bluuebunny/crossref_metadata_2025 huggingface dataset:
Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data
Authors: Vo Duong H.T. , Thorne Thomas
Published: March 2024

Gene interaction networks are graphs in which nodes represent genes and edges represent functional interactions between them. These interactions can be at multiple levels, for instance, gene regulation, protein-protein interaction, or metabolic pathways. To analyse gene interaction networks at a large scale, gene co-expression network analysis is often applied on high-throughput gene expression data such as RNA sequencing data. With the advance in sequencing technology, expression of genes can be measured in individual cells. Single-cell RNA sequencing (scRNAseq) provides insights of cellular development, differentiation and characteristics at transcriptomic level. High sparsity and high-dimensional data structure pose challenges in scRNAseq data analysis. In this study, a sparse inverse covariance matrix estimation framework for scRNAseq data is developed to capture direct functional interactions between genes. Comparative analyses highlight high performance and fast computation of Stein-type shrinkage in high-dimensional data using simulated scRNAseq data. Data transformation approaches also show improvement in performance of shrinkage methods in non-Gaussian distributed data. Zero-inflated modelling of scRNAseq data based on a negative binomial distribution enhances shrinkage performance in zero-inflated data without interference on non zeroinflated count data. The optimal zero-inflated Stein-type shrinkage framework is applied on experimental scRNAseq data which demonstrates its potential to construct sparser gene interaction networks with higher precision.

Availability and implementation

https://github.com/calathea24/ZINBGraphicalModel
Development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography
Authors: Du Daniel X. , Bartnik Adam C. , Duncan Cameron J. R. , Choudhry Usama , Tabachnik Tanya , Sallah Chaim , Najafi Ebrahim , Yang Ding-Shyue , Maxson Jared M. , Fitzpatrick Anthony W. P.
Published: March 2024

Cryo-electron tomography (cryo-ET) is a powerful modality for resolving cellular structures in their native state. While single-particle cryo-electron microscopy (cryo-EM) excels in determining protein structures purified from recombinant or endogenous sources, cryo-ET suffers from low contrast in crowded cellular milieux. A novel experimental approach to enhance contrast in cryo-ET is to manipulate the phase of scattered pulsed electrons using ultrafast pulsed photons. Here, we outline the experimental design of a proof-of-concept electron microscope and demonstrate synchronization between electron packets and laser pulses. Further, we show ultrabright photoemission of electrons from an alloy field emission tip using femtosecond ultraviolet pulses. These experiments pave the way towards exploring the utility of the ponderomotive effect using pulsed radiation to increase phase contrast in cryo-ET of subcellular protein complexesin situ, thus advancing the field of cell biology.
Frontoparietal structural network disconnections correlate with outcome after a severe stroke
Authors: Frontzkowski Lukas , Fehring Felix , Frey Benedikt M. , Wróbel Paweł P. , Reibelt Antonia , Higgen Focko , Wolf Silke , Backhaus Winifried , Braaß Hanna , Koch Philipp J. , Choe Chi-un , Bönstrup Marlene , Cheng Bastian , Thomalla Götz , Gerloff Christian , Quandt Fanny , Schulz Robert
Published: March 2024

Structural disconnectome analyses have provided valuable insights into how a stroke lesion results in widespread network disturbances and how these relate to deficits, recovery patterns, and outcome. Previous analyses have primarily focused on patients with relatively mild to moderate deficits. However, outcomes vary among survivors of severe strokes, and the mechanisms of recovery remain poorly understood. This study assesses the association between lesion-induced network disconnection and outcome after severe stroke. Thirty-eight ischaemic stroke patients underwent MRI brain imaging early after stroke and longitudinal clinical follow-up. Lesion information was integrated with normative connectome data to infer individual disconnectome profiles on a localized regional and region-to-region pathway level. Ordinal logistic regressions were computed to link disconnectome information to the modified Rankin Scale after 3-6 months. Disconnections of ipsilesional frontal, parietal and temporal cortical brain areas were significantly associated with a worse motor outcome after a severe stroke, adjusted for the initial deficit, lesion volume, and age. The analysis of the underlying pathways mediating this association revealed location specific results: For frontal, prefrontal and temporal brain areas, the association was primarily driven by relatively sparse intrahemispheric disconnections. In contrast, the ipsilesional primary motor cortex, the dorsal premotor cortex, and various parietal brain regions showed a remarkable involvement of either frontoparietal intrahemispheric or additionally interhemispheric disconnections. These results indicate that localized disconnection of multiple regions embedded in the structural frontoparietal network correlates with worse outcome after severe stroke. Specifically, primary motor and parietal cortices might gain a particular importance as they structurally link frontoparietal networks of both hemispheres. These data shed novel light on the significance of distinct brain networks for recovery after severe stroke.
Epidemiological, phylogenetic, and resistance heterogeneity amongAcinetobacter baumanniiin a major US Deep South healthcare center
Authors: Graffice Emma , Moates Derek B. , Leal Sixto M. , Amerson-Brown Megan , Calix Juan J.
Published: March 2024

