bluuebunny/crossref_metadata_2025_split huggingface dataset:
SINGLe: Accurate detection of single nucleotide polymorphisms using nanopore sequencing in gene libraries
Authors: Rocío Espada , Nikola Zarevski , Adèle Dramé-Maigné , Yannick Rondelez 
Published: March 2020

AbstractNanopore sequencing is a powerful single molecule DNA sequencing technology which offers high throughput and long sequence reads. Nevertheless, its high native error rate limits the direct detection of point mutations in individual reads of amplicon libraries, as these mutations are difficult to distinguish from the sequencing noise.In this work, we developed SINGLe (SNPs In Nanopore reads of Gene Libraries), a computational method to reduce the noise in nanopore reads of amplicons containing point variations. Our approach uses the fact that all reads are very similar to a wild type sequence, for which we experimentally characterize the position-specific systematic sequencing error pattern. We then use this information to reweight the confidence given to nucleotides that do not match the wild type in individual variant reads. We tested this method in a set of variants of KlenTaq, where the true mutation rate was well below the sequencing noise. SINGLe improves between 4 and 9 fold the signal to noise ratio, in comparison to the data returned by the basecaller guppy. Downstream, this approach improves variants clustering and consensus calling.SINGLe is simple to implement and requires only a few thousands reads of the wild type sequence of interest, which can be easily obtained by multiplexing in a single minION run. It does not require any modification in the experimental protocol, it does not imply a large loss of sequencing throughput, and it can be incorporated downstream of standard basecalling.
Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis
Authors: Shi Qingya , Pei Fen , Perlmutter David H. , Liu Bing , Bahar Ivet 
Published: March 2020

AbstractAutophagy plays an essential role in cell survival/death and functioning. Modulation of autophagy has been recognized as a promising therapeutic strategy against diseases/disorders associated with uncontrolled growth or accumulation of biomolecular aggregates, organelles or cells including those caused by cancer, aging, neurodegeneration, and liver diseases such as α1-antitrypsin deficiency. Numerous pharmacological agents that enhance or suppress autophagy have been discovered. However, their molecular mechanisms of action are far from clear. Here we collected a set of 225 autophagy modulators and carried out a comprehensive quantitative systems pharmacology (QSP) analysis of their targets using both existing databases and predictions made by our machine learning algorithm. Autophagy modulators include several highly promiscuous drugs (e.g. artenimol and olanzapine acting as activator, fostamatinib as inhibitor, or melatonin as dual-modulator), as well as selected drugs uniquely targeting specific proteins (∼30% of modulators). They are mediated by three layers of regulation: (i) pathways involving core autophagy-related (ATG) proteins such as mTOR, AKT, and AMPK; (ii) upstream signaling events that regulates the activity of ATG pathways such as calcium-, cAMP-, and MAPK-signaling pathways; and (iii) transcription factors regulating the expression ATG proteins such as TFEB, TFE3, HIF-1, FoxO, and NF-κB. Our results suggest that PKA serves as a linker bridging between various signal transduction events and autophagy. These new insights contribute to a better assessment of the mechanism of action of autophagy modulators as well as their side effects, development of novel polypharmacological strategies, and identification of drug repurposing opportunities.
miRSwitch: Detecting microRNA arm shift and switch events
Authors: Kern Fabian , Amand Jeremy , Senatorov Ilya , Isakova Alina , Backes Christina , Meese Eckart , Keller Andreas , Fehlmann Tobias 
Published: March 2020

AbstractArm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30,521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues inHomo sapiensandMus musculus. In summary, miRSwitch offers a broad range of customised arm switch analyses along with comprehensive visualisations, and is freely available at:https://www.ccb.uni-saarland.de/mirswitch/.
Task design and assignment of full-text generation on mass Chinese historical archives in digital humanities
Authors: Liang Jihong , Wang Hao , Li Xiaojing 
Published: March 2020

