Probing Factors Influencing Students' Graph Comprehension Regarding Four Operations in Kinematics Graphs

ERIC Educational Resources Information Center

Phage, Itumeleng B.; Lemmer, Miriam; Hitge, Mariette

2017-01-01

Students' graph comprehension may be affected by the background of the students who are the readers or interpreters of the graph, their knowledge of the context in which the graph is set, and the inferential processes required by the graph operation. This research study investigated these aspects of graph comprehension for 152 first year…

Theoretical Bound of CRLB for Energy Efficient Technique of RSS-Based Factor Graph Geolocation

NASA Astrophysics Data System (ADS)

Kahar Aziz, Muhammad Reza; Heriansyah; Saputra, EfaMaydhona; Musa, Ardiansyah

2018-03-01

To support the increase of wireless geolocation development as the key of the technology in the future, this paper proposes theoretical bound derivation, i.e., Cramer Rao lower bound (CRLB) for energy efficient of received signal strength (RSS)-based factor graph wireless geolocation technique. The theoretical bound derivation is crucially important to evaluate whether the energy efficient technique of RSS-based factor graph wireless geolocation is effective as well as to open the opportunity to further innovation of the technique. The CRLB is derived in this paper by using the Fisher information matrix (FIM) of the main formula of the RSS-based factor graph geolocation technique, which is lied on the Jacobian matrix. The simulation result shows that the derived CRLB has the highest accuracy as a bound shown by its lowest root mean squared error (RMSE) curve compared to the RMSE curve of the RSS-based factor graph geolocation technique. Hence, the derived CRLB becomes the lower bound for the efficient technique of RSS-based factor graph wireless geolocation.

Solving very large, sparse linear systems on mesh-connected parallel computers

NASA Technical Reports Server (NTRS)

Opsahl, Torstein; Reif, John

1987-01-01

The implementation of Pan and Reif's Parallel Nested Dissection (PND) algorithm on mesh connected parallel computers is described. This is the first known algorithm that allows very large, sparse linear systems of equations to be solved efficiently in polylog time using a small number of processors. How the processor bound of PND can be matched to the number of processors available on a given parallel computer by slowing down the algorithm by constant factors is described. Also, for the important class of problems where G(A) is a grid graph, a unique memory mapping that reduces the inter-processor communication requirements of PND to those that can be executed on mesh connected parallel machines is detailed. A description of an implementation on the Goodyear Massively Parallel Processor (MPP), located at Goddard is given. Also, a detailed discussion of data mappings and performance issues is given.

A graph model for preventing railway accidents based on the maximal information coefficient

NASA Astrophysics Data System (ADS)

Shao, Fubo; Li, Keping

2017-01-01

A number of factors influences railway safety. It is an important work to identify important influencing factors and to build the relationship between railway accident and its influencing factors. The maximal information coefficient (MIC) is a good measure of dependence for two-variable relationships which can capture a wide range of associations. Employing MIC, a graph model is proposed for preventing railway accidents which avoids complex mathematical computation. In the graph, nodes denote influencing factors of railway accidents and edges represent dependence of the two linked factors. With the increasing of dependence level, the graph changes from a globally coupled graph to isolated points. Moreover, the important influencing factors are identified from many factors which are the monitor key. Then the relationship between railway accident and important influencing factors is obtained by employing the artificial neural networks. With the relationship, a warning mechanism is built by giving the dangerous zone. If the related factors fall into the dangerous zone in railway operations, the warning level should be raised. The built warning mechanism can prevent railway accidents and can promote railway safety.

A Comparison of a Relational and Nested-Relational IDEF0 Data Model

DTIC Science & Technology

1990-03-01

develop, some of the problems inherent iu the hierarchical 5 model were circumvented by the more sophisticated network model. Like the hierarchical model...uetwork database consists of a collection of records connected via links. Unlike the hierarchical model, the network model allows arbitrary graphs as...opposed to trees. Thus, each node may have everal owners and may, in turn, own any number of other records. The network model provides a lchanism by

Effects of biotic and abiotic factors on the oxygen content of green sea turtle nests during embryogenesis.

PubMed

Chen, Chiu-Lin; Wang, Chun-Chun; Cheng, I-Jiunn

2010-10-01

Several biotic and abiotic factors can influence nest oxygen content during embryogenesis. Several of these factors were determined during each developmental stage of green sea turtle embryos on Wan-an Island, Penghu Archipelago, Taiwan. We examined oxygen content in 7 nests in 2007 and 11 in 2008. Oxygen in the adjacent sand, total and viable clutch sizes, air, sand and nest temperatures, and sand characters of each nest were also determined. Oxygen content was lower in late stages than in the early and middle stages. It was also lower in the middle layer than in the upper and bottom layers. Nest temperature showed opposite trends, reaching its maximum value in late stages of development. Nest oxygen content was influenced by fraction of viable eggs, total clutch sizes, sand temperatures, maximum nest temperature and maximum change in the nest temperature during incubation. Clutch size during embryogenesis was the most influential factor overall. However, the major influential factors were different for different developmental stages. In the first half of the incubation, the development rate was low, and the change in the nest oxygen content was influenced mainly by the clutch size. During the second half, the rapid embryonic development rate became the dominant factor, and hatchling activities caused even greater oxygen consumption during the last stage of development.

Discrete geometric analysis of message passing algorithm on graphs

NASA Astrophysics Data System (ADS)

Watanabe, Yusuke

2010-04-01

We often encounter probability distributions given as unnormalized products of non-negative functions. The factorization structures are represented by hypergraphs called factor graphs. Such distributions appear in various fields, including statistics, artificial intelligence, statistical physics, error correcting codes, etc. Given such a distribution, computations of marginal distributions and the normalization constant are often required. However, they are computationally intractable because of their computational costs. One successful approximation method is Loopy Belief Propagation (LBP) algorithm. The focus of this thesis is an analysis of the LBP algorithm. If the factor graph is a tree, i.e. having no cycle, the algorithm gives the exact quantities. If the factor graph has cycles, however, the LBP algorithm does not give exact results and possibly exhibits oscillatory and non-convergent behaviors. The thematic question of this thesis is "How the behaviors of the LBP algorithm are affected by the discrete geometry of the factor graph?" The primary contribution of this thesis is the discovery of a formula that establishes the relation between the LBP, the Bethe free energy and the graph zeta function. This formula provides new techniques for analysis of the LBP algorithm, connecting properties of the graph and of the LBP and the Bethe free energy. We demonstrate applications of the techniques to several problems including (non) convexity of the Bethe free energy, the uniqueness and stability of the LBP fixed point. We also discuss the loop series initiated by Chertkov and Chernyak. The loop series is a subgraph expansion of the normalization constant, or partition function, and reflects the graph geometry. We investigate theoretical natures of the series. Moreover, we show a partial connection between the loop series and the graph zeta function.

Arctic foxes, lemmings, and canada goose nest survival at cape Churchill, Manitoba

USGS Publications Warehouse

Reiter, M.E.; Andersen, D.E.

2011-01-01

We examined factors influencing Canada Goose (Branta canadensis interior) annual nest success, including the relative abundance of collared lemmings (Dicrostonyx richardsoni), arctic fox (Alopex lagopus) den occupancy, nest density, and spring phenology using data collected during annual Canada Goose breeding area surveys at Cape Churchill, Manitoba. Nest density and arctic fox den occupancy strongly influenced Canada Goose nest success. High nest density resulted in higher nest success and high den occupancy reduced nest success. Nest success was not influenced by lemming abundance in the current or previous year as predicted by the "bird-lemming" hypothesis. Reducing arctic fox abundance through targeted management increased nest survival of Canada Geese; a result that further emphasizes the importance of arctic fox as nest predators in this system. The spatial distribution of nest predators, at least for dispersed-nesting geese, may be most important for nest survival, regardless of the abundance of small mammals in the local ecosystem. Further understanding of the factors influencing the magnitude and variance in arctic fox abundance in this region, and the spatial scale at which these factors are realized, is necessary to fully explain predator-prey-alternative prey dynamics in this system. ?? 2011 by the Wilson Ornithological Society.

Factors affecting songbird nest survival in riparian forests in a Midwestern agricultural landscape

Treesearch

Rebecca G. Peak; Frank R. Thompson; Terry L. Shaffer

2004-01-01

We investigated factors affecting nest success of songbirds in riparian forest and buffers in northeastern Missouri. We used an information-theoretic approach to determine support for hypotheses concerning effects of nest-site, habitat-patch, edge, and temporal factors on nest success of songbirds in three narrow (55-95 m) and three wide (400-530 m) riparian forests...

Rapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width.

PubMed

De Sa, Christopher; Zhang, Ce; Olukotun, Kunle; Ré, Christopher

2015-12-01

Gibbs sampling on factor graphs is a widely used inference technique, which often produces good empirical results. Theoretical guarantees for its performance are weak: even for tree structured graphs, the mixing time of Gibbs may be exponential in the number of variables. To help understand the behavior of Gibbs sampling, we introduce a new (hyper)graph property, called hierarchy width . We show that under suitable conditions on the weights, bounded hierarchy width ensures polynomial mixing time. Our study of hierarchy width is in part motivated by a class of factor graph templates, hierarchical templates , which have bounded hierarchy width-regardless of the data used to instantiate them. We demonstrate a rich application from natural language processing in which Gibbs sampling provably mixes rapidly and achieves accuracy that exceeds human volunteers.

A topo-graph model for indistinct target boundary definition from anatomical images.

PubMed

Cui, Hui; Wang, Xiuying; Zhou, Jianlong; Gong, Guanzhong; Eberl, Stefan; Yin, Yong; Wang, Lisheng; Feng, Dagan; Fulham, Michael

2018-06-01

It can be challenging to delineate the target object in anatomical imaging when the object boundaries are difficult to discern due to the low contrast or overlapping intensity distributions from adjacent tissues. We propose a topo-graph model to address this issue. The first step is to extract a topographic representation that reflects multiple levels of topographic information in an input image. We then define two types of node connections - nesting branches (NBs) and geodesic edges (GEs). NBs connect nodes corresponding to initial topographic regions and GEs link the nodes at a detailed level. The weights for NBs are defined to measure the similarity of regional appearance, and weights for GEs are defined with geodesic and local constraints. NBs contribute to the separation of topographic regions and the GEs assist the delineation of uncertain boundaries. Final segmentation is achieved by calculating the relevance of the unlabeled nodes to the labels by the optimization of a graph-based energy function. We test our model on 47 low contrast CT studies of patients with non-small cell lung cancer (NSCLC), 10 contrast-enhanced CT liver cases and 50 breast and abdominal ultrasound images. The validation criteria are the Dice's similarity coefficient and the Hausdorff distance. Student's t-test show that our model outperformed the graph models with pixel-only, pixel and regional, neighboring and radial connections (p-values <0.05). Our findings show that the topographic representation and topo-graph model provides improved delineation and separation of objects from adjacent tissues compared to the tested models. Copyright © 2018 Elsevier B.V. All rights reserved.

OpenMP Parallelization and Optimization of Graph-based Machine Learning Algorithms

DTIC Science & Technology

2016-05-01

composed of hyper - spectral video sequences recording the release of chemical plumes at the Dugway Proving Ground. We use the 329 frames of the...video. Each frame is a hyper - spectral image with dimension 128 × 320 × 129, where 129 is the dimension of the channel of each pixel. The total number of...j=1 . Then we use the nested for- loop to calculate the values of WXY by the formula (1). We then put the corresponding value in an array which

Extracting Loop Bounds for WCET Analysis Using the Instrumentation Point Graph

NASA Astrophysics Data System (ADS)

Betts, A.; Bernat, G.

2009-05-01

Every calculation engine proposed in the literature of Worst-Case Execution Time (WCET) analysis requires upper bounds on loop iterations. Existing mechanisms to procure this information are either error prone, because they are gathered from the end-user, or limited in scope, because automatic analyses target very specific loop structures. In this paper, we present a technique that obtains bounds completely automatically for arbitrary loop structures. In particular, we show how to employ the Instrumentation Point Graph (IPG) to parse traces of execution (generated by an instrumented program) in order to extract bounds relative to any loop-nesting level. With this technique, therefore, non-rectangular dependencies between loops can be captured, allowing more accurate WCET estimates to be calculated. We demonstrate the improvement in accuracy by comparing WCET estimates computed through our HMB framework against those computed with state-of-the-art techniques.

An Efficient Scheme for Updating Sparse Cholesky Factors

NASA Technical Reports Server (NTRS)

Raghavan, Padma

2002-01-01

Raghavan had earlier developed the software package DCSPACK which can be used for solving sparse linear systems where the coefficient matrix is symmetric and positive definite (this project was not funded by NASA but by agencies such as NSF). DSCPACK-S is the serial code and DSCPACK-P is a parallel implementation suitable for multiprocessors or networks-of-workstations with message passing using MCI. The main algorithm used is the Cholesky factorization of a sparse symmetric positive positive definite matrix A = LL(T). The code can also compute the factorization A = LDL(T). The complexity of the software arises from several factors relating to the sparsity of the matrix A. A sparse N x N matrix A has typically less that cN nonzeroes where c is a small constant. If the matrix were dense, it would have O(N2) nonzeroes. The most complicated part of such sparse Cholesky factorization relates to fill-in, i.e., zeroes in the original matrix that become nonzeroes in the factor L. An efficient implementation depends to a large extent on complex data structures and on techniques from graph theory to reduce, identify, and manage fill. DSCPACK is based on an efficient multifrontal implementation with fill-managing algorithms and implementation arising from earlier research by Raghavan and others. Sparse Cholesky factorization is typically a four step process: (1) ordering to compute a fill-reducing numbering, (2) symbolic factorization to determine the nonzero structure of L, (3) numeric factorization to compute L, and, (4) triangular solution to solve L(T)x = y and Ly = b. The first two steps are symbolic and are performed using the graph of the matrix. The numeric factorization step is of dominant cost and there are several schemes for improving performance by exploiting the nested and dense structure of groups of columns in the factor. The latter are aimed at better utilization of the cache-memory hierarchy on modem processors to prevent cache-misses and provide execution rates (operations/second) that are close to the peak rates for dense matrix computations. Currently, EPISCOPACY is being used in an application at NASA directed by J. Newman and M. James. We propose the implementation of efficient schemes for updating the LL(T) or LDL(T) factors computed in DSCPACK-S to meet the computational requirements of their project. A brief description is provided in the next section.

Rapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width

PubMed Central

De Sa, Christopher; Zhang, Ce; Olukotun, Kunle; Ré, Christopher

2016-01-01

Gibbs sampling on factor graphs is a widely used inference technique, which often produces good empirical results. Theoretical guarantees for its performance are weak: even for tree structured graphs, the mixing time of Gibbs may be exponential in the number of variables. To help understand the behavior of Gibbs sampling, we introduce a new (hyper)graph property, called hierarchy width. We show that under suitable conditions on the weights, bounded hierarchy width ensures polynomial mixing time. Our study of hierarchy width is in part motivated by a class of factor graph templates, hierarchical templates, which have bounded hierarchy width—regardless of the data used to instantiate them. We demonstrate a rich application from natural language processing in which Gibbs sampling provably mixes rapidly and achieves accuracy that exceeds human volunteers. PMID:27279724

Statistical mechanics of high-density bond percolation

NASA Astrophysics Data System (ADS)

Timonin, P. N.

2018-05-01

High-density (HD) percolation describes the percolation of specific κ -clusters, which are the compact sets of sites each connected to κ nearest filled sites at least. It takes place in the classical patterns of independently distributed sites or bonds in which the ordinary percolation transition also exists. Hence, the study of series of κ -type HD percolations amounts to the description of classical clusters' structure for which κ -clusters constitute κ -cores nested one into another. Such data are needed for description of a number of physical, biological, and information properties of complex systems on random lattices, graphs, and networks. They range from magnetic properties of semiconductor alloys to anomalies in supercooled water and clustering in biological and social networks. Here we present the statistical mechanics approach to study HD bond percolation on an arbitrary graph. It is shown that the generating function for κ -clusters' size distribution can be obtained from the partition function of the specific q -state Potts-Ising model in the q →1 limit. Using this approach we find exact κ -clusters' size distributions for the Bethe lattice and Erdos-Renyi graph. The application of the method to Euclidean lattices is also discussed.

Waterbird nest-site selection is influenced by neighboring nests and island topography

USGS Publications Warehouse

Hartman, Christopher; Ackerman, Joshua T.; Takekawa, John Y.; Herzog, Mark

2016-01-01

Avian nest-site selection is influenced by factors operating across multiple spatial scales. Identifying preferred physical characteristics (e.g., topography, vegetation structure) can inform managers to improve nesting habitat suitability. However, social factors (e.g., attraction, territoriality, competition) can complicate understanding physical characteristics preferred by nesting birds. We simultaneously evaluated the physical characteristics and social factors influencing selection of island nest sites by colonial-nesting American avocets (Recurvirostra americana) and Forster's terns (Sterna forsteri) at 2 spatial scales in San Francisco Bay, 2011–2012. At the larger island plot (1 m2) scale, we used real-time kinematics to produce detailed topographies of nesting islands and map the distribution of nests. Nesting probability was greatest in island plots between 0.5 m and 1.5 m above the water surface, at distances <10 m from the water's edge, and of moderately steep (avocets) or flat (terns) slopes. Further, avocet and tern nesting probability increased as the number of nests initiated in adjacent plots increased up to a peak of 11–12 tern nests, and then decreased thereafter. Yet, avocets were less likely to nest in plots adjacent to plots with nesting avocets, suggesting an influence of intra-specific territoriality. At the smaller microhabitat scale, or the area immediately surrounding the nest, we compared topography, vegetation, and distance to nearest nest between nest sites and paired random sites. Topography had little influence on selection of the nest microhabitat. Instead, nest sites were more likely to have vegetation present, and greater cover, than random sites. Finally, avocet, and to a lesser extent tern, nest sites were closer to other active conspecific or heterospecific nests than random sites, indicating that social attraction played a role in selection of nest microhabitat. Our results demonstrate key differences in nest-site selection between co-occurring avocets and terns, and indicate the effects of physical characteristics and social factors on selection of nesting habitat are dependent on the spatial scale examined. Moreover, these results indicate that islands with abundant area between 0.5 m and 1.5 m above the water surface, within 10 m of the water's edge, and containing a mosaic of slopes ranging from flat to moderately steep would provide preferred nesting habitat for avocets and terns. © 2016 The Wildlife Society.

Multiple Illuminant Colour Estimation via Statistical Inference on Factor Graphs.

PubMed

Mutimbu, Lawrence; Robles-Kelly, Antonio

2016-08-31

This paper presents a method to recover a spatially varying illuminant colour estimate from scenes lit by multiple light sources. Starting with the image formation process, we formulate the illuminant recovery problem in a statistically datadriven setting. To do this, we use a factor graph defined across the scale space of the input image. In the graph, we utilise a set of illuminant prototypes computed using a data driven approach. As a result, our method delivers a pixelwise illuminant colour estimate being devoid of libraries or user input. The use of a factor graph also allows for the illuminant estimates to be recovered making use of a maximum a posteriori (MAP) inference process. Moreover, we compute the probability marginals by performing a Delaunay triangulation on our factor graph. We illustrate the utility of our method for pixelwise illuminant colour recovery on widely available datasets and compare against a number of alternatives. We also show sample colour correction results on real-world images.

Influence of age and selected environmental factors on reproductive performance of canvasbacks

USGS Publications Warehouse

Serie, Jerome R.; Trauger, David L.; Austin, Jane E.

1992-01-01

Age, productivity, and other factors affecting breeding performance of canvasbacks (Aythya valisineria) are poorly understood. Consequently, we tested whether reproductive performance of female canvasbacks varied with age and selected environmental factors in southwestern Manitoba from 1974 to 1980. Neither clutch size, nest parasitism, nest success, nor the number of ducklings/brood varied with age. Return rates, nest initiation dates, renesting, and hen success were age-related. Return rates averaged 21% for second-year (SY) and 69% for after-second-year (ASY) females (58% for third-year and 79% for after-third-year females). Additionally, water conditions and spring temperatures influenced chronology of arrival, timing of nesting, and reproductive success. Nest initiation by birds of all ages was affected by minimum April temperatures. Clutch size was higher in nests initiated earlier. Interspecific nest parasitism did not affect clutch size, nest success, hen success, or hatching success. Nest success was lower in dry years (17%) than in moderately wet (54%) or wet (60%) years. Nests per female were highest during wet years. No nests of SY females were found in dry years. In years of moderate to good wetland conditions, females of all ages nested. Predation was the primary factor influencing nest success. Hen success averaged 58% over all years. The number of ducklings surviving 20 days averaged 4.7/brood. Because SY females have lower return rates and hen success than ASY females, especially during drier years, management to increase canvasback populations might best be directed to increasing first year recruitment (no. of females returning to breed) and to increasing overall breeding success by reducing predation and enhancing local habitat conditions during nesting.

Transformations of Mathematical and Stimulus Functions

PubMed Central

Ninness, Chris; Barnes-Holmes, Dermot; Rumph, Robin; McCuller, Glen; Ford, Angela M; Payne, Robert; Ninness, Sharon K; Smith, Ronald J; Ward, Todd A; Elliott, Marc P

2006-01-01

Following a pretest, 8 participants who were unfamiliar with algebraic and trigonometric functions received a brief presentation on the rectangular coordinate system. Next, they participated in a computer-interactive matching-to-sample procedure that trained formula-to-formula and formula-to-graph relations. Then, they were exposed to 40 novel formula-to-graph tests and 10 novel graph-to-formula tests. Seven of the 8 participants showed substantial improvement in identifying formula-to-graph relations; however, in the test of novel graph-to-formula relations, participants tended to select equations in their factored form. Next, we manipulated contextual cues in the form of rules regarding mathematical preferences. First, we informed participants that standard forms of equations were preferred over factored forms. In a subsequent test of 10 additional novel graph-to-formula relations, participants shifted their selections to favor equations in their standard form. This preference reversed during 10 more tests when financial reward was made contingent on correct identification of formulas in factored form. Formula preferences and transformation of novel mathematical and stimulus functions are discussed. PMID:17020211

Factors determining presence of passerines breeding within White Stork Ciconia ciconia nests

NASA Astrophysics Data System (ADS)

Zbyryt, Adam; Jakubas, Dariusz; Tobolka, Marcin

2017-10-01

Nests of White Stork Ciconia ciconia are commonly used by various passerines as nesting sites. In this study, we investigated factors determining presence and number of pairs of species breeding within White Stork nests in an extensive farmland in NE Poland. In 133 (57%) out of 233 White Stork nests, we found at least one breeding pair of passerine bird. These were from three species: House Sparrows Passer domesticus (68% of 133 nests with co-breeding), Tree Sparrows Passer montanus (65%), and Starlings Sturnus vulgaris (30%). The probability of breeding passerines within White Stork nests increased with increasing nest thickness, and was significantly higher in currently occupied nests. Sparrows were more likely to breed in White Stork nests located on electricity poles, situated closer to settlements and surrounded mainly by arable fields where meadows were not prevalent. In this paper, we show that White Stork nests are favorable nesting sites for passerines, as they are well insulated and provide an anti-predatory shield.

Reproductive Performance of a Declining Forest Passerine in Relation to Environmental and Social Factors: Implications for Species Conservation

PubMed Central

Grendelmeier, Alex; Arlettaz, Raphaël; Gerber, Michael; Pasinelli, Gilberto

2015-01-01

Identifying factors influencing a species' ecological niche and demography is a prerequisite for species conservation. However, our understanding of the interplay between demographic rates and biotic/abiotic factors is still poor for most species of conservation concern. We evaluated relevance of eight hypotheses relating to timing of breeding, temporal nest exposure, nest concealment, topography, tree structure, predation risk and disturbance, density dependence and weather for explaining variation in reproductive performance of the declining wood warbler Phylloscopus sibilatrix in northern Switzerland. Reproductive performance was monitored with cameras at 136 nests from 2010 to 2012 and was associated to temporal exposure, timing of breeding and concealment of nests. Daily nest survival was positively related to the number of grass and sedge tussocks, nest concealment and nest age. Clutch size and number of fledglings decreased, the later in the season a nest was initiated. Nest survival over an average nesting period of 31 days was 46.9 ± 0.07% (mean ± SE), daily nest survival rate was 0.976 ± 0.002. As for many ground-breeding birds, nest predation was the principal cause of nest failure, accounting for 79% of all nest losses. Conservation measures should aim at increasing the area of relatively homogenous forest stands featuring suitable habitats characterized by abundant and accessible grass and sedge tussocks. In managed forests, such conditions can be found in stands of middle age (i.e. pole wood) with little to no shrub layer. PMID:26172954

Reproductive Performance of a Declining Forest Passerine in Relation to Environmental and Social Factors: Implications for Species Conservation.

PubMed

Grendelmeier, Alex; Arlettaz, Raphaël; Gerber, Michael; Pasinelli, Gilberto

2015-01-01

Identifying factors influencing a species' ecological niche and demography is a prerequisite for species conservation. However, our understanding of the interplay between demographic rates and biotic/abiotic factors is still poor for most species of conservation concern. We evaluated relevance of eight hypotheses relating to timing of breeding, temporal nest exposure, nest concealment, topography, tree structure, predation risk and disturbance, density dependence and weather for explaining variation in reproductive performance of the declining wood warbler Phylloscopus sibilatrix in northern Switzerland. Reproductive performance was monitored with cameras at 136 nests from 2010 to 2012 and was associated to temporal exposure, timing of breeding and concealment of nests. Daily nest survival was positively related to the number of grass and sedge tussocks, nest concealment and nest age. Clutch size and number of fledglings decreased, the later in the season a nest was initiated. Nest survival over an average nesting period of 31 days was 46.9 ± 0.07% (mean ± SE), daily nest survival rate was 0.976 ± 0.002. As for many ground-breeding birds, nest predation was the principal cause of nest failure, accounting for 79% of all nest losses. Conservation measures should aim at increasing the area of relatively homogenous forest stands featuring suitable habitats characterized by abundant and accessible grass and sedge tussocks. In managed forests, such conditions can be found in stands of middle age (i.e. pole wood) with little to no shrub layer.

Factors affecting nest survival of Henslow's Sparrows (Ammodramus henslowii) in southern Indiana

USGS Publications Warehouse

Crimmins, Shawn M.; McKann, Patrick C.; Robb, Joseph R.; Lewis, Jason P.; Vanosdol, Teresa; Walker, Benjamin A.; Williams, Perry J.; Thogmartin, Wayne E.

2016-01-01

Populations of Henslow’s Sparrows have declined dramatically in recent decades, coinciding with widespread loss of native grassland habitat. Prescribed burning is a primary tool for maintaining grassland patches, but its effects on nest survival of Henslow’s Sparrows remains largely unknown, especially in conjunction with other factors. We monitored 135 nests of Henslow’s Sparrows at Big Oaks National Wildlife Refuge in southern Indiana from 1998–2001 in an effort to understand factors influencing nest survival, including prescribed burning of habitat. We used a mixed-effects implementation of the logistic exposure model to predict daily nest survival in an information theoretic framework. We found that daily survival declined near the onset of hatching and increased with the height of standing dead vegetation, although this relationship was weak. We found only nominal support to suggest that time since burn influenced nest survival. Overall, nest age was the most important factor in estimating daily nest survival rates. Our daily survival estimate from our marginal model (0.937) was similar to that derived from the Mayfield method (0.944) suggesting that our results are comparable to previous studies using the Mayfield approach. Our results indicate that frequent burning to limit woody encroachment into grassland habitats might benefit Henslow’s Sparrow, but that a variety of factors ultimately influence daily nest survival. However, we note that burning too frequently can also limit occupancy by Henslow’s Sparrows. We suggest that additional research is needed to determine the population-level consequences of habitat alteration and if other extrinsic factors influence demographics of Henslow’s Sparrows.

Assessing and Understanding Line Graph Interpretations Using a Scoring Rubric of Organized Cited Factors

ERIC Educational Resources Information Center

Boote, Stacy K.

2014-01-01

This study examined how 12- and 13-year-old students' mathematics and science background knowledge affected line graph interpretations and how interpretations were affected by graph question levels. A purposive sample of 14 students engaged in think aloud interviews while completing an excerpted Test of Graphing in Science. Data were…

Claw-Free Maximal Planar Graphs

DTIC Science & Technology

1989-01-01

1976, 212-223. 110] M.D. Plummer, On n-extendable graphs, Discrete Math . 31, 1980, 201-210. 1111 , A theorem on matchings in the plane, Graph Theory...in Memory of G.A. Dirac, Ann. Discrete Math . 41, North-Holland, Amsterdam, 1989, 347-354. 1121 N. Sbihi, Algorithme de recherche d’un stable de...cardinalitA maximum dans un graphe sans 6toile, Discrete Math . 29, 1980, 53-76. 1131 D. Sumner, On Tutte’s factorization theorem, Graphs and Combinatorics

Factors influencing occupancy of nest cavities in recently burned forests

Treesearch

Victoria A. Saab; Jonathan Dudley; William L. Thompson

2004-01-01

Recently burned forests in western North America provide nesting habitat for many species of cavity-nesting birds. However, little is understood about the time frame and the variables affecting occupancy of postfire habitats by these birds. We studied factors influencing the occupancy and reuse of nest cavities from 1–7 years after fire in two burned sites of western...

Collaborative Robotic Instruction: A Graph Teaching Experience

ERIC Educational Resources Information Center

Mitnik, Ruben; Recabarren, Matias; Nussbaum, Miguel; Soto, Alvaro

2009-01-01

Graphing is a key skill in the study of Physics. Drawing and interpreting graphs play a key role in the understanding of science, while the lack of these has proved to be a handicap and a limiting factor in the learning of scientific concepts. It has been observed that despite the amount of previous graph-working experience, students of all ages…

Habitat Selection and Reproductive Success of Lewis's Woodpecker (Melanerpes lewis) at Its Northern Limit

PubMed Central

Zhu, Xiang; Srivastava, Diane S.; Martin, Kathy

2012-01-01

Lewis's Woodpecker (Melanerpes lewis) has experienced population declines in both Canada and the United States and in 2010 was assigned a national listing of threatened in Canada. We conducted a two-year study (2004–2005) of this species at its northern range limit, the South Okanagan Valley in British Columbia, Canada. Our main objective was to determine whether the habitat features that influenced nest-site selection also predicted nest success, or whether other factors (e.g. cavity dimensions, clutch initiation date or time of season) were more important. Nest tree decay class, density of suitable cavities and total basal area of large trees were the best predictors of nest-site selection, but these factors were unrelated to nesting success. Estimates of demographic parameters (mean ± SE) included daily nest survival rate (0.988±0.003, years combined), nest success (0.52±0.08), clutch size (5.00±0.14 eggs), female fledglings per successful nest (1.31±0.11), and annual productivity (0.68±0.12 female fledglings per nest per year). Although higher nest survival was associated with both early and late initiated clutches, early-initiated clutches allowed birds to gain the highest annual productivity as early clutches were larger. Nests in deep cavities with small entrances experienced lower predation risk especially during the peak period of nest predation. We concluded that nest-site selection can be predicted by a number of easily measured habitat variables, whereas nest success depended on complicated ecological interactions among nest predators, breeding behaviors, and cavity features. Thus, habitat-based conservation strategies should also consider ecological factors that may not be well predicted by habitat. PMID:23028525

Factors influencing predation associated with visits to artificial goose nests

USGS Publications Warehouse

Vacca, M. Michele; Handel, Colleen M.

1988-01-01

Artificial goose nests were used to determine what factors might increase predation after visits to nests of Cackling Canada Geese (Branta canadensis minima). We tested whether leaving the nest uncovered, marking the nest location with a flag, or placing the nest on an island or peninsula would increase the rate of predation. Predators destroyed significantly more of the nests with eggs exposed to view (61%) than of the nests with eggs covered with goose down (35%) (P < 0.05). However, the rate of predation was only slightly higher among nests located on peninsulas than on islands and equal proportions of flagged and unflagged nests were destroyed. We also determined that investigators attracted predators to the study area and caused an increase in predation at uncovered nests immediately after the visit. Covering the eggs with down essentially negated the effect of attracting predators when visiting the nest. Among the 46 nests destroyed, 78% were destroyed by birds and 22% by mammals. Results of our study suggested that visibility of exposed eggs rather than nest markers provided important cues to avian predators and that islands probably provided some refuge from mammalian predators. Investigators can take steps to minimize their impact on nesting success and should incorporate a measure of that impact in their studies.

Nest survival is influenced by parental behaviour and heterospecifics in a mixed-species colony

USGS Publications Warehouse

Brussee, Brianne E.; Coates, Peter S.; Hothem, Roger L.; Howe, Kristy; Casazza, Michael L.; Eadie, John M.

2016-01-01

Studies of avian nest success often focus on examining influences of variation in environmental and seasonal factors. However, in-depth evaluations can also incorporate variation in individual incubation behaviour to further advance our understanding of avian reproductive ecology. We examined these relationships in colonially nesting Black-crowned Night-Herons Nycticorax nycticorax using intensive video-monitoring methods to quantify incubation behaviours. We modelled nest survival as a function of both extrinsic factors and incubation behaviours over a 3-year period (2010–12) on Alcatraz Island, USA. Model-averaged parameter estimates indicated that nest survival increased as a function of greater incubation constancy (% of time spent incubating eggs within a 24-h period), and average daily precipitation throughout the nesting stage. Common Ravens Corvus corax are the only known nest predator of Night-Herons on Alcatraz Island, as on many other coastal Pacific islands. We also investigated the effects of heterospecific nesting of California Gulls Larus californicus and Western Gulls Larus occidentalis in a mixed-species colony with Night-Herons, based on nesting proximity data collected over a 2-year period (2011–12). This second analysis indicated that, in addition to incubation behaviours, nesting heterospecifics are an important factor for explaining variation in Night-Heron nest survival. However, contrary to our original expectation, we found that Night-Herons experienced increased nest survival with increasing distance from gull colony boundaries. These results may apply to other areas with multiple colonial nesting species and similar predator communities and climatic patterns.

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

NASA Astrophysics Data System (ADS)

Bramer, David; Wei, Guo-Wei

2018-02-01

Protein structural fluctuation, measured by Debye-Waller factors or B-factors, is known to correlate to protein flexibility and function. A variety of methods has been developed for protein Debye-Waller factor prediction and related applications to domain separation, docking pose ranking, entropy calculation, hinge detection, stability analysis, etc. Nevertheless, none of the current methodologies are able to deliver an accuracy of 0.7 in terms of the Pearson correlation coefficients averaged over a large set of proteins. In this work, we introduce a paradigm-shifting geometric graph model, multiscale weighted colored graph (MWCG), to provide a new generation of computational algorithms to significantly change the current status of protein structural fluctuation analysis. Our MWCG model divides a protein graph into multiple subgraphs based on interaction types between graph nodes and represents the protein rigidity by generalized centralities of subgraphs. MWCGs not only predict the B-factors of protein residues but also accurately analyze the flexibility of all atoms in a protein. The MWCG model is validated over a number of protein test sets and compared with many standard methods. An extensive numerical study indicates that the proposed MWCG offers an accuracy of over 0.8 and thus provides perhaps the first reliable method for estimating protein flexibility and B-factors. It also simultaneously predicts all-atom flexibility in a molecule.

Figure-Ground Segmentation Using Factor Graphs

PubMed Central

Shen, Huiying; Coughlan, James; Ivanchenko, Volodymyr

2009-01-01

Foreground-background segmentation has recently been applied [26,12] to the detection and segmentation of specific objects or structures of interest from the background as an efficient alternative to techniques such as deformable templates [27]. We introduce a graphical model (i.e. Markov random field)-based formulation of structure-specific figure-ground segmentation based on simple geometric features extracted from an image, such as local configurations of linear features, that are characteristic of the desired figure structure. Our formulation is novel in that it is based on factor graphs, which are graphical models that encode interactions among arbitrary numbers of random variables. The ability of factor graphs to express interactions higher than pairwise order (the highest order encountered in most graphical models used in computer vision) is useful for modeling a variety of pattern recognition problems. In particular, we show how this property makes factor graphs a natural framework for performing grouping and segmentation, and demonstrate that the factor graph framework emerges naturally from a simple maximum entropy model of figure-ground segmentation. We cast our approach in a learning framework, in which the contributions of multiple grouping cues are learned from training data, and apply our framework to the problem of finding printed text in natural scenes. Experimental results are described, including a performance analysis that demonstrates the feasibility of the approach. PMID:20160994

Ticks as a factor in nest desertion of California brown pelicans

USGS Publications Warehouse

King, Kirke A.; Keith, James O.; Mitchell, Christine A.; Keirans, James E.

1977-01-01

In summary, our observations suggest that O. denmarki may be an important environmental factor influencing the distribution and success of Brown Pelican nests in the Gulf of California. More information on these relationships may be unobtainable without seriously disturbing and destroying large numbers of nests.

Presenting simulation results in a nested loop plot.

PubMed

Rücker, Gerta; Schwarzer, Guido

2014-12-12

Statisticians investigate new methods in simulations to evaluate their properties for future real data applications. Results are often presented in a number of figures, e.g., Trellis plots. We had conducted a simulation study on six statistical methods for estimating the treatment effect in binary outcome meta-analyses, where selection bias (e.g., publication bias) was suspected because of apparent funnel plot asymmetry. We varied five simulation parameters: true treatment effect, extent of selection, event proportion in control group, heterogeneity parameter, and number of studies in meta-analysis. In combination, this yielded a total number of 768 scenarios. To present all results using Trellis plots, 12 figures were needed. Choosing bias as criterion of interest, we present a 'nested loop plot', a diagram type that aims to have all simulation results in one plot. The idea was to bring all scenarios into a lexicographical order and arrange them consecutively on the horizontal axis of a plot, whereas the treatment effect estimate is presented on the vertical axis. The plot illustrates how parameters simultaneously influenced the estimate. It can be combined with a Trellis plot in a so-called hybrid plot. Nested loop plots may also be applied to other criteria such as the variance of estimation. The nested loop plot, similar to a time series graph, summarizes all information about the results of a simulation study with respect to a chosen criterion in one picture and provides a suitable alternative or an addition to Trellis plots.

Non-planar one-loop Parke-Taylor factors in the CHY approach for quadratic propagators

NASA Astrophysics Data System (ADS)

Ahmadiniaz, Naser; Gomez, Humberto; Lopez-Arcos, Cristhiam

2018-05-01

In this work we have studied the Kleiss-Kuijf relations for the recently introduced Parke-Taylor factors at one-loop in the CHY approach, that reproduce quadratic Feynman propagators. By doing this, we were able to identify the non-planar one-loop Parke-Taylor factors. In order to check that, in fact, these new factors can describe non-planar amplitudes, we applied them to the bi-adjoint Φ3 theory. As a byproduct, we found a new type of graphs that we called the non-planar CHY-graphs. These graphs encode all the information for the subleading order at one-loop, and there is not an equivalent of these in the Feynman formalism.

Diversity of great gray owl nest sites and nesting habitats in California

Treesearch

Joanna X. Wu; Rodney B. Siegel; Helen L. Loffland; Morgan W. Tingley; Sarah L. Stock; Kevin N. Roberts; John J. Keane; Joseph R. Medley; Roy Bridgman; Chris Stermer

2015-01-01

The great gray owl (Strix nebulosa) is listed by the state of California as endangered, with a population estimate of fewer than 300 individuals in the state. Nest-site availability has been suggested as a limiting factor for population growth in California, but information on nest types and nesting habitat has been based on a small number of nests...

Nest-site habitat of cavity-nesting birds at the San Joaquin Experimental Range

Treesearch

Kathryn L. Purcell; Jared. Verner

2008-01-01

Detailed information about the nesting habitats of birds, including those needed for successful nesting, can provide a better understanding of the ecological factors that permit coexistence of different species and may aid in conservation efforts. From 1989 through 1994, we studied the nesting habitat of secondary cavity-nesting birds in oak woodlands at the San...

Species associations and habitat influence the range-wide distribution of breeding Canada Geese (Branta canadensis interior) on Western Hudson Bay

USGS Publications Warehouse

Reiter, Matthew E.; Andersen, David E.; Raedeke, Andrew H.; Humburg, Dale D.

2017-01-01

Inter- and intra-specific interactions are potentially important factors influencing the distribution of populations. Aerial survey data, collected during range-wide breeding population surveys for Eastern Prairie Population (EPP) Canada Geese (Branta canadensis interior), 1987–2008, were evaluated to assess factors influencing their nesting distribution. Specifically, associations between nesting Lesser Snow Geese (Chen caerulescens caerulescens) and EPP Canada Geese were quantified; and changes in the spatial distribution of EPP Canada Geese were identified. Mixed-effects Poisson regression models of EPP Canada Goose nest counts were evaluated within a cross-validation framework. The total count of EPP Canada Goose nests varied moderately among years between 1987 and 2008 with no long-term trend; however, the total count of nesting Lesser Snow Geese generally increased. Three models containing factors related to previous EPP Canada Goose nest density (representing recruitment), distance to Hudson Bay (representing brood-habitat), nesting habitat type, and Lesser Snow Goose nest density (inter-specific associations) were the most accurate, improving prediction accuracy by 45% when compared to intercept-only models. EPP Canada Goose nest density varied by habitat type, was negatively associated with distance to coastal brood-rearing areas, and suggested density-dependent intra-specific effects on recruitment. However, a non-linear relationship between Lesser Snow and EPP Canada Goose nest density suggests that as nesting Lesser Snow Geese increase, EPP Canada Geese locally decline and subsequently the spatial distribution of EPP Canada Geese on western Hudson Bay has changed.

Effects of spatial disturbance on common loon nest site selection and territory success

USGS Publications Warehouse

McCarthy, K.P.; DeStefano, S.

2011-01-01

The common loon (Gavia immer) breeds during the summer on northern lakes and water bodies that are also often desirable areas for aquatic recreation and human habitation. In northern New England, we assessed how the spatial nature of disturbance affects common loon nest site selection and territory success. We found through classification and regression analysis that distance to and density of disturbance factors can be used to classify observed nest site locations versus random points, suggesting that these factors affect loon nest site selection (model 1: Correct classification = 75%, null = 50%, K = 0.507, P < 0.001; model 2: Correct classification = 78%, null = 50%, K = 0.551, P < 0.001). However, in an exploratory analysis, we were unable to show a relation between spatial disturbance variables and breeding success (P = 0.595, R 2 = 0.436), possibly because breeding success was so low during the breeding seasons of 2007-2008. We suggest that by selecting nest site locations that avoid disturbance factors, loons thereby limit the effect that disturbance will have on their breeding success. Still, disturbance may force loons to use sub-optimal nesting habitat, limiting the available number of territories, and overall productivity. We advise that management efforts focus on limiting disturbance factors to allow breeding pairs access to the best nesting territories, relieving disturbance pressures that may force sub-optimal nest placement. ?? 2011 The Wildlife Society.

A Novel Strategy Using Factor Graphs and the Sum-Product Algorithm for Satellite Broadcast Scheduling Problems

NASA Astrophysics Data System (ADS)

Chen, Jung-Chieh

This paper presents a low complexity algorithmic framework for finding a broadcasting schedule in a low-altitude satellite system, i. e., the satellite broadcast scheduling (SBS) problem, based on the recent modeling and computational methodology of factor graphs. Inspired by the huge success of the low density parity check (LDPC) codes in the field of error control coding, in this paper, we transform the SBS problem into an LDPC-like problem through a factor graph instead of using the conventional neural network approaches to solve the SBS problem. Based on a factor graph framework, the soft-information, describing the probability that each satellite will broadcast information to a terminal at a specific time slot, is exchanged among the local processing in the proposed framework via the sum-product algorithm to iteratively optimize the satellite broadcasting schedule. Numerical results show that the proposed approach not only can obtain optimal solution but also enjoys the low complexity suitable for integral-circuit implementation.

Parameterized Complexity Results for General Factors in Bipartite Graphs with an Application to Constraint Programming

NASA Astrophysics Data System (ADS)

Gutin, Gregory; Kim, Eun Jung; Soleimanfallah, Arezou; Szeider, Stefan; Yeo, Anders

The NP-hard general factor problem asks, given a graph and for each vertex a list of integers, whether the graph has a spanning subgraph where each vertex has a degree that belongs to its assigned list. The problem remains NP-hard even if the given graph is bipartite with partition U ⊎ V, and each vertex in U is assigned the list {1}; this subproblem appears in the context of constraint programming as the consistency problem for the extended global cardinality constraint. We show that this subproblem is fixed-parameter tractable when parameterized by the size of the second partite set V. More generally, we show that the general factor problem for bipartite graphs, parameterized by |V |, is fixed-parameter tractable as long as all vertices in U are assigned lists of length 1, but becomes W[1]-hard if vertices in U are assigned lists of length at most 2. We establish fixed-parameter tractability by reducing the problem instance to a bounded number of acyclic instances, each of which can be solved in polynomial time by dynamic programming.

An Improved Multi-Sensor Fusion Navigation Algorithm Based on the Factor Graph

PubMed Central

Zeng, Qinghua; Chen, Weina; Liu, Jianye; Wang, Huizhe

2017-01-01

An integrated navigation system coupled with additional sensors can be used in the Micro Unmanned Aerial Vehicle (MUAV) applications because the multi-sensor information is redundant and complementary, which can markedly improve the system accuracy. How to deal with the information gathered from different sensors efficiently is an important problem. The fact that different sensors provide measurements asynchronously may complicate the processing of these measurements. In addition, the output signals of some sensors appear to have a non-linear character. In order to incorporate these measurements and calculate a navigation solution in real time, the multi-sensor fusion algorithm based on factor graph is proposed. The global optimum solution is factorized according to the chain structure of the factor graph, which allows for a more general form of the conditional probability density. It can convert the fusion matter into connecting factors defined by these measurements to the graph without considering the relationship between the sensor update frequency and the fusion period. An experimental MUAV system has been built and some experiments have been performed to prove the effectiveness of the proposed method. PMID:28335570

An Improved Multi-Sensor Fusion Navigation Algorithm Based on the Factor Graph.

PubMed

Zeng, Qinghua; Chen, Weina; Liu, Jianye; Wang, Huizhe

2017-03-21

An integrated navigation system coupled with additional sensors can be used in the Micro Unmanned Aerial Vehicle (MUAV) applications because the multi-sensor information is redundant and complementary, which can markedly improve the system accuracy. How to deal with the information gathered from different sensors efficiently is an important problem. The fact that different sensors provide measurements asynchronously may complicate the processing of these measurements. In addition, the output signals of some sensors appear to have a non-linear character. In order to incorporate these measurements and calculate a navigation solution in real time, the multi-sensor fusion algorithm based on factor graph is proposed. The global optimum solution is factorized according to the chain structure of the factor graph, which allows for a more general form of the conditional probability density. It can convert the fusion matter into connecting factors defined by these measurements to the graph without considering the relationship between the sensor update frequency and the fusion period. An experimental MUAV system has been built and some experiments have been performed to prove the effectiveness of the proposed method.

Scalable effective-temperature reduction for quantum annealers via nested quantum annealing correction

NASA Astrophysics Data System (ADS)

Vinci, Walter; Lidar, Daniel A.

2018-02-01

Nested quantum annealing correction (NQAC) is an error-correcting scheme for quantum annealing that allows for the encoding of a logical qubit into an arbitrarily large number of physical qubits. The encoding replaces each logical qubit by a complete graph of degree C . The nesting level C represents the distance of the error-correcting code and controls the amount of protection against thermal and control errors. Theoretical mean-field analyses and empirical data obtained with a D-Wave Two quantum annealer (supporting up to 512 qubits) showed that NQAC has the potential to achieve a scalable effective-temperature reduction, Teff˜C-η , with 0 <η ≤2 . We confirm that this scaling is preserved when NQAC is tested on a D-Wave 2000Q device (supporting up to 2048 qubits). In addition, we show that NQAC can also be used in sampling problems to lower the effective-temperature of a quantum annealer. Such effective-temperature reduction is relevant for machine-learning applications. Since we demonstrate that NQAC achieves error correction via a reduction of the effective-temperature of the quantum annealing device, our results address the problem of the "temperature scaling law for quantum annealers," which requires the temperature of quantum annealers to be reduced as problems of larger sizes are attempted to be solved.

Age and breeding success related to nest position in a White stork Ciconia ciconia colony

NASA Astrophysics Data System (ADS)

Vergara, Pablo; Aguirre, José I.

2006-11-01

Coloniality is a breeding system that may produce benefits in terms of breeding success, although these advantages could vary according to factors such as colony size or nest position. We studied breeder's age in relation to nest position (peripheral or central) within the colony. In addition, we studied the relationship between breeding success and nest position, controlling for breeder's age, a highly correlated factor, in a White Stork Ciconia ciconia colony over a 7-year period. Our results show that central nests are mainly occupied by adult birds and had lower failure rates. However, controlling for breeder's age, nest position per se did not explain breeding success. The scarce predation and the lack of human disturbance in the study colony could explain the absence of differences in breeding success between different nest positions within the colony.

Constructing compact and effective graphs for recommender systems via node and edge aggregations

DOE PAGES

Lee, Sangkeun; Kahng, Minsuk; Lee, Sang-goo

2014-12-10

Exploiting graphs for recommender systems has great potential to flexibly incorporate heterogeneous information for producing better recommendation results. As our baseline approach, we first introduce a naive graph-based recommendation method, which operates with a heterogeneous log-metadata graph constructed from user log and content metadata databases. Although the na ve graph-based recommendation method is simple, it allows us to take advantages of heterogeneous information and shows promising flexibility and recommendation accuracy. However, it often leads to extensive processing time due to the sheer size of the graphs constructed from entire user log and content metadata databases. In this paper, we proposemore » node and edge aggregation approaches to constructing compact and e ective graphs called Factor-Item bipartite graphs by aggregating nodes and edges of a log-metadata graph. Furthermore, experimental results using real world datasets indicate that our approach can significantly reduce the size of graphs exploited for recommender systems without sacrificing the recommendation quality.« less

Factors affecting predation at songbird nests in old fields

Treesearch

Dirk E. Burhans; Donald Dearborn; Frank R. III Thompson; John Faaborg

2002-01-01

We determined the effects of microhabitat, year, weather, time of season, stage of the nesting cycle, and brood parasitism on nest predation from a 7-year dataset on field sparrows (Spizella pusilla) and indigo buntings (Passerina cyanea) in central Missouri, USA. Year, site, and the interaction of species and 2-week interval of the season were important factors...

Complexity of chemical graphs in terms of size, branching, and cyclicity.

PubMed

Balaban, A T; Mills, D; Kodali, V; Basak, S C

2006-08-01

Chemical graph complexity depends on many factors, but the main ones are size, branching, and cyclicity. Some molecular descriptors embrace together all these three parameters, which cannot then be disentangled. The topological index J (and its refinements that include accounting for bond multiplicity and the presence of heteroatoms) was designed to compensate in a significant measure for graph size and cyclicity, and therefore it contains information mainly on branching. In order to separate these factors, two new indices (F and G) related with J are proposed, which allow to group together graphs with the same size into families of constitutional formulas differing in their branching and cyclicity. A comparison with other topological indices revealed that a few other topological indices vary similarly with index G, notably DN2S4 among the triplet indices, and TOTOP among the indices contained in the Molconn-Z program. This comparison involved all possible chemical graphs (i.e. connected planar graphs with vertex degrees not higher than four) with four through six vertices, and all possible alkanes with four through nine carbon atoms.

Influence of olfactory and visual cover on nest site selection and nest success for grassland-nesting birds.

PubMed

Fogarty, Dillon T; Elmore, R Dwayne; Fuhlendorf, Samuel D; Loss, Scott R

2017-08-01

Habitat selection by animals is influenced by and mitigates the effects of predation and environmental extremes. For birds, nest site selection is crucial to offspring production because nests are exposed to extreme weather and predation pressure. Predators that forage using olfaction often dominate nest predator communities; therefore, factors that influence olfactory detection (e.g., airflow and weather variables, including turbulence and moisture) should influence nest site selection and survival. However, few studies have assessed the importance of olfactory cover for habitat selection and survival. We assessed whether ground-nesting birds select nest sites based on visual and/or olfactory cover. Additionally, we assessed the importance of visual cover and airflow and weather variables associated with olfactory cover in influencing nest survival. In managed grasslands in Oklahoma, USA, we monitored nests of Northern Bobwhite ( Colinus virginianus ), Eastern Meadowlark ( Sturnella magna ), and Grasshopper Sparrow ( Ammodramus savannarum ) during 2015 and 2016. To assess nest site selection, we compared cover variables between nests and random points. To assess factors influencing nest survival, we used visual cover and olfactory-related measurements (i.e., airflow and weather variables) to model daily nest survival. For nest site selection, nest sites had greater overhead visual cover than random points, but no other significant differences were found. Weather variables hypothesized to influence olfactory detection, specifically precipitation and relative humidity, were the best predictors of and were positively related to daily nest survival. Selection for overhead cover likely contributed to mitigation of thermal extremes and possibly reduced detectability of nests. For daily nest survival, we hypothesize that major nest predators focused on prey other than the monitored species' nests during high moisture conditions, thus increasing nest survival on these days. Our study highlights how mechanistic approaches to studying cover informs which dimensions are perceived and selected by animals and which dimensions confer fitness-related benefits.

Effects of spatial disturbance on common loon nest site selection and territory success

USGS Publications Warehouse

McCarthy, Kyle P.; DeStefano, Stephen

2011-01-01

The common loon (Gavia immer) breeds during the summer on northern lakes and water bodies that are also often desirable areas for aquatic recreation and human habitation. In northern New England, we assessed how the spatial nature of disturbance affects common loon nest site selection and territory success. We found through classification and regression analysis that distance to and density of disturbance factors can be used to classify observed nest site locations versus random points, suggesting that these factors affect loon nest site selection (model 1: Correct classification = 75%, null = 50%, K = 0.507, P < 0.001; model 2: Correct classification = 78%, null = 50%, K = 0.551, P < 0.001). However, in an exploratory analysis, we were unable to show a relation between spatial disturbance variables and breeding success (P = 0.595, R2 = 0.436), possibly because breeding success was so low during the breeding seasons of 2007–2008. We suggest that by selecting nest site locations that avoid disturbance factors, loons thereby limit the effect that disturbance will have on their breeding success. Still, disturbance may force loons to use sub-optimal nesting habitat, limiting the available number of territories, and overall productivity. We advise that management efforts focus on limiting disturbance factors to allow breeding pairs access to the best nesting territories, relieving disturbance pressures that may force sub-optimal nest placement.

The Antsy Social Network: Determinants of Nest Structure and Arrangement in Asian Weaver Ants.

PubMed

Devarajan, Kadambari

2016-01-01

Asian weaver ants (Oecophylla smaragdina) are arboreal ants that are known to form mutualistic complexes with their host trees. They are eusocial ants that build elaborate nests in the canopy in tropical areas. A colony comprises of multiple nests, usually on multiple trees, and the boundaries of the colony may be difficult to identify. However, they provide the ideal model for studying group living in invertebrates since there are a definite number of nests for a given substrate, the tree. Here, we briefly examine the structure of the nests and the processes involved in the construction and maintenance of these nests. We have described the spatial arrangement of weaver ant nests on trees in two distinct tropical clusters, a few hundred kilometres apart in India. Measurements were made for 13 trees with a total of 71 nests in the two field sites. We have considered a host of biotic and abiotic factors that may be crucial in determining the location of the nesting site by Asian weaver ants. Our results indicate that tree characteristics and architecture followed by leaf features help determine nest location in Asian weaver ants. While environmental factors may not be as influential to nest arrangement, they seem to be important determinants of nest structure. The parameters that may be considered in establishing the nests could be crucial in picking the evolutionary drivers for colonial living in social organisms.

Using survival analysis of artificial and Real Brewer's sparrow (Spizella breweri breweri) nests to model site level and nest site factors associated with nest success in the South Okanagan region of Canada

Treesearch

Pam Krannitz Kym Welstead

2005-01-01

Predation is the predominant cause of nest failure for the Brewer's Sparrow (Spizella breweri breweri), a provincially red-listed shrub-steppe species that has experienced significant declines throughout most of its range. We monitored Brewer’s Sparrow nests and conducted an artificial nest experiment, in the South Okanagan Valley,...

Species and temporal factors affect predator-specific rates of nest predation for forest songbirds in the midwest

Treesearch

W. Andrew Cox; Frank R. III Thompson; John Faaborg

2012-01-01

Knowledge of the relative contributions of predator species to overall rates of nest predation can improve our understanding of why predation risk varies, but the identity of predators is seldom known. We used video technology to identify nest predators of the tree-nesting Acadian Flycatcher (Empidonax virescens) and the shrub-nesting Indigo Bunting...

Predation of Songbird Nests Differs By Predator and Between Field and Forest Habitats

Treesearch

Frank R., III Thompson; Dirk E. Burhans

2003-01-01

Our understanding of factors affecting nest predation and ability to mitigate high nest predation rates is hampered by a lack of information on the importance of various nest predator species in different habitats and landscapes. We identified predators of songbird nests in old-field and forest habitats in central Missouri, USA, with miniature video cameras. We used an...

Contrasting patterns of nest survival and postfledging survival in ovenbirds and Acadian flycatchers in Missouri forest fragments

Treesearch

Julianna M. A. Jenkins; Frank R. Thompson; John Faaborg

2016-01-01

We can improve our ability to assess population viability and forecast population growth under different scenarios by understanding factors that limit population parameters in each stage of the annual cycle. Postfledging mortality rates may be as variable as nest survival across regions and fragmentation gradients, although factors that negatively impact nest survival...

Less is less: a systematic review of graph use in meta-analyses.

PubMed

Schild, Anne H E; Voracek, Martin

2013-09-01

Graphs are an essential part of scientific communication. Complex datasets, of which meta-analyses are textbook examples, benefit the most from visualization. Although a number of graph options for meta-analyses exist, the extent to which these are used was hitherto unclear. A systematic review on graph use in meta-analyses in three disciplines (medicine, psychology, and business) and nine journals was conducted. Interdisciplinary differences, which are mirrored in the respective journals, were revealed, that is, graph use correlates with external factors rather than methodological considerations. There was only limited variation in graph types (with forest plots as the most important representatives), and diagnostic plots were very rare. Although an increase in graph use over time could be observed, it is unlikely that this phenomenon is specific to meta-analyses. There is a gaping discrepancy between available graphic methods and their application in meta-analyses. This may be rooted in a number of factors, namely, (i) insufficient dissemination of new developments, (ii) unsatisfactory implementation in software packages, and (iii) minor attention on graphics in meta-analysis reporting guidelines. Using visualization methods to their full capacity is a further step in using meta-analysis to its full potential. Copyright © 2013 John Wiley & Sons, Ltd.

Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance

PubMed Central

Lin, Jing; Pramono, Zacharias Aloysius Dwi; Maurer-Stroh, Sebastian

2016-01-01

The multiple circulating human influenza A virus subtypes coupled with the perpetual genomic mutations and segment reassortment events challenge the development of effective therapeutics. The capacity to drug most RNAs motivates the investigation on viral RNA targets. 123,060 segment sequences from 35,938 strains of the most prevalent subtypes also infecting humans–H1N1, 2009 pandemic H1N1, H3N2, H5N1 and H7N9, were used to identify 1,183 conserved RNA target sequences (≥15-mer) in the internal segments. 100% theoretical coverage in simultaneous heterosubtypic targeting is achieved by pairing specific sequences from the same segment (“Duals”) or from two segments (“Doubles”); 1,662 Duals and 28,463 Doubles identified. By combining specific Duals and/or Doubles to form a target graph wherein an edge connecting two vertices (target sequences) represents a Dual or Double, it is possible to hedge against antiviral resistance besides maintaining 100% heterosubtypic coverage. To evaluate the hedging potential, we define the hedge-factor as the minimum number of resistant target sequences that will render the graph to become resistant i.e. eliminate all the edges therein; a target sequence or a graph is considered resistant when it cannot achieve 100% heterosubtypic coverage. In an n-vertices graph (n ≥ 3), the hedge-factor is maximal (= n– 1) when it is a complete graph i.e. every distinct pair in a graph is either a Dual or Double. Computational analyses uncover an extensive number of complete graphs of different sizes. Monte Carlo simulations show that the mutation counts and time elapsed for a target graph to become resistant increase with the hedge-factor. Incidentally, target sequences which were reported to reduce virus titre in experiments are included in our target graphs. The identity of target sequence pairs for heterosubtypic targeting and their combinations for hedging antiviral resistance are useful toolkits to construct target graphs for different therapeutic objectives. PMID:26771381

Using Artificial Nests to Study Nest Predation in Birds

ERIC Educational Resources Information Center

Belthoff, James R.

2005-01-01

A simple and effective field exercise that demonstrates factors affecting predation on bird nests is described. With instructor guidance, students in high school biology or college-level biology, ecology, animal behavior, wildlife management or ornithology laboratory courses can collaborate to design field experiments related to nest depredation.

Factor determining prochard nest predation along a wetland gradient

USGS Publications Warehouse

Albrecht, T.; Horak, D.; Kreisinger, J.; Weidinger, K.; Klvana, P.; Michot, T.C.

2006-01-01

Waterfowl management on breeding grounds focuses on improving nest success, but few studies have compared waterfowl nest success and factors affecting nest survival along a wetland gradient and simultaneously identified nest predators. We monitored nests (n = 195) of common pochards (Aythya ferina) in Trebon Basin Biosphere Reserve, Czech Republic, during 1999-2002. Daily nest survival rates (DSRs, logistic-exposure) declined from island (0.985, 95% confidence interval, 0.978-0.991) to overwater (0.962, 0.950-0.971) and terrestrial (0.844, 0.759-0.904) nests. The most parsimonious model for DSRs included habitat class (DSRs: island > overwater > terrestrial) and nest visibility. Nest survival was improved by reduced nest visibility, increased water depth, and increased distance from the nest to habitat edge in littoral habitats. On islands, nest success increased with advancing date and increased distance to open water. A model of constant nest survival best explained the data for terrestrial nests. There were no observer effects on DSRs in any habitat. In 2003, artificial nests (n = 180; 120 contained a wax-filled egg) were deployed on study plots. The model that best explained variation in DSRs for artificial nests included only 1 variable: habitat class (DSRs: island ??? overwater > terrestrial). Mammalian predation of artificial nests (by foxes [Vulpes vulpes] and martens [Martes spp.]) was more likely in terrestrial habitats than in littoral habitats or on islands. By contrast, corvids and marsh harriers (Circus aeruginosus) prevailed among predators of overwater and island nests. Our data indicate that artificial islands and wide strips of littoral vegetation may represent secure breeding habitats for waterfowl because those habitats allow nests to be placed in areas that are not accessible to, or that are avoided by, mammalian predators. Management actions should be aimed at preserving these habitats. This, along with creation of new artificial islands, could help to enhance breeding productivity of pochards and possibly other waterfowl species inhabiting man-made ponds.

Graphs as a Managerial Tool: A Case Study of Du Pont's Use of Graphs in the Early Twentieth Century.

ERIC Educational Resources Information Center

Yates, JoAnne

1985-01-01

Sketches the development of business graphs in America. Examines their early use at Du Pont and the origin of the chart room around 1920, an important factor in the executive control systems at Du Pont. Draws lessons from this case study for managers and teachers of business communication. (PD)

Advanced techniques for modeling avian nest survival

USGS Publications Warehouse

Dinsmore, S.J.; White, Gary C.; Knopf, F.L.

2002-01-01

Estimation of avian nest survival has traditionally involved simple measures of apparent nest survival or Mayfield constant-nest-survival models. However, these methods do not allow researchers to build models that rigorously assess the importance of a wide range of biological factors that affect nest survival. Models that incorporate greater detail, such as temporal variation in nest survival and covariates representative of individual nests represent a substantial improvement over traditional estimation methods. In an attempt to improve nest survival estimation procedures, we introduce the nest survival model now available in the program MARK and demonstrate its use on a nesting study of Mountain Plovers (Charadrius montanus Townsend) in Montana, USA. We modeled the daily survival of Mountain Plover nests as a function of the sex of the incubating adult, nest age, year, linear and quadratic time trends, and two weather covariates (maximum daily temperature and daily precipitation) during a six-year study (1995–2000). We found no evidence for yearly differences or an effect of maximum daily temperature on the daily nest survival of Mountain Plovers. Survival rates of nests tended by female and male plovers differed (female rate = 0.33; male rate = 0.49). The estimate of the additive effect for males on nest survival rate was 0.37 (95% confidence limits were 0.03, 0.71) on a logit scale. Daily survival rates of nests increased with nest age; the estimate of daily nest-age change in survival in the best model was 0.06 (95% confidence limits were 0.04, 0.09) on a logit scale. Daily precipitation decreased the probability that the nest would survive to the next day; the estimate of the additive effect of daily precipitation on the nest survival rate was −1.08 (95% confidence limits were −2.12, −0.13) on a logit scale. Our approach to modeling daily nest-survival rates allowed several biological factors of interest to be easily included in nest survival models and allowed us to generate more biologically meaningful estimates of nest survival.

Integer Flows and Circuit Covers of Graphs and Signed Graphs

NASA Astrophysics Data System (ADS)

Cheng, Jian

The work in Chapter 2 is motivated by Tutte and Jaeger's pioneering work on converting modulo flows into integer-valued flows for ordinary graphs. For a signed graphs (G, sigma), we first prove that for each k ∈ {2, 3}, if (G, sigma) is (k - 1)-edge-connected and contains an even number of negative edges when k = 2, then every modulo k-flow of (G, sigma) can be converted into an integer-valued ( k + 1)-ow with a larger or the same support. We also prove that if (G, sigma) is odd-(2p+1)-edge-connected, then (G, sigma) admits a modulo circular (2 + 1/ p)-flows if and only if it admits an integer-valued circular (2 + 1/p)-flows, which improves all previous result by Xu and Zhang (DM2005), Schubert and Steffen (EJC2015), and Zhu (JCTB2015). Shortest circuit cover conjecture is one of the major open problems in graph theory. It states that every bridgeless graph G contains a set of circuits F such that each edge is contained in at least one member of F and the length of F is at most 7/5∥E(G)∥. This concept was recently generalized to signed graphs by Macajova et al. (JGT2015). In Chapter 3, we improve their upper bound from 11∥E( G)∥ to 14/3 ∥E(G)∥, and if G is 2-edgeconnected and has even negativeness, then it can be further reduced to 11/3 ∥E(G)∥. Tutte's 3-flow conjecture has been studied by many graph theorists in the last several decades. As a new approach to this conjecture, DeVos and Thomassen considered the vectors as ow values and found that there is a close relation between vector S1-flows and integer 3-NZFs. Motivated by their observation, in Chapter 4, we prove that if a graph G admits a vector S1-flow with rank at most two, then G admits an integer 3-NZF. The concept of even factors is highly related to the famous Four Color Theorem. We conclude this dissertation in Chapter 5 with an improvement of a recent result by Chen and Fan (JCTB2016) on the upperbound of even factors. We show that if a graph G contains an even factor, then it contains an even factor H with. ∥E(H)∥ ≥ 4/7 (∥ E(G)∥+1)+ 1/7 ∥V2 (G)∥, where V2( G) is the set of vertices of degree two.

Factors influencing nesting success of burrowing owls in southeastern Idaho

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gleason, R.S.; Johnson, D.R.

1985-01-31

A burrowing owl (Athene cunicularia) population nesting on the Idaho National Engineering Laboratory (INEL) in southeastern Idaho utilized burrows excavated by badgers (Taxidea taxus) or natural cavities in lava flows as nesting sites. The size of the population was small (N = 13-14 pairs) in relation to the number of available nesting sites, suggesting that factors other than burrow availability limited this population. Rodents and Jerusalem crickets (Stenopelmatus fuscus) represented the primary prey utilized during the nesting season. This population demonstrated both a numerical (brood size) and functional (dietary) response to a decrease in the density of three species ofmore » rodents on the INEL during a drought in 1977. 11 references, 1 figure, 2 table.« less

Female turtles from hot nests: is it duration of incubation or proportion of development at high temperatures that matters?

PubMed

Georges, Arthur

1989-11-01

Mean daily temperature in natural nests of freshwater turtles with temperature-dependent sex determination is known to be a poor predictor of hatchling sex ratios when nest temperatures fluctuate. To account for this, a model was developed on the assumption that females will emerge from eggs when more than half of embryonic development occurs above the threshold temperature for sex determination rather than from eggs that spend more than half their time above the threshold. The model is consistent with previously published data and in particular explains the phenomenon whereby the mean temperature that best distinguishes between male and female nests decreases with increasing variability in nest temperature. The model, if verified by controlled experiments, has important implications for our understanding of temperature-dependent sex determination in natural nests. Both mean nest temperature and "hours spent above the threshold" will be poor predictors of hatchling sex ratios. Studies designed to investigate latitudinal trends and inter-specific differences in the threshold temperature will need to consider latitudinal and inter-specific variation in the magnitude of diel fluctuations in nest temperature, and variation in factors influencing the magnitude of those fluctuations, such as nest depth. Furthermore, any factor that modifies the relationship between developmental rate and temperature can be expected to influence hatchling sex ratios in natural nests, especially when nest temperatures are close to the threshold.

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera.

PubMed

Meireles, Ricardo Camargos de; Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F; Fernandes, Raphael B A; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common.

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera

PubMed Central

Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F.; Fernandes, Raphael B. A.; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common. PMID:29381768

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

PubMed

Spadafore, Maxwell; Najarian, Kayvan; Boyle, Alan P

2017-11-29

Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, these methods provide no information describing how TFs interact with one another when they do bind. TFs tend to bind the genome in clusters, and current methods to identify these clusters are either limited in scope, unable to detect relationships beyond motif similarity, or not applied to TF-TF interactions. Here, we present a proximity-based graph clustering approach to identify TF clusters using either ChIP-seq or motif search data. We use TF co-occurrence to construct a filtered, normalized adjacency matrix and use the Markov Clustering Algorithm to partition the graph while maintaining TF-cluster and cluster-cluster interactions. We then apply our graph structure beyond clustering, using it to increase the accuracy of motif-based TFBS searching for an example TF. We show that our method produces small, manageable clusters that encapsulate many known, experimentally validated transcription factor interactions and that our method is capable of capturing interactions that motif similarity methods might miss. Our graph structure is able to significantly increase the accuracy of motif TFBS searching, demonstrating that the TF-TF connections within the graph correlate with biological TF-TF interactions. The interactions identified by our method correspond to biological reality and allow for fast exploration of TF clustering and regulatory dynamics.

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations

NASA Technical Reports Server (NTRS)

Shapiro, Bruce E.; Levchenko, Andre; Meyerowitz, Elliot M.; Wold, Barbara J.; Mjolsness, Eric D.

2003-01-01

Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions and transcriptional activation. Multi-compartment systems are represented as graphs with STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or output as systems of equations that can be read by other programs. Cellerator simulations are fully extensible and portable to any operating system that supports Mathematica, and can be indefinitely nested within larger data structures to produce highly scaleable models.

A Scalable Distributed Syntactic, Semantic, and Lexical Language Model

DTIC Science & Technology

2012-09-01

Here pa(τ) denotes the set of parent states of τ. If the recursive factorization refers to a graph , then we have a Bayesian network (Lauritzen 1996...Broadly speaking, however, the recursive factorization can refer to a representation more complicated than a graph with a fixed set of nodes and edges...factored language (FL) model (Bilmes and Kirchhoff 2003) is close to the smoothing technique we propose here, the major difference is that FL

Enclosed nests may provide greater thermal than nest predation benefits compared with open nests across latitudes

USGS Publications Warehouse

Martin, Thomas E.; Boyce, Andy J.; Fierro-Calderon, Karolina; Mitchell, Adam E.; Armstad, Connor E.; Mouton, James C.; Bin Soudi, Evertius E.

