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A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species.

BACKGROUND: The available Leptospira multilocus sequence typing (MLST) scheme supported by a MLST website is limited to L. interrogans and L. kirschneri. Our aim was to broaden the utility of this scheme to incorporate a total of seven pathogenic species. METHODOLOGY AND FINDINGS: We modified the existing scheme by replacing one of the seven MLST loci (fadD was changed to caiB), as the former gene did not appear to be present in some pathogenic species. Comparison of the original and modified schemes using data for L. interrogans and L. kirschneri demonstrated that the discriminatory power of

Molecular epidemiology of rabies in Ukraine.

To investigate the circulation of rabies virus in Ukraine, 78 rabies virus isolates were acquired from 14 states in 2002 and 2008-2010 for characterization. Partial sequences of nucleoprotein (359 nt) and glycoprotein (344 nt) genes were compared with those from neighbouring countries. The analysis identified 39 unique nucleoprotein genes and two geographically distinct RV variants belonging to the cosmopolitan lineage. The Ukrainian samples were similar to the North-East European lineage (NEE) (n = 19) and Russian group C (n = 20). The group C viruses were mainly isolated in Eastern Ukraine,

Phylogenetic analysis of the spirochete Borrelia microti, a potential agent of relapsing fever in Iran.

We report a role for Borrelia microti as a cause of relapsing fever in Iran supported by robust epidemiological evidence. The molecular identity of this spirochete and its relation with other relapsing fever borreliae have, until now, been poorly delineated. We analyzed an isolate of B. microti, obtained from Ornithodoros erraticus ticks, by sequencing four loci (16S rRNA, flaB, glpQ, intragenic spacer [IGS]) and comparing these sequences with those of other relapsing fever borreliae. Phylogenetic analysis using concatenated sequences of 16S rRNA, flaB, and glpQ grouped B. microti alongside th

Global distribution and genetic diversity of Bartonella in bat flies (Hippoboscoidea, Streblidae, Nycteribiidae).

Recently, a growing number Bartonella spp. have been identified as causative agents for a broadening spectrum of zoonotic diseases, emphasizing their medical importance. Many mammalian reservoirs and vectors however are still unknown, hindering our understanding of pathogen ecology and obscuring epidemiological connections. New Bartonella genotypes were detected in a global sampling of 19 species of blood-feeding bat flies (Diptera, Hippoboscoidea, Nycteribiidae, Streblidae) from 20 host bat species, suggesting an important role of bat flies in harboring bartonellae. Evolutionary relationships

Genetic variation in jasmonic acid- and spider mite-induced plant volatile emission of cucumber accessions and attraction of the predator Phytoseiulus persimilis.

Cucumber plants (Cucumis sativus L.) respond to spider-mite (Tetranychus urticae) damage with the release of specific volatiles that are exploited by predatory mites, the natural enemies of the spider mites, to locate their prey. The production of volatiles also can be induced by exposing plants to the plant hormone jasmonic acid. We analyzed volatile emissions from 15 cucumber accessions upon herbivory by spider mites and upon exposure to jasmonic acid using gas chromatography-mass spectrometry. Upon induction, cucumber plants emitted over 24 different compounds, and the blend of induced vola

Genomics and evolution of Aedes-borne flaviviruses.

We analysed the complete coding sequences of all recognized species of Aedes-borne flavivirus, including previously uncharacterized viruses within the yellow fever virus (YFV), Spondweni virus (SPOV) and dengue virus (DENV) groups. Two major phylogenetic lineages were revealed: one included the YFV and Entebbe bat virus groups, and the other included the DENV, SPOV and Culex-borne flavivirus groups. This analysis supported previous evidence that Culex-borne flaviviruses have evolved from ancestral Aedes-borne viruses. However, the topology at the junction between these lineages remains complex

Microarray analysis reveals differences in gene expression of circulating CD8(+) T cells in melanoma patients and healthy donors.

Circulating T cells from many cancer patients are known to be dysfunctional and undergo spontaneous apoptosis. We used microarray technology to determine whether gene expression differences exist in T cells from melanoma patients versus healthy subjects, which may underlie these abnormalities. To maximize the resolution of our data, we sort purified CD8(+) subsets and amplified the extracted RNA for microarray analysis. These analyses show subtle but statistically significant expression differences for 10 genes in T cells from melanoma patients versus healthy controls, which were additionally

Learning difficulties, social intelligence, and self-concept: connections to bully-victim problems.

