Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Feasibility randomised controlled trial comparing TRAK-ACL digital rehabilitation intervention plus treatment as usual versus treatment as usual for patients following anterior cruciate ligament reconstruction

Objectives: To evaluate the feasibility of trialling taxonomy for the rehabilitation of knee conditions-ACL (TRAK-ACL), a digital health intervention that provides health information, personalised exercise plans and remote clinical support combined with treatment as usual (TAU), for people following ACL reconstruction. Methods: The study design was a two-arm parallel randomised controlled trial (RCT). Eligible participants were English-speaking adults who had undergone ACL reconstruction within the last 12 weeks, had access to the internet and could provide informed consent. Recruitment took place at three sites in the UK. TRAK-ACL intervention was an interactive website informed by behaviour change technique combined with TAU. The comparator was TAU. Outcomes were: recruitment and retention; completeness of outcome measures at follow-up; fidelity of intervention delivery and engagement with the intervention. Individuals were randomised using a computer-generated random number sequence. Blinded assessors allocated groups and collected outcome measures. Results: Fifty-nine people were assessed for eligibility at two of the participating sites, and 51 were randomised; 26 were allocated to TRAK-ACL and 25 to TAU. Follow-up data were collected on 44 and 40 participants at 3 and 6 months, respectively. All outcome measures were completed fully at 6 months except the Client Service Receipt Inventory. Two patients in each arm did not receive the treatment they were randomised to. Engagement with TRAK-ACL intervention was a median of 5 logins (IQR 3-13 logins), over 18 weeks (SD 12.2 weeks). Conclusion: TRAK-ACL would be suitable for evaluation of effectiveness in a fully powered RCT

HFE variants and the expression of iron-related proteins in breast cancer-associated lymphocytes and macrophages

Disponível em: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264664/The association of HFE (High Iron FE) major variants with breast cancer risk and behavior has been a matter of discussion for a long time. However, their impact on the expression of iron-related proteins in the breast cancer tissue has never been addressed. In the present study, hepcidin, ferroportin 1, transferrin receptor 1 (TfR1), and ferritin expressions, as well as tissue iron deposition were evaluated in a collection of samples from breast cancers patients and analyzed according to the patients’ HFE genotype. Within the group of patients with invasive carcinoma, those carrying the p.Cys282Tyr variant in heterozygosity presented a higher expression of hepcidin in lymphocytes and macrophages than wild-type or p.His63Asp carriers. An increased expression of TfR1 was also observed in all the cell types analyzed but only in p.Cys282Tyr/p.His63Asp compound heterozygous patients. A differential impact of the two HFE variants was further noticed with the observation of a significantly higher percentage of p.Cys282Tyr heterozygous patients presenting tissue iron deposition in comparison to p.His63Asp heterozygous. In the present cohort, no significant associations were found between HFE variants and classical clinicopathological markers of breast cancer behavior and prognosis. Although limited by a low sampling size, our results provide a new possible explanation for the previously reported impact of HFE major variants on breast cancer progression, i.e., not by influencing systemic iron homeostasis but rather by differentially modulating the local cellular expression of iron-related proteins and tissue iron deposition.OM is a recipient of the PhD grant SFRH/BD/2011/78184 from Fundação para a Ciência e Tecnologia (FCT). The authors also acknowledge financial support from ICBAS/AI&NSUMIB and by national funds through FCT and Ministério da Educação e Ciência (MEC) and when applicable co-funded by FEDER funds within the partnership agreement PT2020 related with the research unit number 4293.info:eu-repo/semantics/publishedVersio

Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability.