2017-01-01

Nest structure is thought to provide benefits that have fitness consequences for several taxa. Traditionally, reduced nest predation has been considered the primary benefit underlying evolution of nest structure, whereas thermal benefits have been considered a secondary or even non-existent factor. Yet, the relative roles of these factors on nest structures remain largely unexplored.Enclosed nests have a constructed or natural roof connected to sides that allow a restricted opening or tube entrance that provides cover in all directions except the entrance, whereas open nests are cups or platforms that are open above. We show that construction of enclosed nests is more common among songbirds (Passeriformes) in tropical and southern hemisphere regions than in north temperate regions. This geographic pattern may reflect selection from predation risk, under long-standing assumptions that nest predation rates are higher in southern regions and that enclosed nests reduce predation risk compared with open cup nests. We therefore compared nest predation rates between enclosed vs. open nests in 114 songbird species that do not nest in tree holes among five communities of coexisting birds, and for 205 non-hole-nesting species from the literature, across northern temperate, tropical, and southern hemisphere regions.Among coexisting species, enclosed nests had lower nest predation rates than open nests in two south temperate sites, but not in either of two tropical sites or a north temperate site. Nest predation did not differ between nest types at any latitude based on literature data. Among 319 species from both our field studies and the literature, enclosed nests did not show consistent benefits of reduced predation and, in fact, predation was not consistently higher in the tropics, contrary to long-standing perspectives.Thermal benefits of enclosed nests were indicated based on three indirect results. First, species that built enclosed nests were smaller than species using open nests both among coexisting species and among species from the literature. Smaller species lose heat fastest and thereby may gain important thermal benefits from reduced convective cooling. Second, eggs were warmed by parents for less time in species with enclosed nests, as can be expected if egg cooling rates are slower. Finally, species using enclosed nests exhibited enhanced growth of mass and wings compared with species using open nests, suggesting reduced thermoregulatory costs allowed increased energy for growth.Enclosed nests may therefore provide more consistent thermal than nest predation benefits, counter to long-standing perspectives.

Nest tree use by the endangered Virginia northern flying squirrel in the central Appalachian Mountains

Treesearch

Jennifer M. Menzel; W. Mark Ford; John W. Edwards; Michael A. Menzel

2004-01-01

Little is known about nest tree use of the endangered Virginia northern flying squirrel (Glaucomys sabrinus fuscus). Because nesting sites could be a limiting factor, it is important to understand the denning ecology to further manage and protect this subspecies. We compared characteristics of nest trees used by Virginia northern flying squirrels...

Factors influencing depredation of artificial duck nests

USGS Publications Warehouse

Esler, Daniel N.; Grand, James B.

1993-01-01

Because artificial nests can facilitate controlled experiments of nest success, we used them to assess whether human visitation, nest density, vegetation structure, and proximity to habitat edge could affect depredation of duck nests on Yukon Flats National Wildlife Refuge, Alaska. More (P < 0.01) nests in a plot visited daily (100%) were depredated than those in plots visited at intervals of 7 (40%), 14 (35%), or 28 days (45%). More (P < 0.01) nests were depredated in a plot with 10 nests/ha (95%) than nests in a plot of a lower density (2/ha; 40%). Vegetation height, vegetation density, distance to a wetland, distance to forest edge, or distance to the nearest ecotone did not differ (P > 0.05) between depredated and undisturbed nests. We suggest that daily visitation of duck nests increases depredation, but longer intervals, typical of most nest studies, do not. High nesting densities, which could occur when flooding limits nesting habitat, may result in higher depredation rates.

Use of artificial nests to investigate predation on freshwater turtle nests

Treesearch

Michael N. Marchand; John A. Litvaitis; Thomas J. Maier; Richard M. DeGraaf

2002-01-01

Habitat fragmentation has raised concerns that populations of generalist predators have increased and are affecting a diverse group of prey. Previous research has included the use of artificial nests to investigate the role of predation on birds that nest on or near the ground. Because predation also is a major factor limiting populations of freshwater turtles, we...

The nest-concealment hypothesis: New insights from a comparative analysis

USGS Publications Warehouse

Borgmann, Kathi L.; Conway, Courtney J.

2015-01-01

Selection of a breeding site is critical for many animals, especially for birds whose offspring are stationary during development. Thus, birds are often assumed to prefer concealed nest sites. However, 74% of studies (n = 106) that have evaluated this relationship for open-cup nesting songbirds in North America failed to support the nest-concealment hypothesis. We conducted a comparative analysis to identify factors that contribute to variation in the ability of researchers to find support for the nest-concealment hypothesis. We found that some of the discrepancy among studies can be explained by interspecific differences in morphological and extrinsic factors that affect nest predation. Moreover, methods that investigators used to estimate concealment affected whether studies found support for the nest-concealment hypothesis; 33% of the studies that used quantitative estimates found support for the nest-concealment hypothesis whereas only 10% of the studies that used qualitative estimates found support. The timing of measurements also explained some of the ambiguity; studies that provided little information regarding the timing of their foliage density estimates were less likely to support the nest-concealment hypothesis. Species with more conspicuous male plumage were less likely to support the nest-concealment hypothesis when we analyzed studies that used visual estimates. Whereas species with more conspicuous female plumage were more likely to support the nest-concealment hypothesis when we analyzed studies that used quantitative measures. Our results demonstrate that support for the nest-concealment hypothesis has been equivocal, but that some of the ambiguity can be explained by morphological traits and methods used to measure concealment.

Factors affecting detection of burrowing owl nests during standardized surveys

USGS Publications Warehouse

Conway, C.J.; Garcia, V.; Smith, M.D.; Hughes, K.

2008-01-01

Identifying causes of declines and evaluating effects of management practices on persistence of local populations of burrowing owls (Athene cunicularia) requires accurate estimates of abundance and population trends. Moreover, regulatory agencies in the United States and Canada typically require surveys to detect nest burrows prior to approving developments or other activities in areas that are potentially suitable for nesting burrowing owls. In general, guidelines on timing of surveys have been lacking and surveys have been conducted at different times of day and in different stages of the nesting cycle. We used logistic regression to evaluate 7 factors that could potentially affect probability of a surveyor detecting a burrowing owl nest. We conducted 1,444 detection trials at 323 burrowing owl nests within 3 study areas in Washington and Wyoming, USA, between February and August 2000-2002. Detection probability was highest during the nestling period and increased with ambient temperature. The other 5 factors that we examined (i.e., study area, time of day, timing within the breeding season, wind speed, % cloud cover) interacted with another factor to influence detection probability. Use of call-broadcast surveys increased detection probability, even during daylight hours when we detected >95% of owls visually. Optimal timing of surveys will vary due to differences in breeding phenology and differences in nesting behavior across populations. Nevertheless, we recommend ???3 surveys per year: one that coincides with the laying and incubation period, another that coincides with the early nestling period, and a third that coincides with the late nestling period. In northern latitudes, surveys can be conducted throughout the day.

Massive Scale Cyber Traffic Analysis: A Driver for Graph Database Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joslyn, Cliff A.; Choudhury, S.; Haglin, David J.

2013-06-19

We describe the significance and prominence of network traffic analysis (TA) as a graph- and network-theoretical domain for advancing research in graph database systems. TA involves observing and analyzing the connections between clients, servers, hosts, and actors within IP networks, both at particular times and as extended over times. Towards that end, NetFlow (or more generically, IPFLOW) data are available from routers and servers which summarize coherent groups of IP packets flowing through the network. IPFLOW databases are routinely interrogated statistically and visualized for suspicious patterns. But the ability to cast IPFLOW data as a massive graph and query itmore » interactively, in order to e.g.\\ identify connectivity patterns, is less well advanced, due to a number of factors including scaling, and their hybrid nature combining graph connectivity and quantitative attributes. In this paper, we outline requirements and opportunities for graph-structured IPFLOW analytics based on our experience with real IPFLOW databases. Specifically, we describe real use cases from the security domain, cast them as graph patterns, show how to express them in two graph-oriented query languages SPARQL and Datalog, and use these examples to motivate a new class of "hybrid" graph-relational systems.« less

Toward the optimization of normalized graph Laplacian.

PubMed

Xie, Bo; Wang, Meng; Tao, Dacheng

2011-04-01

Normalized graph Laplacian has been widely used in many practical machine learning algorithms, e.g., spectral clustering and semisupervised learning. However, all of them use the Euclidean distance to construct the graph Laplacian, which does not necessarily reflect the inherent distribution of the data. In this brief, we propose a method to directly optimize the normalized graph Laplacian by using pairwise constraints. The learned graph is consistent with equivalence and nonequivalence pairwise relationships, and thus it can better represent similarity between samples. Meanwhile, our approach, unlike metric learning, automatically determines the scale factor during the optimization. The learned normalized Laplacian matrix can be directly applied in spectral clustering and semisupervised learning algorithms. Comprehensive experiments demonstrate the effectiveness of the proposed approach.

Factors influencing nesting success of king eiders on northern Alaska's Coastal Plain

USGS Publications Warehouse

Bentzen, R.L.; Powell, A.N.; Suydam, R.S.

2008-01-01

King eider (Somateria spectabilis) populations have declined markedly in recent decades for unknown reasons. Nest survival is one component of recruitment, and a female's chance of reproductive success increases with her ability to choose an appropriate nesting strategy. We estimated variation in daily nest survival of king eiders at 2 sites, Teshekpuk and Kuparuk, Alaska, USA, 2002-2005. We evaluated both a priori and exploratory competing models of nest survival that considered importance of nest concealment, seclusion, and incubation constancy as strategies to avoid 2 primary egg predators, avian (Larus spp., Stercorarius spp., and Corvus corax) and fox (Alopex lagopus). We used generalized nonlinear techniques to examine factors affecting nest survival rates and information-theoretic approaches to select among competing models. Estimated nest survival, accounting for a nest visitation effect, varied considerably across sites and years (0.21-0.57); however, given our small sample size, much of this variation maybe attributable to sampling variation (??process = 0.007, 95% CI: 0.003-0.070). Nest survival was higher at Kuparuk than Teshekpuk in all years; however, due to the correlative nature of our data, we cannot determine the underlying causes with any certainty. We found mixed support for the concealed breeding strategy, females derived no benefit from nesting in areas with more willow (Salix spp.; measure of concealment) except that the observer effect diminished as willow cover increased. We suggest these patterns are due to conflicting predation pressures. Nest survival was not higher on islands (measure of seclusion) or with increased incubation constancy but was higher post-fox removal, indicating that predator control on breeding grounds could be a viable management option. Nest survival was negatively affected by our nest visitations, most likely by exposing the nest to avian scavengers. We recommend precautions be taken to limit the effects of nest visits in future studies and to consider them as a possible negative bias in estimated nest survival. Future models of the impacts of development within the breeding grounds of king eider should consider the influence of humans in the vicinity of nests.

Structure and strategy in encoding simplified graphs

NASA Technical Reports Server (NTRS)

Schiano, Diane J.; Tversky, Barbara

1992-01-01

Tversky and Schiano (1989) found a systematic bias toward the 45-deg line in memory for the slopes of identical lines when embedded in graphs, but not in maps, suggesting the use of a cognitive reference frame specifically for encoding meaningful graphs. The present experiments explore this issue further using the linear configurations alone as stimuli. Experiments 1 and 2 demonstrate that perception and immediate memory for the slope of a test line within orthogonal 'axes' are predictable from purely structural considerations. In Experiments 3 and 4, subjects were instructed to use a diagonal-reference strategy in viewing the stimuli, which were described as 'graphs' only in Experiment 3. Results for both studies showed the diagonal bias previously found only for graphs. This pattern provides converging evidence for the diagonal as a cognitive reference frame in encoding linear graphs, and demonstrates that even in highly simplified displays, strategic factors can produce encoding biases not predictable solely from stimulus structure alone.

Embryonic death is linked to maternal identity in the leatherback turtle (Dermochelys coriacea).

PubMed

Rafferty, Anthony R; Santidrián Tomillo, Pilar; Spotila, James R; Paladino, Frank V; Reina, Richard D

2011-01-01

Leatherback turtles have an average global hatching success rate of ~50%, lower than other marine turtle species. Embryonic death has been linked to environmental factors such as precipitation and temperature, although, there is still a lot of variability that remains to be explained. We examined how nesting season, the time of nesting each season, the relative position of each clutch laid by each female each season, maternal identity and associated factors such as reproductive experience of the female (new nester versus remigrant) and period of egg retention between clutches (interclutch interval) affected hatching success and stage of embryonic death in failed eggs of leatherback turtles nesting at Playa Grande, Costa Rica. Data were collected during five nesting seasons from 2004/05 to 2008/09. Mean hatching success was 50.4%. Nesting season significantly influenced hatching success in addition to early and late stage embryonic death. Neither clutch position nor nesting time during the season had a significant affect on hatching success or the stage of embryonic death. Some leatherback females consistently produced nests with higher hatching success rates than others. Remigrant females arrived earlier to nest, produced more clutches and had higher rates of hatching success than new nesters. Reproductive experience did not affect stage of death or the duration of the interclutch interval. The length of interclutch interval had a significant affect on the proportion of eggs that failed in each clutch and the developmental stage they died at. Intrinsic factors such as maternal identity are playing a role in affecting embryonic death in the leatherback turtle.

A Graph is Worth a Thousand Words: How Overconfidence and Graphical Disclosure of Numerical Information Influence Financial Analysts Accuracy on Decision Making

PubMed Central

Leite, Rodrigo Oliveira; de Aquino, André Carlos Busanelli

2016-01-01

Previous researches support that graphs are relevant decision aids to tasks related to the interpretation of numerical information. Moreover, literature shows that different types of graphical information can help or harm the accuracy on decision making of accountants and financial analysts. We conducted a 4×2 mixed-design experiment to examine the effects of numerical information disclosure on financial analysts’ accuracy, and investigated the role of overconfidence in decision making. Results show that compared to text, column graph enhanced accuracy on decision making, followed by line graphs. No difference was found between table and textual disclosure. Overconfidence harmed accuracy, and both genders behaved overconfidently. Additionally, the type of disclosure (text, table, line graph and column graph) did not affect the overconfidence of individuals, providing evidence that overconfidence is a personal trait. This study makes three contributions. First, it provides evidence from a larger sample size (295) of financial analysts instead of a smaller sample size of students that graphs are relevant decision aids to tasks related to the interpretation of numerical information. Second, it uses the text as a baseline comparison to test how different ways of information disclosure (line and column graphs, and tables) can enhance understandability of information. Third, it brings an internal factor to this process: overconfidence, a personal trait that harms the decision-making process of individuals. At the end of this paper several research paths are highlighted to further study the effect of internal factors (personal traits) on financial analysts’ accuracy on decision making regarding numerical information presented in a graphical form. In addition, we offer suggestions concerning some practical implications for professional accountants, auditors, financial analysts and standard setters. PMID:27508519

A Graph is Worth a Thousand Words: How Overconfidence and Graphical Disclosure of Numerical Information Influence Financial Analysts Accuracy on Decision Making.

PubMed

Cardoso, Ricardo Lopes; Leite, Rodrigo Oliveira; de Aquino, André Carlos Busanelli

2016-01-01

Previous researches support that graphs are relevant decision aids to tasks related to the interpretation of numerical information. Moreover, literature shows that different types of graphical information can help or harm the accuracy on decision making of accountants and financial analysts. We conducted a 4×2 mixed-design experiment to examine the effects of numerical information disclosure on financial analysts' accuracy, and investigated the role of overconfidence in decision making. Results show that compared to text, column graph enhanced accuracy on decision making, followed by line graphs. No difference was found between table and textual disclosure. Overconfidence harmed accuracy, and both genders behaved overconfidently. Additionally, the type of disclosure (text, table, line graph and column graph) did not affect the overconfidence of individuals, providing evidence that overconfidence is a personal trait. This study makes three contributions. First, it provides evidence from a larger sample size (295) of financial analysts instead of a smaller sample size of students that graphs are relevant decision aids to tasks related to the interpretation of numerical information. Second, it uses the text as a baseline comparison to test how different ways of information disclosure (line and column graphs, and tables) can enhance understandability of information. Third, it brings an internal factor to this process: overconfidence, a personal trait that harms the decision-making process of individuals. At the end of this paper several research paths are highlighted to further study the effect of internal factors (personal traits) on financial analysts' accuracy on decision making regarding numerical information presented in a graphical form. In addition, we offer suggestions concerning some practical implications for professional accountants, auditors, financial analysts and standard setters.

Seven Wonders of the Ancient and Modern Quadratic World.

ERIC Educational Resources Information Center

Taylor, Sharon E.; Mittag, Kathleen Cage

2001-01-01

Presents four methods for solving a quadratic equation using graphing calculator technology: (1) graphing with the CALC feature; (2) quadratic formula program; (3) table; and (4) solver. Includes a worksheet for a lab activity on factoring quadratic equations. (KHR)

Influences of Species Interactions With Aggressive Ants and Habitat Filtering on Nest Colonization and Community Composition of Arboreal Twig-Nesting Ants.

PubMed

Philpott, Stacy M; Serber, Zachary; De la Mora, Aldo

2018-04-05

Ant community assembly is driven by many factors including species interactions (e.g., competition, predation, parasitism), habitat filtering (e.g., vegetation differences, microclimate, food and nesting resources), and dispersal. Canopy ant communities, including dominant and twig-nesting ants, are structured by all these different factors, but we know less about the impacts of species interactions and habitat filters acting at the colonization or recruitment stage. We examined occupation of artificial twig nests placed in shade trees in coffee agroecosystems. We asked whether species interactions-aggression from the dominant canopy ant, Azteca sericeasur Longino (Hymenoptera: Formicidae)-or habitat filtering-species of tree where nests were placed or surrounding vegetation-influence colonization, species richness, and community composition of twig-nesting ants. We found 20 species of ants occupying artificial nests. Nest occupation was lower on trees with A. sericeasur, but did not differ depending on tree species or surrounding vegetation. Yet, there were species-specific differences in occupation depending on A. sericeasur presence and tree species. Ant species richness did not vary with A. sericeasur presence or tree species. Community composition varied with A. sericeasur presence and surrounding vegetation. Our results suggest that species interactions with dominant ants are important determinants of colonization and community composition of twig-nesting ants. Habitat filtering at the level of tree species did not have strong effects on twig-nesting ants, but changes in coffee management may contribute to differences in community composition with important implications for ant conservation in agricultural landscapes, as well as biological control of coffee pests.

Catastrophic health expenditure: a comparative analysis of empty-nest and non-empty-nest households with seniors in Shandong, China.

PubMed

Yang, Tingting; Chu, Jie; Zhou, Chengchao; Medina, Alexis; Li, Cuicui; Jiang, Shan; Zheng, Wengui; Sun, Liyuan; Liu, Jing

2016-07-05

The aim of this study was to compare the catastrophic health expenditure (CHE) prevalence and its determinants between empty-nest and non-empty-nest elderly households. Shandong province of China. A total of 2761 elderly households are included in the analysis. CHE incidence among elderly households was 44.9%. The CHE incidence of empty-nest singles (59.3%, p=0.000, OR=3.19) and empty-nest couples (52.9%, p=0.000, OR=2.45) are both statistically higher than that of non-empty-nest elderly households (31.4%). An inverse association was observed between CHE incidence and income level in all elderly household types. Factors including 1 or more household elderly members with non-communicable chronic diseases in the past 6 months, 1 or more elderly household members being hospitalised in the past year and lower household income, are significant risk factors for CHE in all 3 household types (p<0.05). Health insurance status was found to be a significant determinant of CHE among empty-nest singles and non-empty-nest households (p<0.05). CHE incidence among elderly households is high in China. Empty-nest households are at higher risk for CHE than non-empty-nest households. Based on these findings, we suggest that special insurance be developed to broaden the coverage of health services and heighten the reimbursement rate for empty-nest elderly in the existing health insurance schemes. Financial and social protection interventions are also essential for identified at-risk subgroups among different types of elderly households. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Catastrophic health expenditure: a comparative analysis of empty-nest and non-empty-nest households with seniors in Shandong, China

PubMed Central

Yang, Tingting; Chu, Jie; Zhou, Chengchao; Medina, Alexis; Li, Cuicui; Jiang, Shan; Zheng, Wengui; Sun, Liyuan; Liu, Jing

2016-01-01

Objective The aim of this study was to compare the catastrophic health expenditure (CHE) prevalence and its determinants between empty-nest and non-empty-nest elderly households. Setting Shandong province of China. Participants A total of 2761 elderly households are included in the analysis. Results CHE incidence among elderly households was 44.9%. The CHE incidence of empty-nest singles (59.3%, p=0.000, OR=3.19) and empty-nest couples (52.9%, p=0.000, OR=2.45) are both statistically higher than that of non-empty-nest elderly households (31.4%). An inverse association was observed between CHE incidence and income level in all elderly household types. Factors including 1 or more household elderly members with non-communicable chronic diseases in the past 6 months, 1 or more elderly household members being hospitalised in the past year and lower household income, are significant risk factors for CHE in all 3 household types (p<0.05). Health insurance status was found to be a significant determinant of CHE among empty-nest singles and non-empty-nest households (p<0.05). Conclusions CHE incidence among elderly households is high in China. Empty-nest households are at higher risk for CHE than non-empty-nest households. Based on these findings, we suggest that special insurance be developed to broaden the coverage of health services and heighten the reimbursement rate for empty-nest elderly in the existing health insurance schemes. Financial and social protection interventions are also essential for identified at-risk subgroups among different types of elderly households. PMID:27381206

Population-specific demographic estimates provide insights into declines of Lark Buntings (Calamospiza melanocorys)

USGS Publications Warehouse

Yackel Adams, A.A.; Skagen, S.K.; Savidge, J.A.

2007-01-01

Many North American prairie bird populations have recently declined, and the causes of these declines remain largely unknown. To determine whether population limitation occurs during breeding, we evaluated the stability of a population of prairie birds using population-specific values for fecundity and postfledging survival. During 2001-2003, we radiomarked 67 female Lark Buntings (Calamospiza melanocorys) to determine annual fecundity and evaluate contributing factors such as nest survival and breeding response (number of breeding attempts and dispersal). Collectively, 67 females built 112 nests (1.67 ± 0.07 nests female−1 season−1; range: 1–3); 34 were second nests and 11 were third nests. Daily nest survival estimates were similar for initial and later nests with overall nest survival (DSR19) of 30.7% and 31.7%, respectively. Nest predation was the most common cause of failure (92%). Capture and radiomarking of females did not affect nest survival. Lark Bunting dispersal probabilities increased among females that fledged young from initial nests and females that lost their original nests late in the season. Conservative and liberal estimates of mean annual fecundity were 0.96 ±0.11 and 1.24 ± 0.09 female offspring per female, respectively. Given the fecundity and juvenile-survival estimates for this population, annual adult survival values of 71–77% are necessary to achieve a stable population. Because adult survival of prairie passerines ranges between 55% and 65%, this study area may not be capable of sustaining a stable population in the absence of immigration. We contrast our population assessment with one that assumes indirect values of fecundity and juvenile survival. To elucidate limiting factors, estimation of population-specific demographic parameters is desirable. We present an approach for selecting species and areas for evaluation of population stability.

Landscape alterations influence differential habitat use of nesting buteos and ravens within sagebrush ecosystem: implications for transmission line development

USGS Publications Warehouse

Coates, Peter S.; Howe, Kristy B.; Casazza, Michael L.; Delehanty, David J.

2014-01-01

A goal in avian ecology is to understand factors that influence differences in nesting habitat and distribution among species, especially within changing landscapes. Over the past 2 decades, humans have altered sagebrush ecosystems as a result of expansion in energy production and transmission. Our primary study objective was to identify differences in the use of landscape characteristics and natural and anthropogenic features by nesting Common Ravens (Corvus corax) and 3 species of buteo (Swainson's Hawk [Buteo swainsoni], Red-tailed Hawk [B. jamaicensis], and Ferruginous Hawk [B. regalis]) within a sagebrush ecosystem in southeastern Idaho. During 2007–2009, we measured multiple environmental factors associated with 212 nest sites using data collected remotely and in the field. We then developed multinomial models to predict nesting probabilities by each species and predictive response curves based on model-averaged estimates. We found differences among species related to nesting substrate (natural vs. anthropogenic), agriculture, native grassland, and edge (interface of 2 cover types). Most important, ravens had a higher probability of nesting on anthropogenic features (0.80) than the other 3 species (Artemisia spp.), favoring increased numbers of nesting ravens and fewer nesting Ferruginous Hawks. Our results indicate that habitat alterations, fragmentation, and forthcoming disturbances anticipated with continued energy development in sagebrush steppe ecosystems can lead to predictable changes in raptor and raven communities.

Nest success of snowy plovers (Charadrius nivosus) in the Southern high plains of Texas

USGS Publications Warehouse

Saalfeld, S.T.; Conway, Warren C.; Haukos, D.A.; Johnson, W.P.

2011-01-01

Snowy Plovers (Charadrius nivosus) nesting on edges of saline lakes within the Southern High Plains (SHP) of Texas are threatened by habitat degradation due to reduced artesian spring flow, making many saline lakes unsuitable for nesting and migrating shorebirds. Factors influencing nest success were evaluated, current nest success estimates in the SHP of Texas were compared to estimates obtained ten years prior, and causes and timing of nest failures determined. Overall, 215 nests were monitored from three saline lakes in 20082009, with nest success estimates from Program MARK ranging from 7-33% ( x??= 22%). The leading causes of nest failures were attributed to predation (40%) and weather (36%). Nest success was negatively influenced by number of plants within 707-cm 2 plot, positively influenced by percent surface water availability, and at one saline lake, negatively influenced by day during the nesting season (i.e., nest success declined later in the nesting season). When compared to estimates ten years prior (19981999), mean nest success has declined by 31%. If nesting Snowy Plovers continue to experience increased predation rates, decreased hydrological integrity, and habitat alterations, populations will continue to decline throughout this region.

Discovery of a new Kittlitz's murrelet nest: Clues to habitat selection and nest-site fidelity

USGS Publications Warehouse

Piatt, John F.; Naslund, Nancy L.; van Pelt, Thomas I.

1999-01-01

On 13 June 1993, a new Kittlitz's murrelet (Brachyramphus brevirostris) nest was discovered near Red Mountain on the Kenai Peninsula, Alaska. The nest was on a 22° slope at about 900 m elevation with a northeast aspect, and contained a 60.2 × 40.6 mm egg that weighed 49.0 g. Downy feathers and weathered fecal material found at the nest indicated re-use from a previous year, suggesting possible nest site fidelity. The nest was located in an area scoured by winds and free of snow during early spring, suggesting that this may be an important mesoscale factor influencing selection of nesting habitat. Proximity to suitable foraging habitat, particularly sheltered bays and glacial river outflows, may affect breeding habitat choice over larger spatial scales.

Factors associated with duck nest success in the prairie pothole region of Canada

USGS Publications Warehouse

Greenwood, Raymond J.; Sargeant, Alan B.; Johnson, Douglas H.; Cowardin, Lewis M.; Shaffer, Terry L.

1995-01-01

Populations of some dabbling ducks have declined sharply in recent decades and information is needed to understand reasons for this. During 1982-85, we studied duck nesting for 1-4 years in 17 1.6 by 16.0-km, high-density duck areas in the Prairie Pothole Region (PPR) of Canada, 9 in parkland and 8 in prairie. We estimated nest-initiation dates, habitat preferences, nest success, and nest fates for mallards (Anas platyrhynchos), gadwalls (A. strepera), blue-winged teals (A. discors), northern shovelers (A. clypeata), and northern pintails (A. acuta). We also examined the relation of mallard production to geographic and temporal variation in wetlands, breeding populations, nesting effort, and hatch rate.Average periods of nest initiation were similar for mallards and northern pintails, and nearly twice as long as those of gadwalls, blue-winged teals, and northern shovelers. Median date of nest initiation was related to presence of wet wetlands (contained visible standing water), spring precipitation, and May temperature. Length of initiation period was related to presence of wet wetlands and precipitation in May, June temperature, and nest success; it was negatively related overall to drought that prevailed over much of Prairie Canada during the study, especially in 1984.Mallards, gadwalls, and northern pintails nested most often in brush in native grassland, blue-winged teals in road rights-of-way, and northern shovelers in hayfields and small (< 2 ha) untilled tracts of upland habitat (hereafter called Odd area). Among 8 habitat classes that composed all suitable nesting habitat of each study area, nest success estimates averaged 25% in Woodland, 19% in Brush, 18% in Hayland, 16% in Wetland, 15% in Grass, 11% in Odd area, 8% in Right-of-way, and 2% in Cropland. We detected no significant difference in nest success among species: mallard (11%), gadwall (14%), blue-winged teal (15%), northern shoveler (12%), and northern pintail (7%). Annual nest success (pooled by study area and averaged [unweighted] over all study areas) was 17% in 1982, 15% in 1983, 7% in 1984, and 14% in 1985.We estimated that predators destroyed 72% of mallard, gadwall, blue-winged teal, and northern shoveler nests and 65% of northern pintail nests. In prairie, average nest success decreased about 4 percentage points for every 10 percentage points increase in Cropland, suggesting that under conditions of 1982-85, local populations of these species probably were not stable when Cropland exceeded about 56% of available habitat. We found recent remains of 573 dead ducks during 1983-85; most were females (Anas spp.) apparently killed by predators. In some years, mallards and northern pintails were more numerous among dead ducks than we expected. More females than males were found dead among mallards and northern shovelers, suggesting higher vulnerability of females. Of factors we examined, nest-success rate appeared to be the most influential factor in determining mallard production. Nest success varied both geographically and annually.

Factors influencing nest survival and productivity of Red-throated Loons (Gavia stellata) in Alaska

USGS Publications Warehouse

Rizzolo, Daniel; Schmutz, Joel A.; McCloskey, Sarah E.; Fondell, Thomas F.

2014-01-01

Red-throated Loon (Gavia stellata) numbers in Alaska have fluctuated dramatically over the past 3 decades; however, the demographic processes contributing to these population dynamics are poorly understood. To examine spatial and temporal variation in productivity, we estimated breeding parameters at 5 sites in Alaska: at Cape Espenberg and the Copper River Delta we estimated nest survival, and at 3 sites within the Yukon-Kuskokwim Delta we estimated nest survival and productivity. Nest survival varied broadly among sites and years; annual estimates (lower, upper 95% confidence interval) ranged from 0.09 (0.03, 0.29) at Cape Espenberg in 2001 to 0.93 (0.76, 0.99) at the Copper River Delta in 2002. Annual variation among sites was not concordant, suggesting that site-scale factors had a strong influence on nest survival. Models of nest survival indicated that visits to monitor nests had a negative effect on nest daily survival probability, which if not accounted for biased nest survival strongly downward. The sensitivity of breeding Red-throated Loons to nest monitoring suggests other sources of disturbance that cause incubating birds to flush from their nests may also reduce nest survival. Nest daily survival probability at the Yukon-Kuskokwim Delta was negatively associated with an annual index of fox occurrence. Survival through the incubation and chick-rearing periods on the Yukon-Kuskokwim Delta ranged from 0.09 (0.001, 0.493) to 0.50 (0.04, 0.77). Daily survival probability during the chick-rearing period was lower for chicks that had a sibling in 2 of 3 years, consistent with the hypothesis that food availability was limited. Estimates of annual productivity on the Yukon-Kuskokwim Delta ranged from 0.17 to 1.0 chicks per pair. Productivity was not sufficient to maintain population stability in 2 of 3 years, indicating that nest depredation by foxes and poor foraging conditions during chick rearing can have important effects on productivity.

Counting the number of Feynman graphs in QCD

NASA Astrophysics Data System (ADS)

Kaneko, T.

2018-05-01

Information about the number of Feynman graphs for a given physical process in a given field theory is especially useful for confirming the result of a Feynman graph generator used in an automatic system of perturbative calculations. A method of counting the number of Feynman graphs with weight of symmetry factor was established based on zero-dimensional field theory, and was used in scalar theories and QED. In this article this method is generalized to more complicated models by direct calculation of generating functions on a computer algebra system. This method is applied to QCD with and without counter terms, where many higher order are being calculated automatically.

Marsh nesting by mallards

USGS Publications Warehouse

Krapu, G.L.; Talent, L.G.; Dwyer, T.J.

1979-01-01

Nest-site selection by mallard (Anas platyrhynchos) hens was studied on a 52-km2, privately owned area in the Missouri Coteau of south-central North Dakota during 1974-77. Sixty-six percent of 53 nests initiated by radio-marked and unmarked hens were in wetlands in dense stands of emergent vegetation and usually within 50 m of the wetland edge. These findings and other sources of information suggest that significant numbers of mallards breeding in the Prairie Pothole Region nest in marsh habitat. Potential factors contributing to mallard use of marsh habitat for nesting purposes are discussed. Management considerations associated with marsh nesting by mallards are described and research needs are identified.

Probabilistic graphs as a conceptual and computational tool in hydrology and water management

NASA Astrophysics Data System (ADS)

Schoups, Gerrit

2014-05-01

Originally developed in the fields of machine learning and artificial intelligence, probabilistic graphs constitute a general framework for modeling complex systems in the presence of uncertainty. The framework consists of three components: 1. Representation of the model as a graph (or network), with nodes depicting random variables in the model (e.g. parameters, states, etc), which are joined together by factors. Factors are local probabilistic or deterministic relations between subsets of variables, which, when multiplied together, yield the joint distribution over all variables. 2. Consistent use of probability theory for quantifying uncertainty, relying on basic rules of probability for assimilating data into the model and expressing unknown variables as a function of observations (via the posterior distribution). 3. Efficient, distributed approximation of the posterior distribution using general-purpose algorithms that exploit model structure encoded in the graph. These attributes make probabilistic graphs potentially useful as a conceptual and computational tool in hydrology and water management (and beyond). Conceptually, they can provide a common framework for existing and new probabilistic modeling approaches (e.g. by drawing inspiration from other fields of application), while computationally they can make probabilistic inference feasible in larger hydrological models. The presentation explores, via examples, some of these benefits.

Ground-nesting by the chimpanzees of the Nimba Mountains, Guinea: environmentally or socially determined?

PubMed

Koops, Kathelijne; Humle, Tatyana; Sterck, Elisabeth H M; Matsuzawa, Tetsuro

2007-04-01

The chimpanzees (Pan troglodytes verus) of the Nimba Mountains, Guinea, West Africa, commonly make both elaborate ("night") and simple ("day") nests on the ground. In this study we investigated which factors might influence ground-nesting in this population, and tested two ecological hypotheses: 1) climatic conditions, such as high wind speeds at high altitudes, may deter chimpanzees from nesting in trees; and 2) a lack of appropriate arboreal nesting opportunities may drive the chimpanzees to nest on the ground. In addition to testing these two hypotheses, we explored whether ground-nesting is a sex-linked behavior. Data were collected monthly between August 2003 and May 2004 along transects and ad libitum. To identify the sex of ground-nesting individuals, we used DNA extracted from hair samples. The results showed that the occurrence and distribution of ground nests were not affected by climatic conditions or a lack of appropriate nest trees. Support was found for the notion that ground-nesting is a sex-linked behavior, as males were responsible for building all of the elaborate ground nests and most of the simple ground nests sampled. Elaborate ground nests occurred mostly in nest groups associated with tree nests, whereas simple ground nests usually occurred without tree nests in their vicinity. These results suggest that ground-nesting may be socially, rather than ecologically, determined.

Complexity and approximability for a problem of intersecting of proximity graphs with minimum number of equal disks

NASA Astrophysics Data System (ADS)

Kobylkin, Konstantin

2016-10-01

Computational complexity and approximability are studied for the problem of intersecting of a set of straight line segments with the smallest cardinality set of disks of fixed radii r > 0 where the set of segments forms straight line embedding of possibly non-planar geometric graph. This problem arises in physical network security analysis for telecommunication, wireless and road networks represented by specific geometric graphs defined by Euclidean distances between their vertices (proximity graphs). It can be formulated in a form of known Hitting Set problem over a set of Euclidean r-neighbourhoods of segments. Being of interest computational complexity and approximability of Hitting Set over so structured sets of geometric objects did not get much focus in the literature. Strong NP-hardness of the problem is reported over special classes of proximity graphs namely of Delaunay triangulations, some of their connected subgraphs, half-θ6 graphs and non-planar unit disk graphs as well as APX-hardness is given for non-planar geometric graphs at different scales of r with respect to the longest graph edge length. Simple constant factor approximation algorithm is presented for the case where r is at the same scale as the longest edge length.

Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican parrot

USGS Publications Warehouse

Beissenger, S.R.; Wunderle, J.M.; Meyers, J.M.; Saether, B.-E.; Engen, S.

2008-01-01

The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk analysis, then examine evidence for the importance of specific processes maintaining the bottleneck using the multiple competing hypotheses approach, and finally integrate these results through a sensitivity analysis of a demographic model using life-stage simulation analysis (LSA) to determine the relative importance of genetic, demographic, environmental, and catastrophic processes on population growth. Annual population growth has been slow and variable (1.0 6 5.2 parrots per year, or an average k?1.05 6 0.19) from 16 parrots (1973) to a high of 40-42 birds (1997-1998). A risk analysis based on population prediction intervals (PPI) indicates great risk and large uncertainty, with a range of 22?83 birds in the 90% PPI only five years into the future. Four primary factors (reduced hatching success due to inbreeding, failure of adults to nest, nest failure due to nongenetic causes, and reduced survival of adults and juveniles) were responsible for maintaining the bottleneck. Egghatchability rates were low (70.6% per egg and 76.8% per pair), and hatchability increased after mate changes, suggesting inbreeding effects. Only an average of 34% of the population nested annually, which was well below the percentage of adults that should have reached an age of first breeding (41-56%). This chronic failure to nest appears to have been caused primarily by environmental and/or behavioral factors, and not by nest-site scarcity or a skewed sex ratio. Nest failure rates from nongenetic causes (i.e., predation, parasitism, and wet cavities) were low (29%) due to active management (protecting nests and fostering captive young into wild nests), diminishing the importance of nest failure as a limiting factor. Annual survival has been periodically reduced by catastrophes (hurricanes), which have greatly constrained population growth, but survival rates were high under non-catastrophic conditions. Although the importance of factors maintaining the Puerto Rican Parrot bottleneck varied throughout the 30-year period of study, we determined their long-term influence using LSA simulations to correlate variation in demographic rates with variation in population growth (k). The bottleneck appears to have been maintained primarily by periodic catastrophes (hurricanes) that reduced adult survival, and secondarily by environmental and/or behavioral factors that resulted in a failure of many adults to nest. The influence of inbreeding through reduced hatching success played a much less significant role, even when additional effects of inbreeding on the production and mortality of young were incorporated into the LSA. Management actions needed to speed recovery include (1) continued nest guarding to minimize the effects of nest failure due to nongenetic causes; (2) creating a second population at another location on the island --a process that was recently initiated--to reduce the chance that hurricane strikes will cause extinction; and (3) determining the causes of the low percentage of breeders in the population and ameliorating them, which would have a large impact on population growth.

Relevance of graph literacy in the development of patient-centered communication tools.

PubMed

Nayak, Jasmir G; Hartzler, Andrea L; Macleod, Liam C; Izard, Jason P; Dalkin, Bruce M; Gore, John L

2016-03-01

To determine the literacy skill sets of patients in the context of graphical interpretation of interactive dashboards. We assessed literacy characteristics of prostate cancer patients and assessed comprehension of quality of life dashboards. Health literacy, numeracy and graph literacy were assessed with validated tools. We divided patients into low vs. high numeracy and graph literacy. We report descriptive statistics on literacy, dashboard comprehension, and relationships between groups. We used correlation and multiple linear regressions to examine factors associated with dashboard comprehension. Despite high health literacy in educated patients (78% college educated), there was variation in numeracy and graph literacy. Numeracy and graph literacy scores were correlated (r=0.37). In those with low literacy, graph literacy scores most strongly correlated with dashboard comprehension (r=0.59-0.90). On multivariate analysis, graph literacy was independently associated with dashboard comprehension, adjusting for age, education, and numeracy level. Even among higher educated patients; variation in the ability to comprehend graphs exists. Clinicians must be aware of these differential proficiencies when counseling patients. Tools for patient-centered communication that employ visual displays need to account for literacy capabilities to ensure that patients can effectively engage these resources. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A distributed algorithm to maintain and repair the trail networks of arboreal ants.

PubMed

Chandrasekhar, Arjun; Gordon, Deborah M; Navlakha, Saket

2018-06-18

We study how the arboreal turtle ant (Cephalotes goniodontus) solves a fundamental computing problem: maintaining a trail network and finding alternative paths to route around broken links in the network. Turtle ants form a routing backbone of foraging trails linking several nests and temporary food sources. This species travels only in the trees, so their foraging trails are constrained to lie on a natural graph formed by overlapping branches and vines in the tangled canopy. Links between branches, however, can be ephemeral, easily destroyed by wind, rain, or animal movements. Here we report a biologically feasible distributed algorithm, parameterized using field data, that can plausibly describe how turtle ants maintain the routing backbone and find alternative paths to circumvent broken links in the backbone. We validate the ability of this probabilistic algorithm to circumvent simulated breaks in synthetic and real-world networks, and we derive an analytic explanation for why certain features are crucial to improve the algorithm's success. Our proposed algorithm uses fewer computational resources than common distributed graph search algorithms, and thus may be useful in other domains, such as for swarm computing or for coordinating molecular robots.

Selection of arboreal termitaria for nesting by cooperatively breeding Micronesian Kingfishers Todiramphus cinnamominus reichenbachii

USGS Publications Warehouse

Kesler, Dylan C.; Haig, Susan M.

2005-01-01

Limited nest-site availability appears to be an important factor in the evolution of delayed dispersal and cooperative breeding in some cavity-nesting species. The cooperatively breeding Pohnpei subspecies of Micronesian Kingfisher Todiramphus cinnamominus reichenbachii excavates nest cavities from the nests of arboreal termites Nasutitermes spp., or termitaria. In this first published description of nest-sites for this subspecies, we used surveys, remote sensing and radiotelemetry to evaluate the relationship between nest-site availability and co-operation. Results illustrate that nest termitaria are higher in the forest canopy, larger in volume and occur in areas with more contiguous canopy cover than unused termitaria. Nest termitaria were selected independently of the proximity to forest edges and territory boundaries, and we found no difference in characteristics of termitaria used by cooperative groups and breeding pairs. Logistic regression modelling indicated that termitaria with nest-like characteristics were not limited in abundance, suggesting that neither the prospects of inheriting nesting resources nor limited nest-site abundance are probable explanations for delayed dispersal in the Pohnpei subspecies of Micronesian Kingfisher.

Graph Embedding Techniques for Bounding Condition Numbers of Incomplete Factor Preconditioning

NASA Technical Reports Server (NTRS)

Guattery, Stephen

1997-01-01

We extend graph embedding techniques for bounding the spectral condition number of preconditioned systems involving symmetric, irreducibly diagonally dominant M-matrices to systems where the preconditioner is not diagonally dominant. In particular, this allows us to bound the spectral condition number when the preconditioner is based on an incomplete factorization. We provide a review of previous techniques, describe our extension, and give examples both of a bound for a model problem, and of ways in which our techniques give intuitive way of looking at incomplete factor preconditioners.

Observations of indirect filial cannibalism in response to nest failure of Black-crowned Night-Herons (Nycticorax nycticorax)

USGS Publications Warehouse

Brussee, Brianne E.; Coates, Peter S.; Dwight, Ian; Young, Laura G.

2017-01-01

During 2011, four separate instances of indirect filial cannibalism, whereby adults consumed their young that died from unknown causes, were observed using video-monitoring techniques in a nesting colony of Black-crowned Night-Herons (Nycticorax nycticorax) on Alcatraz Island. Though they were not observed actively killing their young, in all four observations adult Black-crowned Night-Herons consumed their young following death (i.e., indirect filial cannibalism). We could not determine cause of chick mortality, but parental neglect was likely a contributing factor in at least two instances. Indirect filial cannibalism is not commonly documented among birds, and understanding how cannibalism contributes to nest failure can help researchers better understand factors that limit nesting populations.

Effects of human recreation on the incubation behavior of American Oystercatchers

USGS Publications Warehouse

McGowan, C.P.; Simons, T.R.

2006-01-01

Human recreational disturbance and its effects on wildlife demographics and behavior is an increasingly important area of research. We monitored the nesting success of American Oystercatchers (Haematopus palliatus) in coastal North Carolina in 2002 and 2003. We also used video monitoring at nests to measure the response of incubating birds to human recreation. We counted the number of trips per hour made by adult birds to and from the nest, and we calculated the percent time that adults spent incubating. We asked whether human recreational activities (truck, all-terrain vehicle [ATV], and pedestrian traffic) were correlated with parental behavioral patterns. Eleven a priori models of nest survival and behavioral covariates were evaluated using Akaike's Information Criterion (AIC) to see whether incubation behavior influenced nest survival. Factors associated with birds leaving their nests (n = 548) included ATV traffic (25%), truck traffic (17%), pedestrian traffic (4%), aggression with neighboring oystercatchers or paired birds exchanging incubation duties (26%), airplane traffic (1%) and unknown factors (29%). ATV traffic was positively associated with the rate of trips to and away from the nest (??1 = 0.749, P < 0.001) and negatively correlated with percent time spent incubating (??1 = -0.037, P = 0.025). Other forms of human recreation apparently had little effect on incubation behaviors. Nest survival models incorporating the frequency of trips by adults to and from the nest, and the percentage of time adults spent incubating, were somewhat supported in the AIC analyses. A low frequency of trips to and from the nest and, counter to expectations, low percent time spent incubating were associated with higher daily nest survival rates. These data suggest that changes in incubation behavior might be one mechanism by which human recreation affects the reproductive success of American Oystercatchers.

High Performance Semantic Factoring of Giga-Scale Semantic Graph Databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joslyn, Cliff A.; Adolf, Robert D.; Al-Saffar, Sinan

2010-10-04

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors.« less

Factors influencing occupancy of nest cavities in recently burned forests

USGS Publications Warehouse

Saab, V.A.; Dudley, J.; Thompson, W.L.

2004-01-01

Recently burned forests in western North America provide nesting habitat for many species of cavity-nesting birds. However, little is understood about the time frame and the variables affecting occupancy of postfire habitats by these birds. We studied factors influencing the occupancy and reuse of nest cavities from 1-7 years after fire in two burned sites of western Idaho during 1994-1999. Tree cavities were used for nesting by 12 species of cavity nesters that were classified by the original occupant (strong excavator, weak excavator, or nonexcavator) of 385 nest cavities. We used logistic regression to model cavity occupancy by strong excavators (n = 575 trials) and weak excavators (n = 206 trials). Year after fire had the greatest influence on occupancy of nest cavities for both groups, while site of the burn was secondarily important in predicting occupancy by strong excavators and less important for weak excavators. Predicted probability of cavity occupancy was highest during the early years (1-4) after fire, declined over time (5-7 years after fire), and varied by site, with a faster decline in the smaller burned site with a greater mosaic of unburned forest. Closer proximity and greater interspersion of unburned forest (15% unburned) may have allowed a quicker recolonization by nest predators into the smaller burn compared to the larger burn with few patches of unburned forest (4% unburned). In combination with time and space effects, the predicted probability of cavity occupancy was positively affected by tree and nest heights for strong and weak excavators, respectively.

Nesting ecology of Townsend's warblers in relation to habitat characteristics in a mature boreal forest

USGS Publications Warehouse

Matsuoka, S.M.; Handel, Colleen M.; Roby, D.D.

1997-01-01

We investigated the nesting ecology of Townsend's Warblers (Dendroica townsendi) from 1993-1995 in an unfragmented boreal forest along the lower slopes of the Chugach Mountains in southcentral Alaska. We examined habitat characteristics of nest sites in relation to factors influencing reproductive success. Almost all territory-holding males (98%, n = 40) were successful in acquiring mates. Nest success was 54% (n = 24 nests), with nest survivorship greater during incubation (87%) than during the nestling period (62%). Most nesting failure (80%) was attributable to predation, which occurred primarily during the nestling period. Fifty-five percent of nests containing nestling were infested with the larvae of bird blow-flies (Protocalliphora braueri and P. spenceri), obligatory blood-feeding parasites. The combined effects of Protocalliphora infestation and inclement weather apparently resulted in nestling mortality in 4 of the 24 nests. Nests that escaped predation were placed in white spruce with larger diameter than those lost to predation: nests that escaped blow-fly parasitism were located higher in nest trees and in areas with lower densities of woody shrubs than those that were infested. The availability of potential nest sites with these key features may be important in determining reproductive success in Townsend's Warblers.

Variation in nesting behavior of eight species of spider mites, Stigmaeopsis having sociality

NASA Astrophysics Data System (ADS)

Saito, Yutaka; Zhang, Yan-Xuan; Mori, Kotaro; Ito, Katsura; Sato, Yukie; Chittenden, Anthony R.; Lin, Jian-Zhen; Chae, Younghae; Sakagami, Takane; Sahara, Ken

2016-10-01

Nesting behavior is considered to be an important element of social living in animals. The spider mites belonging to the genus Stigmaeopsis spend their lives within nests produced from silk threads. Several of these species show cooperative sociality, while the others are subsocial. In order to identify the origins of this social behavior, comparisons of nest sizes, nesting behaviors (making nests continuously or separately), and their associated traits (fecal deposition patterns) were made for eight cogeneric Stigmaeopsis species showing various levels of social development. All of these species inhabit bamboo plants (Poaceae). We initially addressed the proximate factor of nest size variation. The variation in nest size of the eight species corresponded well with the variation in dorsal seta sc1 length, suggesting that nest size variation among species may have a genetic basis. The time spent within a nest (nest duration) increased with nest size on the respective host plants. Nest arrangement patterns varied among species showing different sized nests: Large nest builders continuously extended their nests, while middle and small nest-building species built new separate nests, which resulted in different social interaction times among species, and is thought to be closely related to social development. Fecal deposition behaviors also varied among Stigmaeopsis species, suggesting diversity in anti-predatory adaptations. Finally, we discuss how the variation in sociality observed within this genus is likely the result of nest size variation that initially evolved as anti-predator strategies.

Variation in nesting behavior of eight species of spider mites, Stigmaeopsis having sociality.

PubMed

Saito, Yutaka; Zhang, Yan-Xuan; Mori, Kotaro; Ito, Katsura; Sato, Yukie; Chittenden, Anthony R; Lin, Jian-Zhen; Chae, Younghae; Sakagami, Takane; Sahara, Ken

2016-10-01

Nesting behavior is considered to be an important element of social living in animals. The spider mites belonging to the genus Stigmaeopsis spend their lives within nests produced from silk threads. Several of these species show cooperative sociality, while the others are subsocial. In order to identify the origins of this social behavior, comparisons of nest sizes, nesting behaviors (making nests continuously or separately), and their associated traits (fecal deposition patterns) were made for eight cogeneric Stigmaeopsis species showing various levels of social development. All of these species inhabit bamboo plants (Poaceae). We initially addressed the proximate factor of nest size variation. The variation in nest size of the eight species corresponded well with the variation in dorsal seta sc1 length, suggesting that nest size variation among species may have a genetic basis. The time spent within a nest (nest duration) increased with nest size on the respective host plants. Nest arrangement patterns varied among species showing different sized nests: Large nest builders continuously extended their nests, while middle and small nest-building species built new separate nests, which resulted in different social interaction times among species, and is thought to be closely related to social development. Fecal deposition behaviors also varied among Stigmaeopsis species, suggesting diversity in anti-predatory adaptations. Finally, we discuss how the variation in sociality observed within this genus is likely the result of nest size variation that initially evolved as anti-predator strategies.

The importance of microclimate variation in determining size, growth and survival of avian offspring: experimental evidence from a cavity nesting passerine.

PubMed

Dawson, Russell D; Lawrie, Cheyenne C; O'Brien, Erin L

2005-07-01

Organisms are expected to balance energy allocation in such a way that fitness is maximized. While much research has focussed on allocation strategies of reproducing parents, in particular birds, relatively little attention has been paid to how nestlings allocate energy while in the nest. Nestling birds are faced with a trade-off between devoting energy to growth or to thermoregulation, and in altricial species it is likely that the thermal environment of the nest site influences the nature of this trade-off. Here, we experimentally investigate how altering the microclimate of nests affects the growth, size and survival, as well as cell-mediated immune (CMI) response, of nestling tree swallows (Tachycineta bicolor) in a temperate environment. We place air-activated heating pads in nests of swallows when young were between 4 days and 16 days of age, and compared performance of offspring to control nests. Our manipulation raised temperatures of heated nests by approximately 5 degrees C compared to control nests. Offspring in heated nests had enhanced survival while in the nest, and we also found that they were heavier and had longer ninth primary feathers at 16 days of age. In addition, heating nest boxes resulted in significantly faster growth of primaries, and there was a trend for growth rates of mass to also be higher in heated nests. There were no significant differences between heated and control nests in growth rate or size of tarsus at age 16 days, and we speculate that this lack of response to elevated nest temperatures may be due to growth of skeletal structures being limited by other factors such as calcium availability. We also found no difference between heated and control nests in CMI response. Nonetheless, our results show overall that increasing temperatures of nests has significant benefits that enhance the fitness of offspring. As provisioning rates to offspring did not differ between heated and control nests, we suspect that the beneficial effects of heating were not the consequence of changes in parental behaviour. Our results provide insight into factors, other than food supply, that have important consequences in determining reproductive success of birds breeding in temperate environments.

Nest placement of the giant Amazon river turtle, Podocnemis expansa, in the Araguaia River, Goiás State, Brazil.

PubMed

Ferreira, Paulo Dias Júnior; Castro, Paulo de Tarso Amorim

2005-05-01

The giant Amazon river turtle (Podocnemis expansa) nests on extensive sand bars on the margins and interior of the channel during the dry season. The high concentration of nests in specific points of certain beaches indicates that the selection of nest placement is not random but is related to some geological aspects, such as bar margin inclination and presence of a high, sandy platform. The presence of access channels to high platform points or ramp morphology are decisive factors in the choice of nesting areas. The eroded and escarped margins of the beaches hinder the Amazon river turtle arriving at the most suitable places for nesting. Through the years, changes in beach morphology can alter nest distribution.

Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot

USGS Publications Warehouse

Newmark, W.D.; Stanley, T.R.

2011-01-01

Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds.

Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot.

PubMed

Newmark, William D; Stanley, Thomas R

2011-07-12

Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds.

Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot

PubMed Central

Newmark, William D.; Stanley, Thomas R.

2011-01-01

Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds. PMID:21709237

A comparison of artificial incubation and natural incubation hatching success of gopher tortoise (Gopherus polyphemus) eggs in southern Mississippi

USGS Publications Warehouse

Noel, Krista M.; Qualls, Carl P.; Ennen, Joshua R.

2012-01-01

Recent studies have found that Gopher Tortoise, Gopherus polyphemus, populations in southern Mississippi exhibit low recruitment, due in part to very low hatching success of their eggs. We sought to determine if the cause(s) of this low hatching success was related to egg quality (intrinsic factors), unsuitability of the nest environment (extrinsic factors), or a combination of the two. In 2003, hatching success was monitored simultaneously for eggs from the same clutches that were incubated in the laboratory and left to incubate in nests. A subset of randomly chosen eggs from each clutch was incubated in the laboratory under physical conditions that were known to be conducive to successful hatching to estimate the proportion of eggs that were capable of hatching in a controlled setting. Hatching success in the laboratory was compared with that of eggs incubated in natural nests to estimate the proportion of eggs that failed to hatch presumably from extrinsic factors. Laboratory hatching success was 58.8%, suggesting that roughly 40% of the eggs were intrinsically incapable of hatching even when incubated under controlled conditions. Hatching success in natural nests, 16.7%, was significantly lower than hatching success in the laboratory, suggesting that approximately 42.1% of eggs were capable of hatching but failed to hatch due to some extrinsic aspect(s) of the nest environment. Thus, the low hatching success of Gopher Tortoise eggs in southern Mississippi appears to be attributable to a combination of intrinsic (egg quality) and extrinsic (nest environment) factors.

Seasonal variation in nest placement of Abert's Towhees

Treesearch

Deborah M. Finch

1983-01-01

Several meteorological variables are known to influence the heat budgets of nesting birds (e.g., Walsberg and King 1978a, b). Such factors include air temperature, incident radiation, wind, and humidity. If the microclimate of the nest is unfavorable, parent birds may become inattentive, exposing eggs or nestlings to excessive heat or cold. They may then desert the...

A smoothed residual based goodness-of-fit statistic for nest-survival models

Treesearch

Rodney X. Sturdivant; Jay J. Rotella; Robin E. Russell

2008-01-01

Estimating nest success and identifying important factors related to nest-survival rates is an essential goal for many wildlife researchers interested in understanding avian population dynamics. Advances in statistical methods have led to a number of estimation methods and approaches to modeling this problem. Recently developed models allow researchers to include a...

Nest site characteristics and nesting success of the Western Burrowing Owl in the eastern Mojave Desert

USGS Publications Warehouse

Longshore, Kathleen M.; Crowe, Dorothy E.

2013-01-01

We evaluated nest site selection at two spatial scales (microsite, territory) and reproductive success of Western Burrowing Owls (Athene cunicularia hypugaea) at three spatial scales (microsite, territory, landscape) in the eastern Mojave Desert. We used binary logistic regression within an information-theoretic approach to assess factors influencing nest site choice and nesting success. Microsite-scale variables favored by owls included burrows excavated by desert tortoise (Gopherus agassizii), burrows with a large mound of excavated soil at the entrance, and a greater number of satellite burrows within 5 m of the nest burrow. At the territory scale, owls preferred patches with greater cover of creosote bush (Larrea tridentata) within 50 m of the nest burrow. An interaction between the presence or absence of a calcic soil horizon layer over the top of the burrow (microsite) and the number of burrows within 50 m (territory) influenced nest site choice. Nesting success was influenced by a greater number of burrows within 5 m of the nest burrow. Total cool season precipitation was a predictor of nesting success at the landscape scale. Conservation strategies can rely on management of habitat for favored and productive nesting sites for this declining species.

How do Neoseiulus californicus (Acari: Phytoseiidae) females penetrate densely webbed spider mite nests?

PubMed

Montserrat, M; de la Peña, F; Hormaza, J I; González-Fernández, J J

2008-02-01

The persea mite Oligonychus perseae is a pest of avocado trees that builds extremely dense webbed nests that protect them against natural enemies, including phytoseiid mites. Nests have one or two marginal entrances that are small and flattened. The predatory mite Neoseiulus californicus co-occurs with O. perseae in the avocado orchards of the south-east of Spain. Penetration inside nests through the entrances by this predator is thought to be hindered by its size and its globular-shaped body. However, in the field it has repeatedly been found inside nests that were clearly ripped. Perhaps penetration of the nests has been facilitated by nest wall ripping caused by some other species or by unfavourable abiotic factors. However, to assess whether N. californicus is also able to enter the nest of O. perseae by itself, we carried out laboratory experiments and made a short film. They show how this predator manages to overcome the webbed wall, and that it can penetrate and forage inside nests of O. perseae.

Partitioning sparse matrices with eigenvectors of graphs

NASA Technical Reports Server (NTRS)

Pothen, Alex; Simon, Horst D.; Liou, Kang-Pu

1990-01-01

The problem of computing a small vertex separator in a graph arises in the context of computing a good ordering for the parallel factorization of sparse, symmetric matrices. An algebraic approach for computing vertex separators is considered in this paper. It is shown that lower bounds on separator sizes can be obtained in terms of the eigenvalues of the Laplacian matrix associated with a graph. The Laplacian eigenvectors of grid graphs can be computed from Kronecker products involving the eigenvectors of path graphs, and these eigenvectors can be used to compute good separators in grid graphs. A heuristic algorithm is designed to compute a vertex separator in a general graph by first computing an edge separator in the graph from an eigenvector of the Laplacian matrix, and then using a maximum matching in a subgraph to compute the vertex separator. Results on the quality of the separators computed by the spectral algorithm are presented, and these are compared with separators obtained from other algorithms for computing separators. Finally, the time required to compute the Laplacian eigenvector is reported, and the accuracy with which the eigenvector must be computed to obtain good separators is considered. The spectral algorithm has the advantage that it can be implemented on a medium-size multiprocessor in a straightforward manner.

An integrated analysis of micro- and macro-habitat features as a tool to detect weather-driven constraints: A case study with cavity nesters.

PubMed

Campobello, D; Lindström, J; Di Maggio, R; Sarà, M

2017-01-01

The effects of climate change on animal populations may be shaped by habitat characteristics at both micro- and macro-habitat level, however, empirical studies integrating these two scales of observation are lacking. As analyses of the effects of climate change commonly rely on data from a much larger scale than the microhabitat level organisms are affected at, this mismatch risks hampering progress in developing understanding of the details of the ecological and evolutionary responses of organisms and, ultimately, effective actions to preserve their populations. Cavity nesters, often with a conservation status of concern, are an ideal model because the cavity is a microenvironment potentially different from the macroenvironment but nonetheless inevitably interacting with it. The lesser kestrel (Falco naumanni) is a cavity nester which was until recently classified by as Vulnerable species. Since 2004, for nine years, we collected detailed biotic and abiotic data at both micro- and macro-scales of observation in a kestrel population breeding in the Gela Plain (Italy), a Mediterranean area where high temperatures may reach lethal values for the nest content. We show that macroclimatic features needed to be integrated with both abiotic and biotic factors recorded at a microscale before reliably predicting nest temperatures. Among the nest types used by lesser kestrels, we detected a preferential occupation of the cooler nest types, roof tiles, by early breeders whereas, paradoxically, late breeders nesting with hotter temperatures occupied the overheated nest holes. Not consistent with such a suggested nest selection, the coolest nest type did not host a higher reproductive success than the overheated nests. We discussed our findings in the light of cavity temperatures and nest types deployed within conservation actions assessed by integrating selected factors at different observation scales.

Factors influencing reproductive performance of northern bobwhite in South Florida

USGS Publications Warehouse

Rolland, V.; Hostetler, J.A.; Hines, T.C.; Percival, H.F.; Oli, M.K.

2011-01-01

Reproductive success is a critical component of individual fitness, and also an important determinant of growth rates of populations characterized by early maturity and high fecundity. We used radiotelemetry data collected during 2003-2008 to estimate reproductive parameters in a declining northern bobwhite (Colinus virginianus) population in South Florida, and to test hypotheses regarding factors influencing these parameters. The overall clutch size was 12.10 ?? 0.22, but females laid more eggs in their first clutch (12.43 ?? 0.24) than in subsequent clutches (10.19 ?? 0.53) within a nesting season. Daily nest survival was higher for first (0.966 ?? 0.003) than subsequent nests (0.936 ?? 0.011). Hatchability (proportion of laid eggs that hatched conditional upon nest survival to hatching) was 0.853 ?? 0.008, but was higher for nests incubated by females (0.873 ?? 0.009) than those incubated by males (0.798 ?? 0.018). The proportion of individuals attempting a second nest was 0.112 ?? 0.024 and 0.281 ?? 0.040 when the first nest was successful and failed, respectively. Hatchability was lower when the nesting habitat was burned the previous winter. We found no evidence that food strip density (a management practice to provide supplemental food) influenced any of the reproductive parameters. Mean summer temperature affected hatchability, nest survival, and proportion of nests incubated by males. Overall, the reproductive output in our study population was lower than that reported for most other bobwhite populations, indicating that low reproductive performance may have contributed to bobwhite population declines in our study site. These results suggest that current management practices, particularly those related to habitat and harvest management, need careful evaluation. ?? 2010 Springer-Verlag.

An integrated analysis of micro- and macro-habitat features as a tool to detect weather-driven constraints: A case study with cavity nesters

PubMed Central

Campobello, D.; Lindström, J.; Di Maggio, R.; Sarà, M.

2017-01-01

The effects of climate change on animal populations may be shaped by habitat characteristics at both micro- and macro-habitat level, however, empirical studies integrating these two scales of observation are lacking. As analyses of the effects of climate change commonly rely on data from a much larger scale than the microhabitat level organisms are affected at, this mismatch risks hampering progress in developing understanding of the details of the ecological and evolutionary responses of organisms and, ultimately, effective actions to preserve their populations. Cavity nesters, often with a conservation status of concern, are an ideal model because the cavity is a microenvironment potentially different from the macroenvironment but nonetheless inevitably interacting with it. The lesser kestrel (Falco naumanni) is a cavity nester which was until recently classified by as Vulnerable species. Since 2004, for nine years, we collected detailed biotic and abiotic data at both micro- and macro-scales of observation in a kestrel population breeding in the Gela Plain (Italy), a Mediterranean area where high temperatures may reach lethal values for the nest content. We show that macroclimatic features needed to be integrated with both abiotic and biotic factors recorded at a microscale before reliably predicting nest temperatures. Among the nest types used by lesser kestrels, we detected a preferential occupation of the cooler nest types, roof tiles, by early breeders whereas, paradoxically, late breeders nesting with hotter temperatures occupied the overheated nest holes. Not consistent with such a suggested nest selection, the coolest nest type did not host a higher reproductive success than the overheated nests. We discussed our findings in the light of cavity temperatures and nest types deployed within conservation actions assessed by integrating selected factors at different observation scales. PMID:28319183

Object recognition in images via a factor graph model

NASA Astrophysics Data System (ADS)

He, Yong; Wang, Long; Wu, Zhaolin; Zhang, Haisu

2018-04-01

Object recognition in images suffered from huge search space and uncertain object profile. Recently, the Bag-of- Words methods are utilized to solve these problems, especially the 2-dimension CRF(Conditional Random Field) model. In this paper we suggest the method based on a general and flexible fact graph model, which can catch the long-range correlation in Bag-of-Words by constructing a network learning framework contrasted from lattice in CRF. Furthermore, we explore a parameter learning algorithm based on the gradient descent and Loopy Sum-Product algorithms for the factor graph model. Experimental results on Graz 02 dataset show that, the recognition performance of our method in precision and recall is better than a state-of-art method and the original CRF model, demonstrating the effectiveness of the proposed method.

High performance semantic factoring of giga-scale semantic graph databases.

DOE Office of Scientific and Technical Information (OSTI.GOV)

al-Saffar, Sinan; Adolf, Bob; Haglin, David

2010-10-01

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors, including basic properties, connected components, namespace interaction, and typed paths.« less

Breeding phenology of birds: mechanisms underlying seasonal declines in the risk of nest predation.

PubMed

Borgmann, Kathi L; Conway, Courtney J; Morrison, Michael L

2013-01-01

Seasonal declines in avian clutch size are well documented, but seasonal variation in other reproductive parameters has received less attention. For example, the probability of complete brood mortality typically explains much of the variation in reproductive success and often varies seasonally, but we know little about the underlying cause of that variation. This oversight is surprising given that nest predation influences many other life-history traits and varies throughout the breeding season in many songbirds. To determine the underlying causes of observed seasonal decreases in risk of nest predation, we modeled nest predation of Dusky Flycatchers (Empidonax oberholseri) in northern California as a function of foliage phenology, energetic demand, developmental stage, conspecific nest density, food availability for nest predators, and nest predator abundance. Seasonal variation in the risk of nest predation was not associated with seasonal changes in energetic demand, conspecific nest density, or predator abundance. Instead, seasonal variation in the risk of nest predation was associated with foliage density (early, but not late, in the breeding season) and seasonal changes in food available to nest predators. Supplemental food provided to nest predators resulted in a numerical response by nest predators, increasing the risk of nest predation at nests that were near supplemental feeders. Our results suggest that seasonal changes in foliage density and factors associated with changes in food availability for nest predators are important drivers of temporal patterns in risk of avian nest predation.

Breeding Phenology of Birds: Mechanisms Underlying Seasonal Declines in the Risk of Nest Predation

PubMed Central

Borgmann, Kathi L.; Conway, Courtney J.; Morrison, Michael L.

2013-01-01

Seasonal declines in avian clutch size are well documented, but seasonal variation in other reproductive parameters has received less attention. For example, the probability of complete brood mortality typically explains much of the variation in reproductive success and often varies seasonally, but we know little about the underlying cause of that variation. This oversight is surprising given that nest predation influences many other life-history traits and varies throughout the breeding season in many songbirds. To determine the underlying causes of observed seasonal decreases in risk of nest predation, we modeled nest predation of Dusky Flycatchers (Empidonax oberholseri) in northern California as a function of foliage phenology, energetic demand, developmental stage, conspecific nest density, food availability for nest predators, and nest predator abundance. Seasonal variation in the risk of nest predation was not associated with seasonal changes in energetic demand, conspecific nest density, or predator abundance. Instead, seasonal variation in the risk of nest predation was associated with foliage density (early, but not late, in the breeding season) and seasonal changes in food available to nest predators. Supplemental food provided to nest predators resulted in a numerical response by nest predators, increasing the risk of nest predation at nests that were near supplemental feeders. Our results suggest that seasonal changes in foliage density and factors associated with changes in food availability for nest predators are important drivers of temporal patterns in risk of avian nest predation. PMID:23776566

The influence of coyotes on an urban Canada goose population in the Chicago metropolitan area

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Justin L.; /Ohio State U.

Canada geese (Branta canadensis) have become common in many urban areas, often creating nuisance problems for human residents. The presence of urban geese has raised concerns about the spread of disease, increased erosion, excessive noise, eutrophication of waterways, and general nuisance problems. Goose populations have grown due to an increase in urbanization resulting in an abundance of high quality food (urban grass) and suitable nesting sites, as well as a decrease in some predators. I monitored nest predation in the Chicago suburbs during the 2004 and 2005 nesting seasons using 3 nest monitoring techniques to identify predators: video cameras, plasticinemore » eggs, and sign from nest using a classification tree analysis. Of 58 nests monitored in 2004 and 286 in 2005, only raccoons (Procyon lotor) and coyotes (Canis latrans) were identified as nest predators. Raccoons were responsible for 22-25% of depredated nests, but were rarely capable of depredating nests that were actively defended by a goose. Coyotes were responsible for 75-78% of all Canada goose nest depredation and were documented killing one adult goose and feeding on several others. The coyote is a top-level predator that had increased in many metropolitan areas in recent years. To determine if coyotes were actively hunting geese or eggs during the nesting season, I analyzed coyote habitat selection between nesting and pre-nesting or post-nesting seasons. Coyote home ranges (95% Minimum Convex Polygon) were calculated for 19 coyotes to examine third order habitat selection related to goose nest abundance. A 100 m buffer (buffer habitat) was created and centered on each waterway edge and contained 90% of all nests. Coyotes showed selection for habitats during all seasons. Buffer habitat was the top ranked habitat in both pre-nesting and nesting seasons, but dropped to third ranked in post-nesting season. Habitat selection across seasons was compared using a repeated measures MANOVA. Habitat selection between pre-nesting and nesting seasons (P=0.72) were similar, while between post-nesting and nesting seasons there was a nearly significant difference (P=0.07). The insignificant change in habitat use across seasons suggests that coyotes did not switch habitat use to take advantage of goose nests. Alternatively, the change in ranking of buffer habitat across seasons suggests that coyotes may have switched habitat use to take advantage of goose nests. The results are not clear as large individual variation between coyotes due to differences in habitat availability, and social status interfere with the results of the analysis. Even though I failed to find strong support for coyotes actively hunting goose nests, they nevertheless were the primary nest predator in the area and may influence Canada goose populations. To determine the potential influence of coyotes on the Canada goose population, I created a Canada goose matrix population model that included variables such as coyote predation on adults and nests as well as coyote influence on nest desertion. Using the base population model I calculated the Canada goose population to be increasing with {lambda} = 1.055. The removal of all coyote influence on the goose population would allow {lambda} to increase to 1.214. Nest predation was the most important factor related to coyotes: the removal of coyote nest predation from the model resulted in a population growth rate {lambda} = 1.157. Modeling results suggest coyotes are serving as a limiting factor for the Canada goose population within the Chicago metropolitan area.« less

Histories of Puerto Rican parrot nests in the Caribbean National Forest/Luquillo Experimental Forest, 1973-2000

USGS Publications Warehouse

Wunderle, J.M.; Snyder, N.F.R.; Muiznieks, B.; Wiley, J.W.; Meyers, J.M.

