bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal Change of Microbial Diversity and Its Relation with Soil Chemical Properties in Orchard
Authors: Luo Xuhui , Wang Mingkuang , Hu Guiping , Weng Boqi 
Published: April 2019

AbstractThis study aimed to determine the microbial diversity of different soil depths (0-5 and 5-20 cm) in a subtropical orchard during different seasons (i.e., Spring, Summer and Autumn) for enrich the knowledgements on micorbes roles in orchard ecosystem balance. In tracking experiments conducted in an orchard (established in 1996), the phospholipid fatty acid (PLFA) biomarker method was employed to know soil microbial system. Total PLFAs concentration did not vary significantly between soil depths but changed between seasons. It peaked in the summer at 258.97 ± 23.48 μg g-1soil from 0-5 cm and at 270.99 ± 58.94 μg g-1soil from 5-20 cm. A total of 33 microbial fatty acid biomarkers were observed and identified in the sampled soil. Quantities of PLFAs for 29 microbe groups varied significantly between seasons, except for 15:0 iso 3OH, 15:1 iso G, 16:0 2OH, and 17:0 iso 3OH. The bacterial PLFAs and fungal and actinomycotic PLFAs in the orchard soil collected in Summer were significantly higher than in the Spring or Autumn (P< 0.01). The number of soil microorganism species (Richness) and the Simpson and Shannon-Wiener indexes were all the highest in summer. The total PLFAs, bacterial PLFAs, fungal PLFAs, actinomycotic PLFAs, Richness, or the Simpson and Shannon-Wiener indexes were all significantly negatively correlated with soil pH, total carbon (TOC), total nitrogen (TN) and cation-exchange capacity (CEC) (P< 0.05).
NOTCH1 signaling establishes the medullary thymic epithelial cell progenitor pool during mouse fetal development
Authors: Li Jie , Gordon Julie , Chen Edward L. Y. , Wu Luying , Zúñiga-Pflücker Juan Carlos , Manley Nancy R. 
Published: April 2019

AbstractThe cortical and medullary thymic epithelial cell (cTEC and mTEC) lineages are essential for inducing T cell lineage commitment, T cell positive selection and the establishment of self-tolerance, but the mechanisms controlling their fetal specification and differentiation are poorly understood. Here, we show that Notch signaling is required to specify and expand the mTEC lineage. Notch1 is expressed by and active in TEC progenitors. Deletion of Notch1 in TECs resulted in depletion of mTEC progenitors and dramatic reductions in mTECs during fetal stages, consistent with defects in mTEC specification and progenitor expansion. Conversely, forced Notch signaling in all TEC resulted in widespread expression of mTEC progenitor markers and profound defects in TEC differentiation. In addition, lineage-tracing analysis indicated that all mTECs have a history of receiving a Notch signal, consistent with Notch signaling occurring in mTEC progenitors. Interestingly, this lineage analysis also showed that cTECs are divided between Notch lineage-positive and lineage-negative populations, identifying a previously unknown complexity in the cTEC lineage.
Congruence of location-specific transcriptional programs in intestinal organoids during long-term culture
Authors: van der Hee B. , Madsen O. , Smidt H. , Wells J.M. 
Published: April 2019

AbstractThe emergence of intestinal organoids, as a stem cell-based self-renewable model system, has led to many studies on intestinal development and cell-cell signaling. However, potential issues regarding the phenotypic stability and reproducibility of the methodology during culture still needs to be addressed for different organoids. Here we investigated the transcriptomes of intestinal organoids derived from the same pig as well as batch-to-batch variation of organoids derived from different pigs over long-term passage. The set of genes expressed in organoids closely resembled that of the tissue of origin, including location specific functions, for at least 17 passages. Minor differences in gene expression were observed between individual organoid cultures. In contrast, most tissue-specific genes were not expressed in the transformed jejunum cell line IPECJ2, which also showed gene expression consistent with cancer phenotypes. We conclude that intestinal organoids provide a robust and stable model for translational research with clear advantages over transformed cells.
Cryo-EM Structures of Four Polymorphic TDP-43 Amyloid Cores
Authors: Cao Qin , Boyer David R. , Sawaya Michael R. , Ge Peng , Eisenberg David S. 
Published: April 2019

