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The increasing availability of short-read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr, a pipeline that processes short-read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low-coverage WGS (

A atual conjuntura global aponta para um futuro no qual Drones serão essenciais como resposta a desastres. Neste âmbito, um dos desafios tecnológicos é permitir o uso integrado de Drones com plataformas de recarga móveis, aumentando, assim, o tempo de voo em missões de busca e resgate. Trata-se de um problema de otimização de difícil solução por resolvedores convencionais. Por essa razão, desenvolvemos uma abordagem heurística para encontrar boas respostas. Simulamos a metodologia proposta na Mina Córrego do Feijão, em Brumadinho, Minas Gerais, onde houve o rompimento de uma barragem de rejeitos de minério. Os resultados obtidos apontam que a metodologia proposta pode auxiliar operações de busca e resgate, fornecendo uma resposta rápida e, portanto, aumentando as chances de encontrar vítimas.

In this study we describe a method for the detection of biomolecules (in the polypeptide m/z range) directly from the surface of plant leaves by using Mass Spectrometry Imaging. The plant-pathogen interaction between Arabidopsis thaliana and the bacterium Xanthomonas campestris pv. campestris was analyzed by comparing infected and non-infected leaf discs submitted to mass spectrometry. The total surface area of ion distribution was calculated for both samples, revealing 23 ions, out of which 3 showed statistical significance. Although these ions were not identified, the results showed that this approach can be successfully applied for the detection of potential polypeptide biomarkers directly on leaf tissue, which is a major challenge in MALDI-Imaging studies.

Mammary pathogenic

A partir da demanda por estratégias para fomentar o acesso e permanência de meninas e mulheres nas ciências, o presente artigo relata a experiência desenvolvida até o momento no projeto “Ciência em Jogo: intercâmbio de vivências na criação de jogo narrativo sobre mulheres e meninas na ciência”. A metodologia está fundamentada na concepção de educação emancipatória de Freire e se realiza na modalidade não-formal, com estudantes dos territórios em que se encontra a Fundação Oswaldo Cruz. As etapas envolveram a experimentação de RPG, a discussão sobre ciência e saúde e a criação, pelas jovens, da ambientação inicial e de personagens baseadas nas vivências de mulheres cientistas. Pretende-se aplicar o RPG em contextos educacionais e espaços museais, a fim de contribuir para a equidade de gênero na ciência.

Laboratory technicians are the backbone of academic research and teaching laboratories, undertaking many tasks such as keeping the chemical inventory up to date, which includes systematic identific...

This paper proposes a one-terminal traveling wave (TW)-based transmission line earth fault distance protection function. It only needs the detection of the first incident modal earth fault-induced TWs, so that, the challenging detection of wavefronts reflected from the fault point is not required. Both the sampling frequency effect and inaccuracies on the wave propagation velocity are considered in order to define the distance protection zone. Simulated fault records were played back in an actual relay, allowing the comparison between a commercially existing time-domain distance protection element and the proposed one. The proposed function is more accurate and significantly reduces transmission line distance protection tripping times without dependability losses.

Metagenomic approaches in conjunction with high-throughput sequencing (HTS) have been employed for the discovery of novel plant-associated viral species, including members of the Geminiviridae family. In the present work, the HTS strategy allowed for the identification of genetically divergent tomato-associated geminivirus 1 (TaGV1) isolates from tomato and table beet in Brasilia-DF, Brazil. The complete genomes of these novel isolates displayed 2573 nucleotides in length (recovered by Sanger sequencing) with 83% identity to previously reported TaGV1 isolates and ≈ 63% identity with a range of capulaviruses. Phylogenetic analyses of all the available TaGV1 isolates, using either their complete genomes or Rep gene (C1:C2) sequences, indicated the genus Capulavirus as the closest group, whereas the CP (V1) gene information indicated the closest relationship with members of the genus Topocuvirus. Southern hybridization confirmed the TaGV1 association with one out of five and two out of 15 original field-collected table beet and tomato leaf samples, respectively. Leaf curling and overall size reduction were observed in two out of seven Nicotiana benthamiana plants in biolistic inoculation assays with an infectious TaGV1 clone (obtained from one novel isolate from tomato). However, no systemic infection was detected in the inoculated tomato and table beet seedlings. Additional infectivity assays with a new set of table beet and tomato accessions as well as a large number of indicator plants are needed to establish the host range of these new TaGV1 isolates.

