Bora wind effects on common structures in the Vipava valleyMarija Bervida
, 2020, doctoral dissertation
Abstract: Strong and gusty north-east wind called Bora is common in south-west regions of Slovenia, as well as along the Adriatic coast. Its intermittent behavior, related to variable strength, frequency and duration, has brought out scientific curiosity for decades. Bora affects human life and causes problems for structures built in Bora affected areas. In Slovenia, Bora is the strongest in the Vipava valley. The motivation for this research is the need to evaluate Bora wind effects on structures, commonly found in the Vipava valley region, using a high resolution computational fluid dynamics (CFD) modeling approach. To date, there are several experimental and computational constraints for accurate representation of Bora in a CFD model, therefore, the main aim of this dissertation is to build foundations for Bora wind simulations using CFD and its method of finite
volumes. The dissertation incorporates the analysis of experimental measurements of Bora wind, as well as numerical modeling studies.
Vertical mean wind speed profile characteristics of Bora were analyzed based on experimental measurements at Razdrto just above the Vipava valley. The obtained results contributed to the choice of Bora mean wind profiles applied at the inflow of computational models. Guidelines regarding the choice of the associated wind profile parameters were given and a new relationship between these parameters was found. As orographic barriers to the north of the Vipava valley
are known to give rise to Bora and to define the specific properties of the Bora flow, numerical modeling studies were in the first place focused on the implementation of the real-scale complex terrain into a CFD model. Simulation of wind flow over orographic barrier in Vipava valley was performed using Raynolds averaged Navier-Stokes approach, providing a first estimation of the flow field over a small hill of
As resolving the turbulence characteristics of Bora is very important for the estimation of wind loads on structures, modeling studies converged towards a more appropriate approach - Large eddy simulations (LES). A crucial step in setting up an accurate LES is the generation of appropriate inflow, which was investigated for the case of atmospheric boundary layer (ABL) flow. The synthetic method PRFG^3 for the generation of unsteady inflow was tested and adapted as a source of an ABL flow with desired turbulence flow properties. Based on its performance, in particular on adequate reproduction of target turbulence intensities and length scales, it was found that PRFG^3 method may be used to generate velocity inflow with desired turbulence properties in LES. Finally, simulations of wind flow coming from Bora direction over the Vipava valley were performed with the aim to depict the effects of underlying orography on the flow within and above the valley. Modeling results were found to be comparable with the results of lidar based remote sensing of vertical atmospheric structures within and above the valley.
Keywords: Vipava valley, Bora wind, Wind profile, Orography, Atmospheric boundary layer, Computational fluid dynamics, Numerical simulations
Published: 17.06.2020; Views: 1625; Downloads: 16
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FUNCTIONALIZED NANOBODIES AS DIAGNOSTIC REAGENTS FOR THE DETECTION OF TOXIC MICROALGAESandra Oloketuyi
, 2020, doctoral dissertation
Abstract: Early detection and monitoring of toxic microalgae remains a challenge that will be necessary to overcome for understanding harmful algal bloom events and their consequent ecological and environmental impacts. Although there are diagnostic techniques based on microscopy, fluorescence in situ hybridization (FISH), DNA microarrays, real-time PCR, sandwich hybridization assays employed for the detection of harmful algal species, such techniques are not suitable for field monitoring and especially for the quantification of Alexandrium minutum due to abundance of cryptic species that cannot be differentiated based on morphology or genomic traits. These approaches are also time-consuming and laborious, hence there is need for alternative simple, rapid and cost-effective methods. In this study, our aim was to develop different nanobody-based capture strategies for the detection of A. minutum. Nanobodies were successfully displayed on the surface of Escherichia coli to facilitate detection of A. minutum. The method is simple and cost effective as no antibody purification step is necessary. As an alternative, A. minutum was quantified by exploiting the peroxidase activity of a G-quadruplex DNAzyme covalently bound to nanobodies and by means of a label free electrochemical immunosensor which exploit nanobodies bound via an irreversible SpyTag-SpyCatcher system as the specific immunocapture element. Such immunosensor was prepared by immobilizing the SpyTagged anti-A. minutum nanobody (SpyTagged C1) by means of a selfassembled monolayer (SAMs) of L- cysteine (L-Cys) displayed onto a gold nanoparticle-modified glassy carbon electrode. Electrochemical Impedance Spectroscopy (EIS) was performed to measure the electrical response of the circuit as the function of A. minutum immunocaptured cells. The results of EIS studies confirmed that the sensing chip detected A. minutum selectively, exhibited a wide dynamic range spanning from 103 to 109 cell L-1 and a limit of detection of 3.1× 103 cell L-1. The immunosensor data can be recorded and then analyzed with a portable potentiostat. Such device can be interfaced with a smart phone, a condition suitable for the rapid A. minutum quantification in situ.
