Reconstruction properties of selective Rips complexes

Selective Rips complexes associated to two parameters are certain subcomplexes of Rips complexes consisting of thin simplices. They are designed to detect more closed geodesics than their Rips counterparts. In this paper we introduce a general definition of selective Rips complexes with countably many parameters and prove basic reconstruction properties associated with them. In particular, we prove that selective Rips complexes of a closed Riemannian manifold (X) attain the homotopy type of (X) at small scales. We also completely classify the resulting persistent fundamental group and (1)-dimensional persistent homology

Production and characterisation of aegerolysin and protein with MACPF domain from entomopathogenic fungus Beauveria bassiana.

Perforini so proteini, ki s tvorjenjem por v membrane predstavljajo velik biotehnološki potencial na biofarmacevtskih, analitičnih in agronomskih področjih. Znanih je več različnih perforinov in proteinskih parov, ki skupaj tvorijo pore, njihov širok spekter možne uporabe pa kliče po novih raziskavah. Pomembno je natančno poznavanje njihovih molekularnih mehanizmov, ki vplivajo na njihovo biološko funkcijo in možne aplikacije. V tej diplomski nalogi smo se odločili preveriti potencial entomopatogene glive Beauveria bassiana, njenega egerolizina in proteina z domeno MACPF, z namenom ugotavljanja njune interakcije pri formiranju por. Izbrali smo dva gena, za katera je obstajala verjetnost, da glivi omogočata entomopatogeno delovanje s tvorbo por v žuželčjo kutikulo. Tekom raziskave smo uspešno klonirali in izrazili oba proteina v rekombinantni bakteriji, egerolizin smo uspešno izolirali v čisti obliki. Na njem smo uspešno izvedli več analitskih metod, ki so pokazale, da smo protein najverjetneje pridobili v pravilnem zvitju. Sedimentacijski test in površinska plazmonska resonanca sta pokazala močno vezavo egerolizina na kombinacijo lipidov ceramid fosfoetanolamin in sfingomielin, kar nakazuje na predvideno biološko funkcijo. Za natančnejšo določitev bioloških funkcij obeh proteinov in dokončno preverbo njunih potencialov kot pesticidnih sredstev in morebitne druge aplikacije pa so zagotovo potrebne nadaljnje analize.Perforins are proteins that have a large biotechnological potential in biopharmaceutical, analytic and agronomical fields because of their pore forming abilities. There is already a wide spectre of known perforins and protein couples that jointly form pores, but their wide spectre of potential use calls for new research. Analysis of molecular mechanisms that effect their biological function as well as their potential applications is crucial. In this thesis we decided to discover potential of entomopathogenic fungi Beauveria bassiana, its aegerolylin and protein with MACPF domain with a goal of discovering their interaction in formulation of pores. We selected two genes, for which there was a plausibility, that they are enabling fungi its entomopathogenic activity, with formation of pores into insect cuticle. During the research we successfully cloned and expressed both proteins from recombinant bacterium and successfully isolated aegerolysin in a pure form. On this protein we than preceded to conduct analytical methods, that confirmed, that we most likely gained it in its native form. Sedimentation test and SPR showed strong bonds of aegerolysin to lipid combination of ceramide phosphoethanolamine and sphingomyelin which matches predicted biological function. For exact determination of biological functions of both proteins and final discovery of their potential use as pesticide and other applications further research is needed

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach

Pediatric T-cell acute lymphoblastic leukemia

The most common pediatric malignancy is acute lymphoblastic leukemia (ALL), of which T-cell ALL (T-ALL) comprises 10–15% of cases. T-ALL arises in the thymus from an immature thymocyte as a consequence of a stepwise accumulation of genetic and epigenetic aberrations. Crucial biological processes, such as differentiation, self-renewal capacity, proliferation, and apoptosis, are targeted and deranged by several types of neoplasia-associated genetic alteration, for example, translocations, deletions, and mutations of genes that code for proteins involved in signaling transduction, epigenetic regulation, and transcription. Epigenetically, T-ALL is characterized by gene expression changes caused by hypermethylation of tumor suppressor genes, histone modifications, and miRNA and lncRNA abnormalities. Although some genetic and gene expression patterns have been associated with certain clinical features, such as immunophenotypic subtype and outcome, none has of yet generally been implemented in clinical routine for treatment decisions. The recent advent of massive parallel sequencing technologies has dramatically increased our knowledge of the genetic blueprint of T-ALL, revealing numerous fusion genes as well as novel gene mutations. The challenges now are to integrate all genetic and epigenetic data into a coherent understanding of the pathogenesis of T-ALL and to translate the wealth of information gained in the last few years into clinical use in the form of improved risk stratification and targeted therapies. Here, we provide an overview of pediatric T-ALL with an emphasis on the acquired genetic alterations that result in this disease

