bluuebunny/crossref_metadata_2025_split huggingface dataset:
SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks
Authors: Schirmeisen Kamila , Naiman Karel , Fréon Karine , Besse Laetitia , Chakraborty Shrena , Carr Antony M. , Kramarz Karol , Lambert Sarah AE 
Published: November 2023

AbstractNuclear pores complexes (NPCs) are genome organizers, defining a particular nuclear compartment enriched for SUMO protease and proteasome activities, and acting as docking sites for DNA repair. In fission yeast, the anchorage of perturbed replication forks to NPCs is an integral part of the recombination-dependent replication restart mechanism (RDR) that resumes DNA synthesis at terminally dysfunctional forks. By mapping DNA polymerase usage, we report that SUMO protease Ulp1-associated NPCs ensure efficient initiation of restarted DNA synthesis, whereas proteasome-associated NPCs sustain the progression of restarted DNA polymerase. In contrast to Ulp1-dependent events, this last function occurs independently of SUMO chains formation. By analyzing the role of the nuclear basket, the nucleoplasmic extension of the NPC, we reveal that the activities of Ulp1 and the proteasome cannot compensate for each other and affect RDR dynamics in distinct ways. Our work probes the mechanisms by which the NPC environment ensures optimal RDR.Highlights● Ulp1-associated NPCs ensure efficient initiation of restarted DNA synthesis, in a SUMO chain-dependent manner● Proteasome-associated NPCs foster the progression of restarted DNA synthesis, in a SUMO chain-independent manner● The nucleoporin Nup60 promotes the spatial sequestration of Ulp1 at the nuclear periphery● Ulp1 and proteasome activities are differently required for optimal recombination-mediated fork restart.
Oyster aquaculture enhances sediment microbial diversity– Insights from a multi-omics study
Authors: Stevens Joshua T.E. , Ray Nicholas E. , Al-Haj Alia N. , Fulweiler Robinson W. , Chowdhury Priyanka Roy 
Published: November 2023

AbstractThe global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.ImportanceSediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.
Sensory progenitors influence patterning of the mammalian auditory sensory epithelium
Authors: Young Caryl A. , Burt Emily , Munnamalai Vidhya 
Published: November 2023

AbstractDuring embryonic development Wnt signaling has been shown to influence proliferation and sensory formation in the cochlea. How the dual nature of Wnt signaling is coordinated is unknown. In this study, we define a novel role for a Wnt regulated gene,Mybl2,which was already known to be important for proliferation, in influencing patterning and determining the size of the sensory epithelium in the murine cochlea. Using a quantitative spatial analysis approach and analyzingMybl2loss-of-function cochleas, we show thatMybl2simultaneously specifies the progenitor niche and the size of the sensory domain, and influences the positioning of the medial sensory domain boundary viaJag1regulation during the mid-gestational stages.Mybl2conditional knockout resulted in a decrease of proliferation within the progenitor niche. During the late embryonic stages, conditional knockout ofMybl2produced a wider sensory epithelium across the radial axis with an increase in ectopic inner hair cell formation. These data suggest thatMybl2-positive progenitors play a role in boundary formation and patterning the sensory epithelium.Summary StatementMybl2is a Wnt-regulated gene encoding a transcription factor that is expressed in the cochlear progenitor niche and influences the boundary formation between the niche and the sensory domain during mid-cochlear developmental stages, thereby impacting the size of the sensory epithelium.
Exploring viral particle, soil, and extraction buffer physicochemical characteristics and their impacts on extractable viral communities
Authors: Fudyma Jane D. , ter Horst Anneliek M. , Santos-Medellín Christian , Sorensen Jess , Gogul Grant , Hillary Luke , Geonczy Sara , Pett-Ridge Jennifer , Emerson Joanne B. 
Published: November 2023

