bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jointly Defining Cell Types from Multiple Single-Cell Datasets Using LIGER
Authors: Liu Jialin , Gao Chao , Sodicoff Joshua , Kozareva Velina , Macosko Evan Z. , Welch Joshua D. 
Published: April 2020

AbstractHigh-throughput single-cell sequencing technologies hold tremendous potential for defining cell types in an unbiased fashion using gene expression and epigenomic state. A key challenge in realizing this potential is integrating single-cell datasets from multiple protocols, biological contexts, and data modalities into a joint definition of cellular identity. We previously developed an approach called Linked Inference of Genomic Experimental Relationships (LIGER) that uses integrative nonnegative matrix factorization to address this challenge. Here, we provide a step-by-step protocol for using LIGER to jointly define cell types from multiple single-cell datasets. The main steps of the protocol include data preprocessing and normalization, joint factorization, quantile normalization and joint clustering, and visualization. We describe how to jointly define cell types from single-cell RNA-seq and single-nucleus ATAC-seq data, but similar steps apply across a wide range of other settings and data types, including cross-species analysis, single-nucleus DNA methylation, and spatial transcriptomics. Our protocol contains examples of expected results, describes common pitfalls, and relies only on our freely available, open-source R implementation of LIGER. We also provide Rmarkdown tutorials showing the outputs from each individual code segment. The analysis process can be performed in 1 - 4 h depending on dataset size and assumes no specialized bioinformatics training.
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors
Authors: Lewis Joshua E. , Forshaw Tom E. , Boothman David A. , Furdui Cristina M. , Kemp Melissa L. 
Published: April 2020

AbstractRedox cofactor production is integral towards antioxidant generation, clearance of reactive oxygen species, and overall tumor response to ionizing radiation treatment. To identify systems-level alterations in redox metabolism which confer resistance to radiation therapy, we developed a bioinformatics pipeline for integrating multi-omics data into personalized genome-scale flux balance analysis models of 716 radiation-sensitive and 199 radiation-resistant tumors. These models collectively predicted that radiation-resistant tumors reroute metabolic flux to increase mitochondrial NADPH stores and ROS scavenging. Simulated genome-wide knockout screens agreed with experimental siRNA gene knockdowns in matched radiation-sensitive and –resistant cancer cell lines, revealing gene targets involved in mitochondrial NADPH production, central carbon metabolism, and folate metabolism that allow for selective inhibition of glutathione production and H2O2clearance in radiation-resistant cancers. This systems approach represents a significant advancement in developing quantitative genome-scale models of redox metabolism and identifying personalized metabolic targets for improving radiation sensitivity in individual cancer patients.
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
Authors: Sarkar Hirak , Srivastava Avi , Bravo Héctor Corrada , Love Michael I. , Patro Rob 
Published: April 2020

AbstractMotivationAdvances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcriptlevel abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects.ResultsWe introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly-reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently supported, and deriving transcriptional groups where the inferential uncertainty is too high to support a transcript-level result.AvailabilityTerminus is implemented in Rust, and is freely-available and open-source. It can be obtained fromhttps://github.com/COMBINE-lab/Terminus.Contactrob@cs.umd.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
The sustainability in alcohol consumption: the “drink responsibly” frontier
Authors: Farace Biasino , Apicella Andrea , Tarabella Angela 
Published: April 2020

PurposeThe excessive consumption of alcohol in numerous countries in the world, combined with the progressively younger age of the consumers, made it necessary for companies to use instruments of communication aimed at the development of consumption responsibility, so as to prevent reckless behaviour and the health risks thereto associated. The purpose of this paper is to assess the visibility and effectiveness of responsible consumption messages used for the sale of the product “beer” (on packaging and in advertisements); the study used a sample audience made up of teenagers and young adults from southern Italy.Design/methodology/approachThe methodology used was that of the focus group. Three interview sessions were conducted, one dedicated to teenagers, age 16–17 years, and two dedicated to young adult panels, age 20–24 years. A ten-question questionnaire was designed prior to the conduction of the focus groups, and it was used in all the sessions.FindingsThe study shows the weak efficacy of the “drink responsibly” communication campaigns carried out by beer manufacturers. The totality of the interviewees failed to remember the existence of the “drink responsibly” messages and, even after supplementary visual stimulation, they were mostly disinterested, defining the fact that companies from the alcoholic drinks industry carry out consumption awareness campaigns as an out-and-out nonsensical contradiction.Originality/valueThe survey draws attention to the perception by young audiences of the more recent “drink responsibly” communication campaigns carried out by beer manufacturers, aiming at encouraging a more responsible attitude to alcohol consumption. There still are not many such inquests aimed at determining the response of young people to the use of slogans and commercials connected to responsible drinking in the literature; therefore, this study aimed at filling this gap. In fact, the authors believe this study is important for assessing the effectiveness of such instruments for achieving greater responsibility in the use of alcoholic drinks, so as to develop better awareness in the ranks of youths. Among the new communication strategies that were proposed to the participants, there were video commercials containing responsible consumption messages and the new prohibition marks placed directly on the product labels.
Relationship between slack resources and performance: temporal symmetry and duration of effects
Authors: Agusti-Perez Maria , Galan Jose Luis , Acedo Francisco J. 
Published: April 2020

