bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic next-generation sequencing of osteoarticular tissue for the diagnosis of suspected osteoarticular tuberculosis
Authors: Yan Guangxuan , Liu Zhifeng , Teng Tianlu , Dong Weijie , Lan Tinglong , Fan Jun , Tang Kai , Qin Shibing , Nie Wenjuan 
Published: November 2024

ABSTRACT

The objective of the study is to determine the accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing osteoarticular tuberculosis (TB) infection and to compare it with mycobacteria growth indicator tube (MGIT) and Xpert assays. We retrospectively analyzed 162 patients admitted with suspected osteoarticular TB. Osteoarticular tissue (66.67%) and abscess specimens (33.33%) from patients were tested for MGIT, GeneXpert/RIF, and mNGS. mNGS assay detected 76 cases (46.9%) with bacterial, 63 cases (38.9%) with mycobacterial, 22 cases (13.6%) with fungal, and 1 case (0.6%) with actinomycetal organisms. These 162 pathogens were classified into 21 species. The most frequent species detected was
Mycobacterium tuberculosis complex
(29.0%), followed by
Staphylococcus aureus
(20.4%),
Mycobacterium abscessus
(5.6%), and
Candida albicans
(5.6%). Taking the “gold standard” TB diagnosis as the standard, the positive predictive values of mNGS, Xpert, and MGIT culture were both 100.00%. The negative predictive values of mNGS, Xpert, and MGIT culture and assays were 94.26%, 98.29%, and 88.46%, respectively. The sensitivity of mNGS detection (85.11%) was similar to that of Xpert (95.74%) and higher than that of MGIT culture (68.08%). The specificities of mNGS detection, Xpert, and MGIT culture were both 100.00%. The area under the curve value of the mNGS assay was 0.895 (95% CI: 0.830, 0.960), which was greater than that of the MGIT culture-based assay of 0.840 (95% CI: 0.757, 0.924), which was similar to 0.979 (95% CI: 0.945, 1.000) for Xpert assay. The pathogen detection rate of mNGS in diagnosing suspected osteoarticular TB exceeded that of conventional methods.

IMPORTANCE

In the detection of unknown infectious disease pathogens, the overall efficacy of traditional detection methods, such as culture, is low, and traditional PCR testing is also limited to the gene sequences of known pathogenic microorganisms. Metagenomic next-generation sequencing (mNGS) performs DNA sequencing by studying the entire microbial community genome in a given sample, without the need for isolation and culture. Previous studies have shown that mNGS performs better on pulmonary and extrapulmonary samples when compared with Xpert, traditional pathogenetic tests, and even parallel diagnostics. However, it should be emphasized that only a few studies have explored the performance of mNGS in detecting
Mycobacterium tuberculosis
in clinical samples associated with bone and joint infections. We conducted this retrospective study to provide additional data to support the use of mNGS in the clinical setting to identify pathogens within abscesses or tissue samples associated with bone and joint infections.
Molybdenum isotopes demonstrate that multistage upgrading is required to generate heavy rare earth element–enriched carbonatites
Authors: Zhao Xiao-Chen , Yan Shuang , Niu He-Cai , Yang Wu-Bin , Li Ning-Bo , Li Jie , Zhang Le , McCoy-West Alex J. 
Published: November 2024