In this article, quantum mechanical/molecular mechanical (QM/MM) methods were used to study the full catalytic mechanism of xanthine oxidase (XO). XO catalyzes the conversion of xanthine (XAN) to uric acid (URC), in the presence of a molybdenum cofactor (Moco). The mechanism occurs through four reaction steps. Initially, the proton from the hydroxyl group of Moco passes to Glu1261 and the activated hydroxyl group makes a nucleophilic attack on XAN. Then, a hydride is transferred from the tetrahedral intermediate to the sulfur atom of the Moco, reducing Mo(VI) to Mo(IV). In the third step, one molecule of URC is formed through its protonation by Arg880. Once this reaction is complete, FAD is reduced to FADH2, oxidizing Mo(IV) to its initial oxidation state of Mo(VI). The enzymatic turnover is achieved with the reaction of one water molecule with the Moco. The rate-limiting step of the full catalytic mechanism is the hydride transfer that requires a free activation barrier of 16.9 kcal mol−1, which closely agrees with the experimental kcat value (18.3 s−1), which corresponds to approximately 15.7 kcal mol−1. This work also elucidates the key role played by Arg880 in the catalytic mechanism and the importance of Glu802 in the binding of the substrate. Both residues were previously shown to be important by mutagenesis studies, but their role was still not clearly understood. Additionally, it was observed that the presence of a tunnel of water molecules located close to Moco and Glu1261 is important for the enzymatic turnover. The determined transition state structures can now be used to help the development of transition-state analog inhibitors targeting XO.

The hot-wire gas metal arc welding (HW-GMAW) process is widely used to increase the melting rate of a secondary wire through Joule heating without significantly increasing the total heat input to the substrate. Because there is limit-ed knowledge regarding the associated arc dynamics and its influence on bead geometry, the present study considers how these are affected by the hot-wire polarity (negative or positive), hot-wire feed rate, and hot-wire orientation using a two-factor full factorial experiment with three replicates. During welding, high-speed imaging synchronized with current and voltage acquisition to study the arc dynamics. After this, each replicated weld was cut into three cross sections, which were examined by standard metallography. The preliminary results suggest that the arc was stable within the range of process parameters studied. The arc polarity played a role on arc position relative to the hot wire, with a decrease in penetration depth observed when the arc was attracted to the hot wire.

Purpose BRCA1 pathogenic variant heterozygotes are at a substantially increased risk for breast and ovarian cancer. The widespread uptake of testing has led to a significant increase in the detection of missense variants in BRCA1, the vast majority of which are variants of uncertain clinical significance (VUS), posing a challenge to genetic counseling. Here, we harness a wealth of functional data for thousands of variants to aid in variant classification. Methods We have collected, curated, and harmonized functional data for 2701 missense variants representing 24.5% of possible missense variants in BRCA1. Results were harmonized across studies by converting data into binary categorical variables (functional impact versus no functional impact). Using a panel of reference variants we identified a subset of assays with high sensitivity and specificity (≥80%) and apply the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines to assign evidence criteria for classification. Results Integration of data from validated assays provided ACMG/AMP evidence criteria in favor of pathogenicity for 297 variants or against pathogenicity for 2058 representing 96.2% of current VUS functionally assessed. We also explore discordant results and identify limitations in the approach. Conclusion High quality functional data are available for BRCA1 missense variants and provide evidence for classification of 2355 VUS according to their pathogenicity.

RESUMO Foram padronizados os graus de lesões dos sacos aéreos em perus com aerossaculite, associadas com a presença de isolados de enterobactérias nesses órgãos. Um total de 110 amostras de sacos aéreos de perus machos com aerossaculite foi coletado para o estudo. Durante o processo de abate, as amostras foram coletadas por meio de swabs e submetidas a três métodos de armazenamento (imediato, congelado ou pré-incubado após congelamento) para posterior comparação das suas eficiências de isolamento. Os gêneros da família Enterobacteriaceae foram identificados pelas séries bioquímicas EPM, MILi e citrato de Simmons. O crescimento bacteriano ocorreu em 43,64% das amostras. Neste estudo, quatro padrões de lesões de aerossaculite foram identificados de acordo com as características patológicas dos sacos aéreos. Os principais gêneros de enterobactérias identificadas foram: Escherichia coli, Citrobacter, Proteus, Edwardsiella, Morganella, Kluyvera, Salmonella e Klebsiella. Foi observado que os graus padronizados como 3 e 4 apresentaram maior variedade de gêneros bacterianos. O armazenamento imediato apresentou maior porcentagem de positividade, 41,82%, no entanto o pré-incubado após congelamento se apresentou mais eficaz em relação à quantidade de colônias. ABSTRACT The degrees of air sac lesions in turkeys with airsacculitis were standardized, associated with the presence of Enterobacteriaceae isolated from these organs. A total of 110 samples of air sacs from male turkeys with airsacculitis were collected and analyzed. During the slaughtering process, the sample collection was done using swabs and submitted to three storage methods (immediate, frozen, or pre incubated after freezing) for further comparison of their isolated efficiency. The bacterial genera of the family Enterobacteriaceae were identified biochemical series EPM, MILi and Simmons citrate. Bacterial growth occurred in 43.64% of samples. In this study, four patterns of aerossaculitis lesions were identified according to the pathological characteristics of air sacs. The frequencies of the Enterobacteriaceae isolated identified in the samples were: Escherichia coli, Citrobacter, Proteus, Edwardsiella, Morganell, Kluyvera, Salmonella and Klebsiella. Otherwise, it was observed that the levels already standardized as level three and four showed higher variety of genus. The immediate storage showed higher percentage of positivity at 41.82%, however, the pre incubated after freezing showed more efficiency in relation to the quantity of colonies.

The severe yellowing disease (amarelao) on melon plants is a serious problem in Brazil, although the causative agent remained unknown for a long time. Recently, recombinant isolates of cucurbit aphid‐borne yellows virus (CABYV) were reported as the possible causative agents of this disease on melon plants. Although aphids are known to be the vectors of the common type of CABYV isolates, almost no aphid colony was observed in the major melon fields in Brazil with high incidence of the severe yellowing disease. In contrast, whiteflies are often abundant. Based on this observation, the hypothesis of the transmission of recombinant CABYV by whiteflies was evaluated. After thorough transmission experiments, we found that this recombinant CABYV isolate was transmitted by the whitefly Bemisia tabaci MEAM1, but not by Aphis gossipii. Furthermore, the host response by whitefly‐based inoculation in cucurbits and other indicator plants showed differences in host range when compared to the common type of CABYV. Due to its transmissibility by the whitefly and the distant relationship of the P3/P5 protein to CABYV, the name “cucurbit whitefly‐borne yellows virus” is proposed for this recombinant CABYV. This is the second report of polerovirus transmission by the whitefly B. tabaci, following the report of pepper whitefly‐borne vein yellows virus.

Glass lapping residues (RLV) are fine tailings from the processing of glass for civil construction, commonly non-recyclable. The present study analyzed the use of these residues in Portland cement mortar composition, partially replacing the conventional aggregate, aiming at better compaction. Percentages of residues were adopted at 0% (reference), 5%, 10% and 20% by mass, replacing the fine conventional aggregate (sand). The binder used was Portland cement CP IV-32. The RLV and fine aggregate were submitted to physical tests, through grain size analysis, grain shape and specific mass; RLV and cement, in turn, submitted to chemical analysis by X-ray spectrometry, to identify the compounds. To evaluate the compressive strength and compaction analysis of the composite in the hardened state, cylindrical specimens 50x100 mm were produced. ANOVA (Analisys of Variance) and Coefficient of Variation showed that the RLV added in 5% resulted in lower voids indexes and moisture absorption than the conventional one. The tests also showed best mechanical performance on compression analisys (30,2 MPa) for 5% of residues in the composite, surpassing the conventional one.

