Developing advanced MR imaging to assess spinal cord function and tract integrity.

The overall purpose of this thesis is to develop a way to match diffusion and functional acquisition techniques in the spinal cord (SC) in order to offer a comprehensive assessment of factors responsible for functional and structural integrity. I began by optimising a pipeline to acquire and process spinal functional data and I finished by matching the functional information with that derived from diffusion imaging (DI) performed during the same scan session as fM RI. In order to characterize the interactions between local structural connections (derived from DI) and functional activation of the SC it has been necessary to develop an imaging protocol that acquires transverse SC images with both modalities, matching their spatial and geometrical characteristics. This is because transverse cord images possess the relevant anatomical information in terms of grey-white matter structure and allow better localisation of the functional response and structural properties within the spinal cord. My main contribution to the field has been: 1. To demonstrate that it is possible to use the “ZOOM” sequence for spinal fM RI 2. To characterize the signal obtained and the comparison of different image analysis approaches 3. To propose a final pipeline for acquisition and analysis of spinal fM RI 4. To demonstrate that there is a dependency of pathological functional and structural changes The same ZOOM-EPI sequence has been applied for all the functional studies reported in this thesis. The outcome of the optimisation for spinal fMRI has been matched by a DI protocol, using standard DI parameters for spinal microstructural characterization and constitutes the final MR protocol used in a pilot study including a group of healthy controls and a group of patients affected by multiple sclerosis (MS). Based on the gathered experience and results from data acquired and analysed over the years I have concluded with some recommendations for future studies and development strategies for structural and functional MRI of the spinal cor

qCLEF: A Proposal to Evaluate Quantum Annealing for Information Retrieval and Recommender Systems

Quantum Computing (QC) has been a focus of research for many researchers over the last few years. As a result of technological development, QC resources are also becoming available and usable to solve practical problems in the Information Retrieval (IR) and Recommender Systems (RS) fields. Nowadays IR and RS need to perform complex operations on very large datasets. In this scenario, it could be possible to increase the performance of these systems both in terms of efficiency and effectiveness by employing QC and, especially, Quantum Annealing (QA). The goal of this work is to design a Lab composed of different Shared Tasks that aims to: compare the performance of QA approaches with respect to their counterparts using traditional hardware;identify new ways of formulating problems so that they can be solved with quantum annealers;allow researchers from to different fields (e.g., Information Retrieval, Operations Research..) to work together and learn more about QA technologies. This Lab uses the QC resources provided by CINECA, one of the most important computing centers worldwide, thanks to an already met agreement. In addition, we also show a possible implementation of the required infrastructure which uses Docker containers and the Kubernetes orchestrator to ensure scalability, fault tolerance and that can be deployed on the cloud

Brewers' spent grain as substrates for production of cellulolytic and hemicellulolytic enzymes by different Aspergillus species

Brewers' spent grain (BSG) is the major by-product of the brewing industry, representing around 85% of the total by-products generated. It is a lignocellulosic material containing about 38% cellulose, 29% hemicellulose, chiefly arabinoxylans, and 13% lignin. The production of cellulolytic and hemicellulolytic enzymes using this material as substrate represent an eco-friendly strategy for the lignocellulosic biomass hydrolysis, generating fermentable sugars that can be converted into high- added value products, such as bioethanol, lactic acid, xylitol and others. Thus, this work aimed to evaluate the potential of cellulolytic and hemicellulolytic enzymes production by some Aspergillus species cultivated in BSG. Fungi were grown in minimum media, pH 6.5, with 1% BSG and inoculum was done with 107spores/mL, cultivated at 30°C, 120 rpm, for 5 days. Every 24 hours 2 mL of the samples were collected. The enzymatic activity was performed after the incubation of the crude extract with 1% Linear arabinan, Xylan from beechwood, Xyloglucan, Locust bean gum and CMC, at 50°C for 60 minutes and the reducing sugars were determined using dinitrosalicylic acid (DNS). Synthetic substrates (2 mM of PNP--L-arabinofuranoside, PNP--D-xylopyranoside, PNP--Dglucopyranoside and PNP--D-cellobioside) were also used at the same conditions. The extract from A. niveus showed the best arabinanase (0.284 U/mL) and -glucosidase (0.126 U/mL) activities after 48 and 96 hours of cultivation, respectively. On the other hand, the extract from A. brasiliensis presented the best activities of -L-arabinofuranosidase (0.129 U/mL), -xylosidase (0.265 U/mL) and xylanase (2.15 U/mL) when cultivated for 48 hours. After 72 hours, this fungus also showed the best activities for xyloglucanase (1.06 U/mL), mannanase (0.617 U/mL) and endoglucanase (0.254 U/mL). The extract produced by A. flavus presented the best cellobiohydrolase activity with 0.113 U/mL after 120 hours of cultivation. It is important to mention that A. awamori, A. clavatus and A. terreus also showed good levels of different enzymes produced but they were not the best producers. These data suggest the great potential of different cellulolytic and hemicellulolytic enzymes production using BSG as substrate, which represents an eco-friendly destination for the residues and can generate high-added value products with great biotechnological application.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Institutos Nacionais de Ciência e Tecnologia (INCT)Fundação para a Ciência e a Tecnologia (FCT)info:eu-repo/semantics/publishedVersio

