bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of
Streptococcus pneumoniae
isolates occurring in optochin-susceptible and optochin-resistant variants by analyzing whole-genome sequencing data
Authors: Vohrnová Sandra , Kozáková Jana , Honskus Michal
Published: February 2025

The paper presents the study of a set of isolates of
Streptococcus pneumoniae
, which comprised two heterogeneous subpopulations, one of which was susceptible and the other resistant to optochin. The aim of the study was to compare the results of serotyping, multilocus sequence typing (MLST), ribosomal multilocus sequence typing (rMLST), and variation analysis of these subpopulations and to investigate the genetic probable causes of optochin resistance. The strains studied were cultured from samples taken from patients with invasive pneumococcal disease in the Czech Republic in 2019 and 2020. A total of 10 studied pairs of isolates were subject to serotyping and whole-genome sequencing (WGS). None of the typing methods (serotyping, MLST, or rMLST) applied to pairs of optochin-susceptible and optochin-resistant isolates revealed differences in serotype, sequence type, or ribosomal sequence type. The WGS data analysis identified point mutations in ATP (adenosine triphosphate) synthase genes in 8 of the 10 optochin-resistant isolates. In seven optochin-resistant isolates, the mutation was found in the
atp
C gene and in one isolate in the
atp
A gene. One of the mutations in the
atp
C gene has not yet been published in the literature; it is a mutation at position 143T > C with an amino acid change of Val48Ala. In 8 out of the 10 optochin-resistant isolates, the possible genetic basis for resistance was identified, involving point mutations in the
atp
A and
atp
C genes. In the remaining two isolates, no clear genetic explanation for the optochin resistance in
S. pneumoniae
was found, based on current knowledge.

IMPORTANCE

Globally, among the most fundamental tests used for the identification of
Streptococcus pneumoniae
isolates is determining susceptibility to optochin. In the last 2 decades, optochin-resistant strains have been frequently reported in the literature, which can lead to the misidentification of
S. pneumoniae
. This study compares whole-genome sequencing data of optochin-susceptible and optochin-resistant subpopulations of
S. pneumoniae
isolates and investigates the genetic probable causes of resistance in the genomes of optochin-resistant subpopulations.
Prospective evaluation of real-world performance and clinical impact of the Biofire FilmArray joint infection panel
Authors: Berinson Benjamin , Tanida Konstantin , Spenke Laura , Krivec Lukas , Keller Johannes , Rolvien Tim , Christner Martin , Lütgehetmann Marc , Aepfelbacher Martin , Klatte Till Orla , Rohde Holger
Published: February 2025

Limitations of culture-based diagnostic approaches in pathogen detection in joint infections (JI) can be overcome by amplification-based, molecular assays. Recently, a syndromic panel PCR (spPCR) assay (Biofire JI panel; BJA) was approved for pathogen identification from synovial fluid (SF). Here, the performance and the clinical impact of the BJA were assessed in comparison to standard of care diagnostics in a prospective cohort of patients presenting with symptoms consistent with JI. One hundred sixty-five synovial fluids underwent analysis using the BJA. The results were compared with culture-based diagnostics. Discrepant results were re-analyzed using species-specific PCRs or 16S-rDNA sequencing. Clinical data from patients were collected to evaluate the impact on patient management. Twenty-seven of 165 (16.3%) synovial fluid cultures grew bacterial pathogens. In 24/27 cases, the BJA results were concordant. In one case, the cultured pathogen was missed, but three additional pathogens were identified. In 11 culture-negative cases, BJA identified a pathogen. Mean turnaround time in culture-positive samples was 14:11 h and 35:17 h in BJA and culture, respectively. In 11 cases, antibiotic therapy was optimized, based on BJA results. This study demonstrates high sensitivity and specificity (96.3% and 97.8%, respectively) of BJA, as well as a shorter turnaround time than culture-based techniques (21 h faster). Based on analysis of clinical data, antibiotic therapy was optimized due to BJA results in 11 cases. Care must be taken, as important pathogens in prosthetic JI are not included in the panel, restricting its value here.

