rof. dr. Peter Purg: Novi izobraževalni modeli med umetnostjo, znanostjo in tehnologijami za družbene inovacije. : Preplet projektov MAST, DIVA in KONS.Peter Purg
, prispevek na konferenci brez natisa
Ključne besede: interdisiplinarnost, inovativnost, leonardo da vinci, MAST, KONS, DIVA, izobraževanje, model, inoviranje
Objavljeno v RUNG: 18.10.2019; Ogledov: 2702; Prenosov: 0
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What effect does VOC sampling time have on derived OH reactivity?Hannah Sonderfeld
, Iain R White
, Iain C A Goodall
, James R Hopkins
, Alistair C Lewis
, Ralf Koppmann
, Paul S Monks
, 2016, izvirni znanstveni članek
Opis: State-of-the-art techniques allow for rapid measurements of total OH reactivity. Unknown sinks of OH and oxidation processes in the atmosphere have been attributed to what has been termed ĝ€missingĝ€ OH reactivity. Often overlooked are the differences in timescales over which the diverse measurement techniques operate. Volatile organic compounds (VOCs) acting as sinks of OH are often measured by gas chromatography (GC) methods which provide low-frequency measurements on a timescale of hours, while sampling times are generally only a few minutes. Here, the effect of the sampling time and thus the contribution of unmeasured VOC variability on OH reactivity is investigated. Measurements of VOC mixing ratios by proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) conducted during two field campaigns (ClearfLo and PARADE) in an urban and a semi-rural environment were used to calculate OH reactivity. VOCs were selected to represent variability for different compound classes. Data were averaged over different time intervals to simulate lower time resolutions and were then compared to the mean hourly OH reactivity. The results show deviations in the range of 1 to 25%. The observed impact of VOC variability is found to be greater for the semi-rural site.The selected compounds were scaled by the contribution of their compound class to the total OH reactivity from VOCs based on concurrent gas chromatography measurements conducted during the ClearfLo campaign. Prior to being scaled, the variable signal of aromatic compounds results in larger deviations in OH reactivity for short sampling intervals compared to oxygenated VOCs (OVOCs). However, once scaled with their lower share during the ClearfLo campaign, this effect was reduced. No seasonal effect on the OH reactivity distribution across different VOCs was observed at the urban site.
Ključne besede: Hydroxyl radical, Atmospheric chemistry, Box model
Objavljeno v RUNG: 18.07.2019; Ogledov: 2351; Prenosov: 0
A map-matching algorithm dealing with sparse cellular fingerprint observationsAndrea Dalla Torre
, Paolo Gallo
, Donatella Gubiani
, Chris Marshall
, Angelo Montanari
, Federico Pittino
, Andrea Viel
, 2019, izvirni znanstveni članek
Opis: The widespread availability of mobile communication makes mobile devices a resource for the collection of data about mobile infrastructures and user mobility. In these contexts, the problem of reconstructing the most likely trajectory of a device on the road network on the basis of the sequence of observed locations (map-matching problem) turns out to be particularly relevant. Different contributions have demonstrated that the reconstruction of the trajectory of a device with good accuracy is technically feasible even when only a sparse set of GNSS positions is available. In this paper, we face the problem of coping with sparse sequences of cellular fingerprints. Compared to GNSS positions, cellular fingerprints provide coarser spatial information, but they work even when a device is missing GNSS positions or is operating in an energy saving mode. We devise a new map-matching algorithm, that exploits the well-known Hidden Markov Model and Random Forests to successfully deal with noisy and sparse cellular observations. The performance of the proposed solution has been tested over a medium-sized Italian city urban environment by varying both the sampling of the observations and the density of the fingerprint map as well as by including some GPS positions into the sequence of fingerprint observations.
Ključne besede: Map-matching algorithm, trajectory, cellular fingerprint, Hidden Markov Model
Objavljeno v RUNG: 11.06.2019; Ogledov: 2871; Prenosov: 95
Celotno besedilo (3,93 MB)
Modelling of Macrosegregation of a Low-Frequency Electromagnetic Direct Chill Casting by a Meshless MethodVanja Hatić
, 2019, doktorska disertacija
Opis: The main aim of the dissertation is to develop a meshless model that describes the solidification and macrosegregation phenomena during the direct chill casting (DCC) of aluminium alloys under the influence of a low-frequency electromagnetic field. Macrosegregation is an undesired consequence of alloy solidification. It represents one of the major casting defects and substantially reduces the quality of the finished product. On the other hand, low-frequency electromagnetic casting (LFEC) is a process that promises to increase greatly the product quality, including the reduction of macrosegregation. The modelling of both processes is of tremendous importance to the metallurgical industry, due to the high costs of experiments during production.
