Efficient crack length measurement using A* shortest path methodology for a phase-field fracture framework

Accurately measuring a crack length is a crucial aspect of experimental fracture tests. In this work, we present an innovative application of the A* (A-star) shortest path methodology to track different shapes of cracks from numerical simulations. This approach is highly efficient, significantly improving the speed and accuracy of crack length measurements. Furthermore, we introduce a modified weight cost function that follows the crack path in the damage field, enhancing the accuracy of our method. The effectiveness of the proposed procedure is shown by fabricating damage fields with different geometry and good agreement when compared to the exact values. In addition, we evaluate a time-dependent crack propagation case, achieving high accuracy. We present all features and steps of the procedure to showcase its efficacy in accurately measuring the length of a crack path. Finally, we validate our method using a phase-field fracture framework and compare it with the compliance technique. The results show that the proposed method is applicable in finite element analyses with recovering accurate resultsThe authors would like to acknowledge CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) for the scholarship under grant 88882.435204/2019-01. J.A. Avila is a Serra Hunter Fellow and a CNPq fellow.Postprint (published version

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Bioinformatics and molecular biology tools for diagnosis, prevention, treatment and prognosis of COVID-19

Since December 2019, a new form of Severe Acute Respiratory Syndrome (SARS) has emerged worldwide, caused by SARS coronavirus 2 (SARS-CoV-2). This disease was called COVID-19 and was declared a pandemic by the World Health Organization in March 2020. Symptoms can vary from a common cold to severe pneumonia, hypoxemia, respiratory distress, and death. During this period of world stress, the medical and scientific community were able to acquire information and generate scientific data at unprecedented speed, to better understand the disease and facilitate vaccines and therapeutics development. Notably, bioinformatics tools were instrumental in decoding the viral genome and identifying critical targets for COVID-19 diagnosis and therapeutics. Through the integration of omics data, bioinformatics has also improved our understanding of disease pathogenesis and virus-host interactions, facilitating the development of targeted treatments and vaccines. Furthermore, molecular biology techniques have accelerated the design of sensitive diagnostic tests and the characterization of immune responses, paving the way for precision medicine approaches in treating COVID-19. Our analysis highlights the indispensable contributions of bioinformatics and molecular biology to the global effort against COVID-19. In this review, we aim to revise the COVID-19 features, diagnostic, prevention, treatment options, and how molecular biology, modern bioinformatic tools, and collaborations have helped combat this pandemic. An integrative literature review was performed, searching articles on several sites, including PUBMED and Google Scholar indexed in referenced databases, prioritizing articles from the last 3 years. The lessons learned from this COVID-19 pandemic will place the world in a much better position to respond to future pandemics

Serum soluble mediator profiles and networks during acute infection with distinct DENV serotypes

Conselho Nacional de Desenvolvimento Cientifico e Tecnologico - CNPq. Funding was also obtained from Fundacao de Amparo a Pesquisa do Estado do Amazonas (FAPEAM/PPP-CNPq, EDITAL N. 016/2014), Ministerio da Saude do Brasil (Chamada Publica no 01/2012, Convenio # 776823/2012) and INCT para Febres Hemorragicas Virais (INCT-FHV - 573739/2008-0).Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilU.S. Food and Drug Administration. Center for Biologics Evaluation and Research. Office of Blood Research and Review. Silver Spring, MD, United States.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Microbiologia. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil / Universidade Federal de Minas Gerais. Faculdade de Medicina. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios e Sarampo. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação de Medicina Tropical Dr. Heitor Vieira Dourado. Instituto de Pesquisa Clínica Carlos Borborema. Manaus, AM, Brazil / Universidade Federal do Amazonas. Escola de Enfermagem de Manaus. Manaus, AM, BrazilFundação de Medicina Tropical Dr. Heitor Vieira Dourado. Instituto de Pesquisa Clínica Carlos Borborema. Manaus, AM, Brazil / Universidade Federal do Amazonas. Escola de Enfermagem de Manaus. Manaus, AM, BrazilFundação de Medicina Tropical Dr. Heitor Vieira Dourado. Instituto de Pesquisa Clínica Carlos Borborema. Manaus, AM, BrazilFundação de Medicina Tropical Dr. Heitor Vieira Dourado. Instituto de Pesquisa Clínica Carlos Borborema. Manaus, AM, BrazilUniversidade Federal do Amazonas. Escola de Enfermagem de Manaus. Manaus, AM, BrazilFundação de Medicina Tropical Dr. Heitor Vieira Dourado. Instituto de Pesquisa Clínica Carlos Borborema. Manaus, AM, Brazil / Universidade Federal do Amazonas. Escola de Enfermagem de Manaus. Manaus, AM, Brazil / Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas. Diretoria de Ensino e Pesquisa. Manaus, AM, BrazilUniversidade Federal de Uberlândia. Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia. Laboratório de Bioinformática e Análises Moleculares. Patos de Minas, MG, BrazilUniversidade Federal de Uberlândia. Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia. Laboratório de Bioinformática e Análises Moleculares. Patos de Minas, MG, BrazilMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.A panoramic analysis of chemokines, pro-inflammatory/regulatory cytokines, and growth factors was performed in serum samples from patients with acute DENV infection (n=317) by a high-throughput microbeads array. Most soluble mediators analyzed were increased in DENV patients regardless of the DENV serotype. The substantial increase (>= 10-fold) of CXCL10, IL-6, and IFN-gamma, and decreased levels of PDGF (= 3-9-fold) were selectively observed in DENV2 as compared to DENV1 and DENV4. Heatmap and biomarker signatures further illustrated the massive release of soluble mediators observed in DENV patients, confirming the marked increase of several soluble mediators in DENV2. Integrative correlation matrices and networks showed that DENV infection exhibited higher connectivity among soluble mediators. Of note, DENV2 displayed a more complex network, with higher connectivity involving a higher number of soluble mediators. The timeline kinetics (Day 0-1, D2, D3, D4-6) analysis additionally demonstrated differences among DENV serotypes. While DENV1 triggers a progressive increase of soluble mediators towards D3 and with a decline at D4-6, DENV2 and DENV4 develop with a progressive increase towards D4-6 with an early plateau observed in DENV4. Overall, our results provided a comprehensive overview of the immune response elicited by DENV infection, revealing that infection with distinct DENV serotypes causes distinct profiles, rhythms, and dynamic network connectivity of soluble mediators. Altogether, these findings may provide novel insights to understand the pathogenesis of acute infection with distinct DENV serotypes

