bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serial passage of PDCoV in cell culture reduces its pathogenicity and its damage of gut microbiota homeostasis in piglets
Authors: Zhang Yunfei , Si Lulu , Gao Junlong , Shu Xiangli , Qiu Congrui , Zhang Yue , Zu Shaopo , Hu Hui 
Published: February 2024

ABSTRACT

Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that mainly causes diarrhea in suckling piglets, and also has the potential for cross-species transmission. However, there are still no commercial vaccines available to prevent and control PDCoV infection. In this study, PDCoV strain HNZK-02 was serially propagated
in vitro
for up to 150 passages and the amino acid changes have mainly occurred in the S protein during serial passage which caused structure change. PDCoV HNZK-02-passage 5 (P5)-infected piglets exhibited acute and severe watery diarrhea, an obvious intestinal damage, while the piglets infected with PDCoV HNZK-02-P150 showed no obvious clinical signs, weak intestinal lesions, and lower viral loads in rectal swabs and various tissues. Compared with the PDCoV HNZK-02-P5 infection, HNZK-02-P150 infection resulted in a decrease in intestinal mucosal permeability and pro-inflammatory cytokines. Moreover, PDCoV HNZK-02-P5 infection had significantly reduced bacterial diversity and increased relative abundance of opportunistic pathogens, while PDCoV HNZK-02-P150 infection did not significantly affect the bacterial diversity, and the relative abundance of probiotics increased. Furthermore, the alterations of gut microbiota were closely related to the change of pro-inflammatory factor. Metagenomics prediction analysis demonstrated that HNZK-02-P150 modulated the tyrosine metabolism, Nucleotide-binding and oligomerization domain (NOD)-like receptor signaling pathway, and lipopolysaccharide biosynthesis, which coincided with lower inflammatory response and intestinal permeability in the piglets infected with HNZK-02-P150. In conclusion, the PDCoV HNZK-02 was successfully attenuated by serial passage
in vitro
, and the changes of S gene, metabolic function, and gut microbiota may contribute to the attenuation. The PDCoV HNZK-02-P150 may have the potential for developing live-attenuated vaccine.

IMPORTANCE

Porcine deltacoronavirus (PDCoV) is an enteropathogen causing severe diarrhea, dehydration, and death in nursing piglets, devastating great economic losses for the global swine industry, and has cross-species transmission and zoonotic potential. There are currently no approved treatments or vaccines available for PDCoV. In addition, gut microbiota has an important relationship with the development of many diseases. Here, the PDCoV virulent HNZK-02 strain was successfully attenuated by serial passage on cell cultures, and the pathogenesis and effects on the gut microbiota composition and metabolic function of the PDCoV HNZK-02-P5 and P150 strains were investigated in piglets. We also found the genetic changes in the S protein during passage
in vitro
and the gut microbiota may contribute to the pathogenesis of PDCoV, while their interaction molecular mechanism would need to be explored further.
Accurate detection of influenza A virus by use of a novel cross-priming isothermal amplification-based point-of-care assay
Authors: Deng Jiankai , Zhu Hongji , An Shu , Huang Hao , Wang Ruizhi , Chen Yaoming , Chen Peisong , Yu Xuegao 
Published: February 2024

ABSTRACT

Influenza virus is known to cause respiratory tract infections of varying severity in individuals of all ages. The EasyNAT Rapid Flu assay is a newly developed
in vitro
diagnostic test that employs cross-priming isothermal amplification (CPA) to detect and differentiate influenza A and B viruses in human nasopharyngeal (NP) swabs. The aim of this study is to determine the performance characteristics of the EasyNAT Rapid Flu assay for rapid detection of influenza virus. The limit of detection (LOD) and cross-reactivity of the EasyNAT Rapid Flu assay were assessed. The clinical performance of the assay was evaluated using NP swab samples that were tested with real-time reverse-transcription polymerase chain reaction (RT-PCR) and Xpert Xpress Flu/RSV assay. The LOD for the detection of influenza A and B using the EasyNAT Rapid Flu assay was found to be 500 copies/mL. Furthermore, the assay exhibited no cross-reactivity with other common respiratory viruses tested. For the 114 NP swab samples tested for influenza A using both the EasyNAT Rapid Flu assay and real-time RT-PCR, the two assays demonstrated a high level of agreement (
κ
= 0.963,
P
< 0.001), with a positive percentage agreement (PPA) of 97.7% and a negative percentage agreement (NPA) of 98.6%. Similarly, for the 43 NP swab samples tested for influenza A and B using both the EasyNAT Rapid Flu assay and Xpert Xpress Flu/RSV assay, the two assays showed a high level of agreement (
κ
= 0.933,
P
< 0.001), with the overall rate of agreement (ORA) of 97.7% for influenza A and 100% for influenza B. The EasyNAT Rapid Flu assay demonstrates excellent performance in the detection of influenza A, highlighted by its strong agreement with RT-PCR-based assays.

