Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data

Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group

Survey of Intestinal Parasites Including Associated Risk Factors Among Food Vendors and Slaughterhouse Workers in Metro Manila, Philippines

Infections by intestinal parasites are considered as one of the major health concerns in developing countries afflicting different groups of people including food handlers and food vendors and are linked to poor personal hygiene and sanitation. This raises public health issues as food vendors and handlers may potentially become agents for the fecal-oral transmission of intestinal parasitic infections to consumers. This study focused on determining the prevalence of intestinal parasites among slaughter house workers and food vendors and examined their personal and food hygiene practices. A small-scale survey was conducted and selected a total of 91 slaughter house workers and food vendors from different areas in Metro Manila. Microscopic examination ofthe fecal samples collected was done following standard procedures by the World Health Organization (WHO) thru direct smear, formalin-ethyl acetate sedimentation and staining methods. Participants were also interviewed on their food and personal hygiene practices using a questionnaire. The overall prevalence of parasitic infection was 90% with helminthic predominating protozoan infections. Eight (8) different intestinal parasites were identified: Entamoeba histolytica/Entamoeba dispar (15.6%), Balantidium coli (8.4%), Giardia lamblia (4.2%), Ascaris lumbricoides (30%), Trichuris trichiura (14.9%), Ancyclostoma duodenale/ Necator americanus (2.3%). Taenia spp. (2.4%), and Enterobius vermicularis (2.9%). Other amoeba-like protozoans (19.2%) were also observed suggestive of exposure to fecal materials. Based on the results obtained, there is high levels of parasitic infections among slaughter house workers and food vendors. Raising awareness on proper food handling, improved personal hygiene and sanitation is needed to prevent further transmission of parasites to the public. Keywords: Food handlers, Food safety, Intestinal parasites, Neglected Tropical Diseases, Public Health

Levantamiento y cruzamiento de las informaciones sobre evaluación clínica, diagnóstico e intervenciones de fisioterapia

Objetivo: descrever a experiência para desenvolver um registro eletrônico em fisioterapia baseado na Classificação Internacional de Funcionalidade, Incapacidade e Saúde através do mapeamento e cruzamento de informações da avaliação clínica, diagnóstico e intervenções fisioterapêuticas. Método: relato de experiência, organizado em quatro etapas: Aprofundamento teórico da Classificação Internacional de Funcionalidade; Aprofundamento teórico da avaliação em fisioterapia; Estruturação dos dados de avaliação, dos diagnósticos e intervenção fisioterapêutica; Informatização e integração de forma sistematizada dos dados da avaliação clínica, dos diagnósticos e intervenções. Resultados: a estruturação dos dados foi dividida por sistemas do corpo humano. Sendo assim, para o sistema respiratório construiu-se 15 tópicos de avaliação, 145 diagnósticos e 74 intervenções; para o sistema neuromusculoesquelético construiu-se 37 tópicos de avaliação, 132 diagnósticos e 65 intervenções; para o sistema cardiovascular construiu-se cinco tópicos de avaliação, 23 diagnósticos e cinco intervenções e para o sistema gastrointestinal e renal construiu-se sete tópicos de avaliação, 21 diagnósticos e uma intervenção. Desta forma, foram construídos 64 itens de avaliação, 318 diagnósticos baseados na Classificação de Funcionalidade e 145 intervenções fisioterapêuticas. Conclusão: o mapeamento das informações sobre avaliação fisioterapêutica, diagnósticos e intervenções para integrar um registro eletrônico em fisioterapia tornará o uso da Classificação Internacional de Funcionalidade, Incapacidade e Saúde mais segura e rápida possibilitando sua aplicabilidade diária na clínica hospitalar.Objective: to describe the experience of developing an electronic health record in physiotherapy based on the International Classification of Functioning Disability and Health through the mapping and cross-referencing of clinical evaluation information, diagnosis and physiotherapeutic interventions. Method: an experience report, organized in four stages: Theoretical development of the International Classification of Functionality; Theoretical development of evaluation in physiotherapy; Structuring of evaluation data, diagnoses and physiotherapeutic intervention; Computerization and systematized integration of data from clinical evaluation, diagnoses and interventions. Results: the structure of the data was divided by systems of the human body. Thus, for the respiratory system, 15 evaluation topics, 145 diagnoses and 74 interventions were constructed; for the neuromusculoskeletal system, 37 evaluation topics, 132 diagnoses and 65 interventions were constructed; for the cardiovascular system, five evaluation topics, 23 diagnoses and five interventions were constructed; and seven assessment topics, 21 diagnoses and one intervention were constructed for the gastrointestinal and renal systems. Thus, 64 evaluation items were constructed, 318 diagnoses based on the Functionality Classification and 145 physiotherapeutic interventions. Conclusion: the mapping of information regarding physiotherapeutic evaluation, diagnoses and interventions to integrate an electronic physiotherapy records will make use of the International Classification of Functioning, Disability and Health safer and faster, allowing it to be applied in the hospital setting.Objetivo: describir la experiencia para desarrollar un registro electrónico en fisioterapia basado en la Clasificación Internacional de Funcionalidad, Incapacidad y Salud a través del levantamiento y cruzamiento de informaciones de la evaluación clínica, diagnóstico e intervenciones fisioterapéuticas. Método: relato de experiencia realizado en cuatro etapas: Profundización teórica de la Clasificación Internacional de Funcionalidad; Profundización teórica de la evaluación en fisioterapia; Estructuración de los datos de evaluación, diagnósticos e intervención fisioterapéutica; Informatización e integración de forma sistematizada de los datos de la evaluación clínica, diagnósticos e intervenciones. Resultados: la estructuración de los datos fue dividida por sistemas del cuerpo humano. Así, para el sistema respiratorio se construyeron 15 tópicos de evaluación, 145 diagnósticos y 74 intervenciones. Para el sistema neuromusculoesquelético se construyeron 37 tópicos de evaluación, 132 diagnósticos y 65 intervenciones. Para el sistema cardiovascular se construyeron cinco tópicos de evaluación, 23 diagnósticos y cinco intervenciones y para el sistema gastrointestinal y renal se construyeron siete tópicos de evaluación, 21 diagnósticos y una intervención. De esta forma, se construyeron 64 ítems de evaluación, 318 diagnósticos basados en la Clasificación de Funcionalidad y 145 intervenciones fisioterapéuticas. Conclusión: el levantamiento de las informaciones sobre la evaluación fisioterapéutica, diagnósticos e intervenciones para integrar un registro electrónico en fisioterapia hará que el uso de la Clasificación Internacional de Funcionalidad, Incapacidad y Salud sea más seguro y rápido, posibilitando su aplicabilidad diaria en la clínica hospitalaria.info:eu-repo/semantics/publishedVersio

Physiological lentiviral vectors for the generation of improved CAR-T cells

Anti-CD19 chimeric antigen receptor (CAR)-T cells have achieved impressive outcomes for the treatment of relapsed and refractory B-lineage neoplasms. However, important limitations still remain due to severe adverse events (i.e., cytokine release syndrome and neuroinflammation) and relapse of 40%-50% of the treated patients. Most CAR-T cells are generated using retroviral vectors with strong promoters that lead to high CAR expression levels, tonic signaling, premature exhaustion, and overstimulation, reducing efficacy and increasing side effects. Here, we show that lentiviral vectors (LVs) expressing the transgene through a WAS gene promoter (AW-LVs) closely mimic the T cell receptor (TCR)/CD3 expression kinetic upon stimulation. These AW-LVs can generate improved CAR-T cells as a consequence of their moderate and TCR-like expression profile. Compared with CAR-T cells generated with human elongation factor alpha (EF1 alpha)-driven-LVs, AW-CAR-T cells exhibited lower tonic signaling, higher proportion of naive and stem cell memory T cells, less exhausted phenotype, and milder secretion of tumor necrosis factor alpha (TNF-alpha) and interferon (IFN)-gamma after efficient destruction of CD19(+) lymphoma cells, both in vitro and in vivo. Moreover, we also showed their improved efficiency using an in vitro CD19(+) pancreatic tumor model. We finally demonstrated the feasibility of large-scale manufacturing of AW-CAR-T cells in guanosine monophosphate (GMP)-like conditions. Based on these data, we propose the use of AWLVs for the generation of improved CAR-T products

Genome wide association study of Preserved Ratio Impaired Spirometry (PRISm)

