Funkcionalni i molekularni učinci prehrane bogate mastima u štakora s promijenjenom homeostazom serotonina

Održavanje energijske ravnoteže je složena fiziološka funkcija čija disregulacija može rezultirati pretilošću i metaboličkim poremećajima poput dijabetesa. Ovim radom željelo se doprinijeti boljem razumijevanju uloge serotonina (5HT) u mehanizmima regulacije energijske homeostaze, korištenjem sublinija štakora s konstitucijski povišenom (5HT-visoka) ili sniženom (5HT-niska) aktivnošću serotonina. Životinje iz obiju sublinija podvrgnute su visokokaloričnoj prehrani s visokim udjelom masti te je uspoređen njihov funkcionalni i molekularni odgovor na takav metabolički izazov. U skladu s prethodnim nalazima, životinje iz 5HT-visoke sublinije su u uvjetima standardne prehrane imale lošije metaboličko zdravlje od 5HT-niskih životinja. Međutim, 5HT-niske životinje su u odgovoru na visokokaloričnu prehranu pokazale veću sklonost debljanju, slabiju regulaciju glikemije, jači razvoj rezistencije na inzulin te veće promjene u ekspresiji različitih gena u hipotalamusu i bijelom masnom tkivu. Dobiveni rezultati pokazuju da je konstitucijski snižena aktivnost serotonina povezana s većom osjetljivošću na štetne učinke visokokalorične prehrane.Maintenance of energy balance is a complex physiological function, dysregulation of which can lead to obesity and metabolic disorders such as diabetes. Here, we aimed to contribute to a better understanding of the role of serotonin (5HT) in the mechanisms regulating energy homeostasis, by using sublines of rats with constitutionally increased (5HT-high) or decreased (5HT-low) activity of 5HT. Animals from both sublines were subjected to a high-calorie, high-fat diet and compared for their functional and molecular response to this metabolic challenge. Consistent with previous findings, when administered conventional diet, animals from the 5HT-high subline had poorer metabolic health than animals from 5HT-low subline. However, in response to a high-fat diet, 5HT-low animals showed a greater tendency to gain weight, poorer glycemic control, higher development of insulin resistance, and more pronounced changes in the expression of various metabolic genes in the hypothalamus and adipose tissue. The obtained results suggest that constitutionally decreased activity of 5HT is associated with a higher susceptibility to adverse effects of a high-calorie diet

Green synthesis of organopalladium photosensitizers

Razvijanje čišćih, bržih i ekonomski isplativijih preparativnih metoda za različite vrsta spojeva jedan je od ciljeva zelene i održive kemije. Izvedivost ovog koncepta zelene kemije prikazana je na sintezi organopaladijevih spojeva (paladocikla), važnih zbog njihove široke primjene u organskoj sintezi i jedinstvenih optičkih svojstava. Shodno tome, većina sintetskih koraka u ovom radu provedena je reakcijama u čvrstom stanju primjenom metoda mehanokemije ili ubrzanog starenja. Paladocikli s jednom ili dvije veze metal–ugljik i metal–donor dobiveni su aktivacijom veze(a) C–H u azobenzenima različitim katalizatorima paladija(II), a izmjena njihovih anionskih ili neutralnih liganada rezultirala je u derivatima s drugačijom reaktivnošću i optičkim svojstvima. Opisane reakcije praćene su in situ i ex situ spektroskopskim metodama što je omogućilo karakterizaciju vrsta uključenih u reakcije, izravan uvid u dinamiku i reakcijske putove, uvid u faktore koji kontroliraju reaktivnost i selektivnost, te optimizaciju procesa mljevenja. Ovi rezultati omogućit će primjenu razvijenih metoda i koncepata u sintezi novih organopaladijevih spojeva u okolišu prihvatljivim reakcijskim uvjetima, u izravnoj i selektivnoj zamjeni veze C–H drugim funkcionalnim skupinama, te u razvoju novih katalizatora.The development of clean, fast, and cost-effective preparative methods for various types of compounds is one of the objectives of green chemistry. The feasibility of this green chemistry concept was demonstrated on the synthesis of organopalladium compounds (palladacycles), important due to their wide application in organic synthesis and unique optical properties. Consequently, the majority of synthetic steps in this thesis were performed by solid-state synthetic method, mechanochemistry and accelerated aging. Palladacycles with one or two metal-carbon and metal-donor bonds were prepared via C–H bond(s) activation in azobenzenes by various Pd(II) catalysts, and the exchange of their anionic or neutral ligands resulted in derivatives with different reactivity and optical properties. The described reactions were monitored in situ and ex situ by spectroscopic methods, which enabled the characterization of the species involved in the reactions, direct insight into the reaction pathways, insight into the factors controlling reactivity and selectivity, and optimization of the grinding process. These results will enable the application of developed methods and concepts in the synthesis of new organopalladium compounds, in the direct and selective replacement of the C–H bond by other functional groups, and in the development of new catalysts

Stereochemistry of 2,2'-iminodiacetamide and bis(2-pyridine-2-ylmethyl)amine complexes and their application in enantioselective catalysis

U okviru ove disertacije proučavana je stereokemija kompleksa 2,2'-iminodiacetamida i bis(piridin-2-ilmetil)amina, te je ispitan utjecaj supstituenata na ligandu, aniona, i nekovalentnih interakcija. Pripravljeni ligandi podijeljeni su u četiri skupine. Priređeno je 8 različito supstituiranih iminodiacetamidnih liganada (A) te je istražen utjecaj supstituenata na stereokemiju metalnih kompleksa. S H-supstituiranim ligandom dobivena je kristalna struktura cis-fac kompleksa, dok su s ostalim ligandima dobiveni trans-fac izomeri. S izopropilsupstituiranim bis(piridin-2-ilmetil)aminskim ligandom (B) priređeni su kompleksi koristeći Cu(II) i Zn(II) s različitim anionima. Ovisno o anionu, dobivene su kristalne strukture monomera, dimera, cis-fac-ML2 kompleksa te ciklički trimer koji veže CO2 iz zraka. Kompleksi Fe(II) s 2 cikloheksandiaminska derivata (C) ispitani su u katalitičkim reakcijama kao mimici enzima flavon sintaze. Također je priređeno 7 bis(piridin-2-ilmetil)aminskih i 5 iminodiacetamidnih liganada (D) s različitom duljinom CH2 poveznice i različitim kiralnim skupinama kako bi se istražio utjecaj strukturnih promjena na koordinacijska svojstva liganada u kompleksima Cu(II) i Zn(II). Ligandi s 3 CH2 skupine tvorili su komplekse ML2 stehiometrije, dok je kod liganada s 2 CH2 skupine došlo do koordinacije pokrajnjeg lanca i stvaranja ML kompleksa. Kompleksi ML stehiometrije pokazali su aktivnost u DNA cijepanju.In this dissertation, the stereochemistry of 2,2'-iminodiacetamide and bis(pyridin-2-ylmethyl) amine ligand complexes was studied, focusing on the influence of substituents on the ligand, anion and noncovalent interactions. The prepared ligands were divided into four groups. Eight differently substituted iminodiacetamide ligands (A) were prepared. A cis-fac crystal structure was obtained with the H-substituted ligand, while the other ligands gave trans-fac isomers. Complexes with Cu(II) and Zn(II) were prepared with a isopropyl-substituted bis(2-pyridine- 2-ylmethyl)amine ligand (B). Depending on the anion, crystal structures of monomers, dimers, a cis-fac-ML2 complex and a cyclic trimer that binds CO2 from air were obtained. Fe(II) complexes with two cyclohexanediamine derivatives (C) were investigated in catalytic reactions as flavone synthase mimics. Furthermore, 7 bis(2-pyridine-2-ylmethyl)amine and 5 iminodiacetamide ligands (D) with different lengths of CH2 linkers and different chiral groups were prepared to study the influence of structural changes on the coordination properties of these ligands in Cu(II) and Zn(II) complexes. Ligands with 3 CH2 groups formed ML2 complexes, while ligands with 2 CH2 groups showed side chain coordination and formation of ML complexes. Complexes of ML stoichiometry showed DNA cleavage activity

Računalno istraživanje reakcija slobodnih radikala s halogeniranim organskim spojevima u vodenim otopinama

U disertaciji su istraženi mehanizmi i kinetike reakcija slobodnih radikala s halogeniranim organskim spojevima u nepuferiranim i puferiranim (bikarbonatnim i fosfatnim) vodenim otopinama. Rad obuhvaća istraživanje reaktivnosti α-aminoalkilnih C-radikala: α-aminoetilnog (•CH(CH_3 ) NH_2) i N-metil--aminoetilnog (•CH(CH_3 ) NHCH_3), zatim glicil radikal aniona (•CH(NH_2 ) COO^-) i atoma vodika (H^•) s trima halogenacetatima – klor-, brom- i jodacetatom – te s halogeniranom nukleobazom 5-bromuracilom. U reakcijama je uočeno nekoliko kompetitivnih mehanizama, od kojih je najznačajniji spregnuti prijenos protona i elektrona (PCET). Otapalo voda isprva je opisano implicitno, modelom PCM, a potom je istražen utjecaj eksplicitne molekule vode na mehanizme i reakcijsku energetiku. Na temelju parametara izračunatih teorijom funkcionala elektronske gustoće (DFT) određeni su dominantni reakcijski mehanizmi i kinetike reakcija. Kod izračuna konstanti brzina uporabljena je konvencionalna teorija prijelaznog stanja i njezina varijacijska inačica uz semiklasične popravke na tuneliranje. Sustavnim istraživanjem izmjensko-korelacijskih funkcionala duž Jakovljevih ljestvi DFT-a nađeni su funkcionali koji daju najbolje slaganje s izmjerenim konstantama brzina za niz radikalskih reakcija.In this doctoral thesis the reaction mechanisms and kinetics of free radical reactions with halogenated organic compounds in non-buffered and buffered (bicarbonate and phosphate) aqueous solutions were investigated. This includes a study of the reactivity of C-centered α-aminoalkyl radicals: •CH(CH_3 ) NH_2, •CH(CH_3 ) NHCH_3, glycyl radical anion •CH(NH_2 ) COO^- and hydrogen atom (H^•) with haloacetates: chloro-, bromo- and iodoacetate and a halogenated nucleobase 5-bromouracil. Reactions exhibit a variety of fundamentally important competing mechanisms, of which the most important one is the proton coupled electron transfer. The solvent was initially described implicitly, and then the influence of explicit water molecules on the mechanisms and reaction energetics was explored. Based on the parameters calculated by the theory of density functional theory (DFT), the dominant reaction mechanisms and reaction kinetics were determined. The reaction rate constants were calculated employing the conventional and variational transition state theory with semiclassical corrections for the tunneling. By systematically climbing up the Jacob's ladders of DFT, for the set of radical reactions, we investigated which types of exchange-correlation functionals produce the rate constants in best agreement with the measured ones

