Preparing Evaluation Set for Complex Problems of Recognition and Disambiguation of Named Entities through Crowdsourcing

Práca sa zaoberá prípravou vyhodnocovacej sady pre problémy rozpoznávania a zjednoznačňovania pomenovaných entít. Vyhodnocovacia sada je výsledkom automatizovaného spracovania a crowdsourcingu. Vyhodnocovacia sada môže byť použitá na testovanie pokročilých prípadov v rozpoznávaní a zjednoznačňovaní pomenovaných entít.This Master's Thesis prepares Evaluation Set for Problems of Recognition and Disambiguation of Named Entities. Evaluation Set is created using Automatization and Crowdsourcing. Evaluation Set can be used in testing Edge Cases in Recognition and Disambiguation of Named Entities.

Machine Learning for Question Answering in Czech

Táto diplomová práca sa zaoberá učením neurónových sietí na odpovedanie otázok v češtine. Neurónové siete sú vytvorené v jazyku Python použitím knižnice PyTorch. Vytvorené sú na základe štruktúry LSTM. Učené sú na českej dátovej sade SQAD. Pretože dátová sada je menšia ako anglické dátové sady, rozširujem neurónové siete o algoritmické postupy. Pre jednoduchšiu aplikáciu algoritmov a lepšiu presnosť rozdeľujem odpovedanie na otázku do menších častí.This Master's thesis deals with teaching neural network question answering in Czech. Neural networks are created in Python programming language using the PyTorch library. They are created based on the LSTM structure. They are trained on the Czech SQAD dataset. Because Czech data set is smaller than the English data sets, I opted to extend neural networks with algorithmic procedures. For easier application of algorithmic procedures and better accuracy, I divide question answering into smaller parts.

Human Endogenous Retrovirus HC2 Is a New Member of the S71 Retroviral Subgroup with a Full-LengthpolGene

AbstractWe have isolated and characterized a new human endogenous provirus, which is closely related to the human retrovirus S71, but unlike S71 has a full-lengthpolgene. Two degenerate oligonucleotide primers based on highly conserved motifs within the active sites of two retroviral proteins (the protease and reverse transcriptase) were designed and used for PCR. An amplified product of 847 bp in length, which showed significant homology to protease and reverse transcriptase of several retroviruses, was used for high stringency hybridization with a human genomic library. The MuLV-related endogenous retrovirus sequence, designated HC2, was isolated and completely sequenced. HC2 is a provirus with completegagandpolgenes and a 3′ LTR; the 5′ LTR andenvgene are missing. Thegagandpolgenes appear complete, since they contain sequences homologous to the matrix protein, capsid protein, and nucleocapsid protein of gag and to the protease, reverse transcriptase, tether, RNase H, and integrase of pol. Phylogenetic analysis suggests that although HC2 and S71 are MuLV-related retroviruses, their characters are quite distinct, being placed outside of a clade containing most of the previously characterized MuLV-related retroviruses such as GaLV, FeLV, BaEV, and SSV/SSAV

Neutrophil extracellular traps in urinary tract infection

BackgroundUrinary tract infections (UTI) are common types of bacterial infection in children. UTI treatment is aimed to prevent complications including hypertension, proteinuria, and progression to chronic kidney disease. Activated neutrophils release chromatin-based structures associated with antimicrobial proteins called neutrophil extracellular traps (NETs). We aimed to describe the role of NET-associated markers in children with UTI as well as the role of NETs formation in a mouse model of UTI.Materials and methodsMarkers of NETs including extracellular DNA (ecDNA), myeloperoxidase (MPO) and cathelicidin were analyzed in children with febrile UTI caused by E.coli (n = 98, aged 0.3–1.3 years) and in healthy controls (n = 50, 0.5–5.2 years). Moreover, an acute experimental model of UTI was performed on PAD4 knock-out mice with diminished NETs formation (n = 18), and on wild-type mice (n = 15).ResultsChildren with UTI had significantly higher urinary NETs markers including total ecDNA, nuclear DNA and mitochondrial DNA, altogether with MPO and cathelicidin. The concentrations of MPO and cathelicidin positively correlated with ecDNA (r = 0.53, p ≤ 0.001; r = 0.56, p ≤ 0.001, respectively) and the number of leukocytes in the urine (r = 0.29, p ≤ 0.05; r = 0.27, p ≤ 0.05, respectively). Moreover, urinary MPO was positively associated with cathelicidin (r = 0.61, p ≤ 0.001). In the experimental model, bacterial load in the bladder (20-fold) and kidneys (300-fold) was significantly higher in PAD4 knock-out mice than in wild-type mice.ConclusionHigher urinary NETs makers—ecDNA, MPO and cathelicidin and their correlation with leukocyturia in children with UTI confirmed our hypothesis about the association between NETs and UTI in children. Higher bacterial load in mice with diminished NETs formation suggests that NETs are not only a simple consequence of UTI, but might play a direct role in the prevention of pyelonephritis and other UTI complications

Sex differences in long-term effects of collagen-induced arthritis in middle-aged mice

