bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interconversion of tripartite and bipartite systems for site-specificO-sialylation of flagellin in Gram-negative and Gram-positive bacteria
Authors: Unay Jovelyn , Kint Nicolas , Viollier Patrick 
Published: December 2023

ABSTRACTMany bacteria decorate flagellin with sialic acid-like sugars such as pseudaminic acid (Pse) by O-glycosylation on serine or threonine residues. Evidence for sufficiency of sialylation by a conserved flagellin glycosyltransferase (fGT) system is lacking, presumably because of (a) missing component(s). Here, we reconstituted two Maf-type fGTs from the Gram-negative bacteriumShewanella oneidensisMR-1 in a heterologous host producing a Pse donor sugar. While Maf-1 is sufficient for flagellin glycosylation, Maf-2 reconstitution requires a newly identified,cis-encoded and conserved specificity factor GlfM, predicted to form a four-helix bundle. While GlfM binds Maf-2 to form a ternary complex with flagellin, the C-terminal tetratricopeptide repeat (TPR) domain of Maf-1 confers flagellin acceptor and O-glycosylation specificity at preferred serine residues. GlfM from Gram-negative and Gram-positive bacteria are functional, providing evidence for convergent evolution of specialized flagellin modification systems with acceptor serine selectivity, while also shaping the interconversion of bacterial tripartite and bipartite O-glycosylation systems.
Spatial and Temporal Resolution of Cyanobacterial Bloom Chemistry Reveals an Open-OceanTrichodesmium thiebautiias a Talented Producer of Specialized Metabolites
Authors: Via Christopher W. , Grauso Laura , McManus Kelly M. , Kirk Riley D. , Kim Andrew M. , Webb Eric A. , Held Noelle A. , Saito Mak A. , Scarpato Silvia , Zimba Paul. V. , Moeller Peter. D. R. , Mangoni Alfonso , Bertin Matthew J. 
Published: December 2023

ABSTRACTWhile the ecological role thatTrichodesmiumsp. play in nitrogen fixation has been widely studied, little information is available on potential specialized metabolites that are associated with blooms and standing stockTrichodesmiumcolonies. While a collection of biological material from aT. thiebautiibloom event from North Padre Island, TX in 2014 indicated that this species was a prolific producer of chlorinated specialized metabolites, additional spatial and temporal resolution was needed. We have completed these metabolite comparison studies, detailed in the current report, utilizing LC-MS/MS-based molecular networking to visualize and annotate the specialized metabolite composition of theseTrichodesmiumblooms and colonies in the Gulf of Mexico (GoM) and other waters. Our results showed thatT. thiebautiiblooms and colonies found in the GoM have a remarkably consistent specialized metabolome. Additionally, we isolated and characterized one new macrocyclic compound fromT. thiebautii, trichothilone A (1), which was also detected in three independent cultures ofT. erythraeum. Genome mining identified genes predicted to synthesize certain functional groups in theT. thiebautiimetabolites. These results provoke intriguing questions of how these specialized metabolites affectTrichodesmiumecophysiology, symbioses with marine invertebrates, and niche development in the global oligotrophic ocean.
ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data
Authors: Prillo Sebastian , Ravoor Akshay , Yosef Nir , Song Yun S. 
Published: December 2023

