bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tetracycline resistance in
Listeria monocytogenes
and
L. innocua
from wild black bears (
Ursus americanus
) in the United States is mediated by novel transposable elements
Authors: Brown Phillip , Hernandez Kevin , Parsons Cameron , Chen Yi , Gould Nicholas , DePerno Christopher S. , Niedermeyer Jeffrey , Kathariou Sophia 
Published: October 2023

ABSTRACT

Listeria monocytogenes
is a facultative intracellular foodborne pathogen and the causative agent of the severe disease listeriosis. It is found ubiquitously in the environment and exhibits innate resistance to certain antimicrobials, but acquired antimicrobial resistance remains relatively uncommon. Given the potentially dire health outcomes associated with listeriosis, acquisition of antimicrobial resistance (AMR) by this pathogen is of considerable public health concern. AMR in
L. monocytogenes
has been surveyed frequently in strains of clinical and food origin, but much less commonly in wildlife. We analyzed 158 strains of
L. monocytogenes
and 27 of non-pathogenic
Listeria
spp. isolated from wild black bears (
Ursus americanus
) for resistance to a panel of antimicrobials. AMR was uncommon and noted mostly for tetracycline. Tetracycline resistance was more common in
Listeria innocua
than in
L. monocytogenes
. All tetracycline-resistant
L. monocytogenes
strains belonged to sequence type ST1039 and harbored the Tn
916
-like
tet
(M) transposon Tn
916.1039
in a conserved chromosomal location. In contrast, three different tetracycline resistance elements, i.e., the
tet
(M) elements Tn
5801.UAM
and Tn
5801.551
and the
tet
(S) element Tn
6000.205
, were identified among tetracycline-resistant strains of
L. innocua
. The greater prevalence and diversity of tetracycline resistance elements among bear-derived non-pathogenic
Listeria
strains suggest the potential of the latter to serve as reservoirs for retention and diversification of AMR determinants in this wildlife host and warrant their further monitoring and study.

IMPORTANCE

Listeria monocytogenes
causes severe foodborne illness and is the only human pathogen in the genus
Listeria
. Previous surveys of AMR in
Listeria
focused on clinical sources and food or food processing environments, with AMR in strains from wildlife and other natural ecosystems remaining under-explored. We analyzed 185 sequenced strains from wild black bears (
Ursus americanus
) from the United States, including 158 and 27
L
.
monocytogenes
and
L. innocua
, respectively. Tetracycline resistance was the most prevalent resistance trait. In
L
. monocytogenes, it was encountered exclusively in serotype 4b strains with the novel Tn
916
-like element Tn
916.1039
. In contrast, three distinct, novel tetracycline resistance elements (Tn
5801.UAM
,
Tn5801.551
, and Tn
6000.205
) were identified in
L. innocua
. Interestingly,
Tn5801.551
was identical to elements in
L. monocytogenes
from a major foodborne outbreak in the United States in 2011. The findings suggest the importance of wildlife and non-pathogenic
Listeria
species as reservoir for resistance elements in
Listeria
.
Recombinant outer membrane vesicles delivering eukaryotic expression plasmid of cytokines act as enhanced adjuvants against
Helicobacter pylori
infection in mice
Authors: Liu Qiong , Li Biaoxian , Lu Jiahui , Zhang Yejia , Shang Yinpan , Li Yi , Gong Tian , Zhang Chengsheng 
Published: October 2023

ABSTRACT

The widespread prevalence of
Helicobacter pylori
(
H. pylori
) infection remains a great challenge to human health. The existing vaccines are not ideal for preventing
H. pylori
infection; thus, exploring highly effective adjuvants may improve the immunoprotective efficacy of
H. pylori
vaccines. In a previous study, we found that the outer membrane vesicles (OMVs), a type of nanoscale particle spontaneously produced by Gram-negative bacteria, could act as adjuvants to boost the immune responses to vaccine antigens. In this study, we explored the potential application of OMVs as delivery vectors for adjuvant development. We constructed recombinant OMVs containing eukaryotic expression plasmid of cytokines, including interleukin 17A or interferon-γ, and evaluated their function as adjuvants in combination with inactivated whole-cell vaccine (WCV) or UreB as vaccine antigens. Our results showed that recombinant OMVs as adjuvants could induce stronger humoral and mucosal immune responses in mice than wild-type
H. pylori
OMVs and the cholera toxin (CT) adjuvant. Additionally, the recombinant OMVs significantly promoted Th1/Th2/Th17-type immune responses. Furthermore, the recombinant OMV adjuvant induced more potent clearance of
H. pylori
than CT and wild-type OMVs. Our findings suggest that the recombinant OMVs coupled with cytokines may become potent adjuvants for the development of novel and effective vaccines against
H. pylori
infection.
Long-term outcomes of deep anterior lamellar versus penetrating keratoplasty for keratoconus
Authors: Borderie Vincent Michel , Georgeon Cristina , Sandali Otman , Bouheraoua N 
Published: October 2023

AimsTo compare the long-term outcomes of deep anterior lamellar keratoplasty (DALK) with penetrating keratoplasty (PK) in keratoconus.MethodsRetrospective comparative case series (228 DALKs and 274 PKs). A biphasic linear model was used to describe the postoperative outcome of the endothelial cell density (ECD). Visual acuity, specular microscopy, corneal topography and optical coherence tomography findings were recorded.ResultsGraft survival of the 502 keratoconus eyes was 96.7 at 10 years and 95.6% at 20 years. Visual acuity improved from 20/378±5.1 lines preoperatively to 20/32±2.1 lines at 30 months. The corneal ECD decreased from 2494±382 cells/mm2to 1521±659 cells/mm2at 10 years. The mean simulated keratometry increased from 44.88±2.54 D at 1 year to 46.60±3.0 D at 3 years. The mean follow-up was 103.4 months for DALKs and 106.1 months for PKs. The cumulated incidence of postoperative ocular hypertension requiring treatment was significantly higher in PKs than in DALKs. The early- and late-phase rates of ECD loss were significantly lower in DALKs than in PKs. These figures in DALKs were 50% of those observed in PKs. The simulated mean keratometry was significantly higher in DALKs than in PKs in the mid but not in the long term. No significant differences in visual acuity were observed between both groups. Manual dissection-DALK featured slower visual recovery than PK and big bubble-DALK, whereas big bubble-DALK and PK featured similar visual recovery.ConclusionsDALK featuring higher endothelial survival and lower risk of postoperative ocular hypertension may be superior to PK when indicated for keratoconus.
Team USA injury and illness incidence at the 2022 Beijing Winter Olympic and Paralympic Games
Authors: Anderson Travis , Cali Malia G , Clark Stephanie C , Hasley Ike , Larson Emily G , Noble-Taylor Kayle E , Robinson David M , Post Eric , Finnoff Jonathan T , Adams William M 
Published: October 2023

ObjectiveThe purpose of this study was to determine the injury and illness incidence from Team USA athletes from the 2022 Beijing Winter Olympic and Paralympic Games and assess any sex-based differences or differences between Olympic and Paralympic athletes.MethodsTeam USA Olympic (n=231, 48.5% female) and Team USA Paralympic (n=63, 22.2% female) athletes had medical encounters documented during the Games. Injuries and illnesses were defined according to the 2020 International Olympic Committee Consensus Statement and reviewed for accuracy by a physician. Incidence rates were calculated per 1000 athlete-days and further analysed by sex, sport, anatomical location, type of illness, injury event and injury mechanism, with incident rate ratios (IRRs) used for group comparisons.ResultsThere were no differences in illness (Olympic illness, IRR=0.99 (95% CI 0.48 to 2.07), p=0.998; Paralympic illness, IRR=1.43 (95% CI 0.41 to 4.97), p=0.572) or injury rates (Olympic injury, IRR=0.63 (95% CI 0.39 to 1.03), p=0.062; Paralympic injury, IRR=1.01 (95% CI 0.43 to 2.35), p=0.988) between male and female (reference group) athletes. However, Olympic athletes had significantly lower illness (IRR=0.41 (95% CI 0.22 to 0.76), p=0.003) and injury (IRR=0.56 (95% CI 0.37 to 0.87), p=0.009) risks compared with Paralympic athletes.ConclusionNo significant sex-related differences in injury or illness were detected in Team USA Olympic or Paralympic participating in the 2022 Beijing Winter Games. However, Paralympic athletes exhibited higher rates of injury and illness compared with their Olympic counterparts. This study highlights delegation-specific epidemiological data which may facilitate more focused approaches for injury and illness prevention.
Advances in molecular pathology, diagnosis, and treatment of amyotrophic lateral sclerosis
Authors: Ilieva Hristelina , Vullaganti Mithila , Kwan Justin 
Published: October 2023