Acinetobacter baumannii(Ab) disease in the U.S. is commonly attributed to outbreaks of one or two monophyletic carbapenem resistance (CR)Ablineages that vary by region. However, there is limited knowledge regardingAbepidemiology and population structure in the U.S. Deep South, and few studies compare contemporary CR and carbapenem-susceptible (Cs)Ab, despite prevalence of the latter. We performed a 12-year time series analysis ofAbcases in a large hospital in Birmingham, AL, and 89 isolates from an ongoing surveillance project started in November 2021 were analyzed by whole genome sequencing and antibiotic susceptibility testing (AST). Cumulative CR rate among 2462 cases since 2011 was 19.4%, with increased rates during winter months resulting from seasonal changes in CsAbincidence. Sequenced CRAbbelonged to clonal complex (CC) 1, CC108, CC250, CC2, and CC499. Most CRAbCCs were comprised of isolates that clustered apart from U.S. counterparts in phylogenetic analysis, despite being identified in unrelated cases occurring ≥3 months apart. In contrast, 38/47 (81%) CsAbisolates each belonged to a distinct CC. CRAbisolates displayed lineage-distinct AST features, including unique carbapenem resistance genetic determinants and presumptive heteroresistance behaviors unique to CC108 and CC499 isolates. This first comprehensive analysis ofAbcases in the U.S. Deep South revealed epidemiological trends consistent with those in other regions and an unusually high degree of phylogenetic diversity among regional CRAbisolates. We also describe emergent U.S. CRAblineages whose unconventional antimicrobial resistance features must be integrated into ongoing diagnostic, treatment, and surveillance efforts.
Quantifying brain health in acute ischemic stroke through effective reserve
Authors: Schirmer Markus D. , Alhadid Kenda , Regenhardt Robert W. , Rost Natalia S.
Published: March 2024

Objective

To quantify brain health using a measure of reserve that incorporates pre-existing pathology.

Methods

We analyzed two retrospective ischemic stroke cohorts (GASROS and SALVO) with neuroimaging and 90-day modified Rankin Scores (mRS) available. White matter hyperintensity (WMHv), brain, and intracranial volumes were automatically extracted, and brain parenchymal fraction (BPF) calculated. The latent variable effective reserve (eR) was modeled using age, WMHv, and BPF or brain volume in GASROS. Models were compared using Bayes Information Criterion (BIC). The best model’s eR estimates were categorized into quartiles and evaluated in SALVO.

Results

GASROS included 476 (median age: 65.8; 65.3% male) and SALVO included 43 (median age: 69.2; 62.8% male) patients. Inverse associations between eR and mRS was seen in both models, with brain volume outperforming BPF (path coefficients: -0.67, -0.48, respectively; p < 0.001; |ΔBIC| = 362). Quartile-based eR stratification in SALVO showed a similar inverse trend, with worse outcomes in the low reserve group (mRS≤2 - highest vs lowest quartile: 85/90% vs 59/45% for GASROS/SALVO).

Conclusions

Expanding the concept of eR, highlights its clinical translational potential. The strong link between higher eR and better outcomes underscores its value as a protective brain health metric.
MultiSCRIPT-Cycle 1- A Pragmatic trial embedded within the Swiss Multiple Sclerosis Cohort (SMSC) on neurofilament light chain monitoring to inform personalized treatment decisions in Multiple Sclerosis: a study protocol for a randomized clinical trial
Authors: Janiaud Perrine , Zecca Chiara , Salmen Anke , Benkert Pascal , Schädelin Sabine , Orleth Annette , Demuth Lilian , Maceski Aleksandra Maleska , Granziera Cristina , Oechtering Johanna , Leppert David , Derfuss Tobias , Achtnichts Lutz , Findling Oliver , Roth Patrick , Lalive Patrice , Uginet Marjolaine , Müller Stefanie , Pot Caroline , Hoepner Robert , Disanto Giulio , Gobbi Claudio , Rooshenas Leila , Schwenkglenks Matthias , Lambiris Mark J , Kappos Ludwig , Kuhle Jens , Yaldizli Özgür , Hemkens Lars G
Published: March 2024

Background

Treatment decisions for persons with relapsing-remitting multiple sclerosis (RRMS) rely on clinical and radiological disease activity, the benefit-harm profile of drug therapy, and preferences of patients and physicians. However, there is limited evidence to support evidence-based personalized decision-making on how to adapt disease modifying therapies treatments targeting no evidence of disease activity, while achieving better patient-relevant outcomes, fewer adverse events and improved care. Serum neurofilament light chain (sNfL) is a sensitive measure of disease activity that captures and prognosticates disease worsening in RRMS. sNfL might therefore be instrumental for a patient-tailored treatment adaptation. We aim to assess whether 6-monthly sNfL monitoring in addition to usual care improves patient-relevant outcomes compared to usual care alone.

