BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.

The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.

A network-based approach to understanding gene-biological processes affecting economically important traits of Nelore cattle.

This study aimed to build gene-biological process networks with differentially expressed genes associated with economically important traits of Nelore cattle from 17 previous studies. The genes were clustered into three groups by evaluated traits: group 1, production traits; group 2, carcass traits; and group 3, meat quality traits. For each group, a gene-biological process network analysis was performed with the differentially expressed genes in common. For production traits, 37 genes were found in common, of which 13 genes were enriched for six Gene Ontology (GO) terms; these terms were not functionally grouped. However, the enriched GO terms were related to homeostasis, the development of muscles and the immune system. For carcass traits, four genes were found in common. Thus, it was not possible to functionally group these genes into a network. For meat quality traits, the analysis revealed 222 genes in common. CSRP3 was the only gene differentially expressed in all three groups. Non-redundant biological terms for clusters of genes were functionally grouped networks, reflecting the cross-talk between all biological processes and genes involved. Many biological processes and pathways related to muscles, the immune system and lipid metabolism were enriched, such as striated muscle cell development and triglyceride metabolic processes. This study provides insights into the genetic mechanisms of production, carcass and meat quality traits of Nelore cattle. This information is fundamental for a better understanding of the complex traits and could help in planning strategies for the production and selection systems of Nelore cattle.

Cell annotation using scRNA-seq data: A protein-protein interaction network approach.

Pathway analysis is an important step in the interpretation of single cell transcriptomic data, as it provides powerful information to detect which cellular processes are active in each individual cell. We have recently developed a protein-protein interaction network-based framework to quantify pluripotency associated pathways from scRNA-seq data. On this occasion, we extend this approach to quantify the activity of a pathway associated with any biological process, or even any list of genes. A systems-level characterization of pathway activities across multiple cell types provides a broadly applicable tool for the analysis of pathways in both healthy and disease conditions. Dysregulated cellular functions are a hallmark of a wide spectrum of human disorders, including cancer and autoimmune diseases. Here, we illustrate our method by analyzing various biological processes in healthy and cancer breast samples. Using this approach we found that tumor breast cells, even when they form a single group in the UMAP space, keep diverse biological programs active in a differentiated manner within the cluster.•We implement a protein-protein interaction network-based approach to quantify the activity of different biological processes.•The methodology can be used for cell annotation in scRNA-seq studies and is freely available as R package.

Apical Sealing and Bioactivity of an Experimental Gutta-Percha Containing Niobium Phosphate Bioglass.

This study evaluated the apical sealing ability and bioactivity of an experimental gutta-percha containing niobium phosphate bioglass. Thirty-six human premolars were endodontically prepared and divided into three groups: GPC-filling with conventional gutta-percha; GBC-filling with bioceramic gutta-percha (EndoSequence BC); GNB-filling with experimental gutta-percha containing niobophosphate. Teeth were stored in tubes containing 2 mL of simulated body fluid (SBF) solution in an oven for 30 days. Then, the samples were immersed in lanthanum nitrate solution and analyzed for apical nanoleakage (NI) with a scanning electron microscope (SEM/EDS) and transmission electron microscope (TEM). Gutta-percha specimens were immersed for 28 days (SBF) and analyzed in SEM/EDS and X-ray diffraction (XRD) to assess bioactivity. NI data originated from the SEM/EDS were analyzed using the Kruskal-Wallis test (α = 5%). NI data originated from TEM and bioactivity were descriptively reported. Statistical analysis did not detect a significant difference between groups (p = 0.13) for NI. In the bioactivity analysis, an abundant layer of hydroxyapatite was identified only in the surface of the GNB group samples. The gutta-percha containing niobophosphate bioglass promoted an apical sealing similar to EndoSequence BC, in addition to demonstrating bioactivity through the deposition of hydroxyapatite on the surface of the material after immersion in SBF.

Genes and proteins associated with ribeye area and meat tenderness in a commercial Nellore cattle population.

