bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial metabolite deoxycholic acid shapes microbiota againstCampylobacter jejunichicken colonization
Authors: Alrubaye Bilal , Abraha Mussie , Almansour Ayidh , Bansal Mohit , Wang Hong , Kwon Young Min , Huang Yan , Hargis Billy , Sun Xiaolun 
Published: March 2019

ABSTRACTDespite reducing the prevalent foodborne pathogenCampylobacter jejuniin chickens decreases campylobacteriosis, few effective approaches are available. The aim of this study was to use microbial metabolic product bile acids to reduceC. jejunichicken colonization. Broiler chicks were fed with deoxycholic acid (DCA), lithocholic acid (LCA), or ursodeoxycholic acid (UDCA). The birds were also transplanted with DCA modulated anaerobes (DCA-Anaero) or aerobes (DCA-Aero). The birds were infected with human clinical isolateC. jejuni81-176 or chicken isolateC. jejuniAR101. Notably,C. jejuni81-176 was readily colonized intestinal tract at d16 and reached an almost plateau at d21. Remarkably, DCA excludedC. jejunicecal colonization at 100, 99.997, and 100% at 16, 21, and 28 days of age. Neither chicken ages of infection nor LCA or UDCA alteredC. jejuniAR101 chicken colonization level, while DCA reduced 91% of the bacterium in chickens at d28. Notably, DCA diet reduced phylum Firmicutes but increased Bacteroidetes compared to infected control birds. Importantly, DCA-Anaero attenuated 93% ofC. jejunicolonization at d28 compared to control infected birds. In conclusion, DCA shapes microbiota composition againstC. jejunicolonization in chickens, suggesting a bidirectional interaction between microbiota and microbial metabolites.
Multiplexing cell-cell communication
Authors: Sexton John T. , Tabor Jeffrey J. 
Published: March 2019

AbstractThe engineering of advanced multicellular behaviors, such as the programmed growth of biofilms or tissues, requires cells to communicate multiple aspects of physiological information. Unfortunately, few cell-cell communication systems have been developed for synthetic biology. Here, we engineer a genetically-encoded channel selector device that enables a single communication system to transmit two separate intercellular conversations. Our design comprises multiplexer and demultiplexer sub-circuits constructed from a total of 12 CRISPRi-based transcriptional logic gates, an acyl homoserine lactone-based communication module, and three inducible promoters that enable small molecule control over the conversations. Experimentally-parameterized mathematical models of the sub-components predict the steady state and dynamical performance of the full system. Multiplexed cell-cell communication has applications in synthetic development, metabolic engineering, and other areas requiring the coordination of multiple pathways amongst a community of cells.One Sentence SummaryWe have engineered a synthetic genetic system that enables bacteria to have two separate conversations over a single chemical “wire” by separating the conversations in time.
Adaptive introgression as a driver of local adaptation to climate in European white oaks
Authors: Leroy Thibault , Louvet Jean-Marc , Lalanne Céline , Le Provost Grégoire , Labadie Karine , Aury Jean-Marc , Delzon Sylvain , Plomion Christophe , Kremer Antoine 
Published: March 2019

AbstractLatitudinal and elevational gradients provide valuable experimental settings for studies of the potential impact of global warming on forest tree species. The availability of long-term phenological surveys in common garden experiments for traits associated with climate, such as bud flushing, for sessile oaks (Quercus petraea), provides an ideal opportunity to investigate this impact.We sequenced 18 sessile oak populations, and used available sequencing data for three other closely related European white oak species (Q. pyrenaica, Q. pubescens, Q. robur), to explore the evolutionary processes responsible for shaping the genetic variation across latitudinal and elevational gradients in extant sessile oaks. We used phenotypic surveys in common garden experiments and climatic data for the population of origin, to perform genome-wide scans for population differentiation, genotype-environment (GEA) and genotype-phenotype associations (GPA).The inferred historical relationships betweenQ. petraeapopulations suggest that interspecific gene flow occurred betweenQ. roburandQ. petraeapopulations from cooler or wetter areas. A genome-wide scan of differentiation betweenQ. petraeapopulations identified SNPs displaying strong interspecific relative divergence between these two species. These SNPs followed genetic clines along climatic or phenotypic gradients, providing further support for the likely contribution of introgression to the adaptive divergence ofQ. petraeapopulations.Overall, the results of this study indicate that adaptive introgression ofQ. roburalleles has occurred. We discuss the results of this study in the framework of the post-glacial colonization scenario, in which introgression and diversifying selection have been proposed as essential drivers ofQ. petraeamicroevolution.
Long-term iron deficiency and iron supplementation exacerbate acute DSS-induced colitis and are associated with significant dysbiosis
Authors: Mahalhal Awad , Burkitt Michael D. , Duckworth Carrie A. , Hold Georgina L. , Campbell Barry J. , Pritchard D. Mark , Probert Chris S. 
Published: March 2019

