bluuebunny/crossref_metadata_2025_split huggingface dataset:
stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues
Authors: Pham Duy , Tan Xiao , Xu Jun , Grice Laura F. , Lam Pui Yeng , Raghubar Arti , Vukovic Jana , Ruitenberg Marc J. , Nguyen Quan 
Published: May 2020

ABSTRACTSpatial Transcriptomics is an emerging technology that adds spatial dimensionality and tissue morphology to the genome-wide transcriptional profile of cells in an undissociated tissue. Integrating these three types of data creates a vast potential for deciphering novel biology of cell types in their native morphological context. Here we developed innovative integrative analysis approaches to utilise all three data types to first find cell types, then reconstruct cell type evolution within a tissue, and search for tissue regions with high cell-to-cell interactions. First, for normalisation of gene expression, we compute a distance measure using morphological similarity and neighbourhood smoothing. The normalised data is then used to find clusters that represent transcriptional profiles of specific cell types and cellular phenotypes. Clusters are further sub-clustered if cells are spatially separated. Analysing anatomical regions in three mouse brain sections and 12 human brain datasets, we found the spatial clustering method more accurate and sensitive than other methods. Second, we introduce a method to calculate transcriptional states by pseudo-space-time (PST) distance. PST distance is a function of physical distance (spatial distance) and gene expression distance (pseudotime distance) to estimate the pairwise similarity between transcriptional profiles among cells within a tissue. We reconstruct spatial transition gradients within and between cell types that are connected locally within a cluster, or globally between clusters, by a directed minimum spanning tree optimisation approach for PST distance. The PST algorithm could model spatial transition from non-invasive to invasive cells within a breast cancer dataset. Third, we utilise spatial information and gene expression profiles to identify locations in the tissue where there is both high ligand-receptor interaction activity and diverse cell type co-localisation. These tissue locations are predicted to be hotspots where cell-cell interactions are more likely to occur. We detected tissue regions and ligand-receptor pairs significantly enriched compared to background distribution across a breast cancer tissue. Together, these three algorithms, implemented in a comprehensive Python software stLearn, allow for the elucidation of biological processes within healthy and diseased tissues.
TreeMap: A Structured Approach to Fine Mapping of eQTL Variants
Authors: Liu Li , Chandrashekar Pramod , Zeng Biao , Sanderford Maxwell D. , Kumar Sudhir , Gibson Greg 
Published: May 2020

AbstractMotivationExpression quantitative trait loci (eQTL) harbor genetic variants modulating gene transcription. Fine mapping of regulatory variants at these loci is a daunting task due to the juxtaposition of causal and linked variants at a locus as well as the likelihood of interactions among multiple variants. This problem is exacerbated in genes with multiple cis-acting eQTL, where superimposed effects of adjacent loci further distort the association signals.ResultsWe developed a novel algorithm, TreeMap, that identifies putative causal variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus. Guided by the hierarchical structure of linkage disequilibrium, TreeMap performs an organized search for individual and multiple causal variants. Via extensive simulations, we show that TreeMap detects co-regulating variants more accurately than current methods. Furthermore, its high computational efficiency enables genome-wide analysis of long-range eQTL. We applied TreeMap to GTEx data of brain hippocampus samples and transverse colon samples to search for eQTL in gene bodies and in 4 Mbps gene-flanking regions, discovering numerous distal eQTL. Furthermore, we found concordant distal eQTL that were present in both brain and colon samples, implying long-range regulation of gene expression.AvailabilityTreeMap is available as an R package enabled for parallel processing athttps://github.com/liliulab/treemap.
A novel tolerance index to identify heat tolerance in cultivated and wild barley genotypes
Authors: Bahrami Forouzan , Arzani Ahmad , Rahimmalek Mehdi 
Published: May 2020

AbstractThermal stress at the reproductive stage poses a substantial constraint on cereal production worldwide. This study was conducted to assess tolerance to terminal high-temperature stress in 45 wild (Hordeum vulgaressp.spontaneum)genotypes, 4 cultivars (H. vulgaressp.vulgare), 98 F3 and 79 BC1F2 families derived from hybridization of the most tolerant wild genotype and a susceptible cultivar ‘Mona’. Results of analysis of variance showed the significant genotypic and high-temperature stress effects on all the traits studied. In contrast to the cultivated genotypes, the wild ones were found less affected by high-temperature stress. The multivariate analysis highlighted the additional high-temperature tolerance components in the tolerant families and wild genotypes. Grain yield strongly correlated (p< 0.01) with stress tolerance, yield stability, and heat tolerance indices. The reduction in the reproduction period caused by high-temperature was much higher in cultivated genotypes than in wild ones. In conclusion, the ingenuous-focused strategies like escape/avoidance are being used primarily to cope with heat stress by cultivars, while adaptive-focused coping strategies such as tolerance are being implemented by wild barley.
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors
Authors: Hörberg Johanna , Moreau Kevin , Reymer Anna 
Published: May 2020