To identify genetic causes of intellectual disability (ID), we screened a cohort of 986 individuals with moderate to severe ID for variants in 565 known or candidate ID-associated genes using targeted next-generation sequencing. Likely pathogenic rare variants were found in ∼11% of the cases (113 variants in 107/986 individuals: ∼8% of the individuals had a likely pathogenic loss-of-function [LoF] variant, whereas ∼3% had a known pathogenic missense variant). Variants in SETD5, ATRX, CUL4B, MECP2, and ARID1B were the most common causes of ID. This study assessed the value of sequencing a cohort of probands to provide a molecular diagnosis of ID, without the availability of DNA from both parents for de novo sequence analysis. This modeling is clinically relevant as 28% of all UK families with dependent children are single parent households. In conclusion, to diagnose patients with ID in the absence of parental DNA, we recommend investigation of all LoF variants in known genes that cause ID and assessment of a limited list of proven pathogenic missense variants in these genes. This will provide 11% additional diagnostic yield beyond the 10%-15% yield from array CGH alone.Action Medical Research (SP4640); the Birth Defect Foundation (RG45448); the Cambridge National Institute for Health Research Biomedical Research Centre (RG64219); the NIHR Rare Diseases BioResource (RBAG163); Wellcome Trust award WT091310; The Cell lines and DNA bank of Rett Syndrome, X-linked mental retardation and other genetic diseases (member of the Telethon Network of Genetic Biobanks (project no. GTB12001); the Genetic Origins of Congenital Heart Disease Study (GO-CHD)- funded by British Heart Foundation (BHF)This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/humu.2290

Koncentracija Сa,P i Mg u krvnom serumu jagnjadi hranjenih smešama sa različitim dodatkom preparata na bazi prirodnog zeolita

This work has an aim to explore the effects of the product based on the natural zeolit during the fattening of the lambs and also the effects on contents of calcium, phosphorus and magnesium in blood serum. The experiment lasted 15 days in the closed area of the Agricultural school in Kraljevo, and the lambs were divided into three groups of 15 lambs ( Control group –C, Experimental group E1 and E2). They were fed with sheep’s milk, concentrate for lambs’ fattening and meadow hay. The lambs in the experimental groups, in contrast to Control group, were fed with the different concentration of the preparation based on the natural zeolit (O1=1%, O2=1.5%), so that the manifested differences would be treated as the resault of the different concentration of the zeolit that was added to the lambs’ food.At the end of the experiment the differences in the parameters of the lambs’ blood serum were distinguished and especially in the concentration of calcium, phosphorus and magnesium.Istraživanja u ovom radu postavljena su sa ciljem da se ispitaju efekti korišćenja preparata na bazi prirodnog zeolita u ishrani jagnjadi u tovu kao i utvrđivanje efekata na sadržaj kalcijuma, fosfora i magnezijuma u krvnom serumu. Ogled je izveden u trajanju od 90 dana, u zatvorenom objektu Poljoprivredne škole u Kraljevu, a eksperimentalne životinje su podeljene u tri grupe po 15. jagnjadi (Kontrolna-K i Ogledne-O1 i O2). Obrok se sastojao od ovčjeg mleka, koncentrata za tov jagnjadi i livadskog sena. Jagnjad oglednih grupa, za razliku od kontrolne, dobijala su različite koncentracije preparata na bazi prorodnog zeolita (O1=1%, O2=1.5%), kako bi se na taj način ispoljene razlike tretirale kao posledica sadržaja različite količine dodatog zeolita u hrani. Na kraju ogleda su utvrđene razlike u ispitivanim parametrima iz krvnog seruma jagnjadi i to u koncentraciji kalcijuma , fosfora i magnezijuma

Scheduling Analysis of Imprecise Mixed-Criticality Real-Time Tasks

In this paper, we study the scheduling problem of the imprecise mixed-criticality model (IMC) under earliest deadline first with virtual deadline (EDF-VD) scheduling upon uniprocessor systems. Two schedulability tests are presented. The first test is a concise utilization-based test which can be applied to the implicit deadline IMC task set. The suboptimality of the proposed utilization-based test is evaluated via a widely-used scheduling metric, speedup factors. The second test is a more effective test but with higher complexity which is based on the concept of demand bound function (DBF). The proposed DBF-based test is more generic and can apply to constrained deadline IMC task set. Moreover, in order to address the high time cost of the existing deadline tuning algorithm, we propose a novel algorithm which significantly improve the efficiency of the deadline tuning procedure. Experimental results show the effectiveness of our proposed schedulability tests, confirm the theoretical suboptimality results with respect to speedup factor, and demonstrate the efficiency of our proposed algorithm over the existing deadline tunning algorithm. In addition, issues related to the implementation of the IMC model under EDF-VD are discussed.Computer Systems, Imagery and Medi

Rare Genetic Variation in 135 Families With Family History Suggestive of X-Linked Intellectual Disability.

