bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples
Authors: Brochu Hayden N. , Zhang Qimin , Song Kuncheng , Wang Ling , Deare Emily A. , Williams Jonathan D. , Icenhour Crystal R. , Iyer Lakshmanan K. 
Published: February 2025

ABSTRACT

Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets
Atopobium
(
Fannyhessea
)
vaginae
,
Megasphaera-1
, and
Bacterial Vaginosis Associated Bacterium (BVAB)−2
. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3–V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3–V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3–V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (
P
< 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct
Lactobacilli
, and expanded the identification of BV-associated bacterial and metabolic biomarkers.

IMPORTANCE
Bacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.
Wild raccoons (
Procyon lotor
) as a potential reservoir of cytolethal distending toxin-producing
Providencia
strains in Japan
Authors: Obi Okechukwu John , Hinenoya Atsushi , Awasthi Sharda Prasad , Hatanaka Noritoshi , Faruque Shah M. , Yamasaki Shinji 
Published: February 2025

ABSTRACT

In view of increasing reports of infections due to virulent
Providencia
species including cytolethal distending toxin (
cdt
) gene-positive strains, it is important to identify the reservoirs and transmission routes of such pathogenic strains. Raccoons considered to be a source of zoonotic pathogens were monitored for the presence of
Providencia
species in Japan and analyzed for
cdt
genes. Of 384 wild raccoon rectal swabs analyzed, 60% were positive for
Providencia
species, of which 20% carried
cdt
-genes. Among seven
Providencia
species isolated (
P. alcalifaciens, P. rustigianii, P. rettgeri, P. stuartii, P. heimbachae, P. vermicola,
and
P. huaxiensis
),
cdt
genes were distributed in
P. alcalifcaiens
(63%),
P. rustigianii
(16%), and novel in
P. rettgeri
(21%). Complete
cdt
gene clusters were identified in
P. alcalifaciens
and
P. rustigianii
strains, whereas
P. rettgeri
had intact
cdtB
but truncated
cdtA
and
cdtC
genes. Phylogenetic analyses showed divergent pulsotypes among the
cdt
gene-positive
Providencia
strains. Cytotoxicity assay revealed that
P. alcalifaciens
and
P. rustigianii
produced CDT more toxic to eukaryotic cells compared to human clinical strains, which were neutralized by anti-PaCdtB serum. As expected, the
P. rettgeri
strains with truncated
cdt
genes had no biological activity. Molecular analysis revealed that all the
cdt
genes were located on plasmids as determined by S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern hybridization assay. Intriguingly, the
cdtB
gene in
P. rustigianii
strains was detected on dual plasmids. Notably, all the
cdt
gene-positive
Providencia
strains were found to carry plasmid-mediated T3SS-related genes. These results suggest that wild raccoons are possible reservoir of virulent
Providencia
strains in Japan.

IMPORTANCE

Providencia
species considered normal flora are occasionally associated with gastroenteritis in healthy humans. Cytolethal distending toxin (CDT), a bacterial virulence factor found in various Gram-negative bacteria and associated with gastroenteritis and extra-intestinal infection has also been reported in at least two
Providencia
species (
P. alcalifaciens
and
P. rustigianii
). Determination of the transmission routes of such virulent
Providencia
is crucial for the implementation of evidence-based control programs. In this study, we identified raccoons as the probable reservoir of the
cdt
gene-positive
Providencia
strains in Japan. Interestingly, CDTs produced by raccoon-derived
Providencia
strains exerted more toxic effects on the eukaryotic cells compared to the clinical
Providencia
strains. In addition, the identification of a novel
cdt
gene cluster in another species
P. rettgeri
isolated from raccoons suggests that
Providencia
may be categorized as an emerging zoonotic pathogen.
Knowledge, attitudes and practices regarding arteriovenous fistulas among uremic patients undergoing haemodialysis in China: a cross-sectional study
Authors: Huang Sifeng , Liu Xianli , Liu Yuhong , Liu Dongmei 
Published: February 2025

