bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying shared and unique gene content across 17 microbial ecosystems
Authors: Zimmerman Samuel , Tierney Braden T , Patel Chirag J , Kostic Aleksandar D 
Published: July 2022

AbstractMeasuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies including -- 6 human-associated, 7 non-human-host-associated, and 4 in other non-human host environments. In total, we identified 117,629,181 non-redundant genes. The vast majority of genes (66%) occurred in only one sample (i.e. “singletons”). By contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report datasets of other ecology-associated genes (e.g. abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g. at gene-sequence identifies that are too restrictive). We provide our results and the sets of environmentally-differentiating genes described above at http://www.microbial-genes.bio.ImportanceThe amount of shared genetic elements has not been quantified between the human microbiome and other host and non-host associated microbiomes. Here we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as “near-complete” are far from it. Additionally, over two-thirds of all genes only appear in a single sample and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.
Clostridioides difficile bile salt hydrolase activity has substrate specificity and affects biofilm formation
Authors: Aguirre Andrea Martinez , Sorg Joseph A. 
Published: July 2022

AbstractThe Clostridioides difficile pathogen is responsible for nosocomial infections. Germination is an essential step for the establishment of C. difficile infection (CDI) because toxins that are secreted by vegetative cells are responsible for the symptoms of CDI. Germination can be stimulated by the combinatorial actions of certain amino acids and either conjugated or deconjugated cholic acid-derived bile salts. During synthesis in the liver, cholic acid- and chenodeoxycholic acid-class bile salts are conjugated with either taurine or glycine at the C24 carboxyl. During GI transit, these conjugated bile salts are deconjugated by microbes that express bile salt hydrolases (BSHs). Here, we surprisingly find that several C. difficile strains have BSH activity. We observed this activity in both C. difficile vegetative cells and in spores and that the observed BSH activity was specific to taurine-derived bile salts. Additionally, we find that this BSH activity can produce cholate for metabolic conversion to deoxycholate by C. scindens. The C. scindens-produced deoxycholate signals to C. difficile to initiate biofilm formation. Our results show that C. difficile BSH activity has the potential to influence the interactions between microbes and this could extend to the GI setting.ImportanceBoth primary and secondary bile salts are well-established to impact C. difficile spore germination and vegetative growth. Here, we find that C. difficile vegetative cells, and spores, have bile salt hydrolase activity that is specific to taurine-derived bile salts. When grown in co-culture with the secondary bile salt-producing bacterium, C. scindens, we find that C. difficile-mediated deconjugation of taurocholate, ‘feeds’ C. scindens cholate. C. scindens 7α-dehydroxylates cholate to deoxycholate. The C. scindens-produced deoxycholate then stimulates biofilm formation by C. difficile cells. Thus, this suggests that the bile salt hydrolase activity expressed by several C. difficile strains could be responsible for modulating in vivo biofilm formation and maintenance in a host.
Enriching Representation Learning Using 53 Million Patient Notes through Human Phenotype Ontology Embedding
Authors: Daniali Maryam , Galer Peter D. , Lewis-Smith David , Parthasarathy Shridhar , Kim Edward , Salvucci Dario D. , Miller Jeffrey M. , Haag Scott , Helbig Ingo 
Published: July 2022

AbstractThe Human Phenotype Ontology (HPO) is a dictionary of more than 15,000 clinical phenotypic terms with defined semantic relationships, developed to standardize their representation for phenotypic analysis. Over the last decade, the HPO has been used to accelerate the implementation of precision medicine into clinical practice. In addition, recent research in representation learning, specifically in graph embedding, has led to notable progress in automated prediction via learned features. Here, we present a novel approach to phenotype representation by incorporating phenotypic frequencies based on 53 million full-text health care notes from more than 1.5 million individuals. We demonstrate the efficacy of our proposed phenotype embedding technique by comparing our work to existing phenotypic similarity-measuring methods. Using phenotype frequencies in our embedding technique, we are able to identify phenotypic similarities that surpass the current computational models. In addition, we show that our embedding technique aligns with domain experts’ judgment at a level that exceeds their agreement. We show that our proposed technique efficiently represents complex and multidimensional phenotypes in HPO format, which can then be used as input for various downstream tasks that require deep phenotyping, including patient similarity analyses and disease trajectory prediction.
Integrative multi-omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention-Deficit/Hyperactivity Disorder
Authors: Hubers Nikki , Hagenbeek Fiona A. , Pool René , Déjean Sébastien , Harms Amy C. , Roetman Peter J. , van Beijsterveldt Catharina E. M. , Fanos Vassilios , Ehli Erik A. , Vermeiren Robert R. J. M. , Bartels Meike , Hottenga Jouke Jan , Hankemeier Thomas , Dongen Jenny van , Boomsma Dorret I. 
Published: July 2022

