Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization.

Colorectal cancer (CRC) is the third most common cancer and the second most deathly worldwide. It is a very heterogeneous disease that can develop via distinct pathways where metastasis is the primary cause of death. Therefore, it is crucial to understand the molecular mechanisms underlying metastasis. RNA-sequencing is an essential tool used for studying the transcriptional landscape. However, the high-dimensionality of gene expression data makes selecting novel metastatic biomarkers problematic. To distinguish early-stage CRC patients at risk of developing metastasis from those that are not, three types of binary classification approaches were used: (1) classification methods (decision trees, linear and radial kernel support vector machines, logistic regression, and random forest) using differentially expressed genes (DEGs) as input features; (2) regularized logistic regression based on the Elastic Net penalty and the proposed iTwiner-a network-based regularizer accounting for gene correlation information; and (3) classification methods based on the genes pre-selected using regularized logistic regression. Classifiers using the DEGs as features showed similar results, with random forest showing the highest accuracy. Using regularized logistic regression on the full dataset yielded no improvement in the methods' accuracy. Further classification using the pre-selected genes found by different penalty factors, instead of the DEGs, significantly improved the accuracy of the binary classifiers. Moreover, the use of network-based correlation information (iTwiner) for gene selection produced the best classification results and the identification of more stable and robust gene sets. Some are known to be tumor suppressor genes (OPCML-IT2), to be related to resistance to cancer therapies (RAC1P3), or to be involved in several cancer processes such as genome stability (XRCC6P2), tumor growth and metastasis (MIR602) and regulation of gene transcription (NME2P2). We show that the classification of CRC patients based on pre-selected features by regularized logistic regression is a valuable alternative to using DEGs, significantly increasing the models' predictive performance. Moreover, the use of correlation-based penalization for biomarker selection stands as a promising strategy for predicting patients' groups based on RNA-seq data.

Kidney Cancer Biomarker Selection Using Regularized Survival Models.

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of RCC showing a significant percentage of mortality. One of the priorities of kidney cancer research is to identify RCC-specific biomarkers for early detection and screening of the disease. With the development of high-throughput technology, it is now possible to measure the expression levels of thousands of genes in parallel and assess the molecular profile of individual tumors. Studying the relationship between gene expression and survival outcome has been widely used to find genes associated with cancer survival, providing new information for clinical decision-making. One of the challenges of using transcriptomics data is their high dimensionality which can lead to instability in the selection of gene signatures. Here we identify potential prognostic biomarkers correlated to the survival outcome of ccRCC patients using two network-based regularizers (EN and TCox) applied to Cox models. Some genes always selected by each method were found (COPS7B, DONSON, GTF2E2, HAUS8, PRH2, and ZNF18) with known roles in cancer formation and progression. Afterward, different lists of genes ranked based on distinct metrics (logFC of DEGs or ß coefficients of regression) were analyzed using GSEA to try to find over- or under-represented mechanisms and pathways. Some ontologies were found in common between the gene sets tested, such as nuclear division, microtubule and tubulin binding, and plasma membrane and chromosome regions. Additionally, genes that were more involved in these ontologies and genes selected by the regularizers were used to create a new gene set where we applied the Cox regression model. With this smaller gene set, we were able to significantly split patients into high/low risk groups showing the importance of studying these genes as potential prognostic factors to help clinicians better identify and monitor patients with ccRCC.

Direitos da criança e adolescente hospitalizados à luz da gestão da clínica / Derechos de los niños y adolescentes hospitalizados a la luz de la gestión de la clínica / Rights of hospitalized children and adolescents in light of clinic management