ObjectivesThis study aimed to investigate the relationship between knowledge, attitude and practice (KAP) regarding arteriovenous fistula (AVF) care in uremic patients undergoing haemodialysis (HD).DesignA web-based cross-sectional study was conducted among uremic patients receiving HD at the First Affiliated Hospital of Chongqing Medical University between April 2023 and June 2023.SettingThe study took place at the First Affiliated Hospital of Chongqing Medical University.ParticipantsA total of 522 valid questionnaires were collected from patients undergoing HD, representing 85.57% of the 610 patients eligible for the study.InterventionsPathway analysis was used to assess the interplay among KAP scores related to AVF care in the participants.Primary and secondary outcome measuresThe study evaluated KAP scores (ranging 0–20, 8–40 and 6–30, respectively) to gauge patients’ KAP regarding AVF care.ResultsThe findings indicated that patients exhibited adequate knowledge, positive attitudes and proactive practices towards AVF care. Patients’ knowledge directly influenced their attitudes and practices, with attitudes also positively impacting practices. Additionally, knowledge indirectly affected practices through attitudes.ConclusionsUremic patients undergoing HD demonstrated satisfactory understanding, favourable attitudes and proactive behaviours concerning AVF care. The pathway analysis provided insights into the relationships between KAP, illustrating the direct and indirect effects of these factors on each other in the context of AVF care among patients.
Effect of melatonin versus placebo for prevention of delirium among medically hospitalised patients: study protocol for a single-centre, double-blinded, randomised controlled trial (project RESTORE)
Authors: Al-Maqbali Juhaina Salim , Al-Busaidi Salim , Al Farsi Rajaa Saleh , Al Rasbi Sara , Al Zeedy Khalfan , Al Huraizi Aisha Ramadhan , Al Alawi Abdullah M 
Published: February 2025

IntroductionDelirium, a common neuropsychiatric condition in hospitalised older adults, is associated with increased mortality, longer hospital stays and cognitive decline. The potential of melatonin to prevent delirium by improving sleep patterns and regulating circadian rhythms is promising, though existing evidence is mixed. This study aims to evaluate the efficacy of melatonin in preventing delirium in medically hospitalised patients aged 65 years and older.Methods and analysisThis randomised, double-blind, placebo-controlled trial will enrol 240 patients aged 65 or older admitted to general medical wards at Sultan Qaboos University Hospital starting from September 2024. Participants will be randomly assigned to receive either 5 mg or 8 mg of melatonin or a placebo nightly for up to 5 days. The primary outcome is the incidence of delirium, assessed using the 3 min Diagnostic Confusion Assessment Method during the first 5 days. Secondary outcomes include the duration of delirium, sleep patterns and other clinical measures, such as hospital length of stay and 28-day readmission.Ethics and disseminationThe study protocol has received ethical approval from the Medical Research Ethics Committee at Sultan Qaboos University (REF. NO. SQU-EC/024\2024, MREC #3240). All participants or their legal proxies will provide informed consent prior to enrolment. Results will be disseminated through peer-reviewed publications and conference presentations, contributing to the global evidence base on delirium prevention strategies in hospitalised older adults.Trial registration numberClinicalTrials.gov under the identifierNCT06509191.
Role of informal carers in medication management for people with long-term conditions: a systematic review
Authors: Alkhaldi Maha , Lindsey Laura , Richardson Charlotte 
Published: February 2025

