Stochastic Generator of Earthquakes for Mainland France

Mainland France is characterized by low-to-moderate seismic activity, yet it is known that major earthquakes could strike this territory (e.g., Liguria in 1887 or Basel in 1356). Assessing this French seismic hazard is thus necessary in order to support building codes and to lead prevention actions towards the population. The Probabilistic Seismic Hazard Assessment (PSHA) is the classical approach used to estimate the seismic hazard. One way to apply PSHA is to generate synthetic earthquakes by propagating information from past seismicity and building various seismic scenarios. In this paper, we present an implementation of a stochastic generator of earthquakes and discuss its relevance to mimic the seismicity of low-to-moderate seismic areas. The proposed stochastic generator produces independent events (main shocks) and their correlated seismicity (only aftershocks). Main shocks are simulated first in time and magnitude considering all available data in the area, and then localized in space with the use of a probability map and regionalization. Aftershocks are simulated around main shocks by considering both the seismic moment ratio and distribution of the aftershock’s proportion. The generator is tested with mainland France data.

Apical and basal auxin sources pattern shoot branching in a moss

Shoot branching mechanisms where branches arise in association with leaves – referred to as lateral or axillary branching – evolved by convergence in the sporophyte of vascular plants and the gametophyte of bryophytes, and accompanied independent events of plant architectural diversification. Previously, we showed that three hormonal cues, including auxin, have been recruited independently to co-ordinate branch patterning in flowering plant leafy shoots and moss gametophores (Coudert, Palubicki et al., 2015). Moreover, auxin-mediated apical dominance, which relies on local auxin production, has been proposed as a unifying molecular regulatory mechanism of branch development across land plants. Whilst our previous work in the moss Physcomitrium patens has gathered indirect evidence supporting the notion that auxin synthesized in gametophore apices regulates branch formation at a distance, direct genetic evidence for a role of auxin biosynthesis in gametophore branching control is still lacking. Here, we show that gametophore apex decapitation promotes branch emergence through massive and rapid transcriptional reprogramming of auxin-responsive genes and altering auxin biosynthesis gene activity. Specifically, we identify a subset of P. patens TRYPTOPHAN AMINO-TRANSFERASE (TAR) and YUCCA FLAVIN MONOOXYGENASE-LIKE (YUC) auxin biosynthesis genes expressed in apical and basal regions of the gametophore, and show that they are essential for branch initiation and outgrowth control. Our results demonstrate that local auxin biosynthesis coordinates branch patterning in moss and thus constitutes a shared and ancient feature of shoot architecture control in land plants.

Bus Travel Time Reliability Incorporating Stop Waiting Time and In-vehicle Travel Time with AVL Data

Improving bus operation quality can attract more commuters to use bus transit, and therefore reduces the share of car and alleviates traffic congestion. One important index of bus operation quality is the bus travel time reliability, which in this paper is defined to be the probability when the sum of bus stop waiting time and in-vehicle travel time is less than a certain threshold. We formulate the bus travel time reliability by the convolution of independent events’ probabilities, and elaborate the calculation method using Automatic Vehicle Location (AVL) data. Next, the No.63 Bus Line in Harbin City is used to test the applicability of the proposed method, and analyze the influence factors of the bus travel time reliability. The numerical results show that factors such as weather, workday, departure time, travel distance, and the distance from the boarding stop to the bus departure station will significantly affect the travel time reliability. At last, some general conclusions and future research are summarized.

Investigating Affective Responding to Daily Positive Events Among Adolescents Using Ecological Momentary Assessment

The experience of positive events is associated with increased positive affect, which can beneficially impact the physical and mental health outcomes of adolescents. Despite an increase in important life events during adolescence, little research has examined the influence of positive events on affect in this population. This study used Ecological Momentary Assessment to investigate individual differences in the effects of daily positive events on momentary positive and negative affect and event-specific positive affect among 136 adolescents ( M age = 13.03 years). Results indicated that interpersonal and independent events elicited greater event-specific positive affect than non-interpersonal and dependent events. Dependent interpersonal events were associated with the greatest positive affect compared to other combinations of event types. Gender did not moderate these effects. These findings may address the gap in the literature regarding the types of daily positive events that elicit the most positive affect in adolescents, and in turn, may enhance well-being.

Analysis of the probability of connectivity of a telecommunications network based on the reduction of several non-connectivity events to a union of independent events

Introduction: For large and structurally complex telecommunication networks, calculating the connectivity probability turns out to be a very cumbersome and time-consuming process due to the huge number of elements in the resulting expression. The most expedient way out of this situation is a method based on the representation of a network connectivity event in the form of sums of products of incompatible events. However, this method also requires performing additional operations on sets in some cases. Purpose: To eliminate the main disadvantages of the method using multi-variable inversion. Results: It is shown that the connectivity event of a graph should be interpreted as a union of connectivity events of all its subgraphs, which leads to the validity of the expression for the connectivity event of the network in the form of a union of connectivity events of typical subgraphs (path, backbone, and in general, a multi-pole tree) of the original random graph. An iterative procedure is proposed for bringing a given number of connectivity events to the union of independent events by sequentially adding subgraph disjoint events. The possibility of eliminating repetitive routine procedures inherent in methods using multi-variable inversion is proved by considering not the union of connectivity events (incoherence) degenerating into the sum of incompatible products, but the intersection of opposite events, which also leads to a similar sum. However, to obtain this sum, there is no need to perform a multi-variable inversion for each of the terms over all those previously analyzed. Practical relevance: The obtained analytical relations can be applied in the analysis of reliability, survivability or stability of complex telecommunications networks.

Bacillus anthracis Phylogeography: New Clues From Kazakhstan, Central Asia

This article describes Bacillus anthracis strains isolated in Kazakhstan since the 1950s until year 2016 from sixty-one independent events associated with anthrax in humans and animals. One hundred and fifty-four strains were first genotyped by Multiple Locus VNTR (variable number of tandem repeats) Analysis (MLVA) using 31 VNTR loci. Thirty-five MLVA31 genotypes were resolved, 28 belong to the A1/TEA group, five to A3/Sterne-Ames group, one to A4/Vollum and one to the B clade. This is the first report of the presence of the B-clade in Kazakhstan. The MLVA31 results and epidemiological data were combined to select a subset of seventy-nine representative strains for draft whole genome sequencing (WGS). Strains from Kazakhstan significantly enrich the known phylogeny of the Ames group polytomy, including the description of a new branch closest to the Texas, United States A.Br.Ames sublineage stricto sensu. Three among the seven currently defined branches in the TEA polytomy are present in Kazakhstan, “Tsiankovskii”, “Heroin”, and “Sanitary Technical Institute (STI)”. In particular, strains from the STI lineage are largely predominant in Kazakhstan and introduce numerous deep branching STI sublineages, demonstrating a high geographic correspondence between “STI” and Kazakhstan, Central Asia. This observation is a strong indication that the TEA polytomy emerged after the last political unification of Asian steppes in the fourteenth century of the Common Era. The phylogenetic analysis of the Kazakhstan data and of currently available WGS data of worldwide origin strengthens our understanding of B. anthracis geographic expansions in the past seven centuries.

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000–5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.

Laboratory methods to decipher epigenetic signatures: a comparative review

Epigenetics refers to nucleotide sequence-independent events, and heritable changes, including DNA methylation and histone modification (as the two main processes), contributing to the phenotypic features of the cell. Both genetics and epigenetics contribute to determining the outcome of regulatory gene expression systems. Indeed, the flexibility of epigenetic effects and stability of genetic coding lead to gene regulation complexity in response signals. Since some epigenetic changes are significant in abnormalities such as cancers and neurodegenerative diseases, the initial changes, dynamic and reversible properties, and diagnostic potential of epigenomic phenomena are subject to epigenome-wide association studies (EWAS) for therapeutic aims. Based on recent studies, methodological developments are necessary to improve epigenetic research. As a result, several methods have been developed to explore epigenetic alterations at low, medium, and high scales, focusing on DNA methylation and histone modification detection. In this research field, bisulfite-, enzyme sensitivity- and antibody specificity-based techniques are used for DNA methylation, whereas histone modifications are gained based on antibody recognition. This review provides a mechanism-based understanding and comparative overview of the most common techniques for detecting the status of epigenetic effects, including DNA methylation and histone modifications, for applicable approaches from low- to high-throughput scales.

Onset and stepwise extensions of recombination suppression are common in mating-type chromosomes of Microbotryum anther-smut fungi

Sex chromosomes and mating-type chromosomes can display large genomic regions without recombination. Recombination suppression often extended stepwise with time away from the sex- or mating-type-determining genes, generating evolutionary strata of differentiation between alternative sex or mating-type chromosomes. In anther-smut fungi of the Microbotryum genus, recombination suppression evolved repeatedly, linking the two mating-type loci and extended multiple times in regions distal to the mating-type genes. Here, we obtained high-quality genome assemblies of alternative mating types for four Microbotryum fungi. We found an additional event of independent chromosomal rearrangements bringing the two mating-type loci on the same chromosome followed by recombination suppression linking them. We also found, in a new clade analysed here, that recombination suppression between the two mating-type loci occurred in several steps, with first an ancestral recombination suppression between one of the mating-type locus and its centromere; later, completion of recombination suppression up to the second mating-type locus occurred independently in three species. The estimated dates of recombination suppression between the mating-type loci ranged from 0.15 to 3.58 million years ago. In total, this makes at least nine independent events of linkage between the mating-type loci across the Microbotryum genus. Several mating-type locus linkage events occurred through the same types of chromosomal rearrangements, where similar chromosome fissions at centromeres represent convergence in the genomic changes leading to the phenotypic convergence. These findings further highlight Microbotryum fungi as excellent models to study the evolution of recombination suppression.

spaceNtime: an R package for estimating abundance of unmarked animals using camera-trap photographs

The space to event (STE), time to event (TTE), and instantaneous sampling (IS) methods were developed to estimate abundance of unmarked animals from camera trap images (Moeller et al. in Ecosphere 9(8):e02331, 2018). The space and time to event models use camera data in a different way than other abundance estimation methods do. Instead of using counts of animals over independent events, STE uses a measure of sampled space before the first detection of the target species, and TTE uses the time until the first detection. We introduce , a free and open-source R package designed to assist in the implementation of the STE and TTE models, along with the IS estimator. This package takes the user through the steps of transforming data, defining sampling effort, selecting sampling occasions, building encounter histories, and estimating abundance from camera data using these three methods. The package is designed for users with a baseline level of knowledge of R and statistics, without requiring expertise in either.