bluuebunny/crossref_metadata_2025_split huggingface dataset:
reComBat: batch-effect removal in large-scale multi-source gene-expression data integration
Authors: Adamer Michael F. , Brüningk Sarah C. , Tejada-Arranz Alejandro , Estermann Fabienne , Basler Marek , Borgwardt Karsten 
Published: November 2021

AbstractMotivationWith the steadily increasing abundance of omics data produced all over the world under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch-effect removal for entire databases lies in the large number of batches and biological variation which can result in design matrix singularity. This problem can currently not be solved satisfactorily by any common batch-correction algorithm.ResultsWe present reComBat, a regularized version of the empirical Bayes method to overcome this limitation and benchmark it against popular approaches for the harmonization of public gene expression data (both microarray and bulkRNAsq) of the human opportunistic pathogen Pseudomonas aeruginosa. Batch-effects are successfully mitigated while biologically meaningful gene expression variation is retained. reComBat fills the gap in batch-correction approaches applicable to large-scale, public omics databases and opens up new avenues for data-driven analysis of complex biological processes beyond the scope of a single study.Contactmichael.adamer@bsse.ethz.chAvailabilityThe code is available at https://github.com/BorgwardtLab/reComBat, all data and evaluation code can be found at https://github.com/BorgwardtLab/batchCorrectionPublicData
Stress Resistance Heat Shock Protein 70 (HSP70) Analysis in Sorghum (Sorghum bicolor L.) at Genome-Wide Level
Authors: Amare Kasahun , Kebede Mulugeta 
Published: November 2021

ABSTRACTHeat shock proteins (HSP70) play an important role in many biological processes. However, as typical in Sorghum bicolor, the systematic identification of the HSP70 gene is very limited, and the role of the Hsp70 gene in the evolution of Sorghum bicolor has not been described systematically a lot. To overcome the gap, Insilco analysis of HSP70 gene family was conducted.The investigation was utilizing the bioinformatics method to analyze the HSP70 gene family and it has been identified that 30 HSP70 genes from the genome sequence of Sorghum bicolor. A comprehensive analysis of these 30 identified genes undertaking the analysis of gene structure, phylogeny, and physicochemical properties, subcellular localization, and promoter region analysis. The gene structure visualization analyses revealed that 22 genes contains both 5’ and 3’ UTRS and one 5’ and one 3’ gene and 6 genes without UTR. The highest number of introns was recorded as 12 and those genes have shown that without in any intron. In the promoter region analysis, ten protein motifs are identified and characterized and 2219 cis-acting elements are identified. Among those, the promoter enhancer elements share the highest number (1411) and light-responsive elements share the next value (335). The physicochemical properties analysis revealed that 23 families have an acidic nature while four families are basic and the rests are neutral. In general, the different analyses performed disclosed their structural organization, subcellular localization, physicochemical properties, cis-acting elements, phylogenetic, and understress conditions. This study provides further information for the functional characterization of HSP70 and helps to understand the mechanisms of abiotic stress tolerance under diverse stress conditions in Sorghum bicolor.
Crosstalk between guanosine nucleotides regulates cellular heterogeneity in protein synthesis during nutrient limitation
Authors: Diez Simon , Hydorn Molly , Whalen Abigail , Dworkin Jonathan 
Published: November 2021

AbstractPhenotypic heterogeneity of microbial populations can facilitate survival in dynamic environments by generating sub-populations of cells that may have differential fitness in a future environment. Bacillus subtilis cultures experiencing nutrient limitation contain distinct sub-populations of cells exhibiting either comparatively high or low protein synthesis activity. This heterogeneity requires the production of phosphorylated guanosine nucleotides (pp)ppGpp by three synthases: SasA, SasB, and RelA. Here we show that these enzymes differentially affect this bimodality: RelA and SasB are necessary to generate the sub-population of cells exhibiting low protein synthesis whereas SasA is necessary to generate cells exhibiting comparatively higher protein synthesis. The RelA product (pppGpp) allosterically activates SasB and we find, in contrast, that the SasA product (pGpp) competitively inhibits this activation. Finally, we provide in vivo evidence that this antagonistic interaction mediates the observed heterogeneity in protein synthesis. This work therefore identifies the mechanism underlying phenotypic heterogeneity in the central physiological process of protein synthesis.Author SummaryUpon encountering conditions that are unfavorable to growth, such as nutrient limitation, bacteria enter into a quiescent phenotype that is mediated by group of guanosine nucleotides collectively known as (pp)pGpp. These nucleotides direct the down-regulation of energy intensive processes and are essential for a striking heterogeneity in protein synthesis observed during exit from rapid growth. Here, we show that a network of (pp)pGpp synthases is responsible for this heterogeneity and describe a mechanism that allows for the integration of multiple signals into the decision to down regulate the most energy intensive process in a cell.
Re-entry into mitosis and regeneration of intestinal stem cells through enteroblast dedifferentiation in Drosophila midguts
Authors: Tian Aiguo , Morejon Virginia , Kohoutek Sarah , Huang Yi-Chun , Deng Wu-Min , Jiang Jin 
Published: November 2021