Learning skills, social intelligence, and self-concept were related to each other and to bully-victim problems among fifth-grade children (7 … r hand, was not related to LD. LD children's proposed victim status was in some degree supported by cluster analysis: a group of LD children emerged, who not only scored high on bullying, but also tended to be victimized by others. In addition, two groups of bullies appeared: one whose members could be interpreted as socially unskilled and another as socially skil …

Symptom burden survey and symptom clusters in patients with cervical cancer: a cross-sectional survey.

Abstract Purpose The purpose of this study is to determine the incidence and severity of symptoms of patients with cervical cancer within 6 months after radiotherapy and chemotherapy, form a symptom burden report, evaluate the distribution characteristics of symptoms, identify symptom clusters, and provide a basis for clinical doctors and nurses to improve the symptom management of patients with cervical cancer after radiotherapy and chemotherapy. Methods The patients with cervical cancer within 6 months after radiotherapy and chemotherapy were recruited to investigate their symptom burden. Ex

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… Symptom cluster recognition methods mainly include principal component analysis (PCA), confirmative factor analysis (CFA), hierarchical cluster analysis (HCA), and exploratory factor analysis (EFA). … This method is currently a widely used clinical symptom cluster identification method, mainly including principal components analysis (PCA), common factor analysis (CFA), and hierarchical cluster analysis (HCA) [ 32 , 33 ]. …

The predictive ability of "TyG_CVAI" for incident stroke in individuals with different glycemic metabolic status: A national cohort study.

The triglyceride-glucose-Chinese visceral adiposity index (TyG_CVAI) has been validated as an effective predictor of early stroke. However, its predictive efficacy across different glycemic metabolic states remains unexplored. This study utilized data from the China Health and Retirement Longitudinal Study, including 7744 stroke-free participants. Participants were categorized into 3 glycemic groups: diabetes mellitus (DM), prediabetes mellitus (Pre-DM), and normal glucose regulation (NGR). K-means clustering further divided participants into 2 clusters based on TyG_CVAI fluctuations: Cluster

CD163+ macrophage density in perimysial connective tissue associated with prognosis in IMNM.

OBJECTIVE: The pathological features of immune-mediated necrotizing myopathy (IMNM) are dominated by the infiltration of macrophages. We aimed to perform a histopathologic semiquantitative analysis to investigate the relationship between macrophage markers and prognosis. METHODS: Semiquantitative analysis of histologic features was performed in 62 samples of IMNM. Independent risk factors were identified through univariate and multivariate regression analysis. Cluster analysis was performed using the partitioning around the medoids (PAM) method. Decision tree modeling was utilized to efficien…

Neonatal outcomes of preterm infants with pulmonary hypertension: clustering based on prenatal risk factors.

BACKGROUND: To investigate association of prenatal risk factors and neonatal outcomes of preterm infants with pulmonary hypertension (PH). METHODS: A prospective cohort study of very-low-birth-weight infants born at 22-29 weeks' gestation who received PH-specific treatment during hospitalization. Infants were classified using a two-step cluster analysis based on gestational age (GA), small-for-gestational-age (SGA), exposure to antenatal corticosteroids (ACS), histologic chorioamnionitis (HCA), and oligohydramnios. RESULTS: Among 910 infants, six clusters were identified: cluster A (HCA, n =…

Identification of PsA phenotypes with machine learning analytics using data from two phase III clinical trials of guselkumab in a bio-naïve population of patients with PsA.

OBJECTIVES: Psoriatic arthritis (PsA) phenotypes are typically defined by their clinical components, which may not reflect patients' overlapping symptoms. This post hoc analysis aimed to identify hypothesis-free PsA phenotype clusters using machine learning to analyse data from the phase III DISCOVER-1/DISCOVER-2 clinical trials. METHODS: Pooled data from bio-naïve patients with active PsA receiving guselkumab 100 mg every 8/4 weeks were retrospectively analysed. Non-negative matrix factorisation was applied as an unsupervised machine learning technique to identify PsA phenotype clusters; bas

Species-specific elemental profiles in three hymenoptera species under shared environmental exposure: implications for biomonitoring.

This study compared the elemental composition of worker honey bees (Apis mellifera), German wasps (Vespula germanica), and European hornets … lements, while PC2 (22.4%) distinguished honey bees from wasps based on macroelements. Hierarchical cluster analysis confirmed this separation, with hornets forming a distinct cluster and bees and wasps forming separate subclusters. These differences reflect species-specific exposure pathways, foraging range, and physiological regulation of element uptake rather t …

De novo clustering of long-read amplicons improves phylogenetic insight into microbiome data.

Long-read amplicon profiling through read classification limits phylogenetic analysis of amplicons while community analysis of multicopy genes, relying on unique molecular identifier (UMI) corrections, often demands deep sequencing. To address this, we present a long amplicon consensus analysis (LACA) workflow employing multiple de novo clustering approaches based on sequence dissimilarity. LACA controls the average error rate of corrected sequences below 1% for the Oxford Nanopore Technologies (ONT) R9.4.1 and ONT R10.3 data, 0.2% for ONT R10.4.1, and 0.1% for high-accuracy ONT Duplex and Pac

Microbiome-Based Colon Cancer Patient Stratification and Survival Analysis.

BACKGROUND: Colorectal cancer (CRC) is any cancer that starts in the colon or the rectum and presents a significant health concern. It is the third most diagnosed and the second deadliest cancer, with an estimated 153,020 new cases and 52,550 deaths in 2023. The severity of colon cancer may be attributed to its ability to avoid the host immune system and growth suppressors, its asymptomatic nature in the early stages, its association with a continually ageing population and unfavourable diet and obesity. The composition of the gut microbiome plays an important role in the development of CRC an

Evaluation study of congelex laxative granules based on HPLC fingerprint, multi-component content determination, and chemometrics.

Congelex Laxative Granules is an in-house preparation of Hebei Provincial Hospital of Traditional Chinese Medicine. This study aims to estab … nide, wedelolactone, aurantio-obtusin, and chrysophanol, were quantitatively analyzed. Hierarchical Cluster Analysis (HCA), principal component analysis (PCA), and orthogonal partial least squares-discriminant analysis (OPLS-DA) were used to comprehensively evaluate sample quality. Results indicated that the 20 batches could be divided into two categories, with co …

Prospective Spatiotemporal Cluster Detection Using SaTScan: Tutorial for Designing and Fine-Tuning a System to Detect Reportable Communicable Disease Outbreaks.

Staff at public health departments have few training materials to learn how to design and fine-tune systems to quickly detect acute, localized, community-acquired outbreaks of infectious diseases. Since 2014, the Bureau of Communicable Disease at the New York City Department of Health and Mental Hygiene has analyzed reportable communicable diseases daily using SaTScan. SaTScan is a free software that analyzes data using scan statistics, which can detect increasing disease activity without a priori specification of temporal period, geographic location, or size. The Bureau of Communicable Diseas

Epidemiological characteristics and spatiotemporal clustering of scarlet fever in Liaoning Province, China, 2010-2019.

BACKGROUND: To explore the epidemiological characteristics and spatiotemporal distribution of scarlet fever in Liaoning Province, which could provide scientific evidence for the formulation and improvement of prevention and control strategies and measures. METHODS: Data on scarlet fever cases and population were obtained from the China Information System for Disease Control and Prevention in Liaoning Province between 2010 and 2019. We examined the spatial and spatiotemporal clusters of scarlet fever across Liaoning Province using the Moran's I, local indicators of spatial association, local G

Saliva based non invasive screening of Oral Submucous Fibrosis using ATR-FTIR spectroscopy.

Oral Submucous Fibrosis (OSMF) is a type of precancerous condition of Oral cancer and considered to have the greatest malignant potential. Biopsy is an ultimate option for the conformation of the malignancy. But the invasiveness of the procedure makes it interdict. Therefore, there is an urgent need to identify effective screening and diagnostic methods which would be less invasive, rapid, more accurate and cost effective. Here, we used Attenuated Total Reflection- Fourier transform infrared spectroscopy (ATR-FTIR) with Chemometric analysis coupled with estimation of total salivary protein to