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ObjectiveClinical observations and a limited number of research studies provide evidence that the fragile X premutation may confer risk for autism, executive dysfunction, and psychopathology. The link to autism spectrum symptoms and social cognition deficits with the premutation remains uncertain, and thus was the focus of the present investigation.MethodOur sample included 131 individuals, 42 men/22 women with the FMR1 premutation (mean age = 31.83 ± 8.59 years) with a normal neurological exam, and 48 men/19 women healthy age-matched controls (mean age = 29.48 ± 7.29 years). Individuals completed a comprehensive neuropsychological battery with additional assessments for social cognition, broad autism spectrum, and obsessive-compulsive (OC) symptoms.ResultsPremutation carriers self-reported higher rates of autism-related symptoms (Autism Quotient; p = .001). Among males only, premutation carriers showed more atypical social interaction (p

This article discusses the effectiveness and safety of powered endoscopic resection (EndoRotor) treatment for scarred polyps (manipulated lesions) that occur after the treatment of large polyps with conventional endoscopic and/or surgical methods. The study, conducted at Nottingham University Hospitals NHS Trust, included 42 patients who received EndoRotor treatment. The primary outcome was the complete eradication of the polyps, which was achieved in 93% of patients within three treatment sessions. The study concludes that EndoRotor is a safe and effective treatment for scarred polyps, with most patients achieving complete eradication within three sessions. [Extracted from the article]

This article presents the findings of a retrospective study conducted in Barcelona, Spain and Nottingham, United Kingdom on the safety and efficacy of a double balloon overtube device in facilitating complex endoscopic therapeutic procedures. The study included 42 patients with loopy bowels or colostomies who underwent overtube-assisted procedures. The device was found to be useful in overcoming difficult access, preventing air leakage, and completing the intervention in the majority of cases. The study concludes that the device can safely and effectively reduce procedure time and improve outcomes in patients with difficult colonic anatomy and complex polyps. [Extracted from the article]

Abstract: Background: Submucosal lifting of lesions prior to endoscopic resection is crucial to reduce complications and improve the technical feasibility of the procedure. Aim: To compare a self-assembled hydro-jet system vs. standard needle injection for tissue elevation prior to endoscopic resection of colorectal lesions. Methods: Randomised study performed at a single tertiary care institution. Consecutive patients with colonoscopic diagnosis of sessile polyps or non-polypoid lesions >5mm or laterally spreading tumours. Outcome measures: successful elevation, time to proper elevation, completeness of excision, cautery damage, and general histological diagnostic quality (blinded pathologic assessment). Results: 79 patients were randomised to hydro-jet (40 patients, group A) and needle (39 patients, group B) elevation. Successful elevation was achieved in 97.5% and 94.8%, respectively. Time to proper elevation was 8±5s vs. 18±3s (p <0.05). In group A, histology showed selective accumulation of fluid in the submucosa with intact collagen fibres. Damage to muscularis mucosa was never noted in the specimens of group A and in 7 cases of group B (p <0.01). Artefacts from “cautery effect” were very limited. Radial margins of resection could be adequately evaluated in all cases and were negative. Conclusions: The hydro-jet system is as effective and safe as standard needle injection for tissue elevation prior to endoscopic resection of colorectal lesions, but it is significantly faster. [Copyright &y& Elsevier]

Abstract Background Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval. Results The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI. Conclusion We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components. Availability OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl

Abstract Background Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources. Experimental data sets from metabolomics studies need to be integrated with one another, but also with data produced by other types of omics studies in the spirit of systems biology, hence the pressing need for vocabularies and ontologies in metabolomics. However, it is time-consuming and non trivial to construct these resources manually. Results We describe a methodology for rapid development of controlled vocabularies, a study originally motivated by the needs for vocabularies describing metabolomics technologies. We present case studies involving two controlled vocabularies (for nuclear magnetic resonance spectroscopy and gas chromatography) whose development is currently underway as part of the Metabolomics Standards Initiative. The initial vocabularies were compiled manually, providing a total of 243 and 152 terms. A total of 5,699 and 2,612 new terms were acquired automatically from the literature. The analysis of the results showed that full-text articles (especially the Materials and Methods sections) are the major source of technology-specific terms as opposed to paper abstracts. Conclusions We suggest a text mining method for efficient corpus-based term acquisition as a way of rapidly expanding a set of controlled vocabularies with the terms used in the scientific literature. We adopted an integrative approach, combining relatively generic software and data resources for time- and cost-effective development of a text mining tool for expansion of controlled vocabularies across various domains, as a practical alternative to both manual term collection and tailor-made named entity recognition methods.