Following the paths of the agrarian reform and confiscations between 1945-1949: the example of the Lemež family

Zaplembe premoženja predstavljajo eno temeljnih vprašanj slovenske povojne zgodovine. Njihovo poznavanje je eden izmed osnovnih pogojev za razumevanje nekaterih revolucionarnih sprememb in dogajanj po letu 1945. Če hočemo obdobje po vojni razumeti, moramo misliti na posameznike in njihove usode. Poznavanje problematike povojnih zaplemb je ključno za razumevanje preobrazbe zasebne lastnine v državno. Kot večina agrarnih reform v zgodovini je bila tudi agrarna reforma po drugi svetovni vojni v Jugoslaviji izpeljana s ciljem pridobiti premoženje in ne s ciljem zadostitve tistim, ki jih ukrep zadeva. Z agrarno reformo v Sloveniji, izpeljano leta 1946, so veleposestnikom, Cerkvi in večjim kmetom odvzeli zemljo in jo razdelili pod geslom »zemljo tistemu, ki jo obdeluje«. Kljub tovrstnemu ukrepu je veliko zemlje ostalo v državnih rokah. Velik poudarek v pričujočem delu je predvsem na represiji do kmečkega prebivalstva, natančneje do rodbine Lemež. Posebna pozornost je namenjena razlastitvam, zaplembam in sodnim procesom. Poglavje o političnih sodnih procesih zoper rodbino Lemež je skoraj v celoti pisano na osnovi proučevanja arhivskega gradiva, saj literature o posameznih kmečkih oškodovancih agrarne reforme ni na razpolago veliko. Posebej pomembno poglavje v magistrski nalogi je psihološki vpliv na družino Lemež, ki je v celoti napisano na podlagi osebnih izpovedi družinskih članov.The confiscation of assets is one of the fundamental questions of the Slovenian post-war history. Knowledge of confiscations of assets is one of the basic conditions for understanding some revolutionary changes and events since the year 1945. If we want to understand the post-war period, we need to think of individuals and their fates. Knowing the problem of post-war confiscations is crucial for understanding the transformation of private property into state property. Like most agricultural reforms in history, the agrarian reform after the Second World War in Yugoslavia was carried out with the goal of acquiring property and not with the goal of meeting those affected by the measure. With the agrarian reform in Slovenia, carried out in 1946, they deprived the landowners, the Church and large farmers of their land and distributed it under the slogan »Land for those who work on it. « Despite this kind of measure, a lot of land remained in the hands of the state. The emphasis in the presented work is mainly on the repression against the agricultural population, and more specifically against the family Lemež. A special attention is given to expropriation, confiscation and judicial processes. The chapter on political trials against the family Lemež is almost entirely written on the basis of the study of archival documents, since not a lot of the literature on individual aggrieved farmers in the agrarian reform is available. Particularly relevant chapter in the master\u27s thesis is the psychological impact on the Lemež family, which is written entirely on the basis of personal confessions of the family members

ARBELOS

Diplomsko delo obravnava geometrijski lik, ki se imenuje arbelos ali čevljarski nož. Z njim se je ukvarjal že Arhimed, kasneje pa so se mu posvečali še mnogi drugi matematiki. V delu je predstavljenih več zanimivih krogov in njihove lastnosti: Arhimedova dvojčka, Paposova veriga, Apolonijev krog, Bankoffov krog in Schochova kroga.This thesis discusses the geometric form called Arbelos or the Shoemaker´s Knife. It was studied by Archimedes and was later delt with by numerous other mathematicians. The work presents several interesting circles and their properties: Twin Circles of Archimedes, Pappus Chain, Apollonius Circle, Bankoff Circle and Schoch´s Circles

Regulation of immune cells in the periphery and central nervous system after X-ray irradiation

