bluuebunny/crossref_metadata_2025_split huggingface dataset:
A proteomic analysis of atrial fibrillation in a prospective longitudinal cohort (AGES-Reykjavik study)
Authors: Jonmundsson Thorarinn , Steindorsdottir Anna E , Austin Thomas R , Frick Elisabet A , Axelsson Gisli T , Launer Lenore , Psaty Bruce M , Loureiro Joseph , Orth Anthony P , Aspelund Thor , Emilsson Valur , Floyd James S , Jennings Lori , Gudnason Vilmundur , Gudmundsdottir Valborg 
Published: November 2023

Abstract

Aims
Atrial fibrillation (AF) is associated with high risk of comorbidities and mortality. Our aim was to examine causal and predictive relationships between 4137 serum proteins and incident AF in the prospective population-based Age, Gene/Environment Susceptibility-Reykjavik (AGES-Reykjavik) study.

Methods and results
The study included 4765 participants, of whom 1172 developed AF. Cox proportional hazards regression models were fitted for 4137 baseline protein measurements adjusting for known risk factors. Protein associations were tested for replication in the Cardiovascular Health Study (CHS). Causal relationships were examined in a bidirectional, two-sample Mendelian randomization analysis. The time-dependent area under the receiver operating characteristic curve (AUC)-statistic was examined as protein levels and an AF-polygenic risk score (PRS) were added to clinical risk models. The proteomic signature of incident AF consisted of 76 proteins, of which 63 (83%) were novel and 29 (38%) were replicated in CHS. The signature included both N-terminal prohormone of brain natriuretic peptide (NT-proBNP)-dependent (e.g. CHST15, ATP1B1, and SVEP1) and independent components (e.g. ASPN, AKR1B, and LAMA1/LAMB1/LAMC1). Nine causal candidates were identified (TAGLN, WARS, CHST15, CHMP3, COL15A1, DUSP13, MANBA, QSOX2, and SRL). The reverse causal analysis suggested that most AF-associated proteins were affected by the genetic liability to AF. N-terminal prohormone of brain natriuretic peptide improved the prediction of incident AF events close to baseline with further improvements gained by the AF-PRS at all time points.

Conclusion
The AF proteomic signature includes biologically relevant proteins, some of which may be causal. It mainly reflects an NT-proBNP-dependent consequence of the genetic liability to AF. N-terminal prohormone of brain natriuretic peptide is a promising marker for incident AF in the short term, but risk assessment incorporating a PRS may improve long-term risk assessment.
How do adolescents experience the decision-making process on travel mode choice?
Authors: Renninger Denise , Reimers Anne K , Marzi Isabel , Beck Franziska , Krieger Claus , Demetriou Yolanda 
Published: November 2023

Abstract
Active travel can contribute to multiple health benefits in youth. Previous research has identified several factors influencing travel behavior. This study investigates how adolescents process these factors during their decision-making process on travel mode choice. Semi-structured interviews were conducted with 13 adolescents (11–14 years) and analysed using deductive–inductive thematic analysis. Four themes were generated from which the decision-making process on mode choice was conceptualized according to adolescents. The step-by-step process in which travel mode options were gradually reduced, was dependent on the context (Theme 1), the perceived availability of travel mode choice options, which was influenced by factors beyond the individual’s perceived control (Theme 2), and on adolescents’ pros/cons assessment to identify the most convenient option. Adolescents’ habitually used travel mode influenced the decision at several stages throughout the process (Theme 4). To promote healthy travel behaviors, interventions should consider contextual circumstances, balance between enabling autonomous choices and promoting advantages of active travel modes, address individual travel modes and include practices that foster conscious processing of decision-making.
Diverse O-methyltransferases catalyze the biosynthesis of floral benzenoids that repel aphids from the flowers of waterlily Nymphaea prolifera
Authors: Liu Guanhua , Fu Jianyu , Wang Lingyun , Fang Mingya , Zhang Wanbo , Yang Mei , Yang Xuemin , Xu Yingchun , Shi Lin , Ma Xiaoying , Wang Qian , Chen Hui , Yu Cuiwei , Yu Dongbei , Chen Feng , Jiang Yifan 
Published: November 2023

