bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of long and short enhancers in melanoma cell states
Authors: Mauduit David , Minnoye Liesbeth , Taskiran Ibrahim Ihsan , de Waegeneer Maxime , Christiaens Valerie , Hulselmans Gert , Demeulemeester Jonas , Wouters Jasper , Aerts Stein 
Published: July 2021

AbstractUnderstanding how enhancers drive cell type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assay (MPRA) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state specific H3K27 acetylation close to differentially expressed genes. A more in-depth evaluation of those regions was then pursued by investigating the activity of ATAC-seq peaks found therein along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions and we were able to precisely locate the active regions within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity, while SOX and MITF both influence MEL enhancer activity with SOX being required to achieve high levels of activity. Overall, our MPRA assays shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity as reporters across melanoma cell states.
Mutated in Colorectal Cancer (MCC) is a centrosomal protein that relocalizes to the ncMTOC during intestinal cell differentiation
Authors: Tomaz Lucian B. , Liu Bernard A. , Ong Sheena L. M. , Tan Ee Kim , Meroshini M. , Tolwinski Nicholas S. , Williams Christopher S. , Gingras Anne-Claude , Leushacke Marc , Dunn N. Ray 
Published: July 2021

AbstractMutated in Colorectal Cancer (MCC) encodes a coiled-coil protein implicated, as its name suggests, in the pathogenesis of hereditary human colon cancer. To date, however, the contributions of MCC to intestinal homeostasis remain unclear. Here, we examine the subcellular localization of MCC, both at the mRNA and protein levels, in the adult intestinal epithelium. Our findings reveal that Mcc transcripts are restricted to proliferating crypt cells, including Lgr5+ stem cells, and that Mcc protein is distinctly associated with the centrosome in these cells. Upon intestinal cellular differentiation, Mcc is redeployed to the non-centrosomal microtubule organizing center (ncMTOC) at the apical domain of villus cells. Using intestinal organoids, we show that the shuttling of the Mcc protein depends on phosphorylation by Casein Kinases 1δ/ε, which are critical modulators of WNT signaling. Together, our findings support a putative role for MCC in establishing and maintaining the cellular architecture of the intestinal epithelium as a component of both the centrosome and ncMTOC.
Complete Mitochondrial and Plastid DNA Sequences of the Freshwater Green Microalga Medakamo hakoo
Authors: Takusagawa Mari , Kato Shoichi , Matsunaga Sachihiro , Maruyama Shinichiro , Tsujimoto-Inui Yayoi , Nozaki Hisayoshi , Yagisawa Fumi , Ohnuma Mio , Kuroiwa Haruko , Kuroiwa Tsuneyoshi , Misumi Osami 
Published: July 2021

AbstractHere we report the complete organellar genome sequences of Medakamo hakoo, a green alga identified in freshwater in Japan. It has 90.8-kb plastid and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein coding genes, respectively, representing the smallest organellar genome among currently known core Trebouxiophyceae.
m6A is required for resolving progenitor identity during planarian stem cell differentiation
Authors: Dagan Yael , Yesharim Yarden , Bonneau Ashley R. , Schwartz Schraga , Reddien Peter W. , Wurtzel Omri 
Published: July 2021

AbstractRegeneration requires accurate production of missing cell lineages. Cell production is driven by changes to gene expression, which is shaped by multiple layers of regulation. Here, we find that the ubiquitous mRNA base-modification, m6A, is required for proper cell fate choice and cellular maturation in planarian stem cells (neoblasts). We mapped m6A-enriched regions in 7,600 planarian genes, and found that perturbation of the m6A pathway resulted in progressive deterioration of tissues and death. Using single cell RNA sequencing of >20,000 cells following perturbation of the pathway, we discovered that m6A negatively regulates transcription of histone variants, and that inhibition of the pathway resulted in accumulation of undifferentiated cells throughout the animal in an abnormal transcriptional state. Analysis of >1000 planarian gene expression datasets revealed that the inhibition of the chromatin modifying complex NuRD had almost indistinguishable consequences, unraveling an unappreciated link between m6A and chromatin modifications. Our findings reveal that m6A is critical for planarian stem cell homeostasis and gene regulation in regeneration.
Barcode Fusion Genetics-Protein-fragment Complementation Assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery
Authors: Evans-Yamamoto Daniel , Rouleau François D. , Nanda Piyush , Makanae Koji , Liu Yin , Després Philippe C. , Matsuo Hitoshi , Seki Motoaki , Dube Alexandre K. , Ascencio Diana , Yachie Nozomu , Landry Christian R. 
Published: July 2021

