Genomic co-processor for long read assembly

Genomics data is transforming medicine and our understanding of life in fundamental ways; however, it is far outpacing Moore's Law. Third-generation sequencing technologies produce 100X longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. In order to enable the vast potential of exponentially growing genomics data, domain specific acceleration provides one of the few remaining approaches to continue to scale compute performance and efficiency, since general-purpose architectures are struggling to handle the huge amount of data needed for genome alignment. The aim of this project is to implement a genomic-coprocessor targeting HPC FPGAs starting from the Darwin FPGA co-processor. In this scenario, the final objective is the simulation and implementation of the algorithms described by Darwin using Alveo boards, exploiting High Bandwidth Memory (HBM) to increase its performance

Disseny, realització i test d'un microprocessador

L’objectiu general d’aquest treball de fi de grau és obtenir un microprocessador implementat en un dispositiu lògic programable capaç d’executar qualsevol programa en llenguatge assemblador que contingui les instruccions suportades pel microprocessador.Així doncs, s’ha realitzat el disseny de dos tipus de microprocessador basats en l’arquitectura MIPS, un microprocessador pipelinedi un multi cicle, els quals suporten les mateixes instruccions, 52 en total, però difereixen en la microarquitectura, d’aquesta manera s’ha dut a terme una comparativa entre els dos. El disseny s’ha realitzat en llenguatge de descripció de hardware VHDL mitjançant el software Vivado.Posteriorment s’ha dut a terme la implementació dels dos microprocessadors sobre una FPGA Nexys 4DDR, a fi de verificar el seu correcte funcionament carregant varis programes a la seva memòria d’instruccions

Disseny, realització i test d'un microprocessador

L’objectiu general d’aquest treball de fi de grau és obtenir un microprocessador implementat en un dispositiu lògic programable capaç d’executar qualsevol programa en llenguatge assemblador que contingui les instruccions suportades pel microprocessador.Així doncs, s’ha realitzat el disseny de dos tipus de microprocessador basats en l’arquitectura MIPS, un microprocessador pipelinedi un multi cicle, els quals suporten les mateixes instruccions, 52 en total, però difereixen en la microarquitectura, d’aquesta manera s’ha dut a terme una comparativa entre els dos. El disseny s’ha realitzat en llenguatge de descripció de hardware VHDL mitjançant el software Vivado.Posteriorment s’ha dut a terme la implementació dels dos microprocessadors sobre una FPGA Nexys 4DDR, a fi de verificar el seu correcte funcionament carregant varis programes a la seva memòria d’instruccions

Electronegative LDL Is Associated with Plaque Vulnerability in Patients with Ischemic Stroke and Carotid Atherosclerosis

Owing to the high risk of recurrence, identifying indicators of carotid plaque vulnerability in atherothrombotic ischemic stroke is essential. In this study, we aimed to identify modified LDLs and antioxidant enzymes associated with plaque vulnerability in plasma from patients with a recent ischemic stroke and carotid atherosclerosis. Patients underwent an ultrasound, a CT-angiography, and an 18F-FDG PET. A blood sample was obtained from patients (n = 64, 57.8% with stenosis ≥50%) and healthy controls (n = 24). Compared to the controls, patients showed lower levels of total cholesterol, LDL cholesterol, HDL cholesterol, apolipoprotein B (apoB), apoA-I, apoA-II, and apoE, and higher levels of apoJ. Patients showed lower platelet-activating factor acetylhydrolase (PAF-AH) and paraoxonase-1 (PON-1) enzymatic activities in HDL, and higher plasma levels of oxidized LDL (oxLDL) and electronegative LDL (LDL(−)). The only difference between patients with stenosis ≥50% and p p p < 0.033), indicating that an increased proportion of LDL(−) is associated with vulnerable atherosclerotic plaque

Electronegative LDL Is Associated with Plaque Vulnerability in Patients with Ischemic Stroke and Carotid Atherosclerosis

