bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmid manipulation of bacterial behaviour through translational regulatory crosstalk
Authors: Thompson Catriona M A , Hall James P. J. , Chandra Govind , Martins Carlo , Saalbach Gerhard , Bird Susannah , Ford Samuel , Little Richard H. , Piazza Ainelen , Harrison Ellie , Jackson Robert W. , Brockhurst Michael A. , Malone Jacob G. 
Published: June 2022

AbstractBeyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator controlling the host proteome through direct interaction with host mRNAs and interference with the host’s translational regulatory network. This mRNA interference leads to largescale proteomic changes in metabolic genes, key regulators and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.Significance StatementPlasmids are recognised for their important role in bacterial evolution as drivers of horizontal gene transfer. Less well understood are the effects of plasmids upon bacterial behaviours by manipulating the expression of key bacterial phenotypes. Until now, examples of plasmid manipulation of their bacterial hosts were limited to highly targeted transcriptional control of a few related traits. In contrast, here we describe the first plasmid global translational regulator evolved to control the bacterial behavioural switch from a motile to a sessile lifestyle and bacterial metabolism, mediated through manipulation of the bacterial proteome. Moreover, this global translational regulator is common across divergent plasmids in a wide range of bacterial host taxa, suggesting that plasmids may commonly control bacterial lifestyle in the clinic, agricultural fields, and beyond.
An ANI gap within bacterial species that advances the definitions of intra-species units
Authors: Rodriguez-R Luis M. , Conrad Roth E. , Viver Tomeu , Feistel Dorian J. , Lindner Blake G. , Venter Fanus , Orellana Luis , Amann Rudolf , Rossello-Mora Ramon , Konstantinidis Konstantinos T. 
Published: June 2022

AbstractLarge-scale surveys of prokaryotic communities (metagenomes) as well as isolate genomes have revealed that their diversity is predominantly organized in sequence-discrete units that may be equated to species. Specifically, genomes of the same species commonly show genome-aggregate average nucleotide identity (ANI) >95% among themselves and ANI <90% to members of other species, while genomes showing ANI 90-95% are comparatively rare. However, it remains unclear if such “discontinuities” or gaps in ANI values can be observed within species and thus, used to advance and standardize intra-species units such as strains and sequence types. By analyzing 18,123 complete isolate genomes from 330 bacterial species with at least ten genome representatives each as well as available long-read metagenomes, we show that such a discontinuity exists between 99.2-99.8% (mean 99.5%) ANI. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with ∼20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity.
Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: in vitro and in vivo
Authors: Lecinski Sarah , Shepherd Jack W. , Bunting Kate , Dresser Lara , Quinn Steven D. , MacDonald Chris , Leake Mark C. 
Published: June 2022

AbstractIn eukaryotes, intracellular physicochemical properties like macromolecular crowding and cytoplasmic viscoelasticity influence key processes such as metabolic activities, molecular diffusion, and protein folding. However, mapping crowding and viscoelasticity in living cells remains challenging. One approach uses passive rheology in which diffusion of exogenous fluorescent particles internalised in cells is tracked and physicochemical properties inferred from derived mean square displacement relations. Recently, the crGE2.3 Förster Resonance Energy Transfer (FRET) biosensor was developed to quantify crowding in cells, though it is unclear how this readout depends on viscoelasticity and the molecular weight of the crowder. Here, we present correlative, multidimensional data to explore diffusion and molecular crowding characteristics of molecular crowding agents using super-resolved fluorescence microscopy and ensemble time-resolved spectroscopy. We firstly characterise in vitro and then apply these insights to live cells of budding yeast Saccharomyces cerevisiae. It is to our knowledge the first time this has been attempted. We demonstrate that these are usable both in vitro and in the case of endogenously expressed sensors in live cells. Finally, we present a method to internalise fluorescent beads as in situ viscoelasticity markers in the cytoplasm of live yeast cells, and discuss limitations of this approach including impairment of cellular function.
Integration networks in IT-enabled transformation programs
Authors: Fernandez Walter , Klein Gary , Jiang James , Khan Rasheed M. 
Published: June 2022

PurposeDiscover how organizations effectively integrate the temporary program outputs into the permanent organization.Design/methodology/approachA grounded theory approach deriving knowledge from interviews, field observations and documentary evidence.FindingsA network of actors integrates the multiteam program system into the overall organization, generating alternate political and implementation impetus.Research limitations/implicationsThe paper significantly contributes to the literature of IT-enabled programs by surfacing processes, mechanisms and structures that simultaneously address extant concerns in the program management literature.Practical implicationsThe directives of current research and program standards of professional societies identify an individual responsible for integrating the program output into the organization. The study indicates greater autonomy on the responsible actor requiring adjusting to changing stakeholder groups.Originality/valueThe authors add a missing link in understanding how programs can institute effective work structures to address emerging program conflicts and issues, suggesting strategies to foster interaction between temporary and permanent organizations.
Social embeddedness and food justice at farmers markets: the model farmers market program
Authors: He Arden , Morales Alfonso 
Published: June 2022

