Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations.

PubMed

Liu, Gangbiao; Zou, Yangyun; Cheng, Qiqun; Zeng, Yanwu; Gu, Xun; Su, Zhixi

2014-04-01

The age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint differences, genes in different functional categories might show dissimilar retention patterns after duplication. It is known that genes in some functional categories are highly duplicated in the early stage of vertebrate evolution. However, the correlations of the age distribution pattern of gene duplication between the different functional categories are still unknown. To investigate this issue, we developed a robust pipeline to date the gene duplication events in the human genome. We successfully estimated about three-quarters of the duplication events within the human genome, along with the age distribution pattern in each Gene Ontology (GO) slim category. We found that some GO slim categories show different distribution patterns when compared to the whole genome. Further hierarchical clustering of the GO slim functional categories enabled grouping into two main clusters. We found that human genes located in the duplicated copy number variant regions, whose duplicate genes have not been fixed in the human population, were mainly enriched in the groups with a high proportion of recently duplicated genes. Moreover, we used a phylogenetic tree-based method to date the age of duplications in three signaling-related gene superfamilies: transcription factors, protein kinases and G-protein coupled receptors. These superfamilies were expressed in different subcellular localizations. They showed a similar age distribution as the signaling-related GO slim categories. We also compared the differences between the age distributions of gene duplications in multiple subcellular localizations. We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome.

Chromosome inversions and ecological plasticity in the main African malaria mosquitoes

PubMed Central

Ayala, Diego; Acevedo, Pelayo; Pombi, Marco; Dia, Ibrahima; Boccolini, Daniela; Costantini, Carlo; Simard, Frédéric; Fontenille, Didier

2017-01-01

Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes. PMID:28071788

Small-scale topography modulates elevational α-, β- and γ-diversity of Andean leaf beetles.

PubMed

Thormann, Birthe; Ahrens, Dirk; Espinosa, Carlos Iván; Armijos, Diego Marín; Wagner, Thomas; Wägele, Johann W; Peters, Marcell K

2018-05-01

Elevational diversity gradients are typically studied without considering the complex small-scale topography of large mountains, which generates habitats of strongly different environmental conditions within the same elevational zones. Here we analyzed the importance of small-scale topography for elevational diversity patterns of hyperdiverse tropical leaf beetles (Coleoptera: Chrysomelidae). We compared patterns of elevational diversity and species composition of beetles in two types of forests (on mountain ridges and in valleys) and analyzed whether differences in the rate of species turnover among forest habitats lead to shifts in patterns of elevational diversity when scaling up from the local study site to the elevational belt level. We sampled beetle assemblages at 36 sites in the Podocarpus National Park, Ecuador, which were equally distributed over two forest habitats and three elevational levels. DNA barcoding and Poisson tree processes modelling were used to delimitate putative species. On average, local leaf beetle diversity showed a clear hump-shaped pattern. However, only diversity in forests on mountain ridges peaked at mid-elevation, while beetle diversity in valleys was similarly high at low- and mid-elevation and only declined at highest elevations. A higher turnover of species assemblages at lower than at mid-elevations caused a shift from a hump-shaped diversity pattern found at the local level to a low-elevation plateau pattern (with similar species numbers at low and mid-elevation) at the elevational belt level. Our study reveals an important role of small-scale topography and spatial scale for the inference on gradients of elevational species diversity.

Celestial polarization patterns during twilight.

PubMed

Cronin, Thomas W; Warrant, Eric J; Greiner, Birgit

2006-08-01

Scattering of sunlight produces patterns of partially linearly polarized light in the sky throughout the day, and similar patterns appear at night when the Moon is bright. We studied celestial polarization patterns during the period of twilight, when the Sun is below the horizon, determining the degree and orientation of the polarized-light field and its changes before sunrise and after sunset. During twilight, celestial polarized light occurs in a wide band stretching perpendicular to the location of the hidden Sun and reaching typical degrees of polarization near 80% at wavelengths >600 nm. In the tropics, this pattern appears approximately 1 h before local sunrise or disappears approximately 1 h after local sunset (within 10 min. after the onset of astronomical twilight at dawn, or before its end at dusk) and extends with little change through the entire twilight period.

Spatial and temporal repeatability in parasite community structure of tropical fish hosts.

PubMed

Vidal-Martínez, V M; Poulin, R

2003-10-01

An assessment is made of the repeatability of parasite community structure in space for a marine fish, and in space and time for a freshwater fish from south-eastern Mexico. The marine fish species was the red grouper, Epinephelus morio (collected from 9 localities), and the freshwater species was the cichlid, Cichlasoma urophthalmus (collected from 6 localities: including monthly at 2 localities for 1 year, and bimonthly at 1 locality in 1990 and 1999). Pairwise interspecific associations and analyses of nested patterns in the distributions of parasite species among hosts were used in both fish species, with comparisons over time made only with the cichlid. Positive interspecific associations, and nested patterns were noted in some localities for both fish species, and/or at some sampling times for the cichlid fish. However, non-random patterns in the structure of parasite communities in these 2 host species only were observed sporadically. When present, nestedness in both fish species was apparently linked with a positive association between total infection intensities and fish size. Additionally, adjacent localities were more likely to display similar parasite community structure than distant ones. This preliminary result suggests that distance between localities is an important determinant of predictability in parasite community structure.

Visual identification and similarity measures used for on-line motion planning of autonomous robots in unknown environments

NASA Astrophysics Data System (ADS)

Martínez, Fredy; Martínez, Fernando; Jacinto, Edwar

2017-02-01

In this paper we propose an on-line motion planning strategy for autonomous robots in dynamic and locally observable environments. In this approach, we first visually identify geometric shapes in the environment by filtering images. Then, an ART-2 network is used to establish the similarity between patterns. The proposed algorithm allows that a robot establish its relative location in the environment, and define its navigation path based on images of the environment and its similarity to reference images. This is an efficient and minimalist method that uses the similarity of landmark view patterns to navigate to the desired destination. Laboratory tests on real prototypes demonstrate the performance of the algorithm.

Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

NASA Astrophysics Data System (ADS)

Hedayati, R.; Mirzaali, M. J.; Vergani, L.; Zadpoor, A. A.

2018-03-01

Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of "action-at-a-distance" metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular) materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson's ratios as a way of making "action-at-a-distance" metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable) robotics and exosuits.

Water Quality and Herbivory Interactively Drive Coral-Reef Recovery Patterns in American Samoa

PubMed Central

Houk, Peter; Musburger, Craig; Wiles, Phil

2010-01-01

Background Compared with a wealth of information regarding coral-reef recovery patterns following major disturbances, less insight exists to explain the cause(s) of spatial variation in the recovery process. Methodology/Principal Findings This study quantifies the influence of herbivory and water quality upon coral reef assemblages through space and time in Tutuila, American Samoa, a Pacific high island. Widespread declines in dominant corals (Acropora and Montipora) resulted from cyclone Heta at the end of 2003, shortly after the study began. Four sites that initially had similar coral reef assemblages but differential temporal dynamics four years following the disturbance event were classified by standardized measures of ‘recovery status’, defined by rates of change in ecological measures that are known to be sensitive to localized stressors. Status was best predicted, interactively, by water quality and herbivory. Expanding upon temporal trends, this study examined if similar dependencies existed through space; building multiple regression models to identify linkages between similar status measures and local stressors for 17 localities around Tutuila. The results highlighted consistent, interactive interdependencies for coral reef assemblages residing upon two unique geological reef types. Finally, the predictive regression models produced at the island scale were graphically interpreted with respect to hypothesized site-specific recovery thresholds. Conclusions/Significance Cumulatively, our study purports that moving away from describing relatively well-known patterns behind recovery, and focusing upon understanding causes, improves our foundation to predict future ecological dynamics, and thus improves coral reef management. PMID:21085715

Water quality and herbivory interactively drive coral-reef recovery patterns in American Samoa.

PubMed

Houk, Peter; Musburger, Craig; Wiles, Phil

2010-11-10

Compared with a wealth of information regarding coral-reef recovery patterns following major disturbances, less insight exists to explain the cause(s) of spatial variation in the recovery process. This study quantifies the influence of herbivory and water quality upon coral reef assemblages through space and time in Tutuila, American Samoa, a Pacific high island. Widespread declines in dominant corals (Acropora and Montipora) resulted from cyclone Heta at the end of 2003, shortly after the study began. Four sites that initially had similar coral reef assemblages but differential temporal dynamics four years following the disturbance event were classified by standardized measures of 'recovery status', defined by rates of change in ecological measures that are known to be sensitive to localized stressors. Status was best predicted, interactively, by water quality and herbivory. Expanding upon temporal trends, this study examined if similar dependencies existed through space; building multiple regression models to identify linkages between similar status measures and local stressors for 17 localities around Tutuila. The results highlighted consistent, interactive interdependencies for coral reef assemblages residing upon two unique geological reef types. Finally, the predictive regression models produced at the island scale were graphically interpreted with respect to hypothesized site-specific recovery thresholds. Cumulatively, our study purports that moving away from describing relatively well-known patterns behind recovery, and focusing upon understanding causes, improves our foundation to predict future ecological dynamics, and thus improves coral reef management.

Similarity of plant functional traits and aggregation pattern in a subtropical forest

USGS Publications Warehouse

Zhang, Bo; Lu, Xiaozhen; Jiang, Jiang; DeAngelis, Donald L.; Fu, Zhiyuan; Zhang, Jinchi

2017-01-01

The distribution of species and communities in relation to environmental heterogeneity is a central focus in ecology. Co-occurrence of species with similar functional traits is an indication that communities are determined in part by environmental filters. However, few studies have been designed to test how functional traits are selectively filtered by environmental conditions at local scales. Exploring the relationship between soil characteristics and plant traits is a step toward understanding the filtering hypothesis in determining plant distribution at local scale. Toward this end, we mapped all individual trees (diameter >1 cm) in a one-ha subtropical forest of China in 2007 and 2015. We measured topographic and detailed soil properties within the field site, as well as plant leaf functional traits and demographic rates of the seven most common tree species. A second one-ha study plot was established in 2015, to test and validate the general patterns that were drawn from first plot. We found that variation in species distribution at local scale can be explained by soil heterogeneity and plant functional traits. (From first plot). (1) Species dominant in habitats with high soil ammonium nitrogen and total phosphorus tended to have high specific leaf area (SLA) and relative growth rate (RGR). (2) Species dominant in low-fertility habitats tended to have high leaf dry matter content (LDMC), ratio of chlorophyll a and b (ratioab), and leaf thickness (LT). The hypothesis that functional traits are selected in part by environmental filters and determine plant distribution at local scale was confirmed by the data of the first plot and a second regional site showed similar species distribution patterns.

Perception of shapes targeting local and global processes in autism spectrum disorders.

PubMed

Grinter, Emma J; Maybery, Murray T; Pellicano, Elizabeth; Badcock, Johanna C; Badcock, David R

2010-06-01

Several researchers have found evidence for impaired global processing in the dorsal visual stream in individuals with autism spectrum disorders (ASDs). However, support for a similar pattern of visual processing in the ventral visual stream is less consistent. Critical to resolving the inconsistency is the assessment of local and global form processing ability. Within the visual domain, radial frequency (RF) patterns - shapes formed by sinusoidally varying the radius of a circle to add 'bumps' of a certain number to a circle - can be used to examine local and global form perception. Typically developing children and children with an ASD discriminated between circles and RF patterns that are processed either locally (RF24) or globally (RF3). Children with an ASD required greater shape deformation to identify RF3 shapes compared to typically developing children, consistent with difficulty in global processing in the ventral stream. No group difference was observed for RF24 shapes, suggesting intact local ventral-stream processing. These outcomes support the position that a deficit in global visual processing is present in ASDs, consistent with the notion of Weak Central Coherence.

Whole Brain Functional Connectivity Pattern Homogeneity Mapping.

PubMed

Wang, Lijie; Xu, Jinping; Wang, Chao; Wang, Jiaojian

2018-01-01

Mounting studies have demonstrated that brain functions are determined by its external functional connectivity patterns. However, how to characterize the voxel-wise similarity of whole brain functional connectivity pattern is still largely unknown. In this study, we introduced a new method called functional connectivity homogeneity (FcHo) to delineate the voxel-wise similarity of whole brain functional connectivity patterns. FcHo was defined by measuring the whole brain functional connectivity patterns similarity of a given voxel with its nearest 26 neighbors using Kendall's coefficient concordance (KCC). The robustness of this method was tested in four independent datasets selected from a large repository of MRI. Furthermore, FcHo mapping results were further validated using the nearest 18 and six neighbors and intra-subject reproducibility with each subject scanned two times. We also compared FcHo distribution patterns with local regional homogeneity (ReHo) to identify the similarity and differences of the two methods. Finally, FcHo method was used to identify the differences of whole brain functional connectivity patterns between professional Chinese chess players and novices to test its application. FcHo mapping consistently revealed that the high FcHo was mainly distributed in association cortex including parietal lobe, frontal lobe, occipital lobe and default mode network (DMN) related areas, whereas the low FcHo was mainly found in unimodal cortex including primary visual cortex, sensorimotor cortex, paracentral lobule and supplementary motor area. These results were further supported by analyses of the nearest 18 and six neighbors and intra-subject similarity. Moreover, FcHo showed both similar and different whole brain distribution patterns compared to ReHo. Finally, we demonstrated that FcHo can effectively identify the whole brain functional connectivity pattern differences between professional Chinese chess players and novices. Our findings indicated that FcHo is a reliable method to delineate the whole brain functional connectivity pattern similarity and may provide a new way to study the functional organization and to reveal neuropathological basis for brain disorders.

Evidence for nucleolar subcompartments in Dictyostelium

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

Catalano, Andrew, E-mail: acatalano@ccny.cuny.edu; O’Day, Danton H., E-mail: danton.oday@utoronto.ca; Department of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario M5S 3G5

2015-01-24

Highlights: • Two nucleolar subcompartments (NoSC1, NoSC2) were found in Dictyostelium. • Specific nucleolar proteins localize to different nucleolar subcompartments. • Specific proteins exit NoSC1 and NoSC2 differently upon Actinomycin D treatment. • KRKR appears to function as an NoSC2 nucleolar subcompartment localization signal. - Abstract: The nucleolus is a multifunctional nuclear compartment usually consisting of two to three subcompartments which represent stages of ribosomal biogenesis. It is linked to several human diseases including viral infections, cancer, and neurodegeneration. Dictyostelium is a model eukaryote for the study of fundamental biological processes as well as several human diseases however comparatively littlemore » is known about its nucleolus. Unlike most nucleoli it does not possess visible subcompartments at the ultrastructural level. Several recently identified nucleolar proteins in Dictyostelium leave the nucleolus after treatment with the rDNA transcription inhibitor actinomycin-D (AM-D). Different proteins exit in different ways, suggesting that previously unidentified nucleolar subcompartments may exist. The identification of nucleolar subcompartments would help to better understand the nucleolus in this model eukaryote. Here, we show that Dictyostelium nucleolar proteins nucleomorphin isoform NumA1 and Bud31 localize throughout the entire nucleolus while calcium-binding protein 4a localizes to only a portion, representing nucleolar subcompartment 1 (NoSC1). SWI/SNF complex member Snf12 localizes to a smaller area within NoSC1 representing a second nucleolar subcompartment, NoSC2. The nuclear/nucleolar localization signal KRKR from Snf12 localized GFP to NoSC2, and thus also appears to function as a nucleolar subcompartment localization signal. FhkA localizes to the nucleolar periphery displaying a similar pattern to that of Hsp32. Similarities between the redistribution patterns of Dictyostelium nucleolar proteins during nucleolar disruption as a result of either AM-D treatment or mitosis support these subcompartments. A model for the AM-D-induced redistribution patterns is proposed.« less

Clustering Of Left Ventricular Wall Motion Patterns

NASA Astrophysics Data System (ADS)

Bjelogrlic, Z.; Jakopin, J.; Gyergyek, L.

1982-11-01

A method for detection of wall regions with similar motion was presented. A model based on local direction information was used to measure the left ventricular wall motion from cineangiographic sequence. Three time functions were used to define segmental motion patterns: distance of a ventricular contour segment from the mean contour, the velocity of a segment and its acceleration. Motion patterns were clustered by the UPGMA algorithm and by an algorithm based on K-nearest neighboor classification rule.

A novel approach for SEMG signal classification with adaptive local binary patterns.

PubMed

Ertuğrul, Ömer Faruk; Kaya, Yılmaz; Tekin, Ramazan

2016-07-01

Feature extraction plays a major role in the pattern recognition process, and this paper presents a novel feature extraction approach, adaptive local binary pattern (aLBP). aLBP is built on the local binary pattern (LBP), which is an image processing method, and one-dimensional local binary pattern (1D-LBP). In LBP, each pixel is compared with its neighbors. Similarly, in 1D-LBP, each data in the raw is judged against its neighbors. 1D-LBP extracts feature based on local changes in the signal. Therefore, it has high a potential to be employed in medical purposes. Since, each action or abnormality, which is recorded in SEMG signals, has its own pattern, and via the 1D-LBP these (hidden) patterns may be detected. But, the positions of the neighbors in 1D-LBP are constant depending on the position of the data in the raw. Also, both LBP and 1D-LBP are very sensitive to noise. Therefore, its capacity in detecting hidden patterns is limited. To overcome these drawbacks, aLBP was proposed. In aLBP, the positions of the neighbors and their values can be assigned adaptively via the down-sampling and the smoothing coefficients. Therefore, the potential to detect (hidden) patterns, which may express an illness or an action, is really increased. To validate the proposed feature extraction approach, two different datasets were employed. Achieved accuracies by the proposed approach were higher than obtained results by employed popular feature extraction approaches and the reported results in the literature. Obtained accuracy results were brought out that the proposed method can be employed to investigate SEMG signals. In summary, this work attempts to develop an adaptive feature extraction scheme that can be utilized for extracting features from local changes in different categories of time-varying signals.

Differences in species richness patterns between unicellular and multicellular organisms.

PubMed

Hillebrand, Helmut; Watermann, Frank; Karez, Rolf; Berninger, Ulrike-G

2001-01-01

For unicellular organisms, a lack of effects of local species richness on ecosystem function has been proposed due to their locally high species richness and their ubiquitous distribution. High dispersal ability and high individual numbers may enable unicellular taxa to occur everywhere. Using our own and published data sets on uni- and multicellular organisms, we conducted thorough statistical analyses to test whether (1) unicellular taxa show higher relative local species richness compared to multicellular taxa, (2) unicellular taxa show lower slopes of the species:area relationships and species:individuals relationships, and (3) the species composition of unicellular taxa is less influenced by geographic distance compared to multicellular taxa. We found higher local species richness compared to the global species pool for unicellular organisms than for metazoan taxa. The difference was significant if global species richness was conservatively estimated but not if extrapolated, and therefore higher richness estimates were used. Both microalgae and protozoans showed lower slopes between species richness and sample size (area or individuals) compared to macrozoobenthos, also indicating higher local species richness for unicellular taxa. The similarity of species composition of both benthic diatoms and ciliates decreased with increasing geographic distance. This indicated restricted dispersal ability of protists and the absence of ubiquity. However, a steeper slope between similarity and distance was found for polychaetes and corals, suggesting a stronger effect of distance on the dispersal of metazoans compared to unicellular taxa. In conclusion, we found partly different species richness patterns among uni- and multicellular eukaryotes, but no strict ubiquity of unicellular taxa. Therefore, the effect of local unicellular species richness on ecosystem function has to be reanalyzed. Macroecological patterns suggested for multicellular organisms may differ in unicellular communities.

Evaluation of camouflage pattern performance of textiles by human observers and CAMAELEON

NASA Astrophysics Data System (ADS)

Heinrich, Daniela H.; Selj, Gorm K.

2017-10-01

Military textiles with camouflage pattern are an important part of the protection measures for soldiers. Military operational environments differ a lot depending on climate and vegetation. This requires very different camouflage pattern to achieve good protection. To find the best performing pattern for given environments we have in earlier evaluations mainly applied observer trials as evaluation method. In these camouflage evaluation test human observers were asked to search for targets (in natural settings) presented on a high resolution PC screen, and the corresponding detection times were recorded. Another possibility is to base the evaluation on simulations. CAMAELEON is a licensed tool that ranks camouflaged targets by their similarity with local backgrounds. The similarity is estimated through the parameters local contrast, orientation of structures in the pattern and spatial frequency, by mimicking the response and signal processing in the visual cortex of the human eye. Simulations have a number of advantages over observer trials, for example, that they are more flexible, cheaper, and faster. Applying these two methods to the same images of camouflaged targets we found that CAMAELEON simulation results didn't match observer trial results for targets with disruptive patterns. This finding now calls for follow up studies in order to learn more about the advantages and pitfalls of CAMAELEON. During recent observer trials we studied new camouflage patterns and the effect of additional equipment, such as combat vests. In this paper we will present the results from a study comparing evaluation results of human based observer trials and CAMAELEON.

Dirac electrons in Moiré superlattice: From two to three dimensions

NASA Astrophysics Data System (ADS)

Hu, Chen; Michaud-Rioux, Vincent; Kong, Xianghua; Guo, Hong

2017-11-01

Moiré patterns in van der Waals (vdW) heterostructures bring novel physical effects to the materials. We report theoretical investigations of the Moiré pattern formed by graphene (Gr) on hexagonal boron nitride (h BN). For both the two-dimensional (2D) flat-sheet and the freestanding three-dimensional (3D) wavelike film geometries, the behaviors of Dirac electrons are strongly modulated by the local high-symmetry stacking configurations of the Moiré pattern. In the 2D flat sheet, the secondary Dirac cone (SDC) dispersion emerges due to the stacking-selected localization of SDC wave functions, while the original Dirac cone (ODC) gap is suppressed due to an overall effect of ODC wave functions. In the freestanding 3D wavelike Moiré structure, we predict that a specific local stacking in the Moiré superlattice is promoted at the expense of other local stackings, leading to an electronic structure more similar to that of the perfectly matching flat Gr/h BN than that of the flat-sheet 2D Moiré pattern. To capture the overall picture of the Moiré superlattice, supercells containing 12 322 atoms are simulated by first principles.

One Shot Detection with Laplacian Object and Fast Matrix Cosine Similarity.

PubMed

Biswas, Sujoy Kumar; Milanfar, Peyman

2016-03-01

One shot, generic object detection involves searching for a single query object in a larger target image. Relevant approaches have benefited from features that typically model the local similarity patterns. In this paper, we combine local similarity (encoded by local descriptors) with a global context (i.e., a graph structure) of pairwise affinities among the local descriptors, embedding the query descriptors into a low dimensional but discriminatory subspace. Unlike principal components that preserve global structure of feature space, we actually seek a linear approximation to the Laplacian eigenmap that permits us a locality preserving embedding of high dimensional region descriptors. Our second contribution is an accelerated but exact computation of matrix cosine similarity as the decision rule for detection, obviating the computationally expensive sliding window search. We leverage the power of Fourier transform combined with integral image to achieve superior runtime efficiency that allows us to test multiple hypotheses (for pose estimation) within a reasonably short time. Our approach to one shot detection is training-free, and experiments on the standard data sets confirm the efficacy of our model. Besides, low computation cost of the proposed (codebook-free) object detector facilitates rather straightforward query detection in large data sets including movie videos.

Subcellular localization patterns and their relationship to photodynamic activity of pyropheophorbide-a derivatives.

PubMed

MacDonald, I J; Morgan, J; Bellnier, D A; Paszkiewicz, G M; Whitaker, J E; Litchfield, D J; Dougherty, T J

1999-11-01

To determine if subcellular localization is important to photodynamic therapy (PDT) efficacy, an in vitro fluorescence microscopy study was conducted with a congeneric series of pyropheophorbide-a derivatives in human pharyngeal squamous cell carcinoma (FaDu) cells and murine radiation-induced fibrosarcoma (RIF) mutant cells. In the FaDu cells the octyl, decyl and dodecyl ether derivatives localized to the lysosomes at extracellular concentrations less than needed to produce a 50% cell kill (LD50). At extracellular concentrations equal or greater than the LD50 the compounds localized mainly to mitochondria. The propyl, pentyl, hexyl and heptyl ether derivatives localized mainly to the mitochondria at all concentrations studied. This suggested that mitochondria are a sensitive PDT target for these derivatives. Similar experiments were performed with two Photofrin-PDT resistant RIF cell lines, one of which was found to be resistant to hexyl ether derivative (C6) mediated-PDT and the other sensitive to C6-PDT relative to the parent line. At extracellular concentrations of C6 below the LD50 of each cell line, the mutants exhibited lysosomal localization. At concentrations above these values the patterns shifted to a mainly mitochondrial pattern. In these cell lines mitochondrial localization also correlated with PDT sensitivity. Localization to mitochondria or lysosomes appeared to be affected by the aggregation state of the congeners, all of which are highly aggregated in aqueous medium. Monomers apparently were the active fraction of these compounds because equalizing the extracellular monomer concentrations produced equivalent intracellular concentrations, photoxicity and localization patterns. Compounds that were mainly aggregates localized to the lysosomes where they were rendered less active. Mitochondria appear to be a sensitive target for pyropheophorbide-a-mediated photodamage, and the degree of aggregation seems to be a determinant of the localization site.