Owing to the high risk of recurrence, identifying indicators of carotid plaque vulnerability in atherothrombotic ischemic stroke is essential. In this study, we aimed to identify modified LDLs and antioxidant enzymes associated with plaque vulnerability in plasma from patients with a recent ischemic stroke and carotid atherosclerosis. Patients underwent an ultrasound, a CT-angiography, and an 18F-FDG PET. A blood sample was obtained from patients (n = 64, 57.8% with stenosis &ge;50%) and healthy controls (n = 24). Compared to the controls, patients showed lower levels of total cholesterol, LDL cholesterol, HDL cholesterol, apolipoprotein B (apoB), apoA-I, apoA-II, and apoE, and higher levels of apoJ. Patients showed lower platelet-activating factor acetylhydrolase (PAF-AH) and paraoxonase-1 (PON-1) enzymatic activities in HDL, and higher plasma levels of oxidized LDL (oxLDL) and electronegative LDL (LDL(&minus;)). The only difference between patients with stenosis &ge;50% and &lt;50% was the proportion of LDL(&minus;). In a multivariable logistic regression analysis, the levels of LDL(&minus;), but not of oxLDL, were independently associated with the degree of carotid stenosis (OR: 5.40, CI: 1.15&ndash;25.44, p &lt; 0.033), the presence of hypoechoic plaque (OR: 7.52, CI: 1.26&ndash;44.83, p &lt; 0.027), and of diffuse neovessels (OR: 10.77, CI: 1.21&ndash;95.93, p &lt; 0.033), indicating that an increased proportion of LDL(&minus;) is associated with vulnerable atherosclerotic plaque

Effect of general anaesthesia on functional outcome in patients with anterior circulation ischaemic stroke having endovascular thrombectomy versus standard care: a meta-analysis of individual patient data

Background: General anaesthesia (GA) during endovascular thrombectomy has been associated with worse patient outcomes in observational studies compared with patients treated without GA. We assessed functional outcome in ischaemic stroke patients with large vessel anterior circulation occlusion undergoing endovascular thrombectomy under GA, versus thrombectomy not under GA (with or without sedation) versus standard care (ie, no thrombectomy), stratified by the use of GA versus standard care. Methods: For this meta-analysis, patient-level data were pooled from all patients included in randomised trials in PuMed published between Jan 1, 2010, and May 31, 2017, that compared endovascular thrombectomy predominantly done with stent retrievers with standard care in anterior circulation ischaemic stroke patients (HERMES Collaboration). The primary outcome was functional outcome assessed by ordinal analysis of the modified Rankin scale (mRS) at 90 days in the GA and non-GA subgroups of patients treated with endovascular therapy versus those patients treated with standard care, adjusted for baseline prognostic variables. To account for between-trial variance we used mixed-effects modelling with a random effect for trials incorporated in all models. Bias was assessed using the Cochrane method. The meta-analysis was prospectively designed, but not registered. Findings: Seven trials were identified by our search; of 1764 patients included in these trials, 871 were allocated to endovascular thrombectomy and 893 were assigned standard care. After exclusion of 74 patients (72 did not undergo the procedure and two had missing data on anaesthetic strategy), 236 (30%) of 797 patients who had endovascular procedures were treated under GA. At baseline, patients receiving GA were younger and had a shorter delay between stroke onset and randomisation but they had similar pre-treatment clinical severity compared with patients who did not have GA. Endovascular thrombectomy improved functional outcome at 3 months both in patients who had GA (adjusted common odds ratio (cOR) 1·52, 95% CI 1·09–2·11, p=0·014) and in those who did not have GA (adjusted cOR 2·33, 95% CI 1·75–3·10, p&lt;0·0001) versus standard care. However, outcomes were significantly better for patients who did not receive GA versus those who received GA (covariate-adjusted cOR 1·53, 95% CI 1·14–2·04, p=0·0044). The risk of bias and variability between studies was assessed to be low. Interpretation: Worse outcomes after endovascular thrombectomy were associated with GA, after adjustment for baseline prognostic variables. These data support avoidance of GA whenever possible. The procedure did, however, remain effective versus standard care in patients treated under GA, indicating that treatment should not be withheld in those who require anaesthesia for medical reasons