SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms

The reconstruction of phylogenomic trees containing multiple genes is best achieved by using a supermatrix. The advent of NGS technology made it easier and cheaper to obtain multiple gene data in one sequencing run. When numerous genes and organisms are used in the phylogenomic analysis, it is difficult to organize all information and manually align the gene sequences to further concatenate them. This study describes SPLACE, a tool to automatically SPLit, Align, and ConcatenatE the genes of all species of interest to generate a supermatrix file, and consequently, a phylogenetic tree, while handling possible missing data. In our findings, SPLACE was the only tool that could automatically align gene sequences and also handle missing data; and, it required only a few minutes to produce a supermatrix FASTA file containing 83 aligned and concatenated genes from the chloroplast genomes of 270 plant species. It is an open-source tool and is publicly available at https://github.com/reinator/splace

Schistosoma Mansoni Reinfection: Analysis of Risk Factors By Classification and Regression Tree (CART) Modeling.

Praziquantel (PZQ) is an effective chemotherapy for schistosomiasis mansoni and a mainstay for its control and potential elimination. However, it does not prevent against reinfection, which can occur rapidly in areas with active transmission. A guide to ranking the risk factors for Schistosoma mansoni reinfection would greatly contribute to prioritizing resources and focusing prevention and control measures to prevent rapid reinfection. The objective of the current study was to explore the relationship among the socioeconomic, demographic, and epidemiological factors that can influence reinfection by S. mansoni one year after successful treatment with PZQ in school-aged children in Northeastern Minas Gerais state Brazil. Parasitological, socioeconomic, demographic, and water contact information were surveyed in 506 S. mansoni-infected individuals, aged 6 to 15 years, resident in these endemic areas. Eligible individuals were treated with PZQ until they were determined to be negative by the absence of S. mansonieggs in the feces on two consecutive days of Kato-Katz fecal thick smear. These individuals were surveyed again 12 months from the date of successful treatment with PZQ. A classification and regression tree modeling (CART) was then used to explore the relationship between socioeconomic, demographic, and epidemiological variables and their reinfection status. The most important risk factor identified for S. mansoni reinfection was their “heavy” infection at baseline. Additional analyses, excluding heavy infection status, showed that lower socioeconomic status and a lower level of education of the household head were also most important risk factors for S. mansoni reinfection. Our results provide an important contribution toward the control and possible elimination of schistosomiasis by identifying three major risk factors that can be used for targeted treatment and monitoring of reinfection. We suggest that control measures that target heavily infected children in the most economically disadvantaged households would be most beneficial to maintain the success of mass chemotherapy campaigns

Anti-EGFR therapy: strategies in head and neck squamous cell carcinoma.

Epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor that activates downstream signaling pathways, including the Ras-MEK-Erk and PI3K-AKT pathways, leading to cell proliferation, resistance to apoptosis, angiogenesis and the ability to metastasize. EGFR overexpression is a significant finding in cancer, particularly in head and neck cancer, where it is also associated with a poor prognosis. In recent years, several molecules have been designed to inhibit EGFR activation. Among the many available anti-EGFR drugs, only cetuximab was approved for the treatment of head and neck cancers. However, no predictive biomarkers of cetuximab response are currently known. In the present review, we provide an updated assessment of EGFR biology and its clinical impact in head and neck cancers. A special emphasis is placed on novel patents of EGFR-inhibitors that are anticipated to diversify the anti-EGFR therapies available to treat head and neck cancers. In particular, we outline a new class of irreversible multi-target inhibitors (e.g. afatinib, icotinib, CUDC-101), which may significantly contribute to new head and neck cancer therapies.The authors would like to acknowledge Dr. Laura Mussel white for critical revision of the manuscript. André L. Carvalho and Rui M. Reis have a National Counsel of Technological and Scientific Development (CNPq) scholarship. A.C.C, has a FAPESP (2013/13834-7) scholarship.info:eu-repo/semantics/publishedVersio

