bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes
Authors: Shitrit Alina , Nisnevich Valerya , Rozenshtein Nofar , Kobo Hila , Phan Hoang Van , Tay Savaş , Szpara Moriah , Weitzman Matthew D. , Drayman Nir , Kobiler Oren 
Published: November 2023

ABSTRACT
Genomic rearrangements contribute to the enhancement of genetic diversity in populations. However, non-canonical rearrangements (NCRs) such as deletions, insertions, and inversions have the potential to trigger genomic instability. In the case of DNA viruses, NCRs can lead to generation of defective viral genomes (DVGs). To study NCRs in herpes simplex virus type 1 (HSV-1) genomes, we enriched DVGs formation by undiluted serial passaging on various cell types. We found that viral passaging on cell type that enables more viral genomes to initiate replication induces higher amplitude and frequency of cyclic patterns associated with DVGs formation. Despite differences in the rates of DVG accumulation, cell lines displayed comparable quantities of distinct NCRs, indicating that fluctuations caused by DVGs may impose bottlenecks on population genetic diversity. These findings propose additional roles for DVGs in modulating viral genetic diversity. Each cell type exhibited a unique population of NCRs, suggesting that NCRs accumulate in a cell type-specific manner. Interestingly, we identified a higher prevalence of short homologies and short reverse complementary in the parental sequences of NCR junction sites across all cell types. These shared sequence characteristics were also observed in NCRs identified in sequences obtained from clinical samples. The fundamental properties of HSV-1 NCR formation uncovered in this study may have broader implications for other DNA viruses.

IMPORTANCE
Mutations and genetic rearrangements are the primary driving forces of evolution. Viruses provide valuable model systems for investigating these mechanisms due to their rapid evolutionary rates and vast genetic variability. To investigate genetic rearrangements in the double-stranded DNA genome of herpes simplex virus type 1, the viral population was serially passaged in various cell types. The serial passaging led to formation of defective genomes, resulted from cell-specific non-canonical rearrangements (NCRs). Interestingly, we discovered shared sequence characteristics underlying the formation of these NCRs across all cell types. Moreover, most NCRs identified in clinical samples shared these characteristics. Based on our findings, we propose a model elucidating the formation of NCRs during viral replication within the nucleus of eukaryotic cells.
The phage fought the cells, and the phage won: a satellite symposium at the ASV 2023 annual meeting
Authors: Parent Kristin N. 
Published: November 2023

ABSTRACT

This satellite symposium was focused on the molecular arms race between bacteria and their predators, the bacteriophages: who’s the friend and who’s the foe? This
Gem
recounts highlights of the talks and presents food for thought and additional reflections on the current state of the field.
HIV-2 inhibits HIV-1 gene expression via two independent mechanisms during cellular co-infection
Authors: Yapo Vincent , Majumder Kinjal , Tedbury Philip R. , Wen Xin , Ong Yee T. , Johnson Marc C. , Sarafianos Stefan G. 
Published: November 2023

ABSTRACT
Human immunodeficiency virus (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS). The two main forms of HIV are HIV-1 and HIV-2; in the clinic, each is predominantly found in the context of monoinfection. However, dual infections are found in regions where HIV-1 and HIV-2 coexist, such as West Africa. Both viruses can induce AIDS; however, HIV-2 is generally less pathogenic than HIV-1 and progresses more slowly to AIDS. Additionally, there are reports that HIV-2 infection can reduce HIV-1-associated pathogenesis in dual-infected patients, and in cell culture. However, the mechanisms underlying these protective effects are not well understood. To decipher these mechanisms, we performed dual infections with HIV-1 and HIV-2 in cell culture. We demonstrated that HIV-1 and HIV-2 can co-infect individual cells. HIV-2 infection was found to inhibit HIV-1 infection when performed prior to or simultaneously with HIV-1 infection. Two distinct mechanisms were identified. First, HIV-2 induces an interferon (IFN) response that broadly inhibits gene expression. Second, in the absence of IFN production, HIV-1-specific inhibition was found to be conferred by the HIV-2 trans-activation response (TAR) element. The HIV-2 TAR (TAR-2) element appears to inhibit HIV-1 long terminal repeat (LTR) promoter activity through competition with the HIV-1 TAR element for HIV-1 Tat binding. We show that this results in suppression of HIV-1 LTR-driven transcription by stalling RNA polymerase II early transcription complexes at the HIV-1 LTR promoter region.

