bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic surveillance of
Clostridioides difficile
transmission and virulence in a healthcare setting
Authors: Newcomer Erin P. , Fishbein Skye R. S. , Zhang Kailun , Hink Tiffany , Reske Kimberly A. , Cass Candice , Iqbal Zainab H. , Struttmann Emily L. , Burnham Carey-Ann D. , Dubberke Erik R. , Dantas Gautam 
Published: February 2024

ABSTRACT

Clostridioides difficile
infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and the genomic determinants of disease outcomes. Across two wards over 6 months, we selectively cultured
C. difficile
from patients (
n
= 384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most
C. difficile
isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (
n
= 79), 19 (24%) patients were colonized with toxigenic
C. difficile
on admission to the hospital. We defined 25 strain networks at ≤2 core gene single nucleotide polymorphisms; two of these networks contain strains from different patients. Strain networks were temporally linked (
P
< 0.0001). To understand the genomic correlates of the disease, we conducted WGS on an additional cohort of
C. difficile
(
n
= 102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic
C. difficile
isolates are associated with the presence of
cdtR
, nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes (
tcdABER and cdtR
) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate that toxigenic and nontoxigenic
C. difficile
contamination persist in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to
C. difficile
colonization and disease.

IMPORTANCE

Clostridioides difficile
infection remains a leading cause of hospital-associated diarrhea, despite increased antibiotic stewardship and transmission prevention strategies. This suggests a changing genomic landscape of
C. difficile
. Our study provides insight into the nature of prevalent
C. difficile
strains in a hospital setting and transmission patterns among carriers. Longitudinal sampling of surfaces and patient stool revealed that both toxigenic and nontoxigenic strains of
C. difficile
clade 1 dominate these two wards. Moreover, quantification of transmission in carriers of these clade 1 isolates underscores the need to revisit infection prevention measures in this patient group. We identified unique genetic signatures associated with virulence in this clade. Our data highlight the complexities of preventing transmission of this pathogen in a hospital setting and the need to investigate the mechanisms of
in vivo
persistence and virulence of prevalent lineages in the host gut microbiome.
Initiation of the Cascade arc
Authors: Tepper Jeffrey H. , Clark Kenneth P. 
Published: February 2024

Abstract
The Cascade arc (western North America) is the world’s youngest continental arc, and because the down-going Juan de Fuca plate is young, it is also the hottest end member among subduction zones worldwide. We present evidence that the arc initiated &lt;5 m.y. after accretion of the Siletzia oceanic terrane terminated the earlier subduction system and caused the northern portion of the Farallon slab to break off. Cascade magmatism began ca. 46 Ma with a new trench outboard of Siletzia, a reconfiguration commonly attributed to a seaward jump of the subduction zone. However, the presence of young buoyant oceanic lithosphere that would have resisted being forced into the mantle and the very rapid reestablishment of arc magmatism are hard to reconcile with initiation of a new subduction zone by this process. We propose an alternative mechanism in which the arc was reestablished as the intact southern portion of Farallon slab migrated northward from California (United States), converting a transform margin to a convergent one. This model utilizes plate reconstructions, petrology, mantle tomography, and geochronology to explain how subduction was initiated in a setting where the slab was young and hot and why the earliest Cascade magmatism occurred toward the middle rather than an end of the arc.
Prevalence of depression, stress and suicide tendency among individuals with long COVID and determinants: a protocol of a systematic review and meta-analysis
Authors: Bidhendi-Yarandi Razieh , Biglarian Akbar , Bakhshi Enayatollah , Khodaei-Ardakani Mohammad-Reza , Behboudi-Gandevani Samira 
Published: February 2024

BackgroundIt is well known that the COVID-19 pandemic has had a devastating impact on mental health, especially among individuals with long COVID. This systematic review and meta-analysis aims to investigate the prevalence of depression, stress and suicide tendencies among individuals with long COVID, as well as to explore the factors that contribute to these conditions.Methods and analysisA comprehensive review of literature will be conducted in various databases of including PubMed, including Medline, Embase, PsycINFO, CINAHL and Cochrane Library. The studies to be included in this review will be published in the English language, and the time frame of included studies will be from the date of inception of COVID-19 until 30 December 2023. Two independent reviewers will identify studies for inclusion based on a screening questionnaire, and the JBI standardised critical appraisal checklist for studies reporting prevalence data will be used to assess the methodological quality. The strength of the body of evidence will be assessed using the Grading of Recommendations Assessment, Development and Evaluation approach. To analyse the data, a robust Bayesian approach will be applied using the STATA software package (V.14; STATA) and JASP software. The findings of this systematic review and meta-analysis will provide valuable insights into the prevalence of depression, stress and suicide tendencies among individuals with long COVID, as well as the factors that contribute to these conditions.Ethics and disseminationThere is no research ethics board approval required. The dissemination plan is to publish results in a peer-reviewed academic journal.PROSPERO registration numberCRD42022346858.
“Just as curry is needed to eat rice, antibiotics are needed to cure fever”—a qualitative study of individual, community and health system-level influences on community antibiotic practices in rural West Bengal, India
Authors: Gautham Meenakshi , Bhattacharyya Sanghita , Maity Suroshree , Roy Mayura Biswas , Balasubramaniam Priya , Ebata Ayako , Bloom Gerald 
Published: February 2024

ObjectivesTo understand community antibiotic practices and their drivers, comprehensively and in contextually sensitive ways, we explored the individual, community and health system-level factors influencing community antibiotic practices in rural West Bengal in India.DesignQualitative study using focus group discussions and in-depth interviews.SettingTwo contrasting village clusters in South 24 Parganas district, West Bengal, India. Fieldwork was conducted between November 2019 and January 2020.Participants98 adult community members (42 men and 56 women) were selected purposively for 8 focus group discussions. In-depth interviews were conducted with 16 community key informants (7 teachers, 4 elected village representatives, 2 doctors and 3 social workers) and 14 community health workers.ResultsSignificant themes at the individual level included sociodemographics (age, gender, education), cognitive factors (knowledge and perceptions of modern antibiotics within non-biomedical belief systems), affective influences (emotive interpretations of appropriate medicine consumption) and economic constraints (affordability of antibiotic courses and overall costs of care). Antibiotics were viewed as essential fever remedies, akin to antipyretics, with decisions to halt mid-course influenced by non-biomedical beliefs associating prolonged use with toxicity. Themes at the community and health system levels included the health stewardship roles of village leaders and knowledge brokering by informal providers, pharmacists and public sector accredited social health activists. However, these community resources lacked sufficient knowledge to address people’s doubts and concerns. Qualified doctors were physically and socially inaccessible, creating a barrier to seeking their expertise.ConclusionsThe interplay of sociodemographic, cognitive and affective factors, and economic constraints at the individual level, underscores the complexity of antibiotic usage. Additionally, community leaders and health workers emerge as crucial players, yet their knowledge gaps and lack of empowerment pose challenges in addressing public concerns. This comprehensive analysis highlights the need for targeted interventions that address both individual beliefs and community health dynamics to promote judicious antibiotic use.
Prevalence of and risk factors for myopia among urban and rural children in Northeast China: protocol for a school-based cross-sectional study
Authors: Zheng Tianli , Jiang Shuang , Fu Weiwei , Liu Hua , Ding Shangshang , Xv Daoliang , Zhang Hetong , Zheng Tianyou , Yang Xiaodong 
Published: February 2024

IntroductionThe worldwide prevalence of myopia is high and continues to increase. In this study, a school screening programme for myopia will be implemented using the whole-process information method. The purpose of this study is to investigate the prevalence of myopia in urban and rural areas of Northeast China and to determine the factors related to myopia.Methods and analysisThis is a school-based cross-sectional study. Our study population will include 6000 school-aged children from 2 urban and 2 rural schools in Jinzhou, China. The study will be conducted using our self-developed internet-based intelligent data collection, transmission, storage and analysis system. Examination parameters include uncorrected distance visual acuity, presenting distance visual acuity, non-cycloplegic autorefraction, height, weight, waist circumference, hip circumference, spinal curvature and dental caries. The examination report will be automatically sent to parents, who will complete the questionnaire, and appropriate statistical analysis will be performed. The main outcome is the prevalence of myopia, defined as an equivalent spherical degree ≤−0.5 D.Ethics and disseminationEthical approval was obtained from the Third Affiliated Hospital of Jinzhou Medical University (number: JYDSY-KXYJ-IEC-2023-018). Findings will be published in a peer-reviewed journal. Subjects and their parents (or other authorised agents) give informed consent prior to study participation.Trial registration numberChiCTR2300072893.
Knowledge and attitude towards stroke among the population of one rural community in southern Thailand: a survey
Authors: Wanichanon Worawit , Ananchaisarp Thareerat , Buathong Napakkawat , Choomalee Kittisakdi 
Published: February 2024

ObjectiveTo evaluate attitude and knowledge of stroke in a rural community in southern Thailand.DesignA survey.SettingA community in southern Thailand.ParticipantsAll community members aged ≥18 years who were at home during the survey were invited to participate.Primary and secondary outcome measuresLevel of attitude and knowledge score towards stroke were assessed, and the associated factors were evaluated.MethodsThe questionnaire used in this survey was developed from a literature review, and the content validity and reliability were tested before use. Logistic and linear regression were used to determine factors associated with the level of attitude and knowledge score towards stroke.ResultsAmong 247 participants, most were Muslim and the median age was 54.0 years. The median (Q1, Q3) score of stroke risk factors was 5 (2, 7) (full score: 9). Participants who knew about stroke, had an acquaintance diagnosed with stroke and had a high level of attitude had significantly higher scores. Two-thirds of the participants had a low-to-moderate level of attitude. Furthermore, most high-risk participants (99/113) had a low to no chance awareness of their risk to stroke. The median (Q1, Q3) score of stroke warning symptoms was 6 (3, 7) (full score: 10). The participants who had received education via the Face Arm Speech Time (FAST) campaign demonstrated a significantly higher proportion of correct answers to the symptoms mentioned in the FAST.ConclusionAbout half of the participants in this community did not know some of the risk factors and warning symptoms of stroke. Moreover, most participants had a low-to-moderate level of attitude and underestimated their risk to stroke even in the high cardiovascular risk participants. The FAST may help people memorise the typical warning symptoms of stroke.
Faecal microbial transfer and complex carbohydrates mediate protection against COPD
Authors: Budden Kurtis F , Shukla Shakti D , Bowerman Kate L , Vaughan Annalicia , Gellatly Shaan L , Wood David L A , Lachner Nancy , Idrees Sobia , Rehman Saima Firdous , Faiz Alen , Patel Vyoma K , Donovan Chantal , Alemao Charlotte A , Shen Sj , Amorim Nadia , Majumder Rajib , Vanka Kanth S , Mason Jazz , Haw Tatt Jhong , Tillet Bree , Fricker Michael , Keely Simon , Hansbro Nicole , Belz Gabrielle T , Horvat Jay , Ashhurst Thomas , van Vreden Caryn , McGuire Helen , Fazekas de St Groth Barbara , King Nicholas J C , Crossett Ben , Cordwell Stuart J , Bonaguro Lorenzo , Schultze Joachim L , Hamilton‐Williams Emma E , Mann Elizabeth , Forster Samuel C , Cooper Matthew A , Segal Leopoldo N , Chotirmall Sanjay H , Collins Peter , Bowman Rayleen , Fong Kwun M , Yang Ian A , Wark Peter A B , Dennis Paul G , Hugenholtz Philip , Hansbro Philip M 
Published: February 2024

Objective
Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear.

