Discovery and validation of serologic biomarkers for the diagnosis and prognosis of invasive candidiasis by computational immunomics

Invasive candidiasis (IC) is an opportunistic systemic mycosis caused by Candida species (commonly Candida albicans) that continues to pose a significant public health problem worldwide. Despite great advances in antifungal therapy and changes in clinical practices, IC remains a major infectious cause of morbidity and mortality in severely immunocompromised or critically ill patients, and further accounts for substantial healthcare costs. Its impact on patient clinical outcome and economic burden could be ameliorated by timely initiation of appropriate antifungal therapy. However, early detection of IC is extremely difficult because of its unspecific clinical signs and symptoms, and the inadequate accuracy and time delay of the currently available diagnostic or risk stratification methods. In consequence, the diagnosis of IC is often attained in advanced stages of infection (leading to delayed therapeutic interventions and ensuing poor clinical outcomes) or, unfortunately, at autopsy. In addition to the difficulties encountered in diagnosing IC at an early stage, the initial therapeutic decision-making process is also hindered by the insufficient accuracy of the currently available tools for predicting clinical outcomes in individual IC patients at presentation. Therefore, it is not surprising that clinicians are generally unable to early detect IC, and identify those IC patients who are most likely to suffer fatal clinical outcomes and may benefit from more personalized therapeutic strategies at presentation. Better diagnostic and prognostic biomarkers for IC are thus needed to improve the clinical management of this life-threatening and costly opportunistic fungal infection...

A possibility for non-invasive diagnosis of superficial scald in 'Rocha' pear based on chlorophyll a fluorescence, colorimetry, and the relation between alpha-farnesene and conjugated trienols

This study aimed to identify physiological markers in superficially scalded 'Rocha' pear (Pyrus communis L 'Rocha') that would relate to chlorophyll a fluorescence (CF), allowing a non-invasive diagnosis of the disorder. Conditions chosen before shelf life provided two fruit groups with different developing patterns and severity of superficial scald: T fruit fully developed the disorder in storage, while C fruit developed it progressively throughout shelf life. Principal component analysis (PCA) of all the measured variables, and simple linear correlations among several major parameters and scald index (SI)/shelf life showed that scald and ripening/aging were concurring processes, and that it was not possible to isolate a particular variable that could deliver a direct non-invasive diagnosis of the disorder. For both fruit groups the SI resulted from the balance between the reducing power (OD200) and the content of conjugated trienols (CTos) and alpha-farnesene (alpha-Farn) in the fruit peel. At OD200 > 150 there was a linear relationship between CTos and OD200, suggesting that the level of antioxidants was self-adjusted in order to compensate the CTos level. However, at OD200 < 150 this relationship disappeared. A consistent linear relationship between dos and alpha-Farn existed throughout shelf life in both fruit groups, contrarily to the early storage stage, when those compounds do not relate linearly. The CF variables F-0, F-v/F-m, and the colorimetric variables, L* and h degrees were used in multi-linear regressions with other physiological variables. The regressions were made on one of the fruit groups and validated through the other. Reliable regressions to alpha-Farn and CTos were obtained (R approximate to 0.6; rmsec approximate to rmsep). Our results suggest that a model based on CF and colorimetric parameters could be used to diagnose non-invasively both the contents and the relationship between alpha-Farn and CTos and hence the stage of scald development. (C) 2011 Elsevier By. All rights reserved.

A possibility for non-invasive diagnosis of superficial scald in 'Rocha' pear based on chlorophyll a fluorescence, colorimetry, and the relation between alpha-farnesene and conjugated trienols