Methods

Pragmatic multicenter, 1:1 randomized, platform trial embedded in the Swiss MS Cohort (SMSC). All patients with RRMS in the SMSC for ≥1 year are eligible. We plan to include 915 patients with RRMS, randomly allocated to two groups with different care strategies, one of them new (group A), one of them usual care (group B). In group A, 6-monthly monitoring of sNfL will together with information on relapses, disability and magnetic resonance imaging (MRI) inform personalized treatment decisions (e.g., escalation or de-escalation) supported by pre-specified algorithms. In group B, patients will receive usual care with their usual 6- or 12- monthly visits. Two primary outcomes will be used: 1) evidence of disease activity (EDA3: occurrence of relapses, disability worsening, or MRI activity) and 2) quality of life (MQoL-54) using 24-month follow-up. The new treatment strategy with sNfL will be considered superior to usual care if either more patients have no EDA3, or their health-related quality of life increases. Data collection will be embedded within the SMSC using established trial-level quality procedures.

Discussion

MultiSCRIPT aims to be a platform where research and care are optimally combined to generate evidence to inform personalized decision-making in usual care. This approach aims to foster better personalized treatment and care strategies, at low cost and with rapid translation to clinical practice.

Trial registration

NCT06095271
Phenotypic spectrum ofFAM47E-SHROOM3haplotype composition in a general population sample
Authors: Ghasemi-Semeskandeh Dariush , König Eva , Foco Luisa , Dordevic Nikola , Gögele Martin , Rainer Johannes , Ralser Markus , Acoba Dianne , Domingues Francisco S. , Peters Dorien J. M. , Pramstaller Peter P. , Pattaro Cristian
Published: March 2024

Genome-wide association studies identified a locus on chromosome 4q21.1, spanning theFAM47E,STBD1,CCDC158, andSHROOM3genes, as associated with kidney function markers. Functional studies implicatedSHROOM3, encoding an actin-binding protein involved in cell shaping, into podocyte barrier damage. Despite the locus was also found associated with electrolytes, hematological and cardiovascular traits, systematic explorations of functional variants across all the genes in the locus are lacking.

We reconstructed haplotypes covering the whole locus on 12,834 participants to the Cooperative Health Research in South Tyrol (CHRIS) study, using genotypes imputed on a whole-exome sequencing reference panel of a subsample of 3,422 participants. Haplotypes included 146 exonic and intronic variants over the four genes and were tested for association with 73 serum, urine and anthropometric traits, 172 serum metabolite and 148 plasma protein concentrations using linear regression models.

We identified 11 haplotypes with 2% to 24% frequency. Compared to the most common haplotype, most haplotypes were associated with higher levels of the creatinine-based estimated glomerular filtration rate and lower serum magnesium levels. The second most common haplotype (12% frequency) was additionally associated with lower dodecanoyl-, hydroxyvaleryl- and tiglyl-carnitine serum concentrations. A haplotype of 4% frequency was also associated with lower red blood cell count, hemoglobin, and hematocrit levels. A haplotype of 2% frequency was associated with serum glutamine and putrescine concentrations. Cluster analysis revealed distinct groups of traits and of haplotypes.

TheFAM47E-SHROOM3locus exhibits haplotype variability that corresponds to marked pleiotropic effects, implicating the existence of population subgroups with distinct biomarker profiles.
Effectiveness of COVID-19 Vaccines: A Vaccinated-Only Approach
Authors: Foppa Ivo M.
Published: March 2024

We used a modified screening method that ensures quasi-exchangeability of comparison groups to estimate COVID-19 vaccine effectiveness in people resident in the Federal State of Hessen, Germany. COVID-19 vaccination history of vaccinated subjects with reported symptomatic SARS-CoV-2 infection was used to determine vaccination status. Subjects with their first COVID-19 vaccination within 7 days before the imputed date of infection were considered unvaccinated. Vaccination is assumed not to have a relevant effect on outcome risk for the first seven days and to be fully developed after between 14 and 21 days. The immunization profile of the source population was estimated from the number of subjects vaccinated by dose, date and age group as recorded in the Hessian COVID-19 vaccination registry. Effect estimates were obtained using logistic regression, fitted by a Bayesian approach. The first dose of COVID-19 vaccines had a measurable effect during the predominance of the Alpha and Delta variants of SARS-CoV-2, but a smaller effect during Omicron predominance. Only during Alpha and Delta predominance did the second dose provide an added benefit. During Omicron predominance, the third dose provided additional protection, but that effect was smaller than for the Delta period. Comparison of our estimates with estimates using a conventional, not quasi-exchangeable, approach revealed substantial differences in some cases, without any recognizable pattern.

PACS

0000, 1111

MSC

0000, 1111

Graphical Abstract

Highlights

We propose a vaccine effectiveness (VE) study design for COVID-19 that is based on a modification of the screening method. The modification ensures quasi-exchangeable: Only vaccinated subjects are considered, COVID-19 cases on the one hand and subjects registered in the COVID-19 vaccination registry. Risk comparisons are calculated for individuals who received theirn-th vaccination one to two weeks apart, assuming no relevant vaccine effect within a week.

The first dose of COVID-19 vaccines had a measurable effect during the predominance of the Alpha and Delta variants of SARS-CoV-2, but a smaller effect during Omicron predominance. Only during Alpha and Delta predominance did the second dose provide an added benefit. During Omicron predominance, the third dose provided additional protection, but that effect was smaller than for the Delta period.