Utjecaj otpadnih voda farmaceutskih industrija na razvoj i širenje otpornosti na antibiotike

Cilj rada bio je istražiti utjecaj ispusta otpadnih voda iz dviju lokalnih farmaceutskih industrija na recipijentni vodeni okoliš, s naglaskom na razvoj i širenje otpornosti na antibiotike te sastav bakterijskih zajednica. Kemijskom analizom potvrđene su relativno visoke koncentracije antibiotika u otpadnim vodama tih industrija te znatno više koncentracije antibiotika u sedimentima recipijentnih voda nizvodno od ispusta u odnosu na referentnu lokaciju uzvodno od ispusta. Funkcionalnom metagenomikom identificirani su poznati i potencijalno novi geni za otpornost na ciljane antibiotike u otpadnim vodama i sedimentima. Kvantifikacijom odabranih gena otpornosti utvrđene su značajno više količine u sedimentima na lokaciji ispusta i nizvodno od ispusta u odnosu na referentnu uzvodnu lokaciju. Egzogenom izolacijom plazmida potvrđeno je povećano horizontalno širenje gena otpornosti na makrolide i/ili tetracikline u sedimentima onečišćenima otpadnim vodama farmaceutskih industrija. Filogenetskom analizom nukleotidnih sekvenci gena ermB potvrđena je njihova visoka sličnost između okolišnih bakterijskih izolata porijeklom iz riječnog sedimenta izrazito onečišćenog makrolidima i kliničkih izolata streptokoka, što ukazuje na mogući prijenos ovog gena između bakterija kliničkog i okolišnog podrijetla. Sekvenciranjem amplikona 16S rRNA gena utvrđene su značajne prostorne i sezonske promjene u sastavu bakterijskih zajednica izloženih sedimenata. Rezultati ovog istraživanja ukazali su na problem onečišćenja okoliša otpadnim vodama farmaceutskih industrija, što može predstavljati potencijalnu opasnost za zdravlje ljudi i okoliša.The aim of this work was to explore the impact of the wastewater discharge from two local pharmaceutical industries on the recipient freshwater environments, particularly regarding the development and spread of antibiotic resistance and bacterial communities composition. Chemical analyses confirmed relatively high antibiotic concentrations in the wastewater from those industries and considerably higher antibiotic concentrations in recipient sediments downstream from the discharge site when compared with upstream reference site. Functional metagenomics revealed already known and potentially novel genes for resistance to targeted antibiotics in wastewater and sediments. Significantly higher concentrations of selected resistance genes were found in sediments at the disharge site and downstream from the pharmaceutical industries discharge site relative to the upstream reference site. Exogenous plasmid isolation revealed the increased horizontal transfer of macrolide and/or tetracycline resistance genes in antibiotic-polluted sediments. Phylogenetic analysis confirmed high similarity of the nucletiode sequences of the ermB gene between environmental bacterial isolates that originated from highly macrolide-polluted river sediments and clinical streptococcal isolates indicating potential transfer of this gene between bacteria of environmental and clinical origin. Sequencing of 16S rRNA gene amplicons revealed significant spatial and seasonal changes in bacterial communities composition of wastewater-exposed sediments. The results of this study highlight the problem of environmental pollution with pharmaceutical wastewater, which may pose a potential threat to both human and environmental health