IMPORTANCE
Twenty-five years after the first report that HIV-2 infection can reduce HIV-1-associated pathogenesis in dual-infected patients, the mechanisms are still not well understood. We explored these mechanisms in cell culture and showed first that these viruses can co-infect individual cells. Under specific conditions, HIV-2 inhibits HIV-1 through two distinct mechanisms, a broad-spectrum interferon response and an HIV-1-specific inhibition conferred by the HIV-2 TAR. The former could play a prominent role in dually infected individuals, whereas the latter targets HIV-1 promoter activity through competition for HIV-1 Tat binding when the same target cell is dually infected. That mechanism suppresses HIV-1 transcription by stalling RNA polymerase II complexes at the promoter through a minimal inhibitory region within the HIV-2 TAR. This work delineates the sequence of appearance and the modus operandi of each mechanism.
Metagenome-assembled genomes from particle-associated microbial communities in the mesopelagic zone of the Pacific Ocean
Authors: Hollensteiner Jacqueline , Schneider Dominik , Poehlein Anja , Himmelbach Axel , Daniel Rolf 
Published: November 2023

ABSTRACT

We report 10 particle-associated metagenome-assembled genomes (MAGs) from the mesopelagic zone of Pacific Ocean seawaters. MAGs comprise members of
Flavobacteria Halomonas
,
Blastomonas
,
Brevundimonas
,
Alteromonas, Shingomonas
,
Sphingopyxis
,
Tabrizicola, Proteobacteria
, and
Gammaproteobacteria
. Functional annotation suggests that these bacteria are involved in central particulate organic carbon conversion, nitrogen cycling, and phosphorus cycling.
Association between administration or recommendation of the human papillomavirus vaccine and primary care physicians’ knowledge about vaccination during proactive recommendation suspension: a nationwide cross-sectional study in Japan
Authors: Sakanishi Yuta , Takeuchi Jiro , Suganaga Rei , Nakayama Kuniko , Nishioka Yosuke , Chiba Hiroshi , Kishi Tomomi , Machino Ako , Mastumura Mami , Okada Tadao , Suzuki Tomio 
Published: November 2023

ObjectiveThe Japanese government suspended the proactive recommendation of the human papillomavirus vaccine (HPVv) in 2013, and the vaccination rate of HPVv declined to <1% during 2014–2015. Previous studies have shown that the recommendation by a physician affects a recipient’s decision to receive a vaccine, and physicians’ accurate knowledge about vaccination is important to increase vaccine administration. This study aimed to evaluate the association between physicians’ knowledge of vaccination and the administration or recommendation of HPVv by primary care physicians (PCPs) in the absence of proactive recommendations from the Japanese government.DesignCross-sectional study analysed data obtained through a web-based, self-administered questionnaire survey.SettingThe questionnaire was distributed to Japan Primary Care Association (JPCA) members.ParticipantsJPCA members who were physicians and on the official JPCA mailing list (n=5395) were included.Primary and secondary outcome measuresThe primary and secondary outcomes were the administration and recommendation of HPVv, respectively, by PCPs. The association between PCPs’ knowledge regarding vaccination and each outcome was determined based on their background and vaccination quiz scores and a logistic regression analysis to estimate the adjusted ORs (AORs).ResultsWe received responses from 1084 PCPs and included 981 of them in the analysis. PCPs with a higher score on the vaccination quiz were significantly more likely to administer the HPVv for routine and voluntary vaccination (AOR 2.28, 95% CI 1.58 to 3.28; AOR 2.71, 95% CI 1.81 to 4.04, respectively) and recommend the HPVv for routine and voluntary vaccination than PCPs with a lower score (AOR 2.17, 95% CI 1.62 to 2.92; AOR 1.88, 95% CI 1.32 to 2.67, respectively).ConclusionsThese results suggest that providing accurate knowledge regarding vaccination to PCPs may improve their administration and recommendation of HPVv, even in the absence of active government recommendations.
Clinical staging across eating disorders: a scoping review protocol
Authors: Hyam Lucy Elizabeth , Phillips Matthew , Gracie Lara , Allen Karina , Schmidt Ulrike 
Published: November 2023

IntroductionClinical staging models in psychiatry assert that there are earlier, less severe or more malleable forms of illness that are distinguishable from later, more chronic forms of illness, and that these stages may have different prognostic and treatment implications. Previous reviews on clinical staging in eating disorders (EDs) suggest a staging heuristic could be useful for anorexia nervosa, but less research is available on how this applies to other EDs. An up-to-date review is required to synthesise new and heterogenous avenues of research. This scoping review aims to explore the extent and types of evidence in relation to illness staging for EDs and how these concepts are associated with treatment response and outcomes.Methods and analysisThis protocol was developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol extension for Scoping Reviews checklist and the Joanna Briggs Institute Reviewer’s Manual. We will consider any documents providing evidence for clinical staging such as those which describe full or partial staging models, for all EDs, across various domains of assessment and functioning. Participants will include clinical or non-clinical population samples with full-syndrome EDs or disordered eating behaviour. PubMed, PsycINFO, MEDLINE and Web of Science databases will be systematically searched for relevant literature. Two authors will export documents and screen titles, abstracts and full texts. Data will be extracted into a charting form drafted by the authors. A narrative summary of the documents will be conducted in line with the study aims. Finally, clinical and research recommendations will be outlined.Ethics and disseminationEthical approval will not be required to synthesise published and unpublished literature. The study will be published in a peer-reviewed journal and shared at conferences, via social media, and in other communications.
Protocol of a randomised trial of teriparatide followed by zoledronic acid to reduce fracture risk in adults with osteogenesis imperfecta
Authors: Hald Jannie D , Keerie Catriona , Weir Christopher J , Javaid Muhammad K , Lam Wayne , Osborne Patricia , Walsh Jennifer , Langdahl Bente L , Ralston Stuart H 
Published: November 2023

IntroductionOsteogenesis imperfecta (OI) is a rare genetic disease associated with multiple fractures throughout life. It is often treated with osteoporosis medications but their effectiveness at preventing fractures is unknown. The Treatment of Osteogenesis Imperfecta with Parathyroid Hormone and Zoledronic Acid trial will determine if therapy with teriparatide (TPTD) followed by zoledronic acid (ZA) can reduce the risk of clinical fractures in OI.Methods and analysisIndividuals aged ≥18 years with a clinical diagnosis of OI are eligible to take part. At baseline, participants will undergo a spine X-ray, and have bone mineral density (BMD) measured by dual-energy X-ray absorptiometry (DXA) at the spine and hip. Information on previous fractures and previous bone targeted treatments will be collected. Questionnaires will be completed to assess pain and other aspects of health-related quality of life (HRQoL). Participants will be randomised to receive a 2-year course of TPTD injections 20 µg daily followed by a single intravenous infusion of 5 mg ZA, or to receive standard care, which will exclude the use of bone anabolic drugs. Participants will be followed up annually, have a repeat DXA at 2 years and at the end of study. Spine X-rays will be repeated at the end of study. The duration of follow-up will range between 2 and 8 years. The primary endpoint will be new clinical fractures confirmed by X-ray or other imaging. Secondary endpoints will include participant reported fractures, BMD and changes in pain and HRQoL.Ethics and disseminationThe study received ethical approval in December 2016. Following completion of the trial, a manuscript will be submitted to a peer-reviewed journal. The results will inform clinical practice by determining if TPTD/ZA can reduce the risk of fractures in OI compared with standard care.Trial registration numberISRCTN15313991.
Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial
Authors: Zhu Jiaying , Sun Chuqing , Li Min , Hu Guoru , Zhao Xing-Ming , Chen Wei-Hua 
Published: November 2023

Objective
We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis.