Conceptual recurrence plots: revealing patterns in human discourse.

PubMed

Angus, Daniel; Smith, Andrew; Wiles, Janet

2012-06-01

Human discourse contains a rich mixture of conceptual information. Visualization of the global and local patterns within this data stream is a complex and challenging problem. Recurrence plots are an information visualization technique that can reveal trends and features in complex time series data. The recurrence plot technique works by measuring the similarity of points in a time series to all other points in the same time series and plotting the results in two dimensions. Previous studies have applied recurrence plotting techniques to textual data; however, these approaches plot recurrence using term-based similarity rather than conceptual similarity of the text. We introduce conceptual recurrence plots, which use a model of language to measure similarity between pairs of text utterances, and the similarity of all utterances is measured and displayed. In this paper, we explore how the descriptive power of the recurrence plotting technique can be used to discover patterns of interaction across a series of conversation transcripts. The results suggest that the conceptual recurrence plotting technique is a useful tool for exploring the structure of human discourse.

The spectrum of dermatoscopic patterns in blue nevi.

PubMed

Di Cesare, Antonella; Sera, Francesco; Gulia, Andrea; Coletti, Gino; Micantonio, Tamara; Fargnoli, Maria Concetta; Peris, Ketty

2012-08-01

Blue nevi are congenital or acquired, dermal dendritic melanocytic proliferations that can simulate melanocytic and nonmelanocytic lesions including melanoma, cutaneous metastasis of melanoma, Spitz/Reed nevi, and basal cell carcinoma. We sought to investigate global and local dermatoscopic patterns of blue nevi compared with melanomas and basal cell carcinomas. We retrospectively analyzed global and local features in 95 dermatoscopic images of blue nevi and in 190 melanomas and basal cell carcinomas that were selected as control lesions on the basis of similar pigmentation. Lesion pigmentation was classified as monochromatic, dichromatic, or multichromatic. A global pattern characterized by homogeneous pigmentation was observed in all of 95 (100%) blue nevi. Eighty of 95 (84.2%) blue nevi presented a homogeneous pattern consisting of one color (blue, black, or brown) or two colors (blue-brown, blue-gray, or blue-black). Fifteen of 95 (15.8%) blue nevi had a multichromatic (blue, gray, black, brown, and/or red) pigmentation. In all, 47 of 95 (49.5%) blue nevi were characterized by pigmentation in the absence of pigment network or any other local dermatoscopic features. And 48 of 95 (50.5%) blue nevi showed local dermatoscopic patterns including whitish scarlike depigmentation, dots/globules, vascular pattern, streaks, and networklike pattern. The study was retrospective and involved only Caucasian people of Italian origin. The characteristic feature of blue nevi is a homogeneous pigmentation that is blue, blue-gray, blue-brown, or blue-black. We showed that a wide spectrum of local dermatoscopic features (whitish scarlike depigmentation, dots/globules, peripheral streaks or vessels) may also be present. In such cases, clinical and dermatoscopic distinction from melanoma or nonmelanocytic lesions may be difficult or impossible, and surgical excision is necessary. Copyright © 2011 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

Inferring biodiversity maintenance mechanisms from ecological pattern

NASA Astrophysics Data System (ADS)

Ostling, Annette

Among a set of competitors for a single common resource, the best will simply exclude the others. Yet in nature we can see astounding diversity of competing species. Do close similarities in species' response to the local environment primarily explain their coexistence? Or is this diversity possible because of differences between species that stabilize their coexistence? And if so, what particular differences between species are important in particular communities? Some ecological communities lend themselves to experimental manipulation to begin to answer these questions. Yet for many other communities, such as tree species in forests, the logistical hurdles to this approach are daunting. Faster progress could be made in ecology if insight into biodiversity maintenance mechanisms could be gained from patterns exhibited in local ecological communities, such as how coexisting species are distributed in their ecological traits and relative abundance. Hurdles that we need to overcome to be able to gain such insight include: 1) further developing neutral theory, a quantitative process-based null model of community pattern resulting when species similarities are what allow their coexistence, and 2) better understanding what patterns to expect when species differences dominate instead, particularly in the context of stochasticity and immigration. I will describe our ongoing research to overcome these hurdles, to provide better tools for analyzing observed pattern. National Science Foundation Advancing Theory in Biology Grant 1038678, Danish National Research Foundation Grant DNRF 96 for the Center of Macroecology, Evolution and Climate.

Spontaneous Magnetic Alignment by Yearling Snapping Turtles: Rapid Association of Radio Frequency Dependent Pattern of Magnetic Input with Novel Surroundings

PubMed Central

Landler, Lukas; Painter, Michael S.; Youmans, Paul W.; Hopkins, William A.; Phillips, John B.

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF (‘RF off → RF off’), but were disoriented when subsequently exposed to RF (‘RF off → RF on’). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF (‘RF on → RF off’), but aligned towards magnetic south when tested with RF (‘RF on → RF on’). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space. PMID:25978736

Spontaneous magnetic alignment by yearling snapping turtles: rapid association of radio frequency dependent pattern of magnetic input with novel surroundings.

PubMed

Landler, Lukas; Painter, Michael S; Youmans, Paul W; Hopkins, William A; Phillips, John B

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF ('RF off → RF off'), but were disoriented when subsequently exposed to RF ('RF off → RF on'). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF ('RF on → RF off'), but aligned towards magnetic south when tested with RF ('RF on → RF on'). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space.

Dietary patterns are associated with metabolic syndrome in adult Samoans.

PubMed

DiBello, Julia R; McGarvey, Stephen T; Kraft, Peter; Goldberg, Robert; Campos, Hannia; Quested, Christine; Laumoli, Tuiasina Salamo; Baylin, Ana

2009-10-01

The prevalence of metabolic syndrome has reached epidemic levels in the Samoan Islands. In this cross-sectional study conducted in 2002-2003, dietary patterns were described among American Samoan (n = 723) and Samoan (n = 785) adults (> or =18 y) to identify neo-traditional and modern eating patterns and to relate these patterns to the presence of metabolic syndrome using Adult Treatment Panel III criteria. The neo-traditional dietary pattern, similar across both polities, was characterized by high intake of local foods, including crab/lobster, coconut products, and taro, and low intake of processed foods, including potato chips and soda. The modern pattern, also similar across both polities, was characterized by high intake of processed foods such as rice, potato chips, cake, and pancakes and low intake of local foods. The neo-traditional dietary pattern was associated with significantly higher serum HDL-cholesterol in American Samoa (P-trend = 0.05) and a decrease in abdominal circumference in American Samoa and Samoa (P-trend = 0.004 and 0.01, respectively). An inverse association was found with metabolic syndrome, although it did not reach significance (P = 0.23 in American Samoa; P = 0.13 in Samoa). The modern pattern was significantly positively associated with metabolic syndrome in Samoa (prevalence ratio = 1.21 for the fifth compared with first quintile; 95% CI: 0.93.1.57; P-trend = 0.05) and with increased serum triglyceride levels in both polities (P < 0.05). Reduced intake of processed foods high in refined grains and adherence to a neo-traditional eating pattern characterized by plant-based fiber, seafood, and coconut products may help to prevent growth in the prevalence of metabolic syndrome in the Samoan islands.

Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

NASA Astrophysics Data System (ADS)

Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

2018-04-01

The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

Fast and robust multimodal image registration using a local derivative pattern.

PubMed

Jiang, Dongsheng; Shi, Yonghong; Chen, Xinrong; Wang, Manning; Song, Zhijian

2017-02-01

Deformable multimodal image registration, which can benefit radiotherapy and image guided surgery by providing complementary information, remains a challenging task in the medical image analysis field due to the difficulty of defining a proper similarity measure. This article presents a novel, robust and fast binary descriptor, the discriminative local derivative pattern (dLDP), which is able to encode images of different modalities into similar image representations. dLDP calculates a binary string for each voxel according to the pattern of intensity derivatives in its neighborhood. The descriptor similarity is evaluated using the Hamming distance, which can be efficiently computed, instead of conventional L1 or L2 norms. For the first time, we validated the effectiveness and feasibility of the local derivative pattern for multimodal deformable image registration with several multi-modal registration applications. dLDP was compared with three state-of-the-art methods in artificial image and clinical settings. In the experiments of deformable registration between different magnetic resonance imaging (MRI) modalities from BrainWeb, between computed tomography and MRI images from patient data, and between MRI and ultrasound images from BITE database, we show our method outperforms localized mutual information and entropy images in terms of both accuracy and time efficiency. We have further validated dLDP for the deformable registration of preoperative MRI and three-dimensional intraoperative ultrasound images. Our results indicate that dLDP reduces the average mean target registration error from 4.12 mm to 2.30 mm. This accuracy is statistically equivalent to the accuracy of the state-of-the-art methods in the study; however, in terms of computational complexity, our method significantly outperforms other methods and is even comparable to the sum of the absolute difference. The results reveal that dLDP can achieve superior performance regarding both accuracy and time efficiency in general multimodal image registration. In addition, dLDP also indicates the potential for clinical ultrasound guided intervention. © 2016 The Authors. Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

77 FR 35839 - Special Local Regulation and Security Zone: War of 1812 Bicentennial Commemoration, Port of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... Commemoration, Port of Boston, MA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast..., MA. Recommendations to employ a similar pattern to that which was used during the Sail Boston 2009...

Quantum beating patterns observed in the energetics of Pb film nanostructures.

PubMed

Czoschke, P; Hong, Hawoong; Basile, L; Chiang, T-C

2004-07-16

We have studied the nanoscale structural evolution of Pb films grown at 110 K on a Si(111) substrate as they are annealed to increasingly higher temperatures. Surface x-ray diffraction from a synchrotron source is used to observe the morphology evolve from an initial smooth film through various metastable states before reaching a state of local equilibrium, at which point the coverage of different height Pb structures is analyzed and related to the thickness-dependent surface energy. Rich patterns are seen in the resulting energy landscape similar to the beating patterns heard from the interference of two musical notes of similar pitch. The explanation is, however, very simple, as demonstrated by a model calculation based on the confinement of free electrons to a quantum well.

Quantum Beating Patterns Observed in the Energetics of Pb Film Nanostructures

NASA Astrophysics Data System (ADS)

Czoschke, P.; Hong, Hawoong; Basile, L.; Chiang, T.-C.

2004-07-01

We have studied the nanoscale structural evolution of Pb films grown at 110K on a Si(111) substrate as they are annealed to increasingly higher temperatures. Surface x-ray diffraction from a synchrotron source is used to observe the morphology evolve from an initial smooth film through various metastable states before reaching a state of local equilibrium, at which point the coverage of different height Pb structures is analyzed and related to the thickness-dependent surface energy. Rich patterns are seen in the resulting energy landscape similar to the beating patterns heard from the interference of two musical notes of similar pitch. The explanation is, however, very simple, as demonstrated by a model calculation based on the confinement of free electrons to a quantum well.

Predicting local adaptation in fragmented plant populations: implications for restoration genetics

PubMed Central

Pickup, Melinda; Field, David L; Rowell, David M; Young, Andrew G

2012-01-01

Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7–600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration. PMID:23346235

Heritable stress response dynamics revealed by single-cell genealogy

PubMed Central

2018-01-01

Cells often respond to environmental stimuli by activating specific transcription factors. Upon exposure to glucose limitation stress, it is known that yeast Saccharomyces cerevisiae cells dephosphorylate the general stress response factor Msn2, leading to its nuclear localization, which in turn activates the expression of many genes. However, the precise dynamics of Msn2 nucleocytoplasmic translocations and whether they are inherited over multiple generations in a stress-dependent manner are not well understood. Tracking Msn2 localization events in yeast lineages grown on a microfluidic chip, here we report how cells modulate the amplitude, duration, frequency, and dynamic pattern of the localization events in response to glucose limitation stress. Single yeast cells were found to modulate the amplitude and frequency of Msn2 nuclear localization, but not its duration. Moreover, the Msn2 localization frequency was epigenetically inherited in descendants of mother cells, leading to a decrease in cell-to-cell variation in localization frequency. An analysis of the time dynamic patterns of nuclear localizations between genealogically related cell pairs using an information theory approach found that the magnitude of pattern similarity increased with stress intensity and was strongly inherited by the descendant cells at the highest stress level. By dissecting how general stress response dynamics is contributed by different modulation schemes over long time scales, our work provides insight into which scheme evolution might have acted on to optimize fitness in stressful environments. PMID:29675464

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.

PubMed

Xia, Li C; Steele, Joshua A; Cram, Jacob A; Cardon, Zoe G; Simmons, Sheri L; Vallino, Joseph J; Fuhrman, Jed A; Sun, Fengzhu

2011-01-01

The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa.

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

PubMed Central

2011-01-01

Background The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. Results We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. Conclusions The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa. PMID:22784572

Potential coastal impacts of contemporary changing climate on South Asian seas states

NASA Astrophysics Data System (ADS)

Gable, F. J.; Aubrey, D. G.

1990-01-01

The threat of man-induced global change on the nations of the South Asian seas region varies from place to place because of differences in exposure to monsoons and stoms, differences in local tectonics and subsidence, and variations in air and sea climates. Because several nations are involved, some having subsistence budgets, and given the cost of deriving independently a comprehensive response to global change, the similarities and differences between national settings must be identified soon. These comparisons will form the basis for local response strategies: the similarities provide a basis for responses similar to that of other nations and the differences provide for local adaptation. That climate change on the South Asian coastal region will have an impact is certain: its economics, environment, and coastal land uses are dominated to a certain extent by this marine influence. The extent of these impacts, however, is uncertain. Accompanying global change will be changes in sea level, differences in storm climate, and altered precipitation patterns; science cannot define today what pattern these changes will take. Because global change is inevitable—although its magnitude, timing, and geographic distribution are unknown—the South Asian seas region should begin the appropriate research and planning studies to set forth a reasoned response to global change, for implementation when scientific evidence for global change is more quantitative.

Intracellular Localization and Cellular Factors Interaction of HTLV-1 and HTLV-2 Tax Proteins: Similarities and Functional Differences

PubMed Central

Bertazzoni, Umberto; Turci, Marco; Avesani, Francesca; Di Gennaro, Gianfranco; Bidoia, Carlo; Romanelli, Maria Grazia

2011-01-01

Human T-lymphotropic viruses type 1 (HTLV-1) and type 2 (HTLV-2) present very similar genomic structures but HTLV-1 is more pathogenic than HTLV-2. Is this difference due to their transactivating Tax proteins, Tax-1 and Tax-2, which are responsible for viral and cellular gene activation? Do Tax-1 and Tax-2 differ in their cellular localization and in their interaction pattern with cellular factors? In this review, we summarize Tax-1 and Tax-2 structural and phenotypic properties, their interaction with factors involved in signal transduction and their localization-related behavior within the cell. Special attention will be given to the distinctions between Tax-1 and Tax-2 that likely play an important role in their transactivation activity. PMID:21994745

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

PubMed Central

Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

2013-01-01

Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

Stable orthogonal local discriminant embedding for linear dimensionality reduction.

PubMed

Gao, Quanxue; Ma, Jingjie; Zhang, Hailin; Gao, Xinbo; Liu, Yamin

2013-07-01

Manifold learning is widely used in machine learning and pattern recognition. However, manifold learning only considers the similarity of samples belonging to the same class and ignores the within-class variation of data, which will impair the generalization and stableness of the algorithms. For this purpose, we construct an adjacency graph to model the intraclass variation that characterizes the most important properties, such as diversity of patterns, and then incorporate the diversity into the discriminant objective function for linear dimensionality reduction. Finally, we introduce the orthogonal constraint for the basis vectors and propose an orthogonal algorithm called stable orthogonal local discriminate embedding. Experimental results on several standard image databases demonstrate the effectiveness of the proposed dimensionality reduction approach.

Phylogenetic turnover along local environmental gradients in tropical forest communities.

PubMed

Baldeck, C A; Kembel, S W; Harms, K E; Yavitt, J B; John, R; Turner, B L; Madawala, S; Gunatilleke, N; Gunatilleke, S; Bunyavejchewin, S; Kiratiprayoon, S; Yaacob, A; Supardi, M N N; Valencia, R; Navarrete, H; Davies, S J; Chuyong, G B; Kenfack, D; Thomas, D W; Dalling, J W

2016-10-01

While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3 % and 0.4-8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved.

LSHSIM: A Locality Sensitive Hashing based method for multiple-point geostatistics

NASA Astrophysics Data System (ADS)

Moura, Pedro; Laber, Eduardo; Lopes, Hélio; Mesejo, Daniel; Pavanelli, Lucas; Jardim, João; Thiesen, Francisco; Pujol, Gabriel

2017-10-01

Reservoir modeling is a very important task that permits the representation of a geological region of interest, so as to generate a considerable number of possible scenarios. Since its inception, many methodologies have been proposed and, in the last two decades, multiple-point geostatistics (MPS) has been the dominant one. This methodology is strongly based on the concept of training image (TI) and the use of its characteristics, which are called patterns. In this paper, we propose a new MPS method that combines the application of a technique called Locality Sensitive Hashing (LSH), which permits to accelerate the search for patterns similar to a target one, with a Run-Length Encoding (RLE) compression technique that speeds up the calculation of the Hamming similarity. Experiments with both categorical and continuous images show that LSHSIM is computationally efficient and produce good quality realizations. In particular, for categorical data, the results suggest that LSHSIM is faster than MS-CCSIM, one of the state-of-the-art methods.

Spatial pattern in Antarctica: what can we learn from Antarctic bacterial isolates?

PubMed

Chong, Chun Wie; Goh, Yuh Shan; Convey, Peter; Pearce, David; Tan, Irene Kit Ping

2013-09-01

A range of small- to moderate-scale studies of patterns in bacterial biodiversity have been conducted in Antarctica over the last two decades, most suggesting strong correlations between the described bacterial communities and elements of local environmental heterogeneity. However, very few of these studies have advanced interpretations in terms of spatially associated patterns, despite increasing evidence of patterns in bacterial biogeography globally. This is likely to be a consequence of restricted sampling coverage, with most studies to date focusing only on a few localities within a specific Antarctic region. Clearly, there is now a need for synthesis over a much larger spatial to consolidate the available data. In this study, we collated Antarctic bacterial culture identities based on the 16S rRNA gene information available in the literature and the GenBank database (n > 2,000 sequences). In contrast to some recent evidence for a distinct Antarctic microbiome, our phylogenetic comparisons show that a majority (~75 %) of Antarctic bacterial isolates were highly similar (≥99 % sequence similarity) to those retrieved from tropical and temperate regions, suggesting widespread distribution of eurythermal mesophiles in Antarctic environments. However, across different Antarctic regions, the dominant bacterial genera exhibit some spatially distinct diversity patterns analogous to those recently proposed for Antarctic terrestrial macroorganisms. Taken together, our results highlight the threat of cross-regional homogenisation in Antarctic biodiversity, and the imperative to include microbiota within the framework of biosecurity measures for Antarctica.

Flavonoid Accumulation Patterns of Transparent Testa Mutants of Arabidopsis1

PubMed Central

Peer, Wendy Ann; Brown, Dana E.; Tague, Brian W.; Muday, Gloria K.; Taiz, Lincoln; Murphy, Angus S.

2001-01-01

Flavonoids have been implicated in the regulation of auxin movements in Arabidopsis. To understand when and where flavonoids may be acting to control auxin movement, the flavonoid accumulation pattern was examined in young seedlings and mature tissues of wild-type Arabidopsis. Using a variety of biochemical and visualization techniques, flavonoid accumulation in mature plants was localized in cauline leaves, pollen, stigmata, and floral primordia, and in the stems of young, actively growing inflorescences. In young Landsberg erecta seedlings, aglycone flavonols accumulated developmentally in three regions, the cotyledonary node, the hypocotyl-root transition zone, and the root tip. Aglycone flavonols accumulated at the hypocotyl-root transition zone in a developmental and tissue-specific manner with kaempferol in the epidermis and quercetin in the cortex. Quercetin localized subcellularly in the nuclear region, plasma membrane, and endomembrane system, whereas kaempferol localized in the nuclear region and plasma membrane. The flavonoid accumulation pattern was also examined in transparent testa mutants blocked at different steps in the flavonoid biosynthesis pathway. The transparent testa mutants were shown to have precursor accumulation patterns similar to those of end product flavonoids in wild-type Landsberg erecta, suggesting that synthesis and end product accumulation occur in the same cells. PMID:11402185

Flavonoid accumulation patterns of transparent testa mutants of arabidopsis

NASA Technical Reports Server (NTRS)

Peer, W. A.; Brown, D. E.; Tague, B. W.; Muday, G. K.; Taiz, L.; Murphy, A. S.

2001-01-01

Flavonoids have been implicated in the regulation of auxin movements in Arabidopsis. To understand when and where flavonoids may be acting to control auxin movement, the flavonoid accumulation pattern was examined in young seedlings and mature tissues of wild-type Arabidopsis. Using a variety of biochemical and visualization techniques, flavonoid accumulation in mature plants was localized in cauline leaves, pollen, stigmata, and floral primordia, and in the stems of young, actively growing inflorescences. In young Landsberg erecta seedlings, aglycone flavonols accumulated developmentally in three regions, the cotyledonary node, the hypocotyl-root transition zone, and the root tip. Aglycone flavonols accumulated at the hypocotyl-root transition zone in a developmental and tissue-specific manner with kaempferol in the epidermis and quercetin in the cortex. Quercetin localized subcellularly in the nuclear region, plasma membrane, and endomembrane system, whereas kaempferol localized in the nuclear region and plasma membrane. The flavonoid accumulation pattern was also examined in transparent testa mutants blocked at different steps in the flavonoid biosynthesis pathway. The transparent testa mutants were shown to have precursor accumulation patterns similar to those of end product flavonoids in wild-type Landsberg erecta, suggesting that synthesis and end product accumulation occur in the same cells.

Dynamical phenomena at the inner edge of the Keeler gap

NASA Astrophysics Data System (ADS)

Tajeddine, Radwan; Nicholson, Philip D.; Tiscareno, Matthew S.; Hedman, Matthew M.; Burns, Joseph A.; El Moutamid, Maryame

2017-06-01

We analyze several thousand Cassini ISS images in order to study the inner edge of the Keeler gap in Saturn's outer A ring. We find strong evidence for an m = 32 perturbation with a mean amplitude of radial variation of 4.5 km. Phase analysis yields a pattern speed consistent with the mean motion of Prometheus, indicating that this pattern is generated by the 32:31 Inner Lindblad resonance with Prometheus. In addition, we find evidence of 18-lobed and 20-lobed patterns with amplitudes of ∼1.5 km. These patterns, whose rotation rates correspond to resonance locations ∼4 km interior to the gap edge, are believed to be normal modes. The former is probably related to the nearby 18:17 (m = 18) resonance with Pandora. In addition to these resonant and normal mode patterns, we also observe multiple localized features that appear to move at the local keplerian rate and that persist for only a few months. One hypothesis is that different groups of ring particles at the inner edge of the gap may be reacting differently to the resonance with Prometheus, with local variations in the forced eccentricity and/or pericenter; an alternative hypothesis is the existence of several unseen objects embedded at or near the inner edge of the Keeler gap, similar to those suspected to exist at the outer edges of the A and B rings. In either case, observations of the ring edge at opposite ansae demonstrate that the localized features must be on eccentric orbits.

A unified model explains commonness and rarity on coral reefs.