Endiinski spojevi u višekomponentnim reakcijama

Trokomponentna Passerinijeva i četverokomponentna Ugijeva reakcija pripadaju skupini višekomponentnih reakcija koje uključuju izocijanidnu komponentu. Do sada u literaturi nije opisana primjena ovih reakcija u sintezi spojeva s endiinskim motivom. Stoga je cilj istraživanja provedenih u okviru ove doktorske disertacije bio primjena Passerinijeve i Ugijeve reakcije u sintezi endiinskih peptidomimetika. Pripravljena su četiri aldehida s različitom duljinom alkilne razmaknice u iskorištenju 78 - 96 %. Dobiveni aldehidi korišteni su u Passerinijevoj i Ugijevoj reakciji te je sintetiziran dvadeset jedan Passerinijev produkt u iskorištenju 29 - 92 % i trideset dva Ugijeva produkta u iskorištenju 13 - 93 %. Dokazana je mogućnost postmodifikacija Passerinijevih i Ugijevih produkata. Pripravljen je jedan postmodificirani Passerinijev produkt u 50%-tnom iskorištenju te dvadeset pet Sonogashirinih produkata u iskorištenju 34 - 99 %. Ciklizacijom Sonogashirinih produkata dobiveno je šesnaest makrocikličkih spojeva s endiinskim motivom i esterskom vezom u iskorištenju 9 - 68 %

Računalni postupci za modeliranje i analizu medijske agende temeljeni na strojnome učenju