PurposeAlthough slack resources and their relationship to performance have been widely studied in the literature, the temporal symmetry of this relationship, and the duration of its effects, are still unknown aspects and are the objective of this paper.Design/methodology/approachTo evaluate this effect, an exploratory study has been designed on a sample of 449 Spanish industrial companies over a period of 12 years, assessing the impact of idle resources on economic and financial profitability. By means of hierarchical regressions, the short- term, medium- term and long-term effects of slack resources have been evaluated.FindingsThe results show that the impact on performance depends on the type of resource considered. Available slack has a consistent and positive effect on economic profitability in the short term. Other types of slack show persistent effects on performance, but, in the case of the recoverable slack, with a negative sign that contradicts the benefits provided by these resources. Finally, potential slack only has a permanent effect on financial profitability, but the sign changes depending on the economic context under consideration. There are also differences in the duration of the effects according to the type of resources.Originality/valueThis paper advances the knowledge about the slack-performance relationship over time that has been scarcely studied.
Providing healthcare through “value shops”: impact on professional fulfilment for physicians and nurses
Authors: Gadolin Christian , Andersson Thomas , Eriksson Erik , Hellström Andreas 
Published: April 2020

PurposeThe purpose of this paper is to empirically explore and demonstrate the ability of healthcare professionals to attain professional fulfilment when providing healthcare inspired by “value shops”.Design/methodology/approachA qualitative case study incorporating interviews and observations was conducted.FindingsThe empirical data suggest that the professional fulfilment of both physicians and nurses is facilitated when care is organized through “value shops”. Both groups of professionals state that they are able to return to their “professional core”.Originality/valueThe beneficial outcomes of organizing healthcare inspired by the “value shop” have previously been explored in terms of efficiency and quality. However, the professional fulfilment of healthcare professionals when providing such care has not been explicitly addressed. Professional fulfilment is vital in order to safeguard high-quality care, as well as healthcare professionals' involvement and engagement in implementing quality improvements. This paper highlights the fact that care provision inspired by the “value shop” may facilitate professional fulfilment, which further strengthens the potential positive outcomes of the “value shop” when utilized in a healthcare setting.
Misallocation and reallocation of resources in Vietnamese manufacturing firms
Authors: Nguyen Phuong Thi , Nguyen Minh Khac 
Published: April 2020