ABSTRACTBarcode fusion genetics (BFG) utilizes deep sequencing to improve the throughput of protein-protein interaction (PPI) screening in pools. BFG has been implemented in Yeast two-hybrid (Y2H) screens (BFG-Y2H). While Y2H requires test protein pairs to localize in the nucleus for reporter reconstruction, Dihydrofolate Reductase Protein-Fragment Complementation Assay (DHFR-PCA) allows proteins to localize in broader subcellular contexts and proves to be largely orthogonal to Y2H. Here, we implemented BFG to DHFR-PCA (BFG-PCA). This plasmid-based system can leverage ORF collections across model organisms to perform comparative analysis, unlike the original DHFR-PCA that requires yeast genomic integration. The scalability and quality of BFG-PCA were demonstrated by screening human and yeast interactions for >11,000 protein pairs. BFG-PCA showed high-sensitivity and high-specificity for capturing known interactions for both species. BFG-Y2H and BFG-PCA capture distinct sets of PPIs, which can partially be explained based on the domain orientation of the reporter tags. BFG-PCA is a high-throughput protein interaction technology to interrogate binary PPIs that exploits clone collections from any species of interest, expanding the scope of PPI assays.
Tannins and gut health in broilers: Effects of a blend of chestnut and quebracho tannins on gut health and performance of broiler chickens
Authors: Redondo Enzo A. , Redondo Leandro M. , Bruzzone Octavio A. , Diaz-Carrasco Juan M. , Cabral Claudio , Garces Victorino , Liñeiro Maximo , Fernandez-Miyakawa Mariano E. 
Published: July 2021

ABSTRACTConsumer demands and increased regulations on the use of antimicrobials in farm animals accentuated the need to develop strategies to replace antimicrobial growth promoters (AGPs) in food-producing animals. The present study evaluates the productive and gut health outcomes during the implementation of AGPs free programs based on the inclusion of a tannin blend compared with AGPs based program under commercial conditions. In the first trial, 6 farms were randomly assigned to AGP or tannin-based programs. In a second trial, both programs were applied simultaneously in one farm and the results were studied over 1 year. Although productive results from both trials were similar among treatments, evaluations of gut health indicators show improvements in the tannins treated flocks. Frequency and severity of intestinal gross lesions were reduced in jejunum (42% vs 23%; p<0.05 – 1.37 vs. 0.73; p<0.01, respectively) and ileum (25% vs. 10%; p<0.0.5 – 1.05 vs. 0.58; p<0.01) in tannins treated birds. Results from 16S studies, show that cecal microbiota diversity was not differentially affected by AGPs or tannins, but changes in the relative abundance of certain taxa were described, including Lactobacillus and Bifidobacterium groups. Additional evaluations using an in vivo model for C. perfringens necrotic enteritis showed that tannins treated birds had reduced incidence of gross lesions in jejunum (43.75 vs. 74.19%; p<0.01) and ileum (18.75% vs. 45.16%; p<0.05) compared with control. These results suggest that AGPs can be replaced by tannins feed additives, and contribute in the implementation of antimicrobial-free programs in broilers without affecting health or performance.
Structural insights into tick-borne encephalitis virus neutralization and animal protection by a therapeutic antibody
Authors: Baykov Ivan K. , Chojnowski Grzegorz , Pachl Petr , Matveev Andrey L. , Moor Nina A. , Emelianova Lyudmila A. , Rezacova Pavlina M. , Lamzin Victor S. , Tikunova Nina V. 
Published: July 2021