Comparison with a conventional approach revealed substantial differences in some cases, that did not follow a clear pattern.
Spatial Transcriptomic Analysis Identifies Epithelium-Macrophage Crosstalk in Endometriotic Lesions
Authors: Burns Gregory W. , Fu Zhen , Vegter Erin L. , Madaj Zachary B. , Greaves Erin , Flores Idhaliz , Fazleabas Asgerally T.
Published: March 2024

The mechanisms underlying the pathophysiology of endometriosis, characterized by the presence of endometrium-like tissue outside the uterus, remain poorly understood. This study aimed to identify cell type-specific gene expression changes in superficial peritoneal endometriotic lesions and elucidate the crosstalk among the stroma, epithelium, and macrophages compared to patient-matched eutopic endometrium. Surprisingly, comparison between lesions and eutopic endometrium revealed transcriptional similarities, indicating minimal alterations in the sub-epithelial stroma and epithelium of lesions. Spatial transcriptomics highlighted increased signaling between the lesion epithelium and macrophages, emphasizing the role of the epithelium in driving lesion inflammation. We propose that the superficial endometriotic lesion epithelium orchestrates inflammatory signaling and promotes a pro-repair phenotype in macrophages, providing a new role for Complement 3 in lesion pathobiology. This study underscores the significance of considering spatial context and cellular interactions in uncovering mechanisms governing disease in endometriotic lesions.
Sulfoquinovosyl diacylglycerol is required for dimerization of theRhodobacter sphaeroidesRC-LH1 core complex
Authors: Martin Elizabeth C. , Bowie Adam G.M. , Reid Taylor Wellfare , Hunter C. Neil , Hitchcock Andrew , Swainsbury David J.K.
Published: March 2024

The reaction centre-light harvesting 1 (RC-LH1) core complex is indispensable for anoxygenic photosynthesis. In the purple bacteriumRhodobacter(Rba.)sphaeroidesRC-LH1 is produced both as a monomer in which 14 LH1 subunits form a crescent-shaped antenna around one RC, and as a dimer, where 28 LH1 subunits form an S-shaped antenna surrounding two RCs. The PufX polypeptide augments the five RC and LH subunits, and in addition to providing an interface for dimerization, PufX also prevents LH1 ring closure, introducing a channel for quinone exchange that is essential for photoheterotrophic growth. Structures ofRba. sphaeroidesRC-LH1 complexes revealed several new components; protein-Y, which helps to form a quinone channel; protein-Z, of unknown function but which is unique to dimers; and a tightly bound sulfoquinovosyl diacylglycerol (SQDG) lipid that interacts with two PufX arginines. This lipid lies at the dimer interface alongside weak density for a second molecule, previously proposed to be an ornithine lipid. In this work we have generated strains ofRba. sphaeroideslacking protein-Y, protein-Z, SQDG or ornithine lipids to assess the roles of these previously unknown components in the assembly and activity of RC-LH1. We show that whilst the removal of either protein-Y, protein-Z or ornithine lipids has only subtle effects, SQDG is essential for the formation of RC-LH1 dimers but its absence has no functional effect on the monomeric complex.
Circular RNA Obelisk-S.sis highly abundant inStreptococcus sanguinisSK36
Authors: Maddamsetti Rohan , You Lingchong
Published: March 2024

A new class of viroid-like circular RNAs, called Obelisks, was recently reported by Zheludevet al.1. They identify a specific 1137 nt Obelisk, called Obelisk-S.s, in monoculture transcriptomes ofStreptococcus sanguinisSK36, a commensal bacterium of the human oral microbiome. Here, we report that Obelisk-S.s. is highly abundant in SK36, despite its absence from the SK36 genome (i.e., as DNA). In 11 out of 17 monoculture SK36 RNA-seq datasets examined, Obelisk-S.s. is more abundant than any mRNA. Given its abundance, we hypothesized that multiple Obelisk-S.svariants could coexist within SK36. We found three Obelisk-S.smutations at 5-10% allele frequency in some samples: a R162R synonymous mutation in one set of replicate transcriptomes, and an I48I synonymous mutation and an intergenic mutation in another set of replicate transcriptomes. A simple mathematical model shows how high Obelisk abundance can transiently stabilize intracellular Obelisk populations, and how extreme Obelisk abundances may stabilize intracellular Obelisk populations indefinitely. Evolution experiments with SK36 could test this theory and could shed light on how Obelisks function and evolve within their microbial hosts.
Elucidating Microbial Iron Corrosion Mechanisms with a Hydrogenase-Deficient Strain ofDesulfovibrio vulgaris
Authors: Wang Di , Ueki Toshiyuki , Ma Peiyu , Xu Dake , Lovley Derek R.
Published: March 2024