Abstract There are thousands of biology databases with hundreds of terminologies, reporting guidelines, representations models, and exchange formats to help annotate, report, and share bioscience investigations. It is evident, however, that researchers and bioinformaticians struggle to navigate the various standards and to find the appropriate database to collect, manage, and share data. Further, policy makers, funders, and publishers lack sufficient information to formulate their guidelines. In this paper, we highlight a number of key issues that can be used to turn these challenges into new opportunities. It is time for all stakeholders to work together to reconcile cause and effect and make the data-sharing culture functional and efficient.

Abstract Background A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. Results We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Conclusion Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data.

Abstract Background Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies is the lack of a unified methodology. Different methodologies have been proposed for different scenarios, but there is no agreed-upon standard methodology for building ontologies. The involvement of geographically distributed domain experts, the need for domain experts to lead the design process, the application of the ontologies and the life cycles of bio-ontologies are amongst the features not considered by previously proposed methodologies. Results Here, we present a methodology for developing ontologies within the biological domain. We describe our scenario, competency questions, results and milestones for each methodological stage. We introduce the use of concept maps during knowledge acquisition phases as a feasible transition between domain expert and knowledge engineer. Conclusion The contributions of this paper are the thorough description of the steps we suggest when building an ontology, example use of concept maps, consideration of applicability to the development of lower-level ontologies and application to decentralised environments. We have found that within our scenario conceptual maps played an important role in the development process.

Background: Thyroid thermoablative techniques have been developed as an alternative to surgery for the treatment of symptomatic benign nodes, with the advantage of being minimally invasive, repeatable, with a minimal complication rate, and avoiding the perioperative risks and irreversible consequences of surgery., Methods: A series of patients undergoing laser thermoablation by the same team of endocrinologists operating in 2 centers from May 2016 to December 2022 is presented. The procedure was performed in patients with compressive symptomatology determined by a thyroid node typed TIR 2, or TIR 3A with rejection of the surgical option. We analyzed cases that required surgery because of persistent compressive symptoms, reduction failure, or increase in volume., Results: From May 2016 to December 2022, 207 thermoablative procedures were performed (187 patients). Single ablative session was unresolved in 28 patients (15%). The proportion of nodes with TIR 3A cytology was significantly higher (21.4 vs 7.0%). In this group, the response in terms of volumetric reduction 6 months after the procedure was significantly lower (5.7% vs 50%). Ten patients (5.3%) underwent surgery, whose histological outcome demonstrated malignancy in 50% of cases., Conclusions: Data show the importance of timely re-evaluation with referral to surgical treatment for patients presenting a less than 20% volume reduction 6 months after thermoablation, in order to ensure promptly effective treatment of misrecognized malignancies., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: Postmenopausal androgen excess often occurs due to the imbalance between the rapid decline in ovarian estrogen and a relatively gradual decline in androgen secretion. The rapid onset of hirsutism, alopecia, and acne, on the other hand, is a rare occurrence and requires further investigation in order to rule out an underlying neoplasm., Case Report: A 54-year-old woman arrived at the endocrinology outpatient clinic for the appearance of hirsutism and defluvium capitis in the past 9 months. She had hypertrichosis of the face, trunk, and mammary areolae and reduced timbre of voice. Circulating androgens were higher than normal levels (testosterone: 7.7 ng/mL, DHEAS: 5437 mcg/L, 17-OH-progesterone: 3.1 nmol/L), gonadotropin and prolactin levels were normal, and Nugent test was negative. Abdominal CT scan was negative for adrenal lesions, while transvaginal ovarian ultrasonography revealed a left adnexal formation (19x18x24 mm) compatible with stromal neoplasm. A bilateral hysteroannessiectomy was performed. Histological examination was diagnostic for multiple ovarian Leydig cell tumors., Conclusion: The most frequent cause of postmenopausal hyperandrogenism is polycystic ovary syndrome. It is necessary to exclude the presence of neoplastic causes (ovarian or adrenal androgen- secreting tumors). In case of marked virilization and severe hyperandrogenism, it is useful to perform transvaginal ultrasonography to search for the presence of ovarian hypertrichosis or androgen-secreting ovarian tumors and a CT/RM scan to study the adrenal glands. The best treatment for hyperandrogenism of neoplastic origin is surgery. Patients who are not candidates for this approach are candidates for therapy with GnRH agonists., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Endoscopic resection (ER) of colorectal polyps has become a daily practice in most endoscopic units providing a colorectal cancer screening program and requires the availability of local experts and high-end endoscopic devices. ER procedures have evolved over the past few years from endoscopic mucosal resection (EMR) to more advanced techniques, such as endoscopic submucosal dissection and endo-scopic full-thickness resection. Complete resection and disease eradication are the ultimate goals of ER-based techniques, and novel devices have been developed to achieve these goals. The EndoRotor ® Endoscopic Powered Resection System (Interscope Medical, Inc., Northbridge, Massachusetts, United States) is one such device. The EndoRotor is a powered resection tool for the removal of alimentary tract mucosa, including post-EMR persistent lesions with scarring, and has both CE Mark and FDA clearance. This review covers available published evidence documenting the usefulness of EndoRotor for the management of recurrent colorectal polyps., Competing Interests: Conflict-of-interest statement: Dr. Parra-Blanco reports other from Inter scope, during the conduct of the study; other from Lumendi and CREO medical, other from Puramatrix, outside the submitted work., (©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.)