PurposeThis research identifies the level of misallocation in Vietnamese manufacturing sector for the period 2000–2015. Meltiz and Polanec dynamic productivity decomposition is used to compare the relative productivity contributions from surviving, entering and exiting firms to aggregate productivity change by the type of ownership. Heckman's two-step model is used to examine the effect of misallocation and industry- and firm-level factors on entry or exit decision and market share of firms in Vietnamese manufacturing sector.Design/methodology/approachThe level of misallocation and efficiency gains in total factor productivity (TFP) are assessed using Hsieh and Klenow (2009) productivity decomposition framework for the period 2000–2015. The dynamic productivity decomposition of Meltiz and Polanec (2015) is used to compare the relative contributions from surviving, entering and exiting firms to aggregate productivity change. The effects of misallocation and other factors on entry or exit decisions and market share of firms are determined by using Heckman choice model.FindingsThe results indicate three main points. Firstly, resource misallocation is found to be highest among state-owned enterprise (SOEs) and low technology industries. TFP is found to 81.2% greater if there is no resource misallocation among firms. Secondly, the aggregate productivity change for the entering, exiting and surviving firms is 35% due to productivity reallocation among three groups. Finally, the decision of entry or exit as well as the market share of firms are influenced by misallocation and industry- and firm-level factors such as Vietnam's WTO entry, tax policy, financial frictions, industrial concentration, technology gap, capital intensity, human capital, scale of firm, time entry and FDI spillovers. The result finds the higher misallocation level is, the lower the probability and market share for a new firm to enter in the industry is.Research limitations/implicationsThe main limitation of the study is that the market is assumed perfectly competitive and the method has only decomposed misallocation of resources to those arising from output and capital distortions. The results of Heckman choice model only clarify on the sub-sample of state-owned enterprises and low technology firms.Originality/valueThe focus of many previous research papers on resource misallocation was generally to look at the level of misallocation in developed countries. However, knowledge about the effect of misallocation and other factors on entry or exit decisions and market share of firms is limited, particularly in the context of developing countries. This paper clarifies the level of misallocation in Vietnamese manufacturing sector and the effect of misallocation and other factors on entry or exit decisions and market share of firms.
Interactive research in production start-up—application and outcomes
Authors: Berglund Martina , Harlin Ulrika , Säfsten Kristina 
Published: April 2020

PurposeThe purpose of this paper is to reflect on interactive research as a means to create relevant knowledge in the domain of operations management in general and specifically in the context of production start-up.Design/methodology/approachThe reflection on the use of interactive research in production start-ups was based on a study of two completed interactive research projects. The lens for reflection was a framework including context, quality of relationship, quality of the research process itself and outcomes.FindingsThe context was industrial manufacturing companies in Sweden, with different kind of challenges related to production start-ups, such as collaboration between involved functions and suppliers, competence development and work routines. Indicators of the quality of relationship between researchers and practitioners were initiated development activities and new collaboration between functions, within the company, between companies and in supply chains. The reflection of the quality of the research process itself was based on an interactive research process including four iterative steps with regular follow-ups allowing joint practitioner and researcher reflection on the progress. Identified outcomes included increased awareness and competence on how to deal with production start-ups, improvements of communication, work procedures and structures, better use of competences, increased cross-functional dialogue and cultural understanding.Practical implicationsImplications for practitioners are the possibilities for knowledge creation through interactive collaboration in research projects enabling exchange between researchers from complementary fields and other companies dealing with production start-ups.Originality/valueThe interactive research approach enables joint knowledge creation in a fast-changing context such as production start-ups as well as value-adding results both for practitioners in industry and for academia.
Identity play and the stories we live by
Authors: Ghaempanah Babak , Khapova Svetlana N. 
Published: April 2020

PurposeThe purpose of this paper is to advance our understanding of identity play process by including the stories we live by in depth. Over the past decade, identity play literature has placed more emphasis on the role of self-narratives. Yet, the “stories we live by”, including the told or untold stories of past and imagined events of the future, have not been considered in depth in these self-narratives.Design/methodology/approachThis conceptual paper draws on the personal construct theory, narrative identity and constructivist psychotherapy literatures and attempts to include the stories we live by in scholarly conceptualizations and explorations of identity play processes.FindingsDrawing on the personal construct theory, narrative identity and constructivist psychotherapy literatures this paper offers a comprehensive conceptual model of how the stories we live by infuse individual identity construction processes. The model highlights the inter-connectivity among stories we live by, identity play, identity work, sensemaking and social validation. Looking through the lens of the personal construct theory and taking these inter-connectivities into account lead to the observation of temporality in identity construction and the plurivocality of self-narratives.Originality/valueThis paper looks at identity play through the lens of the personal construct theory. However, self-narratives are seen as a medium for manifestation of personal constructs. Thus, this paper also draws on the narrative identity literature and dialogical-self concept, which helps access the multiplicity of the self-narratives to widen our grasp of personal constructs. This paper combines discourse of deconstruction with the dialogical-self concept and provides more means for the explication of identity play.
A user preference modelling method for the assessment of visual complexity in building façade
Authors: Hussein Dheyaa 
Published: April 2020