PurposeThe purpose of this paper is to explore the task design and assignment of full-text generation on mass Chinese historical archives (CHAs) by crowdsourcing, with special attention paid to how to best divide full-text generation tasks into smaller ones assigned to crowdsourced volunteers and to improve the digitization of mass CHAs and the data-oriented processing of the digital humanities.Design/methodology/approachThis paper starts from the complexities of character recognition of mass CHAs, takes Sheng Xuanhuai archives crowdsourcing project of Shanghai Library as a case study, and makes use of the theories of archival science, including diplomatics of Chinese archival documents, and the historical approach of Chinese archival traditions as the theoretical basis and analysis methods. The results are generated through the comprehensive research.FindingsThis paper points out that volunteer tasks of full-text generation include transcription, punctuation, proofreading, metadata description, segmentation, and attribute annotation in digital humanities and provides a metadata element set for volunteers to use in creating or revising metadata descriptions and also provides an attribute tag set. The two sets can be used across the humanities to construct overall observations about texts and the archives of which they are a part. Along these lines, this paper presents significant insights for application in outlining the principles, methods, activities, and procedures of crowdsourced full-text generation for mass CHAs.Originality/valueThis study is the first to explore and identify the effective design and allocation of tasks for crowdsourced volunteers completing full-text generation on CHAs in digital humanities.
The impact of urban façade quality on affective feelings
Authors: Hollander Justin B. , Anderson Eric C. 
Published: March 2020

PurposeMuch of the current literature on streetscape design emphasizes a need for well-articulated edge conditions to enhance pedestrian-orientation and the reason appears to lie in evolutionary biology: humans have a psychological preference for wall-hugging due to a well-established trait in other species: thigmotaxis.Design/methodology/approachThis study seeks to explore the relationship between urban facades and affective feelings through an empirical study, which asks: how do people perceive edge conditions in urban environments? Through a study of affect relative to edge conditions, greater insight can be generated as to the human experience in the built environment. We conducted a laboratory experiment with 76 subjects who each viewed 40 images of urban facades and rated each based on their emotional reaction.FindingsEach subject also completed two validated individual trait difference measures. We found that those images depicting thigmotaxic facades were more highly rated than other facades.Originality/valueHigh quality edge environment resulted in people feeling more pleasant than low quality edges.
Dynamic capabilities for SME participation in public procurement
Authors: Akenroye Temidayo O. , Owens Jonathan D. , Elbaz Jamal , Durowoju Olatunde A. 
Published: March 2020

PurposeAlthough small- and medium-sized enterprises (SMEs) play major roles in most economies in terms of job creation, innovation and contribution to national income, they are often underrepresented in public procurement markets. This paper aims to explore how the dynamic capabilities theory can improve SME participation in public procurement.Design/methodology/approachThrough a systematic literature review, the paper identifies common barriers to the effective participation of SMEs in public procurement and explores the applicability of the dynamic capabilities theory in addressing these barriers.FindingsA theoretical analysis was conducted to identify possible relationships between the factors reported in the literature as barriers to SME participation in public procurement and different components of the dynamic capabilities of firms (i.e. sensing, seizing, reconfiguring and learning). Seven key propositions were generated to guide future research.Research limitations/implicationsDespite its contributions, this paper is based solely on a systematic literature review and theoretical analysis. Future studies could use meta-analysis to review multiple studies relating to the nexus between SMEs and public procurement, hence improving methodological rigour.Practical implicationsThe paper contributes to the ongoing debate about whether and how SMEs can leverage their resources and capabilities to develop self-help strategies to improve participation in public procurement, an area yet underexplored in the literature.Originality/valueThis is one of the few studies examining the implications of firm-level capabilities of SME activity in public procurement markets. The findings may be beneficial to SME managers/owners, particularly regarding firms' ability to leverage resources and capabilities to participate effectively in public procurement.
An investigation of key predictors of organizational citizenship behavior of civil servants
Authors: Obedgiu Vincent , Nkurunziza Gideon , Simiyu Gabriel , Lubogoyi Bumaali 
Published: March 2020

