Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America

Tambaqui or cachama (Colossoma macropomum) is one of the most important neo-tropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water tempera-ture is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High- throughput sequencing to generate genome-wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and un-covering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed pop-ulations of tambaqui in South America using single- nucleotide polymorphism (SNP) markers obtained with double-digest restriction site-associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (lo-cated in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288– 0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p< 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aq-uaculture, were identified to be under positive selection, suggesting local adapta-tion to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programsConselho Nacional de Desenvolvimento Científico e Tecnológico, Grant/Award Number: 140740/2016–3, 311559/2018– 2 and 422670/2018-9; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Fundação de Amparo à Pesquisa do Estado de São Paulo, Grant/Award Number: 2016/18294–9, 2016/21011– 9, 2017/19717-3, 2017/26900–9, 2018/08416–5, 2019/08972-8 and 2019/10662-7; Comisión Nacional de Investigación Científica y Tecnológica.S

Assessment of risk scores to predict mortality of COVID-19 patients admitted to the intensive care unit

ObjectivesTo assess the ABC2-SPH score in predicting COVID-19 in-hospital mortality, during intensive care unit (ICU) admission, and to compare its performance with other scores (SOFA, SAPS-3, NEWS2, 4C Mortality Score, SOARS, CURB-65, modified CHA2DS2-VASc, and a novel severity score).Materials and methodsConsecutive patients (≥ 18 years) with laboratory-confirmed COVID-19 admitted to ICUs of 25 hospitals, located in 17 Brazilian cities, from October 2020 to March 2022, were included. Overall performance of the scores was evaluated using the Brier score. ABC2-SPH was used as the reference score, and comparisons between ABC2-SPH and the other scores were performed by using the Bonferroni method of correction. The primary outcome was in-hospital mortality.ResultsABC2-SPH had an area under the curve of 0.716 (95% CI 0.693–0.738), significantly higher than CURB-65, SOFA, NEWS2, SOARS, and modified CHA2DS2-VASc scores. There was no statistically significant difference between ABC2-SPH and SAPS-3, 4C Mortality Score, and the novel severity score.ConclusionABC2-SPH was superior to other risk scores, but it still did not demonstrate an excellent predictive ability for mortality in critically ill COVID-19 patients. Our results indicate the need to develop a new score, for this subset of patients

Turnover of neutrophils mediated by Fas ligand drives Leishmania major infection.

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2015-02-10T13:44:26Z No. of bitstreams: 1 Ribeiro-Gomes FL Turnover...pdf: 2439307 bytes, checksum: 63344954ef36fc4b33455b01fa48f302 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2015-02-10T13:44:35Z (GMT) No. of bitstreams: 1 Ribeiro-Gomes FL Turnover...pdf: 2439307 bytes, checksum: 63344954ef36fc4b33455b01fa48f302 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2015-02-10T13:55:47Z (GMT) No. of bitstreams: 1 Ribeiro-Gomes FL Turnover...pdf: 2439307 bytes, checksum: 63344954ef36fc4b33455b01fa48f302 (MD5)Made available in DSpace on 2015-02-10T13:55:47Z (GMT). No. of bitstreams: 1 Ribeiro-Gomes FL Turnover...pdf: 2439307 bytes, checksum: 63344954ef36fc4b33455b01fa48f302 (MD5) Previous issue date: 2005Federal University of Rio de Janeiro. Instituto de Biofísica Carlos Chagas Filho. Rio de Janeiro, RJ, BrasilFederal University of Rio de Janeiro. Instituto de Biofísica Carlos Chagas Filho. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, BrasilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrasilFederal University of Rio de Janeiro. Instituto de Biofísica Carlos Chagas Filho. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrasilUniversity of São Paulo. Instituto de Ciências Biomédicas. São Paulo, SP, BrasilFederal University of Rio de Janeiro. Instituto de Biofísica Carlos Chagas Filho. Rio de Janeiro, RJ, BrasilApoptosis mediated by Fas ligand (FasL) initiates inflammation characterized by neutrophilic infiltration. Neutrophils undergo apoptosis and are ingested by macrophages. Clearance of dead neutrophils leads to prostaglandin- and transforming growth factor-beta-dependent replication of Leishmania major in macrophages from susceptible mice. How L. major induces neutrophil turnover in a physiological setting is unknown. We show that BALB/c FasL-sufficient mice are more susceptible to L. major infection than are FasL-deficient mice. FasL promotes the apoptosis of infected resident macrophages and attracts neutrophils. Furthermore, FasL-sufficient neutrophils exacerbate L. major replication in macrophages, whereas FasL-deficient neutrophils induce parasite killing. These contrasting effects are due to delaying apoptosis and the clearance of FasL-deficient neutrophils. The transfer of neutrophils exacerbates infection in FasL-sufficient mice but reduces infection in FasL-deficient mice. Depletion of neutrophils abolishes the susceptibility of FasL-sufficient mice. These data illustrate a deleterious role of the FasL-mediated turnover of neutrophils on L. major infection

Table_3_Assessment of risk scores to predict mortality of COVID-19 patients admitted to the intensive care unit.docx

ObjectivesTo assess the ABC2-SPH score in predicting COVID-19 in-hospital mortality, during intensive care unit (ICU) admission, and to compare its performance with other scores (SOFA, SAPS-3, NEWS2, 4C Mortality Score, SOARS, CURB-65, modified CHA2DS2-VASc, and a novel severity score).Materials and methodsConsecutive patients (≥ 18 years) with laboratory-confirmed COVID-19 admitted to ICUs of 25 hospitals, located in 17 Brazilian cities, from October 2020 to March 2022, were included. Overall performance of the scores was evaluated using the Brier score. ABC2-SPH was used as the reference score, and comparisons between ABC2-SPH and the other scores were performed by using the Bonferroni method of correction. The primary outcome was in-hospital mortality.ResultsABC2-SPH had an area under the curve of 0.716 (95% CI 0.693–0.738), significantly higher than CURB-65, SOFA, NEWS2, SOARS, and modified CHA2DS2-VASc scores. There was no statistically significant difference between ABC2-SPH and SAPS-3, 4C Mortality Score, and the novel severity score.ConclusionABC2-SPH was superior to other risk scores, but it still did not demonstrate an excellent predictive ability for mortality in critically ill COVID-19 patients. Our results indicate the need to develop a new score, for this subset of patients.</p

Table_2_Assessment of risk scores to predict mortality of COVID-19 patients admitted to the intensive care unit.docx

ObjectivesTo assess the ABC2-SPH score in predicting COVID-19 in-hospital mortality, during intensive care unit (ICU) admission, and to compare its performance with other scores (SOFA, SAPS-3, NEWS2, 4C Mortality Score, SOARS, CURB-65, modified CHA2DS2-VASc, and a novel severity score).Materials and methodsConsecutive patients (≥ 18 years) with laboratory-confirmed COVID-19 admitted to ICUs of 25 hospitals, located in 17 Brazilian cities, from October 2020 to March 2022, were included. Overall performance of the scores was evaluated using the Brier score. ABC2-SPH was used as the reference score, and comparisons between ABC2-SPH and the other scores were performed by using the Bonferroni method of correction. The primary outcome was in-hospital mortality.ResultsABC2-SPH had an area under the curve of 0.716 (95% CI 0.693–0.738), significantly higher than CURB-65, SOFA, NEWS2, SOARS, and modified CHA2DS2-VASc scores. There was no statistically significant difference between ABC2-SPH and SAPS-3, 4C Mortality Score, and the novel severity score.ConclusionABC2-SPH was superior to other risk scores, but it still did not demonstrate an excellent predictive ability for mortality in critically ill COVID-19 patients. Our results indicate the need to develop a new score, for this subset of patients.</p

Table_1_Assessment of risk scores to predict mortality of COVID-19 patients admitted to the intensive care unit.docx

ObjectivesTo assess the ABC2-SPH score in predicting COVID-19 in-hospital mortality, during intensive care unit (ICU) admission, and to compare its performance with other scores (SOFA, SAPS-3, NEWS2, 4C Mortality Score, SOARS, CURB-65, modified CHA2DS2-VASc, and a novel severity score).Materials and methodsConsecutive patients (≥ 18 years) with laboratory-confirmed COVID-19 admitted to ICUs of 25 hospitals, located in 17 Brazilian cities, from October 2020 to March 2022, were included. Overall performance of the scores was evaluated using the Brier score. ABC2-SPH was used as the reference score, and comparisons between ABC2-SPH and the other scores were performed by using the Bonferroni method of correction. The primary outcome was in-hospital mortality.ResultsABC2-SPH had an area under the curve of 0.716 (95% CI 0.693–0.738), significantly higher than CURB-65, SOFA, NEWS2, SOARS, and modified CHA2DS2-VASc scores. There was no statistically significant difference between ABC2-SPH and SAPS-3, 4C Mortality Score, and the novel severity score.ConclusionABC2-SPH was superior to other risk scores, but it still did not demonstrate an excellent predictive ability for mortality in critically ill COVID-19 patients. Our results indicate the need to develop a new score, for this subset of patients.</p

ABC-SPH risk score for in-hospital mortality in COVID-19 patients : development, external validation and comparison with other available scores

The majority of available scores to assess mortality risk of coronavirus disease 2019 (COVID-19) patients in the emergency department have high risk of bias. Therefore, this cohort aimed to develop and validate a score at hospital admission for predicting in-hospital mortality in COVID-19 patients and to compare this score with other existing ones. Consecutive patients (≥ 18 years) with confirmed COVID-19 admitted to the participating hospitals were included. Logistic regression analysis was performed to develop a prediction model for in-hospital mortality, based on the 3978 patients admitted between March-July, 2020. The model was validated in the 1054 patients admitted during August-September, as well as in an external cohort of 474 Spanish patients. Median (25-75th percentile) age of the model-derivation cohort was 60 (48-72) years, and in-hospital mortality was 20.3%. The validation cohorts had similar age distribution and in-hospital mortality. Seven significant variables were included in the risk score: age, blood urea nitrogen, number of comorbidities, C-reactive protein, SpO/FiO ratio, platelet count, and heart rate. The model had high discriminatory value (AUROC 0.844, 95% CI 0.829-0.859), which was confirmed in the Brazilian (0.859 [95% CI 0.833-0.885]) and Spanish (0.894 [95% CI 0.870-0.919]) validation cohorts, and displayed better discrimination ability than other existing scores. It is implemented in a freely available online risk calculator (https://abc2sph.com/). An easy-to-use rapid scoring system based on characteristics of COVID-19 patients commonly available at hospital presentation was designed and validated for early stratification of in-hospital mortality risk of patients with COVID-19