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The elongation of Caenorhabditis elegans embryos allows examination of mechanical interactions between adjacent tissues. Muscle contractions during late elongation induce the remodeling of epidermal circumferential actin filaments through mechanotransduction. Force inputs from the muscles deform circumferential epidermal actin filament, which causes them to be severed, eventually reformed, and shortened. This squeezing force drives embryonic elongation. We investigated the possible role of the nonmuscle myosins NMY-1 and NMY-2 in this process using nmy-1 and nmy-2 thermosensitive alleles. Our findings show these myosins act redundantly in late elongation, since double nmy-2(ts); nmy-1(ts) mutants immediately stop elongation when raised to 25°C. Their inactivation does not reduce muscle activity, as measured from epidermis deformation, suggesting that they are directly involved in the multistep process of epidermal remodeling. Furthermore, NMY-1 and NMY-2 inactivation is reversible when embryos are kept at the nonpermissive temperature for a few hours. However, after longer exposure to 25°C double mutant embryos fail to resume elongation, presumably because NMY-1 was seen to form protein aggregates. We propose that the two C. elegans nonmuscle myosin II act during actin remodeling either to bring severed ends or hold them., Competing Interests: Conflicts of interest: The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Objective: To present a series of experiments: (1) to evaluate the impact of pre-annotation on the speed of manual annotation of clinical trial announcements; and (2) to test for potential bias, if pre-annotation is utilized., Methods: To build the gold standard, 1400 clinical trial announcements from the clinicaltrials.gov website were randomly selected and double annotated for diagnoses, signs, symptoms, Unified Medical Language System (UMLS) Concept Unique Identifiers, and SNOMED CT codes. We used two dictionary-based methods to pre-annotate the text. We evaluated the annotation time and potential bias through F-measures and ANOVA tests and implemented Bonferroni correction., Results: Time savings ranged from 13.85% to 21.5% per entity. Inter-annotator agreement (IAA) ranged from 93.4% to 95.5%. There was no statistically significant difference for IAA and annotator performance in pre-annotations., Conclusions: On every experiment pair, the annotator with the pre-annotated text needed less time to annotate than the annotator with non-labeled text. The time savings were statistically significant. Moreover, the pre-annotation did not reduce the IAA or annotator performance. Dictionary-based pre-annotation is a feasible and practical method to reduce the cost of annotation of clinical named entity recognition in the eligibility sections of clinical trial announcements without introducing bias in the annotation process.

Background: Mannose-binding lectin (MBL) is a pattern-recognition molecule of the innate immune system and may be involved in the pathogenesis of inflammatory bowel disease (IBD). Our aim was to assess the prevalence of MBL deficiency in a cohort of patients with paediatric-onset IBD and study whether it is associated with the clinical manifestations, serum antibody formation, or genetic factors., Methods: This prospective study included 159 paediatric patients (mean age: 14.0 years) with IBD [107 patients with Crohn disease (CD) and 52 patients with ulcerative colitis (UC)]. Furthermore, 95 controls were investigated. Serum samples were determined for MBL by enzyme-linked immunosorbent assay (ELISA) and for serologic markers [autoantibodies against Saccharomyces cerevisiae (ASCA) and perinuclear components of neutrophils (pANCA)] by indirect immunofluorescent assay. NOD2/CARD15 variants were tested by polymerase chain reaction/restriction fragment length polymorphism., Results: The MBL serum concentration was significantly lower in IBD patients(both with CD and UC) compared to controls (IBD, p=0.007, CD, p=0.04, UC p=0.004). Prevalence of low MBL level (<500 ng/mL) was significantly higher in both CD and UC groups compared to controls (p=0.002 and p=0.006). Furthermore, low MBL level was associated with isolated ileal involvement (p=0.01) and MBL deficiency (<100 ng/mL) with male gender (p=0.004) in patients with CD. We failed to confirm any correlation between MBL deficiency and serum autoantibodies or NOD2/CARD15 variants., Conclusions: Our results suggest that low MBL associated with paediatric-onset IBD and ileal CD may be considered an additional marker of the IBD pathogenesis., (Copyright © 2012 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.)

Objective: (1) To evaluate a state-of-the-art natural language processing (NLP)-based approach to automatically de-identify a large set of diverse clinical notes. (2) To measure the impact of de-identification on the performance of information extraction algorithms on the de-identified documents., Material and Methods: A cross-sectional study that included 3503 stratified, randomly selected clinical notes (over 22 note types) from five million documents produced at one of the largest US pediatric hospitals. Sensitivity, precision, F value of two automated de-identification systems for removing all 18 HIPAA-defined protected health information elements were computed. Performance was assessed against a manually generated 'gold standard'. Statistical significance was tested. The automated de-identification performance was also compared with that of two humans on a 10% subsample of the gold standard. The effect of de-identification on the performance of subsequent medication extraction was measured., Results: The gold standard included 30 815 protected health information elements and more than one million tokens. The most accurate NLP method had 91.92% sensitivity (R) and 95.08% precision (P) overall. The performance of the system was indistinguishable from that of human annotators (annotators' performance was 92.15%(R)/93.95%(P) and 94.55%(R)/88.45%(P) overall while the best system obtained 92.91%(R)/95.73%(P) on same text). The impact of automated de-identification was minimal on the utility of the narrative notes for subsequent information extraction as measured by the sensitivity and precision of medication name extraction., Discussion and Conclusion: NLP-based de-identification shows excellent performance that rivals the performance of human annotators. Furthermore, unlike manual de-identification, the automated approach scales up to millions of documents quickly and inexpensively.

Background, Aims: According to Porto Criteria upper gastrointestinal (UGI) endoscopy is recommended in patients with suspected inflammatory bowel disease (IBD). Nevertheless, previous studies revealed frequent involvement of UGI tract even in patients with ulcerative colitis (UC). The aim of the present study was to determine the diagnostic role of esophagogastroduodenoscopy (EGD) and assess the prevalence and different aspects of UGI involvement in children registered in the Hungarian Pediatric IBD Registry (HUPIR) from 1st of January 2007 to 31th of December 2009., Methods: Twenty seven institutes provided prospective follow-up data about newly diagnosed IBD patients to HUPIR. The registry was based on detailed questionnaire (76 parameters) involving anamnestic data, laboratory findings, activity indexes, diagnostic procedures, endoscopic examinations (EGD and ileocolonoscopy), and histological data. Localization and phenotype of disease were based on the Montreal classification criteria., Results: During the 3-year period 420 children were diagnosed with IBD, 265 (63%) of them had Crohn's disease (CD), 130 (31%) UC, and 25 (6%) IBD-unclassified (IBD-U). The mean age at diagnosis was 13.2 years (range: 1.2-18 years). EGD was performed in 237 patients (56%), in most cases in patients suffering from CD. Macroscopic lesions on EGD were noted in 64% of patients with CD and 40% of children with UC. Characteristic lesions for CD (ulcer, erosion, aphthous lesion, and granuloma) were noted in 31% of CD patients, however, EGD helped to establish the final diagnosis in 9% of CD patients (diagnostic yield, 9%)., Conclusions: There was a high frequency of UGI involvement in children with CD and UC. One third of CD patients showed significant lesions at upper endoscopy and one patient out of ten had real diagnostic help from EGD., (Copyright © 2011 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.)

We have analysed BP180 mRNA expression in normal human keratinocytes. Here we report the presence in normal keratinocytes of two COL17A1 transcripts which differ by 0.6 kb in length. Both mRNAs hybridized on Northern blot with probes directed to sequences encoding intracellular and extracellular fragments of BP180. By BLAST homology search alignments we extended the 3' untranslated region (3'UTR) of the known BP180 mRNA sequence by 877 bases to completion. Three of 20 cDNAs identified by BLAST searches contained a 610 bp deletion in this new 3'UTR sequence. Northern blot analysis with a probe complementary to this deleted sequence showed binding only to the larger mRNA. The deletion of 610 nucleotides in the smaller mRNA was verified by reverse transcription-PCR and sequencing. Genomic PCR showed the new sequence to be an extension of exon 56 of the COL17A1 gene which suggests that the second mRNA is generated by differential splicing. In normal keratinocytes the level of the smaller transcript was 5-15% of that of the larger transcript whereas in a squamous cell carcinoma cell line this ratio was reversed, the smaller mRNA being three times more abundant than the larger mRNA. The biological significance of this newly identified transcript in protein synthesis and tissue expression or in cell differentiation, proliferation or adhesion is as yet unknown.