AbstractTick-borne encephalitis virus (TBEV) causes about 5-6 thousand cases annually, while there is still no effective treatment for this virus. To fill this gap, a high-affinity chimeric anti-TBEV antibody ch14D5 has previously been constructed, and high protective activity in a murine TBEV model has been shown for this antibody. However, the mechanism of action of this antibody and the recognized epitope have not been known yet. In this study, it is shown by X-ray crystallography that this antibody recognizes a unique epitope on the lateral ridge of the D3 domain of glycoprotein E, which is readily accessible for binding. The orientation of this antibody relative to the virion surface makes bivalent binding possible, which facilitates the cross-linking of glycoprotein E molecules and thus blocking of surface rearrangements required for infection. Since the antibody tightly binds to this protein even at pH ∼ 5.0, it locks the virion in an acidic environment inside the late endosomes or phagosomes and, therefore, effectively blocks the fusion of the viral and endosomal/phagosomal membranes. We believe that this is why the ch14D5 antibody does not induce an antibody-dependent enhancement of infectionin vivo, which is critical in the development of antibody-based therapeutic agents. In addition, the structure of the antibody-glycoprotein E interface can be used for the rational design of this antibody for enhancing its properties.
Integrative analysis of the salt stress response in cyanobacteria
Authors: Klähn Stephan , Mikkat Stefan , Riediger Matthias , Georg Jens , Hess Wolfgang R. , Hagemann Martin 
Published: July 2021

AbstractMicroorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacteriumSynechocystissp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data. A dynamic reorganization of the transcriptome and proteome occurred during the first hours after salt shock, e.g. involving the upregulation of genes to activate compatible solute biochemistry balancing osmotic pressure. The massive accumulation of glucosylglycerol then had a measurable impact on the overall carbon and nitrogen metabolism. In addition, we observed the coordinated induction of putative regulatory RNAs and of several proteins known for their involvement in other stress responses. Overall, salt-induced changes in the proteome and transcriptome showed good correlations, especially among the stably up-regulated proteins and their transcripts. We define an extended salt stimulon comprising proteins directly or indirectly related to compatible solute metabolism, ion and water movements, and a distinct set of regulatory RNAs involved in post-transcriptional regulation. Our comprehensive data set provides the basis for engineering cyanobacterial salt tolerance and to further understand its regulation.
Supply chain resilience in the face of uncertainty: how horizontal and vertical collaboration can help?
Authors: Lotfi Maryam , Larmour Abby 
Published: July 2021

PurposeThe COVID-19 outbreak highlights that many supply chains are exposed to unforeseen disruptions, that risks are unavoidable, and that the international nature of supply chains can seriously disrupt normal operations. Therefore, the need for Supply Chain Resilience (SCRES) is more imperative than ever. Furthermore, collaboration in supply chains may have benefitted the response to the COVID-19 outbreak. The aim of this research is to gain a deeper understanding of how collaboration with both types of horizontal and vertical collaboration in the supply chain affects its resilience.Design/methodology/approachA thematic analysis of the literature is used to investigate the concepts of both vertical and horizontal collaboration and supply chain resilience separately, then integrating identified themes to understand the relationship between them through a thematic map.FindingsThe thematic analysis indicates that the more firms collaborate in the supply chain, the more resilient they will be. Furthermore, both horizontal and vertical collaboration between supply chain partners will enhance resilience. This relationship is positively moderated by governance in the partnership and negatively moderated by competition in the partnership.Originality/valueThis is one of the first papers to provide in-depth insights into how collaboration, with both types of horizontal and vertical collaboration, affects supply chain resilience. Neither of previous articles provide an understanding of how both types of collaboration enables supply chain resilience.
Crank-Nicolson Scheme for Solving the Modified Nonlinear Schrodinger Equation
Authors: Alanazi A. A. , Alamri Sultan Z. , Shafie S. , Mohd Puzi Shazirawati 
Published: July 2021

Purpose
The purpose of this paper is to obtain the nonlinear Schrodinger equation (NLSE) numerical solutions in the presence of the first-order chromatic dispersion using a second-order, unconditionally stable, implicit finite difference method. In addition, stability and accuracy are proved for the resulting scheme.