AbstractPatients taking oral iron supplementation often suffer from gastrointestinal side effects. We have previously shown that acute alterations in oral iron exacerbate dextran sodium sulphate (DSS) induced colitis and are associated with dysbiosis. As patients take iron supplementation for long periods, we asked whether this too would influence colitis and the microbiome. We assessed the impact of long-term changes in dietary iron, by feeding chow containing 100ppm, 200ppm and 400ppm (reflecting a deficient, normal or supplemented diet, respectively) for up to 9 weeks to female wild-type C57BL/6 (WT) mice in presence or absence of chronic colitis, or acute colitis induced after 8 weeks, induced by DSS. Assessment was made based on (i) clinical and histological severity of colitis, and (ii) faecal microbial diversity, as assessed by sequencing the V4 region of16SrRNA. In mice with long term changes to their dietary iron, reduced iron intake (100ppm iron diet) was associated with increased weight loss and histology scoring in the acute colitis model. Chronic colitis was not influenced by altering dietary iron however there was a clear change in the faecal microbiome in the 100 and 400ppm iron DSS-treated groups and in controls consuming the 400ppm iron diet. Proteobacteria levels increased significantly at day-63 compared to baseline and Bacteroidetes levels decreased in the 400ppm iron DSS group at day-63 compared to baseline; mirroring our previously published work in acute colitis. Long term dietary iron alterations clearly affects gut microbiota signatures but do not appear to exacerbate chronic colitis. However, acute colitis is exacerbated by changes in dietary iron. More work is needed to understand the impact of iron supplementation of the pathologenesis of IBD and rise that possiblity that the change in the microbiome, in patients with colitis, is a consequence of the increase in luminal iron and not simply the presence of colitis.
Mutational profiling of lipomas
Authors: Kanojia Deepika , Dakle Pushkar , Mayakonda Anand , Parameswaran Rajeev , Puhaindran Mark E , Min Victor Lee Kwan , Madan Vikas , Koeffler H Phillip 
Published: March 2019

AbstractLipomas are benign fatty tumors with a high prevalence rate, mostly found in adults but have a good prognosis. Until now, reason for lipoma occurrence not been identified. We performed whole exome sequencing to define the mutational spectrum in ten lipoma patients along with their matching control samples. We identified 412 somatic variants including missense mutations, splice site variants, frameshift indels, and stop gain/lost. Kinase genes and transcriptions factors were among the validated mutated genes critical for cell proliferation and survival. Pathway analysis revealed enrichment of calcium, Wnt and phospholipase D signaling in patients. Whole exome sequencing in lipomas identified mutations in genes with a possible role in development and progression of lipomas.Author SummaryWe presented genomic insight into the development of lipomas, the most common benign tumor of soft tissue. Until date, no one knows the cause of lipoma development and its progression. Our group for the first time profiled ten lipoma patients’ samples and their matching normal controls to delineate the somatic mutation pattern using whole exome sequencing. Interestingly, exome-profiling results highlighted the potential role of important kinase genes and transcription factors in lipoma development. In addition, calcium, Wnt and phospholipase D signaling pathway speculated to be involve in pathogenesis of this disease.
The Long Pentraxin 3 (PTX3) Suppresses Immunity to Cutaneous Leishmaniasis by Negatively Regulating Th17 Response
Authors: Gupta Gaurav , Jia Ping , Sharma Rohit , Zayats Romaniya , Viana Sayonara M. , Shan Lianyu , Mou Zhriong , Barral Aldina , Boaventura Viviane S. , Murooka Thomas T. , Soussi-Gounni Abdel , de Oliveira Camila I. , Uzonna Jude E. 
Published: March 2019

AbstractThe long Pentraxin 3 (PTX3), a soluble pattern recognition molecule, plays a critical role in inflammation, tissue repair and wound healing. Here, we show that PTX3 regulates disease pathogenesis in cutaneous leishmaniasis (CL). PTX3 expression is increased in active skin lesions in patients and mice during CL, with higher levels being expressed in individuals with severe disease. PTX3 deficient (PTX3-/-) mice were highly resistant toL. majorinfection and the enhanced resistance was associated with increased IL-17 response. Neutralization of IL-17A abolished this enhanced resistance while treatment with recombinant PTX3 resulted in reduced IL-17A response and increased susceptibility toL. majorinfection. Naïve CD4+T cells from PTX3-/-mice displayed increased differentiation into Th17 cells, which was reversed in the presence of recombinant PTX3. The enhanced Th17 response observed in PTX3-/-cells was associated with increasedLeishmaniaspecific IL-6 production from dendritic cells along with enhanced expression of Th17-specific transcription factors including RORγt, AhR and STAT3. Addition of recombinant PTX3 significantly inhibited the expression of Th17-specific transcription factors and dramatically reduced the frequency of Th17 cells in Th17-polarizing cultures of PTX3-/-CD4+T cells. Collectively, our results show that PTX3 contributes to the pathogenesis of CL by suppressing Th17 differentiation and IL-17A production.Author SummaryCutaneous leishmaniasis (CL) is caused by several species ofLeishmania. Currently, there is no approved vaccine against human CL because of the poor understanding of the mechanisms that regulate disease pathogenesis and correlates of protective immunity. Because the long pentraxin 3 (PTX3, a soluble pattern recognition molecule that forms an integral part of the host innate immunity), regulates inflammation and tissue repair, which are critical physiological events associated with resolution of skin lesions during CL, we investigated its role in disease pathogenesis.Here, we show that PTX3 levels were elevated in skin-lesions in patients and mice during CL. Using a loss of function approach, we showed that PTX3 contributes to pathogenesis, and this was associated with increased IL-17A responses. Neutralization and recombinant cytokine treatment studies showed that the increased resistance of PTX3 deficient mice toL. majoris due to enhanced Th17 response in these mice. We further show that PTX3 negatively regulates IL-6 production by dendritic cells and the expression of IL-17A-specific transcription factors (including RORγT, STAT3, IRF4, BATF and AhR) in CD4+T cells. Collectively, these findings show that PTX3 is a negative regulator of Th17 response and protective immunity duringL. majorinfection.
A catalog of CasX genome editing sites in common model organisms
Authors: Roberson Elisha D.O. 
Published: March 2019

AbstractDpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria. In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast (Saccharomyces cerevisiae), flatworms (Caenorhabditis elegans), flies (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus), rats (Rattus norvegicus), and humans (Homo sapiens). Across those genomes there were >27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6 – 45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain. The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor.
Strategic orientations and firm innovativeness: a necessary condition analysis
Authors: Tho Nguyen Dinh 
Published: March 2019

PurposeThe purpose of this paper is to decipher the levels of three strategic orientations – learning orientation, entrepreneurial orientation (proactiveness and risk taking) and marketing orientation (responsiveness to customers, responsiveness to competitors, responsiveness to the macro-environment and business relationship quality) – that are necessary for firm innovativeness.Design/methodology/approachData were collected from a sample of 316 firms in Ho Chi Minh City, Vietnam. Multiple regression analysis (MRA) was employed to examine the net effects of seven factors (learning orientation, proactiveness, risk taking, responsiveness to customers, responsiveness to competitors, responsiveness to changes in the macro-environment and business relationship quality) on firm innovativeness. Necessary condition analysis (NCA) was then employed to discover the level of these factors as necessary conditions for firm innovativeness.FindingsThe results produced by MRA show that learning orientation, proactiveness, responsiveness to customers and responsiveness to competitors have positive effects on firm innovativeness. The results from the NCA reveal that six out of seven conditions exhibit varying necessary levels for firm innovativeness.Practical implicationsThe findings are relevant to senior managers and suggest that the levels of strategic orientations necessary for firm innovativeness vary. Firms therefore should pay attention not only to the net effects (beta weights) but also to their necessary levels. Based on their resources and capabilities, firms should take into account the necessary level of each strategic orientation in order to achieve their innovativeness goal.Originality/valueThis study is among the first to decipher the levels of three strategic orientations (learning orientation, entrepreneurial orientation and marketing orientation) that are necessary for firm innovativeness.
Business value of integrated BIM-based asset management
Authors: Munir Mustapha , Kiviniemi Arto , Jones Stephen W. 
Published: March 2019

Purpose
Currently, building information modelling (BIM) is largely seen as a 3D model, not as an information model or information management tool. This wrong perception of BIM and low interest in 3D asset management (AM) is one of the major reasons for the slow adoption by clients in the architectural, engineering and construction (AEC) industry. The purpose of this paper is to identify the techniques and strategies of streamlining AM systems for BIM-based integration, and how the information is captured from physical assets towards BIM-based integration for clients to derive value from BIM investments.

Design/methodology/approach
A qualitative case study strategy was used to study the strategic implementation process of integrating BIM with AM systems and the business value of BIM in AM by a large asset owner in the UK.