Importance: The relationship between Enterococcus faecalis vaginal colonization and urinary tract infections (UTIs) remains uncertain., Objective: We aimed to evaluate the surface invasion capability of E faecalis isolates from patients with and without UTIs as a potential readout of pathogenicity., Study Design: Participants were females from urogynecology clinics, comprising symptomatic UTI and asymptomatic non-UTI patients, categorized by the presence or absence of E faecalis-positive cultures identified via standard urine culture techniques. Vaginal and urine samples from patients were plated on enterococci selective medium, and E faecalis isolates detected in both cohorts were species specific identified using 16S rRNA sequencing. Clinical isolates were inoculated on semisolid media, and both external colonies and underneath colony prints formed by agar-penetrating enterococci were imaged. External growth and invasiveness were quantified by determining colony-forming units of the noninvading and agar-penetrating cells and compared with the E faecalis OG1RF., Results: We selected E faecalis isolates from urine and vaginal samples of 4 patients with and 4 patients without UTIs. Assays demonstrated that most isolates formed similarly sized external colonies with comparable colony-forming unit. Surface invasion differed across patients and isolation sites compared with OG1RF. The vaginal isolate from UTI patient 1, who had the most recurrences, exhibited significantly greater agar-invading capacity compared with OG1RF., Conclusions: Our pilot study indicates that ex vivo invasion assays may unveil virulence traits in E faecalis from UTI patients. Enhanced enterococcal surface penetration could increase urogenital invasion risk. Further research is needed to correlate penetration with disease severity in a larger patient group., Competing Interests: The authors have declared they have no conflicts of interest., (Copyright © 2024 American Urogynecologic Society. All rights reserved.)

Competing Interests: Dr Adolfo Parra-Blanco is a consultant for Lumendi company and is an advisory member for Lumendi, received speaker honorarium from Interscope and from 3D Matrix.No competing interest for the other two authors.

Enterococcus faecalis is a normal commensal of the human gastrointestinal tract (GIT). However, upon disruption of gut homeostasis, this nonmotile bacterium can egress from its natural niche and spread to distal organs. While this translocation process can lead to life-threatening systemic infections, the underlying mechanisms remain largely unexplored. Our prior work showed that E. faecalis migration across diverse surfaces requires the formation of matrix-covered multicellular aggregates and the synthesis of exopolysaccharides, but how enterococcal cells are reprogrammed during this process is unknown. Whether surface penetration endows E. faecalis with adaptive advantages is also uncertain. Here, we report that surface penetration promotes the generation of a metabolically and phenotypically distinct E. faecalis population with an enhanced capacity to endure various forms of extracellular stress. Surface-invading enterococci demonstrated major ultrastructural alterations in their cell envelope characterized by increased membrane glycolipid content. These changes were accompanied by marked induction of specific transcriptional programs enhancing cell envelope biogenesis and glycolipid metabolism. Notably, the surface-invading population demonstrated superior tolerance to membrane-damaging antimicrobials, including daptomycin and β-defensins produced by epithelial cells. Genetic mutations impairing glycolipid biosynthesis sensitized E. faecalis to envelope stressors and reduced the ability of this bacterium to penetrate semisolid surfaces and translocate through human intestinal epithelial cell monolayers. Our study reveals that surface penetration induces distinct transcriptional, metabolic, and ultrastructural changes that equip E. faecalis with enhanced capacity to resist external stressors and thrive in its surrounding environment. IMPORTANCE Enterococcus faecalis inhabits the GIT of multiple organisms, where its establishment could be mediated by the formation of biofilm-like aggregates. In susceptible individuals, this bacterium can overgrow and breach intestinal barriers, a process that may lead to lethal systemic infections. While the formation of multicellular aggregates promotes E. faecalis migration across surfaces, little is known about the metabolic and physiological states of the enterococci encased in these surface-penetrating structures. The present study reveals that E. faecalis cells capable of migrating through semisolid surfaces genetically reprogram their metabolism toward increased cell envelope and glycolipid biogenesis, which confers superior tolerance to membrane-damaging agents. E. faecalis's success as a pathobiont depends on its antimicrobial resistance, as well as on its rapid adaptability to overcome multiple environmental challenges. Thus, targeting adaptive genetic and/or metabolic pathways induced during E. faecalis surface penetration may be useful to better confront infections by this bacterium in the clinic.