Abstract
Although the past two decades have produced exciting discoveries in the genetics and pathology of amyotrophic lateral sclerosis (ALS), progress in developing an effective therapy remains slow. This review summarizes the critical discoveries and outlines the advances in disease characterization, diagnosis, imaging, and biomarkers, along with the current status of approaches to ALS care and treatment. Additional knowledge of the factors driving disease progression and heterogeneity will hopefully soon transform the care for patients with ALS into an individualized, multi-prong approach able to prevent disease progression sufficiently to allow for a dignified life with limited disability.
Effectiveness of lifestyle interventions for improving the physical health of children and adolescents taking antipsychotic medications: protocol for a systematic review and meta-analysis
Authors: Hawker Patrick , Bellamy Jessica , McHugh Catherine , Wong Tsz Ying , Williams Katrina , Wood Amanda , Anderson Vicki , Tonge Bruce J , Ward Philip , Sciberras Emma , Bellgrove Mark A , Silk Tim , Lin Ping-I , Eapen Valsamma 
Published: October 2023

IntroductionChildren and adolescents are increasingly prescribed antipsychotic medications off-label in the treatment of behavioural disorders. While antipsychotic medications are effective in managing behavioural issues, they carry a significant risk of adverse events that compromise ongoing physical health. Of particular concern is the negative impact antipsychotic medications have on cardiometabolic health. Interventions that aim to modify lifestyle habits have the potential to alleviate the adverse effects of antipsychotic medication by enhancing weight management, increasing physical activity, promoting better nutritional practices, improving dietary habits and promoting healthier sleep patterns and sleep hygiene. However, a comprehensive review has not been performed to ascertain the effectiveness of lifestyle interventions for children and adolescents who are at increased risk of antipsychotic-induced compromises to their physical health.Methods and analysisThis systematic review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. Four databases will be searched without any year constraints to identify randomised controlled trials that are published in the English language and report a lifestyle intervention compared with usual care with any physical health outcome measure. Trial registers and results repositories will be scoured to identify additional studies. Two reviewers will independently conduct screening, data extraction and quality assessment and compare the results. Quantitative data will be synthesised, where appropriate, through a random-effects meta-analysis model. Otherwise, data will be reported in a qualitative (narrative) synthesis. Heterogeneity will be quantified using the I2statistic. The Cochrane Risk of Bias 2 tool will be used for risk of bias assessment. The Grading of Recommendations, Assessment, Development and Evaluation system will be used to evaluate the cumulative body of evidence.Ethics and disseminationEthics approval is not required. The publication plan will target high-impact, peer-reviewed journals that fall under the scope of Psychiatry and Mental Health.PROSPERO registration numberCRD42022380277.
Prevalence of metabolic syndrome and metabolic dysfunction-associated fatty liver disease in Malaysia 2023: study protocol for a community-based nationwide cross-sectional survey
Authors: Wan Kim Sui , Mat Rifin Halizah , Mohd Yusoff Muhammad Fadhli , Yoga Ratnam Kishwen Kanna , Chan Wah Kheong , Mohamad Masni , Mohd Noor Nurain , Mustapha Feisul , Ahmad Noor Ani 
Published: October 2023

IntroductionMetabolic syndrome (MetS) is a cluster of cardio-metabolic dysfunctions characterised by increased fasting plasma glucose, waist circumference, blood pressure, triglycerides and reduction in high-density lipoprotein cholesterol. Meanwhile, metabolic dysfunction-associated fatty liver disease (MAFLD) is the new term for fatty liver associated with MetS. People with MetS or MAFLD have higher risks for adverse cardiovascular outcomes and mortalities. However, large-scale data on MetS and MAFLD prevalence in Malaysia is mainly unknown. This study aims to determine the prevalence of MetS and MAFLD among the general adult population in Malaysia.Methods and analysisThis is a community-based nationwide cross-sectional study in Malaysia. The data collection period is from July 2023 until September 2023, with a planned sample size of 1296 participants. We use a two-stage proportionate stratified random sampling method to ensure national representativeness. The definition of MetS follows the Harmonised Joint Interim Statement in 2009. A diagnosis of MAFLD is made if a participant has fatty liver, defined as having a Fatty Liver Index ≥60 and has type 2 diabetes, a body mass index ≥23 kg/m2, or ≥2 metabolic risk abnormalities. Complex sample analysis will be conducted, and the disease prevalence will be reported with 95% CIs, unweighted counts and estimated populations.Ethics and disseminationThe protocol has been approved by the Medical Research and Ethics Committee of the Ministry of Health Malaysia (NMRR ID-22–02845-GUT). The findings will be disseminated through a formal report, policy brief, scientific publications, conference presentations, social media, print media and stakeholder engagement activities.
Cardiac arrhythmia and hypoglycaemia in patients receiving haemodialysis with and without diabetes (the CADDY study): protocol for a Danish multicentre cohort study
Authors: Kofod Dea Haagensen , Diederichsen Søren Zöga , Bomholt Tobias , Ørbæk Andersen Mads , Rix Marianne , Liem Ylian , Lindhard Kristine , Post Hansen Henrik , Rydahl Casper , Lindhardt Morten , Schandorff Kristine , Lange Theis , Nørgaard Kirsten , Almdal Thomas Peter , Svendsen Jesper Hastrup , Feldt-Rasmussen Bo , Hornum Mads 
Published: October 2023

IntroductionPatients receiving haemodialysis are at increased risk of arrhythmias and sudden cardiac death, but data on arrhythmia burden and the pathophysiology remain limited. Among potential risk factors, hypoglycaemia is proposed as a possible trigger of lethal arrhythmias. The development of implantable loop recorders (ILR) and continuous glucose monitoring (CGM) enables long-term continuous ECG and glycaemic monitoring. The current article presents the protocol of a study aiming to increase the understanding of arrhythmias and risk factors in patients receiving haemodialysis. The findings will provide a detailed exploration of the burden and nature of arrhythmias in these patients including the potential association between hypoglycaemia and arrhythmias.Methods and analysisThe study is an investigator-initiated, prospective, multicentre cohort study recruiting 70 patients receiving haemodialysis: 35 with diabetes and 35 without diabetes. Participants are monitored with ILRs and CGM for 18 months follow-up. Data collection further includes a monthly collection of predialysis blood samples and dialysis parameters. The primary outcome is the presence of clinically significant arrhythmias defined as a composite of bradycardia, ventricular tachycardia, or ventricular fibrillation. Secondary outcomes include the characterisation of clinically significant arrhythmias and other arrhythmias, glycaemic characteristics, and mortality. The data analyses include an assessment of the association between arrhythmias and hypoglycaemia and hyperglycaemia, baseline clinical variables, and parameters related to kidney failure and the haemodialysis procedure.Ethics and disseminationThe study has been approved by the Ethics Committee of the Capital Region of Denmark (H-20069767). The findings will be presented at national and international congresses as well as in international peer-reviewed scientific journals.Trial registration numberNCT04841304.
NovelTFGmutation causes autosomal-dominant spastic paraplegia and defects in autophagy
Authors: Xu Ling , Wang Yaru , Wang Wenqing , Zhang Rui , Zhao Dandan , Yun Yan , Liu Fuchen , Zhao Yuying , Yan Chuanzhu , Lin Pengfei 
Published: October 2023

BackgroundMutations in the tropomyosin receptor kinase fused (TFG) gene are associated with various neurological disorders, including autosomal recessive hereditary spastic paraplegia (HSP), autosomal dominant hereditary motor and sensory neuropathy with proximal dominant involvement (HMSN-P) and autosomal dominant type of Charcot-Marie-Tooth disease type 2.MethodsWhole genome sequencing and whole-exome sequencing were used, followed by Sanger sequencing for validation. Haplotype analysis was performed to confirm the inheritance mode of the novelTFGmutation in a large Chinese family with HSP. Additionally, another family diagnosed with HMSN-P and carrying the reportedTFGmutation was studied. Clinical data and muscle pathology comparisons were drawn between patients with HSP and patients with HMSN-P. Furthermore, functional studies using skin fibroblasts derived from patients with HSP and patients with HMSN-P were conducted to investigate the pathomechanisms ofTFGmutations.ResultsA novel heterozygousTFGvariant (NM_006070.6: c.125G>A (p.R42Q)) was identified and caused pure HSP. We further confirmed that the well-documented recessively inherited spastic paraplegia, caused by homozygousTFGmutations, exists in a dominantly inherited form. Although the clinical features and muscle pathology between patients with HSP and patients with HMSN-P were distinct, skin fibroblasts derived from both patient groups exhibited reduced levels of autophagy-related proteins and the presence of TFG-positive puncta.ConclusionsOur findings suggest that autophagy impairment may serve as a common pathomechanism among different clinical phenotypes caused byTFGmutations. Consequently, targeting autophagy may facilitate the development of a uniform treatment for TFG-related neurological disorders.
Functional annotation with expression validation identifies novel metastasis-relevant genes from post-GWAS risk loci in sporadic colorectal carcinomas
Authors: Thean Lai Fun , Wong Michelle , Lo Michelle , Tan Iain , Wong Evelyn , Gao Fei , Tan Emile , Tang Choong Leong , Cheah Peh Yean 
Published: October 2023