Rad se bavi računalnim postupcima analize medijske agende (engl. Media Agenda) temeljenima na tematskim modelima (engl. Topic Models) te metodama vrednovanja tematskih modela. Analiza medijske agende provodi se radi stjecanja uvida u strukturu i zastupljenost medijskih tema, što je od interesa za društvenoznanstvena istraživanja te za medijsku industriju i druge komercijalne i političke aktere. Računalni postupci analize medijske agende omogućuju auto- matsko otkrivanje tema u velikim skupovima tekstova i mjerenje njihove zastupljenosti. Ovi postupci pružaju analitičaru uvid u teme prisutne u medijima i uvid u zastupljenost tema u poje- dinim medijima i vremenskim razdobljima te omogućuju analizu korelacije zastupljenosti tema sa podacima poput ljudske percepcije njihove važnosti. Cilj istraživanja bio je razvoj računalnih postupaka za eksplorativnu analizu i mjerenje me- dijske agende temeljenih na tematskim modelima, klasi modela strojnog učenja pogodnih za analizu tematske strukture teksta. Istraživanje obuhvaća razvoj postupaka primjene tematskih modela na otkrivanje medijskih tema i mjerenje njihove zastupljenosti te razvoj računalnih alata za unaprijed̄enje i provedbu tih postupaka. Ti alati obuhvaćaju metode vrednovanja tematskih modela te programsku potporu za implementaciju postupaka analize agende i vrednovanja mo- dela. Primjena postupaka na analizu medijskih tekstova brzo je pokazala potrebu za razvojem novih metoda vrednovanja tematskih modela radi povećanja efikasnosti na modelima temelje- nih postupaka. Iz tog je razloga poseban naglasak istraživanja bio na razvoju i analizi metoda vrednovanja tematskih modela. Prvo je provedeno istraživanje postupaka primjene tematskih modela na analizu medijske agende. Na temelju istraživanja postojećih postupaka predložen je poboljšani postupak koji se sastoji od tri koraka: koraka otkrivanja tema, koraka definicije tema i koraka mjerenja tema. Predloženi postupak otklanja uočene nedostatke ranijih metoda: upotrebu samo jednog modela za otkrivanje tema, nemogućnost prilagodbe i definicije novih tema te izostanak kvantitativnog vrednovanja metoda mjerenja. Postupak je primijenjen u dvije analize medijske agende prove- dene na zbirkama američkih i hrvatskih političkih vijesti. Na temelju opažanja i podataka iz tih analiza uočena je potreba za mjerom interpretabilnosti tema modela te za metodom mjerenja pokrivenosti skupa koncepata od strane modela. Drugi istraženi problem bio je problem mjerenja interpretabilnosti tema modela. Standardni pristup ovom problemu je mjerenje semantičke koherentosti tema, a postojeće mjere koherent- nosti temelje se na računanju koherentosti skupa uz temu vezanih riječi. Ove mjere pokazale su se nepogodnima u slučaju prolaznih medijskih tema karakteriziranih semantički nepovezanim riječima. Predložena je nova klasa mjera koherentosti medijskih tema temeljenih na uz teme vezanim dokumentima. Vrednovanje niza predloženih mjera na skupovima engleskih i hrvat- skih medijskih tema otkrilo je najbolju mjeru koja računa koherentnost agregacijom lokalne povezanosti grafa dokumenata. Provedena je kvantitativna i kvalitativna usporedba razvijenih mjera dokumentne koherentosti s postojećim mjerama koherentnosti riječi koja je otkrila kom- plementarnost ova dva tipa mjera. Treći istraženi problem je problem pokrivenosti tema, motiviran podacima iz primjene pos- tupka analize medijske agende, koji su pokazali da jedan tematski model pokriva samo dio svih otkrivenih koncepata. Problem pokrivenosti nadilazi domenu medijskih tekstova i unatoč važnosti ovog problema dosadašnja istraživanja na tu temu su rudimentarana. Problem pokri- venosti razmotren je u općenitosti i definiran kao problem mjerenja poklapanja izmed̄u skupa automatski naučenih tema modela i skupa referentnih tema koji sadrži od ljudi uočene koncepte. Predložena je metoda izrade skupa referentnih tema i dvije metode mjerenja pokrivenosti teme- ljene na računanju poklapanja tema. Predložene mjere vrednovane su na dva raznorodna skupa podataka, medijskom i biološkom, te primijenjene na analizu četiri različite klase standardnih tematskih modela. Završni korak istraživanja postupka analize medijske agende bio je poboljšanje postupka na temelju predloženih metoda vrednovanja tematskih modela i iskustava iz primjena postupka na analizu hrvatskih i američkih medija. Glavna poboljšanja odnose se na korak eksplorativne analize odnosno otkrivanja tema i temelje se na razvijenim mjerama pokrivenosti i dokumentne koherentosti tema. Ova poboljšanja imaju za cilj brže otkrivanje većeg broja koncepata. Ostala poboljšanja odnose se na povećanje efikasnosti postupka interpretacije tema modela. Tijekom istraživanja postupka analize medijske agende i metoda vrednovanja tematskih mo- dela uočen je niz problema vezanih uz upotrebu, izgradnju, pohranu i dohvat tematskih modela i vezanih resursa. Ovi problemi javljaju se kod implementacije grafičkog korisničkog sučelja za provedbu postupka i kod provedbe eksperimenata vrednovanja. Rješavanju ovih problema pristupilo se sustavno i oblikovan je radni okvir za izgradnju i upravljanje resursima u temat- skom modeliranju. Arhitektura okvira temelji se na četiri načela koja u kombinaciji definiraju općenitu i fleksibilnu metodu izrade programske potpore za primjenu i vrednovanje tematskih modela. Razvijeni su i grafičko korisničko sučelje za eksplorativnu analizu i potporu mjere- nju zastupljenosti tema te aplikacija namijenjena izradi zbirki medijskih tekstova koja tijekom duljeg vremenskog razdoblja sakuplja tekstove iz niza web-izvora.This thesis focuses on computational methods for media agenda analysis based on topic mo- dels and methods of topic model evaluation. The goal of a media agenda analysis is gaining insights into the structure and frequency of media topics. Such analyses are of interest for social scientists studying news media, journalists, media analysts, and other commercial and political actors. Computational methods for media agenda analysis enable automatic discovery of topics in large corpora of news text and measuring of topics’ frequency. Data obtained by such analyses provides insights into the type and structure of topics occurring in the media, enables the analysis of topic cooccurrence, and analysis of correlation between topics and other variables such as text metadata and human perception of topic significance. The goal of the research presented in the thesis is development of efficient computational methods for the discovery of topics that constitute the media agenda and methods for measu- ring frequencies of these topics. The proposed methods are based on topic models – a class of unsupervised machine learning models widely used for exploratory analysis of topical text structure. The research encompasses the development of applications of topic models for dis- covery of media topics and for measuring topics’ frequency, as well as development of methods for improvement and facilitation of these applications. The improvement and facilitation met- hods encompass methods of topic model evaluation and software tools for working with topic models. Methods of topic model evaluation can be used for selection of high-quality models and for accelerating the process of topic discovery. Namely, topic models are a useful tool, but due to the stohasticity of the model learning algorithms the quality of learned topics varies. For this reason the methods of topic model evaluation have the potential to increase the efficiency of the methods based on topic models. Media agenda consists of a set of topics discussed in the media, and the problem of media agenda analysis consists of two sub-tasks: discovery of the topics on the agenda and measu- ring the frequencies of these topics. The first contribution of the thesis is a method for media agenda analysis based on topic models that builds upon previous approaches to the problem and addresses their deficiencies. Three notable deficiencies are: usage of a single topic model for topic discovery, lack of possibility to define new topics that match the analyst’s interests,\ud and the lack of precise evaluation of methods for measuring topics’ frequency. In addition to addressing the identified deficiencies, the method also systematizes the previous approaches to the problem and is evaluated in two case studies of media agenda analysis. The proposed experimental method for media agenda analysis consists of three steps: topic discovery, topic definition, and topic measuring steps. In order to achieve better topic coverage, the discovery step is based not on a single model but on a set of topic models. The type and number of topic models used depends on available model implementations and the time available for topic annotation, while the hyperparameter defining the number of model topics depends on the desired generality of learned topics. Reaso- nable default settings for model construction are proposed based on the existing agenda analysis studies and an iterative procedure for tuning the number of topics is described. After the topic models are constructed, topic discovery is performed by human inspection and interpretation of the topics. Topic interpretation produces semantic topics (concepts) that are recorded in a reference table of semantic topics that serves as a record of topics and as a tool for synchroni- zation of human annotators. After all the model topics are inspected, annotators can optionally perform the error correcting step of revising the semantic topics, as well as the step of building a taxonomy of semantic topics. Topic discovery is supported with a graphical user interface developed for topic inspection and annotation. The step of topic definition is based on semantic topics obtained during topic discovery. The purpose of topic definition is to define new semantic topics that closely match the analyst’s exact interests. The possibility of defining new semantic topics is an important difference between the proposed and the existing media agenda analysis approaches. Namely, the existing approaches base the analysis only on model-produced topics, although there is no guarantee that these topics will match the concepts of interest to the analyst. During topic definition, the analysts infers definitions of new semantic topics based on previously discovered topics and describes these topics with word lists. Discovered semantic topics that already closely match the concepts of interest are used without modification. During the step of topic measuring the frequencies of semantic topics obtained during the discovery and definition steps are measured. Topic frequency is defined as the number of news articles in which a topic occurrs, and the measuring