2003-01-01

This publication summarizes the histories of all known Puerto Rican parrot nests in the Caribbean National Forest/Luquillo Experimental Forest from 1973 through 2000. Included for each nest, when known, are the identifies of the pair, clutch size, known fertile and infertile eggs, number of eggs that hatched, number of chicks that survived, sources of mortality, fostering (source, destination. or both), number of young fledged from the pair and from the nest, and percentage of days the nest was guarded. This information is useful for detecting and assessing potential changes in reproductive output and nest threats and is fundamental for understanding some of the demographic and genetic factors influencing the wild parrot population.

Weighted graph based ordering techniques for preconditioned conjugate gradient methods

NASA Technical Reports Server (NTRS)

Clift, Simon S.; Tang, Wei-Pai

1994-01-01

We describe the basis of a matrix ordering heuristic for improving the incomplete factorization used in preconditioned conjugate gradient techniques applied to anisotropic PDE's. Several new matrix ordering techniques, derived from well-known algorithms in combinatorial graph theory, which attempt to implement this heuristic, are described. These ordering techniques are tested against a number of matrices arising from linear anisotropic PDE's, and compared with other matrix ordering techniques. A variation of RCM is shown to generally improve the quality of incomplete factorization preconditioners.

Coordinates and intervals in graph-based reference genomes.

PubMed

Rand, Knut D; Grytten, Ivar; Nederbragt, Alexander J; Storvik, Geir O; Glad, Ingrid K; Sandve, Geir K

2017-05-18

It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords .

Multiple directed graph large-class multi-spectral processor

NASA Technical Reports Server (NTRS)

Casasent, David; Liu, Shiaw-Dong; Yoneyama, Hideyuki

1988-01-01

Numerical analysis techniques for the interpretation of high-resolution imaging-spectrometer data are described and demonstrated. The method proposed involves the use of (1) a hierarchical classifier with a tree structure generated automatically by a Fisher linear-discriminant-function algorithm and (2) a novel multiple-directed-graph scheme which reduces the local maxima and the number of perturbations required. Results for a 500-class test problem involving simulated imaging-spectrometer data are presented in tables and graphs; 100-percent-correct classification is achieved with an improvement factor of 5.

Adaptive nest clustering and density-dependent nest survival in dabbling ducks

USGS Publications Warehouse

Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.

2014-01-01

Density-dependent population regulation is observed in many taxa, and understanding the mechanisms that generate density dependence is especially important for the conservation of heavily-managed species. In one such system, North American waterfowl, density dependence is often observed at continental scales, and nest predation has long been implicated as a key factor driving this pattern. However, despite extensive research on this topic, it remains unclear if and how nest density influences predation rates. Part of this confusion may have arisen because previous studies have studied density-dependent predation at relatively large spatial and temporal scales. Because the spatial distribution of nests changes throughout the season, which potentially influences predator behavior, nest survival may vary through time at relatively small spatial scales. As such, density-dependent nest predation might be more detectable at a spatially- and temporally-refined scale and this may provide new insights into nest site selection and predator foraging behavior. Here, we used three years of data on nest survival of two species of waterfowl, mallards and gadwall, to more fully explore the relationship between local nest clustering and nest survival. Throughout the season, we found that the distribution of nests was consistently clustered at small spatial scales (˜50–400 m), especially for mallard nests, and that this pattern was robust to yearly variation in nest density and the intensity of predation. We demonstrated further that local nest clustering had positive fitness consequences – nests with closer nearest neighbors were more likely to be successful, a result that is counter to the general assumption that nest predation rates increase with nest density.

Factors Affecting Florida Scrub-Jay Nest Survival on Ocala National Forest, Florida

Treesearch

Kathleen Franzreb; Stan Zarnoch

2011-01-01

One of the main populations of the Florida scrub-jay (Aphelocoma coerulescens), a federally threatened species, occurs on Ocala National Forest, Florida. We determined the nest survival rate (DSR) of 474 nests of Florida scrub-jays in stands subject to sand pine reforestation management after timber harvesting or wildfire on Ocala National Forest. We used the...

Nesting characteristics of mourning doves in central New Mexico: Response to riparian forest change

Treesearch

D. Max Smith; Deborah M. Finch; David L. Hawksworth

2012-01-01

Riparian forests of the American Southwest are especially prone to changes in composition and structure due to natural and anthropogenic factors. To determine how breeding mourning doves (Zenaida macroura) respond to these changes, we examined nest site use and nest survival in control plots, fuel reduction plots before and after mechanical thinning, and post-wildfire...

Geographic Gossip: Efficient Averaging for Sensor Networks

NASA Astrophysics Data System (ADS)

Dimakis, Alexandros D. G.; Sarwate, Anand D.; Wainwright, Martin J.

Gossip algorithms for distributed computation are attractive due to their simplicity, distributed nature, and robustness in noisy and uncertain environments. However, using standard gossip algorithms can lead to a significant waste in energy by repeatedly recirculating redundant information. For realistic sensor network model topologies like grids and random geometric graphs, the inefficiency of gossip schemes is related to the slow mixing times of random walks on the communication graph. We propose and analyze an alternative gossiping scheme that exploits geographic information. By utilizing geographic routing combined with a simple resampling method, we demonstrate substantial gains over previously proposed gossip protocols. For regular graphs such as the ring or grid, our algorithm improves standard gossip by factors of $n$ and $\\sqrt{n}$ respectively. For the more challenging case of random geometric graphs, our algorithm computes the true average to accuracy $\\epsilon$ using $O(\\frac{n^{1.5}}{\\sqrt{\\log n}} \\log \\epsilon^{-1})$ radio transmissions, which yields a $\\sqrt{\\frac{n}{\\log n}}$ factor improvement over standard gossip algorithms. We illustrate these theoretical results with experimental comparisons between our algorithm and standard methods as applied to various classes of random fields.

Information Graph Flow: A Geometric Approximation of Quantum and Statistical Systems

NASA Astrophysics Data System (ADS)

Vanchurin, Vitaly

2018-05-01

Given a quantum (or statistical) system with a very large number of degrees of freedom and a preferred tensor product factorization of the Hilbert space (or of a space of distributions) we describe how it can be approximated with a very low-dimensional field theory with geometric degrees of freedom. The geometric approximation procedure consists of three steps. The first step is to construct weighted graphs (we call information graphs) with vertices representing subsystems (e.g., qubits or random variables) and edges representing mutual information (or the flow of information) between subsystems. The second step is to deform the adjacency matrices of the information graphs to that of a (locally) low-dimensional lattice using the graph flow equations introduced in the paper. (Note that the graph flow produces very sparse adjacency matrices and thus might also be used, for example, in machine learning or network science where the task of graph sparsification is of a central importance.) The third step is to define an emergent metric and to derive an effective description of the metric and possibly other degrees of freedom. To illustrate the procedure we analyze (numerically and analytically) two information graph flows with geometric attractors (towards locally one- and two-dimensional lattices) and metric perturbations obeying a geometric flow equation. Our analysis also suggests a possible approach to (a non-perturbative) quantum gravity in which the geometry (a secondary object) emerges directly from a quantum state (a primary object) due to the flow of the information graphs.

Information Graph Flow: A Geometric Approximation of Quantum and Statistical Systems

NASA Astrophysics Data System (ADS)

Vanchurin, Vitaly

2018-06-01

Given a quantum (or statistical) system with a very large number of degrees of freedom and a preferred tensor product factorization of the Hilbert space (or of a space of distributions) we describe how it can be approximated with a very low-dimensional field theory with geometric degrees of freedom. The geometric approximation procedure consists of three steps. The first step is to construct weighted graphs (we call information graphs) with vertices representing subsystems (e.g., qubits or random variables) and edges representing mutual information (or the flow of information) between subsystems. The second step is to deform the adjacency matrices of the information graphs to that of a (locally) low-dimensional lattice using the graph flow equations introduced in the paper. (Note that the graph flow produces very sparse adjacency matrices and thus might also be used, for example, in machine learning or network science where the task of graph sparsification is of a central importance.) The third step is to define an emergent metric and to derive an effective description of the metric and possibly other degrees of freedom. To illustrate the procedure we analyze (numerically and analytically) two information graph flows with geometric attractors (towards locally one- and two-dimensional lattices) and metric perturbations obeying a geometric flow equation. Our analysis also suggests a possible approach to (a non-perturbative) quantum gravity in which the geometry (a secondary object) emerges directly from a quantum state (a primary object) due to the flow of the information graphs.

Density and Distribution of Xylocopa Nests (Hymenoptera: Apidae) in Caatinga Areas in the Surroundings of Passion Fruit Crops.

PubMed

Martins, C F; de Siqueira, K M M; Kiill, L H P; Sá, I I S; Aguiar, C M L

2014-08-01

Due to their importance as pollinators of many plant species, this study aimed to know the nest density, spatial distribution, and nesting substrates used by Xylocopa species in the Caatinga, a xerophilous vegetation of Northeastern Brazil. Three areas of Caatinga in the surroundings of passion fruit crops were sampled. The bee species found in these areas were Xylocopa grisescens Lepeletier and Xylocopa frontalis (Olivier). All nests were in Commiphora leptophloeos (Burseraceae) trees (n = 113). Phytosociological analysis showed that this tree species presented the highest absolute density (212.5 individuals/ha) and index of importance value (52.7). The distribution pattern of the C. leptophloeos was aggregated. The nests were located in dead and dried branches with an average diameter of 5.3 ± 2.0 cm (n = 43). The mean number of nests/tree was 3.1 ± 2.8 (n = 113). The less disturbed area showed 6.7 nests/ha and 4.2 nests/tree. In the disturbed areas, 0.9 nests/ha and 2.4 to 2.7 nests/tree were observed. The availability of substrate for nesting in the studied areas and its importance as a limiting factor for nesting are discussed.

Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests

PubMed Central

Trottier-Paquet, Myriam; Bêty, Joël; Lamarre, Vincent; Lecomte, Nicolas

2016-01-01

Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter “conspicuous behaviour”), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs. PMID:27602257

Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests.

PubMed

Giroux, Marie-Andrée; Trottier-Paquet, Myriam; Bêty, Joël; Lamarre, Vincent; Lecomte, Nicolas

2016-01-01

Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter "conspicuous behaviour"), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs.

A Factor Graph Approach to Automated GO Annotation

PubMed Central

Spetale, Flavio E.; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

2016-01-01

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

A Factor Graph Approach to Automated GO Annotation.

PubMed

Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

2016-01-01

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.

Effects of habitat on avian productivity in abandoned pecan orchards in southern Georgia

USGS Publications Warehouse

Patnode, K.A.; White, D.H.

1992-01-01

Daily survival rates (DSRs) of nests, eggs and nestlings were determined for Mourning Doves (Zenaida macroura), Northern Cardinals (Cardinalis cardinalis), Brown Thrashers (Toxostoma rufum) and Northern Mockingbirds (Mimus polyglottos) occupying abandoned pecan orchards in a highly fragmented and intensively farmed area of southern Georgia. The effects of nest placement parameters, seasonal factors and habitat disruptions on DSRs for all species combined were statistically analyzed. Egg and nestling DSRs varied significantly by month of nesting, percent cover, vegetative form and position of nest in substrate. Causes of nest failure (no fledglings produced) in order of decreasing importance were predation by small mammals/snakes, avian predation, predation by large mammals, and abandonment. Results provide further evidence that the importance of nest placement and habitat disruptions in nesting success is influenced by foraging strategies of the predator community. Site-specific predator/habitat complexes may be a more appropriate criterion than habitat conditions alone for evaluating avian nesting habitat

Changing nest placement of Hawaiian Common Amakihi during the breeding cycle

USGS Publications Warehouse

van Riper, Charles; Kern, M. D.; Sogge, M. K.

1993-01-01

We studied the nesting behavior of the Common Amakihi (Hemignathus virens) from 1970-1981 on the island of Hawaii to determine if the species alters nest placement over a protracted 9-month breeding season. Birds preferentially chose the southwest quadrant of trees in which to build nests during all phases of the breeding season. It appeared that ambient temperature (Ta) was a contributing factor to differential nest placement between early and late phases of the annual breeding cycle. When Ta is low during the early (December-March) breeding period, Common Amakihi selected exposed nesting locations that benefitted them with maximum solar insolation. However, in the later phase of the breeding period (April-July) when Ta was much higher, renesting birds selected nest sites deeper in the canopy in significantly taller trees. This is one of the few documented examples in which a species changes location of nest during a breeding season, thus allowing exploitation of temporally differing microclimatic conditions.

Synchrony of Piping Plover breeding populations in the U.S. Northern Great Plains

USGS Publications Warehouse

Roche, Erin A.; Shaffer, Terry L.; Dovichin, Colin M.; Sherfy, Mark H.; Anteau, Michael J.; Wiltermuth, Mark T.

2016-01-01

Local populations that fluctuate synchronously are at a greater risk of extinction than those that do not. The closer the geographic proximity of populations, the more prone they are to synchronizing. Shorebird species select habitat broadly, and many breed across regions with diverse nesting habitat types. Under these conditions, nearby populations may experience conditions sufficiently different to prevent population synchrony, despite dispersal. In the U.S. Northern Great Plains, the Piping Plover (Charadrius melodus), federally listed as Threatened, is a migratory shorebird species that nests on the shorelines of rivers, reservoirs, and alkaline lakes. We assessed the degree to which local plover breeding population abundances were correlated (population synchrony), changed over time (population stability), and were influenced by environmental factors such as available habitat, precipitation, and within-season reservoir level rise. We found that the abundances of breeding populations nesting in riverine and reservoir habitats were the most synchronous, while populations nesting in alkaline lake habitats exhibited the greatest stability. Changes in local breeding population abundances were not explained by a single factor across habitat types. However, the abundances of local populations nesting in alkaline lake and river shoreline habitats were positively correlated with changes in nesting habitat availability. Our results suggest that dispersal among populations nesting in either river or reservoir and alkaline lake shoreline habitat may have an overall stabilizing effect on the persistence of the Great Plains Piping Plover metapopulation.

Hatching success and predation of Bog Turtle (Glyptemys muhlenbergii) eggs in New Jersey and Pennsylvania

USGS Publications Warehouse

Zappalorti, Robert T.; Tutterow, Annalee M.; Pittman, Shannon E.; Lovich, Jeffrey E.

2017-01-01

Nest-site selection by most turtles affects the survival of females and their offspring. Although bog turtles (Glyptemys muhlenbergii) do not typically leave their wetlands for nesting, nest-site selection can impact hatching success and hatchling survival. Between 1974 and 2012, we monitored the fates of 258 bog turtle eggs incubated in the field and 91 eggs incubated under laboratory conditions from 11 different bogs, fens, or wetland complexes in New Jersey and Pennsylvania. Laboratory-incubated eggs exhibited the greatest hatching success (81%), but we did not detect a significant difference in hatching success between nests protected with predator excluder cages (43%) and unprotected nests (33%). However, we found significantly lower predation rates in protected nests, suggesting that while predator excluder cages successfully reduced predation, other environmental factors persisted to reduce egg survival in the field. Natural hatching success was potentially reduced by poor weather conditions, which may have resulted in embryo developmental problems, dehydration, or embryos drowning in the egg. Our results suggest that egg depredation, coupled with embryo developmental problems and infertility, are limiting factors to hatching success in our study populations. Using predator excluder cages to protect bog turtle eggs in the field, or incubating eggs in the laboratory and releasing hatchlings at original nesting areas, may be an effective conservation tool for recovering populations of this federally threatened species.

Tactic changes in dusky frillgoby Bathygobius fuscus sneaker males: effects of body size and nest availability.

PubMed

Takegaki, T; Kaneko, T; Matsumoto, Y

2013-02-01

Field and laboratory studies were conducted to examine the effects of nest availability and body size on changes in male mating tactics from sneaking to nest-holding in the dusky frillgoby Bathygobius fuscus. In the field, the body size of nest-holding males decreased from early to mid-breeding season, suggesting the possibility of a change in the tactics of sneaker males to nest-holding. Many sneaker males did not use vacant spawning nests even when size-matched nests were available, but they continued to reproduce as sneakers. Similarly, in aquarium experiments with available vacant nests, some sneaker males became nest-holders irrespective of their body size, but some did not. These results showed that nest availability is not a limiting factor for changes in tactics by sneaker males in this species. Because tactic-unchanged sneaker males were co-housed with larger nest-holding males in the tanks, the body size of nearby nest-holding males may have affected the decision to change tactics for sneaker males. Moreover, smaller individuals among tactic-changed males tended to spend more time until spawning, probably because they had relatively larger costs and smaller benefits of reproduction as nest-holding males compared to larger males. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Use of a nesting platform by Gull-billed Terns and Black Skimmers at the Salton Sea, California

USGS Publications Warehouse

Molina, Kathy C.; Ricca, Mark A.; Miles, A. Keith; Schoneman, Christian

2009-01-01

In 2006, we constructed an elevated nesting platform at the Salton Sea, California, and monitored its use by Gull-billed Terns and Black Skimmers over three subsequent breeding seasons. Black Skimmers were the first to colonize the platform with a total of five nests in 2006. In 2007 Gull-billed Terns colonized the platform with a total of 28 nests and the number of Black Skimmer nests increased to 20. Neither species nested on the platform in 2008. Low success for both species was probably influenced by at least two factors. First, when both species nested on the platform, nest densities were higher than is typical of their colonies on larger, earthen islands, and colony success may have been reduced by overcrowding. Second, lack of access to water may have reduced chicks' ability to thermoregulate effectively in the hot environment of the Salton Sea. Refinements to the size, design, and location of artificial nesting habitats are necessary to enhance productivity of colonial groundnesting birds at the Salton Sea successfully.

Spawning chronology, nest site selection and nest success of smallmouth bass during benign streamflow conditions

USGS Publications Warehouse

Dauwalter, D.C.; Fisher, W.L.

2007-01-01

We documented the nesting chronology, nest site selection and nest success of smallmouth bass Micropterus dolomieu in an upstream (4th order) and downstream (5th order) reach of Baron Fork Creek, Oklahoma. Males started nesting in mid-Apr. when water temperatures increased to 16.9 C upstream, and in late-Apr. when temperatures increased to 16.2 C downstream. Streamflows were low (77% upstream to 82% downstream of mean Apr. streamflow, and 12 and 18% of meanjun. streamflow; 47 and 55 y of record), and decreased throughout the spawning period. Larger males nested first upstream, as has been observed in other populations, but not downstream. Upstream, progeny in 62 of 153 nests developed to swim-up stage. Downstream, progeny in 31 of 73 nests developed to swim-up. Nesting densities upstream (147/km) and downstream (100/km) were both higher than any densities previously reported. Males selected nest sites with intermediate water depths, low water velocity and near cover, behavior that is typical of smallmouth bass. Documented nest failures resulted from human disturbance, angling, and longear sunfish predation. Logistic exposure models showed that water velocity at the nest was negatively related and length of the guarding male was positively related to nest success upstream. Male length and number of degree days were both positively related to nest success downstream. Our results, and those of other studies, suggest that biological factors account for most nest failures during benign (stable, low flow) streamflow conditions, whereas nest failures attributed to substrate mobility or nest abandonment dominate when harsh streamflow conditions (spring floods) coincide with the spawning season.

Terrestrial nest-building by wild chimpanzees (Pan troglodytes): implications for the tree-to-ground sleep transition in early hominins.

PubMed

Koops, Kathelijne; McGrew, William C; Matsuzawa, Tetsuro; Knapp, Leslie A

2012-07-01

Nest-building is a great ape universal and arboreal nesting in chimpanzees and bonobos suggests that the common ancestor of Pan and Homo also nested in trees. It has been proposed that arboreal nest-building remained the prevailing pattern until Homo erectus, a fully terrestrial biped, emerged. We investigated the unusual occurrence of ground-nesting in chimpanzees (Pan troglodytes), which may inform on factors influencing the tree-to-ground sleep transition in the hominin lineage. We used a novel genetic approach to examine ground-nesting in unhabituated chimpanzees at Seringbara in the Nimba Mountains, Guinea. Previous research showed that ground-nesting at Seringbara was not ecologically determined. Here, we tested a possible mate-guarding function of ground-nesting by analyzing DNA from shed hairs collected from ground nests and tree nests found in close proximity. We examined whether or not ground-nesting was a group-level behavioral pattern and whether or not it occurred in more than one community. We used multiple genetic markers to identify sex and to examine variation in mitochondrial DNA control region (HV1, HV2) sequences. Ground-nesting was a male-biased behavior and males constructed more elaborate ("night") nests than simple ("day") nests on the ground. The mate-guarding hypothesis was not supported, as ground and associated tree nests were built either by maternally-related males or possibly by the same individuals. Ground-nesting was widespread and likely habitual in two communities. We suggest that terrestrial nest-building may have already occurred in arboreally-adapted early hominins before the emergence of H. erectus. Copyright © 2012 Wiley Periodicals, Inc.

New heterogeneous test statistics for the unbalanced fixed-effect nested design.

PubMed

Guo, Jiin-Huarng; Billard, L; Luh, Wei-Ming

2011-05-01

When the underlying variances are unknown or/and unequal, using the conventional F test is problematic in the two-factor hierarchical data structure. Prompted by the approximate test statistics (Welch and Alexander-Govern methods), the authors develop four new heterogeneous test statistics to test factor A and factor B nested within A for the unbalanced fixed-effect two-stage nested design under variance heterogeneity. The actual significance levels and statistical power of the test statistics were compared in a simulation study. The results show that the proposed procedures maintain better Type I error rate control and have greater statistical power than those obtained by the conventional F test in various conditions. Therefore, the proposed test statistics are recommended in terms of robustness and easy implementation. ©2010 The British Psychological Society.

Contrasting nest survival patterns for ducks and songbirds in northern mixed-grass prairie

USGS Publications Warehouse

Grant, Todd; Shaffer, Terry L.; Madden, Elizabeth M.; Nenneman, Melvin P.

2017-01-01

Management actions intended to protect or improve habitat for ducks may benefit grassland-nesting passerines, but scant information is available to explore this assumption. During 1998–2003, we examined nest survival of ducks and songbirds to determine whether effects of prescribed fire and other habitat features (e.g., shrub cover and distance to habitat edges) were similar for ducks and passerines breeding in North Dakota. We used the logistic-exposure method to estimate survival of duck and songbird nests (n = 3,171). We used an information-theoretic approach to identify factors that most influenced nest survival. Patterns of nest survival were markedly different between taxonomic groups. For ducks, nest survival was greater during the first postfire nesting season (daily survival rate [DSR] = 0.957, 85% CI = 0.951–0.963), relative to later postfire nesting seasons (DSR = 0.946, 85% CI = 0.942–0.950). Furthermore duck nest survival and nest densities were inversely related. Duck nest survival also was greater as shrub cover decreased and as distance from cropland and wetland edges increased. Passerines had lower nest survival during the first postfire nesting season (DSR = 0.934, 85% CI = 0.924–0.944), when densities also were low compared to subsequent postfire nesting seasons (DSR = 0.947, 85% CI = 0.944–0.950). Parasitism by brown-headed cowbirds (Molothrus ater) reduced passerine nest survival and this effect was more pronounced during the first postfire nesting season compared to subsequent nesting seasons. Passerine nest survival was greater as shrub cover decreased and perhaps for more concealed nests. Duck and songbird nest survival rates were not correlated during this study and for associated studies that examined additional variables using the same dataset, suggesting that different mechanisms influenced their survival. Based on our results, ducks should not be considered direct surrogates for passerines when predicting effects of prescribed fire, shrub cover, and habitat edges on nest survival.

Genetic algorithm and graph theory based matrix factorization method for online friend recommendation.

PubMed

Li, Qu; Yao, Min; Yang, Jianhua; Xu, Ning

2014-01-01

Online friend recommendation is a fast developing topic in web mining. In this paper, we used SVD matrix factorization to model user and item feature vector and used stochastic gradient descent to amend parameter and improve accuracy. To tackle cold start problem and data sparsity, we used KNN model to influence user feature vector. At the same time, we used graph theory to partition communities with fairly low time and space complexity. What is more, matrix factorization can combine online and offline recommendation. Experiments showed that the hybrid recommendation algorithm is able to recommend online friends with good accuracy.

The Effects of Describing Antecedent Stimuli and Performance Criteria in Task Analysis Instruction for Graphing

ERIC Educational Resources Information Center

Tyner, Bryan C.; Fienup, Daniel M.

2016-01-01

Task analyses are ubiquitous to applied behavior analysis interventions, yet little is known about the factors that make them effective. Numerous task analyses have been published in behavior analytic journals for constructing single-subject design graphs; however, learner outcomes using these task analyses may fall short of what could be…

Butterfly in the Quantum World; The story of the most fascinating quantum fractal

NASA Astrophysics Data System (ADS)

Satija, Indubala I.

2016-08-01

``Butterfly in the Quantum World'' by Indu Satija, with contributions by Douglas Hofstadter, is the first book ever to tell the story of the ``Hofstadter butterfly'', a beautiful and fascinating graph lying at the heart of the quantum theory of matter. The butterfly came out of a simple-sounding question: What happens if you immerse a crystal in a magnetic field? What energies can the electrons take on? From 1930 onwards, physicists struggled to answer this question, until 1974, when graduate student Douglas Hofstadter discovered that the answer was a graph consisting of nothing but copies of itself nested down infinitely many times. This wild mathematical object caught the physics world totally by surprise, and it continues to mesmerize physicists and mathematicians today. The butterfly plot is intimately related to many other important phenomena in number theory and physics, including Apollonian gaskets, the Foucault pendulum, quasicrystals, the quantum Hall effect, and many more. Its story reflects the magic, the mystery, and the simplicity of the laws of nature, and Indu Satija, in a wonderfully personal style, relates this story, enriching it with a vast number of lively historical anecdotes, many photographs, beautiful visual images, and even poems, making her book a great feast, for the eyes, for the mind and for the soul.

Graph Theoretic and Motif Analyses of the Hippocampal Neuron Type Potential Connectome.

PubMed

Rees, Christopher L; Wheeler, Diek W; Hamilton, David J; White, Charise M; Komendantov, Alexander O; Ascoli, Giorgio A

2016-01-01

We computed the potential connectivity map of all known neuron types in the rodent hippocampal formation by supplementing scantly available synaptic data with spatial distributions of axons and dendrites from the open-access knowledge base Hippocampome.org. The network that results from this endeavor, the broadest and most complete for a mammalian cortical region at the neuron-type level to date, contains more than 3200 connections among 122 neuron types across six subregions. Analyses of these data using graph theory metrics unveil the fundamental architectural principles of the hippocampal circuit. Globally, we identify a highly specialized topology minimizing communication cost; a modular structure underscoring the prominence of the trisynaptic loop; a core set of neuron types serving as information-processing hubs as well as a distinct group of particular antihub neurons; a nested, two-tier rich club managing much of the network traffic; and an innate resilience to random perturbations. At the local level, we uncover the basic building blocks, or connectivity patterns, that combine to produce complex global functionality, and we benchmark their utilization in the circuit relative to random networks. Taken together, these results provide a comprehensive connectivity profile of the hippocampus, yielding novel insights on its functional operations at the computationally crucial level of neuron types.

Graph theory applied to noise and vibration control in statistical energy analysis models.

PubMed

Guasch, Oriol; Cortés, Lluís

2009-06-01

A fundamental aspect of noise and vibration control in statistical energy analysis (SEA) models consists in first identifying and then reducing the energy flow paths between subsystems. In this work, it is proposed to make use of some results from graph theory to address both issues. On the one hand, linear and path algebras applied to adjacency matrices of SEA graphs are used to determine the existence of any order paths between subsystems, counting and labeling them, finding extremal paths, or determining the power flow contributions from groups of paths. On the other hand, a strategy is presented that makes use of graph cut algorithms to reduce the energy flow from a source subsystem to a receiver one, modifying as few internal and coupling loss factors as possible.

Time-specific patterns of nest survival for ducks and passerines breeding in North Dakota

USGS Publications Warehouse

Shaffer, Terry L.; Grant, Todd A.

2012-01-01

In many bird species, survival can vary with the age of the nest, with the date a nest was initiated, or among years within the same nesting area. A literature review showed that patterns of survival vary in relation to nest age and date and are often contradictory. Inconsistencies could be a result of temporal variation in the environment or life-history differences among species. We examined patterns of nest survival in relation to nest age, date, and year for several duck and passerine species nesting at a single location in North Dakota during 1998–2003. We predicted that if environment shaped nest survival patterns, then temporal patterns in survival might be similar among three species of upland nesting ducks, and also among three species of grassland passerines nesting at the same site. We expected that survival patterns would differ between ducks and passerines because of relatively disparate life histories and differences in predators that prey on their nests. Nest survival was rarely constant among years, seasonally, or with age of the nest for species that we studied. As predicted, the pattern of survival was similar among duck species, driven mainly by differences in nest survival associated with nest initiation date. The pattern of survival also was similar among passerine species, but nest survival was more influenced by nest age than by date. Our findings suggest that some but not all variation in temporal patterns of nest survival in grassland birds reported in the literature can be explained on the basis of temporal environmental variation. Because patterns of survival were dissimilar among ducks and passerines, it is likely that mechanisms such as predation or brood parasitism have variable influences on productivity of ducks and passerines nesting in the same area. Our results indicate that biologists and managers should not assume that temporal environmental variations, especially factors that affect nest survival, act similarly on all grassland birds.

A framework for graph-based synthesis, analysis, and visualization of HPC cluster job data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayo, Jackson R.; Kegelmeyer, W. Philip, Jr.; Wong, Matthew H.

The monitoring and system analysis of high performance computing (HPC) clusters is of increasing importance to the HPC community. Analysis of HPC job data can be used to characterize system usage and diagnose and examine failure modes and their effects. This analysis is not straightforward, however, due to the complex relationships that exist between jobs. These relationships are based on a number of factors, including shared compute nodes between jobs, proximity of jobs in time, etc. Graph-based techniques represent an approach that is particularly well suited to this problem, and provide an effective technique for discovering important relationships in jobmore » queuing and execution data. The efficacy of these techniques is rooted in the use of a semantic graph as a knowledge representation tool. In a semantic graph job data, represented in a combination of numerical and textual forms, can be flexibly processed into edges, with corresponding weights, expressing relationships between jobs, nodes, users, and other relevant entities. This graph-based representation permits formal manipulation by a number of analysis algorithms. This report presents a methodology and software implementation that leverages semantic graph-based techniques for the system-level monitoring and analysis of HPC clusters based on job queuing and execution data. Ontology development and graph synthesis is discussed with respect to the domain of HPC job data. The framework developed automates the synthesis of graphs from a database of job information. It also provides a front end, enabling visualization of the synthesized graphs. Additionally, an analysis engine is incorporated that provides performance analysis, graph-based clustering, and failure prediction capabilities for HPC systems.« less

Fast Decentralized Averaging via Multi-scale Gossip

NASA Astrophysics Data System (ADS)

Tsianos, Konstantinos I.; Rabbat, Michael G.

We are interested in the problem of computing the average consensus in a distributed fashion on random geometric graphs. We describe a new algorithm called Multi-scale Gossip which employs a hierarchical decomposition of the graph to partition the computation into tractable sub-problems. Using only pairwise messages of fixed size that travel at most O(n^{1/3}) hops, our algorithm is robust and has communication cost of O(n loglogn logɛ - 1) transmissions, which is order-optimal up to the logarithmic factor in n. Simulated experiments verify the good expected performance on graphs of many thousands of nodes.

Graphs to estimate an individualized risk of breast cancer.

PubMed

Benichou, J; Gail, M H; Mulvihill, J J

1996-01-01

Clinicians who counsel women about their risk for developing breast cancer need a rapid method to estimate individualized risk (absolute risk), as well as the confidence limits around that point. The Breast Cancer Detection Demonstration Project (BCDDP) model (sometimes called the Gail model) assumes no genetic model and simultaneously incorporates five risk factors, but involves cumbersome calculations and interpolations. This report provides graphs to estimate the absolute risk of breast cancer from the BCDDP model. The BCDDP recruited 280,000 women from 1973 to 1980 who were monitored for 5 years. From this cohort, 2,852 white women developed breast cancer and 3,146 controls were selected, all with complete risk-factor information. The BCDDP model, previously developed from these data, was used to prepare graphs that relate a specific summary relative-risk estimate to the absolute risk of developing breast cancer over intervals of 10, 20, and 30 years. Once a summary relative risk is calculated, the appropriate graph is chosen that shows the 10-, 20-, or 30-year absolute risk of developing breast cancer. A separate graph gives the 95% confidence limits around the point estimate of absolute risk. Once a clinician rules out a single gene trait that predisposes to breast cancer and elicits information on age and four risk factors, the tables and figures permit an estimation of a women's absolute risk of developing breast cancer in the next three decades. These results are intended to be applied to women who undergo regular screening. They should be used only in a formal counseling program to maximize a woman's understanding of the estimates and the proper use of them.

Using Behavior Over Time Graphs to Spur Systems Thinking Among Public Health Practitioners.

PubMed

Calancie, Larissa; Anderson, Seri; Branscomb, Jane; Apostolico, Alexsandra A; Lich, Kristen Hassmiller

2018-02-01

Public health practitioners can use Behavior Over Time (BOT) graphs to spur discussion and systems thinking around complex challenges. Multiple large systems, such as health care, the economy, and education, affect chronic disease rates in the United States. System thinking tools can build public health practitioners' capacity to understand these systems and collaborate within and across sectors to improve population health. BOT graphs show a variable, or variables (y axis) over time (x axis). Although analyzing trends is not new to public health, drawing BOT graphs, annotating the events and systemic forces that are likely to influence the depicted trends, and then discussing the graphs in a diverse group provides an opportunity for public health practitioners to hear each other's perspectives and creates a more holistic understanding of the key factors that contribute to a trend. We describe how BOT graphs are used in public health, how they can be used to generate group discussion, and how this process can advance systems-level thinking. Then we describe how BOT graphs were used with groups of maternal and child health (MCH) practitioners and partners (N = 101) during a training session to advance their thinking about MCH challenges. Eighty-six percent of the 84 participants who completed an evaluation agreed or strongly agreed that they would use this BOT graph process to engage stakeholders in their home states and jurisdictions. The BOT graph process we describe can be applied to a variety of public health issues and used by practitioners, stakeholders, and researchers.

Cognitive and attitudinal predictors related to graphing achievement among pre-service elementary teachers

NASA Astrophysics Data System (ADS)

Szyjka, Sebastian P.

The purpose of this study was to determine the extent to which six cognitive and attitudinal variables predicted pre-service elementary teachers' performance on line graphing. Predictors included Illinois teacher education basic skills sub-component scores in reading comprehension and mathematics, logical thinking performance scores, as well as measures of attitudes toward science, mathematics and graphing. This study also determined the strength of the relationship between each prospective predictor variable and the line graphing performance variable, as well as the extent to which measures of attitude towards science, mathematics and graphing mediated relationships between scores on mathematics, reading, logical thinking and line graphing. Ninety-four pre-service elementary education teachers enrolled in two different elementary science methods courses during the spring 2009 semester at Southern Illinois University Carbondale participated in this study. Each subject completed five different instruments designed to assess science, mathematics and graphing attitudes as well as logical thinking and graphing ability. Sixty subjects provided copies of primary basic skills score reports that listed subset scores for both reading comprehension and mathematics. The remaining scores were supplied by a faculty member who had access to a database from which the scores were drawn. Seven subjects, whose scores could not be found, were eliminated from final data analysis. Confirmatory factor analysis (CFA) was conducted in order to establish validity and reliability of the Questionnaire of Attitude Toward Line Graphs in Science (QALGS) instrument. CFA tested the statistical hypothesis that the five main factor structures within the Questionnaire of Attitude Toward Statistical Graphs (QASG) would be maintained in the revised QALGS. Stepwise Regression Analysis with backward elimination was conducted in order to generate a parsimonious and precise predictive model. This procedure allowed the researcher to explore the relationships among the affective and cognitive variables that were included in the regression analysis. The results for CFA indicated that the revised QALGS measure was sound in its psychometric properties when tested against the QASG. Reliability statistics indicated that the overall reliability for the 32 items in the QALGS was .90. The learning preferences construct had the lowest reliability (.67), while enjoyment (.89), confidence (.86) and usefulness (.77) constructs had moderate to high reliabilities. The first four measurement models fit the data well as indicated by the appropriate descriptive and statistical indices. However, the fifth measurement model did not fit the data well statistically, and only fit well with two descriptive indices. The results addressing the research question indicated that mathematical and logical thinking ability were significant predictors of line graph performance among the remaining group of variables. These predictors accounted for 41% of the total variability on the line graph performance variable. Partial correlation coefficients indicated that mathematics ability accounted for 20.5% of the variance on the line graphing performance variable when removing the effect of logical thinking. The logical thinking variable accounted for 4.7% of the variance on the line graphing performance variable when removing the effect of mathematics ability.

Distortions in memory for visual displays

NASA Technical Reports Server (NTRS)

Tversky, Barbara

1989-01-01

Systematic errors in perception and memory present a challenge to theories of perception and memory and to applied psychologists interested in overcoming them as well. A number of systematic errors in memory for maps and graphs are reviewed, and they are accounted for by an analysis of the perceptual processing presumed to occur in comprehension of maps and graphs. Visual stimuli, like verbal stimuli, are organized in comprehension and memory. For visual stimuli, the organization is a consequence of perceptual processing, which is bottom-up or data-driven in its earlier stages, but top-down and affected by conceptual knowledge later on. Segregation of figure from ground is an early process, and figure recognition later; for both, symmetry is a rapidly detected and ecologically valid cue. Once isolated, figures are organized relative to one another and relative to a frame of reference. Both perceptual (e.g., salience) and conceptual factors (e.g., significance) seem likely to affect selection of a reference frame. Consistent with the analysis, subjects perceived and remembered curves in graphs and rivers in maps as more symmetric than they actually were. Symmetry, useful for detecting and recognizing figures, distorts map and graph figures alike. Top-down processes also seem to operate in that calling attention to the symmetry vs. asymmetry of a slightly asymmetric curve yielded memory errors in the direction of the description. Conceptual frame of reference effects were demonstrated in memory for lines embedded in graphs. In earlier work, the orientation of map figures was distorted in memory toward horizontal or vertical. In recent work, graph lines, but not map lines, were remembered as closer to an imaginary 45 deg line than they had been. Reference frames are determined by both perceptual and conceptual factors, leading to selection of the canonical axes as a reference frame in maps, but selection of the imaginary 45 deg as a reference frame in graphs.

Why wasp foundresses change nests: relatedness, dominance, and nest quality.

PubMed

Seppä, Perttu; Queller, David C; Strassmann, Joan E

2012-01-01

The costs and benefits of different social options are best understood when individuals can be followed as they make different choices, something that can be difficult in social insects. In this detailed study, we follow overwintered females of the social wasp Polistes carolina through different nesting strategies in a stratified habitat where nest site quality varies with proximity to a foraging area, and genetic relatedness among females is known. Females may initiate nests, join nests temporarily or permanently, or abandon nests. Females can become helpers or egglayers, effectively workers or queens. What they actually do can be predicted by a combination of ecological and relatedness factors. Advantages through increased lifetime success of individuals and nests drives foundresses of the social wasp Polistes from solitary to social nest founding. We studied reproductive options of spring foundresses of P. carolina by monitoring individually-marked wasps and assessing reproductive success of each foundress by using DNA microsatellites. We examined what behavioral decisions foundresses make after relaxing a strong ecological constraint, shortage of nesting sites. We also look at the reproductive consequences of different behaviors. As in other Polistes, the most successful strategy for a foundress was to initiate a nest as early as possible and then accept others as subordinates. A common feature for many P. carolina foundresses was, however, that they reassessed their reproductive options by actively monitoring other nests at the field site and sometimes moving permanently to new nests should that offer better (inclusive) fitness prospects compared to their original nests. A clear motivation for moving to new nests was high genetic relatedness; by the end of the foundress period all females were on nests with full sisters.

Nest visits and capture events affect breeding success of Yellow-billed and Pacific loons

USGS Publications Warehouse

Uher-Koch, Brian D.; Schmutz, Joel A.; Wright, Kenneth G.

2015-01-01

Accurate estimates of breeding success are essential for understanding population dynamics and for managing populations. Unfortunately, research activities to collect these data can negatively impact the breeding success of the study species and bias estimates of breeding success. Despite the potential for negative impacts, few studies have documented the effect of capturing incubating adults on nest survival or compared nest survival following different capture methods. In this study we evaluate the impacts of investigator disturbance associated with captures and nest visits on nest survival of Yellow-billed Loons (Gavia adamsii) and Pacific Loons (Gavia pacifica) in the National Petroleum Reserve-Alaska (NPR-A), an area of conservation concern, in 2011–2013. In an effort to reduce capture-related nest failures, we developed a new suspended dive net technique to catch territorial aquatic birds while off their nests. We then compared nest survival following suspended dive net captures to bow-net trap captures of breeding adult loons. Daily nest survival following bow-net trap or suspended dive net capture was about 30% lower than when adults were not captured. The effect of captures on nest survival was similar between bow-net trap and suspended dive net capture methods. Nest visits without captures also negatively impacted nest survival, although less than captures. If not accounted for, nest visitation biased daily survival rates of nests downward 6%. Effects of investigator disturbance did not differ by species or between years. Our results suggest that any source of disturbance that displaces incubating adult loons could potentially reduce nest survival. To maximize breeding success, human disturbance factors should be limited near loon nests.

Nesting ecology of Whimbrels in boreal Alaska

USGS Publications Warehouse

Harwood, Christopher M.; Gill, Robert E.; Powell, Abby

2016-01-01

Breeding ecology studies of boreal waders have been relatively scarce in North America. This paucity is due in part to boreal habitats being difficult to access, and boreal waders being widely dispersed and thus difficult to monitor. Between 2008 and 2014 we studied the nesting ecology of Whimbrels Numenius phaeopus hudsonicus in interior Alaska, a region characterized by an active wildfire regime. Our objectives were to (1) describe the nesting ecology of Whimbrels in tundra patches within the boreal forest, (2) assess the influence of habitat features at multiple scales on nest-site selection, and (3) characterize factors affecting nest survival. Whimbrels nested in the largest patches and exhibited a consistently compressed annual breeding schedule. We hypothesized that these Whimbrels would exhibit synchronous and clustered nesting, but observed synchronous nesting in only 2009 and 2011, and evidence of clustered nesting at just one study area in 2009, providing limited support for the hypothesis. Nests tended to be on hummocks and exhibited lateral concealment around the bowl, suggesting a trade-off between a greater view from the nest and concealment. However, our analysis failed to identify other important habitat features at scales from 1–400 m from the nest. Our best-supported nest survival model showed a strong difference between our two main study areas, but this difference remains largely unexplained. Given the increased frequency, severity, and extent of wildfires predicted under climate change scenarios, our study highlights the importance of monitoring the persistence of boreal tundra patches and the Whimbrels breeding therein.

A real-time expert system for self-repairing flight control

NASA Technical Reports Server (NTRS)

Gaither, S. A.; Agarwal, A. K.; Shah, S. C.; Duke, E. L.

1989-01-01

An integrated environment for specifying, prototyping, and implementing a self-repairing flight-control (SRFC) strategy is described. At an interactive workstation, the user can select paradigms such as rule-based expert systems, state-transition diagrams, and signal-flow graphs and hierarchically nest them, assign timing and priority attributes, establish blackboard-type communication, and specify concurrent execution on single or multiple processors. High-fidelity nonlinear simulations of aircraft and SRFC systems can be performed off-line, with the possibility of changing SRFC rules, inference strategies, and other heuristics to correct for control deficiencies. Finally, the off-line-generated SRFC can be transformed into highly optimized application-specific real-time C-language code. An application of this environment to the design of aircraft fault detection, isolation, and accommodation algorithms is presented in detail.

Why are Tailored Messages More Effective? A Multiple Mediation Analysis of a Breast Cancer Screening Intervention.

PubMed

Jensen, Jakob D; King, Andy J; Carcioppolo, Nicholas; Davis, LaShara

2012-10-01

Past research has found that tailoring increases the persuasive effectiveness of a message. However, the observed effect has been small and the explanatory mechanism remains unknown. To address these shortcomings, a tailoring software program was created that personalized breast cancer screening pamphlets according to risk, health belief model constructs, and visual preference. Women aged 40 and older ( N = 119) participated in a 2 (tailored vs. stock message) × 2 (charts/graphs vs. illustrated visuals) × 3 (nested replications of the visuals) experiment. Participants provided with tailored illustrated pamphlets expressed greater breast cancer screening intentions than those provided with other pamphlets. In a test of 10 different mediators, perceived message relevance was found to fully mediate the tailoring × visual interaction.

Experimental shifts in egg-nest contrasts do not alter egg rejection responses in an avian host-brood parasite system.

PubMed

Hauber, Mark E; Aidala, Zachary; Igic, Branislav; Shawkey, Matthew D; Moskát, Csaba

2015-09-01

Obligate brood parasitic birds exploit their hosts to provide care for unrelated young in the nest. Potential hosts can reduce the cost of parasitism by rejecting foreign eggs from the nest. Observational, comparative, and experimental studies have concluded that most hosts use the coloration and patterning of eggshells to discriminate between own and foreign eggs in the nest. However, an alternative hypothesis is that birds use the colour contrasts between eggshells and the nest lining to identify parasitic eggs (egg-nest contrast hypothesis). In support of this hypothesis, we found that the avian perceivable chromatic contrasts between dyed eggs and unmanipulated nest linings significantly and negatively covaried with the rejection rates of different dyed eggs of the great reed warbler Acrocephalus arundinaceus, a frequently parasitized host of the common cuckoo Cuculus canorus. To experimentally test whether egg-nest contrasts influence rejection, we reciprocally dyed both eggs and the nest lining of this host species with one of two colours: orange and green. Contrary to the egg-nest contrast hypothesis, host rejection patterns in response to dyed eggs were not altered by dyeing nests, relative to unmanipulated control eggs and nests. In turn, experimental egg colour was the only significant predictor of egg rejection rate. Our results demonstrate that egg-nest contrast is a collateral, not a causal factor in egg rejection, and confirm the conclusions of previous studies that hosts can rely on the parasitic egg's appearance itself to recognize the foreign egg in the nest.

A multiscale analysis of nest predation on Least Bell's Vireos (Vireo bellii pusillus)

USGS Publications Warehouse

Kus, Barbara E.; Peterson, Bonnie L.; Deutschman, Douglas H.

2008-01-01

We examined variables influencing nest predation on the endangered Least Bell's Vireo (Vireo bellii pusillus) at three spatial scales to determine what nest-site, habitat, or landscape characteristics affect the likelihood of nest predation and to determine the spatial distribution of predation risk and the variables influencing it. We used MARK to calculate daily survival rates of Least Bell's Vireo nests and applied an information-theoretic approach to evaluate support for logistic regression models of the effect of habitat variables on predation risk. Analysis of data for 195 nests collected during 1999 and 2000 at the San Luis Rey River and Pilgrim Creek in southern California revealed no effect of fine-scale factors, including nest height, supporting plant species, and three measures of nest concealment, on the likelihood of predation. At the intermediate scale, distances to the riparian-habitat edge and to internal gaps in the canopy were unrelated to nest survival. Surrounding land-use type was a poor predictor of predation risk, with the exception of proximity to golf course–park habitat and wetland. Nests within 400 m of golf course–park were only 20% as likely to avoid predation as nests >400 m from this habitat, and nests near wetland were more than twice as likely to survive as nests distant from wetland. Spatially, predation appeared to be random throughout the site, with localized clustering evident in the vicinity of golf course–park and wetland. Our results suggest that the landscape may be the most appropriate scale at which to manage nest predation in this system.

Daily survival rate for nests and chicks of Least Terns (Sternula antillarum) at natural nest sites in South Carolina

USGS Publications Warehouse

Brooks, Gillian L.; Sanders, Felicia J.; Gerard, Patrick D.; Jodice, Patrick G.R.

2013-01-01

Although a species of conservation concern, little is known about the reproductive success of Least Terns (Sternula antillarum) throughout the southeastern USA where availability of natural beaches for nesting is limited. Daily survival rate (DSR) of nests and chicks was examined at four natural nesting sites in Cape Romain National Wildlife Refuge, South Carolina, 2009–2010. Measures of nest success (n = 257 nests) ranged from 0–93% among colony sites. The DSR of nests was primarily related to colony site, but year and estimates of predation risk also were related to DSR. Predation was the principal cause of identifiable nest loss, accounting for 47% of nest failures when the two years of data were pooled. The probability (± SE) of a chick surviving from hatching to fledging = 0.449 ± 0.01 (n = 92 chicks). DSR of chicks was negatively related to tide height and rainfall. Therefore, productivity of Least Terns is being lost during both the nesting and chick stage through a combination of biotic and abiotic factors that may prove difficult to fully mitigate or manage. Although natural nesting sites within Cape Romain National Wildlife Refuge intermittently produce successful nests, the consistency of productivity over the long term is still unknown. Given that the long term availability of anthropogenic nest sites (e.g., rooftops, dredge-spoil islands) for Least Terns is questionable, further research is required both locally and throughout the region to assess the extent to which natural sites act as population sources or sinks.

Levels of line graph question interpretation with intermediate elementary students of varying scientific and mathematical knowledge and ability: A think aloud study

NASA Astrophysics Data System (ADS)

Keller, Stacy Kathryn

This study examined how intermediate elementary students' mathematics and science background knowledge affected their interpretation of line graphs and how their interpretations were affected by graph question levels. A purposive sample of 14 6th-grade students engaged in think aloud interviews (Ericsson & Simon, 1993) while completing an excerpted Test of Graphing in Science (TOGS) (McKenzie & Padilla, 1986). Hand gestures were video recorded. Student performance on the TOGS was assessed using an assessment rubric created from previously cited factors affecting students' graphing ability. Factors were categorized using Bertin's (1983) three graph question levels. The assessment rubric was validated by Padilla and a veteran mathematics and science teacher. Observational notes were also collected. Data were analyzed using Roth and Bowen's semiotic process of reading graphs (2001). Key findings from this analysis included differences in the use of heuristics, self-generated questions, science knowledge, and self-motivation. Students with higher prior achievement used a greater number and variety of heuristics and more often chose appropriate heuristics. They also monitored their understanding of the question and the adequacy of their strategy and answer by asking themselves questions. Most used their science knowledge spontaneously to check their understanding of the question and the adequacy of their answers. Students with lower and moderate prior achievement favored one heuristic even when it was not useful for answering the question and rarely asked their own questions. In some cases, if students with lower prior achievement had thought about their answers in the context of their science knowledge, they would have been able to recognize their errors. One student with lower prior achievement motivated herself when she thought the questions were too difficult. In addition, students answered the TOGS in one of three ways: as if they were mathematics word problems, science data to be analyzed, or they were confused and had to guess. A second set of findings corroborated how science background knowledge affected graph interpretation: correct science knowledge supported students' reasoning, but it was not necessary to answer any question correctly; correct science knowledge could not compensate for incomplete mathematics knowledge; and incorrect science knowledge often distracted students when they tried to use it while answering a question. Finally, using Roth and Bowen's (2001) two-stage semiotic model of reading graphs, representative vignettes showed emerging patterns from the study. This study added to our understanding of the role of science content knowledge during line graph interpretation, highlighted the importance of heuristics and mathematics procedural knowledge, and documented the importance of perception attentions, motivation, and students' self-generated questions. Recommendations were made for future research in line graph interpretation in mathematics and science education and for improving instruction in this area.

A Constant-Factor Approximation Algorithm for the Link Building Problem

NASA Astrophysics Data System (ADS)

Olsen, Martin; Viglas, Anastasios; Zvedeniouk, Ilia

In this work we consider the problem of maximizing the PageRank of a given target node in a graph by adding k new links. We consider the case that the new links must point to the given target node (backlinks). Previous work [7] shows that this problem has no fully polynomial time approximation schemes unless P = NP. We present a polynomial time algorithm yielding a PageRank value within a constant factor from the optimal. We also consider the naive algorithm where we choose backlinks from nodes with high PageRank values compared to the outdegree and show that the naive algorithm performs much worse on certain graphs compared to the constant factor approximation scheme.

Body size mediates social and environmental effects on nest building behaviour in a fish with paternal care.

PubMed

Lehtonen, Topi K; Lindström, Kai; Wong, Bob B M

2015-07-01

Body size, social setting, and the physical environment can all influence reproductive behaviours, but their interactions are not well understood. Here, we investigated how male body size, male-male competition, and water turbidity influence nest-building behaviour in the sand goby (Pomatoschistus minutus), a marine fish with exclusive paternal care. We found that environmental and social factors affected the nest characteristics of small and large males differently. In particular, association between male size and the level of nest elaboration (i.e. the amount of sand piled on top of the nest) was positive only under clear water conditions. Similarly, male size and nest entrance size were positively associated only in the absence of competition. Such interactions may, in turn, help to explain the persistence of variation in reproductive behaviours, which-due to their importance in offspring survival-are otherwise expected to be under strong balancing selection.

Daily survival rates for nests of Black Skimmers from a core breeding area of the Southeastern USA

USGS Publications Warehouse

Brooks, Gillian L.; Sanders, Felicia J.; Gerard, Patrick D.; Jodice, Patrick G.R.

2014-01-01

Little is known about the reproductive success of Black Skimmers (Rynchops niger) throughout the southeastern USA where availability of undisturbed beaches for nesting is limited. Daily survival rates (DSR) of nests were examined at three nesting sites in Cape Romain National Wildlife Refuge (CRNWR), South Carolina, USA, 2009–2010. The percent of successful nests (n  =  346 nests) ranged from 42–69% among colony sites when data were pooled across both years. The DSR of nests was primarily related to colony site, predation risk, height of high tide, and clutch size. Predation and overwash were the principal causes of identifiable nest loss, each accounting for ∼33% of nest failures during the two study years. Because of the challenges of resighting skimmer chicks, we were not able to measure chick survival effectively and therefore accurate measures of productivity remain elusive. High variability in nest success among sites within close proximity to each other (<20 km) suggests factors at local scales such as disturbance, predation, and overwash events strongly influenced nest success of Black Skimmers during these 2 years as opposed to more region-wide stressors such as tropical storms or food availability. Although time-intensive techniques to control predators do exist, management options to limit flooding and overwash are far more limited. Conservation of Black Skimmers in the southeastern USA would benefit from coordinated, multi-state efforts to measure nest and chick survival.

Renesting by dusky Canada geese on the Copper River Delta, Alaska

USGS Publications Warehouse

Fondell, Thomas F.; Grand, James B.; Miller, David A.W.; Anthony, R. Michael

2006-01-01

The population of dusky Canada geese (Branta canadensis occidentalis; hereafter duskies) breeding on the Copper River Delta (CRD), Alaska, USA, has been in long-term decline, largely as a result of reduced productivity. Estimates of renesting rates by duskies may be useful for adjusting estimates of the size of the breeding population derived from aerial surveys and for understanding population dynamics. We used a marked population of dusky females to obtain estimates of renesting propensity and renesting interval on the CRD, 1999–2000. Continuation nests, replacement nests initiated without a break in the laying sequence, resulted only after first nests were destroyed in the laying stage with ≤4 eggs laid. Renesting propensity declined with nest age from 72% in mid-laying to 30% in early incubation. Between first nests and renests, mean interval was 11.9 ± 0.6 days, mean distance was 74.5 m (range 0–214 m), and clutch size declined 0.9 ± 0.4 eggs. We incorporated our renesting estimates and available estimates of other nesting parameters into an individual-based model to predict the proportion of first nests, continuation nests, and renests, and to examine female success on the CRD, 1997–2000. Our model predicted that 19–36% of nests each year were continuation nests and renests. Also, through 15 May (the approx. date of breeding ground surveys), 1.1–1.3 nests were initiated per female. Thus, the number of nests per female would have a significant, though relatively consistent, effect on adjusting the relation between numbers of nests found on ground surveys versus numbers of birds seen during aerial surveys. We also suggest a method that managers could use to predict nests per female using nest success of early nests. Our model predicted that relative to observed estimates of nest success, female success was 32–100% greater, due to replacement nests. Thus, although nest success remains low, production for duskies was higher than previously thought. For dusky Canada geese, managers need to consider both continuation nests and renests in designing surveys and in calculating adjustment factors for the expansion of aerial survey data using nest densities.

Orbit-product representation and correction of Gaussian belief propagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Jason K; Chertkov, Michael; Chernyak, Vladimir

We present a new interpretation of Gaussian belief propagation (GaBP) based on the 'zeta function' representation of the determinant as a product over orbits of a graph. We show that GaBP captures back-tracking orbits of the graph and consider how to correct this estimate by accounting for non-backtracking orbits. We show that the product over non-backtracking orbits may be interpreted as the determinant of the non-backtracking adjacency matrix of the graph with edge weights based on the solution of GaBP. An efficient method is proposed to compute a truncated correction factor including all non-backtracking orbits up to a specified length.

Mapping risk for nest predation on a barrier island

USGS Publications Warehouse

Hackney, Amanda D.; Baldwin, Robert F.; Jodice, Patrick G.R.

2013-01-01

Barrier islands and coastal beach systems provide nesting habitat for marine and estuarine turtles. Densely settled coastal areas may subsidize nest predators. Our purpose was to inform conservation by providing a greater understanding of habitat-based risk factors for nest predation, for an estuarine turtle. We expected that habitat conditions at predated nests would differ from random locations at two spatial extents. We developed and validated an island-wide model for the distribution of predated Diamondback terrapin nests using locations of 198 predated nests collected during exhaustive searches at Fisherman Island National Wildlife Refuge, USA. We used aerial photographs to identify all areas of possible nesting habitat and searched each and surrounding environments for nests, collecting location and random-point microhabitat data. We built models for the probability of finding a predated nest using an equal number of random points and validated them with a reserve set (N = 67). Five variables in 9 a priori models were used and the best selected model (AIC weight 0.98) reflected positive associations with sand patches near marshes and roadways. Model validation had an average capture rate of predated nests of 84.14 % (26.17–97.38 %, Q1 77.53 %, median 88.07 %, Q3 95.08 %). Microhabitat selection results suggest that nests placed at the edges of sand patches adjacent to upland shrub/forest and marsh systems are vulnerable to predation. Forests and marshes provide cover and alternative resources for predators and roadways provide access; a suggestion is to focus nest protection efforts on the edges of dunes, near dense vegetation and roads.

Quantifying avian nest survival along an urbanization gradient using citizen- and scientist-generated data.

PubMed

Ryder, Thomas B; Reitsma, Robert; Evans, Brian; Marra, Peter P

2010-03-01

Despite the increasing pace of urbanization little is known about the factors that limit bird populations (i.e., population-level processes) within the urban/suburban land-use matrix. Here, we report rates of nest survival within the matrix of an urban land-use gradient in the greater Washington, D.C., USA, area for five common songbirds using data collected by scientists and citizens as part of a project called Neighborhood Nestwatch. Using program MARK, we modeled the effects of species, urbanization at multiple spatial scales (canopy cover and impervious surface), and observer (citizen vs. scientist) on nest survival of four open-cup and one cavity-nesting species. In addition, artificial nests were used to determine the relative impacts of specific predators along the land-use gradient. Our results suggest that predation on nests within the land-use matrix declines with urbanization but that there are species-specific differences. Moreover, variation in nest survival among species was best explained by urbanization metrics measured at larger "neighborhood" spatial scales (e.g., 1000 m). Trends were supported by data from artificial nests and suggest that variable predator communities (avian vs. mammalian) are one possible mechanism to explain differential nest survival. In addition, we assessed the quality of citizen science data and show that citizens had no negative effect on nest survival and provided estimates of nest survival comparable to Smithsonian biologists. Although birds nesting within the urban matrix experienced higher nest survival, individuals also faced a multitude of other challenges such as contaminants and invasive species, all of which could reduce adult survival.

Dynamics of habitat selection in birds: adaptive response to nest predation depends on multiple factors.

PubMed

Devries, J H; Clark, R G; Armstrong, L M

2018-05-01

According to theory, habitat selection by organisms should reflect underlying habitat-specific fitness consequences and, in birds, reproductive success has a strong impact on population growth in many species. Understanding processes affecting habitat selection also is critically important for guiding conservation initiatives. Northern pintails (Anas acuta) are migratory, temperate-nesting birds that breed in greatest concentrations in the prairies of North America and their population remains below conservation goals. Habitat loss and changing land use practices may have decoupled formerly reliable fitness cues with respect to nest habitat choices. We used data from 62 waterfowl nesting study sites across prairie Canada (1997-2009) to examine nest survival, a primary fitness metric, at multiple scales, in combination with estimates of habitat selection (i.e., nests versus random points), to test for evidence of adaptive habitat choices. We used the same habitat covariates in both analyses. Pintail nest survival varied with nest initiation date, nest habitat, pintail breeding pair density, landscape composition and annual moisture. Selection of nesting habitat reflected patterns in nest survival in some cases, indicating adaptive selection, but strength of habitat selection varied seasonally and depended on population density and landscape composition. Adaptive selection was most evident late in the breeding season, at low breeding densities and in cropland-dominated landscapes. Strikingly, at high breeding density, habitat choice appears to become maladaptive relative to nest predation. At larger spatial scales, the relative availability of habitats with low versus high nest survival, and changing land use practices, may limit the reproductive potential of pintails.

Species richness and distributions of boreal waterbirds in relation to nesting and brood-rearing habitats

USGS Publications Warehouse

Lewis, Tyler L.; Lindberg, Mark S.; Schmutz, Joel A.; Bertram, Mark R.; Dubour, Adam J.

2015-01-01

Identification of ecological factors that drive animal distributions allows us to understand why distributions vary temporally and spatially, and to develop models to predict future changes to populations–vital tools for effective wildlife management and conservation. For waterbird broods in the boreal forest, distributions are likely driven by factors affecting quality of nesting and brood-rearing habitats, and the influence of these factors may extend beyond singles species, affecting the entire waterbird community. We used occupancy models to assess factors influencing species richness of waterbird broods on 72 boreal lakes, along with brood distributions of 3 species of conservation concern: lesser scaup (Aythya affinis), white-winged scoters (Melanitta fusca), and horned grebe (Podiceps auritus). Factors examined included abundance of invertebrate foods (Amphipoda, Diptera, Gastropoda, Hemiptera, Odonata), physical lake attributes (lake area, emergent vegetation), water chemistry (nitrogen, phosphorus, chlorophyll a concentrations), and nesting habitats (water edge, non-forest cover). Of the 5 invertebrates, only amphipod density was related to richness and occupancy, consistently having a large and positive relationship. Despite this importance to waterbirds, amphipods were the most patchily distributed invertebrate, with 17% of the study lakes containing 70% of collected amphipods. Lake area was the only other covariate that strongly and positively influenced species richness and occupancy of scaup, scoters, and grebes. All 3 water chemistry covariates, which provided alternative measures of lake productivity, were positively related to species richness but had little effect on scaup, scoter, and grebe occupancy. Conversely, emergent vegetation was negatively related to richness, reflecting avoidance of overgrown lakes by broods. Finally, nesting habitats had no influence on richness and occupancy, indicating that, at a broad spatial scale, brood distributions are largely driven by the presence of quality brood-rearing lakes, not nesting habitats. Our findings are relevant to generating conservation plans or management goals; specifically, boreal lakes with abundant amphipods and surface areas >25 ha are important habitat for waterbird broods and merit conservation, especially given the patchy distribution of amphipods. Moreover, these high quality brood-rearing lakes are much rarer, and thus more constraining, than are quality nesting habitats, which are likely abundant in the boreal.

Nest-site selection and reproductive success of greater sage-grouse in a fire-affected habitat of northwestern Nevada

USGS Publications Warehouse

Lockyer, Zachary B.; Coates, Peter S.; Casazza, Michael L.; Espinosa, Shawn; Delehanty, David J.

2015-01-01

Identifying links between micro-habitat selection and wildlife reproduction is imperative to population persistence and recovery. This information is particularly important for landscape species such as greater sage-grouse (Centrocercus urophasianus; sage-grouse). Although this species has been widely studied, because environmental factors can affect sage-grouse populations, local and regional studies are crucial for developing viable conservation strategies. We studied the habitat-use patterns of 71 radio-marked sage-grouse inhabiting an area affected by wildfire in the Virginia Mountains of northwestern Nevada during 2009–2011 to determine the effect of micro-habitat attributes on reproductive success. We measured standard vegetation parameters at nest and random sites using a multi-scale approach (range = 0.01–15,527 ha). We used an information-theoretic modeling approach to identify environmental factors influencing nest-site selection and survival, and determine whether nest survival was a function of resource selection. Sage-grouse selected micro-sites with greater shrub canopy cover and less cheatgrass (Bromus tectorum) cover than random sites. Total shrub canopy, including sagebrush (Artemisia spp.) and other shrub species, at small spatial scales (0.8 ha and 3.1 ha) was the single contributing selection factor to higher nest survival. These results indicate that reducing the risk of wildfire to maintain important sagebrush habitats could be emphasized in sage-grouse conservation strategies in Nevada. Managers may seek to mitigate the influx of annual grass invasion by preserving large intact sagebrush-dominated stands with a mixture of other shrub species. For this area of Nevada, the results suggest that ≥40% total shrub canopy cover in sage-grouse nesting areas could yield improved reproductive success. 

Factors affecting chick provisioning by Caspian Terns nesting in the Columbia River estuary

USGS Publications Warehouse

Anderson, Scott K.; Roby, D.D.; Lyons, Donald E.; Collis, K.

2005-01-01

We investigated factors affecting chick provisioning by radio-tagged Caspian Terns (Sterna caspia) nesting in a large colony on East Sand Island in the Columbia River estuary during 2001. Caspian Tern predation on juvenile salmonids (Oncorhynchus spp.) in the estuary prompted resource managers to relocate ca. 9,000 pairs of terns nesting on Rice Island (river km 34) to East Sand Island (river km 8), where terns were expected to consume fewer salmonids in favor of marine forage fishes. This study investigated factors influencing foraging success, diet composition, and overall reproductive success at the managed Caspian Tern colony. Our results indicated that daytime colony attendance by nesting terns averaged 64% and decreased throughout the chick-rearing period, while duration of foraging trips averaged 47 min and increased during the same period; these seasonal changes were more strongly related to date than chick age. Average meal delivery rates to 2-chick broods (0.88 meals h-1) were 2.6 times greater than to 1-chick broods (0.33 meals h-1). Parents delivered more juvenile salmonids to chicks during ebb tides than flood tides, but meal delivery rates to the nest remained constant, suggesting diet composition tracks relative availability of prey species. Foraging trips resulting in delivery of juvenile salmonids averaged 68% longer than foraging trips for schooling marine forage fishes, indicating higher availability of marine prey near the colony. High availability of marine forage fish in the Columbia River estuary during 2001 was apparently responsible for high colony attendance, short foraging trips, high chick meal delivery rates, and high nesting success of Caspian Terns on East Sand Island.

Potential sources of intra-population variation in the overwintering strategy of painted turtle (Chrysemys picta) hatchlings.

PubMed

Riley, Julia L; Tattersall, Glenn J; Litzgus, Jacqueline D

2014-12-01

Many temperate animals spend half their lives in a non-active, overwintering state, and multiple adaptations have evolved to enable winter survival. One notable vertebrate model is Chrysemys picta, whose hatchlings display dichotomous overwintering strategies: some hatchlings spend their first winter aquatically after nest emergence in the autumn, whereas others overwinter terrestrially within their natal nest with subsequent emergence in the spring. The occurrence of these strategies varies among populations and temporally within populations; however, factors that determine the strategy employed by a nest in nature are unknown. We examined potential factors that influence intra-population variation in the overwintering strategy of C. picta hatchlings over two winters in Algonquin Park, Ontario. We found that environmental factors may be a trigger for the hatchling overwintering strategy: autumn-emerging nests were sloped towards the water and were surrounded by a relatively higher percentage of bare ground compared with spring-emerging nests. Autumn-emerging hatchlings were also relatively smaller. Overwintering strategy was not associated with clutch oviposition sequence, or mammalian or avian predation attempts. Instead, autumn emergence from the nest was associated with the direct mortality threat of predation by sarcophagid fly larvae. Body condition and righting response, measured as proxies of hatchling fitness, did not differ between overwintering strategies. Costs and benefits of overwintering aquatically versus terrestrially in hatchling C. picta are largely unknown, and have the potential to affect population dynamics. Understanding winter survival has great implications for turtle ecology, thus we emphasize areas for future research on dichotomous overwintering strategies in temperate hatchling turtles. © 2014. Published by The Company of Biologists Ltd.

Greater sage-grouse nest predators in the Virginia Mountains of northwestern Nevada

USGS Publications Warehouse

Lockyer, Zachary B.; Coates, Peter S.; Casazza, Michael L.; Espinosa, Shawn; Delehanty, David J.

2013-01-01

Greater sage-grouse Centrocercus urophasianus, hereafter sage-grouse, populations have declined across their range due to the loss, degradation, and fragmentation of habitat. Habitat alterations can lead not only to vegetative changes but also to shifts in animal behavior and predator composition that may influence population vital rates, such as nest success. For example, common ravens Corvus corax are sage-grouse nest predators, and common raven abundance is positively associated with human-caused habitat alterations. Because nest success is a central component to sage-grouse population persistence, research that identifies factors influencing nest success will better inform conservation efforts. We used videography to unequivocally identify sage-grouse nest predators within the Virginia Mountains of northwestern Nevada, USA, from 2009 to 2011 and used maximum likelihood to calculate daily probability of nest survival. In the Virginia Mountains, fires, energy exploration, and other anthropogenic activities have altered historic sage-grouse habitat. We monitored 71 sage-grouse nests during the study, placing video cameras at 39 nests. Cumulative nest survival for all nests was 22.4% (95% CI, 13.0–33.4%), a survival rate that was significantly lower than other published results for sage-grouse in the Great Basin. Depredation was the primary cause for nest failure in our study (82.5%), and common ravens were the most frequent sage-grouse nest predator, accounting for 46.7% of nest depredations. We also successfully documented a suite of mammalian and reptilian species depredating sage-grouse nests, including some predators never previously confirmed in the literature to be sage-grouse nest predators (i.e., bobcats Lynx rufus and long-tailed weasels Mephitis frenata). Within the high elevation, disturbed habitat of the Virginia Mountains, low sage-grouse nest success may be limiting sage-grouse population growth. These results suggest that management actions that restore habitat in the Virginia Mountains and decrease anthropogenic subsidies of ravens will benefit sage-grouse.

The effects of heterospecifics and climatic conditions on incubation behavior within a mixed-species colony

USGS Publications Warehouse

Coates, Peter S.; Brussee, Brianne E.; Hothem, Roger L.; Howe, Kristy H.; Casazza, Michael L.; Eadie, John M.

2016-01-01

Parental incubation behavior largely influences nest survival, a critical demographic process in avian population dynamics, and behaviors vary across species with different life history breeding strategies. Although research has identified nest survival advantages of mixing colonies, behavioral mechanisms that might explain these effects is largely lacking. We examined parental incubation behavior using video-monitoring techniques on Alcatraz Island, California, of black-crowned night-heron Nycticorax nycticorax(hereinafter, night-heron) in a mixed-species colony with California gulls Larus californicus and western gulls L. occidentalis. We first quantified general nesting behaviors (i.e. incubation constancy, and nest attendance), and a suite of specific nesting behaviors (i.e. inactivity, vigilance, preening, and nest maintenance) with respect to six different daily time periods. We employed linear mixed effects models to investigate environmental and temporal factors as sources of variation in incubation constancy and nest attendance using 211 nest days across three nesting seasons (2010–2012). We found incubation constancy (percent of time on the eggs) and nest attendance (percent of time at the nest) were lower for nests that were located < 3 m from one or more gull nest, which indirectly supports the predator protection hypothesis, whereby heterospecifics provide protection allowing more time for foraging and other self-maintenance activities. To our knowledge, this is the first empirical evidence of the influence of one nesting species on the incubation behavior of another. We also identified distinct differences between incubation constancy and nest attentiveness, indicating that these biparental incubating species do not share similar energetic constraints as those that are observed for uniparental species. Additionally, we found that variation in incubation behavior was a function of temperature and precipitation, where the strength of these effects was dependent on the time of day. Overall, these findings strengthen our understanding of incubation behavior and nest ecology of a colonial-nesting species.

Factors affecting hatch success of hawksbill sea turtles on Long Island, Antigua, West Indies.

PubMed

Ditmer, Mark Allan; Stapleton, Seth Patrick

2012-01-01

Current understanding of the factors influencing hawksbill sea turtle (Eretmochelys imbricata) hatch success is disparate and based on relatively short-term studies or limited sample sizes. Because global populations of hawksbills are heavily depleted, evaluating the parameters that impact hatch success is important to their conservation and recovery. Here, we use data collected by the Jumby Bay Hawksbill Project (JBHP) to investigate hatch success. The JBHP implements saturation tagging protocols to study a hawksbill rookery in Antigua, West Indies. Habitat data, which reflect the varied nesting beaches, are collected at egg deposition, and nest contents are exhumed and categorized post-emergence. We analyzed hatch success using mixed-model analyses with explanatory and predictive datasets. We incorporated a random effect for turtle identity and evaluated environmental, temporal and individual-based reproductive variables. Hatch success averaged 78.6% (SD: 21.2%) during the study period. Highly supported models included multiple covariates, including distance to vegetation, deposition date, individual intra-seasonal nest number, clutch size, organic content, and sand grain size. Nests located in open sand were predicted to produce 10.4 more viable hatchlings per clutch than nests located >1.5 m into vegetation. For an individual first nesting in early July, the fourth nest of the season yielded 13.2 more viable hatchlings than the initial clutch. Generalized beach section and inter-annual variation were also supported in our explanatory dataset, suggesting that gaps remain in our understanding of hatch success. Our findings illustrate that evaluating hatch success is a complex process, involving multiple environmental and individual variables. Although distance to vegetation and hatch success were inversely related, vegetation is an important component of hawksbill nesting habitat, and a more complete assessment of the impacts of specific vegetation types on hatch success and hatchling sex ratios is needed. Future research should explore the roles of sand structure, nest moisture, and local weather conditions.

Factors Affecting Hatch Success of Hawksbill Sea Turtles on Long Island, Antigua, West Indies

PubMed Central

Ditmer, Mark Allan; Stapleton, Seth Patrick

2012-01-01

Current understanding of the factors influencing hawksbill sea turtle (Eretmochelys imbricata) hatch success is disparate and based on relatively short-term studies or limited sample sizes. Because global populations of hawksbills are heavily depleted, evaluating the parameters that impact hatch success is important to their conservation and recovery. Here, we use data collected by the Jumby Bay Hawksbill Project (JBHP) to investigate hatch success. The JBHP implements saturation tagging protocols to study a hawksbill rookery in Antigua, West Indies. Habitat data, which reflect the varied nesting beaches, are collected at egg deposition, and nest contents are exhumed and categorized post-emergence. We analyzed hatch success using mixed-model analyses with explanatory and predictive datasets. We incorporated a random effect for turtle identity and evaluated environmental, temporal and individual-based reproductive variables. Hatch success averaged 78.6% (SD: 21.2%) during the study period. Highly supported models included multiple covariates, including distance to vegetation, deposition date, individual intra-seasonal nest number, clutch size, organic content, and sand grain size. Nests located in open sand were predicted to produce 10.4 more viable hatchlings per clutch than nests located >1.5 m into vegetation. For an individual first nesting in early July, the fourth nest of the season yielded 13.2 more viable hatchlings than the initial clutch. Generalized beach section and inter-annual variation were also supported in our explanatory dataset, suggesting that gaps remain in our understanding of hatch success. Our findings illustrate that evaluating hatch success is a complex process, involving multiple environmental and individual variables. Although distance to vegetation and hatch success were inversely related, vegetation is an important component of hawksbill nesting habitat, and a more complete assessment of the impacts of specific vegetation types on hatch success and hatchling sex ratios is needed. Future research should explore the roles of sand structure, nest moisture, and local weather conditions. PMID:22802928

Evaluating nest supplementation as a recovery strategy for the endangered rodents of the Florida Keys

USGS Publications Warehouse

Cove, Michael V.; Simons, Theodore R.; Gardner, Beth; Maurer, Andrew S.; O'Connell, Allan F.

2017-01-01

The Key Largo woodrat (Neotoma floridana smalli) and Key Largo cotton mouse (Peromyscus gossypinus allapaticola) are federally endangered subspecies endemic to the tropical hardwood hammocks of Key Largo, Florida. Woodrats are considered generalists in habitat and diet, yet a steady decline in natural stick nests and capture rates over the past several decades suggests that they are limited by the availability of nesting habitat due to habitat loss and fragmentation. The more specialized Key Largo cotton mouse appears to rely on old growth hammock, a habitat type that is rare following past land clearing. In 2004, the U.S. Fish and Wildlife Service started building supplemental nest structures to restore habitat quality and connectivity for these endangered rodents, but nest use requires evaluation. We used camera traps and occupancy models to evaluate the factors influencing woodrat and cotton mouse use of the supplemental nests. We detected woodrats at 65 and cotton mice at 175 of 284 sampled nest structures, with co-occurrence at 38 nests. Woodrat nest use followed a gradient from low nest use in the north to high nest use in the south, which might relate to the proximity of free-ranging domestic cat (Felis catus) colonies in residential developments. Cotton mouse nest use, however, was related positively to mature hammock and related negatively to disturbed areas (e.g. scarified lands). The two species occurred independently of each other. Stick-stacking behavior was observed at supplemental nests and, although it was correlated with detection of woodrats, it was not a strong predictor of their occurrence. We suggest that nest supplementation can be an important tool for species recovery as habitat quality continues to improve with succession.

Linking snake behavior to nest predation in a Midwestern bird community.

PubMed

Weatherhead, Patrick J; Carfagno, Gerardo L F; Sperry, Jinelle H; Brawn, Jeffrey D; Robinson, Scott K

2010-01-01

Nest predators can adversely affect the viability of songbird populations, and their impact is exacerbated in fragmented habitats. Despite substantial research on this predator-prey interaction, however, almost all of the focus has been on the birds rather than their nest predators, thereby limiting our understanding of the factors that bring predators and nests into contact. We used radiotelemetry to document the activity of two snake species (rat snakes, Elaphe obsoleta; racers, Coluber constrictor) known to prey on nests in Midwestern bird communities and simultaneously monitored 300 songbird nests and tested the hypothesis that predation risk should increase for nests when snakes were more active and in edge habitat preferred by both snake species. Predation risk increased when rat snakes were more active, for all nests combined and for two of the six bird species for which we had sufficient nests to allow separate analyses. This result is consistent with rat snakes being more important nest predators than racers. We found no evidence, however, that nests closer to forest edges were at greater risk. These results are generally consistent with the one previous study that investigated rat snakes and nest predation simultaneously. The seemingly paradoxical failure to find higher predation risk in the snakes' preferred habitat (i.e., edge) might be explained by the snakes using edges at least in part for non-foraging activities. We propose that higher nest predation in fragmented habitats (at least that attributable to snakes) results indirectly from edges promoting larger snake populations, rather than from edges directly increasing the risk of nest predation by snakes. If so, the notion of edges per se functioning as ecological "traps" merits further study.

Connections between Graphical Gaussian Models and Factor Analysis

ERIC Educational Resources Information Center

Salgueiro, M. Fatima; Smith, Peter W. F.; McDonald, John W.

2010-01-01

Connections between graphical Gaussian models and classical single-factor models are obtained by parameterizing the single-factor model as a graphical Gaussian model. Models are represented by independence graphs, and associations between each manifest variable and the latent factor are measured by factor partial correlations. Power calculations…

Mixed-grass prairie passerines exhibit weak and variable responses to patch size

USGS Publications Warehouse

Davis, S.K.; Brigham, R.M.; Shaffer, T.L.; James, P.C.

2006-01-01

Much of our current understanding of the demographic effects of habitat fragmentation on bird populations is derived from studies of passerines in forests and tallgrass prairie surrounded by woody vegetation. We quantified grassland bird density, nest survival, and productivity in 41 native mixed-grass prairie pastures during 1997-2000 in southern Saskatchewan, Canada. Pastures ranged in size from 18 ha to 11,600 ha and were typically surrounded by agriculture (i.e., ranching and annual cropping). Grassland passerines did not respond strongly or uniformly to patch size. Sprague's Pipit (Anthus spragueii) was the only species whose density increased with pasture size. Patch size had minimal influence on nest survival of Sprague's Pipit or Clay-colored Sparrow (Spizella pallida); whereas nest survival increased with patch size for Savannah Sparrow (Passerculus sandwichensis) and declined for Baird's Sparrow (Ammodramus bairdii), Chestnut-collared Longspur (Calcarius ornatus), and Western Meadowlark (Sturnella neglecta). Time-specific factors (i.e., nest age, date, and year) were more important predictors of nest survival than patch size. Exploratory analyses indicated that effects of edge distance, pasture shape, or landscape on nest survival were just as likely as patch-size effects. However, effects of edge on Chestnut-collared Longspurs may be governed by landscape-level factors, because nest survival decreased with distance to edge in landscapes with increased amounts of cropland. Our results indicate that mixed-grass prairie parcels ≥18 ha play a role in the conservation of several grassland passerine species currently in decline, but the conservation of Sprague's Pipit likely depends on maintaining larger tracts of native prairie.

Separation of cell survival, growth, migration, and mesenchymal transdifferentiation effects of fibroblast secretome on tumor cells of head and neck squamous cell carcinoma.

PubMed

Metzler, Veronika Maria; Pritz, Christian; Riml, Anna; Romani, Angela; Tuertscher, Raphaela; Steinbichler, Teresa; Dejaco, Daniel; Riechelmann, Herbert; Dudás, József

2017-11-01

Fibroblasts play a central role in tumor invasion, recurrence, and metastasis in head and neck squamous cell carcinoma. The aim of this study was to investigate the influence of tumor cell self-produced factors and paracrine fibroblast-secreted factors in comparison to indirect co-culture on cancer cell survival, growth, migration, and epithelial-mesenchymal transition using the cell lines SCC-25 and human gingival fibroblasts. Thereby, we particularly focused on the participation of the fibroblast-secreted transforming growth factor beta-1.Tumor cell self-produced factors were sufficient to ensure tumor cell survival and basic cell growth, but fibroblast-secreted paracrine factors significantly increased cell proliferation, migration, and epithelial-mesenchymal transition-related phenotype changes in tumor cells. Transforming growth factor beta-1 generated individually migrating disseminating tumor cell groups or single cells separated from the tumor cell nest, which were characterized by reduced E-cadherin expression. At the same time, transforming growth factor beta-1 inhibited tumor cell proliferation under serum-starved conditions. Neutralizing transforming growth factor beta antibody reduced the cell migration support of fibroblast-conditioned medium. Transforming growth factor beta-1 as a single factor was sufficient for generation of disseminating tumor cells from epithelial tumor cell nests, while other fibroblast paracrine factors supported tumor nest outgrowth. Different fibroblast-released factors might support tumor cell proliferation and invasion, as two separate effects.

X-Ray Form Factor, Attenuation and Scattering Tables

National Institute of Standards and Technology Data Gateway

SRD 66 X-Ray Form Factor, Attenuation and Scattering Tables (Web, free access)   This database collects tables and graphs of the form factors, the photoabsorption cross section, and the total attenuation coefficient for any element (Z <= 92).

Model of the best-of-N nest-site selection process in honeybees.

PubMed

Reina, Andreagiovanni; Marshall, James A R; Trianni, Vito; Bose, Thomas

2017-05-01

The ability of a honeybee swarm to select the best nest site plays a fundamental role in determining the future colony's fitness. To date, the nest-site selection process has mostly been modeled and theoretically analyzed for the case of binary decisions. However, when the number of alternative nests is larger than two, the decision-process dynamics qualitatively change. In this work, we extend previous analyses of a value-sensitive decision-making mechanism to a decision process among N nests. First, we present the decision-making dynamics in the symmetric case of N equal-quality nests. Then, we generalize our findings to a best-of-N decision scenario with one superior nest and N-1 inferior nests, previously studied empirically in bees and ants. Whereas previous binary models highlighted the crucial role of inhibitory stop-signaling, the key parameter in our new analysis is the relative time invested by swarm members in individual discovery and in signaling behaviors. Our new analysis reveals conflicting pressures on this ratio in symmetric and best-of-N decisions, which could be solved through a time-dependent signaling strategy. Additionally, our analysis suggests how ecological factors determining the density of suitable nest sites may have led to selective pressures for an optimal stable signaling ratio.

Fibroblast growth factor-10 signals development of von Brunn's nests in the exstrophic bladder

PubMed Central

Eastman, Rocky; Leaf, Elizabeth M.; Zhang, Dianzhong; True, Lawrence D.; Sweet, Robert M.; Seidel, Kristy; Siebert, Joseph R.; Grady, Richard; Mitchell, Michael E.

2010-01-01

von Brunn's nests have long been recognized as precursors of benign lesions of the urinary bladder mucosa. We report here that von Brunn's nests are especially prevalent in the exstrophic bladder, a birth defect that predisposes the patient to formation of bladder cancer. Cells of von Brunn's nest were found to coalesce into a stratified, polarized epithelium which surrounds itself with a capsule-like structure rich in types I, III, and IV collagen. Histocytochemical analysis and keratin profiling demonstrated that nested cells exhibited a phenotype similar, but not identical, to that of urothelial cells of transitional epithelium. Immunostaining and in situ hybridization analysis of exstrophic tissue demonstrated that the FGF-10 receptor is synthesized and retained by cells of von Brunn's nest. In contrast, FGF-10 is synthesized and secreted by mesenchymal fibroblasts via a paracrine pathway that targets basal epithelial cells of von Brunn's nests. Small clusters of 10pRp cells, positive for both FGF-10 and its receptor, were observed both proximal to and inside blood vessels in the lamina propria. The collective evidence points to a mechanism where von Brunn's nests develop under the control of the FGF-10 signal transduction system and suggests that 10pRp cells may be the original source of nested cells. PMID:20719973

Model of the best-of-N nest-site selection process in honeybees

NASA Astrophysics Data System (ADS)

Reina, Andreagiovanni; Marshall, James A. R.; Trianni, Vito; Bose, Thomas

2017-05-01

The ability of a honeybee swarm to select the best nest site plays a fundamental role in determining the future colony's fitness. To date, the nest-site selection process has mostly been modeled and theoretically analyzed for the case of binary decisions. However, when the number of alternative nests is larger than two, the decision-process dynamics qualitatively change. In this work, we extend previous analyses of a value-sensitive decision-making mechanism to a decision process among N nests. First, we present the decision-making dynamics in the symmetric case of N equal-quality nests. Then, we generalize our findings to a best-of-N decision scenario with one superior nest and N -1 inferior nests, previously studied empirically in bees and ants. Whereas previous binary models highlighted the crucial role of inhibitory stop-signaling, the key parameter in our new analysis is the relative time invested by swarm members in individual discovery and in signaling behaviors. Our new analysis reveals conflicting pressures on this ratio in symmetric and best-of-N decisions, which could be solved through a time-dependent signaling strategy. Additionally, our analysis suggests how ecological factors determining the density of suitable nest sites may have led to selective pressures for an optimal stable signaling ratio.

Importance of individual species of predators on nesting success of ducks in the Canadian prairie pothole region

USGS Publications Warehouse

Johnson, Douglas H.; Sargeant, Alan B.; Greenwood, Raymond J.

1989-01-01

We followed 3094 upland nests of several species of ducks. Clutches in most nests were lost to predation. We related daily nest predation rates to indices of activity of eight egg-eating predators, precipitation during the nesting season, and measures of wetland conditions. Activity indices of red fox (Vulpes vulpes), striped skunk (Mephitis mephitis), and raccoon (Procyon lotor) activity were positively correlated, as were activity indices of coyote (Canis latrans), Franklin's ground squirrel (Spermophilus franklinii), and black-billed magpie (Pica pica). Indices of fox and coyote activity were strongly negatively correlated (r = -0.51), as were those of badger (Taxidea taxus) and skunk (r = -0.46). Nest predation rates in the early part of the breeding season were positively related to indices of fox, American crow (Corvus brachyrhynchos), and badger activity. Predation rates in the latter part of the season were positively related to indices of fox and skunk activity. Predation rates on early-season nests were lower in areas and years in which larger fractions of seasonal wetlands contained water. For late-season nests, a similar relationship held involving semipermanent wetlands. We suspect that the wetland measures, which reflect precipitation during some previous period, also indicate vegetation growth and the abundance of buffer prey, factors that may influence nest predation rates.

The ART of mating: alternative reproductive tactics and mating success in a nest-guarding fish.

PubMed

Mascolino, S; Benvenuto, C; Gubili, C; Sacchi, C; Boufana, B; Mariani, S

2016-12-01

Behavioural observations in the field of male Mediterranean damselfish Chromis chromis were combined with molecular analyses, using bi-parentally and maternally inherited markers, to investigate reproductive success patterns of alternative reproductive tactics (ARTs) in terms of number of eggs sired and number of females contributing to each nest. Cuckoldry was observed in every nest sampled, with at least two and up to seven sneaker males per nest. The nesting male, however, always significantly fertilized the greater number of eggs (on average 49%) in each clutch, whereas each sneaker fertilized around 7% of the clutch. The average number of females whose eggs were fertilized by nesting males was 6·76 (range 2-13), while each sneaker on average fertilized the eggs of 1·74 (range 1-8) females. Using this sibship reconstruction, some of the factors involved in the regulation of the dynamic equilibrium of reproductive success were investigated between the two ARTs shown by C. chromis males. Results show that the sneakers' reproductive success was positively linked to egg clutch size; the density of individuals in the nesting area negatively affected the size of egg clutches; the rate of defence behaviours performed by nesting males negatively influenced the number of females contributing to each nest. © 2016 The Fisheries Society of the British Isles.

The influence of regional hydrology on nesting behavior and nest fate of the American alligator

USGS Publications Warehouse

Ugarte, Cristina A.; Bass, Oron L.; Nuttle, William; Mazzotti, Frank J.; Rice, Kenneth G.; Fujisaki, Ikuko; Whelan, Kevin R.T.

2013-01-01

Hydrologic conditions are critical to the nesting behavior and reproductive success of crocodilians. In South Florida, USA, growing human settlement has led to extensive surface water management and modification of historical water flows in the wetlands, which have affected regional nesting of the American alligator (Alligator mississippiensis). Although both natural and anthropogenic factors are considered to determine hydrologic conditions, the aspects of hydrological patterns that affect alligator nest effort, flooding (partial and complete), and failure (no hatchling) are unclear. We deconstructed annual hydrological patterns using harmonic models that estimated hydrological matrices including mean, amplitude, timing of peak, and periodicity of surface water depth and discharge and examined their effects on alligator nesting using survey data from Shark Slough, Everglades National Park, from 1985 to 2005. Nest effort increased in years with higher mean and lesser periodicity of water depth. A greater proportion of nests were flooded and failed when peak discharge occurred earlier in the year. Also, nest flooding rates were greater in years with greater periodicity of water depth, and nest failure rate was greater when mean discharge was higher. This study guides future water management decisions to mitigate negative impacts on reproduction of alligators and provides wildlife managers with a tool for assessing and modifying annual water management plans to conserve crocodilians and other wetland species.

Chimpanzees (Pan troglodytes) Flexibly Use Introduced Species for Nesting and Bark Feeding in a Human-Dominated Habitat.

PubMed

McCarthy, Maureen S; Lester, Jack D; Stanford, Craig B

2017-01-01

As habitat loss and fragmentation place growing pressure on endangered nonhuman primate populations, researchers find increasing evidence for novel responses in behavior. In western Uganda between the Budongo and Bugoma Forests, chimpanzees ( Pan troglodytes schweinfurthii ) inhabit a mosaic landscape comprising forest fragments, human settlements, and agricultural land. We recorded nests and feeding evidence of unhabituated chimpanzees in this region over a 12-mo period. We found extensive evidence of nesting in introduced tree species, including eucalyptus ( Eucalyptus grandis ), guava ( Psidium guajava ), cocoa ( Theobroma cacao ), and Caribbean pine ( Pinus caribaea ). In addition, we found instances of ground nesting, nest reuse, and composite nests constructed from branches of multiple trees. This evidence may indicate a lack of suitable nesting trees or attempts by chimpanzees to nest in areas of riparian forest that allow them to avoid human detection. We also found new evidence for eucalyptus bark feeding by chimpanzees. Such evidence suggests chimpanzees respond flexibly to mitigate anthropogenic pressures in human-dominated landscapes. The limits of such flexibility remain unknown. Further research is needed to examine systematically the factors influencing the use of such resources and to understand better the extent to which chimpanzees can persist while relying on them.

A review of the nest protection hypothesis: does inclusion of fresh green plant material in birds' nests reduce parasite infestation?

PubMed

Scott-Baumann, James F; Morgan, Eric R

2015-07-01

The use of aromatic plants and their essential oils for ectoparasite treatment is a field of growing interest. Several species of birds regularly introduce aromatic herbs into their nests putatively to reduce parasites. The behaviour is most often seen in cavity nesting birds and after nest building has finished. The plants are included in a non-structural manner and are often strongly aromatic. Various different hypotheses have been proposed regarding the function of this behaviour; from the plants altering some non-living factor in the nest (crypsis, water loss and insulation hypotheses) to them being involved in mate selection (mate hypothesis) or even having a beneficial effect, direct or indirect, on chicks (drug or nest protection hypothesis, NPH). Many studies have been carried out over the years observing and experimentally testing these hypotheses. This review focuses on studies involving the most popular of these hypotheses, the NPH: that plants decrease nest parasites or pathogens, thereby conveying positive effects to the chicks, allowing the behaviour to evolve. Studies providing observational evidence towards this hypothesis and those experimentally testing it are discussed.

Nest survival of piping plovers at a dynamic reservoir indicates an ecological trap for a threatened population

USGS Publications Warehouse

Anteau, Michael J.; Shaffer, Terry L.; Sherfy, Mark H.; Sovada, Marsha A.; Stucker, Jennifer H.; Wiltermuth, Mark T.

2012-01-01

In the past 60 years, reservoirs have reshaped riverine ecosystems and transformed breeding habitats used by the threatened piping plover (Charadrius melodus; hereafter plover). Currently, 29% of the Northern Great Plains plover population nests at reservoirs that might function as ecological traps because reservoirs have more diverse habitat features and greater dynamics in water levels than habitats historically used by breeding plovers. We examined factors influencing daily survival rates (DSR) of 346 plover nests at Lake Sakakawea (SAK; reservoir) during 2006–2009 by evaluating multiple a priori models, and we used our best model to hindcast nest success of plovers during 1985–2009. Our observed and hindcast estimates of nest success were low compared to published estimates. Previous findings indicate that plovers prefer nest sites that are low relative to water level. We found that elevation of nests above the water level had a strong positive correlation with DSR because water levels of SAK typically increased throughout the nesting period. Habitat characteristics on the reservoir differ from those that shaped nest-site selection for plovers. Accordingly, extraordinary nest loss occurs there in many years, largely due to inundation of nests, and based on low fledging rates those losses were not compensated by potential changes in chick survival. Therefore, our example supports the concept of ecological traps in birds because it addresses quantitative assessments of habitat preference and productivity over 25 years (since species listing) and affects a large portion of the population.

An aerial sightability model for estimating ferruginous hawk population size

USGS Publications Warehouse

Ayers, L.W.; Anderson, S.H.

1999-01-01

Most raptor aerial survey projects have focused on numeric description of visibility bias without identifying the contributing factors or developing predictive models to account for imperfect detection rates. Our goal was to develop a sightability model for nesting ferruginous hawks (Buteo regalis) that could account for nests missed during aerial surveys and provide more accurate population estimates. Eighteen observers, all unfamiliar with nest locations in a known population, searched for nests within 300 m of flight transects via a Maule fixed-wing aircraft. Flight variables tested for their influence on nest-detection rates included aircraft speed, height, direction of travel, time of day, light condition, distance to nest, and observer experience level. Nest variables included status (active vs. inactive), condition (i.e., excellent, good, fair, poor, bad), substrate type, topography, and tree density. A multiple logistic regression model identified nest substrate type, distance to nest, and observer experience level as significant predictors of detection rates (P < 0.05). The overall model was significant (??26 = 124.4, P < 0.001, n = 255 nest observations), and the correct classification rate was 78.4%. During 2 validation surveys, observers saw 23.7% (14/59) and 36.5% (23/63) of the actual population. Sightability model predictions, with 90% confidence intervals, captured the true population in both tests. Our results indicate standardized aerial surveys, when used in conjunction with the predictive sightability model, can provide unbiased population estimates for nesting ferruginous hawks.

Long term productivity of canvasbacks (Aythya valisineria) in a snowpack-driven desert marsh

USGS Publications Warehouse

Kruse, Kammie L.; Lovvorn, James R.; Takekawa, John Y.; Mackay, Jeffrey

2003-01-01

Ruby Lake, Nevada, is a large palustrine wetland that hosts the southern-most major breeding population of Canvasbacks (Aythya valisineria). That arid marsh, fed by springs derived from mountain snowpack, differs in climate and hydrology from glaciated potholes of the northern prairies where most Canvasbacks breed. Fourteen years of nesting data on Canvasbacks over a 31 year period (1970–2000) were analyzed to determine factors affecting breeding performance at Ruby Lake and whether they differed from those in the prairies. Long-term Mayfield nest success at Ruby Lake (50% of all nests) was in the range of that in the northern prairies (21–65%). Of all Canvasback nests, 73% were parasitized (mostly by Redheads [Aythya americana]) as compared to 83–97% in a large Manitoba marsh and 57–65% in Manitoba potholes. However, as in the northern prairies, nest parasitism generally had little or no effect on either nest success or percentage of host eggs that hatched. In Manitoba potholes, nest success was unrelated to habitat variables measured; but successful nests at Ruby Lake were over shallower water, farther from shore, in wider bands of emergent vegetation, and surrounded by lower stem densities than unsuccessful nests. Water level is the key factor in breeding performance of Canvasbacks at both Ruby Lake and the northern prairies; however, the source of water differs (mountain snowpack at Ruby Lake, direct precipitation in the prairies) and effects of water-level variations are reversed. In small prairie potholes (mostly <0.4 ha) with many mammalian predators, productivity of Canvasbacks (which build floating nests) is increased by high water that floods the emergent fringe. At Ruby Lake, a very large marsh (2,830 ha) with mostly avian predators, Canvasback productivity is decreased by high water that floods interior emergent stands too deeply. Water level at Ruby Lake was highly correlated (multiple R2 = 0.91) with mountain snowpack up to three years earlier, emphasizing the strong effect of climatic variations on wetland birds in that arid region.

Nesting phenology of marine turtles: insights from a regional comparative analysis on green turtle (Chelonia mydas).

PubMed

Dalleau, Mayeul; Ciccione, Stéphane; Mortimer, Jeanne A; Garnier, Julie; Benhamou, Simon; Bourjea, Jérôme

2012-01-01

Changes in phenology, the timing of seasonal activities, are among the most frequently observed responses to environmental disturbances and in marine species are known to occur in response to climate changes that directly affects ocean temperature, biogeochemical composition and sea level. We examined nesting seasonality data from long-term studies at 8 green turtle (Chelonia mydas) rookeries that include 21 specific nesting sites in the South-West Indian Ocean (SWIO). We demonstrated that temperature drives patterns of nesting seasonality at the regional scale. We found a significant correlation between mean annual Sea Surface Temperature (SST) and dates of peak nesting with rookeries exposed to higher SST having a delayed nesting peak. This supports the hypothesis that temperature is the main factor determining peak nesting dates. We also demonstrated a spatial synchrony in nesting activity amongst multiple rookeries in the northern part of the SWIO (Aldabra, Glorieuses, Mohéli, Mayotte) but not with the eastern and southern rookeries (Europa, Tromelin), differences which could be attributed to females with sharply different adult foraging conditions. However, we did not detect a temporal trend in the nesting peak date over the study period or an inter-annual relation between nesting peak date and SST. The findings of our study provide a better understanding of the processes that drive marine species phenology. The findings will also help to predict their ability to cope with climate change and other environmental perturbations. Despite demonstrating this spatial shift in nesting phenology, no trend in the alteration of nesting dates over more than 20 years was found.

Buteo Nesting Ecology: Evaluating Nesting of Swainson's Hawks in the Northern Great Plains.

PubMed

Inselman, Will M; Datta, Shubham; Jenks, Jonathan A; Jensen, Kent C; Grovenburg, Troy W

2015-01-01

Swainson's hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson's hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson's hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, SDist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%-42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson's hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson's hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson's hawks arriving to the breeding grounds.

Nesting Phenology of Marine Turtles: Insights from a Regional Comparative Analysis on Green Turtle (Chelonia mydas)

PubMed Central

Dalleau, Mayeul; Ciccione, Stéphane; Mortimer, Jeanne A.; Garnier, Julie; Benhamou, Simon; Bourjea, Jérôme

2012-01-01

Changes in phenology, the timing of seasonal activities, are among the most frequently observed responses to environmental disturbances and in marine species are known to occur in response to climate changes that directly affects ocean temperature, biogeochemical composition and sea level. We examined nesting seasonality data from long-term studies at 8 green turtle (Chelonia mydas) rookeries that include 21 specific nesting sites in the South-West Indian Ocean (SWIO). We demonstrated that temperature drives patterns of nesting seasonality at the regional scale. We found a significant correlation between mean annual Sea Surface Temperature (SST) and dates of peak nesting with rookeries exposed to higher SST having a delayed nesting peak. This supports the hypothesis that temperature is the main factor determining peak nesting dates. We also demonstrated a spatial synchrony in nesting activity amongst multiple rookeries in the northern part of the SWIO (Aldabra, Glorieuses, Mohéli, Mayotte) but not with the eastern and southern rookeries (Europa, Tromelin), differences which could be attributed to females with sharply different adult foraging conditions. However, we did not detect a temporal trend in the nesting peak date over the study period or an inter-annual relation between nesting peak date and SST. The findings of our study provide a better understanding of the processes that drive marine species phenology. The findings will also help to predict their ability to cope with climate change and other environmental perturbations. Despite demonstrating this spatial shift in nesting phenology, no trend in the alteration of nesting dates over more than 20 years was found. PMID:23056527

Daily nest survival rates of Gunnison Sage-Grouse (Centrocercus minimus): assessing local- and landscape-scale drivers

USGS Publications Warehouse

Stanley, Thomas R.; Aldridge, Cameron L.; Joanne Saher,; Theresa Childers,

2015-01-01

The Gunnison Sage-Grouse (Centrocercus minimus) is a species of conservation concern and is a candidate for listing under the U.S. Endangered Species Act because of substantial declines in populations from historic levels. It is thought that loss, fragmentation, and deterioration of sagebrush (Artemisia spp.) habitat have contributed to the decline and isolation of this species into seven geographically distinct subpopulations. Nest survival is known to be a primary driver of demography of Greater Sage-Grouse (C. urophasianus), but no unbiased estimates of daily nest survival rates (hereafter nest survival) exist for Gunnison Sage-Grouse or published studies identifying factors that influence nest survival. We estimated nest survival of Gunnison Sage-Grouse for the western portion of Colorado's Gunnison Basin subpopulation, and assessed the effects and relative importance of local- and landscape-scale habitat characteristics on nest survival. Our top performing model was one that allowed variation in nest survival among areas, suggesting a larger landscape-area effect. Overall nest success during a 38-day nesting period (egg-laying plus incubation) was 50% (daily survival rate; SE  =  0.982 [0.003]), which is higher than previous estimates for Gunnison Sage-Grouse and generally higher than published for the closely related Greater Sage-Grouse. We did not find strong evidence that local-scale habitat variables were better predictors of nest survival than landscape-scale predictors, nor did we find strong evidence that any of the habitat variables we measured were good predictors of nest survival. Nest success of Gunnison Sage-Grouse in the western portion of the Gunnison Basin was higher than previously believed.

Mitigation effectiveness for improving nesting success of greater sage-grouse influenced by energy development.

PubMed

Kirol, Christopher P; Sutphin, Andrew L; Bond, Laura; Fuller, Mark R; Maechtle, Thomas L

Sagebrush ( Artemisia spp.) habitats being developed for oil and gas reserves are inhabited by sagebrush obligate species-including the greater sage-grouse ( Centrocercus urophasianus ; sage-grouse) that is currently being considered for protection under the U.S. Endangered Species Act. Numerous studies suggest increasing oil and gas development may exacerbate species extinction risks. Therefore, there is a great need for effective on-site mitigation to reduce impacts to co-occurring wildlife such as sage-grouse. Nesting success is a primary factor in avian productivity and declines in nesting success are also thought to be an important contributor to population declines in sage-grouse. From 2008 to 2011 we monitored 296 nests of radio-marked female sage-grouse in a natural gas (NG) field in the Powder River Basin, Wyoming, USA and compared nest survival in mitigated and non-mitigated development areas and relatively unaltered areas to determine if specific mitigation practices were enhancing nest survival. Nest survival was highest in relatively unaltered habitats followed by mitigated, and then non-mitigated NG areas. Reservoirs used for holding NG discharge water had the greatest support as having a direct relationship to nest survival. Within a 5 km 2 area surrounding a nest, the probability of nest failure increased by about 15% for every 1.5 km increase in reservoir water edge. Reducing reservoirs was a mitigation focus and sage-grouse nesting in mitigated areas were exposed to almost half of the amount of water edge compared to those in non-mitigated areas. Further, we found that an increase in sagebrush cover was positively related to nest survival. Consequently, mitigation efforts focused on reducing reservoir construction and reducing surface disturbance, especially when the surface disturbance results in sagebrush removal, are important to enhancing sage-grouse nesting success.

Nesting behavior of Palila, as assessed from video recordings

USGS Publications Warehouse

Laut, M.E.; Banko, P.C.; Gray, E.M.

2003-01-01

We quantified nesting behavior of Palila (Loxiodes bailleui), an endangered Hawaiian honeycreeper, by recording at nests during three breeding seasons using a black-and-white video camera connected to a Videocassette recorder. A total of seven nests was observed. We measured the following factors for daylight hours: percentage of time the female was on the nest (attendance), length of attendance bouts by the female, length of nest recesses, and adult provisioning rates. Comparisons were made between three stages of the 40-day nesting cycle: incubation (day 1-day 16), early nestling stage (day 17-day 30 [i.e., nestlings ??? 14 days old]), and late nestling stage (day 31-day 40 [i.e., nestlings > 14 days old]). Of seven nests observed, four fledged at least one nestling and three failed. One of these failed nests was filmed being depredated by a feral cat (Felis catus). Female nest attendance was near 82% during the incubation stage and decreased to 21% as nestlings aged. We did not detect a difference in attendance bout length between stages of the nesting cycle. Mean length of nest recesses increased from 4.5 min during the incubation stage to over 45 min during the late nestling stage. Mean number of nest recesses per hour ranged from 1.6 to 2.0. Food was delivered to nestlings by adults an average of 1.8 times per hour for the early nestling stage and 1.5 times per hour during the late nestling stage and did not change over time. Characterization of parental behavior by video had similarities to but also key differences from findings taken from blind observations. Results from this study will facilitate greater understanding of Palila reproductive strategies.

Mitigation effectiveness for improving nesting success of greater sage-grouse influenced by energy development

PubMed Central

Kirol, Christopher P.; Sutphin, Andrew L.; Bond, Laura; Fuller, Mark R.; Maechtle, Thomas L.

2015-01-01

Sagebrush (Artemisia spp.) habitats being developed for oil and gas reserves are inhabited by sagebrush obligate species—including the greater sage-grouse (Centrocercus urophasianus; sage-grouse) that is currently being considered for protection under the U.S. Endangered Species Act. Numerous studies suggest increasing oil and gas development may exacerbate species extinction risks. Therefore, there is a great need for effective on-site mitigation to reduce impacts to co-occurring wildlife such as sage-grouse. Nesting success is a primary factor in avian productivity and declines in nesting success are also thought to be an important contributor to population declines in sage-grouse. From 2008 to 2011 we monitored 296 nests of radio-marked female sage-grouse in a natural gas (NG) field in the Powder River Basin, Wyoming, USA and compared nest survival in mitigated and non-mitigated development areas and relatively unaltered areas to determine if specific mitigation practices were enhancing nest survival. Nest survival was highest in relatively unaltered habitats followed by mitigated, and then non-mitigated NG areas. Reservoirs used for holding NG discharge water had the greatest support as having a direct relationship to nest survival. Within a 5 km2 area surrounding a nest, the probability of nest failure increased by about 15% for every 1.5 km increase in reservoir water edge. Reducing reservoirs was a mitigation focus and sage-grouse nesting in mitigated areas were exposed to almost half of the amount of water edge compared to those in non-mitigated areas. Further, we found that an increase in sagebrush cover was positively related to nest survival. Consequently, mitigation efforts focused on reducing reservoir construction and reducing surface disturbance, especially when the surface disturbance results in sagebrush removal, are important to enhancing sage-grouse nesting success. PMID:26366042

A Functional Analytic Approach To Computer-Interactive Mathematics

PubMed Central

2005-01-01

Following a pretest, 11 participants who were naive with regard to various algebraic and trigonometric transformations received an introductory lecture regarding the fundamentals of the rectangular coordinate system. Following the lecture, they took part in a computer-interactive matching-to-sample procedure in which they received training on particular formula-to-formula and formula-to-graph relations as these formulas pertain to reflections and vertical and horizontal shifts. In training A-B, standard formulas served as samples and factored formulas served as comparisons. In training B-C, factored formulas served as samples and graphs served as comparisons. Subsequently, the program assessed for mutually entailed B-A and C-B relations as well as combinatorially entailed C-A and A-C relations. After all participants demonstrated mutual entailment and combinatorial entailment, we employed a test of novel relations to assess 40 different and complex variations of the original training formulas and their respective graphs. Six of 10 participants who completed training demonstrated perfect or near-perfect performance in identifying novel formula-to-graph relations. Three of the 4 participants who made more than three incorrect responses during the assessment of novel relations showed some commonality among their error patterns. Derived transfer of stimulus control using mathematical relations is discussed. PMID:15898471

A functional analytic approach to computer-interactive mathematics.

PubMed

Ninness, Chris; Rumph, Robin; McCuller, Glen; Harrison, Carol; Ford, Angela M; Ninness, Sharon K

2005-01-01

Following a pretest, 11 participants who were naive with regard to various algebraic and trigonometric transformations received an introductory lecture regarding the fundamentals of the rectangular coordinate system. Following the lecture, they took part in a computer-interactive matching-to-sample procedure in which they received training on particular formula-to-formula and formula-to-graph relations as these formulas pertain to reflections and vertical and horizontal shifts. In training A-B, standard formulas served as samples and factored formulas served as comparisons. In training B-C, factored formulas served as samples and graphs served as comparisons. Subsequently, the program assessed for mutually entailed B-A and C-B relations as well as combinatorially entailed C-A and A-C relations. After all participants demonstrated mutual entailment and combinatorial entailment, we employed a test of novel relations to assess 40 different and complex variations of the original training formulas and their respective graphs. Six of 10 participants who completed training demonstrated perfect or near-perfect performance in identifying novel formula-to-graph relations. Three of the 4 participants who made more than three incorrect responses during the assessment of novel relations showed some commonality among their error patterns. Derived transfer of stimulus control using mathematical relations is discussed.

The effects of ant nests on soil fertility and plant performance: a meta-analysis.

PubMed

Farji-Brener, Alejandro G; Werenkraut, Victoria

2017-07-01

Ants are recognized as one of the major sources of soil disturbance world-wide. However, this view is largely based on isolated studies and qualitative reviews. Here, for the first time, we quantitatively determined whether ant nests affect soil fertility and plant performance, and identified the possible sources of variation of these effects. Using Bayesian mixed-models meta-analysis, we tested the hypotheses that ant effects on soil fertility and plant performance depend on the substrate sampled, ant feeding type, latitude, habitat and the plant response variable measured. Ant nests showed higher nutrient and cation content than adjacent non-nest soil samples, but similar pH. Nutrient content was higher in ant refuse materials than in nest soils. The fertilizer effect of ant nests was also higher in dry habitats than in grasslands or savannas. Cation content was higher in nests of plant-feeding ants than in nests of omnivorous species, and lower in nests from agro-ecosystems than in nests from any other habitat. Plants showed higher green/root biomass and fitness on ant nests soils than in adjacent, non-nest sites; but plant density and diversity were unaffected by the presence of ant nests. Root growth was particularly higher in refuse materials than in ant nest soils, in leaf-cutting ant nests and in deserts habitats. Our results confirm the major role of ant nests in influencing soil fertility and vegetation patterns and provide information about the factors that mediate these effects. First, ant nests improve soil fertility mainly through the accumulation of refuse materials. Thus, different refuse dump locations (external or in underground nest chambers) could benefit different vegetation life-forms. Second, ant nests could increase plant diversity at larger spatial scales only if the identity of favoured plants changes along environmental gradients (i.e. enhancing β-diversity). Third, ant species that feed on plants play a relevant role fertilizing soils, which may balance their known influence as primary consumers. Fourth, the effects of ant nests as fertility islands are larger in arid lands, possibly because fertility is intrinsically lower in these habitats. Overall, this study provide novel and quantitative evidence confirming that ant nests are key soil modifiers, emphasizing their role as ecological engineers. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Reaction factoring and bipartite update graphs accelerate the Gillespie Algorithm for large-scale biochemical systems.

PubMed

Indurkhya, Sagar; Beal, Jacob

2010-01-06

ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models.

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

PubMed Central

Indurkhya, Sagar; Beal, Jacob

2010-01-01

ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models. PMID:20066048

Nonlinear optimization simplified by hypersurface deformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stillinger, F.H.; Weber, T.A.

1988-09-01

A general strategy is advanced for simplifying nonlinear optimization problems, the ant-lion method. This approach exploits shape modifications of the cost-function hypersurface which distend basins surrounding low-lying minima (including global minima). By intertwining hypersurface deformations with steepest-descent displacements, the search is concentrated on a small relevant subset of all minima. Specific calculations demonstrating the value of this method are reported for the partitioning of two classes of irregular but nonrandom graphs, the prime-factor graphs and the pi graphs. We also indicate how this approach can be applied to the traveling salesman problem and to design layout optimization, and that itmore » may be useful in combination with simulated annealing strategies.« less

Density and nest survival of golden-cheeked warblers: Spatial scale matters

Treesearch

Jennifer L. Reidy; Frank R., III Thompson; Lisa O' Donnell

2017-01-01

Conservation and management plans often rely on indicators such as species occupancy or density to define habitat quality, ignoring factors that influence reproductive success, and potentially limiting conservation achievements. We examined relationships between predicted density and nest survival with environmental features at multiple spatial scales for the golden-...

Fabrication of imaging X-ray optics

NASA Astrophysics Data System (ADS)

Catura, R. C.; Joki, E. G.; Brookover, W. J.

The design, fabrication, and performance of optics for X-ray astronomy and laboratory applications are described and illustrated with diagrams, drawings, graphs, photographs, and sample images. Particular attention is given to the Wolter I telescope developed for spectroscopic observation of 8-30-A cosmic X-ray sources from a rocketborne X-ray Objective Grating Spectrometer; this instrument employs three nested paraboloid-hyperboloid mirrors of 5083 Al alloy, figured by diamond turning and covered with a thin coating of acrylic lacquer prior to deposition of a 40-nm-thick layer of Sn. In calibration tests at NASA Marshall, the FWHM of the line-spread function at 1.33 nm was found to be 240 microns, corresponding to 21 arcsec. Also presented are the results of reflectivity measurements on C and W multilayers sputtered on Si and fusion glass substrates.

Reproductive indices in natural nests of giant Amazon river turtles Podocnemis expansa (Schweigger, 1812) (Testudines, Podocnemididae) in the Environmental Protection Area Meanders of the Araguaia River.

PubMed

Alves-Júnior, J R F; Lustosa, A P G; Bosso, A C S; Balestra, R A M; Bastos, L F; Miranda, L B; Santos, A L Q

2012-02-01

A count was made of unhatched eggs and hatchling live and dead Podocnemis expansa turtles in 327 natural nests located on the beaches of the Environmental Protection Area (EPA) Meanders of the Araguaia River, to determine the percentage of hatching (94.63%), non-hatching (5.37%), survival (94.24%) and hatchling mortality (5.76%), and the average percentage of dead hatchlings during the 15 days in the nursery (0.97%). The mean number of hatchlings per nest was determined from the sum of the number of live and dead hatchlings divided by the total number of nests, while the mean number of eggs per nest was determined from the sum of live and dead hatchlings and unhatched eggs divided by the number of nests. These calculations yielded the following mean values: live hatchlings (88.98 ± 23.94), dead hatchlings (0.37 ± 0.93), unhatched eggs (5.07 ± 9.57), and total number of eggs (94.42 ± 21.30). The reproductive efficiency of the wild population of P. expansa can be affected by many environmental factors such as temperature, humidity and rainfall. In addition, man-made factors like the presence of chemicals in the water and the potential for infectious disease also have significant impact. The reproductive indices data obtained from this study are indispensable for future investigations of hatching anomalies.

Demographic consequences of nest box use for Red-footed Falcons Falco vespertinus in Central Asia

USGS Publications Warehouse

Bragin, Evgeny A.; Bragin, Alexander E.; Katzner, Todd

2017-01-01

Nest box programs are frequently implemented for the conservation of cavity-nesting birds, but their effectiveness is rarely evaluated in comparison to birds not using nest boxes. In the European Palearctic, Red-footed Falcon Falco vespertinus populations are both of high conservation concern and are strongly associated with nest box programs in heavily managed landscapes. We used a 21-year monitoring dataset collected on 753 nesting attempts by Red-footed Falcons in unmanaged natural or semi-natural habitats to provide basic information on this poorly known species; to evaluate long-term demographic trends; and to evaluate response of demographic parameters of Red-footed Falcons to environmental factors including use of nest boxes. We observed significant differences among years in laying date, offspring loss, and numbers of fledglings produced, but not in egg production. Of these four parameters, offspring loss and, to a lesser extent, number of fledglings exhibited directional trends over time. Variation in laying date and in numbers of eggs were not well explained by any one model, but instead by combinations of models, each with informative terms for nest type. Nevertheless, laying in nest boxes occurred 2.10 ± 0.70 days earlier than in natural nests. In contrast, variation in both offspring loss and numbers of fledglings produced were fairly well explained by a single model including terms for nest type, nest location, and an interaction between the two parameters (65% and 81% model weights respectively), with highest offspring loss in nest boxes on forest edges. Because, for other species, earlier laying dates are associated with more fit individuals, this interaction highlighted a possible ecological trap, whereby birds using nest boxes on forest edges lay eggs earlier but suffer greater offspring loss and produce lower numbers of fledglings than do those in other nesting settings. If nest boxes increase offspring loss for Red-footed Falcons in heavily managed landscapes where populations are at greater risk, or for the many other species of rare or endangered birds supported by nest box programs, these processes could have important demographic and conservation consequences.

Influence of human development and predators on nest survival of tundra birds, Arctic Coastal Plain, Alaska.

PubMed

Liebezeit, J R; Kendall, S J; Brown, S; Johnson, C B; Martin, P; McDonald, T L; Payer, D C; Rea, C L; Streever, B; Wildman, A M; Zack, S

2009-09-01

Nest predation may influence population dynamics of birds on the Arctic Coastal Plain (ACP) of Alaska, USA. Anthropogenic development on the ACP is increasing, which may attract nest predators by providing artificial sources of food, perches, den sites, and nest sites. Enhanced populations or concentrations of human-subsidized predators may reduce nest survival for tundra-nesting birds. In this study, we tested the hypothesis that nest survival decreases in proximity to human infrastructure. We monitored 1257 nests of 13 shorebird species and 619 nests of four passerine species at seven sites on the ACP from 2002 to 2005. Study sites were chosen to represent a range of distances to infrastructure from 100 m to 80 km. We used Cox proportional hazards regression models to evaluate the effects of background (i.e., natural) factors and infrastructure on nest survival. We documented high spatial and temporal variability in nest survival, and site and year were both included in the best background model. We did not detect an effect of human infrastructure on nest survival for shorebirds as a group. In contrast, we found evidence that risk of predation for passerine nests increased within 5 km of infrastructure. This finding provides quantitative evidence of a relationship between infrastructure and nest survival for breeding passerines on the ACP. A posteriori finer-scale analyses (within oil field sites and individual species) suggested that Red and Red-necked Phalaropes combined (Phalaropus fulicarius, P. lobatus) had lower productivity closer to infrastructure and in areas with higher abundance of subsidized predators. However, we did not detect such a relationship between infrastructure and nest survival for Semipalmated and Pectoral Sandpipers (Calidris pusilla, C. melanotos), the two most abundant shorebirds. High variability in environmental conditions, nest survival, and predator numbers between sites and years may have contributed to these inconsistent results. We recommend targeted management actions to minimize anthropogenic effects and suggest new research needed on this issue as expanding development is planned for the ACP of Alaska. In particular, we recommend research on demography of key predators and their importance with respect to nest survival, and experimental studies that better address challenges posed by high natural variability.

Climate and predation dominate juvenile and adult recruitment in a turtle with temperature-dependent sex determination.

PubMed

Schwanz, Lisa E; Spencer, Ricky-John; Bowden, Rachel M; Janzen, Fredric J

2010-10-01

Conditions experienced early in life can influence phenotypes in ecologically important ways, as exemplified by organisms with environmental sex determination. For organisms with temperature-dependent sex determination (TSD), variation in nest temperatures induces phenotypic variation that could impact population growth rates. In environments that vary over space and time, how does this variation influence key demographic parameters (cohort sex ratio and hatchling recruitment) in early life stages of populations exhibiting TSD? We leverage a 17-year data set on a population of painted turtles, Chrysemys picta, to investigate how spatial variation in nest vegetation cover and temporal variation in climate influence early life-history demography. We found that spatial variation in nest cover strongly influenced nest temperature and sex ratio, but was not correlated with clutch size, nest predation, total nest failure, or hatching success. Temporal variation in climate influenced percentage of total nest failure and cohort sex ratio, but not depredation rate, mean clutch size, or mean hatching success. Total hatchling recruitment in a year was influenced primarily by temporal variation in climate-independent factors, number of nests constructed, and depredation rate. Recruitment of female hatchlings was determined by stochastic variation in nest depredation and annual climate and also by the total nest production. Overall population demography depends more strongly on annual variation in climate and predation than it does on the intricacies of nest-specific biology. Finally, we demonstrate that recruitment of female hatchlings translates into recruitment of breeding females into the population, thus linking climate (and other) effects on early life stages to adult demographics.

Developing nondestructive techniques for managing conflicts between fisheries and double-crested cormorant colonies

USGS Publications Warehouse

Suzuki, Yasuko; Roby, Daniel D.; Lyons, Donald E.; Courtot, Karen; Collis, Ken

2015-01-01

Double-crested cormorants (Phalacrocorax auritus) have been identified as the source of significant mortality to juvenile salmonids (Oncorhynchus spp.) in the Columbia River Basin. Management plans for reducing the size of a large colony on East Sand Island (OR, USA) in the Columbia River estuary are currently being developed. We evaluated habitat enhancement and social attraction as nondestructive techniques for managing cormorant nesting colonies during 2004–2007. We tested these techniques on unoccupied plots adjacent to the East Sand Island cormorant colony. Cormorants quickly colonized these plots and successfully raised young. Cormorants also were attracted to nest and raised young on similar plots at 2 islands approximately 25 km from East Sand Island; 1 island had a history of successful cormorant nesting whereas the other was a site where cormorants had previously nested unsuccessfully. On a third island with no history of cormorant nesting or nesting attempts, these techniques were unsuccessful at attracting cormorants to nest. Our results suggest that some important factors influencing attraction of nesting cormorants using these techniques include history of cormorant nesting, disturbance, and presence of breeding cormorants nearby. These techniques may be effective in redistributing nesting cormorants away from areas where fish stocks of conservation concern are susceptible to predation, especially if sites with a recent history of cormorant nesting are available within their foraging or dispersal range. Published 2015. Wiley Periodicals, Inc. This article is a US Government work and, as such, is in the public domain in the United States of America.

Buteo Nesting Ecology: Evaluating Nesting of Swainson’s Hawks in the Northern Great Plains

PubMed Central

Inselman, Will M.; Datta, Shubham; Jenks, Jonathan A.; Jensen, Kent C.; Grovenburg, Troy W.

2015-01-01

Swainson’s hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson’s hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson’s hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, S Dist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%–42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson’s hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson’s hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson’s hawks arriving to the breeding grounds. PMID:26327440

Habitat comparisons and productivity in nesting common terns on the mid-Atlantic coast

USGS Publications Warehouse

Erwin, R.M.; Smith, D.C.

1985-01-01

Nesting Common Terns (Sterna hirundo) were studied at a number of barrier beaches and small islands of tidal salt marsh in New Jersey and the Eastern Shore of Maryland-Virginina from 1980 through 1982. Data were collected on clutch sizes, nest spacing, and nesting success. The principal null hypothesis tested was that no difference in reproductive success exists between beach and marsh habitats. Nests were monitored from egg-laying in mid-May until mid-July when young fledged. Clutch sizes varied among colonies and across years but no systematic effect of year, habitat, or colony size on mean clutch size per colony was detected. Analyses of nest productivity (estimated using both the Mayfield method and using a colony average) failed to reveal significant effects of habitat or colony size but showed a stronger year effect. Storm tide flooding and egg chick disappearance (presumably predation by Herring Gulls Larus argentatus and Laughing Gulls L. atricilla nesting nearby) accounted for most nest failures. Losses due to both these mortality factors were unpredictable from year to year. Nest spacing in salt marsh colonies was much closer than it was on barrier beaches. In mixed-species colonies with Black Skimmers (Rynchops niger), distances between tern and skimmer nests were also much smaller in marsh colonies than they were on beaches. The limited amount of wrack (windrows of dead, matted vegetation) preferred by marsh-nesting terns probably explains these spacing differences. Several lines of evidence suggest that terns prefer beaches to marshes for nesting, however, the uncertainty of predation and flooding may often obscure any intrinsic differences in habitat quality. Long-term field studies are essential for testing hypotheses related to differential fitness of individuals among habitats.

Patch size and edge proximity are useful predictors of brood parasitism but not nest survival of grassland birds.

PubMed

Benson, Thomas J; Chiavacci, Scott J; Ward, Michael P

2013-06-01

Declines of migratory birds have led to increased focus on causative factors for these declines, including the potential adverse effects of habitat fragmentation on reproductive success. Although numerous studies have addressed how proximity to a habitat edge, patch size, or landscape context influence nest survival or brood parasitism, many have failed to find the purported effects. Furthermore, many have sought to generalize patterns across large geographic areas and habitats. Here, we examined evidence for effects of edge proximity, patch size, and landscape context on nest survival and brood parasitism of grassland birds, a group of conservation concern. The only consistent effect was a positive association between edge proximity and brood parasitism. We examined effects of patch size on nest survival (37 studies) and brood parasitism (30 studies) representing 170 and 97 different estimates, respectively, with a total sample size of > 14000 nests spanning eastern North America. Nest survival weakly increased with patch size in the Great Plains, but not in the Midwestern or Eastern United States, and brood parasitism was inversely related to patch size and consistently greater in the Great Plains. The consistency in brood parasitism relative to nest survival patterns is likely due to parasitism being caused by one species, while nest survival is driven by a diverse and variable suite of nest predators. Often, studies assume that predators responsible for nest predation, the main driver of nest success, either are the same or exhibit the same behaviors across large geographic areas. These results suggest that a better mechanistic understanding of nest predation is needed to provide meaningful conservation recommendations for improving grassland bird productivity, and that the use of general recommendations across large geographic areas should only be undertaken when sufficient data are available from all regions.

Predation and infanticide influence ideal free choice by a parrot occupying heterogeneous tropical habitats.

PubMed

Bonebrake, Timothy C; Beissinger, Steven R

2010-06-01

The ideal free distribution (IFD) predicts that organisms will disperse to sites that maximize their fitness based on availability of resources. Habitat heterogeneity underlies resource variation and influences spatial variation in demography and the distribution of populations. We relate nest site productivity at multiple scales measured over a decade to habitat quality in a box-nesting population of Forpus passerinus (green-rumped parrotlets) in Venezuela to examine critical IFD assumptions. Variation in reproductive success at the local population and neighborhood scales had a much larger influence on productivity (fledglings per nest box per year) than nest site or female identity. Habitat features were reliable cues of nest site quality. Nest sites with less vegetative cover produced greater numbers of fledglings than sites with more cover. However, there was also a competitive cost to nesting in high-quality, low-vegetative cover nest boxes, as these sites experienced the most infanticide events. In the lowland local population, water depth and cover surrounding nest sites were related with F. passerinus productivity. Low vegetative cover and deeper water were associated with lower predation rates, suggesting that predation could be a primary factor driving habitat selection patterns. Parrotlets also demonstrated directional dispersal. Pairs that changed nest sites were more likely to disperse from poor-quality nest sites to high-quality nest sites rather than vice versa, and juveniles were more likely to disperse to, or remain in, the more productive of the two local populations. Parrotlets exhibited three characteristics fundamental to the IFD: habitat heterogeneity within and between local populations, reliable habitat cues to productivity, and active dispersal to sites of higher fitness.

Nest ectoparasites increase physiological stress in breeding birds: an experiment.

PubMed

Martínez-de la Puente, Josué; Merino, Santiago; Tomás, Gustavo; Moreno, Juan; Morales, Judith; Lobato, Elisa; Martínez, Javier

2011-02-01

Parasites are undoubtedly a biotic factor that produces stress. Heat shock proteins (HSPs) are important molecules buffering cellular damage under adverse conditions. During the breeding season, blue tit Cyanistes caeruleus (L.) adults are affected by blood parasites, nest-dwelling parasites and biting flies, potentially affecting their HSP-mediated responses. Here, we treated females with primaquine to reduce blood parasites and fumigated nests with permethrin to reduce nest-dwelling parasites to test whether these treatments affect HSP60 level during the breeding season. Medicated females, but not controls, had a significant reduction of the intensity of infection by Haemoproteus spp. blood parasites. However, final intensity of infection did not differ significantly between groups, and we did not find an effect of medication on change in HSP60 level. Fumigation reduced the abundance of nest-dwelling parasites (mites, fleas and blowfly larvae) and engorged biting midges in nests. Females breeding in non-fumigated nests increased HSP60 levels during the season more than those breeding in fumigated nests. Furthermore, the change in HSP60 level was positively correlated with the abundance of biting midges. These results show how infections by nest ectoparasites during the breeding period can increase the level of HSPs and suggest that biting midges impose physiological costs on breeding female blue tits. Although plausible, the alternative that biting midges prefer to feed on more stressed birds is poorly supported by previous studies.

A Fuzzy Rule-Base Model for Classification of Spirometric FVC Graphs in Chronical Obstructive Pulmonary Diseases

DTIC Science & Technology

2001-10-25

questionnaire was filled out before test which is very important criteria for each subject for investigating are smoking cigarettes, having asthma, chronic...9, 12]. Secondly, observed FVC and FEV1 data plotted are taken under investigation. According to the questionnaire filled out, subjects... questionnaire filled in by each subject on the result of the diagnosing (categorizing FVC graphs) COPD, elimination of erroneous factors affecting

Patch size and landscape effects on density and nesting success of grassland birds

USGS Publications Warehouse

Winter, Maiken; Johnson, Douglas H.; Shaffer, Jill A.; Donovan, Therese M.; Svedarsky, W. Daniel

2006-01-01

Current management recommendations for grassland birds in North America emphasize providing large patches of grassland habitat within landscapes that have few forest or shrubland areas. These Bird Conservation Areas are being proposed under the assumption that large patches of habitat in treeless landscapes will maintain viable populations of grassland birds. This assumption requires that patch size and landscape features affect density and nesting success of grassland birds, and that these effects are consistent among years and regions and across focal species. However, these assumptions have not yet been validated for grassland birds, and the relative importance of local vegetation structure, patch size, and landscape composition on grassland bird populations is not well known. In addition, factors influencing grassland bird nesting success have been investigated mostly in small-scale and short-duration studies. To develop management guidelines for grassland birds, we tested the spatial and temporal repeatability of the influence of patch size and landscape composition on density and nesting success of 3 grassland passerines, after controlling for local-scale vegetation structure, climate, and—when analyzing nest success—bird density. We conducted our study during 4 years (1998–2001) in 44 study plots that were set up in 3 regions of the northern tallgrass prairie in Minnesota and North Dakota, USA. In these study plots we measured density and nesting success of clay-colored sparrows (Spizella pallida), Savannah sparrows (Passerculus sandwichensis), and bobolinks (Dolichonyx oryzivorus). Statistical models indicated that density was influenced by patch size, landscape, region, and local vegetation structure more so than by local vegetation structure alone. Both magnitude and direction of the response of density to patch size varied among regions, years, and species. In contrast, the direction of landscape effects was consistent among regions, years, and between Savannah sparrows and bobolinks. In each species, this landscape effect was independent of patch size. Nesting success was not clearly influenced by patch size or landscape composition, and none of the factors that influenced avian density also influenced nesting success in any of the 3 species. General statements on “optimal habitat” for grassland birds should therefore be viewed cautiously. Instead, long-term studies in different regions as well as a deeper understanding of the local system are needed to determine which factors are most important for grassland birds in a particular area.

Heat or insulation: behavioral titration of mouse preference for warmth or access to a nest.

PubMed

Gaskill, Brianna N; Gordon, Christopher J; Pajor, Edmond A; Lucas, Jeffrey R; Davis, Jerry K; Garner, Joseph P

2012-01-01

In laboratories, mice are housed at 20-24°C, which is below their lower critical temperature (≈30°C). This increased thermal stress has the potential to alter scientific outcomes. Nesting material should allow for improved behavioral thermoregulation and thus alleviate this thermal stress. Nesting behavior should change with temperature and material, and the choice between nesting or thermotaxis (movement in response to temperature) should also depend on the balance of these factors, such that mice titrate nesting material against temperature. Naïve CD-1, BALB/c, and C57BL/6 mice (36 male and 36 female/strain in groups of 3) were housed in a set of 2 connected cages, each maintained at a different temperature using a water bath. One cage in each set was 20°C (Nesting cage; NC) while the other was one of 6 temperatures (Temperature cage; TC: 20, 23, 26, 29, 32, or 35°C). The NC contained one of 6 nesting provisions (0, 2, 4, 6, 8, or 10g), changed daily. Food intake and nest scores were measured in both cages. As the difference in temperature between paired cages increased, feed consumption in NC increased. Nesting provision altered differences in nest scores between the 2 paired temperatures. Nest scores in NC increased with increasing provision. In addition, temperature pairings altered the difference in nest scores with the smallest difference between locations at 26°C and 29°C. Mice transferred material from NC to TC but the likelihood of transfer decreased with increasing provision. Overall, mice of different strains and sexes prefer temperatures between 26-29°C and the shift from thermotaxis to nest building is seen between 6 and 10 g of material. Our results suggest that under normal laboratory temperatures, mice should be provided with no less than 6 grams of nesting material, but up to 10 grams may be needed to alleviate thermal distress under typical temperatures.

Selection of nest-site habitat by interior least terns in relation to sandbar construction

USGS Publications Warehouse

Sherfy, M.H.; Stucker, J.H.; Buhl, D.A.

2012-01-01

Federally endangered interior least terns (Sternula antillarum) nest on bare or sparsely vegetated sandbars on midcontinent river systems. Loss of nesting habitat has been implicated as a cause of population declines, and managing these habitats is a major initiative in population recovery. One such initiative involves construction of mid-channel sandbars on the Missouri River, where natural sandbar habitat has declined in quantity and quality since the late 1990s. We evaluated nest-site habitat selection by least terns on constructed and natural sandbars by comparing vegetation, substrate, and debris variables at nest sites (na =a 798) and random points (na =a 1,113) in bare or sparsely vegetated habitats. Our logistic regression models revealed that a broader suite of habitat features was important in nest-site selection on constructed than on natural sandbars. Odds ratios for habitat variables indicated that avoidance of habitat features was the dominant nest-site selection process on both sandbar types, with nesting terns being attracted to nest-site habitat features (gravel and debris) and avoiding vegetation only on constructed sandbars, and avoiding silt and leaf litter on both sandbar types. Despite the seemingly uniform nature of these habitats, our results suggest that a complex suite of habitat features influences nest-site choice by least terns. However, nest-site selection in this social, colonially nesting species may be influenced by other factors, including spatial arrangement of bare sand habitat, proximity to other least terns, and prior habitat occupancy by piping plovers (Charadrius melodus). We found that nest-site selection was sensitive to subtle variation in habitat features, suggesting that rigor in maintaining habitat condition will be necessary in managing sandbars for the benefit of least terns. Further, management strategies that reduce habitat features that are avoided by least terns may be the most beneficial to nesting least terns. ?? 2011 The Wildlife Society.

Selection of nest-site habitat by interior least terns in relation to sandbar construction

USGS Publications Warehouse

Sherfy, Mark H.; Stucker, Jennifer H.; Buhl, Deborah A.

2012-01-01

Federally endangered interior least terns (Sternula antillarum) nest on bare or sparsely vegetated sandbars on midcontinent river systems. Loss of nesting habitat has been implicated as a cause of population declines, and managing these habitats is a major initiative in population recovery. One such initiative involves construction of mid-channel sandbars on the Missouri River, where natural sandbar habitat has declined in quantity and quality since the late 1990s. We evaluated nest-site habitat selection by least terns on constructed and natural sandbars by comparing vegetation, substrate, and debris variables at nest sites (n = 798) and random points (n = 1,113) in bare or sparsely vegetated habitats. Our logistic regression models revealed that a broader suite of habitat features was important in nest-site selection on constructed than on natural sandbars. Odds ratios for habitat variables indicated that avoidance of habitat features was the dominant nest-site selection process on both sandbar types, with nesting terns being attracted to nest-site habitat features (gravel and debris) and avoiding vegetation only on constructed sandbars, and avoiding silt and leaf litter on both sandbar types. Despite the seemingly uniform nature of these habitats, our results suggest that a complex suite of habitat features influences nest-site choice by least terns. However, nest-site selection in this social, colonially nesting species may be influenced by other factors, including spatial arrangement of bare sand habitat, proximity to other least terns, and prior habitat occupancy by piping plovers (Charadrius melodus). We found that nest-site selection was sensitive to subtle variation in habitat features, suggesting that rigor in maintaining habitat condition will be necessary in managing sandbars for the benefit of least terns. Further, management strategies that reduce habitat features that are avoided by least terns may be the most beneficial to nesting least terns.

Diagnostic value of nested-PCR for identification of Malassezia species in dandruff

NASA Astrophysics Data System (ADS)

Jusuf, N. K.; Nasution, T. A.; Ullyana, S.

2018-03-01

Dandruff or pityriasis simplex is a condition of abnormal occurrence of formation of yellowish white scales from the scalp. Many factors play a role in the pathogenesis of dandruff, i.e.colonization of Malassezia species. Examination of Malassezia species previously done by culture as the gold standard. However, there are various difficulties in doing the culture. Identification method with anested-polymerase chain reaction (nested-PCR) is expected to provide quickly and easily detected. This study aimedto determine the diagnostic value of nested-PCR in the identification of Malassezia species in dandruff. From 21 subjects, scales from the scalp were taken and sent to the laboratory for nested-PCR identification. Statistical analysis of diagnostic test carried out to determine sensitivity, specificity, positive predictive value, and negative predictive value. The results showed nested-PCR detected 10 sample (47.6%) positive for Malassezia species consist of M. sympodialis (23.8%); M. slooffiae (9.5%); M. furfur (4.8%); M. globosa and M. furfur (4.8%); and M. restricta and M. sympodialis (4.8%). Detection of Malassezia species by nested-PCR has 100% in sensitivity whereas the specificity was 55%. Nested-PCR test has high sensitivity. Therefore nested-PCR may be considered for a faster and simpler alternative examination in identification for Malassezia species in dandruff.

Effects of environmental factors on incubation patterns of Greater Sage-Grouse

USGS Publications Warehouse

Coates, Peter S.; Delehanty, David J.

2008-01-01

Birds in which only one sex incubates the eggs are often faced with a direct conflict between foraging to meet metabolic needs and incubation. Knowledge of environmental and ecological factors that shape life-history strategies of incubation is limited. We used continuous videography to make precise measurements of female Greater Sage-Grouse (Centrocercus urophasianus) incubation constancy (percentage of time spent at the nest in a 24-hour period) and recess duration. We used an information-theoretic approach to evaluate incubation patterns in relation to grouse age, timing of incubation, raven abundance, microhabitat, weather, and food availability. Overall, sage-grouse females showed an incubation constancy of 96% and a distinctive bimodal distribution of brief incubation recesses that peaked at sunset and 30 min prior to sunrise. Grouse typically returned to their nests during low light conditions. Incubation constancy of yearlings was lower than that of adults, particularly in the later stages of incubation. Yearlings spent more time away from nests later in the morning and earlier in the evening compared to adults. Video images revealed that nearly all predation events by Common Ravens (Corvus corax), the most frequently recorded predator at sage-grouse nests, took place during mornings and evenings after sunrise and before sunset, respectively. These were the times of the day when sage-grouse typically returned from incubation recesses. Recess duration was negatively related to raven abundance. We found evidence that incubation constancy increased with greater visual obstruction, usually from vegetation, of nests. An understanding of how incubation patterns relate to environmental factors will help managers make decisions aimed at increasing productivity through successful incubation.

Phenological adjustment in arctic bird species: relative importance of snow melt and ecological factors

USGS Publications Warehouse

Liebezeit, Joseph R.; Gurney, K. E. B.; Budde, Michael E.; Zack, Steve; Ward, David H.

2014-01-01

Previous studies have documented advancement in clutch initiation dates (CIDs) in response to climate change, most notably for temperate-breeding passerines. Despite accelerated climate change in the Arctic, few studies have examined nest phenology shifts in arctic breeding species. We investigated whether CIDs have advanced for the most abundant breeding shorebird and passerine species at a long-term monitoring site in arctic Alaska. We pooled data from three additional nearby sites to determine the explanatory power of snow melt and ecological variables (predator abundance, green-up) on changes in breeding phenology. As predicted, all species (semipalmated sandpiper, Calidris pusilla, pectoral sandpiper, Calidris melanotos, red-necked phalarope, Phalaropus lobatus, red phalarope, Phalaropus fulicarius, Lapland longspur, Calcarius lapponicus) exhibited advanced CIDs ranging from 0.40 to 0.80 days/year over 9 years. Timing of snow melt was the most important variable in explaining clutch initiation advancement (“climate/snow hypothesis”) for four of the five species, while green-up was a much less important explanatory factor. We found no evidence that high predator abundances led to earlier laying dates (“predator/re-nest hypothesis”). Our results support previous arctic studies in that climate change in the cryosphere will have a strong impact on nesting phenology although factors explaining changes in nest phenology are not necessarily uniform across the entire Arctic. Our results suggest some arctic-breeding shorebird and passerine species are altering their breeding phenology to initiate nesting earlier enabling them to, at least temporarily, avoid the negative consequences of a trophic mismatch.

A hierarchical nest survival model integrating incomplete temporally varying covariates

PubMed Central

Converse, Sarah J; Royle, J Andrew; Adler, Peter H; Urbanek, Richard P; Barzen, Jeb A

2013-01-01

Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the biting-insect hypothesis and other hypotheses for nesting failure in this reintroduced population; resulting inferences will support ongoing efforts to manage this population via an adaptive management approach. Wider application of our approach offers promise for modeling the effects of other temporally varying, but imperfectly observed covariates on nest survival, including the possibility of modeling temporally varying covariates collected from incubating adults. PMID:24340185

A hierarchical nest survival model integrating incomplete temporally varying covariates

USGS Publications Warehouse

Converse, Sarah J.; Royle, J. Andrew; Adler, Peter H.; Urbanek, Richard P.; Barzan, Jeb A.

2013-01-01

Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the biting-insect hypothesis and other hypotheses for nesting failure in this reintroduced population; resulting inferences will support ongoing efforts to manage this population via an adaptive management approach. Wider application of our approach offers promise for modeling the effects of other temporally varying, but imperfectly observed covariates on nest survival, including the possibility of modeling temporally varying covariates collected from incubating adults.

An intelligent allocation algorithm for parallel processing

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Homaifar, Abdollah; Ananthram, Kishan G.

1988-01-01

The problem of allocating nodes of a program graph to processors in a parallel processing architecture is considered. The algorithm is based on critical path analysis, some allocation heuristics, and the execution granularity of nodes in a program graph. These factors, and the structure of interprocessor communication network, influence the allocation. To achieve realistic estimations of the executive durations of allocations, the algorithm considers the fact that nodes in a program graph have to communicate through varying numbers of tokens. Coarse and fine granularities have been implemented, with interprocessor token-communication duration, varying from zero up to values comparable to the execution durations of individual nodes. The effect on allocation of communication network structures is demonstrated by performing allocations for crossbar (non-blocking) and star (blocking) networks. The algorithm assumes the availability of as many processors as it needs for the optimal allocation of any program graph. Hence, the focus of allocation has been on varying token-communication durations rather than varying the number of processors. The algorithm always utilizes as many processors as necessary for the optimal allocation of any program graph, depending upon granularity and characteristics of the interprocessor communication network.

Analyzing cross-college course enrollments via contextual graph mining

PubMed Central

Liu, Xiaozhong; Chen, Yan

2017-01-01

The ability to predict what courses a student may enroll in the coming semester plays a pivotal role in the allocation of learning resources, which is a hot topic in the domain of educational data mining. In this study, we propose an innovative approach to characterize students’ cross-college course enrollments by leveraging a novel contextual graph. Specifically, different kinds of variables, such as students, courses, colleges and diplomas, as well as various types of variable relations, are utilized to depict the context of each variable, and then a representation learning algorithm node2vec is applied to extracting sophisticated graph-based features for the enrollment analysis. In this manner, the relations between any pair of variables can be measured quantitatively, which enables the variable type to transform from nominal to ratio. These graph-based features are examined by the random forest algorithm, and experiments on 24,663 students, 1,674 courses and 417,590 enrollment records demonstrate that the contextual graph can successfully improve analyzing the cross-college course enrollments, where three of the graph-based features have significantly stronger impacts on prediction accuracy than the others. Besides, the empirical results also indicate that the student’s course preference is the most important factor in predicting future course enrollments, which is consistent to the previous studies that acknowledge the course interest is a key point for course recommendations. PMID:29186171

Analyzing cross-college course enrollments via contextual graph mining.

PubMed

Wang, Yongzhen; Liu, Xiaozhong; Chen, Yan

2017-01-01

The ability to predict what courses a student may enroll in the coming semester plays a pivotal role in the allocation of learning resources, which is a hot topic in the domain of educational data mining. In this study, we propose an innovative approach to characterize students' cross-college course enrollments by leveraging a novel contextual graph. Specifically, different kinds of variables, such as students, courses, colleges and diplomas, as well as various types of variable relations, are utilized to depict the context of each variable, and then a representation learning algorithm node2vec is applied to extracting sophisticated graph-based features for the enrollment analysis. In this manner, the relations between any pair of variables can be measured quantitatively, which enables the variable type to transform from nominal to ratio. These graph-based features are examined by the random forest algorithm, and experiments on 24,663 students, 1,674 courses and 417,590 enrollment records demonstrate that the contextual graph can successfully improve analyzing the cross-college course enrollments, where three of the graph-based features have significantly stronger impacts on prediction accuracy than the others. Besides, the empirical results also indicate that the student's course preference is the most important factor in predicting future course enrollments, which is consistent to the previous studies that acknowledge the course interest is a key point for course recommendations.

Effects of grazing on nesting of the Oriental pratincole (Glareola maldivarum) in Bueng Boraphet Wetland, Thailand.

PubMed

Chaiyarat, Rattanawat; Eiam-Ampai, Kairat

2014-02-01

Livestock grazing may negatively impact bird nesting in wetland habitats. This study evaluated the effect of grazing on the nests of the Oriental pratincole (Glareola maldivarum) along the grassland of a wetland at six study sites with different densities of grazing cattle and buffalo. Species richness, density, cover, and height of vegetation in the study areas were different (P < 0.05). The density of cattle and buffalo at the various sites affected vegetation composition and amount, which in turn influenced bird nest density. The estimated trampling rates, number of fledglings, and number of trampled eggs were different among study sites (P < 0.05). The density of cattle and buffalo has an influence on nest failure rates. The factors that influenced the mortality rates of the Oriental pratincole were trampling and unhatched eggs. Only 48.5% of the nests were successful at sites where cattle and buffalo continuously grazed in the grasslands at high densities. Thus, increases in the density of cattle and buffalo will reduce the number of nests of the Oriental pratincole, which may result in a reduction of the overall population in the future.

Determinants of stingless bee nest density in lowland dipterocarp forests of Sabah, Malaysia.

PubMed

Eltz, Thomas; Brühl, Carsten A; van der Kaars, Sander; Linsenmair, Eduard K

2002-03-01

We measured the nest density of stingless bees (Apidae, Meliponini) in undisturbed and logged-over dipterocarp forests in Sabah, northern Borneo, and evaluated hypotheses on proximate factors leading to the observed variation: population control mediated by (1) nest predation, (2) limitation of nest trees, or (3) food limitation. Per-area nest density varied twentyfold across 14 forest sites and was significantly affected by locality, but not by the degree and history of disturbance. Nest density was generally high in sites located in the Sepilok Forest fragment (mean 8.4 nests/ha), bordering mangroves or plantations. In contrast, nest densities in continuous forests were all low (between 0 and 2.1 nests/ha, mean 0.5 nests/ha). Yearly nest mortality was low (13.5-15.0%) over 4 years of observation and did not vary between forest localities, thus limiting the potential of nest predation (1) in creating the observed variation in nest density. The presence of potential nest trees (2), though positively correlated with nest density, explained only a minute fraction of the observed variation. Nest density was best explained by differences in the pollen resources (3) available to the bees (quantified by analysis of pollen in bee garbage). Across five selected sites the amount of nonforest pollen (from mangrove or crop plants) included in diets of Trigona collina was positively correlated with T. collina nest density. External pollen sources are a likely supplement to bee diets at times when little flowering occurs inside the forest, thus increasing overall bee carrying capacity. Pollen limitation was also indicated by direct measurements of pollen import and foraging activity of T. collina in three selected sites: Pollen traps installed at nests in high-density Sepilok captured significantly more corbicular pollen than colonies in low-density Deramakot. At the same time, morning foraging activity was also greater in Sepilok, indicating a regulatory increase in foraging in response to high pollen availability. We conclude that the abundance of stingless bees in forests in Sabah is chiefly dependent on the local availability of food resources. Bee populations strongly benefit from edge effects and increased foraging habitat diversity. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00442-001-0848-6.

SPECTRAL GRAPH THEORY AND GRAPH ENERGY METRICS SHOW EVIDENCE FOR THE ALZHEIMER’S DISEASE DISCONNECTION SYNDROME IN APOE-4 RISK GENE CARRIERS

PubMed Central

Daianu, Madelaine; Mezher, Adam; Jahanshad, Neda; Hibar, Derrek P.; Nir, Talia M.; Jack, Clifford R.; Weiner, Michael W.; Bernstein, Matt A.; Thompson, Paul M.

2015-01-01

Our understanding of network breakdown in Alzheimer’s disease (AD) is likely to be enhanced through advanced mathematical descriptors. Here, we applied spectral graph theory to provide novel metrics of structural connectivity based on 3-Tesla diffusion weighted images in 42 AD patients and 50 healthy controls. We reconstructed connectivity networks using whole-brain tractography and examined, for the first time here, cortical disconnection based on the graph energy and spectrum. We further assessed supporting metrics - link density and nodal strength - to better interpret our results. Metrics were analyzed in relation to the well-known APOE-4 genetic risk factor for late-onset AD. The number of disconnected cortical regions increased with the number of copies of the APOE-4 risk gene in people with AD. Each additional copy of the APOE-4 risk gene may lead to more dysfunctional networks with weakened or abnormal connections, providing evidence for the previously hypothesized “disconnection syndrome”. PMID:26413205

SPECTRAL GRAPH THEORY AND GRAPH ENERGY METRICS SHOW EVIDENCE FOR THE ALZHEIMER'S DISEASE DISCONNECTION SYNDROME IN APOE-4 RISK GENE CARRIERS.

PubMed

Daianu, Madelaine; Mezher, Adam; Jahanshad, Neda; Hibar, Derrek P; Nir, Talia M; Jack, Clifford R; Weiner, Michael W; Bernstein, Matt A; Thompson, Paul M

2015-04-01

Our understanding of network breakdown in Alzheimer's disease (AD) is likely to be enhanced through advanced mathematical descriptors. Here, we applied spectral graph theory to provide novel metrics of structural connectivity based on 3-Tesla diffusion weighted images in 42 AD patients and 50 healthy controls. We reconstructed connectivity networks using whole-brain tractography and examined, for the first time here, cortical disconnection based on the graph energy and spectrum. We further assessed supporting metrics - link density and nodal strength - to better interpret our results. Metrics were analyzed in relation to the well-known APOE -4 genetic risk factor for late-onset AD. The number of disconnected cortical regions increased with the number of copies of the APOE -4 risk gene in people with AD. Each additional copy of the APOE -4 risk gene may lead to more dysfunctional networks with weakened or abnormal connections, providing evidence for the previously hypothesized "disconnection syndrome".

Urban waterfowl population: Ecological evaluation of management and planning

NASA Astrophysics Data System (ADS)

Greer, David M.

1982-05-01

An urban population of ducks in Puyallup, Washington, USA was studied for 14 consecutive months beginning in November 1978. Observations were made weekly from four study sites where ducks would congregate at early morning hours. Factors contributing to the presence of waterfowl in Puyallyup included abundant food supplies and a creek corridor that connected fragmented habitats in the urban area to the larger rural populations of waterfowl. Mallards ( Anas platyrhynchos) were the most abundant of the 13 species observed and were the only ducks remaining during the nesting season. Habitat size and complexity were important factors influencing the species diversity of a particular site. Nesting success of mallards was poor due to limited distribution of nesting habitat, intraspecific aggression, and human disturbance. Both site-specific and more broad-based strategies are suggested for managing and planning for duck populations in urban areas.

The Stability Analysis Method of the Cohesive Granular Slope on the Basis of Graph Theory.

PubMed

Guan, Yanpeng; Liu, Xiaoli; Wang, Enzhi; Wang, Sijing

2017-02-27

This paper attempted to provide a method to calculate progressive failure of the cohesivefrictional granular geomaterial and the spatial distribution of the stability of the cohesive granular slope. The methodology can be divided into two parts: the characterization method of macro-contact and the analysis of the slope stability. Based on the graph theory, the vertexes, the edges and the edge sequences are abstracted out to characterize the voids, the particle contact and the macro-contact, respectively, bridging the gap between the mesoscopic and macro scales of granular materials. This paper adopts this characterization method to extract a graph from a granular slope and characterize the macro sliding surface, then the weighted graph is analyzed to calculate the slope safety factor. Each edge has three weights representing the sliding moment, the anti-sliding moment and the braking index of contact-bond, respectively, . The safety factor of the slope is calculated by presupposing a certain number of sliding routes and reducing Weight repeatedly and counting the mesoscopic failure of the edge. It is a kind of slope analysis method from mesoscopic perspective so it can present more detail of the mesoscopic property of the granular slope. In the respect of macro scale, the spatial distribution of the stability of the granular slope is in agreement with the theoretical solution.

Combining Human and Machine Intelligence to Derive Agents' Behavioral Rules for Groundwater Irrigation

NASA Astrophysics Data System (ADS)

Hu, Y.; Quinn, C.; Cai, X.

2015-12-01

One major challenge of agent-based modeling is to derive agents' behavioral rules due to behavioral uncertainty and data scarcity. This study proposes a new approach to combine a data-driven modeling based on the directed information (i.e., machine intelligence) with expert domain knowledge (i.e., human intelligence) to derive the behavioral rules of agents considering behavioral uncertainty. A directed information graph algorithm is applied to identifying the causal relationships between agents' decisions (i.e., groundwater irrigation depth) and time-series of environmental, socio-economical and institutional factors. A case study is conducted for the High Plains aquifer hydrological observatory (HO) area, U.S. Preliminary results show that four factors, corn price (CP), underlying groundwater level (GWL), monthly mean temperature (T) and precipitation (P) have causal influences on agents' decisions on groundwater irrigation depth (GWID) to various extents. Based on the similarity of the directed information graph for each agent, five clusters of graphs are further identified to represent all the agents' behaviors in the study area as shown in Figure 1. Using these five representative graphs, agents' monthly optimal groundwater pumping rates are derived through the probabilistic inference. Such data-driven relationships and probabilistic quantifications are then coupled with a physically-based groundwater model to investigate the interactions between agents' pumping behaviors and the underlying groundwater system in the context of coupled human and natural systems.

What Drives Crude Oil Prices?

EIA Publications

2017-01-01

An assessment of the various factors that may influence oil prices - physical market factors as well as those related to trading and financial markets. The analysis describes seven key factors that could influence oil markets and explores possible linkages between each factor and oil prices. Regularly updated graphs are included to illustrate aspects of those relationships.

Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau

PubMed Central

An, Bei; Shu, Meilin

2017-01-01

We investigated population dynamics, breeding pairs, breeding habitat selection, nest density, distance between neighboring nests, nest survival, reproductive success, and recruitment rate for Black-necked Cranes (BNC, Grus nigricollis) during 2013–2015 in Yanchiwan National Nature Reserve (YCW), Gansu, China. Numbers of BNC and breeding pairs remained relatively stable at around 140 individuals and 40 pairs. Recruitment rates ranged from 15.7% to 25.8%. The average nest distance was 718.66 ± 430.50 m (2013), 1064.51 ± 323.99 m (2014) and 534.99 ± 195.45 m (2015). Average nest survival rate, hatching success, and breeding success of all 29 nests were 65.56 ± 5.09%, 57.04 ± 6.12% and 32.78% ± 2.55. Water depth, water body area, and distance to land were positively related to nest survival, while disturbance level showed a negative relationship. However, nest site selection of BNC was determined by habitat type, disturbance and water depth. BNC often foraged in mudflats and freshwater marsh but seldom foraged in saline-alkali wet meadows due to food density and quantity in April, the month when BNC choose nest sites. Conservation strategies based on habitats should consider ecological factors that may not be well predicted by nest site selection. Shifts within core-use areas from satellite tracking of BNC demonstrated that maintaining populations demands that conservation areas are large enough to permit breeding BNC changes in space use. Our results are important for conservation management and provide quantitative reproductive data for this species. PMID:28168110

Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau.

PubMed

Zhang, Lixun; An, Bei; Shu, Meilin; Yang, Xiaojun

2017-01-01

We investigated population dynamics, breeding pairs, breeding habitat selection, nest density, distance between neighboring nests, nest survival, reproductive success, and recruitment rate for Black-necked Cranes (BNC, Grus nigricollis ) during 2013-2015 in Yanchiwan National Nature Reserve (YCW), Gansu, China. Numbers of BNC and breeding pairs remained relatively stable at around 140 individuals and 40 pairs. Recruitment rates ranged from 15.7% to 25.8%. The average nest distance was 718.66 ± 430.50 m (2013), 1064.51 ± 323.99 m (2014) and 534.99 ± 195.45 m (2015). Average nest survival rate, hatching success, and breeding success of all 29 nests were 65.56 ± 5.09%, 57.04 ± 6.12% and 32.78% ± 2.55. Water depth, water body area, and distance to land were positively related to nest survival, while disturbance level showed a negative relationship. However, nest site selection of BNC was determined by habitat type, disturbance and water depth. BNC often foraged in mudflats and freshwater marsh but seldom foraged in saline-alkali wet meadows due to food density and quantity in April, the month when BNC choose nest sites. Conservation strategies based on habitats should consider ecological factors that may not be well predicted by nest site selection. Shifts within core-use areas from satellite tracking of BNC demonstrated that maintaining populations demands that conservation areas are large enough to permit breeding BNC changes in space use. Our results are important for conservation management and provide quantitative reproductive data for this species.

Habitat edges affect patterns of artificial nest predation along a wetland-meadow boundary

NASA Astrophysics Data System (ADS)

Suvorov, Petr; Svobodová, Jana; Albrecht, Tomáš

2014-08-01

Wetland habitats are among the most endangered ecosystems in the world. However, little is known about factors affecting the nesting success of birds in pristine grass-dominated wetlands. During three breeding periods we conducted an experiment with artificial ground nests to test two basic mechanisms (the matrix and ecotonal effects) that may result in edge effects on nest predation in grass-dominated wetland habitats. Whereas the matrix effect model supposes that predator penetrate from habitat of higher predator density to habitat of lower predator density, thus causing an edge effect in the latter, according to the ecotonal effect model predators preferentially use edge habitats over habitat interiors. In addition, we tested the edge effect in a wetland habitat using artificial shrub nests that simulated the real nests of small open-cup nesting passerines. In our study area, the lowest predation rates on ground nests were found in wetland interiors and were substantially higher along the edges of both wetland and meadow habitat. However, predation was not significantly different between meadow and wetland interiors, indicating that both mechanisms can be responsible for the edge effect in wetland edges. An increased predation rate along wetland edges was also observed for shrub nests, and resembled the predation pattern of real shrub nests in the same study area. Though we are not able to distinguish between the two mechanisms of the edge effect found, our results demonstrate that species nesting in wetland edges bordering arable land may be exposed to higher predation. Therefore, an increase in the size of wetland patches that would lead to a reduced proportion of edge areas might be a suitable management practice to protect wetland bird species in cultural European landscapes.

Sandhill crane abundance and nesting ecology at Grays Lake, Idaho

USGS Publications Warehouse

Austin, J.E.; Henry, A.R.; Ball, I.J.

2007-01-01

We examined population size and factors influencing nest survival of greater sandhill cranes (Grus canadensis tabida) at Grays Lake National Wildlife Refuge, Idaho, USA, during 1997-2000. Average local population of cranes from late April to early May, 1998-2000, was 735 cranes, 34% higher than that reported for May 1970-1971. We estimated 228 (SE = 30) nests in the basin core (excluding renests), 14% higher than a 1971 estimate. Apparent nest success in our study (x?? = 60%, n = 519 nests) was lower than reported for Grays Lake 30-50 years earlier. Daily survival rates (DSRs) of all nests averaged 0.9707 (41.2%). The best model explaining nest survival included year and water depth and their interaction. Nest survival was highest (DSR = 0.9827) in 1998 compared with other years (0.9698-0.9707). Nest survival changed little relative to water depth in 1998, when flooding was extensive and alternative prey (microtines) irrupted, but declined markedly with lower water levels in 2000, the driest year studied. Hypotheses relating nest survival to vegetation height, land use (idle, summer grazing, fall grazing), and date were not supported. In a before-after-control-impact design using 12 experimental fields, nest survival differed among years but not among management treatments (idle, fall graze, fall burn, and summer-graze-idle rotation), nor was there an interaction between year and treatments. However, DSRs in fall-burn fields declined from 0.9781 in 1997-1998 to 0.9503 in 1999-2000 (posttreatment). Changes in the predator community have likely contributed to declines in nest success since the 1950s and 1970s. Our results did not support earlier concerns about effects of habitat management practices on crane productivity. Nest survival could best be enhanced by managing spring water levels. Managers should continue censuses during late April to evaluate long-term relationships to habitat conditions and management.

Mitigation effectiveness for improving nesting success of greater sage-grouse influenced by energy development

USGS Publications Warehouse

Kirol, Christopher P.; Sutphin, Andrew L.; Bond, Laura S.; Fuller, Mark R.; Maechtle, Thomas L.

2015-01-01

Sagebrush Artemisia spp. habitats being developed for oil and gas reserves are inhabited by sagebrush obligate species — including the greater sage-grouse Centrocercus urophasianus (sage-grouse) that is currently being considered for protection under the U.S. Endangered Species Act. Numerous studies suggest increasing oil and gas development may exacerbate species extinction risks. Therefore, there is a great need for effective on-site mitigation to reduce impacts to co-occurring wildlife such as sage-grouse. Nesting success is a primary factor in avian productivity and declines in nesting success are also thought to be an important contributor to population declines in sage-grouse. From 2008 to 2011 we monitored 296 nests of radio-marked female sage-grouse in a natural gas (NG) field in the Powder River Basin, Wyoming, USA, and compared nest survival in mitigated and non-mitigated development areas and relatively unaltered areas to determine if specific mitigation practices were enhancing nest survival. Nest survival was highest in relatively unaltered habitats followed by mitigated, and then non-mitigated NG areas. Reservoirs used for holding NG discharge water had the greatest support as having a direct relationship to nest survival. Within a 5-km2 area surrounding a nest, the probability of nest failure increased by about 15% for every 1.5 km increase in reservoir water edge. Reducing reservoirs was a mitigation focus and sage-grouse nesting in mitigated areas were exposed to almost half of the amount of water edge compared to those in non-mitigated areas. Further, we found that an increase in sagebrush cover was positively related to nest survival. Consequently, mitigation efforts focused on reducing reservoir construction and reducing surface disturbance, especially when the surface disturbance results in sagebrush removal, are important to enhancing sage-grouse nesting success.

Nest site selection by Kentish plover suggests a trade-off between nest-crypsis and predator detection strategies.

PubMed

Gómez-Serrano, Miguel Ángel; López-López, Pascual

2014-01-01

Predation is one of the main causes of adult mortality and breeding failure for ground-nesting birds. Micro-habitat structure around nests plays a critical role in minimizing predation risk. Plovers nest in sites with little vegetation cover to maximize the incubating adult visibility, but many studies suggest a trade-off between nest-crypsis and predator detection strategies. However, this trade-off has not been explored in detail because methods used so far do not allow estimating the visibility with regards to critical factors such as slope or plant permeability to vision. Here, we tested the hypothesis that Kentish plovers select exposed sites according to a predator detection strategy, and the hypothesis that more concealed nests survive longer according to a crypsis strategy. To this end, we obtained an accurate estimation of the incubating adult's field of vision through a custom built inverted periscope. Our results showed that plovers selected nest sites with higher visibility than control points randomly selected with regards to humans and dogs, although nests located in sites with higher vegetation cover survived longer. In addition, the flushing distance (i.e., the distance at which incubating adults leave the nest when they detect a potential predator) decreased with vegetation cover. Consequently, the advantages of concealing the nest were limited by the ability to detect predators, thus indirectly supporting the existence of the trade-off between crypsis and predator detection. Finally, human disturbance also constrained nest choice, forcing plovers to move to inland sites that were less suitable because of higher vegetation cover, and modulated flushing behavior, since plovers that were habituated to humans left their nests closer to potential predators. This constraint on the width of suitable breeding habitat is particularly relevant for the conservation of Kentish Plover in sand beaches, especially under the current context of coastal regression and increase of recreational activities.

Nest Site Selection by Kentish Plover Suggests a Trade-Off between Nest-Crypsis and Predator Detection Strategies

PubMed Central

Gómez-Serrano, Miguel Ángel; López-López, Pascual

2014-01-01

Predation is one of the main causes of adult mortality and breeding failure for ground-nesting birds. Micro-habitat structure around nests plays a critical role in minimizing predation risk. Plovers nest in sites with little vegetation cover to maximize the incubating adult visibility, but many studies suggest a trade-off between nest-crypsis and predator detection strategies. However, this trade-off has not been explored in detail because methods used so far do not allow estimating the visibility with regards to critical factors such as slope or plant permeability to vision. Here, we tested the hypothesis that Kentish plovers select exposed sites according to a predator detection strategy, and the hypothesis that more concealed nests survive longer according to a crypsis strategy. To this end, we obtained an accurate estimation of the incubating adult's field of vision through a custom built inverted periscope. Our results showed that plovers selected nest sites with higher visibility than control points randomly selected with regards to humans and dogs, although nests located in sites with higher vegetation cover survived longer. In addition, the flushing distance (i.e., the distance at which incubating adults leave the nest when they detect a potential predator) decreased with vegetation cover. Consequently, the advantages of concealing the nest were limited by the ability to detect predators, thus indirectly supporting the existence of the trade-off between crypsis and predator detection. Finally, human disturbance also constrained nest choice, forcing plovers to move to inland sites that were less suitable because of higher vegetation cover, and modulated flushing behavior, since plovers that were habituated to humans left their nests closer to potential predators. This constraint on the width of suitable breeding habitat is particularly relevant for the conservation of Kentish Plover in sand beaches, especially under the current context of coastal regression and increase of recreational activities. PMID:25208045

Winter severity and phenology of spring emergence from the nest in freshwater turtles.

PubMed

Baker, Patrick Joseph; Iverson, John B; Lee, Richard E; Costanzo, Jon P

2010-07-01

Although many species of freshwater turtles emigrate to water soon after hatching, the offspring of some species overwinter on land and move to aquatic habitats in the following spring. Timing of emigration can affect the hatchlings' fitness, but the factors underlying phenology of nest emergence are incompletely understood. We tested the supposition that cold stress imposed during hibernation can influence the timing of nest emergence in three species of turtles in the central USA. In each year of the 6-year study, Chrysemys picta emerged in late March and early April and, on average, these hatchlings left their nests 2 weeks earlier than those of Graptemys geographica and 4 weeks earlier than those of Trachemys scripta. Emergence of conspecific hatchlings from different nests usually occurred over 3-7 weeks, but in some years lasted several additional weeks. Relatively few nests had siblings that emerged on the same day (i.e., synchronously); complete emergence of the typical sibling group required 1 to 2 weeks. In winter, subzero cold occurred with regularity in the nests of all species, though C. picta experienced the lowest temperatures owing to their shallower nests. However, for no species did emergence date or length of the emergence period correlate with winter minimum temperature and, at the level of the individual nest, neither did emergence synchrony or duration. Despite encountering lower temperatures, hatchlings of C. picta emigrated from their nests before those of sympatric species, suggesting that the fitness benefits of early emergence may lead to the improvement of cold-hardiness adaptations in northern populations of turtles.

Winter severity and phenology of spring emergence from the nest in freshwater turtles

NASA Astrophysics Data System (ADS)

Baker, Patrick Joseph; Iverson, John B.; Lee, Richard E.; Costanzo, Jon P.

2010-07-01

Although many species of freshwater turtles emigrate to water soon after hatching, the offspring of some species overwinter on land and move to aquatic habitats in the following spring. Timing of emigration can affect the hatchlings’ fitness, but the factors underlying phenology of nest emergence are incompletely understood. We tested the supposition that cold stress imposed during hibernation can influence the timing of nest emergence in three species of turtles in the central USA. In each year of the 6-year study, Chrysemys picta emerged in late March and early April and, on average, these hatchlings left their nests 2 weeks earlier than those of Graptemys geographica and 4 weeks earlier than those of Trachemys scripta. Emergence of conspecific hatchlings from different nests usually occurred over 3-7 weeks, but in some years lasted several additional weeks. Relatively few nests had siblings that emerged on the same day (i.e., synchronously); complete emergence of the typical sibling group required 1 to 2 weeks. In winter, subzero cold occurred with regularity in the nests of all species, though C. picta experienced the lowest temperatures owing to their shallower nests. However, for no species did emergence date or length of the emergence period correlate with winter minimum temperature and, at the level of the individual nest, neither did emergence synchrony or duration. Despite encountering lower temperatures, hatchlings of C. picta emigrated from their nests before those of sympatric species, suggesting that the fitness benefits of early emergence may lead to the improvement of cold-hardiness adaptations in northern populations of turtles.

Ovarian Brenner tumour: a morphologic and immunohistochemical analysis suggesting an origin from fallopian tube epithelium.

PubMed

Kuhn, Elisabetta; Ayhan, Ayse; Shih, Ie-Ming; Seidman, Jeffrey D; Kurman, Robert J

2013-12-01

Brenner tumours (BTs), like other epithelial ovarian tumours, are thought to develop from the ovarian surface epithelium. We hypothesised that BTs arise from transitional metaplasia near the tuboperitoneal junction which, when embedded in the ovary as Walthard cell nests, may progress to BTs. The aim of this study was to validate this hypothesis by a morphologic and immunohistochemical (IHC) analysis. The IHC analysis revealed that fallopian tube secretory cells, transitional metaplasia, Walthard cell nests and the epithelial component of BTs shared a similar IHC profile, consistently expressing AKR1C3 (an enzyme involved in androgen biosynthesis) and androgen receptor, but not calretinin. The tumour stromal cells that immediately surrounded the epithelial nests showed strong expression of calretinin, inhibin and steroidogenic factor 1 (markers of steroidogenic cells) in the majority of BTs. Using a highly sensitive immunofluorescent staining method, we detected small groups of cilia in transitional metaplasia and Walthard cell nests, multifocal stretches of cilia and/or ciliated vacuoles in benign BTs and well-developed cilia in atypical proliferative BTs. Our findings suggest a tubal origin of BTs through transitional metaplasia and Walthard cell nests, based on their anatomic proximity, similar IHC profile and the presence of cilia. In addition, we hypothesise a role of androgenic stimulation in the pathogenesis of BT, based on the IHC staining pattern of calretinin, inhibin and steroidogenic factor 1 expressed in the luteinised stromal cells surrounding the epithelial nests of the tumours, and AKR1C3 and androgen receptor expressed in both the epithelial and stromal components. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sex Differences in the Effects of Captivity on Hippocampus Size in Brown-Headed Cowbirds (Molothrus ater obscurus)

PubMed Central

Day, Lainy B.; Guerra, Marjorie; Schlinger, Barney A.; Rothstein, Stephen I.

2010-01-01

In brood parasitic cowbirds, hippocampus (Hp) size is correlated with environmental spatial memory demands. Searching for host nests is the presumed causal factor influencing cowbird Hp size, because Hp volumes vary across species, sexes, and seasons according to nest-searching participation. Brown-headed cowbirds have female-only nest searching and, at least in the eastern subspecies, a larger Hp in females than in males, suggesting that nest searching influences cowbird Hp size. We predicted that female brown-headed cowbirds housed in aviaries lacking host nests would have a smaller Hp than wild-caught females whereas males would be unaffected. We found that the Hp was smaller in captive females, but not males, compared to their wild-caught counterparts. This did not appear to be due to general effects of an impoverished environment on all brain regions. Our results imply that interruption of nest searching in cowbirds prevents seasonal increase in Hp size in females. Future studies should isolate which behavioral differences between wild and captive birds contributed to captivity-induced changes in Hp volume in females while not affecting males. PMID:18513123

Trap-Nesting Bees in Montane Grassland (Campo Rupestre) and Cerrado in Brazil: Collecting Generalist or Specialist Nesters.

PubMed

Araújo, P C S; Lourenço, A P; Raw, A

2016-10-01

Species richness and seasonal abundance of solitary bees were investigated in rocky, montane grassland (campo rupestre) (1180 m asl) and cerrado sensu stricto (680 m asl) in the Biribiri State Park, Diamantina, state of Minas Gerais, Brazil. Three hundred nineteen nest traps of bamboo canes and black cardboard tubes were monthly inspected at each site during 15 months. A total of eight species of bees built 97 nests. Four species were common to both sites. Tetrapedia aff. curvitarsis Friese and Tetrapedia aff. peckoltii Friese were the most abundant at campo rupestre and cerrado s.s., respectively, followed by Centris analis (Fabricius) in campo rupestre and Centris tarsata Smith in cerrado s.s. The nesting peaks occurred in May in campo rupestre and in February in cerrado s.s. Three cuckoo bees and one bee-fly were collected as natural enemies. The findings suggest that differences between the sites were related more to ecological factors (floral resources, natural nest sites) than to the altitudinal difference. The species richness was similar to that in other habitats with open vegetation. We demonstrate the need to use several types of trap-nest to increase the range of species sampled; some species used only one of the two types traps provided. We also comment on the limitations of trap-nests in cerrado vegetation. Most cerrado species of bees are very selective in their choice for a nesting site, but bees that use trap-nests are more generalists.

Space use by white-headed woodpeckers and selection for recent forest disturbances

Treesearch

Teresa J. Lorenz; Kerri T. Vierling; Jeffrey M. Kozma; Janet E. Millard; Martin G. Raphael

2015-01-01

White-headed woodpeckers (Picoides albolarvatus) are important cavity excavators that recently have become the focus of much research because of concerns over population declines. Past studies have focused on nest site selection and survival but information is needed on factors influencing their space use when away from the nest. We examined space...

Association of weather and nest-site structure with reproductive success in California spotted owls

Treesearch

Malcolm North; George Steger; Renee Denton; Gary Eberlein; Tom Munton; Ken Johnson

2000-01-01

Although the spotted owl (Strix occidentalis) has been intensively studied, factors influencing its reproduction are not well understood. We examined a 9-year demographic study of 51-86 pairs of the California spotted owl (S. o. occidentalis), weather conditions, and forest structure at nest sites in oak (Quercus sp.) woodland and...

Factors affecting golden-cheeked warbler nest survival in urban and rural landscapes

Treesearch

Jenifer L. Reidy; Frank R. Thompson; Rebecca G. Peak

2009-01-01

We evaluated hypotheses concerning temporal, landscape, and habitat effects on nest survival of golden-cheeked warblers (Dendroica chrysoparia) in an urban and a rural landscape during the breeding seasons of 2005 and 2006 in central Texas, USA. We found support for temporal effects of year and cubic effect of date and included them in candidate...

Songbird abundance and parasatism differ between urban and rural shrublands

Treesearch

Dirk E. Burhans; Frank R. Thompson

2006-01-01

Many studies have examined differences in avian community composition between urban and rural habitats, but few, if any, have looked at nesting success of urban shrubland birds in a replicated fashion while controlling for habitat. We tested factors affecting nest survival, parasitism by the Brown-headed Cowbird (Molothrus ater), and species abundance in shrubland...

Factors that influence vital rates of Seaside and Saltmarsh sparrows in coastal New Jersey, USA

PubMed Central

Roberts, Samuel G.; Longenecker, Rebecca A.; Etterson, Matthew A.; Ruskin, Katharine J.; Elphick, Chris S.; Olsen, Brian J.; Shriver, W. Gregory

2018-01-01

As saltmarsh habitat continues to disappear, understanding the factors that influence saltmarsh breeding bird population dynamics is an important step for the conservation of these declining species. Using five years (2011 – 2015) of demographic data, we evaluated and compared Seaside (Ammodramus maritimus) and Saltmarsh (A. caudacutus) sparrow apparent adult survival and nest survival at the Edwin B. Forsythe National Wildlife Refuge, New Jersey, USA. We determined the effect of site management history (unditched vs. ditched marsh) on adult and nest survival to aid in prioritizing future management or restoration actions. Seaside Sparrow apparent adult survival (61.6%, 95% CI: 52.5 – 70.0%) averaged >1.5 times greater than Saltmarsh Sparrow apparent adult survival (39.9%, 95% CI: 34.0 – 46.2%). Nest survival and predation and flooding rates did not differ between species, and predation was the primary cause of failure for both species. Apparent adult survival and nest survival did not differ between unditched and ditched marshes for either species, indicating that marsh ditching history may not affect breeding habitat quality for these species. With predation as the primary cause of nest failure for both species in New Jersey, we suggest that future research should focus on identification of predator communities in salt marshes and the potential for implementing predator-control programs to limit population declines. PMID:29479129

Quantum Graphical Models and Belief Propagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leifer, M.S.; Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo Ont., N2L 2Y5; Poulin, D.

Belief Propagation algorithms acting on Graphical Models of classical probability distributions, such as Markov Networks, Factor Graphs and Bayesian Networks, are amongst the most powerful known methods for deriving probabilistic inferences amongst large numbers of random variables. This paper presents a generalization of these concepts and methods to the quantum case, based on the idea that quantum theory can be thought of as a noncommutative, operator-valued, generalization of classical probability theory. Some novel characterizations of quantum conditional independence are derived, and definitions of Quantum n-Bifactor Networks, Markov Networks, Factor Graphs and Bayesian Networks are proposed. The structure of Quantum Markovmore » Networks is investigated and some partial characterization results are obtained, along the lines of the Hammersley-Clifford theorem. A Quantum Belief Propagation algorithm is presented and is shown to converge on 1-Bifactor Networks and Markov Networks when the underlying graph is a tree. The use of Quantum Belief Propagation as a heuristic algorithm in cases where it is not known to converge is discussed. Applications to decoding quantum error correcting codes and to the simulation of many-body quantum systems are described.« less

Productivity of forest birds at Hakalau Forest NWR

USGS Publications Warehouse

Paxton, Eben H.; Cummins, George C; Kendall, Steven J.

2014-01-01

Hawai‘i has some of the most endangered avian species in the world, which face numerous threats from habitat loss, disease, climate change, and introduced species. This report details the results of a two-year productivity study of all forest bird species at Hakalau National Wildlife Refuge, Hawai‘i Island. We found and monitored nests from seven native species and three common non-native species of forest birds at three sites across the refuge. In addition to gathering important baseline information on productivity of forest birds, we examined differences in productivity between years, sites, and as a function of nest height. The weather differed greatly between the two years, with much more rain occurring in 2014. The daily survival rate (DSR) of nests was found to have an inverse relationship with the amount of rainfall, and accordingly was much lower in 2014 compared to 2013. Nest success was lower at a regenerating forest site compared with mature rainforest, indicating negative environmental factors affecting nest success may be exacerbated in reforested areas which have lower canopies. Nest success was also impacted by nest height, with a positive relationship in the drier 2013, and a negative relationship in 2014 for the canopy nesting honeycreepers. The large difference in weather and DSR between years illustrates the need for long term demographic studies that can capture the vital rates of this community of birds.

Determinants of abundance and effects of blood-sucking flying insects in the nest of a hole-nesting bird.

PubMed

Tomás, Gustavo; Merino, Santiago; Martínez-de la Puente, Josué; Moreno, Juan; Morales, Judith; Lobato, Elisa

2008-05-01

Compared to non-flying nest-dwelling ectoparasites, the biology of most species of flying ectoparasites and its potential impact on avian hosts is poorly known and rarely, if ever, reported. In this study we explore for the first time the factors that may affect biting midge (Diptera: Ceratopogonidae) and black fly (Diptera: Simuliidae) abundances in the nest cavity of a bird, the hole-nesting blue tit Cyanistes caeruleus, and report their effects on adults and nestlings during reproduction. The abundance of biting midges was positively associated with nest mass, parental provisioning effort and abundance of blowflies and black flies, while negatively associated with nestling condition. Furthermore, a medication treatment to reduce blood parasitaemias in adult birds revealed that biting midges were more abundant in nests of females whose blood parasitaemias were experimentally reduced. This finding would be in accordance with these insect vectors attacking preferentially uninfected or less infected hosts to increase their own survival. The abundance of black flies in the population was lower than that of biting midges and increased in nests with later hatching dates. No significant effect of black fly abundance on adult or nestling condition was detected. Blood-sucking flying insects may impose specific, particular selection pressures on their hosts and more research is needed to better understand these host-parasite associations.

Written violence policies and risk of physical assault against Minnesota educators.

PubMed

Feda, Denise M; Gerberich, Susan G; Ryan, Andrew D; Nachreiner, Nancy M; McGovern, Patricia M

2010-12-01

Few research studies on school violence policies use quantitative methods to evaluate the impact of policies on workplace violence. This study analyzed nine different written violence policies and their impact on work-related physical assault in educational settings. Data were from the Minnesota Educators' Study. This large, nested case control study included cases (n=372) who reported physical assaults within the last year, and controls (n=1116) who did not. Multivariate logistic regression analyses, using directed acyclic graphs, estimated risk of assault. Results of the adjusted multivariate model suggested decreased risks of physical assault were associated with the presence of policies regarding how to report sexual harassment, verbal abuse, and threat (OR 0.53; 95 per cent CI: 0.30-0.95); assurance of confidential reporting of events (OR 0.67; 95 per cent CI: 0.44-1.04); and zero tolerance for violence (OR 0.70; 95 per cent CI: 0.47-1.04).

Multi-level multi-task learning for modeling cross-scale interactions in nested geospatial data

USGS Publications Warehouse

Yuan, Shuai; Zhou, Jiayu; Tan, Pang-Ning; Fergus, Emi; Wagner, Tyler; Sorrano, Patricia

2017-01-01

Predictive modeling of nested geospatial data is a challenging problem as the models must take into account potential interactions among variables defined at different spatial scales. These cross-scale interactions, as they are commonly known, are particularly important to understand relationships among ecological properties at macroscales. In this paper, we present a novel, multi-level multi-task learning framework for modeling nested geospatial data in the lake ecology domain. Specifically, we consider region-specific models to predict lake water quality from multi-scaled factors. Our framework enables distinct models to be developed for each region using both its local and regional information. The framework also allows information to be shared among the region-specific models through their common set of latent factors. Such information sharing helps to create more robust models especially for regions with limited or no training data. In addition, the framework can automatically determine cross-scale interactions between the regional variables and the local variables that are nested within them. Our experimental results show that the proposed framework outperforms all the baseline methods in at least 64% of the regions for 3 out of 4 lake water quality datasets evaluated in this study. Furthermore, the latent factors can be clustered to obtain a new set of regions that is more aligned with the response variables than the original regions that were defined a priori from the ecology domain.

[Nested species subsets of amphibians and reptiles in Thousand Island Lake].

PubMed

Wang, Xi; Wang, Yan-Ping; Ding, Ping

2012-10-01

Habitat fragmentation is a main cause for the loss of biological diversity. Combining line-transect methods to survey the amphibians and reptiles on 23 islands on Thousand Island Lake in Zhejiang province, along with survey data on nearby plant species and habitat variables collected by GIS, we used the"BINMATNEST (binary matrix nestedness temperature calculator)" software and the Spearman rank correlation to examine whether amphibians and reptiles followed nested subsets and their influencing factors. The results showed that amphibians and reptiles were significantly nested, and that the island area and habitat type were significantly associated with their nested ranks. Therefore, to effectively protect amphibians and reptiles in the Thousand Islands Lake area we should pay prior attention to islands with larger areas and more habitat types.

Evolution of sexual dichromatism in relation to nesting habits in European passerines: a test of Wallace's hypothesis.

PubMed

Soler, J J; Moreno, J

2012-08-01

Wallace proposed in 1868 that natural rather than sexual selection could explain the striking differences in avian plumage dichromatism. Thus, he predicted that nesting habits, through their association with nest predation, could drive changes in sexual dichromatism by enabling females in cavity nesters to become as conspicuous as males, whereas Darwin (1871, The Descent of Man and Selection in Relation to Sex, John Murray, London) argued that sexual selection was the sole explanation for dichromatism. Sexual dichromatism is currently used as indicating the strength of sexual selection, and therefore testing Wallace's claim with modern phylogentically controlled methodologies is of prime interest for comparing the roles of natural and sexual selection in affecting the evolution of avian coloration. Here, we have related information on nest attendance, sexual dichromatism and nesting habits (open and cavity nesting) to male and female plumage conspicuousness in European passerines. Nest incubation attendance does not explain male or female plumage conspicuousness but nest type does. Moreover, although females of monochromatic and cavity nesting species are more conspicuous than females of other species, males of monochromatic and open nesting species are those with more cryptic plumage. Finally, analyses of character evolution suggest that changes in nesting habits influence the probability of changes in both dichromatism and plumage conspicuousness of males but do not significantly affect those in females. These results strongly suggest a role of nesting habits in the evolution of plumage conspicuousness of males, and a role for sexual selection also in females, both factors affecting the evolution of sexual dichromatism. We discuss our findings in relation to the debate that Darwin and Wallace maintained more than one century ago on the importance of natural and sexual selection in driving the evolution of plumage conspicuousness and sexual dichromatism in birds, and conclude that our results partly support the evolutionary scenarios envisaged by both extraordinary scientists. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Identifying effective actions to guide volunteer-based and nationwide conservation efforts for a ground-nesting farmland bird.

PubMed

Santangeli, Andrea; Arroyo, Beatriz; Millon, Alexandre; Bretagnolle, Vincent

2015-08-01

1. Modern farming practices threaten wildlife in different ways, and failure to identify the complexity of multiple threats acting in synergy may result in ineffective management. To protect ground-nesting birds in farmland, monitoring and mitigating impacts of mechanical harvesting is crucial. 2. Here, we use 6 years of data from a nationwide volunteer-based monitoring scheme of the Montagu's harrier, a ground-nesting raptor, in French farmlands. We assess the effectiveness of alternative nest protection measures and map their potential benefit to the species. 3. We show that unprotected nests in cultivated land are strongly negatively affected by harvesting and thus require active management. Further, we show that protection from harvesting alone (e.g. by leaving a small unharvested buffer around the nest) is impaired by post-harvest predation at nests that become highly conspicuous after harvest. Measures that simultaneously protect from harvesting and predation (by adding a fence around the nest) significantly enhance nest productivity. 4. The map of expected gain from nest protection in relation to available volunteers' workforce pinpoints large areas of high expected gain from nest protection that are not matched by equally high workforce availability. This mismatch suggests that the impact of nest protection can be further improved by increasing volunteer efforts in key areas where they are low relative to the expected gain they could have. 5. Synthesis and applications . This study shows that synergistic interplay of multiple factors (e.g. mechanical harvesting and predation) may completely undermine the success of well-intentioned conservation efforts. However, identifying areas where the greatest expected gains can be achieved relative to effort expended can minimize the risk of wasted volunteer actions. Overall, this study underscores the importance of citizen science for collecting large-scale data useful for producing science and ultimately informs large-scale evidence-based conservation actions within an adaptive management framework.

Beyond Low-Rank Representations: Orthogonal clustering basis reconstruction with optimized graph structure for multi-view spectral clustering.

PubMed

Wang, Yang; Wu, Lin

2018-07-01

Low-Rank Representation (LRR) is arguably one of the most powerful paradigms for Multi-view spectral clustering, which elegantly encodes the multi-view local graph/manifold structures into an intrinsic low-rank self-expressive data similarity embedded in high-dimensional space, to yield a better graph partition than their single-view counterparts. In this paper we revisit it with a fundamentally different perspective by discovering LRR as essentially a latent clustered orthogonal projection based representation winged with an optimized local graph structure for spectral clustering; each column of the representation is fundamentally a cluster basis orthogonal to others to indicate its members, which intuitively projects the view-specific feature representation to be the one spanned by all orthogonal basis to characterize the cluster structures. Upon this finding, we propose our technique with the following: (1) We decompose LRR into latent clustered orthogonal representation via low-rank matrix factorization, to encode the more flexible cluster structures than LRR over primal data objects; (2) We convert the problem of LRR into that of simultaneously learning orthogonal clustered representation and optimized local graph structure for each view; (3) The learned orthogonal clustered representations and local graph structures enjoy the same magnitude for multi-view, so that the ideal multi-view consensus can be readily achieved. The experiments over multi-view datasets validate its superiority, especially over recent state-of-the-art LRR models. Copyright © 2018 Elsevier Ltd. All rights reserved.

Smothering in UK free-range flocks. Part 2: investigating correlations between disease, housing and management practices.

PubMed

Rayner, A C; Gill, R; Brass, D; Willings, T H; Bright, A

2016-09-10

Smothering, when birds group together in a way that results in death from suffocation, is a welfare and economic concern for the egg industry. This questionnaire-based study explored correlations between disease, housing, management practices and smothering on free-range farms. A binomial logistic regression approach was used to test whether question responses predicted occurrence of nest box smothers (NBS) and panic and recurring smothers (PSRS) on farms. Breed (P=0.008) and nest box manufacturer (P=0.014) predicted NBS. Breed and nest box design have been previously reported to affect nesting behaviour. The affect of nest box manufacturer found in this study may illustrate the effect of nest box design features or house layouts. Nest box manufacturer (P=0.009), feeding oyster grit or grain on the litter (P<0.001) and range use on a sunny day (P<0.001) also predicted PSRS. Implementing some management practices to encourage desirable behaviours (eg ranging) may contribute to smothering, whereas some management practices such as those aimed at occupying birds may be beneficial, illustrating the delicate balance of factors involved in free-range egg production. It is hoped that these results will stimulate further work exploring the suitability of housing design and management of laying hens in light of smothering. British Veterinary Association.

How numbers of nesting sea turtles can be overestimated by nearly a factor of two

PubMed Central

Esteban, Nicole; Mortimer, Jeanne A.

2017-01-01

Estimating the absolute number of individuals in populations and their fecundity is central to understanding the ecosystem role of species and their population dynamics as well as allowing informed conservation management for endangered species. Estimates of abundance and fecundity are often difficult to obtain for rare or cryptic species. Yet, in addition, here we show for a charismatic group, sea turtles, that are neither cryptic nor rare and whose nesting is easy to observe, that the traditional approach of direct observations of nesting has likely led to a gross overestimation of the number of individuals in populations and underestimation of their fecundity. We use high-resolution GPS satellite tags to track female green turtles throughout their nesting season in the Chagos Archipelago (Indian Ocean) and assess when and where they nested. For individual turtles, nest locations were often spread over several tens of kilometres of coastline. Assessed by satellite observations, a mean of 6.0 clutches (range 2–9, s.d. = 2.2) was laid by individuals, about twice as many as previously assumed, a finding also reported in other species and ocean basins. Taken together, these findings suggest that the actual number of nesting turtles may be almost 50% less than previously assumed. PMID:28202810

How numbers of nesting sea turtles can be overestimated by nearly a factor of two.

PubMed

Esteban, Nicole; Mortimer, Jeanne A; Hays, Graeme C

2017-02-22

Estimating the absolute number of individuals in populations and their fecundity is central to understanding the ecosystem role of species and their population dynamics as well as allowing informed conservation management for endangered species. Estimates of abundance and fecundity are often difficult to obtain for rare or cryptic species. Yet, in addition, here we show for a charismatic group, sea turtles, that are neither cryptic nor rare and whose nesting is easy to observe, that the traditional approach of direct observations of nesting has likely led to a gross overestimation of the number of individuals in populations and underestimation of their fecundity. We use high-resolution GPS satellite tags to track female green turtles throughout their nesting season in the Chagos Archipelago (Indian Ocean) and assess when and where they nested. For individual turtles, nest locations were often spread over several tens of kilometres of coastline. Assessed by satellite observations, a mean of 6.0 clutches (range 2-9, s.d. = 2.2) was laid by individuals, about twice as many as previously assumed, a finding also reported in other species and ocean basins. Taken together, these findings suggest that the actual number of nesting turtles may be almost 50% less than previously assumed. © 2017 The Author(s).

Factors limiting the domestic density of Triatoma infestans in north-west Argentina: a longitudinal study.

PubMed Central

Cecere, M. C.; Gürtler, R. E.; Chuit, R.; Cohen, J. E.

1998-01-01

Reported are the environmental and demographic risk factors associated with the domestic infestation and density of Triatoma infestans in three heavily infested rural villages in Santiago del Estero Province, Argentina. In a one-factor unadjusted analysis, the number of T. infestans captured per person-hour was associated significantly and negatively with the use of domestic insecticides by householders, type of thatch used in the roofs and the age of the house; and positively with the following: degree of cracking of the indoor walls and presence of hens nesting indoors. In one model, using multiple linear regression and a backward stepwise elimination procedure, most of the variation in the overall abundance of T. infestans was explained by insecticide use and the presence of hens nesting indoors; in another model using the same procedure it was explained by insecticide use, bug density in 1988 and previous spraying with deltamethrin in 1985. Variations in bug density per capture stratum (household goods, beds, walls and roof) were explained by the bug density in other strata and by one or two of the following risk factors: hens nesting indoors, type of roof, presence of cracks in the walls and number of people living in the house. Bug density might be locally controlled by the availability of refuges in the roofs and walls, by the presence of hens nesting indoors and by the use of domestic insecticides. Certain local materials, such as a grass known as simbol, could be successfully used in rural housing improvement programmes aimed at reducing the availability of refuges for insects in the roof. PMID:9803588

Factors limiting the domestic density of Triatoma infestans in north-west Argentina: a longitudinal study.

PubMed

Cecere, M C; Gürtler, R E; Chuit, R; Cohen, J E

1998-01-01

Reported are the environmental and demographic risk factors associated with the domestic infestation and density of Triatoma infestans in three heavily infested rural villages in Santiago del Estero Province, Argentina. In a one-factor unadjusted analysis, the number of T. infestans captured per person-hour was associated significantly and negatively with the use of domestic insecticides by householders, type of thatch used in the roofs and the age of the house; and positively with the following: degree of cracking of the indoor walls and presence of hens nesting indoors. In one model, using multiple linear regression and a backward stepwise elimination procedure, most of the variation in the overall abundance of T. infestans was explained by insecticide use and the presence of hens nesting indoors; in another model using the same procedure it was explained by insecticide use, bug density in 1988 and previous spraying with deltamethrin in 1985. Variations in bug density per capture stratum (household goods, beds, walls and roof) were explained by the bug density in other strata and by one or two of the following risk factors: hens nesting indoors, type of roof, presence of cracks in the walls and number of people living in the house. Bug density might be locally controlled by the availability of refuges in the roofs and walls, by the presence of hens nesting indoors and by the use of domestic insecticides. Certain local materials, such as a grass known as simbol, could be successfully used in rural housing improvement programmes aimed at reducing the availability of refuges for insects in the roof.

Nest-niche differentiation in two sympatric columbid species from a Mediterranean Tetraclinis woodland: Considerations for forest management

NASA Astrophysics Data System (ADS)

Hanane, Saâd; Yassin, Mohamed

2017-01-01

Studies of niche partitioning among Columbid species have mainly addressed food habits and foraging activities, while partitioning in relation to nest-niche differentiation has been little studied. Here we investigate whether two sympatric columbid species-Woodpigeon (Columba palumbus) and Turtle dove (Streptopelia turtur)-occupy similar niches. A total of 74 nests were monitored: 37 nests for each species. The study, conducted in June 2016, attempted to determine the factors that may play a role in nest-niche differentiation among the two sympatric columbid species in a Moroccan Thuya (Tetraclinis articulata) forest. We used Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) to test the relevance of nest placement, proximity of food resources, forest edge and human presence variables in the nest distribution of the two species. The results show substantial niche segregation in the T. articulata nest-trees selected by Woodpigeons and Turtle doves, with selection depending primarily on the tree size and nest height. Observed nest-niche partitioning may diminish the potential for competition between these species and enhance opportunities for their coexistence. Management policies and practices aimed at ensuring the presence of mixed-sized class of Thuya trees must be prioritized. We recommend additional studies designed to: (1) reproduce the same experimental approach on other Mediterranean Thuya forests to improve our understanding of the effects of different levels of anthropogenic disturbance on the breeding behaviour of these two game species; (2) better understand the spatio-temporal dynamics of Woodpigeon and Turtle dove coexistence in the region; and (3) better identify the spatio-temporal extent of the effect of forest management on Woodpigeon and Turtle dove site occupancy.

Assessments of habitat preferences and quality depend on spatial scale and metrics of fitness

USGS Publications Warehouse

Chalfoun, A.D.; Martin, T.E.

2007-01-01

1. Identifying the habitat features that influence habitat selection and enhance fitness is critical for effective management. Ecological theory predicts that habitat choices should be adaptive, such that fitness is enhanced in preferred habitats. However, studies often report mismatches between habitat preferences and fitness consequences across a wide variety of taxa based on a single spatial scale and/or a single fitness component. 2. We examined whether habitat preferences of a declining shrub steppe songbird, the Brewer's sparrow Spizella breweri, were adaptive when multiple reproductive fitness components and spatial scales (landscape, territory and nest patch) were considered. 3. We found that birds settled earlier and in higher densities, together suggesting preference, in landscapes with greater shrub cover and height. Yet nest success was not higher in these landscapes; nest success was primarily determined by nest predation rates. Thus landscape preferences did not match nest predation risk. Instead, nestling mass and the number of nesting attempts per pair increased in preferred landscapes, raising the possibility that landscapes were chosen on the basis of food availability rather than safe nest sites. 4. At smaller spatial scales (territory and nest patch), birds preferred different habitat features (i.e. density of potential nest shrubs) that reduced nest predation risk and allowed greater season-long reproductive success. 5. Synthesis and applications. Habitat preferences reflect the integration of multiple environmental factors across multiple spatial scales, and individuals may have more than one option for optimizing fitness via habitat selection strategies. Assessments of habitat quality for management prescriptions should ideally include analysis of diverse fitness consequences across multiple ecologically relevant spatial scales. ?? 2007 The Authors.

Reproductive ecology of Emperor Geese: Survival of adult females

USGS Publications Warehouse

Petersen, Margaret R.

1992-01-01

Life history theory predicts a decrease in survival with increased reproductive effort of individuals. This relationship, however, is highly variable among and within species. I studied the nesting success and survival of adult female Emperor Geese during 1982-1986 and found no direct evidence that differential reproductive effort as measured by the number of eggs laid or hatching success had a significant negative effect on survival to the next breeding season. Incubated clutch size, hatched clutch size, number of parasitic eggs, nest initiation date, hatch date, and mass at hatch were not related to subsequent survival. Of the factors I examined, only an attempt to nest the previous season was related to survival of a female. I suggest that the higher probability of survival among non-nesting adult female Emperor Geese was primarily related to hunting pressure on the nesting area between spring and fall migration. The probability of survival was increased for females with larger clutches, suggesting a positive relationship between brood size and survival.

Experimental quantum annealing: case study involving the graph isomorphism problem.

PubMed

Zick, Kenneth M; Shehab, Omar; French, Matthew

2015-06-08

Quantum annealing is a proposed combinatorial optimization technique meant to exploit quantum mechanical effects such as tunneling and entanglement. Real-world quantum annealing-based solvers require a combination of annealing and classical pre- and post-processing; at this early stage, little is known about how to partition and optimize the processing. This article presents an experimental case study of quantum annealing and some of the factors involved in real-world solvers, using a 504-qubit D-Wave Two machine and the graph isomorphism problem. To illustrate the role of classical pre-processing, a compact Hamiltonian is presented that enables a reduced Ising model for each problem instance. On random N-vertex graphs, the median number of variables is reduced from N(2) to fewer than N log2 N and solvable graph sizes increase from N = 5 to N = 13. Additionally, error correction via classical post-processing majority voting is evaluated. While the solution times are not competitive with classical approaches to graph isomorphism, the enhanced solver ultimately classified correctly every problem that was mapped to the processor and demonstrated clear advantages over the baseline approach. The results shed some light on the nature of real-world quantum annealing and the associated hybrid classical-quantum solvers.

Experimental quantum annealing: case study involving the graph isomorphism problem

PubMed Central

Zick, Kenneth M.; Shehab, Omar; French, Matthew

2015-01-01

Quantum annealing is a proposed combinatorial optimization technique meant to exploit quantum mechanical effects such as tunneling and entanglement. Real-world quantum annealing-based solvers require a combination of annealing and classical pre- and post-processing; at this early stage, little is known about how to partition and optimize the processing. This article presents an experimental case study of quantum annealing and some of the factors involved in real-world solvers, using a 504-qubit D-Wave Two machine and the graph isomorphism problem. To illustrate the role of classical pre-processing, a compact Hamiltonian is presented that enables a reduced Ising model for each problem instance. On random N-vertex graphs, the median number of variables is reduced from N2 to fewer than N log2 N and solvable graph sizes increase from N = 5 to N = 13. Additionally, error correction via classical post-processing majority voting is evaluated. While the solution times are not competitive with classical approaches to graph isomorphism, the enhanced solver ultimately classified correctly every problem that was mapped to the processor and demonstrated clear advantages over the baseline approach. The results shed some light on the nature of real-world quantum annealing and the associated hybrid classical-quantum solvers. PMID:26053973

Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

PubMed Central

Hériché, Jean-Karim; Lees, Jon G.; Morilla, Ian; Walter, Thomas; Petrova, Boryana; Roberti, M. Julia; Hossain, M. Julius; Adler, Priit; Fernández, José M.; Krallinger, Martin; Haering, Christian H.; Vilo, Jaak; Valencia, Alfonso; Ranea, Juan A.; Orengo, Christine; Ellenberg, Jan

2014-01-01

The advent of genome-wide RNA interference (RNAi)–based screens puts us in the position to identify genes for all functions human cells carry out. However, for many functions, assay complexity and cost make genome-scale knockdown experiments impossible. Methods to predict genes required for cell functions are therefore needed to focus RNAi screens from the whole genome on the most likely candidates. Although different bioinformatics tools for gene function prediction exist, they lack experimental validation and are therefore rarely used by experimentalists. To address this, we developed an effective computational gene selection strategy that represents public data about genes as graphs and then analyzes these graphs using kernels on graph nodes to predict functional relationships. To demonstrate its performance, we predicted human genes required for a poorly understood cellular function—mitotic chromosome condensation—and experimentally validated the top 100 candidates with a focused RNAi screen by automated microscopy. Quantitative analysis of the images demonstrated that the candidates were indeed strongly enriched in condensation genes, including the discovery of several new factors. By combining bioinformatics prediction with experimental validation, our study shows that kernels on graph nodes are powerful tools to integrate public biological data and predict genes involved in cellular functions of interest. PMID:24943848

The Empty Nest Syndrome: Ways to Enhance Quality of Life

ERIC Educational Resources Information Center

Chen, Dianbing; Yang, Xinxiao; Aagard, Steve Dale

2012-01-01

Empty nest syndrome occurs as a result of urbanization and loosened relationships among family members. It may threaten the life quality of older adults and stability of society as a whole. This survey was designed to investigate the situation and factors that influence the life quality of a sample of older adults in a western state. Thirty-five…

Fire and shade effects on ground cover structure in Kirtland's warbler habitat

Treesearch

John R. Probst; Deahn DonnerWright

2003-01-01

Researchers and managers have suggested that a narrow range of ground-cover structure resulting from fire might be necessary for suitable Kirtland`s warbler nesting conditions. Yet, Kirtland`s warblers have bred successfully in numerous unburned stands and there is little direct evidence to indicate that ground cover structure is a limiting factor for nest sites or...

Compilation of annual reports of the Navy ELF (Extremely Low Frequency) communications system ecological monitoring program (1983). Volume 2: Tabs F-J

NASA Astrophysics Data System (ADS)

Fischer, R. L.; Beaver, D. L.; Asher, J. H.; Hill, R. W.; Burton, T. M.

1984-07-01

The climatic factors which are known to impinge upon the biological behavior patterns of the megachilid bees were measured. Statistical testing of man-made influences such as ELF into the environment were pursued, with emphasis on nest architecture, pollen collection, and ability to orient to nest sites.

A highly sensitive single-tube nested PCR assay for the detection of Pineapple mealybug wilt associated virus-2 (PMWaV-2)

USDA-ARS?s Scientific Manuscript database

An assay was developed for the detection of Pineapple mealybug wilt associated virus-2 (PMWaV-2), an important factor in the etiology of mealybug wilt of pineapple. The assay combines reverse transcription of RNA isolated from pineapple with a specific and very sensitive, single, closed-tube nested ...

Development of a Kemp’s ridley sea turtle stock assessment model

USGS Publications Warehouse

Gallaway, Benny J.; Gazey, William; Caillouet, Charles W.; Plotkin, Pamela T.; Abreu Grobois, F. Alberto; Amos, Anthony F.; Burchfield, Patrick M.; Carthy, Raymond R.; Castro Martinez, Marco A.; Cole, John G.; Coleman, Andrew T.; Cook, Melissa; DiMarco, Steven F.; Epperly, Sheryan P.; Fujiwara, Masami; Gamez, Daniel Gomez; Graham, Gary L.; Griffin, Wade L.; Illescas Martinez, Francisco; Lamont, Margaret M.; Lewison, Rebecca L.; Lohmann, Kenneth J.; Nance, James M.; Pitchford, Jonathan; Putman, Nathan F.; Raborn, Scott W.; Rester, Jeffrey K.; Rudloe, Jack J.; Sarti Martinez, Laura; Schexnayder, Mark; Schmid, Jeffrey R.; Shaver, Donna J.; Slay, Christopher; Tucker, Anton D.; Tumlin, Mandy; Wibbels, Thane; Zapata Najera, Blanca M.

2016-01-01

We developed a Kemp’s ridley (Lepidochelys kempii) stock assessment model to evaluate the relative contributions of conservation efforts and other factors toward this critically endangered species’ recovery. The Kemp’s ridley demographic model developed by the Turtle Expert Working Group (TEWG) in 1998 and 2000 and updated for the binational recovery plan in 2011 was modified for use as our base model. The TEWG model uses indices of the annual reproductive population (number of nests) and hatchling recruitment to predict future annual numbers of nests on the basis of a series of assumptions regarding age and maturity, remigration interval, sex ratios, nests per female, juvenile mortality, and a putative ‘‘turtle excluder device effect’’ multiplier starting in 1990. This multiplier was necessary to fit the number of nests observed in 1990 and later. We added the effects of shrimping effort directly, modified by habitat weightings, as a proxy for all sources of anthropogenic mortality. Additional data included in our model were incremental growth of Kemp’s ridleys marked and recaptured in the Gulf of Mexico, and the length frequency of stranded Kemp’s ridleys. We also added a 2010 mortality factor that was necessary to fit the number of nests for 2010 and later (2011 and 2012). Last, we used an empirical basis for estimating natural mortality, on the basis of a Lorenzen mortality curve and growth estimates. Although our model generated reasonable estimates of annual total turtle deaths attributable to shrimp trawling, as well as additional deaths due to undetermined anthropogenic causes in 2010, we were unable to provide a clear explanation for the observed increase in the number of stranded Kemp’s ridleys in recent years, and subsequent disruption of the species’ exponential growth since the 2009 nesting season. Our consensus is that expanded data collection at the nesting beaches is needed and of high priority, and that 2015 be targeted for the next stock assessment to evaluate the 2010 event using more recent nesting and in-water data.

Effect of Methodological and Ecological Approaches on Heterogeneity of Nest-Site Selection of a Long-Lived Vulture

PubMed Central

Moreno-Opo, Rubén; Fernández-Olalla, Mariana; Margalida, Antoni; Arredondo, Ángel; Guil, Francisco

2012-01-01

The application of scientific-based conservation measures requires that sampling methodologies in studies modelling similar ecological aspects produce comparable results making easier their interpretation. We aimed to show how the choice of different methodological and ecological approaches can affect conclusions in nest-site selection studies along different Palearctic meta-populations of an indicator species. First, a multivariate analysis of the variables affecting nest-site selection in a breeding colony of cinereous vulture (Aegypius monachus) in central Spain was performed. Then, a meta-analysis was applied to establish how methodological and habitat-type factors determine differences and similarities in the results obtained by previous studies that have modelled the forest breeding habitat of the species. Our results revealed patterns in nesting-habitat modelling by the cinereous vulture throughout its whole range: steep and south-facing slopes, great cover of large trees and distance to human activities were generally selected. The ratio and situation of the studied plots (nests/random), the use of plots vs. polygons as sampling units and the number of years of data set determined the variability explained by the model. Moreover, a greater size of the breeding colony implied that ecological and geomorphological variables at landscape level were more influential. Additionally, human activities affected in greater proportion to colonies situated in Mediterranean forests. For the first time, a meta-analysis regarding the factors determining nest-site selection heterogeneity for a single species at broad scale was achieved. It is essential to homogenize and coordinate experimental design in modelling the selection of species' ecological requirements in order to avoid that differences in results among studies would be due to methodological heterogeneity. This would optimize best conservation and management practices for habitats and species in a global context. PMID:22413023

Influence of corticosterone treatment on nestling begging in Florida scrub-jays (Aphelocoma coerulescens).

PubMed

Elderbrock, Emily K; Small, Thomas W; Schoech, Stephan J

2018-04-01

Altricial young are dependent on adults for protection and food, and they display nutritional need by begging to elicit feeding from parents. Begging at high levels can be energetically expensive and attract predators; thus, an individual must balance its nutritional needs with these potential costs. Further, because a parent is limited in the amount of food it can provide, begging can contribute to both parent-offspring conflict and sibling-sibling competition. Many extrinsic and intrinsic factors may contribute to begging behavior. One intrinsic factor of interest is corticosterone (CORT), a metabolic hormone hypothesized to play a role in regulating a nestling's begging behavior. We investigated the hypothesis that increased exposure to CORT influences nestling begging behavior in an altricial species, the Florida scrub-jay (Aphelocoma coerulescens). We treated one nestling per treatment nest with a twice-daily dose of exogenous hormone via a CORT-injected waxworm, whereas a second individual received a vehicle-injected waxworm. We monitored individual nestling and adult behavior at all nests with the use of high-definition video cameras on several days during treatment. We found no difference in begging rate between CORT fed and vehicle fed nestlings within a treatment nest. Further, to determine whether CORT treatment had indirect effects on the entire brood, we monitored additional nests, in which nestlings were not manipulated. When treatment and controls were compared, overall begging rates of nestlings in treatment nests were greater than those in control nests. This result suggests that CORT treatment of an individual altered its behavior, as well as that of its siblings. Copyright © 2017 Elsevier Inc. All rights reserved.

GC[Formula: see text]NMF: A Novel Matrix Factorization Framework for Gene-Phenotype Association Prediction.

PubMed

Zhang, Yaogong; Liu, Jiahui; Liu, Xiaohu; Hong, Yuxiang; Fan, Xin; Huang, Yalou; Wang, Yuan; Xie, Maoqiang

2018-04-24

Gene-phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene-phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among genes. While due to sparseness of curated gene-phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene-phenotype association detection. In this paper, we propose a novel method by exploiting weighted graph constraint learned from hierarchical structures of phenotype data and group prior information among genes by inheriting advantages of Non-negative Matrix Factorization (NMF), called Weighted Graph Constraint and Group Centric Non-negative Matrix Factorization (GC[Formula: see text]NMF). Specifically, first we introduce the depth of parent-child relationships between two adjacent phenotypes in hierarchical phenotypic data as weighted graph constraint for a better phenotype understanding. Second, we utilize intra-group correlation among genes in a gene group as group constraint for gene understanding. Such information provides us with the intuition that genes in a group probably result in similar phenotypes. The model not only allows us to achieve a high-grade prediction performance, but also helps us to learn interpretable representation of genes and phenotypes simultaneously to facilitate future biological analysis. Experimental results on biological gene-phenotype association datasets of mouse and human demonstrate that GC[Formula: see text]NMF can obtain superior prediction accuracy and good understandability for biological explanation over other state-of-the-arts methods.

American white pelicans breeding in the northern plains: productivity, behavior, movements, and migration

USGS Publications Warehouse

Sovada, Marsha A.; Pietz, Pamela J.; Woodward, Robert O.; Bartos, Alisa J.; Buhl, Deborah A.; Assenmacher, Michael J.

