Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors

Funding Information: This research was funded by Fundação para a Ciência e Tecnologia (FCT) Portugal, grant number UIDB/50006/2020 (LAQV-REQUIMTE), UIDP/04378/2020 and UIDB/04378/2020 (UCIBIO) and LA/P/0140/2020 (i4HB), the European Commission GLYCOTwinning (GA 101079417), the EJPRD ProDGNE (EJPRD/0001/2020 EU 825575) and SI I&DT, DCMatters (AVISO Nº 17/SI/2019) REF 47212. F.P. gratefully acknowledges FCT for an Assistant Research Position (CEECIND/01649/2021). Publisher Copyright: © 2023 by the authors.Computational approaches in immune-oncology therapies focus on using data-driven methods to identify potential immune targets and develop novel drug candidates. In particular, the search for PD-1/PD-L1 immune checkpoint inhibitors (ICIs) has enlivened the field, leveraging the use of cheminformatics and bioinformatics tools to analyze large datasets of molecules, gene expression and protein–protein interactions. Up to now, there is still an unmet clinical need for improved ICIs and reliable predictive biomarkers. In this review, we highlight the computational methodologies applied to discovering and developing PD-1/PD-L1 ICIs for improved cancer immunotherapies with a greater focus in the last five years. The use of computer-aided drug design structure- and ligand-based virtual screening processes, molecular docking, homology modeling and molecular dynamics simulations methodologies essential for successful drug discovery campaigns focusing on antibodies, peptides or small-molecule ICIs are addressed. A list of recent databases and web tools used in the context of cancer and immunotherapy has been compilated and made available, namely regarding a general scope, cancer and immunology. In summary, computational approaches have become valuable tools for discovering and developing ICIs. Despite significant progress, there is still a need for improved ICIs and biomarkers, and recent databases and web tools have been compiled to aid in this pursuit.publishersversionpublishe

POLÍTICAS PÚBLICAS PARA MULHERES ENCARCERADAS NO BRASIL: UM INSTRUMENTO GARANTIDOR DA DIGNIDADE

RESUMONo Brasil, a situação de mulheres encarceradas ainda se encontra inserida em um panorama frágil em face da incipiência das políticas públicas. De acordo com o levantamento nacional de informações penitenciárias (INFOPEN Mulheres) produzido em 2017 é necessário considerar e garantir os direitos humanos destas mulheres e, para isso, se requer o aprimoramento de políticas que atendam às suas necessidades e tutelem seus direitos específicos. Nesse sentido, este ensaio tem por objetivo analisar os dados existentes neste último relatório com o intuito de verificar se há políticas públicas destinadas às mulheres encarceradas no Brasil e se a dignidade das mulheres presas está sendo observada. Para tanto utilizou-se dos métodos descritivo, exploratório, quali-quantitativo, bem como revisão bibliográfica. Inicialmente, o artigo demonstrou a situação da mulher encarcerada no Brasil. Logo após, abordou-se as políticas públicas necessárias à garantia dos direitos previstos no âmbito interno e internacional. Constatou-se ao final a necessidade de implementação de políticas públicas para as mulheres encarceradas com o intuito de diminuir o encarceramento provisório bem como instrumento garantidor da dignidade da mulher presa. PALAVRAS-CHAVE: Dignidade da Pessoa Humana; Mulheres Encarceradas; Políticas Públicas. ABSTRACTIn Brazil, the situation of imprisoned women is still framed in a fragile scenario in the face of the incipience of public policies. According to the national survey of penitentiary information (INFOPEN Women) produced in 2017, it is necessary to consider and guarantee the human rights of these women, and for that, it is necessary to improve policies that meet their needs and protect their specific rights. In this sense, the purpose of this essay is to analyze the data available in this last report in order to verify if there are public policies aimed at women incarcerated in Brazil and whether the dignity of women prisoners is being observed. For this purpose, descriptive, exploratory, qualitative and quantitative methods were used as well as bibliographic review. Initially, the article demonstrated the situation of women incarcerated in Brazil. Shortly afterwards, the public policies necessary to guarantee the rights foreseen in the internal and international scope were discussed. The need to implement public policies for incarcerated women with a view to reducing provisional incarceration as well as an instrument guaranteeing the dignity of women prisoners was confirmed. KEYWORDS: Dignity of the Human Person; Incarcerated Women; Public Policy