Keywords: Alexandrium minutum, nanobodies, bioreagents, immunosensor, toxic microalgae
Published: 17.06.2020; Views: 1612; Downloads: 79
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DEVELOPMENT OF A NOVEL PCR-BASED ASSAY FOR HIGH-RISK HUMAN PAPILLOMAVIRUS DETECTION AND GENOTYPING IN SELF COLLECTED CERVICOVAGINAL SAMPLES: A NEW POSSIBILITY FOR THE CERVICAL CANCER SCREENINGAlice Avian
, 2020, doctoral dissertation
Abstract: Human Papillomavirus (HPV) infection is the causative agent for the invasive cervical cancer and its precancerous lesions, furthermore, there are growing evidences of HPV being a relevant factor in other anogenital cancers as well as head and neck cancers. Most sexually active women become infected with HPV at least once in their lifetime, but less than 10% of women becomes persistently infected, and it is precisely the persistent infection that contributes to the development of cervical cancer.
The preventive effect of cervical cancer screening largely depends in the high women participation and coverage; indeed, a large number of cervical cancers diagnoses normally arise among under-screened and unscreened women. Increase in the screening coverage is essential to improve the effectiveness of cervical screening programmes.
The main purpose of this PhD project was to solve some of the most relevant problems in the cervical cancer screening programmes, as the increase of cost-effectiveness and the amelioration of the screening coverage.
My work was focused on the development and validation of the first Ulisse BioMed S.p.A. product, the HPV Selfy™ test, an innovative PCR-based kit for the direct detection and genotyping of 12 high-risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58 and 59) and 2 possible/probable high-risk (66 and 68), specifically optimized for the analysis of self-collected vaginal specimens.
The core of this innovative test is based on high-resolution melting (HRM) analysis, a recently developed technique for fast, high-throughput post-PCR analysis of variance in nucleic acid sequences, that characterizes the amplicons by studying thermal denaturation of double-stranded DNA. Based on this approach and through the design of different HPV type-specific primer pairs and the development of a specific master mix, unique melting peaks in a single fluorescence channel were obtained, allowing the multiple detection and genotyping of 14 HPV types in a single PCR well.
Three different clinical studies have been carried out to validate the assay on the vaginal self-collected samples with truly amazing results regarding the assay’s performance, but also for self-sampling acceptability by women. Moreover, data collected in these studies suggest a future possible use of this test for the hard-to-reach women, as an alternative of the conventional clinician-collected sample, in order to increase the cervical cancer screening coverage.
Keywords: Human Papillomavirus, HPV test, cervical cancer screening, prevention, diagnostic test, High resolution melting, HRM, genotyping, PCR, Self-sampling, clinical validation.
Published: 17.06.2020; Views: 1182; Downloads: 21
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Managing karst in Coastal British Columbia, CanadaPaul Andre Griffiths
, 2020, doctoral dissertation
Abstract: This thesis provides a detailed description and analysis of the system used for managing karst in the forests of coastal British Columbia (BC), where the major land- use activity is industrial forestry. In 2004, BC shifted from a more prescriptive forest management model (the Forest Practices Code) to a less regulated, results-based approach based primarily on the Forest and Range Practices Act (FRPA). The dissertation examines how this results-based management approach for forest resources has worked – or not worked – with respect to karst.
The research focused on the five key realms of an environmental management system as defined by the International Standards Organization (ISO 14001 standard): 1) Legislation and Policy, 2) Planning, 3) Implementation, 4) Checking/Corrective Action, and 5) Management Review. The research also examined the roles of professional reliance (another major foundational element of the FRPA model), karst research, and organizational capacity as external factors which influence on the functioning of the karst management system. A combination of interviews, surveys, document reviews and field observations were used to collect qualitative information relevant to all aspects of the karst management system.