This study aimed to identify physiological markers in superficially scalded 'Rocha' pear (Pyrus communis L 'Rocha') that would relate to chlorophyll a fluorescence (CF), allowing a non-invasive diagnosis of the disorder. Conditions chosen before shelf life provided two fruit groups with different developing patterns and severity of superficial scald: T fruit fully developed the disorder in storage, while C fruit developed it progressively throughout shelf life. Principal component analysis (PCA) of all the measured variables, and simple linear correlations among several major parameters and scald index (SI)/shelf life showed that scald and ripening/aging were concurring processes, and that it was not possible to isolate a particular variable that could deliver a direct non-invasive diagnosis of the disorder. For both fruit groups the SI resulted from the balance between the reducing power (OD200) and the content of conjugated trienols (CTos) and alpha-farnesene (alpha-Farn) in the fruit peel. At OD200 > 150 there was a linear relationship between CTos and OD200, suggesting that the level of antioxidants was self-adjusted in order to compensate the CTos level. However, at OD200 < 150 this relationship disappeared. A consistent linear relationship between dos and alpha-Farn existed throughout shelf life in both fruit groups, contrarily to the early storage stage, when those compounds do not relate linearly. The CF variables F-0, F-v/F-m, and the colorimetric variables, L* and h degrees were used in multi-linear regressions with other physiological variables. The regressions were made on one of the fruit groups and validated through the other. Reliable regressions to alpha-Farn and CTos were obtained (R approximate to 0.6; rmsec approximate to rmsep). Our results suggest that a model based on CF and colorimetric parameters could be used to diagnose non-invasively both the contents and the relationship between alpha-Farn and CTos and hence the stage of scald development. (C) 2011 Elsevier By. All rights reserved.

Objective evaluation of surgical competency for minimally invasive surgery with a collection of simple tests

Objective: This study aims at determining if a collection of 16 motor tests on a physical simulator can objectively discriminate and evaluate practitioners' competency level, i.e. novice, resident, and expert. Methods: An experimental design with three study groups (novice, resident, and expert) was developed to test the evaluation power of each of the 16 simple tests. An ANOVA and a Student Newman-Keuls (SNK) test were used to analyze results of each test to determine which of them can discriminate participants' competency level. Results: Four of the 16 tests used discriminated all of the three competency levels and 15 discriminated at least two of the three groups (α= 0.05). Moreover, other two tests differentiate beginners\' level from intermediate, and other seven tests differentiate intermediate level from expert. Conclusion: The competency level of a practitioner of minimally invasive surgery can be evaluated by a specific collection of basic tests in a physical surgical simulator. Reduction of the number of tests needed to discriminate the competency level of surgeons can be the aim of future research.

Non-invasive winding fault detection for induction machines based on stray flux magnetic sensors

Non-intrusive monitoring of health state of induction machines within industrial process and harsh environments poses a technical challenge. In the field, winding failures are a major fault accounting for over 45% of total machine failures. In the literature, many condition monitoring techniques based on different failure mechanisms and fault indicators have been developed where the machine current signature analysis (MCSA) is a very popular and effective method at this stage. However, it is extremely difficult to distinguish different types of failures and hard to obtain local information if a non-intrusive method is adopted. Typically, some sensors need to be installed inside the machines for collecting key information, which leads to disruption to the machine operation and additional costs. This paper presents a new non-invasive monitoring method based on GMRs to measure stray flux leaked from the machines. It is focused on the influence of potential winding failures on the stray magnetic flux in induction machines. Finite element analysis and experimental tests on a 1.5-kW machine are presented to validate the proposed method. With time-frequency spectrogram analysis, it is proven to be effective to detect several winding faults by referencing stray flux information. The novelty lies in the implement of GMR sensing and analysis of machine faults.

Utility and safety of invasive (fractional flow reserve) and non-invasive (cardiac magnetic resonance imaging) diagnostic tests in patients with NSTEMI

