Introduction: Studies investigating genetic risk factors for susceptibility to rheumatoid arthritis (RA) studied anti-citrullinated peptide antibody (CCP)-positive RA more frequently than anti-CCP-negative RA. One of the reasons for this is the perception that anti-CCP-negative RA may include patients that fulfilled criteria for RA but belong to a wide range of diagnoses. We aimed to evaluate the validity of this notion and explored whether clinical subphenotypes can be discerned within anti-CCP-negative RA.
Methods: The 318 patients with anti-CCP-negative RA (1987 ACR criteria), included in the Leiden Early Arthritis Clinic between 1993 and 2006, were studied for baseline characteristics and radiologic progression data during a mean follow-up of 5 years. Grouping was studied both at variable and patient levels. Principal components analysis and partial least-squares regression were applied to study for clustering of variables. A cluster analysis was performed to look for clustering of patients.
Results: The simultaneous presence of patient characteristics at disease presentation was observed for several groups; however, the three largest groups of patients' characteristics explained only 26.5% of the total variance. Plotting the contribution of each patient to these three groups did not reveal clustering of patients. Comparable observations were made when data on progression of joint destruction were studied in relation to baseline clinical data. A cluster analysis, evaluating whether patients resemble each other, revealed no grouping of patients. Altogether, no clinically distinguishable subphenotypes were observed.
Conclusions: The current data provide evidence that, for risk-factor studies, anti-CCP-negative RA patients can be studied as one group.
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http://dx.doi.org/10.1186/ar3505 | DOI Listing |
Nat Methods
January 2025
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-wide genotype-phenotype maps comprising CRISPR-Cas9-based knockouts of >20,000 genes in >30 million cells. Our optical pooled cell profiling platform (PERISCOPE) combines a destainable high-dimensional phenotyping panel (based on Cell Painting) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries.
View Article and Find Full Text PDFChembiochem
January 2025
Osaka University: Osaka Daigaku, International Center for Biotechnology, JAPAN.
Bacillibactin (BB) is a microbial siderophore produced by Bacillus species. BB is biosynthesized from 2,3-dihydroxybenzoic acid (2,3-DHB), Gly, and L-Thr by nonribosomal peptide synthetase (NRPS) enzymes DhbE, DhbB, and DhbF. The biosynthetic gene cluster (dhb) is also conserved in some strains of thermophilic genera, Geobacillus, Anoxybacillus and Parageobacillus.
View Article and Find Full Text PDFJ Infect
January 2025
National Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, PR China; Hubei Hongshan Laboratory, Wuhan, PR China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, PR China. Electronic address:
Objectives: Emerging human pathogens of animal origin have become an increasing public health concern in recent years. The aim of this study was to investigate the transmission of group B streptococcus (GBS) clonal complex (CC) 61 strains in the southern Chinese population and analyze their genetic characteristics.
Methods: Whole-genome sequencing was performed on 693 clinical isolates of GBS collected from southern China between 2016 and 2021, and the prevalence of human CC61 isolates was investigated by genomic epidemiology.
Background: Investigators and funding organizations desire knowledge on topics and trends in publicly funded research but current efforts for manual categorization have been limited in breadth and depth of understanding.
Purpose: We present a semi-automated analysis of 21 years of R-type National Cancer Institute (NCI) grants to departments of radiation oncology and radiology using natural language processing (NLP).
Methods: We selected all non-education R-type NCI grants from 2000 to 2020 awarded to departments of radiation oncology/radiology with affiliated schools of medicine.
J Hazard Mater
January 2025
Dept. of Science Education, Ewha Womans University, Seoul 03760, South Korea. Electronic address:
Although sulfur-bearing minerals are valuable resources, they pose significant environmental risks to river ecosystems by releasing hazardous leachate. Accurately tracing these sources is crucial but challenging due to overlapping chemical signatures and pollutant transport dynamics in river systems. This study investigates seasonal and spatial variations in sulfate (SO) and trace element contributions in mining districts of the upper Nakdong River basin, South Korea.
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