problem is cast as the problem of multi-label classification in which each news article is being tagged with one or more semantic topics. This formulation allows for precise quantitative evaluation of methods for measuring topic frequency. Two measuring methods are considered. The baseline is a supervised method using the method of binary relevance in combination with a linear kernel SVM model. The second method is a newly proposed weakly supervised approach, in which the measured semantic topics are first described by sets of highly discriminative words, after which a new LDA model is constructed in such a way that the topics of the model correspond to measured topics, which is achieved via prior probabilities of model topics. The method for selecting words highly discriminative for a semantic topic represents the main difference between the proposed and the previous weakly supervised approaches. This method consists of inspecting, for each measured semantic topic, closely related model topics, and selecting words highly discriminative for the topic by means of inspecting word-related documents and assessing their correspondence with the topic. The proposed three-step method for media agenda analysis is applied to two media agenda analyses: the analysis of mainstream US political news and the analysis of mainstream Croatian political news in the election period. The applications of the proposed method show that the topic discovery step gives a good overview of the media agenda and leads to the discovery of useful topics, and that the usage of more than one topic model leads to a more comprehensive set of topics. The two analyses also demonstrate the necessity of the proposed topic definition step – in the case of US news new sensible topics corresponding to issues are pinpointed during this step, while in the case of Croatian election-related news the analysis is based entirely on newly defined semantic topics that describe the pre- and post-election processes. Quantitative evaluation of topic frequency measuring shows that the proposed weakly supervised approach works better than the supervised SVM-based method since it achieves better or comparable performance with less labeling effort. In contrast to the supervised method, weakly supervi- sed models have a higher recall and work well for smaller topics. Qualitative evaluation of measuring models confirms the quality of the proposed approach – measured topic frequency correlates well with real-world events and the election-related conclusions based on measuring models are in line with conclusions drawn from social-scientific studies. Observations from two media agenda analysis studies and the analysis of collected topic data underlined two problems related to methods of topic model evaluation. The first is the problem of measuring topic quality – the studies both confirmed variations in topic quality and indicated the inadequacy of existing word-based measures of topic coherence. The second is the problem of topic coverage – while the data confirms the limited ability of a single topic model to cover all the semantic topics, no available methods for measuring topic coverage exist, so it is not possible to identify the high-coverage models. These observations motivated the development of new methods of topic model evaluation – document-based coherence measures and methods for topic coverage analysis. As described, the analysis of topics produced during the applications of topic discovery confirmed variations in topics’ quality and underlined the need for better measures of topic quality. The analysis also indicated that existing word-based measures of topic coherence are inadequate for evaluating quality of media topics often characterized by semantically unrelated word sets. Based on the observation that media topics can be successfully interpreted using topic-related documents, a new class of document-based topic coherence measures is proposed. The proposed measures calculate topic coherence in three steps: selection of topic-related documents, document vectorization, and computation of the coherence score from document vectors. Topic-related documents are selected using a simple model-independent strategy – a fixed number of documents with top document-topic weights is selected. Two families of docu- ment vectorization methods are considered. The first family consists of two standard methods based on calculation of word and document frequencies: probabilistic bag-of-words vectoriza- tion and tf-idf vectorization. Methods in the second family vectorize documents by aggregating either CBOW or GloVe word embeddings. Three types of methods are considered for cohe- rence score computation: distance-based methods that model coherence via mutual document distance, probability-based methods that model coherence as probabilistic compactness of do- cument vectors, and graph-based methods that model coherence via connectivity of the docu- ment graph. The space of all the coherence measures is parametrized and sensible parameter values are defined to obtain a smaller set of several thousand measures. Then the selection and evaluation of the coherence measures is performed, using model topics manually labeled with document-based coherence scores and using the area under the ROC curve (AUC) as the per- formance criterion. The measures are partitioned in structural categories and the best measure from each category is selected using AUC on the development set as a criterion. These best measures are then evaluated on two test sets containing English and Croatian news topics. The evaluation of document-based coherence measures shows that the graph-based measu- res achieve best results. Namely, best approximators of human coherence scores are the graph- based measures that use frequency-based document vectorization, build sparse graphs of locally connected documents and calculate coherence by aggregating a local connectivity score such as closeness centrality. Quantitative evaluation of word-based measures confirms the observations that word-based measures fail to approximate document-based coherence scores well and qu- alitative evaluation of coherence measures indicates that document- and word-based coherence measures complement each other and should be used in combination to obtain a more complete model of topic coherence. Motivated by the data from the topic discovery steps performed in two media agenda analyses and by the obvious need to increase the number of topics discovered by a single topic model, the problem of topic coverage is defined and solutions are proposed. This problem occurrs in ap- plication of topic models to any text domain, i.e., it is domain-independent and extends beyond applications to media text. The problem of topic coverage consists of measuring how automati- cally learned model topics cover a set of reference topics – topical concepts defined by humans. Two basic aspects of the problem are the reference topics that represent the concepts topic mo- dels are expected to cover and the measures of topic coverage that calculate a score measuring overlap between the model topics and reference topics. Finally, the third aspect encompasses evaluation of a set of topic models using a reference set and coverage measures. The coverage experiments are conducted using two datasets that correspond to two separate text domains – news media texts and biological texts. Each dataset contains a text corpus, a set of reference topics, and a set of topic models. Reference topics consist of topics that standard topic models are expected to be able to cover. These topics are constructed by human inspection, selection, and modification of model-learned topics. Both sets of reference topics are representative of useful topics discovered during the process of exploratory text analysis. Two approaches to measuring topic coverage are developed – an approach based on super- vised approximation of topic matching and an unsupervised approach based on integrating co- verage across a range of topic-matching criteria. The supervised approach is based on building a classification model that approximates human intuition of topic matching. A binary classifier is learned from a set of topic pairs annotated with matching scores. Four standard classification models are considered: logistic regression, support vector machine, random forest, and multi- layer perceptron. Topic pairs are represented as distances of topic-related word and document vectors using four distinct distance measures: cosine, hellinger, L1 , and L2. Model selection and evaluation shows that the proposed method approximates human scores very well, and that logistic regression is the best-performing model. The second proposed method for measuring coverage uses a measure of topic distance and a distance threshold to approximate the equality of a reference topic and a model topic. The threshold value is varied and for each threshold coverage is calculated as a proportion of reference topics that are matched by at least one model topic at a distance below the threshold. Varying the threshold results in a curve with threshold values on the x-axis and coverage scores on the y-axis. The final coverage score is calculated as the area under this curve. This unsupervised measure of coverage, dubbed area under the coverage-distance curve, correlates very well with the supervised measures of coverage, while the curve itself is a useful tool for visual analysis of topic coverage. This measure enables the users to quickly perform coverage measurements on new domains, without the need to annotate topic pairs in order to construct a supervised coverage measure. Using the proposed coverage measures and two sets of reference topics, coverage experi- ments in two distinct text domains are performed. Experiments consist of measuring coverages obtained by a set of topic models of distinct types constructed using different hyperparameters. In addition to demonstrating application of coverage methods, the experiments show that the NMF model has high coverage scores, is robust to domain change and able to discover topics on a high level of precision. Nonparametric model based on Pitman-Yor priors achieves the best coverage for news topics. Two proposed methods of topic model evaluation – document-based coherence measures and methods devised for solving the coverage problem – are applied in order to improve the previously proposed topic-model-based method of media agenda analysis. The improvements refer to the step of topic discovery and lead to quicker discovery of a larger number of concepts. This is achieved by using more interpretable models with higher coverage, and by ordering mo- del topics, befo