Abstract
Carbonatites with heavy rare earth element (HREE) enrichment are a rare and intriguing prospect for economic geology research, due to the growing global demand for HREEs in various industries. However, debate persists over the mechanism responsible for HREE enrichment in carbonatites, with the mantle source, magmatic-hydrothermal evolution, or a combination of these factors proposed to be responsible. This study examines three adjacent Late Triassic carbonatites (from the Huanglongpu, Huayangchuan, and Jialu carbonatite dike systems) in the Lesser Qinling of Central China and uses Mo isotope systematics to provide unique insights into the HREE enrichment process of these magmas. All three carbonatites exhibit elevated total REE (ΣREE) concentrations (up to 4600 ppm), along with significant HREE enrichment (ΣHREE/ΣREE = 0.1–0.4). Notably, Jialu carbonatite stands out for having the highest total HREE concentrations (≥360 ppm) and ΣHREE/ΣREE ratios (0.2–0.4). Regardless of their variable degrees of HREE enrichment, the three carbonatites display similar Sr-Nd-Pb isotope signatures, which indicates a shared enriched mantle source. The Huanglongpu and Huayangchuan carbonatites mostly display significantly lighter δ98/95Mo (−1.71‰ to −0.15‰) values than the depleted mantle, which indicates an origin from an enriched mantle influenced by recycled pelagic clays and Fe-Mn nodules. Both types of marine sediments are enriched in REEs and would have undergone initial HREE enrichment during slab dehydration and metamorphism, resulting in an HREE-enriched mantle source region. In contrast, Jialu carbonatite possesses significantly heavier δ98/95Mo (0.13‰–1.89‰), which is indicative of the subsequent influence of hydrothermal processes. Additional evidence of this hydrothermal influence at Jialu is preserved in calcite crystal fluid inclusions, elevated δ18O (8.71‰–10.72‰), non-charge-and-radius–controlled (CHARAC) Y/Ho ratios (36–41), and low Sr concentrations (&lt;4800 ppm). Secondary upgrading of HREEs at Jialu occurred due to preferential complexation and transportation during hydrothermal exsolution. This study demonstrates that maximum HREE enrichment in carbonatites is achieved through a two-stage process that involves both a refertilized mantle source and late-stage hydrothermal exsolution.
Subductability of continental lithosphere
Authors: Wang Yang , Li Zhong-Hai 
Published: November 2024

Abstract
Multiple lines of evidence from geological and geophysical observations indicate the deep subduction of continental lithosphere; however, the potential and driving forces of (self-sustained) continental subduction remain unclear. Here, systematic thermal-petrological models were conducted to quantitatively evaluate the subductability of continental lithosphere by analyzing its density structure and slab-pull evolution during subduction. The results indicate that the metamorphic densification of deeply subducted continental lithosphere (upper, middle, lower crust and lithospheric mantle) could provide considerable driving force for continental deep subduction. The numerical models further indicate that, if a Phanerozoic or Proterozoic continental lithosphere is dragged to a large depth of &gt;300 km, then the continental slab pull overcomes the overall resistance force. Consequently, the continental subduction occurs self-consistently without any drag from the preceding oceanic slab. For Archean continental lithosphere, it is more difficult for self-sustained subduction to occur, due to the highly depleted mantle composition. In addition, we also systematically quantified the effects of multiple factors, including the scraping of continental crust, subduction velocity, subduction angle, and variable bulk-rock compositions of continental crust. Finally, a representative case study of the Himalayan orogen revealed that the slab pull of presently subducting Indian continental lithosphere ranges from 13 TN/m to 29 TN/m, providing a major contribution for the ongoing India-Asia collision.
Anterograde placement of drug-coated balloon for ureteroileal anastomosis stricture
Authors: Rico Luis , Maqueda Martin , Blas Leandro , Contreras Pablo 
Published: November 2024

We describe a case of ureteral stricture after radical cystectomy with orthotopic neobladder. The patient presented 4 months after laparoscopic radical cystectomy with intracorporeal orthotopic ileal neobladder, with fever and left lower back pain.Laboratory analysis showed leucocytosis and elevated C reactive protein and creatine levels. CT scan showed left hydronephrosis and slow excretion of the intravenous contrast medium with a narrowing at the left ureteroileal anastomosis.A nephrostomy was placed and, 6 weeks later, the anterograde placement of a drug-coated balloon with paclitaxel was placed. Inflation to rated burst pressure occurred for 3–5 min, the drug-coated balloon was removed and a new nephrostomy tube was placed without ureteral stent placement. We performed a kidney ultrasound 30 days after the drug-coated balloon placement with the nephrostomy tube closed showing no left hydronephrosis and the nephrostomy tube was removed.
Addressing data quality issues to assess clinical and epidemiological risk factors for COVID-19 among documented cases in Liberia: a single-centre, retrospective, observational study
Authors: Harmon-Gray Wahdae-Mai , Hessou Heounohu , Adeiza Mukhtar , Brown Jerry , Wright Antoinette H , Skrip Laura 
Published: November 2024

