Effects of current on early stages of focused ion beam nano-machining

In this report we investigate the effects of focused ion beam machining at low doses in the range of 1015–1016 ions cm-2 for currents below 300 pA on Si(100) substrates. The effects of similar doses with currents in the range 10–300 pA were compared. The topography of resulting structures has been characterized using atomic force microscope, while crystallinity of the Si was assessed by means of Raman spectroscopy. These machining parameters allow a controllable preparation of structures either protruding from, or recessed into, the surface with nanometre precision

Reviewer Integration and Performance Measurement for Malware Detection

We present and evaluate a large-scale malware detection system integrating machine learning with expert reviewers, treating reviewers as a limited labeling resource. We demonstrate that even in small numbers, reviewers can vastly improve the system's ability to keep pace with evolving threats. We conduct our evaluation on a sample of VirusTotal submissions spanning 2.5 years and containing 1.1 million binaries with 778GB of raw feature data. Without reviewer assistance, we achieve 72% detection at a 0.5% false positive rate, performing comparable to the best vendors on VirusTotal. Given a budget of 80 accurate reviews daily, we improve detection to 89% and are able to detect 42% of malicious binaries undetected upon initial submission to VirusTotal. Additionally, we identify a previously unnoticed temporal inconsistency in the labeling of training datasets. We compare the impact of training labels obtained at the same time training data is first seen with training labels obtained months later. We find that using training labels obtained well after samples appear, and thus unavailable in practice for current training data, inflates measured detection by almost 20 percentage points. We release our cluster-based implementation, as well as a list of all hashes in our evaluation and 3% of our entire dataset.Comment: 20 papers, 11 figures, accepted at the 13th Conference on Detection of Intrusions and Malware & Vulnerability Assessment (DIMVA 2016

Does the thermal mismatch hypothesis predict disease outcomes in different morphs of a terrestrial salamander?

Many aspects of ectotherm physiology are temperature‐dependent. The immune system of temperate‐dwelling ectothermic host species is no exception and their immune function is often downregulated in cold temperatures. Likewise, species of ectothermic pathogens experience temperature‐mediated effects on rates of transmission and/or virulence. Although seemingly straightforward, predicting the outcomes of ectothermic host−pathogen interactions is quite challenging. A recent hypothesis termed the thermal mismatch hypothesis posits that cool‐adapted host species should be most susceptible to pathogen infection during warm temperature periods whereas warm‐adapted host species should be most susceptible to pathogens during periods of cool temperatures. We explore this hypothesis using two ecologically and physiologically differentiated color morphs of the Eastern Red‐backed Salamander (Plethodon cinereus) and a pathogenic chytrid fungus (Batrachochytrium dendrobatidis; hereafter Bd ) using a fully factorial laboratory experiment. At cool temperatures, unstriped salamanders (i.e., those that are tolerant of warm temperatures) had a significantly higher probability of Bd infection compared with cool‐tolerant striped salamanders, consistent with the thermal mismatch hypothesis. However, we found no support for this hypothesis when salamanders were exposed to Bd at warm temperatures: the probability of Bd infection in the cool‐tolerant striped salamanders was nearly identical in both cool and warm temperatures, opposite the predictions of the thermal mismatch hypothesis. Our results are most consistent with the fact that Bd grows poorly at warm temperatures. Alternatively, our data could indicate that the two color morphs do not differ in their tolerance to warm temperatures but that striped salamanders are more tolerant to cool temperatures than unstriped salamanders. Research Highlights: In a test of the thermal mismatch hypothesis, we found that in cool temperatures, warm‐tolerant salamanders had higher parasitism compared with cool‐tolerant salamanders. There was no difference in parasitism for salamanders in warm temperatures

Repeatability of foraging behavior following a simulated predation attempt depends on color morph, sex, and foraging metric in Red-backed salamanders (Plethodon cinereus)

Behavioral repeatability greatly affects the capacity of an individual to respond to varying environments. When multiple behaviors within individuals are repeatable and correlated across time or across contexts, it is termed a behavioral syndrome. However, not all behaviors exhibit the same level of repeatability, and relatively few studies have examined repeatability in amphibians. We examined the repeatability of foraging behavior in the Eastern Red-backed salamander (Plethodon cinereus), a color-polymorphic terrestrial salamander, following a simulated predation attempt. We tested several hypotheses: (1) Simulated predation would negatively affect foraging, increasing latency to feed and decreasing the number of prey items eaten in a fixed time period compared to a control group; (2) Because striped color morphs of P. cinereus are more aggressive, striped individuals would exhibit “bold” behavior by resuming foraging sooner and consuming more prey; and (3) Foraging behavior would be more repeatable for males. We found that the predation treatment inhibited foraging behavior, although neither morphs nor sexes differed in either forging metric. The number of prey eaten was repeatable for all groups of salamanders. Latency to feed, however, was not repeatable for control salamanders. Simulated predation induced repeatable latencies, but when morphs and sexes were analyzed separately, only unstriped and male salamanders were repeatable, suggesting characteristics of these groups related to behavioral syndromes drive this response. We speculate that the greater repeatability of the unstriped morph’s latency to feed may result from more frequent encounters with predators in the leaf litter matrix while foraging. Striped salamanders from the source population, in turn, exhibit greater territorial success, and thus may experience more variation in encounters with predators and conspecifics over the course of their lifespans. Our results illustrate the need to carefully define the behavior and subset of the population to be tested when studying behavioral repeatability or behavioral syndromes

Male mate preference as an agent of fecundity selection in a polymorphic salamander

Color polymorphisms are associated with variation in other traits which may affect individual fitness, and these color‐trait associations are expected to contribute to nonrandom mating in polymorphic species. The red‐backed salamander (Plethodon cinereus) exhibits a polymorphism in dorsal pattern: striped and unstriped, and previous studies have suggested that they may mate nonrandomly. However, the mechanism(s) contributing to this behavior remain unclear. Here we consider the role that male preference may have in driving mating behavior in P. cinereus. We limit our focus to striped individuals because this morph is most likely to be choosy given their dominant, aggressive behavioral profiles relative to unstriped males. Specifically, we evaluated (a) whether striped males preferentially associate with females with respect to her dorsum color, size, and body condition and (b) if so, whether female traits are evaluated via visual or chemical cues. We also considered whether the frequency of another male social behavior, nose taps, was associated with matepreferences. We found that striped male P. cinereus nose tapped more often to preferred females. However, males only assessed potential mates via chemical cues, preferring larger females overall. Reproductive phenology data on a sample of gravid females drawn from the same population indicated that the color morphs do not differ in reproductive traits, but larger females have greater fecundity. Given our findings, we conclude that female P. cinereus are under fecundity selection, mediated by male preference. In this manner, male mating behavior contributes to observations of nonrandom mate associations in this population of P. cinereus

Female Salamanders Experience Higher Parasitism Compared to Males: A Cost of Female Reproduction?

Males tend to experience higher rates of parasitism compared to females, a phenomenon associated with ecological factors, the fact that males engage in risky behaviors, and because testosterone is known to be immunosuppressive. However, females could experience higher rates of parasitism if energy is allocated from costly immune responses towards producing eggs. We used pooled data sets from laboratory experiments to investigate sex-specific differences in salamander (Plethodon cinereus) resistance to the emerging fungal pathogen Batrachochytrium dendrobatidis (‘‘Bd’’). Contrary to our predictions, we found that female salamanders had a higher prevalence of infection (~56%) and carried a higher Bd infection burden (455 zoospores equivalents per sample) compared to male salamanders (which had a Bd infection prevalence of ~24% and an average infection burden of 58 zoospore equivalents per sample). We also found that female reproductive investment (i.e., mass of eggs) positively correlated with Bd infection burden, suggesting that females who previously invested more into reproduction carried a higher Bd infection burden. Collectively, our findings might indicate that female salamanders experience a cost of reproduction in the form of decreased disease resistance

Development of Recrystallization Texture and Microstructure in Cold Rolled Copper

