In this paper, we propose a technique for time series clustering using community detection in complex networks. Firstly, we present a method to transform a set of time series into a network using ...different distance functions, where each time series is represented by a vertex and the most similar ones are connected. Then, we apply community detection algorithms to identify groups of strongly connected vertices (called a community) and, consequently, identify time series clusters. Still in this paper, we make a comprehensive analysis on the influence of various combinations of time series distance functions, network generation methods and community detection techniques on clustering results. Experimental study shows that the proposed network-based approach achieves better results than various classic or up-to-date clustering techniques under consideration. Statistical tests confirm that the proposed method outperforms some classic clustering algorithms, such as k-medoids, diana, median-linkage and centroid-linkage in various data sets. Interestingly, the proposed method can effectively detect shape patterns presented in time series due to the topological structure of the underlying network constructed in the clustering process. At the same time, other techniques fail to identify such patterns. Moreover, the proposed method is robust enough to group time series presenting similar pattern but with time shifts and/or amplitude variations. In summary, the main point of the proposed method is the transformation of time series from time-space domain to topological domain. Therefore, we hope that our approach contributes not only for time series clustering, but also for general time series analysis tasks.
Quantitative Polymerase Chain Reaction (qPCR) is currently the most sensitive technique used for absolute and relative quantification of a target gene transcript, requiring the use of appropriated ...reference genes for data normalization. To accurately estimate the relative expression of target tomato (Solanum lycopersicum L.) genes responsive to several virus species in reverse transcription qPCR analysis, the identification of reliable reference genes is mandatory. In the present study, ten reference genes were analyzed across a set of eight samples: two tomato contrasting genotypes ('Santa Clara', susceptible, and its near-isogenic line 'LAM 157', resistant); subjected to two treatments (inoculation with Tomato chlorotic mottle virus (ToCMoV) and its mock-inoculated control) and in two distinct times after inoculation (early and late). Reference genes stability was estimated by three statistical programs (geNorm, NormFinder and BestKeeper). To validate the results over broader experimental conditions, a set of ten samples, corresponding to additional three tomato-virus pathosystems that included tospovirus, crinivirus and tymovirus + tobamovirus, was analyzed together with the tomato-ToCMoV pathosystem dataset, using the same algorithms. Taking into account the combined analyses of the ranking order outputs from the three algorithms, TIP41 and EF1 were identified as the most stable genes for tomato-ToCMoV pathosystem, and TIP41 and EXP for the four pathosystems together, and selected to be used as reference in the forthcoming expression qPCR analysis of target genes in experimental conditions involving the aforementioned tomato-virus pathosystems.
Network science established itself as a prominent tool for modeling time series and complex systems. This modeling process consists of transforming a set or a single time series into a network. Nodes ...may represent complete time series, segments, or single values, while links define associations or similarities between the represented parts. R is one of the main programming languages used in data science, statistics, and machine learning, with many packages available. However, no single package provides the necessary methods to transform time series into networks. This paper presents a detailed revision of the main transformation methods in the literature and their implementation in the ts2net package in R. The package provides time series distance functions that can be easily computed in parallel and in supercomputers to process larger data sets and methods to transform distance matrices into networks. ts2net also provides methods to transform a single time series into a network, such as recurrence networks, visibility graphs, and transition networks. Together with other packages, ts2net permits the use of network science and graph mining tools to extract information from time series.
Central banks have usually employed short-term rates as the main instrument of monetary policy. In the last decades, however, forward guidance has also become a central tool. This paper combines two ...sources of extraneous information - high frequency surprises and narrative evidence - with sign restrictions in a structural vector autoregressive (VAR) model to disentangle forward guidance from conventional monetary policy. Results show that conventional monetary policy has the expected effects on industrial production even in a recent US sample and that forward guidance is an effective policy tool, being at least as strong as conventional monetary policy.
To uncover the selective forces shaping life-history trait evolution across species, we investigate the genomic basis underlying adaptations to seasonal habitat desiccation in African killifishes, ...identifying the genetic variants associated with positive and relaxed purifying selection in 45 killifish species and 231 wild individuals distributed throughout sub-Saharan Africa. In annual species, genetic drift led to the expansion of nuclear and mitochondrial genomes and caused the accumulation of deleterious genetic variants in key life-history modulating genes such as mtor, insr, ampk, foxo3, and polg. Relaxation of purifying selection is also significantly associated with mitochondrial function and aging in human populations. We find that relaxation of purifying selection prominently shapes genomes and is a prime candidate force molding the evolution of lifespan and the distribution of genetic variants associated with late-onset diseases in different species.