This research reveals inadequacies in all five realms of BC’s current karst management framework, including gaps in legislation, a lack of implementation of existing standards and guidelines, and non-existent effectiveness and compliance monitoring. The results suggest that BC’s shift to ‘self-regulation’ has yielded unsatisfactory results so far for karst resources and has hindered progress toward implementing a fully integrated science-based ecosystem approach to karst management in the study area. Professional reliance failures are identified as one of the key factors contributing to a breakdown of the management system for karst.
This is the first comprehensive study that examines the systems and processes used for managing karst in coastal BC, and consolidates knowledge for government, industry, and others that wish to study or better understand BC’s approach and methods for managing karst. The findings will be useful for private and public forest sector organizations endeavoring to implement fully-functional and effective systems for managing karst in a forestry context. This information may also have more specific applications for managing karst.
Keywords: karst ecosystems, protection and management, legislation, policies, standards and guidelines, environmental degradation, forestry impacts, professional reliance, British Columbia, Canada
Published: 02.03.2020; Views: 1444; Downloads: 27
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Dissecting the role of REEP1 in preventing Tau-mediated neurodegeneration in a D.melanogaster Alzheimer's disease modelAlessio Guglielmi
, 2019, doctoral dissertation
Abstract: Tau is natively an unfolded protein that promotes the assembly and the stability of the
axonal microtubules in the central nervous system. Increased formation of Tau protein
aggregates has been causatively implicated in several neurodegenerative diseases called
tauopathies. In the present study, we used the Drosophila melanogaster system to express
the longest isoform of human Tau (2N4R) in the nervous system of adult flies, recreating
the main features of the human pathology. Herein, this Tau-mediated neurodegeneration
model was used as a platform to perform genetic screenings to identify putative modifiers
of Tau toxicity. Our strategy exploited the modulation of genes considered as risk factors of
Alzheimer’s disease (AD), Frontotemporal Dementias and other neurodegenerative
diseases by RNA interference in vivo. This approach allowed us to identify a new gene
which participates in the neuronal response against Tau induced neurotoxicity in
Drosophila: D-Reep1, homologue of human REEP1 gene (h-Reep1). D-Reep1 knockout flies
showed no apparent phenotypes in physiological growing and developmental conditions,
however, they showed peculiar sensitivity to stress conditions. In addition, D-Reep1
knockout enhanced the neurodegeneration mediated by Tau expression in Drosophila eyes.
On the contrary, the overexpression of UAS-D-Reep1 and UAS-h-Reep1 abolished the
typical rough eye phenotype induced by the presence of Tau. The Co-expression of D-Reep1
in Tau backgrounds did not alter the phosphorylation pattern of this protein while, the
presence of D-Reep1 seemed to prevent the formation of Tau aggregates in vivo. Thus, the
data support the idea that D-Reep1 exerts a protective role on Tau induced toxicity which is
independent of its phosphorylation status. In this work, I analysed the mechanisms behind
the neuroprotective role of D-Reep1 and, in particular, I found that REEP1 is involved in the
regulation of the unfolded protein response (UPR) through the PERK-ATF4 cascade within
the ER. By the activation of this pathway, the neurotoxic aggregates of Tau are removed
from Drosophila neuronal tissues rescuing the normal characteristics of the affected
tissues. Evidences also suggest that the activation of autophagy was behind the removal of
Tau aggregates, providing new molecular information about the physiological role of D
Reep1 in the nervous system.
Keywords: AD Alzheimer Disease APP Amyloid precursor protein CNS Central Nervous System DM Drosophila melanogaster HSP Hereditary Spastic Paraplegia LN Lewy’s neurite MT Microtubule MAP Microtubule associated protein MT Microtubule/s MTBD Microtubule binding domain NFT Neurofibrillary tangle NP Neuritic plaques PHF Paired helical filament PS1 Presenilin 1 PS2 Presenilin 2 SPG Spastic Paraplegia ThS Thioflavin S
Published: 06.12.2019; Views: 1467; Downloads: 55
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Zr/Cu-TiO2 CATALYSTS FOR PHOTOCATALYTIC WATER TREATMENTOlena Pliekhova
, 2019, doctoral dissertation
Abstract: This work entitled «Zr/Cu-TiO2 catalysts for photocatalytic water treatment» tackles a problem of tons of dyes discharged everyday mainly from textile industries. This is a huge concern because of dyes persistence, toxicity and potential to the bioaccumulation in living organisms. Here, a small contribution to overall problem is presented.