Design/methodology/approach
The conserved quantities such as mass, momentum and energy are calculated for the system governed by the NLSE. Moreover, the robustness of the scheme is confirmed by conducting various numerical tests using the Crank-Nicolson method on different cases of solitons to discuss the effects of the factor considered on solitons properties and on conserved quantities.

Findings
The Crank-Nicolson scheme has been derived to solve the NLSE for optical fibers in the presence of the wave packet drift effects. It has been founded that the numerical scheme is second-order in time and space and unconditionally stable by using von-Neumann stability analysis. The effect of the parameters considered in the study is displayed in the case of one, two and three solitons. It was noted that the reliance of NLSE numeric solutions properties on coefficients of wave packets drift, dispersions and Kerr nonlinearity play an important control not only the stable and unstable regime but also the energy, momentum conservation laws. Accordingly, by comparing our numerical results in this study with the previous work, it was recognized that the obtained results are the generalized formularization of these work. Also, it was distinguished that our new data are regarding to the new communications modes that depend on the dispersion, wave packets drift and nonlinearity coefficients.

Originality/value
The present study uses the first-order chromatic. Also, it highlights the relationship between the parameters of dispersion, nonlinearity and optical wave properties. The study further reports the effect of wave packet drift, dispersions and Kerr nonlinearity play an important control not only the stable and unstable regime but also the energy, momentum conservation laws.
How do founder-CEOs sell their remaining ownership shares? Theory and evidence
Authors: Niu Xu 
Published: July 2021

PurposeIn this paper, the author attempts to answer an important question upon founder-CEOs' exiting: How do they sell their remaining ownership shares? The literature has largely been silent on this question, and therefore is missing an important piece of the puzzle on the final stage of the founding entrepreneurs' involvement in their companies.Design/methodology/approachThe author uses both theoretical models and empirical methods to examine how founder-CEOs sell their remaining ownership shares.FindingsThe author finds that founder-CEOs of high-growth firms and those with high managerial ability are more likely to sell remaining ownership shares gradually rather than suddenly. Moreover, if either the growth or the managerial ability is high, founder-CEOs managing firms with high volatility tend to sell gradually.Originality/valueThis paper provides insights into the final stage of founding entrepreneurs' involvement in companies. The methodology of pattern recognition also helps investors and regulators in tracking and monitoring stock trading of founders and other company insiders.
Does crop specialization improve agricultural productivity and commercialization? Insight from the Northern Savannah Ecological Zone of Ghana
Authors: Sekyi Samuel , Quaidoo Christopher , Wiafe Emmanuel Agyapong 
Published: July 2021

PurposeThis paper aims to analyze the effects of crop specialization on agricultural productivity and commercialization for farmers who produce high-value crops in the Northern Savannah Ecological Zone of Ghana.Design/methodology/approachThe study used the USAID/Ghana Feed the Future (FTF) survey, which collected data on high-value crops (i.e. maize, rice and soya). Data for the analysis consists of 2,903 farm households. The study utilized the three-stage generalized method of moment estimation technique to deal with the potential endogeneity of crop specialization within the context of productivity and commercialization and heteroscedasticity issues in the data.FindingsThe study found that crop specialization positively relates to agricultural productivity and commercialization, suggesting that increased crop specialization in the production of high-value stimulates productivity and opens market opportunities for farm households. These findings imply that crop specialization seems more beneficial to farmers as it significantly improves productivity and commercialization.Research limitations/implicationsThe study was conducted in the Northern Savannah Ecological Zone of Ghana and not the entire country.Originality/valueTo the best of the authors' knowledge, this study is the first to have jointly modeled crop specialization, agricultural productivity and commercialization. The main advantage of using this system approach is that it uses more information, thereby providing more precise parameter estimates.
Predicting bid protests: what should sourcing teams (not) do?
Authors: Hawkins Timothy G. , Gravier Michael J. , Niranjan Suman 
Published: July 2021

Purpose
The purpose of this study is to better understand the effectiveness of buyers’ defensive measures to thwart bid protests in government procurements.