A biomechanical perspective on perineal injuries during childbirth

Background and objective: Childbirth trauma is a major health concern that affects millions of women worldwide. Severe degrees of perineal trauma, designated as obstetric anal sphincter injuries (OASIS), and levator ani muscle (LAM) injuries are associated with long-term morbidity. While significant research has been conducted on LAM avulsions, less attention has been given to perineal trauma and OASIS, which affect up to 90% and 11% of vaginal deliveries, respectively. Despite being widely discussed, childbirth trauma remains unpredictable. This work aims to enhance the modeling of the maternal musculature during childbirth, with a particular focus on understanding the mechanisms underlying the often overlooked perineal injuries. Methods: A geometrical model of the pelvic floor muscles (PFM) and perineum (including the perineal body, ischiocavernosus, bulbospongiosus, superficial and deep transverse perineal muscles) was created. The muscles were characterized by a transversely isotropic visco-hyperelastic constitutive model. Two simulations of vaginal delivery were conducted with the fetus in the vertex presentation and occipito-anterior position, with and without the perineum. Results: The simulation that considered the perineum exhibited higher stresses over an extended area of the PFM, which suggests that including additional structures can impact the obtained results. The maximum stretch of the urogenital hiatus was 2.94 and the maximum stress was 23.86 kPa. The perineal body reached a maximum stretch of 1.95, which was more pronounced near the urogenital hiatus, where perineal tears may occur. The external anal sphincter's transverse diameter decreased by 51% and the maximum principal stresses were observed in the area close to the perineal body, where OASIS can occur. Conclusions: The present study emphasizes the importance of including most structures involved in vaginal delivery in its biomechanical analysis and represents another step further in the understanding of perineal injuries and OASIS. The superior region of the perineal body and its connection to the urogenital hiatus and anal sphincter have been identified as the most critical regions, highly susceptible to injury

Use of natural rubber membranes as support for powder TiO2 and Ag/TiO2 photocatalysts

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)The purpose of this study was to synthesize TiO2-polymer composites able to act as photocatalyst membranes. TiO2 catalysts were prepared using the sol-gel method to contain 0.0, 0.5, 1.0, and 2.0 wt.% of embedded Ag particles, subsequently incorporated into natural rubber latex at a weight fraction of 15%. Samples of these ceramic powders were suspended in a latex emulsion (natural rubber), cast in Petri dishes and slowly dried in an oven. The resulting materials were evaluated by X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray, diffuse reflectance spectroscopy, differential scanning calorimetry, thermogravimetry, and photocatalytic assaying using methylene blue as an organic pollutant reference. All composite membranes exhibited good photoactivity conferred by TiO2 powder, with 98% dye fading after 300 min of ultraviolet irradiation.The purpose of this study was to synthesize TiO2-polymer composites able to act as photocatalyst membranes. TiO2 catalysts were prepared using the sol-gel method to contain 0.0, 0.5, 1.0, and 2.0 wt.% of embedded Ag particles, subsequently incorporated in273575583CNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORFUNDECT - FUNDAÇÃO DE APOIO AO DESENVOLVIMENTO DO ENSINO, CIÊNCIA E TECNOLOGIA DO ESTADO DE MATO GROSSO DO SUL |Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)sem informaçãosem informaçãosem informaçãosem informaçãoThe authors wish to thank the Brazilian funding agencies Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and Fundação de Apoio ao Desenvolvimento do Ensino, Ciênci

Avaliação da função renal em ratos wistar com insuficiência renal

A incidência e a prevalência da doença renal crónica continuam a aumentar em todo o mundo. O modelo de redução de 5/6 de massa renal (5/6 RMR) é um dos procedimentos experimentais mais utilizados para a indução e o estudo das alterações associadas a uma insuficiência renal crónica. A resposta adaptativa do rim à redução cirúrgica do número de nefrónios parece ser suficientemente semelhante às características fisiopatológicas das nefropatias progressivas humanas. Neste estudo foram utilizados seis ratos machos da estirpe Wistar. Os animais foram anestesiados com xilazina (10 mg/kg) e ketamina (75 mg/kg). Em três animais foi realizada a redução de 5/6 de massa renal e nos restantes três a cirurgia foi simulada. Os animais foram divididos em dois grupos experimentais: grupo SO: animais em que a cirurgia foi simulada; e grupo RMR: animais submetidos à RMR. Foi realizada uma recolha de sangue e de urina no estado basal e depois mensalmente, durante 2 meses. Os animais submetidos à RMR apresentaram um aumento do fluxo urinário, um aumento das concentrações plasmáticas de ureia e de creatinina, uma diminuição da depuração de creatinina e um aumento das concentrações plasmáticas de potássio. Portanto, a redução cirúrgica de massa renal foi acompanhada por um declínio da função renal

Avaliação da função renal em ratos wistar com insuficiência renal

A incidência e a prevalência da doença renal crónica continuam a aumentar em todo o mundo. O modelo de redução de 5/6 de massa renal (5/6 RMR) é um dos procedimentos experimentais mais utilizados para a indução e o estudo das alterações associadas a uma insuficiência renal crónica. A resposta adaptativa do rim à redução cirúrgica do número de nefrónios parece ser suficientemente semelhante às características fisiopatológicas das nefropatias progressivas humanas. Neste estudo foram utilizados seis ratos machos da estirpe Wistar. Os animais foram anestesiados com xilazina (10 mg/kg) e ketamina (75 mg/kg). Em três animais foi realizada a redução de 5/6 de massa renal e nos restantes três a cirurgia foi simulada. Os animais foram divididos em dois grupos experimentais: grupo SO: animais em que a cirurgia foi simulada; e grupo RMR: animais submetidos à RMR. Foi realizada uma recolha de sangue e de urina no estado basal e depois mensalmente, durante 2 meses. Os animais submetidos à RMR apresentaram um aumento do fluxo urinário, um aumento das concentrações plasmáticas de ureia e de creatinina, uma diminuição da depuração de creatinina e um aumento das concentrações plasmáticas de potássio. Portanto, a redução cirúrgica de massa renal foi acompanhada por um declínio da função renal

Mining clinical attributes of genomic variants through assisted literature curation in Egas

The veritable deluge of biological data over recent years has led to the establishment of a considerable number of knowledge resources that compile curated information extracted from the literature and store it in structured form, facilitating its use and exploitation. In this article, we focus on the curation of inherited genetic variants and associated clinical attributes, such as zygosity, penetrance or inheritance mode, and describe the use of Egas for this task. Egas is a web-based platform for text-mining assisted literature curation that focuses on usability through modern design solutions and simple user interactions. Egas offers a flexible and customizable tool that allows defining the concept types and relations of interest for a given annotation task, as well as the ontologies used for normalizing each concept type. Further, annotations may be performed on raw documents or on the results of automated concept identification and relation extraction tools. Users can inspect, correct or remove automatic text-mining results, manually add new annotations, and export the results to standard formats. Egas is compatible with the most recent versions of Google Chrome, Mozilla Firefox, Internet Explorer and Safari and is available for use at https://demo.bmd-software.com/egas/

The heat transfer modelling for bone metastatic lesion minimization using two different cement types

Bone tumors grow when cells divide without any control, forming a tissue mass. Bone tumors could be benign or malignant, and primary or metastatic due to systemic cancer cells dissemination. They destroy bone and lead to pathological fractures. The main objective of this work is to study the thermal effect induced by the bone cement polymerization, in the bone metastatic tumor minimization. To assess the clinical effect, it is important to test this methodology before its application and obtain sustained results. In this work, a numerical model was developed to predict the temperature distribution produced by cement polymerization. Thus, distinct tests were produced for different two cements types and amounts introduced in a cortical and spongy bone metastatic lesion, with or without an intramedullary titanium nail. The bone cement was introduced to fill in a metastatic lytic lesion area, which the main objective is playing a promising role for bone tumor necrosis due to thermal effects and biomechanical stabilization for function and pain relief.info:eu-repo/semantics/publishedVersio