Benchmark of Selected Digital Image Processing Algorithms Implemented in Python

Tato bakalářská práce se zabývá digitálním zpracováním obrazu v Pythonu, popisem vybraných algoritmů, jejich implementací a použitou technologií. Porovnává rychlosti běhu vybraných algoritmů na zpracování obrazu v C++ a Pythonu, potom Pyhonu s využitím speciální knihovny Numpy a mezi překladači PyPy a Cython.This Bachelor thesis deals with the digital image processing in Python, description of selected algorithms their implementation and used technology. Specifically, it is focused on comparison of speed among selected algorithms, implemented in languages C++ and Python, Python with NumPy library and compilers PyPy and Cython.460 - Katedra informatikydobř

Synonymous and Nonsynonymous Distances Help Untangle Convergent Evolution and Recombination

When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because different segments of the sequence alignment support different phylogenies. Similarly, convergent selective pressures at the molecular level can also lead to phylogenetic tree incongruence across the sequence alignment. Current methods for detection of phylogenetic incongruence are not equipped to distinguish between these two different mechanisms and assume that the incongruence is a result of recombination or other horizontal transfer of genetic information. We propose a new recombination detection method that can make this distinction, based on synonymous codon substitution distances. Although some power is lost by discarding the information contained in the nonsynonymous substitutions, our new method has lower false positive probabilities than the comparable recombination detection method when the phylogenetic incongruence signal is due to convergent evolution. We apply our method to three empirical examples, where we analyze: 1) sequences from a transmission network of the human immunodeficiency virus, 2) tlpB gene sequences from a geographically diverse set of 38 Helicobacter pylori strains, and 3) Hepatitis C virus sequences sampled longitudinally from one patient.Comment: 21 pages, 8 figures, updated abstrac

Задачи и структура информационно-коммуникационной системы «умного» органического хозяйства

The authors showed that the organic production is an actively growing global business: in 2017, it occupied more than 1.4 percent of all agricultural land on the planet. The authors emphasized the relevance of digitalization with the constant growth of the database, which the farmer needs to process quickly and effi ciently. (Research purpose) To form the structure of the information and communication system for the «smart» crop organic farming and the database necessary for its training and ensuring its functioning. (Materials and methods) The prior research was used, as well as previously created databases and information from the existing literature. Since 2016, a multifactorial experiment with potatoes has been carried out as part of an organic crop rotation to fi ll the information base with experimental data. (Results and discussion) The structure of the information and communication system of the “smart” organic crop production has been formed. It is based on the territory digital map and agricultural crop digital models. In the course of the work of the system, we decided to make daily changes to the digital model of agricultural crops based on the incoming agroecological information, as well as to prepare recommendations on the relevant choice and use of the planned technological operations. It was found out that in a fouryear fi eld experiment, the potato yield in the control variant (without the introduction of compost and pesticides) averaged 21.7 tons per hectare, and when using compost and biofungicide Kartofi n, it increased to 26.7 tons per hectare. The authors calculated multiple linear regression equations describing the dependence of the nitrogen mineral form content in the soil in June on the sum of the active temperatures during this period and the compost dose (the correlation coeffi cient is 0.658); and the dependence of potato yield on the nitrogen mineral form content in the soil in the fi rst ten days of June and the sum of active temperatures in May-June (the correlation coeffi cient is 0.667). (Conclusions) The authors presented the structure of the information and communication system of an organic agricultural enterprise, substantiated the possibility of its full implementation as a tool that helps agricultural producers to carry out environmentally safe, competitive and effi cient organic production at a totally new level.Показали, что производство органической продукции – это активно растущий мировой бизнес: в 2017 году он занимал более 1,4 процента всех сельскохозяйственных угодий планеты. Подчеркнули актуальность цифровизации на фоне постоянного роста базы данных, которые фермеру необходимо оперативно и эффективно обрабатывать. (Цель исследования) Сформировать структуру информационно-коммуникационной системы «умного» растениеводческого органического хозяйства и необходимую базу данных для ее обучения и обеспечения функционирования. (Материалы и методы) Использовали ранее выполненные исследования, включая созданные базы данных и информацию из литературных источников. С 2016 года для заполнения экспериментальными данными информационной базы проводится многофакторный опыт c картофелем в рамках органического севооборота. (Результаты и обсуждение) Сформировали структуру информационно-коммуникационной системы «умного» растениеводческого органического хозяйства. За ее основу приняли цифровую карту территории и цифровые модели сельскохозяйственных культур. Решили в ходе работы системы ежедневно вносить изменения в цифровую модель сельскохозяйственной культуры на основе поступающей агроэкологической информации, а также подготовить рекомендации по оптимальному выбору и использованию очередных технологических операций. Выявили, что в полевом опыте за четыре года урожайность картофеля в контрольном варианте (без внесения компоста и пестицидов) составила в среднем 21,7 тонны на гектар, а при использовании компоста и биофунгицида Картофин она увеличилась до 26,7 тонны на гектар. Рассчитали уравнения множественной линейной регрессии, описывающие зависимость содержания минеральных форм азота в почве в июне от суммы активных температур в этот период и дозы компоста (коэффициент корреляции 0,658) и зависимость урожайности картофеля от содержания в почве минеральных форм азота в первую декаду июня и суммы активных температур в мае – июне (коэффициент корреляции 0,667). (Выводы) Представили структуру информационно-коммуникационной системы органического сельхозпредприятия, обосновали возможность ее полной реализации в качестве инструмента, помогающего агропроизводителям осуществлять экологически безопасное, конкурентоспособное и эффективное органическое производство на новом уровне