AbstractCRISPR/Cas9 gene editing technology has enabled lineage tracing for thousands of cellsin vivo. However, most of the analysis of CRISPR/Cas9 lineage tracing data has so far been limited to the reconstruction of single-cell treetopologies, which depict lineage relationships between cells, but not the amount of time that has passed between ancestral cell states and the present. Time-resolved trees, known aschronograms, would allow one to study the evolutionary dynamics of cell populations at an unprecedented level of resolution. Indeed, time-resolved trees would reveal the timing of events on the tree, the relative fitness of subclones, and the dynamics underlying phenotypic changes in the cell population – among other important applications. In this work, we introduce the first scalable and accurate method to refine any given single-cell tree topology into a single-cell chronogram by estimating its branch lengths. To do this, we leverage a statistical model of CRISPR/Cas9 cutting with missing data, paired with a conservative version of maximum parsimony that reconstructs only the ancestral states that we are confident about. As part of our method, we propose a novel approach to represent and handle missing data – specifically, double-resection events – which greatly simplifies and speeds up branch length estimation without compromising quality. All this leads to a convex maximum likelihood estimation (MLE) problem that can be readily solved in seconds with off-the-shelf convex optimization solvers. To stabilize estimates in low-information regimes, we propose a simple penalized version of MLE using a minimum branch length and pseudocounts. We benchmark our method using simulations and show that it performs well on several tasks, outperforming more naive baselines. Our method, which we name ‘ConvexML’, is available through the cassiopeia open source Python package.
High yield, low magnesium flexizyme reactions in a water-ice eutectic phase
Authors: Davisson Joshua A. , Alejo Jose L. , Blank Mace , Kalb Evan M. , Prasad Angelin , Knudson Isaac J. , Schepartz Alanna , Engelhart Aaron E. , Adamala Katarzyna P. 
Published: December 2023

AbstractFlexizymes enable the stoichiometric acylation of tRNAs with a variety of compounds, enabling thein vitrotranslation of peptides with both non-natural backbones and side chains. However, flexizyme reactions have several drawbacks, including single-turnover kinetics, high Mg(II) carryover inhibitingin vitrotranslation, and rapid product hydrolysis. Here we present flexizyme reactions utilizing an ice-eutectic phase, with high yields, 30X lower Mg(II), and long-term product stability. The eutectic flexizyme reactions increase the ease of use and flexibility of flexizyme aminoacylation, and increase thein vitroprotein production.
Aberrant expression prediction across human tissues
Authors: Hölzlwimmer Florian R. , Lindner Jonas , Wagner Nils , Casale Francesco Paolo , Yépez Vicente A. , Gagneur Julien 
Published: December 2023

AbstractDespite the frequent implication of aberrant gene expression in diseases, algorithms predicting aberrantly expressed genes of an individual are lacking. To address this need, we compiled an aberrant expression prediction benchmark covering 8.2 million rare variants from 633 individuals across 48 tissues. While not geared toward aberrant expression, the deleteriousness score CADD and the loss-of-function predictor LOFTEE showed mild predictive ability (1-1.5% average precision). Leveraging these and further variant annotations, we next trained AbExp, a model that yielded 10% average precision by combining in a tissue-specific fashion expression variability with variant effects on isoforms and on aberrant splicing. Integrating expression measurements from clinically accessible tissues led to another two-fold improvement. Furthermore, we show on UK Biobank blood traits that performing rare variant association testing using the continuous and tissue-specific AbExp variant scores instead of LOFTEE variant burden increases gene discovery sensitivity and enables improved phenotype predictions.
High-speed Auto-Polarization Synchronization Modulation Three-dimensional Structured Illumination Microscopy
Authors: Li Yaning , Cao Ruijie , Ren Wei , Fu Yunzhe , Hou Yiwei , Zhong Suyi , Zhanghao Karl , Li Meiqi , Xi Peng 
Published: December 2023

AbstractIn recent years, notable progress has been achieved in both the hardware and algorithms of structured illumination microscopy (SIM). Nevertheless, the advancement of 3DSIM has been impeded by challenges arising from the speed and intricacy of polarization modulation. In this study, we introduce a high-speed modulation 3DSIM system, leveraging the polarization maintaining and modulation capabilities of a digital micro-mirror device (DMD) in conjunction with an electro-optic modulator. The DMD-3DSIM system yields a 2-fold enhancement in both lateral (133 nm) and axial (300 nm) resolution compared to wide-field imaging, and can acquire a data set comprising 29 sections of 1024×1024 pixels, with 15 ms exposure time and 6.75 s per volume. The versatility of the DMD-3DSIM approach was exemplified through the imaging of various specimens, including fluorescent beads, nuclear pores, microtubules, actin filaments, and mitochondria within cells, as well as plant and animal tissues. Notably, polarized 3DSIM elucidated the orientation of actin filaments. Furthermore, the implementation of diverse deconvolution algorithms further enhances three-dimensional resolution. The DMD-based 3DSIM system presents a rapid and reliable methodology for investigating biomedical phenomena, boasting capabilities encompassing 3D superresolution, fast temporal resolution, and polarization imaging.
IL-1β disrupts blood-brain barrier development by inhibiting endothelial Wnt/β-catenin signaling
Authors: Fetsko Audrey R. , Sebo Dylan J. , Budzynski Lilyana B. , Scharbarth Alli , Taylor Michael R. 
Published: December 2023