AbstractMany adult tissues and organs including the intestine rely on resident stem cells to maintain homeostasis. In mammalian intestines, upon ablation of resident stem cells, the progenies of intestinal stem cells (ISCs) such as secretory cells and tuft cells can dedifferentiate to generate ISCs to drive epithelial regeneration, but whether and how the ISC progenies dedifferentiate to generate ISCs under physiological conditions remains unknown. Here we show that infection of pathogenic bacteria induces enteroblasts (EBs) as one type of ISC progenies to re-enter the mitotic cycle in the Drosophila intestine. The re-entry into mitosis is dependent on epithermal growth factor receptor (EGFR)-Ras signaling and ectopic activation of EGFR-Ras signaling in EBs is sufficient to drive EBs cell-autonomously to re-enter into mitosis. In addition, we examined whether EBs gain ISC identity as a prerequisite to divide, but the immunostaining with stem cell marker Delta shows that these dividing EBs do not gain ISC identity. After employing lineage tracing experiments, we further demonstrate that EBs dedifferentiate to generate functional ISCs after symmetric divisions of EBs. Together, our study in Drosophila intestines uncovers a new role of EGFR-Ras signaling in regulating re-entry into mitosis and dedifferentiation during regeneration and reveals a novel mechanism by which ISC progenies undergo dedifferentiation through a mitotic division, which has important implication to mammalian tissue homeostasis and tumorigenesis.
Gene Expression in Lung Epithelial Cells Following Interaction withPneumocystis cariniiand its Specific Life Forms Yields Insights into Host Gene Responses to Infection
Authors: Kottom Theodore J. , Carmona Eva M. , Limper Andrew H. 
Published: November 2021

ABSTRACTPneumocystisspp. interacts with epithelial cells in the alveolar spaces of the lung. It is thought that the binding ofPneumocystisto host cell epithelium is needed for life cycle completion and proliferation. The effect of this interaction on lung epithelial cells have previously shown that the trophic form of this organism greatly inhibits p34cdc2activity, a serine/threonine kinase required for transition from G2to M phase in the cell cycle. To gain further insight into the host response during Pneumocystis pneumonia (PCP), we used microarray technology to profile epithelial cell (A549) gene expression patterns followingPneumocystis cariniiinteraction. Furthermore, we isolated separate populations of cyst and trophic forms ofP. carinii, which were then applied to the lung epithelial cells. Differential expression of genes involved in various cellular functions dependent on the specificP. cariniilife form in contact with the A549 cell were identified. The reliability of our data was further confirmed by Northern blot analysis on a number of selected up or down regulated transcripts. The transcriptional response toP. cariniiwas dominated by cytokines, apoptotic, and anti-apoptotic related genes. These results reveal several previously unknown effects ofP. cariniion the lung epithelial cell and provide insight into the complex interactions of host and pathogen.
Substrate stiffness modulates integrin α5 expression and ECM-associated gene expression in fibroblasts
Authors: Verma Brijesh Kumar , Chatterjee Aritra , Kondaiah Paturu , Gundiah Namrata 
Published: November 2021

AbstractBiomaterials, like polydimethylsiloxane (PDMS), are soft, biocompatible, and tuneable, which makes them useful to delineate specific substrate factors that regulate the complex landscape of cell-substrate interactions. We used a commercial formulation of PDMS to fabricate substrates with moduli 40 kPa, 300 kPa, and 1.5 MPa, and cultured HMF3S fibroblasts on them. Gene expression analysis was performed by RT-PCR and Western blotting. Cellular and nuclear morphologies were analyzed using confocal imaging, and MMP-2 and MMP-9 activities were determined with gelatin zymography. Results, comparing mechanotransduction on PDMS substrates with control petridishes, show that substrate stiffness modulates cell morphologies and proliferations. Cell nuclei were rounded on compliant substrates and correlated with increased tubulin expression. Proliferations were higher on stiffer substrates with cell cycle arrest on softer substrates. Integrin α5 expression decreased on lower stiffness substrates, and correlated with inefficient TGF-β activation. Changes to the activated state of the fibroblast on higher stiffness substrates were linked to altered TGF-β secretion. Collagen I, collagen III, and MMP-2 expression levels were lower on compliant PDMS substrates as compared to stiffer ones; there was little MMP-9 activity on substrates. These results demonstrate critical feedback mechanisms between substrate stiffness and ECM regulation by fibroblasts which is highly relevant in diseases like tissue fibrosis.
The effect of borrower country financial system and corporate governance system types on the spread of syndicated loans
Authors: Moutinho Nuno , Alves Carlos Francisco , Martins Francisco 
Published: November 2021

Purpose
This study aims to analyse the effect of borrower’s countries on syndicated loan spreads, featuring countries according to institutional factors, namely, financial systems and corporate governance systems.

