High Specificity Research Articles

[Practical application of the Paris system for reporting urinary cytology].

Objective: To validate the diagnostic performance of the Paris system for reporting urinary cytology (TPS). Methods: A total of 7 046 urine cytology samples from 3 402 patients collected in the Department of Pathology, Beijing Hospital, China from January 2020 to January 2022 were analyzed. 488 patients had a biopsy or resection specimen during the follow-up period of 6 months. The sensitivity, specificity, risk of malignancy (ROM) and risk of high-grade malignancy (ROHM) of the TPS were evaluated using histological diagnosis as the golden standard. Results: Among the 7 046 samples, high-grade urothelial carcinoma (HGUC) accounted for 5.7% (399/7 046), suspicious for high-grade urothelial carcinoma (SHGUC) for 3.2% (227/7 046), atypical urothelial cells (AUC) for 8.4% (593/7 046), and negative for high-grade urothelial carcinoma (NHGUC) for 72.9% (5 139/7 046) including low-grade urothelial neoplasm (LGUN) for 0.8% (59/7 046) and insufficient samples for 9.8% (688/7 046). 488 patients had a bladder biopsy or resection in the follow-up of six months, including 314 males and 174 females, aged 27 to 92 years (average, 66 years). The ROHM of TPS was 94.7% in HGUC, 83.3% in SHGUC, 41.3% in AUC and 18.8% in NHGUC. The sensitivity and specificity of urine cytology were 70.1% (169/241) and 97.0% (162/167), respectively. The negative predictive value of NHGUC was 69.2% (162/234). Conclusions: The study has shown that TPS classification has high sensitivity and specificity, high ROHM for HGUC and SHGUC, and high negative predictive value for NHGUC. The application of TPS reporting system can better interpret the clinical significance of cytology samples, improve the accuracy of urine cytopathology and ensure continuous diagnostic consistency.

Personalized lung care: Bronchopulmonary dysplasia risk prediction tool tailored for neonates born in resource-limited settings.

Predicting bronchopulmonary dysplasia (BPD) to assess the risk-benefit of therapy is necessary considering the side effects of medications. We developed and validated an instrument for predicting BPD and compared it with an instrument currently used for neonates born in a Brazilian hospital. This was a retrospective cohort study of patients born between 2016 and 2020 with a gestational age (GA) between 23 and 30 weeks. Predictive equations were elaborated using methods of component variable selection collected on the 14th day of life; 70% of the sample was randomly selected for the construction of risk prediction equations and the remaining 30% for their validation, application, and comparison with the National Institute of Child Health and Human Development (NICHD) instrument. The sensitivity, specificity, and predictive values of the equations were calculated. The equation that used variables with p < 5% in Fisher's exact test presented the best results: specificity of 98% and positive predictive value of 93% and could be used for BPD prediction of all small-for-gestational-age (SGA) infants. The NICHD calculator applied to our population had a specificity of 93% and a positive predictive value of 75% and could not be applied to extremely SGA infants. Our tool can predict the risk of BPD on the 14th day of life, has higher specificity and positive predictive value to our population than the NICHD instrument, and can be suitable for SGA infants. The results must be confirmed by applying it to other populations to validate our tool.

Evaluation of urea breath test as a diagnostic tool for Helicobacter pylori infection in adult dyspeptic patients

In this editorial, we discuss the article in the World Journal of Gastroenterology . The article conducts a meta-analysis of the diagnostic accuracy of the urea breath test (UBT), a non-invasive method for detecting Helicobacter pylori (H. pylori) infection in humans. It is based on radionuclide-labeled urea. Various methods, both invasive and non-invasive, are available for diagnosing H. pylori infection, including endoscopy with biopsy, serology for immunoglobulin titers, stool antigen analysis, and UBT. Several guidelines recommend UBTs as the primary choice for diagnosing H. pylori infection and for reexamining after eradication therapy. It is used to be the first choice non-invasive test due to their high accuracy, specificity, rapid results, and simplicity. Moreover, its performance remains unaffected by the distribution of H. pylori in the stomach, allowing a high flow of patients to be tested. Despite its widespread use, the performance characteristics of UBT have been inconsistently described and remain incompletely defined. There are two UBTs available with Food and Drug Administration approval: The 13C and 14C tests. Both tests are affordable and can provide real-time results. Physicians may prefer the 13C test because it is non-radioactive, compared to 14C which uses a radioactive isotope, especially in young children and pregnant women. Although there was heterogeneity among the studies regarding the diagnostic accuracy of both UBTs, 13C-UBT consistently outperforms the 14C-UBT. This makes the 13C-UBT the preferred diagnostic approach. Furthermore, the provided findings of the meta-analysis emphasize the significance of precise considerations when choosing urea dosage, assessment timing, and measurement techniques for both the 13C-UBT and 14C-UBT, to enhance diagnostic precision.