Utjecaj utišavanja integrinskih podjedinica α u stanicama melanoma čovjeka na osjetljivost na protutumorske lijekove i pokretljivost

Terapija protutumorskim lijekovima nije metoda odabira za metastatski melanom, ali se koristi u liječenju melanoma koji ne odgovaraju na ciljanu terapiju. Ovaj rad istražuje na modelu četiri stanične linije melanoma čovjeka utjecaj utišavanja integrinskih podjedinica α (α3, α4 ili αv) na osjetljivost na protutumorske lijekove (cisplatinu, paklitaksel ili vinkristin) i pokretljivost. U staničnoj liniji melanoma RPMI-7951, u kojoj utišavanje integrinske podjedinice αv povećava osjetljivost na cisplatinu, paklitaksel ili vinkristin, i smanjuje pokretljivost, istražen je sastav kompleksa adhezije, tj. adhesoma integrina αv. Rezultati ovog rada doprinose razumijevanju signalnih puteva integrina u melanomu, kao i razvoju kombiniranih terapija.Chemotherapy is not a preffered treatment option for metastatic melanoma, but is used in the treatment of melanoma which do not respond to targeted therapy. This disertation studies, in a panel of four human melanoma cell lines, the effect of integrin subunits α (α3, α4 or αv) knockdown on the modulation of sensitivity to chemoterapy drugs (cisplatin, paclitaxel or vincristine) and motility. In melanoma cell line RPMI-7951, in which integrin αv knockdown increases sensitivity to cisplatin, paclitaxel or vincristine, the composition of integrin αv adhesion complexes (IAC), i.e. adhesome, was analysed. Results of this work contribute to the understanding of integrin signaling pathways in melanoma and to the development of the combinational therapy for melanoma

Fotokemijska dekarboksilacija ftalimidnih derivata

U okviru ove doktorske disertacije provedena je sinteza novih derivata ftalimida i istraživanje fotokemijske reaktivnosti tih spojeva. Novopripravljene molekule su ftalimidni derivati adamantanskih aminokiselina, pri čemu je istražen utjecaj udaljenosti između ftalimidnog kromofora (akceptor elektrona) i karboksilne skupine (donor elektrona) na učinkovitost fotoinduciranog prijenosa elektrona (PET) i dekarboksilacije. Udaljenost tih skupina ima značajan utjecaj na učinkovitost dekarboksilacije istraživanih spojeva, a intramolekulski PET je najsporiji stupanj cijelog procesa. Nadalje, istražen je i utjecaj različitih supstituenata vezanih na položaju 4 ftalimidnog kromofora na fotofizička svojstva i fotokemijsku reaktivnost. Ftalimide s elektron-donorskim supstituentom općenito karakterizira reaktivnost i iz singletnog i iz tripletnog pobuđenog stanja. Fluorescencija tih spojeva je u kompeticiji s PET-om, a populacija tripletnog pobuđenog stanja u odsutnosti senzibilizatora je neučinkovita. S druge strane, ftalimidi s elektron-akceptorskim supstituentom reagiraju uglavnom iz tripletnog pobuđenog stanja. Međutim, nitro-derivat je drukčiji budući da ima reaktivnost karakterističnu za nitrobenzenski kromofor. Istraživan je i utjecaj supramolekulske kontrole s ciklodekstrinima (CD) na [3 + 2] cikloadiciju alkena i fotogeneriranih azometin-ilida iz odabranih ftalimida. Kompleksiranjem adamantilftalimidnog derivata s β-CD povećava se iskorištenje adukata

Biochemical characterization of a dual enzymatic activity hydrolase from moss Physcomitrella patens

Nudix-dipeptidil-peptidaza III je biljni enzim s dvojnom hidrolaznom aktivnošću: dipeptidil-peptidaznom (DPP III) i fosfataznom (Nudix). Biokemijski su okarakterizirani homolozi iz mahovine (Physcomitrella patens) i uročnjaka (Arabidopsis thaliana). C-terminalna domena oba homologa predstavlja atipičnu DPP III s obzirom na aktivno mjesto (pentapeptid HEXXH umjesto heksapeptida HEXXGH u tipičnim DPP III), te je slabije aktivna prema sintetskim supstratima u usporedbi s tipičnim, do sada istraženim DPP III. N-terminalna domena je član nadporodice Nudix proteina. Utvrđeno je da Nudix domena ima fosfataznu aktivnost prema supstratima izopentenil-difosfatu i dimetilalil-difosfatu, prekursorima u sintezi izoprenoida. Funkcionalnim istraživanjima na mutantama mahovine P. patens koje ne eksprimiraju ovaj enzim pokazano je da on sudjeluje u metabolizmu biljnih hormona citokinina. Preliminarni rezultati analize ekspresije gena u mahovini u prisutnosti stresora sugeriraju da enzim Nudix-DPP III sudjeluje u odgovoru biljaka na stres (sušu, solni i oksidacijski stres). Zaključno, predložen je naziv izopentenil-difosfat-fosfohidrolaza za novopronađenu enzimsku aktivnost.Nudix-dipeptidyl peptidase III is a plant enzyme with dual hydrolase activity: dipeptidylpeptidase III (DPP III) and phosphatase (Nudix). Homologues from moss (Physcomitrella patens) and angiosperm (Arabidopsis thaliana) were biochemically characterized. C-terminal domain of both homologues represents an atypical DPP III considering the active site (pentapeptide HEXXH instead of hexapeptide HEXXGH in typical DPPs III), and it is less active towards synthetic supstrates than typical, formerly characterized DPPs III. N-terminal domain is a member of Nudix superfamily. It was established that it has phosphatase activity towards isopentenyl-diphosphate and dimethylallyl-diphosphate, precursors in isoprenoid sythesis. Functional research on moss P. patens knock-out mutants showed that this enzyme is involved in cytokinin metabolism. Preliminary analysis of gene expression in the presence of stressors suggests that Nudix-DPP III enzyme is involved in plant response to stress (drought, salt and oxidative stress). Finally, the name isopentenyl diphosphate phosphohydrolase is suggested for the newly identified enzyme activity