Sulfate-reducing microorganisms extensively contribute to the corrosion of ferrous metal infrastructure. There is substantial debate over their corrosion mechanisms. We investigated Fe0corrosion withDesulfovibrio vulgaris, the sulfate reducer most often employed in corrosion studies. Cultures were grown with both lactate and Fe0as potential electron donors to replicate the common environmental condition in which organic substrates help fuel the growth of corrosive microbes. Fe0was corroded in cultures of aD. vulgarishydrogenase-deficient mutant with the 1:1 correspondence between Fe0loss and H2accumulation expected for Fe0oxidation coupled to H+reduction to H2. This result and the extent of sulfate reduction indicated thatD. vulgariswas not capable of direct Fe0-to-microbe electron transfer even though it was provided with a supplementary energy source in the presence of abundant ferrous sulfide. Corrosion in the hydrogenase-deficient mutant cultures was greater than in sterile controls, demonstrating the H2removal was not necessary for the enhanced corrosion observed in the presence of microbes. The parental H2-consuming strain corroded more Fe0than the mutant strain, which could be attributed to H2oxidation coupled to sulfate reduction producing sulfide that further stimulated Fe0oxidation. The results suggest that H2consumption is not necessary for microbially enhanced corrosion, but H2oxidation can indirectly promote corrosion by increasing sulfide generation from sulfate reduction. The finding that,D. vulgariswas incapable of direct electron uptake from Fe0reaffirms that direct metal-to-microbe electron transfer has yet to be rigorously described in sulfate-reducing microbes.

Impact Statement

The economic impact of microbial corrosion of iron-containing metals is substantial. A better understanding of how microbes accelerate corrosion is expected to lead to the development of methods to prevent corrosion. The results presented here refute the suggestion, frequently made in the microbiology literature, that microbial H2uptake stimulates Fe0corrosion. Also refuted, are previous claims thatDesulfovibrio vulgarisis capable of directly extracting electrons from Fe0. The results are consistent with the concept that sulfide produced by sulfate-reducers promotes Fe0oxidation with the production of H2.The results illustrate that appropriate mutants can provide rigor to corrosion mechanism studies.
Weak entanglement improves quantum communication using only product measurements
Authors: Piveteau Amélie , Abbott Alastair A. , Muhammad Sadiq , Bourennane Mohamed , Tavakoli Armin
Published: March 2024

We show that weakly entangled states can improve communication over a qubit channel using only separate, interference-free, measurements of individual photons. We introduce a communication task corresponding to the cryptographic primitive known as secret sharing and show that all steerable two-qubit isotropic states provide a quantum advantage in the success rate using only product measurements. Furthermore, we show that such measurements can even reveal communication advantages from noisy partially entangled states that admit no quantum steering. We then go further and consider a stochastic variant of secret sharing based on more-sophisticated, yet standard, partial Bell-state analyzers, and show that this reveals advantages also for a range of unsteerable isotropic states. By preparing polarization qubits in unsteerable states, we experimentally demonstrate increased success rates of both secret-sharing tasks beyond the best entanglement-unassisted qubit protocol. Our results reveal the capability of simple and scalable measurements in entanglement-assisted quantum communication to overcome large amounts of noise.

Published by the American Physical Society
2024
Atomic excitation trapping in dissimilar chirally coupled atomic arrays
Authors: Handayana I Gusti Ngurah Yudi , Wu Chun-Chi , Goswami Sumit , Chen Ying-Cheng , Jen H. H.
Published: March 2024

An atomic array coupled to a one-dimensional nanophotonic waveguide allows photon-mediated dipole-dipole interactions and nonreciprocal decay channels. Such an array possesses many intriguing quantum phenomena due to its distinctive and emergent quantum correlations. In this atom-waveguide quantum system, we theoretically investigate the atomic excitation dynamics and its transport property, specifically at an interface of dissimilar atomic arrays with different interparticle distances. We find that the atomic excitation dynamics is highly dependent on the interparticle distances of dissimilar arrays and the directionality of nonreciprocal couplings. By tuning these parameters, a dominant excitation reflection can be achieved at the interface of the arrays in the single excitation case. We further study two effects on the transport property—of external drive and of single excitation delocalization over multiple atoms—where we manifest a rich interplay between multisite excitation and the relative phase in determining the transport properties. Finally, we present an intriguing trapping effect of atomic excitation by designing multiple zones of dissimilar arrays. Similar to the single excitations, multiple excitations are reflected from the array interfaces and trapped as well, although complete trapping of many excitations together is relatively challenging at long time due to a faster combined decay rate. Our results can provide insights into nonequilibrium quantum dynamics in dissimilar arrays, and they can shed light on confining and controlling quantum registers useful for quantum information processing.

Published by the American Physical Society
2024
Wait! What’s my job? Role ambiguity and role conflict as predictors of commitment among faculty
Authors: Homayed Assil , Karkoulian Silva , Srour F. Jordan
Published: March 2024

Purpose

Faculty play a unique role in universities performing duties along the three fronts of teaching, research and service. While it might be teaching that contributes most to the bottom line of a small university, it is often research by which faculty merit is judged. This study explores the relationships between role ambiguity, role conflict and commitment (affective, normative and continuance) as mediated by job satisfaction among faculty members.

Design/methodology/approach

A sample of 133 faculty members at a US-accredited university in Lebanon served as the basis for this study. The faculty members completed a survey covering scales on role ambiguity, role conflict, commitment and job satisfaction in addition to demographic variables.