PurposeDespite the progressive values espoused by farmers' market patrons, markets have been shown to be exclusive to low-income people of color. This paper examines a particular food security program at a farmers market to ask how social embeddedness and moral economy can be incorporated to dignify underrepresented groups at the market.Design/methodology/approachThis case study uses an embeddedness framework to analyze the design of a community-oriented food security program at a farmers market.FindingsSocial embeddedness contributed to the success of the program in a number of meaningful ways: face-to-face community outreach reached target populations at a human level, and engendered spontaneous support from organizations with shared values. Graphics and text used in marketing material can make transparent the moral economy of the market. However, as soon as social embeddedness is legitimized within a program design, suppressed tensions emerge that are associated with the perceived dichotomy between academic, technically-oriented professionals and on-the-ground community members. In particular, the selection of personnel from the community itself led to interpersonal tensions as well as technical difficulties.Research limitations/implicationsThe analysis proceeds from an administrative point of view, and does not include direct interviews with market attendees or vendors.Practical implicationsThe findings suggest that long-term support is necessary for the implementation of socially embedded food security programs, so that personnel can build trust and technical competence over time.Originality/valueThis paper offers solutions to the limitations of farmers markets as sites for food security programs, and uniquely contextualizes policy administration in a social embeddedness lens.
Sustainable exploration of coffee extracts (coffea arabica l.) for dyeing of microwave-treated bio-mordanted cotton fabric
Authors: Adeel Shahid , Rehman Fazal-Ur , Amin Ayesha , Amin Nimra , Batool Fatima , Hassan Atya , Ozomay Meral 
Published: June 2022

Purpose
This study aims to observe the coloring efficacy of coffee-based natural brown colorant for cotton dyeing under microwave (MW) treatment.

Design/methodology/approach
The colorant extracted in particular (neutral and acidic) media was stimulated by MW treatment up to 6 min. Dyeing variables were optimized and 2–10 g/100 mL of sustainable anchors (mordants) have been used to get colorfast shades.

Findings
It has been found that un-irradiated acidic extract (RE) containing 5% of table salt at 80 °C for 50 min has given high color yield onto MW-irradiated cotton fabric (RC = 2 min). The utilization of 2% of Fe, 10% of tannic acid and 10% of sodium potassium tartrate before bio-coloration, whereas 4% of Fe, 10% of tannic acid and 6% of sodium potassium tartrate after bio-coloration has given good color characteristics. In comparison the application of 6% of pomegranate and turmeric extracts before bio-coloration and 6% of pomegranate and 10% of turmeric extracts after bio-coloration have given good color characteristics. New bio-mordants can be added to get more new colorfast shades.

Research limitations/implications
There is no research limitation for this work. New bio-mordants can be added to get more new colorfast shades.

Practical implications
This work has practical application for artisans, textile industry and handicrafts. It is concluded that colorant from coffee beans can be possible alternative of synthetic brown dyes and inclusion of MW rays for extraction and plant molecules as shade developers can make process more green.

Social implications
Socially, it has good impact on eco-system and global community because the effluent load is not carcinogenic in nature.

Originality/value
The work is original and contains value-added product for textiles and other allied fields.
Communist Ideological Imprinting and the Transformation of State‐owned Enterprises
Authors: Zhang Liang , Ren Yeyao , Wu Jianzu 
Published: June 2022

AbstractDespite an increasingly similar institutional environment for state‐owned enterprises (SOEs), some SOEs adapt to transformation more rapidly than others. We seek answers to this puzzle by examining how founding institutional environments shape the timing of SOE transformation. We first employ imprinting theory to argue that SOEs founded in different environments are imprinted with different political ideologies that influence their subsequent transformation timing. Using a dataset from the Annual Census of Chinese Industrial Enterprises from 1998 to 2007, we find that SOEs’ communist ideological imprint negatively affects their faster transformation. Drawing on insights from institutional theory, we also consider the contextual factors that influence the strength and decay of the imprint. We find that SOEs affiliated with central government at founding develop a stronger imprint, but mimetic force and regional marketization in the current environment weaken the negative effect of the imprint on faster SOE transformation. We discuss the contributions to the literature on SOE transformation and imprinting and the research at the intersection of imprinting and institutional theory.
Autochthonous Dolomitization and Dissolution in the Microbial Carbonate Rocks of the Fengjiawan Formation in the Ordos Basin
Authors: ZHANG Jing , ZHANG Baomin , ZHANG Shuichang , WANG Huajian 
Published: June 2022