PubMed

Connolly, Sean R; Hughes, Terry P; Bellwood, David R

2017-04-01

Abundance patterns in ecological communities have important implications for biodiversity maintenance and ecosystem functioning. However, ecological theory has been largely unsuccessful at capturing multiple macroecological abundance patterns simultaneously. Here, we propose a parsimonious model that unifies widespread ecological relationships involving local aggregation, species-abundance distributions, and species associations, and we test this model against the metacommunity structure of reef-building corals and coral reef fishes across the western and central Pacific. For both corals and fishes, the unified model simultaneously captures extremely well local species-abundance distributions, interspecific variation in the strength of spatial aggregation, patterns of community similarity, species accumulation, and regional species richness, performing far better than alternative models also examined here and in previous work on coral reefs. Our approach contributes to the development of synthetic theory for large-scale patterns of community structure in nature, and to addressing ongoing challenges in biodiversity conservation at macroecological scales. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Generalization in visual recognition by the honeybee (Apis mellifera): a review and explanation.

PubMed

Horridge, Adrian

2009-06-01

During a century of studies on honeybee vision, generalization was the word for the acceptance of an unfamiliar pattern in the place of the training pattern, or the ability to learn a common factor in a group of related patterns. The ideas that bees generalize one pattern for another, detect similarity and differences, or form categories, were derived from the use of the same terms in the human cognitive sciences. Recent work now reveals a mechanistic explanation for bees. Small groups of ommatidia converge upon feature detectors that respond selectively to certain parameters that are in the pattern: modulation in the receptors, edge orientations, or to areas of black or colour. Within each local region of the eye the responses of each type of feature detector are summed to form a cue. The cues are therefore not in the pattern, but are local totals in the bee. Each cue has a quality, a quantity and a position on the eye, like a neuron response. This summation of edge detector responses destroys the local pattern based on edge orientation but preserves a coarse, sparse and simplified version of the panorama. In order of preference, the cues are: local receptor modulation, positions of well-separated black areas, a small black spot, colour and positions of the centres of each cue, radial edges, the averaged edge orientation and tangential edges. A pattern is always accepted by a trained bee that detects the expected cues in the expected places and no unexpected cues. The actual patterns are irrelevant. Therefore we have an explanation of generalization that is based on experimental testing of trained bees, not by analogy with other animals. Historically, generalization appeared when the training patterns were regularly interchanged to make the bees examine them. This strategy forced the bees to ignore parameters outside the training pattern, so that learning was restricted to one local eye region. This in turn limited the memory to one cue of each type, so that recognition was ambiguous because the cues were insufficient to distinguish all patterns. On the other hand, bees trained on very large targets, or by landing on the pattern, learned cues in several eye regions, and were able to recognize the coarse configural layout.

Patterns of failure after involved field radiotherapy for locally advanced esophageal squamous cell carcinoma.

PubMed

Li, Duo-Jie; Li, Hong-Wei; He, Bin; Wang, Geng-Ming; Cai, Han-Fei; Duan, Shi-Miao; Liu, Jing-Jing; Zhang, Ya-Jun; Cui, Zhen; Jiang, Hao

2016-01-01

To retrospectively analyze the patterns of failure and the treatment effects of involved-field irradiation (IFI) on patients treated with locally advanced esophageal squamous cell carcinoma (ESCC) and to determine whether IFI is practicable in these patients. A total of 79 patients with locally advanced ESCC underwent three dimensional conformal (3D)CRT) or intensity modulated radiotherapy (IMRT) using IFI or elective nodal irradiation (ENI) according to the target volume. The patterns of failure were defined as local/regional, in-field, out)of)field regional lymph node (LN) and distant failure. With a median follow)up of 32.0 months, failures were observed in 66 (83.6%) patients. The cumulative incidence of local/regional failure (55.8 vs 52.8%) and in)field regional lymph node failure (25.6 vs 19.4%) showed no statistically significant difference between the IFI and the ENI group (p=0.526 and 0.215, respectively). Out)of)field nodal relapse rate of only 7.0% was seen in the IFI group. Three)year survival rates for the ENI and IFI group were 22.2 and 18.6%, respectively (p=0.240), and 3)year distant metastasis rates were 27.8 and 32.6%, respectively (p=0.180). The lung V10, V20, V30 and mean lung dose of the ENI group were greater than those of the IFI group, while the mean lung dose and V10 had statistically significant difference. The patterns of failure and survival rates in the IFI group were similar as in the ENI group; the regional recurrence and distant metastasis are the main cause of treatment failure. IFI is feasible for locally advanced ESCC. Further investigation is needed to increase local control and decrease distant metastasis in these patients.

GC-MS analyses and chemometric processing to discriminate the local and long-distance sources of PAHs associated to atmospheric PM2.5.

PubMed

Masiol, Mauro; Centanni, Elena; Squizzato, Stefania; Hofer, Angelika; Pecorari, Eliana; Rampazzo, Giancarlo; Pavoni, Bruno

2012-09-01

This study presents a procedure to differentiate the local and remote sources of particulate-bound polycyclic aromatic hydrocarbons (PAHs). Data were collected during an extended PM(2.5) sampling campaign (2009-2010) carried out for 1 year in Venice-Mestre, Italy, at three stations with different emissive scenarios: urban, industrial, and semirural background. Diagnostic ratios and factor analysis were initially applied to point out the most probable sources. In a second step, the areal distribution of the identified sources was studied by applying the discriminant analysis on factor scores. Third, samples collected in days with similar atmospheric circulation patterns were grouped using a cluster analysis on wind data. Local contributions to PM(2.5) and PAHs were then assessed by interpreting cluster results with chemical data. Results evidenced that significantly lower levels of PM(2.5) and PAHs were found when faster winds changed air masses, whereas in presence of scarce ventilation, locally emitted pollutants were trapped and concentrations increased. This way, an estimation of pollutant loads due to local sources can be derived from data collected in days with similar wind patterns. Long-range contributions were detected by a cluster analysis on the air mass back-trajectories. Results revealed that PM(2.5) concentrations were relatively high when air masses had passed over the Po Valley. However, external sources do not significantly contribute to the PAHs load. The proposed procedure can be applied to other environments with minor modifications, and the obtained information can be useful to design local and national air pollution control strategies.

Cerium anomaly at microscale in fossils.

PubMed

Gueriau, Pierre; Mocuta, Cristian; Bertrand, Loïc

2015-09-01

Patterns in rare earth element (REE) concentrations are essential instruments to assess geochemical processes in Earth and environmental sciences. Excursions in the "cerium anomaly" are widely used to inform on past redox conditions in sediments. This proxy resources to the specificity of cerium to adopt both the +III and +IV oxidation states, while most rare earths are purely trivalent and share very similar reactivity and transport properties. In practical terms, the level of cerium anomaly is established through elemental point quantification and profiling. All these models rely on a supposed homogeneity of the cerium oxidation state within the samples. However, this has never been demonstrated, whereas the cerium concentration can significantly vary within a sample, as shown for fossils, which would vastly complicate interpretation of REE patterns. Here, we report direct micrometric mapping of Ce speciation through synchrotron X-ray absorption spectroscopy and production of local rare earth patterns in paleontological fossil tissues through X-ray fluorescence mapping. The sensitivity of the approach is demonstrated on well-preserved fishes and crustaceans from the Late Cretaceous (ca. 95 million years (Myr) old). The presence of Ce under the +IV form within the fossil tissues is attributed to slightly oxidative local conditions of burial and agrees well with the limited negative cerium anomaly observed in REE patterns. The [Ce(IV)]/[Ce(tot)] ratio appears remarkably stable at the microscale within each fossil and is similar between fossils from the locality. Speciation maps were obtained from an original combination of synchrotron microbeam X-ray fluorescence, absorption spectroscopy, and diffraction, together with light and electron microscopy. This work also highlights the need for more systematic studies of cerium geochemistry at the microscale in paleontological contexts, in particular across fossil histologies.

Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints

PubMed Central

Singh, Aarti; Poczos, Barnabas; Erickson, Kirk I.; Tseng, Wen-Yih I.; Verstynen, Timothy D.

2016-01-01

Quantifying differences or similarities in connectomes has been a challenge due to the immense complexity of global brain networks. Here we introduce a noninvasive method that uses diffusion MRI to characterize whole-brain white matter architecture as a single local connectome fingerprint that allows for a direct comparison between structural connectomes. In four independently acquired data sets with repeated scans (total N = 213), we show that the local connectome fingerprint is highly specific to an individual, allowing for an accurate self-versus-others classification that achieved 100% accuracy across 17,398 identification tests. The estimated classification error was approximately one thousand times smaller than fingerprints derived from diffusivity-based measures or region-to-region connectivity patterns for repeat scans acquired within 3 months. The local connectome fingerprint also revealed neuroplasticity within an individual reflected as a decreasing trend in self-similarity across time, whereas this change was not observed in the diffusivity measures. Moreover, the local connectome fingerprint can be used as a phenotypic marker, revealing 12.51% similarity between monozygotic twins, 5.14% between dizygotic twins, and 4.51% between none-twin siblings, relative to differences between unrelated subjects. This novel approach opens a new door for probing the influence of pathological, genetic, social, or environmental factors on the unique configuration of the human connectome. PMID:27846212

Convergent and Divergent Signaling in PAMP-Triggered Immunity and Effector-Triggered Immunity.

PubMed

Peng, Yujun; van Wersch, Rowan; Zhang, Yuelin

2018-04-01

Plants use diverse immune receptors to sense pathogen attacks. Recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors localized on the plasma membrane leads to PAMP-triggered immunity (PTI). Detection of pathogen effectors by intracellular or plasma membrane-localized immune receptors results in effector-triggered immunity (ETI). Despite the large variations in the magnitude and duration of immune responses triggered by different PAMPs or pathogen effectors during PTI and ETI, plasma membrane-localized immune receptors activate similar downstream molecular events such as mitogen-activated protein kinase activation, oxidative burst, ion influx, and increased biosynthesis of plant defense hormones, indicating that defense signals initiated at the plasma membrane converge at later points. On the other hand, activation of ETI by immune receptors localized to the nucleus appears to be more directly associated with transcriptional regulation of defense gene expression. Here, we review recent progress in signal transductions downstream of different groups of plant immune receptors, highlighting the converging and diverging molecular events.

Internalization and localization of basal insulin peglispro in cells.

PubMed

Moyers, Julie S; Volk, Catherine B; Cao, Julia X C; Zhang, Chen; Ding, Liyun; Kiselyov, Vladislav V; Michael, M Dodson

2017-10-15

Basal insulin peglispro (BIL) is a novel, PEGylated insulin lispro that has a large hydrodynamic size compared with insulin lispro. It has a prolonged duration of action, which is related to a delay in insulin absorption and a reduction in clearance. Given the different physical properties of BIL compared with native insulin and insulin lispro, it is important to assess the cellular internalization characteristics of the molecule. Using immunofluorescent confocal imaging, we compared the cellular internalization and localization patterns of BIL, biosynthetic human insulin, and insulin lispro. We assessed the effects of BIL on internalization of the insulin receptor (IR) and studied cellular clearance of BIL. Co-localization studies using antibodies to either insulin or PEG, and the early endosomal marker EEA1 showed that the overall internalization and subcellular localization pattern of BIL was similar to that of human insulin and insulin lispro; all were rapidly internalized and co-localized with EEA1. During ligand washout for 4 h, concomitant loss of insulin, PEG methoxy group, and PEG backbone immunostaining was observed for BIL, similar to the loss of insulin immunostaining observed for insulin lispro and human insulin. Co-localization studies using an antibody to the lysosomal marker LAMP1 did not reveal evidence of lysosomal localization for insulin lispro, human insulin, BIL, or PEG using either insulin or PEG immunostaining reagents. BIL and human insulin both induced rapid phosphorylation and internalization of human IR. Our findings show that treatment of cells with BIL stimulates internalization and localization of IR to early endosomes. Both the insulin and PEG moieties of BIL undergo a dynamic cellular process of rapid internalization and transport to early endosomes followed by loss of cellular immunostaining in a manner similar to that of insulin lispro and human insulin. The rate of clearance for the insulin lispro portion of BIL was slower than the rate of clearance for human insulin. In contrast, the PEG moiety of BIL can recycle out of cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Exploring the patterns and evolution of self-organized urban street networks through modeling

NASA Astrophysics Data System (ADS)

Rui, Yikang; Ban, Yifang; Wang, Jiechen; Haas, Jan

2013-03-01

As one of the most important subsystems in cities, urban street networks have recently been well studied by using the approach of complex networks. This paper proposes a growing model for self-organized urban street networks. The model involves a competition among new centers with different values of attraction radius and a local optimal principle of both geometrical and topological factors. We find that with the model growth, the local optimization in the connection process and appropriate probability for the loop construction well reflect the evolution strategy in real-world cities. Moreover, different values of attraction radius in centers competition process lead to morphological change in patterns including urban network, polycentric and monocentric structures. The model succeeds in reproducing a large diversity of road network patterns by varying parameters. The similarity between the properties of our model and empirical results implies that a simple universal growth mechanism exists in self-organized cities.

Numerical simulation of the effects of urban land-use changes on the local climate of multiple desert cities

NASA Astrophysics Data System (ADS)

Kamal, S. M.; Huang, H. P.; Myint, S. W.

2016-12-01

This study quantifies the effect of urbanization on local climate by numerical simulations for multiple desert cities with a wide range of urban size, baseline climatology, and composition of land cover. The numerical experiments use the Weather Research and Forecasting (WRF) model with multiple layers of nesting centered at a desert city. To extract the influence of land-use changes, twin runs are performed with each pair driven by the same time-varying lateral boundary conditions from reanalysis but different land surface conditions from Landsat observations for 1985 and 2010. The differences in the meteorological fields between the two runs are interpreted as the effects of land-use changes due to urbanization from 1985-2010. Using this strategy, simulations are carried out for five desert cities: (1) Las Vegas, United States, (2) Hotan, China, (3) Kharga, Egypt, (4) Beer Sheva, Israel, and (5) Jodhpur, India. The results of the simulations reveal a common pattern of the climatic effect of desert urbanization with nighttime warming but daytime cooling over areas where urbanization occurred. This effect is mainly confined to the urban area and is not sensitive to the size of the city or the detail of land cover in the surrounding non-urban areas. The pattern is similar in winter and summer. Exceptions to this pattern are found in a few cases in which the noisiness of local circulation, specifically monsoon and land-sea breeze, overwhelms the climatic signal induced by land-use changes. Although the local climatic responses to urbanization are qualitatively similar for the five desert cities, quantitative differences exist in the magnitudes of nighttime warming and daytime cooling. The possible reasons for those secondary differences are discussed.

Excitatory Local Interneurons Enhance Tuning of Sensory Information

PubMed Central

Assisi, Collins; Stopfer, Mark; Bazhenov, Maxim

2012-01-01

Neurons in the insect antennal lobe represent odors as spatiotemporal patterns of activity that unfold over multiple time scales. As these patterns unspool they decrease the overlap between odor representations and thereby increase the ability of the olfactory system to discriminate odors. Using a realistic model of the insect antennal lobe we examined two competing components of this process –lateral excitation from local excitatory interneurons, and slow inhibition from local inhibitory interneurons. We found that lateral excitation amplified differences between representations of similar odors by recruiting projection neurons that did not receive direct input from olfactory receptors. However, this increased sensitivity also amplified noisy variations in input and compromised the ability of the system to respond reliably to multiple presentations of the same odor. Slow inhibition curtailed the spread of projection neuron activity and increased response reliability. These competing influences must be finely balanced in order to decorrelate odor representations. PMID:22807661

Commonalities in Educational Technology Policy Initiatives among Nations.

ERIC Educational Resources Information Center

Schnitz, James E.; Azbell, Janet

While education systems from nation to nation differ significantly according to national character and local requirements, developments in public policy initiatives regarding the use of technology in schools have followed similar patterns among nations as diverse as the United States, Great Britain, Denmark, Italy, Viet Nam, Germany, France,…

Spatio-temporal patterns of bacteria caused by collective motion

NASA Astrophysics Data System (ADS)

Kitsunezaki, So

2006-04-01

In incubation experiments on bacterial colonies of Proteus mirabilis, collective motion of bacteria is found to generate macroscopic turbulent patterns on the surface of agar media. We propose a mathematical model to describe the time evolution of the positional and directional distributions of motile bacteria in such systems, and investigate this model both numerically and analytically. It is shown that as the average density of bacteria increases, nonuniform swarming patterns emerge from a uniform stationary state. For a sufficient large density, we find that spiral patterns are caused by interactions between the local bacteria densities and the rotational mode of the collective motion. Unidirectional spiral patterns similar to those observed in experiments appear in the case in which the equilibrium directional distribution is asymmetric.

Comparison of techniques for approximating ocean bottom topography in a wave-refraction computer model

NASA Technical Reports Server (NTRS)

Poole, L. R.

1975-01-01

A study of the effects of using different methods for approximating bottom topography in a wave-refraction computer model was conducted. Approximation techniques involving quadratic least squares, cubic least squares, and constrained bicubic polynomial interpolation were compared for computed wave patterns and parameters in the region of Saco Bay, Maine. Although substantial local differences can be attributed to use of the different approximation techniques, results indicated that overall computed wave patterns and parameter distributions were quite similar.

Phase demodulation method from a single fringe pattern based on correlation with a polynomial form.

PubMed

Robin, Eric; Valle, Valéry; Brémand, Fabrice

2005-12-01

The method presented extracts the demodulated phase from only one fringe pattern. Locally, this method approaches the fringe pattern morphology with the help of a mathematical model. The degree of similarity between the mathematical model and the real fringe is estimated by minimizing a correlation function. To use an optimization process, we have chosen a polynomial form such as a mathematical model. However, the use of a polynomial form induces an identification procedure with the purpose of retrieving the demodulated phase. This method, polynomial modulated phase correlation, is tested on several examples. Its performance, in terms of speed and precision, is presented on very noised fringe patterns.

Seeing a straight line on a curved surface: decoupling of patterns from surfaces by single IT neurons

PubMed Central

Ratan Murty, N. Apurva

2016-01-01

We have no difficulty seeing a straight line drawn on a paper even when the paper is bent, but this inference is in fact nontrivial. Doing so requires either matching local features or representing the pattern after factoring out the surface shape. Here we show that single neurons in the monkey inferior temporal (IT) cortex show invariant responses to patterns across rigid and nonrigid changes of surfaces. We recorded neuronal responses to stimuli in which the pattern and the surrounding surface were varied independently. In a subset of neurons, we found pattern-surface interactions that produced similar responses to stimuli across congruent pattern and surface transformations. These interactions produced systematic shifts in curvature tuning of patterns when overlaid on convex and flat surfaces. Our results show that surfaces are factored out of patterns by single neurons, thereby enabling complex perceptual inferences. NEW & NOTEWORTHY We have no difficulty seeing a straight line on a curved piece of paper, but in fact, doing so requires decoupling the shape of the surface from the pattern itself. Here we report a novel form of invariance in the visual cortex: single neurons in monkey inferior temporal cortex respond similarly to congruent transformations of patterns and surfaces, in effect decoupling patterns from the surface on which they are overlaid. PMID:27733595

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists.

PubMed

Lentendu, Guillaume; Mahé, Frédéric; Bass, David; Rueckert, Sonja; Stoeck, Thorsten; Dunthorn, Micah

2018-05-30

Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests. © 2018 John Wiley & Sons Ltd.

Self-organised silicide nanodot patterning by medium-energy ion beam sputtering of Si(100): local correlation between the morphology and metal content.

PubMed

Redondo-Cubero, A; Galiana, B; Lorenz, K; Palomares, F J; Bahena, D; Ballesteros, C; Hernandez-Calderón, I; Vázquez, L

2016-11-04

We have produced self-organised silicide nanodot patterns by medium-energy ion beam sputtering (IBS) of silicon targets with a simultaneous and isotropic molybdenum supply. Atomic force microscopy (AFM) studies show that these patterns are qualitatively similar to those produced thus far at low ion energies. We have determined the relevance of the ion species on the pattern ordering and properties. For the higher ordered patterns produced by Xe(+) ions, the pattern wavelength depends linearly on the ion energy. The dot nanostructures are silicide-rich as assessed by x-ray photoelectron spectroscopy (XPS) and emerge in height due to their lower sputtering yield, as observed by electron microscopy. Remarkably, a long wavelength corrugation is observed on the surface which is correlated with both the Mo content and the dot pattern properties. Thus, as assessed by electron microscopy, the protrusions are Mo-rich with higher and more spaced dots on their surface whereas the valleys are Mo-poor with smaller dots that are closer to each other. These findings indicate that there is a correlation between the local metal content of the surface and the nanodot pattern properties both at the nanodot and the large corrugation scales. These results contribute to advancing the understanding of this interesting nanofabrication method and aid in developing a comprehensive theory of nanodot pattern formation and evolution.

Protein functional features are reflected in the patterns of mRNA translation speed.

PubMed

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

Phylogenetic relatedness and leaf functional traits, not introduced status, influence community assembly.

PubMed

Lemoine, Nathan P; Shue, Jessica; Verrico, Brittany; Erickson, David; Kress, W John; Parker, John D

2015-10-01

Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity explain local abundance of both native and introduced species, which would suggest similar assembly mechanisms regardless of origin. Using a chronosequence of invaded temperate forest stands, we tested whether the occurrence and abundance of both introduced and native species were predicted by phylogenetic relatedness, functional overlap, and key environmental characteristics including forest age. Environmental filtering against functionally and phylogenetically distinct species strongly dictated the occurrence and abundance of both introduced and native species, with slight modifications of these patterns according to forest age. Thus, once functional and evolutionary novelty were quantified, introduced status provided little information about species' presence or abundance, indicating largely similar sorting mechanisms for both native and introduced species.

Multiscale Trend Analysis for Pampa Grasslands Using Ground Data and Vegetation Sensor Imagery

PubMed Central

Scottá, Fernando C.; da Fonseca, Eliana L.

2015-01-01

This study aimed to evaluate changes in the aboveground net primary productivity (ANPP) of grasslands in the Pampa biome by using experimental plots and changes in the spectral responses of similar vegetation communities obtained by remote sensing and to compare both datasets with meteorological variations to validate the transition scales of the datasets. Two different geographic scales were considered in this study. At the local scale, an analysis of the climate and its direct influences on grassland ANPP was performed using data from a long-term experiment. At the regional scale, the influences of climate on the grassland reflectance patterns were determined using vegetation sensor imagery data. Overall, the monthly variations of vegetation canopy growth analysed using environmental changes (air temperature, total rainfall and total evapotranspiration) were similar. The results from the ANPP data and the NDVI data showed the that variations in grassland growth were similar and independent of the analysis scale, which indicated that local data and the relationships of local data with climate can be considered at the regional scale in the Pampa biome by using remote sensing. PMID:26197320

Subtropical Interactions: Comparing Galling Insect and Host Plant Diversity in Southern Brazil and Florida.

PubMed

D S Mendonça, M; Stiling, P

2017-11-22

Gall-inducing insects seem to have a diversity pattern distinct from the usual latitudinal decrease in species, with more species occurring in xeric environments instead. Many questions regarding galler diversity over geographical scales remain unanswered: for example, little is known about beta diversity, and the role super host plants play in local/regional richness. Our aim was to compare galling insect and host plant diversity in different biogeographical regions, but under similar environmental conditions. We sampled short stature coastal woodlands on sandy soils of the Atlantic coast in both USA (Florida) and Brazil (Rio Grande do Sul, RS), between 25° and 30° latitude. Little-used 200-m long trails were searched during 90 min for galls; there were four trails in USA and five in Brazil. Gall functional traits (galled plant organ, gall shape and colour) proportions were not different between Florida and RS. Local galling and host plant species richness also did not differ, and neither did regional galling diversity. The beta diversity pattern, however, was distinct: sites in Florida have more similar galling faunas than sites in RS. Common diversity patterns indicate common environmental biotic (plant diversity, vegetation structure) and abiotic (climate, soil) factors might be contributing to these similar responses. As Brazilian sites are in the Atlantic forest hotspot, a high galling insect beta diversity might be caused by a higher heterogeneity at larger scales-sample-based rarefaction curves were ascending for Brazil, but not for USA. Myrtaceans were super hosts in Brazil, but not in Florida, where oaks take up this role.

Discovering Cortical Folding Patterns in Neonatal Cortical Surfaces Using Large-Scale Dataset

PubMed Central

Meng, Yu; Li, Gang; Wang, Li; Lin, Weili; Gilmore, John H.

