Greyscale to binary image conversion

V první části bakalářské práce jsou popsány základní pojmy v oblasti získávání a popisu digitálního obrazu. Další část teoreticky popisuje možnosti zpracovávání obrazu, které jsou nutným základem pro správné oddělení textu od pozadí a tím pádem správný převod šedotónového snímku na binární. Dále byl proveden rozbor úlohy s přípravou dat pro zpracovávání. Následně byly aplikovány metody pro převod šedotónových snímků na binární a sestavena uživatelská aplikace. Posledním krokem je zhodnocení praktické realizace převodu, jeho subjektivní testování na dotazovaných respondentech a objektivní testování pomocí OCR softwaru.In the first part of the bachelor’s thesis are described the basic terms in obtaining and description of a digital image. The next part describes the theory about possibilities of image processing, which are essential for the correct separation of the text from the background, and thus for the correct conversion grayscale image to binary image. Then was performed the analysis of the task with the preparation of data for image processing. Then were applied different methods for converting grayscale to binary images and it was compiled user application. The final step is to evaluate the practical realization of the conversion, the subjective testing of respondents and objektive testing with the OCR software.

CATSNAP : a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing

Understanding the evolutionary conservation of complex eukaryotic transcriptomes significantly illuminates the physiological relevance of alternative splicing (AS). Examining the evolutionary depth of a given AS event with ordinary homology searches is generally challenging and time-consuming. Here, we present CATSNAP, an algorithmic pipeline for assessing the conservation of putative protein isoforms generated by AS. It employs a machine learning approach following a database search with the provided pair of protein sequences. We used the CATSNAP algorithm for analyzing the conservation of emerging experimentally characterized alternative proteins from plants and animals. Indeed, most of them are conserved among other species. CATSNAP can detect the conserved functional protein isoforms regardless of the AS type by which they are generated. Notably, we found that while the primary amino acid sequence is maintained, the type of AS determining the inclusion or exclusion of protein regions varies throughout plant phylogenetic lineages in these proteins. We also document that this phenomenon is less seen among animals. In sum, our algorithm highlights the presence of unexpectedly frequent hotspots where protein isoforms recurrently arise to carry physiologically relevant functions. The user web interface is available at https://catsnap.cesnet.cz/.peer-reviewe

Click chemistry-based tracking reveals putative cell wall-located auxin binding sites in expanding cells

Abstract Auxin is a key plant regulatory molecule, which acts upon a plethora of cellular processes, including those related to cell differentiation and elongation. Despite the stunning progress in all disciplines of auxin research, the mechanisms of auxin-mediated rapid promotion of cell expansion and underlying rearrangement of cell wall components are poorly understood. This is partly due to the limitations of current methodologies for probing auxin. Here we describe a click chemistry-based approach, using an azido derivative of indole-3-propionic acid. This compound is as an active auxin analogue, which can be tagged in situ. Using this new tool, we demonstrate the existence of putative auxin binding sites in the cell walls of expanding/elongating cells. These binding sites are of protein nature but are distinct from those provided by the extensively studied AUXIN BINDING PROTEIN 1 (ABP1). Using immunohistochemistry, we have shown the apoplastic presence of endogenous auxin epitopes recognised by an anti-IAA antibody. Our results are intriguingly in line with previous observations suggesting some transcription-independent (non-genomic) activity of auxin in cell elongation

Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana

Summary Advanced transcriptome sequencing has uncovered that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the plant model Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionary-conserved transcripts PIN7a and PIN7b. PIN7a and PIN7b, differing in a 4-amino acid motif, exhibit almost identical expression pattern and subcellular localization. We reveal that they closely associate and mutually influence their mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, unveiling an additional regulatory level of auxin-mediated plant development.Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.Peer reviewe

