Eliciting the Functional Taxonomy from protein annotations and taxa

The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules

A Simulation Tool for Computing Energy Optimal Motion Parameters of Industrial Robots

This paper presents a novel robot simulation tool, fully interfaced with a common Robot Offline Programming software (i.e. Delmia Robotics), which allows to automatically compute energy-optimal motion parameters, for a given end-effector path, by tuning the joint speed/acceleration during point-to-point motions whenever allowed by the manufacturing constraints. The main advantage of this method, as compared to other optimization routines that are not conceived for a seamless integration with commercial industrial manipulators, is that the computed parameters are the same required by the robot controls, so that the results can generate ready-to-use energy-optimal robot code

PERFIL DE SUSCEPTIBILIDADE A ANTIMICROBIANOS DOS PRINCIPAIS AGENTES CAUSADORES DE OTITE EXTERNA EM CÃES E GATOS

Otite externa canina é uma enfermidade comum na rotina clínica de pequenosanimais se caracterizando por inflamação aguda ou crônica da orelha externa, sendomais frequente em cães do que em gatos. Possui etiologia multifatorial classificada emfatores predisponentes, primários e perpetuantes. Os principais agentes infecciosossecundários descritos na literatura associados a casos de otite externa são bactérias,leveduras e fungos. As bactérias mais encontradas na literatura destacam-seStaphylococcus spp., Streptococcus spp., Pseudomonas spp. e Proteus spp. Dentre osagentes fungicos e leveduras, o patógeno mais comum para perpetuar otite canina éMalassezia spp. e mais raramente Candida sp. e outros organismos fúngicos saprófitas.A baixa efetividade dos fármacos pode ser justificada, em parte, pela produção de β-lactamases por linhagens de Staphylococcus spp., enterobactérias e Pseudomonasaeruginosa e o uso há décadas da neomicina no tratamento tópico da otite canina.Apesar da preocupação emergente com a resistência múltipla de bactérias aosantimicrobianos convencionais de uso veterinário poucos estudos no Brasil tem sidoconduzidos com intuito de investigar a presença de linhagens multirresistentes isoladasde otite canina. Desse modo, a, presente pesquisa tem o objetivo de verificar a presençados principais microrganismos causadores de otite em cães e gatos, bem como verificaro perfil de susceptibilidade a antimicrobianos. As coletas foram realizadas em clínicas depequenos animais, pet shops, Organizações não governamentais (ONG). E osprocedimentos metodológicos foram realizados no Laboratório de Microbiologia daUniversidade do Oeste de Santa Catarina – UNOESC, campus de São Miguel do Oeste –SC. Dos 34 animais coletados, houve crescimento microbiológico de 20 amostras. Osmicroorganismos isolados nos exames microbiológicos foram identificados como:Staphylococcus sp. (7cepas), 35%; Staphylococcus aureus (11cepas), 55%;Pseudomonas aeruginosa (2 cepas), 10%

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of potential quadruplex-forming sequences (PQS) in the genome of all known viruses that can infect humans. We show that occurrence and location of PQSs are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the PQS classification. For each virus we provide: i) the list of all PQS present in the genome (positive and negative strands), ii) their position in the viral genome, iii) the degree of conservation among strains of each PQS in its genome context, iv) the statistical significance of PQS abundance. This information is accessible from a database to allow the easy navigation of the results: http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus. The availability of these data will greatly expedite research on G-quadruplex in viruses, with the possibility to accelerate finding therapeutic opportunities to numerous and some fearsome human diseases

ESTUDO ANATOMOPATOLÓGICO NEOPLASIAS MAMÁRIAS EM CADELAS E GATAS ATENDIDAS NO HOSPITAL VETERINÁRIO DA UNIVERSIDADE DE SANTA CRUZ DO SUL – RS, BRASIL

Mammary tumors are frequent in bitches and cats. This study aimed to evaluate the frequency of canine and feline mammary tumors, their size, histopathological type and the relationship between the occurrence of mammary neoplasms and the fertile status of the animal. The data in this study are from patients treated at the HV-UNISC-RS during the period from December 2020 to August 2021. The tumors of 21 females, 19 bitches and 2 cats were analyzed, with a mean age of around 9 years, ranging from 2 to 13 years. Of these, 90.40% were not neutered. Histopathological analysis of mammary chains resulted in the diagnosis of 49 tumors, of which 48 were diagnosed as neoplastic and 1 presented non-neoplastic alterations. Regarding the biological behavior of neoplasms, 81.25% were malignant and 18.75% benign. The size ranged from 0.7 to 10 centimeters in diameter. In cats, tubular carcinoma was more prevalent (60.00%), with carcinoma in situ (20.00%) and phyllodes tumor (20.00%) also being reported. In bitches, it was carcinoma in mixed tumor (34.88%), followed by tubular carcinoma (18.60%), micropapillary carcinoma (13.95%), malignant adenomyoepithelioma (6.66%), benign adenomyoepithelioma (4.65%), benign mixed tumor and tubular adenoma (4.65%), carcinoma in situ, solid carcinoma, tubulopapillary carcinoma, ductal adenoma and fibroma (2.32%). The incidence of mammary tumor is higher in bitches due to prolonged exposure to estrogen. Most of the females with neoplasms were not neutered or had used exogenous hormones, thus emphasizing the importance of castration of canine and feline females and the contraindication of the use of progestogens.Tumores mamários são frequentes em cadelas e gatas. Este estudo teve por objetivo avaliar a frequência dos tumores mamários caninos e felinos, o tamanho, o tipo histopatológico e a relação entre a ocorrência de neoplasias mamárias com a situação fértil do animal. Os dados deste estudo são de pacientes atendidos no HV-UNISC-RS durante o período de dezembro de 2020 a agosto de 2021. Foram analisados os tumores de 21 fêmeas, 19 cadelas e 2 gatas, com idade média em torno de 9 anos, variando entre 2 a 13 anos. Destas, 90,40% não eram castradas. A análise histopatológica das cadeias mamárias resultou no diagnóstico de 49 tumores, dos quais 48 foram diagnosticados como neoplásicos e 1 apresentou alterações não neoplásicas. Quanto ao comportamento biológico das neoplasias, 81,25% eram malignos e 18,75% benignos. O tamanho variou entre 0,7 a 10 centímetros de diâmetro. Em gatas, teve maior prevalência o carcinoma tubular (60,00%), sendo relatados ainda carcinoma in situ (20,00%) e tumor filoides (20,00%). Em cadelas, foi o carcinoma em tumor misto (34,88%), seguido pelo carcinoma tubular (18,60%), carcinoma micropapilar (13,95%), adenomioepitelioma maligno (6,66%), adenomioepitelioma benigno (4,65%), tumor misto benigno e adenoma tubular (4,65%), carcinoma in situ, carcinoma sólido, carcinoma túbulo-papilar, adenoma ductal e fibroma (2,32%). A incidência de tumor mamário é maior em cadelas por conta da exposição prolongada ao estrógeno. A maioria das fêmeas com neoplasias não eram castradas ou haviam feito uso de hormônios exógenos, salientando assim, a importância da castração de fêmeas caninas e felinas e a contraindicação do uso de progestágenos

Lopinavir/Ritonavir and Darunavir/Cobicistat in Hospitalized COVID-19 Patients: Findings From the Multicenter Italian CORIST Study

Background: Protease inhibitors have been considered as possible therapeutic agents for COVID-19 patients. Objectives: To describe the association between lopinavir/ritonavir (LPV/r) or darunavir/cobicistat (DRV/c) use and in-hospital mortality in COVID-19 patients. Study Design: Multicenter observational study of COVID-19 patients admitted in 33 Italian hospitals. Medications, preexisting conditions, clinical measures, and outcomes were extracted from medical records. Patients were retrospectively divided in three groups, according to use of LPV/r, DRV/c or none of them. Primary outcome in a time-to event analysis was death. We used Cox proportional-hazards models with inverse probability of treatment weighting by multinomial propensity scores. Results: Out of 3,451 patients, 33.3% LPV/r and 13.9% received DRV/c. Patients receiving LPV/r or DRV/c were more likely younger, men, had higher C-reactive protein levels while less likely had hypertension, cardiovascular, pulmonary or kidney disease. After adjustment for propensity scores, LPV/r use was not associated with mortality (HR = 0.94, 95% CI 0.78 to 1.13), whereas treatment with DRV/c was associated with a higher death risk (HR = 1.89, 1.53 to 2.34, E-value = 2.43). This increased risk was more marked in women, in elderly, in patients with higher severity of COVID-19 and in patients receiving other COVID-19 drugs. Conclusions: In a large cohort of Italian patients hospitalized for COVID-19 in a real-life setting, the use of LPV/r treatment did not change death rate, while DRV/c was associated with increased mortality. Within the limits of an observational study, these data do not support the use of LPV/r or DRV/c in COVID-19 patients

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries