Adversarial training to improve robustness of adversarial deep neural classifiers in the NOvA experiment

The NOvA experiment is a long-baseline neutrino oscillation experiment. Consisting of two functionally identical detectors situated off-axis in Fermilab’s NuMI neutrino beam. The Near Detector observes the unoscillated beam at Fermilab, while the Far Detector observes the oscillated beam 810 km away. This allows for measurements of the oscillation probabilities for multiple oscillation channels, ν_µ → ν_µ, anti ν_µ → anti ν_µ, ν_µ → ν_e and anti ν_µ → anti ν_e, leading to measurements of the neutrino oscillation parameters, sinθ_23, ∆m^2_32 and δ_CP. These measurements are produced from an extensive analysis of the recorded data. Deep neural networks are deployed at multiple stages of this analysis. The Event CVN network is deployed for the purposes of identifying and classifying the interaction types of selected neutrino events. The effects of systematic uncertainties present in the measurements on the network performance are investigated and are found to cause negligible variations. The robustness of these network trainings is therefore demonstrated which further justifies their current usage in the analysis beyond the standard validation. The effects on the network performance for larger systematic alterations to the training datasets beyond the systematic uncertainties, such as an exchange of the neutrino event generators, are investigated. The differences in network performance corresponding to the introduced variations are found to be minimal. Domain adaptation techniques are implemented in the AdCVN framework. These methods are deployed for the purpose of improving the Event CVN robustness for scenarios with systematic variations in the underlying data

Erratum to ‘Bateman's principles and human sex roles’

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Tracking Cyber Adversaries with Adaptive Indicators of Compromise

A forensics investigation after a breach often uncovers network and host indicators of compromise (IOCs) that can be deployed to sensors to allow early detection of the adversary in the future. Over time, the adversary will change tactics, techniques, and procedures (TTPs), which will also change the data generated. If the IOCs are not kept up-to-date with the adversary's new TTPs, the adversary will no longer be detected once all of the IOCs become invalid. Tracking the Known (TTK) is the problem of keeping IOCs, in this case regular expressions (regexes), up-to-date with a dynamic adversary. Our framework solves the TTK problem in an automated, cyclic fashion to bracket a previously discovered adversary. This tracking is accomplished through a data-driven approach of self-adapting a given model based on its own detection capabilities. In our initial experiments, we found that the true positive rate (TPR) of the adaptive solution degrades much less significantly over time than the naive solution, suggesting that self-updating the model allows the continued detection of positives (i.e., adversaries). The cost for this performance is in the false positive rate (FPR), which increases over time for the adaptive solution, but remains constant for the naive solution. However, the difference in overall detection performance, as measured by the area under the curve (AUC), between the two methods is negligible. This result suggests that self-updating the model over time should be done in practice to continue to detect known, evolving adversaries.Comment: This was presented at the 4th Annual Conf. on Computational Science & Computational Intelligence (CSCI'17) held Dec 14-16, 2017 in Las Vegas, Nevada, US

Head Size of Male and Female Lizards Increases with Population Density Across Island Populations in the Bahamas

In polygynous lizards, male–male competition is an important driver of morphologic and behavioral traits associated with intraspecific dominance. The extent to which females engage in aggressive behavior and thus contribute to competition-driven morphologic variation is not well studied. We used injury frequencies of brown anoles (Anolis sagrei) in 16 island populations to test the hypothesis that injury-inducing aggressive encounters increase with population density in both male and female lizards. We further asked whether intraspecific competition is a potential driver of phenotypic traits related to dominance by using population density as proxy for intraspecific competition. We found that the proportion of individuals with injuries was greater in populations with higher densities, suggesting that agonistic competitive interactions increase with population density. Size-adjusted head length of male and female lizards increased with population density, suggesting that larger heads might be advantageous when intraspecific competition is strong. We detected differences in morphology and injury frequency among islands for both males and females, which suggests that agonistic competitive interactions among females may be stronger than previously appreciated. Further research is needed to determine whether aggressive encounters involving females are restricted to intrasexual competition or whether they also involve males, and how morphologic traits of females are related to competitive dominance and reproductive success

Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian

Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within‐pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome‐wide SNPs generated using a double‐digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that withinpond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes

Effects of black tea on body composition and metabolic outcomes related to cardiovascular disease risk: a randomized controlled trial

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence (http://creativecommons.org/licenses/by/3.0/)There is increasing evidence that tea and its non-caffeine components (primarily flavonoids) contribute to cardiovascular health. Randomized controlled trials have shown that tea can improve cardiovascular disease risk factors. We have previously reported a non-caffeine associated beneficial effect of regular black tea consumption on blood pressure and its variation. Objective: To explore the non-caffeine associated effects of black tea on body weight and body fat distribution, and cardiovascular disease related metabolic outcomes. Design: regular tea-drinking men and women (n ¼ 111; BMI 20–35 kg m 2) were recruited to a randomized controlled double-blind 6 month parallel-designed trial. Participants consumed 3 cups per day of either powdered black tea solids (tea) or a flavonoid-free flavour- and caffeine-matched placebo (control). Body weight, waist- and hip-circumference, endothelial function and plasma biomarkers were assessed at baseline, 3 months and 6 months. Results: Compared to control, regular ingestion of black tea over 3 months inhibited weight gain ( 0.64 kg, p ¼ 0.047) and reduced waist circumference ( 1.88 cm, P ¼ 0.035) and waist-to-hip ratio ( 0.03, P ¼ 0.005). These effects were no longer significant at 6 months. There were no significant effects observed on fasting glucose, insulin, plasma lipids or endothelial function. Conclusion: Our study suggests that short-term regular ingestion of black tea over 3 months can improve body weight and body fat distribution, compared to a caffeine-matched control beverage. However, there was no evidence that these effects were sustained beyond 3 months

Cell boundary confinement sets the size and position of the E. coli chromosome

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome

Evolution and development of fruits of Erycina pusilla and other orchid species

Fruits play a crucial role in seed dispersal. They open along dehiscence zones. Fruit dehiscence zone formation has been intensively studied in Arabidopsis thaliana. However, little is known about the mechanisms and genes involved in the formation of fruit dehiscence zones in species outside the Brassicaceae. The dehiscence zone of A. thaliana contains a lignified layer, while dehiscence zone tissues of the emerging orchid model Erycina pusilla include a lipid layer. Here we present an analysis of evolution and development of fruit dehiscence zones in orchids. We performed ancestral state reconstructions across the five orchid subfamilies to study the evolution of selected fruit traits and explored dehiscence zone developmental genes using RNA-seq and qPCR. We found that erect dehiscent fruits with non-lignified dehiscence zones and a short ripening period are ancestral characters in orchids. Lignified dehiscence zones in orchid fruits evolved multiple times from non-lignified zones. Furthermore, we carried out gene expression analysis of tissues from different developmental stages of E. pusilla fruits. We found that fruit dehiscence genes from the MADS-box gene family and other important regulators in E. pusilla differed in their expression pattern from their homologs in A. thaliana. This suggests that the current A. thaliana fruit dehiscence model requires adjustment for orchids. Additionally, we discovered that homologs of A. thaliana genes involved in the development of carpel, gynoecium and ovules, and genes involved in lipid biosynthesis were expressed in the fruit valves of E. pusilla, implying that these genes may play a novel role in formation of dehiscence zone tissues in orchids. Future functional analysis of developmental regulators, lipid identification and quantification can shed more light on lipid-layer based dehiscence of orchid fruits