Identifying global centers of unsustainable commercial harvesting of species

Overexploitation is one of the main threats to biodiversity, but the intensity of this threat varies geographically. We identified global concentrations, on land and at sea, of 4543 species threatened by unsustainable commercial harvesting. Regions under high-intensity threat (based on accessibility on land and on fishing catch at sea) cover 4.3% of the land and 6.1% of the seas and contain 82% of all species threatened by unsustainable harvesting and > 80% of the ranges of Critically Endangered species threatened by unsustainable harvesting. Currently, only 16% of these regions are covered by protected areas on land and just 6% at sea. Urgent actions are needed in these centers of unsustainable harvesting to ensure that use of species is sustainable and to prevent further species' extinctions.Peer reviewe

The role of cardiac biomarkers and epicardial fat in the diagnosis of heart failure in patients with various types of atrial fibrillation

Aim. To assess the level of various cardiac biomarkers and the volume of epicardial adipose tissue (EAT) in patients with heart failure (HF) depending on the type of atrial fibrillation (AF).Material and methods. This prospective observational study included 69 patients with symptomatic AF, as well as with manifestations of New York Heart Association (NYHA) class II-III HF. All patients were examined before catheter ablation for AF. The following investigations were performed: echocardiography, computed tomography, myocardial perfusion scintigraphy, immunochemical analysis of cardiac biomarkers (brain natriuretic peptide (BNP), high-sensitivity troponin I (hs-TnI)), as well as biochemical analysis of high-sensitivity C reactive protein (hsCRP). Patients were divided into 2 groups, depending on the AF type, into paroxysmal and non-paroxysmal (persistent and long-standing persistent).Results. The analysis included 69 patients with various AF types and symptomatic HF. There were significantly more patients with HF confirmed by an elevated BNP level in the group with non-paroxysmal type (27 (71%) vs 5 (16%), p<0,00001). Comparison analysis showed that in group 2 the mean BNP level was significantly higher than in group 1 (135,5 pg/ml [75,2;303,2] vs 40 pg/ml [20,7;56,9], respectively, p<0,00001). The hs-TnI level was higher in group 2 (2,5 [1,7;5,1] vs 1,9 [0,8;3,9], respectively, p=0,19), but there was no significant difference between the groups. The level of hsCRP did not differ in both groups. In group 1, the EAT volume was 139 [117,5;171] vs 169 [130;209,5] in group 2 (p=0,03).Conclusion. The type of AF plays a role in the interpretation of cardiac specific enzymes, and BNP levels and EAT volume are higher in patients with the non-paroxysmal form

Some aspects of gene association with high sport achievements

Most papers on sport genetics identify differences between genotypes of athletes and a control group. It is obvious that the genetic differences should also be among sportsmen with different qualifications. Additionally, athletes’ performance depends not only on their genotypes, but also on the gene activities, which can be different during the training process in various athletes.The aim of the study was to compare genotypes of athletes with different qualifications and to analyze the change in expression of some genes responsible for the physical performance. Genotypes of 143 elite sportsmen of 18 national teams were analyzed by PCR method. A comparison of the genotypes of Masters of Sports, International Masters of Sports and Honored Masters of Sports showed that the frequencies of favorable gene variants were higher in the genotypes of more qualified athletes; it proves an appropriate genetic potential necessity for high achievements in sports. The analysis of UCP2, HIF1A and MTHFR gene expression changes in response to two-week hypoxiс training was performed on 15 skaters of high qualification. We found that average UCP2 and MTHFR mRNA levels had significantly increased after the training but the expression of the HIF1A gene had reduced. At the same time, individual athlete variability in UCP2, HIF1A and MTHFR gene expression was revealed. Genotype influence on gene expression was shown with the help of the UCP2 gene – its activity was higher in sportsmen with Val/Val than with Val/Ala or Ala/Ala genotypes. Consequently, genotyping and analysis of gene expression is very important for athlete selection and training