2017-01-01

The cortical folding of the human brain is highly complex and variable across individuals. Mining the major patterns of cortical folding from modern large-scale neuroimaging datasets is of great importance in advancing techniques for neuroimaging analysis and understanding the inter-individual variations of cortical folding and its relationship with cognitive function and disorders. As the primary cortical folding is genetically influenced and has been established at term birth, neonates with the minimal exposure to the complicated postnatal environmental influence are the ideal candidates for understanding the major patterns of cortical folding. In this paper, for the first time, we propose a novel method for discovering the major patterns of cortical folding in a large-scale dataset of neonatal brain MR images (N = 677). In our method, first, cortical folding is characterized by the distribution of sulcal pits, which are the locally deepest points in cortical sulci. Because deep sulcal pits are genetically related, relatively consistent across individuals, and also stable during brain development, they are well suitable for representing and characterizing cortical folding. Then, the similarities between sulcal pit distributions of any two subjects are measured from spatial, geometrical, and topological points of view. Next, these different measurements are adaptively fused together using a similarity network fusion technique, to preserve their common information and also catch their complementary information. Finally, leveraging the fused similarity measurements, a hierarchical affinity propagation algorithm is used to group similar sulcal folding patterns together. The proposed method has been applied to 677 neonatal brains (the largest neonatal dataset to our knowledge) in the central sulcus, superior temporal sulcus, and cingulate sulcus, and revealed multiple distinct and meaningful folding patterns in each region. PMID:28229131

Reproduction of overall spontaneous pain pattern by manual stimulation of active myofascial trigger points in fibromyalgia patients

PubMed Central

2011-01-01

Introduction It has previously been reported that local and referred pain from active myofascial trigger points (MTPs) in the neck and shoulder region contribute to fibromyalgia (FM) pain and that the pain pattern induced from active MTPs can reproduce parts of the spontaneous clinical FM pain pattern. The current study investigated whether the overall spontaneous FM pain pattern can be reproduced by local and referred pain from active MTPs located in different muscles. Methods A spontaneous pain pattern in FM was recorded in 30 FM patients and 30 healthy subjects served as controls. Local and referred pain patterns induced from active (patients) and latent (controls) MTPs were recorded following manual stimulation. The existence of MTPs was confirmed by intramuscular electromyographical registration of spontaneous electrical activity. Results Local and referred pain areas induced from key active MTPs in FM were larger than pain areas from latent MTPs in healthy controls (P < 0.001), but were similar to the overall spontaneous FM pain area in FM (P > 0.05). The induced pain area was positively associated with current spontaneous pain intensity in FM (P < 0.01). The locations of key active MTPs in FM patients were found to have latent MTPs in healthy subjects. The muscles containing key active MTPs in FM are often observed in the muscles of extensor digitorum, trapezius, infraspinatus in the upper part of the body and of quadratus lumborum, gluteus medius in the lower part of the body. Conclusions The overall spontaneous FM pain pattern can be reproduced by mechanical stimulation of active MTPs located in different muscles, suggesting that fibromyalgia pain is largely composed of pain arising from muscle pain and spasm. Targeting active MTPs and related perpetuating factors may be an important strategy in FM pain control. Trial registration ISRCTN ISRCTN43167547. PMID:21426569

On the unsteady gravity-capillary wave pattern found behind a slow moving localized pressure distribution

NASA Astrophysics Data System (ADS)

Masnadi, N.; Duncan, J. H.

2013-11-01

The non-linear response of a water surface to a slow-moving pressure distribution is studied experimentally using a vertically oriented carriage-mounted air-jet tube that is set to translate over the water surface in a long tank. The free surface deformation pattern is measured with a full-field refraction-based method that utilizes a vertically oriented digital movie camera (under the tank) and a random dot pattern (above the water surface). At towing speeds just below the minimum phase speed of gravity-capillary waves (cmin ~ 23 cm/s), an unsteady V-shaped pattern is formed behind the pressure source. Localized depressions are generated near the source and propagate in pairs along the two arms of the V-shaped pattern. These depressions are eventually shed from the tips of the pattern at a frequency of about 1 Hz. It is found that the shape and phase speeds of the first depressions shed in each run are quantitatively similar to the freely-propagating gravity-capillary lumps from potential flow calculations. In the experiments, the amplitudes of the depressions decrease by approximately 60 percent while travelling 12 wavelengths. The depressions shed later in each run behave in a less consistent manner, probably due to their interaction with neighboring depressions.

An immunohistochemical study of APG-2 protein in the rat hippocampus after transient forebrain ischemia.

PubMed

Lee, Mun-Yong; Choi, Yun-Sik; Choi, Jeong-Sun; Min, Do Sik; Chun, Myung-Hoon; Kim, Ok Nyu; Lee, Sang Bok; Kim, Seong Yun

2002-01-11

The cellular localization and spatiotemporal expression pattern of APG-2 protein, a member of the heat shock protein 110 family, were investigated in the rat hippocampus after transient forebrain ischemia. The spatiotemporal patterns of immunoreactivity of both APG-2 and glial fibrillary acidic protein were very similar, indicating that reactive astrocytes express APG-2, which was confirmed by double immunofluorescence histochemistry. Colocalization of APG-2 and a neuronal marker NeuN in the neurons of the CA2 and CA3 subfields was also confirmed.

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

Riggs, J.B.

An experimental test model, which is dynamically similar to an actual UCC (Under ground Coal Conversion) system, has been used to determine fluid flow patterns and local heat transfer that occur in the UCC burn cavity. This study should provide insight into the little understood mechanisms (i.e., heat transfer and oxygen transport to the cavity walls) which control maximum cavity width, and therefore resource recovery during UCC. The experimental system is operational and producing physically realistic results. The qualitative results of this study have shown the dominant effect of free convection on the flow pattern of the system.

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

Rodríguez-González, R.; Martínez-Orozco, J. C.; Madrigal-Melchor, J.

In this work we use the standard T-matrix method to study the tunneling of Dirac electrons through graphene multilayers. A graphene sheet is deposited on top of slabs of Silicon-Oxide (SiO{sub 2}) and Silicon-Carbide (SiC) substrates, in which we applied the Cantor’s series. We calculate the transmittance as a function of energy for different incident angles and different generations of the Cantor’s series. Comparing the transmittance, we found three types of self-similarity: (a) local - into generations, (b) between incident angles and (c) between generations. We also compute the angular distribution of the transmittance for fixed energies finding a self-similarmore » pattern between generations. To our knowledge is the first time that four different self-similar patterns are presented in Cantor-based multilayers.« less

Is the clinicopathological pattern of colorectal carcinoma similar in the state and private healthcare systems of South Africa? Analysis of a Durban colorectal cancer database.

PubMed

Ntombela, Xolani H; Zulu, Babongile Mw; Masenya, Molikane; Sartorius, Ben; Madiba, Thandinkosi E

2017-10-01

Previous state hospital-based local studies suggest varying population-based clinicopathological patterns of colorectal cancer (CRC). Patients diagnosed with CRC in the state and private sector hospitals in Durban, South Africa over a 12-month period (January-December 2009) form the basis of our study. Of 491 patients (172 state and 319 private sector patients), 258 were men. State patients were younger than private patients. Anatomical site distribution was similar in both groups with minor variations. Stage IV disease was more common in state patients. State patients were younger, presented with advanced disease and had a lower resection rate. Black patients were the youngest, presented with advanced disease and had the lowest resection rate.

Model-based document categorization employing semantic pattern analysis and local structure clustering

NASA Astrophysics Data System (ADS)

Fume, Kosei; Ishitani, Yasuto

2008-01-01

We propose a document categorization method based on a document model that can be defined externally for each task and that categorizes Web content or business documents into a target category in accordance with the similarity of the model. The main feature of the proposed method consists of two aspects of semantics extraction from an input document. The semantics of terms are extracted by the semantic pattern analysis and implicit meanings of document substructure are specified by a bottom-up text clustering technique focusing on the similarity of text line attributes. We have constructed a system based on the proposed method for trial purposes. The experimental results show that the system achieves more than 80% classification accuracy in categorizing Web content and business documents into 15 or 70 categories.

Geometry Of Discrete Sets With Applications To Pattern Recognition

NASA Astrophysics Data System (ADS)

Sinha, Divyendu

1990-03-01

In this paper we present a new framework for discrete black and white images that employs only integer arithmetic. This framework is shown to retain the essential characteristics of the framework for Euclidean images. We propose two norms and based on them, the permissible geometric operations on images are defined. The basic invariants of our geometry are line images, structure of image and the corresponding local property of strong attachment of pixels. The permissible operations also preserve the 3x3 neighborhoods, area, and perpendicularity. The structure, patterns, and the inter-pattern gaps in a discrete image are shown to be conserved by the magnification and contraction process. Our notions of approximate congruence, similarity and symmetry are similar, in character, to the corresponding notions, for Euclidean images [1]. We mention two discrete pattern recognition algorithms that work purely with integers, and which fit into our framework. Their performance has been shown to be at par with the performance of traditional geometric schemes. Also, all the undesired effects of finite length registers in fixed point arithmetic that plague traditional algorithms, are non-existent in this family of algorithms.

New York State's Extreme School Segregation: Inequality, Inaction and a Damaged Future

ERIC Educational Resources Information Center

Kucsera, John

2014-01-01

The fight for equal educational opportunity in New York has followed a pattern similar to other diverse or racially transforming states. From the 1950s to 1980s, the issue of school desegregation was an important issue. Local civil rights pressure, the courts, and legislation attempted to desegregate large urban school systems through both…

Gender Inequalities in the Education of the Second Generation in Western Countries

ERIC Educational Resources Information Center

Fleischmann, Fenella; Kristen, Cornelia

2014-01-01

Drawing on comparative analyses from nine Western countries, we ask whether local-born children from a wide range of immigrant groups show patterns of female advantage in education that are similar to those prevalent in their host Western societies. We consider five outcomes throughout the educational career: test scores or grades at age 15,…

Pattern and process of biotic homogenization in the New Pangaea

PubMed Central

Baiser, Benjamin; Olden, Julian D.; Record, Sydne; Lockwood, Julie L.; McKinney, Michael L.

2012-01-01

Human activities have reorganized the earth's biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. Furthermore, change in pairwise similarity is itself dependent on two distinct processes, spatial turnover in species composition and changes in gradients of species richness. Most past research has failed to disentangle the effect of these two mechanisms on homogenization patterns. Here, we use recent statistical advances and collate a global database of homogenization studies (20 studies, 50 datasets) to provide the first global investigation of the homogenization process across major faunal and floral groups and elucidate the relative role of changes in species richness and turnover. We found evidence of homogenization (change in similarity ranging from −0.02 to 0.09) across nearly all taxonomic groups, spatial extent and grain sizes. Partitioning of change in pairwise similarity shows that overall change in community similarity is driven by changes in species richness. Our results show that biotic homogenization is truly a global phenomenon and put into question many of the ecological mechanisms invoked in previous studies to explain patterns of homogenization. PMID:23055062

Pattern and process of biotic homogenization in the New Pangaea.

PubMed

Baiser, Benjamin; Olden, Julian D; Record, Sydne; Lockwood, Julie L; McKinney, Michael L

2012-12-07

Human activities have reorganized the earth's biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. Furthermore, change in pairwise similarity is itself dependent on two distinct processes, spatial turnover in species composition and changes in gradients of species richness. Most past research has failed to disentangle the effect of these two mechanisms on homogenization patterns. Here, we use recent statistical advances and collate a global database of homogenization studies (20 studies, 50 datasets) to provide the first global investigation of the homogenization process across major faunal and floral groups and elucidate the relative role of changes in species richness and turnover. We found evidence of homogenization (change in similarity ranging from -0.02 to 0.09) across nearly all taxonomic groups, spatial extent and grain sizes. Partitioning of change in pairwise similarity shows that overall change in community similarity is driven by changes in species richness. Our results show that biotic homogenization is truly a global phenomenon and put into question many of the ecological mechanisms invoked in previous studies to explain patterns of homogenization.

Are adaptation costs necessary to build up a local adaptation pattern?

PubMed

Magalhães, Sara; Blanchet, Elodie; Egas, Martijn; Olivieri, Isabelle

2009-08-03

Ecological specialization is pervasive in phytophagous arthropods. In such specialization mode, limits to host range are imposed by trade-offs preventing adaptation to several hosts. The occurrence of such trade-offs is inferred by a pattern of local adaptation, i.e., a negative correlation between relative performance on different hosts. To establish a causal link between local adaptation and trade-offs, we performed experimental evolution of spider mites on cucumber, tomato and pepper, starting from a population adapted to cucumber. Spider mites adapted to each novel host within 15 generations and no further evolution was observed at generation 25. A pattern of local adaptation was found, as lines evolving on a novel host performed better on that host than lines evolving on other hosts. However, costs of adaptation were absent. Indeed, lines adapted to tomato had similar or higher performance on pepper than lines evolving on the ancestral host (which represent the initial performance of all lines) and the converse was also true, e.g. negatively correlated responses were not observed on the alternative novel host. Moreover, adapting to novel hosts did not result in decreased performance on the ancestral host. Adaptation did not modify host ranking, as all lines performed best on the ancestral host. Furthermore, mites from all lines preferred the ancestral to novel hosts. Mate choice experiments indicated that crosses between individuals from the same or from a different selection regime were equally likely, hence development of reproductive isolation among lines adapted to different hosts is unlikely. Therefore, performance and preference are not expected to impose limits to host range in our study species. Our results show that the evolution of a local adaptation pattern is not necessarily associated with the evolution of an adaptation cost.

A hierarchical framework for investigating epiphyte assemblages: networks, meta-communities, and scale.

PubMed

Burns, K C; Zotz, G

2010-02-01

Epiphytes are an important component of many forested ecosystems, yet our understanding of epiphyte communities lags far behind that of terrestrial-based plant communities. This discrepancy is exacerbated by the lack of a theoretical context to assess patterns in epiphyte community structure. We attempt to fill this gap by developing an analytical framework to investigate epiphyte assemblages, which we then apply to a data set on epiphyte distributions in a Panamanian rain forest. On a coarse scale, interactions between epiphyte species and host tree species can be viewed as bipartite networks, similar to pollination and seed dispersal networks. On a finer scale, epiphyte communities on individual host trees can be viewed as meta-communities, or suites of local epiphyte communities connected by dispersal. Similar analytical tools are typically employed to investigate species interaction networks and meta-communities, thus providing a unified analytical framework to investigate coarse-scale (network) and fine-scale (meta-community) patterns in epiphyte distributions. Coarse-scale analysis of the Panamanian data set showed that most epiphyte species interacted with fewer host species than expected by chance. Fine-scale analyses showed that epiphyte species richness on individual trees was lower than null model expectations. Therefore, epiphyte distributions were clumped at both scales, perhaps as a result of dispersal limitations. Scale-dependent patterns in epiphyte species composition were observed. Epiphyte-host networks showed evidence of negative co-occurrence patterns, which could arise from adaptations among epiphyte species to avoid competition for host species, while most epiphyte meta-communities were distributed at random. Application of our "meta-network" analytical framework in other locales may help to identify general patterns in the structure of epiphyte assemblages and their variation in space and time.

Change in Pattern of Relapse After Antiangiogenic Therapy in High-Grade Glioma

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

Narayana, Ashwatha, E-mail: ashwatha.narayana@nyumc.org; Department of Neurosurgery, New York University Langone Medical Center, New York, NY; Kunnakkat, Saroj D.

2012-01-01

Purpose: Local recurrence is the dominant pattern of relapse in high-grade glioma (HGG) after conventional therapy. The recent use of antiangiogenic therapy has shown impressive radiologic and clinical responses in adult HGG. The preclinical data suggesting increased invasiveness after angiogenic blockade have necessitated a detailed analysis of the pattern of recurrence after therapy. Methods and Materials: A total of 162 consecutive patients with HGG, either newly diagnosed (n = 58) or with recurrent disease (n = 104) underwent therapy with bevacizumab at 10 mg/kg every 2 weeks and conventional chemotherapy with or without involved field radiotherapy until disease progression. Themore » pattern of recurrence and interval to progression were the primary aims of the present study. Diffuse invasive recurrence (DIR) was defined as the involvement of multiple lobes with or without crossing the midline. Results: At a median follow-up of 7 months (range, 1-37), 105 patients had recurrence, and 79 patients ultimately developed DIR. The interval to progression was similar in the DIR and local recurrence groups (6.5 and 6.3 months, p = .296). The hazard risk of DIR increased exponentially with time and was similar in those with newly diagnosed and recurrent HGG (R{sup 2} = 0.957). The duration of bevacizumab therapy increased the interval to recurrence (p < .0001) and improved overall survival (p < .0001). However, the pattern of relapse did not affect overall survival (p = .253). Conclusion: Along with an increase in median progression-free survival, bevacizumab therapy increased the risk of DIR in HGG patients. The risk of increased invasion with prolonged angiogenic blockade should be addressed in future clinical trials.« less

A segmentation approach for a delineation of terrestrial ecoregions

NASA Astrophysics Data System (ADS)

Nowosad, J.; Stepinski, T.

2017-12-01

Terrestrial ecoregions are the result of regionalization of land into homogeneous units of similar ecological and physiographic features. Terrestrial Ecoregions of the World (TEW) is a commonly used global ecoregionalization based on expert knowledge and in situ observations. Ecological Land Units (ELUs) is a global classification of 250 meters-sized cells into 4000 types on the basis of the categorical values of four environmental variables. ELUs are automatically calculated and reproducible but they are not a regionalization which makes them impractical for GIS-based spatial analysis and for comparison with TEW. We have regionalized terrestrial ecosystems on the basis of patterns of the same variables (land cover, soils, landform, and bioclimate) previously used in ELUs. Considering patterns of categorical variables makes segmentation and thus regionalization possible. Original raster datasets of the four variables are first transformed into regular grids of square-sized blocks of their cells called eco-sites. Eco-sites are elementary land units containing local patterns of physiographic characteristics and thus assumed to contain a single ecosystem. Next, eco-sites are locally aggregated using a procedure analogous to image segmentation. The procedure optimizes pattern homogeneity of all four environmental variables within each segment. The result is a regionalization of the landmass into land units characterized by uniform pattern of land cover, soils, landforms, climate, and, by inference, by uniform ecosystem. Because several disjoined segments may have very similar characteristics, we cluster the segments to obtain a smaller set of segment types which we identify with ecoregions. Our approach is automatic, reproducible, updatable, and customizable. It yields the first automatic delineation of ecoregions on the global scale. In the resulting vector database each ecoregion/segment is described by numerous attributes which make it a valuable GIS resource for global ecological and conservation studies.

MotionFlow: Visual Abstraction and Aggregation of Sequential Patterns in Human Motion Tracking Data.

PubMed

Jang, Sujin; Elmqvist, Niklas; Ramani, Karthik

2016-01-01

Pattern analysis of human motions, which is useful in many research areas, requires understanding and comparison of different styles of motion patterns. However, working with human motion tracking data to support such analysis poses great challenges. In this paper, we propose MotionFlow, a visual analytics system that provides an effective overview of various motion patterns based on an interactive flow visualization. This visualization formulates a motion sequence as transitions between static poses, and aggregates these sequences into a tree diagram to construct a set of motion patterns. The system also allows the users to directly reflect the context of data and their perception of pose similarities in generating representative pose states. We provide local and global controls over the partition-based clustering process. To support the users in organizing unstructured motion data into pattern groups, we designed a set of interactions that enables searching for similar motion sequences from the data, detailed exploration of data subsets, and creating and modifying the group of motion patterns. To evaluate the usability of MotionFlow, we conducted a user study with six researchers with expertise in gesture-based interaction design. They used MotionFlow to explore and organize unstructured motion tracking data. Results show that the researchers were able to easily learn how to use MotionFlow, and the system effectively supported their pattern analysis activities, including leveraging their perception and domain knowledge.

Predicting the impact of urban flooding using open data.

PubMed

Tkachenko, Nataliya; Procter, Rob; Jarvis, Stephen

2016-05-01

This paper aims to explore whether there is a relationship between search patterns for flood risk information on the Web and how badly localities have been affected by flood events. We hypothesize that localities where people stay more actively informed about potential flooding experience less negative impact than localities where people make less effort to be informed. Being informed, of course, does not hold the waters back; however, it may stimulate (or serve as an indicator of) such resilient behaviours as timely use of sandbags, relocation of possessions from basements to upper floors and/or temporary evacuation from flooded homes to alternative accommodation. We make use of open data to test this relationship empirically. Our results demonstrate that although aggregated Web search reflects average rainfall patterns, its eigenvectors predominantly consist of locations with similar flood impacts during 2014-2015. These results are also consistent with statistically significant correlations of Web search eigenvectors with flood warning and incident reporting datasets.

Local pH oscillations witness autocatalytic self-organization of biomorphic nanostructures

NASA Astrophysics Data System (ADS)

Montalti, M.; Zhang, G.; Genovese, D.; Morales, J.; Kellermeier, M.; García-Ruiz, J. M.

2017-02-01

Bottom-up self-assembly of simple molecular compounds is a prime pathway to complex materials with interesting structures and functions. Coupled reaction systems are known to spontaneously produce highly ordered patterns, so far observed in soft matter. Here we show that similar phenomena can occur during silica-carbonate crystallization, the emerging order being preserved. The resulting materials, called silica biomorphs, exhibit non-crystallographic curved morphologies and hierarchical textures, much reminiscent of structural principles found in natural biominerals. We have used a fluorescent chemosensor to probe local conditions during the growth of such self-organized nanostructures. We demonstrate that the pH oscillates in the local microenvironment near the growth front due to chemical coupling, which becomes manifest in the final mineralized architectures as intrinsic banding patterns with the same periodicity. A better understanding of dynamic autocatalytic crystallization processes in such simple model systems is key to the rational development of advanced materials and to unravel the mechanisms of biomineralization.

A Query Expansion Framework in Image Retrieval Domain Based on Local and Global Analysis

PubMed Central

Rahman, M. M.; Antani, S. K.; Thoma, G. R.

2011-01-01

We present an image retrieval framework based on automatic query expansion in a concept feature space by generalizing the vector space model of information retrieval. In this framework, images are represented by vectors of weighted concepts similar to the keyword-based representation used in text retrieval. To generate the concept vocabularies, a statistical model is built by utilizing Support Vector Machine (SVM)-based classification techniques. The images are represented as “bag of concepts” that comprise perceptually and/or semantically distinguishable color and texture patches from local image regions in a multi-dimensional feature space. To explore the correlation between the concepts and overcome the assumption of feature independence in this model, we propose query expansion techniques in the image domain from a new perspective based on both local and global analysis. For the local analysis, the correlations between the concepts based on the co-occurrence pattern, and the metrical constraints based on the neighborhood proximity between the concepts in encoded images, are analyzed by considering local feedback information. We also analyze the concept similarities in the collection as a whole in the form of a similarity thesaurus and propose an efficient query expansion based on the global analysis. The experimental results on a photographic collection of natural scenes and a biomedical database of different imaging modalities demonstrate the effectiveness of the proposed framework in terms of precision and recall. PMID:21822350

Contrasting patterns of selection between MHC I and II across populations of Humboldt and Magellanic penguins.

PubMed

Sallaberry-Pincheira, Nicole; González-Acuña, Daniel; Padilla, Pamela; Dantas, Gisele P M; Luna-Jorquera, Guillermo; Frere, Esteban; Valdés-Velásquez, Armando; Vianna, Juliana A

2016-10-01

The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow. We hypothesize that high gene flow among populations of Humboldt and Magellanic penguins limits local adaptation in MHC I and MHC II, and signatures of selection differ between markers, locations, and species. We evaluated the MHC I and II diversity using 454 next-generation sequencing of 100 Humboldt and 75 Magellanic penguins from seven different breeding colonies. Higher genetic diversity was observed in MHC I than MHC II for both species, explained by more than one MHC I loci identified. Large population sizes, high gene flow, and/or similar selection pressures maintain diversity but limit local adaptation in MHC I. A pattern of isolation by distance was observed for MHC II for Humboldt penguin suggesting local adaptation, mainly on the northernmost studied locality. Furthermore, trans-species alleles were found due to a recent speciation for the genus or convergent evolution. High MHC I and MHC II gene diversity described is extremely advantageous for the long-term survival of the species.