The volume-averaging formulation is used for the modelling of the solid-liquid interaction. The conservation equations for mass, energy, momentum, and species are used to model the solidification of aluminium-alloy billets in axysimmetry. The electromagnetic-induction equation is coupled with the melt flow. It is used to calculate the magnetic vector potential and the Lorentz force. The Lorentz force is time-averaged and included in the momentum-conservation equation, which intensifies the melt flow. The effect of Joule heating is neglected in the energy conservation due to its insignificant contribution. The semi-continuous casting process is modelled with the Eulerian approach. This implies that the global computational domain is fixed in space. The inflow of the liquid melt is assumed at the top boundary and the outflow of the solid metal is assumed at the bottom. It is assumed that the whole mushy area is a rigid porous media, which is modelled with the Darcy law. The Kozeny-Carman relation is used for the permeability definition. The incompressible mass conservation is ensured by the pressure correction, which is performed with the fractional step method. The conservation equations and the induction equation are posed in the cylindrical coordinate system. A linearised eutectic binary phase diagram is used to predict the solute redistribution in the solid and liquid phases. The micro model uses the lever rule to determine the temperature and the liquid fraction field from the transport equations.
The partial differential equations are solved with the meshless-diffuse-approximate method (DAM). The DAM uses weighted least squares to determine a locally smooth approximation from a discrete set of data. The second-order polynomials are used as the trial functions, while the Gaussian function is used as the weight function. The method is localised by defining a smooth approximation for each computational node separately. This is performed by associating each node with a unique local neighbourhood, which is used for the minimisation. There are 14 nodes included in the local subdomains for the DCC and LFEC simulations. The stability of the advective term is achieved with a shift of the Gaussian weight in the upwind direction. This approach is called the adaptive upwind weight function and is used in the DAM for the first time. The Explicit-Euler scheme is used for temporal discretisation.
The use of a meshless method and the automatic node-arrangement generation makes it possible to investigate the complicated flow structures, which are formed in geometrically complex inflow conditions in a straightforward way. A realistic inflow geometry and mould can therefore be included in the model. The number of computational nodes is increased in the mushy zone and decreased in the solid phase, due to the optimisation of the computational time and memory. The computational node arrangement is automatically adapted with time, as the position of the mushy zone is changed in shape and position.
Ključne besede: low-frequency electromagnetic casting, direct chill casting, macrosegregation, electromagnetic stirring, aluminium alloys, meshless methods, diffuse-approximate method, multiphysics model, solidification
Objavljeno v RUNG: 25.04.2019; Ogledov: 3176; Prenosov: 145
Celotno besedilo (28,80 MB)
New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in waterArtem Badasyan
, Matjaž Valant
, 2018, objavljeni povzetek znanstvenega prispevka na konferenci
Opis: During the past decade the experimental studies of biopolymer conformations have reached an
unprecedented level of detailization and allow to study single molecules in vivo . Processing of
experimental data essentially relies on theoretical approaches to conformational transitions in
biopolymers . However, the models that are currently used, originate from the early 1960's and
contain several unjustified assumptions, widely accepted at that time. Thus, the view on the
conformational transitions in the polypeptides as a two-state process has very limited applicability
because the all-or-none transition mechanism takes place only in short polypeptides with sizes
comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is
phenomenological and does not allow for a microscopic model for water; the implicit consideration of
the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy
difference on temperature can only be justified through the assumption of an ideal gas with a constant
heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation  of the
Zimm-Bragg model  with the term describing the water-polypeptide interactions . The analytical
solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat
and cold denaturation. On the example of several sets of experimental data we show, that our formula
results in a significantly better fit, as compared to the existing approaches. Moreover, the application
of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an
information, inaccessible before.
 I. König, A. Zarrine-Afsar, M. Aznauryan, A. Soranno, B. Wunderlich, F. Dingfelder, J. C. Stüber, A. Plückthun, D.
Nettels, B. Schuler, (2015), Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic
cells/Nature Methods, 12, 773-779.
 J. Seelig, H.-J. Schönfeld, (2016), Thermal protein unfolding by differential scanning calorimetry and circular
dichroism spectroscopy. Two-state model versus sequential unfolding/Quarterly Reviews of Biophysics, 49, e9, 1-24.
 A.V. Badasyan, A. Giacometti, Y. Sh. Mamasakhlisov, V. F. Morozov, A. S. Benight, (2010), Microscopic formulation
of the Zimm-Bragg model for the helix-coil transition/Physical Review E, 81, 021921.
 B. H. Zimm, J. K. Bragg, (1959), Theory of the Phase Transition between Helix and Random Coil in Polypeptide
Chains/Journal of Chemical Physics, 31, 526.