PurposeThis study aims to provide a method to assess the perceptual impact of the visual complexity of building façades.Design/methodology/approachThe research identifies the number of design elements and the variation in their position and colour as variables of visual complexity. It introduces the concepts of vertices and corners as atomic indicators on which the measurement of these variables is built. It measures visual complexity and its variables in images of building façades and analyses their relationships with participants' reactions. It reports on the effect of visual complexity on preferences, the adequacy of different methods in measuring visual complexity and the perceptual impact of each of its variables.FindingsThe research demonstrates that visual complexity can be assessed through the measure of its variables and their statistical mapping to users' preferences.Originality/valueThe manuscript provides the foundation for a planning/assessment tool for the visual control of the built environment using computer systems based on the preferences of residents through the examination of the relationship between the users and their environment. It creates a paradigm, which introduces a robust concept in the visual analysis of urban design.
A case study of disaster decision‐making in the presence of anomalies and absence of recognition
Authors: Curnin Steven , Brooks Benjamin , Owen Christine 
Published: April 2020

AbstractThis paper provides an insight into the complexities of decision‐making during an unprecedented disaster. We used the critical decision method to explore a series of decision points that were made for a low probability yet high consequence decision that was made by the commander of the Australian Urban Search and Rescue team deployed to Fukushima in 2011. The findings identified that in a situation with no similarities to previous experiences, the commander used a process of anomaly detection to trigger a situational assessment, following this with mental simulation and consultation of his actions. In this unparalleled case study, hazard‐specific expertise also supported the decision‐making process. The paper offers practitioners and academia an example of high consequence decision‐making in a unique situation as well as the opportunity to reflect on the models of decision‐making previously identified as useful in these operational environments.
Ultrasonographic evaluation of subclinical enthesitis in patients with psoriasis
Authors: Bolkan Günaydın Elzem , Aladağ Perihan , Tecer Duygu , Yenice Işıl Saadet , Adışen Esra , Göğüş Feride Nur 
Published: April 2020

AbstractAimThe primary objective of this study was to assess the ultrasonographic signs of subclinical enthesitis in patients with psoriasis. Secondary objective was to examine the associations between the clinical assessments of enthesitis, severity of psoriasis, and the ultrasonographic signs of enthesitis.MethodThis study included 30 patients with psoriasis who did not have clinically detectable arthritis or enthesitis and 30 healthy volunteers as a control group. In the patient group, PASI, NAPSI, MASES, and SPARCC scores were calculated, and in the control group, MASES and SPARCC scores were calculated. Acute, chronic, and total enthesitis scores were calculated by ultrasonographic examination of the enthesis points that are assessed during calculation of SPARCC score, performed by a researcher blinded to the clinical assessments.ResultIn the ultrasonographic assessment, total enthesitis score was significantly higher in the patient group compared with the control group (P = .04). There was no significant difference between the groups regarding acute or chronic enthesitis scores. NAPSI, PASI, MASES, or SPARCC scores did not show correlation with the ultrasonographically acute, chronic, or total enthesitis scores. There was a low‐level correlation between MASES and SPARCC scores in the patient group, which was statistically significant (P = .03). No significant correlation was found between other clinical scores. There was no significant difference between patient and control groups in terms of MASES and SPARCC scores.ConclusionEntheseal changes may be frequently observed in patients with psoriasis who are asymptomatic. Musculoskeletal ultrasonography (MUS) may be utilized to detect such abnormalities at the early period.
New insight into the role of substance P/neurokinin‐1 receptor system in breast cancer progression and its crosstalk with microRNAs
Authors: Ebrahimi Safieh , Javid Hosein , Alaei Amin , Hashemy Seyed Isaac 
Published: April 2020

AbstractThe neuropeptide substance P (SP) triggers a variety of tumor‐promoting signaling pathways through the activation of neurokinin‐1receptor (NK1R), a class of neurokinin G protein‐coupled receptors superfamily. Recent researches in our and other laboratories have shown the overexpression of both SP and NK1R in breast cancer (BC) patients. SP/NK1R signaling is strongly implicated in the pathogenesis of BC through affecting cell proliferation, migration, metastasis, angiogenesis, and resistance. Therefore, SP/NK1R signaling responses must be rigorously regulated; otherwise, they would contribute to a more aggressive BC phenotype. Recently, microRNAs (miRNAs) as a specific class of epigenetic regulators have been shown to regulate NK1R and thus, controlling SP/NK1R signaling responses in BC. This review summarizes the current knowledge of the role of SP/NK1R signaling and its therapeutic potentials in BC. We also provide an overview regarding the effects of miRNA‐mediated NK1R regulatory mechanisms in controlling BC tumorigenesis to gain a clearer view and thus better management of cancer.