Resumo Objetivo Analisar o (des)cumprimento dos Direitos da Criança e Adolescente hospitalizados à luz da gestão da clínica. Métodos Pesquisa de métodos mistos, explanatória sequencial, realizada entre setembro e dezembro de 2019, em hospital universitário do Centro-Oeste do Brasil. Participaram 60 acompanhantes, oito profissionais e quatro estudantes da área da saúde, em setores de internação de crianças e adolescentes. Aplicou-se escala Likert com os vinte direitos na etapa quantitativa, e entrevista semiestruturada na qualitativa, com análise descritiva e de conteúdo, respectivamente. Os dados foram integrados por conexão e analisados à luz de princípios da gestão da clínica. Resultados Na etapa quantitativa, identificaram-se direitos com menores percentuais de cumprimento: permanecer ao lado da mãe ao nascer, receber aleitamento materno, apoio psicológico, recreação, acompanhamento do currículo escolar e morte digna. Nos resultados qualitativos identificou-se desconhecimento da resolução pelos participantes, considerando parcialmente cumpridos os direitos: não permanecer internado desnecessariamente, ter acompanhante, não ser separado da mãe ao nascer, receber aleitamento materno, não sentir dor, conhecimento da enfermidade, desfrutar de recreação e programas educacionais, receber informação, todos os recursos para cura, proteção contra maus tratos, preservação de imagem, não ser utilizado pela mídia e ter morte digna. Identificaram-se princípios da gestão da clínica limitados, exigindo estratégias de fomento no hospital. Conclusão Princípios da gestão da clínica mostraram-se fragilizados, especialmente os de orientação às necessidades de saúde e integralidade, transparência e responsabilização social..

Resumen Objetivo Analizar el (in)cumplimiento de los Derechos del Niño y del Adolescente hospitalizados a la luz de la gestión de la clínica. Métodos Investigación con métodos mixtos, explanatoria secuencial, realizada entre septiembre y diciembre de 2019, en un hospital universitario del medio oeste de Brasil. Participaron 60 acompañantes, ocho profesionales y cuatro estudiantes del área de la salud, en sectores de internación de niños y de adolescentes. Se aplicó una escala Likert con los veinte derechos en la etapa cuantitativa, y entrevista semiestructurada en la cualitativa, con análisis descriptivo y de contenido, respectivamente. Los datos se integraron por conexión y fueron analizados a la luz de principios de la gestión de la clínica. Resultados En la etapa cuantitativa, se identificaron derechos con menores porcentajes de cumplimiento: permanecer al lado de la madre al nascer, lactancia materna, apoyo psicológico, recreación, acompañamiento del currículum escolar y muerte digna. En los resultados cualitativos se identificó un desconocimiento de la resolución de parte de los participantes, considerando parcialmente cumplidos los derechos: no permanecer internado sin necesidad, tener un acompañante, no separarse de la madre en el nacimiento, lactancia materna, no sentir dolor, conocimiento de la enfermedad, disfrutar de la recreación y programas educativos, recibir información, todos los recorridos para la curación, protección contra malos tratos, preservación de la imagen, no ser utilizado por los medios y tener una muerte digna. Se identificaron principios de la gestión de la clínica limitados, exigiendo estrategias de fomento en el hospital. Conclusión Principios de la gestión de la clínica se mostraron fragilizados, especialmente los de orientación a las necesidades de salud e integralidad, transparencia y responsabilización social.

Abstract Objective To analyze the (non)compliance with the rights of hospitalized children and adolescents in light of clinic management. Methods This is a mixed methods research, sequential explanatory, carried out between September and December 2019, in a university hospital in center-western Brazil. Sixty companions, eight professionals and four health care students participated in hospitalization sectors for children and adolescents. A Likert-type scale was applied with the twenty rights in the quantitative stage, and semi-structured interviews in the qualitative stage, with descriptive and content analysis, respectively. Data were integrated by connection and analyzed in light of clinic management principles. Results In the quantitative stage, rights were identified with the lowest percentages of compliance: staying by the mother's side at birth, being breastfed, psychological support, recreation, monitoring the school curriculum and dignified death. In the qualitative results, it was identified that participants did not know about the resolution, considering that the rights were partially complied with: not being hospitalized unnecessarily, having a companion, not being separated from the mother at birth, being breastfed, not feeling pain, knowing the disease, enjoying recreation and educational programs, receiving information, all resources for healing, protection against abuse, preservation of image, not being used by the media and having a dignified death. Limited principles of clinic management were identified, requiring development strategies in the hospital. Conclusion Principles of clinic management were weakened, especially those related to health needs and comprehensiveness, transparency and social accountability.

TCox: Correlation-Based Regularization Applied to Colorectal Cancer Survival Data.

Colorectal cancer (CRC) is one of the leading causes of mortality and morbidity in the world. Being a heterogeneous disease, cancer therapy and prognosis represent a significant challenge to medical care. The molecular information improves the accuracy with which patients are classified and treated since similar pathologies may show different clinical outcomes and other responses to treatment. However, the high dimensionality of gene expression data makes the selection of novel genes a problematic task. We propose TCox, a novel penalization function for Cox models, which promotes the selection of genes that have distinct correlation patterns in normal vs. tumor tissues. We compare TCox to other regularized survival models, Elastic Net, HubCox, and OrphanCox. Gene expression and clinical data of CRC and normal (TCGA) patients are used for model evaluation. Each model is tested 100 times. Within a specific run, eighteen of the features selected by TCox are also selected by the other survival regression models tested, therefore undoubtedly being crucial players in the survival of colorectal cancer patients. Moreover, the TCox model exclusively selects genes able to categorize patients into significant risk groups. Our work demonstrates the ability of the proposed weighted regularizer TCox to disclose novel molecular drivers in CRC survival by accounting for correlation-based network information from both tumor and normal tissue. The results presented support the relevance of network information for biomarker identification in high-dimensional gene expression data and foster new directions for the development of network-based feature selection methods in precision oncology.

Implications of PEGylation of Carbon Nanotubes for Central Nervous System Bioavailability.

BACKGROUND AND OBJECTIVE: In this mini-review, we have compiled the most recent and comparable information to shed light on the action of PEGylation in the biodistribution of carbon nanotubes (CNT) in the central nervous system (CNS). It is well known that due to the complexity of the CNS and the severity of the outcome following changes in this system, this is one of the areas where there are more investments in research to develop new technologies and approaches for more effective and less invasive treatments. The CNS is highly protected against toxic and invasive microorganisms thanks to the blood brain barrier (BBB), but this protection also prevents the passage of potentially beneficial molecules for the treatment of neurological disorders. Nanotechnology attempts to develop nanocompounds that are biocompatible and non-immunogenic, and that are able to cross the BBB in therapeutic amounts without causing damage and to diffuse through nerve tissue. These compounds should also be cleared and biodistributed properly, being capable of performing drug delivery exclusively for CNS pathologies, such as neurodegenerative diseases (Parkinson's and Alzheimer's) and brain tumors. CONCLUSION: In this way, this review focuses on CNT PEGylation, aiming to help in the development of viable and effective nanomedicines for neuroscience applications.

Biodistribution and toxicological study of PEGylated single-wall carbon nanotubes in the zebrafish (Danio rerio) nervous system.

Nanotechnology has been proven to be increasingly compatible with pharmacological and biomedical applications. Therefore, we evaluated the biological interactions of single-wall carbon nanotubes functionalized with polyethylene glycol (SWNT-PEG). For this purpose, we analyzed biochemical, histological, behavioral and biodistribution parameters to understand how this material behaves in vitro and in vivo using the fish Danio rerio (zebrafish) as a biological model. The in vitro results for fish brain homogenates indicated that SWNT-PEG had an effect on lipid peroxidation and GSH (reduced glutathione) content. However, after intraperitoneal exposure, SWNT-PEG proved to be less biocompatible and formed aggregates, suggesting that the PEG used for the nanoparticle functionalization was of an inappropriate size for maintaining product stability in a biological environment. This problem with functionalization may have contributed to the low or practically absent biodistribution of SWNT-PEG in zebrafish tissues, as verified by Raman spectroscopy. There was an accumulation of material in the abdominal cavity that led to inflammation and behavioral disturbances, as evaluated by a histological analysis and an open field test, respectively. These results provide evidence of a lack of biocompatibility of SWNTs modified with short chain PEGs, which leads to the accumulation of the material, tissue damage and behavioral alterations in the tested subjects.

Metodologia de intervenção psicossocial e acompanhamento do processo grupal com unidades produtivas em projeto de inclusão produtiva da APRECIA / Methodology for psychosocial intervention and group process work with productive unities within the productive inclusion project of APRECIA

O artigo apresenta a metodologia de intervenção psicossocial com unidades produtivas em um projeto de inclusão produtiva desenvolvidopela APRECIA em parceria com a SEDS-MG. Enfatiza o trabalho com a demanda bem como a interrelação entre o processo grupal, aprodução e a auto-organização dos grupos. Descreve os princípios, estratégias e instrumentos utilizados no processo de intervençãopsicossocial.

The paper presents the methodology for psychosocial intervention with productive unities within a project of productive inclusion developed by APRECIA in partnership with SEDS-MG. It emphasizes the group demand as well as the interrelationship among the group process,production and self-organization. It describes the principles, strategies and tools utilized in the process of psychosocial intervention.