IMPORTANCE
The newly developed EasyNAT Rapid Flu assay is an innovative cross-priming isothermal amplification-based method designed for detecting influenza A and B viruses at point-of-care settings. This study aims to thoroughly assess the analytical and clinical performance of the assay, offering valuable insights into its potential advantages and limitations. The findings of this research hold significant implications for clinical practice.
Gibraltar subduction zone is invading the Atlantic
Authors: Duarte João C. , Riel Nicolas , Rosas Filipe M. , Popov Anton , Schuler Christian , Kaus Boris J.P. 
Published: February 2024

Abstract
Subduction initiation is a cornerstone of the Wilson cycle. It marks the turning point in an ocean's lifetime, allowing its lithosphere to be recycled into the mantle. However, formation of new subduction zones in Atlantic-type oceans is challenging, given that it commonly involves the action of an external force, such as the slab pull from a nearby subduction zone, a far-field compression, or the impact of a plume. Notwithstanding, the Atlantic already has two subduction zones, the Lesser Antilles and the Scotia arcs. These subduction zones have been forced from the nearby Pacific subduction zones. The Gibraltar arc is another place where a subduction zone is invading the Atlantic. This corresponds to a direct migration of a subduction zone that developed in the closing Mediterranean Basin. Nevertheless, few authors consider the Gibraltar subduction to be still active because it has significantly slowed down in the past millions of years. Here, we use new gravity-driven geodynamic models that reproduce the evolution of the Western Mediterranean, show how the Gibraltar arc formed, and test if it is still active. The results suggest that the arc will propagate further into the Atlantic after a period of quiescence. The models also show how a subduction zone starting in a closing ocean (Ligurian Ocean) can migrate into a new opening ocean (Atlantic) through a narrow oceanic corridor. Subduction invasion is likely a common mechanism of subduction initiation in Atlantic-type oceans and a fundamental process in the recent geological evolution of Earth.
Rare encounter: facial vein thrombosis and thrombophlebitis as a complication of acute submandibular sialadenitis
Authors: Goebel Frieder , Knopf Katrin , Fiedler Lukas S 
Published: February 2024

Thrombosis and thrombophlebitis of the facial vein represent exceptionally rare diagnoses, particularly when occurring as complications of acute sialadenitis of the submandibular gland. This case report details the experience of a middle-aged man initially presenting at a tertiary care ear, nose and throat department with right submandibular gland sialadenitis. Despite initiating outpatient treatment involving oral antibiotics and sialagogues, the patient returned after a week with persistent and worsening pain, accompanied by swelling of the right submandibular gland and cheek. Using ultrasound, the accurate diagnosis was promptly identified, revealing thrombosis in the facial vein.The patient underwent a comprehensive treatment regimen involving anticoagulation and intravenous antibiotics. With a subsequent reduction in pain and swelling, the patient was discharged, continuing oral anticoagulation and antibiotics. Outpatient follow-up revealed a complete recovery 3 weeks later. This case underscores the importance of timely and precise diagnostic measures in managing rare complications associated with sialadenitis.
Association of non-alcoholic fatty liver disease with cardiovascular disease and all cause death in patients with type 2 diabetes mellitus: nationwide population based study
Authors: Kim Kyung-Soo , Hong Sangmo , Han Kyungdo , Park Cheol-Young 
Published: February 2024

Abstract

Objective
To investigate the risk of non-alcoholic fatty liver disease (NAFLD) for cardiovascular disease and all cause death in patients with type 2 diabetes mellitus (T2DM).

Design
Nationwide population based study.