Влияние глубокого рыхления междурядий на физические свойства дерново-подзолистой почвы и урожайность органического картофеля

The purpose of this research is to study the effect of deep loosening of row spacings on the physical properties of the soil and yield of organic potatoes. Two variants of soil cultivation were used in row spacings: usual and 25 cm deep. The soil cultivation was carried out with a row-crop chisel cultivator. Its design was developed at the institute. Analysis of the data obtained as a result of experimental studies showed that deep loosening of row spacings had a positive effect on soil compaction both in the inter-row width and directly in the plough ridge. The soil compaction in the row spacing during normal tillage was in average above 20 %, and in the ridge by an average of 13 % compared to deep tillage. The assimilation of moisture by the soil with when using of deep loosening of row spacings also had a positive trend, especially under condition of a large amount of precipitation in a short period of time. Thus, with a loss of 34 mm, the soil in the variant with loosening the row spacings in a larger volume absorbed moisture and the moisture indicators increased sharply in layers, at 15 cm by 27 %, at 25 cm by 20 %, at 35 cm by 5 %. Potato yield increased by 8.7 % when using deep loosening of row spacings. The obtained results of experimental studies should be used as recommendations when carrying out technological operations aimed at caring for potato plantings.Целью данного исследования является изучение влияния глубокого рыхления междурядий на физические свойства почвы и урожайность органического картофеля. В междурядьях использовалось два варианта обработки почвы: обычный и на глубину 25 см. Обработка почвы проводилась с помощью пропашного культиватора-глубокорыхлителя, конструкция которого разработана в ИАЭП. Анализ данных, полученных в результате экспериментальных исследований, показал, что глубокое рыхление междурядий положительно сказалось на уплотнении почвы как по ширине междурядий, так и непосредственно в гребне. Уплотнение почвы в междурядьях при обычной обработке почвы было в среднем выше 20 %, а на гребне в среднем на 13 % по сравнению с глубокой обработкой почвы. Усвоение влаги почвой с использованием глубокого рыхления междурядий также имело положительную динамику, особенно в условиях выпадения большого количества осадков за короткий промежуток времени. Таким образом, при выпадении 34 мм почва в варианте с рыхлением междурядий в большем объеме усвоила влагу и показатели влажности резко повысились в слоях, на 15 см – на 27 %, на 25 см – на 20 %, на 35 см – на 5 %. Урожайность картофеля увеличилась на 8,7 % при использовании глубокого рыхления междурядий. Полученные результаты экспериментальных рекомендуется использовать при проведении технологических операций, направленных на уход за посадками картофеля

Influence of characteristics of epicardial adipose tissue and myocardial sympathetic innervation on the development of late recurrence of atrial fibrillation after radiofrequency ablation

Aim. To investigate the relationship between radiological characteristics of epicardial adipose tissue (EAT) and myocardial sympathetic activity, as well as to study their association with late recurrence of atrial fibrillation (AF) after radiofrequency ablation (RFA).Material and methods. This prospective study included 26 people with persistent and long-standing persistent AF scheduled for interventional AF treatment. Before the RFA procedure, all patients underwent cardiac 123I-metaiodobenzylguanidine (123I-MIBG) scintigraphy to assess the myocardial sympathetic innervation and contrast-enhanced cardiac multislice computed tomography to assess pulmonary vein anatomy, left atrial volume, and EAT volume. Clinical follow-up, including 12-lead electrocardiography (ECG) and 24-hour ECG monitoring, was carried out 3, 6 and 12 months after RFA.Results. After the end of follow-up, the patients were divided into two groups: with AF recurrence (group 1, n=8) and without AF recurrence (group 2, n=18). Multivariate logistic analysis found that only the 123I-MIBG washout rate (odds ratio, 1,0943; 95% confidence interval, 1,0138-1,1812) proved to be an independent predictor of late AF recurrence after RFA. ROC analysis revealed that a 123I-MIBG washout rate >21% with a sensitivity of 75% and a specificity of 83,3% (AUC=0,844; p<0,001) predicts late AF recurrence after RFA.Conclusion. Parameters of myocardial sympathetic activity, assessed by 123I-MIBG myocardial scintigraphy, are associated with late AF recurrence after RFA in patients with persistent and long-standing persistent AF. There were no reliable data confirming associations between myocardial sympathetic innervation and radiological EAT indicators, as well as the effect of the latter on the risk of AF recurrence after RFA