ObjectivesTo explore the literature about the role of unpaid informal carers in medication management for people with long-term conditions.DesignSystematic review designed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.Information sourceMEDLINE (Ovid), Embase (Ovid), PsycINFO, Cumulated Index in Nursing and Allied Health Literature (EBSCO), Scopus and Web of Science were searched from inception until April 2024. Additional papers were identified by searching backwards and forwards the reference lists of included papers.Eligibility criteriaPrimary research studies were included if they reported medication-related activities undertaken by carers for people with long-term conditions. Qualitative and mixed methods studies were considered without restriction on language or country.Data extraction and synthesisRelevant data were extracted and summarised in a table. The Mixed Method Appraisal Tool was used for quality assessment. Data were narratively synthesised.ResultsFrom 12 473 identified records, 107 underwent full text screening and 20 studies were included. Family carers were the predominant type of carer. Spouses and adult children constituted the largest caregiving dyads. Based on the required skills, two groups of roles were identified: physical roles, such as prescription management, and cognitive roles, such as decision-making. Carers used different strategies and tools to undertake medication-related activities including compliance aids and alarms. However, carers reported challenges in their experiences of caregiving, flagging up their need for additional support and education to commence such activities.ConclusionInformal carers undertake a wide variety of medication-related activities. The studies emphasised the need to support families as partners in health outcomes. This systematic review identifies the importance of bridging the gap between carers and healthcare providers. More efforts are needed to empower carers towards better and safer caregiving. Future work could address how to optimise carer involvement and engagement and provide best practice recommendations for carers’ support.PROSPERO registration numberCRD42024506694.
Key clinical findings from the IMPROVE-UK quality improvement projects: an overview
Authors: Phillips Andrew James , Bowen Rebecca , Wells Mary , McNeish Iain , Sundar Sudha 
Published: February 2025

IntroductionSurvival from ovarian cancer in the UK is poor compared with international comparators. The Ovarian Cancer Audit Feasibility Pilot demonstrated variation in 1-year and 5-year survival across the UK as well as significant variation in treatment rates. In 2020, IMPROVE-UK was established as the first major programme to address inequalities in ovarian cancer management and survival across the UK, to develop a legacy of best practice sharing across the country and to establish and evaluate quality improvement projects that could drive care at scale.MethodsFollowing a competitive process, seven quality improvement projects were funded to address inequalities in care and identify strategies to improve and equalise survival rates for all women with ovarian cancer in the UK, to address health inequalities from geography, age or ethnicity.ResultsProjects addressed the secondary care diagnostic pathway, genomic testing, prehabilitation and improving treatment-related decision-making, particularly decisions for surgery. All seven projects at least partial achieved their aims with numerous areas across all projects identified where processes could be refined and incorporated into standard care to improve outcomes of women diagnosed with ovarian cancer. Dissemination of information regarding best practice has been undertaken.ConclusionIMPROVE-UK was the first programme of its kind addressing significant inequalities of care in women with ovarian cancer. We demonstrate systematic quality improvement projects in ovarian cancer targeting various aspects of the treatment journey. Scaling up the results of the improve UK pilots is likely to improve survival in the UK and potentially internationally.
Measurements of the quantum yield of silicon using Geiger-mode avalanching photodetectors
Authors: Lewis Harry , Mahtab Mahsa , Retière Fabrice , De St. Croix Austin , Raymond Kurtis , Henriksson-Ward Maia , Morrison Nicholas , Zhang Aileen , Capra Andrea , Underwood Ryan 
Published: February 2025

Abstract
Accurate characterization of quantum yield is crucial to the reconstruction of energy depositions in silicon at the eV scale. This work presents a new method for experimentally calculating quantum yield using vacuum UV-sensitive silicon photomultipliers (SiPMs), which can be used to determine the probabilities that a UV photon absorbed in a silicon crystal will produce one, two, or three electron–hole pairs. Results are presented which fully constrain the distribution at photon energies up to 7.75 eV. This method works by exploiting the saturation of photon detection efficiency which occurs when these devices are biased sufficiently high above their avalanche breakdown voltage. The measured quantum yield values are lower than those that have been previously reported by experimental data and modelling – this is expected to impact the sensitivity of experiments searching for light dark matter through direct detection in semiconductors, and should also be taken into account when characterizing the performance of UV photodetectors with high quantum efficiency. Measurements have been taken using a Hamamatsu VUV4 and an FBK VUV-HD3 device, showing good agreements between devices, and at a range of temperatures from 163–233 K. The validity of the method is assessed using supplementary measurements of absolute photon detection efficiency, and an additional novel method of measuring average quantum yield using DC current–voltage measurements of SiPMs is presented and used for corroboration.
Lag synchronization in an unidirectional ring of memristive neurons
Authors: Vijayan Vijeesh , Natiq Hayder , Momani Shaher , Pham Viet-Thanh , Perc Matjaž 
Published: February 2025