Exploring the frontiers of therapeutic breadth of antifungal peptides: A new avenue in antifungal drugs.

The growing prevalence of fungal infections alongside rising resistance to antifungal drugs poses a significant challenge to public health safety. At the close of the 2000s, major pharmaceutical firms began to scale back on antimicrobial research due to repeated setbacks and diminished economic gains, leaving only smaller companies and research labs to pursue new antifungal solutions. Among various natural sources explored for novel antifungal compounds, antifungal peptides (AFPs) emerge as particularly promising. Despite their potential, AFPs receive less focus than their antibacterial counterparts. These peptides have been sourced extensively from nature, including plants, animals, insects, and especially bacteria and fungi. Furthermore, with advancements in recombinant biotechnology and computational biology, AFPs can also be synthesized in lab settings, facilitating peptide production. AFPs are noted for their wide-ranging efficacy, in vitro and in vivo safety, and ability to combat biofilms. They are distinguished by their high specificity, minimal toxicity to cells, and reduced likelihood of resistance development. This review aims to comprehensively cover AFPs, including their sources-both natural and synthetic-their antifungal and biofilm-fighting capabilities in laboratory and real-world settings, their action mechanisms, and the current status of AFP research.

Gonadotropin elevation is ootoxic to ovulatory oocytes and inhibits oocyte maturation, and activin decoy receptor ActRIIB:Fc therapeutically restores maturation

BackgroundElevated FSH often occurs in women of advanced maternal age (AMA, age ≥ 35) and in infertility patients undergoing controlled ovarian stimulation (COS). There is controversy on whether high endogenous FSH contributes to infertility and whether high exogenous FSH adversely impacts patient pregnancy rates.MethodsThe senescence-accelerated mouse-prone-8 (SAMP8) model of female reproductive aging was employed to assess the separate impacts of age and high FSH activity on the percentages (%) of viable and mature ovulated oocytes recovered after gonadotropin treatment. Young and midlife mice were treated with the FSH analog equine chorionic gonadotropin (eCG) to model both endogenous FSH elevation and exogenous FSH elevation. Previously we showed the activin inhibitor ActRIIB:Fc increases oocyte quality by preventing chromosome and spindle misalignments. Therefore, ActRIIB:Fc treatment was performed in an effort to increase % oocyte viability and % oocyte maturation.ResultsThe high FSH activity of eCG is ootoxic to ovulatory oocytes, with greater decreases in % viable oocytes in midlife than young mice. High FSH activity of eCG potently inhibits oocyte maturation, decreasing the % of mature oocytes to similar degrees in young and midlife mice. ActRIIB:Fc treatment does not prevent eCG ootoxicity, but it restores most oocyte maturation impeded by eCG.ConclusionsFSH ootoxicity to ovulatory oocytes and FSH maturation inhibition pose a paradox given the well-known pro-growth and pro-maturation activities of FSH in the earlier stages of oocyte growth. We propose the FOOT Hypothesis (“FSH OoToxicity Hypothesis), that FSH ootoxicity to ovulatory oocytes comprises a new driver of infertility and low pregnancy success rates in DOR women attempting spontaneous pregnancy and in COS/IUI patients, especially AMA women. We speculate that endogenous FSH elevation also contributes to reduced fecundity in these DOR and COS/IUI patients.Restoration of oocyte maturation by ActRIB:Fc suggests that activin suppresses oocyte maturation in vivo. This contrasts with prior studies showing activin A promotes oocyte maturation in vitro. Improved oocyte maturation with agents that decrease endogenous activin activity with high specificity may have therapeutic benefit for COS/IVF patients, COS/IUI patients, and DOR patients attempting spontaneous pregnancies.