ABSTRACTSoil viruses are expected to be pivotal members of soil ecosystems, and recent advances in viral size fraction metagenomic (viromic) approaches have substantially improved our ability to interrogate soil viral ecology. However, the first step of viromics relies on extraction buffers to effectively remove viral particles from the soil matrix for downstream analysis, and viral extraction efficiency at this stage could be affected by the interplay between viral particles, soils, and extraction buffer chemistry. Here, we investigated whether extraction buffer chemistry affected extractable viral community composition measured by viromics from different soil types, for both biological (samples collected 1 meter apart) and technical (subsamples from the same soil homogenate) replicates. We first investigated protein-supplemented phosphate-buffered saline pH (PPBS, pHs 4.5, 5.5, 6.5, and 7.5) on a forest, grassland and wetland soil that exhibited different soil edaphic properties, and then we tested different buffer chemistries (PPBS, Carbonated Buffer, Glycine, and Saline Magnesium) on just the wetland soil. Spatial distance, or where the sample was taken in the field (i.e., biological replicate), was the primary driver of extractable viral community composition across all buffers and soils tested. Differences in viral community composition according to extraction buffer properties were only observed in the grassland technical replicates at PPBS buffer pH 4.5, as well as in both the wetland technical and biological replicates treated with different buffer chemistries, but the effects of buffer chemistry were secondary to spatial distance in all cases where spatial distance was a factor. The lack of buffering capacity in the grassland soil technical replicates likely increased sorption of some viral particles at pH 4.5, but neither protein composition nor isoelectric point (both calculated bioinformatically) explained this phenomenon. Given that most soil viral ecological studies to date include sample collection schemes over distances much farther apart than the 1-meter distances considered here, results suggest that extraction buffer chemistry is likely of much lower importance than ecological considerations, such as spatial distance, in the design of future soil viral ecological investigations.HIGHLIGHTSSpatial distance was the main driver of extractable viral community composition.Extraction buffer chemistry secondarily structured wetland viral communities.At pH 4.5, PPBS buffer likely increased viral sorption in homogenized grassland soil.Increased sorption was not explained by estimated viral protein isoelectric points.
Right ventricular pressure-strain relationship-derived myocardial work reflects contractility: validation with invasive pressure-volume analysis
Authors: Lakatos Bálint Károly , Rako Zvonimir , Szijártó Ádám , da Rocha Bruno R. Brito , Richter Manuel J. , Fábián Alexandra , Gall Henning , Ghofrani Hossein A. , Kremer Nils , Seeger Werner , Zedler Daniel , Yildiz Selin , Yogeswaran Athiththan , Merkely Béla , Tello Khodr , Kovács Attila 
Published: November 2023

BackgroundThree-dimensional (3D) echocardiography-derived right ventricular (RV) ejection fraction (EF) and global longitudinal strain (GLS) are valuable RV functional markers; nevertheless, they are substantially load-dependent. Global myocardial work index (GMWI) adjusts myocardial deformation to instantaneous pressure; therefore, it may better reflect contractility. Accordingly, we aimed to calculate RV GMWI using 3D echocardiography and examine its relationship with RV contractility’s gold standard invasive measurement.MethodsSixty patients (65±14 years, 65% female) with suspected or established pulmonary hypertension were enrolled. Detailed 3D echocardiography was performed to quantify RV EF and GLS using the ReVISION software. Patients underwent RV pressure-conductance catheterization to obtain the RV pressure curve and to assess contractility (end-systolic elastance - Ees) and ventriculo-arterial coupling (Ees/arterial elastance - Ees/Ea). RV GMWI was calculated using the RV GLS and the RV pressure trace curve.ResultsWhile neither RV EF (r=-0.143, p=0.275) nor GLS (r=-0.067, p=0.611) correlated with Ees, GMWI showed a strong correlation with it (r=0.669, p<0.001). In contrast, RV EF and GLS showed a relationship with Ees/Ea (RVEF: r=0.552; GLS: r=0.460, both p<0.001). By dividing the population based on the Reveal Lite 2 risk classification, EF and GLS showed a significant decrease only in the high-risk group (low vs. intermediate vs. high risk; EF: 48.8±6.6 vs. 44.0±9.4 vs. 35.0±7.8%, ANOVA p<0.001; GLS: 18.6±3.6 vs. 17.0±4.5 vs. 13.3±3.9%, ANOVA p<0.001), whereas GMWI already showed an increase in the intermediate group (550±267 vs. 831±361 vs. 797±265 mmHg%, ANOVA p<0.01).ConclusionsRV EF and GLS reflect ventriculo-arterial coupling, while GMWI strongly correlates with contractility. RV GMWI may emerge as a useful clinical tool for risk stratification and follow-up in patients with pulmonary hypertension.
The non-mitotic role of HMMR in regulating the localization of TPX2 and the dynamics of microtubules in neurons
Authors: Chen Yi-Ju , Tseng Shun-Cheng , Chen Peng-Tzu , Hwang Eric 
Published: November 2023