Setting
Longitudinal cohort study in Korea.

Participants
7 796 763 participants in the National Health Screening Programme in 2009 were divided into three groups based on NAFLD status: no NAFLD (fatty liver index<30); grade 1 NAFLD (30≤fatty liver index<60); and grade 2 NAFLD (fatty liver index≥60). Median follow-up was 8.13 years.

Main outcome measures
The primary outcome was incident cardiovascular disease (myocardial infarction, ischaemic stroke) or all cause death.

Results
Of 7 796 763 participants, 6.49% (n=505 763) had T2DM. More patients with T2DM had grade 1 NAFLD (34.06%) and grade 2 NAFLD (26.73%) than those without T2DM (grade 1 NAFLD: 21.20%; grade 2 NAFLD: 10.02%). The incidence rate (per 1000 person years) of cardiovascular disease and all cause death increased in the order of no NAFLD, grade 1 NAFLD, and grade 2 NAFLD, and the incidence rates in patients with T2DM were higher than those in patients without T2DM. The five year absolute risk for cardiovascular disease and all cause death increased in the order of no NAFLD, grade 1 NAFLD, and grade 2 NAFLD in patients without and with T2DM (no NAFLD, without T2DM: 1.03, 95% confidence interval 1.02 to 1.04, and 1.25, 1.24 to 1.26, respectively; grade 1 NAFLD, without T2DM: 1.23, 1.22 to 1.25, and 1.50, 1.48 to 1.51, respectively; grade 2 NAFLD, without T2DM: 1.42, 1.40 to 1.45, and 2.09, 2.06 to 2.12, respectively; no NAFLD, with T2DM: 3.34, 3.27 to 3.41, and 3.68, 3.61 to 3.74, respectively; grade 1 NAFLD, with T2DM: 3.94, 3.87 to 4.02, and 4.25, 4.18 to 4.33, respectively; grade 2 NAFLD, with T2DM: 4.66, 4.54 to 4.78, and 5.91, 5.78 to 6.05, respectively). Patients with T2DM and without NAFLD had a higher five year absolute risk for cardiovascular disease and all cause death than those without T2DM and with grade 2 NAFLD. Risk differences for cardiovascular disease and all cause death between no NAFLD and grade 1 or grade 2 NAFLD were higher in patients with T2DM than in those without T2DM.

Conclusions
NAFLD in patients with T2DM seems to be associated with a higher risk of cardiovascular disease and all cause death, even in patients with mild NAFLD. Risk differences for cardiovascular disease and all cause death between the no NAFLD group and the grade 1 or grade 2 NAFLD groups were higher in patients with T2DM than in those without T2DM.
Non-pharmacological therapies for pain management in paediatric intensive care units: a protocol for a scoping review
Authors: Alencar Isabele Gouveia Muniz de , Dantas Joyce Karolayne dos Santos , Matias de Araújo Sara Cristina , Fernandes Thatiane Evelyn de Lima , de Araújo Pedro Lucas Oliveira , da Costa Alex Batista , Takahashi Juliana A , Oliveira Jonas Sâmi Albuquerque de 
Published: February 2024

IntroductionIn critically ill children, pain management is complex owing to cognitive development and the nature of hospitalisation in paediatric intensive therapy units. Although there are many protocols and guidelines for pain control via pharmacological interventions, non-pharmacological practices should also be explored and disseminated for their potential benefit.Methods and analysisA systematic literature search will be performed using the following databases: Academic Search Premier, Cumulative Index to Nursing and Allied Health Literature, Cochrane Library, Excerpta Medica Database, Virtual Health Library, Medical Literature Analysis and Retrieval System Online, ScienceDirect, Scopus, Web of Science Core Collection, Theses fromCoordenação de Aperfeiçoamento de Pessoal de Nível Superior, Dart Europe, Open Access Theses and Dissertations and grey literature from Google Scholar. The research will consider quantitative and qualitative studies, mixed-method studies, systematic reviews, text articles, opinion articles, letters to editors and editorials in any language and from any database. The following will be eligible for inclusion: (1) newborns, infants, children and adolescents; and (2) non-pharmacological therapies used for pain in paediatric intensive care.Ethics and disseminationThis study does not require ethical approval. The results of this research will be disseminated through social media channels and podcasts about pain in children.Trial registration numberThis protocol has been registered with the Open Science Framework (DOI 10.17605/OSF.IO/DZHKT).
Non-communicable disease care in Sierra Leone: a mixed-methods study of the drivers and barriers to retention in care for hypertension
Authors: Dibba Yusupha , Kachimanga Chiyembekezo , Gassimu Joseph , Kulinkina Alexandra V , Bukhman Gene , Gilbert Hannah N , Adler Alma J , Mukherjee Joia S 
Published: February 2024

ObjectiveTo retrospectively analyse routinely collected data on the drivers and barriers to retention in chronic care for patients with hypertension in the Kono District of Sierra Leone.DesignConvergent mixed-methods study.SettingKoidu Government Hospital, a secondary-level hospital in Kono District.ParticipantsWe conducted a descriptive analysis of key variables for 1628 patients with hypertension attending the non-communicable disease (NCD) clinic between February 2018 and August 2019 and qualitative interviews with 21 patients and 7 staff to assess factors shaping patients’ retention in care at the clinic.OutcomesThree mutually exclusive outcomes were defined for the study period: adherence to the treatment protocol (attending >80% of scheduled visits); loss-to-follow-up (LTFU) (consecutive 6 months of missed appointments) and engaged in (but not fully adherent) with treatment (<80% attendance).Results57% of patients were adherent, 20% were engaged in treatment and 22% were LTFU. At enrolment, in the unadjusted variables, patients with higher systolic and diastolic blood pressures had better adherence than those with lower blood pressures (OR 1.005, 95% CI 1.002 to 1.009, p=0.004 and OR 1.008, 95% CI 1.004 to 1.012, p<0.001, respectively). After adjustment, there were 14% lower odds of adherence to appointments associated with a 1 month increase in duration in care (OR 0.862, 95% CI 0.801 to 0.927, p<0.001). Qualitative findings highlighted the following drivers for retention in care: high-quality education sessions, free medications and good interpersonal interactions. Challenges to seeking care included long wait times, transport costs and misunderstanding of the long-term requirement for hypertension care.ConclusionFree medications, high-quality services and health education may be effective ways of helping NCD patients stay engaged in care. Facility and socioeconomic factors can pose challenges to retention in care.
Impact of intraosseous regional administration of tranexamic acid in total knee arthroplasty on perioperative blood loss: a protocol for a randomised controlled trial
Authors: Wei Zhanqi , Yu Muyang , Xu Yiming , Weng Xisheng , Feng Bin 
Published: February 2024

IntroductionTotal knee arthroplasty (TKA) is a common surgical intervention to treat joint diseases. However, TKA is associated with significant blood loss. Tranexamic acid (TXA) has been used to reduce perioperative bleeding and postoperative blood transfusion. This study aims to explore the effectiveness and safety of intraosseous regional administration (IORA) of TXA in TKA and compare differences in perioperative blood loss between IORA of TXA, intravenous infusion of TXA, and combined IORA and intravenous infusion of TXA.Methods and analysisThis randomised controlled trial will enrol 105 patients with osteoarthritis who meet the inclusion criteria for unilateral TKA. Patients were randomly divided into three groups using the random number table method. Group A received 1.0 g of TXA via IORA, group B received 1.0 g of TXA via intravenous infusion 15 min prior to the tourniquet release, and group C received both IORA of 1.0 g of TXA and intravenous infusion of 1.0 g of TXA. The primary outcome measure is perioperative total blood loss. Secondary outcomes include bleeding events, venous thromboembolism events, inflammation reactions, other complications and knee function assessments.Ethics and disseminationThis study has been approved by the Ethics Committee of Peking Union Medical College Hospital and registered in the Chinese Clinical Trial Registry. Informed consent will be obtained from all the patients before enrolment. The trial will be conducted in accordance with the principles of the Declaration of Helsinki and the International Conference on Harmonization Good Clinical Practice guidelines. The results of this study will be disseminated through peer-reviewed publications, conference presentations and social media platforms. The findings will provide valuable insights into the use of IORA of TXA in TKA and may lead to the development of new strategies for perioperative blood management in joint replacement surgery.Trial registration numberThe Ethics Committee of Peking Union Medical College Hospital (approval number: K2371); Chinese Clinical Trial Registry (trial registration number: ChiCTR2200066293).
Good School Toolkit-Secondary Schools to prevent violence against students: protocol for a pilot cluster randomised controlled trial
Authors: Devries Karen , Tanton Clare , Knight Louise , Nakuti Janet , Nanyunja Barbrah , Laruni Yvonne , Amollo Mathew , Apota John , Opobo Timothy , Pearlman Jodie , Allen Elizabeth , Bonell Chris , Naker Dipak 
Published: February 2024