Slitter rewinder control

Diplomová práce řeší řízení tahových sekcí odvíjení a navíjení na podélné řezačce obalového materiálu. Práce byla vypracována ve spolupráci s firmou SOMA, která poskytla stroj pro testování a měření v práci popsaných poznatků. Teoretická část se zabývá funkcí podélné řezačky, možnými mechanickými přístupy k řízení tahových sekcí a konkrétním řešením mechaniky pro řízení tahových sekcí na použitém stroji. Dále je popsán vybraný hardware pro řízení tahových sekcí a jeho použití na stroji. Ostatní kapitoly se soustřeďují na jednotlivé měřící řetězce, kalibrace, výpočty žádaných veličin a řízení stroje. Poslední část práce porovnává teoretická a naměřená data a zhodnocuje výsledky práce.This diploma thesis deals with the control of unwinding and winding tension sections on the slitter rewinder for packaging material. The essay was created in collaboration with SOMA company, which provided a machine for testing and measuring. The theoretical part describes the function of bitter rewinder, possible mechanical approaches of control the tension sections, and real mechanics of control on our machine. The next part explores selected hardware and its use on the rewinder. Further chapters are focused on the individual measuring chains, calibration, computations of required quantities and control algorithms. The last part compares the theoretical and measured values and evaluates the results of this essay.

Asymmetric deformation of bubble shape: cause or effect of vortex-shedding?

Two perpendicular projections of rising bubbles were observed in counter-current downstream diverging flow. Evidently, the bubbles did not enter the boundary layer at the channel wall and a plug liquid flow assumption was acceptable in our experimental equipment. This confirmed that the experiment was appropriate for simulation of bubble rises in a quiescent liquid column. Recent data obtained by a high-speed camera permitted recording over a period of 60 s. Image analysis by a tailor-made program provided a time-series of quantities related to the position, size, and shape of bubbles. In addition to determination of the aspect ratio of the equivalent oblate ellipsoid, deviation from this shape was investigated in respect of the difference between the bubble’s centre of mass and the geometrical centre of bubble projection. Autocorrelation of the data indicated that the bubble inclination oscillated harmonically with a frequency of 5–10 Hz; cross correlation showed that the horizontal shift of the centre of mass, as well as the horizontal velocity, increased with increasing bubble inclination, and the vertical shift of the centre of mass increased with an increases in the absolute value of the bubble inclination. There is no significant phase shift in the oscillation of these quantities. The bulky bottom side of the bubbles is in accordance with the model of bubble oscillation induced by instability of the equilibrium of gravity and surface tension forces. The oscillation frequency dependence on surface forces (Eötvös number) is evident, while viscosity does not play a significant role in low-viscosity liquids. Therefore, vortex-shedding is more likely to be an effect of the oscillation and not its cause.Web of Science681797

In Vivo Reporters for Visualizing Alternative Splicing of Hormonal Genes

Rapid progress in plant molecular biology in recent years has uncovered the main players in hormonal pathways and characterized transcriptomic networks associated with hormonal response. However, the role of RNA processing, in particular alternative splicing (AS), remains largely unexplored. Here, using example genes involved in cytokinin signaling, brassinosteroid synthesis and auxin transport, we present a set of reporters devised to visualize their AS events in vivo. These reporters show a differential tissue-specific expression of certain transcripts and reveal that expression of some of the them can be changed by the application of the exogenous hormone. Finally, based on the characterized AS event of the PIN7 auxin efflux carrier, we designed a system that allows a rapid genetic screening for the factors upstream of this AS event. Our innovative toolset can be therefore highly useful for exploring novel regulatory nodes of hormonal pathways and potentially helpful for plant researchers focusing on developmental aspects of AS

On bubble rising in countercurrent flow

A single bubble of typical volume 20 mm³ ≤ VB ≤ 400 mm³ was placed in downward conically diverging flow of low and moderate viscous liquids (aqueous solutions of glycerine and of electrolytes (NaCl, Na3PO4, MgSO4), and butanol). Experiments were performed over a range of Reynolds number 60≤Re≤2200, Weber number 1≤We≤14, Tadaki number 1≤Ta≤10, Eötvös number 1≤Eo≤22, and bubble aspect ratio 0.4≤b/a≤0.9. The bubble shape, bubble position and motion were investigated by direct observation of two plane projection of bubble by high speed camera. Typical sampling frequency was 150 fps. Relatively long records, (approximately 9000 frames per one bubble observation) allow us to get relevant statistics of treated data. Bubble aspect ratio has been determined from both projection planes. Dimensionless front area of observed bubble has been introduced as suitable parameter for correlation with Eötvös number. Model of static bubble and classical Wellek correlation were employed as asymptotes. Bubble rising velocity has been determined and tested for each single bubble with respect to liquid properties. Velocity data are plotted within the frame given by several theoretical predictions for pure and contaminated liquids. Dimensional analysis is used considering viscosity and surface tension effect. New simple correlation of bubble rising velocity separating the effects of viscosity and surface tension is presented.Web of Science10art. no. A3

