Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests.

For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular classifiers such as Kraken use -mers, recent research indicates that using maximal exact matches (MEMs) can lead to better classifications. For example, we can ■ build an augmented FM-index over the the genomes in the tree concatenated in left-to-right order; ■ for each MEM in a read, find the interval in the suffix array containing the starting positions of that MEM's occurrences in those genomes; ■ find the minimum and maximum values stored in that interval; ■ take the lowest common ancestor (LCA) of the genomes containing the characters at those positions.

Molecular Characterization of a Novel Infecting Raspberry.

Raspberry plants, valued for their fruits, are vulnerable to a range of viruses that adversely affect their yield and quality. Utilizing high-throughput sequencing (HTS), we identified a novel virus, tentatively named raspberry enamovirus 1 (RaEV1), in three distinct raspberry plants. This study provides a comprehensive characterization of RaEV1, focusing on its genomic structure, phylogeny, and possible transmission routes.

Mononuclear or Coordination Polymer Complexes? Both Are Possible for 3,6,9-Trioxaundecanedioic Acid.

Investigating the driving forces leading to the formation of a specific supramolecular architecture among a wide spectrum of all the possibly obtainable structures is not an easy task. The contemporary literature provides several models for correctly predicting the thermodynamically accessible structures that can originate from a library of building blocks. Definitions are rigid by their very nature, so their application may sometimes require a shift in perspective.

Online teaching of practical classes under the Covid-19 restrictions.

COVID -19 pandemic and its restrictions bring new challenges to all aspects and phases of higher education. At universities, new remote formats have been developed and deployed for lectures and laboratory exercises. This article addresses challenges and introduces the new experience with lectures and laboratory classes during the pandemic time at the Department of Measurement of the Czech Technical University in Prague, Faculty of Electrical Engineering.

Heterogeneous Electrochemical Ammonia Oxidation with a Ru-bda Oligomer Anchored on Graphitic Electrodes via CH-π Interactions.

Molecular catalysts can promote ammonia oxidation, providing mechanistic insights into the electrochemical N cycle for a carbon-free fuel economy. We report the ammonia oxidation activity of carbon anodes functionalized with the oligomer {[Ru(bda-κ- )(4,4'-bpy)](4,4'-bpy)}, , where bda is [2,2'-bipyridine]-6,6'-dicarboxylate and 4,4'-bpy is 4,4'-bipyridine. Electrocatalytic studies in propylene carbonate demonstrate that the Ru-based hybrid anode used in a 3-electrode configuration transforms NH to N and H in a 1:3 ratio with near-unity faradaic efficiency at an applied potential of 0.

Mixed Infection of Blackcurrant with a Novel Cytorhabdovirus and Black Currant-Associated Nucleorhabdovirus.

A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined and verified using high-throughput sequencing. The genomic organization of BCRV2 was characteristic of cytorhabdoviruses (family ) and included seven genes: 3 ́- N-P´-P-P3-M-G-L -5 ́.

Online teaching at CTU in Prague aka university under COVID restrictions.

Covid-19 related restrictions bring new challenges to all aspects and phases of higher education. At universities, new remote formats are deployed or even developed both for lectures and laboratory exercises. This article addresses new challenges and describes the experience with lessons during the pandemic time at the Department of Measurement of the Czech Technical University in Prague, Faculty of Electrical Engineering.

Evaluation of digital watermarking on subjective speech quality.

New methods of securing the distribution of audio content have been widely deployed in the last twenty years. Their impact on perceptive quality has, however, only been seldomly the subject of recent extensive research. We review digital speech watermarking state of the art and provide subjective testing of watermarked speech samples.

Synthesis, Structure, and Ammonia Oxidation Catalytic Activity of Ru-NH Complexes Containing Multidentate Polypyridyl Ligands.

Ammonia (electro)oxidation with molecular catalysts is a rapidly developing topic with wide practical applications ahead. We report here the catalytic ammonia oxidation reaction (AOR) activity using [Ru(tda-κ-NO)(py)], , (tda is 2,2':6',2''-terpyridine-6,6''-dicarboxylate; py is pyridine) as a catalyst precursor. Furthermore, we also describe the rich chemistry associated with the reaction of Ru-tda and Ru-tPa (tPa is 2,2':6',2''-terpyridine-6,6''-diphosphonate) complexes with NH and NH using [Ru(tda-κ-NO)(dmso)Cl] (dmso is dimethyl sulfoxide) and [Ru(tPa-κ-NO)(py)], , as synthetic intermediates, respectively.

PFP Compressed Suffix Trees.

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string , it produces a dictionary and a parse of overlapping phrases such that BWT() can be computed from and in time and workspace bounded in terms of their combined size |PFP()|.

Dynamic Helicates Self-Assembly from Homo- and Heterotopic Dynamic Covalent Ligand Strands.

The understanding and the application of reversible covalent reactions and coordination chemistry together with the proper design of the molecular frameworks, allow to achieve not only well-defined output architectures but also different grades of complex behavior. In this work, the dynamic nature of the helical systems offers an additional level of complexity by combining self-sorting on two levels: 1) the build-up of the ligand strand constituents from their components through dynamic covalent chemistry; 2) the assembly of the helicates from the ligands and the metal cations through dynamic metallo-supramolecular chemistry. The information encoded in the ligands constituent molecule was read differently (and accurately at the same time) by metal cations that varied in the coordination algorithms.

A Ru-bda Complex with a Dangling Carboxylate Group: Synthesis and Electrochemical Properties.

Ruthenium complexes containing the tetradentate 2,2'-bipyridine-6,6'-dicarboxylato (bda) equatorial ligand and ortho-subsituted pyridines in the axial position have been prepared and characterized using spectroscopic, crystallographic and electrochemical techniques. Complexes [Ru(Hbda)(DMSO)(pyC)] () and [Ru(bda)(DMSO)(pyA)] () (where pyC is 2-pyridinecarboxylate, pyA is pyridine-2-ylmethanol and DMSO is dimethyl sulfoxide) have been isolated in moderate to high yields. The solid state structures of (-H) and reveal the strong chelate effect of the axial pyridine ligand that coordinates in a bidentate fashion leaving the bda equatorial ligand coordinating in a tridentate mode.

Subjective speech quality measurement with and without parallel task: Laboratory test results comparison.

This paper focuses on a novel methodology of subjective speech quality measurement and repeatability of its results between laboratory conditions and simulated environmental conditions. A single set of speech samples was distorted by various background noises and low bit-rate coding techniques. This study aimed to compare results of subjective speech quality tests with and without a parallel task deploying the ITU-T P.

SOPanG: online text searching over a pan-genome.

Motivation: The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far.

Results: We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

Assessment of ECG and respiration recordings from simulated emergency landings of ultra light aircraft.

Pilots of ultra light aircraft have limited training resources, but with the use of low cost simulators it might be possible to train and test some parts of their training on the ground. The purpose of this paper is to examine possibility of stress inducement on a low cost flight simulator. Stress is assessed from electrocardiogram and respiration.

Deciphering the growth pattern and phytohormonal content in Saskatoon berry (Amelanchier alnifolia) in response to in vitro cytokinin application.

Clonal propagation plays a critical integral role in the growth and success of a global multi-billion dollar horticulture industry through a constant supply of healthy stock plants. The supply chain depends on continuously improving the micropropagation process, thus, understanding the physiology of in vitro plants remains a core component. We evaluated the influence of exogenously applied cytokinins (CKs, N-benzyladenine = BA, isopentenyladenine = iP, meta-topolin = mT, 6-(3-hydroxybenzylamino)-9-(tetrahydropyran-2-yl)purine = mTTHP) in Murashige and Skoog (MS)-supplemented media on organogenic response and accumulation of endogenous CK and indole-3-acetic acid (IAA) metabolites.

Coevolution and ratiometric behaviour in metal cation-driven dynamic covalent systems.

Dynamic Covalent Libraries (DCLs) have been used to demonstrate coevolution behaviour on a molecular level using dynamic covalent molecules such as imines and hydrazones. Two systems are presented: the first system is based on a dialdehyde and two diamines in combination with Zn(ii) and Hg(ii) to form a 2 × 2 Constitutional Dynamic Network (CDN) of four complexes of macrocyclic bis-imines. Whereas the two metal ions, when reacted separately form a complex with each macrocycle with low selectivity, when applied together, each cation yields selectively a complex with one of the two macrocycles.

Training a Constitutional Dynamic Network for Effector Recognition: Storage, Recall, and Erasing of Information.

Constitutional dynamic libraries (CDLs) of hydrazones, acylhydrazones, and imines undergo reorganization and adaptation in response to chemical effectors (herein metal cations) via component exchange and selection. Such CDLs can be subjected to training by exposition to given effectors and keep memory of the information stored by interaction with a specific metal ion. The long-term storage of the acquired information into the set of constituents of the system allows for fast recognition on subsequent contacts with the same effector(s).

Gallium(III) complexes of NOTA-bis (phosphonate) conjugates as PET radiotracers for bone imaging.

Ligands with geminal bis(phosphonic acid) appended to 1,4,7-triazacyclonone-1,4-diacetic acid fragment through acetamide (NOTAM(BP) ) or methylenephosphinate (NO2AP(BP) ) spacers designed for (68) Ga were prepared. Ga(III) complexation is much faster for ligand with methylenephosphinate spacer than that with acetamide one, in both chemical (high reactant concentrations) and radiolabeling studies with no-carrier-added (68) Ga. For both ligands, formation of Ga(III) complex was slower than that with NOTA owing to the strong out-of-cage binding of bis(phosphonate) group.

Calix[4]arenes with intramolecularly bridged meta positions prepared via Pd-catalysed double C-H activation.

The introduction of a 2-pyridylsulfoxide moiety into the upper rim of calix[4]arenes enabled the synthesis of unprecedented derivatives with intramolecularly bridged meta positions of two neighbouring aromatic subunits. Palladium-catalysed double C-H activation thus represents a straightforward way to a completely novel type of calixarenes.

Preparation, biological activity and endogenous occurrence of N6-benzyladenosines.

Cytokinin activity of forty-eight 6-benzyladenosine derivatives at both the receptor and cellular levels as well as their anticancer properties were compared in various in vitro assays. The compounds were prepared by the condensation of 6-chloropurine riboside with corresponding substituted benzylamines and characterized by standard collection of physico-chemical methods. The majority of synthesized derivatives exhibited high activity in all three of the cytokinin bioassays used (tobacco callus, wheat leaf senescence and Amaranthus bioassay).

Preparation and biological activity of 6-benzylaminopurine derivatives in plants and human cancer cells.

To study the structure-activity relationships of aromatic cytokinins, the cytokinin activity at both the receptor and cellular levels, as well as CDK inhibitory and anticancer properties of 38 6-benzylaminopurine (BAP) derivatives were compared in various in vitro assays. The compounds were prepared by the condensation of 6-chloropurine with corresponding substituted benzylamines. The majority of synthesised derivatives exhibited high activity in all three of the cytokinin bioassays employed (tobacco callus, wheat senescence and Amaranthus bioassay).

New cytokinin metabolites in IPT transgenic Arabidopsis thaliana plants.

Two novel cytokinin metabolites were identified in transgenic Arabidopsis thaliana (L.) Heynh. plants containing the bacterial IPT gene under the transcriptional control of a heat-regulated promoter.