A prospective randomised controlled clinical trial of treatment decisions informed by invasive functional testing of coronary artery disease severity compared with standard angiography-guided management was implemented in 350 patients with a recent non-ST elevation myocardial infarction (NSTEMI) admitted to 6 hospitals in the National Health Service. The main aims of this study were to examine the utility of both invasive fractional flow reserve (FFR) and non-invasive cardiac magnetic resonance imaging (MRI) amongst patients with a recent diagnosis of NSTEMI. In summary, the findings of this thesis are: (1) the use of FFR combined with intravenous adenosine was feasible and safe amongst patients with NSTEMI and has clinical utility; (2) there was discordance between the visual, angiographic estimation of lesion significance and FFR; (3). The use of FFR led to changes in treatment strategy and an increase in prescription of medical therapy in the short term compared with an angiographically guided strategy; (4) in the incidence of major adverse cardiac events (MACE) at 12 months follow up was similar in the two groups. Cardiac MRI was used in a subset of patients enrolled in two hospitals in the West of Scotland. T1 and T2 mapping methods were used to delineate territories of acute myocardial injury. T1 and T2 mapping were superior when compared with conventional T2-weighted dark blood imaging for estimation of the ischaemic area-at-risk (AAR) with less artifact in NSTEMI. There was poor correlation between the angiographic AAR and MRI methods of AAR estimation in patients with NSTEMI. FFR had a high accuracy at predicting inducible perfusion defects demonstrated on stress perfusion MRI. This thesis describes the largest randomized trial published to date specifically looking at the clinical utility of FFR in the NSTEMI population. We have provided evidence of the diagnostic and clinical utility of FFR in this group of patients and provide evidence to inform larger studies. This thesis also describes the largest ever MRI cohort, including with myocardial stress perfusion assessments, specifically looking at the NSTEMI population. We have demonstrated the diagnostic accuracy of FFR to predict reversible ischaemia as referenced to a non-invasive gold standard with MRI. This thesis has also shown the futility of using dark blood oedema imaging amongst all comer NSTEMI patients when compared to novel T1 and T2 mapping methods.

Occurrence of plastic debris in the stomach of the invasive crab Eriocheir sinensis

The Chinese mitten crab is known as a pest causing damage to fishing gears and fish. On the other hand, this highly invasive species is considered a delicacy by Asian migrants and therefore commercially fished and sold in many countries. The ingestion of plastic by the Chinese mitten crab Eriocheir sinensis from the Baltic coastal waters (Poland) and the Tagus Estuary (Portugal) was studied based on stomach content analysis. As many as 13% of the 302 analysed males and females (38.07–89.07 mm carapace width) from both regions, contained microplastic in the form of strands and balls. Most of them were transparent. Ingested plastic particles were identified as fragments of fishing gears. Contamination with plastic may have a negative impact on this species as well as on higher trophic levels feeding on crabs.

Phytotoxic activity of compounds from Moutabea guianensis aubl. on Amazonian invasive species.

Este estudo teve como objetivo estabelecer as variações na atividade fitotóxica dos extratos hexânico, acetato de etila e metanólico das raízes de Moutabea guianensis, e das substâncias cafeato de metila e escopoletina isoladas do extrato acetato de etila, variando a concentração e as espécies receptores. Foram desenvolvidos bioensaios de atividades fitotóxicas de germinação (a 25 °C e 12 horas de fotoperíodo) e de desenvolvimento da radícula e do hipocótilo (25 °C e 24 horas de fotoperíodo). A germinação das sementes de Mimosa pudica foi sensível aos extratos hexânico, acetato de etila e metanólico a 1% (w/v), com efeitos de inibição em 92%, 100% e 100%, respectivamente. A análise comparativa da atividade fitotóxica das substâncias testadas revelou que a escopoletina apresentou um potencial de inibição mais elevado no bioensaio de germinação de sementes frente a Mimosa pudica. Senna obtusifolia não foi sensível às substâncias testadas. Cafeato de metila apresentou maior potencial de inibição no bioensaio de desenvolvimento da radícula e hipocótilo, e a intensidade dos efeitos alelopáticos variou com as concentrações.

Practical Management of the Endangered African Wild Dog (Lycaon Pictus): Implementation of Research Methodologies, Management Tools and Validation of Non-Invasive Endocrinology Applications

The porpoise of this study was to implement research methodologies and assess the effectiveness and impact of management tools to promote best practices for the long term conservation of the endangered African wild dog (Lycaon pictus). Different methods were included in the project framework to investigate and expand the applicability of these methodologies to free-ranging African wild dogs in the southern African region: ethology, behavioural endocrinology and ecology field methodologies were tested and implemented. Additionally, research was performed to test the effectiveness and implication of a contraceptive implant (Suprenolin) as a management tool for the species of a subpopulation hosted in fenced areas. Attention was especially given to social structure and survival of treated packs. This research provides useful tools and advances the applicability of these methods for field studies, standardizing and improving research instruments in the field of conservation biology and behavioural endocrinology. Results reported here provide effective methodologies to expand the applicability of non-invasive endocrine assessment to previously prohibited fields, and validation of sampling methods for faecal hormone analysis. The final aim was to fill a knowledge gap on behaviours of the species and provide a common ground for future researchers to apply non-invasive methods to this species research and to test the effectiveness of the contraception on a managed metapopulation.

Percutaneous Cement Discoplasty: Biomechanical and clinical assessment of a minimally invasive treatment of lumbar intervertebral disc disease

With population ageing, spine diseases have an increasing prevalence and induce high economic and social costs. The development of minimally invasive surgeries allows reducing the surgery-associated risks in elderly and polymorbid patients, and save costs by treating more patients in shorter time and reducing the complications. Percutaneous Cement Discoplasty (PCD) is a minimally invasive technique developed to treat highly degenerated intervertebral discs exhibiting a vacuum phenomenon. Filling the disc with bone cement creates a stand-alone spacer which partially restores the disc height and re-opens the foraminal space. PCD has recently been introduced to clinical use. However, the spine biomechanics following this treatment remained unravelled. The aim of this PhD thesis is to bridge the clinical experience with in vitro methodologies, to provide a multilateral evaluation of PCD outcome and a better understanding of its impact on the spine biomechanics, and of its possible contraindications. Firstly, a suitable in vitro porcine model to test the biomechanics of discoplasty by comparing specimens in the preoperative and postoperative conditions was developed. The methodology was then applied to investigate the biomechanics of discoplasty in cadaveric human segments. The in vitro specimens were mechanically investigated in flexion and extension, while a DIC system quantified the range of motion, disc height, and strains on the disc surface. Then, a versatile tool to measure the impact of discoplasty on the foramen space was developed and applied both to clinical and experimental work. The vertebrae reconstructed from CT scans were registered to match the loading configuration, using ex vivo DIC measurements under loading. The foramen volumetric changes caused by PCD was measured using a 3D geometrical method clinically developed by the research group. In conclusion, this project significantly extended the understanding of PCD biomechanics, highlighting its benefits in the treatment of advanced cases of intervertebral disc degeneration.

The environmental DNA in the risk assessment and decision making processes for the invasive species management in agri-food sector, hydraulic security and biodiversity conservation

The use of environmental DNA (eDNA) analysis as a monitoring tool is becoming more and more widespread. The eDNA metabarcoding methods allow rapid community assessments of different target taxa. This work is focused on the validation of the environmental DNA metabarcoding protocol for biodiversity assessment of freshwater habitats. Scolo Dosolo was chosen as study area and three sampling points were defined for traditional and eDNA analyses. The gutter is a 205 m long anthropic canal located in Sala Bolognese (Bologna, Italy). Fish community and freshwater invertebrate metazoans were the target groups for the analysis. After a preliminary study in summer 2019, 2020 was devoted to the sampling campaign with winter (January), spring (May), summer (July) and autumn (October) surveys. Alongside with the water samplings for the eDNA study, also traditional fish surveys using the electrofishing technique were performed to assess fish community composition; census on invertebrates was performed using an entomological net and a surber sampler. After in silico analysis, the MiFish primer set amplifying a fragment of the 12s rRNA gene was selected for bony fishes. For invertebrates the FWHF2 + FWHR2N primer combination, that amplifies a region of the mitochondrial coi gene, was chosen. Raw reads were analyzed through a bioinformatic pipeline based on OBITools metabarcoding programs package and QIIME2. The OBITools pipeline retrieved seven fish taxa and 54 invertebrate taxa belonging to six different phyla, while QIIME2 recovered eight fish taxa and 45 invertebrate taxa belonging to the same six phyla as the OBITools pipeline. The metabarcoding results were then compared with the traditional surveys data and bibliographic records. Overall, the validated protocol provides a reliable picture of the biodiversity of the study area and an efficient support to the traditional methods.