Krystalická struktura a tepelné chování tetradraselné soli kyseliny oktahydroimidazo-[4,5-d]imidazol-1,3,4,6-tetrasulfonové (TACOS-K)

The tetrahydrate of the tetrapotassium salt of octahydroimidazo-[4,5-d]imidazol-1,3,4,6-tetrasulfonic acid (TACOS-K), an new energetic material, was investigated in terms of its crystal structure, heat of combustion, thermal stability and decomposition kinetics. Its heat of combustion is -5487±96 J.g-1 from which a heat of formation of -3150 kJ.mol-1 was estimated. It has been found that this compound has a hexagonal crystal space group with a density of 2.026 g.mol-1/150 K. The organic anionic skeleton of the TACOS-K molecule is distinctly deformed. Six tetraanions interconnected by a coordination to the potassium cations and hydrogen bridges to water molecules form hydrophilic as well as hydrophobic cavities. As an intermediate to synthesize cis-1,3,4,6-tetranitro-octahydroimidazo-[4,5-d]imidazole (BCHMX), it decomposes at around 31°C with a first peak temperature range of 46.6-94.3 °C due to loss of water, depending on the heating rates. Hydrolysis of the N-S bonds might play an important role here. Crystalline water evaporation competes with this hydrolysis. TACOS-K has a residual mass of about 46% at 2°C.min-1, which increases with the heating rate. Peak of the exothermic process occurs at 235.6 °C at the same heating rate with an enthalpy change of 164 J.g-1. Dehydration occurs with an energy barrier of 36.7 kJ mol-1 followed by a shoulder mass loss process with a much higher activation energy 110.6 kJ mol-1, while the activation energy for the main exothermic reaction is about 136.2 kJ mol-1.Tetrahydrát na tetradraselné soli oktahydroimidazo- [4,5-d] imidazol-1,3,4,6-tetrasulfonové kyseliny (TACOS-K) je nový energetický materiál, zkoumaný z hlediska své krystalické struktury, spalného tepla, tepelné stability a rozkladné kinetiky. Jeho spalné teplo je -5487 ± 96 J.g-1, ze kterého bylo odhadnuté slučovací teplo -3150 kJ.mol-1. Bylo zjištěno, že tato sloučenina má hexagonální krystalovou strukturu s hustotou 2.026 g.mol-1 při 150 K. Skelet organického aniontu molekuly TACOS-K je výrazně deformovaný. Šest tetraanionů je koordinačně propojeno s kationtů draslíku a vodíkovými můstky s molekulmi vody tvoří hydrofilní i hydrofobní dutiny. Tento meziprodukt pro syntézu cis-1,3,4,6-tetranitro-oktahydroimidazo- [4,5-d] imidazolu (BCHMX) se rozkládá při teplotě okolo 31 ° C, s prvním vrcholem v rozmezí teplot 46.6-94.3 ° C v důsledku ztráty vody a v závislosti na rychlosti ohřevu. Hydrolýza vazeb N-S zde může hrát důležitou roli. Odpařování krystalické vody soutěží s touto hydrolýzou. V TGA má TACOS-K zbytkovou hmotu 46% při vzestupu teploty 2 ° C.min-1, což se zvyšuje s rychlostí ohřevu. Vrchol exotermického procesu se vyskytuje při 235,6 ° C a při stejné rychlosti ohřevu s entalpickou změnou 164 J.g-1. Dehydratace nastává s energetickou bariéru 36,7 kJ mol-1 s následným hromadným procesem ztráty hmotnosti s mnohem vyšší aktivační energie 110,6 kJ mol-1, zatímco aktivační energie pro hlavní exotermní reakci je asi 136,2 kJ mol-1

Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport-Dependent Auxin Distribution[W]

In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery