Validation of the Portuguese Version of the Short-Form Glasgow Composite Measure Pain Scale (CMPS-SF) According to COSMIN and GRADE Guidelines.

We aimed to validate the CMPS-SF according to COSMIN and GRADE guidelines. Four trained evaluators assessed 208 videos (pre-operative-M1, peak of pain-M2, 1 h after the peak of pain and analgesia (rescue)-M3, and 24 h post-extubation-M4) of 52 dogs, divided into negative controls (n = 10), soft tissue surgeries (n = 22), and orthopedic surgeries (n = 20). The videos were randomized and blinded as to when they were filmed, and were evaluated in two stages, 21 days apart. According to confirmatory analysis, the CMPS-SF is a unidimensional scale. Intra-observer reliability was between 0.80 and 0.99 and inter-observer reliability between 0.73 and 0.86. Criterion validity was confirmed by the correlation between the CMPS-SF and other unidimensional scales (≥0.7). The differences between the scores were M2 ≥ M3 > M4 > M1 (responsiveness), and the scale presented construct validity (higher postoperative pain scores in dogs undergoing surgery versus control). Internal consistency was 0.7 (Cronbach's α) and 0.77 (McDonald's ω), and the item-total correlation was between 0.3 and 0.7, except for "A(ii)-Attention to wound". Specificity and sensitivity were 78-87% and 74-83%, respectively. The cut-off point for rescue analgesia was ≥5 or ≥4 excluding item B(iii) mobility, and the GRADE classification was high, confirming the validity of the scale.

Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North-South collaboration.

Next-generation sequencing technology has revolutionised pathogen surveillance over the last two decades. However, the benefits are not equitably distributed, with developing countries lagging far behind in acquiring the required technology and analytical capacity. Recent declines in the cost associated with sequencing-equipment and running consumables have created an opportunity for broader adoption. During the COVID-19 pandemic, rapid diagnostics development and DNA sequencing revolutionised the ability to diagnose and sequence SARS-CoV-2 rapidly. Socioeconomic inequalities substantially impact the ability to sequence SARS-CoV-2 strains and undermine a developing country's pandemic preparedness. Low- and middle-income countries face additional challenges in establishing, maintaining and expanding genomic surveillance. We present our experience of establishing a genomic surveillance system at the Aga Khan University, Karachi, Pakistan. Despite being at a leading health sciences research institute in the country, we encountered significant challenges. These were related to collecting standardised contextual data for SARS-CoV-2 samples, procuring sequencing reagents and consumables, and challenges with library preparation, sequencing and submission of high-quality SARS-CoV-2 genomes. Several technical roadblocks ensued during the implementation of the genomic surveillance framework, which were resolved in collaboration with our partners. High-quality genome sequences were then deposited on open-access platforms per the best practices. Subsequently, these efforts culminated in deploying Pakistan's first SARS-CoV-2 phyllo surveillance map as a Nextstrain build. Our experience offers lessons for the successful development of Genomic Surveillance Infrastructure in resource-limited settings struck by a pandemic.

Post-COVID-19 Cardiopulmonary Symptoms: Predictors and Imaging Features in Patients after Hospital Discharge. / Sintomas Cardiopulmonares Pós-COVID-19: Preditores e Características de Imagem de Pacientes após a Alta Hospitalar.