Findings

We find that a decrease in role ambiguity strengthens affective and normative commitment but weakens continuance commitment. Structural equation modeling indicates that job satisfaction partially mediates the relationship between role ambiguity and affective commitment, while not mediating the relationship between role ambiguity and normative and continuance commitments. Similar findings hold for job satisfaction as a mediator in the relationship between role conflict and commitment.

Originality/value

Based on statistical modeling, this work (1) puts forth a revised scale for organizational commitment tailored to academia and (2) provides guidance to higher education institutions in terms of the differential impacts on faculty commitment that stem from reducing role-ambiguity versus role-conflict. Managerial recommendations focus on improving normative and affective commitment through the design of policies to reduce role conflict among faculty.
An international snapshot of peer leadership in higher education
Authors: Skalicky Jane , Speed Harriet , van der Meer Jacques , Young Dallin George
Published: March 2024

Purpose

This paper describes an exploratory, international research collaboration that seeks to gain a deeper understanding of the development and experiences of peer leaders in higher education across different international contexts, namely the USA, Canada (CAN), Australasia (Australia and New Zealand) (ANZ), the United Kingdom (UK) and South Africa (SA).

Design/methodology/approach

Data are summarized and compared across each of the participating countries, providing a more global context and depth of perspective on peer leadership (PL) in higher education than is currently available in the literature.

Findings

The findings highlight some apparent differences between countries in relation to student engagement in peer leader roles and the ways in which PL is supported by higher education institutions, as well as some similarities across the different international contexts, particularly in the way peer leaders view the benefits of their involvement in PL.

Originality/value

These insights provide a valuable addition to the literature on PL and practical information to higher education institutions for supporting student leadership development and involvement.
Explore before you restore: Incorporating complex systems thinking in ecosystem restoration
Authors: Maes S. L. , Perring M. P. , Cohen R. , Akinnifesi F. K. , Bargués‐Tobella A. , Bastin J.‐F. , Bauters M. , Bernardino P. N. , Brancalion P. H. S. , Bullock J. M. , Ellison D. , Fayolle A. , Fremout T. , Gann G. D. , Hishe H. , Holmgren M. , Ilstedt U. , Mahy G. , Messier C. , Parr C. L. , Ryan C. M. , Sacande M. , Sankaran M. , Scheffer M. S. , Suding K. N. , Van Meerbeek K. , Verbeeck H. , Verbist B. J. P. , Verheyen K. , Winowiecki L. A. , Muys B.
Published: March 2024

The global movement for ecosystem restoration has gained momentum in response to the Bonn Challenge (2010) and the UN Decade on Ecosystem Restoration (UNDER, 2021–2030). While several science‐based guidelines exist to aid in achieving successful restoration outcomes, significant variation remains in the outcomes of restoration projects. Some of this disparity can be attributed to unexpected responses of ecosystem components to planned interventions.

Given the complex nature of ecosystems, we propose that concepts from Complex Systems Science (CSS) that are linked to non‐linearity, such as regime shifts, ecological resilience and ecological feedbacks, should be employed to help explain this variation in restoration outcomes from an ecological perspective.

Our framework, Explore Before You Restore, illustrates how these concepts impact restoration outcomes by influencing degradation and recovery trajectories. Additionally, we propose incorporating CSS concepts into the typical restoration project cycle through a CSS assessment phase and suggest that the need for such assessment is explicitly included in the guidelines to improve restoration outcomes.

To facilitate this inclusion and make it workable by practitioners, we describe indicators and methods available for restoration teams to answer key questions that should make up such CSS assessment. In doing so, we identify key outstanding science and policy tasks that are needed to further operationalize CSS assessment in restoration.

Synthesis and applications. By illustrating how key Complex Systems Science (CSS) concepts linked to non‐linear threshold behaviour can impact restoration outcomes through influencing recovery trajectories, our framework Explore Before You Restore demonstrates the need to incorporate Complex Systems thinking in ecosystem restoration. We argue that inclusion of CSS assessment into restoration project cycles, and more broadly, into international restoration guidelines, may significantly improve restoration outcomes.
Natural streamflow reconstruction and quantification of hydrological drought in the Soan River basin, Pakistan
Authors: Laraib Muhammad , Iqbal Mudassar , Waseem Muhammad , Arshed Abu Bakar , Sultan Umar , Khan Hayat Ullah , Rahman Awais , Abbas Khawar , Shah Muhammad Ayub , Javaid Samra , Tariq Muhammad Atiq Ur Rehman
Published: March 2024

Climate change and rapid socioeconomic development have exacerbated the damage caused by hydrological droughts. To ensure effective drought defense and infrastructure development, it is essential to investigate variations in hydrological droughts. The primary objective of this study is to reconstruct the natural streamflow by using Soil and Water Assessment Tool (SWAT) hydrological modeling. The hydrological drought at different time scales (1, 3, 6, and 12 months) were measured using the streamflow drought index (SDI). The statistical parameters, including Nash–Sutcliffe Efficiency and the Coefficient of Determination, which yielded values of 0.84 and 0.82 during the calibration period and 0.78 and 0.76 during the validation period, respectively, showed a satisfactory SWAT model performance. Additionally, the Pettit test was used to identify a change point in streamflow within the 1991–2015 timeframe, leading to the division of the study period into two distinct phases: an undisturbed period (1991–1998) and a disturbed period (1999–2015). The SDI index‐based analysis revealed 9.39% moderate drought and 3.13% severe drought during the undisturbed period, while 11.76% moderate drought and 7.35% severe drought may happen due to the human influences that occurred in the disturbed period. These findings enhance the understanding of the hydrological drought variations in the Soan River basin for optimizing the water resources management system and effectively preventing and mitigating drought‐related damages.
Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial genomes
Authors: Zhang Xinyi , Chen Haimei , Ni Yang , Wu Bin , Li Jingling , Burzyński Artur , Liu Chang
Published: March 2024