Display omitted
Display omitted
•Whole-genome sequences of 45 African killifish species•Relaxed selection leads to larger genomes in short-lived, annual killifish•Population bottlenecks affect the distribution of aging variants in fish and humans•Natural polg variants in annual killifish cause high rate of mtDNA mutations
Studying the genomic changes accompanying the repeated evolution of short lifespan in 45 African killifish species reveals that neutral genetic drift, rather than adaptive evolution, explains the accumulation of deleterious gene variants affecting lifespan and aging.
This article reviews evidence for sex differences in vulnerability to addiction with an emphasis on the neural mechanisms underlying these differences. Sex differences in the way that the gonadal ...hormone, estradiol, interacts with the ascending telencephalic dopamine system results in sex differences in motivated behaviors, including drug-seeking. In rodents, repeated psychostimulant exposure enhances incentive sensitization to a greater extent in females than males. Estradiol increases females' motivation to attain psychostimulants and enhances the value of drug related cues, which ultimately increases their susceptibility towards spontaneous relapse. This, along with females’ dampened ability to alter decisions regarding risky behaviors, enhances their vulnerability for escalation of drug use. In males, recent evidence suggests that estradiol may be protective against susceptibility towards drug-preference.
Sex differences in the actions of estradiol are reviewed to provide a foundation for understanding how future research might enhance understanding of the mechanisms of sex differences in addiction-related behaviors, which are dependent on estradiol receptor (ER) subtype and the region of the brain they are acting in. A comprehensive review of the distribution of ERα, ERβ, and GPER1 throughout the rodent brain are provided along with a discussion of the possible ways in which these patterns differentially regulate drug-taking between the sexes.
The article concludes with a brief discussion of the actions of gonadal hormones on the circuitry of the stress system, including the hypothalamic pituitary adrenal axis and regulation of corticotropin-releasing factor. Sex differences in the stress system can also contribute to females’ enhanced vulnerability towards addiction.
•Roles of estradiol in sex differences in vulnerability to addiction.•Variable localization and function of ERα, ERβ, GPER1 throughout the brain.•Estradiol regulation of dopamine in reward pathway.•Sex differences in stress and vulnerability to addiction.•Gaps in the scientific literature are highlighted throughout.
Protest diffusion is a cascade process that can spread over different regions of the planet. The way and the extension that this phenomenon can occur is still not properly understood. Here, we ...empirically investigate this question using protest data from GDELT and ICEWS, two of the most extensive and longest-running data sets freely available. We divide the globe into grid cells and construct a temporal network for each data set where nodes represent cells and links are established between nodes if their protest events co-occur. We show that the temporal networks are small-world, indicating that the cells are directly linked or separated by a few steps on average. Furthermore, the average path lengths are decreasing through the years, which suggests that the world is becoming "smaller". The persistent temporal hubs present in both data sets indicate that protests can spread faster through the hubs. This topological feature is consistent with the hypothesis that protests can quickly diffuse from one region to any other part of the globe.
Cancer treatments are often more successful when the disease is detected early. We evaluated the feasibility and safety of multicancer blood testing coupled with positron emission tomography-computed ...tomography (PET-CT) imaging to detect cancer in a prospective, interventional study of 10,006 women not previously known to have cancer. Positive blood tests were independently confirmed by a diagnostic PET-CT, which also localized the cancer. Twenty-six cancers were detected by blood testing. Of these, 15 underwent PET-CT imaging and nine (60%) were surgically excised. Twenty-four additional cancers were detected by standard-of-care screening and 46 by neither approach. One percent of participants underwent PET-CT imaging based on false-positive blood tests, and 0.22% underwent a futile invasive diagnostic procedure. These data demonstrate that multicancer blood testing combined with PET-CT can be safely incorporated into routine clinical care, in some cases leading to surgery with intent to cure.
Abstract
Neandertal DNA makes up 2–3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene ...flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.
The New Zealand aquaculture industry is based primarily on the production of Greenshell™ mussels, Chinook salmon and Pacific oysters. The industry is primed for development and is anticipating ...increasing its export earnings to NZ$3 billion by 2035. To achieve this target and retain its 'clean and green' image, the industry must be able to demonstrate that its practices are sustainable. Integrated multi-trophic aquaculture (IMTA) systems provide an avenue to address this challenge, with most of the work in New Zealand focusing on the integration of low trophic level high-value species such as sea cucumbers and seaweeds with mussels, providing environmental bioremediation and provision of valuable secondary products (nutraceuticals and pharmaceuticals). Ecophysiological, hydrodynamic and benthic diagenesis models have been developed to underpin this IMTA research into sustainable farming designs. However, many regulatory barriers are still in place, which together with the current lack of investment, market security for these new products and associated operational costs form the main constrains to development. Nevertheless, the recent emergence of aquaculture fora where industry, researchers, and regulators meet to discuss future research and development has invigorated interest in diversification of the sector, inclusive of IMTA within existing coastal areas and upcoming land-based and open-ocean operations.
PDF