Root Type-Specific Reprogramming of Maize Pericycle Transcriptomes by Local High Nitrate Results in Disparate Lateral Root Branching Patterns1[OPEN

PubMed Central

Lithio, Andrew

2016-01-01

The adaptability of root system architecture to unevenly distributed mineral nutrients in soil is a key determinant of plant performance. The molecular mechanisms underlying nitrate dependent plasticity of lateral root branching across the different root types of maize are only poorly understood. In this study, detailed morphological and anatomical analyses together with cell type-specific transcriptome profiling experiments combining laser capture microdissection with RNA-seq were performed to unravel the molecular signatures of lateral root formation in primary, seminal, crown, and brace roots of maize (Zea mays) upon local high nitrate stimulation. The four maize root types displayed divergent branching patterns of lateral roots upon local high nitrate stimulation. In particular, brace roots displayed an exceptional architectural plasticity compared to other root types. Transcriptome profiling revealed root type-specific transcriptomic reprogramming of pericycle cells upon local high nitrate stimulation. The alteration of the transcriptomic landscape of brace root pericycle cells in response to local high nitrate stimulation was most significant. Root type-specific transcriptome diversity in response to local high nitrate highlighted differences in the functional adaptability and systemic shoot nitrogen starvation response during development. Integration of morphological, anatomical, and transcriptomic data resulted in a framework underscoring similarity and diversity among root types grown in heterogeneous nitrate environments. PMID:26811190

Sex-specific local life-history adaptation in surface- and cave-dwelling Atlantic mollies (Poecilia mexicana).

PubMed

Riesch, Rüdiger; Reznick, David N; Plath, Martin; Schlupp, Ingo

2016-03-10

Cavefishes have long been used as model organisms showcasing adaptive diversification, but does adaptation to caves also facilitate the evolution of reproductive isolation from surface ancestors? We raised offspring of wild-caught surface- and cave-dwelling ecotypes of the neotropical fish Poecilia mexicana to sexual maturity in a 12-month common garden experiment. Fish were raised under one of two food regimes (high vs. low), and this was crossed with differences in lighting conditions (permanent darkness vs. 12:12 h light:dark cycle) in a 2 × 2 factorial design, allowing us to elucidate potential patterns of local adaptation in life histories. Our results reveal a pattern of sex-specific local life-history adaptation: Surface molly females had the highest fitness in the treatment best resembling their habitat of origin (high food and a light:dark cycle), and suffered from almost complete reproductive failure in darkness, while cave molly females were not similarly affected in any treatment. Males of both ecotypes, on the other hand, showed only weak evidence for local adaptation. Nonetheless, local life-history adaptation in females likely contributes to ecological diversification in this system and other cave animals, further supporting the role of local adaptation due to strong divergent selection as a major force in ecological speciation.

Sex-specific local life-history adaptation in surface- and cave-dwelling Atlantic mollies (Poecilia mexicana)

PubMed Central

Riesch, Rüdiger; Reznick, David N.; Plath, Martin; Schlupp, Ingo

2016-01-01

Cavefishes have long been used as model organisms showcasing adaptive diversification, but does adaptation to caves also facilitate the evolution of reproductive isolation from surface ancestors? We raised offspring of wild-caught surface- and cave-dwelling ecotypes of the neotropical fish Poecilia mexicana to sexual maturity in a 12-month common garden experiment. Fish were raised under one of two food regimes (high vs. low), and this was crossed with differences in lighting conditions (permanent darkness vs. 12:12 h light:dark cycle) in a 2 × 2 factorial design, allowing us to elucidate potential patterns of local adaptation in life histories. Our results reveal a pattern of sex-specific local life-history adaptation: Surface molly females had the highest fitness in the treatment best resembling their habitat of origin (high food and a light:dark cycle), and suffered from almost complete reproductive failure in darkness, while cave molly females were not similarly affected in any treatment. Males of both ecotypes, on the other hand, showed only weak evidence for local adaptation. Nonetheless, local life-history adaptation in females likely contributes to ecological diversification in this system and other cave animals, further supporting the role of local adaptation due to strong divergent selection as a major force in ecological speciation. PMID:26960566

The heterotrimeric motor protein kinesin-II localizes to the midpiece and flagellum of sea urchin and sand dollar sperm.

PubMed

Henson, J H; Cole, D G; Roesener, C D; Capuano, S; Mendola, R J; Scholey, J M

1997-01-01

We have utilized immunoblotting and light microscopic immunofluorescent staining methods to examine the expression and localization of sea urchin kinesin-II, a heterotrimeric plus end-directed microtubule motor protein (previously referred to as KRP(85/95)), in sea urchin and sand dollar sperm. We demonstrate the presence of the 85 K and 115 K subunits of kinesin-II in sperm and localize these proteins to the sperm flagella and midpiece. The kinesin-II localization pattern is punctate and discontinuous, and in the flagella it is quite distinct from the continuous labeling present in sperm labeled with anti-flagellar dynein. The kinesin-II staining is largely insensitive to prefixation detergent extraction, suggesting that it is not associated with membranous elements in the sperm. In the midpiece the kinesin-II staining is similar to the pattern present in sperm labeled with an anti-centrosomal antibody. To our knowledge, this is the first localization of kinesin-like proteins in mature sperm and corroborates the recent identification and localization of kinesin-like proteins in the flagella and basal body of the unicellular green alga Chlamydomonas. We hypothesize that kinesin-II in the sperm may play functional roles in intraflagellar transport and/or the formation of flagella during spermatogenesis.

Comparative study of LDR (Manchester system) and HDR image-guided conformal brachytherapy of cervical cancer: patterns of failure, late complications, and survival.

PubMed

Narayan, Kailash; van Dyk, Sylvia; Bernshaw, David; Rajasooriyar, Chrishanthi; Kondalsamy-Chennakesavan, Srinivas

2009-08-01

To compare patterns of failure, late toxicities, and survival in locally advanced cervical cancer patients treated by either low-dose-rate (LDR) or conformal high-dose-rate (HDRc) brachytherapy as a part of curative radiotherapy. A retrospective comparative study of 217 advanced cervix cancer patients was conducted; 90 of these patients received LDR and 127 received HDRc brachytherapy. All patients were staged using International Federation of Gynecology and Obstetrics (FIGO) rules, had pretreatment magnetic resonance imaging (MRI), and were treated with concurrent cisplatin chemoradiotherapy. Both groups matched for FIGO stage, MRI tumor volume, and uterine invasion status. Local and pelvic failures were similar 12-13% and 14% both in both groups. Abdominal and systemic failures in LDR group were 21% and 24%, whereas corresponding failures in HDRc group were 20% and 24%. Sixty-eight percent (87/127) of patients treated by HDRc remained asymptomatic, whereas 42% (38/90) of patients were asymptomatic from the bowel and bladder symptoms after treatment with LDR. The 5-year OS rate was 60% (SE = 4%). The 5-year failure-free survival rate was 55% (SE = 3%). There was no significant difference between the groups. Image-guided HDRc planning led to a large decrease in late radiation effects in patients treated by HDRc. Patterns of failure and survival were similar in patients treated either by LDR or HDRc.

Directed seed dispersal of Piper by Carollia perspicillata and its effect on understory plant diversity and folivory.

PubMed

Salazar, Diego; Kelm, Detlev H; Salazar, Diego

2013-11-01

Directed dispersal occurs when seeds are differentially deposited to sites where offspring survivorship is higher than at randomly chosen sites. Traditionally, characteristics of the dispersal target sites that could increase survivorship of the dispersed plants are thought to be intrinsic to the sites. If directed dispersal is constant over extended periods of time, however, it is likely that nonrandom patterns of dispersal could modify the ecological characteristics of the target site in ways that could increase survivorship and fitness of the dispersed plants. Here we report patterns of Piper diversity (richness, equitability, and similarity) and Piper folivory within plots near natural or artificial roosts of Carollia perspicillata vs. similar plots without bat roosts. Plots with bat roosts, both natural and artificial, had significantly higher Piper species diversity. Additionally, we found that plots with a higher Piper species diversity showed less specialist folivory, higher generalist folivory, and lower total herbivore leaf damage than plots with low Piper diversity. Finally, plots with bat roosts also showed less specialist folivory, lower generalist folivory, and lower total folivory when compared to plots without roosts. We propose that long-lasting nonrandom patterns of seed dispersal can change the local ecological characteristics of target sites via changes in plant diversity, and that these changes are likely to reduce the local rates of folivory and, therefore, increase seed and adult plant survivorship.

Experimental investigation on the heat transfer characteristics and flow pattern in vertical narrow channels heated from one side

NASA Astrophysics Data System (ADS)

Huang, Lihao; Li, Gang; Tao, Leren

2016-07-01

Experimental investigation for the flow boiling of water in a vertical rectangular channel was conducted to reveal the boiling heat transfer mechanism and flow patterns map aspects. The onset of nucleate boiling went upward with the increasing of the working fluid mass flow rate or the decreasing of the inlet working fluid temperature. As the vapour quality was increased, the local heat transfer coefficient increased first, then decreased, followed by various flow patterns. The test data from other researchers had a similar pattern transition for the bubble-slug flow and the slug-annular flow. Flow pattern transition model analysis was performed to make the comparison with current test data. The slug-annular and churn-annular transition models showed a close trend with current data except that the vapor phase superficial velocity of flow pattern transition was much higher than that of experimental data.

Species turnover drives β-diversity patterns across multiple spatial scales of plant-galling interactions in mountaintop grasslands.

PubMed

Coelho, Marcel Serra; Carneiro, Marco Antônio Alves; Branco, Cristina Alves; Borges, Rafael Augusto Xavier; Fernandes, Geraldo Wilson

2018-01-01

This study describes differences in species richness and composition of the assemblages of galling insects and their host plants at different spatial scales. Sampling was conducted along altitudinal gradients composed of campos rupestres and campos de altitude of two mountain complexes in southeastern Brazil: Espinhaço Range and Mantiqueira Range. The following hypotheses were tested: i) local and regional richness of host plants and galling insects are positively correlated; ii) beta diversity is the most important component of regional diversity of host plants and galling insects; and iii) Turnover is the main mechanism driving beta diversity of both host plants and galling insects. Local richness of galling insects and host plants increased with increasing regional richness of species, suggesting a pattern of unsaturated communities. The additive partition of regional richness (γ) into local and beta components shows that local richnesses (α) of species of galling insects and host plants are low relative to regional richness; the beta (β) component incorporates most of the regional richness. The multi-scale analysis of additive partitioning showed similar patterns for galling insects and host plants with the local component (α) incorporated a small part of regional richness. Beta diversity of galling insects and host plants were mainly the result of turnover, with little contribution from nesting. Although the species composition of galling insects and host plant species varied among sample sites, mountains and even mountain ranges, local richness remained relatively low. In this way, the addition of local habitats with different landscapes substantially affects regional richness. Each mountain contributes fundamentally to the composition of regional diversity of galling insects and host plants, and so the design of future conservation strategies should incorporate multiple scales.

Divisibility patterns of natural numbers on a complex network.

PubMed

Shekatkar, Snehal M; Bhagwat, Chandrasheel; Ambika, G

2015-09-16

Investigation of divisibility properties of natural numbers is one of the most important themes in the theory of numbers. Various tools have been developed over the centuries to discover and study the various patterns in the sequence of natural numbers in the context of divisibility. In the present paper, we study the divisibility of natural numbers using the framework of a growing complex network. In particular, using tools from the field of statistical inference, we show that the network is scale-free but has a non-stationary degree distribution. Along with this, we report a new kind of similarity pattern for the local clustering, which we call "stretching similarity", in this network. We also show that the various characteristics like average degree, global clustering coefficient and assortativity coefficient of the network vary smoothly with the size of the network. Using analytical arguments we estimate the asymptotic behavior of global clustering and average degree which is validated using numerical analysis.

BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies.

PubMed

Wan, Yinan; Long, Fuhui; Qu, Lei; Xiao, Hang; Hawrylycz, Michael; Myers, Eugene W; Peng, Hanchuan

2015-10-01

Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.

Quantitative Characterization of the Nanoscale Local Lattice Strain Induced by Sr Dopants in La1.92Sr0.08CuO4

NASA Astrophysics Data System (ADS)

Lin, J. Q.; Liu, X.; Blackburn, E.; Wakimoto, S.; Ding, H.; Islam, Z.; Sinha, S. K.

2018-05-01

The nanometer scale lattice deformation brought about by the dopants in the high temperature superconducting cuprate La2 -xSrx CuO4 (x =0.08 ) was investigated by measuring the associated x-ray diffuse scattering around multiple Bragg peaks. A characteristic diffuse scattering pattern was observed, which can be well described by continuum elastic theory. With the fitted dipole force parameters, the acoustic-type lattice deformation pattern was reconstructed and found to be of similar size to lattice thermal vibration at 7 K. Our results address the long-term concern of dopant introduced local lattice inhomogeneity, and show that the associated nanometer scale lattice deformation is marginal and cannot, alone, be responsible for the patched variation in the spectral gaps observed with scanning tunneling microscopy in the cuprates.

Analysis of stationary displacement patterns in rotating machinery subject to local harmonic excitation

NASA Astrophysics Data System (ADS)

Österlind, Tomas; Kari, Leif; Nicolescu, Cornel Mihai

2017-02-01

Rotor vibration and stationary displacement patterns observed in rotating machineries subject to local harmonic excitation are analysed for improved understanding and dynamic characterization. The analysis stresses the importance of coordinate transformation between rotating and stationary frame of reference for accurate results and estimation of dynamic properties. A generic method which can be used for various rotor applications such as machine tool spindle and turbo machinery vibration is presented. The phenomenon shares similarities with stationary waves in rotating disks though focuses on vibration in shafts. The paper further proposes a graphical tool, the displacement map, which can be used for selection of stable rotational speed for rotating machinery. The results are validated through simulation of dynamic response of a milling cutter, which is a typical example of a variable speed rotor operating under different load conditions.

Content based image retrieval using local binary pattern operator and data mining techniques.

PubMed

Vatamanu, Oana Astrid; Frandeş, Mirela; Lungeanu, Diana; Mihalaş, Gheorghe-Ioan

2015-01-01

Content based image retrieval (CBIR) concerns the retrieval of similar images from image databases, using feature vectors extracted from images. These feature vectors globally define the visual content present in an image, defined by e.g., texture, colour, shape, and spatial relations between vectors. Herein, we propose the definition of feature vectors using the Local Binary Pattern (LBP) operator. A study was performed in order to determine the optimum LBP variant for the general definition of image feature vectors. The chosen LBP variant is then subsequently used to build an ultrasound image database, and a database with images obtained from Wireless Capsule Endoscopy. The image indexing process is optimized using data clustering techniques for images belonging to the same class. Finally, the proposed indexing method is compared to the classical indexing technique, which is nowadays widely used.

Common Warming Pattern Emerges Irrespective of Forcing Location

NASA Astrophysics Data System (ADS)

Kang, Sarah M.; Park, Kiwoong; Jin, Fei-Fei; Stuecker, Malte F.

2017-10-01

The Earth's climate is changing due to the existence of multiple radiative forcing agents. It is under question whether different forcing agents perturb the global climate in a distinct way. Previous studies have demonstrated the existence of similar climate response patterns in response to aerosol and greenhouse gas (GHG) forcings. In this study, the sensitivity of tropospheric temperature response patterns to surface heating distributions is assessed by forcing an atmospheric general circulation model coupled to an aquaplanet slab ocean with a wide range of possible forcing patterns. We show that a common climate pattern emerges in response to localized forcing at different locations. This pattern, characterized by enhanced warming in the tropical upper troposphere and the polar lower troposphere, resembles the historical trends from observations and models as well as the future projections. Atmospheric dynamics in combination with thermodynamic air-sea coupling are primarily responsible for shaping this pattern. Identifying this common pattern strengthens our confidence in the projected response to GHG and aerosols in complex climate models.

Specifying and Sustaining Pigmentation Patterns in Domestic and Wild Cats

PubMed Central

Kaelin, Christopher B.; Xu, Xiao; Hong, Lewis Z.; David, Victor A.; McGowan, Kelly A.; Schmidt-Küntzel, Anne; Roelke, Melody E.; Pino, Javier; Pontius, Joan; Cooper, Gregory M.; Manuel, Hermogenes; Swanson, William F.; Marker, Laurie; Harper, Cindy K.; van Dyk, Ann; Yue, Bisong; Mullikin, James C.; Warren, Wesley C.; Eizirik, Eduardo; Kos, Lidia; O’Brien, Stephen J.; Barsh, Gregory S.; Menotti-Raymond, Marilyn

2013-01-01

Color markings among felid species display both a remarkable diversity and a common underlying periodicity. A similar range of patterns in domestic cats suggests a conserved mechanism whose appearance can be altered by selection. We identified the gene responsible for tabby pattern variation in domestic cats as Transmembrane aminopeptidase Q (Taqpep), which encodes a membrane-bound metalloprotease. Analyzing 31 other felid species, we identified Taqpep as the cause of the rare king cheetah phenotype, in which spots coalesce into blotches and stripes. Histologic, genomic expression, and transgenic mouse studies indicate that paracrine expression of Endothelin3 (Edn3) coordinates localized color differences. We propose a two-stage model in which Taqpep helps to establish a periodic pre-pattern during skin development that is later implemented by differential expression of Edn3. PMID:22997338

Perceptually relevant grouping of image tokens on the basis of constraint propagation from local binary patterns

NASA Astrophysics Data System (ADS)

Behlim, Sadaf Iqbal; Syed, Tahir Qasim; Malik, Muhammad Yameen; Vigneron, Vincent

2016-11-01

Grouping image tokens is an intermediate step needed to arrive at meaningful image representation and summarization. Usually, perceptual cues, for instance, gestalt properties inform token grouping. However, they do not take into account structural continuities that could be derived from other tokens belonging to similar structures irrespective of their location. We propose an image representation that encodes structural constraints emerging from local binary patterns (LBP), which provides a long-distance measure of similarity but in a structurally connected way. Our representation provides a grouping of pixels or larger image tokens that is free of numeric similarity measures and could therefore be extended to nonmetric spaces. The representation lends itself nicely to ubiquitous image processing applications such as connected component labeling and segmentation. We test our proposed representation on the perceptual grouping or segmentation task on the popular Berkeley segmentation dataset (BSD500) that with respect to human segmented images achieves an average F-measure of 0.559. Our algorithm achieves a high average recall of 0.787 and is therefore well-suited to other applications such as object retrieval and category-independent object recognition. The proposed merging heuristic based on levels of singular tree component has shown promising results on the BSD500 dataset and currently ranks 12th among all benchmarked algorithms, but contrary to the others, it requires no data-driven training or specialized preprocessing.

Semantic representation in the white matter pathway

PubMed Central

Fang, Yuxing; Wang, Xiaosha; Zhong, Suyu; Song, Luping; Han, Zaizhu; Gong, Gaolang

2018-01-01

Object conceptual processing has been localized to distributed cortical regions that represent specific attributes. A challenging question is how object semantic space is formed. We tested a novel framework of representing semantic space in the pattern of white matter (WM) connections by extending the representational similarity analysis (RSA) to structural lesion pattern and behavioral data in 80 brain-damaged patients. For each WM connection, a neural representational dissimilarity matrix (RDM) was computed by first building machine-learning models with the voxel-wise WM lesion patterns as features to predict naming performance of a particular item and then computing the correlation between the predicted naming score and the actual naming score of another item in the testing patients. This correlation was used to build the neural RDM based on the assumption that if the connection pattern contains certain aspects of information shared by the naming processes of these two items, models trained with one item should also predict naming accuracy of the other. Correlating the neural RDM with various cognitive RDMs revealed that neural patterns in several WM connections that connect left occipital/middle temporal regions and anterior temporal regions associated with the object semantic space. Such associations were not attributable to modality-specific attributes (shape, manipulation, color, and motion), to peripheral picture-naming processes (picture visual similarity, phonological similarity), to broad semantic categories, or to the properties of the cortical regions that they connected, which tended to represent multiple modality-specific attributes. That is, the semantic space could be represented through WM connection patterns across cortical regions representing modality-specific attributes. PMID:29624578

Amino acid and nucleotide recurrence in aligned sequences: synonymous substitution patterns in association with global and local base compositions.

PubMed

Nishizawa, M; Nishizawa, K

2000-10-01

The tendency for repetitiveness of nucleotides in DNA sequences has been reported for a variety of organisms. We show that the tendency for repetitive use of amino acids is widespread and is observed even for segments conserved between human and Drosophila melanogaster at the level of >50% amino acid identity. This indicates that repetitiveness influences not only the weakly constrained segments but also those sequence segments conserved among phyla. Not only glutamine (Q) but also many of the 20 amino acids show a comparable level of repetitiveness. Repetitiveness in bases at codon position 3 is stronger for human than for D.melanogaster, whereas local repetitiveness in intron sequences is similar between the two organisms. While genes for immune system-specific proteins, but not ancient human genes (i.e. human homologs of Escherichia coli genes), have repetitiveness at codon bases 1 and 2, repetitiveness at codon base 3 for these groups is similar, suggesting that the human genome has at least two mechanisms generating local repetitiveness. Neither amino acid nor nucleotide repetitiveness is observed beyond the exon boundary, denying the possibility that such repetitiveness could mainly stem from natural selection on mRNA or protein sequences. Analyses of mammalian sequence alignments show that while the 'between gene' GC content heterogeneity, which is linked to 'isochores', is a principal factor associated with the bias in substitution patterns in human, 'within gene' heterogeneity in nucleotide composition is also associated with such bias on a more local scale. The relationship amongst the various types of repetitiveness is discussed.

Amino acid and nucleotide recurrence in aligned sequences: synonymous substitution patterns in association with global and local base compositions

PubMed Central

Nishizawa, Manami; Nishizawa, Kazuhisa

2000-01-01

The tendency for repetitiveness of nucleotides in DNA sequences has been reported for a variety of organisms. We show that the tendency for repetitive use of amino acids is widespread and is observed even for segments conserved between human and Drosophila melanogaster at the level of >50% amino acid identity. This indicates that repetitiveness influences not only the weakly constrained segments but also those sequence segments conserved among phyla. Not only glutamine (Q) but also many of the 20 amino acids show a comparable level of repetitiveness. Repetitiveness in bases at codon position 3 is stronger for human than for D.melanogaster, whereas local repetitiveness in intron sequences is similar between the two organisms. While genes for immune system-specific proteins, but not ancient human genes (i.e. human homologs of Escherichia coli genes), have repetitiveness at codon bases 1 and 2, repetitiveness at codon base 3 for these groups is similar, suggesting that the human genome has at least two mechanisms generating local repetitiveness. Neither amino acid nor nucleotide repetitiveness is observed beyond the exon boundary, denying the possibility that such repetitiveness could mainly stem from natural selection on mRNA or protein sequences. Analyses of mammalian sequence alignments show that while the ‘between gene’ GC content heterogeneity, which is linked to ‘isochores’, is a principal factor associated with the bias in substitution patterns in human, ‘within gene’ heterogeneity in nucleotide composition is also associated with such bias on a more local scale. The relationship amongst the various types of repetitiveness is discussed. PMID:11000273

Squids in the Study of Cerebral Magnetic Field

NASA Astrophysics Data System (ADS)

Romani, G. L.; Narici, L.

The following sections are included: * INTRODUCTION * HISTORICAL OVERVIEW * NEUROMAGNETIC FIELDS AND AMBIENT NOISE * DETECTORS * Room temperature sensors * SQUIDs * DETECTION COILS * Magnetometers * Gradiometers * Balancing * Planar gradiometers * Choice of the gradiometer parameters * MODELING * Current pattern due to neural excitations * Action potentials and postsynaptic currents * The current dipole model * Neural population and detected fields * Spherically bounded medium * SPATIAL CONFIGURATION OF THE SENSORS * SOURCE LOCALIZATION * Localization procedure * Experimental accuracy and reproducibility * SIGNAL PROCESSING * Analog Filtering * Bandpass filters * Line rejection filters * DATA ANALYSIS * Analysis of evoked/event-related responses * Simple average * Selected average * Recursive techniques * Similarity analysis * Analysis of spontaneous activity * Mapping and localization * EXAMPLES OF NEUROMAGNETIC STUDIES * Neuromagnetic measurements * Studies on the normal brain * Clinical applications * Epilepsy * Tinnitus * CONCLUSIONS * ACKNOWLEDGEMENTS * REFERENCES

Fracture labelling of boar spermatozoa for the fucose-binding-protein (FBP).