Despite several studies on genetic markers and differentially expressed genes related to ribeye area (REA) and tenderness traits in beef cattle, there is divergence in the results regarding the genes associated with these traits. Thirteen genes associated with or exhibiting biological functions that might influence such phenotypes were included in this study. A total of five genes for REA (IGF-1, IGF-2, MSTN, NEDD4, and UBE4A) and eight genes for meat tenderness (CAPN1, CAPN2, CAST, HSPB1, DNAJA1, FABP4, SCD, and PRKAG3) were selected from previous studies on beef cattle. Genes and their respective proteins expression were validated in a commercial population of Nellore cattle using quantitative real-time PCR (RT-qPCR) and advanced mass spectrometry (LC/MS-MS) techniques, respectively. The MSTN gene was upregulated in animals with low REA. The CAPN1, CAPN2, CAST, HSPB1, and DNAJA1 genes were upregulated in animals with tough meat. The proteins translated by these genes were not differentially expressed. Our results confirm the potential of some of the studied genes as biomarkers for carcass and meat quality traits in Nellore cattle.

Molecular markers associated with the outcome of tamoxifen treatment in estrogen receptor-positive breast cancer patients: scoping review and in silico analysis.

Tamoxifen (TMX) is used as adjuvant therapy for estrogen receptor-positive (ER+) breast cancer cases due to its affinity and inhibitory effects. However, about 30% of cases show drug resistance, resulting in recurrence and metastasis, the leading causes of death. A literature review can help to elucidate the main cellular processes involved in TMX resistance. A scoping review was performed to find clinical studies investigating the association of expression of molecular markers profiles with long-term outcomes in ER+ patients treated with TMX. In silico analysis was performed to assess the interrelationship among the selected markers, evaluating the joint involvement with the biological processes. Forty-five studies were selected according to the inclusion and exclusion criteria. After clustering and gene ontology analysis, 23 molecular markers were significantly associated, forming three clusters of strong correlation with cell cycle regulation, signal transduction of proliferative stimuli, and hormone response involved in morphogenesis and differentiation of mammary gland. Also, it was found that overexpression of markers in selected clusters is a significant indicator of poor overall survival. The proposed review offered a better understanding of independent data from the literature, revealing an integrative network of markers involved in cellular processes that could modulate the response of TMX. Analysis of these mechanisms and their molecular components could improve the effectiveness of TMX.

Landfill leachate treatment in Brazil - An overview.

The management of municipal solid waste (MSW) presents an ever increasing and more complex challenge in global terms. The disposal of MSW in landfills generates leachate, a liquid highly polluting to the aquatic environment. This review describes the state-of-the-art approaches to treatments applied to leachate in Brazil, highlighting the new technologies and alternatives that are still in the research phase, and compares the leachate treatment technologies applied around the world with the current scenario in Brazil. In Brazilian landfills, along with other technologies, the biological process is commonly applied, since this is a simple and economical approach and often it is the only technique used in small municipalities. The sanitary landfills in large Brazilian cities located in the states of São Paulo and Rio de Janeiro, invest in or outsource landfill activities, where apply advanced treatment technologies, such as membrane filtration. The use of membrane filtration technology in these cases reveals similarities with leachate treatments applied in the developed countries of North America and Europe. Brazilian researchers have highlighted the need to use efficient and economically viable technologies for the treatment of leachate in Brazilian landfills. However, the current scenario of MSW management in Brazil shows deficiencies related to the monitoring of sanitary landfills and limited information is available on the performance of leachate treatment systems.

Longissimus dorsi muscle label-free quantitative proteomic reveals biological mechanisms associated with intramuscular fat deposition.