Production of an enzymatic cocktail by Aspergillus awamori grown on corn straw with stirred tank bioreactor

Increased agroindustrial activity has led to the accumulation of large amounts of lignocellulosic material (LCM). LCM is nature's most abundant source of renewable carbon, representing a valuable industrial substrate with potential for many applications. Thus, the objective of this work was to screen for different holocellulases and to analyze the production of an Aspergillus awamori enzyme cocktail grown in corn straw (CS) using a stirred tank bioreactor. Screening was performed with A. clavatus, A. flavus, A. terreus, A. niveus, A. awamori and A. brasiliensis cultivated in minimal medium (MM), with 1% CS at 30 ºC or 37 ºC (for A. niveus), 120 rpm, for 5 days. Xylanase (XYN) and endoglucanase (EG) activities were evaluated by formation of reducing sugars using dinitrosalicylic acid (DNS). Cellobiohydrolase (CBH), -glucosidase (BGL) and -xylosidase (BXL) were determined by cleavage of PNP--D-cellobioside, PNP--D-glucopyranoside and PNP--D- xylopyranoside, respectively. After screening, a pre-inoculum was prepared with the best enzyme producer using a 500 mL MM flask and incubated at 30 °C, 120 rpm for 48 hours. The increase of enzyme production was performed in a Benchtop BioFlo 310 bioreactor, with 4.5 L of MM and 1% of CS, and was then inoculated the best enzyme producer. Cultivation was performed at 30 °C, pH 6.5, 275 rpm, air flow 2 v.v.m., for 5 days. During the screening, all fungi presented EG, CBH, BGL, XYN and BXL activities. However, A. awamori was chosen to continue the experiments because of its BXL activity which was 12.6 times higher than that produced by A. niveus. At the scale-up stage, XYN production (47.80 U/ mL) increased 4.1-fold compared to flask activity (11.52 U/mL). BXL also showed 1.6-times higher activity, as well as EG, CBH and BGL, which improved 2.3, 3.3 and 1.2 times their activities, respectively. It was concluded that the staggering of cocktail production improved the enzymatic activities and that corn straw is an excellent source of induction. Furthermore, this cocktail has the potential to be applied in the hydrolysis of different LCM due to the range of holocellulases present.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Institutos Nacionais de Ciência e Tecnologia (INCT)Fundação para a Ciência e a Tecnologia (FCT)info:eu-repo/semantics/publishedVersio

Sex-related mortality differences in young adult septic shock patients

Septic shock survival rate and host immune response are intimately interlaced. In the last years, biological and pre-clinical studies demonstrated sex-specific differences in the immune response to infection. In the hypothesis that survival rate is related to the hormonal framework, the aim of the present study was to observe sex-specific differences in 28-day mortality rate between women of childbearing potential and same-age men. This multicenter study was conducted in six Italian intensive care units (ICUs). We enrolled consecutive patients ≤ 55 years old admitted to the Intensive Care Unit from January 2011 to January 2020, who were diagnosed with septic shock at the time of ICU admission or during the ICU stay. We gathered baseline characteristics and outcomes. The primary outcome was 28-day mortality; secondary outcomes included ICU mortality, in-hospital mortality and length of stay in the ICU and in the hospital. Moreover, data from >55 years old patients were collected and analyzed. We enrolled 361 young patients with septic shock: 215 were males (60%) and 146 females (40%). While baseline and ICU characteristics were similar between the two groups, males had a higher 28-day mortality rate (39.5% vs. 29%, p = 0.035), ICU mortality rate (49% vs. 38%, p = 0.040) and hospital mortality rate (61% vs. 50%, p = 0.040) as compared to females. Findings were confirmed in patients with septic shock at ICU admission. Young adult females developed septic shock less frequently than young males, displaying a reduced mortality rate as compared to that of their same-age male counterpart. These findings may stimulate future research and therapies