Design/methodology/approach
This study is an empirical investigation based on a unique sample of more than 85,000 syndicated loans from 122 countries. The paper uses standard and two-stage least squares regression analysis to test whether the types of financial and corporate governance systems affect loan spreads.

Findings
The paper finds that borrowers from countries with financial systems oriented towards the banking-based paradigm pay lower interest rate spreads than those from countries with financial systems oriented towards the market-based paradigm. In addition, there is evidence that borrowers from countries with more developed financial systems pay lower spreads. The results also show that borrowers from countries with an Anglo-Saxon governance system pay higher spreads than borrowers from countries with a Continental governance system.

Research limitations/implications
This study does not consider potential promiscuous relationships that can arise at the ownership structure and governance level between banks and borrowers and may affect loan spreads.

Practical implications
This study suggests that financial and corporate governance systems are essential factors in the financial intermediation process. Furthermore, the evidence indicates that corporates with higher potential agency costs and higher potential information asymmetry are requested to pay higher spreads. Therefore, the opportunities to such corporates invest optimally tend to be scarcer.

Originality/value
The paper highlights the impact of institutional factors on the cost of financing, characterising the countries according to the type of financial system and the type of corporate governance system. The study finds that borrowers from countries with bank-based financial systems pay lower interest rate spreads than those from countries with market-based financial systems. The paper also highlights how the level of financial development affects the cost of financing. The paper focusses on non-financial firms, unlike financial firms, which have been the focus of several empirical studies on topics relating to the cost of funding and corporate governance.
The moderating role of previous venture experience on breadth of learning and innovation and the impacts on SME performance
Authors: Sinha Kanhaiya K. , Saunders Chad , Raby Simon , Dewald Jim 
Published: November 2021

PurposeThe purpose of this paper is to investigate the moderating role of previous venture experience on the relationship between learning breadth and innovation breadth, defined as the range of innovation types within a firm, and the impacts on SME performance.Design/methodology/approachA theoretical model was developed, and hypotheses were tested using step-wise multivariate regressions on survey data from 509 North American SME respondents.FindingsThe results demonstrate that the previous venture experience of a firm's top management plays a key role in enhancing the innovation breadth for a given level of learning breadth. There is a curvilinear relationship between innovation breadth and learning breadth, and increases in innovation breadth lead to increases in firm performance.Practical implicationsThe results indicate that organizations seeking higher performance returns by expanding their breadth of innovations need parallel attention on higher learning breadth in order to adequately capture the value from this broader set of innovations.Originality/valueThe paper contextualizes learning and innovation in the SMEs and argues that the consideration of diversity (breadth) of learning and innovation can help us understand their performance implications across industries. It also extends the effect of previous venture experience (PVE) of the leadership team in explaining performance. Beyond their ability to address external factors, PVE has a moderating effect on the relationship between learning and innovation breadth across the organization. Previous venture experience serves as both a guide and catalyst for investments in learning activities that lead to a broader range of innovation activities across the firm.
PLRSNet: a semantic segmentation network for segmenting plant leaf region under complex background
Authors: Talasila Srinivas , Rawal Kirti , Sethi Gaurav 
Published: November 2021

PurposeExtraction of leaf region from the plant leaf images is a prerequisite process for species recognition, disease detection and classification and so on, which are required for crop management. Several approaches were developed to implement the process of leaf region segmentation from the background. However, most of the methods were applied to the images taken under laboratory setups or plain background, but the application of leaf segmentation methods is vital to be used on real-time cultivation field images that contain complex backgrounds. So far, the efficient method that automatically segments leaf region from the complex background exclusively for black gram plant leaf images has not been developed.Design/methodology/approachExtracting leaf regions from the complex background is cumbersome, and the proposed PLRSNet (Plant Leaf Region Segmentation Net) is one of the solutions to this problem. In this paper, a customized deep network is designed and applied to extract leaf regions from the images taken from cultivation fields.FindingsThe proposed PLRSNet compared with the state-of-the-art methods and the experimental results evident that proposed PLRSNet yields 96.9% of Similarity Index/Dice, 94.2% of Jaccard/IoU, 98.55% of Correct Detection Ratio, Total Segmentation Error of 0.059 and Average Surface Distance of 3.037, representing a significant improvement over existing methods particularly taking into account of cultivation field images.Originality/valueIn this work, a customized deep learning network is designed for segmenting plant leaf region under complex background and named it as a PLRSNet.
University’s support for entrepreneurship and entrepreneurial intention: the mediating role of entrepreneurial climate
Authors: Sim Mandy Siew Chen , Galloway Joshua Edward , Ramos Hazel Melanie , Mustafa Michael James 
Published: November 2021

Purpose
Drawing on institutional theory, this paper seeks to untangle the relationship between university support for entrepreneurship and students’ entrepreneurial intentions. Specifically, this study aims to examine whether entrepreneurial climates within universities mediate the relationship between university support for entrepreneurship and students’ entrepreneurial intention.

Design/methodology/approach
Empirical data is drawn from 195 students across three Malaysian higher education institutions. Partial least squares procedures are used to test the proposed hypotheses.

Findings
Findings show that no element of university support for entrepreneurship had a direct effect on students’ entrepreneurial intentions. However, the entrepreneurial climate was found – to mediate the relationship between perceived business and concept development support and students’ entrepreneurial intentions.

Originality/value
This study represents one of the few efforts in the literature considering the role of entrepreneurial climates within universities in influencing students’ entrepreneurial intention. In considering the mediating role of entrepreneurial climate, in the relationship between university support for entrepreneurship and students’ entrepreneurial intentions, this study provides a complementary and contextualised perspective, to existing studies, which have traditionally focussed on the mediating role of individual attributes. Doing so provides further evidence of entrepreneurial universities in fostering entrepreneurship.
The mediating effect of supply chain flexibility on the relationship between supply chain integration and supply chain performance
Authors: Khanuja Anurodhsingh , Jain Rajesh Kumar 
Published: November 2021

PurposeSupply chain integration (SCI) and flexibility (SCF) are recognised as crucial business practices and capability in the global competitive market. However, limited research has paid attention to study the relationship between SCI, SCF and their impact on supply chain performance (SCP). Therefore, the purpose of this paper is to establish a relationship between integration, flexibility and performance.Design/methodology/approachThe structural equation modelling technique was used to analyse the 187 data collected from Indian organisations through the survey methodology.FindingsFindings indicate that external integration contributes significantly to realise SCF and SCP. Sourcing and logistics flexibility also help to improve the SCP. The mediation analysis showed that the association of customer and supplier integration with SCP is partially and fully mediated by logistics flexibility, respectively. This study suggests that integration influences the SCP when the firm has a strong association with downstream partners and enough capability for logistics flexibility.Research limitations/implicationsThe study has collected cross-sectional data to analyse the relationship between SCI, SCF and SCP. However, as integration requires an effort of the years, longitudinal data and industry-specific studies may provide comprehensive views to validate the results of this study.Originality/valueBuilding on relational view theory and dynamic capability theory, the study has proposed the SCP assessment framework based on the relationship between SCI and SCF.
The impacts of brand personality and self-congruity on consumers' intention to stay in a hotel: does consumer affinity matter?
Authors: Tsaur Sheng-Hshiung , Hsu Fu-Sung , Ching Hsiao-Wei 
Published: November 2021

PurposeThe purposes of this study were to explore the moderating effect of consumer affinity on brand personality and consumers' intention to stay in a hotel, as well as on self-congruity and consumers' intention to stay in a hotel.Design/methodology/approachThis study collected data from 386 inbound tourists to Taiwan. Hierarchical regression analysis was applied to analyze the data.FindingsThe results showed that brand personality, self-congruity and consumer affinity have significant positive effects on consumers' intention to stay in a hotel, respectively. Moreover, consumer affinity has significant moderating effect on brand personality and intention to stay in a hotel, as well as on self-congruity and intention to stay in a hotel.Practical implicationsConsumer affinity is a construct that identifies national attributes, and it strengthens the relationships between brand personality or self-congruity and consumers' intention to stay in a hotel from the level of country-specific affect. The results of this study can provide hotel marketers with reference for marketing management.Originality/valueAlthough past studies have examined the relationship between consumer affinity and purchase intention or behavior, the effect of consumer affinity construct on hotel consumers' intention to stay remains sparse in the hotel context. This study confirmed that consumer affinity has significant moderating effect on brand personality and intention to stay in a hotel, as well as on self-congruity and intention to stay in a hotel.
Student-managed investment funds: seven mismatches and three recommendations
Authors: Lin Crystal Yan 
Published: November 2021

PurposeThe purpose of this paper is to investigate the embedded challenges of student-managed investment funds (SMIFs) and provide recommendations to work with these issues.Design/methodology/approachThe paper analyzes and critiques the ways SMIFs are structured and operated and makes several suggestions.FindingsThe paper details seven unique challenges of SMIFs compared to professionally managed investment funds. The source of these challenges is that SMIFs are set up for educational purposes, which makes the operation and management different from performance-focused investment funds. The paper proposes several recommendations on how to align the educational focus with fund performance.Originality/valueThe paper is original and based on primary research.