DRINet for medical image segmentation

Convolutional neural networks (CNNs) have revolutionized medical image analysis over the past few years. The UNet architecture is one of the most well-known CNN architectures for semantic segmentation and has achieved remarkable successes in many different medical image segmentation applications. The U-Net architecture consists of standard convolution layers, pooling layers, and upsampling layers. These convolution layers learn representative features of input images and construct segmentations based on the features. However, the features learned by standard convolution layers are not distinctive when the differences among different categories are subtle in terms of intensity, location, shape, and size. In this paper, we propose a novel CNN architecture, called Dense-Res-Inception Net (DRINet), which addresses this challenging problem. The proposed DRINet consists of three blocks, namely a convolutional block with dense connections, a deconvolutional block with residual Inception modules, and an unpooling block. Our proposed architecture outperforms the U-Net in three different challenging applications, namely multi-class segmentation of cerebrospinal fluid (CSF) on brain CT images, multi-organ segmentation on abdominal CT images, multi-class brain tumour segmentation on MR images

A new method for the spectroscopic identification of stellar non-radial pulsation modes. II. Mode identification of the Delta Scuti star FG Virginis

We present a mode identification based on new high-resolution time-series spectra of the non-radially pulsating Delta Scuti star FG~Vir (HD 106384, V = 6.57, A5V). From 2002 February to June a global Delta Scuti Network (DSN) campaign, utilizing high-resolution spectroscopy and simultaneous photometry has been conducted for FG~Vir in order to provide a theoretical pulsation model. In this campaign we have acquired 969 Echelle spectra covering 147 hours at six observatories. The mode identification was carried out by analyzing line profile variations by means of the Fourier parameter fit method, where the observational Fourier parameters across the line are fitted with theoretical values. This method is especially well suited for determining the azimuthal order m of non-radial pulsation modes and thus complementary with the method of Daszynska-Daszkiewicz (2002) which does best at identifying the degree l. 15 frequencies between 9.2 and 33.5 c/d were detected spectroscopically. We determined the azimuthal order m of 12 modes and constrained their harmonic degree l. Only modes of low degree (l <= 4) were detected, most of them having axisymmetric character mainly due to the relatively low projected rotational velocity of FG Vir. The detected non-axisymmetric modes have azimuthal orders between -2 and 1. We derived an inclination of 19 degrees, which implies an equatorial rotational rate of 66 km/s.Comment: 14 pages, 26 figure

Peripheral and central mechanisms involved in hormonal control of male and female reproduction

Reproduction involves the integration of hormonal signals acting across multiple systems togenerate a synchronized physiological output. A critical component of reproduction is the luteinizinghormone (LH) surge, which is mediated by estradiol (E2) and neuroprogesterone interacting tostimulate kisspeptin release in the rostral periventricular nucleus of the third ventricle in rats. Recentevidence has shown that both classical and membrane E2 and progesterone signaling is involved inthis pathway. A metabolite of gonadotropin-releasing hormone (GnRH), GnRH-(1-5), has been shownto stimulate GnRH expression, secretion, and has a role in the regulation of lordosis. Additionally,gonadotropin-inhibitory hormone (GnIH) projects to and influences the activity of GnRH neurons inbirds. Stress-induced changes in GnIH have been shown to alter breeding behaviors in birds,demonstrating another molecular control of reproduction. Peripherally, paracrine and autocrineactions within the gonad have been suggested as therapeutic targets for infertility in both males andfemales. Dysfunction of testicular prostaglandin synthesis is a possible cause of idiopathic maleinfertility. Indeed, local production of melatonin and corticotropin-releasing hormone (CRH) couldinfluence spermatogenesis via immune pathways in the gonad. In females, vascular endothelialgrowth factor A (VEGF-A) has been implicated in an angiogenic process that mediates developmentof the corpus luteum and thus fertility via the Notch signaling pathway. Age-induced decreases infertility involve ovarian kisspeptin and its regulation of ovarian sympathetic innervation. Finally,morphological changes in the arcuate nucleus of the hypothalamus influence female sexualreceptivity in rats. The processes mediating these morphological changes have been shown toinvolve rapid effects of E2 controlling synaptogenesis in this hypothalamic nucleus. Together, thisreview highlights new research in these areas, focusing on recent findings in the molecularmechanisms of central and peripheral hormonal control of reproduction.Fil: Rudolph, L. M.. University of California at Los Angeles; Estados UnidosFil: Bentley, G. E.. University of California Berkeley; Estados UnidosFil: Calandra, Ricardo Saul. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Paredes, A. H.. Universidad de Chile; ChileFil: Tesone, Marta. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Wu, T. J.. Uniformed Services University; Estados UnidosFil: Micevych, P. E.. University of California at Los Angeles; Estados Unido