Induction of Hebbian associative plasticity through paired non-invasive brain stimulation of premotor-motor areas to elucidate the network's functional role

The ventral premotor cortex (PMv) is believed to play a pivotal role in a multitude of visuomotor behaviors, such as sensory-guided goal-directed visuomotor transformations, arbitrary visuomotor mapping, and hyper-learnt visuomotor associations underlying automatic imitative tendencies. All these functions are likely carried out through the copious projections connecting PMv to the primary motor cortex (M1). Yet, causal evidence investigating the functional relevance of the PMv-M1 network remains elusive and scarce. In the studies reported in this thesis we addressed this issue using a transcranial magnetic stimulation (TMS) protocol called cortico-cortical paired associative stimulation (ccPAS), which relies on multisite stimulation to induce Hebbian spike-timing dependent plasticity (STDP) by repeatedly stimulating the pathway connecting two target areas to manipulate their connectivity. Firstly, we show that ccPAS protocols informed by both short- and long-latency PMv-M1 interactions effectively modulate connectivity between the two nodes. Then, by pre-activating the network to apply ccPAS in a state-dependent manner, we were able to selectively target specific functional visuo-motor pathways, demonstrating the relevance of PMv-M1 connectivity to arbitrary visuomotor mapping. Subsequently, we addressed the PMv-to-M1 role in automatic imitation, and demonstrated that its connectivity manipulation has a corresponding impact on automatic imitative tendencies. Finally, by combining dual-coil TMS connectivity assessments and ccPAS in young and elderly individuals, we traced effective connectivity of premotor-motor networks and tested their plasticity and relevance to manual dexterity and force in healthy ageing. Our findings provide unprecedent causal evidence of the functional role of the PMv-to-M1 network in young and elderly individuals. The studies presented in this thesis suggest that ccPAS can effectively modulate the strength of connectivity between targeted areas, and coherently manipulate a networks’ behavioral output. Results open new research prospects into the causal role of cortico-cortical connectivity, and provide necessary information to the development of clinical interventions based on connectivity manipulation.

Plasma-activated liquids as promising tools for non-invasive selective treatment of epithelial ovarian cancer

Plasma medicine is a branch of plasma-promising biomedical applications that uses cold atmospheric plasma (CAP) as a therapeutic agent in treating a wide range of medical conditions including cancer. Epithelial ovarian cancer (EOC) is a highly malignant and aggressive form of ovarian cancer, and most patients are diagnosed at advanced stages which significantly reduces the chances of successful treatment. Treatment resistance is also common, highlighting the need for novel therapies to be developed to treat EOC. Research in Plasma Medicine has revealed that plasma has unique properties suitable for biomedical applications and medical therapies, including responses to hormetic stimuli. However, the exact mechanisms by which CAP works at the molecular level are not yet fully understood. In this regard, the main goal of this thesis is to identify a possible adjuvant therapy for cancer, which could exert a cytotoxic effect, without damaging the surrounding healthy cells. An examination of different plasma-activated liquids (PALs) revealed their potential as effective tools for significantly inhibiting the growth of EOC. The dose-response profile between PALs and their targeted cytotoxic effects on EOC cells without affecting healthy cells was established. Additionally, it was validated that PALs exert distinct effects on different subtypes of EOC, possibly linked to the cells' metabolism. This suggests the potential for developing new, personalized anticancer strategies. Furthermore, it was observed that CAP treatment can alter the chemistry of a biomolecule present in PAL, impacting its cytotoxic activity. The effectiveness of the treatment was also preliminarily evaluated in 3D cultures, opening the door for further investigation of a possible correlation between the tumor microenvironment and PALs' resistance. These findings shed light on the intricate interplay between CAP and the liquid substrate and cell behaviour, providing valuable insights for the development of a novel and promising CAP-based cancer treatment for clinical application.