PurposeThe purpose of this paper is to examine the key predictors of organizational citizenship behavior of civil servants in local governments in Uganda.Design/methodology/approachThe study draws on a quantitative approach and cross-sectional survey design. Data were collected using a self-administered closed-ended questionnaire from a sample size of 265 respondents derived using Krejcie and Morgan (1970) from a population of 844 civil servants using stratified simple random sampling technique. Data were analyzed using IBM SPSS statistical software vs 23 and Hypotheses tested using Hayes (2018) Process Macro v3.2 (Model 4).FindingsThe findings revealed that organizational justice has a significant positive effect on organizational commitment, which impact positively on organizational citizenship behavior of civil servants. The study further reveals an indirect-only mediation where organizational justice affects organizational citizenship behavior through organizational commitment. The study proves that there is no direct relationship such a relationship is enhanced through organizational commitment.Originality/valueThis study contributes to knowledge by providing key information on the predictors of organizational citizenship behavior of civil servants. The indirect-only mediation findings give some new insights into theory and literature. This study has eventually changed the direction of the debate popularly held among previous scholars who believe that organizational justice relates to organizational citizenship behavior. This is relevant in understanding the concept of organizational citizenship behavior and filling the practical gap that exists in Ugandan context.
Choice and interest in designed learning environments: the case of FUSE Studios
Authors: DiGiacomo Daniela K. , Van Horne Katie , Penuel William R. 
Published: March 2020

Purpose
Empirical investigation into the e-learning innovation, FUSE Studios, is both timely and relevant because FUSE is rapidly expanding domestically and abroad and there is continued interest in the interdisciplinary fields of information and learning sciences in the constructs of choice and interest as they relate to the provision and design of learning experiences. In particular, this paper aims to contribute to scholarly and design-based conversations on how e-learning innovations – especially those situated within the digital youth and constructionism strands of research – can be designed in ways that support robust opportunities for learning for young people (Reynolds et al., 2019).

Design/methodology/approach
Drawing upon a large corpus of mixed-methods data including computer-generated activity log data, youth survey data and studio facilitator interview data, this paper examines patterns of use and interest-related experience among young people in a range of FUSE Studios settings across the USA.

Findings
The results suggest that student choice within FUSE’s curricular and Studio model tends to support a broad exploration of interests across a wide range of youth, rather than a deep dive into particular Science, Technology, Engineering, Arts, and Mathematics (STEAM) content areas.

Practical implications
Alongside the broad exploration that was found to characterize the patterns of student choice in FUSE Studios, a striking number of students from those surveyed reported that FUSE supported their interest development: they liked the FUSE challenges, were always able to find something of interest to do in the FUSE Studios and saw the FUSE challenges are supportive of their current and future interests. (See similar findings in Stevens et al., 2016). We understand these student self-reported experiences as evidence that the FUSE Studios model did well to encourage meaningful, interest-driven learning experiences for youth.

Originality/value
Committed to making research usable for practice, this paper offers implications for future e-learning designs that seek to make choice and interest central to the organization of activity and environment.
Customer’s expectations and perceptions of reference marketing programs
Authors: Morgado Andre Vilares 
Published: March 2020

Purpose
The purpose of this research is to study organizational purchasing and relationship formation in interactions between customers and suppliers of capital equipment and the factors affecting the ability of reference marketing programs to deliver their expected purchasing benefits.

Design/methodology/approach
This work adopts an inductive research strategy and combines a critical realist approach with a qualitative research method consisting of in-depth interviews with purchasing managers from the energy industry.

Findings
By presenting a new theoretical model that aims to explain the referencing phenomenon, this study offers a deeper understanding of referencing and thus new perspectives on how and under what circumstances the customer–supplier relationship can be leveraged.

Research limitations/implications
Because of the qualitative nature of the research, no claim to statistical significance can be made. The model presented here helps the authors to understand the empirical phenomena as exhibited in the recorded interviews, but it does not allow for statistical generalization. The model allows for a certain degree of analytic inference but only within the study’s boundaries and limitations because the above findings are specific to the electric power industry.

Practical implications
A deeper understanding of this phenomenon allows suppliers to pursue strategies based on efficient reference marketing programs. The paper ends by presenting useful recommendations for reference marketing best practices and suggestions for improving the use of references in organizational purchasing.