SummaryDuring neuroinflammation, the proinflammatory cytokine Interleukin-1β (IL-1β) impacts blood-brain barrier (BBB) function by disrupting brain endothelial tight junctions, promoting vascular permeability, and increasing transmigration of immune cells. Here, we examined the effects of Il-1β on thein vivodevelopment of the BBB. We generated a doxycycline-inducible transgenic zebrafish model that drives secretion of Il-1β in the CNS. To validate the utility of our model, we showed Il-1β dose-dependent mortality, recruitment of neutrophils, and expansion of microglia. Using live imaging, we discovered that Il-1β causes a significant reduction in CNS angiogenesis and barriergenesis. To demonstrate specificity, we rescued the Il-1β induced phenotypes by targeting the zebrafishil1r1gene using CRISPR/Cas9. Mechanistically, we determined that Il-1β disrupts BBB development by decreasing Wnt/β-catenin transcriptional activation in brain endothelial cells. Given that several neurodevelopmental disorders are associated with inflammation, our findings support further investigation into the connections between proinflammatory cytokines, neuroinflammation, and neurovascular development.
ZO-1 regulates Hippo-independent YAP activity and cell proliferation via a GEF-H1- and TBK1-regulated mechanosensitive signalling network
Authors: Haas Alexis J. , Karakus Mert , Zihni Ceniz , Balda Maria S. , Matter Karl 
Published: December 2023

ABSTRACTTight junctions are a barrier-forming cell-cell adhesion complex and have been proposed to regulate cell proliferation. However, the underlying mechanisms are not well understood. Here, we used cells deficient in the junction scaffold ZO-1 alone or together with its paralog ZO-2, which disrupts the junctional barrier. We found that ZO-1 knockout increased cell proliferation, loss of cell density-dependent proliferation control, and promoted cell death. These phenotypes were enhanced by double ZO-1/ZO-2 knockout. Increased proliferation was dependent on YAP and ZONAB, two transcriptional regulators. ZO-1 knockout stimulated YAP nuclear translocation and activity without changes in Hippo-dependent phosphorylation. Knockout promoted TANK-binding Kinase 1 (TBK1) activation and increased expression of the RhoA activator GEF-H1. Knockdown of ZO-3, another paralog interacting with ZO1, was sufficient to induce GEF-H1 expression and YAP activity. GEF-H1, TBK1, and mechanotransduction at focal adhesions were required for YAP/TEAD activation in ZO-1-deficient cells. Thus, ZO-1 controls cell proliferation and Hippo-independent YAP activity by activating a GEF-H1- and TBK1-regulated mechanosensitive signalling network.
Internet of Things adoption: unpacking the role of perceived brand credibility
Authors: Dutta Abhisek , Kovid Raj K. , Drave Vinayak A. , Bhatia Manjot Singh 
Published: December 2023

Purpose
This study aims to examine how perceived brand credibility (PBC) moderates the adoption of the Internet of Things (IoT) and identifies the influencing variables that consumers consider while adopting IoT products and services. The study uses the technology acceptance model (TAM) and extends its constructs by investigating the role of PBC to measure the intention to use IoT.

Design/methodology/approach
To test the proposed relationships, data was gathered using the survey method, from respondents in India, an emerging market. The data was analyzed using partial least square based structural equation modeling (PLS-SEM). Moreover, the study measured the moderating effect of PBC and evaluated the effect of control variables – gender and degree of exposure to IoT.

