Analysis of micro RNA expression in bladder urothelial carcinoma

Introdução: O câncer de bexiga é a segunda neoplasia maligna mais frequente do trato urinário, com 386.000 casos estimados e 150.000 mortes para 2011 no mundo. Noventa e cinco por cento são carcinomas uroteliais (CUB) papilíferos não músculo-invasivos de baixo grau, que apresentam altas taxas de recidiva, mas raramente progridem. Tumores invasivos de alto grau representam 10-20% dos diagnósticos, são altamente agressivos levando à mortalidade elevada. O conhecimento das vias moleculares envolvidas na carcinogênese dessa neoplasia é importante para a identificação de novos marcadores para diagnóstico, acompanhamento, prognóstico e desenvolvimento de novas terapias alvo. Micro RNA (miRNA) são pequenas sequências não codificantes de RNA que regulam a expressão dos genes inibindo a tradução da proteína ou promovendo a degradação do RNA mensageiro, estando atualmente envolvidos em vários processos celulares fisiológicos e patológicos, incluindo o câncer. Objetivos: Caracterizar o perfil de expressão de miRNA no CUB, relacionando-o com os parâmetros prognósticos clássicos para a doença: grau histológico e estadiamento. Além disso, relacionar esse padrão de comportamento dos miRNA com a recidiva tumoral e sobrevida câncer-específica em pacientes tratados cirurgicamente para CUB. Material e Métodos: Catorze miRNA (miR-100, miR-10a, miR-21, miR-205, miR-let7c, miR- 125b, miR-143, miR-145, miR-221, miR-223, miR-15a, miR-16-1, miR-199a e miR- 452) foram isolados de espécimes cirúrgicos de 60 pacientes divididos em 2 grupos: 30 pacientes com CUB não invasivo (pTa) de baixo grau submetidos à RTU de bexiga, 30 com CUB invasivo (pT2-3) de alto grau submetidos à cistectomia radical. O grupo controle é representado por cinco pacientes portadores de bexiga normal sem CUB que realizaram tratamento cirúrgico aberto para tratamento da hiperplasia prostática benigna (HPB). O processamento dos miRNA envolveu três fases: (1) extração do miRNA com kit específico, (2) geração do DNA complementar e (3) amplificação do miRNA por PCR quantitativo em tempo real (qRT-PCR). A expressão de cada miRNA foi obtida através do cálculo 2- CT e os RNU-43 e RNU-48 foram utilizados como controles endógenos. Testes estatísticos foram aplicados para estudar as variáveis envolvidas e curvas de Kaplan-Meyer foram usadas para avaliar a sobrevida livre de recidiva (SLR) e sobrevida câncer-específica (SCE). Resultados: Dos 14 miRNA estudados a maioria apresentou subexpressão nos dois grupos de tumor analisados, com exceção do miR-10a para o grupo pTa de baixo grau e do miR-100, 21 e 205 para os tumores pT2/pT3 de alto grau, onde demonstraram-se superexpressos. Essas diferenças de expressão de miRNA entre os dois grupos foram estatisticamente. Quando estudamos a relação entre expressão de miRNA e a evolução dos pacientes através de curvas de sobrevida, observamos que maiores níveis de expressão do miR-21 relacionou-se com menor SLR para tumores pTa. Ainda, maiores concentrações de miR-10a e miR-145 se associaram com menor SLR e maiores níveis de miR-10a com menor SCE para tumores pT2-3. Conclusões: Demonstramos um predomínio de subexpressão de miRNA em xv carcinomas de bexiga. Os miR-100, miR-10a, miR-21 e miR-205 demonstraram diferenças no perfil de expressão para grau e estadiamento dentro dos dois grupos de tumor, sendo capazes de diferenciá-los. Maiores níveis de miR-21 se relacionaram com menor SLR para tumores pTa de baixo grau, enquanto maiores concentrações de miR-10a estiveram associadas com menor SLR e SCE para tumores pT2/pT3 de alto grauIntroduction: Bladder cancer (BC) is the second most common malignancy of the urinary tract, with 386,000 cases estimated and 150,000 deaths in 2011. Urothelial carcinomas (UC) represent 95% of BC cases, and knowledge of the molecular pathways associated with BC carcinogenesis is crucial to identify new diagnostic and prognostic biomarkers, and development of new target molecular therapies. MicroRNAs (miRNAs) are short non-coding RNA molecules that play important roles in the regulation of gene expression by acting directly on mRNAs, leading to either mRNA degradation or inhibition of translation, involved in many physiological and pathological processes, including cancer. Objectives: To characterize miRNAs expression profiles in UC, associating with classic prognostic factors: grade and stage. Moreover, correlate miRNA expression with tumor recurrence and survival. Material and Methods: Fourteen miRNAs (miR-100, miR-10a, miR-21, miR-205, miR-let7c, miR-125b, miR-143, miR-145, miR-221, miR-223, miR-15a, miR-16-1, miR- 199a e miR-452) were isolated from surgical specimens from 60 patients classified in two groups: 30 patients with low-grade non-invasive pTa UC that underwent TURB, 30 with high-grade invasive pT2/pT3 UC underwent radical cystectomy. The control group consists in five normal bladder tissue taken from patients that underwent retropubic prostatectomy to treat benign prostatic hyperplasia (BPH). miRNA processing involved three phases: (1) miRNA extraction by specific kits, (2) cDNA generation (3) miRNA amplification through qRT-PCR. Expression profiles were obtained by relative quantification determined by 2-ct method. Endogenous control were RNU-43 and RNU-48. Statistic tests were used to study the prognostic variables and Kaplan-Meyer curves were constructed to analyze disease-free (DFS) and disease-specific (DSS) survivals. Results: All miRNAs were underexpressed in both groups, except miR-10a in pTa and miR-100, 21 and 205 in pT2/pT3 tumors, that where over-expressed. miR-100, miR-21, miR-10a and miR-205 differentialy expressed in both groups and this differences were statistically significant. The Kaplan-Meyer survival curves showed that higher levels of miR-21 were related to shorter DFS for pTa group. Also, higher levels of miR-10a and miR-145 were associated with shorter DFS and higher levels of miR-10a were also related to shorter DSS in pT2/pT3 group. Conclusions: The majority of miRNA were shown to be underexpressed in bladder UC. miR-100, miR-10a, miR-21 and miR-205 were differentially expressed considering tumor grade and stage. The miRNA profile was able to distinguish pTa low grade and pT2-3 high grade tumors. Higher levels of miR- 21 were related to shorter DFS in pTa, while higher levels of miR-10a were associated with shorter DFS and DSS in pT2-3, high grade U

