Focusing on the Big Picture: Insights into a Systems Approach to Deep Learning for Satellite Imagery

Deep learning tasks are often complicated and require a variety of components working together efficiently to perform well. Due to the often large scale of these tasks, there is a necessity to iterate quickly in order to attempt a variety of methods and to find and fix bugs. While participating in IARPA's Functional Map of the World challenge, we identified challenges along the entire deep learning pipeline and found various solutions to these challenges. In this paper, we present the performance, engineering, and deep learning considerations with processing and modeling data, as well as underlying infrastructure considerations that support large-scale deep learning tasks. We also discuss insights and observations with regard to satellite imagery and deep learning for image classification.Comment: Accepted to IEEE Big Data 201

Evidence for inbreeding depression in a species with limited opportunity for maternal effects

It is often assumed that mating with close relatives reduces offspring fitness. In such cases, reduced offspring fitness may arise from inbreeding depression (i.e., genetic effects of elevated homozygosity) or from post-mating maternal investment. This can be due to a reduction in female investment after mating with genetically incompatible males ("differential allocation") or compensation for incompatibility ("reproductive compensation"). Here, we looked at the effects of mating with relatives on offspring fitness in mosquitofish, Gambusia holbrooki. In this species, females are assumed to be nonplacental and to allocate resources to eggs before fertilization, limiting differential allocation. We looked at the effects of mating with a brother or with an unrelated male on brood size, offspring size, gestation period, and early offspring growth. Mating with a relative reduced the number of offspring at birth, but there was no difference in the likelihood of breeding, gestation time, nor in the size or growth of these offspring. We suggest that due to limited potential for maternal effects to influence these traits that any reduction in offspring fitness, or lack thereof, can be explained by inbreeding depression rather than by maternal effects. We highlight the importance of considering the potential role of maternal effects when studying inbreeding depression and encourage further studies in other Poeciliid species with different degrees of placentation to test whether maternal effects mask or amplify any genetic effects of mating with relatives.This work was supported bythe Australian Research Council (DP120100339). R.V.-T. is supported by fellowships from Consejo Nacion-al de Ciencia y Tecnologıa-Mexico and the ResearchSchool of Biology

Transcriptomic Profiles of Monocyte-Derived Macrophages in Response to Escherichia coli is Associated with the Host Genetics.

Reactive Nitrogen Species (RNS) are a group of bactericidal molecules produced by macrophages in response to pathogens in a process called oxidative burst. Nitric oxide (NO-) is a member of RNS produced from arginine by inducible Nitric Oxide Synthase (iNOS) enzyme. The activity of iNOS and production of NO- by macrophages following stimulation is one of the indicators of macrophage polarization towards M1/proinflammatory. Production of NO- by bovine monocyte-derived macrophage (MDM) and mouse peritoneal macrophages has been shown to be strongly associated with host genetic with the heritability of 0.776 in bovine MDM and 0.8 in mouse peritoneal macrophages. However, the mechanism of genetic regulation of macrophage response has remained less explored. In the current study, the transcriptome of bovine MDMs was compared between two extreme phenotypes that had been classified as high and low responder based on NO- production. The results showed that 179 and 392 genes were differentially expressed (DE) between high and low responder groups at 3 and 18 hours after exposure to Escherichia coli, respectively. A set of 11 Transcription Factors (TFs) (STAT1, IRF7, SPI1, STAT4, IRF1, HIF1A, FOXO3, REL, NFAT5, HIC1, and IRF4) at 3 hours and a set of 13 TFs (STAT1, IRF1, HIF1A, STAT4, ATF4, TP63, EGR1, CDKN2A, RBL1, E2F1, PRDM1, GATA3, and IRF4) at 18 hours after exposure to E. coli were identified to be differentially regulated between the high and low responder phenotypes. These TFs were found to be divided into two clusters of inflammatory- and hypoxia-related TFs. Functional analysis revealed that some key canonical pathways such as phagocytosis, chemotaxis, antigen presentation, and cell-to-cell signalling are enriched among the over-expressed genes by high responder phenotype. Based on the results of this study, it was inferred that the functional characteristics of bovine MDMs are associated with NO-based classification. Since NO- production is strongly associated with host genetics, this study for the first time shows the distinct proinflammatory profiles of macrophages are controlled by the natural genetic polymorphism in an outbred population. In addition, the results suggest that genetics can be considered as a new dimension in the current model of macrophage polarization which is currently described by the combination of stimulants, only

Group B streptococcal infection and activation of human astrocytes.

BACKGROUND:Streptococcus agalactiae (Group B Streptococcus, GBS) is the leading cause of life-threatening meningitis in human newborns in industrialized countries. Meningitis results from neonatal infection that occurs when GBS leaves the bloodstream (bacteremia), crosses the blood-brain barrier (BBB), and enters the central nervous system (CNS), where the bacteria contact the meninges. Although GBS is known to invade the BBB, subsequent interaction with astrocytes that physically associate with brain endothelium has not been well studied. METHODOLOGY/PRINCIPAL FINDINGS:We hypothesize that human astrocytes play a unique role in GBS infection and contribute to the development of meningitis. To address this, we used a well- characterized human fetal astrocyte cell line, SVG-A, and examined GBS infection in vitro. We observed that all GBS strains of representative clinically dominant serotypes (Ia, Ib, III, and V) were able to adhere to and invade astrocytes. Cellular invasion was dependent on host actin cytoskeleton rearrangements, and was specific to GBS as Streptococcus gordonii failed to enter astrocytes. Analysis of isogenic mutant GBS strains deficient in various cell surface organelles showed that anchored LTA, serine-rich repeat protein (Srr1) and fibronectin binding (SfbA) proteins all contribute to host cell internalization. Wild-type GBS also displayed an ability to persist and survive within an intracellular compartment for at least 12 h following invasion. Moreover, GBS infection resulted in increased astrocyte transcription of interleukin (IL)-1β, IL-6 and VEGF. CONCLUSIONS/SIGNIFICANCE:This study has further characterized the interaction of GBS with human astrocytes, and has identified the importance of specific virulence factors in these interactions. Understanding the role of astrocytes during GBS infection will provide important information regarding BBB disruption and the development of neonatal meningitis

