bluuebunny/crossref_metadata_2025 huggingface dataset:
The Prevalence and Impact of Model Violations in Phylogenetic Analysis
Authors: Naser-Khdour Suha , Minh Bui Quang , Zhang Wenqi , Stone Eric A , Lanfear Robert
Published: September 2019

In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).
Stagnant-lid convection with diffusion and dislocation creep rheology: Influence of a non-evolving grain size
Authors: Schulz Falko , Tosi Nicola , Plesa Ana-Catalina , Breuer Doris
Published: September 2019

Heat transfer in one-plate planets is governed by mantle convection beneath the stagnant lid. Newtonian diffusion creep and non-Newtonian dislocation creep are the main mechanisms controlling large-scale mantle deformation. Diffusion creep strongly depends on the grain size (d), which in turn controls the relative importance of the two mechanisms. However, dislocation creep is usually neglected in numerical models of convection in planetary mantles. These mostly assume linear diffusion creep rheologies, often based on reduced activation parameters (compared to experimental values) that are thought to mimic the effects of dislocation creep and, as a side benefit, also ease the convergence of linear solvers. Assuming Mars-like parameters, we investigated the influence of a non-evolving grain size on Rayleigh–Bénard convection in the stagnant lid regime. In contrast to previous studies based on the Frank–Kamentskii approximation, we used Arrhenius laws for diffusion and dislocation creep—including temperature as well as pressure dependence—based on experimental measurements of olivine deformation. For d ≲ 2.5 mm, convection is dominated by diffusion creep. We observed an approximately equal partitioning between the two mechanisms for d ≈ 5 mm, while dislocation creep dominates for d ≳ 8 mm. Independent estimates of an average grain size of few mm up to 1 cm or more for present-day Mars suggest thus that dislocation creep plays an important role and possibly dominates the deformation. Mimicking dislocation creep convection using an effective linear rheology with reduced activation parameters, as often done in simulations of convection and thermal evolution of Mars, has significant limitations. Although it is possible to mimic mean temperature, mean lid thickness and Nusselt number, there are important differences in the flow pattern, root mean square velocity, and lid shape. The latter in particular affects the amount and distribution of partial melt, suggesting that care should be taken upon predicting the evolution of crust production when using simplified rheologies. The heat transport efficiency expressed in terms of the Nusselt number as a function of the Rayleigh number is thought to depend on the deformation mechanisms at play. We show that the relative volume in which dislocation creep dominates has nearly no influence on the Nusselt–Rayleigh scaling relation when a mixed rheology is used. In contrast, the flow pattern influences the Nusselt number more strongly. We derived a scaling law for the Nusselt number based on the mean lid thickness (〈L〉) and on the effective Rayleigh number (Raeff) obtained by suitably averaging the viscosity beneath the stagnant lid. We found that the Nusselt number follows the scaling $\mathrm{Nu} = 0.37 \langle L \rangle ^{-0.666} \mathrm{Ra}_{\mathrm{eff}}^{0.071}$ regardless of the deformation mechanism.
Is immune recovery different depending on the use of integrase strand transfer inhibitor-, non-nucleoside reverse transcriptase- or boosted protease inhibitor-based regimens in antiretroviral-naive HIV-infected patients?
Authors: Milanés-Guisado Yusnelkis , Gutiérrez-Valencia Alicia , Muñoz-Pichardo Juan Manuel , Rivero Antonio , Trujillo-Rodriguez Maria , Ruiz-Mateos Ezequiel , Espinosa Nuria , Roca-Oporto Cristina , Viciana Pompeyo , López-Cortés Luis F
Published: September 2019

Objectives

To analyse whether integrase inhibitor (InSTI)-based regimens achieve better immunological recovery than NNRTI- or boosted PI (bPI)-based regimens as initial ART.