Clinical significance of a basophil activation test for Japanese beekeepers naturally sensitized to honey bee venom.

The basophil activation test (BAT) has high sensitivity and specificity for diagnosing Hymenoptera venom allergy and is useful for predicting the clinical sensitivity of bee venom-allergic patients after venom immunotherapy. Patients sensitized to Hymenoptera venom are at risk for systemic reactions (SRs) to subsequent stings. Therefore, a tool that can predict the occurrence of SRs and the severity of Hymenoptera stings is needed. We performed BATs on Japanese beekeepers naturally sensitized to honey bee venom (HBV) and analyzed the positive threshold concentration for the occurrence of SRs following honey bee stings (HBS). Sixty-one beekeepers were interviewed and blood samples were taken. Data including history of HBS and the occurrence and severity of SRs to HBS were recorded. Blood samples were exposed to HBV-specific IgE antibodies (sIgE) and BAT was performed. Participants with HBV-sIgE ≥ class 1 were considered sensitized to HBV. The positive threshold for BAT scored as 0.0001, 0.001, 0.01, 0.1, and 1 μg/ml was classified as classes 5, 4, 3, 2, and 1, respectively. Samples negative at 1 μg/ml were classified as class 0. About 40% of beekeepers with a positive BAT threshold ≤ 0.1 μg/ml had SRs after HBS. The mean score of the BAT positivity threshold for beekeepers who developed SRs was significantly lower than that for beekeepers with no history of SRs (2.6 ± 0.8 vs 1.4 ± 1.1, P < 0.01). Analysis of the positive threshold of BAT in Japanese beekeepers naturally sensitized to HBV may be a useful tool for predicting the occurrence of SRs.

Sedimentation field-flow fractionation for rapid phenotypic antimicrobial susceptibility testing: a pilot study.

The increase in antibiotic resistance is a major public health issue. The development of rapid antimicrobial susceptibility testing (AST) methods is becoming a priority to ensure early and appropriate antibiotic therapy. To evaluate sedimentation field-flow fractionation (SdFFF) as a method for performing AST in less than 3 h. SdFFF is based on the detection of early biophysical changes in bacteria, using a chromatographic-type technology. One hundred clinical Escherichia coli strains were studied. A calibrated bacterial suspension was incubated for 2 h at 37°C in the absence (untreated) or presence (treated) of five antibiotics used at EUCAST breakpoint concentrations. Bacterial suspensions were then injected into the SdFFF machine. For each E. coli isolate, retention times and elution profiles of antibiotic-treated bacteria were compared with retention times and elution profiles of untreated bacteria. Algorithms comparing retention times and elution profiles were used to determine if the strain was susceptible or resistant. Performance evaluation was done according to CLSI and the ISO standard 20776-2:2021 with broth microdilution used as the reference method. AST results from SdFFF were obtained in less than 3 h. SdFFF showed high categorical agreement (99.8%), sensitivity (99.5%) and specificity (100.0%) with broth microdilution. Results for each antimicrobial were also in agreement with the ISO 20776-2 recommendations, with sensitivity and specificity of ≥95.0%. This study showed that SdFFF can be used as a rapid, accurate and reliable phenotypic AST method with a turnaround time of less than 3 h.

Sensitivity and specificity of the question “do you have any concerns regarding your mouth related to undergoing surgery?” for predicting perioperative oral health problems in patients with primary esophageal and lung cancer: a retrospective observational study

BackgroundPerioperative oral management contributes to the prevention of dental/systemic complications. However, a professional dental checkup before surgery is generally not performed and relies on the patient’s answer to a simple question by medical professionals other than dentists: “Do you have any concerns regarding your mouth related to undergoing surgery?” Here, we evaluated the sensitivity and specificity of this question for predicting perioperative oral health problems in patients with primary esophageal and primary lung cancer.MethodsWe performed an oral cavity check in all patients before scheduled surgery for primary esophageal and lung cancer. A total of 183 patients were enrolled (M, 112; F, 71; 24–88 years, median, 69 years), consisting of 61 with primary esophageal cancer (M, 46; F, 15; 24–85 years, median, 69 years) and 122 with primary lung cancer (M, 66; F; 56; 33–88 years, median, 69 years). All subjects provided a response to this question, and an oral cavity check was performed by dentists. The sensitivity and specificity of this question for detecting oral health problems were evaluated retrospectively.ResultsOverall sensitivity and specificity for detecting oral health problems were 0.263 and 0.898, respectively. There were no significant differences by sex or disease (primary esophageal or lung cancer).ConclusionThis simple question has low sensitivity but high specificity for detecting oral health problems. Although challenging to detect surgical patients with oral health problems by simply asking questions, the results indicated that patients with oral complaints are more likely to have problems during surgery.

Development of a Specific Aptamer-Modified Nano-System to Treat Esophageal Squamous Cell Carcinoma.

Esophageal squamous cell carcinoma (ESCC) is a prevalent gastrointestinal cancer characterized by high mortality and an unfavorable prognosis. While combination therapies involving surgery, chemotherapy, and radiation therapy are advancing, targeted therapy for ESCC remains underdeveloped. As a result, the overall five-year survival rate for ESCC is still below 20%. Herein, ESCC-specific DNA aptamers and an innovative aptamer-modified nano-system is introduced for targeted drug and gene delivery to effectively inhibit ESCC. The EA1 ssDNA aptamer, which binds robustly to ESCC cells with high specificity and affinity, is identified using cell-based systematic evolution of ligands by exponential enrichment (cell-SELEX). An EA1-modified nano-system is developed using a natural egg yolk lipid nanovector (EA1-EYLNs-PTX/siEFNA1) that concurrently loads paclitaxel (PTX) and a small interfering RNA of Ephrin A1 (EFNA1). This combination counters ESCC's proliferation, migration, invasion, and lung metastasis. Notably, EFNA1 is overexpressed in ESCC tumors with lung metastasis and has an inverse correlation with ESCC patient prognosis. The EA1-EYLNs-PTX/siEFNA1 nano-system offers effective drug delivery and tumor targeting, resulting in significantly improved therapeutic efficacy against ESCC tumors. These insights suggest that aptamer-modified nano-systems can deliver drugs and genes with superior tumor-targeting, potentially revolutionizing targeted therapy in ESCC.

Identification of key eRNAs for intervertebral disc degeneration by integrated multinomial bioinformatics analysis

BackgroundIntervertebral disc degeneration (IVDD) is a common degenerative condition leading to abnormal stress distribution under load, causing intervertebral stenosis, facet joint degeneration, and foraminal stenosis. Very little is known about the molecular mechanism of eRNAs in IVDD.MethodsGene expression profiles of 38 annulus disc samples composed of 27 less degenerated discs (LDs) and 11 more degenerated discs (MDs) were retrieved from the GEO database. Then, differentially expressed enhancer RNAs (DEeRNAs), differentially expressed target genes (DETGs), and differentially expressed transcription factors (DETFs), hallmark of cancer signalling pathways according to GSVA; the types and quantity of immune cells according to CIBERSORT; and immune gene sets according to ssGSEA were analysed to construct an IVDD-related eRNA network. Then, multidimensional validation was performed to explore the interactions among DEeRNAs, DETFs and DEGs in space.ResultsA total of 53 components, 14 DETGs, 15 DEeRNAs, 3 DETFs, 5 immune cells, 9 hallmarks, and 7 immune gene sets, were selected to construct the regulatory network. After validation by online multidimensional databases, 21 interactive DEeRNA-DEG-DETF axes related to IVDD exacerbation were identified, among which the C1S-CTNNB1-CHD4 axis was the most significant.ConclusionBased upon the results of our study, we theorize that the C1S-CTNNB1-CHD4 axis plays a vital role in IVDD exacerbation. Specifically, C1S recruits CTNNB1 and upregulates the expression of CHD4 in IVDD, and subsequently, CHD4 suppresses glycolysis and activates oxidative phosphorylation, thus generating insoluble collagen fibre deposits and leading to the progression of IVDD. Overall, these DEeRNAs could comprise promising therapeutic targets for IVDD due to their high tissue specificity.

TUsing Decision Tree Models and Comprehensive Statewide Data to Predict Opioid Overdoses Following Prison Release.

Identifying predictors of opioid overdose following release from prison is critical for opioid overdose prevention. We leveraged an individually linked, state-wide database from 2015-2020 to predict the risk of opioid overdose within 90 days of release from Massachusetts state prisons. We developed two decision tree modeling schemes: a model fit on all individuals with a single weight for those that experienced an opioid overdose and models stratified by race/ethnicity. We compared the performance of each model using several performance measures and identified factors that were most predictive of opioid overdose within racial/ethnic groups and across models. We found that out of 44,246 prison releases in Massachusetts between 2015-2020, 2,237 (5.1%) resulted in opioid overdose in the 90 days following release. The performance of the two predictive models varied. The single weight model had high sensitivity (79%) and low specificity (56%) for predicting opioid overdose and was more sensitive for White non-Hispanic individuals (sensitivity = 84%) than for racial/ethnic minority individuals. Stratified models had better balanced performance metrics for both White non-Hispanic and racial/ethnic minority groups and identified different predictors of overdose between racial/ethnic groups. Across racial/ethnic groups and models, involuntary commitment (involuntary treatment for alcohol/substance use disorder) was an important predictor of opioid overdose.

Clinical validity of the Italian adaptation of the Uniform Data Set Neuropsychological Test Battery (I-UDSNB) in Mild Cognitive Impairment and Alzheimer’s Disease

BackgroundThe identification and staging of Alzheimer’s Disease (AD) represent a challenge, especially in the prodromal stage of Mild Cognitive Impairment (MCI), when cognitive changes can be subtle. Worldwide efforts were dedicated to select and harmonize available neuropsychological instruments. In Italy, the Italian Network of Neuroscience and Neuro-Rehabilitation has promoted the adaptation of the Uniform Data Set Neuropsychological Test Battery (I-UDSNB), collecting normative data from 433 healthy controls (HC).Here, we aimed to explore the ability of I-UDSNB to differentiate between a) MCI and HC, b) AD and HC, c) MCI and AD.MethodsOne hundred thirty-seven patients (65 MCI, 72 AD) diagnosed after clinical-neuropsychological assessment, and 137 HC were included. We compared the I-UDSNB scores between a) MCI and HC, b) AD and HC, c) MCI and AD, with t-tests. To identify the test(s) most capable of differentiating between groups, significant scores were entered in binary logistic and in stepwise regressions, and then in Receiver Operating Characteristic curve analyses.ResultsTwo episodic memory tests (Craft Story and Five Words test) differentiated MCI from HC subjects; Five Words test, Semantic Fluency (vegetables), and TMT-part B differentiated AD from, respectively, HC and MCI.ConclusionsOur findings indicate that the I-UDSNB is a suitable tool for the harmonized and concise assessment of patients with cognitive decline, showing high sensitivity and specificity for the diagnosis of MCI and AD.

Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression

Immunotherapy with chimeric antigen receptor T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify cancer specific exon targets, here we analyze 1532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We find 2933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n = 148) or the alternatively spliced isoform (n = 9) level. Expression of selected alternatively spliced targets, including the EDB domain of fibronectin 1, and gene targets, such as COL11A1, are validated in pediatric patient derived xenograft tumors. We generate T cells expressing chimeric antigen receptors specific for the EDB domain or COL11A1 and demonstrate that these have antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.

Enhanced Brain Tumor Classification: A Hybrid Classifier Approach

Early detection of brain tumors is crucial for enhancing patient survival rates and treatment effectiveness. Analyzing magnetic resonance imaging (MRI) images by manually is a difficult task. Therefore, there is a requirement for digital techniques to improve the accuracy of tumor diagnosis. Study of this work was to enhance the performance of Machine Learning classifiers rather than move to deep learning. Machine Learning classifiers are advantageous compared to deep learning methods because of their ability to train on small datasets, low computing time complexity, affordability, and ease of adoption by individuals with less expertise The proposed methodology encompasses image processing, segmentation, feature extraction, feature reduction, and classification, leveraging techniques such as Otsu’s thresholding, GLCM, BWT, and PCA to extract pertinent information while minimizing dimensionality. By integrating a hybrid classifier that combines SVM, DT, and KNN, along with ensemble techniques, significant improvements in classification accuracy and robustness are achieved. Experimental results on the TCGA-GBM dataset showcase accuracy of 96.9%, with high specificity (95.14%) and sensitivity (97.14%) for classify normal tumors (benign tumors) and cancerous tumors (malignant tumors). Furthermore, the proposed methodology demonstrates efficiency with relatively low execution time, rendering it suitable for real-world applications.