Background: Preserved Ratio Impaired Spirometry (PRISm) is defined as FEV1 &lt;80% predicted, FEV1/FVC ≥0.70. PRISm is associated with respiratory symptoms and co-morbidities. Our objective was to discover novel genetic signals for PRISm and see if they provide insight into the pathogenesis of PRISm and associated co-morbidities.Methods: We undertook a genome-wide association study (GWAS) of PRISm in UK Biobank participants (Stage 1), and selected SNPs reaching genome-wide significance for replication in 13 cohorts (Stage 2). A combined meta-analysis of Stage 1 and Stage 2 was done to determine top SNPs. We used cross-trait Linkage Disequilibrium score regression to estimate genome-wide genetic correlation between PRISM and pulmonary and extra-pulmonary traits. Phenome-wide association studies of top SNPs was performed. Results: 22 signals reached significance in the joint meta-analysis, including four signals novel for lung function. A strong genome-wide genetic correlation (rg) between PRISm and spirometric COPD (rg = 0.62, p-value &lt;0.001) was observed, and genetic correlation with type II diabetes (rg = 0.12, p-value 0.007). PheWAS showed that 18 of 22 signals were associated with diabetic traits and 7 with blood pressure traits.Discussion: This is the first GWAS to successfully identify SNPs associated with PRISm. Four of the signals; rs7652391 (nearest gene MECOM), rs9431040 (HLX), rs62018863 (TMEM114) and rs185937162 (HLA-B) have not been described in association with lung function before, demonstrating the utility of using different lung function phenotypes in GWAS. Genetic factors associated with PRISm are strongly correlated with risk of both other lung diseases and extra-pulmonary co-morbidity.<br/

A list of land plants of Parque Nacional do Caparaó, Brazil, highlights the presence of sampling gaps within this protected area

Brazilian protected areas are essential for plant conservation in the Atlantic Forest domain, one of the 36 global biodiversity hotspots. A major challenge for improving conservation actions is to know the plant richness, protected by these areas. Online databases offer an accessible way to build plant species lists and to provide relevant information about biodiversity. A list of land plants of “Parque Nacional do Caparaó” (PNC) was previously built using online databases and published on the website "Catálogo de Plantas das Unidades de Conservação do Brasil." Here, we provide and discuss additional information about plant species richness, endemism and conservation in the PNC that could not be included in the List. We documented 1,791 species of land plants as occurring in PNC, of which 63 are cited as threatened (CR, EN or VU) by the Brazilian National Red List, seven as data deficient (DD) and five as priorities for conservation. Fifity-one species were possible new ocurrences for ES and MG states

Impactos dos subsídios agrícolas dos Estados Unidos na expansão do agronegócio brasileiro

Nos fóruns de negociações multilaterais da Organização Mundial de Comércio subsiste veemente debate com intuito de eliminar as subvenções agrícolas nos países desenvolvidos. Contudo, os Estados Unidos têm aumentado o volume desses subsídios, causando distorções no comércio agrícola mundial. Assim, o objetivo desta pesquisa foi avaliar os impactos desses subsídios norte-americanos (Loan Deficiency Payments), concedidos no período de 2002 a 2007, sobre o crescimento do agronegócio brasileiro. Os resultados permitem inferir que a redução dos subsídios nos EUA propiciaria o crescimento da produção agroindustrial brasileira e ampliaria o superávit na balança comercial desse setor, com crescimento conjunto das exportações e importações. Portanto, cortes nesses subsídios contribuiriam para maior competitividade das exportações brasileiras e gerariam oportunidades para o crescimento do agronegócio.In the forums of multilateral negotiations of the World Trade Organization (WTO) there has been a strong debate which tries to eliminate the agricultural subventions in the developed countries. However, the United States has increased the amount of these subsidies causing distortions in the world agricultural trade. Therefore, the purpose of this research has been to evaluate these American subsidies impacts (Loan Deficiency Payments) given between 2002 and 2007 upon the Brazilian agribusiness growth. The findings allow to deduce that the reduction of the subsidies in the United States might promote the growth of the Brazilian agribusiness production and might produce trade surplus in the trade balance in this sector as well as the growth of both exports and imports. Hence the cuts in these subsidies would contribute to a bigger competitiveness of the Brazilian exports and would generate opportunities to the agribusiness growth

State of the world’s plants and fungi 2020

Kew’s State of the World’s Plants and Fungi project provides assessments of our current knowledge of the diversity of plants and fungi on Earth, the global threats that they face, and the policies to safeguard them. Produced in conjunction with an international scientific symposium, Kew’s State of the World’s Plants and Fungi sets an important international standard from which we can annually track trends in the global status of plant and fungal diversity