Originality/value
The available literature on referencing does not clarify the factors that affect the ability of reference marketing to deliver its purchasing benefits. Thus, the facts and circumstances associated with the influence that reference marketing programs have on purchasing behavior have yet to be determined.
Does regional trade promote economic growth? Evidence from Economic Community of West African States (ECOWAS)
Authors: Okoro Agwu Sunday , Ujunwa Augustine , Umar Farida , Ukemenam Angela 
Published: March 2020

PurposeThis paper examines the impact of regional and non-regional trade on economic growth using annual data from Economic Community of West African States (ECOWAS) member countries for the period 2007 to 2017.Design/methodology/approachTrade data were decomposed into regional (trade among ECOWAS Member States) and non-regional (trade between ECOWAS Member States and the rest of the world). We used the dynamic system GMM to estimate the models and introduced exchange rate, unemployment rate, population growth and gross capital formation as controlled variables.FindingsThe results revealed that the estimated coefficient of ECOWAS regional trade is statistically significant and positive in predicting growth, while the non-regional trade coefficient is negative and not statistically significant in predicting growth. Other predictors of growth introduced into the model as controlled variables, such as exchange rate, unemployment rate, population growth and gross capital formation, displayed mixed results. More importantly, population growth, unemployment and exchange rate depreciation hurt economic growth, while gross capital formation promotes economic growth.Practical implicationsThe findings provide strong support in favour of the Krugman (1991) hypothesis that regional trade agreements (RTAs) are a better alternative to global trade.Originality/valueOur decision to disaggregate ECOWAS trade is unique and influenced largely by the objective of the study, which is to establish the type of ECOWAS trade that is a good predictor of growth. The evidence from our findings support the theory that RTAs are a better catalyst to economic growth.
Suggestions for standardization of halal tourism in hospitality industry
Authors: Pamukcu Huseyin , Sariisik Mehmet 
Published: March 2020

PurposeThe purpose of this paper is to determine the expectations of hotel guests regarding the halal standards in the hotels where they stay. Besides, the determination of differences in demographic characteristics of the participants is among the objectives of the research. Thus, taking into consideration the halal standard expectations of the participants, the results that will support the applications of accommodation establishments have been attempted to be figured out.Design/methodology/approachQuantitative research methods were used in this research. Owing to the lack of a specific scale in the related literature, the questionnaire used in the study was created as a result of pilot tests conducted with the expressions mentioned in the theoretical studies. In a sense, this research provides a basis for the development of a scale that was not available in this area. Analysis methods were decided by considering the preconditions for parametric test techniques.FindingsIslamic lifestyle is specified as the most common reason for choosing halal concept hotels. Additionally, there are some other outstanding reasons like halal food, safer holiday etc. Watching TV during the holidays is the least important reason to spend time. It has been determined that the attitude toward halal tourism changes according to gender and women’s attitude toward tourism is more positive than men’s. In addition to this, it is found out that the attitude of halal tourism differs by age for males, while it differs by educational status for women. It is ensured that potential entrepreneurs can achieve significant economic gains by attracting investors’ attention to this market. Besides, the possibility of meeting the holiday needs of the masses with religious sensitivities within the country is revealed by halal tourism. The emergence of sufficient tourism facilities will show that this group will be respected and valued. Hence, this will also contribute positively to social tolerance.Research limitations/implicationsHalal tourism is an issue for almost all tourism (accommodation, eating, recreation, transportation) businesses. However, this dissertation focused on accommodation establishments and other tourism enterprises were excluded from the scope of the study.Practical implicationsIt is believed that this study is authentic in the way it offers a universal halal tourism model for the hospitality industry as well as the comprehensive literature review that it is built on. Thus, it is expected to have a significant impact on both practical and theoretical knowledge.Originality/valueThis study is unique in terms of increasing the satisfaction of the people demanding the halal concept accommodation establishments can apply halal tourism and offering a standardization proposal for that. It is thought that this research is original and that it is important for both the practice field and the theoretical field to provide a standardization which can be applied in accommodation establishments.