PubMed

Friess, A E; Toepfer-Petersen, E; Schill, W B

1987-01-01

Labelling of fractured boar spermatozoa with the FUC-HRP gold method for a fucose-binding-protein (FBP) gave evidence the FBP is localized in the acrosomal matrix. All fracture faces through the acrosome from the rostral end towards the equatorial segment show similar labelling pattern. This labelling is completely blocked by preincubation of the fractured tissue with focoidan.

Antibiotic resistance of Campylobacter in raw retail chickens and imported chicken portions.

PubMed Central

Wilson, I. G.

2003-01-01

Campylobacter isolates from raw retail chickens (n = 434) sampled between 1998 and 2000 were tested for resistance to 12 antibiotics. Among 208 campylobacters tested, more than 90% of isolates were susceptible to 4 out of 9 antibiotics (nalidixic acid, erythromycin, chloramphenicol and gentamicin). Most campylobacters were resistant to 3 antibiotics and multiple resistance was found in 4%. Ciprofloxacin resistance was 11%. Campylobacter contamination (28%) in imported chickens (n = 150) was almost half that found in local whole chickens (50%), but the resistance of imported isolates (n = 42) was similar to that of local campylobacters. Resistance in isolates from imported chicken breasts was generally more common, but to only 4 antibiotics. Resistance patterns of chicken isolates were compared to human clinical isolates (n = 494), and a greater similarity was found between the clinical and local isolates than with imported campylobacters. Lower chloramphenicol resistance was found in clinical Campylobacter isolates than in those from chicken sources. PMID:14959786

Moderate Cortical Cooling Eliminates Thalamocortical Silent States during Slow Oscillation.

PubMed

Sheroziya, Maxim; Timofeev, Igor

2015-09-23

Reduction in temperature depolarizes neurons by a partial closure of potassium channels but decreases the vesicle release probability within synapses. Compared with cooling, neuromodulators produce qualitatively similar effects on intrinsic neuronal properties and synapses in the cortex. We used this similarity of neuronal action in ketamine-xylazine-anesthetized mice and non-anesthetized mice to manipulate the thalamocortical activity. We recorded cortical electroencephalogram/local field potential (LFP) activity and intracellular activities from the somatosensory thalamus in control conditions, during cortical cooling and on rewarming. In the deeply anesthetized mice, moderate cortical cooling was characterized by reversible disruption of the thalamocortical slow-wave pattern rhythmicity and the appearance of fast LFP spikes, with frequencies ranging from 6 to 9 Hz. These LFP spikes were correlated with the rhythmic IPSP activities recorded within the thalamic ventral posterior medial neurons and with depolarizing events in the posterior nucleus neurons. Similar cooling of the cortex during light anesthesia rapidly and reversibly eliminated thalamocortical silent states and evoked thalamocortical persistent activity; conversely, mild heating increased thalamocortical slow-wave rhythmicity. In the non-anesthetized head-restrained mice, cooling also prevented the generation of thalamocortical silent states. We conclude that moderate cortical cooling might be used to manipulate slow-wave network activity and induce neuromodulator-independent transition to activated states. Significance statement: In this study, we demonstrate that moderate local cortical cooling of lightly anesthetized or naturally sleeping mice disrupts thalamocortical slow oscillation and induces the activated local field potential pattern. Mild heating has the opposite effect; it increases the rhythmicity of thalamocortical slow oscillation. Our results demonstrate that slow oscillation can be influenced by manipulations to the properties of cortical neurons without changes in neuromodulation. Copyright © 2015 the authors 0270-6474/15/3513006-14$15.00/0.

Domain Selectivity in the Parahippocampal Gyrus Is Predicted by the Same Structural Connectivity Patterns in Blind and Sighted Individuals.

PubMed

Wang, Xiaoying; He, Chenxi; Peelen, Marius V; Zhong, Suyu; Gong, Gaolang; Caramazza, Alfonso; Bi, Yanchao

2017-05-03

Human ventral occipital temporal cortex contains clusters of neurons that show domain-preferring responses during visual perception. Recent studies have reported that some of these clusters show surprisingly similar domain selectivity in congenitally blind participants performing nonvisual tasks. An important open question is whether these functional similarities are driven by similar innate connections in blind and sighted groups. Here we addressed this question focusing on the parahippocampal gyrus (PHG), a region that is selective for large objects and scenes. Based on the assumption that patterns of long-range connectivity shape local computation, we examined whether domain selectivity in PHG is driven by similar structural connectivity patterns in the two populations. Multiple regression models were built to predict the selectivity of PHG voxels for large human-made objects from white matter (WM) connectivity patterns in both groups. These models were then tested using independent data from participants with similar visual experience (two sighted groups) and using data from participants with different visual experience (blind and sighted groups). Strikingly, the WM-based predictions between blind and sighted groups were as successful as predictions between two independent sighted groups. That is, the functional selectivity for large objects of a PHG voxel in a blind participant could be accurately predicted by its WM pattern using the connection-to-function model built from the sighted group data, and vice versa. Regions that significantly predicted PHG selectivity were located in temporal and frontal cortices in both sighted and blind populations. These results show that the large-scale network driving domain selectivity in PHG is independent of vision. SIGNIFICANCE STATEMENT Recent studies have reported intriguingly similar domain selectivity in sighted and congenitally blind individuals in regions within the ventral visual cortex. To examine whether these similarities originate from similar innate connectional roots, we investigated whether the domain selectivity in one population could be predicted by the structural connectivity pattern of the other. We found that the selectivity for large objects of a PHG voxel in a blind participant could be predicted by its structural connectivity pattern using the connection-to-function model built from the sighted group data, and vice versa. These results reveal that the structural connectivity underlying domain selectivity in the PHG is independent of visual experience, providing evidence for nonvisual representations in this region. Copyright © 2017 the authors 0270-6474/17/374706-12$15.00/0.

Comparing methods of measuring geographic patterns in temporal trends: an application to county-level heart disease mortality in the United States, 1973 to 2010.

PubMed

Vaughan, Adam S; Kramer, Michael R; Waller, Lance A; Schieb, Linda J; Greer, Sophia; Casper, Michele

2015-05-01

To demonstrate the implications of choosing analytical methods for quantifying spatiotemporal trends, we compare the assumptions, implementation, and outcomes of popular methods using county-level heart disease mortality in the United States between 1973 and 2010. We applied four regression-based approaches (joinpoint regression, both aspatial and spatial generalized linear mixed models, and Bayesian space-time model) and compared resulting inferences for geographic patterns of local estimates of annual percent change and associated uncertainty. The average local percent change in heart disease mortality from each method was -4.5%, with the Bayesian model having the smallest range of values. The associated uncertainty in percent change differed markedly across the methods, with the Bayesian space-time model producing the narrowest range of variance (0.0-0.8). The geographic pattern of percent change was consistent across methods with smaller declines in the South Central United States and larger declines in the Northeast and Midwest. However, the geographic patterns of uncertainty differed markedly between methods. The similarity of results, including geographic patterns, for magnitude of percent change across these methods validates the underlying spatial pattern of declines in heart disease mortality. However, marked differences in degree of uncertainty indicate that Bayesian modeling offers substantially more precise estimates. Copyright © 2015 Elsevier Inc. All rights reserved.

A Study on the Model of Detecting the Variation of Geomagnetic Intensity Based on an Adapted Motion Strategy.

PubMed

Li, Hong; Liu, Mingyong; Liu, Kun; Zhang, Feihu

2017-12-25

By simulating the geomagnetic fields and analyzing thevariation of intensities, this paper presents a model for calculating the objective function ofan Autonomous Underwater Vehicle (AUV)geomagnetic navigation task. By investigating the biologically inspired strategies, the AUV successfullyreachesthe destination duringgeomagnetic navigation without using the priori geomagnetic map. Similar to the pattern of a flatworm, the proposed algorithm relies on a motion pattern to trigger a local searching strategy by detecting the real-time geomagnetic intensity. An adapted strategy is then implemented, which is biased on the specific target. The results show thereliabilityandeffectivenessofthe proposed algorithm.

Finger Vein Segmentation from Infrared Images Based on a Modified Separable Mumford Shah Model and Local Entropy Thresholding

PubMed Central

Dermatas, Evangelos

2015-01-01

A novel method for finger vein pattern extraction from infrared images is presented. This method involves four steps: preprocessing which performs local normalization of the image intensity, image enhancement, image segmentation, and finally postprocessing for image cleaning. In the image enhancement step, an image which will be both smooth and similar to the original is sought. The enhanced image is obtained by minimizing the objective function of a modified separable Mumford Shah Model. Since, this minimization procedure is computationally intensive for large images, a local application of the Mumford Shah Model in small window neighborhoods is proposed. The finger veins are located in concave nonsmooth regions and, so, in order to distinct them from the other tissue parts, all the differences between the smooth neighborhoods, obtained by the local application of the model, and the corresponding windows of the original image are added. After that, veins in the enhanced image have been sufficiently emphasized. Thus, after image enhancement, an accurate segmentation can be obtained readily by a local entropy thresholding method. Finally, the resulted binary image may suffer from some misclassifications and, so, a postprocessing step is performed in order to extract a robust finger vein pattern. PMID:26120357

A High-Resolution 3D Separated-Local-Field Experiment by Means of Magic-Angle Turning

PubMed

Hu; Alderman; Pugmire; Grant

1997-05-01

A 3D separated-local-field (SLF) experiment based on the 2D PHORMAT technique is described. In the 3D experiment, the conventional 2D SLF powder pattern for each chemically inequivalent carbon is separated according to their different isotropic chemical shifts. The dipolar coupling constant of a C-H pair, hence the bond distance, and the relative orientation of the chemical-shift tensor to the C-H vector can all be determined for the protonated carbons with a single measurement. As the sample turns at only about 30 Hz in a MAT experiment, the SLF patterns obtained approach those of a stationary sample, and an accuracy in the measurement similar to that obtained on a stationary sample is expected. The technique is demonstrated on 2,6-dimethoxynaphthalene, where the 13 C-1 H separated-local-field powder patterns for the six chemically inequivalent carbons are clearly identified and measured. The observed dipolar coupling for the methoxy carbon is effectively reduced by the fast rotation of the group about its C3 symmetry axis. The average angle between the C-H bond direction and the C3 rotation axis in the OCH3 group is found to be about 66°.

Islands increase genetic subdivision and disrupt patterns of connectivity of intertidal snails in a complex archipelago.

PubMed

Johnson, Michael S; Black, Robert

2006-12-01

The view that marine species with planktonic dispersal have highly connected, demographically open populations is giving way to recognition that populations may often be largely self-recruiting, or demographically closed. This raises the question of what local conditions might favor isolation of populations. To test the importance of islands for local isolation in species with planktonic larvae, we examined allozyme variation among 35 populations of the intertidal snail Austrocochlea constricta in the Houtman Abrolhos Islands, Western Australia, spanning 60 km. Heterogeneity of allozyme frequencies among populations was high, with average F(ST) of 0.237, indicating highly localized populations. Increased subdivision was associated with islands at different scales: between island groups, separated by deep water gaps, and between disconnected sets of islands within groups. At short distances, up to two km, subdivision increased fivefold between islands compared with that between populations on the same island. Along 11 km of continuous, sheltered shore, there was isolation by distance but among a linear series of islands over similar distance, there was greater subdivision at short distances but no association with distance. These patterns had been seen previously in the direct-developing snail Bembicium vittatum, but its finding in A. constricta confirms for a planktonic disperser the importance of this complex archipelago for both retention of locally produced larvae and disruption of patterns of connectivity. Taken together, these results indicate that islands can increase both the "open" and the "closed" components of recruitment and that applicable models of genetic connectivity depend substantially on local conditions.

Local texture and strongly linked conduction in spray-pyrolyzed TlBa2Ca2Cu3O(8+x) deposits

NASA Astrophysics Data System (ADS)

Kroeger, D. M.; Goyal, A.; Specht, E. D.; Wang, Z. L.; Tkaczyk, J. E.; Sutliff, J. A.; Deluca, J. A.

Local texture in polycrystalline TlBa2Ca2 Cu3O(8+x) deposits has been determined from transmission electron microscopy, electron backscatter diffraction patterns and x-ray diffraction. The small-grained deposits had excellent c-axis alignment and contained colonies of grains with similar but not identical a-axis orientations. Most grain boundaries within a colony have small misorientation angles and should not be weak links. It is proposed that long range conduction utilizes a percolative network of small angle grain boundaries at colony intersections.

Antigenic Maps of Influenza A(H3N2) Produced With Human Antisera Obtained After Primary Infection.

PubMed

Fonville, Judith M; Fraaij, Pieter L A; de Mutsert, Gerrie; Wilks, Samuel H; van Beek, Ruud; Fouchier, Ron A M; Rimmelzwaan, Guus F

2016-01-01

Antigenic characterization of influenza viruses is typically based on hemagglutination inhibition (HI) assay data for viral isolates tested against strain-specific postinfection ferret antisera. Here, similar virus characterizations were performed using serological data from humans with primary influenza A(H3N2) infection. We screened sera collected between 1995 and 2011 from children between 9 and 24 months of age for influenza virus antibodies, performed HI tests for the positive sera against 23 influenza viruses isolated between 1989 and 2011, and measured HI titers of antisera against influenza A(H3N2) from 24 ferrets against the same panel of viruses. Of the 17 positive human sera, 6 had a high response, showing HI patterns that would be expected from primary infection antisera, while 11 sera had lower, more dispersed patterns of reactivity that are not easily explained. The antigenic map based on the high-response human HI data was similar to the map created using ferret data. Although the overall structure of the ferret and human antigenic maps is similar, local differences in virus positions indicate that the human and ferret immune system might see antigenic properties of viruses differently. Further studies are needed to establish the degree of similarity between serological patterns in ferret and human data. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

Behavioral states may be associated with distinct spatial patterns in electrocorticogram.

PubMed

Panagiotides, Heracles; Freeman, Walter J; Holmes, Mark D; Pantazis, Dimitrios

2011-03-01

To determine if behavioral states are associated with unique spatial electrocorticographic (ECoG) patterns, we obtained recordings with a microgrid electrode array applied to the cortical surface of a human subject. The array was constructed with the intent of extracting maximal spatial information by optimizing interelectrode distances. A 34-year-old patient with intractable epilepsy underwent intracranial ECoG monitoring after standard methods failed to reveal localization of seizures. During the 8-day period of invasive recording, in addition to standard clinical electrodes a square 1 × 1 cm microgrid array with 64 electrodes (1.25 mm separation) was placed on the right inferior temporal gyrus. Careful review of video recordings identified four extended naturalistic behaviors: reading, conversing on the telephone, looking at photographs, and face-to-face interactions. ECoG activity recorded with the microgrid that corresponded to these behaviors was collected and ECoG spatial patterns were analyzed. During periods of ECoG selected for analysis, no electrographic seizures or epileptiform patterns were present. Moments of maximal spatial variance are shown to cluster by behavior. Comparisons between conditions using a permutation test reveal significantly different spatial patterns for each behavior. We conclude that ECoG recordings obtained on the cortical surface with optimal high spatial frequency resolution reveal distinct local spatial patterns that reflect different behavioral states, and we predict that similar patterns will be found in many if not most cortical areas on which a microgrid is placed.

Structural characteristics of the shock-induced boundary layer separation extended to the leading edge

NASA Astrophysics Data System (ADS)

Tao, Y.; Liu, W. D.; Fan, X. Q.; Zhao, Y. L.

2017-07-01

For a better understanding of the local unstart of supersonic/hypersonic inlet, a series of experiments has been conducted to investigate the shock-induced boundary layer separation extended to the leading edge. Using the nanoparticle-based planar laser scattering, we recorded the fine structures of these interactions under different conditions and paid more attention to their structural characteristics. According to their features, these interactions could be divided into four types. Specifically, Type A wave pattern is similar to the classic shock wave/turbulent boundary layer interaction, and Type B wave configuration consists of an overall Mach reflection above the large scale separation bubble. Due to the gradual decrease in the size of the separation bubble, the separation bubble was replaced by several vortices (Type C wave pattern). Besides, for Type D wave configuration which exists in the local unstart inlet, there appears to be some flow spillage around the leading edge.

Double dissociation of 'what' and 'where' processing in auditory cortex.

PubMed

Lomber, Stephen G; Malhotra, Shveta

2008-05-01

Studies of cortical connections or neuronal function in different cerebral areas support the hypothesis that parallel cortical processing streams, similar to those identified in visual cortex, may exist in the auditory system. However, this model has not yet been behaviorally tested. We used reversible cooling deactivation to investigate whether the individual regions in cat nonprimary auditory cortex that are responsible for processing the pattern of an acoustic stimulus or localizing a sound in space could be doubly dissociated in the same animal. We found that bilateral deactivation of the posterior auditory field resulted in deficits in a sound-localization task, whereas bilateral deactivation of the anterior auditory field resulted in deficits in a pattern-discrimination task, but not vice versa. These findings support a model of cortical organization that proposes that identifying an acoustic stimulus ('what') and its spatial location ('where') are processed in separate streams in auditory cortex.

Aging in the natural world: comparative data reveal similar mortality patterns across primates.

PubMed

Bronikowski, Anne M; Altmann, Jeanne; Brockman, Diane K; Cords, Marina; Fedigan, Linda M; Pusey, Anne; Stoinski, Tara; Morris, William F; Strier, Karen B; Alberts, Susan C

2011-03-11

Human senescence patterns-late onset of mortality increase, slow mortality acceleration, and exceptional longevity-are often described as unique in the animal world. Using an individual-based data set from longitudinal studies of wild populations of seven primate species, we show that contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging; the tendency for males to have shorter life spans and higher age-specific mortality than females throughout much of adulthood is a common feature in many, but not all, primates; and the aging profiles of primate species do not reflect phylogenetic position. These findings suggest that mortality patterns in primates are shaped by local selective forces rather than phylogenetic history.

Finger Vein Recognition Based on Local Directional Code

PubMed Central

Meng, Xianjing; Yang, Gongping; Yin, Yilong; Xiao, Rongyang

2012-01-01

Finger vein patterns are considered as one of the most promising biometric authentication methods for its security and convenience. Most of the current available finger vein recognition methods utilize features from a segmented blood vessel network. As an improperly segmented network may degrade the recognition accuracy, binary pattern based methods are proposed, such as Local Binary Pattern (LBP), Local Derivative Pattern (LDP) and Local Line Binary Pattern (LLBP). However, the rich directional information hidden in the finger vein pattern has not been fully exploited by the existing local patterns. Inspired by the Webber Local Descriptor (WLD), this paper represents a new direction based local descriptor called Local Directional Code (LDC) and applies it to finger vein recognition. In LDC, the local gradient orientation information is coded as an octonary decimal number. Experimental results show that the proposed method using LDC achieves better performance than methods using LLBP. PMID:23202194

Finger vein recognition based on local directional code.

PubMed

Meng, Xianjing; Yang, Gongping; Yin, Yilong; Xiao, Rongyang

2012-11-05

Finger vein patterns are considered as one of the most promising biometric authentication methods for its security and convenience. Most of the current available finger vein recognition methods utilize features from a segmented blood vessel network. As an improperly segmented network may degrade the recognition accuracy, binary pattern based methods are proposed, such as Local Binary Pattern (LBP), Local Derivative Pattern (LDP) and Local Line Binary Pattern (LLBP). However, the rich directional information hidden in the finger vein pattern has not been fully exploited by the existing local patterns. Inspired by the Webber Local Descriptor (WLD), this paper represents a new direction based local descriptor called Local Directional Code (LDC) and applies it to finger vein recognition. In LDC, the local gradient orientation information is coded as an octonary decimal number. Experimental results show that the proposed method using LDC achieves better performance than methods using LLBP.

Fractal regional myocardial blood flows pattern according to metabolism, not vascular anatomy

PubMed Central

Yipintsoi, Tada; Kroll, Keith

2015-01-01

Regional myocardial blood flows are markedly heterogeneous. Fractal analysis shows strong near-neighbor correlation. In experiments to distinguish control by vascular anatomy vs. local vasomotion, coronary flows were increased in open-chest dogs by stimulating myocardial metabolism (catecholamines + atropine) with and without adenosine. During control states mean left ventricular (LV) myocardial blood flows (microspheres) were 0.5–1 ml·g−1·min−1 and increased to 2–3 ml·g−1·min−1 with catecholamine infusion and to ∼4 ml·g−1·min−1 with adenosine (Ado). Flow heterogeneity was similar in all states: relative dispersion (RD = SD/mean) was ∼25%, using LV pieces 0.1–0.2% of total. During catecholamine infusion local flows increased in proportion to the mean flows in 45% of the LV, “tracking” closely (increased proportionately to mean flow), while ∼40% trended toward the mean. Near-neighbor regional flows remained strongly spatially correlated, with fractal dimension D near 1.2 (Hurst coefficient 0.8). The spatial patterns remain similar at varied levels of metabolic stimulation inferring metabolic dominance. In contrast, adenosine vasodilation increased flows eightfold times control while destroying correlation with the control state. The Ado-induced spatial patterns differed from control but were self-consistent, inferring that with full vasodilation the relaxed arterial anatomy dominates the distribution. We conclude that vascular anatomy governs flow distributions during adenosine vasodilation but that metabolic vasoregulation dominates in normal physiological states. PMID:26589329

Fractal regional myocardial blood flows pattern according to metabolism, not vascular anatomy.

PubMed

Yipintsoi, Tada; Kroll, Keith; Bassingthwaighte, James B

2016-02-01

Regional myocardial blood flows are markedly heterogeneous. Fractal analysis shows strong near-neighbor correlation. In experiments to distinguish control by vascular anatomy vs. local vasomotion, coronary flows were increased in open-chest dogs by stimulating myocardial metabolism (catecholamines + atropine) with and without adenosine. During control states mean left ventricular (LV) myocardial blood flows (microspheres) were 0.5-1 ml·g(-1)·min(-1) and increased to 2-3 ml·g(-1)·min(-1) with catecholamine infusion and to ∼4 ml·g(-1)·min(-1) with adenosine (Ado). Flow heterogeneity was similar in all states: relative dispersion (RD = SD/mean) was ∼25%, using LV pieces 0.1-0.2% of total. During catecholamine infusion local flows increased in proportion to the mean flows in 45% of the LV, "tracking" closely (increased proportionately to mean flow), while ∼40% trended toward the mean. Near-neighbor regional flows remained strongly spatially correlated, with fractal dimension D near 1.2 (Hurst coefficient 0.8). The spatial patterns remain similar at varied levels of metabolic stimulation inferring metabolic dominance. In contrast, adenosine vasodilation increased flows eightfold times control while destroying correlation with the control state. The Ado-induced spatial patterns differed from control but were self-consistent, inferring that with full vasodilation the relaxed arterial anatomy dominates the distribution. We conclude that vascular anatomy governs flow distributions during adenosine vasodilation but that metabolic vasoregulation dominates in normal physiological states. Copyright © 2016 the American Physiological Society.

Selecting for extinction: nonrandom disease-associated extinction homogenizes amphibian biotas.

PubMed

Smith, Kevin G; Lips, Karen R; Chase, Jonathan M

2009-10-01

Studying the patterns in which local extinctions occur is critical to understanding how extinctions affect biodiversity at local, regional and global spatial scales. To understand the importance of patterns of extinction at a regional spatial scale, we use data from extirpations associated with a widespread pathogenic agent of amphibian decline, Batrachochytrium dendrobatidis (Bd) as a model system. We apply novel null model analyses to these data to determine whether recent extirpations associated with Bd have resulted in selective extinction and homogenization of diverse tropical American amphibian biotas. We find that Bd-associated extinctions in this region were nonrandom and disproportionately, but not exclusively, affected low-occupancy and endemic species, resulting in homogenization of the remnant amphibian fauna. The pattern of extirpations also resulted in phylogenetic homogenization at the family level and ecological homogenization of reproductive mode and habitat association. Additionally, many more species were extirpated from the region than would be expected if extirpations occurred randomly. Our results indicate that amphibian declines in this region are an extinction filter, reducing regional amphibian biodiversity to highly similar relict assemblages and ultimately causing amplified biodiversity loss at regional and global scales.

Dental morphology and ancestry in Albuquerque, New Mexico Hispanics.