AbstractA functional nervous system is built upon the proper morphogenesis of neurons to establish the intricate connection between them. The microtubule cytoskeleton is known to play various essential roles in this morphogenetic process. While many microtubule-associated proteins (MAPs) have been demonstrated to participate in neuronal morphogenesis, the function of many more remains to be determined. This study focuses on a MAP called HMMR, which was originally identified as a hyaluronan binding protein and later found to possess microtubule and centrosome binding capacity. HMMR exhibits high abundance on neuronal microtubules and altering the level of HMMR significantly affects the morphology of neurons. Instead of confining to the centrosome(s) like cells in mitosis, HMMR localizes to microtubules along axons and dendrites. Furthermore, transiently expressing HMMR enhances the stability of neuronal microtubules and increases the formation frequency of growing microtubules along the neurites. HMMR regulates the microtubule localization of a non-centrosomal microtubule nucleator TPX2 along the neurite, offering an explanation for how HMMR contributes to the promotion of growing microtubules. This study sheds light on how progenitor cells utilize proteins involved in mitosis for non-mitotic functions.
Investigation of the impact of bromodomain inhibition on cytoskeleton stability and contraction
Authors: Bigger-Allen Alexander , Gheinani Ali Hashemi , Adam Rosalyn M. 
Published: November 2023

AbstractInjury to contractile organs such as the heart, vasculature, urinary bladder and gut can stimulate a pathological response that results in loss of normal contractility. PDGF and TGFβ are among the most well studied initiators of the injury response and have been shown to induce aberrant contraction in mechanically active cells of hollow organs including smooth muscle cells (SMC) and fibroblasts. However the mechanisms driving contractile alterations downstream of PDGF and TGFβ in SMC and fibroblasts are incompletely understood, limiting therapeutic interventions. To identify potential molecular targets, we have leveraged the analysis of publicly available data, comparing transcriptomic changes in mechanically active cells stimulated with PDGF and TGFβ and identified a shared molecular profile regulated by MYC and members of the AP-1 transcription factor complex. We also analyzed data sets from SMC and fibroblasts treated in the presence or absence of the MYC inhibitor JQ1. This analysis revealed a unique set of cytoskeleton-associated genes that were sensitive to MYC inhibition. JQ1 was also able to attenuate TGFβ and PDGF induced changes to the cytoskeleton and contraction of smooth muscle cells and fibroblastsin vitro. These findings identify MYC as a key driver of aberrant cytoskeletal and contractile changes in fibroblasts and SMC, and suggest that JQ1 could be used to restore normal contractile function in hollow organs.
Digital transformation: a challenging opportunity for the food industry companies
Authors: Marczewska Magdalena 
Published: November 2023

PurposeCommon availability of digital technologies encouraged companies in almost all industries to focus on exploring various ways of benefiting from their adoption and thus taking steps toward their digital transformation. This paper aims to describe the digital transformation of small and medium enterprises (SMEs) as a challenging opportunity and identify ways in which companies from the food industry address it.Design/methodology/approachThe paper presents empirical evidence based on a case study of the Polish freeze-drying market and companies operating on it. This study adopted a single case study research method to describe the digital transformation journey of SMEs. The sample constitutes a single sectoral case study with more than one unit of analysis – sixteen companies. The undertaken approach follows an embedded case study design and allows for an extensive and multidimensional analysis of rich empirical data.FindingsThe results of this analysis allowed to identify four significant trends describing human resources involvement in the digital transformation of freeze-drying companies in Poland (i.e. visionary top-down, cooperative task-oriented, persuasive bottom-up, chaotic), a detailed catalog of outcomes of digital transformation from the perspective of food industry companies grouped in seven categories and a list of main barriers to digital transformation.Originality/valueThis paper contributes to expanding knowledge on the practices of food industry companies in addressing challenges posed by the development of information technology and the dynamically changing environment after the COVID-19 pandemic. It contributes further to the discussion related to context-, industry- and country-specific barriers to digital transformation, identifying time-related constraints as an essential barrier to digital transformation.
E-waste supply chain risk management: a framework considering omnichannel and circular economy
Authors: Senna Pedro , Marujo Lino Guimarães , Santos Ana Carla de Souza Gomes dos , Ferreira Amanda Chousa , da Silva Luís Alfredo Aragão 
Published: November 2023

PurposeIn the last few years, environmental issues have become a matter of survival. In this sense, e-waste management is among the major problems since it may be a way of mitigating mineral depletion. In this context, the literature lacks e-waste supply chain studies that systematically map supply chain challenges and risks concerning material recovery.Design/methodology/approachGiven this context, the authors' paper conducted a systematic literature review (SLR) to build a framework to identify the constructs of e-waste supply chain risk management.FindingsThe paper revealed the theoretical relationship between important variables to achieve e-waste supply chain risk management via a circular economy (CE) framework. These variables include reverse logistics (RL), closed-loop supply chains (CLSC), supply chain risk management, supply chain resilience and smart cities.Originality/valueThe literature contributions of this paper are as follows: (1) a complete list of the risks of the e-waste supply chains, (2) the techniques being used to identify, assess and mitigate e-waste supply chain risks and (3) the constructs that form the theoretical framework of e-waste supply chain risk management. In addition, the authors' results address important literature gaps identified by researchers and serve as a guide to implementation.
A cross-organizational Lean deployment in an Italian regional healthcare system
Authors: Rosa Angelo , Marolla Giuliano , McDermott Olivia 
Published: November 2023

PurposeThis study explores how Lean was deployed in several hospitals in the Apulia region in Italy over 3.5 years.Design/methodology/approachAn exploratory qualitative design was drawn up based on semi-structured interviews.FindingsThe drivers of Lean in hospitals were to increase patient satisfaction and improve workplace well-being by eliminating non-value-add waste. The participants highlighted three key elements of the pivotal implementation stages of Lean: introduction, spontaneous and informal dissemination and strategic level implementation and highlighted critical success and failure factors that emerged for each of these stages. During the introduction, training and coaching from an external consultant were among the most impactful factors in the success of pilot projects, while time constraints and the adoption of process analysis tools were the main barriers to implementation. The experiences of the Lean teams strongly influence the process of spontaneous dissemination aided by the celebration of project results and the commitment of the departmental hospital heads.Practical implicationsLean culture can spread to allow many projects be conducted spontaneously, but the Lean paradigm can struggle to be adopted strategically. Lean in healthcare can fail because of the lack of alignment of Lean with leadership in healthcare and with their strategic vision, a lack of employees' project management skills and crucially the absence of a Lean steering committee.Originality/valueThe absence of managerial expertise and a will to support Lean implementation do not allow for systemic adoption of Lean. This is one of the first and largest long-term case studies on a Lean cross-regional multi-hospital application in healthcare.
Workplace bullying in pharmacy – a study on prevalence, impacts and barriers to reporting
Authors: Silwal Pushkar , D'Souza Natalia , Aspden Trudi Jane , Scahill Shane 
Published: November 2023

Purpose The study aims to estimate the prevalence of workplace bullying, personal and work-related impacts, reporting practices for bullying, and the reasons for not reporting bullying incidents in the New Zealand pharmacy sector.Design/methodology/approach An online survey was conducted among registered pharmacists and pharmacist interns in New Zealand from June to August 2020. The questionnaire comprises both close-ended and semi-structured free-text questions. Goldberg’s 12-item General Health Questionnaire (GHQ-12) assessed the respondents’ general psychological health status, and a 22-item Negative Acts Questionnaire-Revised (NAQ-R) was used to estimate bullying prevalence together with the self-rated/self-labeled questions. The qualitative information obtained from the free-text responses was used to support and elaborate on the quantitative results.Findings The self-labeled prevalence of workplace bullying was 36.9%, with almost 10% reporting it occurring almost daily to several times per week. The 54.7% prevalence based on the NAQ-R assessment compares well with the prevalence of witnessing the incidents (58.5%). Psychological distress symptoms were experienced by 37.1% in pre-COVID and 45.3% during COVID-year 1. Supervisors or direct managers were the commonest perpetrators (32.7%). Only 28.8% of those who experienced bullying had reported the incidents formally.Research limitations/implicationsThis study is cross-sectional, and the relationships indicated are bi-directional. The consistency of the results is reassuring, however inferring causality of effect is challenging. Future studies and analyses should focus on this. This study suggests that in the pharmacy environment bullying from the top is reasonably prevalent, is not commonly reported and requires the design and implementation of prevention and management strategies that take into account and mitigate these bullying factors. Professional pharmacy leadership organizations, National Health Authority and Pharmacy regulators could play a significant role in awareness and training to reduce bullying with the development and promotion of strategies to curb it and improve reporting.Originality/value This is the first paper to describe the prevalence and impact of workplace bullying, and the practices of reporting bullying incidents in the New Zealand pharmacy sector. Based on empirical evidence, pharmacists represent a small share of total healthcare workforce, yet the overall prevalence of bullying is consistent with professions with much larger numbers such as medicine and nursing.