bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control
Authors: Viny Aaron D. , Bowman Robert L. , Liu Yu , Lavallée Vincent-Philippe , Eisman Shira E. , Xiao Wenbin , Durham Benjamin H. , Navitski Anastasia , Park Jane , Braunstein Stephanie , Azizi Elham , Witkin Matthew , Baslan Timour , Ott Christopher J. , Pe’er Dana , Dekker Job , Koche Richard , Levine Ross L. 
Published: March 2019

AbstractTranscriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show Stag2 deletion in hematopoietic stem/progenitor cells (HSPC) results in altered hematopoietic function, increased self-renewal, and impaired differentiation. ChIP-sequencing revealed that while Stag2 and Stag1 can bind the same loci, a component of Stag2 binding sites are unoccupied by Stag1 even in Stag2-deficient HSPCs. While concurrent loss of Stag2 and Stag1 abrogated hematopoiesis, Stag2 loss alone decreased chromatin accessibility and transcription of lineage-specification genes, including Ebf1 and Pax5, leading to blunted HSPC commitment to the B-cell lineage. Our data illustrate a role for Stag2 in transformation and transcriptional dysregulation distinct from its shared role with Stag1 in chromosomal segregation.One Sentence SummaryStag1 rescues topologically associated domains in the absence of Stag2, but cannot restore chromatin architecture required for hematopoietic lineage commitment
Exploring the extracellular regulation of the tumor angiogenic interaction network using a systems biology model
Authors: Li Ding , Finley Stacey D. 
Published: March 2019

ABSTRACTTumor angiogenesis is regulated by pro- and anti-angiogenic factors. Anti-angiogenic agents target the interconnected network of angiogenic factors to inhibit neovascularization, which subsequently impedes tumor growth. Due to the complexity of this network, optimizing anti-angiogenic cancer treatments requires detailed knowledge at a systems level. In this study, we constructed a tumor tissue-based model to better understand how the angiogenic network is regulated by opposing mediators at the extracellular level. We consider the network comprised of two pro-angiogenic factors: vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (FGF2), and two anti-angiogenic factors: thrombospondin-1 (TSP1) and platelet factor 4 (PF4). The model’s prediction of angiogenic factors’ distribution in tumor tissue reveals the localization of different factors and indicates the angiogenic state of the tumor. We explored how the distributions are affected by the secretion of the pro- and anti-angiogenic factors, illustrating how the angiogenic network is regulated in the extracellular space. Interestingly, we identified a counterintuitive result that the secretion of the anti-angiogenic factor PF4 can enhance pro-angiogenic signaling by elevating the levels of the interstitial and sur-face-level pro-angiogenic species. This counterintuitive situation is pertinent to the clinical setting, such as the release of anti-angiogenic factors in platelet activation or the administration of exogenous PF4 for anti-angiogenic therapy. Our study provides mechanistic insights into this counterintuitive result and highlights the role of heparan sulfate proteoglycans in regulating the interactions between angiogenic factors. This work complements previous studies aimed at understanding formation of angiogenic complexes in tumor tissue and helps in the development of anti-cancer strategies targeting angiogenesis.
Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome
Authors: Reixachs-Solé Marina , Ruiz-Orera Jorge , Albà M Mar , Eyras Eduardo 
Published: March 2019

AbstractThe differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing), a new pipeline for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (Ribosome profiling). We found evidence of translation for 40-50% of the expressed transcript isoforms in human and mouse, with 53% of the expressed genes having more than one translated isoform in human, 33% in mouse. Differential analysis revealed that about 40% of the splicing changes at RNA level were concordant with changes in translation, with 21.7% of changes at RNA level and 17.8% at translation level conserved between human and mouse. Furthermore, orthologous cassette exons preserving the directionality of the change were conserved between human and mouse and enriched in microexons in a comparison between glia and glioma. ORQAS leverages ribosome profiling to uncover a widespread and evolutionary conserved impact of differential splicing on the translation of isoforms and, in particular, of microexon-containing isoforms. ORQAS is available at https://github.com/comprna/orqas
An ATAC-seq atlas of chromatin accessibility in mouse tissues
Authors: Liu Chuanyu , Wang Mingyue , Wei Xiaoyu , Wu Liang , Xu Jiangshan , Dai Xi , Xia Jun , Cheng Mengnan , Yuan Yue , Zhang Pengfan , Li Jiguang , Feng Taiqing , Chen Ao , Zhang Wenwei , Chen Fang , Shang Zhouchun , Zhang Xiuqing , Peters Brock A. , Liu Longqi 
Published: March 2019

AbstractThe Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics in multiple species. A comprehensive reference of ATAC-seq datasets for mammalian tissues is important for the understanding of regulatory specificity and developmental abnormality caused by genetic or environmental alterations. Here, we report an adult mouse ATAC-seq atlas by producing a total of 66 ATAC-seq profiles from 20 primary tissues of both male and female mice. The ATAC-seq read enrichment, fragment size distribution, and reproducibility between replicates demonstrated the high quality of the full dataset. We identified a total of 296,574 accessible elements, of which 26,916 showed tissue-specific accessibility. Further, we identified key transcription factors specific to distinct tissues and found that the enrichment of each motif reflects the developmental similarities across tissues. In summary, our study provides an important resource on the mouse epigenome and will be of great importance to various scientific disciplines such as development, cell reprogramming, and genetic disease.
Post-transcriptional mechanisms distinguish human and chimp forebrain progenitor cells
Authors: Grassi Daniela A , Brattås Per Ludvik , Valdés Jeovanis G , Rezeli Melinda , Jönsson Marie E , Nolbrant Sara , Parmar Malin , Marko-Varga György , Jakobsson Johan 
Published: March 2019

AbstractThe forebrain has expanded in size and complexity during hominoid evolution. The contribution of post-transcriptional control of gene expression to this process is unclear. Using in-depth proteomics in combination with bulk and single-cell RNA sequencing, we analyzed protein and RNA levels of almost 5,000 genes in human and chimpanzee forebrain neural progenitor cells. We found that species differences in protein expression level was often independent of RNA levels, and more frequent than transcriptomic differences. Low-abundant proteins were more likely to show species-specific expression levels, while proteins expressed at a high level appeared to have evolved under stricter constraints. Our study implicates a previously unappreciated broad and important role for post-transcriptional regulatory mechanisms in the evolution of the human forebrain.
Towards a fully automated surveillance of well-being status in laboratory mice using deep learning
Authors: Andresen Niek , Wöllhaf Manuel , Hohlbaum Katharina , Lewejohann Lars , Hellwich Olaf , Thöne-Reineke Christa , Belik Vitaly 
Published: March 2019

AbstractAssessing the well-being of an animal is hindered by the limitations of efficient communication between humans and animals. Instead of direct communication, a variety of behavioral, biochemical, physiological, and physical parameters are employed to evaluate the well-being of an animal. Especially in the field of biomedical research, scientifically sound tools to assess pain, suffering, and distress for experimental animals are highly demanded due to ethical and legal reasons. For mice, the most commonly used laboratory animals, a valuable tool is the Mouse Grimace Scale (MGS), a coding system for facial expressions of pain in mice which has been shown to be accurate and reliable. Currently, MGS scoring is very time and effort consuming as it is manually performed by humans being thoroughly trained in using this method. Therefore, we aim to develop a fully automated system for the surveillance of well-being in mice. Our work introduces a semi-automated pipeline as a first step towards this goal. We use and provide a new data set of images of black-furred laboratory mice that were moving freely, thus the images contain natural variation with regard to perspective and background. The analysis of this data set is therefore more challenging but reflects realistic conditions as it would be obtainable without human intervention. Images were obtained after anesthesia (with isoflurane or ketamine/xylazine combination) and surgery (castration). We deploy two pre-trained state of the art deep convolutional neural network (CNN) architectures (ResNet50 and InceptionV3) and compare to a third CNN architecture without pre-training. Depending on the particular treatment, we achieve an accuracy of up to 99% for binary “pain”/”no-pain” classification.Author summaryIn the field of animal research, it is crucial to assess the well-being of an animal. For mice, the most commonly used laboratory animals, there is a variety of indicators for well-being. Especially the facial expression of a mouse can give us important information on its well-being state. However, currently the surveillance of well-being can only be ensured if a human is present. Therefore, we developed a first approach towards a fully automated surveillance of the well-being status of a mouse. We trained neural networks on face images of black-furred mice, which were either untreated or underwent anesthesia or surgery, to distinguish between an impaired and unimpaired well-being state. Our systems successfully learnt to assess whether the well-being of a mouse was impaired and, depending on the particular treatment, its decision was correct in up to 99%. A tool that visualizes the features used for the decision making process indicated that the decision was mainly based on the facial expressions of a mouse.
Corrosion inhibition and the structure-efficiency relationship study of two cationic surfactants
Authors: Chen Gang , Lin Jiao , Liu Qiaona , Zhang Jie , Wu Ya , Li Hong , Qu Chentun , Song Wenqi 
Published: March 2019

Purpose
As an example of structure-efficiency relationship study, this paper aims to evaluate the corrosion inhibition effect of two cationic surfactants, cetyl-trimethyl ammonium chloride (CTAC) and cetyl-dimethyl-hydroxyethyl ammonium chloride (CDHAC), and to discuss the effect of structure on the performance by thermodynamics methods.

Design/methodology/approach
The effect of the two cationic surfactants, CTAC and CDHAC, on the corrosion of the mild steel in HCl solution was investigated by using weight loss measurements, and the activation energies of CTAC and CDHAC involved in the corrosion inhibition were calculated and discussed.

Findings
The weight loss measurements showed that the corrosion inhibition efficiency of CDHAC was higher than that of CTAC in any case. The effects of the structure on performance were discussed, and the following data are available from the results, all of ΔS are positive, the values of ΔG are both close to −40 kJ·mol-1 and the values of ΔH are 10.960 and 36.996 kJ·mol-1, which indicate that the surfactant molecules are spontaneously adsorbed on the surface of the steel surface, and the adsorption on the steel plate is endothermic chemical adsorption.

Originality/value
The available data show that most organic inhibitors undergo physisorption on the metal surface, while in the presence of non-bonded and p-electrons, the inhibitor molecules may undergo chemisorption. This work showed that the two surfactant molecules are spontaneously adsorbed on the surface of the steel surface, and the adsorption on the steel plate is endothermic chemical adsorption.
How EMNEs choose location for strategic asset seeking in internationalization?
Authors: Gao Qiuling , Li Zijie , Huang Xinli 
Published: March 2019

PurposeBased on the strategy tripod perspective, this study aims to address how emerging economy multinational enterprises (EMNEs) make a strategic decision of choosing a foreign location for their strategic asset seeking and under what mechanism EMNEs make foreign direct investment (FDI) location choice.Design/methodology/approachThis paper first reviews the literature on strategy tripod and strategic asset seeking strategy of EMNEs. Then, six cases of Chinese multinational enterprises operating in manufacturing industry have been introduced, emphasizing on interactions within three dimensions of strategy tripod framework, namely, resource-based dimension, industry-based dimension and institution-based dimension. By triangulating with multiple sources of archival and interview data, this paper identified a conceptual model presenting location choice mechanisms.FindingsBased on a comparative multi-case study, four mechanisms of EMNEs’ location choice when seek strategic asset by FDI within a strategy tripod framework have been revealed. Specifically, EMNEs make their strategic decision of choosing a foreign location for their strategic asset seeking under mechanisms of seeking complementary resources based on industry characteristics; echoing with institutional dimension of home country when exploitation of resource; matching institutional dimension of host country when consider industry fitness; and institutional leveraging combined with understanding of resource and industry dimensions inside strategy tripod.Originality/valueThe findings shed novel insights into the mechanisms under which EMNEs choose their location for strategic asset-seeking FDI. It also broadens the strategy tripod framework by looking deeper into the characteristics of each dimension within a new research context of EMNEs’ FDI location choice.
Modeling the efficiency of Tunisian and Moroccan banks using the SFA approach
Authors: Kallel Hela , Ben Hamad Salah , Triki Mohamed 
Published: March 2019

PurposeThe purpose of this paper is to evaluate and compare bank efficiency between the two Maghreb countries, Tunisia and Morocco, over the period 2005–2014.Design/methodology/approachThe authors follow the stochastic frontier analysis, where the preferred cost model is determined via various hypothesis tests based on the maximum likelihood estimation. Then, the first and the second derivates of the cost function are employed to determine scale elasticities, scale inefficiencies and technological progress.FindingsSpecification tests indicate that the Fourier Flexible form provides better fit to the data set. Further, the estimated model shows that Tunisian and Moroccan banks’ efficiency is positively affected by banking service quality, but negatively influenced by both bank capitalization and GDP growth. Overall, Moroccan banks are found to be the most efficient despite the decrease of efficiency levels in both countries. Additionally, foreign banks have a higher scale inefficiency and, therefore, a lower cost efficiency. Equally, the technical progress raises banking costs in both countries, providing a decrease in efficiency scores.Practical implicationsThe findings of this study provide novel insights to Tunisian and Moroccan policy makers on the relevance of the smaller banks’ consolidation to improve bank efficiency by achieving unrealized economies of scale. Also, more reforms should be implemented in Tunisia to reduce non-performing loans.Originality/valueTo the best of the authors’ knowledge, this study is the first which offers a comparison between Tunisian and Moroccan banks to clarify the sources of inefficiency and to make strategic decisions.
Public value of online financial transparency
Authors: Puron-Cid Gabriel , Reddick Christopher G. , Ganapati Sukumar 
Published: March 2019