Findings
The paper identifies key strategies in the adoption of BIM-based processes by an asset owner, the implementation process, the challenges and the benefits attained. Several barriers were identified as the challenges of adopting BIM-based processes in AM: complexity and cost associated with BIM; irrelevance of 3D geometric data in AM processes; nature of asset ownership structure; managing the asset handover process; managing change within the organisation. Organisations will have to consider the following issues in streaming asset information with BIM: the development for a clear strategy prior to adoption; connecting the strategy to the business goals; and conducting the discovery exercise to identify organisational information needs.

Originality/value
The research addresses a significant gap in the development of techniques and strategies for asset owners to streamline BIM with AM systems and derive business value from such integration. The research context is a case study involving a large owner-operator in the UK that has been able to derive value from BIM systems in their AM processes. The key value of the paper is improving asset owners’ understanding of BIM in AM by demonstrating the implementation strategies, linkage to organisational objectives, challenges, value management process and business value of BIM in AM. Another contribution of the paper is improving the understanding of BIM, which is usually viewed as 3D models and that 3D geometric data do not have much value for AM tasks.
Multi academy trusts in England: a scenario of cooperation with universities
Authors: Massoud Hiba K. , Ayoubi Rami M. , Loutfi Mohamed 
Published: March 2019

Purpose
The purpose of this paper is to present the authors’ views of university–multi academy trusts’ (MATs) opportunities for future interconnectivity that could support successful partnerships.

Design/methodology/approach
The authors developed a matrix of university–MATs partnerships that could help identifying potential scenarios of collaboration between universities and MATs.

Findings
Four potential scenarios of collaborations are proposed (board membership, academic supervision, recruitment support and academic support).

Research limitations/implications
Scholars in the field can further investigate the four proposed scenarios in the matrix in future studies.

Practical implications
The matrix will be useful for universities and MATs management for potential cooperation in the future.

Originality/value
The study proposes four scenarios of cooperation between MATs and universities.
Principal resilience and vitality in extremis
Authors: Simon Susan , Gibson Mark T. 
Published: March 2019

Purpose
High-stakes accountability and continuous multi-faceted pressures of the principalship require leaders to develop a broad range of personal qualities including resilience and personal vitality. Scant research exists on what happens to school principals when careers abruptly and involuntarily end, and the purpose of this paper is sought to hear principals’ accounts of their experiences and to identify whether these personal qualities assist recovery and career re-identification.

Design/methodology/approach
A collaborative English and Australian study of former principals aimed to evaluate effects of involuntary job loss from their own perspectives. In total, 12 case studies involved one-on-one interviews during a two-year period revealing impact of job loss, coping strategies, resilience and personal vitality.

Findings
Successful management indicators were found: personal qualities, including the ability to retain a perspective and big picture view of career journey; an enduring love of teaching; health and fitness; study; getting another suitable post; and psychological and medical support. Time taken to regain pre-existing levels of personal vitality varied significantly based on resilience and contextual circumstances, whilst psychological and social support from family and professional colleagues was invaluable for recovery.

Originality/value
This international study presents an original insight into effects of principals’ sudden job loss – a perspective which has imposing pastoral relevance for employing authorities, professional associations and collegial networks. Aspiring and current principals may feel, “There but for the grace of God, go I”, and it is they who may need ultimately to be prepared for what is an increasingly common occurrence in schools across the world.
Empirical analysis of residential submarket conceptualisation in Ghana
Authors: Gavu Emmanuel Kofi , Owusu-Ansah Anthony 
Published: March 2019

PurposeThe purpose of this paper is to empirically test for submarket existence based on an understanding of the residential rental housing market in Ghana.Design/methodology/approachBased on extant literature and market observations, the authors provide key concepts and an overview of the residential rental market dynamics in Ghana. Reseachers appreciate that submarkets may exist in the Ghanaian rental market but have ignored the empirical testing for submarket existence due to data asymmetries. Based on real estate experts and stakeholder consultations,a prioridelineation of submarkets are constructed based on spatial, structural and a nested approach. Submarket existence is tested using the Kruskal–Wallis H test and Hedonic modelling techniques.FindingsBy using fieldwork data from Accra rental market, the analysis provides credence to the conceptualisation of submarkets and how to empirically test for same. It is argued that researchers should use alternative methods to compare results to make far-reaching conclusions.Research limitations/implicationsExamining the hypothesis that differential rental values exists for submarkets has implications for policy decisions to target submarket constructs differently to improve market maturity.Practical implicationsThe research provides stakeholder investors in the rental space an understanding of market dynamics for profit maximisation, and end-users to maximise utility in deciding where to live – and as such households could benefit from making informed investment decisions on housing.Originality/valueThis research is one of the first attempts to empirically identify and test for submarkets existence in Ghana’s residential rental housing market.