 A. Badasyan, Sh.A. Tonoyan, A. Giacometti, R. Podgornik, V.A. Parsegian, Y.Sh. Mamasakhlisov, V.F. Morozov,
(2014), Unified description of solvent effects in the helix-coil transition/Physical Review E, 89, 022723.
Corresponding author: Artem Badasyan (firstname.lastname@example.org)
Ključne besede: Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition.
Objavljeno v RUNG: 22.10.2018; Ogledov: 2988; Prenosov: 0
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Vrednotenje in izbira merilnih sistemov v avtomobilski industrijiMatevž Ivančič
, 2018, magistrsko delo
Opis: V magistrskem delu smo obravnavali vrednotenje in izbiro merilnih sistemov v avtomobilski industriji. Uporaba merilnih sistemov se nanaša na kontrolo premerov lukenj na komutatorjih, ki so eden izmed elementov električnih motorjev. Kontrola premerov lukenj je pomembna faza proizvodnega procesa, saj s tem preprečimo dobavo neustreznih proizvodov. Odločitveni problem se nanaša na izbor najprimernejšega merilnega sistema, kjer izbiramo med štirimi merilnimi sistemi: ročno kontrolo s kontrolnikom Gre/Ne gre, avtomatsko kontrolo s trnom Gre/Ne gre, avtomatsko kontrolo s trnom Gre/Gre s silo in vzporednim merjenjem sile ter avtomatsko kontrolo s kroglico. Vrednotenje in izbor poteka z uporabo večparametrske metode DEX, pri kateri smo za merilni sistem določili ekonomske, tehnološke in kakovostne kriterije ter jih vključili v model za vse štiri merilne sisteme. Po korakih, ki jih določajo metode večparametrskega vrednotenja, smo izdelali celoten model ter z njim ovrednotili in analizirali merilne sisteme. Analize so obsegale analizo ±1, analizo kaj-če ter analizo prednosti in slabosti. Končni rezultat je predlog najprimernejšega merilnega sistema, to je avtomatski merilni sistem s trnom Gre/Gre s silo in vzporednim merjenjem sile.
Ključne besede: komutator, premer luknje komutatorja, merilni sistem, odločitveni model, večparametrsko odločanje, metoda DEX, program DEXi
Objavljeno v RUNG: 03.10.2018; Ogledov: 4388; Prenosov: 170
Celotno besedilo (2,34 MB)
POLYMORPHISMS IN GENES FOR ENDOTHELIN 1, ENDOTHELIN RECEPTORS AND NITRIC OXIDE SYNTHASE 3 IN PATIENTS WITH DIABETIC RETINOPATHY AND DIABETES MELLITUS TYPE 2 : DISSERTATIONDejan Bregar
, 2018, doktorska disertacija
Opis: The major causes of Diabetes Mellitus Type 2 (T2DM) are multi-factorial consequences of complex interactions between environmental, social and genetic factors. We investigated the genetic risk factors in Slovene patients with T2DM on a model of microvascular complication – Diabetic Retinopathy (DR).
Retrospective case-control study includes a T2DM Slovene population with clinical risk factors for T2DM and DR. Only some of the candidate genes with selected single nucleotid polymorphisms (SNPs) were included: (EDN1 (rs5370, rs3087459, rs1476046), EDNRA (rs5335, rs1801708), EDNRB (rs10507875, rs4885493), NOS3 (rs869109213).
By genotyping with either real-time polymerase chain reaction or standard polymerase chain reaction (PCR) we successfully identified the contribution of variable number of tandem repeats rs869109213 in DR progression (Proliferative Diabetic Retinopathy (PDR)) in Slovene patients with T2DM. The joint effect of individual genotypes of rs10507875 in EDNRB and rs869109213 in NOS3 on DR onset (DR) and DR progression (PDR) was demonstrated as well. The joint effect of the two polymorphisms on DR onset (DR) and DR progression (PDR) was greater than the individual effect of each polymorphism separately in the analyzed genetic models.
Despite genetic research contributions in DR, linkage studies, and Genome-wide association studies the identification of susceptible loci through candidate gene approaches still remains in its early stages. The frequent approach with an ultimate focus on SNP associations with phenotype is likely to underestimate the roles of genetics in human diseases by disregarding not only the joint effect of multiple loci but the complex interaction network between them. By identifying polymorphisms in genetic disorders in a more systematic way, we will be able to deepen our understanding of the regulatory mechanisms and disease etiology which should lead to a more effective development of mechanism-based therapies as well.