Design

Using an
in vivo
mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation.

Results

FMT alleviated hallmark features of COPD (inflammation, alveolar destruction, impaired lung function), gastrointestinal pathology and systemic immune changes. Protective effects were additive to smoking cessation, and transfer of CS-associated microbiota after antibiotic-induced microbiome depletion was sufficient to increase lung inflammation while suppressing colonic immunity in the absence of CS exposure. Disease features correlated with the relative abundance of
Muribaculaceae, Desulfovibrionaceae
and
Lachnospiraceae
family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes.

Conclusion
The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.
Time poverty, health and health-related behaviours in a Southern European city: a gender issue
Authors: Artazcoz Lucía , Cortès-Franch Imma , Arcas M. Marta , Ollé-Espluga Laia , Pérez Katherine 
Published: February 2024

BackgroundDespite its growing interest, time poverty is a neglected issue in public health analysis and policies. The objectives of this study were: (1) to analyse gender differences in paid, unpaid and total working time; (2) to identify gender differences in the factors related to time poverty; and (3) to examine gender differences in the relationship between time poverty, health and health-related behaviours in the city of Barcelona (Spain).MethodsCross-sectional study based on salaried workers aged 16–64 years interviewed in the 2021 Barcelona Health Survey (695 men and 713 women). Time poverty was defined as the top tercile of the total paid and unpaid work. Dependent variables were self-perceived health status, mental health, sleep time, sleep quality and leisure time physical activity.ResultsWomen were more likely to be time poor. In both sexes, time poverty was related to the number of children. Whereas among men time poverty was not associated with any health indicators, among women it was related to poor mental health status (aOR=2.11, 95% CI 1.39 to 3.20), short sleep (aOR=1.54, 95% CI 1.05 to 2.25), poor sleep quality (aOR=1.83, 95% CI 1.25 to 2.68) and low leisure time physical activity (aOR=1.50, 95% CI 1.00 to 2.26).ConclusionsThis study suggests that time use can be an important social determinant of health and of gender inequalities in health. At the local level, in many European cities, time poverty could be reduced, among other interventions, by increasing affordable and good quality public services for the care of dependent persons.
Effectiveness of the Coordinated Return to Work model after orthopaedic surgery for lumbar discectomy and hip and knee arthroplasty: a register-based study
Authors: Lavikainen Piia , Heiskanen Jari , Jalkanen Kari , Lehtimäki Aku-Ville , Vehkala Saara , Kangas Pauliina , Husman Kaj , Vohlonen Ilkka , Martikainen Janne 
Published: February 2024

ObjectivesThis study examined the effectiveness of an individualised Coordinated Return to Work (CRtW) model on the length of the return to work (RTW) period compared with a standard prescription of 2–3 months RTW during recovery after lumbar discectomy and hip and knee arthroplasty among Finnish working-age population.MethodsCohorts on patients aged 18–65 years old with lumbar discectomy or hip or knee arthroplasty were extracted from the electronic health records of eight Finnish hospital districts in 2015–2021 and compiled with retirement and sickness benefits. The overall effect of the CRtW model on the average RTW period was calculated as a weighted average of area-specific mean differences in RTW periods between 1 year before and 1 year after the implementation. Longer-term effects of the model were examined with an interrupted time series design estimated with a segmented regression model.ResultsDuring the first year of the CRtW model, the average RTW period shortened by 9.1 days (95% CI 4.1 to 14.1) for hip arthroplasty and 14.4 days (95% CI 7.5 to 21.3) for knee arthroplasty. The observed differences were sustained over longer follow-up times. For lumbar discectomy, the first-year decrease was not statistically significant, but the average RTW had shortened by 36.2 days (95% CI 33.8 to 38.5) after 4.5 years.ConclusionsThe CRtW model shortened average RTW periods among working-age people during the recovery period. Further research with larger samples and longer follow-up times is needed to ensure the effectiveness of the model as a part of the Finnish healthcare system.
Observable $$\Delta {\textrm{N}}_{\textrm{eff}}$$ in Dirac scotogenic model
Authors: Borah Debasish , Das Pritam , Nanda Dibyendu 
Published: February 2024

