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Dosimetric verification of breast treatment plans delivered using O-ring coplanar linear accelerator
No full textDozimetrijske provjere naprednih radioterapijskih tehnika važan su doprinos osiguranju kvalitete kliničke radioterapije. Njima se osigurava točno, pouzdano i sigurno radioterapijsko liječenje bolesnika.
Ovaj rad usmjeren je na dozimetrijsku provjeru novouspostavljene volumno modulirane lučne radioterapije (VMAT), radioterapijske tehnike za zračenje karcinoma dojke na prstenastom akceleratoru Halcyon. Za potrebe provjere korištene su dvije metode. U prvoj su mjerene raspodjele apsorbirane doze pomoću dioda ugrađenih u plašt cilindričnog matričnog detektora ArcCHECK, a u drugoj su određivane pomoću elektroničkog portalnog slikovnog uređaja (EPID) koji je integriran u Halcyon. Potom su te raspodjele doze uspoređene gama analizom s pripadnim raspodjelama doze izračunatim u računalnom sustavu za planiranje radioterapije (Eclipse). Rezultat gama analize je stupanj prolaznosti gama indeksa. Sva mjerenja provedena su u Kliničkom bolničkom centru Zagreb, u Klinici za onkologiju.
U radu je zatim provedena statistička analiza stupnjeva prolaznosti gama indeksa 33 plana zračenja koji se međusobno razlikuju po kriteriju, broju izocentara, lukova, monitorskih jedinica, načinu normiranja razlike doze, strani tijela i datumu provođenja dozimetrijske provjere. Statistička analiza uključivala je izračun i usporedbu opisne statistike za planove koji imaju zajedničke značajke, Shapiro-Wilkov test i Q-Q grafikone za provjeru normalnosti raspodjele uzorka, Kruskal-Wallisov test za usporedbu medijana raspodjela uzoraka, beta regresijsku analizu kako bi se ispitao utjecaj pojedinih nezavisnih varijabli na stupanj prolaznosti gama indeksa te je izračunata Spearmanova matrica korelacije, kako bi se provjerio trend povezanosti između rezultata mjerenja prolaznosti gama indeksa dobivenih pomoću ArcCHECK-a i pomoću EPID-a.
Iz rezultata statističke analize je za obje metode dozimetrijske provjere zaključeno da uzorci nisu raspodijeljeni prema normalnoj raspodjeli te da lokalno normirana razlika doze i lijeva strana tijela značajno smanjuju stupanj prolaznosti gama indeksa. Iz beta regresijske analize rezultata ArcCHECK mjerenja zaključeno je da rigoroznija optimizacija raspodjele doze s većim brojem lukova značajno povećava stupanj prolaznosti gama indeksa. Broj izocentara, monitorskih jedinica i datum provođenja dozimetrijske provjere utječu manje ili ne utječu uopće na stupanj prolaznosti gama indeksa. Također je pokazano da korelacija između rezultata mjerenja stupnja prolaznosti gama indeksa dobivenih pomoću ArcCHECK-a i pomoću EPID-a varira od slabe do jake.Dosimetric verification of advanced radiotherapy techniques gives an important contribution to the quality assurance program in clinical radiotherapy. Different verification modalities ensure accurate, reliable and safe radiotherapy treatment of cancer patients.
This work focuses on the dosimetric verification of the newly established volumetric modulated VMAT radiotherapy technique for breast cancer irradiation using the Halcyon ring accelerator. Two methods are used for dosimetric verification purposes. In the first, the absorbed dose distributions were measured using diodes embedded in the plate of the ArcCHECK cylindrical matrix detector, and in the second, they were determined using the electronic portal imaging device (EPID) integrated into Halcyon. These dose distributions were then compared by gamma analysis with the corresponding dose distributions calculated with the treatment planning system (Eclipse). The result of the gamma analysis is the gamma index pass rate. All measurements were performed at the University Hospital Centre Zagreb in the Department of Oncology and Radiotherapy.
The statistical analysis was conducted of the gamma index pass rates of 33 radiation treatment plans that differed from each other in terms of pass criteria, number of isocenters, arcs, monitoring units, dose difference normalization, side of the body, and date of dosimetric check. The statistical analysis included the calculation and comparison of descriptive statistics for treatment plans that had common characteristics, the Shapiro-Wilk test and quantile-quantile (Q-Q) plots to check the normality of the sample distribution, the Kruskal-Wallis test to compare the medians of the sample distributions, beta regression analysis to examine the influence of individual independent variables on the gamma index pass rate. The Spearman correlation matrix was calculated to check the trend of the relationship between the gamma index pass rate measurement results obtained using ArcCHECK and EPID.
The results of the statistical analysis for both methods of dosimetric verification showed that the samples were not distributed according to a normal distribution. It was found that the locally normalized dose difference and the treatment of the left side of the body significantly reduced the gamma index pass rate. Beta regression analysis of the ArcCHECK measurement results revealed that a more rigorous dose distribution optimization, involving a larger number of arcs, significantly improved the gamma index pass rate. The number of isocenters, monitor units and the date of the dosimetric verification had little or no effect on the pass rate. Additionally, the correlation between gamma index pass rates measured with ArcCHECK and those obtained using EPID ranged from weak to strong
Impact of multiple stressors on the biological components of freshwater ecosystems
No full textVodeni ekosustavi izloženi su brojnim prirodnim i antropogenim pritiscima. Glavni cilj ovog
istraživanja je praćenje procesa i molekularnih odgovora ključnih sastavnica slatkovodnih
ekosustava prilikom izlaganja višestrukom stresu. U tu svrhu postavljeni su laboratorijski pokusi
na i) tularima i makrofitima izloženima mikroplastici, farmaceuticima i endokrinim modulatorima
te ii) obraštaju izloženom suši i kemijskom onečišćenju. Za istovremenu karakterizaciju stresora i
praćenje molekularnih odgovara organizama razvijena je sveobuhvatna metoda koja omogućuje
detekciju onečišćivala (farmaceutika, endokrinih modulatora i mikroplastike), metabolita i
proteina iz jednog uzorka tkiva. Analizirajući promjene u regulaciji metabolita i ukupnoj količini
proteina, istraživanje na tularima i makrofitima pruža uvid u štetne učinke mikroplastike na vodene
organizme te uspoređuje utjecaj mikroplastike s utjecajima farmaceutika i endokrinih modulatora.
Eksperiment na obraštaju ukazuje na dinamično međudjelovanje mikrobne zajednice i okoliša
prilikom izlaganja stresu uzrokovanom presušivanjem i farmaceuticima. Stres uzrokovan
presušivanjem oblikuje mikrobnu zajednicu, koja pak pod utjecajem onečišćivala mijenja kemijski
sastav okoliša.Freshwater ecosystems are subject to numerous natural and anthropogenic pressures. The main
objective of this research was to investigate the processes and molecular responses of several key
components of freshwater ecosystems while exposed to multiple stressors. To this end, laboratory
experiments were conducted with i) caddisflies and macrophytes exposed to microplastics,
pharmaceuticals and endocrine disruptors, and ii) biofilms exposed to drought and a mixture of
emerging contaminants. A robust method was developed for simultaneous characterisation of
stressors and monitoring the corresponding molecular responses of organisms, allowing the
detection of emerging contaminants (pharmaceuticals, endocrine disrupting compounds and
microplastics), metabolites and proteins from a single tissue sample. By analyzing metabolic and
total protein variations, the experiment on caddisflies and macrophytes provides valuable insights
into adverse effects of microplastics on aquatic organisms and compares the effects of
microplastics with those of pharmaceuticals and endocrine disruptors. The biofilm experiment
shows a dynamic interaction between the microbial community and its environment during
exposure to desiccation and emerging contaminants. Desiccation stress shapes the microbial
community, which in turn, under the influence of emerging contaminants, modulates chemical
composition of the environment
Analysis of mitochondrial genome in patients with severe COVID-19
No full textCijeli svijet je zahvaćen pandemijom virusa SARS-CoV-2 koji uzrokuje bolest COVID-19. To
je uzrokovalo širok spektar društvenih problema poput zdravstvenih i financijskih. Stoga se
ovaj rad usredotočio na pronalazak novih metoda detekcije te otkrivanja rizičnih čimbenika iz
aspekta mitohondrijskog genoma. Mitohondriji su često zahvaćeni virusnim infekcijama i zbog
toga se postavlja pitanje postoji li mitohondrijska makrohaplogrupa koja svoje nositelje stavlja
pod veći rizik od razvijanja težih simptoma. Korištenjem naprednog sekvenciranja, analizirani
su uzorci mitohondrijske DNA zaraženih osoba oboljelih od teških simptoma. Nije dobivena
statistički važna distribucija makrohaplogrupa u usporedbi s uzorcima opće populacije
Republike Hrvatske. Osim distribucije makrohaplogrupa provjerena je prisutnost nesinonimnih
mutacija i heteroplazmijskih mutacija, ali ni tamo nisu dobiveni podatci koji uvelike odstupaju
od opće populacije Republike Hrvatske. Otkrivene su izrazito malo istražene mutacije koje se
u budućnosti trebaju detektirati u drugim istraživanjima kako bi se mogla provesti detaljna
analiza učinka tih mutacija na mitohondrijske proteine. Unatoč manjku novih otkrića,
analizirani uzorci su izrazito vrijedni zbog vremenskog razdoblja u kojemu su prikupljeni te
mogu dati korisne podatke u budućim studijama.The entire world has been caught in the SARS-CoV-2 pandemic, which causes COVID-19. It
caused a wide spectrum of social problems ranging from financial to public health issues.
Because of this, the master thesis focused on discovering new methods of detecting the virus
and discovering new risk factors regarding the mitochondrial genome. Mitochondria are
commonly targeted by viral infections and because of this the question becomes, are some
mitochondrial macrohaplogroups more susceptible to developing more severe symptoms.
Using advanced sequencing, we have analysed the mitochondrial DNA samples of patients with
severe COVID-19. There was no statistical significance detected regarding the distribution of
macrohaplogroups compared to the samples of the general population in Croatia. Besides the
distribution of macrohaplogroups we also analysed non-synonimous mutations and
heteroplasmic mutations. There was also no significant difference detected in that regard. We
found some mutations that have never been described and have to be detected in different
studies in order to conduct a thorough analysis on their impact on the mitochondria. Despite
there being no new discoveries, these samples are very valuable because of the time period they
were obtained in and these results can prove to be very helpful in future studie
A Museum of Geography - A Conceptual Design
No full textU cijelome svijetu postoji samo nekoliko muzeja geografije, ali unatoč tome postoji značajna količina geografskog sadržaja u muzejima različitih profila diljem svijeta. Terenskim istraživanjem muzeja pokazalo se kako prostorna obilježja muzejskih predmeta i prostorni aspekt muzejskih tema predstavljaju bitan faktor prilikom prezentacije sadržaja u muzejima. Uz to, rezultati istraživanja ključnih geografskih riječi su pokazali kako su osnovne geografske teme vrlo popularne u javnosti i prepoznate u društvu. To su bile osnovne postavke prema kojima se dalje stvarao idejni koncept Muzeja geografije, čija se struktura zasniva na tematskoj podjeli geografije. Kroz muzejske odjele različitim metodama prikaza predstavile su se razne društvenogeografske i fizičkogeografske teme. One su se opisale pomoću raznolikih muzejskih predmeta, simulacijskih modela te raznolikog tekstualnog i grafičkog sadržaja.There are only a few museums of geography in the whole world, but despite that there is a significant amount of geographical content in museums of various profiles around the world. The field research showed that the spatial characteristics of museum objects and the spatial aspect of museum themes represent an important factor when presenting the contents in museums. In addition, the results of the research of key geographic words showed that basic geographic topics are very popular among the public and recognized in society. Based on these assumptions, the creation of the conceptual design of the Museum of Geography, whose structure is based on the thematic division of geography, was set. Various socio-geographical and physical-geographical topics will be represented through the museum's departments using different display methods. They will be described using various museum objects, simulation models and various textual and graphic content
Interactive Web-Map of Cultural Activities in Croatia
No full textKulturne djelatnosti dio su kulturnog pejzaža nekog društva, a njihova institucionalizacija kroz kulturne ustanove zauzima fizički prostor te se u njima može vidjeti manifestacija određene kulture. Web-karte, s druge strane, omogućuju interaktivni i dinamični prikaz prostornih podataka kako bi se dala informacija o lokacijama, primjerice, kulturnih ustanova. Glavni cilj ovog rada bio je prikazati odabrane kulturne djelatnosti (kazališta, kinematografi, knjižnice i muzeji) u Republici Hrvatskoj na interaktivnoj web-karti. Za izradu web-karte korišteni su jezici HTML, CSS i JavaScript te Leaflet biblioteka za JavaScript. Također, cilj rada bio je provesti prostornu analizu odabranih kulturnih djelatnosti u Republici Hrvatskoj u 2024. godini te njihova usporedba s podacima iz 1990.Cultural institutions are a part of the cultural landscape of any society. They provide a physical manifestation of culture through the physical space they take up, whether they are a museum collection or a theatre. Web-maps, on the other hand, enable authors to show spatial data in an interactive and dynamic way and to provide information on the location of, for example, cultural institutions. The primary aim of this paper was to show selected cultural institutions (theatres, movie theatres, libraries and museums) in the Republic of Croatia on an interactive web-map. The languages HTML, CSS and JavaScript, as well as the Leaflet library for JavaScript are used to design and make the web-map. Another aim of the paper was to conduct a spatial analysis of the selected cultural institutions for 2024. and to compare them to data from 1990
Beach vulnerability assesment at the island of Hvar
No full textU radu su metodama terenskog rada, daljinskih istraživanja i analizom arhivskog materijala istražena geomorfološka obilježja, evolucija i ranjivost 47 žala na otoku Hvaru. Većina žala, njih 85,1 %, čini geomorfološke sustave s drenažnim bazenima i oblikovana su u plavinskom materijalu na njihovom ušću, 8,5 % žala oblikovano je ispod klifa, dok je najmanje, njih 6,4 % oblikovano u eolskim naslagama. U posljednjih 200 godina žala su izgubila prosječno 44,1 % svoje površine, dok im se obalna linija pomaka prema kopnu za prosječno 5,5 m. Procjena ranjivosti žala pokazala je da je većina žala na otoku Hvaru jako ranjiva te teži prema vrlo jakoj ranjivosti, što se podudara sa značajnim trendom erozije žala tijekom posljednjih ~200 godina te naglašava potrebu za održivim upravljanjem žalima i stalnim praćenjem stanja.This thesis investigates the geomorphological properties, evolution, and vulnerability of 47 beaches on the island of Hvar using fieldwork methods, remote sensing, and analysis of archival material. The majority of the beaches, 85.1%, are part of geomorphological systems with drainage basins and are formed in alluvial material at their outlets, 8.5% are formed beneath cliffs, while the smallest portion, 6.4%, are shaped in aeolian deposits. In the last 200 years, the beaches have lost an average of 44.1% of their surface area, and their shoreline has retreated landward by an average of 5.5 meters. The vulnerability assessment shows that most beaches on the island of Hvar are highly vulnerable and tend toward very high vulnerability, which corresponds to the significant trend of beach erosion over the last ~200 years, highlighting the need for sustainable beach management and continuous monitoring
Modeling the forces responsible for positioning chromosomes in the mitotic spindle
No full textDiobeno vreteno biološki je mikrostroj sastavljen od mikrotubula. Njegova uloga u stanici je pravilno, precizno i robusno razdvajanje kromosoma tijekom stanične diobe, zašto mu je potreban mehanizam odredivanja i regulacije vlastite duljine. Interpolarni mikrotubuli sudjeluju u regulaciji duljine posredstvom motornih proteina u antiparalelnom preklopu dvaju mikrotubula i motornih proteina koji minus krajeve mikrotubula povezuju s polovima diobenog vretena. Ovdje uvodimo teorijski opis sila motornih proteina na minus krajevima u tri inačice. Numeričkim rješavanjem diferencijalne jednadžbe prvog reda za ravnotežu sila pokazujemo da ovisnost sile motornih proteina na minus krajevima o duljini mikrotubula rezultira stabilnom ravnotežnom duljinom vretena koja ovisi o omjeru brzina koračanja motora na polovima i motora u preklopu. Područje preklopa antiparalelnih mikrotubula, čija je duljina u modelu fiksirana, centrira se u inačici modela sa silama ovisnima o duljini mikrotubula, dok u ostalim inačicama ostaje izmaknuta iz središnjeg položaja. Ovi rezultati sugeriraju da bi na minus krajevima mikrotubula mogao postojati mehanizam regulacije duljine diobenog vretena zasnovan na djelovanju motornih proteina ovisnom o duljini mikrotubula.The mitotic spindle is a biological micromachine built from microtubules. Its role in the cell is the regular, precise, and robust separation of chromosomes during cell division, for which it needs a mechanism of measuring and controlling its own length. Interpolar microtubules participate in spindle length control via motor proteins in their antiparallel overlap and motor proteins that connect the spindle poles with microtubule minus ends. Here, we introduce a theoretical description of forces by motor proteins at the minus ends in three variations. By numerically solving the first order force balance ODE, we show that the length dependence of the force by minus end motor proteins results in a stable mitotic spindle length which is determined by the ratio of stepping velocities of overlap motors and minus end motors. The antiparallel microtubule overlap region, whose length is fixed in the model, shows centering behavior in the length dependent model variant, while without length dependence it sustains its initial off-centered position. These results suggest a potential motor protein driven, microtubule-length-dependent mechanism of spindle length regulation at microtubule minus ends
Determining the dynamics of a physical system using interpretable deep learning algorithms
No full textOvaj diplomski rad istražuje primjenu interpretabilnih algoritama dubokog učenja za modeliranje dinamike populacije neurona koristeći podatke vremenskih nizova. Neuronske simulacije generirane Brian 2 simulatorom služe kao primarni skup podataka, replicirajući ponašanje međusobno povezane mreže neurona u kontroliranim uvjetima. U istraživanju se primjenjuje novi duboki konvolucijski okvir osmišljen za multivarijatne vremenske nizove, s naglaskom na interpretabilnost bez gubitka točnosti predikcije. To se postiže arhitekturom sposobnom za hvatanje aktivnosti pojedinačnih neurona i kolektivne dinamike, kao i pružanje uvida u temeljne mehanizme koji upravljaju tim ponašanjima. Prepoznavanjem najbitnijih značajki filtriranjem signala od šuma i aproksimacijom interakcija zadanim funkcijama, model spaja fleksibilnost dubokog učenja i interpretabilnost klasičnih regresija. Fokusirajući se na Izhikievichev model neurona, rad istražuje sposobnost modeliranja sustava vremenskih nizova i interpretabilnost modela. Rezultati pokazuju da ovakav interpretabilni pristup dubokog učenja može učinkovito analizirati i predvidjeti neuronsku dinamiku, povezujući područja strojnog učenja, neuroznanosti i fizike. Također, razvijene su nove ideje za prilagođavanje izlaza modela promatranom sustavu.This thesis explores the application of interpretable deep learning algorithms for modeling the dynamics of neuron populations using time-series data. Neural simulations generated with the Brian 2 simulator serve as the primary dataset, replicating the behavior of interconnected neural networks under controlled conditions. The study employs a novel deep convolutional framework for multivariate time series, emphasizing interpretability without sacrificing predictive accuracy. This is achieved through an architecture capable of capturing the activity of individual neurons and collective dynamics while providing insights into the fundamental mechanisms governing these behaviors. By identifying key features, filtering signals from noise, and approximating interactions with predefined functions, the model combines the flexibility of deep learning with the interpretability of classical regression techniques. Focusing on the Izhikevich neuron model, the work examines the capacity of time-series systems to model and interpret the dynamics. The results demonstrate that such an interpretable deep learning approach can effectively analyze and predict neural dynamics, bridging the fields of machine learning, neuroscience, and physics. Additionally, new ideas were developed for adapting the model's outputs to the observed system
Development of an in vivo tryptofanyl-tRNA synthetase inhibition assay
No full textAminoacil-tRNA-sintetaze (AaRS), predstavljaju dobru metu za razvoj novih antibiotika, jer
postoje značajne razlike između evolucijski očuvanih prokariotskih i eukariotskih enzima. Većina
bakterija koristi jednu konstitutivno eksprimiranu triptofanil-tRNA-sintetazu (TrpRS), no Bacillus
thuringiensis ima i bona fide inducibilnu TrpRS2, kojoj je zasad uloga nepoznata. U prijašnjim
istraživanjima na izoleucil-tRNA-sintetazi je pokazano da je IleRS2 inducibilna te daje bakterijama
otpornost na mupirocin, dok konstitutivna verzija ima bolju učinkovitost u aminoacilaciji.
Postavljena je hipoteza da bi TrpRS2 mogla imati sličnu ulogu. Stoga je klonirana promotorska
regija gena za TrpRS2 iz B. thuringiensis u Bacillus subtilis s povezanim reporterskim genom
(lacZ). Ovaj sintetski sustav omogućio bi brzi probir prirodnih spojeva koji mogu inhibirati
triptofanil-tRNA-sintetazu, što bi moglo doprinijeti razvoju novih antibiotika. Do sada je u
kliničkoj primjeni samo tri inhibitora AaRS: mupirocin, halofuginon i tavaborol.Aminoacyl-tRNA-synthetases (AaRS) represent a good target for the development of new
antibiotics, because there are significant differences between evolutionarily conserved prokaryotic
and eukaryotic enzymes. Most bacteria use one constitutively expressed tryptophanyl-tRNAsynthetase (TrpRS), but Bacillus thuringiensis also has a bona fide inducible TrpRS2, whose role
is currently unknown. In previous research, on isoleucyl-tRNA-synthetase, it was shown that
IleRS2 is responsible for bacterial resistance to mupirocin, while the constitutive version has better
efficiency in aminoacylation. It was hypothesized that TrpRS2 might play a similar role. Therefore,
the promoter region of the TrpRS2 gene from B. thuringiensis was cloned into Bacillus subtilis
with an associated reporter gene (lacZ). This synthetic system would enable rapid screening of
natural compounds that can inhibit tryptophanyl-tRNA-synthetase, which could contribute to the
development of new antibiotics. So far, only three AaRS inhibitors are in clinical use: mupirocin,
halofuginone and tavaborole
Bioraznolikost epibiotskih dijatomeja glavate želve (Caretta caretta)
No full textLogerhead sea turtles host the most diverse range of macroepibionts, such as arthropods, molluscs or macroalgae. The surface of their skin and carapace is initially colonized by microepibiontic biofilm formed by bacteria, fungi and protists. Among them diatoms gained prominent attention as there are several taxa exclusively living on sea turtles. The aim of this study was to compare diatom communities found on loggerhead sea turtles from different geographic locations and to observe the changes in assemblages based on the time loggerheads spent under rehabilitation. The data were collected from carapaces and skins of 91 loggerheads from 2017 to 2022 from four locations in Adriatic and Aegean Sea. Results showed significantly different epibiontic diatom communities among locations. We also found significant difference between diatom communities on sea turtles that were sampled in their natural habitats and turtles held in rehabilitation for longer than 30 days. Poulinea lepidochelicola was the most abundant species in the natural communities, and was completely absent from loggerheads in rehabilitation. However, we found that diatom assemblages on rehabilitated turtles closely resembled those found on pool tank plastic sides. This research contributes to the understanding of the relationship between epizoic diatoms and sea turtles as their hosts.Glavate želve su domaćini raznih epibiontskih organizama kao što su člankonošci, školjkaši i makroalge. Na površini kože i oklopa se inicijalno stvara mikroepibiontski biofilm kojeg formiraju bakterije, gljive i protisti među kojima su najvažnije dijatomeje. Nedavno je otkriveno da nekoliko vrsta dijatomeja živi isključivo na površini morskih kornjača. Cilj ovog istraživanja je bio usporediti zajednice dijatomeja s glavatih želvi s različitih geografskih lokacija te ispitati postoje li razlike između epibiontskih dijatomejskih zajednica ovisno o vremenu koje su želve provele u centrima za oporavak. Podaci su prikupljeni iz uzoraka sakupljenih između 2017-2022 s kože i oklopa 91 glavate želve s četiri lokacije u Jadranskom i Egejskom moru. Rezultati su pokazali značajne razlike između epibiontskih dijatomejskih zajednica s različitih lokacija te između zajednica s želvi koje su uzorkovane u prirodnom staništu i želvi koje su se nalazile u oporavilištima duže od 30 dana. Poulinea lepidochelicola je bila najbrojnija vrsta u prirodnim zajednicama, dok je u potpunosti bila odsutna sa želvi koje su uzorkovane u oporavilištima. Međutim, zajednice dijatomeja na želvama u oporavilištima su bile iznimno slične zajednicama biofilma koji je nađen na stijenkama plastičnih bazena u oporavilištima. Ovo istraživanje pridonosi razumijevanju odnosa između epizojskih dijatomjea i morskih kornjača kao njihovih domaćina