Meso-scale transboundary units for the management of coral reefs in the South China Sea area

Local communities and local government units are recognized as the primary stakeholders and participants in the management of coral reef resources and the primary beneficiaries of small-scale fishing activities in the nearshore areas of the coastal zone. The issues relating to the management of the coastal zone are multi-faceted and some issues are largely intertwined with national policy and development goals. Thus, national governments have jurisdiction over these nearshore coastal resources to harmonize policies, monitor resource use and provide incentives for sustainable use. However, the natural boundaries of these reef resources, the processes that support reef ecosystems, and the local or national affiliation of the people who benefit from them may transcend the boundaries of the local and national management units. Therefore, efforts to arrest the decline in fish catch and loss of biodiversity for reefs require management interventions and assessment activities to be carried out at varying scales. In Southeast Asia, some aspects of reef and reef resources management — particularly in deciding the allocation of catch among competing fisheries, development of sustainable harvest strategies, use of broodstock for restocking or stock enhancement programs, protection of nursery and spawning areas, designation of systems of marine protected areas, and the identification of representative, adequate and comprehensive areas for biodiversity conservation in the region — may require the definition of larger management units. At the regional level, multi-country initiatives will need to define units for the transboundary management of resources. The use of large marine ecosystems (LMEs) to identify and manage fisheries resources may be a starting point; however, given the relatively sedentary nature of coral reef-dwelling and reef-associated organisms compared with other pelagic and demersal species, meso-scale transboundary units within the LMEs have to be defined. This paper provides suggestions for transboundary management units for coral reef and reef-associated resources in Southeast Asia based on information from genetic structures of model organisms in the region. In addition, specific reef areas are identified, which may be important beyond their national boundaries, as potential sources of recruits.Coral reefs, Resource management, Large marine ecosystems, Population genetics, Reef fisheries, Fishery management, South China Sea,

B-spline neural networks based PID controller for Hammerstein systems

A new PID tuning and controller approach is introduced for Hammerstein systems based on input/output data. A B-spline neural network is used to model the nonlinear static function in the Hammerstein system. The control signal is composed of a PID controller together with a correction term. In order to update the control signal, the multi-step ahead predictions of the Hammerstein system based on the B-spline neural networks and the associated Jacobians matrix are calculated using the De Boor algorithms including both the functional and derivative recursions. A numerical example is utilized to demonstrate the efficacy of the proposed approaches

Cone Identification in Choroideremia: Repeatability, Reliability, and Automation Through Use of a Convolutional Neural Network

Purpose: Adaptive optics imaging has enabled the visualization of photoreceptors both in health and disease. However, there remains a need for automated accurate cone photoreceptor identification in images of disease. Here, we apply an open-source convolutional neural network (CNN) to automatically identify cones in images of choroideremia (CHM). We further compare the results to the repeatability and reliability of manual cone identifications in CHM. Methods: We used split-detection adaptive optics scanning laser ophthalmoscopy to image the inner segment cone mosaic of 17 patients with CHM. Cones were manually identified twice by one experienced grader and once by two additional experienced graders in 204 regions of interest (ROIs). An open-source CNN either pre-trained on normal images or trained on CHM images automatically identified cones in the ROIs. True and false positive rates and Dice\u27s coefficient were used to determine the agreement in cone locations between data sets. Interclass correlation coefficient was used to assess agreement in bound cone density. Results: Intra- and intergrader agreement for cone density is high in CHM. CNN performance increased when it was trained on CHM images in comparison to normal, but had lower agreement than manual grading. Conclusions: Manual cone identifications and cone density measurements are repeatable and reliable for images of CHM. CNNs show promise for automated cone selections, although additional improvements are needed to equal the accuracy of manual measurements. Translational Relevance: These results are important for designing and interpreting longitudinal studies of cone mosaic metrics in disease progression or treatment intervention in CHM

Dynamics of D1-brane in I-brane Background

This paper is devoted to the study of the effective field theory description of the probe D1-brane in the background of the system of two stacks of fivebranes in type IIB theory that intersect on $R^{1,1}$. We study the properties of the Dirac-Born-Infeld action for D1-brane moving in this background. We will argue that this action is invariant under an additional symmetry in the near horizon limit and that this new symmetry is closely related to the enhanced symmetry of the I-brane background considered recently in [hep-th/0508025]. We also solve explicitly the equation of motion of D1-brane in the near horizon limit.Comment: 21 pages, references adde

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC) makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals) and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals). We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918) with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes

Simit: A Language for Physical Simulation

Using existing programming tools, writing high-performance simulation code is labor intensive and requires sacrificing readability and portability. The alternative is to prototype simulations in a high-level language like Matlab, thereby sacrificing performance. The Matlab programming model naturally describes the behavior of an entire physical system using the language of linear algebra. However, simulations also manipulate individual geometric elements, which are best represented using linked data structures like meshes. Translating between the linked data structures and linear algebra comes at significant cost, both to the programmer and the machine. High-performance implementations avoid the cost by rephrasing the computation in terms of linked or index data structures, leaving the code complicated and monolithic, often increasing its size by an order of magnitude. In this paper, we present Simit, a new language for physical simulations that lets the programmer view the system both as a linked data structure in the form of a hypergraph, and as a set of global vectors, matrices and tensors depending on what is convenient at any given time. Simit provides a novel assembly construct that makes it conceptually easy and computationally efficient to move between the two abstractions. Using the information provided by the assembly construct, the compiler generates efficient in-place computation on the graph. We demonstrate that Simit is easy to use: a Simit program is typically shorter than a Matlab program; that it is high-performance: a Simit program running sequentially on a CPU performs comparably to hand-optimized simulations; and that it is portable: Simit programs can be compiled for GPUs with no change to the program, delivering 5-25x speedups over our optimized CPU code

Nonabelian gauge field and dual description of fuzzy sphere

In matrix models, higher dimensional D-branes are obtained by imposing a noncommutative relation to coordinates of lower dimensional D-branes. On the other hand, a dual description of this noncommutative space is provided by higher dimensional D-branes with gauge fields. Fuzzy spheres can appear as a configuration of lower dimensional D-branes in a constant R-R field strength background. In this paper, we consider a dual description of higher dimensional fuzzy spheres by introducing nonabelian gauge fields on higher dimensional spherical D-branes. By using the Born-Infeld action, we show that a fuzzy $2k$-sphere and spherical D$2k$-branes with a nonabelian gauge field whose Chern character is nontrivial are the same objects when $n$ is large. We discuss a relationship between the noncommutative geometry and nonabelian gauge fields. Nonabelian gauge fields are represented by noncommutative matrices including the coordinate dependence. A similarity to the quantum Hall system is also studied.Comment: 28 page

Coronal Shock Waves, EUV Waves, and Their Relation to CMEs. III. Shock-Associated CME/EUV Wave in an Event with a Two-Component EUV Transient

On 17 January 2010, STEREO-B observed in extreme ultraviolet (EUV) and white light a large-scale dome-shaped expanding coronal transient with perfectly connected off-limb and on-disk signatures. Veronig et al. (2010, ApJL 716, 57) concluded that the dome was formed by a weak shock wave. We have revealed two EUV components, one of which corresponded to this transient. All of its properties found from EUV, white light, and a metric type II burst match expectations for a freely expanding coronal shock wave including correspondence to the fast-mode speed distribution, while the transient sweeping over the solar surface had a speed typical of EUV waves. The shock wave was presumably excited by an abrupt filament eruption. Both a weak shock approximation and a power-law fit match kinematics of the transient near the Sun. Moreover, the power-law fit matches expansion of the CME leading edge up to 24 solar radii. The second, quasi-stationary EUV component near the dimming was presumably associated with a stretched CME structure; no indications of opening magnetic fields have been detected far from the eruption region.Comment: 18 pages, 10 figures. Solar Physics, published online. The final publication is available at http://www.springerlink.co

Dissolving D0-brane into D2-brane with background B-field

D0-branes on a D2-brane with a constant background B-field are unstable due to the presence of a tachyonic mode and expected to dissolve into the D2-brane to formulate a constant D0-charge density. In this paper we study such a dissolution process in terms of a noncommutative gauge theory. Our results show that the localized D0-brane spreads out over all of space on the D2-brane as the tachyon rolls down into a stable vacuum. D0-branes on a D2-brane can be described as unstable solitons in a noncommutative gauge theory in 2+1 dimensions in the Seiberg-Witten limit. In contrast to the case of annihilation of a non-BPS D-brane, we are free from difficulty of disappearance of DOF, since there exist open strings after the tachyon condensation. We solve an equation of motion of the gauge field numerically, and our results show that the localized soliton smears over all of noncommutative space. In addition, we evaluate distributions of D-brane charge, F-string charge, and energy density via formulas derived in Matrix theory. Our results show that the initial singularities of D0-charge and energy density are resolved by turning on the tachyon, and they disperse over the whole space on the D2-brane during the tachyon condensation process.Comment: 42 pages, 20 figures, JHEP style; references added, clarifications added in section 3.1; references adde

On the Nature and Genesis of EUV Waves: A Synthesis of Observations from SOHO, STEREO, SDO, and Hinode

A major, albeit serendipitous, discovery of the SOlar and Heliospheric Observatory mission was the observation by the Extreme Ultraviolet Telescope (EIT) of large-scale Extreme Ultraviolet (EUV) intensity fronts propagating over a significant fraction of the Sun's surface. These so-called EIT or EUV waves are associated with eruptive phenomena and have been studied intensely. However, their wave nature has been challenged by non-wave (or pseudo-wave) interpretations and the subject remains under debate. A string of recent solar missions has provided a wealth of detailed EUV observations of these waves bringing us closer to resolving their nature. With this review, we gather the current state-of-art knowledge in the field and synthesize it into a picture of an EUV wave driven by the lateral expansion of the CME. This picture can account for both wave and pseudo-wave interpretations of the observations, thus resolving the controversy over the nature of EUV waves to a large degree but not completely. We close with a discussion of several remaining open questions in the field of EUV waves research.Comment: Solar Physics, Special Issue "The Sun in 360",2012, accepted for publicatio