IntroductionIdentification of risk factors for severe COVID-19 can help to inform case management in resource-constrained settings. We aimed to rigorously but retroactively address data issues to identify risk factors for COVID-19 morbidity and mortality among cases seeking care in Liberia.MethodsChart data on confirmed cases were extracted at the national COVID-19 treatment unit. Due to the use of paper charts, assignment of non-unique identifiers and incomplete documentation, data required cleaning to remove duplicates per three sets of predefined criteria. Associations between epidemiological, clinical and demographic variables and indicators of disease severity were assessed using multivariable logistic regression.ResultsThe raw data set for patients classified between 15 March and 1 September 2020 included 2703 cases or 107% more than the 1303 cases reported by the national surveillance system during the same period. The median age of cases was found to be 38 years (IQR: 27–50); most cases were men (65%). The rates of continuous positive airway pressure (CPAP) use for breathing support and of case fatality were 5% (71/1330) and 5% (52/981), respectively. Increased odds of breathing assistance with CPAP use were associated with self-reported diabetes (aOR: 4.37; 95% CI: 1.72 to 10.4) and/or hypertension (aOR: 4.86; 95% CI: 1.81 to 12.2) and increasing age (aOR: 1.06; 95% CI: 1.04 to 1.08). Recent travel history (aOR: 5.13; 95% CI: 1.13 to 19.3) and residence outside of urban Montserrado County (aOR: 22.7; 95% CI: 8.08 to 76.4) were associated with increased odds of death.ConclusionsResults from this retrospective analysis highlight self-reported non-communicable diseases as well as residence outside of largely urbanised Montserrado County as factors associated with COVID-19 severity among presenting cases in Liberia. The findings, both in terms of analytical results and data quality concerns, offer insight into how access to the highly centralised health systems and processes in Liberia may have affected populations distant from the central response in terms not only of COVID-19 disease outcomes but also care-seeking behaviour and surveillance effectiveness. This has implications for surveillance and response across priority diseases.
Exploring cardiovascular involvement in IgG4-related disease: a case series approach with cardiovascular magnetic resonance
Authors: Henry John Aaron , Xavier Roshan , Selvaraj Emmanuel , Burrage Matthew , Thomas Katharine E , Lukaschuk Elena , Zhang Qiang , Ferreira Vanessa M , Piechnik Stefan K , Sabharwal Nikant , Neubauer Stefan , Rider Oliver , Culver Emma L , Lewis Andrew 
Published: November 2024

Background
IgG4-related disease (IgG4-RD) is a relapsing–remitting, fibroinflammatory, multisystem disorder. Cardiovascular involvement from IgG4-RD has not been systematically characterised. In this study, we sought to evaluate consecutive patients with IgG4-RD using a detailed multiparametric cardiovascular magnetic resonance (CMR) imaging protocol.

Methods
We prospectively enrolled 11 patients with histology-confirmed IgG4-RD; with active disease at time of scan. We undertook a detailed multiparametric CMR imaging protocol at 1.5T including cine imaging, native T1 and T2 mapping, stress perfusion imaging with inline quantitation of myocardial blood flow and late gadolinium enhancement (LGE) imaging.

Results

All patients exhibited at least one abnormality on CMR imaging. Abnormal elevation of global or segmental left ventricular myocardial T1 and T2 values was present in four patients, suggesting myocardial oedema or inflammation. Abnormal LGE, suggesting myocardial scar fibrosis, was present in nine patients, with eight displaying a non-ischaemic pattern, and one showing an ischaemic pattern. Four patients fulfilled both Lake Louise Criteria for active myocardial inflammation, while a further six fulfilled one criterion. Myocardial perfusion reserve was normal in all evaluable patients. Ten patients had normal ventricular volumes, mass and systolic function. In addition, thoracic aortitis was identified in three patients who underwent
18
F-flourodeoxyglucose PET/CT imaging, with resolution following anti-B-cell treatment.