BACKGROUND: Most of the evidence about the impact of the post-acute COVID-19 Syndrome (PACS) reports individual symptoms without correlations with related imaging. OBJECTIVES: To evaluate cardiopulmonary symptoms, their predictors and related images in COVID-19 patients discharged from hospital. METHODS: Consecutive patients who survived COVID-19 were contacted 90 days after discharge. The Clinic Outcome Team structured a questionnaire evaluating symptoms and clinical status (blinded for hospitalization data). A multivariate analysis was performed to address the course of COVID-19, comorbidities, anxiety, depression, and post-traumatic stress during hospitalization, and cardiac rehabilitation after discharge. The significance level was set at 5%. RESULTS: A total of 480 discharged patients with COVID-19 (age: 59±14 years, 67.5% males) were included; 22.3% required mechanical ventilation. The prevalence of patients with PACS-related cardiopulmonary symptoms (dyspnea, tiredness/fatigue, cough, and chest discomfort) was 16.3%. Several parameters of chest computed tomography and echocardiogram were similar in patients with and without cardiopulmonary symptoms. The multivariate analysis showed that PACS-related cardiopulmonary-symptoms were independently related to female sex (OR 3.023; 95% CI 1.319-6.929), in-hospital deep venous thrombosis (OR 13.689; 95% CI 1.069-175.304), elevated troponin I (OR 1.355; 95% CI 1.048-1.751) and C-reactive protein during hospitalization (OR 1.060; 95% CI 1.023-1.097) and depression (OR 6.110; 95% CI 2.254-16.558). CONCLUSION: PACS-related cardiopulmonary symptoms 90 days post-discharge are common and multifactorial. Beyond thrombotic and markers of inflammation/myocardial injury during hospitalization, female sex and depression were independently associated with cardiopulmonary-related PACS. These results highlighted the need for a multifaceted approach targeting susceptible patients.

FUNDAMENTO: A maioria da evidência sobre o impacto da síndrome COVID pós-aguda (PACS, do inglês, post-acute COVID-19 syndrome) descreve sintomas individuais sem correlacioná-los com exames de imagens. OBJETIVOS: Avaliar sintomas cardiopulmonares, seus preditores e imagens relacionadas em pacientes com COVID-19 após alta hospitalar. MÉTODOS: Pacientes consecutivos, que sobreviveram à COVID-19, foram contatados 90 dias após a alta hospitalar. A equipe de desfechos clínicos (cega quanto aos dados durante a internação) elaborou um questionário estruturado avaliando sintomas e estado clínico. Uma análise multivariada foi realizada abordando a evolução da COVID-19, comorbidades, ansiedade, depressão, e estresse pós-traumático durante a internação, e reabilitação cardíaca após a alta. O nível de significância usado nas análises foi de 5%. RESULTADOS: Foram incluídos 480 pacientes (idade 59±14 anos, 67,5% do sexo masculino) que receberam alta hospitalar por COVID-19; 22,3% necessitaram de ventilação mecânica. A prevalência de pacientes com sintomas cardiopulmonares relacionados à PACS (dispneia, cansaço/fadiga, tosse e desconforto no peito) foi de 16,3%. Vários parâmetros de tomografia computadorizada do tórax e de ecocardiograma foram similares entre os pacientes com e sem sintomas cardiopulmonares. A análise multivariada mostrou que sintomas cardiopulmonares foram relacionados de maneira independente com sexo feminino (OR 3,023; IC95% 1,319-6,929), trombose venosa profunda durante a internação (OR 13,689; IC95% 1,069-175,304), nível elevado de troponina (OR 1,355; IC95% 1,048-1,751) e de proteína C reativa durante a internação (OR 1,060; IC95% 1,023-1,097) e depressão (OR 6,110; IC95% 2,254-16,558). CONCLUSÃO: Os sintomas cardiopulmonares relacionados à PACS 90 dias após a alta hospitalar são comuns e multifatoriais. Além dos marcadores trombóticos, inflamatórios e de lesão miocárdica durante a internação, sexo feminino e depressão foram associados independentemente com sintomas cardiopulmonares relacionados à PACS. Esses resultados destacaram a necessidade de uma abordagem multifacetada direcionada a pacientes susceptíveis.

Sintomas Cardiopulmonares Pós-COVID-19: Preditores e Características de Imagem de Pacientes após a Alta Hospitalar / Post-COVID-19 Cardiopulmonary Symptoms: Predictors and Imaging Features in Patients after Hospital Discharge