Ključne besede: endothelin 1, EDN1, endothelin receptor A, EDNRA, endothelin receptor B, EDNRB, nitric oxide synthase 3, NOS3, diabetic retinopathy, DR, diabetes mellitus type 2, T2DM, polymorphism, SNP, genetic model
Objavljeno v RUNG: 07.09.2018; Ogledov: 3130; Prenosov: 171
Celotno besedilo (3,06 MB)
MODIFIED U1 RNAs AS SPLICING CORRECTORS IN HUMAN GENETIC DISORDERSKatarzyna Rajkowska
, 2018, doktorska disertacija
Opis: The experimental work of this thesis was performed at the International Centre
for Genetic Engineering and Biotechnology (ICGEB) in the Human Molecular
Genetics Group, under the scientific direction of Prof. Franco Pagani. The project
was developed during the academic years 2014-2017.
Modified U1 RNAs, also named Exon Specific U1s (ExSpeU1s) represent a novel
class of small RNA-based molecules that correct exons splicing defects. To evaluate
their therapeutic potential focused on Familial Dysautonomia (FD), a rare autosomal
recessive disorder characterized by progressive degeneration of the sensory and
autonomic nervous system. More than 99% of patients are homozygous for the T to
C transition in position 6 of the IKBKAP intron 20 (c.2204+6T>C). This substitution
modifies the exon 20 5’ splice site (5’ss) inducing exon skipping in a tissue-specific
manner and reducing the total amount of IKAP protein. The molecular mechanisms
underlying the IKBKAP mis-splicing are not completely clear and there
are no effective treatments.
In this thesis, I investigated the therapeutic potential of ExSpeU1s and the role
of cis- and trans-acting factors that regulates IKBKAP splicing. Using a splicing
functional assay, I identified ExSpeU1s that bind to intron 20 sequences and rescue
the exon 20 skipping defect. Interestingly, their rescue activity was modulated
by several splicing factors and requires a critical exonic splicing enhancer element.
Transfection experiment showed the involvement of both enhancing (TIA1, PTBP1
and PTB4) and inhibitory (SRSF3, hnRNPA1, FOX and FUS) splicing factors
in IKBKAP splicing. To better evaluate the ExSpeU1s therapeutic efficacy,
I transduced FD patient’s fibroblasts with a lentiviral vector expressing the most
active ExSpeU1. This resulted in a complete rescue of the exon skipping defect and
improvement in IKAP protein expression. Most importantly, intraperitoneal delivery
of ExSpeU1s by AAV9 into a transgenic mouse model, that recapitulates
the tissue-specific mis-splicing seen in FD patients, corrected the aberrant splicing
patterns in several tissues increasing the amount of the corresponding IKAP protein.
All together, these results identify novel regulatory splicing factors involved in the
IKBKAP exon 20 regulation and provide the proof of principle that ExSpeU1s
delivered in vivo by AAV vectors represent a novel therapeutic strategy for FD.
Ključne besede: Familial Dysautonomia, IKBKAP, IKAP, splicing, splicing defects, ExSpeU1, U1 snRNA, mouse model, AAV
Objavljeno v RUNG: 26.03.2018; Ogledov: 3962; Prenosov: 123
Celotno besedilo (13,96 MB)
Model vrednotenja primernosti kandidatov za delovna mesta v zdravstvenem domuBoštjan Milič
, 2017, magistrsko delo
V magistrskem delu smo opisali nastali kadrovski odločitveni problem v Zdravstvenem domu Sežana. Obravnavali smo problem vrednotenja primernosti kandidatov za izbrano delovno mesto v zdravstvenem domu. Osredotočili smo se na tri delovna mesta (administratorja, zdravnika stomatologa in zdravnika pediatra) in najprej pridobili podatke o razpisanih delovnih mestih. V razpisih so bili podani kriteriji, s katerimi smo izdelali večparametrski model vrednotenja za vsako delovno mesto posebej. Te modele smo izdelali z računalniškim programom DEXi. Na podlagi tega programa smo vrednotili kandidate za delovna mesta. Izmed 334 prijavljenih kandidatov za delovno mesto administratorja smo z modelom ovrednotili in ugotovili, da je za delovno mesto najprimernejši ekonomist računovodske smeri. Podobno smo izbrali najprimernejša izmed 254 prijavljenih kandidatov za delovno mesto zdravnika stomatologa in med 145 prijavljenimi kandidati za novo delovno mesto zdravnika pediatra. Večparametrski model DEX se je izkazal za odlično alternativo pri izbiri novega kandidata za izbrano delovno mesto. Z uporabo metode šestih klobukov razmišljanja smo potrdili rezultate izbora kandidatov.
Ključne besede: kandidati, delovno mesto, večparametrski model vrednotenja, analiza SWOT, metoda šestih klobukov razmišljanja
Objavljeno v RUNG: 02.03.2018; Ogledov: 4691; Prenosov: 192
Celotno besedilo (1,24 MB)