Abstract
Nymphaea is a key genus of the ANA grade (Amborellales, Nymphaeales, and Austrobaileyales) of basal flowering plants, which serve as a key model to study the early evolution of floral traits. In this study, we comprehensively investigated the emission, biosynthesis, and biological function of the floral scent in a night-blossoming waterlily Nymphaea prolifera. The headspace volatile collection combined with GC–MS analysis showed that the floral scent of N. prolifera is predominately comprised by methylated benzenoids including anisole, veratrole, guaiacol, and methoxyanisole. Moreover, the emission of these floral benzenoids in N. prolifera exhibited temporal and spatial pattern with circadian rhythm and tissue specificity. By creating and mining transcriptomes of N. prolifera flowers, 12 oxygen methyltransferases (NpOMTs) were functionally identified. By in vitro enzymatic assay, NpOMT3, 6, and 7 could produce anisole and NpOMT5, 7, 9, produce guaiacol, whereas NpOMT3, 6, 9, 11 catalyzed the formation of veratrole. Methoxyanisole was identified as the universal product of all NpOMTs. Expression patterns of NpOMTs provided implication for their roles in the production of the respective benzenoids. Phylogenetic analysis of OMTs suggested a Nymphaea-specific expansion of the OMT family, indicating the evolution of lineage-specific functions. In bioassays, anisole, veratrole, and guaiacol in the floral benzenoids were revealed to play the critical role in repelling waterlily aphids. Overall, this study indicates that the basal flowering plant N. prolifera has evolved a diversity and complexity of OMT genes for the biosynthesis of methylated benzenoids that can repel insects from feeding the flowers. These findings provide new insights into the evolutional mechanism and ecological significance of the floral scent from early-diverged flowering plants.
Do the attitudes and practices of Australian pharmacists reflect a need for education and training to provide care for people who are transgender?
Authors: Chaudhary Swapna , Lindsay Daniel , Ray Robin , Glass Beverley D 
Published: November 2023

Abstract

Background
Many transgender and gender diverse (TGD) people access care through community pharmacy in Australia. However, there is limited information available about the role of Australian pharmacists in providing care for TGD people.

Objective
To explore the attitudes, practices, and training needs of pharmacists in the provision of care for TGD people in Australia.

Method
Pharmacists Australia-wide were invited to participate in an online survey through Facebook, e-newsletters of pharmacy organizations and a professional pharmacy journal. Quantitative data were analysed for descriptive and inferential statistics. A Fisher exact test was used to investigate associations between two variables. Results with P value &lt;0.05 were considered statistically significant. Content analysis was used to analyse data from free-text responses.

Result
Of the 169 respondents, the majority were female (75.1%), aged below 40 years (74%) and with less than 10 years of working experience as a pharmacist (58%). Although 95% of the sample agreed that they had an important role in the provision of care for TGD people, only 29.6% were confident about their knowledge of pharmacotherapeutic treatments for gender affirmation. Only 2.4% had received education about TGD care at university, and only 5.3% received any TGD healthcare training over the past 5 years.

Conclusion
Although pharmacists had a positive attitude and recognized their role in TGD care, they expressed a lack of confidence in their knowledge to be a barrier to providing quality care. Most recommended the need for more education about TGD healthcare in pharmacy curricula and continuous professional education activities.
Effects of vaccination on the two-strain transmission dynamics of COVID-19: Dougherty County, Georgia, USA, as a case study
Authors: Pantha Buddhi , Mohammed-Awel Jemal , Vaidya Naveen K 
Published: November 2023

Abstract
The emergence of multiple strains of SARS-COV-2 has made it complicated to predict and control the COVID-19 pandemic. Although some vaccines have been effective in reducing the severity of the disease, these vaccines are designed for a specific strain of the virus and are usually less effective for other strains. In addition, the waning of vaccine-induced immunity, reinfection of recovered people, and incomplete vaccination are challenging to the vaccination program. In this study, we developed a detailed model to describe the multi-strain transmission dynamics of COVID-19 under vaccination. We implemented our model to examine the impact of inter-strain transmission competition under vaccination on the critical outbreak indicators: hospitalized cases, undiagnosed cases, basic reproduction numbers, and the overtake-time by a new strain to the existing strain. In particular, our results on the dependence of the overtake-time on vaccination rates, progression-to-infectious rate, and relative transmission rates provide helpful information for managing a pandemic with circulating two strains. Furthermore, our results suggest that a reduction in the relative transmission rates and a decrease in vaccination dropout rates or an increase in vaccination rates help keep the reproduction number of both strains below unity and keep the number of hospitalized cases and undiagnosed cases at their lowest levels. Moreover, our analysis shows that the second and booster-dose vaccinations are useful for further reducing the reproduction number.
Streptococcus suis Serotype 2 Type IV Secretion Effector SspA-1 Induces Proinflammatory Cytokine Production via TLR2 Endosomal and Type I Interferon Signaling
Authors: Yin Supeng , Yuan Mengmeng , Zhang Sirui , Chen Hongdan , Zhou Jing , He Tongyu , Li Gang , Yu Yanlan , Zhang Fan , Li Ming , Zhao Yan 
Published: November 2023

Abstract
The subtilisin-like protease-1 (SspA-1) plays an important role in the pathogenesis of a highly virulent strain of Streptococcus suis 2. However, the mechanism of SspA-1–triggered excessive inflammatory response is still unknown. In this study, we demonstrated that activation of type I IFN signaling is required for SspA-1–induced excessive proinflammatory cytokine production. Further experiments showed that the TLR2 endosomal pathway mediates SspA-1–induced type I IFN signaling and the inflammatory response. Finally, we mapped the major signaling components of the related pathway and found that the TIR adaptor proteins Mal, TRAM, and MyD88 and the downstream activation of IRF1 and IRF7 were involved in this pathway. These results explain the molecular mechanism by which SspA-1 triggers an excessive inflammatory response and reveal a novel effect of type I IFN in S. suis 2 infection, possibly providing further insights into the pathogenesis of this highly virulent S. suis 2 strain.
Climate Change and Violent Conflict in the Middle East and North Africa
Authors: Kim Kyungmee , Garcia Tània Ferré 
Published: November 2023

Abstract
Previous research has demonstrated that climate change can escalate the risks for violent conflict through various pathways. Existing evidence suggests that contextual factors, such as migration and livelihood options, governance arrangements, and existing conflict dynamics, can influence the pathways through which climate change leads to conflict. This important insight leads to an inquiry to identify sets of conditions and processes that make climate-related violent conflict more likely. In this analytic essay, we conduct a systematic review of scholarly literature published during the period 1989–2022 and explore the climate-conflict pathways in the Middle East and North Africa (MENA) region. Through the systematic review of forty-one peer-reviewed publications in English, we identify that society’s ability to cope with the changing climate and extreme weather events is influenced by a range of factors, including preceding government policies that led to the mismanagement of land and water and existing conflict dynamics in the MENA region. Empirical research to unpack the complex and diverse relationship between the climate shocks and violent conflict in the MENA region needs advancing. Several avenues for future research are highlighted such as more studies on North Africa and the Gulf region, with focus on the implications of floods and heatwaves, and exploring climate implications on non-agriculture sectors including the critical oil sector.
Emergence of a novel ISS1N-optrA-carrying transposon within an integrative and conjugative element from Streptococcus parasuis
Authors: Dai Xingyang , Sun Junjie , Zhao Wenbin , Wang Jianzhong , Zhang Xiaohui , Liu Xiao , Li Aijuan , Zhao Jiaqi , Han Peizhao , Wang Xiaoming , Wang Liping , Huang Jinhu 
Published: November 2023

Abstract

Objectives
To investigate the genetic context and transferability of the oxazolidinone resistance gene optrA in a Streptococcus parasuis isolate.

Methods
The optrA-carrying S. parasuis isolate SFJ45 was characterized by PCR, antimicrobial susceptibility testing, complete genome sequencing and bioinformatic analysis. The transferability of optrA was verified by conjugation, followed by SmaI-PFGE and Southern blotting.

Results
The S. parasuis isolate SFJ45 was positive for optrA, mef(A), msr(D), erm(B), tetAB(P)′, tet(M), aadE, aphA3, catQ, dfrG and mdt(A), conferring an MDR phenotype. The optrA gene was flanked by ISS1N at both termini in the same orientation, representing a novel 8750 bp pseudo-compound transposon, organized as the ISS1N-hth-clb-4hp-optrA-2hp-ISS1N structure. The ISS1N-optrA-carrying transposon was further inserted within an integrative and conjugative element, ICESpsuSFJ45, at 3′ end of the fda gene. Conjugative transfer of the ISS1N-optrA-carrying transposon with ICESpsuSFJ45 was observed from S. parasuis to Streptococcus suis at a frequency of (1.01 ± 3.12) × 10−7.