Dynamic Range Majority Data Structures

Given a set $P$ of coloured points on the real line, we study the problem of answering range $\alpha$-majority (or "heavy hitter") queries on $P$. More specifically, for a query range $Q$, we want to return each colour that is assigned to more than an $\alpha$-fraction of the points contained in $Q$. We present a new data structure for answering range $\alpha$-majority queries on a dynamic set of points, where $\alpha \in (0,1)$. Our data structure uses O(n) space, supports queries in $O((\lg n) / \alpha)$ time, and updates in $O((\lg n) / \alpha)$ amortized time. If the coordinates of the points are integers, then the query time can be improved to $O(\lg n / (\alpha \lg \lg n) + (\lg(1/\alpha))/\alpha))$. For constant values of $\alpha$, this improved query time matches an existing lower bound, for any data structure with polylogarithmic update time. We also generalize our data structure to handle sets of points in d-dimensions, for $d \ge 2$, as well as dynamic arrays, in which each entry is a colour.Comment: 16 pages, Preliminary version appeared in ISAAC 201

Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates

The capsule polysaccharide locus (cps) is the site of the capsule biosynthesis gene cluster in encapsulated Streptococcus pneumoniae. A set of pneumococcal samples and non-pneumococcal streptococci from Denmark, the Gambia, the Netherlands, Thailand, the UK and the USA were sequenced at the cps locus to elucidate serologically mistyped or non-typable isolates. We identified a novel serotype 33B/33C mosaic capsule cluster and previously unseen serotype 22F capsule genes, disrupted and deleted cps clusters, the presence of aliB and nspA genes that are unrelated to capsule production, and similar genes in the non-pneumococcal samples. These data provide greater understanding of diversity at a locus which is crucial to the antigenic diversity of the pathogen and current vaccine strategies

Efficient Processing of Spatial Joins Using R-Trees

Abstract: In this paper, we show that spatial joins are very suitable to be processed on a parallel hardware platform. The parallel system is equipped with a so-called shared virtual memory which is well-suited for the design and implementation of parallel spatial join algorithms. We start with an algorithm that consists of three phases: task creation, task assignment and parallel task execu-tion. In order to reduce CPU- and I/O-cost, the three phases are processed in a fashion that pre-serves spatial locality. Dynamic load balancing is achieved by splitting tasks into smaller ones and reassigning some of the smaller tasks to idle processors. In an experimental performance compar-ison, we identify the advantages and disadvantages of several variants of our algorithm. The most efficient one shows an almost optimal speed-up under the assumption that the number of disks is sufficiently large. Topics: spatial database systems, parallel database systems

Local species assemblages are influenced more by past than current dissimilarities in photosynthetic activity

Most land on Earth has been changed by humans and past changes of land can have lasting influences on current species assemblages. Yet few globally representative studies explicitly consider such influences even though auxiliary data, such as from remote sensing, are readily available. Time series of satellite-derived data have been commonly used to quantify differences in land-surface attributes such as vegetation cover, which will among other things be influenced by anthropogenic land conversions and modifications. Here we quantify differences in current and past (up to five years before sampling) vegetation cover, and assess whether such differences differentially influence taxonomic and functional groups of species assemblages between spatial pairs of sites. Specifically, we correlated between-site dissimilarity in photosynthetic activity of vegetation (the Enhanced Vegetation Index) with the corresponding dissimilarity in local species assemblage composition from a global database using a common metric for both, the Bray-Curtis index. We found that dissimilarity in species assemblage composition was on average more influenced by dissimilarity in past than current photosynthetic activity, and that the influence of past dissimilarity increased when longer time periods were considered. Responses to past dissimilarity in photosynthetic activity also differed among taxonomic groups (plants, invertebrates, amphibians, reptiles, birds and mammals), with reptiles being among the most influenced by more dissimilar past photosynthetic activity. Furthermore, we found that assemblages dominated by smaller and more vegetation-dependent species tended to be more influenced by dissimilarity in past photosynthetic activity than prey-dependent species. Overall, our results have implications for studies that investigate species responses to current environmental changes and highlight the importance of past changes continuing to influence local species assemblage composition. We demonstrate how local species assemblages and satellite-derived data can be linked and provide suggestions for future studies on how to assess the influence of past environmental changes on biodiversity