Introduction: Rheumatoid arthritis (RA) is a chronic inflammatory disorder with high prevalence among middle-aged women. Collagen-induced arthritis (CIA) is the most widely used animal model of RA, however, sex differences and long-term effects of CIA in mice are poorly described in the literature.Aim: Therefore, the present study aimed to analyze the long-term effects of CIA on the joints of middle-aged mice of both sexes and to describe potential sex differences.Materials and methods: CIA was induced in middle-aged DBA/1J mice by immunization with bovine type II collagen and complete Freund’s adjuvant. Saline was administered to control mice. Arthritis score assessment, plethysmometry, and thermal imaging of the joints were performed weekly for 15 weeks. Locomotor activity, micro-computed tomography, joint histology and biochemical analyses were performed at the end of the experiment.Results: Our results indicate a similar prevalence of arthritis in both sexes of mice—67% (8/12) of females and 89% (8/9) males with an earlier onset in males (day 14 vs. day 35). After the arthritis scores peaked on day 56 for males and day 63 for females, they steadily declined until the end of the experiment on day 105. A similar dynamics was observed in paw volume and temperature analyzing different aspects of joint inflammation. Long-term consequences including higher proteinuria (by 116%), loss of bone density (by 33.5%) and joint damage in terms of synovial hyperplasia as well as bone and cartilage erosions were more severe in CIA males compared to CIA females. There were no significant differences in locomotor activity between CIA mice and CTRL mice of any sex.Conclusion: This is the first study to describe the long-term effects of the CIA model in terms of sex differences in DBA/1J mice. Our results indicate sex differences in the dynamics, but not in the extent of arthritis. An earlier onset of arthritis and more severe consequences on joints, bones and kidneys were found in males. The underlying immune pathomechanisms responsible for the limited duration of the arthritis symptoms and the opposite sex difference in comparison to RA patients require further investigation

Cognitive impairment and biomarkers of gut microbial translocation in testicular germ cell tumor survivors

BackgroundSurvivors of testicular germ cell tumors (GCT) may suffer from late cognitive impairment. We hypothesized that disruption of intestinal barrier during chemotherapy and/or radiotherapy may be a contributing factor of cognitive dysfunction within the gut-blood-brain axis.MethodsGCT survivors (N = 142) from National Cancer Institute of Slovakia completed the Functional Assessment of Cancer Therapy Cognitive Function questionnaires during their annual follow-up visit at 9-year median (range 4-32). Biomarkers of gut microbial translocation and dysbiosis high mobility group box-1 (HMGB-1), lipopolysaccharide, d-lactate and sCD14 were measured from peripheral blood obtained during the same visit. Each questionnaire score was correlated with biomarkers. Survivors were treated with orchiectomy only (N = 17), cisplatin-based chemotherapy (N = 108), radiotherapy to the retroperitoneum (N = 11) or both (N = 6).ResultsGCT survivors with higher sCD14 (above median) had worse cognitive function perceived by others (CogOth domain) (mean ± SEM; 14.6 ± 0.25 vs 15.4 ± 0.25, p = 0.019), lower perceived cognitive abilities (CogPCA domain) (20.0 ± 0.74 vs 23.4 ± 0.73, p = 0.025) and lower overall cognitive function score (109.2 ± 0.74 vs 116.7 ± 1.90, p = 0.021). There were no significant cognitive declines associated with HMGB-1, d-lactate and lipopolysaccharide. Survivors treated with ≥ 400mg/m2 vs < 400mg/m2 of cisplatin-based chemotherapy had a higher lipopolysaccharide (567.8 μg/L ± 42.7 vs 462.9 μg/L ± 51.9, (p = 0.03).ConclusionssCD14 is a marker of monocytic activation by lipopolysaccharide and may also serve as a promising biomarker of cognitive impairment in long-term cancer survivors. While chemotherapy and radiotherapy-induced intestinal injury may be the underlying mechanism, further research using animal models and larger patient cohorts are needed to explore the pathogenesis of cognitive impairment in GCT survivors within the gut-brain axis

Extending Presentation Features of Jupyter Notebook

Práca sa zaoberá z prostredím Jupyter Notebook. Rozširuje jeho schopnosti zamerané na prezentáciu programovania. Umožňuje preberať materiály z html dokumentov, vylepšuje vzhľad prezentácií, umožňuje automatizovanú prípravu dokumentu na prezentáciu, upravenie nastavenia pre rozšírenia RISE a úpravu konvertovania dokumentu do formátu LaTeX.This work deals with Jupyter Notebook environment. It extends its abilities for presenting programming, allows downloading of materials from html documents, improves the look of presentations, allows automated preparation of the document for the presentation, editing of RISE settings used for presentation, and editing conversion of the document into LaTeX.

Machine Learning for Question Answering in Czech

This Master's thesis deals with teaching neural network question answering in Czech. Neural networks are created in Python programming language using the PyTorch library. They are created based on the LSTM structure. They are trained on the Czech SQAD dataset. Because Czech data set is smaller than the English data sets, I opted to extend neural networks with algorithmic procedures. For easier application of algorithmic procedures and better accuracy, I divide question answering into smaller parts