AbstractMany euhedral dolomite crystals and related pores are found in the microbial siliceous stromatolite dolomite and siliceous oolitic dolomite in the Fengjiawan Formation of the Mesoproterozoic Jixian System in the southern Ordos Basin. With the application of the microscope, scanning electron microscope, cathodoluminescence and in‐situ trace element imaging, it can be seen that different from the phase I dolomite that was damaged by silicification, the intact euhedral phase II dolomite occurred through dolomitization after silicification, concentrated mainly in the organic‐rich dark laminae of the stromatolite and the dark spheres and cores of the ooids. A considerable number of phase II dolomite crystals were dissolved, giving rise to mold pores and vugs which constituted the matrix pores and also the major pore space of the Fengjiawan Formation. The formation and dissolution of the dolomite were controlled by the microenvironment favorable, respectively, for carbonate precipitation and dissolution under the influence of microbial biological activities and related biochemical reactions. The driving force and material supply of dolomitization and dissolution were confined to the fabrics enriched with microorganisms, which are highly autochthonous. This mechanism may be a key factor for the development of Precambrian dolomite and related reservoirs, in the context of the domination of microbial rocks.
Rectal hyposensitivity: a common pathophysiological finding in patients with constipation and associated hypermobile Ehlers–Danlos syndrome
Authors: Choudhary Anisa , Vollebregt Paul F. , Aziz Qasim , Scott S. Mark , Fikree Asma 
Published: June 2022

SummaryBackground and AimsTo evaluate symptom presentation and underlying pathophysiology of colonic/anorectal dysfunction in females with functional constipation (FC) and hypermobile Ehlers–Danlos syndrome (hEDS)/hypermobility spectrum disorder (HSD)MethodsCase–control study of 67 consecutive female patients with an established diagnosis of hEDS/HSD referred to a specialist centre for investigation of FC (Rome III criteria), age‐matched (1:2 ratio) to 134 female controls with FC scoring 0 on the validated 5‐point joint hypermobility questionnaire. Symptoms and results of colonic/anorectal physiology testing were compared. An independent series of 72 consecutive females with hEDS/HSD, referred to a separate hospital for investigation of FC, was used to validate physiological findings.ResultsFemales with hEDS/HSD were more likely to report constipation for ≥ 5 years (76.1% vs. 61.2%, p = 0.035), and a greater proportion had a high Cleveland Clinic constipation score (≥12: 97.0% vs. 87.3%; p = 0.027). The proportions with delayed whole‐gut transit were similar between groups (35.3% vs. 41.7%; p = 0.462), as were the proportions with functional or structural abnormalities on defaecography (functional: 47.8% vs. 36.6%; p = 0.127; structural: 65.7% vs. 66.4%; p = 0.916). However, rectal hyposensitivity was more common in those with hEDS/HSD (43.3% vs. 20.1%; p = 0.0006); this was confirmed in the validation cohort (rectal hyposensitivity: 45.8%).ConclusionsRectal hyposensitivity is a common pathophysiological factor in females with FC and hEDS/HSD as confirmed in two separate cohorts. The rectal hyposensitivity may be due to altered rectal biomechanics/neuronal pathway dysfunction. Management may be better focused on enhancement of sensory perception (e.g., sensory biofeedback).
“The home isn't like a safe space for them”—Ideals of home and family relationships in children's talk about family adversity and help‐seeking
Authors: Spånberger Weitz Ylva 
Published: June 2022

AbstractThe aim of this study is to explore how schoolchildren reflect on children's help‐seeking in the context of family adversity after participating in lessons about the child welfare services. A thematic narrative analysis was conducted, building on participating pupils' shared reflections on a fictitious story about two siblings living in adverse family circumstances. The analysis suggests that the pupils held a strong belief on children's rights to a safe home with supportive parental relationships, and they expressed an optimistic view on children's opportunities to receive help to achieve positive change when their rights regarding these issues were not met.
ThePI3K/AKTsignalling pathway in inflammation, cell death and glial scar formation after traumatic spinal cord injury: Mechanisms and therapeutic opportunities
Authors: He Xuegang , Li Ying , Deng Bo , Lin Aixin , Zhang Guangzhi , Ma Miao , Wang Yonggang , Yang Yong , Kang Xuewen 
Published: June 2022