Summary ParagraphTDP-43 is an essential DNA/RNA processing protein that undergoes both functional and pathogenic aggregation. Functional TDP-43 aggregates are reversible, forming transient species such as nuclear bodies, stress granules, and myo-granules1–3. In contrast pathogenic TDP-43 aggregates are irreversible, forming stable intracellular amyloid-like inclusions4,5. These inclusions are the primary pathology of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP)6. Disease-associated, hereditary mutations in TDP-43 are known to accelerate the deposition of irreversible aggregates in the cytoplasm7. Reversible TDP-43 aggregation has been shown to precede the formation of irreversible amyloid fibrils similar to the behavior of proteins hnRNPA1 and FUS8–10. Still unknown, however, are the structural features of TDP-43 fibrils that confer both reversibility and irreversibility and how hereditary mutations can impose irreversible aggregation. Here, we determined the structures of amyloid fibrils formed by two segments previously reported to be the pathogenic cores of TDP-43 aggregation7,11,12; these are termed SegA (residues 311-360) and SegB A315E (residues 286-331 containing the ALS hereditary mutation A315E). SegA forms three polymorphs, all with dagger-shaped folds. SegB forms R-shaped folds. All four polymorphs have folds confined to two dimensions, and are stabilized by hydrophobic cores and peripheral hydrogen bonds. Energetic analysis suggests that the dagger-shaped polymorphs are examples of the irreversible fibril structures of TDP-43, whereas the SegB polymorph may participate in both reversible and irreversible fibril structure. Our structure suggests how the A315E mutation may convert this polymorph to the irreversible type and lead to mutation-enhanced pathology.
RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit
Authors: Allepuz-Fuster Paula , O’Brien Michael J. , González-Polo Noelia , Pereira Bianca , Dhoondia Zuzer , Ansari Athar , Calvo Olga 
Published: April 2019

ABSTRACTGene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in therpb4Δ mutant. In contrast to the other looping-defective mutants,rpb4Δ cells do not exhibit a transcription termination defect.RPB4overexpression, however, rescued the transcription termination and gene looping defect ofsua7-1, a mutant of TFIIB. Furthermore,RPB4overexpression rescued thessu72-2gene looping defect, whileSSU72overexpression restored the formation of gene loops inrpb4Δ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised inrpb4Δ cells. These results suggest that the TFIIB-Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB-Ssu72 mediated gene looping.
Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes byEscherichia coli
Authors: Jindal Srijan , Yang Lei , Day Philip J. , Kell Douglas B. 
Published: April 2019

AbstractWe used high-throughput flow cytometry to assess the ability of individual gene knockout strains ofE colito take up two membrane-permeable, cationic fluorescent dyes, viz the carbocyanine diS-C3(5) and the DNA dye SYBR Green. Individual strains showed a large range of distributions of uptake. The range of modal steady-state uptakes for the carbocyanine between the different strains was 36-fold. Knockouts of the ATP synthase α- and β-subunits greatly inhibited uptake, implying that most uptake was ATP-driven rather than being driven by say a membrane potential. Dozens of transporters changed the steady-state uptake of the dye by more than 50% with respect to that of the wild type, in both directions (increased or decreased); knockouts in known influx and efflux transporters behaved as expected, giving confidence in the general strategy. Many of the knockouts with the most reduced uptake were transporter genes of unknown function (‘y-genes’). Similarly, several overexpression variants in the ‘ASKA’ collection had the anticipated, opposite effects. Similar findings were made with SYBR Green (the range being some 69-fold), though despite it too containing a benzimidazole motif there was negligible correlation between its uptake and that of the carbocyanine when compared across the various strains. Overall, we conclude that the uptake of these dyes may be catalysed by a great many transporters of possibly broad and presently unknown specificity. This casts serious doubt upon the use of such dyes as quantitative stains for representing either bioenergetic parameters or the amount of cellular DNA in unfixed cells (in vivo). By contrast, it opens up their potential use as transporter assay substrates in high-throughput screening.
Owners vs executives and decisions vs control
Authors: Andersen Jon Aarum 
Published: April 2019