Modeling, implementation, and analysis of XRCE-DDS applications in distributed multi-processor real-time embedded systems

The Publish-Subscribe paradigm is a design pattern for transparent communication in many recent distributed applications. Data Distribution Service (DDS) is a machine-to-machine communication standard that aims to provide reliable, highperformance, inter-operable, and real-time data exchange based on publish-subscribe paradigm. However, the high resource requirement of DDS limits its usage in low-cost embedded systems. XRCE-DDS is a Client-Agent based standard to enable resource-constrained small embedded systems to connect to the DDS global data space. Current XRCE-DDS implementations suffer from dependencies with host operating systems, target only single processing units, and lack performance analysis methods. In this paper, we present a bare-metal implementation of XRCE-DDS standard on the CompSOC platform as an instance of Multi-Processor System on Chip (MPSoC). The proposed framework includes a hard real-time side hosting the XRCE-DDS Client, and a soft real-time side hosting the XRCE-DDS Agent. A Scenario Aware Data Flow (SADF) model is proposed to capture the dynamism of the system behavior in terms of different execution scenarios. We analyze the long-term expected value for throughput by capturing the probabilistic scenario switching using a proposed Markov model which is experimentally validated

CompROS: A composable ROS2 based architecture for real-time embedded robotic development

Robot Operating System (ROS) is a de-facto standard robot middleware in many academic and industrial use cases. However, utilizing ROS/ROS2 in safety-critical embedded applications with real-time requirement is challenging because of C1) Non-real-time underlying hardware, C2) No control on the host OS scheduler, C3) Unpredictable dynamic memory allocation, C4) High resource requirement, and C5) Unpredictable execution model for ROS nodes. In this paper, we address these limiting factors by proposing a hardwaresoftware architecture-CompROS-for ROS2 based robotic development in a Multi-Processor System on Chip (MPSoC) platform. The proposed hardware architecture consists of a Hard Real-Time (HRT) RISC-V based subsystem implemented in the Programmable Logic (PL) part of the MPSoC platform, a Soft Real-Time (SRT) ARM-based subsystem in the Processing System (PS) part of the MPSoC platform, and a Non-Real-Time (NRT) PC. While the proposed hardware architecture along with a partitioning layer overcomes the first two limiting factors, the rest are managed by the proposed multi-layer software architecture. We make a bare-metal implementation of XRCE-DDS standard for PL-PS communication, while peer-to-peer PL-PL communication is done through a proposed real-time publish-subscribe approach. The reliable communication for PS-PL communication is done through utilizing C-HEAP protocol. Further, we integrate ROS2 software layers on top of the proposed hardware and software layers. Finally, with respect to C5, we present a real-time execution model of ROS2 nodes by a mapping of ROS2 entities to CompROS entities, which is validated through experimental results. We run ROS2 middleware with an executable size of less than 200 KB on an MPSoC platform