2013-01-01

Nearly half of American white pelicans (Pelecanus erythrorhynchos; hereafter pelicans) are believed to nest in several large colonies in the northern plains, yet few studies had been conducted on pelicans in this region until research began in 2004 to investigate the impact of West Nile virus (WNV) on their chicks. The work reported here focused on two of the largest colonies in the region, at Bitter Lake, South Dakota, and Chase Lake, North Dakota, during 2005–10. Pelicans usually began arriving at these two breeding colonies in early April. Egg-laying began during mid-April and nest initiations continued through May. The number of nests documented at these colonies reached a high of about 15,400 at Bitter Lake and 17,300 at Chase Lake, both in 2006. During 2006–8, annual variation in hatching success was high (40 to 100 percent) at video-monitored nests, averaging 61 percent for 82 nests at Bitter Lake and 57 percent for 88 nests at Chase Lake. Although most nests contained two eggs, of those where two chicks hatched, both chicks survived to the crèche stage (about 15 days old) at only two nests. Severe weather events, disturbance, and siblicide were documented causes of early season (before mid-July) mortalities. In the late season (mid-July to fledging), WNV was the most important factor contributing to chick mortality. Nests were nearly always attended by one adult during incubation and brooding. Adults typically exchanged places at the nest around mid-day in all 3 years, apparently taking advantage of thermals to gain altitude for travel to and from foraging areas. The mean time of exchange differed by about an hour between Bitter Lake (1328 central standard time, CST) and Chase Lake (1434 CST) colonies. During incubation, nearly 3 days often passed between adult nest exchanges; after chicks hatched, exchanges usually occurred daily. Exchanges were more frequent and chicks were fed more often at successful nests than at failed nests. Adult pelicans with satellite transmitters that incorporated a Global Positioning System (GPS) foraged primarily in shallow areas of lakes and semipermanent wetlands. These areas coincide with typical habitats of crayfish, salamanders, and rough fish, which were also the foods most commonly seen in pelican regurgitates at the colonies. Several satellite-tracked pelicans made frequent round trips between their breeding colony and foraging areas, most likely to provision their chicks. Typical distances travelled to foraging sites ranged from 30 kilometers to over 90 kilometers. Return times to the colonies (about 1300 and 1500 CST at Bitter Lake and Chase Lake, respectively) supported the colony difference documented at video-monitored nests. Of 28 pelicans tagged with GPS satellite transmitters in 2005–6, 26 survived the first summer and migrated south during fall. Nineteen of these returned to the breeding region (defined as north of the latitude of South Dakota’s southern border) in at least 1 year during 2006–9; collectively, they returned to the breeding region 33 times. Very few pelicans returned to the colony where they had been tagged; many did not breed and concentrated their activities at wetland complexes in South Dakota and North Dakota, but few tagged pelicans temporally overlapped at specific sites. During 2005–9, tagged pelicans collectively made 56 migratory trips south in the fall. Most wintered in Mexico, near the gulf coast and elsewhere; others wintered in Texas, Louisiana, Mississippi, and Florida. Individuals typically returned to the same general areas each winter. Individuals rarely followed the same migratory path on their way south and north, but they often roughly repeated southerly or northerly routes among years. Ensuring a sustainable population of American white pelicans requires identification and mitigation of known threats. The work described herein has identified WNV and severe weather as important factors that potentially limit reproductive success and recruitment in the northern plains. Managers in this region could assess the influence of such factors on productivity at key colonies by annually obtaining aerial photographs during peak nesting, and estimating numbers of chicks fledged from aerial photographs or ground counts. Banding a subsample of chicks in late June or early July, followed by a sweep for bands at the end of the season, would allow estimation of mortality rates of older chicks (that normally would fledge) and help track the influence of WNV or other mortality factors over time and varying environmental conditions.

The Stability Analysis Method of the Cohesive Granular Slope on the Basis of Graph Theory

PubMed Central

Guan, Yanpeng; Liu, Xiaoli; Wang, Enzhi; Wang, Sijing

2017-01-01

This paper attempted to provide a method to calculate progressive failure of the cohesive-frictional granular geomaterial and the spatial distribution of the stability of the cohesive granular slope. The methodology can be divided into two parts: the characterization method of macro-contact and the analysis of the slope stability. Based on the graph theory, the vertexes, the edges and the edge sequences are abstracted out to characterize the voids, the particle contact and the macro-contact, respectively, bridging the gap between the mesoscopic and macro scales of granular materials. This paper adopts this characterization method to extract a graph from a granular slope and characterize the macro sliding surface, then the weighted graph is analyzed to calculate the slope safety factor. Each edge has three weights representing the sliding moment, the anti-sliding moment and the braking index of contact-bond, respectively, E1E2E3E1E2E3. The safety factor of the slope is calculated by presupposing a certain number of sliding routes and reducing Weight E3 repeatedly and counting the mesoscopic failure of the edge. It is a kind of slope analysis method from mesoscopic perspective so it can present more detail of the mesoscopic property of the granular slope. In the respect of macro scale, the spatial distribution of the stability of the granular slope is in agreement with the theoretical solution. PMID:28772596

Biotic and abiotic factors affect the nest environment of embryonic leatherback turtles, Dermochelys coriacea.

PubMed

Wallace, Bryan P; Sotherland, Paul R; Spotila, James R; Reina, Richard D; Franks, Bryan F; Paladino, Frank V

2004-01-01

Clutches of leatherback turtles, Dermochelys coriacea, have lower hatching success than those of other sea turtles, but causes of high embryonic mortality are unknown. We measured characteristics of clutches along with spatial and temporal changes in PO(2) and temperature during incubation to determine the extent to which they affected the developmental environment of leatherback embryos. Minimum PO(2) in nests decreased as both the total number and mass of metabolizing embryos increased. Increases in both the number and mass of metabolizing embryos caused an increase in maximum nest temperature. However, neither PO(2) nor temperature was correlated with hatching success. Our measurements of relatively high nest PO(2) (lowest 17.1 kPa or 16.9% O(2)) indicate that hypoxia apparently does not cause the low hatching success of leatherback clutches. Oxygen partial pressure increased and temperature decreased from the center toward the periphery of leatherback nests. We inferred from these measurements that positions of eggs within nests vary in quality and potentially affect overall developmental success of entire clutches. The large metabolic mass of leatherback clutches and limits to gas flux imposed by the sand create a situation in which leatherback embryos collectively affect their own environment.

Effects of neonicotinoid insecticide exposure and monofloral diet on nest-founding bumblebee queens.

PubMed

Leza, Mar; Watrous, Kristal M; Bratu, Jade; Woodard, S Hollis

2018-06-13

Bumblebees are among the world's most important groups of pollinating insects in natural and agricultural ecosystems. Each spring, queen bumblebees emerge from overwintering and initiate new nests, which ultimately give rise to workers and new reproductives later in the season. Nest initiation and survival are thus key drivers of both bumblebee pollination services and population dynamics. We performed the first laboratory experiment with the model bumblebee species Bombus impatiens that explores how early nesting success is impacted by the effects of temporary or more sustained exposure to sublethal levels of a neonicotinoid-type insecticide (imidacloprid at 5 ppb in nectar) and by reliance on a monofloral pollen diet, two factors that have been previously implicated in bumblebee decline. We found that queens exhibited increased mortality and dramatically reduced activity levels when exposed to imidacloprid, as well as delayed nest initiation and lower brood numbers in the nest, but partially recovered from these effects when they only received early, temporary exposure. The effects of pollen diet on individual queen- and colony-level responses were overshadowed by effects of the insecticide, although a monofloral pollen diet alone was sufficient to negatively impact brood production. These findings speak to the sensitivity of queen bumblebees during the nest initiation phase of the colony cycle, with implications for how queens and their young nests are uniquely impacted by exposure to threats such as pesticide exposure and foraging habitat unsuitability. © 2018 The Author(s).

Laying date, incubation and egg breakage as determinants of bacterial load on bird eggshells: experimental evidence.

PubMed

Soler, Juan José; Ruiz-Rodríguez, Magdalena; Martín-Vivaldi, Manuel; Peralta-Sánchez, Juan Manuel; Ruiz-Castellano, Cristina; Tomás, Gustavo

2015-09-01

Exploring factors guiding interactions of bacterial communities with animals has become of primary importance for ecologists and evolutionary biologists during the last years because of their likely central role in the evolution of animal life history traits. We explored the association between laying date and eggshell bacterial load (mesophilic bacteria, Enterobacteriaceae, Staphylococci, and Enterococci) in natural and artificial magpie (Pica pica) nests containing fresh commercial quail (Coturnix coturnix) eggs. We manipulated hygiene conditions by spilling egg contents on magpie and artificial nests and explored experimental effects during the breeding season. Egg breakage is a common outcome of brood parasitism by great spotted cuckoos (Clamator glandarius) on the nests of magpie, one of its main hosts. We found that the treatment increased eggshell bacterial load in artificial nests, but not in magpie nests with incubating females, which suggests that parental activity prevents the proliferation of bacteria on the eggshells in relation to egg breakage. Moreover, laying date was positively related to eggshell bacterial load in active magpie nests, but negatively in artificial nests. The results suggest that variation in parental characteristics of magpies rather than climatic variation during the breeding season explained the detected positive association. Because the eggshell bacterial load is a proxy of hatching success, the detected positive association between eggshell bacterial loads and laying date in natural, but not in artificial nests, suggests that the generalized negative association between laying date and avian breeding success can be, at least partially, explained by differential bacterial effects.

Sound settlement: noise surpasses land cover in explaining breeding habitat selection of secondary cavity-nesting birds.

PubMed

Kleist, Nathan J; Guralnick, Robert P; Cruz, Alexander; Francis, Clinton D

2017-01-01

Birds breeding in heterogeneous landscapes select nest sites by cueing in on a variety of factors from landscape features and social information to the presence of natural enemies. We focus on determining the relative impact of anthropogenic noise on nest site occupancy, compared to amount of forest cover, which is known to strongly influence the selection process. We examine chronic, industrial noise from natural gas wells directly measured at the nest box as well as site-averaged noise, using a well-established field experimental system in northwestern New Mexico. We hypothesized that high levels of noise, both at the nest site and in the environment, would decrease nest box occupancy. We set up nest boxes using a geospatially paired control and experimental site design and analyzed four years of occupancy data from four secondary cavity-nesting birds common to the Colorado Plateau. We found different effects of noise and landscape features depending on species, with strong effects of noise observed in breeding habitat selection of Myiarchus cinerascens, the Ash-throated Flycatcher, and Sialia currucoides, the Mountain Bluebird. In contrast, the amount of forest cover less frequently explained habitat selection for those species or had a smaller standardized effect than the acoustic environment. Although forest cover characterization and management is commonly employed by natural resource managers, our results show that characterizing and managing the acoustic environment should be an important tool in protected area management. © 2016 by the Ecological Society of America.

Assessment of a Pan-Dermatophyte Nested-PCR Compared with Conventional Methods for Direct Detection and Identification of Dermatophytosis Agents in Animals.

PubMed

Piri, Fahimeh; Zarei Mahmoudabadi, Ali; Ronagh, Ali; Ahmadi, Bahram; Makimura, Koichi; Rezaei-Matehkolaei, Ali

2018-06-26

Conventional direct microscopy with potassium hydroxide (KOH) and culture were found to lack the ability to establish a fast and specific diagnosis of dermatophytosis. A pan-dermatophyte nested-PCR assay was developed using a novel primer pair targeting the translation elongation factor 1-α (Tef-1α) sequences for direct detection and identification of most veterinary relevant dermatophytes in animal samples suspected to dermatophytosis. A total of 140 animal skin and hair samples were subjected to direct microscopy, culture, and ITS-RFLP/ITS-sequencing of culture isolates for the detection and identification of dermatophytosis agents. Nested-PCR sequencing was performed on all the extracted DNAs using a commercial kit after dissolving the specimens by mechanical beating. Nested-PCR was positive in 90% of samples, followed by direct microscopy (85.7%) and culture (75%). The degree of agreement between nested-PCR and direct microscopy (94.4%) was higher than with culture (83.3%). In 105 culture positive cases, the measures of agreement for the identification of dermatophytosis agents were as follows: 100% between nested-PCR sequencing and ITS-RFLP/ITS-sequencing and 63.8% between nested-PCR sequencing and culture. The developed nested-PCR was faster as well as more sensitive and specific than conventional methods for detection and identification of dermatophytes in clinical samples, which was particularly suitable for epidemiological studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Poster presentations at medical conferences: an effective way of disseminating research?

PubMed

Goodhand, J R; Giles, C L; Wahed, M; Irving, P M; Langmead, L; Rampton, D S

2011-04-01

This study aimed to ascertain the value of posters at medical meetings to presenters and delegates. The usefulness of posters to presenters at national and international meetings was evaluated by assessing the numbers of delegates visiting them and the reasons why they visited. Memorability of selected posters was assessed and factors influencing their appeal to expert delegates identified. At both the national and international meetings, very few delegates (< 5%) visited posters. Only a minority read them and fewer asked useful questions. Recall of content was so poor that it prevented identification of factors improving their memorability. Factors increasing posters' visual appeal included their scientific content, pictures/graphs and limited use of words. Few delegates visit posters and those doing so recall little of their content. To engage their audience, researchers should design visually appealing posters by presenting high quality data in pictures or graphs without an excess of words.

Statistical and procedural issues in the use of heated taxidermic mounts

USGS Publications Warehouse

Bakken, G.S.; Kenow, K.P.; Korschgen, C.E.; Boysen, A.F.

2000-01-01

Studies using mounts have an inherently nested error structure; calibration and standardization should use the appropriate procedures and statistics. One example is that individual mount differences are nested within morphological factors related to species, age, or gender; without replication, mount differences may be confused with differences due to morphology. Also, the sensitivity of mounts to orientation to wind or sun is nested within mount; without replication, inadvertent variation in mount positioning may be confused with differences among mounts. Data on heat loss from a of 1-day-old mallard duckling mount are used to illustrate orientation sensitivity. (C) 2000 Elsevier Science Ltd. All rights reserved.

Nest sanitation through defecation: antifungal properties of wood cockroach feces.

PubMed

Rosengaus, Rebeca B; Mead, Kerry; Du Comb, William S; Benson, Ryan W; Godoy, Veronica G

2013-11-01

The wood cockroach Cryptocercus punctulatus nests as family units inside decayed wood, a substrate known for its high microbial load. We tested the hypothesis that defecation within their nests, a common occurrence in this species, reduces the probability of fungal development. Conidia of the entomopathogenic fungus, Metarhizium anisopliae, were incubated with crushed feces and subsequently plated on potato dextrose agar. Relative to controls, the viability of fungal conidia was significantly reduced following incubation with feces and was negatively correlated with incubation time. Although the cockroach's hindgut contained abundant β-1,3-glucanase activity, its feces had no detectable enzymatic function. Hence, these enzymes are unlikely the source of the fungistasis. Instead, the antifungal compound(s) of the feces involved heat-sensitive factor(s) of potential microbial origin. When feces were boiled or when they were subjected to ultraviolet radiation and subsequently incubated with conidia, viability was "rescued" and germination rates were similar to those of controls. Filtration experiments indicate that the fungistatic activity of feces results from chemical interference. Because Cryptocercidae cockroaches have been considered appropriate models to make inferences about the factors fostering the evolution of termite sociality, we suggest that nesting in microbe-rich environments likely selected for the coupling of intranest defecation and feces fungistasis in the common ancestor of wood cockroaches and termites. This might in turn have served as a preadaptation that prevented mycosis as these phylogenetically related taxa diverged and evolved respectively into subsocial and eusocial organizations.

Nest sanitation through defecation: antifungal properties of wood cockroach feces

NASA Astrophysics Data System (ADS)

Rosengaus, Rebeca B.; Mead, Kerry; Du Comb, William S.; Benson, Ryan W.; Godoy, Veronica G.

2013-11-01

The wood cockroach Cryptocercus punctulatus nests as family units inside decayed wood, a substrate known for its high microbial load. We tested the hypothesis that defecation within their nests, a common occurrence in this species, reduces the probability of fungal development. Conidia of the entomopathogenic fungus, Metarhizium anisopliae, were incubated with crushed feces and subsequently plated on potato dextrose agar. Relative to controls, the viability of fungal conidia was significantly reduced following incubation with feces and was negatively correlated with incubation time. Although the cockroach's hindgut contained abundant β-1,3-glucanase activity, its feces had no detectable enzymatic function. Hence, these enzymes are unlikely the source of the fungistasis. Instead, the antifungal compound(s) of the feces involved heat-sensitive factor(s) of potential microbial origin. When feces were boiled or when they were subjected to ultraviolet radiation and subsequently incubated with conidia, viability was "rescued" and germination rates were similar to those of controls. Filtration experiments indicate that the fungistatic activity of feces results from chemical interference. Because Cryptocercidae cockroaches have been considered appropriate models to make inferences about the factors fostering the evolution of termite sociality, we suggest that nesting in microbe-rich environments likely selected for the coupling of intranest defecation and feces fungistasis in the common ancestor of wood cockroaches and termites. This might in turn have served as a preadaptation that prevented mycosis as these phylogenetically related taxa diverged and evolved respectively into subsocial and eusocial organizations.

Host selection by the shiny cowbird

USGS Publications Warehouse

Wiley, J.W.

1988-01-01

Factors important in Shiny Cowbird (Molothrus bonariensis) host selection were examined within the mangrove community in Puerto Rico. Cowbirds did not parasitize birds in proportion to their abundance. The cowbird breeding season coincided with those of its major hosts, which were 'high-quality' foster species (i.e., species that fledge .gtoreq. 55% of cowbirds hatched: Yellow Warbler, Dendroica petechia; Yellow-shouldered Blackbird, Agelaius xanthomus; Black-whiskered Vireo, Vireo altiloquus; Black-cowled Oriole, Icterus dominicensis; Peurto Rican Flycatcher, Myiarchus antillarum; Troupial, Icterus icterus), and did not extend into other periods even though nests of 'low-quality: species (i.e., species that fledge < 55% of cowbird chicks that hatched: Bronze Mannikin, Lonchura cucullata; Greater Antillean Grackle, Quiscalus niger; Gray Kingbird, Tyrannus dominicensis; Northern Mockingbird, Mimus polyglottos; Red-legged Thrush, Turdus plumbeus) were available. Shiny Cowbird food habits and egg size were similar to those of their hosts, suggesting that cowbirds choose hosts partly on the basis of this combination. Cowbirds located host nests primarily by cryptically watching activities of birds in likely habitats. Other nest locating strategies were active searching of suitable habitat and 'flushing' of hosts by the cowbird's noisy approach. Cowbirds closely monitored nest status with frequent visits that peaked on the host's first day of egg laying. Hosts using covered nests (e.g., cavities, domed nests) were as vulnerable to cowbird parasitism as those building open nests.

Mate loss in winter and mallard reproduction

USGS Publications Warehouse

Lercel, Barbara A.; Kaminski, Richard M.; Cox, Robert R.

1999-01-01

Mallards (Anas platyrhynchos) frequently pair during winter, and duck hunting seasons have been extended until the end of January in several southern states in the Mississippi Flyway. Therefore, we simulated dissolution of pair bonds from natural or hunting mortality by removing mates of wild-strain, captive, yearling female mallards in late January 1996 and early February 1997 to test if mate loss in winter would affect subsequent pair formation and reproductive performance. Most (97%) widowed females paired again. Nesting and incubation frequencies, nest-initiation date, days between first and second nests, and egg mass did not differ (P > 0.126) between widowed and control (i.e., no mate loss experienced) females in 1996 and 1997. In 1997, widowed females laid 1.91 fewer eggs in first nests (P = 0.014) and 3.75 fewer viable eggs in second nests (P = 0.056). Computer simulations with a mallard productivity model (incorporating default parameters [i.e., average environmental conditions]) indicated that the observed decreased clutch size of first nests, fewer viable eggs in second nests, and these factors combined had potential to decrease recruitment rates of yearling female mallards 9%, 12%, and 20%. Our results indicate that winter mate loss could reduce reproductive performance by yearling female mallards in some years. We suggest caution regarding extending duck hunting seasons in winter without concurrent evaluations of harvest and demographics of mallard and other duck populations.

Bonabeau model on a fully connected graph

NASA Astrophysics Data System (ADS)

Malarz, K.; Stauffer, D.; Kułakowski, K.

2006-03-01

Numerical simulations are reported on the Bonabeau model on a fully connected graph, where spatial degrees of freedom are absent. The control parameter is the memory factor f. The phase transition is observed at the dispersion of the agents power hi. The critical value fC shows a hysteretic behavior with respect to the initial distribution of hi. fC decreases with the system size; this decrease can be compensated by a greater number of fights between a global reduction of the distribution width of hi. The latter step is equivalent to a partial forgetting.

Predation and nutrients drive population declines in breeding waders.

PubMed

Møller, Anders Pape; Thorup, Ole; Laursen, Karsten

2018-04-20

Allee effects are defined as a decline in per capita fitness at low population density. We hypothesized that predation reduces population size of breeding waders and thereby the efficiency of predator deterrence, while total nitrogen through its effects on primary and secondary productivity increases population size. Therefore, nest predation could have negative consequences for population size because nest failure generally results in breeding dispersal and hence reduced local population density. To test these predictions, we recorded nest predation in five species of waders for 4,745 nests during 1987-2015 at the nature reserve Tipperne, Denmark. Predation rates were generally negatively related to conspecific and heterospecific population density, but positively related to overall population density of the entire wader community. Nest predation and population density were related to ground water level, management (grazing and mowing), and nutrients. High nest predation with a time lag of one year resulted in low overall breeding population density, while high nutrient levels resulted in higher population density. These two factors accounted for 86% of the variance in population size, presumably due to effects of nest predation on emigration, while nutrient levels increased the level of vegetation cover and the abundance of food in the surrounding brackish water. These findings are consistent with the hypothesis that predation may reduce population density through negative density dependence, while total nitrogen at adjacent shallow water may increase population size. Nest predation rates were reduced by high ground water level in March, grazing by cattle and mowing that affected access to and susceptibility of nests to predators. These effects can be managed to benefit breeding waders. © 2018 by the Ecological Society of America.

Habitat use and reproductive success of western snowy plovers at new nesting areas created for California least terns

USGS Publications Warehouse

Powell, Abby N.; Collier, Christine L.

2000-01-01

The Pacific coast population of western snowy plovers (Charadrius alexandrinus nivosus) was listed as threatened under the Endangered Species Act (ESA) in 1993 and its decline is primarily attributed to habitat loss. In southern California, snowy plovers typically nest in association with federally endangered California least terns (Sterna antillarum browni). Since least terns were afforded protection under the ESA, the creation of nesting habitat from dredged materials has been a popular component of habitat restoration to partially compensate for wetland loss in this region. We had a unique opportunity to monitor habitat use and reproductive success at newly created habitats associated with the restoration of Batiquitos Lagoon, San Diego County, California from 1994 to 1998. We also compared hatch and fledge rates and habitat characteristics of snowy plovers nesting at new nesting areas at Batiquitos Lagoon to a nearby natural beach and a dredged-material area created in the 1970s. The number of nesting attempts by snowy plovers increased from 5 in 1994 to a high of 38 in 1997, and plovers nested on 4 of the 5 created areas. Fledge rates at Batiquitos Lagoon varied annually and declined after the initial colonization in 1995. Fledge rate in 1995 was higher at the newly created area than at the older dredged-material and natural beach areas in any other year. Nests on the created areas at Batiquitos Lagoon were surrounded by less vegetative cover, less debris, and shorter vegetation than nests at the older dredged-material and natural beach areas. Nonbreeding snowy plovers used created habitats within the lagoon, and more plovers used the lagoon and its adjacent beach during fall than winter. Predation pressure and habitat quality were important factors determining use and reproductive success on created areas at Batiquitos Lagoon.

Human Factors Evaluation of Advanced Electric Power Grid Visualization Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greitzer, Frank L.; Dauenhauer, Peter M.; Wierks, Tamara G.

This report describes initial human factors evaluation of four visualization tools (Graphical Contingency Analysis, Force Directed Graphs, Phasor State Estimator and Mode Meter/ Mode Shapes) developed by PNNL, and proposed test plans that may be implemented to evaluate their utility in scenario-based experiments.

Manipulating Google's Knowledge Graph Box to Counter Biased Information Processing During an Online Search on Vaccination: Application of a Technological Debiasing Strategy.

PubMed

Ludolph, Ramona; Allam, Ahmed; Schulz, Peter J

2016-06-02

One of people's major motives for going online is the search for health-related information. Most consumers start their search with a general search engine but are unaware of the fact that its sorting and ranking criteria do not mirror information quality. This misconception can lead to distorted search outcomes, especially when the information processing is characterized by heuristic principles and resulting cognitive biases instead of a systematic elaboration. As vaccination opponents are vocal on the Web, the chance of encountering their non‒evidence-based views on immunization is high. Therefore, biased information processing in this context can cause subsequent impaired judgment and decision making. A technological debiasing strategy could counter this by changing people's search environment. This study aims at testing a technological debiasing strategy to reduce the negative effects of biased information processing when using a general search engine on people's vaccination-related knowledge and attitudes. This strategy is to manipulate the content of Google's knowledge graph box, which is integrated in the search interface and provides basic information about the search topic. A full 3x2 factorial, posttest-only design was employed with availability of basic factual information (comprehensible vs hardly comprehensible vs not present) as the first factor and a warning message as the second factor of experimental manipulation. Outcome variables were the evaluation of the knowledge graph box, vaccination-related knowledge, as well as beliefs and attitudes toward vaccination, as represented by three latent variables emerged from an exploratory factor analysis. Two-way analysis of variance revealed a significant main effect of availability of basic information in the knowledge graph box on participants' vaccination knowledge scores (F2,273=4.86, P=.01), skepticism/fear of vaccination side effects (F2,273=3.5, P=.03), and perceived information quality (F2,273=3.73, P=.02). More specifically, respondents receiving comprehensible information appeared to be more knowledgeable, less skeptical of vaccination, and more critical of information quality compared to participants exposed to hardly comprehensible information. Although, there was no significant interaction effect between the availability of information and the presence of the warning, there was a dominant pattern in which the presence of the warning appeared to have a positive influence on the group receiving comprehensible information while the opposite was true for the groups exposed to hardly comprehensible information and no information at all. Participants evaluated the knowledge graph box as moderately to highly useful, with no significant differences among the experimental groups. Overall, the results suggest that comprehensible information in the knowledge graph box positively affects participants' vaccination-related knowledge and attitudes. A small change in the content retrieval procedure currently used by Google could already make a valuable difference in the pursuit of an unbiased online information search. Further research is needed to gain insights into the knowledge graph box's entire potential.

Sunflower (Helianthus annuus) pollination in California's Central Valley is limited by native bee nest site location.

PubMed

Sardiñas, Hillary S; Tom, Kathleen; Ponisio, Lauren Catherine; Rominger, Andrew; Kremen, Claire

2016-03-01

The delivery of ecosystem services by mobile organisms depends on the distribution of those organisms, which is, in turn, affected by resources at local and landscape scales. Pollinator-dependent crops rely on mobile animals like bees for crop production, and the spatial relationship between floral resources and nest location for these central-place foragers influences the delivery of pollination services. Current models that map pollination coverage in agricultural regions utilize landscape-level estimates of floral availability and nesting incidence inferred from expert opinion, rather than direct assessments. Foraging distance is often derived from proxies of bee body size, rather than direct measurements of foraging that account for behavioral responses to floral resource type and distribution. The lack of direct measurements of nesting incidence and foraging distances may lead to inaccurate mapping of pollination services. We examined the role of local-scale floral resource presence from hedgerow plantings on nest incidence of ground-nesting bees in field margins and within monoculture, conventionally managed sunflower fields in California's Central Valley. We tracked bee movement into fields using fluorescent powder. We then used these data to simulate the distribution of pollination services within a crop field. Contrary to expert opinion, we found that ground-nesting native bees nested both in fields and edges, though nesting rates declined with distance into field. Further, we detected no effect of field-margin floral enhancements on nesting. We found evidence of an exponential decay rate of bee movement into fields, indicating that foraging predominantly occurred in less than 1% of medium-sized bees' predicted typical foraging range. Although we found native bees nesting within agricultural fields, their restricted foraging movements likely centralize pollination near nest sites. Our data thus predict a heterogeneous distribution of pollination services within sunflower fields, with edges receiving higher coverage than field centers. To generate more accurate maps of services, we advocate directly measuring the autecology of ecosystem service providers, which vary by crop system, pollinator species, and region. Improving estimates of the factors affecting pollinator populations can increase the accuracy of pollination service maps and help clarify the influence of farming practices on wild bees occurring in agricultural landscapes.

Color normalization of histology slides using graph regularized sparse NMF

NASA Astrophysics Data System (ADS)

Sha, Lingdao; Schonfeld, Dan; Sethi, Amit

2017-03-01

Computer based automatic medical image processing and quantification are becoming popular in digital pathology. However, preparation of histology slides can vary widely due to differences in staining equipment, procedures and reagents, which can reduce the accuracy of algorithms that analyze their color and texture information. To re- duce the unwanted color variations, various supervised and unsupervised color normalization methods have been proposed. Compared with supervised color normalization methods, unsupervised color normalization methods have advantages of time and cost efficient and universal applicability. Most of the unsupervised color normaliza- tion methods for histology are based on stain separation. Based on the fact that stain concentration cannot be negative and different parts of the tissue absorb different stains, nonnegative matrix factorization (NMF), and particular its sparse version (SNMF), are good candidates for stain separation. However, most of the existing unsupervised color normalization method like PCA, ICA, NMF and SNMF fail to consider important information about sparse manifolds that its pixels occupy, which could potentially result in loss of texture information during color normalization. Manifold learning methods like Graph Laplacian have proven to be very effective in interpreting high-dimensional data. In this paper, we propose a novel unsupervised stain separation method called graph regularized sparse nonnegative matrix factorization (GSNMF). By considering the sparse prior of stain concentration together with manifold information from high-dimensional image data, our method shows better performance in stain color deconvolution than existing unsupervised color deconvolution methods, especially in keeping connected texture information. To utilized the texture information, we construct a nearest neighbor graph between pixels within a spatial area of an image based on their distances using heat kernal in lαβ space. The representation of a pixel in the stain density space is constrained to follow the feature distance of the pixel to pixels in the neighborhood graph. Utilizing color matrix transfer method with the stain concentrations found using our GSNMF method, the color normalization performance was also better than existing methods.

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms.

PubMed

Ahsendorf, Tobias; Wong, Felix; Eils, Roland; Gunawardena, Jeremy

2014-12-05

Gene regulation has, for the most part, been quantitatively analysed by assuming that regulatory mechanisms operate at thermodynamic equilibrium. This formalism was originally developed to analyse the binding and unbinding of transcription factors from naked DNA in eubacteria. Although widely used, it has made it difficult to understand the role of energy-dissipating, epigenetic mechanisms, such as DNA methylation, nucleosome remodelling and post-translational modification of histones and co-regulators, which act together with transcription factors to regulate gene expression in eukaryotes. Here, we introduce a graph-based framework that can accommodate non-equilibrium mechanisms. A gene-regulatory system is described as a graph, which specifies the DNA microstates (vertices), the transitions between microstates (edges) and the transition rates (edge labels). The graph yields a stochastic master equation for how microstate probabilities change over time. We show that this framework has broad scope by providing new insights into three very different ad hoc models, of steroid-hormone responsive genes, of inherently bounded chromatin domains and of the yeast PHO5 gene. We find, moreover, surprising complexity in the regulation of PHO5, which has not yet been experimentally explored, and we show that this complexity is an inherent feature of being away from equilibrium. At equilibrium, microstate probabilities do not depend on how a microstate is reached but, away from equilibrium, each path to a microstate can contribute to its steady-state probability. Systems that are far from equilibrium thereby become dependent on history and the resulting complexity is a fundamental challenge. To begin addressing this, we introduce a graph-based concept of independence, which can be applied to sub-systems that are far from equilibrium, and prove that history-dependent complexity can be circumvented when sub-systems operate independently. As epigenomic data become increasingly available, we anticipate that gene function will come to be represented by graphs, as gene structure has been represented by sequences, and that the methods introduced here will provide a broader foundation for understanding how genes work.

A Security Assessment Mechanism for Software-Defined Networking-Based Mobile Networks.

PubMed

Luo, Shibo; Dong, Mianxiong; Ota, Kaoru; Wu, Jun; Li, Jianhua

2015-12-17

Software-Defined Networking-based Mobile Networks (SDN-MNs) are considered the future of 5G mobile network architecture. With the evolving cyber-attack threat, security assessments need to be performed in the network management. Due to the distinctive features of SDN-MNs, such as their dynamic nature and complexity, traditional network security assessment methodologies cannot be applied directly to SDN-MNs, and a novel security assessment methodology is needed. In this paper, an effective security assessment mechanism based on attack graphs and an Analytic Hierarchy Process (AHP) is proposed for SDN-MNs. Firstly, this paper discusses the security assessment problem of SDN-MNs and proposes a methodology using attack graphs and AHP. Secondly, to address the diversity and complexity of SDN-MNs, a novel attack graph definition and attack graph generation algorithm are proposed. In order to quantify security levels, the Node Minimal Effort (NME) is defined to quantify attack cost and derive system security levels based on NME. Thirdly, to calculate the NME of an attack graph that takes the dynamic factors of SDN-MN into consideration, we use AHP integrated with the Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) as the methodology. Finally, we offer a case study to validate the proposed methodology. The case study and evaluation show the advantages of the proposed security assessment mechanism.

A Graph-Algorithmic Approach for the Study of Metastability in Markov Chains

NASA Astrophysics Data System (ADS)

Gan, Tingyue; Cameron, Maria

2017-06-01

Large continuous-time Markov chains with exponentially small transition rates arise in modeling complex systems in physics, chemistry, and biology. We propose a constructive graph-algorithmic approach to determine the sequence of critical timescales at which the qualitative behavior of a given Markov chain changes, and give an effective description of the dynamics on each of them. This approach is valid for both time-reversible and time-irreversible Markov processes, with or without symmetry. Central to this approach are two graph algorithms, Algorithm 1 and Algorithm 2, for obtaining the sequences of the critical timescales and the hierarchies of Typical Transition Graphs or T-graphs indicating the most likely transitions in the system without and with symmetry, respectively. The sequence of critical timescales includes the subsequence of the reciprocals of the real parts of eigenvalues. Under a certain assumption, we prove sharp asymptotic estimates for eigenvalues (including pre-factors) and show how one can extract them from the output of Algorithm 1. We discuss the relationship between Algorithms 1 and 2 and explain how one needs to interpret the output of Algorithm 1 if it is applied in the case with symmetry instead of Algorithm 2. Finally, we analyze an example motivated by R. D. Astumian's model of the dynamics of kinesin, a molecular motor, by means of Algorithm 2.

A Security Assessment Mechanism for Software-Defined Networking-Based Mobile Networks

PubMed Central

Luo, Shibo; Dong, Mianxiong; Ota, Kaoru; Wu, Jun; Li, Jianhua

2015-01-01

Software-Defined Networking-based Mobile Networks (SDN-MNs) are considered the future of 5G mobile network architecture. With the evolving cyber-attack threat, security assessments need to be performed in the network management. Due to the distinctive features of SDN-MNs, such as their dynamic nature and complexity, traditional network security assessment methodologies cannot be applied directly to SDN-MNs, and a novel security assessment methodology is needed. In this paper, an effective security assessment mechanism based on attack graphs and an Analytic Hierarchy Process (AHP) is proposed for SDN-MNs. Firstly, this paper discusses the security assessment problem of SDN-MNs and proposes a methodology using attack graphs and AHP. Secondly, to address the diversity and complexity of SDN-MNs, a novel attack graph definition and attack graph generation algorithm are proposed. In order to quantify security levels, the Node Minimal Effort (NME) is defined to quantify attack cost and derive system security levels based on NME. Thirdly, to calculate the NME of an attack graph that takes the dynamic factors of SDN-MN into consideration, we use AHP integrated with the Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) as the methodology. Finally, we offer a case study to validate the proposed methodology. The case study and evaluation show the advantages of the proposed security assessment mechanism. PMID:26694409

Attributed community mining using joint general non-negative matrix factorization with graph Laplacian

NASA Astrophysics Data System (ADS)

Chen, Zigang; Li, Lixiang; Peng, Haipeng; Liu, Yuhong; Yang, Yixian

2018-04-01

Community mining for complex social networks with link and attribute information plays an important role according to different application needs. In this paper, based on our proposed general non-negative matrix factorization (GNMF) algorithm without dimension matching constraints in our previous work, we propose the joint GNMF with graph Laplacian (LJGNMF) to implement community mining of complex social networks with link and attribute information according to different application needs. Theoretical derivation result shows that the proposed LJGNMF is fully compatible with previous methods of integrating traditional NMF and symmetric NMF. In addition, experimental results show that the proposed LJGNMF can meet the needs of different community minings by adjusting its parameters, and the effect is better than traditional NMF in the community vertices attributes entropy.

Graph-Based Cooperative Localization Using Symmetric Measurement Equations.

PubMed

Gulati, Dhiraj; Zhang, Feihu; Clarke, Daniel; Knoll, Alois

2017-06-17

Precise localization is a key requirement for the success of highly assisted or autonomous vehicles. The diminishing cost of hardware has resulted in a proliferation of the number of sensors in the environment. Cooperative localization (CL) presents itself as a feasible and effective solution for localizing the ego-vehicle and its neighboring vehicles. However, one of the major challenges to fully realize the effective use of infrastructure sensors for jointly estimating the state of a vehicle in cooperative vehicle-infrastructure localization is an effective data association. In this paper, we propose a method which implements symmetric measurement equations within factor graphs in order to overcome the data association challenge with a reduced bandwidth overhead. Simulated results demonstrate the benefits of the proposed approach in comparison with our previously proposed approach of topology factors.

Graph-Based Cooperative Localization Using Symmetric Measurement Equations

PubMed Central

Gulati, Dhiraj; Zhang, Feihu; Clarke, Daniel; Knoll, Alois

2017-01-01

Precise localization is a key requirement for the success of highly assisted or autonomous vehicles. The diminishing cost of hardware has resulted in a proliferation of the number of sensors in the environment. Cooperative localization (CL) presents itself as a feasible and effective solution for localizing the ego-vehicle and its neighboring vehicles. However, one of the major challenges to fully realize the effective use of infrastructure sensors for jointly estimating the state of a vehicle in cooperative vehicle-infrastructure localization is an effective data association. In this paper, we propose a method which implements symmetric measurement equations within factor graphs in order to overcome the data association challenge with a reduced bandwidth overhead. Simulated results demonstrate the benefits of the proposed approach in comparison with our previously proposed approach of topology factors. PMID:28629141

Molecular diagnosis of strongyloidiasis in a population of an endemic area through nested-PCR.

PubMed

Sharifdini, Meysam; Keyhani, Amir; Eshraghian, Mohammad Reza; Beigom Kia, Eshrat

2018-01-01

This study is aimed to diagnose and analyze strongyloidiasis in a population of an endemic area of Iran using nested-PCR, coupled with parasitological methods. Screening of strongyloidiasis infected people using reliable diagnostic techniques are essential to decrease the mortality and morbidity associated with this infection. Molecular methods have been proved to be highly sensitive and specific for detection of Strongyloides stercoralis in stool samples. A total of 155 fresh single stool samples were randomly collected from residents of north and northwest of Khouzestan Province, Iran. All samples were examined by parasitological methods including formalin-ether concentration and nutrient agar plate culture, and molecular method of nested-PCR. Infections with S. stercoralis were analyzed according to demographic criteria. Based on the results of nested-PCR method 15 cases (9.7%) were strongyloidiasis positive. Nested-PCR was more sensitive than parasitological techniques on single stool sampling. Elderly was the most important population index for higher infectivity with S. stercoralis . In endemic areas of S. stercoralis , old age should be considered as one of the most important risk factors of infection, especially among the immunosuppressed individuals.

Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population

PubMed Central

Sofaer, Helen R; Sillett, T Scott; Langin, Kathryn M; Morrison, Scott A; Ghalambor, Cameron K

2014-01-01

Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong. PMID:25077023

Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population.

PubMed

Sofaer, Helen R; Sillett, T Scott; Langin, Kathryn M; Morrison, Scott A; Ghalambor, Cameron K

2014-07-01

Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong.

Bayesian network ensemble as a multivariate strategy to predict radiation pneumonitis risk

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sangkyu, E-mail: sangkyu.lee@mail.mcgill.ca; Ybarra, Norma; Jeyaseelan, Krishinima

2015-05-15

Purpose: Prediction of radiation pneumonitis (RP) has been shown to be challenging due to the involvement of a variety of factors including dose–volume metrics and radiosensitivity biomarkers. Some of these factors are highly correlated and might affect prediction results when combined. Bayesian network (BN) provides a probabilistic framework to represent variable dependencies in a directed acyclic graph. The aim of this study is to integrate the BN framework and a systems’ biology approach to detect possible interactions among RP risk factors and exploit these relationships to enhance both the understanding and prediction of RP. Methods: The authors studied 54 nonsmall-cellmore » lung cancer patients who received curative 3D-conformal radiotherapy. Nineteen RP events were observed (common toxicity criteria for adverse events grade 2 or higher). Serum concentration of the following four candidate biomarkers were measured at baseline and midtreatment: alpha-2-macroglobulin, angiotensin converting enzyme (ACE), transforming growth factor, interleukin-6. Dose-volumetric and clinical parameters were also included as covariates. Feature selection was performed using a Markov blanket approach based on the Koller–Sahami filter. The Markov chain Monte Carlo technique estimated the posterior distribution of BN graphs built from the observed data of the selected variables and causality constraints. RP probability was estimated using a limited number of high posterior graphs (ensemble) and was averaged for the final RP estimate using Bayes’ rule. A resampling method based on bootstrapping was applied to model training and validation in order to control under- and overfit pitfalls. Results: RP prediction power of the BN ensemble approach reached its optimum at a size of 200. The optimized performance of the BN model recorded an area under the receiver operating characteristic curve (AUC) of 0.83, which was significantly higher than multivariate logistic regression (0.77), mean heart dose (0.69), and a pre-to-midtreatment change in ACE (0.66). When RP prediction was made only with pretreatment information, the AUC ranged from 0.76 to 0.81 depending on the ensemble size. Bootstrap validation of graph features in the ensemble quantified confidence of association between variables in the graphs where ten interactions were statistically significant. Conclusions: The presented BN methodology provides the flexibility to model hierarchical interactions between RP covariates, which is applied to probabilistic inference on RP. The authors’ preliminary results demonstrate that such framework combined with an ensemble method can possibly improve prediction of RP under real-life clinical circumstances such as missing data or treatment plan adaptation.« less

Latent Factors in Student-Teacher Interaction Factor Analysis

ERIC Educational Resources Information Center

Le, Thu; Bolt, Daniel; Camburn, Eric; Goff, Peter; Rohe, Karl

2017-01-01

Classroom interactions between students and teachers form a two-way or dyadic network. Measurements such as days absent, test scores, student ratings, or student grades can indicate the "quality" of the interaction. Together with the underlying bipartite graph, these values create a valued student-teacher dyadic interaction network. To…

Predator behaviour and predation risk in the heterogeneous Arctic environment.

PubMed

Lecomte, Nicolas; Careau, Vincent; Gauthier, Gilles; Giroux, Jean-François

2008-05-01

1. Habitat heterogeneity and predator behaviour can strongly affect predator-prey interactions but these factors are rarely considered simultaneously, especially when systems encompass multiple predators and prey. 2. In the Arctic, greater snow geese Anser caerulescens atlanticus L. nest in two structurally different habitats: wetlands that form intricate networks of water channels, and mesic tundra where such obstacles are absent. In this heterogeneous environment, goose eggs are exposed to two types of predators: the arctic fox Vulpes lagopus L. and a diversity of avian predators. We hypothesized that, contrary to birds, the hunting ability of foxes would be impaired by the structurally complex wetland habitat, resulting in a lower predation risk for goose eggs. 3. In addition, lemmings, the main prey of foxes, show strong population cycles. We thus further examined how their fluctuations influenced the interaction between habitat heterogeneity and fox predation on goose eggs. 4. An experimental approach with artificial nests suggested that foxes were faster than avian predators to find unattended goose nests in mesic tundra whereas the reverse was true in wetlands. Foxes spent 3.5 times more time between consecutive attacks on real goose nests in wetlands than in mesic tundra. Their attacks on goose nests were also half as successful in wetlands than in mesic tundra whereas no difference was found for avian predators. 5. Nesting success in wetlands (65%) was higher than in mesic tundra (56%) but the difference between habitats increased during lemming crashes (15%) compared to other phases of the cycle (5%). Nests located at the edge of wetland patches were also less successful than central ones, suggesting a gradient in accessibility of goose nests in wetlands for foxes. 6. Our study shows that the structural complexity of wetlands decreases predation risk from foxes but not avian predators in arctic-nesting birds. Our results also demonstrate that cyclic lemming populations indirectly alter the spatial distribution of productive nests due to a complex interaction between habitat structure, prey-switching and foraging success of foxes.

Stationary Random Metrics on Hierarchical Graphs Via {(min,+)}-type Recursive Distributional Equations

NASA Astrophysics Data System (ADS)

Khristoforov, Mikhail; Kleptsyn, Victor; Triestino, Michele

2016-07-01

This paper is inspired by the problem of understanding in a mathematical sense the Liouville quantum gravity on surfaces. Here we show how to define a stationary random metric on self-similar spaces which are the limit of nice finite graphs: these are the so-called hierarchical graphs. They possess a well-defined level structure and any level is built using a simple recursion. Stopping the construction at any finite level, we have a discrete random metric space when we set the edges to have random length (using a multiplicative cascade with fixed law {m}). We introduce a tool, the cut-off process, by means of which one finds that renormalizing the sequence of metrics by an exponential factor, they converge in law to a non-trivial metric on the limit space. Such limit law is stationary, in the sense that glueing together a certain number of copies of the random limit space, according to the combinatorics of the brick graph, the obtained random metric has the same law when rescaled by a random factor of law {m} . In other words, the stationary random metric is the solution of a distributional equation. When the measure m has continuous positive density on {mathbf{R}+}, the stationary law is unique up to rescaling and any other distribution tends to a rescaled stationary law under the iterations of the hierarchical transformation. We also investigate topological and geometric properties of the random space when m is log-normal, detecting a phase transition influenced by the branching random walk associated to the multiplicative cascade.

Migratory patterns and population structure among breeding and wintering red-breasted mergansers (Mergus serrator) and common mergansers (M. merganser)

USGS Publications Warehouse

Pearce, J.M.; McCracken, K.G.; Christensen, Thomas K.; Zhuravlev, Y.N.

2009-01-01

Philopatry has long been assumed to structure populations of waterfowl and other species of birds genetically, especially via maternally transmitted mitochondrial DNA (mtDNA), yet other migratory behaviors and nesting ecology (use of ground vs. cavity sites) may also contribute to population genetic structure. We investigated the effects of migration and nesting ecology on the population genetic structure of two Holarctic waterfowl, the Red-breasted Merganser (Mergus serrator) and Common Merganser (M. merganser), using mtDNA control-region sequence data. Red-breasted Mergansers (a ground-nesting species) exhibited lower levels of population differentiation across their North American range, possibly as a result of post-Pleistocene range expansion and population growth. By contrast, Common Mergansers (a cavity-nesting species) breeding in western and eastern North America were strongly differentiated, as were continental groups in North America and Europe. Our hypothesis that population differentiation of breeding female Common Mergansers results from limited migration during non-breeding periods was not supported, in that equally heterogeneous mtDNA lineages were observed in males and females on several wintering areas. The interspecific differences in mtDNA patterns for these two closely related species may have resulted from factors related to nesting ecology (ground vs. cavity nesting) and responses to historical climate change.

New concepts regarding the production of waterfowl and other game birds in areas of diversified agriculture

USGS Publications Warehouse

Nelson, H.K.; Duebbert, H.F.

1974-01-01

Many concepts regarding breeding ecology of waterfowl and the influences of environmental factors on annual production have changed in the past 20 years. These influences are especially pronounced in the prairie region of central North America where agriculture becomes more intensive each year. The principal task assigned to this Research Center when established in 1965 was to determine the relative impact of these influences on production and to identify those facets of breeding biology, nesting habitat requirements and other factors that may be altered to increase production on lands dedicated for this purpose. A corollary objective was to develop methods for enhancing production of waterfowl and other ground-nesting birds on private lands in agricultural areas. Some of the highlights of our findings to date, together with the results from current work of others, provide new information on waterfowl that indicates: (1) homing instincts are not as specific as indicated by earlier workers, (2) there are differences in pioneering between species, sexes and age classes, (3) strength and duration of pair bonds vary by species and age classes, (4) territorial tolerances for most species are greater than previously indicated, (5) there is differential productivity by age classes in some species, (6) there has been a gradual decline in nesting success in the prairie region the past 30 years, (7) adverse influences of intensive agriculture are increasing, (8) mammalian predation is an important factor, (9) high quality, secure nesting habitat and a complex of wetland types are the essential components of an optimum production unit, (10) the size and shape of blocks of nesting cover are important management considerations, (11) overharvest of local breeding populations is becoming a serious problem in some areas. Each of these subjects is discussed as related to research objectives and current management problems. Recommendations are presented for obtaining maximum production of waterfowl and other game birds on public and private lands in agricultural areas.

Exactly solved models on planar graphs with vertices in {Z}^3

NASA Astrophysics Data System (ADS)

Kels, Andrew P.

2017-12-01

It is shown how exactly solved edge interaction models on the square lattice, may be extended onto more general planar graphs, with edges connecting a subset of next nearest neighbour vertices of {Z}3 . This is done by using local deformations of the square lattice, that arise through the use of the star-triangle relation. Similar to Baxter’s Z-invariance property, these local deformations leave the partition function invariant up to some simple factors coming from the star-triangle relation. The deformations used here extend the usual formulation of Z-invariance, by requiring the introduction of oriented rapidity lines which form directed closed paths in the rapidity graph of the model. The quasi-classical limit is also considered, in which case the deformations imply a classical Z-invariance property, as well as a related local closure relation, for the action functional of a system of classical discrete Laplace equations.

Classifying Web Pages by Using Knowledge Bases for Entity Retrieval

NASA Astrophysics Data System (ADS)

Kiritani, Yusuke; Ma, Qiang; Yoshikawa, Masatoshi

In this paper, we propose a novel method to classify Web pages by using knowledge bases for entity search, which is a kind of typical Web search for information related to a person, location or organization. First, we map a Web page to entities according to the similarities between the page and the entities. Various methods for computing such similarity are applied. For example, we can compute the similarity between a given page and a Wikipedia article describing a certain entity. The frequency of an entity appearing in the page is another factor used in computing the similarity. Second, we construct a directed acyclic graph, named PEC graph, based on the relations among Web pages, entities, and categories, by referring to YAGO, a knowledge base built on Wikipedia and WordNet. Finally, by analyzing the PEC graph, we classify Web pages into categories. The results of some preliminary experiments validate the methods proposed in this paper.

The relationships between spatial ability, logical thinking, mathematics performance and kinematics graph interpretation skills of 12th grade physics students

NASA Astrophysics Data System (ADS)

Bektasli, Behzat

Graphs have a broad use in science classrooms, especially in physics. In physics, kinematics is probably the topic for which graphs are most widely used. The participants in this study were from two different grade-12 physics classrooms, advanced placement and calculus-based physics. The main purpose of this study was to search for the relationships between student spatial ability, logical thinking, mathematical achievement, and kinematics graphs interpretation skills. The Purdue Spatial Visualization Test, the Middle Grades Integrated Process Skills Test (MIPT), and the Test of Understanding Graphs in Kinematics (TUG-K) were used for quantitative data collection. Classroom observations were made to acquire ideas about classroom environment and instructional techniques. Factor analysis, simple linear correlation, multiple linear regression, and descriptive statistics were used to analyze the quantitative data. Each instrument has two principal components. The selection and calculation of the slope and of the area were the two principal components of TUG-K. MIPT was composed of a component based upon processing text and a second component based upon processing symbolic information. The Purdue Spatial Visualization Test was composed of a component based upon one-step processing and a second component based upon two-step processing of information. Student ability to determine the slope in a kinematics graph was significantly correlated with spatial ability, logical thinking, and mathematics aptitude and achievement. However, student ability to determine the area in a kinematics graph was only significantly correlated with student pre-calculus semester 2 grades. Male students performed significantly better than female students on the slope items of TUG-K. Also, male students performed significantly better than female students on the PSAT mathematics assessment and spatial ability. This study found that students have different levels of spatial ability, logical thinking, and mathematics aptitude and achievement levels. These different levels were related to student learning of kinematics and they need to be considered when kinematics is being taught. It might be easier for students to understand the kinematics graphs if curriculum developers include more activities related to spatial ability and logical thinking.

[A retrieval method of drug molecules based on graph collapsing].

PubMed

Qu, J W; Lv, X Q; Liu, Z M; Liao, Y; Sun, P H; Wang, B; Tang, Z

2018-04-18

To establish a compact and efficient hypergraph representation and a graph-similarity-based retrieval method of molecules to achieve effective and efficient medicine information retrieval. Chemical structural formula (CSF) was a primary search target as a unique and precise identifier for each compound at the molecular level in the research field of medicine information retrieval. To retrieve medicine information effectively and efficiently, a complete workflow of the graph-based CSF retrieval system was introduced. This system accepted the photos taken from smartphones and the sketches drawn on tablet personal computers as CSF inputs, and formalized the CSFs with the corresponding graphs. Then this paper proposed a compact and efficient hypergraph representation for molecules on the basis of analyzing factors that directly affected the efficiency of graph matching. According to the characteristics of CSFs, a hierarchical collapsing method combining graph isomorphism and frequent subgraph mining was adopted. There was yet a fundamental challenge, subgraph overlapping during the collapsing procedure, which hindered the method from establishing the correct compact hypergraph of an original CSF graph. Therefore, a graph-isomorphism-based algorithm was proposed to select dominant acyclic subgraphs on the basis of overlapping analysis. Finally, the spatial similarity among graphical CSFs was evaluated by multi-dimensional measures of similarity. To evaluate the performance of the proposed method, the proposed system was firstly compared with Wikipedia Chemical Structure Explorer (WCSE), the state-of-the-art system that allowed CSF similarity searching within Wikipedia molecules dataset, on retrieval accuracy. The system achieved higher values on mean average precision, discounted cumulative gain, rank-biased precision, and expected reciprocal rank than WCSE from the top-2 to the top-10 retrieved results. Specifically, the system achieved 10%, 1.41, 6.42%, and 1.32% higher than WCSE on these metrics for top-10 retrieval results, respectively. Moreover, several retrieval cases were presented to intuitively compare with WCSE. The results of the above comparative study demonstrated that the proposed method outperformed the existing method with regard to accuracy and effectiveness. This paper proposes a graph-similarity-based retrieval approach for medicine information. To obtain satisfactory retrieval results, an isomorphism-based algorithm is proposed for dominant subgraph selection based on the subgraph overlapping analysis, as well as an effective and efficient hypergraph representation of molecules. Experiment results demonstrate the effectiveness of the proposed approach.

Demographics of piscivorous colonial waterbirds and management implications for ESA-listed salmonids on the Columbia Plateau

USGS Publications Warehouse

Adkins, Jessica Y.; Lyons, Donald E.; Loschl, Peter J.; Roby, Daniel D.; Collis, Ken; Evans, Allen F.; Hostetter, Nathan J.

2014-01-01

We investigated colony size, productivity, and limiting factors for five piscivorous waterbird species nesting at 18 locations on the Columbia Plateau (Washington) during 2004–2010 with emphasis on species with a history of salmonid (Oncorhynchus spp.) depredation. Numbers of nesting Caspian terns (Hydroprogne caspia) and double-crested cormorants (Phalacrocorax auritus) were stable at about 700–1,000 breeding pairs at five colonies and about 1,200–1,500 breeding pairs at four colonies, respectively. Numbers of American white pelicans (Pelecanus erythrorhynchos) increased at Badger Island, the sole breeding colony for the species on the Columbia Plateau, from about 900 individuals in 2007 to over 2,000 individuals in 2010. Overall numbers of breeding California gulls (Larus californicus) and ring-billed gulls (L. delawarensis) declined during the study, mostly because of the abandonment of a large colony in the mid-Columbia River. Three gull colonies below the confluence of the Snake and Columbia rivers increased substantially, however. Factors that may limit colony size and productivity for piscivorous waterbirds nesting on the Columbia Plateau included availability of suitable nesting habitat, interspecific competition for nest sites, predation, gull kleptoparasitism, food availability, and human disturbance. Based on observed population trends alone, there is little reason to project increased impacts to juvenile salmonid survival from tern and cormorant populations. Additional monitoring and evaluation may be warranted to assess future impacts of the growing Badger Island American white pelican colony and those gull colonies located near mainstem dams or associated with Caspian tern colonies where kleptoparasitism is common.

Water Vapor Reaches Mars' Middle Atmosphere During Global Dust Storm

NASA Image and Video Library

2018-01-23

Rising air during a 2007 global dust storm on Mars lofted water vapor into the planet's middle atmosphere, researchers learned from data graphed here, derived from observations by the Mars Climate Sounder instrument on NASA's Mars Reconnaissance Orbiter. The two vertical black lines in the right half of the graph (at about 260 and 310 on the horizontal scale) mark the beginning and end of the most recent global dust storm on Mars, which burst from regional scale to globe-encircling scale in July 2007. The presence of more colored dots, particularly green ones, in the upper portion of the graph between those lines, compared to the upper portion of the graph outside those lines, documents the uplift of water vapor in connection with the global dust storm. The vertical scale is altitude, labeled at left in kilometers above the surface of Mars (50 kilometers is about 30 miles; 80 kilometers is about 50 miles). The color bar below the graph gives the key to how much water vapor each dot represents, in parts per million, by volume, in Mars' atmosphere. Note that green to yellow represents about 100 times as much water as purple does. The horizontal axis of the graph is time, from January 2006 to February 2008. It is labeled with numbers representing the 360 degrees of Mars' orbit around the Sun, from zero to 360 degrees and then further on to include the first 30 degrees of the following Martian year. (The zero point is autumnal equinox -- end of summer -- in Mars' northern hemisphere.) This graph, based on Mars Reconnaissance Orbiter observations, was used in a January 2018 paper in Nature Astronomy by Nicholas Heavens of Hampton University in Hampton, Virginia, and co-authors. The paper presents Martian dust storms' uplifting effect on water vapor as a factor in seasonal patterns that other spacecraft have detected in the rate of hydrogen escaping from the top of Mars' atmosphere. https://photojournal.jpl.nasa.gov/catalog/PIA22080

Factors affecting breeding dispersal of European ducks on Engure Marsh, Latvia

USGS Publications Warehouse

Blums, P.; Nichols, J.D.; Lindberg, M.S.; Hines, J.E.; Mednis, A.

2003-01-01

1. We used up to 35 years of capture-recapture data from nearly 3300 individual female ducks nesting on Engure Marsh, Latvia, and multistate modelling to test predictions about the influence of environmental, habitat and management factors on breeding dispersal probability within the marsh. 2. Analyses based on observed dispersal distances of common pochards and tufted ducks provided no evidence that breeding success in year t influenced dispersal distance between t and t + 1. 3. Breeding dispersal distances (year t to t + 1) of pochards and tufted ducks were associated with a delay in relative nest initiation dates in year t + 1. The delay was greater for pochards (c. 4 days) than for tufted ducks (c. 2 days) when females dispersed > 0.8 km. 4. Northern shovelers and tufted ducks moved from a large island to small islands at low water levels and from small islands to the large island at high water levels before the construction of elevated small islands (1960-82). Following this habitat management (1983-94). breeding fidelity was extremely high and not influenced by water level in the marsh for either species. 5. Because pochard nesting habitats in black-headed gull colonies were saturated during the entire study period, nesting females moved into and out of colonies with similar probabilities. Local survival probabilities and incubation body masses were higher for both yearlings (SY) and adults (ASY) nesting within gull colonies, suggesting that these females were of better quality than females nesting outside of the colonies. 6. Tufted ducks showed higher probabilities of moving from islands to emergent marshes when water levels were higher both before and after habitat management. However, rates of movement for a given water level were higher during the period before management than after. 7. Both pochards and tufted ducks exhibited asymmetric movement with respect to proximity to water, with higher movement probabilities to near-water nesting locations than away from these locations. 8. Multistate capture-recapture models provided analyses that were useful in investigating sources of variation in breeding dispersal probabilities.

The causes of dispersal and the cost of carry-over effects for an endangered bird in a dynamic wetland landscape.

PubMed

Robertson, Ellen P; Fletcher, Robert J; Austin, James D

2017-07-01

The decision to disperse or remain philopatric between breeding seasons has important implications for both ecology and evolution, including the potential for carry-over effects, where an individual's previous history affects its current performance. Carry-over effects are increasingly documented although underlying mechanisms remain unclear. Here we test for potential carry-over effects and their mechanisms by uniting hypotheses for the causes and consequences of habitat selection and dispersal across space and time. We linked hypotheses regarding different types of factors and information (environmental conditions, personal and public information) predicted to impact reproductive success and dispersal for an endangered, wetland-dependent bird, the snail kite (Rostrhamus sociabilis plumbeus). To do so, we coupled structural equation modelling with 20 years of mark-recapture and nesting data across the breeding range of this species to isolate potential direct and indirect effects of these factors. We found that water depth at nest sites explained subsequent emigration rates via an indirect path through the use of personal, not public, information. Importantly, we found that these dispersers tended to initiate nests later the following breeding season. This pattern explained a phenological mismatch of nesting with hydrological conditions, whereby immigrants tended to nest later, late nesters tended to experience lower water depths, higher nest failure occurred at lower water depths and higher nest failure explained subsequent breeding dispersal. These results identified a novel potential mechanism for carry-over effects: a phenological mismatch with environmental conditions (water depth) that occurred potentially due to time costs of dispersal. Our results also highlighted a substantial benefit of philopatry - earlier initiation of reproduction - which allows philopatric individuals to better coincide with environmental conditions that are beneficial for successful reproduction. These results have implications for our mechanistic understanding and prediction of carryover effects, and emphasize that local conservation strategies, such as water management, can explain future demography at distant sites connected through dispersal. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Supporting shared hypothesis testing in the biomedical domain.

PubMed

Agibetov, Asan; Jiménez-Ruiz, Ernesto; Ondrésik, Marta; Solimando, Alessandro; Banerjee, Imon; Guerrini, Giovanna; Catalano, Chiara E; Oliveira, Joaquim M; Patanè, Giuseppe; Reis, Rui L; Spagnuolo, Michela

2018-02-08

Pathogenesis of inflammatory diseases can be tracked by studying the causality relationships among the factors contributing to its development. We could, for instance, hypothesize on the connections of the pathogenesis outcomes to the observed conditions. And to prove such causal hypotheses we would need to have the full understanding of the causal relationships, and we would have to provide all the necessary evidences to support our claims. In practice, however, we might not possess all the background knowledge on the causality relationships, and we might be unable to collect all the evidence to prove our hypotheses. In this work we propose a methodology for the translation of biological knowledge on causality relationships of biological processes and their effects on conditions to a computational framework for hypothesis testing. The methodology consists of two main points: hypothesis graph construction from the formalization of the background knowledge on causality relationships, and confidence measurement in a causality hypothesis as a normalized weighted path computation in the hypothesis graph. In this framework, we can simulate collection of evidences and assess confidence in a causality hypothesis by measuring it proportionally to the amount of available knowledge and collected evidences. We evaluate our methodology on a hypothesis graph that represents both contributing factors which may cause cartilage degradation and the factors which might be caused by the cartilage degradation during osteoarthritis. Hypothesis graph construction has proven to be robust to the addition of potentially contradictory information on the simultaneously positive and negative effects. The obtained confidence measures for the specific causality hypotheses have been validated by our domain experts, and, correspond closely to their subjective assessments of confidences in investigated hypotheses. Overall, our methodology for a shared hypothesis testing framework exhibits important properties that researchers will find useful in literature review for their experimental studies, planning and prioritizing evidence collection acquisition procedures, and testing their hypotheses with different depths of knowledge on causal dependencies of biological processes and their effects on the observed conditions.

Graph-based impact analysis as a framework for incorporating practitioner knowledge in dairy herd health management.

PubMed

Krieger, M; Schwabenbauer, E-M; Hoischen-Taubner, S; Emanuelson, U; Sundrum, A

2018-03-01

Production diseases in dairy cows are multifactorial, which means they emerge from complex interactions between many different farm variables. Variables with a large impact on production diseases can be identified for groups of farms using statistical models, but these methods cannot be used to identify highly influential variables in individual farms. This, however, is necessary for herd health planning, because farm conditions and associated health problems vary largely between farms. The aim of this study was to rank variables according to their anticipated effect on production diseases on the farm level by applying a graph-based impact analysis on 192 European organic dairy farms. Direct impacts between 13 pre-defined variables were estimated for each farm during a round-table discussion attended by practitioners, that is farmer, veterinarian and herd advisor. Indirect impacts were elaborated through graph analysis taking into account impact strengths. Across farms, factors supposedly exerting the most influence on production diseases were 'feeding', 'hygiene' and 'treatment' (direct impacts), as well as 'knowledge and skills' and 'herd health monitoring' (indirect impacts). Factors strongly influenced by production diseases were 'milk performance', 'financial resources' and 'labour capacity' (directly and indirectly). Ranking of variables on the farm level revealed considerable differences between farms in terms of their most influential and most influenced farm factors. Consequently, very different strategies may be required to reduce production diseases in these farms. The method is based on perceptions and estimations and thus prone to errors. From our point of view, however, this weakness is clearly outweighed by the ability to assess and to analyse farm-specific relationships and thus to complement general knowledge with contextual knowledge. Therefore, we conclude that graph-based impact analysis represents a promising decision support tool for herd health planning. The next steps include testing the method using more specific and problem-oriented variables as well as evaluating its effectiveness.

The acute social defeat stress and nest-building test paradigm: A potential new method to screen drugs for depressive-like symptoms.

PubMed

Otabi, Hikari; Goto, Tatsuhiko; Okayama, Tsuyoshi; Kohari, Daisuke; Toyoda, Atsushi

2017-02-01

Psychosocial stress can cause mental conditions such as depression in humans. To develop drug therapies for the treatment of depression, it is necessary to use animal models of depression to screen drug candidates that exhibit anti-depressive effects. Unfortunately, the present methods of drug screening for antidepressants, the forced-swim test and tail-suspension test, are limiting factors in drug discovery because they are not based on the constructive validity of objective phenotypes in depression. Previously, we discovered that the onset of nest building is severely delayed in mice exposed to subchronic mild social defeat stress (sCSDS). Therefore, a novel paradigm combining acute social defeat stress (ASDS) and the nest-building test (SNB) were established for the efficient screening of drugs for depressive-like symptoms. Since ASDS severely delayed the nest-building process as shown in chronically social defeated mice, we sought to rescue the delayed nest-building behavior in ASDS mice. Injecting a specific serotonin 2a receptor antagonist (SR-46349B), the nest-building deficit exhibited by ASDS mice was partially rescued. On the other hand, a selective serotonin reuptake inhibitor (fluoxetine) did not rescue the nest-building deficit in ASDS mice. Therefore, we conclude that the SNB paradigm is an another potential behavioral method for screening drugs for depressive-like symptoms including attention deficit, anxiety, low locomotion, and decreased motivation. Copyright © 2016 Elsevier B.V. All rights reserved.

Managing native predators: Evidence from a partial removal of raccoons (Procyon lotor) on the Outer Banks of North Carolina, USA

USGS Publications Warehouse

Stocking, Jessica J.; Simons, Theodore R.; Parsons, Arielle W.; O'Connell, Allan F.

2017-01-01

Raccoons (Procyon lotor) are important predators of ground-nesting species in coastal systems. They have been identified as a primary cause of nest failure for the American Oystercatcher (Haematopus palliatus) throughout its range. Concerns over the long-term effects of raccoon predation and increased nest success following a hurricane inspired a mark-resight study of the raccoon population on a barrier island off North Carolina, USA. Approximately half of the raccoons were experimentally removed in 2008. Nests (n = 700) were monitored on two adjacent barrier islands during 2004–2013. Daily nest survival estimates were highest for 2004 (0.974 ± 0.005) and lowest for 2007 and 2008 (0.925 ± 0.009 and 0.925 ± 0.010, respectively). The only model in our candidate set that received any support included island and time of season, along with a diminishing effect of the hurricane and a constant, 5-year effect of the raccoon removal. For both hurricane and raccoon removal, however, the support for island-specific effects was weak (β = -0.204 ± 0.116 and 0.146 ± 0.349, respectively). We conclude that either the raccoon reduction was inadequate, or factors other than predation cause more variation in nest success than previously recognized. A multi-faceted approach to management aimed at reducing nest losses to storm overwash, predation, and human disturbance is likely to yield the largest population level benefits.

Mining concepts of health responsibility using text mining and exploratory graph analysis.

PubMed

Kjellström, Sofia; Golino, Hudson

2018-05-24

Occupational therapists need to know about people's beliefs about personal responsibility for health to help them pursue everyday activities. The study aims to employ state-of-the-art quantitative approaches to understand people's views of health and responsibility at different ages. A mixed method approach was adopted, using text mining to extract information from 233 interviews with participants aged 5 to 96 years, and then exploratory graph analysis to estimate the number of latent variables. The fit of the structure estimated via the exploratory graph analysis was verified using confirmatory factor analysis. Exploratory graph analysis estimated three dimensions of health responsibility: (1) creating good health habits and feeling good; (2) thinking about one's own health and wanting to improve it; and 3) adopting explicitly normative attitudes to take care of one's health. The comparison between the three dimensions among age groups showed, in general, that children and adolescents, as well as the old elderly (>73 years old) expressed ideas about personal responsibility for health less than young adults, adults and young elderly. Occupational therapists' knowledge of the concepts of health responsibility is of value when working with a patient's health, but an identified challenge is how to engage children and older persons.

A novel approach to analyzing lung cancer mortality disparities: Using the exposome and a graph-theoretical toolchain

PubMed Central

Juarez, Paul D; Hood, Darryl B; Rogers, Gary L; Baktash, Suzanne H; Saxton, Arnold M; Matthews-Juarez, Patricia; Im, Wansoo; Cifuentes, Myriam Patricia; Phillips, Charles A; Lichtveld, Maureen Y; Langston, Michael A

2017-01-01

Objectives The aim is to identify exposures associated with lung cancer mortality and mortality disparities by race and gender using an exposome database coupled to a graph theoretical toolchain. Methods Graph theoretical algorithms were employed to extract paracliques from correlation graphs using associations between 2162 environmental exposures and lung cancer mortality rates in 2067 counties, with clique doubling applied to compute an absolute threshold of significance. Factor analysis and multiple linear regressions then were used to analyze differences in exposures associated with lung cancer mortality and mortality disparities by race and gender. Results While cigarette consumption was highly correlated with rates of lung cancer mortality for both white men and women, previously unidentified novel exposures were more closely associated with lung cancer mortality and mortality disparities for blacks, particularly black women. Conclusions Exposures beyond smoking moderate lung cancer mortality and mortality disparities by race and gender. Policy Implications An exposome approach and database coupled with scalable combinatorial analytics provides a powerful new approach for analyzing relationships between multiple environmental exposures, pathways and health outcomes. An assessment of multiple exposures is needed to appropriately translate research findings into environmental public health practice and policy. PMID:29152601

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly.

PubMed

Bonizzoni, Paola; Vedova, Gianluca Della; Pirola, Yuri; Previtali, Marco; Rizzi, Raffaella

2016-03-01

The large amount of short read data that has to be assembled in future applications, such as in metagenomics or cancer genomics, strongly motivates the investigation of disk-based approaches to index next-generation sequencing (NGS) data. Positive results in this direction stimulate the investigation of efficient external memory algorithms for de novo assembly from NGS data. Our article is also motivated by the open problem of designing a space-efficient algorithm to compute a string graph using an indexing procedure based on the Burrows-Wheeler transform (BWT). We have developed a disk-based algorithm for computing string graphs in external memory: the light string graph (LSG). LSG relies on a new representation of the FM-index that is exploited to use an amount of main memory requirement that is independent from the size of the data set. Moreover, we have developed a pipeline for genome assembly from NGS data that integrates LSG with the assembly step of SGA (Simpson and Durbin, 2012 ), a state-of-the-art string graph-based assembler, and uses BEETL for indexing the input data. LSG is open source software and is available online. We have analyzed our implementation on a 875-million read whole-genome dataset, on which LSG has built the string graph using only 1GB of main memory (reducing the memory occupation by a factor of 50 with respect to SGA), while requiring slightly more than twice the time than SGA. The analysis of the entire pipeline shows an important decrease in memory usage, while managing to have only a moderate increase in the running time.