Methods

In a retrospective analysis, we selected patients who initiated ART with two NRTIs plus an InSTI, an NNRTI or a bPI and maintained both the same ‘third drug’ and an HIV-RNA <50 copies/mL in ≥95% of determinations once undetectable viral load had been achieved. We compared CD4+ count, %CD4+ and CD4+/CD8+ ratio recovery over 2 years. Data were analysed using mixed-effects regression models for repeated measures.

Results

Of the 836 patients included, 208, 481 and 147 initiated with InSTI, NNRTI and bPI, respectively. For CD4+, %CD4+ and CD4+/CD8+ two main slopes were identified: from month 0 to month 6, with the highest increments; and from month 6 to month 24, with smaller increases every semester. Although the patients on InSTI achieved undetectable viral load faster, for CD4+ and %CD4+ there were no differences in the slopes of change according to the third drug either for the first phase (P = 0.137 and P = 0.393, respectively) or from month 6 onwards (P = 0.834 and P = 0.159, respectively). The increase in CD4+/CD8+ was slightly higher for bPI compared with InSTI (difference of 0.0119, 95% CI 0.0020–0.0205; P = 0.018), but clinically negligible. From month 6 onwards, no differences were found between treatment groups (P = 0.176).

Conclusions

Immune restoration measured as CD4+ count, %CD4+ and CD4+/CD8+ increases was independent of the third antiretroviral drug class used when given with two NRTIs.
Judgment in C-617/17 PZU Życie: ne bis in idem—First Steps towards a Twofold Test for idem?
Authors: Simpson Claire
Published: September 2019

Judgment of 3 April 2019, Powszechny Zakład Ubezpieczeń na Życie S. A, C-617/17, EU: C: 2019: 283.

Fining an undertaking in a single decision for breach of national and EU competition laws does not breach the principle of ne bis in idem.
Thermal desorption induced by chemical reaction on dust surface
Authors: Yamamoto Tetsuo , Miura Hitoshi , Shalabiea Osama M
Published: September 2019

We propose a new mechanism of desorption of molecules from dust surface heated by exothermic reactions and derive a formula for the desorption probability. This theory includes no parameter that is physically ambiguous. It can predict the desorption probabilities not only for one-product reactions but also for multiproduct reactions. Furthermore, it can predict desorption probability of a pre-adsorbed molecule induced by a reaction at a nearby site. This characteristic will be helpful to verify the theory by the experiments which involve complex reaction networks. We develop a quantitative method of comparing the predicted desorption probability with the experiments. This method is also applied to the theories proposed so far. It is shown that each of them reproduces the experiments with similar precision, although the amount of systematic experimental data that give definite desorption probability are limited at present. We point out the importance of clarifying the nature of the substrate used in the experiment, in particular, its thermal diffusivity. We show a way to estimate the substrate properties from systematic desorption experiments without their direct measurements.
OCCASO – III. Iron peak and α elements of 18 open clusters. Comparison with chemical evolution models and field stars
Authors: Casamiquela L , Blanco-Cuaresma S , Carrera R , Balaguer-Núñez L , Jordi C , Anders F , Chiappini C , Carbajo-Hijarrubia J , Aguado D S , del Pino A , Díaz-Pérez L , Gallart C , Pancino E
Published: September 2019

The study of open-cluster chemical abundances provides insights on stellar nucleosynthesis processes and on Galactic chemo-dynamical evolution. In this paper we present an extended abundance analysis of 10 species (Fe, Ni, Cr, V, Sc, Si, Ca, Ti, Mg, O) for red giant stars in 18 OCCASO clusters. This represents a homogeneous sample regarding the instrument features, method, line list and solar abundances from confirmed member stars. We perform an extensive comparison with previous results in the literature, and in particular with the Gaia FGK Benchmark stars Arcturus and $\mu$-Leo. We investigate the dependence of [X/Fe] with metallicity, Galactocentric radius (6.5 kpc < RGC < 11 kpc), age (0.3 Gyr < Age < 10 Gyr), and height above the plane (|z| < 1000 pc). We discuss the observational results in the chemo-dynamical framework, and the radial migration impact when comparing with chemical evolution models. We also use APOGEE DR14 data to investigate the differences between the abundance trends in RGC and |z| obtained for clusters and for field stars.
A deep learning model to emulate simulations of cosmic reionization
Authors: Chardin Jonathan , Uhlrich Grégoire , Aubert Dominique , Deparis Nicolas , Gillet Nicolas , Ocvirk Pierre , Lewis Joseph
Published: September 2019

We present a deep learning model trained to emulate the radiative transfer during the epoch of cosmological reionization. CRADLE (Cosmological Reionization And Deep LEarning) is an auto-encoder convolutional neural network that uses 2D maps of the star number density and the gas density field at z = 6 as inputs and that predicts 3D maps of the times of reionization treion as outputs. These predicted single fields are sufficient to describe the global reionization history of the intergalactic medium in a given simulation. We trained the model on a given simulation and tested the predictions on another simulation with the same parameters but with different initial conditions. The model is successful at predicting treion maps that are in good agreement with the test simulation. We used the power spectrum of the treion field as an indicator to validate our model. We show that the network predicts large scales almost perfectly but is somewhat less accurate at smaller scales. While the current model is already well suited to get average estimates about the reionization history, we expect it can be further improved with larger samples for the training, better data pre-processing and finer tuning of hyper-parameters. Emulators of this kind could be systematically used to rapidly obtain the evolving H ii regions associated with hydro-only simulations and could be seen as precursors of fully emulated physics solvers for future generations of simulations.
On the Interactive Effects of Objective and Subjective Age on Work Outcomes for Men and Women
Authors: Marcus Justin , Fritzsche Barbara A , Ng Yin Lu
Published: September 2019

Based upon theory on successful aging at work and the social identity of age, we hypothesized interactive effects of sex, objective chronological age, and subjective psychological/organizational age on age-based stereotype ratings of older workers, psychological well-being including both burnout and self-esteem, and behavioral self-reports of perceived unfair age and sex discrimination. Study hypotheses were tested using a survey-based sample of N = 1,583 workers from 3 countries, including Turkey, the United States, and Malaysia, and who were employed across a variety of occupations. Potential confounds resultant of socioeconomic status (education level), and the macro environment (country) were statistically controlled. Results generally found support for theoretically expected relations between age and work outcomes. Both psychological and organizational age interacted with chronological age such that different patterns of outcomes were found for men and women. Overall, although older subjective age benefited chronologically older workers, these interactive associations were less beneficial for older women as compared to older men. Implications of study findings for theory and practice are discussed.
Long-Term Cocirculation of Two Strains of Pepino Mosaic Virus in Tomato Crops and Its Effect on Population Genetic Variability
Authors: Alcaide C. , Rabadán M. P. , Juárez M. , Gómez P.
Published: September 2019

Mixed viral infections are common in plants, and the evolutionary dynamics of viral populations may differ depending on whether the infection is caused by single or multiple viral strains. However, comparative studies of single and mixed infections using viral populations in comparable agricultural and geographical locations are lacking. Here, we monitored the occurrence of pepino mosaic virus (PepMV) in tomato crops in two major tomato-producing areas in Murcia (southeastern Spain), supporting evidence showing that PepMV disease-affected plants had single infections of the Chilean 2 (CH2) strain in one area and the other area exhibited long-term (13 years) coexistence of the CH2 and European (EU) strains. We hypothesized that circulating strains of PepMV might be modulating the differentiation between them and shaping the evolutionary dynamics of PepMV populations. Our phylogenetic analysis of 106 CH2 isolates randomly selected from both areas showed a remarkable divergence between the CH2 isolates, with increased nucleotide variability in the geographical area where both strains cocirculate. Furthermore, the potential virus–virus interaction was studied further by constructing six full-length infectious CH2 clones from both areas, and assessing their viral fitness in the presence and absence of an EU-type isolate. All CH2 clones showed decreased fitness in mixed infections and although complete genome sequencing indicated a nucleotide divergence of those CH2 clones by area, the magnitude of the fitness response was irrespective of the CH2 origin. Overall, these results suggest that although agroecological cropping practices may be particularly important for explaining the evolutionary dynamics of PepMV in tomato crops, the cocirculation of both strains may have implications on the genetic variability of PepMV populations.
Dependency in multisensory integration: a copula-based analysis
Authors: Colonius Hans , Diederich Adele
Published: September 2019