Defects and boundary layers in non-Euclidean plates

We investigate the behavior of non-Euclidean plates with constant negative Gaussian curvature using the F\"oppl-von K\'arm\'an reduced theory of elasticity. Motivated by recent experimental results, we focus on annuli with a periodic profile. We prove rigorous upper and lower bounds for the elastic energy that scales like the thickness squared. In particular we show that are only two types of global minimizers -- deformations that remain flat and saddle shaped deformations with isolated regions of stretching near the edge of the annulus. We also show that there exist local minimizers with a periodic profile that have additional boundary layers near their lines of inflection. These additional boundary layers are a new phenomenon in thin elastic sheets and are necessary to regularize jump discontinuities in the azimuthal curvature across lines of inflection. We rigorously derive scaling laws for the width of these boundary layers as a function of the thickness of the sheet

A non-autonomous stochastic discrete time system with uniform disturbances

The main objective of this article is to present Bayesian optimal control over a class of non-autonomous linear stochastic discrete time systems with disturbances belonging to a family of the one parameter uniform distributions. It is proved that the Bayes control for the Pareto priors is the solution of a linear system of algebraic equations. For the case that this linear system is singular, we apply optimization techniques to gain the Bayesian optimal control. These results are extended to generalized linear stochastic systems of difference equations and provide the Bayesian optimal control for the case where the coefficients of these type of systems are non-square matrices. The paper extends the results of the authors developed for system with disturbances belonging to the exponential family

Inbreeding depression does not increase after exposure to a stressful environment: a test using compensatory growth

BACKGROUND: Inbreeding is often associated with a decrease in offspring fitness (‘inbreeding depression’). Moreover, it is generally assumed that the negative effects of inbreeding are exacerbated in stressful environments. This G × E interaction has been explored in many taxa under different environmental conditions. These studies usually manipulate environmental conditions either in adulthood or throughout an individual’s entire life. Far fewer studies have tested how stressful environments only experienced during development subsequently influence the effects of inbreeding on adult traits. RESULTS: We experimentally manipulated the diet (control versus low food) of inbred and outbred juvenile Eastern mosquitofish (Gambusia holbrooki) for three weeks (days 7-28) to test whether experiencing a presumably stressful environment early in life influences their subsequent growth and adult phenotypes. The control diet was a standard laboratory food regime, while fish on the low food diet received less than 25 % of this amount of food. Unexpectedly, despite a large sample size (237 families, 908 offspring) and a quantified 23 % reduction in genome-wide heterozygosity in inbred offspring from matings between full-siblings (f = 0.25), neither inbreeding nor its interaction with early diet affected growth trajectories, juvenile survival or adult size. Individuals did not mitigate a poor start in life by showing ‘compensatory growth’ (i.e. faster growth once the low food treatment ended), but they showed ‘catch-up growth’ by delaying maturation. There was, however, no effect of inbreeding on the extent of catch-up growth. CONCLUSIONS: There were no detectable effects of inbreeding on growth or adult size, even on a low food diet that should elevate inbreeding depression. Thus, the long-term costs of inbreeding due to lower male reproductive success we have shown in another study appear to be unrelated to inbreeding depression for adult male size or the growth rates that are reported in the current study.This work was supported by the Australian Research Council (DP160100285). R.V.-T. is supported by fellowships from Consejo Nacional de Ciencia y Tecnología-México and the Research School of Biology

A massive cluster of Red Supergiants at the base of the Scutum-Crux arm

We report on the unprecedented Red Supergiant (RSG) population of a massive young cluster, located at the base of the Scutum-Crux Galactic arm. We identify candidate cluster RSGs based on {\it 2MASS} photometry and medium resolution spectroscopy. With follow-up high-resolution spectroscopy, we use CO-bandhead equivalent width and high-precision radial velocity measurements to identify a core grouping of 26 physically-associated RSGs -- the largest such cluster known to-date. Using the stars' velocity dispersion, and their inferred luminosities in conjuction with evolutionary models, we argue that the cluster has an initial mass of $\sim$40,000\msun, and is therefore among the most massive in the galaxy. Further, the cluster is only a few hundred parsecs away from the cluster of 14 RSGs recently reported by Figer et al (2006). These two RSG clusters represent 20% of all known RSGs in the Galaxy, and now offer the unique opportunity to study the pre-supernova evolution of massive stars, and the Blue- to Red-Supergiant ratio at uniform metallicity. We use GLIMPSE, MIPSGAL and MAGPIS survey data to identify several objects in the field of the larger cluster which seem to be indicative of recent region-wide starburst activity at the point where the Scutum-Crux arm intercepts the Galactic bulge. Future abundance studies of these clusters will therefore permit the study of the chemical evolution and metallicity gradient of the Galaxy in the region where the disk meets the bulge.Comment: 49 pages, 22 figures. Accepted for publication in ApJ. Version with hi-res figures can be found at http://www.cis.rit.edu/~bxdpci/RSGC2.pd