AbstractThe evolving field of multi-omics combines data and provides methods for simultaneous analysis across several omics levels. Here, we integrated genomics (transmitted and non-transmitted polygenic scores (PGS)), epigenomics and metabolomics data in a multi-omics framework to identify biomarkers for ADHD and investigated the connections among the three omics levels. We first trained single- and next multi-omics models to differentiate between cases and controls in 596 twins (cases=14.8%) from the Netherlands Twin Register (NTR) demonstrating reasonable in-sample prediction through cross-validation. The multi-omics model selected 30 PGSs, 143 CpGs, and 90 metabolites. We confirmed previous associations of ADHD with glucocorticoid exposure and the transmembrane protein familyTMEM, show that the DNA methylation of theMAD1L1gene associated with ADHD has a relation with parental smoking behavior, and present novel findings including associations between indirect genetic effects and CpGs of theSTAP2gene. Out-of-sample prediction in NTR participants (N=258, cases=14.3%) and in a clinical sample (N=145, cases=51%) did not perform well (range misclassification was [0.40, 0.57]). The results highlighted connections between omics levels, with the strongest connections between non-transmitted PGS, CpGs, and amino acid levels and show that multi-omics designs considering interrelated omics levels can help unravel the complex biology underlying ADHD.
How the introduction of new regulatory forms shapes firm self-regulation in the US automobile industry
Authors: Cavazos David 
Published: July 2022

PurposeThe current research aims to explore how the implementation of new regulatory forms contributes to firm self-regulation.Design/methodology/approachLongitudinal analysis of firm-initiated product recalls for 15 manufacturers in the US automobile industry from 1966–2012.FindingsExamining firm-initiated product recalls for 15 manufacturers in the US automobile industry from 1966–2012 has several important findings regarding how the introduction of specific regulatory forms contributes to firm-initiated vehicle recalls. Firms are not likely to self-regulate in response to surveillance or standards-based regulation while information-based regulation results in a greater likelihood of firm self-regulation.Originality/valueThis result suggests that even at the product level; firms become increasingly motivated to self-regulate as regulators introduce information-based regulations.
PMBOK, IPMA and fuzzy-AHP based novel framework for leadership competencies development in megaprojects
Authors: Faisal Mohd. Nishat , Al Subaie Abdulla Abdulaziz , Sabir Lamay Bin , Sharif Khurram Jahangir 
Published: July 2022

PurposeEffective leaders have emerged as the cornerstone of project success. The major purpose of this paper is to propose a framework to categorize and prioritize leadership competencies for project managers in megaprojects.Design/methodology/approachIn the first stage, this study utilizes PMBOK 6th Edition, IPMA ICB 4.0 frameworks to develop a hierarchy-based four clusters of leadership competencies. In the second stage, a Fuzzy-AHP (Analytic Hierarchy Process) approach was employed to prioritize the leadership competencies for an organization dealing in megaprojects. Finally, using ordinal priority approach (OPA), the results of Fuzzy-AHP method are validated.FindingsBased on PMBOK, IPMA and literature, the proposed framework deduced twenty-four leadership competencies and grouped them in four clusters. The Fuzzy-AHP results indicate that among clusters, people competencies cluster is ranked most important, followed by perspective, practice, and innovation competencies. Considering the sub-categories and global weights, culture/values, governance, interpersonal skills, and development and growth emerged as the most important leadership competencies. The results from OPA corroborate the findings of Fuzzy-AHP method.Practical implicationsMegaprojects are characterized by massive investments and extensive economic and social impact. The proposed framework would be an important aid for policymakers to develop suitable strategies and programs to inculcate leadership competencies that would lead to successful project managers and improved project performance.Originality/valueThe need for this research stems from the need to integrate popular project management frameworks in leadership competencies development in project based organizations. The proposed integrated framework, based on PMBOK 6th Edition and IPMA ICB 4.0 competency frameworks, is an original contribution to understand and prioritize leadership competencies for megaproject success.
How public client’s control systems affect contractors’ innovation possibilities
Authors: Järvenpää Anna-Therése , Larsson Johan , Eriksson Per Erik 
Published: July 2022

Purpose
This paper aims to identify how a public client’s use of control systems (process, output and social control) affect innovation possibilities in construction projects.

