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Comparison of algorithms based on the gradient boosting paradigm: Application to real medical and physical datasets
No full textU ovom radu se proučavaju razni pristupi strojnom učenju s naglaskom na algoritme bazirane na paradigmi gradient boostinga, ulazi se u njihovu matematičku pozadinu i u dubine funkcioniranja algoritama. Uspoređuje se efikasnost gradient boostinga, XGBoosta, LightGBM-a, CatBoosta i slučajne šume na dva skupa podataka. Skup podataka Higgsovog bozona nastoji identificirati Higgsov bozon unutar raznih signala. Skup podataka za emboliju nastoji predvidjeti hoće li pacijent preživjeti do svoje sljedeće kontrole. Rezultati navedenih algoritama se mjere njihovom točnošću, opozivom, preciznošću i ROC-AUC vrijednosti. Mjeri se i značajnost značajki pripadnih skupova podataka pomoću Shapleyjevih vrijednosti.This thesis examines various approaches to machine learning, with a focus on algorithms based on the gradient boosting paradigm. It delves into their mathematical foundations and the intricacies of their inner workings. The efficiency of gradient boosting, XGBoost, LightGBM, CatBoost, and random forests is compared using two datasets: the Higgs boson dataset, which aims to identify the Higgs boson among various signals, and the embolism dataset, which seeks to predict patient outcomes based on disease severity and other comorbidities. The performance of these algorithms is evaluated using accuracy, recall, precision, and ROC-AUC values. Additionally, the signficance of the features in each dataset is assessed using Shapley values
INFLUENCE OF METAL SPECIATION ON TOXICITY OF COPPER–BASED NANOPARTICLES IN SELECTED MICROALGA, MUSSEL AND URCHIN SPECIES
No full textNanočestice (eng. nanoparticles, NP) bakra upotrebljavaju se kao antimikrobni aditivi u tekstilnoj industriji, tehnologiji pročišćavanja vode i premazima protiv obraštaja. Upravo upotreba u bojama predstavlja izravniji put za ispuštanje u morski okoliš, zbog degradacije boje u brodskim premazima tijekom vremena gdje mogu utjecati na širok raspon organizama u svim životnim fazama, od embrija do odraslih jedinki. Cilj ovog rada bio je istražiti utjecaj specijacije nanočestica bakra (CuNP), bakrovog (II) oksida (CuONP) i bakrovog (I) oksida (Cu2ONP) i kako abiotički čimbenici (svjetlosna jakost, salinitet i pH vode) utječu na stabilnost NP. Potencijalni toksični učinak specijacije NP ispitan je na morskim organizmima: mikroalgi Dunaliella salina, dagnji Mytilus galloprovincialis te ježincima Arbacia lixula, Paracentrous lividus i Sphaerechinus granularis. Na razini organizma pratila se fotosintetska učinkovitost kod mikroalge, test stres na stres kod dagnje te test spermiotoksičnosti i embriotoksičnosti kod ježinaca, gdje je ispitan negativan utjecaj ovisno o koncentraciji navedenih nanočestica. Na staničnoj razini kod mikroalge istražena je lipidna peroksidacija te aktivnost enzima glutation S–transferaze (GST), katalaze (CAT) i superoksid dismutaze (SOD). Kod dagnje je određena i razina metalotioneina (MT) u probavnoj žlijezdi te aktivnost acetikolinesteraze (AChE), a kod ježinaca test citogenotoksičnosti. Ovi testovi su pokazali korelaciju između razine oksidativnog stresa, aktivacije obrambenih mehanizama i fizikalno-kemijskih karakteristika NP. Općenito, ovaj rad je pokazao kako su Cu2ONP najtoksičnije za sve ispitane organizme, što može imati posljedice u svim razvojnim fazama budući da je to oblik NP bakra koji se naširoko koristi u premazima protiv obraštaja.Copper nanoparticles (NP) are used as antimicrobial additives in the textile industry, water purification technology and anti-fouling coatings. It is their use in such coatings that represents a more direct route for their release into the marine environment where, due to the degradation of the coatings over time, they can affect a wide range of non-target organisms in all life stages, from embryos to adults. The aim of this doctoral thesis was to investigate the influence of speciation of copper (CuNP), copper (II) oxide (CuONP) and copper (I) oxide (Cu2ONP) and how abiotic factors such as light intensity, salinity and water pH can effect the stability of NP. The potential toxicity of these materials was tested on selected marine organisms: microalgae Dunaliella salina, mussels Mytilus galloprovincialis and sea urchins Arbacia lixula, Paracentrous lividus and Sphaerechinus granularis. At the whole organism level, photosynthetic efficiency was monitored in D. salina, physiological state in M. galloprovincialis, and impact on fertilisation ability, transmissible damage to offspring and developmental anomalies in the sea urchins, where a negative influence was shown depending on the NP concentration. At the cellular level, lipid peroxidation and the activity of glutathione S-transferase (GST), catalase (CAT) and superoxide dismutase (SOD) enzymes in microalgae D. salina were determined. Additionally, in M. galloprovincialis, the level of induced metallothionein in the digestive gland and the activity of acetylcholinesterase (AChE) in the gills were determined, while in sea urchins cytogenotoxicity was determined. These tests showed correlation between the level of oxidative stress, the activation of defense mechanisms and the physicochemical properties of NP. Overall, this study demonstrated that Cu2ONP were the most toxic to all organisms, which can have consequences in all developmental stages as this is the form of copper NP widely used in anti-fouling coatings
Composition and provenance of sandstones from Cretaceous-Paleogene deposits of the Gacko area (Bosnia and Herzegovina)
No full textTema ovog rada je odrediti sastav i provenijenciju pješčenjaka uzorkovanih na tri lokaliteta u okolici Gackog u Bosni i Hercegovini. Analizirani pješčenjaci su donjokredne i paleocenske starosti. Korištene su metode petrografska analiza te kvantitativna analiza teške frakcije, obje pomoć polarizacijskog mikroskopa. Metodom petrografske analize određeni su sastav čestica, struktura i tekstura preparata radi sedimentološke klasifikacije uzoraka i određivanja provenijencije klastičnog materijala. Metodom kvantitativne analize teške frakcije determinirani su i prebrojani teški minerali. Petrografskom je analizom utvrđeno sa se radi o arenitima i kalkarenitima. U sva tri uzorka primijećene su frakcije nelistićavih teških minerala: cirkon, turmalin, rutil, granati, Cr-spineli, epidot/zoisit i apatit. Porijeklo detritusa u pješčenjacima vezano je uz procese trošenja ofiolita i jedinica Adria mikroploče.The topic of this study is to determine the composition and provenance of sandstones sampled at three locations in the vicinity of Gacko, Bosnia and Herzegovina. The analyzed sandstones are of Lower Cretaceous and Paleocene age. Petrographic analysis and quantitative heavy mineral analysis methods were used, both with the aid of a polarizing microscope. The petrographic analysis method was used to determine the composition of particles, structure, and texture of the samples, to classify the sediments and establish the provenance of the clastic material. The quantitative heavy mineral analysis method was used to identify and count heavy minerals. Petrographic analysis established that the samples are arenites and calcarenites. All three samples contained fractions of non-micaceous heavy minerals such as zircon, tourmaline, rutile, garnet, Cr-spinel, epidote/zoisite, and apatite. The origin of the detritus in the sandstones is linked to the weathering processes of ophiolites and units of the Adria microplate
Topological orbital angular momentum extraction and twofold protection of vortex transport
No full textVortex phenomena are ubiquitous in nature. In optics, despite the availability of numerous techniques for vortex generation and detection, topological protection of vortex transport with desired orbital angular momentum (OAM) remains a challenge. Here, by use of topological disclination, we demonstrate a scheme to confine and guide vortices featuring arbitrary high-order charges. Such a scheme relies on twofold topological protection: a non-trivial winding in momentum space due to chiral symmetry, and a non-trivial winding in real space due to the complex coupling of OAM modes across the disclination structure. We unveil a vorticity-coordinated rotational symmetry, which sets up a universal relation between the vortex topological charge and the rotational symmetry order of the system. As an example, we construct photonic disclination lattices with a single core but different Cn symmetries and achieve robust transport of an optical vortex with preserved OAM solely corresponding to one selected zero-energy vortex mode at the mid-gap. Furthermore, we show that such topological structures can be used for vortex filtering to extract a chosen OAM mode from mixed excitations. Our results illustrate the fundamental interplay of vorticity, disclination and higher-order topology, which may open a new pathway for the development of OAM-based photonic devices such as vortex guides, fibres and lasers. Topological protection in disclination lattices that relies on non-trivial winding in momentum space and real space is used to confine and guide vortices that feature arbitrary high-order charges. This approach could help in the development of orbital angular momentum-based photonic devices
Simultaneous dispersive interaction of multiple frequency comb lines with a cold atomic cloud
No full textU ovom diplomskom radu proučavan je linearni disperzivni režim interakcije više linija frekventnog češlja s hladnim atomima rubidija unutar optičkog rezonatora. U svrhu promatranja pojedinih linija frekventnog češlja sastavljen je novi dio postava u kojem se stvaraju udari između zrake transmitirane kroz rezonator i kontinuiranog lasera. Mjerenja spektra i signala pojedinih linija potvrdila su da ovakva interakcija dovodi do pomicanja modova optičkog rezonatora. Iz izmjerenih vrijednosti lightshifta određen je broj atoma unutar struka rezonatora za interakciju s različitim linijama. Dobivene vrijednosti međusobno su konzistentne za linije koje se nalaze s iste strane Rb rezonance te je dano moguće objašnjenje za odstupanja dobivena za linije s različitih strana rezonance. Detaljnije je proučena ovisnost transmitirane amplitude jedne linije frekventnog češlja o detuningu pri čemu je uočeno da amplituda ovisi o smjeru promjene detuninga.In this thesis, we studied linear dispersive regime of interaction between multiple frequency comb lines and cold rubidium atoms inside an optical cavity. To observe individual frequency comb lines, we built a new part of the experimental setup, in which beats are created between a beam transmitted through the cavity and a continuous wave laser. Measurements of the spectrum and individual line signals confirmed that this type of interaction leads to a frequency shift of cavity modes. Using lightshift measurements we determined the number of atoms inside the cavity waist for interactions with different comb lines. The obtained values are mutually consistent for comb lines located on the same side of the Rb resonance, and a possible explanation was proposed for the deviations observed for the lines on the opposite sides of the Rb resonance. The dependence of transmitted amplitude on detuning was studied in more detail for one frequency comb line, and it was observed that the amplitude depends on the direction of the detuning change
PLANKTON COMMUNITIES IN THE DEEP KARSTIC LAKE: COMPOSITION AND TROPHIC INTERACTIONS
No full textFitoplankton je dobar pokazatelj ekološkog stanja jer brzo odgovara na okolišne pritiske. Analiza kompozitnih i eufotičkih uzoraka Visovačkog jezera pokazala je visoku razinu sličnosti u kvantitativnom i kvalitativnom sastavu fitoplanktona. Rezultati horizontalne raspodjele ukazuju na odvajanje uzoraka limnetičke i litoralne zone. Usporedivost morfološkog i molekularnog pristupa očituje se u detektiranju funkcionalnih grupa sličnih ekoloških karakteristika te se eDNA metabarkoding može koristiti u monitoringu. Usporedba mrežnih analiza trofičkih interakcija fitoplanktona i bakterioplanktona s drugim jezerima ukazala je kako ne postoji jedinstveni uzorak pojavljivanja određenih skupina bakterija te kako miksotrofija nije prevladavajući način ishrane dominantnih vrsta fitoplanktona Visovačkog jezera. Prema specifičnostima jezera predložene su prilagođene granične vrijednosti koncentracije klorofila a za ocjenu stupnja trofije. Stupanj trofije usporediv je s ekološkim stanjem te je ekološko stanje ocijenjeno dobro, a prema trofiji mezotrofno. Predloženo je mjerenje koncentracije klorofila a za brzu ocjenu, određivanje indeksa za fitoplankton jezera jednom mjesečno te postavljanje bove za praćenje na limnetičkom dijelu.The phytoplankton community is a good bioindicator as it reacts quickly to environmental pressures. The analysis of composite and euphotic samples from Lake Visovačko showed high degree of similarity in quantitative and qualitative composition of phytoplankton. The results of horizontal distribution indicated separation of limnetic and littoral zone samples. The comparability of morphological and molecular approaches was shown in the detection of functional groups with similar ecological characteristics, confirming eDNA metabarcoding as a reliable biomonitoring tool. A network analysis comparison of trophic interactions between phytoplankton and bacterioplankton with other lakes showed no clear pattern of occurrence of certain bacterial groups and that mixotrophy is not the predominant nutrition mode of the dominant phytoplankton species in Lake Visovačko. Regarding lake specificities, the adjusted threshold values for chlorophyll a concentration were proposed to assess the trophic state. It was proposed to measure chlorophyll a concentrations for a rapid daily assessment, to determine the lake phytoplankton index on a monthly basis and to install a buoy in the limnetic part of the Lake
Microtextural relations and genesis of garnet from Srednja Rijeka quarry (Mt. Moslavačka Gora)
No full textNa lokalitetu Srednja rijeka (Moslavačka gora) pronađeni su granati. Nalazili su se unutar leukogranitskih žila koje presjecaju dvotinjčasti granit. Makroskopskom i mikroskopskom analizom leukogranita utvrđene su glavne mineralne vrste: kvarc, K-feldspati, tinjci, andaluzit uz turmalin i granat. Rendgenskom difrakcijom na prahu izdvojenog granata ustanovljeno je da se radi o almandinskom varijetetu granata s dimenzijom jedinične ćelije a0 = 11,54 [Å]. Usporedbom prikupljenih podataka o opaženoj mineralnoj zajednici te podataka prikupljenih rendgenskom difrakcijom na prahu s drugim znanstvenim istraživanjima ustanovljeno je da je temperatura kristalizacije leukogranitnog magmatskog sustava koji sadrži almandinski granat morala biti na početku kristalizacije u okvirima raspona temperatura između 700 i 800 stupnjeva celzijusa te na kraju kristalizacije tlak manji od 400 MPa.Minerals from the garnet mineral group were found at the Srednja rijeka site (Moslavačka gora). They were located within the leucogranite veins that cut through the two-mica granite. Macroscopic and microscopic analysis of leucogranite revealed the main mineral types: quartz, K-feldspars, mica, andalusite along with tourmaline and garnet. By X-ray powder diffraction of the isolated garnet, it was established that it is an almandine variety of garnet with a unit cell dimension of a0 = 11.54 [Å]. By comparing the collected data on the observed mineral and the data collected by X-ray powder diffraction with other scientific research, it was established that the crystallization temperature of the leucogranite magmatic system containing almandine garnet must have been at the beginning of crystallization within the temperature range between 700 and 800 degrees Celsius and at the end of crystallization pressure less than 400 MPa
Regulation and significance of lysophospholipase PNPLA7 in a cellular model of metabolically active tissue
No full textGlavni cilj ove doktorske disertacije bio je istražiti važnost lizofosfolipaze PNPLA7 u staničnom modelu metabolički aktivnih tkiva mišića i jetre te procijeniti ovaj enzim kao metu toksičnih organofosfornih (OP) spojeva s obzirom da značaj i uloga ovog enzima nisu još dovoljno poznati. Dobiveni rezultati pokazuju da utišavanje PNPLA7 smanjuje razinu ionske pumpe NKAα1 te mete u signalnim putevima mTOR i AMPK što upućuje na važnost proteina PNPLA7 u osnovnoj fiziološkoj funkciji stanica. Zatim, pokazano je da povišenje koncentracije glukoze i inzulina rezultira smanjenjem razine PNPLA7 što sugerira da je reguliran ovisno o energetskom statusu stanice i da ima potencijalnu ulogu u metabolizmu energije. Također, izrađen je protokol za prekomjernu ekspresiju proteina u bakteriji Escherichia coli s ciljem kinetičke karakterizacije interakcija PNPLA7 sa supstratima i inhibitorima. Mjerenjem enzimske aktivnosti PNPLA7 u lizatima stanica, pokazano je da su eksprimirane forme patatinska domena i AB-patatinska domena katalitički aktivne prema supstratu p-nitrofenil valeratu i da su inhibirane odabranim OP spojevima. Zaključno, dobiveni rezultati upućuju na važnost PNPLA7 i važnost daljnjih istraživanja ovog enzima u razvoju lijekova za mogući tretman otrovanja OP-ima, ali i za liječenje drugih stanja i bolesti povezanih uz metabolizam lipida.The main goal of this doctoral dissertation was to examine the importance of lysophospholipase PNPLA7 in a cellular model of metabolically active muscle and liver tissue and to evaluate this enzyme as a target of toxic organophosphorus (OP) compounds, given that the significance and role of this enzyme are not yet sufficiently known. The obtained results show that the PNPLA7 silencing reduces the level of the ion pump NKAα1 and targets in the mTOR and AMPK signalling pathways, which points to the importance of PNPLA7 in the basic physiological function of cells. Furthermore, it was shown that an increase in glucose and insulin concentration results in a decrease of PNPLA7 levels, suggesting that it is regulated depending on the energy status of the cell and that it has a potential role in energy metabolism. Moreover, protocol for PNPLA7 overexpression in Escherichia coli was proposed for further kinetic studies of its interactions with substrates and inhibitors. By measuring PNPLA7 enzyme activity in cell lysates with p-nitrophenyl valerate, it was shown that the expressed forms of patatin domain and AB-patatin domain are catalytically active and are inhibited by OP compounds. In summary, the obtained results indicate the significance of PNPLA7 and the importance of further research on this enzyme in the development of drugs for the treatment of OP poisoning or in the treatment of other conditions and diseases related to lipid metabolism
Logistic regression and applications
No full textU prvom poglavlju ovog rada objašnjeni su osnovni pojmovi vezani za logističku regresiju kao i razlike između linearne te logističke regresije. Detaljno je definiran pojam logit funkcije kao i metoda maksimalne vjerodostojnosti kojom se procjenjuju parametri modela. Navedeno je nekoliko testova za testiranje značajnosti koeficijenata te kako se može dobiti procjena pouzdanih intervala za vrijednosti koeficijenata. Objašnjen je pojam omjera izgleda koji je temeljan za razumijevanje interpretacije parametara modela. Zatim je rečeno što ako nisu svi podaci dostupni. Po koracima je naveden postupak koji se najčešće slijedi kako bismo na kraju dobili odgovarajući model te je detaljno opisana stepwise metoda odabira varijabli koje će se nalaziti u modelu. Navedeni su i načini kako možemo usporediti dva modela te kako možemo procijeniti adekvatnost modela. U drugom poglavlju ovog rada prikazani su rezultati dobiveni provođenjem opisanih koraka za odabir varijabli koje će biti u modelu na dva primjera iz područja medicine. Pritom je korišten programski jezik R. U oba primjera kao konačan rezultat dobiveni su modeli koji su prema iznosu površine ispod ROC krivulje ocijenjeni odličnima. U primjeru o srčanom zatajenju dobiveno je da vjerojatnost smrti ovisi o vremenu praćenja pacijenta, o njegovoj dobi, te o vrijednostima kreatinina u krvi i ejekcijske frakcije. Vjerojatnost preživljavanja osoba koje imaju hepatocelularni karcinom može se modelirati u ovisnosti o dobi pacijenta, o tome ima li simptome karcinoma, o statusu njegovog općeg tjelesnog stanja, o tome je li bio i/ili je trenutno zaražen hepatitisom C te o vrijednostima hemoglobina i enzima alkalne fosfataze kao i o vrijednostima njihove međusobne interakcije.In the first chapter of this master thesis we introduced the basic concepts of logistic regression as well as the differences between linear and logistic regression. Logit function and maximum likelihood method for estimating parameters of the model were described in detail. A few statistical tests for testing for the significance of the coefficients and confidence interval estimations of the coefficients were also provided. The concept of odds ratio which is fundamental in understanding how to interpret parameters of the model is also introduced. Additionally, we discussed what to do when there are missing values in the data. We introduced the most common procedure for variable selection step by step and described stepwise procedure in great detail. Lastly, some ways of comparing two models and goodness-of-fit statistics were suggested. In the second chapter we demonstrated variable selection procedure on two medical examples using programming language R. In both examples the final models are considered to be excellent in terms of obtained value of the area under the ROC curve. In the first example regarding the heart failure data we can conclude that probability that patient died depends on their follow-up period, age, serum creatinine value and ejection fraction percentage whereas in the second example about hepatocellular carcinoma we can conclude that probability that patient survived is related to their age, performance status, hemoglobin and alkaline phosphatase values as well as its interaction value, whether they have symptoms of the disease and whether they are and/or were infected with hepatitis C
The effect of proteins, carbohydrates and oils on bioavailability of polyphenols and bioactivities of Ginkgo biloba L. leaf extract
No full textGinkgo biloba L. biljna je vrsta iz porodice Ginkgoaceae i poznata je po imenu „Ginko“ ili prema lokalnim imenima „Yin-xing“ u Kini i „Icho“ u Japanu. Ekstrakt lišća ginka koristi se u fitoterapiji i kao dodatak prehrani. Ima utjecaj na poboljšanje cerebralne cirkulacije, na mršavljenje, antidiabetički, antihipertenzitivni i hipolipemični učinak zbog čega se koriste za liječenje kardiovaskularnih bolesti. Cilj ovog rada je ispitati učinak proteina kazeina, glukoze i ulja na biodostupnost bioaktivnih tvari (fenola, flavonoida, fenolnih i hidroksicimetnih kiselina, flavanola, flavonola, proantocijanidina, terpenskih trilaktona) te na antioksidacijsku i antidijabetičku aktivnost i pomoć pri mršavljenu ekstrakta ginka u uvjetima probave in vitro. Koristeći spektrofotometrijske metode za određivanje koncentracije fitokemikalija, aktivnosti lipaze, α-amilaze, α-glukozidaze, glikacije albumina goveda i antioksidacijske aktivnosti, te analizu uzoraka ginka kromatografijom visoke moći razlučivanja i statističke metode (jednosmjerna ANOVA, Duncan test i analizu glavnih komponenti) utvrdila sam da primjena tableta ginka na prazan želudac ili uz hranu te sastav te hrane ovise o tome koji biološki učinak prvenstveno želimo postići. Što znači da treba imati drugačiji pristup u kombinaciji tableta ginka i hrane ako se radi o poboljšanju cerebralne cirkulacije i pamćenja, antioksidativnom ili antidijabetičkom učinku ili pomoći pri mršavljenju.Ginkgo biloba L. is a plant species from Ginkgoaceae family, and is famous by name „Ginko“ or by local names „Yin-xing“ in China and „Icho“ in Japan. Extract of ginko leves is used in phitotheraphy and as a dietary supplemnet. It has effect on cerebral circulation, weight loss and antidiabetic, antihypertensive and hipolipemic effect wherefore is used for cardiovascular disease treatment. The main purpose of this thesis is to evaluate the effect of proteins, carbohydrates and oils on bioavailability of bioactive compounds (phenols, flavonoids, phenolic and hidroksi cinnamic acids, flavanoids, flavonols, proanthocyanidins, triterpene lactones), antioxidant and antidiabetic effects, and weight loss effect of ginko leaves extracts in conditions of digestion in vitro. Using spectrophotometric methods to determine the concentration of phytochemicals, lipase, α-amylase and α-glucosidase activity, BSA glycation and antioxidant activity, HPLC analysis as well as statistical methods (one-way ANOVA, Duncan test and principal component analysis), I have confirmed that the use of ginkgo tablets on an empty stomach or with food, as well as the composition of these foods, depend on which biological effect we primarily want to achieve. Therefore, a different approach should be taken when combining ginkgo tablets with food