Design
Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups.

Results

Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like
Fusobacterium nucleatum
and
Streptococcus anginosus
. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users.

Conclusion
Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use.

Trial registration number
ChiCTR2300072310.
Genetic variations of type 2 and type 3 von Willebrand diseases in Thailand
Authors: Lauhasurayotin Supanun , Moonla Chatphatai , Ittiwut Rungnapa , Ittiwut Chupong , Songthawee Natsaruth , Komvilaisak Patcharee , Natesirinilkul Rungrote , Sirachainan Nongnuch , Rojnuckarin Ponlapat , Sosothikul Darintr , Suphapeetiporn Kanya 
Published: November 2023

AimsVon Willebrand disease (VWD) is an inherited haemostatic disorder with a wide range of bleeding phenotypes based on von Willebrand factor (VWF) levels. Multiple assays includingVWFgene analysis are employed to correctly diagnose VWD and its subtypes. However, data onVWFmutations among Southeast Asian populations are lacking. We, therefore, aimed to explore genetic variations in Thai patients with type 2 and type 3 VWD by whole exome sequencing (WES).MethodsIn this multicentre study, Thai patients with type 2 and type 3 VWD, according to the definitions and VWF levels recommended by the international guidelines, were recruited. WES was performed using DNA extracted from peripheral blood in all cases. The novel variants were verified by Sanger sequencing.ResultsFifteen patients (73% females; median age at diagnosis 3.0 years) with type 2 (n=12) and type 3 VWD (n=3) from 14 families were enrolled. All patients harboured at least oneVWFvariant. Six missense (p.Arg1374Cys, p.Arg1374His, p.Arg1399Cys, p.Arg1597Trp, p.Ser1613Pro, p.Pro1648Arg) and one splice-site (c.3379+1G>A) variants in theVWFgene were formerly described. Notably, sixVWFvariants, including three missense (p.Met814Ile, p.Trp856Cys, p.Pro2032Leu), one deletion (c.2251delG) and two splice-site (c.7729+4A>C, c.8115+2delT) mutations were novelly identified. Compound heterozygosity contributed to type 2 and type 3 VWD phenotypes in two and one patients, respectively.ConclusionsType 2 and type 3 VWD in Thailand demonstrate the mutational variations amongVWFexons/introns with several unique variants. The WES-based approach potentially provides helpful information to verify VWD diagnosis and facilitate genetic counselling in clinical practice.
Outdoor light at night and mortality in the UK Biobank: a prospective cohort study
Authors: Liang Xue , Wang Zixin , Cai Honglin , Zeng Yi Qian , Chen Jinjian , Wei Xianglin , Dong Guanghui , Huang Yu , Lao Xiang Qian 
Published: November 2023

BackgroundMore than 83% of the world’s population lives under light-polluted skies while information about health effects of outdoor light at night (LAN) is limited. We examined the association of LAN with natural cause (NC) and cardiovascular disease (CVD) mortality using the UK Biobank.MethodsWe included 273 335 participants recruited between 2006 and 2010. Level of LAN was estimated at each participant’s address using time-varying satellite data for a composite of persistent night-time illumination at ~1 km2scale. Information on causes of death until 12 November 2021 was obtained through record linkage. Cox proportional hazards regression was used.ResultsIn the follow-up with an average of 12.4 years, 14 864 NC and 3100 CVD deaths were identified. Compared with the participants exposed to the first quartile of LAN, participants exposed to the highest quartile showed an 8% higher risk of NC mortality (HR: 1.08, 95% CI 1.03 to 1.13) after adjusting for age, sex, social-economic status, shift work, lifestyle factors and body mass index. However, the association disappeared after further adjustment for PM2.5and evening noise, with HRs (95% CIs) of 1.02 (0.97 to 1.07), 1.01 (0.97 to 1.06) and 1.03 (0.97 to 1.08), respectively, for the participants exposed to the second, third and fourth quartiles of LAN. No significant associations were observed between LAN and CVD mortality, either.ConclusionsWe did not observe significant associations of LAN with NC and CVD mortality in this large nationwide cohort. The health effects of LAN remain unclear. Further studies are warranted to address this public health concern.
A proposed renormalization scheme for non-local QFTs and application to the hierarchy problem
Authors: Abu-Ajamieh Fayez , Vempati Sudhir K. 
Published: November 2023