IMPORTANCE

Pathogen detection is critical for targeted management of joint infections; however, cultural detection of pathogens can be challenging. The Biofire Joint Infection Assay (BJA) is a syndromic panel PCR test that allows culture-independent detection of 31 pathogens. The diagnostic performance and clinical impact were evaluated in a cohort of 160 patients with native and prosthetic joint infections. BJA detected concordant pathogens in 24 of 27 culture-positive cases and enabled the detection of additional pathogens in 11 patients. The time to result was significantly shorter than with standard culture-based diagnostics (14 vs 35 h), and BJA allowed optimization of therapy in 11 patients. The data show that BJA is a relevant addition to the diagnostic options for joint infections. Limitations result from incomplete detection of relevant pathogens, especially in prosthetic joint infections. The use of BJA in daily practice must therefore be accompanied by diagnostic stewardship measures.
Simplifying SARS-CoV-2 wastewater-based surveillance using an automated FDA EUA assay
Authors: Sathyanarayana Shivaprasad H. , Robins Ashlee A. , Toledo Diana M. , Gallagher Torrey L. , Tsongalis Gregory J. , Hubbard Jacqueline A. , Lefferts Joel A. , Martin Isabella W.
Published: February 2025

Wastewater-based surveillance (WBS) can track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in communities. Laboratory methods for this testing involve labor-intensive, multi-step processes. This study assessed the feasibility of performing WBS with an off-label use of an automated commercial SARS-CoV-2 assay that had received Emergency Use Authorization for human diagnostic testing from the United States Food and Drug Administration (FDA EUA). Twenty-four-hour composite samples of primary influent wastewater from seven municipalities in New Hampshire and Vermont were collected between September 2020 and February 2021, and were centrifuged upon receipt. An aliquot of fresh supernatant was immediately tested with the Abbott
m
2000 RealTi
m
e SARS-CoV-2 assay (Abbott Molecular, Des Plaines, IL, USA). Corresponding aliquots were then stored at −80°C until they were thawed, polyethylene glycol (PEG) concentrated, and tested by two PCR-based laboratory-developed tests (LDTs). Wastewater samples (103) were tested with successful detection of SARS-CoV-2 viral RNA by all three methods. Bland-Altman analysis showed overall concordant results with a bias of −0.13 and −0.42 log copies/mL detected by the FDA EUA assay compared to the LDTs. Specimen stability assessment demonstrated a decrease of 33.9% measurable viral RNA after three freeze-thaw cycles. SARS-CoV-2 detection in wastewater using an FDA EUA assay on an automated commercial testing platform performed comparably but with more efficient workflow when compared to two LDTs. This sample-to-answer automated method could save time and labor for surveillance testing, but further validation of its ability to quantitate SARS-CoV-2 viral RNA is necessary.

IMPORTANCE

This proof-of-principle study evaluates an off-label use of an automated United States Food and Drug Administration (FDA) Emergency Use Authorization (EUA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human diagnostic assay for wastewater surveillance. Compared to standard, labor-intensive, multi-step methods currently in use for wastewater surveillance testing, an off-label use of an FDA EUA assay on an automated platform offers a sample-to-answer testing requiring less labor and a faster turnaround time.
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

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

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.
The Neoproterozoic glacial broom
Authors: Kirkland C.L. , Strachan R.A. , Archibald D.B. , Murphy J.B.
Published: February 2025

