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Multilingual Entity Linking Using Dense Retrieval
Farhan, Dominik ; Straka, Milan (advisor) ; Bojar, Ondřej (referee)
Entity linking (EL) is the computational process of connecting textual mentions to corresponding entities. Like many areas of natural language processing, the EL field has greatly benefited from deep learning, leading to significant performance improvements. However, present-day approaches are expensive to train and rely on diverse data sources, complicating their reproducibility. In this thesis, we develop multiple systems that are fast to train, demonstrating that competitive entity linking can be achieved without a large GPU cluster. Moreover, we train on a publicly available dataset, ensuring reproducibility and accessibility. Our models are evaluated for 9 languages giving an accurate overview of their strengths. Furthermore, we offer a detailed analysis of bi-encoder training hy- perparameters, a popular approach in EL, to guide their informed selection. Overall, our work shows that building competitive neural network based EL systems that oper- ate in multiple languages is possible even with limited resources, thus making EL more approachable.
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Comparation of ethnic inequality and stereotype of sexual orientation in the TV series "Friends" and "The Big Ben Theory"
Klímová, Petra ; Kruml, Milan (advisor) ; Jirák, Jan (referee)
The aim of this thesis is to observe socio-social phenomena, specifically the balance of ethnic representations and diversity of sexual orientation, in the context of portrayals in the popular media space, television. The tracking of this issue is done on the series The Big Bang Theory. The fundamental questions of the research conducted are whether the series sufficiently portrays racial and ethnic diversity in the cast of actors and actresses, and whether it also sufficiently talks about and portrays LGBT issues. The thesis also touches upon whether and how stereotyping is used in the media content under study. The content also includes a historical anchoring and an overview of the development of television production in the 20th century, along with the characteristics and development of the sitcom itself. Finally, the thesis compares the analysed series The Big Bang Theory with Friends, which was also analysed in the previous thesis "The Problem of Ethnic Inequality and the Stereotype of Sexual Orientation in the TV Series Friends". For the theoretical part of the thesis, a variety of literature was used. The analytical part contains two questionnaire surveys and their results in data. The full conclusion then summarizes all the important information and insights that the thesis and analysis have...
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Evaluation of root system architecture and osmotic adaptation in barley
Klem, Karel ; Findurová, Hana ; Urban, Otmar ; Holub, Petr
Drought tolerance based on improving root system architecture, in particular by increasing rooting depth, increasing root density at deeper layers, or osmotic adjustment, is one of the most effective ways of adapting to drought, especially in conditions where sufficient water remains in the deeper soil layers during the dry season. Moreover, osmotic adjustment is a trait that allows plants to take up water even when water availability is limited, including the deeper soil layers. On the other hand, however, these are traits that are very difficult to evaluate, given their hidden nature or the need to laboriously excavate roots growing in the soil. This is also the reason why, despite their considerable importance, these features have long been overlooked. Breeding for these traits is done only indirectly by evaluating yield response to drought or indirect physiological or morphological parameters. \nIn this methodology, three methods for evaluating root system architecture or osmotic adjustment are presented which allow selection for specific root system architecture traits or osmotic adjustment, to be carried out on a large number of genotypes, using a relatively simple method based on the cultivation of roots on black filter paper, either hydroponically or aeroponically. This method allows a detailed analysis of root system architecture parameters that are important for drought tolerance and also a relatively easy test of osmotic adjustment by inducing osmotic stress with polyethylene glycol (PEG) solution. Both methods have been successfully validated, in the first case in a model experiment with nutrient deficiency, in which the effect on root system architecture is confounded, and in the second case in a set of barley genetic resources and varieties in which previously obtained information on drought tolerance of some genotypes was confirmed. \nAnother of the methods presented is the cultivation of roots in rhizoboxes filled with sand with a grid of spikes that hold the roots in the position in which they grew when washed. This method again allows the root system architecture to be assessed, but in this case under conditions that more closely match real soil conditions. The method was validated in three barley genotypes with contrasting root system vigor. The method used not only demonstrated the expected differences in rooting depth and root density distribution but also showed a relationship to the physiological response to reduced water availability in terms of photosynthetic CO2 assimilation rate. \nTherefore, all the methods presented here are suitable tools to help breeders in the selection of drought-tolerant barley genotypes.
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Methods of Biomedical Informatics in the study of inflammatory bowel disease in children
Čopová, Ivana ; Hradský, Ondřej (advisor) ; Ďuricová, Dana (referee) ; Krupička, Radim (referee)
METHODS OF BIOMEDICAL INFORMATICS IN THE STUDY OF INFLAMMATORY BOWEL DISEASE IN CHILDREN Abstract Inflammatory bowel diseases (IBD) are a group of chronic, polygenic diseases primarily affecting the gastrointestinal tract, with an increasing incidence in both adult and paediatric populations globally. These diseases include Crohn's disease (CD), ulcerative colitis (UC) and so-called IBD unclassified (IBD-U). Faecal calprotectin (FC) is a marker of inflammation in IBD and its levels correlate with disease activity as defined by clinical parameters, endoscopic findings and histology. Current medical practice is associated with the availability of a large amount of clinical data and the desire to apply it effectively in the medical decision-making process in such a way as to achieve the maximum possible reduction in the risk of adverse disease course and the occurrence of disease- and/or treatment-associated complications. The primary goal of this dissertation is to apply biomedical informatics methods to paediatric IBD in the process of validating FC in predicting disease activity and response to treatment, searching for additional potential predictive factors, and developing prediction models for specific clinical situations. We found that the development of FC levels in the early phase of induction therapy...
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Modulation of mitochondrial transfer by influencing mesenchymal stem cells
Fráňová, Markéta ; Krulová, Magdaléna (advisor) ; Rohlenová, Kateřina (referee)
Mesenchymal stem cells (MSCs) have the ability to modulate the immune response. They use several mechanisms to affect the function of immune cells, and mitochondrial transfer is one of them. Recieving mitochondria from MSCs induces metabolic changes in immune cells, thereby promoting their shift to an anti-inflammatory phenotype. Due to their properties, MSCs have a potencial to be used in therapies, for example in a treatment of autoimmune diseases. The problem of MSCs-based therapies is their low efficacy, mainly due to the high mortality of stem cells after transplantation. In order to achieve at least some effect, the large number of cells is needed for application. The required number of cells can be obtained only by in vitro expansion. However, a long-term culture has a negative impact on MSCs and their immunomodulatory properties. Enhancing MSCs function could increase the efficacy of MSCs-based therapies. The aim of this thesis was to determine whether mitochondrial transfer can be modulated by stimulation of MSCs with selected factors. MSCs were treated with rapamycin, insulin-like growth factor 1 (IGF-1), interferon gamma, or oligomycin. Then the effect of these factors on mitochondria and their transfer to immune cells, metabolism, and immunomodulatory properties of MSCs was analyzed. We...
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The uset of HPLC in the field of chiral separations VIII.
Šlapáková, Tereza ; Horáček, Ondřej (advisor) ; Lochman, Lukáš (referee)
Charles University Faculty of Pharmacy in Hradci Králové Department: Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Student: Bc. Tereza Šlapáková Supervisor: RNDr. Ondřej Horáček, Ph.D. Consultant: doc. PharmDr. Radim Kučera, Ph.D. Title of thesis: The uset of HPLC in the field of chiral separations VIII. Carboranes are highly stable, hydrophobic, inorganic compounds that are based on an icosahedral structure composed of boron atoms. Some carborane representatives are chiral, which is mainly due to asymmetric substitution. The establishment of reliable and rapid methods to enable the separation of the enantiomers is necessary, which is important for their future use in practice. The high-performance liquid chromatography method is advantageous for practical application as it is widely used, robust, and applicable to a large range of fields. The aim of this work was to test the behavior of chiral carboranes on polysaccharide columns in HPLC. First, screening was performed by gradient method using six chiral polysaccharide-based stationary phases, the component A of the mobile phase was 50 mmol/l NaClO4, and the component B was ACN or MeOH. Subsequently, the method was converted to isocratic elution. The purpose of this study was to optimize the conditions to create a database of...