AbstractWe propose a renormalization scheme for non-local Quantum Field Theories (QFTs) with infinite derivatives inspired by string theory. Our Non-locality Renormalization Scheme (NRS) is inspired by Dimensional Regularization (DR) in local QFTs and is shown to significantly improve the UV behavior of non-local QFTs. We illustrate the scheme using simple examples from the $$\phi ^{3}$$

ϕ
3

and $$\phi ^{4}$$

ϕ
4

theories, then we evaluate the viability of NRS-enhanced non-local QFTs to solve the hierarchy problem using a simplified toy model. We find that non-locality protects the mass of a light scalar from receiving large corrections from any UV sector to which it couples, as long as the non-locality scale $$\Lambda $$
Λ
is sufficiently smaller than the scale of the UV sector. We also find that NRS eliminates any large threshold corrections from the IR sector.
Demonstration of 75 km-fiber quantum clock synchronization in quantum entanglement distribution network
Authors: Tang Bang-Ying , Tian Ming , Chen Huan , Han Hui , Zhou Han , Li Si-Chen , Xu Bo , Dong Rui-Fang , Liu Bo , Yu Wan-Rong 
Published: November 2023

AbstractThe quantum entanglement distribution network, serviced as the communication infrastructure which distributes quantum information among remote users, enables many applications beyond the reach of classical networks. Recently, the applications such as quantum key distribution and quantum secure direct communication, have been successfully demonstrated in the quantum entanglement distribution network. In this article, we propose a multi-user round-trip quantum clock synchronization (QCS) scheme in the quantum network, which can be implemented with one single entangled photon source located at the server. The server distributes the entangled photons to remote multiple users with the wavelength division multiplexing strategy, and each user feeds partial received photons back to the server. The clock difference between the server and each user is calculated from the one-way and round-trip propagation times, which are determined according to the time correlation of entangled photons. Afterwards, the demonstration has been conducted between the server and a user over a 75-km-long fiber link, where the measured clock difference uncertainty is 4.45 ps, and the time deviation is 426 fs with an average time of 4000 s. Furthermore, the proposed QCS scheme is linearly scalable to many users, with respect to user hardware and number of deployed fibers.
Quantifying inaccuracies in vertical stress determination methods in sedimentary basins; a case study of deep coal-bearing strata in the Cooper Basin, Australia
Authors: Musolino Matthew , King Rosalind , Holford Simon , Hillis Richard 
Published: November 2023

Abstract

Knowledge of subsurface stresses is critical to management and prediction of fluid behaviour in the Earth's crust. However, uncertainties associated with the estimation of vertical stress magnitudes are rarely explored. In settings where the principal stresses are close, small changes of only a few MPa can have drastic effects on, stress regime prediction, fault reactivation and expected fracture behaviour. Using petroleum datasets from the Moomba Gas Field in the Cooper Basin, Australia, we assess the effects of interpolation between gaps in density wireline logs that have been filtered to remove sections of poor density tool contact in coal-bearing sequences. In addition, we compare the sonic velocity–density Nafe–Drake and Gardner transforms by comparing estimates of density from sonic velocity against density from wireline logs. The results indicate that vertical stress could be underestimated by
c.
3 MPa at
c.
3 km in well Moomba 61, using traditional methods. The Gardner transform shows a stronger correlation between sonic and density values for rocks in the Cooper Basin. However, once calibrated to the regional sonic velocity–density trend, the Nafe–Drake transform better matches the density logging tool in Moomba 61. This study delivers a more robust workflow for estimating the vertical stress in basins with deep coal-bearing strata.