Silence is not golden: the hissing calls of tits affect the behaviour of a nest predator.

PubMed

Zub, Karol; Czeszczewik, Dorota; Ruczyński, Ireneusz; Kapusta, Anna; Walankiewicz, Wiesław

2017-01-01

Nest predation is one of the most important mortality factors of birds. Field observations showed that tits (Paridae) produce hissing calls and, usually, have lower breeding losses than nesting Ficedula flycatchers, which do not make such calls. We hypothesise that differences in fledgling success can be directly attributed to the vocal reaction of tits. We tested experimentally whether the hissing calls can affect the behaviour of a potential predator, analysing the response of the Yellow-necked Mouse Apodemus flavicollis to playback of calls of three Parid species. The number of visits by mice to two types of cavities (with playback and control) was not significantly different, but the average time spent by mice in cavities with playback (3.9 s) was significantly shorter than in cavities without playback (26.3 s). This suggests that hissing behaviour of tits significantly changes the exploration activity of predators, which may ultimately increase the breeding success of this group of birds relative to the flycatchers. Nest predation is one of the most important mortality factors of small land birds, but some anti-predatory mechanisms are still poorly recognised. Numerous studies demonstrate that incubating tits make hissing sounds, when a predator is near, but despite almost a century of research, there is little evidence these calls indeed affect behaviour of predators. By using a simple laboratory experiment, we demonstrated that the hissing acoustic signals used by tits may change the behaviour of yellow-necked mice, which are an important predator of cavity-nesting birds in temperate forests. Intruding mice withdrew from cavities where hissing sounds were played back. Our results suggest that the hissing behaviour of tits can change the exploration activity of potential predators and may increase breeding success of this group of birds relative to the flycatchers, which stay silent when their nest is threatened.

Couple Graph Based Label Propagation Method for Hyperspectral Remote Sensing Data Classification

NASA Astrophysics Data System (ADS)

Wang, X. P.; Hu, Y.; Chen, J.

2018-04-01

Graph based semi-supervised classification method are widely used for hyperspectral image classification. We present a couple graph based label propagation method, which contains both the adjacency graph and the similar graph. We propose to construct the similar graph by using the similar probability, which utilize the label similarity among examples probably. The adjacency graph was utilized by a common manifold learning method, which has effective improve the classification accuracy of hyperspectral data. The experiments indicate that the couple graph Laplacian which unite both the adjacency graph and the similar graph, produce superior classification results than other manifold Learning based graph Laplacian and Sparse representation based graph Laplacian in label propagation framework.

Multi-Centrality Graph Spectral Decompositions and Their Application to Cyber Intrusion Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Pin-Yu; Choudhury, Sutanay; Hero, Alfred

Many modern datasets can be represented as graphs and hence spectral decompositions such as graph principal component analysis (PCA) can be useful. Distinct from previous graph decomposition approaches based on subspace projection of a single topological feature, e.g., the centered graph adjacency matrix (graph Laplacian), we propose spectral decomposition approaches to graph PCA and graph dictionary learning that integrate multiple features, including graph walk statistics, centrality measures and graph distances to reference nodes. In this paper we propose a new PCA method for single graph analysis, called multi-centrality graph PCA (MC-GPCA), and a new dictionary learning method for ensembles ofmore » graphs, called multi-centrality graph dictionary learning (MC-GDL), both based on spectral decomposition of multi-centrality matrices. As an application to cyber intrusion detection, MC-GPCA can be an effective indicator of anomalous connectivity pattern and MC-GDL can provide discriminative basis for attack classification.« less

Graphs, matrices, and the GraphBLAS: Seven good reasons

DOE PAGES

Kepner, Jeremy; Bader, David; Buluç, Aydın; ...

2015-01-01

The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istcbigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implementmore » a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.« less

Predation of artificial ground nests on white-tailed prairie dog colonies

USGS Publications Warehouse

Baker, B.W.; Stanley, T.R.; Sedgwick, J.A.

1999-01-01

Prairie dog (Cynomys spp.) colonies are unique to prairie and shrub-steppe landscapes. However, widespread eradication, habitat loss, and sylvatic plague (Yersinia pestis) have reduced their numbers by 98% since historical times. Birds associated with prairie dogs also are declining. Potential nest predators, such as coyotes (Canis latrans), swift foxes (Vulpes velox), and badgers (Taxidea taxus), may be attracted to colonies where a high concentration of prairie dogs serve as available prey. Increased abundance of small mammals, including prairie dogs, also may increase the risk of predation for birds nesting on colonies. Finally, because grazing by prairie dogs may decrease vegetation height and canopy cover, bird nests may be easier for predators to locate. In this study, we placed 1,444 artificial ground nests on and off 74 white-tailed prairie dog (C. leucurus) colonies to test the hypothesis that nest predation rates are higher on colonies than at nearby off sites (i.e., uncolonized habitat). We sampled colonies from 27 May to 16 July 1997 at the following 3 complexes: Coyote Basin, Utah and Colorado; Moxa Arch, Wyoming; and Shirley Basin, Wyoming. Differences in daily predation rates between colonies and paired off sites averaged 1.0% (P = 0.060). When converted to a typical 14-day incubation period, predation rates averaged 14% higher on colonies (57.7 ?? 2.7%; ?? ?? SE) than at off sites (50.4 ?? 3.1%). Comparisons of habitat variables on colonies to off sites showed percent canopy cover of vegetation was similar (P = 0.114), percent bare ground was higher on colonies (P 0.288). Although we found the risk of nest predation was higher on white-tailed prairie dog colonies than at off sites, fitness of birds nesting on colonies might depend on other factors that influence foraging success, reproductive success, or nestling survival.

Breeding productivity and survival of the endangered Hawai'i Creeper in a wet forest refuge on Mauna Kea, Hawai'i

USGS Publications Warehouse

Collins, Mark

2001-01-01

We studied the demography of the endangered Hawai‘i Creeper (Oreomystis muna) from 1994-1999 at three sites in Hakalau Forest National Wildlife Refuge (NWR). Hawai‘i Creepers bred from January to June, with peak breeding in February through May (about 120-l 80 days), and molted from May to August. A small proportion (4.9%) of individuals overlapped breeding and molting activities. We located and monitored the fates of 60 nests. Mean clutch size was 2.1 eggs, nest building required 19 days, incubation was 16 to 17 days, and nestling period lasted 18 days. Of all nest attempts, 25% were abandoned before egg laying, 6.7% were removed for captive propagation, 13.3% had undetermined fates, 38.3% failed during incubation or nestling periods, and 16.7% were successful. Thus, of 33 nests that were active through egg laying and outcome was confirmed, only 30% were successful. The daily survival rate of active nests was 0.960 t 0.009 SE. An average of 1.7 chicks fledged from successful nests. Thirty-two percent of hatch-year birds were alive and in the study area at least one year later. Annual adult survival was high (0.88 t 0.03). The primary factors limiting productivity of Hawai‘i Creeper in Hakalau Forest NWR appear to be low reproductive potential in combination with high rates of nesting failure. Further research into the causes of nest failure, the length of the breeding season, and renesting behavior of females is needed, and protection of the forest from the degrading impacts of introduced mammals is paramount.

Association of empty nest with depressive symptom in a Chinese elderly population: A cross-sectional study.

PubMed

Zhai, Yujia; Yi, Huaiming; Shen, Wei; Xiao, Yuanyuan; Fan, Haixiao; He, Fan; Li, Fudong; Wang, Xinyi; Shang, Xiaopeng; Lin, Junfen

2015-11-15

Empty nest has been becoming the main family pattern among old people, and influencing the traditional family providing for the aged in China. This study aimed to investigate the association of empty nest with depressive symptom in a Chinese elderly population. Our study was based on the baseline investigation of Zhejiang Major Public Health Surveillance which was conducted in 2014. The final analyzed sample consisted of 9215 participants aged no less than 60 years. Subjects completed a questionnaire including demographic characteristics, living arrangements, behavioral risk factors, health status, subjective assessments, and Patient Health Questionnaire-9 scale. More than half of the participants were empty nest elders (57.4%). The overall prevalence of depressive symptom was 10.3%, while it was higher in empty nest group than in non-empty nest group (11.6% vs. 8.6%, P<0.001). A positive association was found between empty nest and depressive symptom, the OR (95%CI) was 1.223(1.045, 1.431). After stratified by gender/age/education level/employment status, this association was just prominent in participants of male, 70 years old and above, primary school education, and retirees. No matter living with spouse or living alone, empty nesters were more likely to have depressive symptoms than non-empty nesters. Cross-sectional study could not make a causation conclusion. The social supports of participants were not been investigated in detail. Empty nest elders, especially those who are male, 70 years old and above, primary school education, and retired, are more vulnerable to depressive symptom. Copyright © 2015 Elsevier B.V. All rights reserved.

Crucial nesting habitat for gunnison sage-grouse: A spatially explicit hierarchical approach

USGS Publications Warehouse

Aldridge, Cameron L.; Saher, D.J.; Childers, T.M.; Stahlnecker, K.E.; Bowen, Z.H.

2012-01-01

Gunnison sage-grouse (Centrocercus minimus) is a species of special concern and is currently considered a candidate species under Endangered Species Act. Careful management is therefore required to ensure that suitable habitat is maintained, particularly because much of the species' current distribution is faced with exurban development pressures. We assessed hierarchical nest site selection patterns of Gunnison sage-grouse inhabiting the western portion of the Gunnison Basin, Colorado, USA, at multiple spatial scales, using logistic regression-based resource selection functions. Models were selected using Akaike Information Criterion corrected for small sample sizes (AIC c) and predictive surfaces were generated using model averaged relative probabilities. Landscape-scale factors that had the most influence on nest site selection included the proportion of sagebrush cover >5%, mean productivity, and density of 2 wheel-drive roads. The landscape-scale predictive surface captured 97% of known Gunnison sage-grouse nests within the top 5 of 10 prediction bins, implicating 57% of the basin as crucial nesting habitat. Crucial habitat identified by the landscape model was used to define the extent for patch-scale modeling efforts. Patch-scale variables that had the greatest influence on nest site selection were the proportion of big sagebrush cover >10%, distance to residential development, distance to high volume paved roads, and mean productivity. This model accurately predicted independent nest locations. The unique hierarchical structure of our models more accurately captures the nested nature of habitat selection, and allowed for increased discrimination within larger landscapes of suitable habitat. We extrapolated the landscape-scale model to the entire Gunnison Basin because of conservation concerns for this species. We believe this predictive surface is a valuable tool which can be incorporated into land use and conservation planning as well the assessment of future land-use scenarios. ?? 2011 The Wildlife Society.

Multi-scale habitat selection in highly territorial bird species: Exploring the contribution of nest, territory and landscape levels to site choice in breeding rallids (Aves: Rallidae)

NASA Astrophysics Data System (ADS)

Jedlikowski, Jan; Chibowski, Piotr; Karasek, Tomasz; Brambilla, Mattia

2016-05-01

Habitat selection often involves choices made at different spatial scales, but the underlying mechanisms are still poorly understood, and studies that investigate the relative importance of individual scales are rare. We investigated the effect of three spatial scales (landscape, territory, nest-site) on the occurrence pattern of little crake Zapornia parva and water rail Rallus aquaticus at 74 ponds in the Masurian Lakeland, Poland. Habitat structure, food abundance and water chemical parameters were measured at nests and random points within landscape plots (from 300-m to 50-m radius), territory (14-m) and nest-site plots (3-m). Regression analyses suggested that the most relevant scale was territory level, followed by landscape, and finally by nest-site for both species. Variation partitioning confirmed this pattern for water rail, but also highlighted the importance of nest-site (the level explaining the highest share of unique variation) for little crake. The most important variables determining the occurrence of both species were water body fragmentation (landscape), vegetation density (territory) and water depth (at territory level for little crake, and at nest-site level for water rail). Finally, for both species multi-scale models including factors from different levels were more parsimonious than single-scale ones, i.e. habitat selection was likely a multi-scale process. The importance of particular spatial scales seemed more related to life-history traits than to the extent of the scales considered. In the case of our study species, the territory level was highly important likely because both rallids have to obtain all the resources they need (nest site, food and mates) in relatively small areas, the multi-purpose territories they defend.

Adjusting protein graphs based on graph entropy.

PubMed

Peng, Sheng-Lung; Tsay, Yu-Wei

2014-01-01

Measuring protein structural similarity attempts to establish a relationship of equivalence between polymer structures based on their conformations. In several recent studies, researchers have explored protein-graph remodeling, instead of looking a minimum superimposition for pairwise proteins. When graphs are used to represent structured objects, the problem of measuring object similarity become one of computing the similarity between graphs. Graph theory provides an alternative perspective as well as efficiency. Once a protein graph has been created, its structural stability must be verified. Therefore, a criterion is needed to determine if a protein graph can be used for structural comparison. In this paper, we propose a measurement for protein graph remodeling based on graph entropy. We extend the concept of graph entropy to determine whether a graph is suitable for representing a protein. The experimental results suggest that when applied, graph entropy helps a conformational on protein graph modeling. Furthermore, it indirectly contributes to protein structural comparison if a protein graph is solid.

Adjusting protein graphs based on graph entropy

PubMed Central

2014-01-01

Measuring protein structural similarity attempts to establish a relationship of equivalence between polymer structures based on their conformations. In several recent studies, researchers have explored protein-graph remodeling, instead of looking a minimum superimposition for pairwise proteins. When graphs are used to represent structured objects, the problem of measuring object similarity become one of computing the similarity between graphs. Graph theory provides an alternative perspective as well as efficiency. Once a protein graph has been created, its structural stability must be verified. Therefore, a criterion is needed to determine if a protein graph can be used for structural comparison. In this paper, we propose a measurement for protein graph remodeling based on graph entropy. We extend the concept of graph entropy to determine whether a graph is suitable for representing a protein. The experimental results suggest that when applied, graph entropy helps a conformational on protein graph modeling. Furthermore, it indirectly contributes to protein structural comparison if a protein graph is solid. PMID:25474347

[Approach to the Development of Mind and Persona].

PubMed

Sawaguchi, Toshiko

2018-01-01

To access medical specialists by health specialists working in the regional health field, the possibility of utilizing the voice approach for dissociative identity disorder (DID) patients as a health assessment for medical access (HAMA) was investigated. The first step is to investigate whether the plural personae in a single DID patient can be discriminated by voice analysis. Voices of DID patients including these with different personae were extracted from YouTube and were analysed using the software PRAAT with basic frequency, oral factors, chin factors and tongue factors. In addition, RAKUGO story teller voices made artificially and dramatically were analysed in the same manner. Quantitive and qualitative analysis method were carried out and nested logistic regression and a nested generalized linear model was developed. The voice from different personae in one DID patient could be visually and easily distinquished using basic frequency curve, cluster analysis and factor analysis. In the canonical analysis, only Roy's maximum root was <0.01. In the nested generalized linear model, the model using a standard deviation (SD) indicator fit best and some other possibilities are shown here. In DID patients, the short transition time among plural personae could guide to the risky situation such as suicide. So if the voice approach can show the time threshold of changes between the different personae, it would be useful as an Access Assessment in the form of a simple HAMA.

Impact analysis of government investment on water projects in the arid Gansu Province of China

NASA Astrophysics Data System (ADS)

Wang, Zhan; Deng, Xiangzheng; Li, Xiubin; Zhou, Qing; Yan, Haiming

In this paper, we introduced three-nested Constant Elasticity of Substitution (CES) production function into a static Computable General Equilibrium (CGE) Model. Through four levels of factor productivity, we constructed three nested production function of land use productivity in the conceptual modeling frameworks. The first level of factor productivity is generated by the basic value-added land. On the second level, factor productivity in each sector is generated by human activities that presents human intervention to the first level of factor productivity. On the third level of factor productivity, water allocation reshapes the non-linear structure of transaction among first and second levels. From the perspective of resource utilization, we examined the economic efficiency of water allocation. The scenario-based empirical analysis results show that the three-nested CES production function within CGE model is well-behaved to present the economy system of the case study area. Firstly, water scarcity harmed economic production. Government investment on water projects in Gansu thereby had impacts on economic outcomes. Secondly, huge governmental financing on water projects bring depreciation of present value of social welfare. Moreover, water use for environment adaptation pressures on water supply. The theoretical water price can be sharply increased due to the increasing costs of factor inputs. Thirdly, water use efficiency can be improved by water projects, typically can be benefited from the expansion of water-saving irrigation areas even in those expanding dry area in Gansu. Therefore, increasing governmental financing on water projects can depreciate present value of social welfare but benefit economic efficiency for future generation.

Discrete bacteria foraging optimization algorithm for graph based problems - a transition from continuous to discrete

NASA Astrophysics Data System (ADS)

Sur, Chiranjib; Shukla, Anupam

2018-03-01

Bacteria Foraging Optimisation Algorithm is a collective behaviour-based meta-heuristics searching depending on the social influence of the bacteria co-agents in the search space of the problem. The algorithm faces tremendous hindrance in terms of its application for discrete problems and graph-based problems due to biased mathematical modelling and dynamic structure of the algorithm. This had been the key factor to revive and introduce the discrete form called Discrete Bacteria Foraging Optimisation (DBFO) Algorithm for discrete problems which exceeds the number of continuous domain problems represented by mathematical and numerical equations in real life. In this work, we have mainly simulated a graph-based road multi-objective optimisation problem and have discussed the prospect of its utilisation in other similar optimisation problems and graph-based problems. The various solution representations that can be handled by this DBFO has also been discussed. The implications and dynamics of the various parameters used in the DBFO are illustrated from the point view of the problems and has been a combination of both exploration and exploitation. The result of DBFO has been compared with Ant Colony Optimisation and Intelligent Water Drops Algorithms. Important features of DBFO are that the bacteria agents do not depend on the local heuristic information but estimates new exploration schemes depending upon the previous experience and covered path analysis. This makes the algorithm better in combination generation for graph-based problems and combination generation for NP hard problems.

The effect of ambient temperature, habitat quality and individual age on incubation behaviour and incubation feeding in a socially monogamous songbird.

PubMed

Amininasab, Seyed Mehdi; Kingma, Sjouke A; Birker, Martje; Hildenbrandt, Hanno; Komdeur, Jan

Incubation is an important aspect of avian life history. The behaviour is energetically costly, and investment in incubation strategies within species, like female nest attentiveness and the feeding by the non-incubating partner during incubation, can therefore vary depending on environmental and individual characteristics. However, little is known about the combined effect of these characteristics. We investigated the importance of ambient temperature, habitat quality, and bird age on female incubation behaviour and male feeding of the incubating female (incubation feeding) in blue tits Cyanistes caeruleus , a socially monogamous songbird. An increase in ambient temperature resulted in a higher nest temperature, and this enabled females to increase the time off the nest for self-maintenance activities. Probably as a consequence of this, an increase in ambient temperature was associated with fewer incubation feedings by the male. Moreover, in areas with more food available (more deciduous trees), females had shorter incubation recesses and males fed females less often. Additionally, males fed young females more, presumably to increase such females' investment in their eggs, which were colder on average (despite the length of recesses and female nest attentiveness being independent of female age). Male age did not affect incubation feeding rate. In conclusion, the patterns of incubation behaviour were related to both environmental and individual characteristics, and male incubation feeding was adjusted to females' need for food according these characteristics, which can facilitate new insights to the study of avian incubation energetics. Parents often invest a substantial amount of energy in raising offspring. How much they do so depends on several environmental factors and on the extent they cooperate to raise the offspring. In birds, males can feed incubating females, which may allow females to stay longer on the nest, which, in turn, may ultimately improve reproductive success. The interplay between environmental factors and such incubation feeding on incubation attendance has, however, received little attention. Here, we show that favourable circumstances (higher ambient temperature and food availability) allowed incubating blue tit females to increase the time off the nest to improve self-maintenance and males to feed them less, whereas males also fed inexperienced partners more often. Thus, we show a concerted effect of several environmental and intrinsic factors on parental effort during incubation, which will help to improve the general understanding of avian incubation and parental care.

Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality

USGS Publications Warehouse

Bruggeman, Jason E.; Swem, Ted; Andersen, David E.; Kennedy, Patricia L.; Nigro, Debora A.

2015-01-01

Intrinsic and extrinsic factors affect vital rates and population-level processes, and understanding these factors is paramount to devising successful management plans for wildlife species. For example, birds time migration in response, in part, to local and broadscale climate fluctuations to initiate breeding upon arrival to nesting territories, and prolonged inclement weather early in the breeding season can inhibit egg-laying and reduce productivity. Also, density-dependent regulation occurs in raptor populations, as territory size is related to resource availability. Arctic Peregrine Falcons (Falco peregrinus tundrius; hereafter Arctic peregrine) have a limited and northern breeding distribution, including the Colville River Special Area (CRSA) in the National Petroleum Reserve–Alaska, USA. We quantified influences of climate, topography, nest productivity, prey habitat, density dependence, and interspecific competition affecting Arctic peregrines in the CRSA by applying the Dail-Madsen model to estimate abundance and vital rates of adults on nesting cliffs from 1981 through 2002. Arctic peregrine abundance increased throughout the 1980s, which spanned the population's recovery from DDT-induced reproductive failure, until exhibiting a stationary trend in the 1990s. Apparent survival rate (i.e., emigration; death) was negatively correlated with the number of adult Arctic peregrines on the cliff the previous year, suggesting effects of density-dependent population regulation. Apparent survival and arrival rates (i.e., immigration; recruitment) were higher during years with earlier snowmelt and milder winters, and apparent survival was positively correlated with nesting season maximum daily temperature. Arrival rate was positively correlated with average Arctic peregrine productivity along a cliff segment from the previous year and initial abundance was positively correlated with cliff height. Higher cliffs with documented higher productivity (presumably indicative of higher-quality habitat), are a priority for continued protection from potential nearby development and disturbance to minimize population-level impacts. Climate change may affect Arctic peregrines in multiple ways, including through access to more snow-free nest sites and a lengthened breeding season that may increase likelihood of nest success. Our work provides insight into factors affecting a population during and after recovery, and demonstrates how the Dail-Madsen model can be used for any unmarked population with multiple years of abundance data collected through repeated surveys.

Identifying Key Drivers of Return Reversal with Dynamical Bayesian Factor Graph.

PubMed

Zhao, Shuai; Tong, Yunhai; Wang, Zitian; Tan, Shaohua

2016-01-01

In the stock market, return reversal occurs when investors sell overbought stocks and buy oversold stocks, reversing the stocks' price trends. In this paper, we develop a new method to identify key drivers of return reversal by incorporating a comprehensive set of factors derived from different economic theories into one unified dynamical Bayesian factor graph. We then use the model to depict factor relationships and their dynamics, from which we make some interesting discoveries about the mechanism behind return reversals. Through extensive experiments on the US stock market, we conclude that among the various factors, the liquidity factors consistently emerge as key drivers of return reversal, which is in support of the theory of liquidity effect. Specifically, we find that stocks with high turnover rates or high Amihud illiquidity measures have a greater probability of experiencing return reversals. Apart from the consistent drivers, we find other drivers of return reversal that generally change from year to year, and they serve as important characteristics for evaluating the trends of stock returns. Besides, we also identify some seldom discussed yet enlightening inter-factor relationships, one of which shows that stocks in Finance and Insurance industry are more likely to have high Amihud illiquidity measures in comparison with those in other industries. These conclusions are robust for return reversals under different thresholds.

Manipulating Google’s Knowledge Graph Box to Counter Biased Information Processing During an Online Search on Vaccination: Application of a Technological Debiasing Strategy

PubMed Central

Allam, Ahmed; Schulz, Peter J

2016-01-01

Background One of people’s major motives for going online is the search for health-related information. Most consumers start their search with a general search engine but are unaware of the fact that its sorting and ranking criteria do not mirror information quality. This misconception can lead to distorted search outcomes, especially when the information processing is characterized by heuristic principles and resulting cognitive biases instead of a systematic elaboration. As vaccination opponents are vocal on the Web, the chance of encountering their non‒evidence-based views on immunization is high. Therefore, biased information processing in this context can cause subsequent impaired judgment and decision making. A technological debiasing strategy could counter this by changing people’s search environment. Objective This study aims at testing a technological debiasing strategy to reduce the negative effects of biased information processing when using a general search engine on people’s vaccination-related knowledge and attitudes. This strategy is to manipulate the content of Google’s knowledge graph box, which is integrated in the search interface and provides basic information about the search topic. Methods A full 3x2 factorial, posttest-only design was employed with availability of basic factual information (comprehensible vs hardly comprehensible vs not present) as the first factor and a warning message as the second factor of experimental manipulation. Outcome variables were the evaluation of the knowledge graph box, vaccination-related knowledge, as well as beliefs and attitudes toward vaccination, as represented by three latent variables emerged from an exploratory factor analysis. Results Two-way analysis of variance revealed a significant main effect of availability of basic information in the knowledge graph box on participants’ vaccination knowledge scores (F2,273=4.86, P=.01), skepticism/fear of vaccination side effects (F2,273=3.5, P=.03), and perceived information quality (F2,273=3.73, P=.02). More specifically, respondents receiving comprehensible information appeared to be more knowledgeable, less skeptical of vaccination, and more critical of information quality compared to participants exposed to hardly comprehensible information. Although, there was no significant interaction effect between the availability of information and the presence of the warning, there was a dominant pattern in which the presence of the warning appeared to have a positive influence on the group receiving comprehensible information while the opposite was true for the groups exposed to hardly comprehensible information and no information at all. Participants evaluated the knowledge graph box as moderately to highly useful, with no significant differences among the experimental groups. Conclusion Overall, the results suggest that comprehensible information in the knowledge graph box positively affects participants’ vaccination-related knowledge and attitudes. A small change in the content retrieval procedure currently used by Google could already make a valuable difference in the pursuit of an unbiased online information search. Further research is needed to gain insights into the knowledge graph box’s entire potential. PMID:27255736

Characterizing Containment and Related Classes of Graphs,

DTIC Science & Technology

1985-01-01

Math . to appear. [G2] Golumbic,. Martin C., D. Rotem and J. Urrutia. "Comparability graphs and intersection graphs" Discrete Math . 43 (1983) 37-40. [G3...intersection classes of graphs" Discrete Math . to appear. [S2] Scheinerman, Edward R. Intersection Classes and Multiple Intersection Parameters of Graphs...graphs and of interval graphs" Canad. Jour. of blath. 16 (1964) 539-548. [G1] Golumbic, Martin C. "Containment graphs: and. intersection graphs" Discrete

Seabirds fighting for land: phenotypic consequences of breeding area constraints at a small remote archipelago.

PubMed

Nunes, Guilherme Tavares; Bertrand, Sophie; Bugoni, Leandro

2018-01-12

Identifying associations between phenotypes and environmental parameters is crucial for understanding how natural selection acts at the individual level. In this context, genetically isolated populations can be useful models for identifying the forces selecting fitness-related traits. Here, we use a comprehensive dataset on a genetically and ecologically isolated population of the strictly marine bird, the brown booby Sula leucogaster, at the tropical and remote Saint Peter and Saint Paul Archipelago, mid-Atlantic Ocean, in order to detect phenotypic adjustments from interindividual differences in diet, foraging behaviour, and nest quality. For this, we took biometrics of all individuals of the colony breeding in 2014 and 2015 and tested their associations with nest quality, diet parameters, and foraging behaviour. While body size was not related to the foraging parameters, the body size of the females (responsible for nest acquisition and defence) was significantly associated with the nest quality, as larger females occupied high-quality nests. Our findings suggest that the small breeding area, rather than prey availability, is a limiting factor, emphasizing the role of on-land features in shaping phenotypic characteristics and fitness in land-dependent marine vertebrates.

Red-shouldered hawk broadcast surveys: Factors affecting detection of responses and population trends

USGS Publications Warehouse

McLeod, M.A.; Andersen, D.E.

1998-01-01

Forest-nesting raptors are often difficult to detect and monitor because they can be secretive, and their nests can be difficult to locate. Some species, however, respond to broadcasts of taped calls, and these responses may be useful both in monitoring population trends and in locating nests. We conducted broadcast surveys on roads and at active red-shouldered hawk (Buteo lineatus) nests in northcentral Minnesota to determine effects of type of call (conspecific or great horned owl [Bubo virginianus]), time of day, and phase of the breeding cycle on red-shouldered hawk response behavior and to evaluate usefulness of broadcasts as a population monitoring tool using area occupied-probability-of-detection techniques. During the breeding seasons of 1994 and 1995, we surveyed 4 10-station road transects 59 times and conducted 76 surveys at 24 active nests. Results of these surveys indicated conspecific calls broadcast prior to hatch and early in the day were the most effective method of detecting red-shouldered hawks. Probability of detection via conspecific calls averaged 0.25, and area occupied was 100%. Computer simulations using these field data indicated broadcast surveys have the potential to be used as a population monitoring tool.

Disentangling the diversity of arboreal ant communities in tropical forest trees.

PubMed

Klimes, Petr; Fibich, Pavel; Idigel, Cliffson; Rimandai, Maling

2015-01-01

Tropical canopies are known for their high abundance and diversity of ants. However, the factors which enable coexistence of so many species in trees, and in particular, the role of foragers in determining local diversity, are not well understood. We censused nesting and foraging arboreal ant communities in two 0.32 ha plots of primary and secondary lowland rainforest in New Guinea and explored their species diversity and composition. Null models were used to test if the records of species foraging (but not nesting) in a tree were dependent on the spatial distribution of nests in surrounding trees. In total, 102 ant species from 389 trees occurred in the primary plot compared with only 50 species from 295 trees in the secondary forest plot. However, there was only a small difference in mean ant richness per tree between primary and secondary forest (3.8 and 3.3 sp. respectively) and considerably lower richness per tree was found only when nests were considered (1.5 sp. in both forests). About half of foraging individuals collected in a tree belonged to species which were not nesting in that tree. Null models showed that the ants foraging but not nesting in a tree are more likely to nest in nearby trees than would be expected at random. The effects of both forest stage and tree size traits were similar regardless of whether only foragers, only nests, or both datasets combined were considered. However, relative abundance distributions of species differed between foraging and nesting communities. The primary forest plot was dominated by native ant species, whereas invasive species were common in secondary forest. This study demonstrates the high contribution of foragers to arboreal ant diversity, indicating an important role of connectivity between trees, and also highlights the importance of primary vegetation for the conservation of native ant communities.

Disentangling the Diversity of Arboreal Ant Communities in Tropical Forest Trees

PubMed Central

Klimes, Petr; Fibich, Pavel; Idigel, Cliffson; Rimandai, Maling

2015-01-01

Tropical canopies are known for their high abundance and diversity of ants. However, the factors which enable coexistence of so many species in trees, and in particular, the role of foragers in determining local diversity, are not well understood. We censused nesting and foraging arboreal ant communities in two 0.32 ha plots of primary and secondary lowland rainforest in New Guinea and explored their species diversity and composition. Null models were used to test if the records of species foraging (but not nesting) in a tree were dependent on the spatial distribution of nests in surrounding trees. In total, 102 ant species from 389 trees occurred in the primary plot compared with only 50 species from 295 trees in the secondary forest plot. However, there was only a small difference in mean ant richness per tree between primary and secondary forest (3.8 and 3.3 sp. respectively) and considerably lower richness per tree was found only when nests were considered (1.5 sp. in both forests). About half of foraging individuals collected in a tree belonged to species which were not nesting in that tree. Null models showed that the ants foraging but not nesting in a tree are more likely to nest in nearby trees than would be expected at random. The effects of both forest stage and tree size traits were similar regardless of whether only foragers, only nests, or both datasets combined were considered. However, relative abundance distributions of species differed between foraging and nesting communities. The primary forest plot was dominated by native ant species, whereas invasive species were common in secondary forest. This study demonstrates the high contribution of foragers to arboreal ant diversity, indicating an important role of connectivity between trees, and also highlights the importance of primary vegetation for the conservation of native ant communities. PMID:25714831

Keeping it regular: Development of thermoregulation in four tropical seabird species.

PubMed

Hart, Lorinda A; Downs, Colleen T; Brown, Mark

2017-02-01

The thermoregulatory capacity of a species can determine which climatic niche it occupies. Its development in avian chicks is influenced by numerous factors. Furthermore, it is suggested that altricial chicks develop their thermoregulatory capacity post-hatching, while precocial chicks develop aspects of this in the egg. We investigated the development of thermoregulation of four co-occurring seabird species in the Seychelles; namely white, ground-nesting white-tailed tropicbirds (Phaethon lepturus) and tree-nesting fairy terns (Gygis alba); and dark plumaged, tree-nesting lesser noddies (Anous tenuirostris) and ground- and tree-nesting brown noddies (A. stolidus). White-tailed tropicbirds have semi-altricial chicks, while the remaining species have semi-precocial chicks. Cloacal temperatures (T b ) were measured at five day intervals from newly hatched chicks and compared over time, and with adult T b s. Initial T b s of all chicks, except fairy terns, were lower than those taken when chicks were older. Brooding cessation generally coincided with feather development, as did an increase in T b. Mean chick T b was significantly lower than mean adult T b for all species, but only white-tailed tropicbird and brown noddy chicks in tree nests differed significantly from mean adult T b when chick T b at five day intervals were considered. There was a significant interactive effect of nest site and age on brown noddy chick T b, but chick colour did not have a significant effect on T b . However, brown noddy chicks on dune crests maintained a constant T b sooner than chicks in tree nests. Our results demonstrate that tropical seabird species have a more delayed onset of thermoregulatory capabilities when compared with those in temperate environments, perhaps as nest sites are less thermally challenging. Nest microhabitats and behavioural thermoregulation, are likely more important during early chick development for these species. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Collection of Features for Semantic Graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eliassi-Rad, T; Fodor, I K; Gallagher, B

2007-05-02

Semantic graphs are commonly used to represent data from one or more data sources. Such graphs extend traditional graphs by imposing types on both nodes and links. This type information defines permissible links among specified nodes and can be represented as a graph commonly referred to as an ontology or schema graph. Figure 1 depicts an ontology graph for data from National Association of Securities Dealers. Each node type and link type may also have a list of attributes. To capture the increased complexity of semantic graphs, concepts derived for standard graphs have to be extended. This document explains brieflymore » features commonly used to characterize graphs, and their extensions to semantic graphs. This document is divided into two sections. Section 2 contains the feature descriptions for static graphs. Section 3 extends the features for semantic graphs that vary over time.« less

Graphing the order of the sexes: constructing, recalling, interpreting, and putting the self in gender difference graphs.

PubMed

Hegarty, Peter; Lemieux, Anthony F; McQueen, Grant

2010-03-01

Graphs seem to connote facts more than words or tables do. Consequently, they seem unlikely places to spot implicit sexism at work. Yet, in 6 studies (N = 741), women and men constructed (Study 1) and recalled (Study 2) gender difference graphs with men's data first, and graphed powerful groups (Study 3) and individuals (Study 4) ahead of weaker ones. Participants who interpreted graph order as evidence of author "bias" inferred that the author graphed his or her own gender group first (Study 5). Women's, but not men's, preferences to graph men first were mitigated when participants graphed a difference between themselves and an opposite-sex friend prior to graphing gender differences (Study 6). Graph production and comprehension are affected by beliefs and suppositions about the groups represented in graphs to a greater degree than cognitive models of graph comprehension or realist models of scientific thinking have yet acknowledged.

Risky business: Site selection by Acadian Flycatchers under threat of nest predation and brood parasitism

USGS Publications Warehouse

HazIer, K.R.; Cooper, R.J.; Twedt, D.J.

2006-01-01

Habitat quality is determined not only by habitat structure and the availability of resources, but also by competitors, cooperators, predators, and parasites. We hypothesized that, for passerines, minimizing risk from avian nest predators and brood parasites is an important factor in selecting a breeding site. Through the early part of two breeding seasons, we spot-mapped locations of Acadian Flycatchers (Empidonax virescens, territory selectors), Red-bellied Woodpeckers (Melanerpes carolinus, nest predators) and Brown-headed Cowbirds (Molothrus ater, brood parasites) in a 56-ha study area within an extensive bottomland hardwood forest. We were thereby able to determine the order of flycatcher territory settlement and nest initiation in relation to risk of predation and parasitism, while accounting for habitat structure. Male settlement was influenced by both habitat structure and risk avoidance. However, risk trom woodpeckers was relatively more important in the first season and risk from cowbirds in the second, evidently due to differences in the relative abundance of predator and brood-parasite in each year. For male flycatchers, settlement choices appear to be flexible in the face of changing 'risk landscapes.' For females, habitat structure was the most important predictor of nest site selection. Even so, there was evidence that females avoided cowbirds. Surprisingly, nest site selection was positively associated with woodpecker abundance in the first season when woodpeckers were present in greater numbers. Possible explanations for this contradictory result are discussed.

Mercury and selenium concentrations in leatherback sea turtles (Dermochelys coriacea): population comparisons, implications for reproductive success, hazard quotients and directions for future research.

PubMed

Perrault, Justin R; Miller, Debra L; Garner, Jeanne; Wyneken, Jeanette

2013-10-01

Leatherback sea turtles (Dermochelys coriacea) are long-distance migrants that travel thousands of km from foraging grounds to breeding and nesting grounds. These extensive journeys are fueled by ingestion of an estimated 300-400 kg of prey/d and likely result in exposure to high concentrations of environmental toxicants (e.g., mercury compounds). Increased bodily concentrations of mercury and its compounds in nesting female turtles may have detrimental effects on reproductive success. Leatherbacks have relatively low reproductive success compared with other sea turtles (global average hatching success ~50-60%). To assess toxicants and necessary nutrients as factors affecting leatherback turtle reproductive success at Sandy Point National Wildlife Refuge (SPNWR), St. Croix, U.S. Virgin Islands, we collected blood from nesting female leatherbacks and tissues from their hatchlings (blood from live turtles, liver and yolk sac from dead turtles). We compared the concentrations in those tissues to hatching and emergence success. We found that on SPNWR, hatching and emergence success were more closely related to seasonal factors than to total mercury and selenium concentrations in both nesting females and hatchlings. Selenium concentrations of nesting females were positively correlated with those of their hatchlings. Mercury and selenium in the liver of hatchlings were positively correlated with one another. Turtles with greater remigration intervals tended to have higher blood selenium concentrations, suggesting that selenium accumulates in leatherbacks through time. Through hazard quotients, we found evidence that selenium may be at or above concentrations that may cause physiologic harm to hatchlings. We also found evidence that population level differences exist for these trace elements. The concentrations of mercury and selenium established in this manuscript form a baseline for future toxicant studies. Copyright © 2013 Elsevier B.V. All rights reserved.

Semi-automatic breast ultrasound image segmentation based on mean shift and graph cuts.

PubMed

Zhou, Zhuhuang; Wu, Weiwei; Wu, Shuicai; Tsui, Po-Hsiang; Lin, Chung-Chih; Zhang, Ling; Wang, Tianfu

2014-10-01

Computerized tumor segmentation on breast ultrasound (BUS) images remains a challenging task. In this paper, we proposed a new method for semi-automatic tumor segmentation on BUS images using Gaussian filtering, histogram equalization, mean shift, and graph cuts. The only interaction required was to select two diagonal points to determine a region of interest (ROI) on an input image. The ROI image was shrunken by a factor of 2 using bicubic interpolation to reduce computation time. The shrunken image was smoothed by a Gaussian filter and then contrast-enhanced by histogram equalization. Next, the enhanced image was filtered by pyramid mean shift to improve homogeneity. The object and background seeds for graph cuts were automatically generated on the filtered image. Using these seeds, the filtered image was then segmented by graph cuts into a binary image containing the object and background. Finally, the binary image was expanded by a factor of 2 using bicubic interpolation, and the expanded image was processed by morphological opening and closing to refine the tumor contour. The method was implemented with OpenCV 2.4.3 and Visual Studio 2010 and tested for 38 BUS images with benign tumors and 31 BUS images with malignant tumors from different ultrasound scanners. Experimental results showed that our method had a true positive rate (TP) of 91.7%, a false positive (FP) rate of 11.9%, and a similarity (SI) rate of 85.6%. The mean run time on Intel Core 2.66 GHz CPU and 4 GB RAM was 0.49 ± 0.36 s. The experimental results indicate that the proposed method may be useful in BUS image segmentation. © The Author(s) 2014.

A conceptual model for quantifying connectivity using graph theory and cellular (per-pixel) approach

NASA Astrophysics Data System (ADS)

Singh, Manudeo; Sinha, Rajiv; Tandon, Sampat K.

2016-04-01

The concept of connectivity is being increasingly used for understanding hydro-geomorphic processes at all spatio-temporal scales. Connectivity is defined as the potential for energy and material flux (water, sediments, nutrients, heat, etc.) to navigate within or between the landscape systems and has two components, structural connectivity and dynamic connectivity. Structural connectivity is defined by the spatially connected features (physical linkages) through which energy and materials flow. Dynamic connectivity is a process defined connectivity component. These two connectivity components also interact with each other by forming a feedback system. This study attempts to explore a method to quantify structural and dynamic connectivity. In fluvial transport systems, sediment and water can flow in either a diffused manner or in a channelized way. At all the scales, hydrological and sediment fluxes can be tracked using a cellular (per-pixel) approach and can be quantified using graphical approach. The material flux, slope and LULC (Land Use Land Cover) weightage factors of a pixel together determine if it will contribute towards connectivity of the landscape/system. In a graphical approach, all the contributing pixels will form a node at their centroid and this node will be connected to the next 'down-node' via a directed edge with 'least cost path'. The length of the edge will depend on the desired spatial scale and its path direction will depend on the traversed pixel's slope and the LULC (weightage) factors. The weightage factors will lie in-between 0 to 1. This value approaches 1 for the LULC factors which promote connectivity. For example, in terms of sediment connectivity, the weightage could be RUSLE (Revised Universal Soil Loss Equation) C-factors with bare unconsolidated surfaces having values close to 1. This method is best suited for areas with low slopes, where LULC can be a deciding as well as dominating factor. The degree of connectivity and its pathways will show changes under different LULC conditions even if the slope remains the same. The graphical approach provides the statistics of connected and disconnected graph elements (edges, nodes) and graph components, thereby allowing the quantification of structural connectivity. This approach also quantifies the dynamic connectivity by allowing the measurement of the fluxes (e.g. via hydrographs or sedimentographs) at any node as well as at any system outlet. The contribution of any sub-system can be understood by removing the remaining sub-systems which can be conveniently achieved by masking associated graph elements.

Maximum likelihood estimation for Cox's regression model under nested case-control sampling.

PubMed

Scheike, Thomas H; Juul, Anders

2004-04-01

Nested case-control sampling is designed to reduce the costs of large cohort studies. It is important to estimate the parameters of interest as efficiently as possible. We present a new maximum likelihood estimator (MLE) for nested case-control sampling in the context of Cox's proportional hazards model. The MLE is computed by the EM-algorithm, which is easy to implement in the proportional hazards setting. Standard errors are estimated by a numerical profile likelihood approach based on EM aided differentiation. The work was motivated by a nested case-control study that hypothesized that insulin-like growth factor I was associated with ischemic heart disease. The study was based on a population of 3784 Danes and 231 cases of ischemic heart disease where controls were matched on age and gender. We illustrate the use of the MLE for these data and show how the maximum likelihood framework can be used to obtain information additional to the relative risk estimates of covariates.

Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting-State Functional MRI Data

PubMed Central

Wang, Jin-Hui; Zuo, Xi-Nian; Gohel, Suril; Milham, Michael P.; Biswal, Bharat B.; He, Yong

2011-01-01

Graph-based computational network analysis has proven a powerful tool to quantitatively characterize functional architectures of the brain. However, the test-retest (TRT) reliability of graph metrics of functional networks has not been systematically examined. Here, we investigated TRT reliability of topological metrics of functional brain networks derived from resting-state functional magnetic resonance imaging data. Specifically, we evaluated both short-term (<1 hour apart) and long-term (>5 months apart) TRT reliability for 12 global and 6 local nodal network metrics. We found that reliability of global network metrics was overall low, threshold-sensitive and dependent on several factors of scanning time interval (TI, long-term>short-term), network membership (NM, networks excluding negative correlations>networks including negative correlations) and network type (NT, binarized networks>weighted networks). The dependence was modulated by another factor of node definition (ND) strategy. The local nodal reliability exhibited large variability across nodal metrics and a spatially heterogeneous distribution. Nodal degree was the most reliable metric and varied the least across the factors above. Hub regions in association and limbic/paralimbic cortices showed moderate TRT reliability. Importantly, nodal reliability was robust to above-mentioned four factors. Simulation analysis revealed that global network metrics were extremely sensitive (but varying degrees) to noise in functional connectivity and weighted networks generated numerically more reliable results in compared with binarized networks. For nodal network metrics, they showed high resistance to noise in functional connectivity and no NT related differences were found in the resistance. These findings provide important implications on how to choose reliable analytical schemes and network metrics of interest. PMID:21818285

Graphing with "LogoWriter."

ERIC Educational Resources Information Center

Yoder, Sharon K.

This book discusses four kinds of graphs that are taught in mathematics at the middle school level: pictographs, bar graphs, line graphs, and circle graphs. The chapters on each of these types of graphs contain information such as starting, scaling, drawing, labeling, and finishing the graphs using "LogoWriter." The final chapter of the…

Seasonal variation in male alternative reproductive tactics.

PubMed

Monroe, M J; Amundsen, T; Utne-Palm, A C; Mobley, K B

2016-12-01

Genetic parentage analyses reveal considerable diversity in alternative reproductive behaviours (e.g. sneaking) in many taxa. However, little is known about whether these behaviours vary seasonally and between populations. Here, we investigate seasonal variation in male reproductive behaviours in a population of two-spotted gobies (Gobiusculus flavescens) in Norway. Male two-spotted gobies guard nests, attract females and care for fertilized eggs. We collected clutches and nest-guarding males early and late in the breeding season in artificial nests and used microsatellite markers to reconstruct parentage from a subset of offspring from each nest. We hypothesized that mating, reproductive success and sneaking should be more prevalent early in the breeding season when competition for mates among males is predicted to be higher. However, parentage analyses revealed similar values of mating, reproductive success and high frequencies of successful sneaking early (30% of nests) and late (27% of nests) in the season. We also found that multiple females with eggs in the same nest were fertilized by one or more sneaker males, indicating that some males in this population engage in a satellite strategy. We contrast our results to previous work that demonstrates low levels of cuckoldry in a population in Sweden. Our results demonstrate marked stability in both the genetic mating system and male alternative reproductive tactics over the breeding season. However, sneaking rates may vary geographically within a species, likely due to local selection influencing ecological factors encountered at different locations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evaluation of a reproductive index to estimate grasshopper sparrow and eastern meadowlark reproductive success

USGS Publications Warehouse

Althoff, Donald P.; Gipson, P.S.; Pontius, J.S.; Japuntich, R.D.

2009-01-01

We compared an index of reproductive success based on breeding behavior to actual nest fates of grasshopper sparrows (Ammodramus savannarum) and eastern meadowlarks (Sturnella magna) on 12 plots (4-ha). Concordance of results between the two methods was 58% for grasshopper sparrows and 42% for eastern meadowlarks on a plot-by-plot basis. The indirect method yielded higher estimates of reproductive activity than nest monitoring for the balance of the plots,. There was little evidence that brown-headed cowbird (Molothrus ater) parasitism influenced the estimates of reproductive success using the indirect method. We concluded that nests and about-to-fledge nestlings were missed during searches on some plots. It may be appropriate to use an indirect method to more efficiently survey territories and/or plots for species with hard-to-find nests or when monitoring large areas. Use of a reproductive index may be appropriate and more time-efficient than nest searching and monitoring for comparing management effects such as burning, grazing, haying, military training, and other localized disturbances that are likely to affect reproductive success of grasshopper sparrows and eastern meadowlarks. However, nest monitoring may be necessary for more precise estimates of productivity necessary for long-term monitoring. Nest monitoring results are also likely to allow for direct comparisons to results from other studies because the index method requires intimate knowledge of the species being evaluated - a factor that could lead to reduced precision because the experience level of technicians relying only on behavioral cues from study-to-study is likely to vary considerably.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Fangyan; Zhang, Song; Chung Wong, Pak

Effectively visualizing large graphs and capturing the statistical properties are two challenging tasks. To aid in these two tasks, many sampling approaches for graph simplification have been proposed, falling into three categories: node sampling, edge sampling, and traversal-based sampling. It is still unknown which approach is the best. We evaluate commonly used graph sampling methods through a combined visual and statistical comparison of graphs sampled at various rates. We conduct our evaluation on three graph models: random graphs, small-world graphs, and scale-free graphs. Initial results indicate that the effectiveness of a sampling method is dependent on the graph model, themore » size of the graph, and the desired statistical property. This benchmark study can be used as a guideline in choosing the appropriate method for a particular graph sampling task, and the results presented can be incorporated into graph visualization and analysis tools.« less

An algorithm for finding a similar subgraph of all Hamiltonian cycles

NASA Astrophysics Data System (ADS)

Wafdan, R.; Ihsan, M.; Suhaimi, D.

2018-01-01

This paper discusses an algorithm to find a similar subgraph called findSimSubG algorithm. A similar subgraph is a subgraph with a maximum number of edges, contains no isolated vertex and is contained in every Hamiltonian cycle of a Hamiltonian Graph. The algorithm runs only on Hamiltonian graphs with at least two Hamiltonian cycles. The algorithm works by examining whether the initial subgraph of the first Hamiltonian cycle is a subgraph of comparison graphs. If the initial subgraph is not in comparison graphs, the algorithm will remove edges and vertices of the initial subgraph that are not in comparison graphs. There are two main processes in the algorithm, changing Hamiltonian cycle into a cycle graph and removing edges and vertices of the initial subgraph that are not in comparison graphs. The findSimSubG algorithm can find the similar subgraph without using backtracking method. The similar subgraph cannot be found on certain graphs, such as an n-antiprism graph, complete bipartite graph, complete graph, 2n-crossed prism graph, n-crown graph, n-möbius ladder, prism graph, and wheel graph. The complexity of this algorithm is O(m|V|), where m is the number of Hamiltonian cycles and |V| is the number of vertices of a Hamiltonian graph.

Reproductive success of Mariana swiftlets (Aerodramus bartschi) on the Hawaiian island of O'ahu

USGS Publications Warehouse

Johnson, Nathan C.; Haig, Susan M.; Mosher, Stephen M.; Hollenbeck, Jeff P.

2017-01-01

Mariana Swiftlets (Aerodramus bartschi) are federally listed as endangered, with populations currently limited to just three islands in the Mariana Islands plus an introduced population on the Hawaiian island of O'ahu. Before efforts are made to reintroduce Mariana Swiftlets to other islands in the Mariana archipelago, additional information is needed concerning their breeding biology. Therefore, our objective was to examine the reproductive biology of Mariana Swiftlets over five annual cycles on the Hawaiian island of O'ahu. This introduced population used a human-made tunnel for roosting and nesting, and was studied as a surrogate to negate interference with endangered populations in the Mariana Islands. Active nests (N = 478) were observed in every month of the year, with peak nesting activity between May and September. All clutches consisted of one egg. Mean duration of incubation and nestling periods were 23.9 d (range = 18–30 d, N = 233) and 55.0 d (range = 41–84 d, N = 228), respectively. Estimated nest success was 63%. Over half (52%) of nest failures were attributed to eggs found on the tunnel floor. Predation by rats (Rattus spp.) was also an important cause of nest failure and often resulted in the loss of most active nests. However, Mariana Swiftlets did re-nest after these predation events. Our results suggest that rat predation of both nests and adults may limit growth of the Mariana Swiftlet population on O'ahu, and could also affect the chances for successful establishment of relocated populations in the Mariana Islands. Another limiting factor on O'ahu is that only one nesting site is apparently available on the island. Current goals for downlisting Mariana Swiftlets from endangered to threatened include establishing populations on Guam, Rota, Aguiguan, and Saipan. To meet these goals, the population of Mariana Swiftlets on O'ahu can be important for testing reintroduction techniques, learning more about the natural history of these swiftlets, and providing individuals for reintroduction efforts in the Mariana Islands.

Mathematical foundations of the GraphBLAS

DOE PAGES

Kepner, Jeremy; Aaltonen, Peter; Bader, David; ...

2016-12-01

The GraphBLAS standard (GraphBlas.org) is being developed to bring the potential of matrix-based graph algorithms to the broadest possible audience. Mathematically, the GraphBLAS defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This study provides an introduction to the mathematics of the GraphBLAS. Graphs represent connections between vertices with edges. Matrices can represent a wide range of graphs using adjacency matrices or incidence matrices. Adjacency matrices are often easier to analyze while incidence matrices are often better for representing data. Fortunately, themore » two are easily connected by matrix multiplication. A key feature of matrix mathematics is that a very small number of matrix operations can be used to manipulate a very wide range of graphs. This composability of a small number of operations is the foundation of the GraphBLAS. A standard such as the GraphBLAS can only be effective if it has low performance overhead. Finally, performance measurements of prototype GraphBLAS implementations indicate that the overhead is low.« less

Spatial analysis of toxic emissions in LCA: a sub-continental nested USEtox model with freshwater archetypes.

PubMed

Kounina, Anna; Margni, Manuele; Shaked, Shanna; Bulle, Cécile; Jolliet, Olivier

2014-08-01

This paper develops continent-specific factors for the USEtox model and analyses the accuracy of different model architectures, spatial scales and archetypes in evaluating toxic impacts, with a focus on freshwater pathways. Inter-continental variation is analysed by comparing chemical fate and intake fractions between sub-continental zones of two life cycle impact assessment models: (1) the nested USEtox model parameterized with sub-continental zones and (2) the spatially differentiated IMPACTWorld model with 17 interconnected sub-continental regions. Substance residence time in water varies by up to two orders of magnitude among the 17 zones assessed with IMPACTWorld and USEtox, and intake fraction varies by up to three orders of magnitude. Despite this variation, the nested USEtox model succeeds in mimicking the results of the spatially differentiated model, with the exception of very persistent volatile pollutants that can be transported to polar regions. Intra-continental variation is analysed by comparing fate and intake fractions modelled with the a-spatial (one box) IMPACT Europe continental model vs. the spatially differentiated version of the same model. Results show that the one box model might overestimate chemical fate and characterisation factors for freshwater eco-toxicity of persistent pollutants by up to three orders of magnitude for point source emissions. Subdividing Europe into three archetypes, based on freshwater residence time (how long it takes water to reach the sea), improves the prediction of fate and intake fractions for point source emissions, bringing them within a factor five compared to the spatial model. We demonstrated that a sub-continental nested model such as USEtox, with continent-specific parameterization complemented with freshwater archetypes, can thus represent inter- and intra-continental spatial variations, whilst minimizing model complexity. Copyright © 2014 Elsevier Ltd. All rights reserved.

On the Existence of Simultaneous Edge Disjoint Realizations of Degree Sequences with ’Few’ Edges

DTIC Science & Technology

1975-08-01

constructing graphs and digraphs with given valences and factors. Discrete Math . 6 (1973) 79-88. 3. M. Keren, Realization of a sun of sequences by a sum...appear. 5. S. Kundu, The k factor conjecture is true. Discrete Math . 6 (1973) 367-376. 6. S. Kundu, Disjoint representation of tree realizable

DESIGN GUIDELINES FOR GOOD HEARING CONDITIONS AND EFFECTIVE NOISE CONTROL IN SCHOOL CLASSROOMS.

ERIC Educational Resources Information Center

KINGSBURY, H.F.; TAYLOR, D.W.

TWO OF THE MOST IMPORTANT OPERATIVE DESIGN FACTORS GOVERNING SPEECH PERCEPTION IN CLASSROOMS HAVE BEEN EXAMINED AND GUIDELINES IN THE FORM OF GRAPHS, ETC. CONSTRUCTED THAT SHOULD BE UNDERSTANDABLE TO AND USABLE BY THOSE ASSOCIATED WITH SCHOOL PLANNING AND DESIGN. THE TWO FACTORS CONSIDERED ARE--(1) PROVISION FOR OPTIMUM REVERBERATION TIME, AND (2)…

Supercomputer Environments

DTIC Science & Technology

1990-01-09

data structures can easily be presented to the user interface. An emphasis of the Graph Browser was the realization of graph views and graph animation ... animation of the graph. Anima- tion of the graph includes changing node shapes, changing node and arc colors, changing node and arc text, and making...many graphs tend to be tree-like. Animtion of a graph is a useful feature. One of the primary goals of GMB was to support animated graphs. For animation

Spatial structure and nest demography reveal the influence of competition, parasitism and habitat quality on slavemaking ants and their hosts

PubMed Central

2011-01-01

Background Natural communities are structured by intra-guild competition, predation or parasitism and the abiotic environment. We studied the relative importance of these factors in two host-social parasite ecosystems in three ant communities in Europe (Bavaria) and North America (New York, West Virginia). We tested how these factors affect colony demography, life-history and the spatial pattern of colonies, using a large sample size of more than 1000 colonies. The strength of competition was measured by the distance to the nearest competitor. Distance to the closest social parasite colony was used as a measure of parasitism risk. Nest sites (i.e., sticks or acorns) are limited in these forest ecosystems and we therefore included nest site quality as an abiotic factor in the analysis. In contrast to previous studies based on local densities, we focus here on the positioning and spatial patterns and we use models to compare our predictions to random expectations. Results Colony demography was universally affected by the size of the nest site with larger and more productive colonies residing in larger nest sites of higher quality. Distance to the nearest competitor negatively influenced host demography and brood production in the Bavarian community, pointing to an important role of competition, while social parasitism was less influential in this community. The New York community was characterized by the highest habitat variability, and productive colonies were clustered in sites of higher quality. Colonies were clumped on finer spatial scales, when we considered only the nearest neighbors, but more regularly distributed on coarser scales. The analysis of spatial positioning within plots often produced different results compared to those based on colony densities. For example, while host and slavemaker densities are often positively correlated, slavemakers do not nest closer to potential host colonies than expected by random. Conclusions The three communities are differently affected by biotic and abiotic factors. Some of the differences can be attributed to habitat differences and some to differences between the two slavemaking-host ecosystems. The strong effect of competition in the Bavarian community points to the scarcity of resources in this uniform habitat compared to the other more diverse sites. The decrease in colony aggregation with scale indicates fine-scale resource hotspots: colonies are locally aggregated in small groups. Our study demonstrates that species relationships vary across scales and spatial patterns can provide important insights into species interactions. These results could not have been obtained with analyses based on local densities alone. Previous studies focused on social parasitism and its effect on host colonies. The broader approach taken here, considering several possible factors affecting colony demography and not testing each one in isolation, shows that competition and environmental variability can have a similar strong impact on demography and life-history of hosts. We conclude that the effects of parasites or predators should be studied in parallel to other ecological influences. PMID:21443778

Spatial structure and nest demography reveal the influence of competition, parasitism and habitat quality on slavemaking ants and their hosts.

PubMed

Scharf, Inon; Fischer-Blass, Birgit; Foitzik, Susanne

2011-03-28

Natural communities are structured by intra-guild competition, predation or parasitism and the abiotic environment. We studied the relative importance of these factors in two host-social parasite ecosystems in three ant communities in Europe (Bavaria) and North America (New York, West Virginia). We tested how these factors affect colony demography, life-history and the spatial pattern of colonies, using a large sample size of more than 1000 colonies. The strength of competition was measured by the distance to the nearest competitor. Distance to the closest social parasite colony was used as a measure of parasitism risk. Nest sites (i.e., sticks or acorns) are limited in these forest ecosystems and we therefore included nest site quality as an abiotic factor in the analysis. In contrast to previous studies based on local densities, we focus here on the positioning and spatial patterns and we use models to compare our predictions to random expectations. Colony demography was universally affected by the size of the nest site with larger and more productive colonies residing in larger nest sites of higher quality. Distance to the nearest competitor negatively influenced host demography and brood production in the Bavarian community, pointing to an important role of competition, while social parasitism was less influential in this community. The New York community was characterized by the highest habitat variability, and productive colonies were clustered in sites of higher quality. Colonies were clumped on finer spatial scales, when we considered only the nearest neighbors, but more regularly distributed on coarser scales. The analysis of spatial positioning within plots often produced different results compared to those based on colony densities. For example, while host and slavemaker densities are often positively correlated, slavemakers do not nest closer to potential host colonies than expected by random. The three communities are differently affected by biotic and abiotic factors. Some of the differences can be attributed to habitat differences and some to differences between the two slavemaking-host ecosystems. The strong effect of competition in the Bavarian community points to the scarcity of resources in this uniform habitat compared to the other more diverse sites. The decrease in colony aggregation with scale indicates fine-scale resource hotspots: colonies are locally aggregated in small groups. Our study demonstrates that species relationships vary across scales and spatial patterns can provide important insights into species interactions. These results could not have been obtained with analyses based on local densities alone. Previous studies focused on social parasitism and its effect on host colonies. The broader approach taken here, considering several possible factors affecting colony demography and not testing each one in isolation, shows that competition and environmental variability can have a similar strong impact on demography and life-history of hosts. We conclude that the effects of parasites or predators should be studied in parallel to other ecological influences.

Oscillometric estimation of central blood pressure: validation of the Mobil-O-Graph in comparison with the SphygmoCor device.

PubMed

Weiss, Wolfgang; Gohlisch, Christopher; Harsch-Gladisch, Christl; Tölle, Markus; Zidek, Walter; van der Giet, Markus

2012-06-01

Hypertension is a major risk factor for a wide range of cardiovascular diseases and is typically identified by measuring blood pressure (BP) at the brachial artery. Although such a measurement may accurately determine diastolic BP, systolic BP is not reflected accurately. Current noninvasive techniques for assessing central aortic BP require additional recording of an arterial pressure wave using a high-fidelity applanation tonometer. Within one measurement cycle, the Mobil-O-Graph BP device uses brachial oscillometric BP waves for a noninvasive estimation of central BP. We therefore validated the Mobil-O-Graph against the SphygmoCor device, which is widely known as the commonly used approach for a noninvasive estimation of central BP. For each individual, we compared three readings of the central BP values obtained by the Mobil-O-Graph and SphygmoCor device consecutively. One hundred individuals (mean age 56.1 ± 15.4 years) were recruited for measurement.Differences between the central BP values of the test device and the SphygmoCor device were calculated for each measurement. The mean difference (95% confidence interval) for the estimated central systolic BP between both devices was -0.6 ± 3.7 mmHg. Comparison of the central BP values measured by the two devices showed a statistically significant linear correlation (R=0.91, P<0.0001). The mean between-method difference was 0.50 mmHg for central systolic BP estimation. The intrarater reproducibility between both the devices was also comparable. Bland and Altman analyses showed that the mean differences (95% confidence interval) between repeated measurements were 1.89 (0.42-3.36) mmHg and 1.36 (-0.16 to 2.83) mmHg for the SphygmoCor and the Mobil-O-Graph device, respectively. Thus, neither of these differences was statistically significantly different from 0. The limits of agreement were -16.34 to 19.73 and -15.23 to 17.17 mmHg for the SphygmoCor and the Mobil-O-Graph device, respectively. Oscillometric noninvasive estimation of central BP with the Mobil-O-Graph BP device is as effective as using the well-established SphygmoCor applanation tonometry device. In comparison, the Mobil-O-Graph combines the widespread benefits of brachial BP measurement and also provides central BP within one measurement.

A graph edit dictionary for correcting errors in roof topology graphs reconstructed from point clouds

NASA Astrophysics Data System (ADS)

Xiong, B.; Oude Elberink, S.; Vosselman, G.

2014-07-01

In the task of 3D building model reconstruction from point clouds we face the problem of recovering a roof topology graph in the presence of noise, small roof faces and low point densities. Errors in roof topology graphs will seriously affect the final modelling results. The aim of this research is to automatically correct these errors. We define the graph correction as a graph-to-graph problem, similar to the spelling correction problem (also called the string-to-string problem). The graph correction is more complex than string correction, as the graphs are 2D while strings are only 1D. We design a strategy based on a dictionary of graph edit operations to automatically identify and correct the errors in the input graph. For each type of error the graph edit dictionary stores a representative erroneous subgraph as well as the corrected version. As an erroneous roof topology graph may contain several errors, a heuristic search is applied to find the optimum sequence of graph edits to correct the errors one by one. The graph edit dictionary can be expanded to include entries needed to cope with errors that were previously not encountered. Experiments show that the dictionary with only fifteen entries already properly corrects one quarter of erroneous graphs in about 4500 buildings, and even half of the erroneous graphs in one test area, achieving as high as a 95% acceptance rate of the reconstructed models.

Belief propagation decoding of quantum channels by passing quantum messages

NASA Astrophysics Data System (ADS)

Renes, Joseph M.

2017-07-01

The belief propagation (BP) algorithm is a powerful tool in a wide range of disciplines from statistical physics to machine learning to computational biology, and is ubiquitous in decoding classical error-correcting codes. The algorithm works by passing messages between nodes of the factor graph associated with the code and enables efficient decoding of the channel, in some cases even up to the Shannon capacity. Here we construct the first BP algorithm which passes quantum messages on the factor graph and is capable of decoding the classical-quantum channel with pure state outputs. This gives explicit decoding circuits whose number of gates is quadratic in the code length. We also show that this decoder can be modified to work with polar codes for the pure state channel and as part of a decoder for transmitting quantum information over the amplitude damping channel. These represent the first explicit capacity-achieving decoders for non-Pauli channels.

Detecting black bear source–sink dynamics using individual-based genetic graphs

PubMed Central

Draheim, Hope M.; Moore, Jennifer A.; Etter, Dwayne; Winterstein, Scott R.; Scribner, Kim T.

2016-01-01

Source–sink dynamics affects population connectivity, spatial genetic structure and population viability for many species. We introduce a novel approach that uses individual-based genetic graphs to identify source–sink areas within a continuously distributed population of black bears (Ursus americanus) in the northern lower peninsula (NLP) of Michigan, USA. Black bear harvest samples (n = 569, from 2002, 2006 and 2010) were genotyped at 12 microsatellite loci and locations were compared across years to identify areas of consistent occupancy over time. We compared graph metrics estimated for a genetic model with metrics from 10 ecological models to identify ecological factors that were associated with sources and sinks. We identified 62 source nodes, 16 of which represent important source areas (net flux > 0.7) and 79 sink nodes. Source strength was significantly correlated with bear local harvest density (a proxy for bear density) and habitat suitability. Additionally, resampling simulations showed our approach is robust to potential sampling bias from uneven sample dispersion. Findings demonstrate black bears in the NLP exhibit asymmetric gene flow, and individual-based genetic graphs can characterize source–sink dynamics in continuously distributed species in the absence of discrete habitat patches. Our findings warrant consideration of undetected source–sink dynamics and their implications on harvest management of game species. PMID:27440668

Detecting black bear source-sink dynamics using individual-based genetic graphs.

PubMed

Draheim, Hope M; Moore, Jennifer A; Etter, Dwayne; Winterstein, Scott R; Scribner, Kim T

2016-07-27

Source-sink dynamics affects population connectivity, spatial genetic structure and population viability for many species. We introduce a novel approach that uses individual-based genetic graphs to identify source-sink areas within a continuously distributed population of black bears (Ursus americanus) in the northern lower peninsula (NLP) of Michigan, USA. Black bear harvest samples (n = 569, from 2002, 2006 and 2010) were genotyped at 12 microsatellite loci and locations were compared across years to identify areas of consistent occupancy over time. We compared graph metrics estimated for a genetic model with metrics from 10 ecological models to identify ecological factors that were associated with sources and sinks. We identified 62 source nodes, 16 of which represent important source areas (net flux > 0.7) and 79 sink nodes. Source strength was significantly correlated with bear local harvest density (a proxy for bear density) and habitat suitability. Additionally, resampling simulations showed our approach is robust to potential sampling bias from uneven sample dispersion. Findings demonstrate black bears in the NLP exhibit asymmetric gene flow, and individual-based genetic graphs can characterize source-sink dynamics in continuously distributed species in the absence of discrete habitat patches. Our findings warrant consideration of undetected source-sink dynamics and their implications on harvest management of game species. © 2016 The Author(s).

Diabetes Interactive Atlas

PubMed Central

Burrows, Nilka R.; Geiss, Linda S.

2014-01-01

The Diabetes Interactive Atlas is a recently released Web-based collection of maps that allows users to view geographic patterns and examine trends in diabetes and its risk factors over time across the United States and within states. The atlas provides maps, tables, graphs, and motion charts that depict national, state, and county data. Large amounts of data can be viewed in various ways simultaneously. In this article, we describe the design and technical issues for developing the atlas and provide an overview of the atlas’ maps and graphs. The Diabetes Interactive Atlas improves visualization of geographic patterns, highlights observation of trends, and demonstrates the concomitant geographic and temporal growth of diabetes and obesity. PMID:24503340

50 CFR 22.27 - Removal of eagle nests.

Code of Federal Regulations, 2010 CFR

2010-10-01

... additional factors that may be relevant to our decision whether to issue the permit, including, but not... (CONTINUED) TAKING, POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF... mitigation, together with the cumulative effects of other permitted take and additional factors affecting...

Comparison and Enumeration of Chemical Graphs

PubMed Central

Akutsu, Tatsuya; Nagamochi, Hiroshi

2013-01-01

Chemical compounds are usually represented as graph structured data in computers. In this review article, we overview several graph classes relevant to chemical compounds and the computational complexities of several fundamental problems for these graph classes. In particular, we consider the following problems: determining whether two chemical graphs are identical, determining whether one input chemical graph is a part of the other input chemical graph, finding a maximum common part of two input graphs, finding a reaction atom mapping, enumerating possible chemical graphs, and enumerating stereoisomers. We also discuss the relationship between the fifth problem and kernel functions for chemical compounds. PMID:24688697

Combinatorial compatibility as habit-controlling factor in lysozyme crystallization I. Monomeric and tetrameric F faces derived graph-theoretically

NASA Astrophysics Data System (ADS)

Strom, C. S.; Bennema, P.

1997-03-01

A series of two articles discusses possible morphological evidence for oligomerization of growth units in the crystallization of tetragonal lysozyme, based on a rigorous graph-theoretic derivation of the F faces. In the first study (Part I), the growth layers are derived as valid networks satisfying the conditions of F slices in the context of the PBC theory using the graph-theoretic method implemented in program FFACE [C.S. Strom, Z. Krist. 172 (1985) 11]. The analysis is performed in monomeric and alternative tetrameric and octameric formulations of the unit cell, assuming tetramer formation according to the strongest bonds. F (flat) slices with thickness Rdhkl ( {1}/{2} < R ≤ 1 ) are predicted theoretically in the forms 1 1 0, 0 1 1, 1 1 1. The relevant energies are established in the broken bond model. The relation between possible oligomeric specifications of the unit cell and combinatorially feasible F slice compositions in these orientations is explored.

Visual texture perception via graph-based semi-supervised learning

NASA Astrophysics Data System (ADS)

Zhang, Qin; Dong, Junyu; Zhong, Guoqiang

2018-04-01

Perceptual features, for example direction, contrast and repetitiveness, are important visual factors for human to perceive a texture. However, it needs to perform psychophysical experiment to quantify these perceptual features' scale, which requires a large amount of human labor and time. This paper focuses on the task of obtaining perceptual features' scale of textures by small number of textures with perceptual scales through a rating psychophysical experiment (what we call labeled textures) and a mass of unlabeled textures. This is the scenario that the semi-supervised learning is naturally suitable for. This is meaningful for texture perception research, and really helpful for the perceptual texture database expansion. A graph-based semi-supervised learning method called random multi-graphs, RMG for short, is proposed to deal with this task. We evaluate different kinds of features including LBP, Gabor, and a kind of unsupervised deep features extracted by a PCA-based deep network. The experimental results show that our method can achieve satisfactory effects no matter what kind of texture features are used.