Families with multiple male children with intellectual disability (ID) are usually suspected of having disease due to a X-linked mode of inheritance and genetic studies focus on analysis of segregating variants in X-linked genes. However, the genetic cause of ID remains elusive in approximately 50% of affected individuals. Here, we report the analysis of next-generation sequencing data in 274 affected individuals from 135 families with a family history suggestive of X-linked ID. Genetic diagnoses were obtained for 19% (25/135) of the families, and 24% (33/135) had a variant of uncertain significance. In 12% of cases (16/135), the variants were not shared within the family, suggesting genetic heterogeneity and phenocopies are frequent. Of all the families with reportable variants (43%, 58/135), we observed that 55% (32/58) were in X-linked genes, but 38% (22/58) were in autosomal genes, while the remaining 7% (4/58) had multiple variants in genes with different modes on inheritance. This study highlights that in families with multiple affected males, X linkage should not be assumed, and both individuals should be considered, as different genetic etiologies are common in apparent familial cases

The role of hemoadsorption in cardiac surgery - a systematic review

BACKGROUND: Extracorporeal blood purification has been widely used in intensive care medicine, nephrology, toxicology, and other fields. During the last decade, with the emergence of new adsorptive blood purification devices, hemoadsorption has been increasingly applied during CPB in cardiac surgery, for patients at different inflammatory risks, or for postoperative complications. Clinical evidence so far has not provided definite answers concerning this adjunctive treatment. The current systematic review aimed to critically assess the role of perioperative hemoadsorption in cardiac surgery, by summarizing the current knowledge in this clinical setting. METHODS: A literature search of PubMed, Cochrane library, and the database provided by CytoSorbents was conducted on June 1st, 2023. The search terms were chosen by applying neutral search keywords to perform a non-biased systematic search, including language variations of terms "cardiac surgery" and "hemoadsorption". The screening and selection process followed scientific principles (PRISMA statement). Abstracts were considered for inclusion if they were written in English and published within the last ten years. Publications were eligible for assessment if reporting on original data from any type of study (excluding case reports) in which a hemoadsorption device was investigated during or after cardiac surgery. Results were summarized according to sub-fields and presented in a tabular view. RESULTS: The search resulted in 29 publications with a total of 1,057 patients who were treated with hemoadsorption and 988 control patients. Articles were grouped and descriptively analyzed due to the remarkable variability in study designs, however, all reported exclusively on CytoSorb$^{®}$ therapy. A total of 62% (18/29) of the included articles reported on safety and no unanticipated adverse events have been observed. The most frequently reported clinical outcome associated with hemoadsorption was reduced vasopressor demand resulting in better hemodynamic stability. CONCLUSIONS: The role of hemoadsorption in cardiac surgery seems to be justified in selected high-risk cases in infective endocarditis, aortic surgery, heart transplantation, and emergency surgery in patients under antithrombotic therapy, as well as in those who develop a dysregulated inflammatory response, vasoplegia, or septic shock postoperatively. Future large randomized controlled trials are needed to better define proper patient selection, dosing, and timing of the therapy

Associations between dog breed and clinical features of mammary epithelial neoplasia in bitches: an epidemiological study of submissions to a single diagnostic pathology centre between 2008-2021

Mammary cancer is one of the most common neoplasms of dogs, primarily bitches. While studies have been carried out identifying differing risk of mammary neoplasia in different dog breeds, few studies have reported associations between dog breeds and clinical features such as number of neoplastic lesions found in an individual case or the likelihood of lesions being benign or malignant. Such epidemiological studies are essential as a foundation for exploring potential genetic drivers of mammary tumour behaviour. Here, we have examined associations between breed, age and neuter status and the odds of a diagnosis of a mammary epithelial-origin neoplastic lesion (as opposed to any other histopathological diagnosis from a biopsied lesion) as well as the odds of a bitch presenting with either a single mammary lesion or multiple lesions, and the odds that those lesions are benign or malignant. The study population consisted of 129,258 samples from bitches, including 13,401 mammary epithelial neoplasms, submitted for histological assessment to a single histopathology laboratory between 2008 and 2021

EnvMine: A text-mining system for the automatic extraction of contextual information

<p>Abstract</p> <p>Background</p> <p>For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.</p> <p>Results</p> <p>EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.</p> <p>Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.</p> <p>Conclusion</p> <p>EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.</p