The notion of copula has attracted attention from the field of contextuality and probability. A copula is a function that joins a multivariate distribution to its one-dimensional marginal distributions. Thereby, it allows characterizing the multivariate dependency separately from the specific choice of margins. Here, we demonstrate the use of copulas by investigating the structure of dependency between processing stages in a stochastic model of multisensory integration, which describes the effect of stimulation by several sensory modalities on human reaction times. We derive explicit terms for the covariance and Kendall's tau between the processing stages and point out the specific role played by two stochastic order relations, the usual stochastic order and the likelihood ratio order, in determining the sign of dependency.

This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
Spooky predictions at a distance: reality, complementarity and contextuality in quantum theory
Authors: Plotnitsky Arkady
Published: September 2019

This article brings together reality, complementarity and contextuality in quantum theory. It clarifies Bohr's concept of complementarity by considering the non-realist epistemology and the corresponding interpretations of quantum mechanics, based in the concept of ‘reality without realism’. Finally, as its main novel contribution, it establishes the connections between complementarity and contextuality.

This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
Assessing the impact of data aggregation in model predictions of HAT transmission and control activities
Authors: Castaño M. Soledad , Ndeffo-Mbah Martial L. , Rock Kat S. , Palmer Cody , Knock Edward , Miaka Erick Mwamba , Ndung’u Joseph M. , Torr Steve , Verlé Paul , Spencer Simon E.F. , Galvani Alison , Bever Caitlin , Keeling Matt J. , Chitnis Nakul
Published: September 2019

Since the turn of the century, the global community has made great progress towards the elimination of gambiense human African trypanosomiasis (HAT). Elimination programs, primarily relying on screening and treatment campaigns, have also created a rich database of HAT epidemiology. Mathematical models calibrated with these data can help to fill remaining gaps in our understanding of HAT transmission dynamics, including key operational research questions such as whether integrating vector control with current intervention strategies is needed to achieve HAT elimination. Here we explore, via an ensemble of models and simulation studies, which aspects of the available data and level of data aggregation, such as separation by disease stage, would be most useful for better understanding transmission dynamics and improving model reliability in making future predictions of control and elimination strategies.

Author summary

Human African tryposonomiasis (HAT), also known as sleeping sickness, is a parasitic disease with over 65 million people estimated to be living at risk of infection. Sleeping sickness consists of two stages: the first one is relatively mild but the second stage is usually fatal if untreated. The World Health Organization has targeted HAT for elimination as a public health problem by 2020 and for elimination of transmission by 2030. Regular monitoring updates indicate that 2020 elimination goals are likely to be achieved. This monitoring relies mainly on case report data that is collected through medical-based control activities — the main strategy employed so far in HAT control. This epidemiological data are also used to calibrate mathematical models that can be used to analyse current interventions and provide projections of potential intensified strategies.

We investigated the role of the type and level of aggregation of this HAT case data on model calibrations and projections. We highlight that the lack of detailed epidemiological information, such as missing stage of disease or truncated time series data, impacts model recommendations for strategy choice: it can misrepresent the underlying HAT epidemiology (for example, the ratio of stage 1 to stage 2 cases) and increase uncertainty in predictions. Consistently including new data from control activities as well as enriching it through cross-sectional (e.g. demographic or behavioural data) and geo-located data is likely to improve modelling accuracy to support planning, monitoring and adapting HAT interventions.
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

Numerous 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

Nations 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

1.2

The 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.