Resumo Fundamento A maioria da evidência sobre o impacto da síndrome COVID pós-aguda (PACS, do inglês, post-acute COVID-19 syndrome) descreve sintomas individuais sem correlacioná-los com exames de imagens. Objetivos Avaliar sintomas cardiopulmonares, seus preditores e imagens relacionadas em pacientes com COVID-19 após alta hospitalar. Métodos Pacientes consecutivos, que sobreviveram à COVID-19, foram contatados 90 dias após a alta hospitalar. A equipe de desfechos clínicos (cega quanto aos dados durante a internação) elaborou um questionário estruturado avaliando sintomas e estado clínico. Uma análise multivariada foi realizada abordando a evolução da COVID-19, comorbidades, ansiedade, depressão, e estresse pós-traumático durante a internação, e reabilitação cardíaca após a alta. O nível de significância usado nas análises foi de 5%. Resultados Foram incluídos 480 pacientes (idade 59±14 anos, 67,5% do sexo masculino) que receberam alta hospitalar por COVID-19; 22,3% necessitaram de ventilação mecânica. A prevalência de pacientes com sintomas cardiopulmonares relacionados à PACS (dispneia, cansaço/fadiga, tosse e desconforto no peito) foi de 16,3%. Vários parâmetros de tomografia computadorizada do tórax e de ecocardiograma foram similares entre os pacientes com e sem sintomas cardiopulmonares. A análise multivariada mostrou que sintomas cardiopulmonares foram relacionados de maneira independente com sexo feminino (OR 3,023; IC95% 1,319-6,929), trombose venosa profunda durante a internação (OR 13,689; IC95% 1,069-175,304), nível elevado de troponina (OR 1,355; IC95% 1,048-1,751) e de proteína C reativa durante a internação (OR 1,060; IC95% 1,023-1,097) e depressão (OR 6,110; IC95% 2,254-16,558). Conclusão Os sintomas cardiopulmonares relacionados à PACS 90 dias após a alta hospitalar são comuns e multifatoriais. Além dos marcadores trombóticos, inflamatórios e de lesão miocárdica durante a internação, sexo feminino e depressão foram associados independentemente com sintomas cardiopulmonares relacionados à PACS. Esses resultados destacaram a necessidade de uma abordagem multifacetada direcionada a pacientes susceptíveis.

Abstract Background Most of the evidence about the impact of the post-acute COVID-19 Syndrome (PACS) reports individual symptoms without correlations with related imaging. Objectives To evaluate cardiopulmonary symptoms, their predictors and related images in COVID-19 patients discharged from hospital. Methods Consecutive patients who survived COVID-19 were contacted 90 days after discharge. The Clinic Outcome Team structured a questionnaire evaluating symptoms and clinical status (blinded for hospitalization data). A multivariate analysis was performed to address the course of COVID-19, comorbidities, anxiety, depression, and post-traumatic stress during hospitalization, and cardiac rehabilitation after discharge. The significance level was set at 5%. Results A total of 480 discharged patients with COVID-19 (age: 59±14 years, 67.5% males) were included; 22.3% required mechanical ventilation. The prevalence of patients with PACS-related cardiopulmonary symptoms (dyspnea, tiredness/fatigue, cough, and chest discomfort) was 16.3%. Several parameters of chest computed tomography and echocardiogram were similar in patients with and without cardiopulmonary symptoms. The multivariate analysis showed that PACS-related cardiopulmonary-symptoms were independently related to female sex (OR 3.023; 95% CI 1.319-6.929), in-hospital deep venous thrombosis (OR 13.689; 95% CI 1.069-175.304), elevated troponin I (OR 1.355; 95% CI 1.048-1.751) and C-reactive protein during hospitalization (OR 1.060; 95% CI 1.023-1.097) and depression (OR 6.110; 95% CI 2.254-16.558). Conclusion PACS-related cardiopulmonary symptoms 90 days post-discharge are common and multifactorial. Beyond thrombotic and markers of inflammation/myocardial injury during hospitalization, female sex and depression were independently associated with cardiopulmonary-related PACS. These results highlighted the need for a multifaceted approach targeting susceptible patients.

AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data.

Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.

Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif.

Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors that has been implicated in immune suppression as well as effector recognition by host resistance proteins. We predicted 55 WY domain containing proteins in the genome of B. lactucae and found substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis of 21 effectors containing WY domains revealed 11 that elicited cell death on wild accessions and domesticated lettuce lines containing resistance genes, indicative of recognition of these effectors by the host immune system. Only two of the 11 recognized effectors contained the canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.