PurposeSome scholars have claimed that CEOs make decisions, while boards of directors control these decisions by applying the concepts of decision management and decision control. These concepts were suggested more than 30 years ago and are still applied in corporate governance research. They are now challenged on the basis of scholarship on corporate governance and management.Design/methodology/approachCorporate governance addresses the authority and responsibility that boards of directors and executives have. Management theory addresses planning and control in corporations.FindingsThe relationship between the owners (the boards of directors) and the top managers is hierarchical. This paper concludes that owners or boards of directors make decisions on main and strategic goals. Decisions cannot be controlled, but the implementation and outcomes of plans can. The latter is managers’ responsibility. The terms “decision management” and “decision control” are undefined and do not describe what takes place in organizations.Research limitations/implicationsThis paper does not contain any new empirical data.Originality/valueManagement theory offers clear definitions of decisions, decision-making and control. The concepts of decision management (initiation and implementation) and decision control (ratification and monitoring) neither properly describe who makes major and strategic decisions nor how and who controls the consequences of these decisions.
Conforming to the host country versus being distinct to our home countries
Authors: Abd Hamid Hamizah , O’Kane Conor , Everett André M. 
Published: April 2019

PurposeThe purpose of this paper is to examine how ethnic migrant entrepreneurs (EMEs) utilise identity work to build legitimacy in a host country. According to optimal distinctiveness theory (ODT), legitimacy is achieved by balancing conformance and distinctiveness. This paper draws on ODT in the context of ethnic migrant entrepreneurship to examine how EMEs both fit in (conformance) and maintain their uniqueness (distinctiveness) in cross-cultural settings.Design/methodology/approachThis study adopts a qualitative approach utilising semi-structured interviews to examine the identity work of EMEs from three distinct countries (Indonesia, Pakistan and South Korea (henceforth Korea)) in one host country (Malaysia).FindingsThe results show that EMEs’ identity work incorporates both the blurring and strengthening of host-home country boundaries. Building on this study’s results, the authors develop a model of identity work and three propositions regarding legitimacy building through identity in the context of ethnic migrant entrepreneurship.Originality/valueThrough the model and propositions, this research contributes to the identity, international entrepreneurship and ethnic migrant entrepreneurship discourse by identifying the mechanisms, focus and key features of identity work for entrepreneurs operating in cross-cultural settings. In so doing, this research also offers an alternative interpretation on the apparent divergent views around identity work in the fields of organisation (advocate isomorphism) and entrepreneurship (advocate uniqueness).
Entrepreneuring as an everyday form of resistance
Authors: Sabella Anton Robert , El-Far Mira Taysir 
Published: April 2019

Purpose
The purpose of this paper is to problematise the dominant conceptualisation of entrepreneurship by recognising the everyday resistance inherent in mundane entrepreneurial practices. Its principle purpose is to show how entrepreneurial activities enacted by ordinary individuals in a marginalised and oppressed context can be an important means of resisting economic adversity, social marginalisation and political (colonial) domination.

Design/methodology/approach
Framed within de Certeau’s conceptualisation of the practices of everyday life, this study utilises a “focussed ethnography”, relying on “participant observation” and “informal interviews”, to explore the perceptions and experiences of Palestinian women street vendors, and how they use everyday entrepreneurial practices in the open-air market of the Old City of Jerusalem to become socially and politically empowered.

Findings
The arguments in this paper demonstrate how marginalised Palestinian women, who are equipped with a genuine critical vision of their reality and a biophiliac attitude, use entrepreneuring to enact new possibilities for themselves and for their families. Through their entrepreneurial act of street vending, these women exemplify a struggle against economic and socio-political constraints, transforming the act of entrepreneuring from a mere economic practice to an all-encompassing human project, one with a more human face.

Originality/value
This paper extends the argument for the complex and dynamic nature of the phenomenon and exposes its political nature, hitherto inadequately addressed in existing literature, as well as uncovers the potential of entrepreneurialism to enhance individual empowerment and contribute to meaningful social change. In addition, it addresses the need for scholarly work that focuses on the everyday entrepreneurial activities carried out by ordinary individuals experiencing various forms of oppression in new and challenging spaces, which are seldom acknowledged within the dominant theoretical and research frameworks.
Maritime Cluster Attractiveness Index
Authors: Lagoudis Ioannis , Madentzoglou Eleftherios M. , Theotokas Ioannis N. , Yip Tsz Leung 
Published: April 2019