The pathways involved in intramuscular fat (IMF) deposition in Longissimus dorsi muscle were investigated using an integrated transcriptome-assisted label-free quantitative proteomic approach by High Definition Mass Spectrometry. We quantified 1582 proteins, of which 164 were differentially abundant proteins (DAPs, p < 0.05) between animals with high (H) and low (L) genomic estimated breeding values (GEBV) for IMF content. Ingenuity pathway analysis (IPA) revealed that these DAPs were mainly involved in glycolysis metabolism, actin cytoskeleton signaling, cell-cell adherens junction and pathways for MAPK and insulin. A comparative study between transcriptomic (mRNA) and proteomic data showed 17 differentially expressed genes corresponding to DAPs, of which three genes/proteins did not agree on the direction of the fold change between groups. Moreover, we investigated microRNAs data to explain these differences in fold change direction, being able to unravel two of the three unexpected mRNA/protein relationships. Results demonstrated that changes in protein/mRNA levels of sarcomere organization, intracellular signal transduction and regulation of actin cytoskeleton, are involved in IMF deposition. These findings provide a deeper understanding of the highly complex regulatory mechanisms involved in IMF deposition in cattle and indicate target pathways for future studies. SIGNIFICANCE: Intramuscular fat is the amount of fat deposited inside muscle and plays an important role in human health and meat quality attributes, influencing energy metabolism of skeletal muscle, as well as, tenderness, flavor, and juiciness of beef. We performed for the first time the utilization of integrated transcriptome-assisted label-free quantitative proteomic approach using High Definition Mass Spectrometry for characterization of the changes in the proteomic profile of the Longissimus dorsi muscle associated with intramuscular fat deposition in cattle. Furthermore, we compared the muscle proteome with the muscle transcriptome (mRNA and microRNAs), obtained by RNA-sequencing, to better understand the relationship between expression of mRNAs and proteins and to unravel essential biological mechanisms involved in bovine skeletal muscle IMF deposition.

Día de los Muertos: Learning About Death Through Observing and Pitching In.

The chapter explores how young children in the state of Puebla, Mexico are socialized with respect to death by observing and pitching in during the annual celebration for día de los muertos. This chapter focuses on observations made of children's participation in practices related to día de los muertos and their experiences with death as explored through ethnographic interviews of preschool children and adults from the cities of Cholula and Puebla. We found that children were included in all aspects of día de los muertos and participated by hanging out, observing, pitching in, and listening. Parents (and grandparents) viewed this active participation as crucial for children to acquire the skills and traditions necessary to be responsible adults in their culture. The current research provides new perspectives regarding the study of children and death within the field of developmental psychology by focusing on how multiple modes of participation are an integral part of young children's socialization with death.

Tecnica mínimamente invasiva (MIPO) y síntesis por vía anterior para el tratamiento de las fracturas diafisarias del húmero / Minimally invasive technique (MIPO) and synthesis by anterior approach for the treatment of humeral shaft fractures

El objetivo del trabajo es evaluar los resultados clínicos, funcionales y radiográficos en el tratamiento con cirugía mínimamente invasiva (MIPO) para las fracturas de la diáfisis humeral, el trabajo fue diseñado bajo la modalidad de serie clínica, del tipo prospectivo, realizado en el Hospital Coromoto durante diciembre del 2007 a enero del 2009, con una población de 11 fracturas de la diáfisis humeral, a los cuales se les realizó técnica MIPO con placas LCP de 4,5 fijada en la anterior de la diáfisis humeral, los resultados se manejaron de acuerdo a las escuelas de valoración de la UCLA para el hombro y de la Clínica de Mayo para el codo (MEPS), obteniendo 82 por ciento de excelentes y 18 por ciento de buenos resultados según la escala de la UCLA, y 73 por ciento de excelentes y 27 por ciento de buenos resultados según la escala MEPS, no se obtuvieron resultados regulares y/o malos tampoco lesiones iatrogénicas del N. radial, no hubo revisiones quirúrgicas ni casos de seudoartrosis, tampoco fallas del implante. La cirugía MIPO es una alternativa segura y eficaz que se corresponde con los nuevos conceptos biológicos.

Evaluate clinical outcomes, functional and radiological treatment minimally invasive surgery (MIPO) for fractures of the humeral diaphysis, the work was designed in the form of clinical series, conducted in a prospective Coromoto Hospital during december 2007 to january 2009, with a population of 11 fractures of the humeral diaphysis, which plate LCP 4.5 set in the front of the humeral diaphysis, the results will be handled according to the assessment scales at UCLA for the men the Mayo Clinic for the elbow, getting 82 percent and 18 percent excellent success according to the scale of UCLA an 73 percent excellent and 27 percent of good performance as the scale of the Mayo Clinic, were not iatrogenic injuries of the N. radio, there was no case of surgical revisions pseudoarthrosis or failure of the implant. Minimally invasive surgery for percutaneous techniques is a safe and effective alternative tha corresponds to new biological concepts.