Findings
The study found that perceived usefulness (PU) and perceived ease of use (PEOU) have a significant influence on customers’ attitudes towards using IoT devices and services. Further, PBC moderates the relationship between attitude and behavioral intention to utilize IoT devices and services. Both components of PBC – brand trustworthiness and trust – have significant moderating effect on the adoption of IoT-based services and devices.

Originality/value
The study tests TAM empirically in a new setting and extends it further. Introducing PBC as a moderating variable improves the understanding of the way consumers adopt IoT technology and hence strengthens the predictive power of TAM. Thus, the study provides rich insights for businesses to effectively position their IoT devices and services among their target users.
Effects of enclosure shape on MHD nanofluid flow and irreversibility in different shaped systems under fluid volume constraint
Authors: Manna Nirmal K. , Saha Abhinav , Biswas Nirmalendu , Ghosh Koushik 
Published: December 2023

Purpose
The purpose of this study is to investigate the influence of enclosure shape on magnetohydrodynamic (MHD) nanofluidic flow, heat transfer and irreversibility in square, trapezoidal and triangular thermal systems under fluid volume constraints, with the aim of optimizing thermal behavior in diverse applications.

Design/methodology/approach
The study uses numerical simulations based on a finite element-based technique to analyze the effects of the Rayleigh number (Ra), Hartmann number (Ha), magnetic field orientation (γ) and nanoparticle concentration (ζ) on heat transfer characteristics and thermodynamic entropy production.

Findings
The key findings reveal that the geometrical design significantly influences fluid velocity, heat transfer and irreversibility. Trapezoidal thermal systems outperform square systems, while triangular systems achieve optimal enhancement. Nanoparticle concentration enhances heat transfer and flow strength at higher Rayleigh numbers. The magnetic field intensity has a significant impact on fluid flow and heat transport in natural convection, with higher Hartmann numbers resulting in reduced flow strength and heat transfer. The study also highlights the influence of various parameters on thermodynamic entropy production.

Research limitations/implications
Further research can explore additional geometries, parameters and boundary conditions to expand the understanding of enclosure shape effects on MHD nanofluidic flow and heat transfer. Experimental validation can complement the numerical simulations presented in this study.

Originality/value
This study provides valuable insights into the impact of enclosure shape on heat transfer performance in MHD nanofluid flow systems. The findings contribute to the optimization of thermal behavior in applications such as electronics cooling and energy systems. The comparison of different enclosure shapes and the analysis of thermodynamic entropy production add novelty to the study.
Anti-corruption disclosure and corporate governance mechanisms: insights from FTSE 100
Authors: Ghazwani Musa , Alamir Ibrahim , Salem Rami Ibrahim A. , Sawan Nedal 
Published: December 2023

Purpose
This study aims to examine the impact of corporate governance (CG) on anti-corruption disclosure (A-CD), paying particular attention to the FTSE 100. Notably, it examines how board and audit committees’ characteristics affect the quantity and quality of anti-corruption disclosure.

Design/methodology/approach
Data from FTSE 100 firms, spanning the period from 2014 to 2020, were analysed using the regression of the Poisson fixed effect and GEE analyses.

Findings
The findings show that gender diversity, audit committee expertise and the independence of the audit committee are positively associated with both quantity and quality of anti-corruption disclosure. Notably, no statistically significant relationships were identified between anti-corruption disclosure and factors such as board size, role duality or board meetings.

Research limitations/implications
The findings provide valuable insights for decision-makers and regulatory bodies, shedding light on the elements that compel UK companies to enhance their anti-corruption disclosure and governance protocols to alleviate corruption and propel efforts towards ethical behaviour.