Design/methodology/approach
Semi-structured interviews about six infrastructure projects were conducted to identify respondents’ views on innovation possibilities. These possibilities were then analyzed from an organizational control perspective within principal–agent relationships between the Swedish Transport Administration (STA) and their contractors.

Findings
How the client uses control systems affects innovation possibilities. Relying on process control could negatively affect innovation opportunities, whereas output control could have a positive influence. In addition, social control seems to have a weak effect, as the STA appears not to use social control to facilitate joint innovation. Public clients must comply with the Public Procurement Act and, therefore, retain the requirements specified in the tendering documents. Much of the steering of the execution is connected to the ex ante phase (before signing the contract), which affects innovation possibilities in the design and execution phases for the contractor.

Research limitations/implications
This study was conducted with only one client, thus limiting its generalizability. However, the findings provide an important stepping stone to further investigation into balancing control systems and creating innovation possibilities in a principal–agent relationship.

Originality/value
Although public procurement has increasingly been emphasized as a major potential source of innovation, studying how a public client’s use of organizational control systems affects innovation possibilities in the construction sector has received scant attention.
The hunt for computerized accounting education in the GCC: a structured literature review
Authors: Thottoli Mohammed Muneerali 
Published: July 2022

PurposeThe objective of this paper is to review and analyze the existing literature on computerized accounting education (CAE) in educational institutions across the Gulf Cooperation Council (GCC) countries and to suggest a research agenda for the future.Design/methodology/approachThe author employs a structured literature review (SLR) approach to analyze CAE research published in the GCC between 1981 and 2021.FindingsThe current study has focused mainly on education in the field of computerized accounting (CA); however, very few research studies have focused on CAE. The author recognized two key topics: the broad concept of CA and the identification of software programs used to teach CA courses.Research limitations/implicationsA future study might extend to address the gap in the knowledge of graduate students’ theoretical concept in accounting with CA program across higher-educational institutions (HEIs) in the GCC.Practical implicationsThe broad topic analyzed by the author leads to highlight the growing need for students’ practical skills in CA, particularly in the GCC, and to give suggestions for future research. This study also provides a kind of advice to educational institutions to implement an appropriate CA program for CA courses.Originality/valueCurrently, there is a lack of SLR on CAE. Findings on the broad topic analyzed in the current study have been addressed by agreeing on a critical assessment of present research and future research goals.
Food supply chain waste reduction for a circular economy in the COVID-19 pandemic: a longitudinal study of New Zealand consumers
Authors: Luo Na , Olsen Tava , Ganguly Subhamoy , Liu Yanping 
Published: July 2022

PurposeFood waste (FW) reduction, of which household wastage comprises a large fraction, has an important role in promoting the circular economy (CE). This study investigates how certain consumer traits impact household FW, particularly in the face of external shocks.Design/methodology/approachThe authors conducted a qualitative and longitudinal study, spanning three periods in New Zealand. A preliminary model is constructed from the outcomes of a survey with 178 participants. Then, the authors carried out 29 semi-structured interviews to refine the preliminary model and adapt it to the analysis of household waste behavior.FindingsDifferent segments of consumers have distinct response patterns in successive lockdowns, and these patterns impact household FW reduction and food supply chain (FSC) management. The key findings include (1) for government, quick responses to quash unhelpful rumors help to reduce public concerns around FSC interruption; (2) for retailers, the pandemic has hastened the growth of online shopping; being able to expand the distribution channel in a short time is a critical issue; and (3) for consumers, the experience of lockdown has different impacts on different groups of consumers. This variation of experience may either enhance or exacerbate FW in households.Originality/valueThis paper complements the existing literature on the FSC and contributes to household FW and CE literature by providing a framework that integrates external impacts, consumer segmentation to reflect on waste management, and the possible applications of the proposed framework.
Destination stereotypes: a phenomenon of destination image
Authors: Karri Venkata Rohan Sharma , Dogra Jeet 
Published: July 2022