Systematic literature review to inform the EULAR recommendations for the use of imaging in crystal-induced arthropathies in clinical practice

ObjectiveTo summarise current data regarding the use of imaging in crystal-induced arthropathies (CiAs) informing a European Alliance of Associations for Rheumatology task force.MethodsWe performed four systematic searches in Embase, Medline...

Application of cytogenetic studies to assess relapse in patients after allogeneic bone marrow transplantation

Ergospirometry is a modern approach to the diagnosis of physical health that involves the use of exercise testing to measure cardiopulmonary function. Aims: To compare the distribution of health characteristics and their relationship between participants, to evaluate the accuracy of hypertension, hyperlipidemia and diabetes in both groups, to measure respiratory rate and heart rate between ergospirometric testing and traditional testing for physical health assessment. Study design: A comparative cross-sectional design to assess ergospirometric testing and traditional testing for physical health assessment. Methodology: The study employed a comparative cross-sectional design, utilizing convenience sampling to recruit participants for ergospirometric testing on a treadmill and the traditional 6-Minute Walk Test. Sample size determination yielded 100 participants (50 per group). Data on sociodemographic, comorbidities, and physiological parameters were collected and analyzed using descriptive statistics, chi-square tests, and independent sample t-tests. Results: The study compared Ergometric testing on a treadmill with the Traditional 6-Minute Walk Test across various parameters. Participants undergoing Ergometric testing were younger with more females and smokers, while the Walk Test group had higher BMI and exercise rates. Ergometric testing revealed higher rates of hypertension (P = 0.034) and hyperlipidemia (P = 0.021) but lower diabetes prevalence (P = 0.016). Additionally, Ergometric testing showed a better detection of respiratory parameters, exercise stress detection (P = 0.009), and cardiovascular parameters as compared to Traditional testing. Furthermore, it has a higher sensitivity 85% and specificity 80% compared to the traditional testing having sensitivity 75%, and specificity 70%. Scientific Novelty: Spirometry testing has made an impact on physical examination today; using advanced technology to achieve the best, sensitivity and specificity marks changes in the actual examination. Conclusion: Ergometric testing (treadmill) shows a significant advantage over traditional testing (6-Minute Walk Test) in diagnosing physical health conditions with a high sensitivity, specificity, and comprehensive parameter assessment.

High-throughput tagging of endogenous loci for rapid characterization of protein function.

To facilitate the interrogation of protein function at scale, we have developed high-throughput insertion of tags across the genome (HITAG). HITAG enables users to rapidly produce libraries of cells, each with a different protein of interest C-terminally tagged. HITAG is based on a modified strategy for performing Cas9-based targeted insertions, coupled with an improved approach for selecting properly tagged lines. Analysis of the resulting clones generated by HITAG reveals high tagging specificity, with most successful tagging events being indel free. Using HITAG, we fuse mCherry to a set of 167 stress granule-associated proteins and elucidate the features that drive a subset of proteins to strongly accumulate within these transient RNA-protein granules.

The grade of obesity affects the noninvasive diagnosis of advanced fibrosis in individuals with MASLD.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is closely associated with obesity. We aimed to assess the impact of obesity on the performance of different noninvasive tests, including liver stiffness measurement (LSM) and Agile3+ (A3+), to detect advanced fibrosis (AF) in a population of patients with MASLD encompassing a wide range of BMI values. A total of 479 patients with MASLD were consecutively included (Lyon Hepatology Institute). Clinical data and noninvasive tests, including FibroTest, LSM, A3+, Fibrosis-4 (FIB-4), magnetic resonance elastography, and liver biopsies, were collected. AF was determined by a composite endpoint, i.e., histological stage ≥ F3, overt diagnosis of cirrhosis by magnetic resonance elastography, or concordant LSM ≥ 9.6 kPa and FibroTest ≥ F3. The median BMI was 35.0 kg/m2, and the prevalence of AF was 28.6%. Patients with BMI ≥ 35 versus <35 had a lower proportion of AF, i.e., 19.3% versus 38.1% (p < 0.001), but higher indeterminate status for AF (34.2% vs. 15.4%; p < 0.001). In the case of BMI ≥ 35, LSM had lower specificity to rule in AF (77.9%) versus A3+ (90.4%), but A3+ had decreased sensitivity to rule out AF. A sequential LSM/A3+ strategy achieved high specificity to rule in AF and lowered the proportion of indeterminate cases in patients with BMI ≥ 35. The grade of obesity affects the detection of MASLD-related AF. A sequential use of LSM/A3+ could improve AF detection in patients with BMI ≥ 35.