Conclusions
In this cohort of patients with histology-confirmed IgG4-RD, multiparametric CMR revealed no changes in gross cardiac structure and function, but frequent myocardial tissue abnormalities. These data suggest a plausible pathophysiological link between IgG4-RD and cardiovascular involvement.
Comparing road traffic injuries by types of road users among children and adolescents in South Korea, 2011–2021
Authors: Yeon Je Sun , Kong So Yeon , Kim Byung Woo , Shin Dong-Min , Moon Sung Hun , Jeon Sung Man , Park Gwan Jin , Chai Hyun Seok , Kim Young Min , Kim Sang Chul 
Published: November 2024

IntroductionRoad traffic injuries (RTIs) are the leading cause of mortality among children and adolescents. This study aimed to compare clinical characteristics and identify factors associated with severe RTIs based on types of road users among children and adolescents with RTIs.MethodsA retrospective multicentre observational study was conducted using the Emergency Department-based Injury In-depth Surveillance registry in South Korea. A total of 78 021 participants younger than 19 years who presented with RTIs to the participating emergency departments from 2011 to 2021 were classified into four groups: passengers, pedestrians, motorcyclists and bicyclists. Demographic and injury-related factors were analysed using a multivariate logistic regression model to determine associations with severe RTIs, as indicated by the Excess Mortality Ratio-based Injury Severity Score of ≥16. The prevalence of traumatic brain injury (TBI), hospitalisations, intensive care unit (ICU) admissions and severe RTIs among road users was compared.ResultsHead injuries were most prevalent in passengers (55.3%), motorcyclists (46.7%) and bicyclists (50.1%). Motorcyclists exhibited the highest proportion of TBI (8.3%), total admissions (28.8%), ICU admissions (8.2%), severe RTIs (41.0%) and mortality (2.0%). Safety devices significantly reduced severe RTIs in passengers and motorcyclists (adjusted OR (95% CI) 0.77 (0.70 to 0.85) and 0.69 (0.62 to 0.76), respectively.ConclusionThe distinct clinical characteristics and factors associated with severe RTIs among different road user types in children and adolescents highlight the need for targeted interventions. Tailoring strategies to the specific requirements of each group is essential for effectively mitigating the occurrence of severe RTIs in this vulnerable demographic.
Association between socioeconomic disadvantage and severe maternal morbidity and mortality in high-income countries: a systematic review
Authors: Geddes-Barton Dorothea , Baldelli Sofia , Karthikappallil Roshan , Bentley Thomas , Omorodion Blessing , Thompson Lucy , Roberts Nia Wyn , Goldacre Raph , Knight Marian , Ramakrishnan Rema 
Published: November 2024

BackgroundSocioeconomic position (SEP) is among the most important determinants of variations in health outcomes. This systematic review aimed to summarise the association between socioeconomic disadvantage and the risk of severe maternal morbidity (SMM) and maternal mortality (MM) across high-income countries.MethodsA comprehensive search was conducted in the MEDLINE, EMBASE, CINAHL and PsycInfo databases and Google Scholar from January 2000 to June 2023. Peer-reviewed papers from observational studies conducted in Organisation for Economic Co-operation and Development countries were included. Meta-analyses of comparable studies, a narrative summary and a harvest plot were undertaken.The risk of bias was assessed using a modified Newcastle-Ottawa tool.ResultsThe final review included 52 papers. In the meta-analyses, compared with the least amount of neighbourhood deprivation, neighbourhood income, neighbourhood poverty and years of education, the ORs for SMM in the highest group were 1.45 (95% CI 1.13 to 1.85), 1.48 (95% CI 1.34 to 1.63), 1.61 (95% CI 0.97 to 2.66) and 1.29 (95% CI 1.22 to 1.37), respectively. Similarly, the ORs for MM among least versus highest amount of neighbourhood deprivation, unemployed versus employed, lower versus higher occupational group and years of education were 2.10 (95% CI 1.57 to 2.81), 1.86 (95% CI 0.95 to 3.66), 1.61 (95% CI 1.03 to 2.51) and 1.90 (95% CI 1.29 to 2.79), respectively.DiscussionIn high-income countries across the different measures of SEP, socioeconomic disadvantage is associated with increased risk for SMM and MM. There is a need for interventions across multiple societal levels that will be effective in reducing these inequitable outcomes.PROSPERO registration numberCRD42023399267.
Downstream healthcare use following breast cancer screening: a register-based cohort study
Authors: Gram Emma Grundtvig , Siersma Volkert , Nicolaisdóttir Dagný Rós , Brandt Brodersen John 
Published: November 2024