AbstractActivator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA-binding sites, our ability to predict new binding sites and explain how the proteins achieve different gene expression levels remains limited. Here we address the role of sequence-specific DNA dynamics for stability and specific binding of AP-1 factors, using microseconds long molecular dynamics simulations. As a model system, we employ yeast AP-1 factor Yap1 binding to three different response elements from two genetic environments. Our data show that Yap1 actively exploits the sequence-specific plasticity of DNA within the response element to form stable protein-DNA complexes. The stability also depends on the four to six flanking nucleotides, adjacent to the response elements. The flanking sequences modulate the conformational adaptability of the response element, making it more shape-efficient to form specific contacts with the protein. Bioinformatics analysis of differential expression of the studied genes supports our conclusions: the stability of Yap1-DNA complexes, modulated by the flanking environment, influences the gene expression levels. Our results provide new insights into mechanisms of protein-DNA recognition and the biological regulation of gene expression levels in eukaryotes.
Board gender diversity and environmental, social and corporate governance performance: evidence from ASEAN banks
Authors: Al-Jaifi Hamdan Amer 
Published: June 2020

PurposeThis study examines the associations between board gender diversity and banks' environmental, social and corporate governance performance in the ASEAN context.Design/methodology/approachThe study uses a sample of yearly observations for ASEAN banks over the period 2011–2016. Generalized method of moments (GMM) regression is used for the main models, and the findings are supported by other robustness tests, namely ordinary least squares (OLS) regression and panel models (fixed and random effect regression).FindingsThe findings imply that board gender diversity positively influences corporate governance performance, although it has no impact on the banks' environmental and social performance.Research limitations/implicationsThis study offers insights to regulators, investors and bank managers concerning board diversity and its impact on environmental, social and corporate governance performance. The findings imply that having a specific percentage of female directors on the board positively influences corporate governance performance. However, the impact of gender diversity on environmental and social performance is not supported.Originality/valueFew empirical studies have examined the impact of gender diversity on non-financial performance. This study contributes to the debate on the importance of gender diversity by providing empirical evidence for the impact of board gender diversity on three non-performance measures (environmental, social and corporate governance) for ASEAN banks, a topic not previously examined. There is scant attention to it in ASEAN countries, which have unique characteristics, and there remains a gap in the literature regarding the impact of board diversity among banks in this region. The findings of the study are confirmed by several robustness tests.
Digital resources integration under the knowledge management model: an analysis based on the structural equation model
Authors: Rafi Muhammad , JianMing Zheng , Ahmad Khurshid 
Published: June 2020

Purpose
In the age of knowledge explosion, modern technology facilitates the acquisition, organization and effective dissemination of information to support academic research. To achieve long-term educational goals, integrating digital resources into a knowledge management model (KMM) has become a necessary prerequisite for university management. The proposed KMM aims to combine resources and technology to facilitate resource management, navigation and cross-database search for advanced research.

Design/methodology/approach
The published literature on digital resource integration was reviewed, and the status of resource organization was discussed with experts to compile research instruments together with the perspectives of serving professionals in universities. The data obtained was systematically processed to develop an integrated resource KMM. Data volume measurement was done with the SPSS software and AMOS was used for path analysis and modeling. After the conceptual model was developed, many assumptions were associated with it, and the software was run on the data set to validate the proposed theoretical model.

Findings
Library resources with four components (digital resources, information technology, financial planning and service promotion) have been successfully integrated into the knowledge management framework to organize resources and provide academic services for researchers. In addition to the organization of digital resources, the two components of knowledge management, such as the explicit knowledge of its technology-oriented nature and the tacit knowledge of its human-centered positions, remained useful to strengthen the integration process.

Practical implications
With the development of digital technology and the internet, information authentication, access and dissemination have become a complex task for information centers. As an integral part of modern digital libraries, the expansion of digital collections requires proper accessibility organization. Owing to the increasing number of digital resources, organization and management require thorough research and appropriate integration mechanisms. This integrated KMM helps to organize heterogeneous information resources and databases in libraries for long-term academic tasks.