Development and evaluation of a multi-target droplet digital PCR assay for highly sensitive and specific detection of Yersinia pestis.

Plague, caused by the bacterium Yersinia pestis, is a zoonotic disease that poses considerable threats to human health. Nucleic acid tests are crucial for plague surveillance and the rapid detection of Y. pestis. However, inhibitors in complex samples such as soil and animal tissues often hamper nucleic acid detection, leading to a reduced rate of identifying low concentrations of Y. pestis. To address this challenge, we developed a sensitive and specific droplet digital polymerase chain reaction (ddPCR) assay for detecting Y. pestis DNA from soil and animal tissue samples. Three genes (ypo2088, caf1, and pla) from Y. pestis were used to develop a multi-target ddPCR assay. The limits of detection (LoD), reproducibility, and specificity were assessed for bacterial genomic DNA samples. The ability of the assay to detect low concentrations of Y. pestis DNA from simulated soil and mouse liver tissue samples was respectively evaluated and compared with that of quantitative real-time PCR (qPCR). The results showed that the ddPCR LoDs ranged from 6.2 to 15.4 copies/reaction for the target genes, with good reproducibility and high specificity for Y. pestis. By testing 130 soil and mouse liver tissue samples spiked with Y. pestis, the ddPCR assay exhibited a better sensitivity than that of the qPCR assay used in the study, with LoDs of 102 colony forming units (CFU)/100 mg soil and 103 CFU/20 mg liver. Moreover, the assay presented good quantitative linearity (R2 = 0.99) for Y. pestis at 103-106 CFU/sample for soil and liver samples. The ddPCR assay presented good performance for detecting Y. pestis DNA from soil and mouse tissue samples, showing great potential for improving the detection rate of low concentrations of Y. pestis in plague surveillance and facilitating the early diagnosis of plague cases.

Xpert-Ultra assay on stool and urine to improve tuberculosis diagnosis in children: the Médecins Sans Frontières experience in Guinea-Bissau and South Sudan

Abstract Background Over half of childhood tuberculosis (TB) remains undiagnosed yearly. WHO recommends Xpert-Ultra as a first paediatric diagnosis test, but microbiological confirmation remains low. We aimed to determine the diagnostic performance of Xpert-Ultra on stool and urine in presumptive paediatric TB cases in two high-TB burden settings. Methods This Médecins sans Frontières cross-sectional multicentric study took place at Simão Mendes hospital, Guinea-Bissau (July 2019 to April 2020) and in Malakal hospital, South Sudan (April 2021 to June 2023). Children 6 months to 15 years with presumptive TB underwent clinical and laboratory assessment, with one respiratory and/or extrapulmonary sample (gold standard (GS)), one stool and one urine specimen analysed with Xpert-Ultra. Results A total of 563 children were enrolled in the study, 133 from Bissau, 400 from Malakal; 30 were excluded. Confirmation of TB was achieved in 75 (14.1%) while 248 (46.5%) had unconfirmed TB. Of 553 with GS specimen, the overall diagnostic yield was 12.4% (66/533). A total of 493 and 524 samples were used to evaluate Xpert-Ultra on stool and on urine, respectively. Compared to GS, sensitivity and specificity of Xpert-Ultra on stool were 62.5%(95%CI:49.4-74) and 98.3%(95%CI:96.7-99.2), whereas on urine were 13.9%(95%CI:7.5-24.3) and 99.4%(95%CI:98.1-99.8), respectively. Nine patients were positive on stool and/or urine but negative on GS. Conclusions Xpert-Ultra on stool showed moderate to high sensitivity and high specificity when compared to GS and an added diagnostic yield when GS was negative. Xpert-Ultra on stool was useful in extrapulmonary cases. Xpert-Ultra in urine showed low test performance. Trial registration NCT06239337