) parts.

Design/methodology/approach
A vibrating FFF three-dimensional printer was set up, with which the samples fabricated in different directions were manufactured separately without and with vibration applied. A series of experimental tests, including tensile tests, dynamics tests and scanning electron microscopy (SEM) tests, were performed on these samples to experimentally quantify the effect of applied vibration on their forming quality.

Findings
It has been found that the applied vibration can significantly increase the tensile strength and plasticity of the samples built in Z-direction, and obviously decrease the orthogonal anisotropy. It can also significantly change the sample’s natural frequency, decrease the resonant response and increase the modal damping ratio, thus improve the anti-vibration capability of FFF samples. In addition, the SEM analysis confirmed that applying vibration into FFF process could improve the forming quality of the fabricated part.

Research limitations/implications
Future research may be focused on investigating the efficiency of applied vibration in improving the forming quality of parts fabricated by the other additive manufacturing techniques.

Practical implications
This study helps to improve the reliability of FFF parts and extend the application range of FFF technology.

Originality/value
A novel method to improve the forming quality of FFF parts is provided and the available information about the performance of dynamics characteristics.
Is workplace bullying always perceived harmful? The cognitive appraisal theory of stress perspective
Authors: Majeed Mehwish , Naseer Saima 
Published: September 2019

The present study expands the literature on bullying by unveiling why and when bullying might produce positive outcomes. Employing the cognitive appraisal theory of stress and coping, we hypothesize eustress as an important mechanism through which bullying might enhance the victim's job performance, career success, and creativity. Moreover, we hypothesized psychological capital as a moderator in the workplace bullying‐eustress relationship. We collected temporally segregated field data at three time intervals with a time lag of 2–3 weeks from matched data of employees and their fellow peers (n = 321) belonging to the service sector of Pakistan. Utilizing PROCESS macro, the results substantiated our hypothesized moderated mediation model, in that workplace bullying led to higher performance, career success and employee creativity through the mechanism of eustress and this indirect effect was stronger for individuals who possessed higher psychological capital. Our study opens up a new avenue in the workplace bullying literature by emphasizing the different side of bullying in an eastern cultural context.