Serotype-associated immune response and network immunoclusters in children and adults during acute Dengue virus infection

Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.U.S. Food and Drug Administration. Center for Biologics Evaluation and Research. Office of Blood Research and Review. Silver Spring, MD, USA.U.S. Food and Drug Administration. Center for Biologics Evaluation and Research. Office of Blood Research and Review. Silver Spring, MD, USA.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Microbiologia. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil / Universidade Federal de Minas Gerais. Faculdade de Medicina. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios e Sarampo. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação de Medicina Tropical Dr. Heitor Vieira Dourado. Manaus, AM, Brazil / Universidade Federal do Amazonas. Manaus, AM, Brazil.Fundação de Medicina Tropical Dr. Heitor Vieira Dourado. Manaus, AM, Brazil.Fundação de Medicina Tropical Dr. Heitor Vieira Dourado. Manaus, AM, Brazil.Universidade Federal do Amazonas. Manaus, AM, Brazil.Fundação de Medicina Tropical Dr. Heitor Vieira Dourado. Manaus, AM, Brazil / Universidade Federal do Amazonas. Manaus, AM, Brazil / Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas. Manaus, AM, Brazil.Universidade Federal de Uberlândia. Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia. Laboratório de Bioinformática e Análises Moleculares. Campus Patos de Minas, MG, Brazil / Universidade Federal de Uberlândia. Faculdade de Engenharia Elétrica. Laboratório de Tecnologias Urbanas e Rurais. Campus Patos de Minas, MG, Brazil.Universidade Federal de Uberlândia. Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia. Laboratório de Bioinformática e Análises Moleculares. Campus Patos de Minas, MG, Brazil / Universidade Federal de Uberlândia. Faculdade de Engenharia Elétrica. Laboratório de Tecnologias Urbanas e Rurais. Campus Patos de Minas, MG, Brazil.Universidade Federal de Uberlândia. Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia. Laboratório de Bioinformática e Análises Moleculares. Campus Patos de Minas, MG, Brazil / Universidade Federal de Uberlândia. Faculdade de Engenharia Elétrica. Laboratório de Tecnologias Urbanas e Rurais. Campus Patos de Minas, MG, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Bioquímica e Imunologia. Belo Horizonte, MG, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade do Estado do Pará. Centro de Ciências Biológicas e da Saúde. Departamento de Patologia. Belém, PA, Brazil.Fundação de Medicina Tropical Dr. Heitor Vieira Dourado. Manaus, AM, Brazil / Universidade Federal do Amazonas. Manaus, AM, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil.The present study was designed as an exploratory investigation to characterize the overall profile of chemokines, growth factors, and pro-inflammatory/regulatory cytokines during acute DENV infection according to DENV-1, DENV-2, DENV-4 serotypes and age: children: 3x), except PDGF in which no fold change was observed. Moreover, despite the age ranges, DENV-1 and DENV-4 presented increased levels of VEGF, IL-6, and TNF-α in serum but decreased levels of PDGF, while DENV-2 exhibited increased levels of CXCL8, CCL4, and IL-12. Noteworthy was that DENV-2 showed increased levels of IL-12, IL-15, IL-17, IL-4, IL-9, and IL-13, and maintained an unaltered levels of PDGF at younger ages (<1–10 yo and 11–20 yo), whereas in older ages (21–40 yo and 41–75 yo), the results showed increased levels of CCL2, IL-6, and TNF-α, but lower levels of PDGF. In general, DENV infection at younger age groups exhibited more complex network immunoclusters as compared to older age groups. Multivariate analysis revealed a clustering of DENV cases according to age for a set of soluble mediators especially in subjects infected with DENV-2 serotype. Altogether, our findings demonstrate that the profile of circulating soluble mediators differs substantially in acute DENV according to age and DENV serotypes suggesting the participation of serotype-associated immune response, which may represent a potential target for development of therapeutics and could be used to assist medical directive for precise clinical management of severe cases

Gas6 drives Zika virus-induced neurological complications in humans and congenital syndrome in immunocompetent mice

Zika virus (ZIKV) has the ability to cross placental and brain barriers, causing congenital malformations in neonates and neurological disorders in adults. However, the pathogenic mechanisms of ZIKV-induced neurological complications in adults and congenital malformations are still not fully understood. Gas6 is a soluble TAM receptor ligand able to promote flavivirus internalization and downregulation of immune responses. Here we demonstrate that there is a correlation between ZIKV neurological complications with higher Gas6 levels and the downregulation of genes associated with anti-viral response, as type I IFN due to Socs1 upregulation. Also, Gas6 gamma-carboxylation is essential for ZIKV invasion and replication in monocytes, the main source of this protein, which was inhibited by warfarin. Conversely, Gas6 facilitates ZIKV replication in adult immunocompetent mice and enabled susceptibility to transplacental infection. Our data indicate that ZIKV promotes the upregulation of its ligand Gas6, which contributes to viral infectivity and drives the development of severe adverse outcomes during ZIKV infection

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data