Nanomedicines: are we lost in translation?

International audience

Macrophages and CD4 T-cells in rheumatoid arthritis and their modulation by JAK inhibitors

Background: Rheumatoid arthritis (RA) is a chronic inflammatory arthritis that causes significant morbidity and mortality and has no cure. Although early treatment strategies and biologic therapies such as TNFα blocking antibodies have revolutionised treatment, there still remains considerable unmet need. JAK kinase inhibitors, which target multiple inflammatory cytokines, have shown efficacy in treating RA although their exact mechanism of action remains to be determined. Stratified medicine promises to deliver the right drug to the right patient at the right time by using predictive ‘omic biomarkers discovered using bioinformatic and “Big Data” techniques. Therefore, knowledge across the realms of clinical rheumatology, applied immunology, bioinformatics and data science is required to realise this goal. Aim: To use bioinformatic tools to analyse the transcriptome of CD14 macrophages derived from patients with inflammatory arthritis and define a JAK/STAT signature. Thereafter to investigate the role of JAK inhibition on inflammatory cytokine production in a macrophage cell contact activation assay. Finally, to investigate JAK inhibition, following RA synovial fluid stimulation of monocytes. Methods and Results: Using bioinformatic software such as limma from the Bioconductor repository, I determined that there was a JAK/STAT signature in synovial CD14 macrophages from patients with RA and this differed from psoriatic arthritis samples. JAK inhibition using a JAK1/3 inhibitor tofacitinib reduced TNFα production when macrophages were cell contact activated by cytokine stimulated CD4 T-cells. Other pro-inflammatory cytokines such as IL-6 and chemokines such as IP-10 were also reduced. RA synovial fluid failed to stimulate monocytes to phosphorylate STAT1, 3 or 6 but CD4 T-cells activated STAT3 with this stimulus. RNA sequencing of synovial fluid stimulated CD4 T-cells showed an upregulation of SOCS3, BCL6 and SBNO2, a gene associated with RA but with unknown function and tofacitinib reversed this. Conclusion: These studies demonstrate that tofacitinib is effective at reducing inflammatory mediator production in a macrophage cell contact assay and also affects soluble factor mediated stimulation of CD4 T-cells. This suggests that the effectiveness of JAK inhibition is due to inhibition of multiple cytokine pathways such as IL-6, IL-15 and interferon. RNA sequencing is a useful tool to identify non-coding RNA transcripts that are associated with synovial fluid stimulation and JAK inhibition but these require further validation. SBNO2, a gene that is associated with RA, may be biomarker of tofacitinib treatment but requires further investigation and validation in wider disease cohorts.

Modelo institucional do processo de estruturação de empresas de desenvolvimento de software: um estudo de múltiplos casos

Some authors have shown the need of understanding the technological structuring process in contemporary firms. From this perspective, the software industry is a very important element because it provides products and services directly to many organizations from many fields. In this case, the Brazilian software industry has some peculiarities that distinguish it from other industries located in developed countries, which makes its understanding even more relevant. There is evidence that local firms take different strategies and structural configurations to enter into a market naturally dominated by large multinational firms. Therefore, this study aims to understand not only the structural configurations assumed by domestic firms but also the dynamic and the process that lead to these different configurations. To do so, this PhD dissertation investigates the institutional environment, its entities and the isomorphic movements, by employing an exploratory, descriptive and explanatory multiple cases study. Eight software development companies from the Recife's information technology Cluster were visited. Also, a form was applied and an interview with one of the main firm s professional was conducted. Although the study is predominantly qualitative, part of the data was analyzed through charts and graphs, providing a companies and environment overview that was very useful to analysis done through the interviews interpretation. As a result, it was realized that companies are structured around hybrids business models from two ideal types of software development companies, which are: software factory and technology-based company. Regarding the development process, it was found that there is a balanced distribution between the traditional and agile development paradigm. Among the traditional methodologies, the Rational Unified Process (RUP) is predominant. The Scrum is the most used methodology among the organizations based on the Agile Manifesto's principles. Regarding the structuring process, each institutional entity acts in such way that generates different isomorphic pressure. Emphasis was given to entities such as customers, research agencies, clusters, market-leading businesses, public universities, incubators, software industry organizations, technology vendors, development tool suppliers and manager s school and background because they relate themselves in a close way with the software firms. About this relationship, a dual and bilateral influence was found. Finally, the structuring level of the organizational field has been also identified as low, which gives a chance to organizational actors of acting independently

Biomarkers of Nitrosative Stress: Development and validation of a new analytical method for 3-Nitrotyrosine quantification

Background: The nitration of tyrosine residues in proteins is associated with nitrosative stress, resulting in the formation of 3-nitrotyrosine (3-NT). 3-NT levels in biological samples have been associated with numerous physiological and pathological conditions. For this reason, several attempts have been made in order to develop methods that accurately quantify 3-NT in biological samples. Regarding chromatographic methods, they seem to be very accurate, showing very good sensibility and specificity. However, accurate quantification of this molecule, which is present at very low concentrations both at physiological and pathological states, is always a complex task and a target of intense research. Objectives: We aimed to develop a simple, rapid, low-cost and sensitive 3-NT quantification method for use in medical laboratories as an additional tool for diagnosis and/or treatment monitoring of a wide range of pathologies. We also aimed to evaluate the performance of the HPLC-based method developed here in a wide range of biological matrices. Material and methods: All experiments were performed on a Hitachi LaChrom Elite® HPLC system and separation was carried out using a Lichrocart® 250-4 Lichrospher 100 RP-18 (5μm) column. The method was further validated according to ICH guidelines. The biological matrices tested were serum, whole blood, urine, B16 F-10 melanoma cell line, growth medium conditioned with the same cell line, bacterial and yeast suspensions. Results: From all the protocols tested, the best results were obtained using 0.5% CH3COOH:MeOH:H2O (15:15:70) as the mobile phase, with detection at wavelengths 215, 276 and 356 nm, at 25ºC, and using a flow rate of 1 mL/min. By using this protocol, it was possible to obtain a linear calibration curve (correlation coefficient = 1), limits of detection and quantification in the order of ng/mL, and a short analysis time (<15 minutes per sample). Additionally, the developed protocol allowed the successful detection and quantification of 3-NT in all biological matrices tested, with detection at 356 nm. Conclusion: The method described in this study, which was successfully developed and validated for 3-NT quantification, is simple, cheap and fast, rendering it suitable for analysis in a wide range of biological matrices.

Cancer appetite and symptom questionnaire (CASQ) for brazilian patients: Cross-cultural adaptation and validation study

Background: Appetite and symptoms, conditions generally reported by the patients with cancer, are somewhat challenging for professionals to measure directly in clinical routine (latent conditions). Therefore, specific instruments are required for this purpose. This study aimed to perform a cultural adaptation of the Cancer Appetite and Symptom Questionnaire (CASQ), into Portuguese and evaluate its psychometric properties on a sample of Brazilian cancer patients. Methods: This is a validation study with Brazilian cancer patients. The face, content, and construct (factorial and convergent) validities of the Cancer Appetite and Symptom Questionnaire, the study tool, were estimated. Further, a confirmatory factor analysis (CFA) was conducted. The ratio of chi-square and degrees of freedom (χ2/df), comparative fit index (CFI), goodness of fit index (GFI) and root mean square error of approximation (RMSEA) were used for fit model assessment. In addition, the reliability of the instrument was estimated using the composite reliability (CR) and Cronbach’s alpha coefficient (α), and the invariance of the model in independent samples was estimated by a multigroup analysis (Δχ2). Results: Participants included 1,140 cancer patients with a mean age of 53.95 (SD = 13.25) years; 61.3% were women. After the CFA of the original CASQ structure, 2 items with inadequate factor weights were removed. Four correlations between errors were included to provide adequate fit to the sample (χ2/df = 8.532, CFI = .94, GFI = .95, and RMSEA = .08). The model exhibited a low convergent validity (AVE = .32). The reliability was adequate (CR = .82 α = .82). The refined model showed strong invariance in two independent samples (Δχ2: λ: p = .855; i: p = .824; Res: p = .390). A weak stability was obtained between patients undergoing chemotherapy and radiotherapy (Δχ2: λ: p = .155; i: p < .001; Res: p < .001), and between patients undergoing chemotherapy combined with radiotherapy and palliative care (Δχ2: λ: p = .058; i: p < .001; Res: p < .001). Conclusion: The Portuguese version of the CASQ had good face and construct validity and reliability. However, the CASQ still presented invariance in independent samples of Brazilian patients with cancer. However, the tool has low convergent validity and weak invariance in samples with different treatments.

Manual do software xcalibre para aplicação do modelo de rasch

Dissertação (mestrado)—Universidade de Brasília, Instituto de Física, Programa de Pós-Graduação de Mestrado Profissional em Ensino de Física, Mestrado Nacional Profissional em Ensino de Física, 2015.

Development and validation of the team learning questionnaire

Nowadays the organizational scenario is changing in several aspects that affect organization commitment. Team learning construct has emerged as a tool to deal with these changes and the dynamic nature of this situation. Although team learning has acquired importance in recent years, instruments to measure team learning should be developed. The aim of this paper is to develop and validate a team learning scale, the Team Learning Questionnaire, attending to four dimensions of team learning: Continued Improvement Seeking, Dialogue Promotion and Open Communication, Collaborative Learning, and Strategic and Proactive Leadership that Promote Learning. Results provide evidence of the reliability and validity of the scale.

Validación y verificación de Software con herramientas avanzadas

Trabajo realizado en la empresa ULMA Embedded Solutions

Transcultural adaptation and validation of the Celiac Dietary Adherence Test: a simple questionnaire to measure adherence to a gluten-free diet

Background and aims: A gluten-free diet is to date the only treatment available to celiac disease sufferers. However, systematic reviews indicate that, depending on the method of evaluation used, only 42% to 91% of patients adhere to the diet strictly. Transculturally adapted tools that evaluate adherence beyond simple self-informed questions or invasive analyses are, therefore, of importance. The aim is to obtain a Spanish transcultural adaption and validation of Leffler's Celiac Dietary Adherence Test. Methods: A two-stage observational transversal study: translation and back translation by four qualified translators followed by a validation stage in which the questionnaire was administered to 306 celiac disease patients aged between 12 and 72 years and resident in Aragon. Factorial structure, criteria validity and internal consistency were evaluated. Results: The Spanish version maintained the 7 items in a 3-factor structure. Feasibility was very high in all the questions answered and the floor and ceiling effects were very low (4.3% and 1%, respectively). The Spearman correlation with the self-efficacy and life quality scales and the self-informed question were statistically significant (p < 0.01). According to the questionnaire criteria, adherence was 72.3%. Conclusion: The Spanish version of the Celiac Dietary Adherence Test shows appropriate psychometric properties and is, therefore, suitable for studying adherence to a gluten-free diet in clinical and research environments.

Remoção de ruídos sísmicos utilizando transformada de wavelet 1D e 2D com software em desenvolvimento

In the Hydrocarbon exploration activities, the great enigma is the location of the deposits. Great efforts are undertaken in an attempt to better identify them, locate them and at the same time, enhance cost-effectiveness relationship of extraction of oil. Seismic methods are the most widely used because they are indirect, i.e., probing the subsurface layers without invading them. Seismogram is the representation of the Earth s interior and its structures through a conveniently disposed arrangement of the data obtained by seismic reflection. A major problem in this representation is the intensity and variety of present noise in the seismogram, as the surface bearing noise that contaminates the relevant signals, and may mask the desired information, brought by waves scattered in deeper regions of the geological layers. It was developed a tool to suppress these noises based on wavelet transform 1D and 2D. The Java language program makes the separation of seismic images considering the directions (horizontal, vertical, mixed or local) and bands of wavelengths that form these images, using the Daubechies Wavelets, Auto-resolution and Tensor Product of wavelet bases. Besides, it was developed the option in a single image, using the tensor product of two-dimensional wavelets or one-wavelet tensor product by identities. In the latter case, we have the wavelet decomposition in a two dimensional signal in a single direction. This decomposition has allowed to lengthen a certain direction the two-dimensional Wavelets, correcting the effects of scales by applying Auto-resolutions. In other words, it has been improved the treatment of a seismic image using 1D wavelet and 2D wavelet at different stages of Auto-resolution. It was also implemented improvements in the display of images associated with breakdowns in each Auto-resolution, facilitating the choices of images with the signals of interest for image reconstruction without noise. The program was tested with real data and the results were good

Design gráfico da pluma de contaminação por compostos orgânicos voláteiss utilizando software CAD na investigação de passivo ambiental em um posto revendedor de combustíveis em Natal/RN

Among the potentially polluting economic activities that compromise the quality of groundwater are the gas stations. The city of Natal has about 120 gas stations, of which only has an environmental license for operation. Discontinuities in the offices were notified by the Public Ministry of Rio Grande do Norte to carry out the environmental adaptations, among which is the investigation of environmental liabilities. The preliminary and confirmatory stages of this investigation consisted in the evaluation of soil gas surveys with two confirmatory chemical analysis of BTEX, PAH and TPH. To get a good evaluation and interpretation of results obtained in the field, it became necessary three-dimensional representation of them. We used a CAD software to graph the equipment installed in a retail service station fuel in Natal, as well as the plumes of contamination by volatile organic compounds. The tool was concluded that contamination is not located in the current system of underground storage of fuel development, but reflects the historical past in which tanks were removed not tight gasoline and diesel

Simulador de escoamento multifásico em poços de petróleo (SEMPP)