Neoproterozoic snowball Earth events reflect globally frigid conditions thought to have stimulated changes in geochemical cycling with planetary biotic response. We investigated the impact of these events on sediment dynamics, focusing on the detrital zircon record within the Dalradian Supergroup of Scotland and Ireland. Utilizing U-Pb detrital zircon ages, we analyzed changes in sediment provenance throughout the stratigraphy via bootstrapped variance metrics. The coefficient of variance for the detrital zircon load exhibits a first-order increase stratigraphically upward, with marked changes at glaciogenic layers. Points of increased variance align with inputs of older detritus compared to lower, preglacial stratigraphic levels, suggesting intensified erosion and downcutting linked to wet-based glacial activity, with postglacial sediment redistribution. Average detrital zircon apparent density also changes through the stratigraphy, with implications for uranium cycling from the continents into the oceans. While early Ediacaran shale geochemistry implies postglacial oceanic oxygenation, loss of proportionally more uranium-rich detrital zircon across glaciogenic layers suggests that modification to continental weathering also fundamentally contributed to Neoproterozoic geochemical shifts.
Supplemental Material: Mesozoic Paleo-Pacific plate subduction effect revealed by 3-D magnetotelluric imaging in the southeastern Great Xing’an Range, Northeast China
Authors: Liang Hongda , Fang Hui , et al.
Published: February 2025

Figures S1-S6.
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

Objectives

This study aimed to investigate the relationship between knowledge, attitude and practice (KAP) regarding arteriovenous fistula (AVF) care in uremic patients undergoing haemodialysis (HD).

Design

A 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.

Setting

The study took place at the First Affiliated Hospital of Chongqing Medical University.

Participants

A total of 522 valid questionnaires were collected from patients undergoing HD, representing 85.57% of the 610 patients eligible for the study.

Interventions

Pathway analysis was used to assess the interplay among KAP scores related to AVF care in the participants.

Primary and secondary outcome measures

The study evaluated KAP scores (ranging 0–20, 8–40 and 6–30, respectively) to gauge patients’ KAP regarding AVF care.

Results

The 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.

Conclusions

Uremic 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

Introduction

Delirium, 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 analysis

This 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 dissemination

The 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 number

ClinicalTrials.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

Objectives

To explore the literature about the role of unpaid informal carers in medication management for people with long-term conditions.

Design

Systematic review designed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

Information source

MEDLINE (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 criteria

Primary 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 synthesis

Relevant data were extracted and summarised in a table. The Mixed Method Appraisal Tool was used for quality assessment. Data were narratively synthesised.

Results

From 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.

Conclusion

Informal 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 number

CRD42024506694.
Promoting equitable genetic testing in ovarian cancer: the demonstration of improvement for molecular ovarian cancer testing (DEMO) project
Authors: Leung Elaine YL , Funingana Ionut Gabriel , Bird Lisa , Alcaraz Marie-Lyne , Evans Anuji , Considine Anna , Freeman Susan , Jimenez-Linan Mercedes , Spencer Catherine , Phanasan Kiran , Winning Julie , Ang Joo Ern , Parkinson Christine , Ong Kai Ren , Butler Samantha , Ridgway Oliver , Charles Ian , Pannell Rachel , Abedin Parveen , Boyle William , Emery Jamie , Salter-Scott Jayne , Williams Sarah , Ganesan Raji , Sundar Sudha , Balega Janos , Brenton James D
Published: February 2025

Parallel genetic testing (testing for both tumour and germline gene changes) after the diagnosis of ovarian cancer should be considered the standard of care and is crucial to support treatment decisions. The demonstration of improvement for molecular ovarian cancer testing (DEMO) project aimed to develop patient-focused tools to promote equitable genetic care in diverse communities with high proportions of patients with limited English proficiency and biopsy guidelines to address the variations in specimen quality in different geographical regions in the UK. Our three work packages (WP) aimed to promote awareness by addressing the information gaps in different community groups (WP1), develop infrastructure to evaluate the different tissue collection pathways in different regions (WP2) and support continuing professional development (CPD) to encourage best practices with the involvement of patients (WP3). Our output included a multimedia multilanguage information package with paired National Health Service-branded written materials to support genetic testing after ovarian cancer diagnosis (https://ovarian.org.uk/demo-uk/), a scalable database to enable a multisite audit of parallel genetic testing pathways and a collection of CPD events that had patient involvement as an essential component. In addition, we have collaborated with patient and community groups to contribute to a national consensus guidance on genetic testing in ovarian cancer. Our co-production work has been recognised by local and regional awards as an exemplar for patient and public involvement (PPI). This has supported the start of a legacy co-production group in gynaeoncology (https://www.dhlnetwork.com/gohildas) to address the critical unmet need for sustainable and equity-oriented PPI to advocate for underserved communities. The DEMO project has contributed to raising awareness of the importance of equitable genetic care in ovarian cancer. We will continue to build on this groundwork to support future quality improvement projects and research, with the ultimate goal of improving the outcomes of patients with ovarian cancer.
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

Introduction

Survival 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.

Methods

Following 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.

Results

Projects 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.

Conclusion

IMPROVE-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.
Assessing the effectiveness of leader rounding for high reliability: a quality improvement initiative
Authors: Murray John S , Clifford Joan
Published: February 2025

High reliability organizations in healthcare are responsible for consistently maintaining high levels of safety and quality over extended periods of time and across multiples service lines and settings. In order to accomplish this, transparent and bi-directional communication across service lines and teams with organizational leaders is essential. Leader rounding for high reliability helps to ensure effective communication takes place. Developing and implementing an evidence-based process for leader rounding for high reliability is important as is determining effectiveness over time. We describe an initiative for assessing effectiveness after an evidence-based process for leader rounding for high reliability was created and implemented for the Veterans Affairs Bedford Healthcare System.
Surveillance of Clostridioides difficile in Canadian retail meat and genomic linkages to community-associated human clinical infections in Canada
Authors: Pidsadny Paula , Du Tim , Hizom Romeo , Ahmed Sean , Tan Derek , Zhanel George , Bay Denice , Reid-Smith Richard , Charlebois Audrey , Golding George
Published: February 2025

Community-associated Clostridioides difficile infections (CA-CDI) remain a concern in Canada, comprising a quarter of cases previously reported through the Canadian Nosocomial Infection Surveillance Program. Previous Canadian studies have reported toxigenic C. difficile isolated from Canadian retail meat, suggesting that it may be a source of exposure for CA-CDI in Canada. In this study, 3/219 (1.4%) of retail pork and 0/99 (0%) of retail beef samples tested positive for toxigenic C. difficile, which were molecularly characterized by PCR ribotyping and whole-genome sequencing. All three isolates were obtained from pork and belonged to sequence types (ST)/ribotypes (RT) that have previously been isolated from human clinical CA-CDI cases in Canada: ST1/RT027, ST8/RT002, and ST10/RT015. Retail meat isolates were susceptible to the antimicrobials tested, save one isolate with intermediate resistance to clindamycin. Genomic comparison to Canadian human clinical CA-CDI isolates with the same corresponding ST/RT types showed two of the three pork isolates clustered with CA-CDI isolates via core-genome multilocus sequencing typing, with single nucleotide variant (SNV) analysis showing further genomic relatedness of 2 SNVs. Retail meat may therefore be a low source of CA-CDI exposure in Canada, with the potential for foodborne transmission of select clones.
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

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

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.
Observational Equality Meets CIC
Authors: Pujet Loïc , Leray Yann , Tabareau Nicolas
Published: February 2025

