bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of COVID-19 Vaccines: A Vaccinated-Only Approach
Authors: Foppa Ivo M. 
Published: March 2024

AbstractWe 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.PACS0000, 1111MSC0000, 1111Graphical AbstractHighlightsWe 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

AbstractThe 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

AbstractThe 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

AbstractA 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

AbstractSulfate-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 StatementThe 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.
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

PurposeFaculty 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/approachA 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.FindingsWe 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/valueBased 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

PurposeThis 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/approachData 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.FindingsThe 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/valueThese 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

Abstract

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

AbstractClimate 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

AbstractTools 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

AbstractBackgroundSuxamethonium 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.MethodsIn 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.ResultsA 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.ConclusionAmong 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

AbstractThe 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

AbstractThe 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.