Flow cytometry immunophenotyping for diagnostic orientation and classification of pediatric cancer based on the euroflow solid tumor orientation tube (Stot)

© 2021 by the authors.Early diagnosis of pediatric cancer is key for adequate patient management and improved outcome. Although multiparameter flow cytometry (MFC) has proven of great utility in the diagnosis and classification of hematologic malignancies, its application to non-hematopoietic pediatric tumors remains limited. Here we designed and prospectively validated a new single eight-color antibody combination—solid tumor orientation tube, STOT—for diagnostic screening of pediatric cancer by MFC. A total of 476 samples (139 tumor mass, 138 bone marrow, 86 lymph node, 58 peripheral blood, and 55 other body fluid samples) from 296 patients with diagnostic suspicion of pediatric cancer were analyzed by MFC vs. conventional diagnostic procedures. STOT was designed after several design–test–evaluate–redesign cycles based on a large panel of monoclonal antibody combinations tested on 301 samples. In its final version, STOT consists of a single 8-color/12-marker antibody combination (CD99-CD8/numyogenin/CD4-EpCAM/CD56/GD2/smCD3-CD19/cyCD3-CD271/CD45). Prospective validation of STOT in 149 samples showed concordant results with the patient WHO/ICCC-3 diagnosis in 138/149 cases (92.6%). These included: 63/63 (100%) reactive/disease-free samples, 43/44 (98%) malignant and 4/4 (100%) benign non-hematopoietic tumors together with 28/38 (74%) leukemia/lymphoma cases; the only exception was Hodgkin lymphoma that required additional markers to be stained. In addition, STOT allowed accurate discrimination among the four most common subtypes of malignant CD45− CD56++ non-hematopoietic solid tumors: 13/13 (GD2++ numyogenin− CD271−/+ nuMyoD1− CD99− EpCAM−) neuroblastoma samples, 5/5 (GD2− numyogenin++ CD271++ nuMyoD1++ CD99−/+ EpCAM−) rhabdomyosarcomas, 2/2 (GD2−/+ numyogenin− CD271+ nuMyoD1− CD99+ EpCAM−) Ewing sarcoma family of tumors, and 7/7 (GD2− numyogenin− CD271+ nuMyoD1− CD99− EpCAM+) Wilms tumors. In summary, here we designed and validated a new standardized antibody combination and MFC assay for diagnostic screening of pediatric solid tumors that might contribute to fast and accurate diagnostic orientation and classification of pediatric cancer in routine clinical practice.This research was funded by the EuroFlow Consortium; Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro, Brazil (FAPERJ), numbers: E26/110.105/2014, E-26/010.101259/2018, and E26/102.191/2013; grant from Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasília, Brazil (CNPQ), Brasília, Brazil, numbers: 303765/2018-6, 409440/2016-7, and 400194/2014-7; and Instituto Desiderata/Chevron, Rio de Janeiro, Brazil, grant “Actions to improve pediatric cancer assistance in RJ”; the EuroFlow Consortium (grant LSHB-CT-2006-018708); Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC; Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Madrid, Spain and FONDOS FEDER), numbers: CB16/12/00400, CB16/12/00233, CB16/12/00369, CB16/12/00489 and CB16/12/00480; grant from Bilateral Cooperation Program between Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-CAPES (Brasília/Brazil) and Dirección General de Políticas Universitárias (DGPU)-Ministério de Educación, Cultura y Deportes (Madrid/Spain) number DGPU 311/15