The research work consists of three main parts: Theoretical background, Experimental and Results and discussion. In the Theoretical background chapter the overall problem is identified and discussed. The main water treatment techniques are presented briefly with their advantages and drawbacks. Photocatalysis assisted with TiO2 is shown as an alternative additional technique with its own pros and cons. Further, a cursory overview of TiO2 modification techniques is made and advantages in using copper and zirconium oxides for TiO2 modification are presented. The reason and possible positive effect of using of two oxides simultaneously for TiO2 modification is indicated. Additionally, a positive impact of solar light for overall rate of dyes degradation assisted with TiO2 is discussed. Within the framework of photosensitization effect, the problem of using dyes for assessment of photocatalytic properties of materials under the visible light is touched on. Photothermal methods as possible beneficial techniques for this purpose are proposed.
In the Experimental chapter, all experimental techniques used in current research work with the technical details specific for the research work are presented. There are methods of materials preparation, photocatalytic tests under different conditions and varying model pollutants, and physico-chemical characterization techniques.
The Results and discussion chapter is divided by three subchapters. Each chapter is dedicated to one hypothesis, which was checked and confirmed or disproved. The first hypothesis is about beneficial loading of copper and zirconium oxides to TiO2. After numerous experiments held, it was concluded that the pair of copper and zirconium oxides is beneficial for simultaneous application on TiO2 surface to promote its performance.
The second subchapter is about zirconium distribution and its impact on the activity of studied materials towards the antraquinone dye Reactive Blue 19. Different techniques such as XRD, TEM, EXAFS and many others were used in order to characterize the materials and to understand the details of the processes taking place. The existence of upper limit of copper oxide loading for its beneficial effect on TiO2 performance was demonstrated. It was observed that zirconium species loading leads to improvement in performance of materials with higher copper loading, which otherwise lowers activity of TiO2 – this is in case when copper only above its optimal level is present. It was concluded that zirconium oxide containing species occupy rutile surface sites in mixed phase TiO2 and this way beneficially influence the material performance towards the dye removal.
The third subchapter is about the visible light TiO2 assisted dye degradation. It is well known that photosensitization mechanism of dye degradation appears under the visible and as a consequence under the solar light irradiation. This leads to the overall enhancement of dyes degradation, which is positive and may be used as a benefit for faster pollutant destruction. However, this fact leads to mishmash in the determination of real photocatalytic activity of materials towards the dye. It was hypothesized that the impact of photosensitization mechanism on the overall material performance against Reactive blue 19 dye (RB19) descends with the dye concentration lowering. Thermal lens spectrometry (TLS) which is sensitive to chemicals at low concentrations was used for hypothesis evaluation.
To summarize the research work achievements, the conclusions of the thesis are given at the end.
Keywords: titanium dioxide, photocatalysis, zirconium/copper, surface modification, water treatment, dyes
Published: 03.12.2019; Views: 2024; Downloads: 54
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Photoactive nanocomposite thin films on glass and thermosensitive substratesNives Vodišek
, 2019, doctoral dissertation
Abstract: Photocatalysis is a well-known process for the last few decades; it is predominantly used for water and air purification, but also for self-cleaning and antibacterial surfaces. The photocatalytic process is one of the advanced oxidation processes, where semiconductors are mainly used as photocatalysts. The most known and used semiconductor is nanosized titania, which can non-selectively decompose organic matters. One of the side effects of nano TiO2 under UV irradiation is photoinduced hydrophilicity, which furthermore improves the self-cleaning effect. The main drawback of TiO2 is that for its activation UV light is needed, which represents only 5 percent of the solar spectrum. Consequently, actinic irradiance power is low and the response of photocatalyst is limited. Novel approaches are being introduced to improve TiO2 response to visible light such as doping, coupling, modification of surface morphology and others.
The thesis consists of five principal chapters. The first chapter is focused on a short literature review and explanation of some basic terms and principles that are related to this thesis.
The aim of the research was to prepare transparent photocatalytically active thin films on glass and thermosensitive substrates. Four thermosensitive substrates were used: polyvinyl chloride (PVC) foil, polymethyl methacrylate (PMMA) sheet and polyester (PES) fabric coated with a polyvinyl and acrylic coating, with (D1) or without (D2) an additional polyvinylidene fluoride topcoat. The synthesis of films was modified with the introduction of zirconium aiming at improving the photocatalytic activity of the TiO2 films, and the final films had a SiO2 phase present for increased mechanical robustness.
The third chapter is dedicated to the experimental part of the thesis. The detailed process of synthesis is described. The sol-gel process was used to prepare initial Ti-Zr sols, colloidal aqueous solutions with TiO2 and ZrO2 nanoparticles derived from titanium and zirconium alkoxides. The four different Ti-Zr sols were prepared with 0, 5, 10 and 20 molar % of Zr according to Ti. The depositing solution was prepared by mixing Ti-Zr sol, SiO2 sol binder, 1-propanol and 2-propoxyethanol, and then thin films were deposited by dip-coating technique. After the deposition, samples did not require high-temperature calcination since the photocatalytic anatase phase was present already after drying the deposited layers. Coated glass slides were put into a furnace at 150 °C, while samples on thermosensitive substrates were just treated by a heat gun. Samples in powder and thin film form were characterized by UV-Vis, FTIR-ATR and laser beam deflection spectroscopy, X-ray diffraction, scanning electron microscopy and thermal analysis. One of the main aspects of the photocatalyst is its activity. Photocatalytic activity of the thin films was determined, either quantitatively by the formation of fluorescent hydroxyterephthalic acid, one of the first degradation products of terephthalic acid deposit, or qualitatively by a visual-based method where degradation of resazurin ink was observed. Two additional methods were used on glass samples, electron paramagnetic resonance, and degradation of methyl stearate by observing the change in water contact angle under UVA irradiation. Mechanical stability of films on various substrates is an essential factor, describing how successful was immobilization of the photocatalytic materials on the substrate. It was determined by the pencil hardness test, i.e., Wolff-Wilborn method.
In the fourth chapter, titled “Results and Discussion,” the most important part of the thesis is placed. Materials characterization and associated discussion of the results are divided into three major parts: i) powder samples characterization; ii) characterization of thin films on a glass substrate, and iii) characterization of films on thermosensitive substrates.
In the conclusions, the main findings of the Ph.D. research work are summarized. One of our initial hypotheses was disapproved, thin films were not more active with a higher content of zirconium. However, they were more durable. All the obtained films were transparent and photoactive, despite the low-temperature synthesis procedure. Besides commonly used glass substrate, immobilization on thermosensitive substrates was also successful.
Keywords: glass substrate, immobilization, nanocomposite, nanomaterials, PES, photocatalysis, PMMA, PVC, self-cleaning surfaces, silica, plastic substrates, thin films, titania, zirconia
Published: 14.10.2019; Views: 1625; Downloads: 91
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SEARCH FOR NEUTRINOS AT EXTREME ENERGIES WITH THE PIERRE AUGER OBSERVATORYMarta Trini
, 2019, doctoral dissertation
Abstract: The detection of Ultra-High-Energy (UHE) neutrinos around and above 10 18 eV (1 EeV) can be the key to
answering the long-standing question of the origin of the UHE cosmic rays. The Pierre Auger Observatory
is the largest experiment that can detect the extensive air showers produced when the cosmic rays and
neutrinos interact in the earth’s atmosphere. In particular, with the Infilled array of the Surface Detector
of the Pierre Auger Observatory we can detect sub-EeV neutrino-induced particle showers. In this thesis
we demonstrate that it is possible to discriminate neutrino-induced showers from the background showers
produced by the more numerous nucleonic cosmic rays. The sensitivity to neutrinos is enhanced in the
inclined directions with respect to the vertical to the ground, where cosmic ray-induced showers starting in
the upper layers of the atmosphere are dominated by the muonic component of the shower, while deeply-
penetrating neutrino showers in contrast exhibit a large electromagnetic component. Based on this idea in
this thesis we have developed a search procedure for UHE neutrinos that consists on selecting inclined
events in the Infilled array of the Pierre Auger Observatory in which the signals in the water-Cherenkov
stations are spread in time, characteristic of the presence of electromagnetic component in the shower. We
have established a complete chain of criteria to first select the inclined events among the sample of all
events triggering the Infilled array, and then identifying those that have a large electromagnetic component
at ground, and hence can be considered as neutrino candidates. We have identified a single variable, the
so-called area-over-peak averaged over all of the stations in each event, as a suitable observable for neutrino
identification purposes. The neutrino selection was established using extensive Monte Carlo simulations of
the neutrino-induced showers in the Infilled array of Auger as well as a fraction of the data assumed to
be totally constituted of background nucleonic cosmic rays. Using these neutrino simulations we have also
computed the exposure of the Infilled array to UHE neutrinos in the period 1 January 04 - 31 December 2017.