Conclusions
ISS1N was found to be associated with optrA spreading for the first time. Integration of the ISS1N-optrA transposon within ICESpsuSFJ45 may lead to the co-selection of optrA with other antimicrobial resistance genes, contributing to its horizontal transfer from S. parasuis to clinically more important bacterial pathogens.
A proteomic perspective on the resistance response of Klebsiella pneumoniae to antimicrobial peptide PaDBS1R1
Authors: Fleitas Osmel , Fontes Wagner , De Souza Camila M , Da Costa Mylena C , Cardoso Marlon H , Castro Mariana S , Sousa Marcelo V , Ricart Carlos A O , Ramada Marcelo H S , Duque Harry M , Porto William F , Silva Osmar N , Franco Octávio L 
Published: November 2023

Abstract

Background
The synthetic antimicrobial peptide, PaDBS1R1, has been reported as a powerful anti-Klebsiella pneumoniae antimicrobial. However, there is only scarce knowledge about whether K. pneumoniae could develop resistance against PaDBS1R1 and which resistance mechanisms could be involved.

Objectives
Identify via label-free shotgun proteomics the K. pneumoniae resistance mechanisms developed against PaDBS1R1.

Methods
An adaptive laboratory evolution experiment was performed to obtain a PaDBS1R1-resistant K. pneumoniae lineage. Antimicrobial susceptibility was determined through microdilution assay. Modifications in protein abundances between the resistant and sensitive lineages were measured via label-free quantitative shotgun proteomics. Enriched Gene Ontology terms and KEGG pathways were identified through over-representation analysis. Data are available via ProteomeXchange with identifier PXD033020.

Results
K. pneumoniae ATCC 13883 parental strain challenged with increased subinhibitory PaDBS1R1 concentrations allowed the PaDBS1R1-resistant K. pneumoniae lineage to emerge. Proteome comparisons between PaDBS1R1-resistant K. pneumoniae and PaDBS1R1-sensitive K. pneumoniae under PaDBS1R1-induced stress conditions enabled the identification and quantification of 1702 proteins, out of which 201 were differentially abundant proteins (DAPs). The profiled DAPs comprised 103 up-regulated proteins (adjusted P value &lt; 0.05, fold change ≥ 2) and 98 down-regulated proteins (adjusted P value &lt; 0.05, fold change ≤ 0.5). The enrichment analysis suggests that PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery could be relevant resistance mechanisms against PaDBS1R1.

Conclusions
Based on experimental evolution and a label-free quantitative shotgun proteomic approach, we showed that K. pneumoniae developed resistance against PaDBS1R1, whereas PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery appear to be relevant resistance mechanisms against PaDBS1R1.
Glycoside hydrolase family 32 enzymes from Bombella spp. catalyze the formation of high-molecular weight fructans from sucrose
Authors: Härer Luca , Ernst Luise , Bechtner Julia , Wefers Daniel , Ehrmann Matthias A 
Published: November 2023

Abstract

Aims
Acetic acid bacteria of the genus Bombella have not been reported to produce exopolysaccharides (EPS). In this study, the formation of fructans by B. apis TMW 2.1884 and B. mellum TMW 2.1889 was investigated.

Methods and Results
Out of eight strains from four different Bombella species, only B. apis TMW 2.1884 and B. mellum TMW 2.1889 showed EPS formation with 50 g l−1 sucrose as substrate. Both EPS were identified as high-molecular weight (HMW) polymers (106–107 Da) by asymmetric flow field-flow fractionation coupled to multi angle laser light scattering and UV detecors (AF4-MALLS/UV) and high performance size exclusion chromatography coupled to MALLS and refractive index detectors (HPSEC-MALLS/RI) analyses. Monosaccharide analysis via trifluoroacetic acid hydrolysis showed that both EPS are fructans. Determination of glycosidic linkages by methylation analysis revealed mainly 2,6-linked fructofuranose (Fruf) units with additional 2,1-linked Fruf units (10%) and 2,1,6-Fruf branched units (7%). No glycoside hydrolase (GH) 68 family genes that are typically associated with the formation of HMW fructans in bacteria could be identified in the genomes. Through heterologous expression in Escherichia coli Top10, an enzyme of the GH32 family could be assigned to the catalysis of fructan formation. The identified fructosyltransferases could be clearly differentiated phylogenetically and structurally from other previously described bacterial fructosyltransferases.

Conclusions
The formation of HMW fructans by individual strains of the genus Bombella is catalyzed by enzymes of the GH32 family. Analysis of the fructans revealed an atypical structure consisting of 2,6-linked Fruf units as well as 2,1-linked Fruf units and 2,1,6-Fruf units.
Systematic review and longitudinal analysis of implementing Artificial Intelligence to predict clinical deterioration in adult hospitals: what is known and what remains uncertain
Authors: van der Vegt Anton H , Campbell Victoria , Mitchell Imogen , Malycha James , Simpson Joanna , Flenady Tracy , Flabouris Arthas , Lane Paul J , Mehta Naitik , Kalke Vikrant R , Decoyna Jovie A , Es’haghi Nicholas , Liu Chun-Huei , Scott Ian A 
Published: November 2023

AbstractObjectiveTo identify factors influencing implementation of machine learning algorithms (MLAs) that predict clinical deterioration in hospitalized adult patients and relate these to a validated implementation framework.Materials and methodsA systematic review of studies of implemented or trialed real-time clinical deterioration prediction MLAs was undertaken, which identified: how MLA implementation was measured; impact of MLAs on clinical processes and patient outcomes; and barriers, enablers and uncertainties within the implementation process. Review findings were then mapped to the SALIENT end-to-end implementation framework to identify the implementation stages at which these factors applied.ResultsThirty-seven articles relating to 14 groups of MLAs were identified, each trialing or implementing a bespoke algorithm. One hundred and seven distinct implementation evaluation metrics were identified. Four groups reported decreased hospital mortality, 1 significantly. We identified 24 barriers, 40 enablers, and 14 uncertainties and mapped these to the 5 stages of the SALIENT implementation framework.DiscussionAlgorithm performance across implementation stages decreased between in silico and trial stages. Silent plus pilot trial inclusion was associated with decreased mortality, as was the use of logistic regression algorithms that used less than 39 variables. Mitigation of alert fatigue via alert suppression and threshold configuration was commonly employed across groups.Conclusions: There is evidence that real-world implementation of clinical deterioration prediction MLAs may improve clinical outcomes. Various factors identified as influencing success or failure of implementation can be mapped to different stages of implementation, thereby providing useful and practical guidance for implementers.
Implementation and evaluation of an electronic health record-integrated app for postpartum monitoring of hypertensive disorders of pregnancy using patient-contributed data collection
Authors: Dullabh Prashila , Heaney-Huls Krysta K , Chiao Andrew B , Callaham Melissa G , Desai Priyanka , Gauthreaux Nicole A , Kashyap Nitu , Lobach David F , Boxwala Aziz 
Published: November 2023

Abstract
Remote monitoring of women experiencing hypertensive disorders of pregnancy (HDP) can provide timely life-saving data, particularly if these data are integrated into existing patient and clinical workflows. This pilot intervention of a smartphone application (app) for postpartum monitoring of hypertensive disorders integrates patient-contributed data into electronic health records (EHRs) to support monitoring and clinical decision-making. Results from the evaluation of the pilot highlight the resources needed when implementing the app, challenges for integrating an app into the EHR, and the usability and utility of the HDP monitoring app for patient and clinician users. The implementation team’s key observations included the importance of a local clinical champion, more robust patient involvement and support for the remote patient monitoring program, an impetus for EHR developers to adopt data integration standards, and a need to expand the capabilities of the standards to support interventions using patient-contributed data.
The Largest Subunit of Human TFIIIC Complex, TFIIIC220, a Lysine Acetyltransferase Targets Histone H3K18
Authors: Basu Moumita , Bhatt Rohini , Sharma Anjali , Boopathi Ramachandran , Das Sadhan , Kundu Tapas K 
Published: November 2023

Abstract
TFIIIC is a multi-subunit complex required for tRNA transcription by RNA polymerase III. Human TFIIIC holo-complex possesses lysine acetyltransferase activity that aids in relieving chromatin-mediated repression for RNA polymerase III-mediated transcription and chromatin assembly. Here we have characterized the acetyltransferase activity of the largest and DNA-binding subunit of TFIIIC complex, TFIIIC220. Purified recombinant human TFIIIC220 acetylated core histones H3, H4 and H2A in vitro. Moreover, we have identified the putative catalytic domain of TFIIIC220 that efficiently acetylates core histones in vitro. Mutating critical residues of the putative acetyl-CoA binding ‘P loop’ drastically reduced the catalytic activity of the acetyltransferase domain. Further analysis showed that the knockdown of TFIIIC220 in mammalian cell lines dramatically reduces global H3K18 acetylation level, which was rescued by overexpression of the putative acetyltransferase domain of human TFIIIC220. Our findings indicated a possibility of a crucial role for TFIIIC220 in maintaining acetylation homeostasis in the cell.