Tools for visualizing genomes are essential for investigating genomic features and their interactions. Currently, tools designed originally for animal mitogenomes and plant plastomes are used to visualize the mitogens of plants but cannot accurately display features specific to plant mitogenomes, such as nonlinear exon arrangement for genes, the prevalence of functional noncoding features and complex chromosomal architecture. To address these problems, a software package, plant mitochondrial genome map (PMGmap), was developed using the Python programming language. PMGmap can draw genes at exon levels; draw cis‐ and trans‐splicing gene maps, noncoding features and repetitive sequences; and scale genic regions by using the scaling of the genic regions on the mitogenome (SAGM) algorithm. It can also draw multiple chromosomes simultaneously. Compared with other state‐of‐the‐art tools, PMGmap showed better performance in visualizing 405 plant mitogenomes, showing potential as an invaluable tool for plant mitogenome research. The web and container versions and the source code of PMGmap can be accessed through the following link: http://www.1kmpg.cn/pmgmap.
Prolonged duration of action of suxamethonium in pregnant and postpartum patients: A registry study
Authors: Dalsten Helene , Crone Vera , Steinmetz Jacob , Rosager Christine L. , Rasmussen Lars S. , Vested Matias
Published: March 2024

Background

Suxamethonium is hydrolysed by butyrylcholinesterase (BChE) and a low BChE activity can result in a prolonged duration of action of suxamethonium. The BChE activity is reduced during pregnancy and postpartum period by up to 33%. However, it can also be reduced by mutations in the BChE gene. In this study, we assessed BChE activity and mutations in the BChE gene in pregnant and postpartum patients with prolonged duration of action of suxamethonium. It was hypothesised that at least 30% of patients with a low BChE activity did not have a mutation in the BChE gene.

Methods

In this registry study we focused on pregnant and postpartum patients with a history of prolonged duration of action of suxamethonium referred to the Danish Cholinesterase Research Unit (DCRU) between March 2007 and January 2023. Primary outcome was the proportion of patients without a mutation among patients with a low BChE activity. Secondary outcomes were the proportion of patients with a low BChE activity and the proportion of patients with a mutation out of the total number of patients.

Results

A total of 40 patients were included and among patients with a low BChE activity, 6% (95% CI: 1%–21%) did not have a mutation. Out of the total number of included patients referred to the DCRU, 90% (95% CI: 76%–97%) had a mutation and 94% (95% CI: 80%–99%) had a low BChE activity.

Conclusion

Among pregnant and postpartum patients with a history of prolonged duration of action of suxamethonium and a low BChE activity, 6% did not have a mutation in the BChE gene.

Our findings suggest that during pregnancy and postpartum clinically relevant prolonged duration of action of suxamethonium rarely occurs in genotypically normal patients.
Comments of the AFAANZ Auditing and Assurance Standards Committee on Proposed International Standard on Auditing 570 (Revised) Going Concern
Authors: Harding Noel , Hay David C. , Dharmasiri Prabashi , Fu Yi (Dale) , Grosse Matthew , Khan Mohammad Jahanzeb , Scott Tom
Published: March 2024

The International Auditing and Assurance Standards Board (IAASB) issued for public comment Proposed International Standard on Auditing 570 (Revised) Going Concern. The Australian Auditing and Assurance Standards Board (AUASB) and New Zealand Auditing and Assurance Standards Board (NZAuASB) also called for comments. The Auditing and Assurance Standards Committee of AFAANZ prepared a submission, based on the findings reported in extant research, informing a number of the questions asked by the IAASB. This technical note presents the formal submission made to the IAASB.
Cadaver preservative properties of a solution composed of honey, ethyl alcohol, liquid paraffin, distilled water and citric acid: Experiments on rabbit cadavers
Authors: Demiraslan Yasin , Gürbüz İftar , Özbek Mehmet , Şahan Yapicier Özlem , Karaca Harun , Özgel Özcan , Öner Hakan
Published: March 2024

