Applicability and potential of monitored reconstruction in computed tomography.

Monitored tomographic reconstruction (MTR) is a potentially powerful tool for dose and time reduction in computed tomography scanning. We are the first to study the issue of practical implementation of MTR protocols in current-generation real-life instruments. We propose an empirical quantitative model for calculating acquisition and reconstruction times.

NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data.

The recognized importance of mutational spectra in molecular evolution is yet to be fully exploited beyond human cancer studies and model organisms. The wealth of intraspecific polymorphism data in the GenBank repository, covering a broad spectrum of genes and species, presents an untapped opportunity for detailed mutational spectrum analysis. Existing methods fall short by ignoring intermediate substitutions on the inner branches of phylogenetic trees and lacking the capability for cross-species mutational comparisons.

BaRDIC: robust peak calling for RNA-DNA interaction data.

Chromatin-associated non-coding RNAs play important roles in various cellular processes by targeting genomic loci. Two types of genome-wide NGS experiments exist to detect such targets: 'one-to-al', which focuses on targets of a single RNA, and 'all-to-al', which captures targets of all RNAs in a sample. As with many NGS experiments, they are prone to biases and noise, so it becomes essential to detect 'peaks'-specific interactions of an RNA with genomic targets.

Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli.

CsqR (YihW) is a local transcription factor that controls expression of yih genes involved in degradation of sulfoquinovose in Escherichia coli. We recently showed that expression of the respective gene cassette might be regulated by lactose. Here, we explore the phylogenetic and functional traits of CsqR.

RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome.

Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs.

Nontriplet feature of genetic code in ciliates is a result of neutral evolution.

The triplet nature of the genetic code is considered a universal feature of known organisms. However, frequent stop codons at internal mRNA positions in ciliates ultimately specify ribosomal frameshifting by one or two nucleotides depending on the context, thus posing a nontriplet feature of the genetic code of these organisms. Here, we sequenced transcriptomes of eight species and assessed evolutionary patterns arising at frameshift sites.

Sense and antisense RNA products of the gene can affect motility and chemotaxis acting independent of the UxuR protein.

Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3'-end of the gene, encoding transcription factor regulating hexuronate metabolism in These overlapping promoters were predicted with rather high scores, effectively bound RNA polymerase and and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between promoter scores and RNA polymerase binding and was higher for promoters located on the antisense strands of the genes, however, sense promoters within the gene were more active.

Simultaneous approximation of a smooth function and its derivatives by deep neural networks with piecewise-polynomial activations.

This paper investigates the approximation properties of deep neural networks with piecewise-polynomial activation functions. We derive the required depth, width, and sparsity of a deep neural network to approximate any Hölder smooth function up to a given approximation error in Hölder norms in such a way that all weights of this neural network are bounded by 1. The latter feature is essential to control generalization errors in many statistical and machine learning applications.

Multiple Sclerosis Is Associated with Immunoglobulin Germline Gene Variation of Transitional B Cells.

The regulatory functions of the B-cell compartment play an important role in the development and suppression of the immune response. Disruption of their anti-inflammatory functions may lead to the acceleration of immunopathological processes, and to autoimmune diseases, in particular. Unfortunately, the exact mechanism underlying the functioning and development of regulatory B cells (Breg) has not yet been fully elucidated.

Measurement of Lepton-Jet Correlation in Deep-Inelastic Scattering with the H1 Detector Using Machine Learning for Unfolding.

The first measurement of lepton-jet momentum imbalance and azimuthal correlation in lepton-proton scattering at high momentum transfer is presented. These data, taken with the H1 detector at HERA, are corrected for detector effects using an unbinned machine learning algorithm (multifold), which considers eight observables simultaneously in this first application. The unfolded cross sections are compared with calculations performed within the context of collinear or transverse-momentum-dependent factorization in quantum chromodynamics as well as Monte Carlo event generators.

K-clique percolation in free association networks and the possible mechanism behind the [Formula: see text] law.

It is important to reveal the mechanisms of propagation in different cognitive networks. In this study, we discuss the k-clique percolation phenomenon as related to the free association networks including the English Small World of Words project (SWOW-EN). We compared different semantic networks and networks of free associations for various languages.

A hierarchy in clusters of cephalopod mRNA editing sites.

RNA editing in the form of substituting adenine with inosine (A-to-I editing) is the most frequent type of RNA editing in many metazoan species. In most species, A-to-I editing sites tend to form clusters and editing at clustered sites depends on editing of the adjacent sites. Although functionally important in some specific cases, A-to-I editing usually is rare.

Molecular Insights into the Role of Cysteine-Rich Peptides in Induced Resistance to Infection in Tomato Based on Transcriptome Profiling.

Cysteine-rich peptides (CRPs) play an important role in plant physiology. However, their role in resistance induced by biogenic elicitors remains poorly understood. Using whole-genome transcriptome sequencing and our CRP search algorithm, we analyzed the repertoire of CRPs in tomato L.

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes.

Tandem alternative splice sites (TASS) is a special class of alternative splicing events that are characterized by a close tandem arrangement of splice sites. Most TASS lack functional characterization and are believed to arise from splicing noise. Based on the RNA-seq data from the Genotype Tissue Expression project, we present an extended catalogue of TASS in healthy human tissues and analyze their tissue-specific expression.

Analysis of English free association network reveals mechanisms of efficient solution of Remote Association Tests.

We study correlations between the structure and properties of a free association network of the English language, and solutions of psycholinguistic Remote Association Tests (RATs). We show that average hardness of individual RATs is largely determined by relative positions of test words (stimuli and response) on the free association network. We argue that the solution of RATs can be interpreted as a first passage search problem on a network whose vertices are words and links are associations between words.

Adaptive evolution at mRNA editing sites in soft-bodied cephalopods.

Background: The bulk of variability in mRNA sequence arises due to mutation-change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection.

New ancient Eastern European genomes illuminate the dispersal of plague in Europe.

, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period.

Passive Underwater Target Tracking: Conditionally Minimax Nonlinear Filtering with Bearing-Doppler Observations.

The paper presents an application of the Conditionally-Minimax Nonlinear Filtering (CMNF) algorithm to the online estimation of underwater vehicle movement given a combination of sonar and Doppler discrete-time noisy sensor observations. The proposed filter postulates recurrent "prediction-correction" form with some predefined basic prediction and correction terms, and then they are optimally fused. The CMNF estimates have the following advantageous features.

Influence of the spacer region between the Shine-Dalgarno box and the start codon for fine-tuning of the translation efficiency in Escherichia coli.

Translation efficiency contributes several orders of magnitude difference in the overall yield of exogenous gene expression in bacteria. In diverse bacteria, the translation initiation site, whose sequence is the primary determinant of the translation performance, is comprised of the start codon and the Shine-Dalgarno box located upstream. Here, we have examined how the sequence of a spacer between these main components of the translation initiation site contributes to the yield of synthesized protein.

Restraining Lysosomal Activity Preserves Hematopoietic Stem Cell Quiescence and Potency.

Quiescence is a fundamental property that maintains hematopoietic stem cell (HSC) potency throughout life. Quiescent HSCs are thought to rely on glycolysis for their energy, but the overall metabolic properties of HSCs remain elusive. Using combined approaches, including single-cell RNA sequencing (RNA-seq), we show that mitochondrial membrane potential (MMP) distinguishes quiescent from cycling-primed HSCs.

On AUV Control with the Aid of Position Estimation Algorithms Based on Acoustic Seabed Sensing and DOA Measurements.

This article discusses various approaches to the control of autonomous underwater vehicles (AUVs) with the aid of different velocity-position estimation algorithms. Traditionally this field is considered as the area of the extended Kalman filter (EKF) application: It became a universal tool for nonlinear observation models and its use is ubiquitous. Meanwhile, the specific characteristics of underwater navigation, such as an incomplete sets of measurements, constraints on the range metering or even impossibility of range measurements, observations provided by rather specific acoustic beacons, sonar observations, and other features seriously narrow the applicability of common instruments due to a high level of uncertainty and nonlinearity.

Non-Specific Lipid Transfer Proteins in Dorof. et Migush.: Identification, Characterization and Expression Profiling in Response to Pathogens and Resistance Inducers.

Non-specific lipid-transfer proteins (nsLTPs) represent a family of plant antimicrobial peptides (AMPs) implicated in diverse physiological processes. However, their role in induced resistance (IR) triggered by non-pathogenic fungal strains and their metabolites is poorly understood. In this work, using RNA-seq data and our AMP search pipeline, we analyzed the repertoire of nsLTP genes in the wheat and studied their expression in response to infection and treatment with the intracellular metabolites of FS-94.

Scent lineups compared across eleven countries: Looking for the future of a controversial forensic technique.

A scent lineup is generally a procedure whereby a dog's alerting behavior is used to establish that the dog detects two scents, one from a crime scene and one from a suspect, as deriving from the same person. The aim of this article is to compare methodologies of using dogs in scent lineups as a means of identifying perpetrators of crimes. It is hoped that this comparative approach, looking at countries where the method is currently or has in the past been used, will help determine what issues should be addressed in order to assure that the scent lineup will have a future as a forensic technique.

Spectral peculiarity and criticality of a human connectome.

We have performed the comparative spectral analysis of structural connectomes for various organisms using open-access data. Our results indicate new peculiar features of connectomes of higher organisms. We found that the spectral density of adjacency matrices of human connectome has maximal deviation from the one of randomized network, compared to other organisms.

Overproduction and purification of the Escherichia coli transcription factors "toxic" to a bacterial cell.

Transcription factors play a crucial role in control of life of a bacterial cell, working as switchers to a different life style or pathogenicity. To reconstruct the network of regulatory events taking place in changing growth conditions, we need to know regulons of as many transcription factors as possible, and motifs recognized by them. Experimentally this can be attained via ChIP-seq in vivo, SELEX and DNAse I footprinting in vitro.