PubMed

Willermet, C M; Edgar, H J H

2009-01-01

The term "Hispanic" groups people from Central and South America and the Caribbean, combining disparate cultures, languages, and ancestry, and masking biological differences. Historical and current admixture patterns within these populations and with indigenous and European-, African-, and/or Asian- derived populations complicate the biological picture. Although "Hispanic" has little biological meaning, it is used widely in epidemiology, disease management, and forensics as a biologically significant group. An interdisciplinary approach combining historical, cultural, and biological data can characterize regional and temporal differences between Hispanic populations. We examined biological distances with a population of central New Mexico Hispanics, as a case study of the local specificity of population history. We collected dental morphological trait frequencies from samples of recent Albuquerque-area Hispanic Americans and several ancestral and contemporary groups. To explore regional admixture patterns we calculated biological distances using the modified Mahalanobis D(2) statistic. Our results indicate that Albuquerque Hispanics are more similar to their European and African ancestral groups than to Native Americans in New Mexico. Additionally, their affinity to Native Americans is greater with prehistoric rather than contemporary samples. We argue that these results reflect a local rather than pan-Hispanic admixture pattern; they underscore that populations are better understood at the local and regional levels. It is undesirable to make sweeping biological generalizations for groups known to be geographically and genetically disparate. This research is part of a growing trend in biological research concerning Hispanics and other groups-an emphasis on local samples, informed by historical, cultural, and biological factors.

Radical External Beam Radiotherapy for Clinically Localized Prostate Cancer in Japan: Changing Trends in the Patterns of Care Process Survey

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

Ogawa, Kazuhiko, E-mail: kogawa@med.u-ryukyu.ac.jp; Nakamura, Katsumasa; Sasaki, Tomonari

2011-12-01

Purpose: To delineate changing trends in radical external beam radiotherapy (EBRT) for prostate cancer in Japan. Methods and Materials: Data from 841 patients with clinically localized prostate cancer treated with EBRT in the Japanese Patterns of Care Study (PCS) from 1996 to 2005 were analyzed. Results: Significant increases in the proportions of patients with stage T1 to T2 disease and decrease in prostate-specific antigen values were observed. Also, there were significant increases in the percentages of patients treated with radiotherapy by their own choice. Median radiation doses were 65.0 Gy and 68.4 Gy from 1996 to 1998 and from 1999more » to 2001, respectively, increasing to 70 Gy from 2003 to 2005. Moreover, conformal therapy was more frequently used from 2003 to 2005 (84.9%) than from 1996 to 1998 (49.1%) and from 1999 to 2001 (50.2%). On the other hand, the percentage of patients receiving hormone therapy from 2003 to 2005 (81.1%) was almost the same as that from 1996 to 1998 (86.3%) and from 1999 to 2001 (89.7%). Compared with the PCS in the United States, patient characteristics and patterns of treatments from 2003 to 2005 have become more similar to those in the United States than those from 1996 to 1998 and those from 1999 to 2001. Conclusions: This study indicates a trend toward increasing numbers of patients with early-stage disease and increasing proportions of patients treated with higher radiation doses with advanced equipment among Japanese prostate cancer patients treated with EBRT during 1996 to 2005 survey periods. Patterns of care for prostate cancer in Japan are becoming more similar to those in the United States.« less

Spatial patterns of giant sequoia (Sequoiadendron giganteum) in two sequoia groves in Sequoia National Park, California

USGS Publications Warehouse

Stohlgren, Thomas J.

1993-01-01

Although Muir Grove and Castle Creek Grove are similar in area, elevation, and number of giant sequoias, various spatial pattern analysis techniques showed that they had dissimilar spatial patterns for similar-sized trees. Two-dimensional and transect two-term local quadrat variance techniques detected general trends in the spatial patterns of different-sized trees, detected multiple-scale patterns within individual size classes, and provided information on the scale and intensity of patches of individual size classes of trees in Muir and Castle Creek groves. In Muir Grove, midsized sequoias (1.5 to 2.4 m DBH classes) had major pattern scales 350–450 m in diameter, whereas the same-sized trees in Castle Creek Grove had pattern scales >1000 m in diameter. Many size classes of trees had minor patches superimposed on larger scale patterns in both groves. There may be different recruitment patterns in core (i.e., central) areas compared with peripheral areas of sequoia groves; core areas of both groves had more small live sequoias and dead sequoias than peripheral areas of the groves. Higher densities of sequoias and, perhaps, more rapid turnover of individuals in core areas may indicate (i) differences in disturbance histories and favorability of microsites in the core and peripheral areas of groves; (ii) different responses to disturbance due to shifts in the species composition of the stand and thus, the relative influences of intra- to inter-specific competition; or (iii) slower growth or lower survivorship rates in marginal habitat (i.e., peripheral areas).

Rickettsia 'in' and 'out': two different localization patterns of a bacterial symbiont in the same insect species.

PubMed

Caspi-Fluger, Ayelet; Inbar, Moshe; Mozes-Daube, Netta; Mouton, Laurence; Hunter, Martha S; Zchori-Fein, Einat

2011-01-01

Intracellular symbionts of arthropods have diverse influences on their hosts, and their functions generally appear to be associated with their localization within the host. The effect of localization pattern on the role of a particular symbiont cannot normally be tested since the localization pattern within hosts is generally invariant. However, in Israel, the secondary symbiont Rickettsia is unusual in that it presents two distinct localization patterns throughout development and adulthood in its whitefly host, Bemisia tabaci (B biotype). In the "scattered" pattern, Rickettsia is localized throughout the whitefly hemocoel, excluding the bacteriocytes, where the obligate symbiont Portiera aleyrodidarum and some other secondary symbionts are housed. In the "confined" pattern, Rickettsia is restricted to the bacteriocytes. We examined the effects of these patterns on Rickettsia densities, association with other symbionts (Portiera and Hamiltonella defensa inside the bacteriocytes) and on the potential for horizontal transmission to the parasitoid wasp, Eretmocerus mundus, while the wasp larvae are developing within the whitefly nymph. Sequences of four Rickettsia genes were found to be identical for both localization patterns, suggesting that they are closely related strains. However, real-time PCR analysis showed very different dynamics for the two localization types. On the first day post-adult emergence, Rickettsia densities were 21 times higher in the "confined" pattern vs. "scattered" pattern whiteflies. During adulthood, Rickettsia increased in density in the "scattered" pattern whiteflies until it reached the "confined" pattern Rickettsia density on day 21. No correlation between Rickettsia densities and Hamiltonella or Portiera densities were found for either localization pattern. Using FISH technique, we found Rickettsia in the gut of the parasitoid wasps only when they developed on whiteflies with the "scattered" pattern. The results suggest that the localization pattern of a symbiont may influence its dynamics within the host.

Recurrent Activation of Neural Circuits during Attention to Global and Local Visual Information.

PubMed

Iglesias-Fuster, Jorge; Piña-Novo, Daniela; Ontivero-Ortega, Marlis; Lage-Castellanos, Agustín; Valdés-Sosa, Mitchell

2018-05-28

The attentional selection of different hierarchical level within compound (Navon) figures has been studied with event related potentials (ERPs), by controlling the ERPs obtained during attention to the global or the local echelon. These studies, using the canonical Navon figures, have produced contradictory results, with doubts regarding the scalp distribution of the effects. Moreover, the evidence about the temporal evolution of the processing of these two levels is not clear. Here, we unveiled global and local letters at distinct times, which enabled separation of their ERP responses. We combine this approach with the temporal generalization methodology, a novel multivariate technique which facilitates exploring the temporal structure of these ERPs. Opposite lateralization patterns were obtained for the selection negativities generated when attending global and local distracters (D statistics, p < .005), with maxima in right and left occipito-temporal scalp regions, respectively (η2 = .111, p < .01; η2 = .042, p < .04). However, both discrimination negativities elicited when comparing targets and distractors at the global or the local level were lateralized to the left hemisphere (η2 = .25, p < .03 and η2 = .142, p < .05 respectively). Recurrent activation patterns were found for both global and local stimuli, with scalp topographies corresponding to early preparatory stages reemerging during the attentional selection process, thus indicating recursive attentional activation. This implies that selective attention to global and local hierarchical levels recycles similar neural correlates at different time points. These neural correlates appear to be mediated by visual extra-striate areas.

Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei.

PubMed

Bass, Hank W; Hoffman, Gregg G; Lee, Tae-Jin; Wear, Emily E; Joseph, Stacey R; Allen, George C; Hanley-Bowdoin, Linda; Thompson, William F

2015-11-01

Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.

Nutritional channels in breast cancer.

PubMed

Godoy, Alejandro; Salazar, Katherine; Figueroa, Carlos; Smith, Gary J; de Los Angeles Garcia, Maria; Nualart, Francisco J

2009-09-01

Breast cancers increase glucose uptake by increasing expression of the facilitative glucose transporters (GLUTs), mainly GLUT1. However, little is known about the relationship between GLUT1 expression and malignant potential in breast cancer. In this study, expression and subcellular localization of GLUT1 was analysed in vivo in breast cancer tissue specimens with differing malignant potential, based on the Scarff-Bloom-Richardson (SBRI, II, III) histological grading system, and in vitro in the breast cancer cell lines, MDA-MB-468 and MCF-7, and in MDA-MB-468 cells grown as xenografts in nude athymic BALB/c male mice. In situ hybridization analyses demonstrated similar levels of GLUT1 mRNA expression in tissue sections from breast cancers of all histological grades. However, GLUT1 protein was expressed at higher levels in grade SBRII cancer, compared with SBRI and SBRIII, and associated with the expression of the proliferation marker PCNA. Immunolocalization analyses in SBRII cancers demonstrated a preferential localization of GLUT1 to the portions of the cellular membrane that faced neighbouring cells and formed 'canaliculi-like structures', that we hypothesize could have a potential role as 'nutritional channels'. A similar pattern of GLUT1 localization was observed in confluent cultures of MDA-MB-468 and MCF-7, and in MDA-MB-468 cells grown as xenografts, but not in the normal breast epithelial cell line HMEC. However, no relationship between GLUT1 expression and malignant potential of human breast cancer was observed. Preferential subcellular localization of GLUT1 could represent a physiological adaptation of a subset of breast cancer cells that form infiltrative tumours with a nodular growth pattern and that therefore need a major diffusion of glucose from blood vessels.

Microgeographic patterns of genetic divergence and adaptation across environmental gradients in Boechera stricta (Brassicaceae)

PubMed Central

Anderson, Jill T.; Perera, Nadeesha; Chowdhury, Bashira; Mitchell-Olds, Thomas

2015-01-01

Abiotic and biotic conditions often vary continuously across the landscape, imposing divergent selection on local populations. We used a provenance trial approach to examine microgeographic variation in local adaptation in Boechera stricta (Brassicaceae), a perennial forb native to the Rocky Mountains. In montane ecosystems, environmental conditions change considerably over short spatial scales, such that neighboring populations can be subject to different selective pressures. Using accessions from southern (Colorado) and northern (Idaho) populations, we characterized spatial variation in genetic similarity via microsatellite markers. We then transplanted genotypes from multiple local populations into common gardens in both regions. Continuous variation in local adaptation emerged for several components of fitness. In Idaho, genotypes from warmer environments (low elevation or south facing sites) were poorly adapted to the north-facing garden. In high and low elevation Colorado gardens, susceptibility to insect herbivory increased with source elevation. In the high elevation Colorado garden, germination success peaked for genotypes that evolved at similar elevations as the garden, and declined for genotypes from higher and lower elevations. We also found evidence for local maladaptation in survival and fecundity components of fitness in the low elevation Colorado garden. This approach is a necessary first step in predicting how global change could affect evolutionary dynamics. PMID:26656218

A comparison of CIC and BTE hearing aids for three-dimensional localization of speech.

PubMed

Best, Virginia; Kalluri, Sridhar; McLachlan, Sara; Valentine, Susie; Edwards, Brent; Carlile, Simon

2010-10-01

Three-dimensional sound localization of speech in anechoic space was examined for eleven listeners with sensorineural hearing loss. The listeners were fitted bilaterally with CIC and BTE hearing aids having similar bandwidth capabilities. The goal was to determine whether differences in microphone placement for these two styles (CICs at the ear canal entrance; BTEs above the pinna) would influence the availability of pinna-related spectral cues and hence localization performance. While lateral and polar angle localization was unaffected by the hearing aid style, the rate of front-back reversals was lower with CICs. This pattern persisted after listeners accommodated to each set of aids for a six week period, although the overall rate of reversals declined. Performance on all measures in all conditions was considerably poorer than in a control group of listeners with normal hearing.

Neighborhood Structural Similarity Mapping for the Classification of Masses in Mammograms.

PubMed

Rabidas, Rinku; Midya, Abhishek; Chakraborty, Jayasree

2018-05-01

In this paper, two novel feature extraction methods, using neighborhood structural similarity (NSS), are proposed for the characterization of mammographic masses as benign or malignant. Since gray-level distribution of pixels is different in benign and malignant masses, more regular and homogeneous patterns are visible in benign masses compared to malignant masses; the proposed method exploits the similarity between neighboring regions of masses by designing two new features, namely, NSS-I and NSS-II, which capture global similarity at different scales. Complementary to these global features, uniform local binary patterns are computed to enhance the classification efficiency by combining with the proposed features. The performance of the features are evaluated using the images from the mini-mammographic image analysis society (mini-MIAS) and digital database for screening mammography (DDSM) databases, where a tenfold cross-validation technique is incorporated with Fisher linear discriminant analysis, after selecting the optimal set of features using stepwise logistic regression method. The best area under the receiver operating characteristic curve of 0.98 with an accuracy of is achieved with the mini-MIAS database, while the same for the DDSM database is 0.93 with accuracy .

Many local pattern texture features: which is better for image-based multilabel human protein subcellular localization classification?

PubMed

Yang, Fan; Xu, Ying-Ying; Shen, Hong-Bin

2014-01-01

Human protein subcellular location prediction can provide critical knowledge for understanding a protein's function. Since significant progress has been made on digital microscopy, automated image-based protein subcellular location classification is urgently needed. In this paper, we aim to investigate more representative image features that can be effectively used for dealing with the multilabel subcellular image samples. We prepared a large multilabel immunohistochemistry (IHC) image benchmark from the Human Protein Atlas database and tested the performance of different local texture features, including completed local binary pattern, local tetra pattern, and the standard local binary pattern feature. According to our experimental results from binary relevance multilabel machine learning models, the completed local binary pattern, and local tetra pattern are more discriminative for describing IHC images when compared to the traditional local binary pattern descriptor. The combination of these two novel local pattern features and the conventional global texture features is also studied. The enhanced performance of final binary relevance classification model trained on the combined feature space demonstrates that different features are complementary to each other and thus capable of improving the accuracy of classification.

Geographic patterns and dynamics of Alaskan climate interpolated from a sparse station record

USGS Publications Warehouse

Fleming, Michael D.; Chapin, F. Stuart; Cramer, W.; Hufford, Gary L.; Serreze, Mark C.

2000-01-01

Data from a sparse network of climate stations in Alaska were interpolated to provide 1-km resolution maps of mean monthly temperature and precipitation-variables that are required at high spatial resolution for input into regional models of ecological processes and resource management. The interpolation model is based on thin-plate smoothing splines, which uses the spatial data along with a digital elevation model to incorporate local topography. The model provides maps that are consistent with regional climatology and with patterns recognized by experienced weather forecasters. The broad patterns of Alaskan climate are well represented and include latitudinal and altitudinal trends in temperature and precipitation and gradients in continentality. Variations within these broad patterns reflect both the weakening and reduction in frequency of low-pressure centres in their eastward movement across southern Alaska during the summer, and the shift of the storm tracks into central and northern Alaska in late summer. Not surprisingly, apparent artifacts of the interpolated climate occur primarily in regions with few or no stations. The interpolation model did not accurately represent low-level winter temperature inversions that occur within large valleys and basins. Along with well-recognized climate patterns, the model captures local topographic effects that would not be depicted using standard interpolation techniques. This suggests that similar procedures could be used to generate high-resolution maps for other high-latitude regions with a sparse density of data.

An embedded face-classification system for infrared images on an FPGA

NASA Astrophysics Data System (ADS)

Soto, Javier E.; Figueroa, Miguel

2014-10-01

We present a face-classification architecture for long-wave infrared (IR) images implemented on a Field Programmable Gate Array (FPGA). The circuit is fast, compact and low power, can recognize faces in real time and be embedded in a larger image-processing and computer vision system operating locally on an IR camera. The algorithm uses Local Binary Patterns (LBP) to perform feature extraction on each IR image. First, each pixel in the image is represented as an LBP pattern that encodes the similarity between the pixel and its neighbors. Uniform LBP codes are then used to reduce the number of patterns to 59 while preserving more than 90% of the information contained in the original LBP representation. Then, the image is divided into 64 non-overlapping regions, and each region is represented as a 59-bin histogram of patterns. Finally, the algorithm concatenates all 64 regions to create a 3,776-bin spatially enhanced histogram. We reduce the dimensionality of this histogram using Linear Discriminant Analysis (LDA), which improves clustering and enables us to store an entire database of 53 subjects on-chip. During classification, the circuit applies LBP and LDA to each incoming IR image in real time, and compares the resulting feature vector to each pattern stored in the local database using the Manhattan distance. We implemented the circuit on a Xilinx Artix-7 XC7A100T FPGA and tested it with the UCHThermalFace database, which consists of 28 81 x 150-pixel images of 53 subjects in indoor and outdoor conditions. The circuit achieves a 98.6% hit ratio, trained with 16 images and tested with 12 images of each subject in the database. Using a 100 MHz clock, the circuit classifies 8,230 images per second, and consumes only 309mW.

Morphometry, Microstructure, and Wear Pattern of Neornithischian Dinosaur Teeth From the Upper Cretaceous Iharkút Locality (Hungary).

PubMed

Virág, Attila; Ősi, Attila

2017-08-01

Teeth of iguanodontian ornithopods and ceratopsians could be remarkably similar, thus the referral of isolated dental material to particular neornithischian clades can be highly problematic. These groups are represented by the rhabdodontid Mochlodon vorosi and the basal coronosaurian Ajkaceratops kozmai in the Upper Cretaceous Csehbánya Formation at Iharkút (western Hungary). Whereas teeth of Mochlodon are common elements at the locality, no dental material belonging to Ajkaceratops was identified until now. Here we used mathematical statistical approaches, as well as tooth wear and dental microstructure analysis in order to decide whether the teeth previously referred to Mochlodon can be treated as a homogenous sample, or some remains belong rather to Ajkaceratops. According to our results, there was a striking morphological and structural convergence between the teeth of both taxa. However, the wear study revealed the existence of two different patterns within the sample. One is characterized by straight and parallel microstriations that suggest orthal movements during the jaw closure. This pattern was associated with Mochlodon. The other pattern appeared only on a few teeth, and it can be differentiated by its distinctive curved microstriations that indicate circumpalinal chewing. Because curved striations have never been described in ornithopods, but are found in several neoceratopsians, this pattern was associated here with Ajkaceratops. Here we present the first teeth that can provisionally be referred to the latter genus. We believe that the methodology discussed in this article will facilitate distinguishing ceratopsian and ornithopod teeth in other localities as well. Anat Rec, 300:1439-1463, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Mapping Forest Structure From Tree Clump And Opening Patterns Across Landscapes With Airborne Lidar To Study Response To Disturbances And Map Habitat

NASA Astrophysics Data System (ADS)

Kane, V. R.; McGaughey, R. J.; Asner, G. P.; Kane, J. T.; Churchill, D.; Vaughn, N.

2016-12-01

Most natural forests are structured as mosaics of tree clumps and openings. These mosaics reflect both the underlying patterns of the biophysical environment and the finer scale patterns of disturbance and regrowth. We have developed methods to quantify and map patterns of tree clumps and openings at scales from within stands to landscapes using airborne LiDAR. While many studies have used LiDAR data to identify individual trees, we also identify clumps as adjacent trees with similar heights within a stand that likely established at a similar time following a disturbance. We characterize openings by both size class and shape complexity. Spatial statistics are used to identify patterns of tree clumps and openings at the local (0.81 ha) scale, and these patterns are then mapped across entire landscapes. We use LiDAR data acquired over Sequoia National Park, California, USA, to show how forest structure varies with patterns of productivity driven by the biophysical environment. We then show how clump and opening patterns vary with different fire histories and how recent drought mortality correlates with different tree clump and opening structural mosaics. We also demonstrate that nesting sites for the California spotted owl, a species of concern, are associated with clumps of large (>32 and especially >48 m) trees but that the surrounding foraging areas consist of a heterogeneous pattern of forest structure. These methods are especially useful for studying clumps of large trees, which dominate above ground forest biomass, and the effects of disturbance on the abundance and pattern of large trees as key forest structures.

The re-emergence of felid camouflage with the decay of predator recognition in deer under relaxed selection

PubMed Central

Stankowich, Theodore; Coss, Richard G

2006-01-01

When a previously common predator disappears owing to local extinction, the strong source of natural selection on prey to visually recognize that predator becomes relaxed. At present, we do not know the extent to which recognition of a specific predator is generalized to similar looking predators or how a specific predator-recognition cue, such as coat pattern, degrades under prolonged relaxed selection. Using predator models, we show that deer exhibit a more rapid and stronger antipredator response to their current predator, the puma, than to a leopard displaying primitive rosettes similar to a locally extinct predator, an early jaguar. Presentation of a novel tiger with a striped coat engendered an intermediate speed of predator recognition and strength of antipredator behaviour. Responses to the leopard model slightly exceeded responses to a non-threatening deer model, suggesting that thousands of years of relaxed selection have led to the loss of recognition of the spotted coat as a jaguar-recognition cue, and that the spotted coat has regained its ability to camouflage the felid form. Our results shed light on the evolutionary arms race between adoption of camouflage to facilitate hunting and the ability of prey to quickly recognize predators by their formerly camouflaging patterns. PMID:17148247

Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of Arabidopsis responding to pathogen infection

PubMed Central

Katagiri, Fumiaki; Glazebrook, Jane

2003-01-01

A major task in computational analysis of mRNA expression profiles is definition of relationships among profiles on the basis of similarities among them. This is generally achieved by pattern recognition in the distribution of data points representing each profile in a high-dimensional space. Some drawbacks of commonly used pattern recognition algorithms stem from their use of a globally linear space and/or limited degrees of freedom. A pattern recognition method called Local Context Finder (LCF) is described here. LCF uses nonlinear dimensionality reduction for pattern recognition. Then it builds a network of profiles based on the nonlinear dimensionality reduction results. LCF was used to analyze mRNA expression profiles of the plant host Arabidopsis interacting with the bacterial pathogen Pseudomonas syringae. In one case, LCF revealed two dimensions essential to explain the effects of the NahG transgene and the ndr1 mutation on resistant and susceptible responses. In another case, plant mutants deficient in responses to pathogen infection were classified on the basis of LCF analysis of their profiles. The classification by LCF was consistent with the results of biological characterization of the mutants. Thus, LCF is a powerful method for extracting information from expression profile data. PMID:12960373

Investigation on the separability of slums by multi-aspect TerraSAR-X dual-co-polarized high resolution spotlight images based on the multi-scale evaluation of local distributions

NASA Astrophysics Data System (ADS)

Schmitt, Andreas; Sieg, Tobias; Wurm, Michael; Taubenböck, Hannes

2018-02-01

Following recent advances in distinguishing settlements vs. non-settlement areas from latest SAR data, the question arises whether a further automatic intra-urban delineation and characterization of different structural types is possible. This paper studies the appearance of the structural type ;slums; in high resolution SAR images. Geocoded Kennaugh elements are used as backscatter information and Schmittlet indices as descriptor of local texture. Three cities with a significant share of slums (Cape Town, Manila, Mumbai) are chosen as test sites. These are imaged by TerraSAR-X in the dual-co-polarized high resolution spotlight mode in any available aspect angle. Representative distributions are estimated and fused by a robust approach. Our observations identify a high similarity of slums throughout all three test sites. The derived similarity maps are validated with reference data sets from visual interpretation and ground truth. The final validation strategy is based on completeness and correctness versus other classes in relation to the similarity. High accuracies (up to 87%) in identifying morphologic slums are reached for Cape Town. For Manila (up to 60%) and Mumbai (up to 54%), the distinction is more difficult due to their complex structural configuration. Concluding, high resolution SAR data can be suitable to automatically trace potential locations of slums. Polarimetric information and the incidence angle seem to have a negligible impact on the results whereas the intensity patterns and the passing direction of the satellite are playing a key role. Hence, the combination of intensity images (brightness) acquired from ascending and descending orbits together with Schmittlet indices (spatial pattern) promises best results. The transfer from the automatically recognized physical similarity to the semantic interpretation remains challenging.