BackgroundFor evaluation of breast cancer screening and informed prioritisation, it is important to examine the downstream healthcare use associated to participation. The objective of this study is to determine the healthcare use among breast cancer screening participants compared with screening-naïve controls.MethodsThe study is a register-based cohort study with 14 years of follow-up. We compare healthcare use among women who participated in the initial phase of the stepwise breast cancer screening implementation in Denmark (stratified on screening result: normal, false positive and breast cancer) compared with those invited in subsequent phases.ResultsScreening participants, especially those with false-positive results, tended to use primary healthcare services more than the screening-naïve group. Women with breast cancer and false positives received more breast imaging compared with the screening-naïve group. False positives consistently had the highest use of drugs compared with the control group. All screening groups had significantly higher use of outpatient clinic visits in the year of and following screening compared with the screening-naïve group. Screening groups were more likely to receive additional diagnoses in the years following screening than the screening-naïve group. There were no significant differences in medical procedures and days of hospitalisation.ConclusionsThe study highlights differences in primary healthcare use among screening groups compared with the screening-naïve group. Since use of primary care services is at the discretion of the women, this implies increased worries about health. Thus, these results indicate increased healthcare-seeking behaviour, especially among women with false-positive results.
Soil nematode communities differ across long-term land-use intensities in relation to soil physical, chemical, and biological parameters
Authors: Arseneault Hannah , Lynch Derek H. , Nyiraneza Judith , Stiles Kyra , Mills Aaron , Fraser Tandra 
Published: November 2024

Soil disturbance, reduced crop diversity, and decreased residue in intensively managed systems can negatively impact soil biological communities and soil health. This study examined the impact of long-term (>20 years) low- (forest, grassland), medium- (diversified annual cropping), and high-intensity (annual cropping, frequently to potatoes) land-use on soil nematode communities and soil health in 59 sites across Prince Edward Island, Canada. Soil samples (0–15 cm) were collected at five locations per site and analysed for soil biological (nematode communities, respiration, soil organic matter, permanganate oxidizable carbon (POXc), soil protein), chemical (pH, N, soil N supply, extractable nutrients), and physical (bulk density, texture) properties. Soil pH and extractable nutrients were lowest in the low-intensity sites, while total C and C:N ratios were highest and decreased with increasing land-use intensity (low > medium > high). Soil respiration, POXc, and protein were lowest for high-intensity sites. Low-intensity sites had greater nematode Shannon diversity and richness, and higher maturity and structure indices than the medium- and high-intensity sites ( p < 0.05), signifying a more structured nematode community. Nematode communities from the high-intensity sites were more degraded and had significantly higher basal indices compared to the low- and medium-intensity sites. At the trophic level, the low-intensity system had higher numbers of omnivores and lower abundance of bacterivores. These differences in nematode trophic composition may result in differences in ecosystem function, including nutrient cycling and biological control.
A review of salt tectonics in Romania's Transylvanian Basin and implications for energy transition
Authors: Tamas Dan Mircea , Dohan Daria , Barabasch Jessica , Tamas Alexandra , Schleder Zsolt , Krezsek Csaba , Urai Janos L. 
Published: November 2024

Salt, pivotal in societal evolution and vital in scientific and economic domains, notably in chemical and hydrocarbon industries, gains relevance amid the climate crisis. As the shift from fossil fuels to sustainable energy sources becomes imperative, salt deposits can advance the energy transition, notably by large-scale hydrogen storage in solution-mined caverns. Other promising applications include carbon capture utilization and storage, and geothermal energy. Due to its potential role in energy transition and the required novel geotechnical solutions, research focusing on salt's contribution remains an emerging field.
The Transylvanian Basin (Romania), provides opportunities for comprehensive multiscale observations, including surface and subsurface data, offering insights into salt deformation. While studies on salt tectonics in the basin exist, it is generally understudied and the focus on energy transition applications is sparse.
This paper aims to review the current state of salt tectonics in the Transylvanian Basin, emphasizing internal deformation complexities, impurity distributions and potential implications for energy transition industries. By shedding light on this significant yet underexplored aspect, this work seeks to stimulate further research interest and prompt comprehensive investigations into salt-related energy transition applications.