bluuebunny/crossref_metadata_2025_split huggingface dataset:
What are the essential determinants of human papillomavirus carcinogenesis?
Authors: Munger Karl , White Elizabeth A. 
Published: October 2024

ABSTRACT

Human papillomavirus (HPV) infection is the leading viral cause of cancer. Over the past several decades, research on HPVs has provided remarkable insight into human cell biology and into the pathology of viral and non-viral cancers. The HPV E6 and E7 proteins engage host cellular proteins to establish an environment in infected cells that is conducive to virus replication. They rewire host cell signaling pathways to promote proliferation, inhibit differentiation, and limit cell death. The activity of the “high-risk” HPV E6 and E7 proteins is so potent that their dysregulated expression is sufficient to drive the initiation and maintenance of HPV-associated cancers. Consequently, intensive research efforts have aimed to identify the host cell targets of E6 and E7, in part with the idea that some or all of the virus-host interactions would be essential cancer drivers. These efforts have identified a large number of potential binding partners of each oncoprotein. However, over the same time period, parallel research has revealed that a relatively small number of genetic mutations drive carcinogenesis in most non-viral cancers. We therefore propose that a high-priority goal is to identify which of the many targets of E6 and E7 are critical drivers of HPV carcinogenesis. By identifying the cancer-driving targets of E6 and E7, it should be possible to better understand the distinct roles of other targets, perhaps in the viral life cycle, and to focus efforts to develop anti-cancer therapies on the subset of virus-host interactions for which therapeutic intervention would have the greatest impact.
Complete genome sequence of a vampire bat-related rabies virus obtained by metagenomics from a patient with encephalitis of unknown etiology, French Guiana
Authors: Hourdel Véronique , Balière Charlotte , Vanhomwegen Jessica , Brisebarre Angela , Grassin Quentin , Manuguerra Jean-Claude , Kallel Hatem , Demar Magalie , Dacheux Laurent , Caro Valérie 
Published: October 2024

ABSTRACT

We report the complete genome sequence of a rabies virus obtained by direct metagenomics from the cerebellum of a gold panner who died of unknown encephalitis in French Guiana. Phylogenetic analysis exhibited a close genetic relationship with vampire bat-related isolates, confirming the second case of human rabies identified in this territory.
Transcriptomic data sets for
Novosphingobium aromaticivorans
grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid
Authors: Metz Fletcher , Myers Kevin S. , Lu Fachuang , Noguera Daniel R. , Donohue Timothy J. 
Published: October 2024

ABSTRACT

The transcriptomes of a 2-pyrone-4,6-dicarboxylic acid-producing strain of
Novosphingobium aromaticivorans
DSM12444 were determined when grown in minimal medium containing glucose alone or glucose plus vanillin, ferulic acid, or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol as carbon sources. Here, we present the RNA-sequencing data we obtained.
Draft genome sequence of
Sanguibacter
species strain 25GB23B1, cultivated from arctic surface seawater
Authors: Mitchell Kiana , Busch Grace , Sharma Indu 
Published: October 2024

ABSTRACT

We report a draft genome sequence for
Sanguibacter
species strain 25GB23B1, isolated from arctic surface seawater off the coast of Alaska. The whole genome sequence will provide knowledge of the bacteria’s relationship to its environment and possibly a new species of
Sanguibacter
.
Pan-genome-scale metabolic modeling of
Bacillus subtilis
reveals functionally distinct groups
Authors: Neal Maxwell , Brakewood William , Betenbaugh Michael , Zengler Karsten 
Published: October 2024

ABSTRACT

Bacillus subtilis
is an important industrial and environmental microorganism known to occupy many niches and produce many compounds of interest. Although it is one of the best-studied organisms, much of this focus including the reconstruction of genome-scale metabolic models has been placed on a few key laboratory strains. Here, we substantially expand these prior models to pan-genome-scale, representing 481 genomes of
B. subtilis
with 2,315 orthologous gene clusters, 1,874 metabolites, and 2,239 reactions. Furthermore, we incorporate data from carbon utilization experiments for eight strains to refine and validate its metabolic predictions. This comprehensive pan-genome model enables the assessment of strain-to-strain differences related to nutrient utilization, fermentation outputs, robustness, and other metabolic aspects. Using the model and phenotypic predictions, we divide
B. subtilis
strains into five groups with distinct patterns of behavior that correlate across these features. The pan-genome model offers deep insights into
B. subtilis’
metabolism as it varies across environments and provides an understanding as to how different strains have adapted to dynamic habitats.