Synergistic effect of static compliance and d-dimers to predict outcome of patients with covid-19-ards: A prospective multicenter study

The synergic combination of D-dimer (as proxy of thrombotic/vascular injury) and static compliance (as proxy of parenchymal injury) in predicting mortality in COVID-19-ARDS has not been systematically evaluated. The objective is to determine whether the combination of elevated D-dimer and low static compliance can predict mortality in patients with COVID-19-ARDS. A “training sample” (March–June 2020) and a “testing sample” (September 2020–January 2021) of adult patients invasively ventilated for COVID-19-ARDS were collected in nine hospitals. D-dimer and compliance in the first 24 h were recorded. Study outcome was all-cause mortality at 28-days. Cutoffs for D-dimer and compliance were identified by receiver operating characteristic curve analysis. Mutually exclusive groups were selected using classification tree analysis with chi-square automatic interaction detection. Time to death in the resulting groups was estimated with Cox regression adjusted for SOFA, sex, age, PaO2/FiO2 ratio, and sample (training/testing). “Training” and “testing” samples amounted to 347 and 296 patients, respectively. Three groups were identified: D-dimer ≤ 1880 ng/mL (LD); D-dimer > 1880 ng/mL and compliance > 41 mL/cmH2O (LD-HC); D-dimer > 1880 ng/mL and compliance ≤ 41 mL/cmH2O (HD-LC). 28-days mortality progressively increased in the three groups (from 24% to 35% and 57% (training) and from 27% to 39% and 60% (testing), respectively; p < 0.01). Adjusted mortality was significantly higher in HD-LC group compared with LD (HR = 0.479, p < 0.001) and HD-HC (HR = 0.542, p < 0.01); no difference was found between LD and HD-HC. In conclusion, combination of high D-dimer and low static compliance identifies a clinical phenotype with high mortality in COVID-19-ARDS

Antibody Response to SARS-CoV-2 Vaccination in Patients following Allogeneic Hematopoietic Cell Transplantation

Vaccines against SARS-CoV-2 have been rapidly approved. Although pivotal studies were conducted in healthy volunteers, little information is available on the safety and efficacy of mRNA vaccines in immunocompromised patients, including recipients of allogeneic hematopoietic cell transplantation (allo-HCT). Here we used a novel assay to analyze patient- and transplantation-related factors and their influence on immune responses to SARS-CoV-2 vaccination over an extended period (up to 6 months) in a large and homogenous group of allo-HCT recipients at a single center in Switzerland. We examined longitudinal antibody responses to SARS-CoV-2 vaccination with BNT162b2 (BioNTech/Pfizer) and mRNA-1273 (Moderna) in 110 allo-HCT recipients and 86 healthy controls. Seroprofiling recording IgG, IgA, and IgM reactivity against SARS-CoV-2 antigens (receptor-binding domain, spike glycoprotein subunits S1 and S2, and nucleocapsid protein) was performed before vaccination, before the second dose, and at 1, 3, and 6 months after the second dose. Patients were stratified to 3 groups: 3 to 6 months post-allo-HCT, 6 to 12 months post-allo-HCT, and >12 months post-allo-HCT. Patients in the 3 to 6 months and 6 to 12 months post-allo-HCT groups developed significantly lower antibody titers after vaccination compared with patients in the >12 months post-allo-HCT group and healthy controls (P 65 years (P = .030), those receiving immunosuppression for prevention or treatment of graft-versus-host disease (GVHD) (P = .033), and patients with relapsed disease (P = .014) displayed low humoral immune responses to the vaccine. In contrast, the intensity of the conditioning regimen, underlying disease (myeloid/lymphoid/other), and presence of chronic GVHD had no impact on antibody levels. Antibody titers achieved the highest levels at 1 month after the second dose of the vaccine but waned substantially in all transplantation groups and healthy controls over time. This analysis of long-term vaccine antibody response is of critical importance to allo-HCT recipients and transplant physicians to guide treatment decisions regarding revaccination and social behavior during the SARS-CoV-2 pandemic. Keywords: Allogeneic hematopoietic cell transplantation; SARS-CoV-2; Vaccinatio