Space environment presents great danger for astronauts' health. One of the major risk factors is exposure to ionizing radiation, which has the potential to ionize atoms and molecules. This can have detrimental effects to cellular mechanisms as well as the biological systems as a whole. Due to the overlap of different biological systems it is impossible to study them individually. Two important organ systems severely affected by ionizing radiation are the immune system and the central nervous system (CNS). The role of irradiated immune cells of the CNS in the pathogenesis of cognitive deficits in addition to those caused by radiation exposure of neuronal cells still needs to be elucidated. The aim of this thesis was to understand the response of microglia with an activated or an inactivated phenotype to different doses of X-irradiation. The murine BV-2 cell line was used as model for microglial cells. DNA damage, apoptotic activity and phagocyic rates after irradiation were determined. For comparison, DNA double strand breaks (DSB) were also measured in the monocyte cell line (U937) after irradiation. While X-irradiation caused a dosedependent increase in DSB, no significant induction of apoptosis or reduction of phagocytotic activity was observed. The responses were comparable for inactivated and activated microglia with an exception of significant results observed in the amount of DNA DSB after irradiation with a dose of 4 Gy. A trend of decreased phagocitic activity was observed in both activated and inactivated phenotype 24 hours post irradiation for the dose of 4 Gy, but did not yield a significant result. The radiation-induced effects 24-hours post irradiation decreased in comparison to the 1- hour post irradiation timepoint which entails the efficiency of the repair mechanisms. Further experiments should be done in order to truly understand the implications of the activated and inactivated phenotype as well as the X-irradiation dose effects on the immune cells of the CNS and the resulting neurological damage or protection

Vztrajna homologija in geometrija

In this thesis we introduce a novel simplicial complex assigned to a decreasing sequence of scales, called the selective Rips complex. It is a generalization of the Vietoris-Rips complex, where a sequence of scales is used instead of a single scale. A simpler version of the selective Rips complexes was previously designed to detect more geometric features than their Rips counterparts. We study the properties of selective Rips complexes and generalize the theory of Vietoris-Rips complexes. We prove the Stability Theorem for selective Rips complexes. The main contributions of this dissertation are various reconstruction results up to the homotopy type using selective Rips complexes. First, we prove that the selective Rips complex of a closed Riemannian manifold X is homotopy equivalent to X for appropriately small scales. When restricted to Vietoris-Rips complexes, we provide a novel proof of the Hausmann\u27s reconstruction result. Next, we present finite reconstruction results with selective Rips complexes and intrinsic Čech complexes. We prove that if a metric space S is close enough to a closed Riemannian manifold X in the Gromov-Hausdorff distance, the selective Rips complex (and also the intrinsic Čech complex) of S is homotopy equivalent to X for appropriately small scales. As a special case, we provide a novel proof of the Latschev\u27s reconstruction result. Finally, we classify the one-dimensional persistence of geodesic spaces arising from selective Rips complexes. We prove that 1-dimensional persistence of Rips and selective Rips complexes are isomorphic up to reparametrization.V tej disertaciji vpeljemo nov simplicialni kompleks imenovan selektivni Ripsov kompleks. Ta kompleks je posplošitev Vietoris-Ripsovega kompleksa, kjer uporabimo zaporedje radijev namesto enega radija. Prvotna verzija selektivnega Ripsovega kompleksa je bila vpeljana z namenom, da zazna več geometrijskih lastnosti kot pripadajoči Ripsov kompleks. S proučevanjem lastnosti selektivnega Ripsovega kompleksa posplošimo že znano teorijo Vietoris-Ripsovih kompleksov. Dokažemo pripadajoč izrek o stabilnosti za selektivne Ripsove komplekse. Najpomembnejši doprinos te disertacije so različni rekonstrukcijski rezultati do homotopskega tipa z uporabo selektivnega Ripsovega kompleksa. Najprej pokažemo, da je selektivni Ripsov kompleks sklenjene Riemannove mnogoterosti X homotopsko ekvivalenten prostoru X za primerno majhne parametre. Ker je Vietoris-Ripsov kompleks poseben primer selektivnega Ripsovega kompleksa, s tem podamo nov dokaz Hausmannovega rekonstrukcijskega rezultata. Nadalje pokažemo končna rekonstrukcijska rezultata z uporabo selektivnega Ripsovega kompleksa in intrinzičnega Čechovega kompleksa: če je metričen prostor S dovolj blizu sklenjeni Riemannovi mnogoterosti X glede na Gromov-Hausdorffovo razdaljo, tedaj je selektivni Ripsov kompleks (oz. intrinzičen Čechov kompleks) na S homotopsko ekvivalenten celotnemu prostoru X. Kot poseben primer s tem podamo nov dokaz Latschevega rekonstrukcijskega rezultata. Nazadnje klasificiramo eno-dimenzionalno vztrajnost geodetskih prostorov porojeno s selektivnimi Ripsovimi kompleksi. Pokažemo, da sta 1-dimenzionalni vztrajnosti Vietoris-Ripsovih in selektivnih Ripsovih kompleksov do reparametirizacije izomorfni

The burden of school and after-school activities on children in the third triad of primary school

Magistrsko delo predstavlja celostni razvoj otrok, obremenjenost, vrste in vzroke utrujenosti, ki se v sodobnem času vse pogosteje pojavljajo. S poznavanjem otrokovih razvojnih značilnosti lahko bolj kakovostno opredelimo nastalo situacijo v vzgojno-izobraževalnem sistemu. Teoretični del predstavlja obremenjenost kot pojav, ki ima že dolgo zgodovino. Je pojav, ki je star toliko kot šola. V sklopu magistrskega dela je bila med učenci tretje triade Osnovne šole Toneta Čufarja izvedena anketa, v kateri so odgovarjali na vprašanja o preživljanju časa po obveznem pouku. Ugotovljeno je bilo, da se 13 otrok ne udeležuje nobene šolske ali obšolske dejavnosti, kar kaže na razvejano mrežo programov, ki jih šola in druge institucije omogočajo za razvijanje interesov. S tem kažejo interes za koristno in zdravo preživljanje prostega časa. V nadaljevanju teoretični del zajema opredelitev dveh delitev interesnih dejavnosti glede na kraj in vsebino. Pri izbiri interesnih dejavnosti ugotovimo, da se otroci pogosto odločajo za šolske in obšolske interesne dejavnosti, ki so različne glede na okoliš izvajanja. Na podlagi lastnih želja so pri otrocih v tretji triadi osnovne šole vsebinsko najbolj zastopane športne dejavnosti. Namen magistrskega dela je bil usmerjen v ugotavljanje, kako zelo se učenci počutijo obremenjene s šolskimi in obšolskimi dejavnostmi in kako zelo te vplivajo na njihov šolski uspeh. Raziskano je bilo, ali se je obiskanost šolskih in obšolskih dejavnosti razlikovala glede na spol. Prav tako so bili ugotovljeni razlogi učencev za vključitev v posamezno vrsto dejavnosti in morebitni vplivi bližnjih oseb na njihovo izbiro. Ugotovljeno je bilo, da je vse več otrok nepravilno obremenjenih. Največkrat se tega zavejo ravno učitelji in mentorji na šolskih in obšolskih dejavnostih, ki poleg staršev prvi zaznajo učenčevo utrujenost.This master\u27s thesis represents the whole child\u27s development, pressure, types and causes of fatigue, which are increasingly occurring in modern times. By knowing the child\u27s developmental characteristics, we can better define the situation in the educational system. The theoretical part represents the pressure as a phenomenon, which has a long history. It\u27s a phenomenon that\u27s as old as school. Within the master\u27s thesis, a survey was conducted among students of the third triad of elementary school of Tone Čufar, in which they answered questions about how their time after compulsory classes is spent. It was found that 13 children do not attend any school or out-of-school activities, which points to a widespread network of programs, enabled by the school and other institutions to develop interests. In this way they show an interest in spending free time in a useful and healthy way. Hereinafter, the theoretical part covers the definition of two divisions of free-time activities by place and content. When choosing free-time activities, we find that children often decide on school and out-of-school activities, which are different according to the environment of their implementation. On the basis of children\u27s own wishes, in the third triad of elementary school, the most represented are sports activity. The purpose of the master\u27s thesis was to determine how much pressure students feel, due to school and out-of-school activities, and what kind of impact these activities have on their academic success. It was researched, whether the attendance of school and out-of-school activities differed by gender. Students\u27 reasons for inclusion in a particular type of activity were also identified. As well as possible impacts people close to them have on their choices. It has been found that more and more children are under incorrect pressure. Most often, this is what teachers and mentors in school and out-of-school activities are aware of, who, in addition to their parents, are the first to notice student\u27s fatigue