IMPORTANCE

As the volume of genomic data and computational power have increased, so has the number of genome-scale metabolic models. These models encapsulate the totality of metabolic functions for a given organism.
Bacillus subtilis
strain 168 is one of the first bacteria for which a metabolic network was reconstructed. Since then, several updated reconstructions have been generated for this model microorganism. Here, we expand the metabolic model for a single strain into a pan-genome-scale model, which consists of individual models for 481
B. subtilis
strains. By evaluating differences between these strains, we identified five distinct groups of strains, allowing for the rapid classification of any particular strain. Furthermore, this classification into five groups aids the rapid identification of suitable strains for any application.
Salivary microbiota reflecting changes in subgingival microbiota
Authors: Jung Jae-Suk , Kook Joong-Ki , Park Soon-Nang , Lim Yun Kyong , Choi Geum Hee , Kim Sunjin , Ji Suk 
Published: October 2024

ABSTRACT

The purpose of this study was to determine whether subgingival microbial changes according to the severity of periodontal disease and following the non-surgical periodontal treatment of periodontitis are reflected in the saliva microbiota. Subgingival and saliva samples were collected from 7 periodontally healthy controls, 14 patients with gingivitis, 12 with moderate periodontitis, and 18 with severe periodontitis. Among subjects who received treatment, seven moderate and seven severe periodontitis patients were selected for post-treatment microbial analysis, and their samples were analyzed at baseline and 6 months after treatment. The V3 and V4 regions of the 16S rRNA gene were sequenced, and correlations of the relative abundance of phyla and health- or periodontitis-dominant species between subgingival plaque and saliva samples were analyzed using Spearman signed-rank tests. Alpha diversity was higher in saliva than subgingival plaque samples, and beta diversity was significantly different between the two samples. However, levels of phyla and most health- or periodontitis-dominant species in salivary microbiota were significantly correlated with those in subgingival plaque. The improvement in clinical parameters following treatment was accompanied by a microbial shift not only in subgingival plaque but also in saliva. The abundance of 2 phyla including Bacteroidetes, 6 genera including
Porphyromonas
and
Treponema
, and 11 species including
Porphyromonas gingivalis
,
Tannerella forsythia
, and
Filifactor alocis
was significantly reduced in saliva following treatment. These results indicate that the salivary microbiota can reflect changes in the subgingival microbiota, suggesting that saliva can be used as a diagnostic tool to monitor the periodontal health status of individuals.

IMPORTANCE
The salivary microbiota has attracted increasing attention as a promising method for monitoring periodontal disease. With regard to the pathogenesis of periodontal disease, however, subgingival plaque microbiota is the dominant etiological factor. Although it has been established that periodontopathogenic bacteria exist in saliva and their distribution differs, depending on the severity of the disease, it is necessary to analyze the extent to which the salivary microbiota reflects the subgingival microbiota. This study explored whether subgingival microbial changes according to the severity of periodontal disease and following the non-surgical periodontal treatment of periodontitis are reflected in the saliva microbiota and concluded that the salivary microbiota can reflect changes in the subgingival microbiota. Saliva can be used as a diagnostic tool to monitor the periodontal health status of individuals.
Exhumation history of the Shanxi Rift, Central Asia, derived from low-temperature thermochronology
Authors: Wang Hongtao , Li Shichao , Yang Xiaopeng , Zuza Andrew V. , Liu Fangbin , Sheldrick Thomas C. , He Xiaoqi , Zhang Jin 
Published: October 2024

Abstract
The Shanxi Rift system in Central Asia is a prominent Cenozoic intraplate rift system within the North China craton that also preserves a record of Mesozoic contractional deformation. The overprinting phases of deformation complicate interpretations of its tectonic history. Here, we present new apatite fission-track (AFT) thermochronology data from the northern flank of the rift system and compile a large thermochronology dataset from around the Shanxi Rift. We also present a new seismic reflection profile for the central Datong Basin to investigate synkinematic basin sediments within the rift. Thermal inverse models of low-temperature thermochronology data reveal temporal and spatial variations in exhumation rates across the rift flanks. The northern rift started exhuming in the Late Jurassic–Early Cretaceous, whereas the central and southern flanks experienced mainly Cenozoic exhumation. Between 50 Ma and 30 Ma, exhumation rates diminished from south to north but markedly accelerated again after 20 Ma. These modeling results reveal that normal faulting along the rift flank was active between 40 Ma and 25 Ma coupled with basin subsidence. The main phase of rifting initiated in the Paleogene, with deformation propagating from southwest to northeast. Postulated Late Jurassic crustal shortening in the Shanxi Rift system followed by Early Cretaceous extension explain the ages in the north, and these dynamics were probably driven by west-dipping flat-slab subduction of the Izanagi (Paleo-Pacific) slab and subsequent slab rollback. Cenozoic rifting across the Shanxi Rift was caused by the combined impacts of Pacific slab dynamics and the growing margin of the Tibetan Plateau.
Diachronous end-Permian terrestrial crises in North and South China
Authors: Chu Daoliang , Song Haijun , Dal Corso Jacopo , Winguth A.M.E. , Gautam Mitali D. , Wignall Paul B. , Grasby Stephen E. , Shu Wenchao , Song Hanchen , Song Huyue , Tian Li , Wu Yuyang , Tong Jinnan 
Published: October 2024

Abstract
Climate breakdown driven by massive volcanic eruptions was the likely cause of the terrestrial Permian–Triassic mass extinction (ca. 252 Ma). However, establishing the relationship between climate factors and terrestrial ecosystem responses is difficult. Furthermore, it is unclear if the pattern and timing of the terrestrial ecosystem crises are consistent across different regions. Our integrated paleontology and geochemistry study indicates that the onset of the terrestrial crisis in North China preceded that in South China by at least 300 k.y. Geological and Earth system modeling suggest that lethal heatwaves and aridity, along with enhanced climate seasonality, were caused by higher atmospheric CO2. The onset of these environmental changes varied regionally and were likely responsible for the diachronous terrestrial crisis. Our results indicate that, rather than a globally synchronous event, cumulative regional extirpations ultimately resulted in a global terrestrial extinction.
The impact of increasing temperatures due to climate change on infectious diseases
Authors: Anikeeva Olga , Hansen Alana , Varghese Blesson , Borg Matthew , Zhang Ying , Xiang Jianjun , Bi Peng 
Published: October 2024

Abstract
Global temperatures will continue to rise due to climate change, with high temperature periods expected to increase in intensity, frequency, and duration. Infectious diseases, including vector-borne diseases such as dengue fever and malaria, waterborne diseases such as cholera, and foodborne diseases such as salmonellosis are influenced by temperature and other climatic variables, thus contributing to higher disease burden and associated healthcare costs, particularly in socioeconomically disadvantaged regions. Targeted efforts and investments are therefore needed to support low and middle income countries to prepare for and respond to the increasing infectious disease threats posed by rising temperatures. This can be facilitated by the development and refinement of robust disease and entomological surveillance and early warning systems with integration of climatic information that promote enhanced understanding of the geographic distribution of disease risk. To enhance healthcare workforce capacity and capability to respond to these public health threats, medical curricula and continuing professional education programmes for healthcare providers must include evidence based components on the impacts of climate change on infectious diseases.
Recent trends in GLP-1 RA and SGLT2i use among people with type 2 diabetes and atherosclerotic cardiovascular disease in the USA
Authors: King Aaron , Tan Xi , Dhopeshwarkar Neil , Bohn Rhonda , Dea Katherine , Leonard Charles E , de Havenon Adam 
Published: October 2024

