Onset of synchronization of Kuramoto oscillators in scale-free networks.

Despite the great attention devoted to the study of phase oscillators on complex networks in the last two decades, it remains unclear whether scale-free networks exhibit a nonzero critical coupling strength for the onset of synchronization in the thermodynamic limit. Here, we systematically compare predictions from the heterogeneous degree mean-field (HMF) and the quenched mean-field (QMF) approaches to extensive numerical simulations on large networks. We provide compelling evidence that the critical coupling vanishes as the number of oscillators increases for scale-free networks characterized by a power-law degree distribution with an exponent 2<γ≤3, in line with what has been observed for other dynamical processes in such networks.

Reciprocal best match graphs.

Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical structure. Here, we investigate the structure of reciprocal best match graphs (RBMGs).

Better Myocardial Function in Aortic Stenosis with Low Left Ventricular Mass: A Mechanism of Protection against Heart Failure Regardless of Stenosis Severity?

About one-tenth to one-third of patients with severe aortic stenosis (AS) do not develop left ventricular hypertrophy (LVH). Intriguingly, the absence of LVH despite severe AS is associated with lower prevalence of heart failure (HF), which challenges the classical notion of LVH as a beneficial compensatory response. Notably, the few studies that have attempted to characterize AS subjects with inadequately low left ventricular (LV) mass relative to LV afterload (i-lowLVM) described better prognosis and enhanced LV performance in AS associated with i-lowLVM, but those reports were limited to severe AS.

Combinatorial properties of phylogenetic diversity indices.

Phylogenetic diversity indices provide a formal way to apportion 'evolutionary heritage' across species. Two natural diversity indices are Fair Proportion (FP) and Equal Splits (ES). FP is also called 'evolutionary distinctiveness' and, for rooted trees, is identical to the Shapley Value (SV), which arises from cooperative game theory.

Reconciling event-labeled gene trees with MUL-trees and species networks.

Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e.

Active Haptic Perception in Robots: A Review.

In the past few years a new scenario for robot-based applications has emerged. Service and mobile robots have opened new market niches. Also, new frameworks for shop-floor robot applications have been developed.

Challenges and recommendations to improve the installability and archival stability of omics computational tools.

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools.

Critical thinking and regional gray matter volume interact to predict representation connection in scientific problem solving.

Representation connection (RC) is a stable ability that significantly predicts the accuracy of scientific innovation problem solving while critical thinking has been strongly related to problem solving. However, the neural mechanisms underlying this relationship have not been assessed. Using voxel-based morphometry (VBM) and scientific innovation problem solving materials, we investigated the correlation between RC and regional gray matter volume (rGMV) in healthy young participants.

Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ.

Background: Gene regulatory networks can be modelled in various ways depending on the level of detail required and biological questions addressed. One of the earliest formalisms used for modeling is a Boolean network, although these models cannot describe most temporal aspects of a biological system. Differential equation models have also been used to model gene regulatory networks, but these frameworks tend to be too detailed for large models and many quantitative parameters might not be deducible in practice.

Alternative characterizations of Fitch's xenology relation.

Horizontal gene transfer (HGT) is an important factor for the evolution of prokaryotes as well as eukaryotes. According to Walter M. Fitch, two genes are xenologs if they are separated by at least one HGT.

Subtyping psychological distress in the population: a semi-parametric network approach.

Aims: The mechanisms underlying both depressive and anxiety disorders remain poorly understood. One of the reasons for this is the lack of a valid, evidence-based system to classify persons into specific subtypes based on their depressive and/or anxiety symptomatology. In order to do this without a priori assumptions, non-parametric statistical methods seem the optimal choice.

Assessment of weather-based influent scenarios for a WWTP: Application of a pattern recognition technique.

This study proposes an integrated approach by combining a pattern recognition technique and a process simulation model, to assess the impact of various climatic conditions on influent characteristics of the largest Italian wastewater treatment plant (WWTP) at Castiglione Torinese. Eight years (viz. 2009-2016) of historical influent data namely influent flow rate (Q), chemical oxygen demand (COD), ammonium (N-NH) and total suspended solids (TSS), in addition to two climatic attributes, average temperature and daily mean precipitation rates (P) from the plant catchment area, are evaluated in this study.

Real-time prediction of influenza outbreaks in Belgium.

Seasonal influenza is a worldwide public health concern. Forecasting its dynamics can improve the management of public health regulations, resources and infrastructure, and eventually reduce mortality and the costs induced by influenza-related absenteism. In Belgium, a network of Sentinel General Practitioners (SGPs) is in place for the early detection of the seasonal influenza epidemic.

Multi-Genome Annotation with AUGUSTUS.

Comparing multiple related genomes can help to improve their structural annotation. The accuracy and consistency of the predicted exon-intron structures of the protein coding genes can be higher when considering all genomes at once rather than annotating one genome at a time.The comparative gene prediction algorithm of AUGUSTUS performs such a multi-genome annotation.

Whole-Genome Annotation with BRAKER.

BRAKER is a pipeline for highly accurate and fully automated gene prediction in novel eukaryotic genomes. It combines two major tools: GeneMark-ES/ET and AUGUSTUS. GeneMark-ES/ET learns its parameters from a novel genomic sequence in a fully automated fashion; if available, it uses extrinsic evidence for model refinement.

Best match graphs.

Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let T be a phylogenetic (gene) tree T and [Formula: see text] an assignment of leaves of T to species. The best match graph [Formula: see text] is a digraph that contains an arc from x to y if the genes x and y reside in different species and y is one of possibly many (evolutionary) closest relatives of x compared to all other genes contained in the species [Formula: see text].

On the uniqueness of the maximum parsimony tree for data with up to two substitutions: An extension of the classic Buneman theorem in phylogenetics.

One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist of various characters (also often referred to as sites). Often, however, tree reconstruction methods based on criteria like maximum parsimony may fail to provide a unique tree for a given dataset, or, even worse, reconstruct the 'wrong' tree (i.

The nested structural organization of the worldwide trade multi-layer network.

Nestedness has traditionally been used to detect assembly patterns in meta-communities and networks of interacting species. Attempts have also been made to uncover nested structures in international trade, typically represented as bipartite networks in which connections can be established between countries (exporters or importers) and industries. A bipartite representation of trade, however, inevitably neglects transactions between industries.

Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony.

In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex v of an evolutionary tree T from the states that are observed at the leaves of the tree. A simple and fast estimation method-maximum parsimony-takes the ancestral state at v to be any state that minimises the number of state changes in T required to explain its evolution on T. In this paper, we investigate the reconstruction accuracy of this estimation method further, under a simple symmetric model of state change, and obtain a number of new results, both for 2-state characters, and r-state characters ([Formula: see text]).

Clustering algorithms: A comparative approach.

Many real-world systems can be studied in terms of pattern recognition tasks, so that proper use (and understanding) of machine learning methods in practical applications becomes essential. While many classification methods have been proposed, there is no consensus on which methods are more suitable for a given dataset. As a consequence, it is important to comprehensively compare methods in many possible scenarios.

Statistical Inconsistency of Maximum Parsimony for k-Tuple-Site Data.

One of the main aims of phylogenetics is to reconstruct the "Tree of Life." In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the evolutionary relationships of these species. Maximum parsimony is one such criterion for tree reconstruction, and it is the one which we will use in this paper.

Unfolding the Complexity of the Global Value Chain: Strength and Entropy in the Single-Layer, Multiplex, and Multi-Layer International Trade Networks.

The worldwide trade network has been widely studied through different data sets and network representations with a view to better understanding interactions among countries and products. Here we investigate international trade through the lenses of the single-layer, multiplex, and multi-layer networks. We discuss differences among the three network frameworks in terms of their relative advantages in capturing salient topological features of trade.

Predicting Genes in Single Genomes with AUGUSTUS.

AUGUSTUS is a tool for finding protein-coding genes and their exon-intron structure in genomic sequences. It does not necessarily require additional experimental input, as it can be applied in so-called ab initio mode. However, extrinsic evidence from various sources such as transcriptome sequencing or the annotations of closely related genomes can be integrated in order to improve the accuracy and completeness of the annotation.

Recovering Quantum Gates from Few Average Gate Fidelities.

Characterizing quantum processes is a key task in the development of quantum technologies, especially at the noisy intermediate scale of today's devices. One method for characterizing processes is randomized benchmarking, which is robust against state preparation and measurement errors and can be used to benchmark Clifford gates. Compressed sensing techniques achieve full tomography of quantum channels essentially at optimal resource efficiency.