Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.

BACKGROUND: Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. RESULTS: We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent). CONCLUSIONS: We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.

Global short-term forecasting of COVID-19 cases.

The continuously growing number of COVID-19 cases pressures healthcare services worldwide. Accurate short-term forecasting is thus vital to support country-level policy making. The strategies adopted by countries to combat the pandemic vary, generating different uncertainty levels about the actual number of cases. Accounting for the hierarchical structure of the data and accommodating extra-variability is therefore fundamental. We introduce a new modelling framework to describe the pandemic's course with great accuracy and provide short-term daily forecasts for every country in the world. We show that our model generates highly accurate forecasts up to seven days ahead and use estimated model components to cluster countries based on recent events. We introduce statistical novelty in terms of modelling the autoregressive parameter as a function of time, increasing predictive power and flexibility to adapt to each country. Our model can also be used to forecast the number of deaths, study the effects of covariates (such as lockdown policies), and generate forecasts for smaller regions within countries. Consequently, it has substantial implications for global planning and decision making. We present forecasts and make all results freely available to any country in the world through an online Shiny dashboard.

Saturnismo após acidente por arma de fogo de grande calibre: relato de caso / Saturnism after accident by large caliber firearm: case report

Saturnismo é a intoxicação que ocorre em atividades ocupacionais com elevada exposição ao chumbo (Pb). Embora seja menos comum, a intoxicação pode ocorrer após incidentes com projétil de arma de fogo (PAF). O presente trabalho descreve um caso clínico-cirúrgico de saturnismo por acidente por PAF em paciente do sexo masculino com exposição a múltiplos fragmentos e níveis limites de chumbo sanguíneo. Sua queixa principal, em consulta bucomaxilofacial, foi ?chumbo pelo corpo?. Após várias cirurgias e controles entre 2007 e 2011 o paciente teve diminuição do chumbo sanguíneo de 44 mcg/dL para 15,6 mcg/dL e melhora de quadros de infecção urinária, depressão e variação de humor. O saturnismo deve ser incluído na investigação diagnóstica de pacientes alvejados por arma de fogo. O adequado diagnóstico de intoxicação certamente auxiliará na apropriada intervenção dos casos.

Saturnism is the poisoning that occurs in activities with high occupational exposure to lead (Pb). Although less common, poisoning can occur after incidents with firearm projectiles (FAP). The present study describes a clinical-surgical case of saturnism by FAP accident in a male patient exposed to multiple fragments and blood lead limiting levels. His main complaint in a maxillofacial consultation was ?lead in the body?. After several surgeries and controls between 2007 and 2011, the patient had decreased blood lead levels from 44 mcg/dL to 15.6 mcg/dL and improvement in urinary tract infections, depressions, and mood changes. Saturnism should be included in the diagnostic investigation of patients wounded by gunshots. The proper poisoning diagnosis certainly will assist in the appropriate intervention

Gout of the Temporomandibular Joint: Report of a Case

Introduction: Gout is an illness characterized by the deposition of monosodium urate crystals in the joints or in soft tissues. The clinical manifestation results from inflammation of limb joints and pain with a rare presentation in the temporomandibular joint (TMJ). Case Report: This study describes a 66-year-old white man with a chief complaint of "occasional pain in the left temporal muscle region." The case disclosed a gout manifestation in the TMJ after physical, radiographic, and ultrasonographic exams, and the patient was referred to proper treatment. Conclusion: Gout manifestation in the TMJ is an unusual presentation, and few reports in the English literature address to the subject. Gout in the TMJ should be included as a differential diagnosis for joint disorders...

Gout of the temporomandibular joint: report of a case.

Introduction Gout is an illness characterized by the deposition of monosodium urate crystals in the joints or in soft tissues. The clinical manifestation results from inflammation of limb joints and pain with a rare presentation in the temporomandibular joint (TMJ). Case Report This study describes a 66-year-old white man with a chief complaint of "occasional pain in the left temporal muscle region." The case disclosed a gout manifestation in the TMJ after physical, radiographic, and ultrasonographic exams, and the patient was referred to proper treatment. Conclusion Gout manifestation in the TMJ is an unusual presentation, and few reports in the English literature address to the subject. Gout in the TMJ should be included as a differential diagnosis for joint disorders.