Design/methodology/approach
A sample of 240 sourcing professionals concerning government source selections is used to analyze a logistic regression model exploring 6 antecedents of bid protests.

Findings
This research implicates the importance of oral presentations of offers, the type of value procured (i.e. services), protest experience, the quantity of document revisions, transaction costs and cost reimbursement contracts in receiving a bid protest.

Originality/value
To the best of the authors’ knowledge, this research is the first to explore sourcing strategy decisions that can contribute to the receipt of a bid protest. It adds clarity to an understudied market of business – the public sector.
Shifting borders of memory: Japan’s Industrial Heritage Information Centre
Authors: Boyle Edward 
Published: July 2021

PurposeThis article examines the borders of memory inherent to a Japanese World Heritage site, and their significance for the 2020 opening of the Industrial Heritage Information Center in Tokyo. The Center was constructed to disseminate information regarding the widely dispersed “Sites of Japan's Meiji Industrial Revolution”, which was recognized as a “serial site” by UNESCO in 2015. As with the original nomination, the opening of this Centre resulted in stringent protests from South Korea, who sought to have UNESCO consider revoking its original listing of these 23 Industrial Sites as collectively constituting the heritage of the world. This Center materializes a “border of memory” between Japan and South Korea that is the outcome of the displacement and re-siting of the heritage associated with Japan's Meiji Industrial Sites.Design/methodology/approachResearch material is derived from nomination documents, site visits, and newspaper reports in order to contextualize and analyse the disputes associated with this particular World Heritage nomination.FindingsThe paper points to how the borders of memory present at heritage sites may shift through contestation. Efforts to fix the meaning of heritage find themselves subverted by connections across such borders of memory.Originality/valueThe paper traces the process by which the geographically-dispersed “Sites of Japan's Meiji Industrial Revolution” have been collectivized through UNESCO's recognition into a single “border of memory” between Japan and Korea, one which the Information Center subsequently succeeded in materializing and reproducing within Japan's national capital.
Predicting entrepreneurial and professional career mindsets in young Nigerian adults
Authors: Adebusuyi Adeola Samuel , Kolawole Samson Olowo , Abu Hassan Salawu , Adebusuyi Olubusayo Foluso , Ajulo Adesina Adewale 
Published: July 2021

Purpose
This study aims to investigate how new graduates in Nigeria can simultaneously pursue entrepreneurial and professional careers. Specifically, this study tested the contextual (socioeconomic status [SES]), person-based (an open personality) and cognitive-person (self-efficacy and outcome expectations) predictors of entrepreneurship, professionalism and leadership.

Design/methodology/approach
The study design is cross-sectional. Data were collected from 363 new graduates from Nigerian tertiary institutions. Hypotheses were generated from social cognitive career self-management (CSM) variables. Research instruments were also revalidated for the Nigerian context, and regression path analysis was used to analyze the data.

Findings
This study’s key findings showed that SES and an open personality are predictors of entrepreneurship, professionalism and leadership (EPL) self-efficacy and intentions, entrepreneurial and job outcome expectations. Second, EPL self-efficacy predicted both entrepreneurial and job outcome expectations and served as a mediating variable for SES and an open personality. Third, entrepreneurial outcome expectations related to EPL intentions, whereas job outcome expectations did not. These results suggest that SES and openness personality trait are crucial for developing a versatile career mindset.

Research limitations/implications
This study demonstrated that individuals’ characteristics (i.e. cognitive and personality) and economic resources are crucial determinants of CSM. As this study is cross-sectional, future research could use a longitudinal approach to determine the cause-effect relationship.

Originality/value
To the best of the authors’ knowledge, this study is the first research to examine how new graduates can simultaneously explore entrepreneurial and professional careers in a developing country like Nigeria using the CSM theory.