IntroductionThis study aimed to assess recent trends in the US use of glucagon-like peptide-1 receptor agonist (GLP-1 RA) and sodium-glucose cotransporter 2 inhibitor (SGLT2i) in people with type 2 diabetes (T2D) and atherosclerotic cardiovascular disease (ASCVD), including incident use following newly diagnosed ASCVD.Research design and methodsThis real-world, retrospective observational study used de-identified data from the TriNetX Dataworks–USA network. A longitudinal analysis of cross-sectional data (interval: January 01, 2018 to December 31, 2022) assessed the yearly prevalent use of GLP-1 RA and SGLT2i. A nested cohort study (January 01, 2017 to January 31, 2023) assessed the proportions of patients with T2D newly prescribed GLP-1 RAs and SGLT2is after incident ASCVD diagnosis.ResultsPrevalent use of GLP-1 RA and/or SGLT2i increased from 9.2% of patients in 2018 to 27.1% in 2022, with eligible annual patient numbers ranging from 279,474 to 348,997. GLP-1 RA-alone use rose from 5.2% to 9.9% and SGLT2i-alone use rose from 2.8% to 12.2% over this interval. Incident use of GLP-1 RA and/or SGLT2i within the year following ASCVD diagnosis increased from 5.9% to 17.0% (2018–2022). For GLP-1 RA alone, this increase was from 3.6% to 7.8%, while for SGLT2i alone, it was from 1.8% to 7.0%.ConclusionsUse of GLP-1 RAs/SGLT2is in patients with T2D and ASCVD has increased in recent years in the USA, but remains suboptimal given the prevalence of ASCVD and its high morbidity and mortality.
Long-term probabilistic forecasts of activity mitigation in English hospitals: a national elicitation exercise providing an outside view based on judgements of experts in support of the New Hospital Programme
Authors: Mohammed Mohammed A , Jemmett Thomas , Cook Josh , Parsons Jake , Wyatt Steven , Beeley Chris , Spilsbury Peter 
Published: October 2024

ObjectivesThe planning process for a new hospital relies on assumptions about future levels of demand. Typically, such assumptions are characterised by point estimates, the flaw-of-averages, base-rate neglect and overoptimism from an inside view. To counteract these limitations, we elicited an outside view of probabilistic forecasts based on judgements of experts about the extent to which various types of hospital activity might be mitigated over 20 years, in support of the New Hospital Programme (NHP) in the English National Health Service.DesignA prospective online elicitation exercise, over two rounds, to forecast the reduction (0% no reduction to 100% total reduction) in 77 types of hospital activity across England via five types of activity mitigation: outpatient attendance avoidance (n=8); inpatient admission avoidance (n=31); A&E attendance avoidance (n=12); outpatient delivery mode (n=4); inpatient length of stay reduction (n=22) and eight types of activity groups.Primary outcomes are the aggregated forecasts representing the percentage reduction (0%–100%) in hospital activity across England based on ‘surprisingly low’ (10th percentile—P10) to ‘surprisingly high’ (90th percentile—P90) forecasts from 17 experts.ResultsWe had 657 forecasts from 17 experts. The most pessimistic forecast was for inpatient avoidance of frail elderly admissions (mean 5.71%, P10=0.43%, P90=16.40%). The most optimistic forecast was for inpatient admission avoidance for vascular surgery (mean 48.27%, P10=19.82%, P90=78.57%). The overall (n=77) aggregate means ranged from a low of 5.71% to a high of 48.27% with an average width of 50.08%. Experts highlighted mainly four types of mitigation mechanisms—prevention, displacement, quality improvement and de-adoption.ConclusionA national elicitation exercise has provided long-term aggregate forecasts across England that make explicit the wide variation and uncertainty associated with future mitigation activities from an outside perspective. These aggregate forecasts may now be incorporated into the NHP, providing a more robust foundation for planning.
Development of a vocational rehabilitation intervention to support return-to-work and well-being following major trauma: a person-based approach
Authors: Radford Kate , Kettlewell Jade , das Nair Roshan , Morriss Richard , Holmes Jain , Kellezi Blerina , Timmons Stephen , Jones Trevor , Tresidder Hereward , Andrews Isobel , Bridger Kay , Patel Priya , Lindley Rebecca , De Dios Perez Blanca , Statham Abigail , Jones Tadeusz , Hoffman Karen , James Marilyn , Kendrick Denise 
Published: October 2024