AbstractObjectsTraumatic spinal cord injury (TSCI) causes neurological dysfunction below the injured segment of the spinal cord, which significantly impacts the quality of life in affected patients. The phosphoinositide 3kinase/serine‐threonine kinase (PI3K/AKT) signaling pathway offers a potential therapeutic target for the inhibition of secondary TSCI. This review summarizes updates concerning the role of the PI3K/AKT pathway in TSCI.Materials and MethodsBy searching articles related to the TSCI field and the PI3K/AKT signaling pathway, we summarized the mechanisms of secondary TSCI and the PI3K/AKT signaling pathway; we also discuss current and potential future treatment methods for TSCI based on the PI3K/AKT signaling pathway.ResultsEarly apoptosis and autophagy after TSCI protect the body against injury; a prolonged inflammatory response leads to the accumulation of pro‐inflammatory factors and excessive apoptosis, as well as excessive autophagy in the surrounding normal nerve cells, thus aggravating TSCI in the subacute stage of secondary injury. Initial glial scar formation in the subacute phase is a protective mechanism for TSCI, which limits the spread of damage and inflammation. However, mature scar tissue in the chronic phase hinders axon regeneration and prevents the recovery of nerve function. Activation of PI3K/AKT signaling pathway can inhibit the inflammatory response and apoptosis in the subacute phase after secondary TSCI; inhibiting this pathway in the chronic phase can reduce the formation of glial scar.ConclusionThe PI3K/AKT signaling pathway has an important role in the recovery of spinal cord function after secondary injury. Inducing the activation of PI3K/AKT signaling pathway in the subacute phase of secondary injury and inhibiting this pathway in the chronic phase may be one of the potential strategies for the treatment of TSCI.
Review of benefits and challenges of co‐supervision in doctoral education
Authors: Kálmán Orsolya , Horváth László , Kardos Dorottya , Kozma Borbála , Feyisa Mebrate Bekele , Rónay Zoltán 
Published: June 2022

AbstractCo‐supervision is a widespread practice in doctoral education; however, little is known about its effective implementation. Co‐supervision is defined here as a form of collaborative supervision where two supervisors guide and support one supervisee's research work in a doctoral study. Four drivers that have contributed to the widespread practice of co‐supervision are identified. We refer to these four drivers as the four Is. The four Is represent emerging policy and institutional strategies focusing on (1) interdisciplinarity, (2) intersectoral collaboration, (3) internationalisation as well as (4) efforts to improve the quality of supervision. This review of research evidence focused on understanding the four Is as drivers of co‐supervision in doctoral education; specifically, by analysing benefits and challenges of co‐supervision. A systematic literature review was conducted using the PRISMA‐P protocol for peer‐reviewed articles between 2005 and 2020. Findings show that the drivers linked to improving the quality of supervision and interdisciplinarity usually coincide, while internationalisation was the least frequently mentioned driver. Although no clear patterns emerge between the four drivers identified and benefits and challenges, we observe that challenges related to co‐supervision are mainly addressed in articles that highlight efforts to improve doctoral education and in articles that addressed interdisciplinary drivers behind co‐supervision.
Can the use of antimicrobials in adult equine patients with acute colitis be justified in the era of antimicrobial stewardship?
Authors: Durie Inge , Galen Gaby van 
Published: June 2022

SummaryThe use of antimicrobials in adult horses with acute colitis is controversial and clear antimicrobial guidelines are lacking. It is generally accepted that antimicrobials should be reserved for patients with specific bacterial enterocolitis such asNeorickettsia risticiiorClostridium difficile; however, in practice, horses show similar clinical signs independently of the underlying aetiology. The clinician is therefore often confronted with the dilemma of rapid initiation of treatment to avoid mortality vs. delayed and selective targeted antimicrobial treatment based on faecal diagnostic testing. The risk of antibiotic associated diarrhoea and the emergence of antimicrobial resistance are other important considerations.
Critical thoughts about critical mass in representative bureaucracy: A theoretical exploration and empirical illustration
Authors: Meier Kenneth J. , Xu Xiaoyang 
Published: June 2022

AbstractStudies of representative bureaucracy frequently reference the need for a critical mass before an underrepresented group can influence policy outputs or outcomes, but the empirical literature is modest and presents mixed findings. This article presents a theoretical exploration to illustrate how critical mass can link individual behavior to organizational contexts. By examining both active representation and symbolic representation at both the individual and organizational level and specifying the different microprocesses of active representation, a series of testable hypotheses are presented. The logic suggests that the concept of critical mass might also be a useful contextual variable to examine other aspects of administrative behavior. Based on the theory, two empirical illustrations from China are presented.