The objective of this study is to assess the efficacy of a solution including honey, ethyl alcohol, liquid paraffin, distilled water and citric acid (HEFS) as a preservative for rabbit cadavers, serving as a potential substitute for formaldehyde. The cadavers underwent preservation using three distinct solutions: 10% formalin, 35% alcohol and HEFS. The cadavers were subjected to a total of four sampling events, occurring at 4‐month intervals, in order to collect specimens for microanatomical, histological, microbiological, mycological, colourimetric, texture and odour analysis. In terms of hardness, suitability for dissection and joint mobility metrics, the cadavers fixed with HEFS had superior qualities to those fixed with formalin. The fixation quality of HEFS for histological analyses was deemed acceptable, except kidney and intestinal tissues. In texture analysis, differences only in the elasticity parameter (p < 0.05) in the same sampling period. A total of 10 (13.9) bacteria isolates were identified among which, Metasolibacillus meyeri 3 (30%) was predominantly followed by Staphylococcus aureus 2 (20%), Bacillus siamensis, Bacillus subtilis, Pseudarthrobacter oxydans, Bacillus licheniformis, Bacillus subtilis subsp. subtilis with a proportion of 1 (10%), respectively, by both microbiological and molecular analysis. However, no anaerobic bacteria and fungi were isolated. A considerable percentage of the students had the perception that HEFS was appropriate for utilization in laboratory settings due to its absence of unpleasant odours and detrimental impact on ocular and respiratory functions. In conclusion, we consider that HEFS may serve as a viable substitute for formalin solution in the preservation of rabbit cadavers.
Review article: Recent advances in ascites and acute kidney injury management in cirrhosis
Authors: Adebayo Danielle , Wong Florence
Published: March 2024

Background

Better understanding of disease pathophysiology has led to advances in managing ascites and its associated complications including hepatorenal syndrome‐acute kidney Injury (HRS‐AKI), especially medicinal and interventional advances.

Aim

To review the latest changes in the management of ascites and HRS‐AKI.

Methods

A literature search was conducted in Pubmed, using the keywords cirrhosis, ascites, renal dysfunction, acute kidney injury, hepatorenal syndrome, beta‐blockers, albumin, TIPS and vasoconstrictors, including only publications in English.

Results

The medicinal advances include earlier treatment of clinically significant portal hypertension to delay the onset of ascites and the use of human albumin solution to attenuate systemic inflammation thus improving the haemodynamic changes associated with cirrhosis. Furthermore, new classes of drugs such as sodium glucose co‐transporter 2 are being investigated for use in patients with cirrhosis and ascites. For HRS‐AKI management, newer pharmacological agents such as vasopressin partial agonists and relaxin are being studied. Interventional advances include the refinement of TIPS technique and patient selection to improve outcomes in patients with refractory ascites. The development of the alfa pump system and the study of outcomes associated with the use of long‐term palliative abdominal drain will also serve to improve the quality of life in patients with refractory ascites.

Conclusions

New treatment strategies emerged from better understanding of the pathophysiology of ascites and HRS‐AKI have shown improved prognosis in these patients. The future will see many of these approaches confirmed in large multi‐centre clinical trials with the aim to benefit the patients with ascites and HRS‐AKI.
Does the proliferation of smartphones reduce consumer search costs? The case of the Korean gasoline market
Authors: Choi Bongseok , Kim Donghun
Published: March 2024

This study treats the introduction of smartphones and access to the Korean gasoline market as a natural experiment, investigating how they affect consumer search costs. We estimate consumer search costs in different regional districts in Seoul and examine how smartphone proliferation affects search costs. Our findings indicate that the widespread use of smartphones reduced consumer search costs, and this reduction was more significant in districts with higher competition across firms. We can also infer that reduced search costs narrowed the market's dispersion of prices and markups.
Intergenerational consequences of racism in the United Kingdom: a qualitative investigation into parents' exposure to racism and offspring mental health and well‐being
Authors: Simela Carl , Akanbi‐Akinlolu Tolúwalàse , Okundi Malaika , Abdalla Hannah , McAdams Tom A. , Harris Androulla , Augustine Alex , Le Huong , Abdinasir Kadra , Ayorech Ziada , Ahmadzadeh Yasmin I.
Published: March 2024

Background

Experiences of racism are linked to negative physical and mental health outcomes among those exposed. According to quantitative research derived mainly from the United States, these negative outcomes can have cascading effects in families, when parents' experiences of racism indirectly impact offspring. New research is warranted for families in the United Kingdom, informed by a qualitative approach to canvassing community knowledge and perspectives, exploring how existing findings relate to lived experiences.

Method

We conducted four online focus groups with 14 parents of school‐aged children and 14 adolescents who had experienced racism in the United Kingdom. Participants were asked what children know of parents' experiences of racism, and how these experiences can impact parent–child interactions, mental health and well‐being. Focus group recordings were transcribed, data coded and analysed through iterative categorisation.

Results

Analyses drew four themes from participants' insights. Together, themes illuminated the pervasive nature of racism experienced by some families in the United Kingdom. Parent and child experiences of racism were connected and co‐occurring, with indirect effects impacting mental health and well‐being in both generations. These experiences were linked to both positive and negative changes in parenting behaviour and parent–child relationships, which could be moderated by intersecting identities such as the parent's generational status for immigration to the United Kingdom. Social cohesion, safe spaces and education programmes were highlighted for future intervention.

Conclusions

Findings corroborate existing literature, while further emphasising a broader bidirectional picture, requiring a family system and intersectional approach to understanding the mental health impact of racism in families. Avenues for future research are discussed to support development of equitable intervention and support strategies to prevent racism and support those affected.