State-based switching multi-rate controller for improving resource utilization on predictable and composable platforms

Resource sharing is a crucial design consideration in design of embedded systems for cost and resource utilization reasons. The system-level performance is negatively influenced by resource sharing due to inter-application interference. For a control application, this further implies a trade-off between the resource utilization and the control performance. For a control application, the sampling rate is an important knob to perform trade-off between resource utilization and the control performance. In this paper, we present a state-base switching multi-rate controller (SSMC) scheme targeting predictable and composable multi-core platforms. In the proposed scheme, the controller switches between multiple sampling rates (or application periods) based on the state of the system i.e., the transient and steady state. We propose two multi-rate control laws targeting SSMC — one using single gain and one using multiple gains over different actuating points. We address the impact of model uncertainty by using a parallel observer system. We validate the effectiveness of the proposed scheme performing hardware-in-the-loop simulations targeting an industrial multi-core platform — Verintec, synthesized on a PYNQ Z2 FPGA board. Finally, we demonstrated that the proposed scheme outperforms the state-of-the-art techniques in terms of resource utilization and the control performance

Expression profile of microrna-145 in urothelial bladder cancer

Purpose Bladder cancer (BC) is the second most common malignancy of the urinary tract, with high mortality. The knowledge of the molecular pathways associated with BC carcinogenesis is crucial to identify new diagnostic and prognostic biomarkers. MicroRNAs (miRNAs) are short non-coding RNA molecules that play important roles in the regulation of gene expression by acting directly on mRNAs. miR-145 has been considered as a tumor suppressor, which targets the c-MYC, MUC-1 and FSCN1 genes. Our aim was to evaluate the expression profile of miR-145 in low-grade non-invasive and high-grade invasive bladder urothelial carcinomas. Materials and Methods We studied 30 specimens of low-grade, non-invasive pTa and 30 of pT2/pT3 high-grade invasive UC obtained by transurethral resection or radical cystectomy, followed over a mean time of 16.1 months. Normal controls were represented by five samples of normal bladder biopsy from patients who underwent retropubic prostatectomy to treat BPH. miRNA extraction and cDNA generation were performed using commercial kits. Analysis was performed by qRT-PCR, and miR-145 expression was calculated using the 2-∆∆ct method; we used RNU-43 and RNU-48 as endogenous controls. Results miR-145 was under-expressed in 73.3% and 86.7% of pTa and pT2/pT3, respectively, with expression means of 1.61 for the former and 0.66 for the last. There were no significant differences in miR-145 expression and histological grade, tumor stage, angiolymphatic neoplastic invasion and tumor recurrence. Conclusion miR-145 is under-expressed in low-grade, non-invasive and high-grade invasive urothelial bladder carcinoma and may play an important role in the carcinogenesis pathway, being an interesting candidate diagnostic marker

Improved Positioning Precision using a Multi-rate Multi-sensor in Industrial Motion Control Systems

Industrial motion control systems, e. pick-andplace tasks in semiconductor manufacturing equipment, require precise positioning for achiering high machine throughput. Linear encoders are the standard industrial sensors used for position feedback due to their relatively low cost, high resolution, and high operating frequency. The challenge is that the linear encoders measure the positions at the points-of-control of the equipment, eg motors, and not at the points-of-interest, e.g. pick-and-place positions The coupling between a point-of-control and the point-of-interest is affected by external disturbances such as mechanical misalignment of the product, friction, and warping of the material, and linear encoders fail to sense these disturbances. Vision-based sensing is a potential alternative to achieve robust sensing and high-precision control. However, vision processing has a long computational delay and affects the machine throughput. In this paper, we propose a multi-rate multi-sensor fusion approach to improve the positioning accuracy of industrial motion control systems with different points-of-control and pointsof-interest. We present a multi-rate Kalman filter with bias correction to fuse accurate but slow and delayed vision sensor data with fast but less accurate linear encoder data for highprecision position control. We validate the proposed method in an evaluation framework by considering an industrial case study of a semiconductor die-bonding machine. A design-space exploration is done to evaluate the performance of the proposed solution with respect to various relevant design parameters. The effectiveness of the proposed solution depends on the type of disturbances and vision processing delay. For the parameter range under consideration, we achieve a positioning accuracy of 1μm