Originality/value
Based on literature studies and discussions with academic experts, integration problems were identified, and raw data were obtained from the library management to find a solution. It is unique research owing to a lack of original work and extensive international literature on resource integration in connection with KMMs. This study has innovative findings that can add value to world literature.
A serious leisure perspective of culinary tourism co-creation: the influence of prior knowledge, physical environment and service quality
Authors: Prayag Girish , Gannon Martin Joseph , Muskat Birgit , Taheri Babak 
Published: June 2020

PurposeRecognising tourists’ increasing desire for authentic destination-specific experiences, the hospitality industry has responded by increasing provision of innovative culinary activities. This study aims to use the concepts of serious leisure and terroir to examine how knowledge, physical environment and service quality influence co-creation within the culinary tourism context.Design/methodology/approachFollowing cooking class participation, 575 domestic Iranian tourists were surveyed. These educational classes provide opportunities to learn about local foods alongside peers in an interactive setting. Consistent with the benefits of serious leisure, this consumption context could prove conducive to stimulating co-creation.FindingsPrior knowledge strongly influences tourists’ reflective and recreational motives for participation (i.e. the benefits of serious leisure). This shapes how tourists evaluate physical environments and service quality therein; influencing value co-creation and supporting serious leisure as the conceptual lens through which to understand experiential culinary consumption.Research limitations/implicationsThe proposed conceptual model was tested on domestic tourists following class participation. However, in suggesting that visually-stimulating, tactile premises with the olfactory appeal can encourage co-created experiences, the findings are relevant to service touch-point management more generally.Originality/valueRecognizing the influential role played by the physical and social aspects of experiential consumption, the serious leisure framework improves an extant understanding of value co-creation.
Masters Highland Games and imaginations of home
Authors: Bowness James 
Published: June 2020

PurposeThis paper aims to explore the journeys of a group of North American Master athletes who travelled to Scotland to compete in the 2014 Masters World Championship Highland Games. Conceptualising, the Masters World Championship Highland Games as a unique form of sport heritage tourism, the paper explores how imaginations of the host venue are caught within individual and collective histories, while also being influenced by the socio-political context of contemporary Scotland.Design/methodology/approachAfter detailing the histories of the Highland games and Scottish emigration, the study draws upon a qualitative methodology to explore how such histories impact the imaginations of the Highland region.FindingsThis paper examines the journeys of athletes to the games, how they understood the games venue space and surrounding areas, and also how the Highland region itself was the site of contested meanings. The study concludes with a discussion of the narratives that frame imaginations of the Highlands and Scotland more broadly.Originality/valueThe paper adds to existing knowledge on sport heritage tourism and considers how conceptualisations of Scotland continue to be renegotiated in light of contemporary political developments.
Social effectiveness of the market economy: measuring and management
Authors: Bogoviz Aleksei V. , Shokhnekh Anna V. , Petrenko Elena S. , Milkina Elizaveta A. 
Published: June 2020

PurposeThe purpose of the paper is to develop the scientific and methodological provision for measuring and managing the social effectiveness of the market economy and its approbation.Design/methodology/approachWith foundation on the classical idea of effectiveness as a ratio of results to costs, and with acknowledgment of incompatibility and inequality of the elements of social effectiveness and the necessity of their ranking, the authors' formula for its evaluation is presented, and the methodology of its application is offered.FindingsIt is substantiated that the economic component of effectiveness of the market economy might have no connection with its social component, moreover, these two components could enter a vivid contradiction. This contradiction is especially vivid in countries with developed market economy. As the example of the USA shows despite the high global economy its market economy shows average statistical social effectiveness. While the experience of Russia shows that even with moderate global competitiveness of the market economy, it is possible to achieve its high social effectiveness. Advantages are achieved due to other social effects – active development of human potential and using the opportunities of the digital economy for social purposes. Social effectiveness of the Russian economy is assessed at 1.602.Originality/valueThe determined differences in the level of social effectiveness of developed and developing market economy predetermined the necessity for applying different measures to manage this effectiveness. A cyclic algorithm for managing the social effectiveness of developed and developing markets has been developed from the examples of the USA and Russia in 2019. It shows that perspectives of increasing the social effectiveness of certain market economies and leveling the disproportions of social effectiveness in the modern global economic system are connected to change of the measures of management with results and costs and for avoiding their mutual neutralization, the authors offer scientific and practical recommendations.
Wild data: how front‐line hospital staff make sense of patients’ experiences
Authors: Montgomery Catherine M. , Chisholm Alison , Parkin Stephen , Locock Louise 
Published: May 2020

