bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biophysical and structural insights into AAV genome ejection
Authors: Gliwa Keely , Hull Joshua , Kansol Austin , Zembruski Victoria , Lakshmanan Renuk , Mietzsch Mario , Chipman Paul , Bennett Antonette , McKenna Robert 
Published: February 2025

ABSTRACT

Recombinant adeno-associated virus (rAAV) is comprised of non-enveloped capsids that can package a therapeutic transgene and are currently being developed and utilized as gene therapy vectors. The therapeutic efficiency of rAAV is dependent on successful cytoplasmic trafficking and transgene delivery to the nucleus. It is hypothesized that an increased understanding of the effects of the cellular environment and biophysical properties of the capsid as it traffics to the nucleus could provide insight to improve vector efficiency. The AAV capsid is exposed to increasing [H
+
] during endo-lysosomal trafficking. Exposure to low pH facilitates the externalization of the viral protein 1 unique region (VP1u). This VP1u contains a phospholipase A2 domain required for endosomal escape and nuclear localization signals that facilitate nuclear targeting and entry. The viral genome is released either after total capsid disassembly or via a concerted DNA ejection mechanism in the nucleus. This study presents the characterization of genome ejection (GE) for two diverse serotypes, AAV2 and AAV5, using temperature. The temperature required to disassemble the virus capsid (T
M
) is significantly higher than the temperature required to expose the transgene (T
E
) for both serotypes. This was verified by quantitative PCR (qPCR) and transmission electron microscopy. Additionally, the absence of VP1/VP2 in the capsids and a decrease in pH increase the temperature of GE. Furthermore, cryo-electron microscopy structures of the AAV5 capsid pre- and post-GE reveal dynamics at the twofold, threefold, and fivefold regions of the capsid interior consistent with a concerted egress of the viral genome.

IMPORTANCE
The development of recombinant adeno-associated virus (rAAV) capsids has grown rapidly in recent years, with five of the eight established therapeutics gaining approval in the past 2 years alone. Clinical progression with AAV2 and AAV5 represents a growing need to further characterize the molecular biology of these viruses. The goal of AAV-based gene therapy is to treat monogenic disorders with a vector-delivered transgene to provide wild-type protein function. A better understanding of the dynamics and conditions enabling transgene release may improve therapeutic efficiency. In addition to their clinical importance, AAV2 and 5 were chosen in this study for their diverse antigenic and biophysical properties compared to more closely related serotypes. Characterization of a shared genome ejection process may imply a conserved mechanism for all rAAV therapies.
Longitudinal changes in the transcriptionally active and intact HIV reservoir after starting ART during acute infection
Authors: Janssens Julie , Wedrychowski Adam , Kim Sun Jin , Isbell Cordelia , Hoh Rebecca , Pillai Satish K. , Henrich Timothy J. , Deeks Steven G. , Roan Nadia R. , Lee Sulggi A. , Yukl Steven A. 
Published: February 2025

ABSTRACT

Even in antiretroviral therapy (ART)-suppressed human immunodeficiency virus (HIV)-infected individuals, there are heterogeneous populations of HIV-expressing cells exhibiting variable degrees of progression through blocks to HIV transcriptional initiation, elongation, completion, and splicing. These HIV-transcribing cells likely contribute to HIV-associated immune activation and inflammation as well as the viral rebound that occurs after stopping ART. However, it is unclear whether the blocks to HIV transcription are present before ART and how the timing and duration of ART may affect the clearance of cells expressing HIV transcripts that differ in their processivity and/or presence of mutations. To investigate these questions, we quantified different types of HIV transcripts and the corresponding HIV DNA regions/proviruses in longitudinal blood samples obtained before ART initiation (T1) and after 6 months (T2) and 1 year (T3) of ART in 16 individuals who initiated ART during acute HIV infection. Before ART, the pattern of HIV transcripts suggested blocks to elongation and splicing, and only ~10% of intact proviruses were transcribing intact HIV RNA. During the first 6 months of ART, we detected progressively greater reductions in initiated, 5′-elongated, mid-transcribed, completed, and multiply spliced HIV transcripts. Completed HIV RNA decayed faster than initiated or 5′-elongated HIV RNA, and intact HIV RNA tended to decay faster than defective HIV RNA. HIV DNA and RNA levels at T1–T3 correlated inversely with baseline CD4+ T-cell counts. Our findings suggest the existence of immune responses that act selectively to reduce HIV transcriptional completion and/or preferentially kill cells making completed or intact HIV RNA.

IMPORTANCE
Even in virologically suppressed HIV-infected individuals, expression of viral products from both intact and defective proviruses may contribute to HIV-associated immune activation and inflammation, which are thought to underlie the organ damage that persists despite suppressive ART. We investigated how the timing of ART initiation and the duration of ART affect the heterogeneous populations of HIV-transcribing cells, including a detailed characterization of the different HIV transcripts produced before ART and the rate at which they decay after ART initiation during acute HIV infection. Even during untreated infection, most cells (~90%) have blocks at some stage of transcription. Furthermore, different HIV transcripts decline at different rates on ART, with the fastest decay of cells making completed and intact HIV RNA. Our results suggest that intrinsic or extrinsic immune responses act selectively to either reduce particular stages of HIV transcription or cause selective killing of cells making particular HIV transcripts.
Effect of host telomerase inhibition on human cytomegalovirus
Authors: Cavanaugh Chloe M. , Betsinger Cora N. , Katchur Nicole , Zhang Sherry , Yang Karen , Nogalski Maciej , Cristea Ileana M. , Notterman Daniel 
Published: February 2025

ABSTRACT

Treatment options remain limited for human cytomegalovirus (HCMV). Host telomerase has been implicated in the pathogenesis and oncogenesis of multiple herpesviruses, most recently including HCMV. In this study, we investigated the effect of telomerase inhibition on HCMV replication, as well as the mechanism of the interaction between HCMV and host telomerase
in vitro
. We found that lytic HCMV infection increases host telomerase activity, at least in part, through modulation of hTERT expression during earlier phases of the HCMV replication cycle. We found telomerase inhibition strongly reduced viral titer for two HCMV strains in a dose-specific manner. Both post-translational pharmaceutical telomerase inhibition and siRNA-mediated knockdown of hTERT reduce HCMV yield. Telomerase inhibition results in both reduction of viral gene and protein expression across the HCMV replication cycle, and suppressed viral genome replication and viral infectivity, suggesting interference with at least early steps of the HCMV viral life cycle. Altogether, our findings indicate telomerase plays an important, perhaps non-canonical role in lytic HCMV infection which includes the support of viral replication and infectivity.

IMPORTANCE

Human cytomegalovirus (HCMV) seroprevalence and morbidity in immunocompromised patients and neonates infected
in utero
remain high globally. Host telomerase has been implicated in the success of multiple infection-induced pathologies, including the success of both lytic infection and oncogenesis in certain herpesviruses. The results of this study suggest a similar biologically important role for host telomerase in lytic HCMV infection. Furthermore, these results may provide the potential for a novel, adjunctive anti-viral treatment for HCMV infection as well as insight into the viral products likely to be involved with HCMV regulation of telomerase.
The Japanese encephalitis virus NS1 protein concentrates ER membranes in a cytoskeleton-independent manner to facilitate viral replication
Authors: Xie Shengda , Lin Xinxin , Yang Qing , Shi Miaolei , Yang Xingmiao , Cao Ziyu , Cao Ruibing 
Published: February 2025

ABSTRACT

Orthoflaviviruses remodel the endoplasmic reticulum (ER) network to construct replication organelles (ROs) for RNA replication. In this study, we demonstrate that the Japanese encephalitis virus (JEV) NS1 protein concentrates ER membranes in the perinuclear region, which provides a substantial membrane source for viral replication. Subsequently, the virus forms main replication organelles within this membrane-concentrated area to facilitate efficient replication. This process relies on the ER localization signal, glycosylation, dimerization, and membrane-binding sites of the NS1 protein. In conclusion, our study highlights the role of the NS1 protein in the formation of the ROs by JEV, providing new insights into orthoflavivirus replication.

IMPORTANCE
Orthoflaviviruses use the endoplasmic reticulum (ER) membranes for replication by forming invaginations to assemble the replication organelles. Here, we found that Japanese encephalitis virus (JEV) utilizes the NS1 protein to concentrate a significant number of ER membranes in the perinuclear area, thereby providing a membrane source for viral replication and facilitating the formation of main replication organelles (MROs). This process depends on the ER localization signals of NS1, as well as its glycosylation, dimerization, and membrane-binding sites, but not on the cytoskeleton. In summary, our study highlights how NS1 remodels ER membranes to facilitate the formation of MROs for JEV, thereby accelerating viral replication.
Understanding road accident injury dynamics in Iran: a growth mixture modelling perspective
Authors: Zarrin Ziba , Gholamizadeh Kamran , Talebi-Ghane Elaheh , Ayubi Erfan , Hamidi Omid 
Published: February 2025

ObjectivesRoad traffic injuries represent a significant public health concern globally. In Iran, road accidents have become a leading cause of death and disability, necessitating urgent attention to injury prevention strategies. This study aims to analyse the trends in injuries resulting from road accidents over a decade. Understanding these trends is crucial for informing targeted interventions and resource allocation, ultimately contributing to the reduction of road traffic injuries.DesignEcological study.SettingThe data were obtained from the official database of the Iranian Legal Medicine Organization, which includes the injury rates of all provinces due to road accidents, from 2012 to 2021.ParticipantsAll records registered with injuries due to road traffic accidents across Iranian provinces.Outcome measuresThe incidence and average annual percentage of injury rates across provinces were illustrated using a map. A piecewise linear mixed-effects model was employed to estimate trends in injury rates, by gender. To identify distinct clusters of provinces exhibiting similar trends in injury rates, a growth mixture model was used over the 10 years.ResultsAmong provinces, Qom (95% CI 18.99 to 37.21) and Sistan and Baluchestan (95% CI 5.41 to 7.66) had the highest and lowest injury rates over the decade, respectively. The annual rate of injuries in Iran increased by 0.52% from 2012 to 2018 and then gradually decreased by 1.16% after 2018. Four distinct classes were identified for the trend of injury rates over the decade: one cluster exhibited a significant decline, two clusters showed sharp increases and the last one had a steady trend.ConclusionsThese results contribute valuable insights into the dynamics of road accident-related injuries in Iran, offering a nuanced understanding of both overarching national trends and the unique patterns observed across provinces. Such knowledge can serve as a foundation for targeted interventions and policy formulations aimed at mitigating the impact of road accidents on public health and safety.
Beyond the embrace: a phenomenological qualitative exploration of the impact of kangaroo mother care (KMC) on couple relationships in China
Authors: He Yiyin , Chen Peizhen , He Chunmei , Ding Jufang , Guo Hongqing , Ding Xin , Yao Wenying 
Published: February 2025

ObjectivesTo explore the impact of kangaroo mother care (KMC), involving both mothers and fathers, on the dynamics of couple relationships.DesignQualitative phenomenological study.SettingA regional comprehensive centre for child healthcare.Participants11 couples engaged in KMC with their infants. We created a semistructured interview guide to conduct face-to-face interviews separately with both wives and husbands. The interviews were audio-recorded and transcribed verbatim, and analysed using Braun and Clarke’s thematic analysis technique.ResultsAnalysis of participants’ narratives revealed three pivotal themes: ‘strengthening of couple relationship’, ‘role adaptation and redefinition’ and ‘conflicts and resolution’. These themes collectively illustrated the complex interplay between enhanced emotional intimacy, renegotiated parental roles and the navigation of conflicts within the context of neonatal caregiving.ConclusionsKMC may have effects on couple relationships beyond its immediate benefits for the infant. It may potentially influence the emotional and relational dynamics between partners. Couples' experiences with KMC practices are multifaceted and complex. Through the intimate act of KMC, couples may experience a deepening of emotional bonds, redefinition of roles and identities, and encounter both challenges and opportunities for conflict resolution. Adopting a more holistic approach to neonatal care including attention to the couple’s relationship and engaging in KMC is suggested.
Examining the association between child development and parental mental health after preterm birth-related stress: a systematic review of the literature and meta-analysis protocol
Authors: Muller Kirsten S , van den Bosch Gerbrich E , Henke Celina E , Daams Joost G , Haverman Lotte , Aarnoudse-Moens Cornelieke S H 
Published: February 2025

IntroductionPreterm infants born before 32 weeks of gestation are generally admitted to a neonatal intensive care unit (NICU) to receive life-saving treatment, resulting in early exposure to stressful events. Yet, NICU admission is not only stressful for the infant but can also have a long-lasting negative impact on parental mental health, who may worry about their child. Parental mental health problems might affect child development through parental behaviour and the parent–infant relationship. Simultaneously, adverse child development after preterm birth can (further) elevate parental stress and mental health problems, straining parental behaviour, the parent–infant relationship and child development. This systematic review and meta-analysis aims to examine the association between preterm-born children’s development (<32 weeks’ gestation) and parental mental health after preterm birth-related stress following NICU admission at any point in time.Methods and analysisA systematic review will be performed and reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A concept-based search on preterm birth, child development and parental mental health is performed using MEDLINE, Embase, PsycINFO and Cochrane Library on 22 March 2024. Eligible are studies with original results on the association between child development after preterm birth (<32 weeks’ gestation) and parental mental health. Independent reviewers will screen the articles, assess study quality using a Newcastle-Ottawa or Cochrane tool and determine the quality of evidence using Grading of Recommendations, Assessment, Development and Evaluation. Meta-analyses are planned on the association between child development and parental mental health after preterm birth.Ethics and disseminationNo ethical approval is required. The results will enhance knowledge of the association between child development and parental mental health after preterm birth-related stress following NICU admission. This might lead to adjustments in follow-up care, optimising outcomes for infants and parents. Findings will be published in an international, peer-reviewed ad open-access journal.PROSPERO registration numberCRD42024518307.
Cohort profile: Outcome Monitoring After Cardiac Surgery (OMACS) – a prospective UK cohort study of cardiac surgery patients at the Bristol Heart Institute
Authors: Joyce Katherine , Maishman Rachel , Walker-Smith Terrie , Smartt Helena , Hopkins Emma , Lambert Penny , Angelini Gianni , Rogers Chris A , Reeves Barnaby , Brierley Rachel , Culliford Lucy 
Published: February 2025

PurposeThe Outcome Monitoring After Cardiac Surgery (OMACS) cohort study was set-up with the aim of establishing a rich source of biological samples and health status data from patients who undergo cardiac surgery. The objectives were to use these data to inform the design of new clinical studies and to provide samples and data to answer research questions.ParticipantsRecruitment began on 23 May 2016 and ended 31 May 2022. Adult patients undergoing cardiac surgery at University Hospitals Bristol and Weston NHS Foundation Trust were screened and approached for consent. Participants could optionally consent to provide biological samples (urine, blood and waste tissue) in addition to data. A total of 4068 patients consented to participate in the study with 2027 consenting to donate samples. Participants were sent quality-of-life follow-up questionnaires at 3 and 12 months after surgery. The clinical data were collected from hospital records/databases.Findings to dateThe OMACS population appears to be representative of the wider cardiac surgery population with similar preoperative demography to those reported on the UK surgery population. To date, eight studies have been carried out by research teams using data from a total of 1165 OMACS participants. Two Studies Within A Trial have been performed by the OMACS study team. The format of the study patient information leaflet was not significantly associated with an increased recruitment rate, and an alternative theory-informed cover letter included with the 12-month follow-up questionnaires was not associated with an increase in questionnaire completion. Additional exploratory research carried out within the OMACS study has been presented at international conferences.Future plansThe OMACS study is now closed. The cohort’s data and samples will be available to share with researchers, providing an opportunity to answer a variety of research questions (eg, evaluating predictors of adverse outcomes after cardiac surgery such as biomarkers, surgical methods and pre-existing conditions). The data and samples will be available for sharing in a linked anonymised format.Trial registration numberISRCTN90204321(date assigned: 21 January 2015).
HER-SAFE study design: an open-label, randomised controlled trial to investigate the safety of withdrawal of pharmacological treatment for recovered HER2-targeted therapy-related cardiac dysfunction
Authors: Dowsing Benjamin , Dehbi Hakim-Moulay , Chung Robin , Pedra Joanna , Worn Orla , Artico Jessica , Schmid Peter , Roylance Rebecca , Kellman Peter , Moon James C , Crake Tom , Westwood Mark , Ghosh Arjun , Andres Maria Sol , Nazir Muhummad Sohaib , Lyon Alexander R , Chen Daniel , Walker Malcolm , Manisty Charlotte H 
Published: February 2025