Originality/value
This study makes a notable contribution to the sparse body of evidence by examining the influence of board and audit committee attributes on anti-corruption disclosure subsequent to the implementation of the UK Bribery Act in 2010. Specifically, to the best of the authors’ knowledge, this study assesses for the first time the impact of board and audit committee mechanisms on both the quantity and quality of anti-corruption disclosure.
Competitive priorities and engagement: can they be a source of satisfaction? Customer-centered model
Authors: Awwad Abdulkareem Salameh , Anouze Abdel Latef , Cudney Elizabeth A. 
Published: December 2023

Purpose This study aims to investigate and test the impact of competitive priorities, in terms of quality, speed, dependability, flexibility, cost and patient engagement, on patient satisfaction with healthcare services. It considers patients’ rather than managers’ points of view to collect responses about competitive priorities.Design/methodology/approach This research employed a cross-sectional survey design to analyze a sample of customers through an empirical study of 488 patients in Qatar’s healthcare service context.Findings The confirmatory factor analysis results show that competitive priorities and engagement positively and significantly impact patient satisfaction.Research limitations/implications Researchers can use this methodology to explore the role of competitive priorities in different service contexts and sectors. The researchers conducted the study in Qatar; therefore, the results are not generalizable to all healthcare sectors. However, regardless of geographic location, the research approach can be used in healthcare.Practical implications Managers can employ the developed scales to diagnose competitive priorities and improve customer service experiences.Originality/value The paper is original as it suggests using competitive priorities as a measurement tool for predicting patient satisfaction compared to prior research that mostly measured competitive priorities based on internal perspectives (managers’ perspectives). Further, this paper is original because it depends on the external perspective (customers’ perspective) for the competitive priorities for measuring patient satisfaction.
Risk and protective factors for self-harm in secure mental health hospitals: a systematic review
Authors: Steene Lisa Maria Beethoven , Gaylor Lisa , Ireland Jane L. 
Published: December 2023

Purpose
The current review aims to focus on how risk and protective factors for self-harm in secure mental health hospitals are captured in the literature.

Design/methodology/approach
Fifty-seven articles were included in a systematic review, drawn from an initial 1,119 articles, post duplicate removal. Databases included Psycinfo, Psycarticles, Psycnet, Web of Science and EBSCO host. A thematic analysis was used, which included a meta-ethnographic approach for considering qualitative papers.

Findings
There was a clear focus on risk factors, with eight identified (in order of occurrence): raised emotional reactivity and poor emotion regulation; poor mental health; traumatic experiences; personality disorder diagnosis and associated traits; increased use of outward aggression – dual harm; constraints of a secure environment and lack of control; previous self-harm and suicide attempts; and hopelessness. Protective factors featured less, resulting in only three themes emerging (in order of occurrence): positive social support and communication; positive coping skills; and hope/positive outlook.

Research limitations/implications
This includes a proposal to move focus away from “risk” factors, to incorporate “needs”, in terms of individual and environmental factors. There is also a need for more attention to focus on developing high quality research in this area.

Originality/value
The research captures an area where a synthesis of research has not been comprehensively undertaken, particularly with regards to capturing protective as well as risk factors.
Indian students' psychological and behavioral aspects on studying abroad decisions amidst fear of uncertainty and social unrest
Authors: Srivastava Khusboo , Dhamija Somesh 
Published: December 2023

PurposeThe study is an attempt to expand the knowledge about the psychological and behavioral aspects of Indian students studying abroad amidst fear of uncertainty and social unrest.Design/methodology/approachThe exploratory study is employed to seek a better and deeper understanding of the possible impact of the potential war on the student abroad study process. In the study, the participants were selected from Delhi NCR of India. The thoughts and opinions of students on studying abroad under the fear of uncertainty were covered in a semi-structured interview.FindingsFive broad themes emerged from the analysis of the interviews that influence students' choices and attitudes toward their decisions on studying abroad. The themes are “safety”, “fear of incomplete degree”, “financial stress”, “parents' apprehension” and “emotional breakdown”.Practical implicationsThe study leveraged an understanding of the mindset of Indian students. Considering the student's doubts and fear over such uncertainty and war-like situations, the higher education policymaker can adopt some measures (hybrid education, short-term programs, student exchange programs, shift in destination, distance learning and new forms of educational technology) to cope with such upcoming challenges, ensuring their safety and pursuing their dreams by taking higher education abroad.Originality/valueThis qualitative study develops a comprehensive understanding of how students perceive such extreme crises and how their thoughts, attitudes and behavior toward studying abroad change. The study contributes to comprehending the student's description of perceptions, emotions, opinions and behaviors under the fear of uncertainty and social unrest.