The notion of equality is at the heart of dependent type theory, as it plays a fundamental role in program specifications and mathematical reasoning. In mainstream proof assistants such as
Agda
,
Lean
and
Coq
, equality is usually defined using Martin-Löf’s identity type, an elegant and simple approach that has stood the test of time since the 1970s. However, this definition also comes with serious downsides: the intensional nature of Martin-Löf’s identity type means that it is impractical for reasoning about functions and predicates, and it is impossible to define quotient types. Recently, observational equality has garnered attention as an alternative method for encoding equality, particularly in proof assistants supporting definitionally proof-irrelevant propositions. However, it has yet to be integrated in any of the three proof assistants mentioned above, as it is not fully compatible with another important feature of type theory: indexed inductive types. In this paper, we propose a systematic approach to reconcile observational equality with indexed inductive types, using a type coercion operator that computes on reflexive identity proofs. The second contribution of this paper is a formal proof that this additional computation rule can be integrated to the system without compromising the decidability of conversion. Finally, we provide an implementation of our observational equality in an extension of
Coq
. This extension is based on the recently introduced rewrite rules, and provides new extensionality principles while remaining fully backward-compatible.
Cyber Physical Games: Rational Multi-Agent Decision-Making in Temporally Non-Deterministic Environments
Authors: Sritriratanarak Warisa , Garcia Paulo
Published: February 2025

We describe a formulation of multi-agents operating within a Cyber-Physical System, resulting in collaborative or adversarial games. We show that the non-determinism inherent in the communication medium between agents and the underlying physical environment gives rise to environment evolution that is a probabilistic function of agents’ strategies. We name these emergent properties Cyber Physical Games and study its properties. We present an algorithmic model that determines the most likely system evolution, approximating Cyber Physical Games through Probabilistic Finite State Automata, which can be used to drive agent strategies towards best performance. We evaluate it on collaborative and adversarial versions of the Iterated Boolean Game, comparing theoretical results with simulated ones, showing that the algorithm can be successfully used to guide agent strategy, outperforming other methods. Results support the validity of the proposed model, and suggest several required research directions to continue evolving our understanding of Cyber Physical System, as well as how to best design agents that must operate within such environments.
Aggregating Digital Identities through Bridging
Authors: Biedermann Ben , Scerri Matthew , Kozlova Victoria , Ellul Joshua
Published: February 2025

Web3's decentralised infrastructure has upended the standardised approach to digital identity established by protocols like OpenID Connect. Web2 and Web3 currently operate in silos, with Web2 leveraging selective disclosure JSON web tokens (SD-JWTs) and Web3 dApps being reliant on on-chain data and sometimes clinging to centralised system data. This fragmentation hinders user experience and the interconnectedness of the digital world. This paper explores the integration of Web3 within the OpenID Connect framework, scrutinising established authentication protocols for their adaptability to decentralised identities. The research examines the interplay between OpenID Connect and decentralised identity concepts, the limitations of existing protocols like OpenID Connect for verifiable credential issuance, OpenID Connect framework for verifiable presentations, and self-issued OpenID provider. As a result, a novel privacy-preserving digital identity bridge is proposed, which aims to answer the research question of whether authentication protocols should inherently support Web3 functionalities and the mechanisms for their integration. Through a Decentralised Autonomous Organisation (DAO) use case, the findings indicate that a privacy-centric bridge can mitigate existing fragmentation by aggregating different identities to provide a better user experience. While the digital identity bridge demonstrates a possible approach to harmonise digital identity across platforms for their use in Web3, the bridging is unidirectional and limits root trust of credentials. The bridge's dependence on centralised systems may further fuel the debate on (de-)centralised identities.
Automated CT Measurement of Total Kidney Volume for Predicting Renal Function Decline after 177Lu Prostate-specific Membrane Antigen–I&T Radioligand Therapy
Authors: Steinhelfer Lisa , Jungmann Friederike , Nickel Manuel , Kaissis Georgios , Hofer Marie-Luise , Tauber Robert , Schmaderer Christoph , Rauscher Isabel , Haller Bernhard , Makowski Marcus R. , Eiber Matthias , Braren Rickmer F.
Published: February 2025

A decrease in total kidney volume after lutetium 177 prostate-specific membrane antigen radioligand therapy predicted renal function decline at 12 months in patients with metastatic castration-resistant prostate cancer.
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.
AI Applications for Thoracic Imaging: Considerations for Best Practice
Authors: Hwang Eui Jin , Goo Jin Mo , Park Chang Min
Published: February 2025

This article describes the status and potential expansion of artificial intelligence in thoracic imaging, including practical issues for its clinical implementation into daily practice as well as challenges and opportunities.
Association between Cystic Fibrosis and Pericardial Calcification Detected at Chest CT in Adults
Authors: Rodriguez-Takeuchi Sara , Tullis Elizabeth , Babaei Jandaghi Ali , Yan Andrew T. , Colak Errol , Hall David A. , Wong Kathy , Jiménez-Juan Laura , McIntyre Kieran , Sykes Jenna , Deva Djeven P. , Callejas Matias F.
Published: February 2025

The prevalence of pericardial calcification at chest CT was higher in adult patients with cystic fibrosis (CF) than in individuals without CF; pericardial calcification progressed over time.
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

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.
Green Nanotechnology: Naturally Sourced Nanoparticles as Antibiofilm and Antivirulence Agents Against Infectious Diseases
Authors: lawal Habiba , Saeed Shamsaldeen Ibrahim , Gaddafi Mohammed Sani , Kamaruzzaman Nor Fadhilah
Published: February 2025

The escalating threat of infectious diseases, exacerbated by antimicrobial resistance (AMR) and biofilm formation, necessitates innovative therapeutic strategies. This review presents a comprehensive exploration of the potential of nanoparticles synthesized from natural sources, including plant extracts, microbial products, and marine compounds, as antimicrobial agents. These naturally derived nanoparticles demonstrated significant antibiofilm and antivirulence effects, with specific examples revealing their capacity to reduce biofilm mass by up to 78% and inhibit bacterial quorum sensing by 65%. The integration of bioactive compounds, such as polyphenols and chitosan, facilitates nanoparticle stability and enhances antimicrobial efficacy, while green synthesis protocols reduce environmental risks. Notably, the review identifies the potential of silver nanoparticles synthesized using green tea extracts, achieving 85% inhibition of polymicrobial growth in vitro. Despite these promising results, challenges such as standardization of synthesis protocols and scalability persist. This study underscores the transformative potential of leveraging naturally sourced nanoparticles as sustainable alternatives to conventional antimicrobials, offering quantitative insights for their future application in combating mono‐ and polymicrobial infections.
Supplementary figure 9 from Single-Cell Transcriptomic Analysis Identifies Senescent Osteocytes That Trigger Bone Destruction in Breast Cancer Metastasis
Authors: Kaur Japneet , Adhikari Manish , Sabol Hayley M. , Anloague Aric , Khan Sharmin , Kurihara Noriyoshi , Diaz-delCastillo Marta , Andreasen Christina Møller , Barnes Charles Lowry , Stambough Jeffrey B. , Palmieri Michela , Reyes-Castro Olivia , Zarrer Jennifer , Taipaleenmäki Hanna , Ambrogini Elena , Almeida Maria , O’Brien Charles A. , Nookaew Intawat , Delgado-Calle Jesus
Published: February 2025

Supplementary figure 9
Supplementary figure 5 from Single-Cell Transcriptomic Analysis Identifies Senescent Osteocytes That Trigger Bone Destruction in Breast Cancer Metastasis
Authors: Kaur Japneet , Adhikari Manish , Sabol Hayley M. , Anloague Aric , Khan Sharmin , Kurihara Noriyoshi , Diaz-delCastillo Marta , Andreasen Christina Møller , Barnes Charles Lowry , Stambough Jeffrey B. , Palmieri Michela , Reyes-Castro Olivia , Zarrer Jennifer , Taipaleenmäki Hanna , Ambrogini Elena , Almeida Maria , O’Brien Charles A. , Nookaew Intawat , Delgado-Calle Jesus
Published: February 2025

Supplementary figure 5