Counting surface-kernel epimorphisms from a co-compact Fuchsian group to a cyclic group with motivations from string theory and QFT

NASA Astrophysics Data System (ADS)

Bibak, Khodakhast; Kapron, Bruce M.; Srinivasan, Venkatesh

2016-09-01

Graphs embedded into surfaces have many important applications, in particular, in combinatorics, geometry, and physics. For example, ribbon graphs and their counting is of great interest in string theory and quantum field theory (QFT). Recently, Koch et al. (2013) [12] gave a refined formula for counting ribbon graphs and discussed its applications to several physics problems. An important factor in this formula is the number of surface-kernel epimorphisms from a co-compact Fuchsian group to a cyclic group. The aim of this paper is to give an explicit and practical formula for the number of such epimorphisms. As a consequence, we obtain an 'equivalent' form of Harvey's famous theorem on the cyclic groups of automorphisms of compact Riemann surfaces. Our main tool is an explicit formula for the number of solutions of restricted linear congruence recently proved by Bibak et al. using properties of Ramanujan sums and of the finite Fourier transform of arithmetic functions.

Mean square cordial labelling related to some acyclic graphs and its rough approximations

NASA Astrophysics Data System (ADS)

Dhanalakshmi, S.; Parvathi, N.

2018-04-01

In this paper we investigate that the path Pn, comb graph Pn⊙K1, n-centipede graph,centipede graph (n,2) and star Sn admits mean square cordial labeling. Also we proved that the induced sub graph obtained by the upper approximation of any sub graph H of the above acyclic graphs admits mean square cordial labeling.

Relating zeta functions of discrete and quantum graphs

NASA Astrophysics Data System (ADS)

Harrison, Jonathan; Weyand, Tracy

2018-02-01

We write the spectral zeta function of the Laplace operator on an equilateral metric graph in terms of the spectral zeta function of the normalized Laplace operator on the corresponding discrete graph. To do this, we apply a relation between the spectrum of the Laplacian on a discrete graph and that of the Laplacian on an equilateral metric graph. As a by-product, we determine how the multiplicity of eigenvalues of the quantum graph, that are also in the spectrum of the graph with Dirichlet conditions at the vertices, depends on the graph geometry. Finally we apply the result to calculate the vacuum energy and spectral determinant of a complete bipartite graph and compare our results with those for a star graph, a graph in which all vertices are connected to a central vertex by a single edge.

Topic Model for Graph Mining.

PubMed

Xuan, Junyu; Lu, Jie; Zhang, Guangquan; Luo, Xiangfeng

2015-12-01

Graph mining has been a popular research area because of its numerous application scenarios. Many unstructured and structured data can be represented as graphs, such as, documents, chemical molecular structures, and images. However, an issue in relation to current research on graphs is that they cannot adequately discover the topics hidden in graph-structured data which can be beneficial for both the unsupervised learning and supervised learning of the graphs. Although topic models have proved to be very successful in discovering latent topics, the standard topic models cannot be directly applied to graph-structured data due to the "bag-of-word" assumption. In this paper, an innovative graph topic model (GTM) is proposed to address this issue, which uses Bernoulli distributions to model the edges between nodes in a graph. It can, therefore, make the edges in a graph contribute to latent topic discovery and further improve the accuracy of the supervised and unsupervised learning of graphs. The experimental results on two different types of graph datasets show that the proposed GTM outperforms the latent Dirichlet allocation on classification by using the unveiled topics of these two models to represent graphs.

Ecological factors related to the widespread distribution of sylvatic Rhodnius ecuadoriensis populations in southern Ecuador

PubMed Central

2012-01-01

Background Chagas disease transmission risk is a function of the presence of triatomines in domestic habitats. Rhodnius ecuadoriensis is one of the main vectors implicated in transmission of Trypanosoma cruzi in Ecuador. This triatomine species is present in domestic, peridomestic and sylvatic habitats in the country. To determine the distribution of sylvatic populations of R. ecuadoriensis and the factors related to this distribution, triatomine searches were conducted between 2005 and 2009 in southern Ecuador. Methods Manual triatomine searches were conducted by skilled bug collectors in 23 communities. Sylvatic searched sites were selected by a) directed sampling, where microhabitats were selected by the searchers and b) random sampling, where sampling points where randomly generated. Domiciliary triatomine searches were conducted using the one man-hour method. Natural trypanosome infection was determined by microscopic examination and PCR. Generalized linear models were used to test the effect of environmental factors on the presence of sylvatic triatomines. Results In total, 1,923 sylvatic individuals were collected representing a sampling effort of 751 man-hours. Collected sylvatic triatomines were associated with mammal and bird nests. The 1,219 sampled nests presented an infestation index of 11.9%, a crowding of 13 bugs per infested nest, and a colonization of 80% of the nests. Triatomine abundance was significantly higher in squirrel (Sciurus stramineus) nests located above five meters from ground level and close to the houses. In addition, 8.5% of the 820 examined houses in the same localities were infested with triatomines. There was a significant correlation between R. ecuadoriensis infestation rates found in sylvatic and synanthropic environments within communities (p = 0.012). Parasitological analysis revealed that 64.7% and 15.7% of the sylvatic bugs examined (n = 300) were infected with Trypanosoma cruzi and T. rangeli respectively, and 8% of the bugs presented mixed infections. Conclusions The wide distribution of sylvatic R. ecuadoriensis populations may jeopardize the effectiveness of control campaigns conducted to eliminate domestic populations of this species. Also, the high T. cruzi infection rates found in sylvatic R. ecuadoriensis populations in southern Ecuador could constitute a risk for house re-infestation and persistent long-term Chagas disease transmission in the region. PMID:22243930

Reproductive success of kittiwakes and murres in sequential stages of the nesting period: Relationships with diet and oceanography

NASA Astrophysics Data System (ADS)

Renner, Heather M.; Drummond, Brie A.; Benson, Anna-Marie; Paredes, Rosana

2014-11-01

Reproductive success is one of the most easily-measured and widely studied demographic parameters of colonial nesting seabirds. Nevertheless, factors affecting the sequential stages (egg laying, incubation, chick-rearing) of reproductive success are less understood. We investigated the separate sequential stages of reproductive success in piscivorous black-legged kittiwakes (Rissa tridactyla) and thick-billed murres (Uria lomvia) using a 36-year dataset (1975-2010) on the major Pribilof Islands (St. Paul and St. George), which have recently had contrasting population trajectories. Our objectives were to evaluate how the proportion of successful nests varied among stages, and to quantify factors influencing the probability of nest success at each stage in each island. We modeled the probability of nest success at each stage using General Linear Mixed Models incorporating broad-scale and local climate variables, and diet as covariates as well as other measures of reproduction such as timing of breeding and reproductive output in the previous year and previous stage. For both species we found: (1) Success in previous stages of the breeding cycle and success in the prior year better explained overall success than any environmental variables. Phenology was also an important predictor of laying success for kittiwakes. (2) Fledging success was lower when chick diets contained oceanic fish found farther from the colonies and small invertebrates, rather than coastal fish species. (3) Differences in reproductive variables at St. Paul and St. George islands did not correspond to population trends between the two islands. Our results highlight the potential importance of adult condition and annual survival to kittiwake and murre productivity and ultimately, populations. Adult condition carrying over from the previous year ultimately seems to drive annual breeding success in a cascade effect. Furthermore, condition and survival appear to be important contributors to population dynamics at each island. Therefore, adult condition and survival prior to breeding, and factors that influence these parameters such as foraging conditions in the non-breeding season, may be important datasets for understanding drivers of seabird demography at the Pribilof Islands.

Ecological factors related to the widespread distribution of sylvatic Rhodnius ecuadoriensis populations in southern Ecuador.

PubMed

Grijalva, Mario J; Suarez-Davalos, Victoria; Villacis, Anita G; Ocaña-Mayorga, Sofia; Dangles, Olivier

2012-01-13

Chagas disease transmission risk is a function of the presence of triatomines in domestic habitats. Rhodnius ecuadoriensis is one of the main vectors implicated in transmission of Trypanosoma cruzi in Ecuador. This triatomine species is present in domestic, peridomestic and sylvatic habitats in the country. To determine the distribution of sylvatic populations of R. ecuadoriensis and the factors related to this distribution, triatomine searches were conducted between 2005 and 2009 in southern Ecuador. Manual triatomine searches were conducted by skilled bug collectors in 23 communities. Sylvatic searched sites were selected by a) directed sampling, where microhabitats were selected by the searchers and b) random sampling, where sampling points where randomly generated. Domiciliary triatomine searches were conducted using the one man-hour method. Natural trypanosome infection was determined by microscopic examination and PCR. Generalized linear models were used to test the effect of environmental factors on the presence of sylvatic triatomines. In total, 1,923 sylvatic individuals were collected representing a sampling effort of 751 man-hours. Collected sylvatic triatomines were associated with mammal and bird nests. The 1,219 sampled nests presented an infestation index of 11.9%, a crowding of 13 bugs per infested nest, and a colonization of 80% of the nests. Triatomine abundance was significantly higher in squirrel (Sciurus stramineus) nests located above five meters from ground level and close to the houses. In addition, 8.5% of the 820 examined houses in the same localities were infested with triatomines. There was a significant correlation between R. ecuadoriensis infestation rates found in sylvatic and synanthropic environments within communities (p = 0.012). Parasitological analysis revealed that 64.7% and 15.7% of the sylvatic bugs examined (n = 300) were infected with Trypanosoma cruzi and T. rangeli respectively, and 8% of the bugs presented mixed infections. The wide distribution of sylvatic R. ecuadoriensis populations may jeopardize the effectiveness of control campaigns conducted to eliminate domestic populations of this species. Also, the high T. cruzi infection rates found in sylvatic R. ecuadoriensis populations in southern Ecuador could constitute a risk for house re-infestation and persistent long-term Chagas disease transmission in the region.

Modeling Temporal Variation in Social Network: An Evolutionary Web Graph Approach

NASA Astrophysics Data System (ADS)

Mitra, Susanta; Bagchi, Aditya

A social network is a social structure between actors (individuals, organization or other social entities) and indicates the ways in which they are connected through various social relationships like friendships, kinships, professional, academic etc. Usually, a social network represents a social community, like a club and its members or a city and its citizens etc. or a research group communicating over Internet. In seventies Leinhardt [1] first proposed the idea of representing a social community by a digraph. Later, this idea became popular among other research workers like, network designers, web-service application developers and e-learning modelers. It gave rise to a rapid proliferation of research work in the area of social network analysis. Some of the notable structural properties of a social network are connectedness between actors, reachability between a source and a target actor, reciprocity or pair-wise connection between actors with bi-directional links, centrality of actors or the important actors having high degree or more connections and finally the division of actors into sub-structures or cliques or strongly-connected components. The cycles present in a social network may even be nested [2, 3]. The formal definition of these structural properties will be provided in Sect. 8.2.1. The division of actors into cliques or sub-groups can be a very important factor for understanding a social structure, particularly the degree of cohesiveness in a community. The number, size, and connections among the sub-groups in a network are useful in understanding how the network, as a whole, is likely to behave.

Effects of two-loop contributions in the pseudofermion functional renormalization group method for quantum spin systems

NASA Astrophysics Data System (ADS)

Rück, Marlon; Reuther, Johannes

2018-04-01

We implement an extension of the pseudofermion functional renormalization group method for quantum spin systems that takes into account two-loop diagrammatic contributions. An efficient numerical treatment of the additional terms is achieved within a nested graph construction which recombines different one-loop interaction channels. In order to be fully self-consistent with respect to self-energy corrections, we also include certain three-loop terms of Katanin type. We first apply this formalism to the antiferromagnetic J1-J2 Heisenberg model on the square lattice and benchmark our results against the previous one-loop plus Katanin approach. Even though the renormalization group (RG) equations undergo significant modifications when including the two-loop terms, the magnetic phase diagram, comprising Néel ordered and collinear ordered phases separated by a magnetically disordered regime, remains remarkably unchanged. Only the boundary position between the disordered and the collinear phases is found to be moderately affected by two-loop terms. On the other hand, critical RG scales, which we associate with critical temperatures Tc, are reduced by a factor of ˜2 indicating that the two-loop diagrams play a significant role in enforcing the Mermin-Wagner theorem. Improved estimates for critical temperatures are also obtained for the Heisenberg ferromagnet on the three-dimensional simple cubic lattice where errors in Tc are reduced by ˜34 % . These findings have important implications for the quantum phase diagrams calculated within the previous one-loop plus Katanin approach which turn out to be already well converged.

Preserving Differential Privacy in Degree-Correlation based Graph Generation

PubMed Central

Wang, Yue; Wu, Xintao

2014-01-01

Enabling accurate analysis of social network data while preserving differential privacy has been challenging since graph features such as cluster coefficient often have high sensitivity, which is different from traditional aggregate functions (e.g., count and sum) on tabular data. In this paper, we study the problem of enforcing edge differential privacy in graph generation. The idea is to enforce differential privacy on graph model parameters learned from the original network and then generate the graphs for releasing using the graph model with the private parameters. In particular, we develop a differential privacy preserving graph generator based on the dK-graph generation model. We first derive from the original graph various parameters (i.e., degree correlations) used in the dK-graph model, then enforce edge differential privacy on the learned parameters, and finally use the dK-graph model with the perturbed parameters to generate graphs. For the 2K-graph model, we enforce the edge differential privacy by calibrating noise based on the smooth sensitivity, rather than the global sensitivity. By doing this, we achieve the strict differential privacy guarantee with smaller magnitude noise. We conduct experiments on four real networks and compare the performance of our private dK-graph models with the stochastic Kronecker graph generation model in terms of utility and privacy tradeoff. Empirical evaluations show the developed private dK-graph generation models significantly outperform the approach based on the stochastic Kronecker generation model. PMID:24723987

A general method for computing Tutte polynomials of self-similar graphs

NASA Astrophysics Data System (ADS)

Gong, Helin; Jin, Xian'an

2017-10-01

Self-similar graphs were widely studied in both combinatorics and statistical physics. Motivated by the construction of the well-known 3-dimensional Sierpiński gasket graphs, in this paper we introduce a family of recursively constructed self-similar graphs whose inner duals are of the self-similar property. By combining the dual property of the Tutte polynomial and the subgraph-decomposition trick, we show that the Tutte polynomial of this family of graphs can be computed in an iterative way and in particular the exact expression of the formula of the number of their spanning trees is derived. Furthermore, we show our method is a general one that is easily extended to compute Tutte polynomials for other families of self-similar graphs such as Farey graphs, 2-dimensional Sierpiński gasket graphs, Hanoi graphs, modified Koch graphs, Apollonian graphs, pseudofractal scale-free web, fractal scale-free network, etc.

Bipartite separability and nonlocal quantum operations on graphs

NASA Astrophysics Data System (ADS)

Dutta, Supriyo; Adhikari, Bibhas; Banerjee, Subhashish; Srikanth, R.

2016-07-01

In this paper we consider the separability problem for bipartite quantum states arising from graphs. Earlier it was proved that the degree criterion is the graph-theoretic counterpart of the familiar positive partial transpose criterion for separability, although there are entangled states with positive partial transpose for which the degree criterion fails. Here we introduce the concept of partially symmetric graphs and degree symmetric graphs by using the well-known concept of partial transposition of a graph and degree criteria, respectively. Thus, we provide classes of bipartite separable states of dimension m ×n arising from partially symmetric graphs. We identify partially asymmetric graphs that lack the property of partial symmetry. We develop a combinatorial procedure to create a partially asymmetric graph from a given partially symmetric graph. We show that this combinatorial operation can act as an entanglement generator for mixed states arising from partially symmetric graphs.

Nest and brood attentiveness in female black ducks

USGS Publications Warehouse

Ringelman, J.K.; Longcore, J.R.; Owen, R.B.

1982-01-01

Incubation rhythms and brood attentiveness of radio-marked Black Ducks (Anas rubripes) were studied in southcentral Maine during 1977-1980. Recess duration and frequency differed between three females nesting near wetlands (x = 82 min, 2.3 recesses/day) and two nesting at upland sites(x = 183 min, I. I recesses/day), but incubation constancy was similar for all birds (x = 86.7%). A fourth wetland-nesting female apparently responded to the absence of down and concealing cover at the nest site by taking shorter and fewer recesses (x= 34 min, 1.0 recesses/day) than did other wetland-nesters with typical nests. Wetland-nesters took longer recesses with increasing air temperature and following long incubation sessions. After their ducklings were two weeks old, two brood-rearing females began leaving their broods to forage on nearby wetlands. Duration of rearing recess (x = 56 min) and total recess time (x = 94 min/day) were less during this mid-rearing stage than during the latter part of rearing (x = 265 min, 488 min/day). The two hen-brood bonds terminated at 43 and 48 days. We suggest that small endogenous nutrient reserves and the low density of invertebrate foods, typical of Black Duck breeding habitat, were critical factors affecting the evolution of Black Duck incubation behavior. Bouts of inattention during brood rearing may have also evolved in relation to food requirements; by foraging on wetlands away from their broods, females avoid competing with offspring for common food resources.

Comparative population structure of cavity-nesting sea ducks

USGS Publications Warehouse

Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

2014-01-01

A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

On the local edge antimagicness of m-splitting graphs

NASA Astrophysics Data System (ADS)

Albirri, E. R.; Dafik; Slamin; Agustin, I. H.; Alfarisi, R.

2018-04-01

Let G be a connected and simple graph. A split graph is a graph derived by adding new vertex v‧ in every vertex v‧ such that v‧ adjacent to v in graph G. An m-splitting graph is a graph which has m v‧-vertices, denoted by mSpl(G). A local edge antimagic coloring in G = (V, E) graph is a bijection f:V (G)\\to \\{1,2,3,\\ldots,|V(G)|\\} in which for any two adjacent edges e 1 and e 2 satisfies w({e}1)\

Survey of Approaches to Generate Realistic Synthetic Graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, Seung-Hwan; Lee, Sangkeun; Powers, Sarah S

A graph is a flexible data structure that can represent relationships between entities. As with other data analysis tasks, the use of realistic graphs is critical to obtaining valid research results. Unfortunately, using the actual ("real-world") graphs for research and new algorithm development is difficult due to the presence of sensitive information in the data or due to the scale of data. This results in practitioners developing algorithms and systems that employ synthetic graphs instead of real-world graphs. Generating realistic synthetic graphs that provide reliable statistical confidence to algorithmic analysis and system evaluation involves addressing technical hurdles in a broadmore » set of areas. This report surveys the state of the art in approaches to generate realistic graphs that are derived from fitted graph models on real-world graphs.« less

Self-organizing maps for learning the edit costs in graph matching.

PubMed

Neuhaus, Michel; Bunke, Horst

2005-06-01

Although graph matching and graph edit distance computation have become areas of intensive research recently, the automatic inference of the cost of edit operations has remained an open problem. In the present paper, we address the issue of learning graph edit distance cost functions for numerically labeled graphs from a corpus of sample graphs. We propose a system of self-organizing maps (SOMs) that represent the distance measuring spaces of node and edge labels. Our learning process is based on the concept of self-organization. It adapts the edit costs in such a way that the similarity of graphs from the same class is increased, whereas the similarity of graphs from different classes decreases. The learning procedure is demonstrated on two different applications involving line drawing graphs and graphs representing diatoms, respectively.

Apparatuses and Methods for Producing Runtime Architectures of Computer Program Modules

NASA Technical Reports Server (NTRS)

Abi-Antoun, Marwan Elia (Inventor); Aldrich, Jonathan Erik (Inventor)

2013-01-01

Apparatuses and methods for producing run-time architectures of computer program modules. One embodiment includes creating an abstract graph from the computer program module and from containment information corresponding to the computer program module, wherein the abstract graph has nodes including types and objects, and wherein the abstract graph relates an object to a type, and wherein for a specific object the abstract graph relates the specific object to a type containing the specific object; and creating a runtime graph from the abstract graph, wherein the runtime graph is a representation of the true runtime object graph, wherein the runtime graph represents containment information such that, for a specific object, the runtime graph relates the specific object to another object that contains the specific object.

Osprey: worldwide sentinel species for assessing and monitoring environmental contamination in rivers, lakes, reservoirs, and estuaries.

PubMed

Grove, Robert A; Henny, Charles J; Kaiser, James L

2009-01-01

In the United States, many fish and wildlife species have been used nationwide to monitor environmental contaminant exposure and effects, including carcasses of the bald eagle (Haliaeetus leucocephalus), the only top avian predator regularly used in the past. Unfortunately, bald eagles are sensitive to investigator intrusion at the nest. Thus, the osprey (Pandion haliaetus) is evaluated as a potential sentinel species for aquatic ecosystems. Several characteristics support the choice of the osprey as a sentinel species, including: (1) fish-eating diet atop the aquatic food web, (2) long-lived with strong nest fidelity, (3) adapts to human landscapes (potentially the most contaminated), (4) tolerates short-term nest disturbance, (5) nests spatially distributed at regular intervals, (6) highly visible nests easily located for study, (7) ability to accumulate most, if not all, lipophilic contaminants, (8) known sensitivity to many contaminants, and (9) nearly a worldwide distribution. These osprey traits have been instrumental in successfully using the species to understand population distribution, abundance, and changes over time; the effects of various contaminants on reproductive success; how contaminants in prey (fish on biomass basis) contribute to egg concentrations (i.e., biomagnification factors); and spatial residue patterns. Data summarized include nesting population surveys, detailed nesting studies, and chemical analyses of osprey egg, organ, blood, and feather samples for contaminants that bioaccumulate and/or biomagnify in aquatic food webs; and biochemical evaluations of blood and various organs. Studies in the United States, Canada, Mexico, Europe, and elsewhere have shown the osprey to be a useful sentinel species for monitoring selected environmental contaminants, including some emerging contaminants in lakes, reservoirs, rivers, and estuaries.

Raptors of the Hanford Site and nearby areas of southcentral Washington

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fitzner, R.E.; Rickard, W.H.; Cadwell, L.L.

1981-05-01

This report is concerned with the birds of prey which use the Hanford Site not only during the nesting season but throughout the year. An ecological treatment of five nesting owls (great horned, long-eared, short-eared, barn and burrowing) and five nesting hawks (marsh hawk, red-tailed hawk, Swainson's hawk, prairie falcon and American kestrel) is provided and supportive information on non-nesting species is presented. Factors which control raptor densities and population dynamics throughout all seasons of the year are discussed. Information is also provided for raptors from other areas of southcentral Washington in order to yield a comprehensive picture of howmore » the Hanford Site fits in with regional bird of prey populations. The following were the objectives of this study: (1) to determine the numbers of birds of prey nesting on the Hanford Site, (2) to document the reproductive chronology of each nesting raptor species, (3) to provide analyses of food habits of birds of prey on the Hanford Site coupled with prey abundance data, (4) to determine the productivity of the dominant large birds of prey on the Hanford Site, (5) to determine the distribution and land use patterns of all raptors on the Hanford Site, (6) to determine the kinds and relative abundance of non-nesting raptors on the Hanford Site and adjacent areas of southcentral Washington (7) to document present land use practices on the Hanford Site and their effects on raptors, (8) to document radionuclide levels in birds of prey on the Hanford Site, and (9) to determine the role of birds of prey in radioecological monitoring.« less

Raptor nest-site use in relation to the proximity of coalbed methane development

USGS Publications Warehouse

Carlile, J.D.; Sanders, Lindsey E.; Chalfoun, Anna D.; Gerow, K.G.

2018-01-01

Raptor nest–site use in relation to the proximity of coalbed–methane development. Energy development such as coalbed–methane (CBM) extraction is a major land use with largely unknown consequences for many animal species. Some raptor species may be especially vulnerable to habitat changes due to energy development given their ecological requirements and population trajectories. Using 12,977 observations of 3,074 nests of 12 raptor species across nine years (2003–2011) in the Powder River Basin, Wyoming, USA, we evaluated relationships between raptor nest–site use and CBM development. Our objectives were to determine temporal trends in nest–use rates, and whether nest–site use was related to the proximity of CBM development. Across the study area, nest–use rates varied across species and years in a non–linear fashion. We developed a novel randomization test to assess differences in use between nests at developed and undeveloped sites, while controlling for annual variation in nest–site use. Red–tailed hawks (Buteo jamaicensis), burrowing owls (Athene cunicularia), and long–eared owls (Asio otus) used nests in undeveloped areas more than nests in developed areas (i.e. nests near CBM development). Differences between development groups were equivocal for the remaining nine species; however, we caution that we likely had lower statistical power to detect differences for rarer species. Our findings suggest potential avoidance of nesting in areas near CBM development by some species and reveal that CBM effects may be fairly consistent across distances between 400–2,415 m from wells. Future work should consider habitat preferences and fitness outcomes, and control for other key factors such as local prey availability, raptor densities, and weather.

Simulation and Sensitivity in a Nested Modeling System for South America. Part II: GCM Boundary Forcing.

NASA Astrophysics Data System (ADS)

Rojas, Maisa; Seth, Anji

2003-08-01

of this study, the RegCM's ability to simulate circulation and rainfall observed in the two extreme seasons was demonstrated when driven at the lateral boundaries by reanalyzed forcing. Seasonal integrations with the RegCM driven by GCM ensemble-derived lateral boundary forcing demonstrate that the nested model responds well to the SST forcing, by capturing the major features of the circulation and rainfall differences between the two years. The GCM-driven model also improves upon the monthly evolution of rainfall compared with that from the GCM. However, the nested model rainfall simulations for the two seasons are degraded compared with those from the reanalyses-driven RegCM integrations. The poor location of the Atlantic intertropical convergence zone (ITCZ) in the GCM leads to excess rainfall in Nordeste in the nested model.An expanded domain was tested, wherein the RegCM was permitted more internal freedom to respond to SST and regional orographic forcing. Results show that the RegCM is able to improve the location of the ITCZ, and the seasonal evolution of rainfall in Nordeste, the Amazon region, and the southeastern region of Brazil. However, it remains that the limiting factor in the skill of the nested modeling system is the quality of the lateral boundary forcing provided by the global model.

The anti-predator role of within-nest emergence synchrony in sea turtle hatchlings.

PubMed

Santos, Robson G; Pinheiro, Hudson Tercio; Martins, Agnaldo Silva; Riul, Pablo; Bruno, Soraya Christina; Janzen, Fredric J; Ioannou, Christos C

2016-07-13

Group formation is a common behaviour among prey species. In egg-laying animals, despite the various factors that promote intra-clutch variation leading to asynchronous hatching and emergence from nests, synchronous hatching and emergence occurs in many taxa. This synchrony may be adaptive by reducing predation risk, but few data are available in any natural system, even for iconic examples of the anti-predator function of group formation. Here, we show for the first time that increased group size (number of hatchlings emerging together from a nest) reduces green turtle (Chelonia mydas) hatchling predation. This effect was only observed earlier in the night when predation pressure was greatest, indicated by the greatest predator abundance and a small proportion of predators preoccupied with consuming captured prey. Further analysis revealed that the effect of time of day was due to the number of hatchlings already killed in an evening; this, along with the apparent lack of other anti-predatory mechanisms for grouping, suggests that synchronous emergence from a nest appears to swamp predators, resulting in an attack abatement effect. Using a system with relatively pristine conditions for turtle hatchlings and their predators provides a more realistic environmental context within which intra-nest synchronous emergence has evolved. © 2016 The Author(s).

Prey use and provisioning rates of urban-nesting Mississippi Kites in west Texas

USGS Publications Warehouse

Welch, Brandi C.; Boal, Clint W.

2015-01-01

Urban ecosystems are attractive to several raptor species, including the Mississippi Kite (Ictinia mississippiensis). To better understand the niche filled by urban-nesting Mississippi Kites, we observed nesting kites at 10 nests for a total of 269 hr during the breeding seasons of 2010 and 2011. We assessed prey delivery rates and prey use within and between years, evaluated the influences of nestling age, time of day, day of year, and local atmospheric conditions on delivery rates, and examined provisioning rates by male and female kites. A 62% decrease in the prey delivery rate, measured by the number of prey deliveries, from 2010 to 2011 was likely attributable to extreme heat and drought during the 2011 breeding season. However, total biomass of identified deliveries increased 38.9% in 2011 due to an increase in the percentage of avian prey (from 1% to 16% of identified deliveries). We suspect that differences in weather conditions between years influenced the type of prey delivered, and our modeling efforts indicated that year, nestling age, time of day, and temperature best explained the number of prey deliveries made per hour. On average, females delivered more prey items than males, but variability among nests suggested additional factors may influence parental effort. Our results suggest that Mississippi Kites exhibit prey switching under differing conditions.

Clinical Usefulness of a One-Tube Nested Reverse Transcription Quantitative Polymerase Chain Reaction Assay for Evaluating Human Epidermal Growth Factor Receptor 2 mRNA Overexpression in Formalin-Fixed and Paraffin-Embedded Breast Cancer Tissue Samples.

PubMed

Wang, Hye-Young; Ahn, Sungwoo; Park, Sunyoung; Kim, SeungIl; Lee, Hyeyoung

2017-01-01

Currently, the two main methods used to analyze human epidermal growth factor receptor 2 (HER2) amplification or overexpression have a limited accuracy and high costs. These limitations can be overcome by the development of complementary quantitative methods. In this study, we analyzed HER2 mRNA expression in clinical formalin-fixed and paraffin-embedded (FFPE) samples using a one-tube nested reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay. We measured expression relative to 3 reference genes and compared the results to those obtained by conventional immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assays with 226 FFPE breast cancer tissue samples. The one-tube nested RT-qPCR assay proved to be highly sensitive and specific based on comparisons with IHC (96.9 and 97.7%, respectively) and FISH (92.4 and 92.9%, respectively) obtained with the validation set. Comparisons with clinicopathological data revealed significant associations between HER2 overexpression and TNM stage (p < 0.01), histological type (p < 0.01), ER status (p < 0.001), PR status (p < 0.05), HER2 status (p < 0.001), and molecular subtypes (p < 0.001). Based on these findings, our one-tube nested RT-qPCR assay is a potentially useful and complementary screening tool for the detection of HER2 mRNA overexpression. © 2016 S. Karger AG, Basel.

Teen Mothers: Selected Socio-Demographic Characteristics and Risk Factors. Report to the Honorable Charles B. Rangel, House of Representatives.

ERIC Educational Resources Information Center

General Accounting Office, Washington, DC. Health, Education, and Human Services Div.

This report provides social and demographic information about teen mothers. Specific information on trends in birth rates for teens, a statistical profile of teen mothers, and sociocultural factors related to these trends are reported. The findings are presented in graphs and figures related to the following issues: (1) teen birth rates, birth…

Identifying Key Drivers of Return Reversal with Dynamical Bayesian Factor Graph

PubMed Central

Zhao, Shuai; Tong, Yunhai; Wang, Zitian; Tan, Shaohua

2016-01-01

In the stock market, return reversal occurs when investors sell overbought stocks and buy oversold stocks, reversing the stocks’ price trends. In this paper, we develop a new method to identify key drivers of return reversal by incorporating a comprehensive set of factors derived from different economic theories into one unified dynamical Bayesian factor graph. We then use the model to depict factor relationships and their dynamics, from which we make some interesting discoveries about the mechanism behind return reversals. Through extensive experiments on the US stock market, we conclude that among the various factors, the liquidity factors consistently emerge as key drivers of return reversal, which is in support of the theory of liquidity effect. Specifically, we find that stocks with high turnover rates or high Amihud illiquidity measures have a greater probability of experiencing return reversals. Apart from the consistent drivers, we find other drivers of return reversal that generally change from year to year, and they serve as important characteristics for evaluating the trends of stock returns. Besides, we also identify some seldom discussed yet enlightening inter-factor relationships, one of which shows that stocks in Finance and Insurance industry are more likely to have high Amihud illiquidity measures in comparison with those in other industries. These conclusions are robust for return reversals under different thresholds. PMID:27893780

Cooperation among cancer cells as public goods games on Voronoi networks.

PubMed

Archetti, Marco

2016-05-07

Cancer cells produce growth factors that diffuse and sustain tumour proliferation, a form of cooperation that can be studied using mathematical models of public goods in the framework of evolutionary game theory. Cell populations, however, form heterogeneous networks that cannot be described by regular lattices or scale-free networks, the types of graphs generally used in the study of cooperation. To describe the dynamics of growth factor production in populations of cancer cells, I study public goods games on Voronoi networks, using a range of non-linear benefits that account for the known properties of growth factors, and different types of diffusion gradients. The results are surprisingly similar to those obtained on regular graphs and different from results on scale-free networks, revealing that network heterogeneity per se does not promote cooperation when public goods diffuse beyond one-step neighbours. The exact shape of the diffusion gradient is not crucial, however, whereas the type of non-linear benefit is an essential determinant of the dynamics. Public goods games on Voronoi networks can shed light on intra-tumour heterogeneity, the evolution of resistance to therapies that target growth factors, and new types of cell therapy. Copyright © 2016 Elsevier Ltd. All rights reserved.

G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases.

PubMed

Wang, Xiaohong; Smalter, Aaron; Huan, Jun; Lushington, Gerald H

2009-01-01

Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and similarity search. With the fast accumulation of graph databases, similarity search in graph databases has emerged as an important research topic. Graph similarity search has applications in a wide range of domains including cheminformatics, bioinformatics, sensor network management, social network management, and XML documents, among others.Most of the current graph indexing methods focus on subgraph query processing, i.e. determining the set of database graphs that contains the query graph and hence do not directly support similarity search. In data mining and machine learning, various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models for supervised learning, graph kernel functions have (i) high computational complexity and (ii) non-trivial difficulty to be indexed in a graph database.Our objective is to bridge graph kernel function and similarity search in graph databases by proposing (i) a novel kernel-based similarity measurement and (ii) an efficient indexing structure for graph data management. Our method of similarity measurement builds upon local features extracted from each node and their neighboring nodes in graphs. A hash table is utilized to support efficient storage and fast search of the extracted local features. Using the hash table, a graph kernel function is defined to capture the intrinsic similarity of graphs and for fast similarity query processing. We have implemented our method, which we have named G-hash, and have demonstrated its utility on large chemical graph databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Most importantly, the new similarity measurement and the index structure is scalable to large database with smaller indexing size, faster indexing construction time, and faster query processing time as compared to state-of-the-art indexing methods such as C-tree, gIndex, and GraphGrep.

GraphReduce: Processing Large-Scale Graphs on Accelerator-Based Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sengupta, Dipanjan; Song, Shuaiwen; Agarwal, Kapil

2015-11-15

Recent work on real-world graph analytics has sought to leverage the massive amount of parallelism offered by GPU devices, but challenges remain due to the inherent irregularity of graph algorithms and limitations in GPU-resident memory for storing large graphs. We present GraphReduce, a highly efficient and scalable GPU-based framework that operates on graphs that exceed the device’s internal memory capacity. GraphReduce adopts a combination of edge- and vertex-centric implementations of the Gather-Apply-Scatter programming model and operates on multiple asynchronous GPU streams to fully exploit the high degrees of parallelism in GPUs with efficient graph data movement between the host andmore » device.« less

Why are some plant-pollinator networks more nested than others?

PubMed

Song, Chuliang; Rohr, Rudolf P; Saavedra, Serguei

2017-10-01

Empirical studies have found that the mutualistic interactions forming the structure of plant-pollinator networks are typically more nested than expected by chance alone. Additionally, theoretical studies have shown a positive association between the nested structure of mutualistic networks and community persistence. Yet, it has been shown that some plant-pollinator networks may be more nested than others, raising the interesting question of which factors are responsible for such enhanced nested structure. It has been argued that ordered network structures may increase the persistence of ecological communities under less predictable environments. This suggests that nested structures of plant-pollinator networks could be more advantageous under highly seasonal environments. While several studies have investigated the link between nestedness and various environmental variables, unfortunately, there has been no unified answer to validate these predictions. Here, we move from the problem of describing network structures to the problem of comparing network structures. We develop comparative statistics, and apply them to investigate the association between the nested structure of 59 plant-pollinator networks and the temperature seasonality present in their locations. We demonstrate that higher levels of nestedness are associated with a higher temperature seasonality. We show that the previous lack of agreement came from an extended practice of using standardized measures of nestedness that cannot be compared across different networks. Importantly, our observations complement theory showing that more nested network structures can increase the range of environmental conditions compatible with species coexistence in mutualistic systems, also known as structural stability. This increase in nestedness should be more advantageous and occur more often in locations subject to random environmental perturbations, which could be driven by highly changing or seasonal environments. This synthesis of theory and observations could prove relevant for a better understanding of the ecological processes driving the assembly and persistence of ecological communities. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Comparing Internet Probing Methodologies Through an Analysis of Large Dynamic Graphs

DTIC Science & Technology

2014-06-01

comparable Internet topologies in less time. We compare these by modeling union of traceroute outputs as graphs, and using standard graph theoretical...topologies in less time. We compare these by modeling union of traceroute outputs as graphs, and using standard graph theoretical measurements as well...We compare these by modeling union of traceroute outputs as graphs, and study the graphs by using vertex and edge count, average vertex degree

GraphBench

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sukumar, Sreenivas R.; Hong, Seokyong; Lee, Sangkeun

2016-06-01

GraphBench is a benchmark suite for graph pattern mining and graph analysis systems. The benchmark suite is a significant addition to conducting apples-apples comparison of graph analysis software (databases, in-memory tools, triple stores, etc.)

Canonic FFT flow graphs for real-valued even/odd symmetric inputs

NASA Astrophysics Data System (ADS)

Lao, Yingjie; Parhi, Keshab K.

2017-12-01

Canonic real-valued fast Fourier transform (RFFT) has been proposed to reduce the arithmetic complexity by eliminating redundancies. In a canonic N-point RFFT, the number of signal values at each stage is canonic with respect to the number of signal values, i.e., N. The major advantage of the canonic RFFTs is that these require the least number of butterfly operations and only real datapaths when mapped to architectures. In this paper, we consider the FFT computation whose inputs are not only real but also even/odd symmetric, which indeed lead to the well-known discrete cosine and sine transforms (DCTs and DSTs). Novel algorithms for generating the flow graphs of canonic RFFTs with even/odd symmetric inputs are proposed. It is shown that the proposed algorithms lead to canonic structures with N/2 +1 signal values at each stage for an N-point real even symmetric FFT (REFFT) or N/2 -1 signal values at each stage for an N-point RFFT real odd symmetric FFT (ROFFT). In order to remove butterfly operations, several twiddle factor transformations are proposed in this paper. We also discuss the design of canonic REFFT for any composite length. Performances of the canonic REFFT/ROFFT are also discussed. It is shown that the flow graph of canonic REFFT/ROFFT has less number of interconnections, less butterfly operations, and less twiddle factor operations, compared to prior works.

Loop series for discrete statistical models on graphs

NASA Astrophysics Data System (ADS)

Chertkov, Michael; Chernyak, Vladimir Y.

2006-06-01

In this paper we present the derivation details, logic, and motivation for the three loop calculus introduced in Chertkov and Chernyak (2006 Phys. Rev. E 73 065102(R)). Generating functions for each of the three interrelated discrete statistical models are expressed in terms of a finite series. The first term in the series corresponds to the Bethe-Peierls belief-propagation (BP) contribution; the other terms are labelled by loops on the factor graph. All loop contributions are simple rational functions of spin correlation functions calculated within the BP approach. We discuss two alternative derivations of the loop series. One approach implements a set of local auxiliary integrations over continuous fields with the BP contribution corresponding to an integrand saddle-point value. The integrals are replaced by sums in the complementary approach, briefly explained in Chertkov and Chernyak (2006 Phys. Rev. E 73 065102(R)). Local gauge symmetry transformations that clarify an important invariant feature of the BP solution are revealed in both approaches. The individual terms change under the gauge transformation while the partition function remains invariant. The requirement for all individual terms to be nonzero only for closed loops in the factor graph (as opposed to paths with loose ends) is equivalent to fixing the first term in the series to be exactly equal to the BP contribution. Further applications of the loop calculus to problems in statistical physics, computer and information sciences are discussed.

[Not Available].

PubMed

Yanashima, Ryoji; Kitagawa, Noriyuki; Matsubara, Yoshiya; Weatheritt, Robert; Oka, Kotaro; Kikuchi, Shinichi; Tomita, Masaru; Ishizaki, Shun

2009-01-01

The scale-free and small-world network models reflect the functional units of networks. However, when we investigated the network properties of a signaling pathway using these models, no significant differences were found between the original undirected graphs and the graphs in which inactive proteins were eliminated from the gene expression data. We analyzed signaling networks by focusing on those pathways that best reflected cellular function. Therefore, our analysis of pathways started from the ligands and progressed to transcription factors and cytoskeletal proteins. We employed the Python module to assess the target network. This involved comparing the original and restricted signaling cascades as a directed graph using microarray gene expression profiles of late onset Alzheimer's disease. The most commonly used method of shortest-path analysis neglects to consider the influences of alternative pathways that can affect the activation of transcription factors or cytoskeletal proteins. We therefore introduced included k-shortest paths and k-cycles in our network analysis using the Python modules, which allowed us to attain a reasonable computational time and identify k-shortest paths. This technique reflected results found in vivo and identified pathways not found when shortest path or degree analysis was applied. Our module enabled us to comprehensively analyse the characteristics of biomolecular networks and also enabled analysis of the effects of diseases considering the feedback loop and feedforward loop control structures as an alternative path.

Asymptote Misconception on Graphing Functions: Does Graphing Software Resolve It?

ERIC Educational Resources Information Center

Öçal, Mehmet Fatih

2017-01-01

Graphing function is an important issue in mathematics education due to its use in various areas of mathematics and its potential roles for students to enhance learning mathematics. The use of some graphing software assists students' learning during graphing functions. However, the display of graphs of functions that students sketched by hand may…

Generalized graph states based on Hadamard matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Shawn X.; Yu, Nengkun; Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1

2015-07-15

Graph states are widely used in quantum information theory, including entanglement theory, quantum error correction, and one-way quantum computing. Graph states have a nice structure related to a certain graph, which is given by either a stabilizer group or an encoding circuit, both can be directly given by the graph. To generalize graph states, whose stabilizer groups are abelian subgroups of the Pauli group, one approach taken is to study non-abelian stabilizers. In this work, we propose to generalize graph states based on the encoding circuit, which is completely determined by the graph and a Hadamard matrix. We study themore » entanglement structures of these generalized graph states and show that they are all maximally mixed locally. We also explore the relationship between the equivalence of Hadamard matrices and local equivalence of the corresponding generalized graph states. This leads to a natural generalization of the Pauli (X, Z) pairs, which characterizes the local symmetries of these generalized graph states. Our approach is also naturally generalized to construct graph quantum codes which are beyond stabilizer codes.« less

Graph processing platforms at scale: practices and experiences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, Seung-Hwan; Lee, Sangkeun; Brown, Tyler C

2015-01-01

Graph analysis unveils hidden associations of data in many phenomena and artifacts, such as road network, social networks, genomic information, and scientific collaboration. Unfortunately, a wide diversity in the characteristics of graphs and graph operations make it challenging to find a right combination of tools and implementation of algorithms to discover desired knowledge from the target data set. This study presents an extensive empirical study of three representative graph processing platforms: Pegasus, GraphX, and Urika. Each system represents a combination of options in data model, processing paradigm, and infrastructure. We benchmarked each platform using three popular graph operations, degree distribution,more » connected components, and PageRank over a variety of real-world graphs. Our experiments show that each graph processing platform shows different strength, depending the type of graph operations. While Urika performs the best in non-iterative operations like degree distribution, GraphX outputforms iterative operations like connected components and PageRank. In addition, we discuss challenges to optimize the performance of each platform over large scale real world graphs.« less

A fast algorithm for vertex-frequency representations of signals on graphs

PubMed Central

Jestrović, Iva; Coyle, James L.; Sejdić, Ervin

2016-01-01

The windowed Fourier transform (short time Fourier transform) and the S-transform are widely used signal processing tools for extracting frequency information from non-stationary signals. Previously, the windowed Fourier transform had been adopted for signals on graphs and has been shown to be very useful for extracting vertex-frequency information from graphs. However, high computational complexity makes these algorithms impractical. We sought to develop a fast windowed graph Fourier transform and a fast graph S-transform requiring significantly shorter computation time. The proposed schemes have been tested with synthetic test graph signals and real graph signals derived from electroencephalography recordings made during swallowing. The results showed that the proposed schemes provide significantly lower computation time in comparison with the standard windowed graph Fourier transform and the fast graph S-transform. Also, the results showed that noise has no effect on the results of the algorithm for the fast windowed graph Fourier transform or on the graph S-transform. Finally, we showed that graphs can be reconstructed from the vertex-frequency representations obtained with the proposed algorithms. PMID:28479645

Graph 500 on OpenSHMEM: Using a Practical Survey of Past Work to Motivate Novel Algorithmic Developments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grossman, Max; Pritchard Jr., Howard Porter; Budimlic, Zoran

2016-12-22

Graph500 [14] is an effort to offer a standardized benchmark across large-scale distributed platforms which captures the behavior of common communicationbound graph algorithms. Graph500 differs from other large-scale benchmarking efforts (such as HPL [6] or HPGMG [7]) primarily in the irregularity of its computation and data access patterns. The core computational kernel of Graph500 is a breadth-first search (BFS) implemented on an undirected graph. The output of Graph500 is a spanning tree of the input graph, usually represented by a predecessor mapping for every node in the graph. The Graph500 benchmark defines several pre-defined input sizes for implementers to testmore » against. This report summarizes investigation into implementing the Graph500 benchmark on OpenSHMEM, and focuses on first building a strong and practical understanding of the strengths and limitations of past work before proposing and developing novel extensions.« less

Graphing trillions of triangles.

PubMed

Burkhardt, Paul

2017-07-01

The increasing size of Big Data is often heralded but how data are transformed and represented is also profoundly important to knowledge discovery, and this is exemplified in Big Graph analytics. Much attention has been placed on the scale of the input graph but the product of a graph algorithm can be many times larger than the input. This is true for many graph problems, such as listing all triangles in a graph. Enabling scalable graph exploration for Big Graphs requires new approaches to algorithms, architectures, and visual analytics. A brief tutorial is given to aid the argument for thoughtful representation of data in the context of graph analysis. Then a new algebraic method to reduce the arithmetic operations in counting and listing triangles in graphs is introduced. Additionally, a scalable triangle listing algorithm in the MapReduce model will be presented followed by a description of the experiments with that algorithm that led to the current largest and fastest triangle listing benchmarks to date. Finally, a method for identifying triangles in new visual graph exploration technologies is proposed.

Important Risk Factors of Mortality Among Children Aged 1-59 Months in Rural Areas of Shahroud, Iran: A Community-based Nested Case-Control Study.

PubMed

Chaman, Reza; Alami, Ali; Emamian, Mohammad Hassan; Naieni, Kourosh Holakouie; Mirmohammadkhani, Majid; Ahmadnezhad, Elham; Entezarmahdi, Rasool; Shati, Mohsen; Shariati, Mohammad

2012-12-01

The aim of the study was to evaluate potential risk factors of children mortality between 1-59 months of age. This nested case-control study was conducted among children born from June 1999 to March 2009 in rural areas of Shahroud, located in the central region of Iran using health care visit reports and follow-up data available in household health records. MORTALITY WAS SIGNIFICANTLY ASSOCIATED WITH BREASTFEEDING DURATION (OR: 0.87, 95% CI: 0.81-0.93), total health care visits (OR: 0.90, 95% CI: 0.83-0.98) and low birth weight (LBW) (OR: 7.38, 95% CI: 1.37-39.67). In our study, a longer breastfeeding period and more frequent health care visits were two important protective factors, while LBW was an important risk factor for 1-59 month child mortality. It seems, that complex and multiple factors may be involved in mortality of under 5-year-old children, so combined efforts would be necessary to improve child health indicators.

Multiple graph regularized protein domain ranking.

PubMed

Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

2012-11-19

Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

Evolutionary graph theory: breaking the symmetry between interaction and replacement

PubMed Central

Ohtsuki, Hisashi; Pacheco, Jorge M.; Nowak, Martin A.

2008-01-01

We study evolutionary dynamics in a population whose structure is given by two graphs: the interaction graph determines who plays with whom in an evolutionary game; the replacement graph specifies the geometry of evolutionary competition and updating. First, we calculate the fixation probabilities of frequency dependent selection between two strategies or phenotypes. We consider three different update mechanisms: birth-death, death-birth and imitation. Then, as a particular example, we explore the evolution of cooperation. Suppose the interaction graph is a regular graph of degree h, the replacement graph is a regular graph of degree g and the overlap between the two graphs is a regular graph of degree l. We show that cooperation is favored by natural selection if b/c > hg/l. Here, b and c denote the benefit and cost of the altruistic act. This result holds for death-birth updating, weak selection and large population size. Note that the optimum population structure for cooperators is given by maximum overlap between the interaction and the replacement graph (g = h = l), which means that the two graphs are identical. We also prove that a modified replicator equation can describe how the expected values of the frequencies of an arbitrary number of strategies change on replacement and interaction graphs: the two graphs induce a transformation of the payoff matrix. PMID:17350049

Multiple graph regularized protein domain ranking

PubMed Central

2012-01-01

Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. PMID:23157331

Recalibration of the GRLWEAP LRFD resistance factor for Oregon DOT.

DOT National Transportation Integrated Search

2011-02-01

The Bridge Section of the Oregon Department of Transportation (ODOT) is responsible for the design of all bridge structures and routinely uses GRLWEAP for controlling pile driving stresses and establishing capacity from the bearing graph. The LRFD re...

Reports on Cancer - Cancer Statistics

Cancer.gov

Interactive tools for access to statistics for a cancer site by gender, race, ethnicity, calendar year, age, state, county, stage, and histology. Statistics include incidence, mortality, prevalence, cost, risk factors, behaviors, tobacco use, and policies and are presented as graphs, tables, or maps.

Alternative Fuels Data Center: Maps and Data

Science.gov Websites

fleet type from 1992-2014 Last update August 2016 View Graph Graph Download Data Generated_thumb20160830 Trend of S&FP AFV acquisitions by fuel type from 1992-2015 Last update August 2016 View Graph Graph transactions from 1997-2014 Last update August 2016 View Graph Graph Download Data Biofuelsatlas BioFuels Atlas

Do honeybees, Apis mellifera scutellata, regulate humidity in their nest?

NASA Astrophysics Data System (ADS)

Human, Hannelie; Nicolson, Sue W.; Dietemann, Vincent

2006-08-01

Honeybees are highly efficient at regulating the biophysical parameters of their hive according to colony needs. Thermoregulation has been the most extensively studied aspect of nest homeostasis. In contrast, little is known about how humidity is regulated in beehives, if at all. Although high humidity is necessary for brood development, regulation of this parameter by honeybee workers has not yet been demonstrated. In the past, humidity was measured too crudely for a regulation mechanism to be identified. We reassess this issue, using miniaturised data loggers that allow humidity measurements in natural situations and at several places in the nest. We present evidence that workers influence humidity in the hive. However, there are constraints on potential regulation mechanisms because humidity optima may vary in different locations of the nest. Humidity could also depend on variable external factors, such as water availability, which further impair the regulation. Moreover, there are trade-offs with the regulation of temperature and respiratory gas exchanges that can disrupt the establishment of optimal humidity levels. As a result, we argue that workers can only adjust humidity within sub-optimal limits.

Use of implanted satellite transmitters to locate Spectacled Eiders at-sea

USGS Publications Warehouse

Petersen, Margaret R.; Douglas, David C.; Mulcahy, Daniel M.

1995-01-01

Population estimates of Spectacled Eiders (Somateria fischeri) on the Yukon-Kuskokwim Delta (YKD), Alaska, suggest that by 1992 the number of birds on this major nesting area had declined to 1,721 pairs, 4% of that estimated in the 1970s (Stehn st al 1993). Consequently, Spectacled Eiders were listed as threatened under the Endangered Species Act. As nesting habitats for this species are believed to have changed little over the past 100 years, hypotheses concerning the cause of this decline include factors away from nesting areas. The non-nesting distribution of this eider is unknown, but birds are believed to molt and winter in the Bering and Chukchi seas (Dau and Kistchinski 1977). Systematic aerial surveys to locate areas where birds concentrate are expensive because of the vast area to be surveyed and dangerous because of restricted daylight and extreme weather conditions. Surveys from ships along the ice margin in the Bering Sea failed to locate concentrations of birds (Irving et al 1968, Everett et al 1989). We initiated a study to determine if at-sea areas used by Spectacled Eiders could be identified using satellite telemetry.

Bayesian model comparison and parameter inference in systems biology using nested sampling.

PubMed

Pullen, Nick; Morris, Richard J

2014-01-01

Inferring parameters for models of biological processes is a current challenge in systems biology, as is the related problem of comparing competing models that explain the data. In this work we apply Skilling's nested sampling to address both of these problems. Nested sampling is a Bayesian method for exploring parameter space that transforms a multi-dimensional integral to a 1D integration over likelihood space. This approach focuses on the computation of the marginal likelihood or evidence. The ratio of evidences of different models leads to the Bayes factor, which can be used for model comparison. We demonstrate how nested sampling can be used to reverse-engineer a system's behaviour whilst accounting for the uncertainty in the results. The effect of missing initial conditions of the variables as well as unknown parameters is investigated. We show how the evidence and the model ranking can change as a function of the available data. Furthermore, the addition of data from extra variables of the system can deliver more information for model comparison than increasing the data from one variable, thus providing a basis for experimental design.

Effects of human disturbance on waterbird nesting and reproductive success at restoration pond SF2, south San Francisco Bay, California

USGS Publications Warehouse

Ackerman, Joshua T.; Herzog, Mark P.; Hartman, Christopher A.

2014-01-01

To determine the effects that human disturbance may have on waterbirds nesting on these newly constructed islands in Pond SF2, we assessed the potential effects of human disturbance features (specifically, access trails, viewing platforms, internal pond berms, exterior levees, and highways) on breeding waterbirds in 2011 and 2012. We found no clear pattern of potential disturbance features on a group of reproductive factors, including nest survival, nest initiation date, and clutch size. Because all the islands were constructed greater than 90 meters from the nearest disturbance feature, Pond SF2 alone did not provide adequate variation in the distance of disturbance features to detect potential detrimental effects for islands closer to disturbance features in other areas of the SBSP Restoration Project. If there is a need for SBSP Restoration Project Management Team to understand how close islands can be built to disturbance features in the future, we suggest a more comprehensive study that includes multiple ponds, other than SF2, with islands at varying distances to disturbance features.

Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

PubMed

Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

2016-08-01

Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages.

GraphReduce: Large-Scale Graph Analytics on Accelerator-Based HPC Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sengupta, Dipanjan; Agarwal, Kapil; Song, Shuaiwen

2015-09-30

Recent work on real-world graph analytics has sought to leverage the massive amount of parallelism offered by GPU devices, but challenges remain due to the inherent irregularity of graph algorithms and limitations in GPU-resident memory for storing large graphs. We present GraphReduce, a highly efficient and scalable GPU-based framework that operates on graphs that exceed the device’s internal memory capacity. GraphReduce adopts a combination of both edge- and vertex-centric implementations of the Gather-Apply-Scatter programming model and operates on multiple asynchronous GPU streams to fully exploit the high degrees of parallelism in GPUs with efficient graph data movement between the hostmore » and the device.« less

SING: Subgraph search In Non-homogeneous Graphs

PubMed Central

2010-01-01

Background Finding the subgraphs of a graph database that are isomorphic to a given query graph has practical applications in several fields, from cheminformatics to image understanding. Since subgraph isomorphism is a computationally hard problem, indexing techniques have been intensively exploited to speed up the process. Such systems filter out those graphs which cannot contain the query, and apply a subgraph isomorphism algorithm to each residual candidate graph. The applicability of such systems is limited to databases of small graphs, because their filtering power degrades on large graphs. Results In this paper, SING (Subgraph search In Non-homogeneous Graphs), a novel indexing system able to cope with large graphs, is presented. The method uses the notion of feature, which can be a small subgraph, subtree or path. Each graph in the database is annotated with the set of all its features. The key point is to make use of feature locality information. This idea is used to both improve the filtering performance and speed up the subgraph isomorphism task. Conclusions Extensive tests on chemical compounds, biological networks and synthetic graphs show that the proposed system outperforms the most popular systems in query time over databases of medium and large graphs. Other specific tests show that the proposed system is effective for single large graphs. PMID:20170516

Do sugar-sweetened beverages cause adverse health outcomes in adults? A systematic review protocol

PubMed Central

2014-01-01

Background Chronic diseases, such as cardiovascular disease and type 2 diabetes, impose significant burden to public health. Most chronic diseases are associated with underlying preventable risk factors, such as elevated blood pressure, blood glucose, and lipids, physical inactivity, excessive sedentary behaviours, overweight and obesity, and tobacco usage. Sugar-sweetened beverages are known to be significant sources of additional caloric intake, and given recent attention to their contribution in the development of chronic diseases, a systematic review is warranted. We will assess whether the consumption of sugar-sweetened beverages in adults is associated with adverse health outcomes and what the potential moderating factors are. Methods/Design Of interest are studies addressing sugar-sweetened beverage consumption, taking a broad perspective. Both direct consumption studies as well as those evaluating interventions that influence consumption (e.g. school policy, educational) will be relevant. Non-specific or multi-faceted behavioural, educational, or policy interventions may also be included subject to the level of evidence that exists for the other interventions/exposures. Comparisons of interest and endpoints of interest are pre-specified. We will include randomized controlled trials, controlled clinical trials, interrupted time series studies, controlled before-after studies, prospective and retrospective comparative cohort studies, case-control studies, and nested case-control designs. The MEDLINE®, Embase, The Cochrane Library, CINAHL, ERIC, and PsycINFO® databases and grey literature sources will be searched. The processes for selecting studies, abstracting data, and resolving conflicts are described. We will assess risk of bias using design-specific tools. To determine sets of confounding variables that should be adjusted for, we have developed causal directed acyclic graphs and will use those to inform our risk of bias assessments. Meta-analysis will be conducted where appropriate; parameters for exploring statistical heterogeneity and effect modifiers are pre-specified. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach will be used for determining the quality of evidence for outcomes. Systematic review registration PROSPERO CRD42014009638 PMID:25248499

Do sugar-sweetened beverages cause adverse health outcomes in adults? A systematic review protocol.

PubMed

Hamel, Candyce; Stevens, Adrienne; Singh, Kavita; Ansari, Mohammed T; Myers, Esther; Ziegler, Paula; Hutton, Brian; Sharma, Arya; Bjerre, Lise M; Fenton, Shannon; Lau, David C W; O'Hara, Kathryn; Reid, Robert; Salewski, Erinn; Shrier, Ian; Willows, Noreen; Tremblay, Mark; Moher, David

2014-09-23

Chronic diseases, such as cardiovascular disease and type 2 diabetes, impose significant burden to public health. Most chronic diseases are associated with underlying preventable risk factors, such as elevated blood pressure, blood glucose, and lipids, physical inactivity, excessive sedentary behaviours, overweight and obesity, and tobacco usage. Sugar-sweetened beverages are known to be significant sources of additional caloric intake, and given recent attention to their contribution in the development of chronic diseases, a systematic review is warranted. We will assess whether the consumption of sugar-sweetened beverages in adults is associated with adverse health outcomes and what the potential moderating factors are. Of interest are studies addressing sugar-sweetened beverage consumption, taking a broad perspective. Both direct consumption studies as well as those evaluating interventions that influence consumption (e.g. school policy, educational) will be relevant. Non-specific or multi-faceted behavioural, educational, or policy interventions may also be included subject to the level of evidence that exists for the other interventions/exposures. Comparisons of interest and endpoints of interest are pre-specified. We will include randomized controlled trials, controlled clinical trials, interrupted time series studies, controlled before-after studies, prospective and retrospective comparative cohort studies, case-control studies, and nested case-control designs. The MEDLINE, Embase, The Cochrane Library, CINAHL, ERIC, and PsycINFO databases and grey literature sources will be searched. The processes for selecting studies, abstracting data, and resolving conflicts are described. We will assess risk of bias using design-specific tools. To determine sets of confounding variables that should be adjusted for, we have developed causal directed acyclic graphs and will use those to inform our risk of bias assessments. Meta-analysis will be conducted where appropriate; parameters for exploring statistical heterogeneity and effect modifiers are pre-specified. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach will be used for determining the quality of evidence for outcomes. PROSPERO CRD42014009638.

GrouseFlocks: steerable exploration of graph hierarchy space.

PubMed

Archambault, Daniel; Munzner, Tamara; Auber, David

2008-01-01

Several previous systems allow users to interactively explore a large input graph through cuts of a superimposed hierarchy. This hierarchy is often created using clustering algorithms or topological features present in the graph. However, many graphs have domain-specific attributes associated with the nodes and edges, which could be used to create many possible hierarchies providing unique views of the input graph. GrouseFlocks is a system for the exploration of this graph hierarchy space. By allowing users to see several different possible hierarchies on the same graph, the system helps users investigate graph hierarchy space instead of a single fixed hierarchy. GrouseFlocks provides a simple set of operations so that users can create and modify their graph hierarchies based on selections. These selections can be made manually or based on patterns in the attribute data provided with the graph. It provides feedback to the user within seconds, allowing interactive exploration of this space.

Spectral partitioning in equitable graphs.

PubMed

Barucca, Paolo

2017-06-01

Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.

Spectral partitioning in equitable graphs

NASA Astrophysics Data System (ADS)

Barucca, Paolo

2017-06-01

Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.

Well-Covered Graphs: A Survey

DTIC Science & Technology

1991-01-01

critical G’s/# G’s -) 0 as IV(G)I -- oo? References [B1] C. Berge, Regularizable graphs, Ann. Discrete Math ., 3, 1978, 11-19. [B2] _ _, Some common...Springer-Verlag, Berlin, 1980, 108-123. [B3] _ _, Some common properties for regularizable graphs, edge-critical graphs, and B-graphs, Ann. Discrete Math ., 12...graphs - an extension of the K6nig-Egervgiry theorem, Discrete Math ., 27, 1979, 23-33. [ER] M.N Ellingham and G.F. Royle, Well-covered cubic graphs

Study of Chromatic parameters of Line, Total, Middle graphs and Graph operators of Bipartite graph

NASA Astrophysics Data System (ADS)

Nagarathinam, R.; Parvathi, N.

2018-04-01

Chromatic parameters have been explored on the basis of graph coloring process in which a couple of adjacent nodes receives different colors. But the Grundy and b-coloring executes maximum colors under certain restrictions. In this paper, Chromatic, b-chromatic and Grundy number of some graph operators of bipartite graph has been investigat

GBS 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

2010-09-30

The Umbra gbs (Graph-Based Search) library provides implementations of graph-based search/planning algorithms that can be applied to legacy graph data structures. Unlike some other graph algorithm libraries, this one does not require your graph class to inherit from a specific base class. Implementations of Dijkstra's Algorithm and A-Star search are included and can be used with graphs that are lazily-constructed.

Information visualisation based on graph models

NASA Astrophysics Data System (ADS)

Kasyanov, V. N.; Kasyanova, E. V.

2013-05-01

Information visualisation is a key component of support tools for many applications in science and engineering. A graph is an abstract structure that is widely used to model information for its visualisation. In this paper, we consider practical and general graph formalism called hierarchical graphs and present the Higres and Visual Graph systems aimed at supporting information visualisation on the base of hierarchical graph models.

Polysemy in the Domain-Specific Pedagogical Use of Graphs in Science Textbooks: The Case of an Electrocardiogram

ERIC Educational Resources Information Center

van Eijck, Michiel; Goedhart, Martin J.; Ellermeijer, Ton

2011-01-01

Polysemy in graph-related practices is the phenomenon that a single graph can sustain different meanings assigned to it. Considerable research has been done on polysemy in graph-related practices in school science in which graphs are rather used as scientific tools. However, graphs in science textbooks are also used rather pedagogically to…

Lamplighter groups, de Brujin graphs, spider-web graphs and their spectra

NASA Astrophysics Data System (ADS)

Grigorchuk, R.; Leemann, P.-H.; Nagnibeda, T.

2016-05-01

We study the infinite family of spider-web graphs \\{{{ S }}k,N,M\\}, k≥slant 2, N≥slant 0 and M≥slant 1, initiated in the 50s in the context of network theory. It was later shown in physical literature that these graphs have remarkable percolation and spectral properties. We provide a mathematical explanation of these properties by putting the spider-web graphs in the context of group theory and algebraic graph theory. Namely, we realize them as tensor products of the well-known de Bruijn graphs \\{{{ B }}k,N\\} with cyclic graphs \\{{C}M\\} and show that these graphs are described by the action of the lamplighter group {{ L }}k={Z}/k{Z}\\wr {Z} on the infinite binary tree. Our main result is the identification of the infinite limit of \\{{{ S }}k,N,M\\}, as N,M\\to ∞ , with the Cayley graph of the lamplighter group {{ L }}k which, in turn, is one of the famous Diestel-Leader graphs {{DL}}k,k. As an application we compute the spectra of all spider-web graphs and show their convergence to the discrete spectral distribution associated with the Laplacian on the lamplighter group.

Visibility graph analysis of very short-term heart rate variability during sleep

NASA Astrophysics Data System (ADS)

Hou, F. Z.; Li, F. W.; Wang, J.; Yan, F. R.

2016-09-01

Based on a visibility-graph algorithm, complex networks were constructed from very short-term heart rate variability (HRV) during different sleep stages. Network measurements progressively changed from rapid eye movement (REM) sleep to light sleep and then deep sleep, exhibiting promising ability for sleep assessment. Abnormal activation of the cardiovascular controls with enhanced 'small-world' couplings and altered fractal organization during REM sleep indicates that REM could be a potential risk factor for adverse cardiovascular event, especially in males, older individuals, and people who are overweight. Additionally, an apparent influence of gender, aging, and obesity on sleep was demonstrated in healthy adults, which may be helpful for establishing expected sleep-HRV patterns in different populations.

The effect of iconicity of visual displays on statistical reasoning: evidence in favor of the null hypothesis.

PubMed

Sirota, Miroslav; Kostovičová, Lenka; Juanchich, Marie

2014-08-01

Knowing which properties of visual displays facilitate statistical reasoning bears practical and theoretical implications. Therefore, we studied the effect of one property of visual diplays - iconicity (i.e., the resemblance of a visual sign to its referent) - on Bayesian reasoning. Two main accounts of statistical reasoning predict different effect of iconicity on Bayesian reasoning. The ecological-rationality account predicts a positive iconicity effect, because more highly iconic signs resemble more individuated objects, which tap better into an evolutionary-designed frequency-coding mechanism that, in turn, facilitates Bayesian reasoning. The nested-sets account predicts a null iconicity effect, because iconicity does not affect the salience of a nested-sets structure-the factor facilitating Bayesian reasoning processed by a general reasoning mechanism. In two well-powered experiments (N = 577), we found no support for a positive iconicity effect across different iconicity levels that were manipulated in different visual displays (meta-analytical overall effect: log OR = -0.13, 95% CI [-0.53, 0.28]). A Bayes factor analysis provided strong evidence in favor of the null hypothesis-the null iconicity effect. Thus, these findings corroborate the nested-sets rather than the ecological-rationality account of statistical reasoning.

New methods for analyzing semantic graph based assessments in science education

NASA Astrophysics Data System (ADS)

Vikaros, Lance Steven

This research investigated how the scoring of semantic graphs (known by many as concept maps) could be improved and automated in order to address issues of inter-rater reliability and scalability. As part of the NSF funded SENSE-IT project to introduce secondary school science students to sensor networks (NSF Grant No. 0833440), semantic graphs illustrating how temperature change affects water ecology were collected from 221 students across 16 schools. The graphing task did not constrain students' use of terms, as is often done with semantic graph based assessment due to coding and scoring concerns. The graphing software used provided real-time feedback to help students learn how to construct graphs, stay on topic and effectively communicate ideas. The collected graphs were scored by human raters using assessment methods expected to boost reliability, which included adaptations of traditional holistic and propositional scoring methods, use of expert raters, topical rubrics, and criterion graphs. High levels of inter-rater reliability were achieved, demonstrating that vocabulary constraints may not be necessary after all. To investigate a new approach to automating the scoring of graphs, thirty-two different graph features characterizing graphs' structure, semantics, configuration and process of construction were then used to predict human raters' scoring of graphs in order to identify feature patterns correlated to raters' evaluations of graphs' topical accuracy and complexity. Results led to the development of a regression model able to predict raters' scoring with 77% accuracy, with 46% accuracy expected when used to score new sets of graphs, as estimated via cross-validation tests. Although such performance is comparable to other graph and essay based scoring systems, cross-context testing of the model and methods used to develop it would be needed before it could be recommended for widespread use. Still, the findings suggest techniques for improving the reliability and scalability of semantic graph based assessments without requiring constraint of how ideas are expressed.

Biometric Subject Verification Based on Electrocardiographic Signals

NASA Technical Reports Server (NTRS)

Dusan, Sorin V. (Inventor); Jorgensen, Charles C. (Inventor)

2014-01-01

A method of authenticating or declining to authenticate an asserted identity of a candidate-person. In an enrollment phase, a reference PQRST heart action graph is provided or constructed from information obtained from a plurality of graphs that resemble each other for a known reference person, using a first graph comparison metric. In a verification phase, a candidate-person asserts his/her identity and presents a plurality of his/her heart cycle graphs. If a sufficient number of the candidate-person's measured graphs resemble each other, a representative composite graph is constructed from the candidate-person's graphs and is compared with a composite reference graph, for the person whose identity is asserted, using a second graph comparison metric. When the second metric value lies in a selected range, the candidate-person's assertion of identity is accepted.

EvoGraph: On-The-Fly Efficient Mining of Evolving Graphs on GPU

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sengupta, Dipanjan; Song, Shuaiwen

With the prevalence of the World Wide Web and social networks, there has been a growing interest in high performance analytics for constantly-evolving dynamic graphs. Modern GPUs provide massive AQ1 amount of parallelism for efficient graph processing, but the challenges remain due to their lack of support for the near real-time streaming nature of dynamic graphs. Specifically, due to the current high volume and velocity of graph data combined with the complexity of user queries, traditional processing methods by first storing the updates and then repeatedly running static graph analytics on a sequence of versions or snapshots are deemed undesirablemore » and computational infeasible on GPU. We present EvoGraph, a highly efficient and scalable GPU- based dynamic graph analytics framework.« less

Genome alignment with graph data structures: a comparison

PubMed Central

2014-01-01

Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

Efficient dynamic graph construction for inductive semi-supervised learning.

PubMed

Dornaika, F; Dahbi, R; Bosaghzadeh, A; Ruichek, Y

2017-10-01

Most of graph construction techniques assume a transductive setting in which the whole data collection is available at construction time. Addressing graph construction for inductive setting, in which data are coming sequentially, has received much less attention. For inductive settings, constructing the graph from scratch can be very time consuming. This paper introduces a generic framework that is able to make any graph construction method incremental. This framework yields an efficient and dynamic graph construction method that adds new samples (labeled or unlabeled) to a previously constructed graph. As a case study, we use the recently proposed Two Phase Weighted Regularized Least Square (TPWRLS) graph construction method. The paper has two main contributions. First, we use the TPWRLS coding scheme to represent new sample(s) with respect to an existing database. The representative coefficients are then used to update the graph affinity matrix. The proposed method not only appends the new samples to the graph but also updates the whole graph structure by discovering which nodes are affected by the introduction of new samples and by updating their edge weights. The second contribution of the article is the application of the proposed framework to the problem of graph-based label propagation using multiple observations for vision-based recognition tasks. Experiments on several image databases show that, without any significant loss in the accuracy of the final classification, the proposed dynamic graph construction is more efficient than the batch graph construction. Copyright © 2017 Elsevier Ltd. All rights reserved.

JavaGenes: Evolving Graphs with Crossover

NASA Technical Reports Server (NTRS)

Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

2000-01-01

Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.