Associated systematic uncertainties on the exposure are also described. Expecting no candidate neutrinos in
the period up to 31 December 2017, and adopting a differential neutrino diffuse flux dN ν /dE ν = k E ν −2 in
the energy range from 0.05 to 1 EeV, we have obtained a 90% C.L. upper limit on the all neutrino flavor,
k 90 < 7.97 × 10 −8 GeV cm −2 s −1 sr −1 .
Keywords: astroparticles, astrophysical neutrinos, cosmic rays showers, Pierre Auger Observatory, Infilled
Published: 03.10.2019; Views: 2314; Downloads: 69
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Factors influencing collected quantities of municipal solid wasteSlavica Schuster
, 2019, doctoral dissertation
Abstract: The first part of the survey, using the survey (enclosed with the annexes), tried in various ways to identify samples and facts by which we could predict the amount of waste collected according to some social and economic indicators of all municipalities of the Republic of Slovenia. Data were collected through surveys to determine the way we work and think about the collection of waste and landfills. For my research I have selected the Republic of Slovenia and its 212 municipalities. It is precisely Slovenia that in many respects represents a bright spot in waste management and management.
In the second part of the research we used statistical methods to find the factors that influence the increase of waste. From the results we have proved our hypotheses and one of the most important is how the average age of people influences the increase of waste. We did the research over a period of 6 years (2012-2017). Where, by comparison, we find that they do not change significantly in structure by age, but of course socio-economic indicators such as average age change.
In the last section, we compared the growth of waste collected with GDP growth. We show that with the growth of GDP, the amount of waste collected also increases. The research is also based on the Republic of Slovenia and beyond. In the second part of the last survey we also included data for EU Member States (28 of them).
Keywords: waste, waste management, amount of waste, socio-economic impacts, Slovenia, wild-landfills, GDP
Published: 02.10.2019; Views: 1749; Downloads: 82
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HOLISTIC GEOMORPHOLOGICAL SPATIAL ANALYSIS OF KARST ON KRK ISLANDEla Šegina
, 2019, doctoral dissertation
Abstract: The intriguing spatial variability of surface features on Krk Island has stimulated the research of this karst area located in the coastal zone of the Dinaric karst in Croatia. Field inspection, ortho-rectified aerial photos (0.5m resolution) and a topographic map (1:5,000) were used for the detection and delineation of detectable karst surface features appearing on the island with the area of 405.5 km². This method resulted in the identification of several yet undefined types of surface features occurring on karst, requiring the revision of the existing classification and re-establishment of a new classification system compatible with the particular field reality. Several morphologic and distributive parameters that had been calculated for each re-classified type of surface feature provided insight into the surface features elementary characteristics, their spatial variability and the correlation to the other types of surface features and to the recent karst relief. This analysis based on a large, accurate dataset, contributed to the general knowledge on karstic surface features, the conditions of surface features in Dinaric karst and to the understanding of the karst surface evolution on Krk Island.
Keywords: karst geomorphology, GIS, spatial analysis, Krk Island, Dinaric karst, Adriatic Sea
Published: 13.09.2019; Views: 1971; Downloads: 122
Fulltext (17,12 MB)