The multiphase flow occurrence in the oil and gas industry is common throughout fluid path, production, transportation and refining. The multiphase flow is defined as flow simultaneously composed of two or more phases with different properties and immiscible. An important computational tool for the design, planning and optimization production systems is multiphase flow simulation in pipelines and porous media, usually made by multiphase flow commercial simulators. The main purpose of the multiphase flow simulators is predicting pressure and temperature at any point at the production system. This work proposes the development of a multiphase flow simulator able to predict the dynamic pressure and temperature gradient in vertical, directional and horizontal wells. The prediction of pressure and temperature profiles was made by numerical integration using marching algorithm with empirical correlations and mechanistic model to predict pressure gradient. The development of this tool involved set of routines implemented through software programming Embarcadero C++ Builder® 2010 version, which allowed the creation of executable file compatible with Microsoft Windows® operating systems. The simulator validation was conduct by computational experiments and comparison the results with the PIPESIM®. In general, the developed simulator achieved excellent results compared with those obtained by PIPESIM and can be used as a tool to assist production systems development

Validation de la reproductibilité d’outils de mesure de la fraction d’éjection du ventricule gauche en médecine nucléaire

La fraction d’éjection du ventricule gauche est un excellent marqueur de la fonction cardiaque. Plusieurs techniques invasives ou non sont utilisées pour son calcul : l’angiographie, l’échocardiographie, la résonnance magnétique nucléaire cardiaque, le scanner cardiaque, la ventriculographie radioisotopique et l’étude de perfusion myocardique en médecine nucléaire. Plus de 40 ans de publications scientifiques encensent la ventriculographie radioisotopique pour sa rapidité d’exécution, sa disponibilité, son faible coût et sa reproductibilité intra-observateur et inter-observateur. La fraction d’éjection du ventricule gauche a été calculée chez 47 patients à deux reprises, par deux technologues, sur deux acquisitions distinctes selon trois méthodes : manuelle, automatique et semi-automatique. Les méthodes automatique et semi-automatique montrent dans l’ensemble une meilleure reproductibilité, une plus petite erreur standard de mesure et une plus petite différence minimale détectable. La méthode manuelle quant à elle fournit un résultat systématiquement et significativement inférieur aux deux autres méthodes. C’est la seule technique qui a montré une différence significative lors de l’analyse intra-observateur. Son erreur standard de mesure est de 40 à 50 % plus importante qu’avec les autres techniques, tout comme l’est sa différence minimale détectable. Bien que les trois méthodes soient d’excellentes techniques reproductibles pour l’évaluation de la fraction d’éjection du ventricule gauche, les estimations de la fiabilité des méthodes automatique et semi-automatique sont supérieures à celles de la méthode manuelle.

INTEGRATION OF INSTRUMENTATION AND PROCESSING SOFTWARE OF A LASER SPECKLE CONTRAST IMAGING SYSTEM

Laser speckle contrast imaging (LSCI) has the potential to be a powerful tool in medicine, but more research in the field is required so it can be used properly. To help in the progression of Michigan Tech's research in the field, a graphical user interface (GUI) was designed in Matlab to control the instrumentation of the experiments as well as process the raw speckle images into contrast images while they are being acquired. The design of the system was successful and is currently being used by Michigan Tech's Biomedical Engineering department. This thesis describes the development of the LSCI GUI as well as offering a full introduction into the history, theory and applications of LSCI.

Methods for Modeling and Analyzing Concurrent Software

Concurrent software executes multiple threads or processes to achieve high performance. However, concurrency results in a huge number of different system behaviors that are difficult to test and verify. The aim of this dissertation is to develop new methods and tools for modeling and analyzing concurrent software systems at design and code levels. This dissertation consists of several related results. First, a formal model of Mondex, an electronic purse system, is built using Petri nets from user requirements, which is formally verified using model checking. Second, Petri nets models are automatically mined from the event traces generated from scientific workflows. Third, partial order models are automatically extracted from some instrumented concurrent program execution, and potential atomicity violation bugs are automatically verified based on the partial order models using model checking. Our formal specification and verification of Mondex have contributed to the world wide effort in developing a verified software repository. Our method to mine Petri net models automatically from provenance offers a new approach to build scientific workflows. Our dynamic prediction tool, named McPatom, can predict several known bugs in real world systems including one that evades several other existing tools. McPatom is efficient and scalable as it takes advantage of the nature of atomicity violations and considers only a pair of threads and accesses to a single shared variable at one time. However, predictive tools need to consider the tradeoffs between precision and coverage. Based on McPatom, this dissertation presents two methods for improving the coverage and precision of atomicity violation predictions: 1) a post-prediction analysis method to increase coverage while ensuring precision; 2) a follow-up replaying method to further increase coverage. Both methods are implemented in a completely automatic tool.