AbstractWe study the possibility of probing the radiative Dirac seesaw model with dark sector particles going inside the loop, popularly referred to as the Dirac scotogenic model via measurements of effective relativistic degrees of freedom $$\Delta {\textrm{N}}_{\textrm{eff}}$$

Δ

N
eff

at cosmic microwave background (CMB) experiments. The loop suppression and additional free parameters involved in neutrino mass generation allow large $$(\sim {\mathcal {O}}(1))$$

(
∼
O
(
1
)
)

coupling of light Dirac neutrinos with the dark sector particles. Such large Yukawa coupling not only dictates the relic abundance of heavy fermion singlet dark matter but also can lead to the thermalisation of the right chiral part of Dirac neutrinos, generating additional relativistic degrees of freedom $$\Delta {\textrm{N}}_{\textrm{eff}}.$$

Δ

N
eff

.

We find that the parameter space consistent with dark matter phenomenology and neutrino mass bounds can also be probed at future cosmic microwave background experiments like CMB-S4 via precision measurements of $$\Delta {\textrm{N}}_{\textrm{eff}}.$$

Δ

N
eff

.

The same parameter space, while leading to loop-suppressed direct detection cross-section of dark matter outside future sensitivities, can also have other interesting and complementary observational prospects via charged lepton flavour violation and collider signatures.
Formulation of Galilean relativistic Born–Infeld theory
Authors: Banerjee Rabin , Bhattacharya Soumya , Majhi Bibhas Ranjan 
Published: February 2024

AbstractIn this paper, we formulate, for the first time, in a systematic manner, Galilean relativistic Born–Infeld action in detail. Exploiting maps connecting Lorentz relativistic and Galilean relativistic vectors, we construct the two limits (electric and magnetic) of Galilean relativistic Born–Infeld action from usual relativistic Born–Infeld theory. An action formalism is thereby derived. From this action, equations of motion are obtained either in the potential or field formulation. Galilean version of duality transformations involving the electric and magnetic fields are defined. They map the electric limit relations to the magnetic ones and vice-versa, exactly as happens for Galilean relativistic Maxwell theory. We also explicitly show the Galilean boost and gauge invariances of the theory in both limits.
Modeling the black holes surrounded by a dark matter halo in the galactic center of M87
Authors: Liu Dong , Yang Yi , Xu Zhaoyi , Long Zheng-Wen 
Published: February 2024

AbstractIn this paper, the structure of a dark matter halo can be well described by the mass model of M87 and the Einasto profile for the cold dark matter model, i.e., $$\rho _{\text {eina}} (r)=\rho _\text {e} \exp ( -2 \alpha ^{-1} ((r/r_\text {e})^\alpha -1 ) )$$

ρ
eina

(
r
)

=

ρ
e

exp

(
-
2

α

-
1

(

(
r
/

r
e

)

α

-
1
)

)

(Wang et al. in Nature 585:39–42, 2020). Under these conditions, we construct a solution of a static spherically symmetric black hole in a dark matter halo. Then, using the Newman–Janis algorithm, we extend this static solution to the case of rotation, and obtain a solution for the Kerr-like black hole. We prove that this solution of the Kerr-like black hole is indeed a solution to the Einstein field equations. Finally, taking M87 as an example, we study and analyze some physical properties of this Kerr-like black hole, and then compare them with the Kerr black hole. Particularly, from the perspective of the black hole shadow and the fact that the Kerr-like black hole and the Kerr black hole is distinguishable, we give the upper limit of the shape parameter of the Einasto density profile, that is approximately $$\alpha <0.22$$

α
<
0.22

, which may provide a new method to further improve and perfect the density profile of dark matter model. These research results for the black hole in a dark matter halo may indirectly provide an effective method for detecting the existence of dark matter.