AbstractPatient‐centred care has become the touchstone of healthcare policy in developed healthcare systems. The ensuing commodification of patients’ experiences has resulted in a mass of data but little sense of whether and how such data are used. We sought to understand how front‐line staff use patient experience data for quality improvement in the National Health Service (NHS). We conducted a 12‐month ethnographic case study evaluation of improvement projects in six NHS hospitals in England in 2016–2017. Drawing on the sociology of everyday life, we show how front‐line staff worked with a notion of data as interpersonal and embodied. In addition to consulting organisationally sanctioned forms of data, staff used their own embodied interactions with patients, carers, other staff and the ward environment to shape improvements. The data staff found useful involved face‐to‐face interaction and dialogue; were visual, emotive, and allowed for immediate action. We draw on de Certeau to re‐conceptualise this as ‘wild data’. We conclude that patient experience data are relational, and have material, social and affective dimensions, which have been elided in the literature to date. Practice‐based theories of the everyday help to envision ‘patient experience’ not as a disembodied tool of managerialism but as an embedded part of healthcare staff professionalism.
Comparison of bioelectrical impedance analysis in healthy pregnant women and patient on hemodialysis
Authors: Hashimoto Seiji , Maoka Tomochika , Yamamoto Rie , Kawashima Keisuke , Nishikawa Akira , Sakurada Katsumi , Koike Takao , Shigematsu Takashi 
Published: May 2020

AbstractPregnant woman undergoing dialysis face challenges such as miscarriage and stillbirth when carrying a baby to term. A complication of prenatal care is the difficulty in properly managing body fluids. We compare fluid volumes between healthy pregnant women and two pregnant women undergoing dialysis using bioelectrical impedance analysis (BIA). Data of 52 healthy pregnant women at various stages of their pregnancy were analyzed for the study. We included these many cases so as to collect sufficient data to compare them with our two cases of women undergoing dialysis who successfully completed their term deliveries. Fluid volumes were measured every week before and after dialysis using BIA. We also measured the levels of human atrial natriuretic peptide after dialysis. During dialysis, the dry weight (DW) of pregnant patients is altered based on the state of the amniotic fluid and fetus. However, evaluating body fluid and DW using radiography is difficult in pregnant women. BIA offers a mostly harmless alternative for such measurements. Using BIA, we were able to easily measure body fluid volume and change the setting of DW for dialysis. Thus, our successful example can serve as a reference for future cases of pregnant women undergoing dialysis. Nevertheless, given that the state of the fetus and amniotic fluid affect the results of dialysis, it is important that we use not only BIA but also a comprehensive evaluation to determine dialysis settings in pregnant women.
Every Cloud has a Silver Lining: Using Silver Concentration to Identify the Number of Sources of Lead used in Shang Dynasty Bronzes
Authors: LIU Ruiliang , POLLARD A. Mark , LIU Cheng , RAWSON Jessica 
Published: June 2020

AbstractThe use of lead, some of which is characterized by a highly radiogenic signature, sharply distinguishes Bronze Age China from the rest of Eurasia. Scholars have long hypothesized that silver can offer an independent proxy to characterize lead minerals. The summary of silver distribution associated with Shang and Western Zhou bronzes in this paper reveals an important difference between the south (Sanxingdui, Hanzhong, Jinsha, Panlongcheng, Xin'gan) and the Central Plains. Correlating silver with lead content as well as with the isotopic signature indicates that south China and the Central Plains had different lead sources during the late Shang period, and also that the highly radiogenic and common lead used at Anyang come from geochemical environments which cannot be distinguished by the level of silver.
August–September Runoff Variation in the Kara Darya River Determined from Juniper (Juniperus turkestanica) Tree Rings in the Pamirs‐Alai Mountains, Kyrgyzstan, Back to 1411 CE
Authors: ZHANG Heli , HE Qing , CHEN Feng , CHONTOEV Dogdurbek , SATYLKANOV Rysbek , ERMENBAEV Bakytbek , CHEN Youping 
Published: June 2020

AbstractA 606 year runoff reconstruction of the Kara Darya River was developed, based on the tree‐ring width chronology of Turkestan juniper (Juniperus turkestanica) from the Pamir‐Alai Mountains of Kyrgyzstan. Preliminary comparison between the snow cover variation and these climate/runoff reconstructions found that Central Asian snow cover may have strong associations with large‐scale ocean‐atmosphere‐land circulations. The runoff reconstruction demonstrated that instrumental runoff was not representative of runoff over the past 606 years. The drought of the 1960s‐1990s resulted in low runoff levels during the past 50 years; however, this probably does not represent a worst‐case scenario for the Kara Darya because the runoff reconstruction showed additional extremely low runoff prior to the 20th century. The reconstruction will provide a long‐term perspective on runoff variation in the Kara Darya River basin, aid sustainable water resource management and be useful in guiding expectations of future variations and water resource planning.