PurposeThe purpose of this paper is to apply Moore’s public value model into the context of e-government research by examining online financial transparency as both an organizational goal and as a driving force for financial sustainability and public officials’ corruption. The empirical context comprises the state governments in the USA.Design/methodology/approachStructural equation modeling is used to examine the relationship between specific contextual factors of the authorizing environment, financial sustainability, public official corruption and online budget transparency.FindingsThe results show that contextual factors like population explain online financial transparency, while financial sustainability and corruption had moderating and negative effects.Practical implicationsGovernments that struggle with issues of financial sustainability and corruption will rely more on online financial transparency. Transparency increases detection of public corruption.Originality/valueThe effects of financial transparency and financial sustainability on corruption have been studied separately. This study fills the gap of understanding the effects of both on corruption as one phenomenon.
Leadership matters: preparation program quality and learning outcomes
Authors: Ni Yongmei , Rorrer Andrea K. , Pounder Diana , Young Michelle , Korach Susan 
Published: March 2019

Purpose
Informed by learning transfer theory, the purpose of this paper is to validate the instrument measuring educational leadership preparation program (LPP) quality attributes and graduates’ leadership learning and to assess the direct and indirect relationships among them, as reported by program graduates.

Design/methodology/approach
This study uses data collected from the 2016 INSPIRE-G Survey, which gathers information from LPP graduates in the USA on their perceptions of program quality and leadership learning. Structural equation modeling was used to determine which program quality factors directly and indirectly influence graduate leadership learning.

Findings
The results suggest significant relationships between the assessed LPP attributes and leadership learning. Faculty quality and program rigor and relevance (PRR) had the strongest association with leadership learning, although the relationship between faculty quality and learning was fully mediated by PRR. Internship experiences and peer relationships were also important predictors of leadership learning. Studying with a cohort had a small but positive relationship with graduates’ leadership learning, although the relationship was fully mediated by perceived peer relationships.

Originality/value
This study further validates the INSPIRE-G Survey and affirms the imperative role of leadership preparation as a predictor to graduate reported learning outcomes and learning transfer. Moreover, this study illustrates the importance of leadership preparation by demonstrating positive relationships between program quality features and reported leadership learning outcomes. Finally, the INSPIRE-G instrument demonstrates its utility as a reliable measure of program quality, which opens the door to large-scale and longitudinal studies of the transfer of learning from leader preparation to practice.
School principals’ systems thinking: antecedents and consequences
Authors: Benoliel Pascale , Shaked Haim , Nadav Nechama , Schechter Chen 
Published: March 2019

PurposeToday’s educational complexities require principals to adopt a more systemic perspective toward school management. Although research has emphasized the benefits associated with the holistic perspective of systems thinking, research in the educational field has been limited. The purpose of this paper is to investigate the mediating role of principals’ systems thinking (PST) in the relationships between instructional leadership (IL) and subject coordinators’ organizational commitment and job satisfaction.Design/methodology/approachData were collected by surveying a sample of 226 subject coordinators from different elementary schools randomly chosen in Israel. Subject coordinators completed questionnaires on their PST competencies, their principals’ IL, job satisfaction and organizational commitment. Structural equation modeling was used to test the research hypotheses.FindingsThe results confirmed the main hypotheses: PST did facilitate subject coordinators’ organizational commitment and job satisfaction. Findings also showed that PST mediated the relationship between IL and subject coordinators’ organizational commitment and job satisfaction.Originality/valueBy integrating research from both educational and non-educational literature, this study contributes to deepen our understanding regarding the antecedents and consequences of the PST as perceived by their subject coordinators, providing a broader leadership framework on their functions in today’s complex school systems.
Relationship between building maintenance sourcing strategy selection factors and performance
Authors: Soh Khai Ying , Chua Shirley Jin Lin , Ali Azlan Shah , Au-Yong Cheong Peng , Alias Anuar 
Published: March 2019

Purpose
The building maintenance management becomes more complicated nowadays, with several sourcing strategies springing up for building maintenance work provisions. Various studies demonstrate that the selection factors and performance measurements are both essential aspects in determining and evaluating the sourcing strategy for building maintenance management. Thus, the purpose of this paper is to examine the relationships between the selection factors and performance measurements of sourcing strategy.

Design/methodology/approach
The paper targeted to evaluate and analyse the perceptions of the building maintenance practitioners regarding the degree of importance of selection factors and performance measurements. Through quantitative approach, the paper adopted stratified random sampling to distribute the questionnaires to the building maintenance practitioners operating in both private and government high-rise office buildings in Kuala Lumpur.

Findings
The findings highlighted the quality factors as the most important selection group factors; meantime, the ability to fulfil client’s need and requirement as well as the ability to deliver the service with reasonable reliability and predictability are identically important performance measurements. There is a significant relationship between the selection factors and performance measurement of sourcing strategy.

Originality/value
This paper provides an impetus research which uncovered the sourcing practices in the industry and guided the sourcing process in determining the appropriate sourcing strategy.