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

EVALUATION OF THE ANTIOXIDANT CAPACITY OF OILS RECOVERED FROM BRAZIL NUT CAKE WITH HEXANE AND ETHANOL

<p>Cold pressing has been the most common technique for oil extraction from Brazil nut (Bertholletia excelsa). As the yield of this process is low, the residual oil present in the cake deserves attention. In order to recovery this residual oil, this study proposed the application of traditional and alternative solvent, as well as, to evaluate the antioxidant capacity of these oils. Oil recovery was carried out using continuous cycle solid-liquid extraction under reflux, using a solid:solvent ratio of 1:15 (g:mL) for 8 hours. Hexane and ethanol were used as solvents and the oil was separated by rotoevaporation at 50 °C. The DPPH method was employed to measure antioxidant capacity. As results, the average yield did not significantly (p>0.05) vary when changing the solvent: 59.19±1.66 g/100g with hexane compared to 59.95±1.73 g/100g with ethanol, indicating that both effectively recovered the oil since the cake has around 60 g/100g of oil in its constitution. However, the evaluation of antioxidant capacity revealed that the oil obtained with ethanol demonstrated a notable inhibition percentage of 78.23±0.31%. This value was considerably higher than that for the commercial oil (29.22±0.33%), obtained by cold pressing, and higher than that for the oil extracted with hexane (48.36±0.27%). These findings suggest that the choice of extraction solvent plays a significant role in the bioactive properties of the residual oil recovered from Brazil nut remaining cake. Ethanol stood out for its ability to extract and preserve the antioxidant compounds present Brazil nut cake, which may be associated with its molecular polarity capable of interacting with the antioxidant components. In addition, ethanol exhibits low toxicity and lower risk to human health and the environment, particularly when compared to hexane, which possesses inherent toxicity. Therefore, ethanol is a promising solvent to recover the residual oil from the remaining Brazil nut cake with higher antioxidant capacity.</p&gt

The MyoSpA Study Protocol

declArAtions ETHICS APPROVAL AND CONSENT TO PARTICIPATE The current study was submitted and approved by the ethical committee of University of Lisbon and Centro Hospitalar de Lisboa Ocidental, Hospital de Egas Moniz, EPE (Reference Number: 20170700050). The study will be conducted in accordance with the International Conference on Harmonization Good Clinical Practice (GCP) and the Declaration of Helsinki. Furthermore, voluntary written informed participants’ consent will be obtained from all subjects before the start of the study procedures. FUNDING This study was supported by iNOVA4Health (consortia to create a multidisdiplinary/translational network at the NOVA University, Lisbon, Portugal) and Portuguese Society of Rheumatology grants.BACKGROUND: Axial Spondyloarthritis (axSpA) is a chronic, inflammatory rheumatic disease that affects the axial skeleton, causing pain, stiffness, and fatigue. Genetics and environmental factors such as microbiota and microtrauma are known causes of disease susceptibility and progression. Murine models of axSpA found a decisive role for biomechanical stress as an inducer of enthesitis and new bone formation. Here, we hypothesize that muscle properties in axSpA patients are compromised and influenced by genetic background. OBJECTIVES: To improve our current knowledge of axSpA physiopathology, we aim to characterize axial and peripheral muscle properties and identify genetic and protein biomarker that might explain such properties. METHODS: A cross-sectional study will be conducted on 48 participants aged 18-50 years old, involving patients with axSpA (according to ASAS classification criteria, symptoms duration < 10 years) and healthy controls matched by gender, age, and levels of physical activity. We will collect epidemiological and clinical data and perform a detailed, whole body and segmental, myofascial characterization (focusing on multifidus, brachioradialis and the gastrocnemius lateralis) concerning: a) Physical Properties (stiffness, tone and elasticity), assessed by MyotonPRO®; b) Strength, by a dynamometer; c) Mass, by bioimpedance; d) Performance through gait speed and 60-second sit-to-stand test; e) Histological and cellular/ molecular characterization through ultrasound-guided biopsies of multifidus muscle; f) Magnetic Resonance Imaging (MRI) characterization of paravertebral muscles. Furthermore, we will perform an integrated transcriptomics and proteomics analysis of peripheral blood samples. DISCUSSION: The innovative and multidisciplinary approaches of this project rely on the elucidation of myofascial physical properties in axSpA and also on the establishment of a biological signature that relates to specific muscle properties. This hitherto unstudied link between gene/protein signatures and muscle properties may enhance our understanding of axSpA physiopathology and reveal new and useful diagnostic and therapeutic targets.publishersversionpublishe