IntroductionNo whole-school interventions which seek to reduce physical, sexual and emotional violence from peers, intimate partners and teachers have been trialled with adolescents. Here, we report a protocol for a pilot trial of the Good School Toolkit-Secondary Schools intervention, to be tested in Ugandan secondary schools. Our main objectives are to (1) refine the intervention, (2) to understand feasibility of delivery of the intervention and (3) to explore design parameters for a subsequent phase III trial.Methods and analysisWe will conduct a pilot cluster randomised controlled trial, with two arms and parallel assignment. Eight schools will be randomly selected from a stratified list of all eligible schools in Kampala and Wakiso Districts. We will conduct a baseline survey and endline survey 18 months after the baseline, with 960 adolescents and 200 teachers. Qualitative data and mixed methods process data collection will be conducted throughout the intervention. Proportion of staff and students reporting acceptability, understanding and implementing with fidelity will be tabulated at endline for intervention schools. Proportions of schools consenting to participation, randomisation and proportions of schools and individual participants completing the baseline and endline surveys will be described in a Consolidated Standards of Reporting Trials diagram.Ethics and disseminationThe ethical requirements of our project are complex. Full approvals have been received from the Mildmay Ethics Committee (0407-2019), the Uganda National Council for Science and Technology (SS 6020) and the London School of Hygiene & Tropical Medicine (16212). Results of this study will be published in peer-reviewed academic journals, and shared with public bodies, policy makers, study participants and the general public in Uganda.Trial registration numberPACTR202009826515511.
Common practices for sociodemographic data reporting in digital mental health intervention research: a scoping review
Authors: Kirvin-Quamme Andrew , Kissinger Jennifer , Quinlan Laurel , Montgomery Robert , Chernenok Mariya , Pirner Maddison C , Pajarito Sarah , Rapoport Stephanie , Wicks Paul , Darcy Alison , Greene Carolyn J , Robinson Athena 
Published: February 2024

BackgroundThe ability of digital mental health interventions (DMHIs) to reduce mental health disparities relies on the recruitment of research participants with diverse sociodemographic and self-identity characteristics. Despite its importance, sociodemographic reporting in research is often limited, and the state of reporting practices in DMHI research in particular has not been comprehensively reviewed.ObjectivesTo characterise the state of sociodemographic data reported in randomised controlled trials (RCTs) of app-based DMHIs published globally from 2007 to 2022.MethodsA scoping review of RCTs of app-based DMHIs examined reporting frequency for 16 sociodemographic domains (eg, gender) and common category options within each domain (eg, woman). The search queried five electronic databases. 5079 records were screened and 299 articles were included.ResultsOn average, studies reported 4.64 (SD=1.79; range 0–9) of 16 sociodemographic domains. The most common were age (97%) and education (67%). The least common were housing situation (6%), residency/location (5%), veteran status (4%), number of children (3%), sexual orientation (2%), disability status (2%) and food security (<1%). Gender or sex was reported in 98% of studies: gender only (51%), sex only (28%), both (<1%) and gender/sex reported but unspecified (18%). Race or ethnicity was reported in 48% of studies: race only (14%), ethnicity only (14%), both (10%) and race/ethnicity reported but unspecified (10%).ConclusionsThis review describes the widespread underreporting of sociodemographic information in RCTs of app-based DMHIs published from 2007 to 2022. Reporting was often incomplete (eg, % female only), unclear (eg, the conflation of gender/sex) and limited (eg, only options representing majority groups were reported). Trends suggest reporting has somewhat improved in recent years. Diverse participant populations must be welcomed and described in DMHI research to broaden learning and the generalisability of results, a prerequisite of DMHI’s potential to reduce disparities in mental healthcare.