Abstract
In recent years, the study of neuronal models has provided significant insights into brain dynamics and neurological disorders. Map-based neuronal models, such as the Rulkov map, have gained considerable popularity due to their computational efficiency and ability to replicate complex neuronal dynamics. We thus here study the collective dynamics of an unidirectional ring network composed of three memristive Rulkov maps, with particular emphasis on synchronization patterns and their dependence on coupling types. By employing electrical and memristive/field couplings, we analyze the emergence of complete synchronization, lag synchronization, and phase synchronization under varying coupling strengths. Our findings highlight how diffusive-based synaptic pathways modulate synchronization and collective behavior in the network. The presented results also offer new perspectives on the role of coupling functions in shaping neuronal synchronization, and they reveal their deeper implications for understanding pathological brain states and for designing neuromorphic systems.
Seismic stratigraphy of the Guinea Plateau before, during and after the opening of the Equatorial Atlantic Gateway
Authors: Aduomahor Benedict , Duarte Debora , Wagner Thomas , Dunkley Jones Tom , Nicholson Uisdean 
Published: February 2025

The Guinea Plateau contains a ∼200-million-year stratigraphic record, encompassing the mid-Cretaceous opening of the Equatorial Atlantic Gateway (EAG). Here we present new 2D seismic data to constrain the structural and stratigraphic evolution of the plateau. Seismic stratigraphic analysis reveals five megasequences of ∼25-65 My duration: M1, a Jurassic syn-rift sequence with prominent seaward-dipping reflections; M2, a late Jurassic-Early Cretaceous post-rift carbonate platform; M3, a late Early Cretaceous transform clastic-dominated sequence; M4, an Albian-Maastrichtian ocean-continent transform to post-transform sequence; and M5, a Maastrichtian-Recent passive margin sequence with low sedimentation rates. These megasequences also contain prominent transgressive-regressive cycles of 5-10 My duration, interpreted to be the result of dynamic topography.
The boundary between M3 and M4 is a major erosional unconformity documenting final continental breakup during the opening of the EAG. Above this, a pronounced Albian to Cenomanian/Turonian marine transgression resulted in marine inundation of the plateau. Structural deformation continued into the early Cenomanian along the Guinea Marginal Ridge, a potential structural barrier that restricted marine connection across the EAG. Bulk geochemical data from the shallow Guinea Plateau indicate that enhanced carbon burial in this setting was primarily driven by the deposition of reworked, oxidised organic matter during OAE, independent of gateway opening.
Case 334: Cryptococcal Meningitis
Authors: Brun-Vergara Maria L. , Zakhari Nader , Torres Carlos H. 
Published: February 2025