ObjectivesMajor trauma centres (MTCs) save lives but rehabilitation to support return-to-work (RTW) is lacking. This paper describes development of a vocational rehabilitation intervention (the ROWTATE intervention) to support RTW following traumatic injury.DesignSequential and iterative person-based approach in four stages—Stage 1:review of evidence about the efficacy and mechanisms of RTW interventions;Stage 2:interviews (n=38) and focus groups (n=25) with trauma survivors and service providers in five UK MTCs to identify the issues, and challenges faced postinjury;Stage 3: codesign workshops (n=43) with trauma stakeholders in MTCs to conceptually test and identify intervention delivery barriers/enablers;Stage 4:meetings (n=7) with intervention development working group (IDWG) to: (1) generate guiding principles, (2) identify key intervention features (process, components, mechanisms) to address unmet rehabilitation needs; (3) generate a logic model and programme theory to illustrate how the intervention works; and (4) develop a training package to support delivery.ResultsTrauma survivors described unmet needs relating to early advice about RTW; psychological support; pain management; hidden disabilities (eg, fatigue); estimating recovery; and community, amputee and musculoskeletal rehabilitation. Mechanisms of effective interventions identified in the review included early intervention, colocation, employer engagement, case coordination and work accommodations. Intervention features identified by IDWG members (n=13) from stages 1 and 2 were use of stepped-care approaches by occupational therapists (OTs) and clinical psychologists (CPs), OT/CP formulation for complex cases, assessment of mental health problems, individually tailored rehabilitation including vocational goal setting, cross-sector coordination/communication, employer engagement, phased RTW, education/advice for family/employers, exploration of work alternatives, ongoing review of physical and mental health needs, work stability monitoring. Conceptual testing ratified the logic model. Geography and long waiting lists were identified as potential delivery barriers.ConclusionsReal-world testing of the intervention is underway in a randomised controlled trial.
Substance use and risk of suicide among adults who sought mental health and addiction specialty services through a centralised intake process in Nova Scotia: a cross-sectional study
Authors: Soboka Matiwos , Stewart Sherry H , Tibbo Philip , Wang JianLi 
Published: October 2024

Objectives
The objectives of this study are as follows: (1) to estimate the prevalence of suicide risk among individuals seeking mental health and addiction (MHA) services in Nova Scotia; (2) to examine the relationship between substance use and suicide risk among this population.

Setting
MHA intake programme, a province-wide centralised intake process established in 2019 by the Department of Health and Wellness of Nova Scotia.

Participants
We included 22 500 MHA intake clients aged 19–64 years old who contacted MHA intake from 2020 to 2021.

Primary outcome measures
During the intake assessment, clients were assessed for suicide risk (past suicide attempt, suicidal ideation during the interview or 2 weeks before the interview).

Results
The lifetime prevalence of suicide attempt was 25.25% in the MHA clients. The prevalence of mild and moderate/high suicide risk was 34.14% and 4.08%, respectively. Clients who used hallucinogens had the highest prevalence of mild and moderate/high suicide risk (61.3% and 12.9%, respectively), followed by amphetamine/methamphetamine (47.6% and 13.3%, respectively) and sedative/hypnotics (47.2% and 8.9%, respectively) users. Stimulant (aOR=1.84, 95% CI 1.23 to 2.75) and hallucinogen (aOR=3.54, 95% CI 1.96 to 6.43) use were associated with increased odds of moderate/high suicide risk compared with denying current use. Additionally, alcohol (aOR=1.17, 95% CI 1.06 to 1.30) and tobacco (aOR=1.20, 95% CI 1.10 to 1.30) use were associated with increased odds of mild suicide risk.

Conclusion
Suicide behaviours were prevalent among clients seeking MHA services. Substance use is an important factor associated with suicide risk in this population. This result underscored the importance of considering substance use patterns when assessing suicide risk and highlighted the need for targeted interventions and preventive measures for individuals engaging in substance use. Future interventional studies are needed to identify and evaluate effective strategies for reducing substance use and suicide risk among clients of MHA central intake.