Bothrops jararaca venom (BjV) can induce mast cell degranulation. In order to investigate the role of mast cells and the interference of the host genetic background in the inflammation induced by BjV, we have used mouse strains selected for maximal (AIRmax) or minimal (AIRmin) acute inflammatory response (AIR). Mice were pretreated with an inhibitor of mast cell degranulation, cromolyn (CROM), and injected in footpads or intraperitoneally (i.p.) with BjV. Pain was measured with von Frey hairs, cell migration in the peritoneum by flow cytometry, and reactive oxygen species (ROS) production by chemiluminescence assays. The nociceptive response to BjV was higher in AIRmax than AIRmin mice; however, this difference was abolished by pretreatment with CROM. BjV induced peritoneal neutrophil (CD11b+ GR-1+) infiltration and ROS secretion in AIRmax mice only, which were partially inhibited by CROM. Our findings evidence a role for mast cells in pain, neutrophil migration, and ROS production triggered by BjV in AIRmax mice that are more susceptible to the action of BjV.

Papaya sticky disease is caused by the association of a fusagra-like and an umbra-like virus, named papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), respectively. Both viral genomes are encapsidated in particles formed by the PMeV ORF1 product, which has the potential to encode a protein with 1563 amino acids (aa). However, the structural components of the viral capsid are unknown. To characterize the structural proteins of PMeV and PMeV2, virions were purified from Carica papaya latex. SDS-PAGE analysis of purified virus revealed two major proteins of ~40 kDa and ~55 kDa. Amino-terminal sequencing of the ~55 kDa protein and LC-MS/MS of purified virions indicated that this protein starts at aa 263 of the deduced ORF1 product as a result of either degradation or proteolytic processing. A yeast two-hybrid assay was used to identify Arabidopsis proteins interacting with two PMeV ORF1 product fragments (aa 321–670 and 961–1200). The 50S ribosomal protein L17 (AtRPL17) was identified as potentially associated with modulated translation-related proteins. In plant cells, AtRPL17 co-localized and interacted with the PMeV ORF1 fragments. These findings support the hypothesis that the interaction between PMeV/PMeV2 structural proteins and RPL17 is important for virus–host interactions.

The objective of this study was to describe the histology and histochemistry of the integument covering the back and stinger of the freshwater stingray Potamotrygon rex, endemic to the Middle Upper Tocantins River. The species has a dark back and yellowish circular spots that extend to the tail, which has one to two stings located in the median portion of the tail. Through histological study it was observed that the epithelia of the back and stinger are composed of non-keratinized stratified pavement epithelial tissue, and are organized in three layers: basal, intermediate and superficial. The differences between the tissues are related to the cell types that compose them. The back is organized with epithelial cells, mucus cells, granulocyte cells and chromatophores. The mucus cells are distributed in different layers along the animal's back, influencing the thickness of the tissue. The tissue that covers the stinger is composed of epithelial cells, chromatophores and specialized cells in protein synthesis. In the histochemistry, the stinger epithelial cells were stained with Bromophenol Blue, especially those of the intermediate layer, which were called specialized cells. In the back the epithelial cells were stained with Bromophenol Blue, Alcian Blue and PAS, and the mucous cells with PAS. In both tissues the presence of protein reserves was detected, areas so called because they are stained strongly with Bromophenol Blue. The results show that the stinger presents activity directed to the production of proteins, and that the back is organized to produce different components, which constitute the cuticle that covers the animal's body. Resumo O objetivo deste estudo foi descrever a histologia e histoquímica do tegumento que reveste o dorso e o ferrão da arraia de água doce Potamotrygon rex, endêmica do Médio Alto Tocantins. A espécie possui o dorso escuro e manchas circulares amareladas que se estendem até a cauda, que possui de um a dois ferrões localizados na porção mediana da cauda. Através do estudo histológico observou-se que os epitélios do dorso e do ferrão são compostos por tecido epitelial pavimentoso estratificado não queratinizado, e estão organizados em três camadas: basal, intermediária e superficial. As diferenças entre os tecidos estão relacionadas aos tipos de células que os compõem. O dorso é organizado com células epiteliais, células mucosas, células de granulócitos e cromatóforos. As células mucosas estão distribuídas em diferentes camadas ao longo do dorso do animal, influenciando na espessura do tecido. O tecido que reveste o ferrão é composto por células epiteliais, cromatóforos e células proteicas. Na histoquímica, as células epiteliais do ferrão foram coradas com Azul de Bromofenol, principalmente as da camada intermediária, que foram denominadas células proteicas. No dorso as células epiteliais foram coradas com Azul de Bromofenol, Azul Alcian e PAS, e as células mucosas com PAS. Em ambos os tecidos também foi detectada a presença de reservatórios de proteínas, áreas assim denominadas por estarem fortemente coradas com Azul de Bromofenol. Os resultados mostram que o ferrão apresenta atividade direcionada à produção de proteínas, e que o dorso se organiza para produzir diferentes componentes que constituem a cutícula que reveste o corpo do animal.

Drought management is currently informed by a variety of approaches, mostly responding to drought crisis when it happens. Toward more effective and integrated drought management, we introduce a conceptual drought diagnosis framework inspired by diagnostic concepts from the field of medicine. This framework comprises five steps: 1. Initial diagnostic assessment; 2. Diagnostic testing; 3. Consultation; 4. Communication of the diagnosis; and 5. Treatment and prognosis. To illustrate the need for the proposed approach, four case studies of recently drought-affected regions were selected: the city of Cape Town, the state of California, the Northeast region of Brazil, and the Horn of Africa. Contrasting elements for these cases include the geographic extent and political boundaries, climate, socio-economics, and the relevance of different water resources (e.g., rainfall, reservoirs, and aquifers). For each case, we identified documented practices and policies and reflected on them in terms of drought misdiagnosis or incomplete diagnosis that have aggravated socio-economic and environmental drought impacts. A common example is the preference for technical solutions (e.g., installing infrastructure to augment water supply), rather than measures that reduce vulnerability. Analysis of these four drought case studies confirmed the anticipated need for a comprehensive approach to drought diagnosis for more successful treatment and prevention of drought. Using an analogy with medical science can be helpful toward comprehensively diagnosing droughts for a variety of contexts and assessing the effectiveness of proposed interventions. This framework can help drought managers to be more proactive in enabling drought-affected regions to become more drought resilient in the future.

This study investigated the renal function of soccer players after an entire game-season. Thirty-five athletes recruited to play for the Macae Futebol Clube were invited for this study, of which 18 athletes completed the entire game season. Blood and 24-hour urine were collected at the beginning (Pre-Season) and the end of the game season (Post-Season). Kidney functions were assessed by calculating the urinary excretion, clearance, and fractional excretion of the selected solutes. Plasma creatinine, sodium, total protein, and osmolality were lower in the Post-Season . In contrast, plasma urea was higher in the Post-Season period. Urinary excretion of urea was reduced while albumin excretion was higher in comparison to Pre-Season. The clearances of creatinine, total proteins, and albumin were higher in the Post-Season period. In accordance, the fractional excretion of albumin increased. On the other hand, the clearance and fractional excretion of urea was lower in the Post-Season period. These results show that soccer-associated exercise throughout the entire game-season induces kidney functions adaptations that may prevent dehydration in these athletes through increased urea reabsorption to conserve water. In addition, this data corroborates to increased glomerular permeability to plasma proteins, such as albumin, that soccer players may experience.

This paper describes a study performed in the Brazilian governmental center, named Cemaden, responsible to monitor natural disasters and sending alerts to the vulnerable community involved. The target of our study is the complex architecture of Cemaden’s Observational Network. It comprises constituent systems (CS) provided by other partners organisms, which operation and maintenance are out of Cemaden con trolling. The correct functioning of those heterogeneous CSs represents a major challenge in this type of system. Thus the comprehension of dependability issues regarding the information flow in the integration of the CSs is essential. Our study compares the current integration architecture based on syntax rules with the use of an ontology-based integration. The advantages of the proposed architecture are discussed in a case study.

Ad hoc teamwork is a research topic in multi-agent systems whereby an agent (the "ad hoc agent") must successfully collaborate with a set of unknown agents (the "teammates") without any prior coordination or communication protocol. However, research in ad hoc teamwork is predominantly focused on agent-only teams, but not in agent-human teams, which we believe is an exciting research avenue and has enormous application potential in human-robot teams. This paper will tap into this potential by proposing HOTSPOT, the first framework for ad hoc teamwork in human-robot teams. Our framework comprises two main modules, addressing the two key challenges in the interaction between a robot acting as the ad hoc agent and human teammates. First, a decision-theoretic module that is responsible for all task-related decision making (task identification, teammate identification, and planning). Second, a communication module that uses natural language processing in order to parse all communication between the robot and the human. To evaluate our framework, we use a task where a mobile robot and a human cooperatively collect objects in an open space, illustrating the main features of our framework in a real-world task.

Umbilical infections in calves comprise a major cause of neonatal mortality and have been related to a variety of microorganisms. E. coli is an opportunistic enteropathogen characterized by a diversity of virulence factors (VF). Nonetheless, the gene profiles that encode VF associated with umbilical infections in calves and their effect on the clinical severity remains unclear. In this scenario, microbial identification (with an emphasis on E. coli), was carried out among 150 neonatal calves (≤30 days of age) with umbilical infections, where the omphalopathies were clinically scored as mild, moderate, or severe. Also, a panel of 16 virulence-encoding genes related to extraintestinal pathogenic E. coli (ExPEC) were investigated, i.e., fimbriae/adhesins (sfa/focDEa, papA, papC, afaBC), toxins (hlyA, sat, cnf1, cdt), siderophores (iroN, irp2, iucD, ireA), invasins (ibeA), and serum resistance (ompT, traT, kpsMT II). Bacteria and yeasts isolates were identified using mass spectrometry. Bacteria, yeasts, and fungi were isolated in 94.7% (142/150) of neonatal calves sampled. E. coli was the agent most frequently isolated (59/150 = 39.3%), in pure culture (27/59 = 45.8%) and combined infections (32/59 = 54.2%), although a great variety (n = 83) of other species of microorganisms were identified. Clinical severity scores of 1, 2, and 3 were observed in 32.2% (19/59), 23.7% (14/59), and 44.1% (26/59) of E. coli infections, respectively. The ExPEC genes detected were related to serum resistance (traT, 42/59 = 72.2%; ompT, 35/59 = 59.3%, kpsMTII, 10/59 = 17%), invasins (ibeA, 11/59 = 18.6%), siderophores (iucD, 9/59 = 15.3%; iroN, 8/59 = 13.6%), and adhesins/fimbriae (papA, 8/59 = 13.6%; papC, 15/59 = 9.6%). The presence of each virulence gene was not associated with the case's clinical score. Among all isolates, 89.8% (53/59) showed in vitro resistance to sulfamethoxazole/trimethoprim and 59.3% to ampicillin (35/59), while 94.1% (55/59) revealed a multidrug resistant profile. Great complexity of bacteria, yeast, and fungi species was identified, reinforcing the umbilical infections of neonatal calves as a polymicrobial disorder. The high occurrence of E. coli (39.3%) highlights the role of this pathogen in the etiology of umbilical infections in calves. Furthermore, a panel of ExPEC genes was investigated for the first time among calves that were clinically scored for case severity. The high prevalence of traT and ompT indicates that these serum resistance-related genes could be used as biomarkers for further investigations of ExPEC isolates from umbilical infections. Our results contribute to the etiological investigation, clinical severity scoring, antimicrobial resistance pattern, and virulence-related to ExPEC genes involved in umbilical infections of neonatal calves.