History A 30-year-old female patient who was 25 weeks pregnant presented to the emergency department with a 1-month history of mild headache and 2 weeks of progressive somnolence and photophobia accompanied by binocular horizontal diplopia and right gaze deviation. The patient also described new neck pain with passive head movements, without neck stiffness. Overall, the pregnancy was uncomplicated, with no high-risk features. Fever, chills, cough, shortness of breath, and abdominal or chest pain were denied. The patient had no history of rash, intravenous drug use, immunosuppressive medication use, or documented congenital abnormalities. She had not traveled recently, although she lived in Vancouver, British Columbia, Canada, 2 years prior to presentation. There was no recent or recurrent bacterial or viral illness. At clinical examination, the patient exhibited a decreased level of alertness and appeared tired. Vital signs were unremarkable, with a normal temperature (37.1 °C). Cranial nerve assessment revealed mild right abducens nerve palsy; neurologic examination was otherwise normal. Fundoscopic examination showed moderate grade 3 papilledema, left greater than right, with obscuration of some of the vessels leaving the disk. A CT scan of the head at admission was interpreted as normal. MRI of the brain performed 5 days later, due to persistent symptoms, revealed infratentorial and supratentorial imaging abnormalities. Lumbar puncture revealed high cerebral spinal fluid (CSF) opening pressure (32 cm H2O; upper limit of normal, 25 cm H2O). The CSF was clear, and analysis revealed an elevated total nucleated cell count (136 ×106/L; reference range, 0–5 ×106/L), with predominant lymphocytic moderate pleocytosis (100 ×106/L; reference range, 0–5 ×106/L) (59% lymphocytes) and normal glucose (3.3 mmol/L; reference range, 2.2–3.9 mmol/L) and normal total protein (0.27 g/L; reference range, 0.16–0.49 g/L) levels. Blood culture results for mycobacteria and anaerobic and aerobic microorganisms showed no growth. Findings from extensive additional diagnostic workup, including serologic testing for herpes simplex virus, varicella-zoster virus, enterovirus, Brucella, Coccidioides, Histoplasma, and mycobacteria, were negative. The HIV test result was negative, and the CD4 lymphocyte count and complement and immunoglobulin levels were within normal range. Autoimmune screening results were also negative.
Influence of Vanadium Doping on the Structural, Magnetic, and Shielding Features of GaFeO3
Authors: Heiba Zein , Ahmed Sameh I. , Mohamed Mohamed Bakr 
Published: February 2025

Abstract
The phase singularity in each sample was tested using the search-match HighScore software. The structural/microstructural parameters of the samples were determined using the Fullprof program based on the Rietveld refinement methodology. The cation distribution across the four crystallographic sites in the GaFeO3 lattice was determined. The integration of vanadium into the lattice results in alterations in cation distribution, inducing distortions in the bond lengths and angles of tetrahedral and octahedral structures. In general, the distortions of octahedrons tend to increase with vanadium doping. The zero field cooling (ZFC) and field cooling (FC) with an applied magnetic field of 100 Oe were performed using a SQUID device. The magnetization field dependence (M-H) of both samples at 10 K was also measured. The Curie temperatures (TC) for both samples were determined. The magnetization of all samples demonstrates obvious hysteretic performance. The coercivity improved slightly from 1.55 kOe to 1.97 kOe, whereas the saturation and remanent magnetization reduced as GaFeO3 was doped with 30% vanadium. A minor rise in LAC and MAC was seen at low and high photon energy ranges, whereas a small reduction in both parameters took place in the medium photon energy range after GaFeO3 was doped with vanadium.
Trauma and Memory in Sebastian Barry’s <i>Old God’s Time</i>
Authors: Abrantes Elisa 
Published: February 2025

Este artigo explora o romance de Sebastian Barry, Old God's Time (2023), utilizando uma abordagem dos Estudos sobre o Trauma (Caruth, 1995; Alexander, 2004; Balaev, 2014) e baseando-se nos conceitos de Ficção de Trauma articulados por Anne Whitehead (2004). O artigo tem por objetivo examinar a representação de traumas culturais individuais e coletivos no romance, com foco na representação das consequências duradouras do abuso infantil nas instituições religiosas da Irlanda. A narrativa é focalizada na perspectiva de um narrador não confiável, entrelaçando histórias pessoais com implicações sociais mais amplas, iluminando assim os efeitos profundos da violência e do abuso que reverberam ao longo dos anos e das gerações. Ao situar o romance dentro do quadro teórico dos Estudos sobre o Trauma, é possível analisar os mecanismos pelos quais o trauma é transmitido na ficção, enfatizando a interação entre memória, testemunho e estrutura narrativa. A análise se estende às características da ficção do trauma, mostrando como a obra de Barry se alinha e contribui para este gênero contemporâneo.