PurposeDespite years of research on destination image (DI), studies have surprisingly failed to investigate how tourists perceive and approach destinations that they are not cognizant about. While prodigious amount of information is available on the dimensionality and nature of DI, little is known about the construct with reference to cognizance, geographical proximity and units. Understanding such an aspect would help destination management organizations (DMOs) in refining their marketing strategies and in improving their destination's competitiveness.Design/methodology/approachThrough an extensive review of literature in areas pertinent to the phenomenon being investigated, this article puts forward a series of propositions, which are then used in the framework entailing the proposed construct of destination stereotypes (DS).FindingsWhile identifying an overlap in concepts pertaining to the fields of marketing and tourism, this study postulates that DS facilitate the extension of a destination's dominant impressions to that of another based on various parameters. It further discusses several courses through which impressions of a particular destination are extended to that of another, thereby putting forward DS as a missing link in tourists' reception of destinations.Practical implicationsDS as a construct helps in identifying the source of an impression which may not be the destination in question but instead another destination. Upon construct validity, the proposed framework would yield insights into other competing destinations and thereby effectively help in altering the extant DI.Originality/valueWhile there have been many studies on tourist stereotypes and DI, it is amongst the first few studies to have discussed stereotypes in the context of destinations and their image, especially with an emphasis on cognizance, geographical proximity and units. Therefore, it acts as a meaningful piece of work towards the progression of the DI literature.
Interplay between lean management and circular production system: implications for zero-waste performance, green value competitiveness, and social reputation
Authors: Afum Ebenezer , Li Yiming , Han Peixiu , Sun Zhuo 
Published: July 2022

PurposeThis study explores the interplay between lean management and circular production systems and their implications on zero-waste performance, green value competitiveness and social reputation.Design/methodology/approachQuestionnaire-based survey methodology is used to obtain empirical data from Ghanaian manufacturing SMEs. A multivariate statistical technique, specifically partial least square structural equation modelling is chosen to test the hypothesized relationships.FindingsThe empirical results confirm that lean management is a vital element in moving SMEs towards the implementation of circular production systems. The results also confirm that lean management and circular production systems combine effectively to bring about significant improvement in zero-waste performance, reinforce green value competitiveness and boost social reputation. The results further confirm the mediation role of circular production system between lean management, zero-waste performance, green value competitiveness and social reputation.Originality/valueAnchored on the tenets of the natural resource-based view theory, resource orchestration theory and stakeholder theory, this study proposes an integrated research model that builds new insights into the relationship between lean management, circular production system, zero-waste performance, green value competitiveness and social reputation. The proposed model directs the actions of SME managers in emerging countries to comprehensively evaluate their production processes to equalize the possible compatibility of lean management and circular production systems to meet their zero-waste performance targets, gain green value competitiveness and stimulate social reputation.
Prosocial messaging during the COVID-19 pandemic: a longitudinal examination of email advertisements
Authors: Deutsch Ashley , Mouton Ashton 
Published: July 2022

PurposeThis study aims to evaluate how brands communicate with consumers through the COVID-19 pandemic and how messaging has shifted over time. The authors identify a typology drawn from extant literature and use it to understand how brands shape consumers’ behavior.Design/methodology/approachThrough a mix of interpretive and thematic analysis, the authors examine 858 US email advertisements and how these messages have evolved throughout the pandemic.FindingsThe authors findings demonstrate brand communication ranges from prosocial to brand messaging and brands employed different strategies at different phases of the pandemic. Specifically, while brands started out emphasizing socially desirable behavior before and directly after a national emergency was declared, COVID-19-related communications shifted to predominantly marketing-related messages later in the pandemic.Originality/valueThis study provides valuable insight into how brands adjust communication strategies through a prolonged cultural trauma and how these messages relate to authenticity, the triple bottom line and a social (versus branded) focus.
Records management practices: are all its factors associated with administrative staff performance in chartered private universities in Uganda?
Authors: Barigye Assumpta , Kasekende Francis , Mwirumubi Richard 
Published: July 2022

Purpose
This paper aims to examine the influence of records management practices on staff performance among administrative staff in private universities in Uganda.

Design/methodology/approach
Using surveys, this study took a cross-sectional descriptive and analytical design. Out of a population of 177, the study targeted a sample size of 123 respondents. Using proportionate random sampling, data were obtained from 104 usable questionnaires. The researchers applied Statistical Package for Social Scientists (SPSS) to test all the four hypotheses. The results are presented in terms of hierarchical regression analysis models.

Findings
Records creation, records maintenance and records disposal are significant predictors of administrative staff performance in chartered private universities in Uganda.

Practical implications
This study is relevant to heads of private universities, as it will guide them to set up and implement records management policies and practices, which are relevant for improving staff performance at work. They will be able to closely adhere to efforts that imply appropriate management of records to promote decision-making, cost reduction and information processing. Private university owners could appraise university management based on whether they can successfully execute records management-related policies and procedures for staff performance.

Originality/value
This study demonstrates that the application of proper records management practices translates into increased administrative staff performance in terms of efficiency and effectiveness within the workplace.