PurposeThe role of clusters in the development and growth of local and national economies has been extensively studied and discussed in global literature. Different methodologies are used for analysing the impact these have in national and regional economies, such as the input–output (IO) and gravity models. This paper aims to detail the methodologies present in the literature and propose a new robust theoretical framework, which facilitates the evaluation and comparison among maritime clusters in terms of attractiveness assisting stakeholders to devise strategies, which will attract companies.Design/methodology/approachAn index is created composed of five key categories, namely, infrastructure, financing, governance, manpower and institution/legislation. For the analysis of the index, multi-attribute utility theory (MAUT) is used as a tool to evaluate the importance and performance of the different attributes using both quantitative and qualitative criteria. The methodology has been tested via the use the Piraeus maritime cluster.FindingsThe framework has been tested on its robustness and friendliness to the user providing useful insights to the stakeholders. Among the results has been the importance of the finance, manpower and infrastructure attributes, which appear to promote the cluster’s attractiveness. In addition, legislation and institutional partnerships, along with Government support, need to take place improve the performance of the cluster.Research limitations/implicationsA key limitation is the fact that the methodology has been tested in a single case. Applying the methodological framework in a wider sample of clusters will significantly improve the present work.Originality/valueThe proposed model takes further existing research in the field via adopting the philosophy of the World Bank’s Logistics Performance Index. Among the benefits of the proposed index is that it offers the flexibility and robustness to compare among different maritime clusters globally and can be readily used as a benchmarking policy tool at national, regional and global levels at any given point in time and attribute dimension.
Why do clients enrol and continue at sports centres?
Authors: Rodríguez Cañamero Sergio , García-Unanue Jorge , Felipe José Luis , Sánchez-Sánchez Javier , Gallardo Leonor 
Published: April 2019

Purpose
The purpose of this paper is to analyse the ways clients find out about a sport centre and the factors that lead them to enrol and influence their satisfaction with their membership. A secondary objective was to determine the reasons for continuing to attend a sport centre and how they influenced satisfaction towards achievement. Finally, the authors aimed to identify differences between reasons for enroling and reasons for continuing at a sport centre.

Design/methodology/approach
A specially developed 16-item questionnaire was sent to 125,000 clients and 21,043 responses were obtained.

Findings
Clients who found out about the centre through a recommendation or the internet were 25 per cent more likely to be satisfied with it than those who knew of the centre due to proximity. Similarly, clients who had a specific motive to continue using the centre, for example, to prepare for a sports competition were twice as likely to be satisfied with their membership as any other group (p<0.001).

Research limitations/implications
It identifies a set of research priorities for the journal and the field.

Practical implications
In conclusion, the option of staying fit is established as the most effective recruitment method for retaining clients at the sport centre.

Originality/value
This paper intends to do is to establish the bases of information and knowledge for the treatment of high motives, as well as for managers of sports centres to remodel their strategies of marketing to attracting customers.
Automated processing strategies for ambient seismic data
Authors: Girard Aaron J. , Shragge Jeffrey 
Published: April 2019

ABSTRACTExtracting body‐wave arrivals from ambient seismic recordings remains a challenging task, largely because ambient records are usually dominated by surface‐wave energy. Most ambient seismic data‐processing strategies aimed at enhancing body‐wave energy focus on a cross‐correlation plus stack methodology. While this approach is useful for interferometric investigations, it effectively squares the magnitude of unwanted coherent noise events (e.g. surface waves, burst‐like or strong monochromatic energy) that commonly overpower ambient body‐wave signal. Accordingly, coherent noise events are usually treated with a binary accept‐or‐reject decision of individual data windows based on root‐mean‐squared energy considerations. Applying a data‐processing workflow to uncorrelated ambient seismic data represents an alternate strategy for mitigating coherent noise. However, this pre‐stack methodology requires significant computational effort due to the often terabyte‐sized data volumes. To make this approach feasible, we outline an automated processing workflow to automatically identify and mitigate coherent noise events that otherwise does not severely degrade the remaining waveforms. After each processing step, we apply a number of quality control measures to monitor the convergence rate of cross‐correlation plus stack waveforms and for evidence of emerging body‐wave reflection events. We apply the processing flow to an ambient seismic data set acquired on a large‐N array at a mine site near Lalor Lake, Manitoba, Canada. Our quality control analyses suggest that automated preprocessing of uncorrelated ambient seismic recordings successfully mitigates unwanted impulsive and monochromatic coherent noise events. Accordingly, we assert that applying an automated data‐processing approach would be beneficial for body‐wave and other imaging and inversion analyses applied to ambient seismic recordings.
Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria
Authors: Spietz Rachel L. , Lundeen Rachel A. , Zhao Xiaowei , Nicastro Daniela , Ingalls Anitra E. , Morris Robert M. 
Published: April 2019

SummaryA hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.