Background
Colorectal cancer (CRC) is the third highest incidence cancer and is the leading cause of cancer mortality worldwide. Metastasis to distal organ is the major cause of cancer mortality. However, the underlying genetic factors are unclear. This study aimed to identify metastasis-relevant genes and pathways for better management of metastasis-prone patients.

Methods
A case-case genome-wide association study comprising 2677 sporadic Chinese CRC cases (1282 metastasis-positive vs 1395 metastasis-negative) was performed using the Human SNP6 microarray platform and analysed with the correlation/trend test based on the additive model. SNP variants with association testing −log10 p value ≥5 were imported into Functional Mapping and Annotation (FUMA) for functional annotation.

Results

Glycolysis was uncovered as the top hallmark gene set. Transcripts from two of the five genes profiled, hematopoietic substrate 1 associated protein X 1 (
HAX1
) and hyaluronan-mediatedmotility receptor (
HMMR
), were significantly upregulated in the metastasis-positive tumours. In contrast to disease-risk variants,
HAX1
appeared to act synergistically with
HMMR
in significantly impacting metastasis-free survival. Examining the subtype datasets with FUMA and Ingenuity Pathway Analysis (IPA) identified distinct pathways demonstrating sexual dimorphism in CRC metastasis.

Conclusions
Combining genome-wide association testing with in silico functional annotation and wet-bench validation identified metastasis-relevant genes that could serve as features to develop subtype-specific metastasis-risk signatures for tailored management of patients with stage I-III CRC.
Evaluation of the promotion criteria in an academic medical centre in Singapore
Authors: Yeo May May , Lim Shih-Hui , Kumar Anshul , Thompson Anne W 
Published: October 2023

IntroductionAcademic medical centres (AMCs) have the tripartite mission of performing research to advance healthcare delivery, educating future clinicians and providing healthcare services. This study investigates the criteria associated with being promoted in a Singaporean AMC.MethodsUsing a dataset of 255 candidates for promotion at the studied AMC, we employ logistic regression to determine if these factors are associated with the likelihood of promotion. Further, we use interaction effects to test if the relationship between the H-index and likelihood of promotion differs across the academic levels of the candidates.ResultsThe logistic regression results based on the best of our three tested models suggest that the H-index is positively associated with promotion for those applying to become clinical associate professors (OR=1.43, p=0.01). Moreover, candidates who provide well-developed education portfolios (OR=3.61, p=0.02) and who have held service/leadership roles (OR=6.72, p<0.001) are more likely to be promoted.ConclusionsThis study affirms the correlation between promotion and the advancement criteria outlined by the AMC. This is important for transparency and trust between the AMC and its faculty in their applications for promotion and success in an academic career. Further, our study is one of the few empirical studies linking promotion criteria to promotion outcomes.
Supercontinents, orogenesis and magmatism: a tribute to the career of J. Brendan Murphy
Authors: Nance R. Damian , Strachan Robin A. , Quesada Cecilio , Lin Shoufa 
Published: October 2023

Abstract
Special Publication 542 is a tribute to the remarkable career of J. Brendan Murphy and features 32 articles by 134 authors from 17 different countries; a testament to the high-profile and far-reaching influence of Brendan's work. The topics are wide-ranging in accord with Brendan's diverse research interests, but fall into three broad categories that encompass Brendan's main fields of influence: (i) supercontinents and the supercontinent cycle, including reconstructions and modelling, (ii) orogenesis and terranes, with a focus on the Appalachian–Variscan and Central Asian orogenic belts and the oceans with which they are associated and (iii) magmatism and magmatic processes, with an emphasis on the geochemistry and isotopic compositions of magmas in arc and rift settings. Like Brendan's own research, the scope of the papers spans the globe from Canada to China and ranges from regional field-based studies to conceptual global analyses. All of the articles, however, are focused on unravelling some critical aspect of geology or aimed at clarifying some crucial geologic process. Hence they also share a theme common to Brendan's many contributions in emphasizing the importance of process-oriented research.