Oxygen free electronic copper, 99.995% purity, of two initial grain sizes, 50 {mu}m and 100 {mu}m, has been cold rolled to six strains of 1.0, 1.5, 2.0, 2.65, 3.5 and 4.5 (von Mises equivalents). The rolled materials were partially and fully recrystallized to study the development of recrystallization textures as a function of grain size, strain and fraction recrystallized. The initial textures were relatively random and the deformation textures show the classic {beta} fiber development. As strain is increased both materials produce increasingly intense cube recrystallization textures, (100), as measured both by x-ray diffraction and the electron backscatter pattern (EBSP) techniques. The strong cube recrystallization textures are a product of a higher than random frequency of cube nucleation sites. An additional factor is that cube regions grow larger than non-cube regions. The explanation of the cube frequency advantage is based on the development of large stored energy differences between cube orientations and neighboring orientations due to recovery of cube sites. Of several possible explanations of the cube orientation size advantage, the most plausible one is solute entrapment. At the higher strains the boundaries of cube grains encounter the deformation texture S components, (123), changing the boundary character to one of 40{degrees}. These boundaries are more resistant to solute accumulation than random high angle boundaries, allowing the boundaries to migrate with less of a solute drag effect than a random high angle boundary

Do genetic structure and landscape heterogeneity impact color morph frequency in a polymorphic salamander?

Landscape heterogeneity plays an important role in population structure and divergence, particularly for species with limited vagility. Here, we used a landscape genetic approach to identify how landscape and environmental variables affect genetic structure and color morph frequency in a polymorphic salamander. The eastern red- backed salamander, Plethodon cinereus, is widely distributed in northeastern North America and contains two common color morphs, striped and unstriped, that are divergent in ecology, behavior, and physiology. To quantify population structure, rates of gene flow, and genetic drift, we amplified 10 microsatellite loci from 648 individuals across 28 sampling localities. This study was conducted in northern Ohio, where populations of P. cinereus exhibit an unusually wide range of morph frequency variation. To test whether genetic distance was more correlated with morph frequency, elevation, canopy cover, waterways, ecological niche or geographic distance, we used resistance distance and least cost path analyses. We then examined whether landscape and environmental variables, genetic distance or geographic distance were correlated with variation in morph frequency. Tests for population structure revealed three genetic clusters across our sampling range, with one cluster monomorphic for the striped morph. Rates of gene flow and genetic drift were low to moderate across sites. Genetic distance was most correlated with ecological niche, elevation and a combination of landscape and environmental variables. In contrast, morph frequency variation was correlated with waterways and geographic distance. Thus, our results suggest that selection is also an important evolutionary force across our sites, and a balance between gene flow, genetic drift and selection interact to maintain the two color morphs

Genetic Analysis of a Cryptic Contact Zone between Mitochondrial Clades of the Eastern Red-Backed Salamander, Plethodon cinereus

When evolutionarily divergent lineages adjoin their geographic ranges after a period of isolation, myriad outcomes can occur, from population anastomosis to the evolution of reproductive isolation by way of reinforcement. Hybrid zones represent natural experiments that may indicate whether lineages will maintain their evolutionary independence. Here, we report on a hybrid zone in the Eastern Red-Backed Salamander, Plethodon cinereus, a highly abundant and wide-ranging terrestrial salamander found in the northeastern United States and in southeastern Canada. An earlier study identified six distinct mitochondrial clades across the range of P. cinereus. Populations of two of these clades were as close as 9.6 km apart in Lorain County, Ohio, USA. To investigate the nature of this contact zone, we sampled 316 individuals from 16 sites along a 53-km transect, and analyzed 10 microsatellite loci and one mitochondrial locus. We found a clinal transition for mtDNA haplotypes. In contrast, most studies of terrestrial plethodontid salamanders commonly exhibit sharp boundaries between mtDNA clades. Microsatellite markers, however, revealed little differentiation and weak population structure, suggesting the nuclear cline, if it exists, lies outside of our sampling region. Explanations for the discordance between the mitochondrial DNA and our microsatellite data include lineage sorting, male-biased dispersal, or historical introgression of mtDNA, among other possibilities. We compare our results with other studies of introgression in terrestrial salamanders, and discuss the causes of mitonuclear discordance