The energetics of the gradual phase

Reseachers compare results with those in the chapter by Moore et al. (1980), who reached five main conclusions about the gradual phase: (1) the typical density of the soft X-ray emitting plasma is between 10 to the 11th power and 10 to the 12th power cm-3 for compact flares and between 10 to the 10th power and 10 to the 11th power cm-3 for a large-area flare; (2) cooling is by conduction and radiation in roughly equal proportions; (3) continual heating is needed in the decay phase of two-ribbon flares; (4) continual heating is probably not needed in compact events; (5) most of the soft-X-ray-emitting plasma results from chromospheric evaporation. The goal was to reexamine these problems with the data from the Solar Maximum Mission (SMM) and other supporting instruments as well as to take advantage of recent theoretical advances. SMM is capable of measuring coronal temperatures more accurately and with a better cadence than has been possible before. The SMM data set is also unique in that the complete transit of an active region was observed, with soft X-ray and UV images being taken every few minutes. Researcher's were therefore able to establish the pre-flare conditions of the region and see whether anything has changed as a result of the flare. The assumptions made in attempting to determine the required plasma parameters are described. The derived parameters for the five prime flares are presented, and the role of numerical simulations is discussed

Flare energetics

In this investigation of flare energetics, researchers sought to establish a comprehensive and self-consistent picture of the sources and transport of energy within a flare. To achieve this goal, they chose five flares in 1980 that were well observed with instruments on the Solar Maximum Mission, and with other space-borne and ground-based instruments. The events were chosen to represent various types of flares. Details of the observations available for them and the corresponding physical parameters derived from these data are presented. The flares were studied from two perspectives, the impulsive and gradual phases, and then the results were compared to obtain the overall picture of the energics of these flares. The role that modeling can play in estimating the total energy of a flare when the observationally determined parameters are used as the input to a numerical model is discussed. Finally, a critique of the current understanding of flare energetics and the methods used to determine various energetics terms is outlined, and possible future directions of research in this area are suggested

Terrestrial laser scanning to reconstruct branch architecture from harvested branches

Quantifying whole branch architecture is critical to understanding tree function, for example, branch surface area controls woody gas exchange. Yet, due to measurement difficulty, branch architecture of small diameter branches (e.g. <10 cm ø) is either modelled, subsampled or ignored. Methods that use Terrestrial Laser Scanning (TLS) are now being widely applied to analyse tree and plot level tree architecture; however, resolving small diameter branches in-situ remains a challenge. Currently, it is suggested accurate reconstruction of small diameter branches can only be achieved by harvest and measurement in controlled conditions. Here we present a new TLS workflow for rapid and accurate reconstruction of complete branch architecture from harvested branches. The workflow sets out scan configuration, post processing (including a novel reectance filter) and fitting of Quantitative Structure Models (QSM) to reconstruct topologically coherent branch models. This is demonstrated on 595 branches (scanned indoors to negate the impact of wind) and compared with 65 branches that were manually measured (i.e. with measuring tape and callipers). Comparison of a suite of morphological and topological traits reveals a good agreement between TLS derived metrics and manual measurements where RMSE (%RMSE) for total branch length = 0.7 m (10%), volume = 0.09 litres (43%), surface area = 0.04 m2 (26%) and N tips = 6.4 (35%). Scanning was faster and invariant to branch size compared with manual measurements which required significantly more personnel time. We recommend measuring a subsample of tip-widths to constrain the QSM taper function as the TLS workflow tends to overestimate tip-width. The workflow presented here allows for a rapid characterisation of branch architecture from harvested branches. Increasing the number of branches analysed (e.g. many branches from a single tree or branches from many species globally) could allow for a comprehensive analysis of the “missing link" between the leaves and larger diameter branches