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Social learning in birds: mechanisms and importance in different contexts
Ernestová, Kamila ; Exnerová, Alice (advisor) ; Stehlík, Patrik (referee)
Social learning, i.e. learning from other individuals of the same or different species can be found in a large number of taxa and the birds are no exception. Authors of a large number of studies focusing on this topic demonstrated the influence of social learning on various aspects of birds' life. Undoubtedly, the most important aspects of birds' life are recognition of predators, mate choice, and acquisition of food and food choice. Tool-related behaviour such as tool making and tool using in order to obtain food is also related to the foraging context. However, social learning often plays a different role in different contexts in different species. The differences in acquisition and use of social learning in some contexts exist even within a single species. These differences are mainly caused by individual personality, sex, age and partly also by social status and different ontogenetic factors influencing individual development. Social learning is a very broad topic with large number of variables and, despite the intensive research, it is still not fully understood. Keywords: social learning, birds, social learning mechanisms, imitation
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Development of effective procedures for transplantation of insulin-producing tissue
Hladíková, Zuzana ; Saudek, František (advisor) ; Kvapil, Milan (referee) ; Průhová, Štěpánka (referee)
Our research has been focused on a new method of transplantation of islets of Langerhans into the greater omentum. Transplantation of pancreatic islets is an established treatment option for selected patients with unstable diabetes. The liver is almost exclusively used as a site for islet transplantation in the clinical setting. Unfortunately, immediately after graft implantation into the portal circulation, a substantial portion of the islets is lost and graft function in the liver may further deteriorate over time. The fate and location of islets implanted in the liver can only be followed with difficulty by radiological methods or biopsies. All these limitations have led to the search for alternative sites for transplantation. The greater omentum is easily surgically accessible, meets the demands of a high blood supply and can accommodate large volumes of transplanted tissue. However, the metabolic function of the islet graft itself in the omentum without fixation never achieved satisfactory long-term results in the experiment. Tissue engineering techniques have been used to improve graft attachment and maintain long-term function in the omentum. In our project, we transplanted islets into the rat omentum using a biocompatible gel consisting of recipient plasma and human thrombin....
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Documentation of old sandstone quarry Goldnen Ranzen (Commite Steinbruch) near Hřensko (Labské pískovce)
Hocková, Eliška ; Lysák, Jakub (advisor) ; Kyncl, Günter (referee)
The aim of this bachelor thesis is to create a large-scale map of the old quarry area Commite Steinbruch near the town Hrensko in the Protected Landscape Area Labské pískovce. The work focuses on capturing the sandstone rocks and showing the remains of the quarrying that slowly blend into the nature. The rock objects are depicted using the contour method and are based on data obtained by drone and detailed airborne laser scanning (LLS). The photogrammetric data was obtained by own mapping in the locality and the LLS data was taken from the GeNeSiS project. Other data for the creation of the topographic database was derived from a geodetic mapping of the quarry and from the own field mapping, for which ArcGIS Field maps was used. The resulting map was processed in ArcGIS Pro software. The map is in digital form and is created at a scale of 1 : 700, its length and width are 430 mm. Key words: old quarry Commite Steinbruch, rock representation, mining remains, large scale map, drone photogrammetry, LLS
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Detection and mitigation of DDoS attacks
Brázda, Mikuláš ; Hranický, Radek (referee) ; Žádník, Martin (advisor)
This work deals with the detection of DDoS attacks in the CESNET3 network infrastructure, utilizing NetFlow record analysis. Considering the dynamic nature of network traffic, it treats the data as an infinite stream. To store and efficiently process large volumes of data, it employs the sketch method, which allows for a compact representation of data without losing key information about the network traffic. The core of the detection mechanism is the adaptive CUSUM algorithm, which accumulates deviations from a long-term moving average. An alert is triggered when a threshold is exceeded. The module was tested on real network data with various parameter settings to demonstrate its properties. The implemented module is part of the NEMEA system.
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