IntroductionA quarter of breast cancers show human epidermal growth factor-2 (HER2) overexpression, where targeted therapy dramatically improves survival. However, cancer therapy-related cardiac dysfunction (CTRCD) occurs in up to 15% of patients. With the interruption of HER2 therapy, if necessary, and the initiation of heart failure therapy (HFT), HER2 CTRCD recovers in over 80% of cases. The need to continue HFT in ‘recovered’ HER2 CTRCD following completion of HER2 therapy is unclear and there are potential significant impacts on patient’s quality of life (QoL). The Randomised Controlled Trial for the Safety of Withdrawal of Pharmacological Treatment for Recovered HER2 Targeted Therapy Related Cardiac Dysfunction (HER-SAFE) aims to evaluate whether HFT can be safely withdrawn in non-high cardiovascular (CV) risk patients with ‘recovered’ HER2 CTRCD.Methods and analysisThis is a multicentre, open-label randomised controlled trial investigating whether withdrawal of HFT is non-inferior to continuation in non-high CV risk, breast cancer survivors with recovered HER2 CTRCD after cancer treatment completion. The primary endpoint is the incidence of guideline-defined cardiac dysfunction or clinical heart failure. Secondary endpoints include changes in cardiac blood biomarkers, cardiovascular magnetic resonance (CMR)-derived strain and tissue mapping and heart failure symptom questionnaires. The study will recruit 90 participants who will undergo serial clinical assessment over 12 months with advanced cardiovascular imaging (CMR scans with automated analysis at baseline, 6 and 12 months), cardiac biomarker measurement (six time points over 12 months), plus complete heart failure QoL and medication disutility questionnaires. This is the first multicentre study to address this significant clinical issue.Ethics and disseminationThis study was approved by the research ethics committee (London—London Bridge, 23/LO/0152). The results will be disseminated in peer-reviewed scientific journals.Trial registration numberNCT05880160.
Strength training for osteoporosis prevention during early menopause (STOP-EM): a pilot study protocol for a single centre randomised waitlisted control trial in Canada
Authors: Alexander Christina J , Kaluta Leah , Whitman Patrick W , Billington Emma O , Burt Lauren A , Gabel Leigh 
Published: February 2025

IntroductionWomen lose up to 10% of their bone mass around menopause and the decade following. There is a need for proactive approaches to preserve bone mass and quality around menopause. Existing work has found that high-intensity resistance and impact training (HiRIT) can improve bone and muscle measures in late postmenopausal women. However, this has not been investigated in perimenopausal and early postmenopausal women who are in the midst of the menopausal transition.Methods and analysisThis study is a 9-month randomised controlled feasibility trial evaluating a HiRIT programme in perimenopausal and early postmenopausal women. The primary objective of this study is to determine the feasibility of HiRIT in 40 perimenopausal and early postmenopausal women (45–60 years). Participants will be randomised 1:1 into a supervised HiRIT exercise intervention and waitlisted control. The primary outcomes are recruitment, retention and adherence to the exercise intervention. Secondary outcomes include bone (bone mineral density, microarchitecture and strength), muscle (mass, strength and power), physical function (balance and aerobic fitness) and quality of life measures. Feasibility will be assessed based on a priori criterion for success and secondary outcomes will be assessed via multiple linear regressions. The study will be considered feasible if>50% of interested and eligible participants are recruited, if there is>60% adherence to the two times per week, 9-month exercise intervention and if at least 65% of the sample complete the final study visit.Feasibility outcomes will be used to inform a larger, future trial aimed at identifying the efficacy of the exercise intervention for improving various health outcomes, including bone density and muscle mass.Secondary exploratory outcomes will provide insight into the effect of exercise on muscle and bone in perimenopausal and early postmenopausal women.Ethics and disseminationThis study has been approved by the Conjoint Health Research Ethics Board of the University of Calgary REB22-1632. The results of this study will be disseminated at national and international conferences and published in academic journals.Trail registration numberClinicalTrials.gov:NCT05961371. (Protocol V.1.2, 28 September 2023)