1.1

IMPORTANCE

Bacillus 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

Functions 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

Circadian 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.

Highlights

Loss of DYSC differentially impacts morning and evening oscillators

Reduced JET activity rescues the dysc and slo arrhythmic phenotype

Reduced JET activity causes synaptic defects at the larval NMJ

JET opposes DYSC and SLO function at the NMJ synapse
Origin of co-operativity in the activation of dimeric transcription factors
Authors: Welch Martin , Brasen Jens Christian , Workman Christopher T. , Sams Thomas
Published: September 2019

Cooperative behavior in the binding of ligands to a protein is often viewed as a complex phenomenon where conformational changes induced by the binding of the first ligand leads to tighter binding of subsequent ligands. We revisit the ligand-dependent activation of dimeric transcription factors and show that this process may appear cooperative even when it results from independent lig- and binding events. This effect is further accentuated through binding of the activated transcription factor to its cognate operator site on the DNA, where we demonstrate that cooperative activation is a stable fixed point. Our analysis nicely accounts for the apparent co-operativity inherent in the biological activity of many dimeric transcription factors.
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

Ascosphaera 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

Clustering 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

Research 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

MicroRNAs(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.
Behavioral and immunohistochemical characterization of rapid reconditioning following extinction of contextual fear
Authors: Williams Amy R. , Kim Earnest S. , Lattal K. Matthew
Published: September 2019

A fundamental property of extinction is that the behavior that is suppressed during extinction can be unmasked through a number of postextinction procedures. Of the commonly studied unmasking procedures (spontaneous recovery, reinstatement, contextual renewal, and rapid reacquisition), rapid reacquisition is the only approach that allows a direct comparison between the impact of a conditioning trial before or after extinction. Thus, it provides an opportunity to evaluate the ways in which extinction changes a subsequent learning experience. In five experiments, we investigate the behavioral and neurobiological mechanisms of postextinction reconditioning. We show that rapid reconditioning of unsignaled contextual fear after extinction in male Long–Evans rats is associative and not affected by the number or duration of extinction sessions that we examined. We then evaluate c-Fos expression and histone acetylation (H4K8) in the hippocampus, amygdala, prefrontal cortex, and bed nucleus of the stria terminalis. We find that in general, initial conditioning has a stronger impact on c-Fos expression and acetylation than does reconditioning after extinction. We discuss implications of these results for theories of extinction and the neurobiology of conditioning and extinction.
Inhibitory learning of phototaxis by honeybees in a passive-avoidance task
Authors: Marchal Paul , Villar Maria Eugenia , Geng Haiyang , Arrufat Patrick , Combe Maud , Viola Haydée , Massou Isabelle , Giurfa Martin
Published: September 2019

Honeybees are a standard model for the study of appetitive learning and memory. Yet, fewer attempts have been performed to characterize aversive learning and memory in this insect and uncover its molecular underpinnings. Here, we took advantage of the positive phototactic behavior of bees kept away from the hive in a dark environment and established a passive-avoidance task in which they had to suppress positive phototaxis. Bees placed in a two-compartment box learned to inhibit spontaneous attraction to a compartment illuminated with blue light by associating and entering into that chamber with shock delivery. Inhibitory learning resulted in an avoidance memory that could be retrieved 24 h after training and that was specific to the punished blue light. The memory was mainly operant but involved a Pavlovian component linking the blue light and the shock. Coupling conditioning with transcriptional analyses in key areas of the brain showed that inhibitory learning of phototaxis leads to an up-regulation of the dopaminergic receptor gene Amdop1 in the calyces of the mushroom bodies, consistently with the role of dopamine signaling in different forms of aversive learning in insects. Our results thus introduce new perspectives for uncovering further cellular and molecular underpinnings of aversive learning and memory in bees. Overall, they represent an important step toward comparative learning studies between the appetitive and the aversive frameworks.
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

Purpose

The 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/approach

The 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.

Findings

The 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 implications

The 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 implications

The 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/value

The 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.