A fast non-local means algorithm based on integral image and reconstructed similar kernel

NASA Astrophysics Data System (ADS)

Lin, Zheng; Song, Enmin

2018-03-01

Image denoising is one of the essential methods in digital image processing. The non-local means (NLM) denoising approach is a remarkable denoising technique. However, its time complexity of the computation is high. In this paper, we design a fast NLM algorithm based on integral image and reconstructed similar kernel. First, the integral image is introduced in the traditional NLM algorithm. In doing so, it reduces a great deal of repetitive operations in the parallel processing, which will greatly improves the running speed of the algorithm. Secondly, in order to amend the error of the integral image, we construct a similar window resembling the Gaussian kernel in the pyramidal stacking pattern. Finally, in order to eliminate the influence produced by replacing the Gaussian weighted Euclidean distance with Euclidean distance, we propose a scheme to construct a similar kernel with a size of 3 x 3 in a neighborhood window which will reduce the effect of noise on a single pixel. Experimental results demonstrate that the proposed algorithm is about seventeen times faster than the traditional NLM algorithm, yet produce comparable results in terms of Peak Signal-to- Noise Ratio (the PSNR increased 2.9% in average) and perceptual image quality.

Motion-based signaling in sympatric species of Australian agamid lizards.

PubMed

Ramos, Jose A; Peters, Richard A

2017-08-01

Signaling species occurring in sympatry are often exposed to similar environmental constraints, so similar adaptations to enhance signal efficacy are expected. However, potentially opposing selective pressures might be present to ensure species recognition. Here, we analyzed the movement-based signals of two pairs of sympatric lizard species to consider how reliable communication is maintained while avoiding misidentification. Our novel approach allows us to quantify signal contrast with plant motion noise at any site we measure, including those utilized by other species. Ctenophorus caudicinctus and Gowidon longirostris differed in display complexity and motor pattern use. They also differed in overall morphology, but their signal contrast scores are strikingly similar. These results demonstrate similar adaptations to their shared environment while maintaining species recognition cues. In contrast, Ctenophorus fordi and Ctenophorus pictus are much closer in appearance, but C. pictus produces considerably higher signal contrast scores, which we suggest is attributable to the absence of territoriality in C. fordi. Taken together, our data provide evidence for adaptation to the local environment in movement-based signals, while also meeting species recognition requirements, but the selective pressure to deal with local conditions is mediated by signal function.

Rickettsia ‘In’ and ‘Out’: Two Different Localization Patterns of a Bacterial Symbiont in the Same Insect Species

PubMed Central

Caspi-Fluger, Ayelet; Inbar, Moshe; Mozes-Daube, Netta; Mouton, Laurence; Hunter, Martha S.; Zchori-Fein, Einat

2011-01-01

Intracellular symbionts of arthropods have diverse influences on their hosts, and their functions generally appear to be associated with their localization within the host. The effect of localization pattern on the role of a particular symbiont cannot normally be tested since the localization pattern within hosts is generally invariant. However, in Israel, the secondary symbiont Rickettsia is unusual in that it presents two distinct localization patterns throughout development and adulthood in its whitefly host, Bemisia tabaci (B biotype). In the “scattered” pattern, Rickettsia is localized throughout the whitefly hemocoel, excluding the bacteriocytes, where the obligate symbiont Portiera aleyrodidarum and some other secondary symbionts are housed. In the “confined” pattern, Rickettsia is restricted to the bacteriocytes. We examined the effects of these patterns on Rickettsia densities, association with other symbionts (Portiera and Hamiltonella defensa inside the bacteriocytes) and on the potential for horizontal transmission to the parasitoid wasp, Eretmocerus mundus, while the wasp larvae are developing within the whitefly nymph. Sequences of four Rickettsia genes were found to be identical for both localization patterns, suggesting that they are closely related strains. However, real-time PCR analysis showed very different dynamics for the two localization types. On the first day post-adult emergence, Rickettsia densities were 21 times higher in the “confined” pattern vs. “scattered” pattern whiteflies. During adulthood, Rickettsia increased in density in the “scattered” pattern whiteflies until it reached the “confined” pattern Rickettsia density on day 21. No correlation between Rickettsia densities and Hamiltonella or Portiera densities were found for either localization pattern. Using FISH technique, we found Rickettsia in the gut of the parasitoid wasps only when they developed on whiteflies with the “scattered” pattern. The results suggest that the localization pattern of a symbiont may influence its dynamics within the host. PMID:21712994

Children’s friendships in super-diverse localities: Encounters with social and ethnic difference

PubMed Central

Iqbal, Humera; Neal, Sarah; Vincent, Carol

2016-01-01

This article explores how children make, manage, or avoid friendships in super-diverse primary school settings. We draw on interviews and pictorial data from 78 children, aged 8–9 years across three local London primary schools to identify particular friendship groupings and the extent to which they followed existing patterns of social division. Children in the study did recognise social and cultural differences, but their friendship perceptions, affections, conflicts and practices meant that the way in which difference impacted relationships was partial and unstable. Friendship practices in the routine settings of school involved interactions across difference, but also entrenchments around similarity. PMID:28232774

Molecular inference of sources and spreading patterns of Plasmodium falciparum malaria parasites in internally displaced persons settlements in Myanmar-China border area.

PubMed

Lo, Eugenia; Zhou, Guofa; Oo, Winny; Lee, Ming-Chieh; Baum, Elisabeth; Felgner, Philip L; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

2015-07-01

In Myanmar, civil unrest and establishment of internally displaced persons (IDP) settlement along the Myanmar-China border have impacted malaria transmission. The growing IDP populations raise deep concerns about health impact on local communities. Microsatellite markers were used to examine the source and spreading patterns of Plasmodium falciparum between IDP settlement and surrounding villages in Myanmar along the China border. Genotypic structure of P. falciparum was compared over the past three years from the same area and the demographic history was inferred to determine the source of recent infections. In addition, we examined if border migration is a factor of P. falciparum infections in China by determining gene flow patterns across borders. Compared to local community, the IDP samples showed a reduced and consistently lower genetic diversity over the past three years. A strong signature of genetic bottleneck was detected in the IDP samples. P. falciparum infections from the border regions in China were genetically similar to Myanmar and parasite gene flow was not constrained by geographical distance. Reduced genetic diversity of P. falciparum suggested intense malaria control within the IDP settlement. Human movement was a key factor to the spread of malaria both locally in Myanmar and across the international border. Copyright © 2015 Elsevier B.V. All rights reserved.

The statistics of local motion signals in naturalistic movies

PubMed Central

Nitzany, Eyal I.; Victor, Jonathan D.

2014-01-01

Extraction of motion from visual input plays an important role in many visual tasks, such as separation of figure from ground and navigation through space. Several kinds of local motion signals have been distinguished based on mathematical and computational considerations (e.g., motion based on spatiotemporal correlation of luminance, and motion based on spatiotemporal correlation of flicker), but little is known about the prevalence of these different kinds of signals in the real world. To address this question, we first note that different kinds of local motion signals (e.g., Fourier, non-Fourier, and glider) are characterized by second- and higher-order correlations in slanted spatiotemporal regions. The prevalence of local motion signals in natural scenes can thus be estimated by measuring the extent to which each of these correlations are present in space-time patches and whether they are coherent across spatiotemporal scales. We apply this technique to several popular movies. The results show that all three kinds of local motion signals are present in natural movies. While the balance of the different kinds of motion signals varies from segment to segment during the course of each movie, the overall pattern of prevalence of the different kinds of motion and their subtypes, and the correlations between them, is strikingly similar across movies (but is absent from white noise movies). In sum, naturalistic movies contain a diversity of local motion signals that occur with a consistent prevalence and pattern of covariation, indicating a substantial regularity of their high-order spatiotemporal image statistics. PMID:24732243

The statistics of local motion signals in naturalistic movies.

PubMed

Nitzany, Eyal I; Victor, Jonathan D

2014-04-14

Extraction of motion from visual input plays an important role in many visual tasks, such as separation of figure from ground and navigation through space. Several kinds of local motion signals have been distinguished based on mathematical and computational considerations (e.g., motion based on spatiotemporal correlation of luminance, and motion based on spatiotemporal correlation of flicker), but little is known about the prevalence of these different kinds of signals in the real world. To address this question, we first note that different kinds of local motion signals (e.g., Fourier, non-Fourier, and glider) are characterized by second- and higher-order correlations in slanted spatiotemporal regions. The prevalence of local motion signals in natural scenes can thus be estimated by measuring the extent to which each of these correlations are present in space-time patches and whether they are coherent across spatiotemporal scales. We apply this technique to several popular movies. The results show that all three kinds of local motion signals are present in natural movies. While the balance of the different kinds of motion signals varies from segment to segment during the course of each movie, the overall pattern of prevalence of the different kinds of motion and their subtypes, and the correlations between them, is strikingly similar across movies (but is absent from white noise movies). In sum, naturalistic movies contain a diversity of local motion signals that occur with a consistent prevalence and pattern of covariation, indicating a substantial regularity of their high-order spatiotemporal image statistics.

Evidence for local adaptation and pleiotropic effects associated with melanization in a plant pathogenic fungus.

PubMed

Zhu, Wen; Zhan, Jiasui; McDonald, Bruce A

2018-06-01

We combined a common garden experimental design with digital image analysis to determine how melanization responds to temperature and fungicide stress in 126 strains of Rhynchosporium commune sampled from nine global field populations. We found that different temperatures and fungicide stress significantly affected the degree of melanization. The nine field populations showed similar patterns in response to the different temperatures. Significant correlations were found between the degree of melanization and the local environment, including mean annual temperature, latitude, and relative humidity, suggesting that melanization is a locally adaptive trait. We also found that melanization is positively correlated with both virulence and fungicide resistance. These findings suggest that melanization has pleiotropic effects in Rhynchosporium commune. Copyright © 2018 Elsevier Inc. All rights reserved.

Segmental expression of Pax3/7 and engrailed homologs in tardigrade development.

PubMed

Gabriel, Willow N; Goldstein, Bob

2007-06-01

How morphological diversity arises through evolution of gene sequence is a major question in biology. In Drosophila, the genetic basis for body patterning and morphological segmentation has been studied intensively. It is clear that some of the genes in the Drosophila segmentation program are functioning similarly in certain other taxa, although many questions remain about when these gene functions arose and which taxa use these genes similarly to establish diverse body plans. Tardigrades are an outgroup to arthropods in the Ecdysozoa and, as such, can provide insight into how gene functions have evolved among the arthropods and their close relatives. We developed immunostaining methods for tardigrade embryos, and we used cross-reactive antibodies to investigate the expression of homologs of the pair-rule gene paired (Pax3/7) and the segment polarity gene engrailed in the tardigrade Hypsibius dujardini. We find that in H. dujardini embryos, Pax3/7 protein localizes not in a pair-rule pattern but in a segmentally iterated pattern, after the segments are established, in regions of the embryo where neurons later arise. Engrailed protein localizes in the posterior ectoderm of each segment before ectodermal segmentation is apparent. Together with previous results from others, our data support the conclusions that the pair-rule function of Pax3/7 is specific to the arthropods, that some of the ancient functions of Pax3/7 and Engrailed in ancestral bilaterians may have been in neurogenesis, and that Engrailed may have a function in establishing morphological boundaries between segments that is conserved at least among the Panarthropoda.

LandEx - Fast, FOSS-Based Application for Query and Retrieval of Land Cover Patterns

NASA Astrophysics Data System (ADS)

Netzel, P.; Stepinski, T.

2012-12-01

The amount of satellite-based spatial data is continuously increasing making a development of efficient data search tools a priority. The bulk of existing research on searching satellite-gathered data concentrates on images and is based on the concept of Content-Based Image Retrieval (CBIR); however, available solutions are not efficient and robust enough to be put to use as deployable web-based search tools. Here we report on development of a practical, deployable tool that searches classified, rather than raw image. LandEx (Landscape Explorer) is a GeoWeb-based tool for Content-Based Pattern Retrieval (CBPR) contained within the National Land Cover Dataset 2006 (NLCD2006). The USGS-developed NLCD2006 is derived from Landsat multispectral images; it covers the entire conterminous U.S. with the resolution of 30 meters/pixel and it depicts 16 land cover classes. The size of NLCD2006 is about 10 Gpixels (161,000 x 100,000 pixels). LandEx is a multi-tier GeoWeb application based on Open Source Software. Main components are: GeoExt/OpenLayers (user interface), GeoServer (OGC WMS, WCS and WPS server), and GRASS (calculation engine). LandEx performs search using query-by-example approach: user selects a reference scene (exhibiting a chosen pattern of land cover classes) and the tool produces, in real time, a map indicating a degree of similarity between the reference pattern and all local patterns across the U.S. Scene pattern is encapsulated by a 2D histogram of classes and sizes of single-class clumps. Pattern similarity is based on the notion of mutual information. The resultant similarity map can be viewed and navigated in a web browser, or it can download as a GeoTiff file for more in-depth analysis. The LandEx is available at http://sil.uc.edu

Local versus landscape-scale effects of anthropogenic land-use on forest species richness

NASA Astrophysics Data System (ADS)

Buffa, G.; Del Vecchio, S.; Fantinato, E.; Milano, V.

2018-01-01

The study investigated the effects of human-induced landscape patterns on species richness in forests. For 80 plots of fixed size, we measured human disturbance (categorized as urban/industrial and agricultural land areas), at 'local' and 'landscape' scale (500 m and 2500 m radius from each plot, respectively), the distance from the forest edge, and the size and shape of the woody patch. By using GLM, we analyzed the effects of disturbance and patch-based measures on both total species richness and the richness of a group of specialist species (i.e. the 'ancient forest species'), representing more specific forest features. Patterns of local species richness were sensitive to the structure and composition of the surrounding landscape. Among the landscape components taken into account, urban/industrial land areas turned out as the most threatening factor for both total species richness and the richness of the ancient forest species. However, the best models evidenced a different intensity of the response to the same disturbance category as well as a different pool of significant variables for the two groups of species. The use of groups of species, such as the ancient forest species pool, that are functionally related and have similar ecological requirements, may represent an effective solution for monitoring forest dynamics under the effects of external factors. The approach of relating local assessment of species richness, and in particular of the ancient forest species pool, to land-use patterns may play an important role for the science-policy interface by supporting and strengthening conservation and regional planning decision making.

The Interrelationship Between Temperature Changes in the Free Atmosphere and Sea Surface Temperature Changes

NASA Astrophysics Data System (ADS)

Newell, Reginald E.; Wu, Zhong-Xiang

1992-03-01

Fields of sea surface temperature anomalies from the Global Ocean Surface Temperature Atlas (GOSTA) and microwave sounding measurements (MSU) of temperature in the troposphere are examined separately and together for the 1979-1988 period. Global correlation patterns of both sets of fields are investigated at a range of leads and lags up to 6 months and exhibit a wide range of correlation structure. There are regions, such as the tropical eastern Pacific, where sea surface temperature anomalies persist for several months and are associated with local air temperature anomalies; in this particular example, about 0.7°C air temperature change is associated with a 1.0°C sea temperature change. By contrast, some ocean regions and many atmospheric regions, mostly in middle and high latitude, show only local spatial correlations that disappear completely in a month or two. The most persistent and extensive spatial correlation patterns are quite different for the sea and the air. In the sea the "butterfly" pattern of the Pacific is the most important and reverses sign between the eastern equatorial Pacific and the western Pacific and subtropics. In the warm phase the temperature anomalies associated with this pattern are similar to the correlation pattern. For the atmosphere the main correlation pattern is an equatorial belt with no sign changes in the tropics; this pattern is linked to the oceanic El Niño mode. In the warm phase the temperature anomalies show peak values on both sides of the equator in the eastern and central Pacific. Based mainly on the results from the spatial patterns, certain regions are selected for intercomparison of time series. In the tropical eastern Pacific the sea leads the air by about a month while in the Gulf Stream and Kuroshio regions the sequence is reversed.

Accurate Sound Localization in Reverberant Environments is Mediated by Robust Encoding of Spatial Cues in the Auditory Midbrain

PubMed Central

Devore, Sasha; Ihlefeld, Antje; Hancock, Kenneth; Shinn-Cunningham, Barbara; Delgutte, Bertrand

2009-01-01

In reverberant environments, acoustic reflections interfere with the direct sound arriving at a listener’s ears, distorting the spatial cues for sound localization. Yet, human listeners have little difficulty localizing sounds in most settings. Because reverberant energy builds up over time, the source location is represented relatively faithfully during the early portion of a sound, but this representation becomes increasingly degraded later in the stimulus. We show that the directional sensitivity of single neurons in the auditory midbrain of anesthetized cats follows a similar time course, although onset dominance in temporal response patterns results in more robust directional sensitivity than expected, suggesting a simple mechanism for improving directional sensitivity in reverberation. In parallel behavioral experiments, we demonstrate that human lateralization judgments are consistent with predictions from a population rate model decoding the observed midbrain responses, suggesting a subcortical origin for robust sound localization in reverberant environments. PMID:19376072

Spatial distribution of 12 class B notifiable infectious diseases in China: A retrospective study.

PubMed

Zhu, Bin; Fu, Yang; Liu, Jinlin; Mao, Ying

2018-01-01

China is the largest developing country with a relatively developed public health system. To further prevent and eliminate the spread of infectious diseases, China has listed 39 notifiable infectious diseases characterized by wide prevalence or great harm, and classified them into classes A, B, and C, with severity decreasing across classes. Class A diseases have been almost eradicated in China, thus making class B diseases a priority in infectious disease prevention and control. In this retrospective study, we analyze the spatial distribution patterns of 12 class B notifiable infectious diseases that remain active all over China. Global and local Moran's I and corresponding graphic tools are adopted to explore and visualize the global and local spatial distribution of the incidence of the selected epidemics, respectively. Inter-correlations of clustering patterns of each pair of diseases and a cumulative summary of the high/low cluster frequency of the provincial units are also provided by means of figures and maps. Of the 12 most commonly notifiable class B infectious diseases, viral hepatitis and tuberculosis show high incidence rates and account for more than half of the reported cases. Almost all the diseases, except pertussis, exhibit positive spatial autocorrelation at the provincial level. All diseases feature varying spatial concentrations. Nevertheless, associations exist between spatial distribution patterns, with some provincial units displaying the same type of cluster features for two or more infectious diseases. Overall, high-low (unit with high incidence surrounded by units with high incidence, the same below) and high-high spatial cluster areas tend to be prevalent in the provincial units located in western and southwest China, whereas low-low and low-high spatial cluster areas abound in provincial units in north and east China. Despite the various distribution patterns of 12 class B notifiable infectious diseases, certain similarities between their spatial distributions are present. Substantial evidence is available to support disease-specific, location-specific, and disease-combined interventions. Regarding provinces that show high-high/high-low patterns of multiple diseases, comprehensive interventions targeting different diseases should be established. As to the adjacent provincial units revealing similar patterns, coordinated actions need to be taken across borders.

Global Mapping of the Yeast Genetic Interaction Network

NASA Astrophysics Data System (ADS)

Tong, Amy Hin Yan; Lesage, Guillaume; Bader, Gary D.; Ding, Huiming; Xu, Hong; Xin, Xiaofeng; Young, James; Berriz, Gabriel F.; Brost, Renee L.; Chang, Michael; Chen, YiQun; Cheng, Xin; Chua, Gordon; Friesen, Helena; Goldberg, Debra S.; Haynes, Jennifer; Humphries, Christine; He, Grace; Hussein, Shamiza; Ke, Lizhu; Krogan, Nevan; Li, Zhijian; Levinson, Joshua N.; Lu, Hong; Ménard, Patrice; Munyana, Christella; Parsons, Ainslie B.; Ryan, Owen; Tonikian, Raffi; Roberts, Tania; Sdicu, Anne-Marie; Shapiro, Jesse; Sheikh, Bilal; Suter, Bernhard; Wong, Sharyl L.; Zhang, Lan V.; Zhu, Hongwei; Burd, Christopher G.; Munro, Sean; Sander, Chris; Rine, Jasper; Greenblatt, Jack; Peter, Matthias; Bretscher, Anthony; Bell, Graham; Roth, Frederick P.; Brown, Grant W.; Andrews, Brenda; Bussey, Howard; Boone, Charles

2004-02-01

A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

Rapid tsunami models and earthquake source parameters: Far-field and local applications

USGS Publications Warehouse

Geist, E.L.

2005-01-01

Rapid tsunami models have recently been developed to forecast far-field tsunami amplitudes from initial earthquake information (magnitude and hypocenter). Earthquake source parameters that directly affect tsunami generation as used in rapid tsunami models are examined, with particular attention to local versus far-field application of those models. First, validity of the assumption that the focal mechanism and type of faulting for tsunamigenic earthquakes is similar in a given region can be evaluated by measuring the seismic consistency of past events. Second, the assumption that slip occurs uniformly over an area of rupture will most often underestimate the amplitude and leading-wave steepness of the local tsunami. Third, sometimes large magnitude earthquakes will exhibit a high degree of spatial heterogeneity such that tsunami sources will be composed of distinct sub-events that can cause constructive and destructive interference in the wavefield away from the source. Using a stochastic source model, it is demonstrated that local tsunami amplitudes vary by as much as a factor of two or more, depending on the local bathymetry. If other earthquake source parameters such as focal depth or shear modulus are varied in addition to the slip distribution patterns, even greater uncertainty in local tsunami amplitude is expected for earthquakes of similar magnitude. Because of the short amount of time available to issue local warnings and because of the high degree of uncertainty associated with local, model-based forecasts as suggested by this study, direct wave height observations and a strong public education and preparedness program are critical for those regions near suspected tsunami sources.

Early differential sensitivity of evoked-potentials to local and global shape during the perception of three-dimensional objects.

PubMed

Leek, E Charles; Roberts, Mark; Oliver, Zoe J; Cristino, Filipe; Pegna, Alan J

2016-08-01

Here we investigated the time course underlying differential processing of local and global shape information during the perception of complex three-dimensional (3D) objects. Observers made shape matching judgments about pairs of sequentially presented multi-part novel objects. Event-related potentials (ERPs) were used to measure perceptual sensitivity to 3D shape differences in terms of local part structure and global shape configuration - based on predictions derived from hierarchical structural description models of object recognition. There were three types of different object trials in which stimulus pairs (1) shared local parts but differed in global shape configuration; (2) contained different local parts but shared global configuration or (3) shared neither local parts nor global configuration. Analyses of the ERP data showed differential amplitude modulation as a function of shape similarity as early as the N1 component between 146-215ms post-stimulus onset. These negative amplitude deflections were more similar between objects sharing global shape configuration than local part structure. Differentiation among all stimulus types was reflected in N2 amplitude modulations between 276-330ms. sLORETA inverse solutions showed stronger involvement of left occipitotemporal areas during the N1 for object discrimination weighted towards local part structure. The results suggest that the perception of 3D object shape involves parallel processing of information at local and global scales. This processing is characterised by relatively slow derivation of 'fine-grained' local shape structure, and fast derivation of 'coarse-grained' global shape configuration. We propose that the rapid early derivation of global shape attributes underlies the observed patterns of N1 amplitude modulations. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms.

PubMed

Esteves, Francisco F; Springhorn, Alexander; Kague, Erika; Taylor, Erika; Pyrowolakis, George; Fisher, Shannon; Bier, Ethan

2014-09-01

In a broad variety of bilaterian species the trunk central nervous system (CNS) derives from three primary rows of neuroblasts. The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2.2, ind/gsh and msh/msx in Drosophila melanogaster/vertebrates, which are expressed in corresponding non-overlapping patterns along the dorsal-ventral axis. While this conserved suite of "neural identity" gene expression strongly suggests a common ancestral origin for the patterning systems, it is unclear whether the original regulatory mechanisms establishing these patterns have been similarly conserved during evolution. In Drosophila, genetic evidence suggests that Bone Morphogenetic Proteins (BMPs) act in a dosage-dependent fashion to repress expression of neural identity genes. BMPs also play a dose-dependent role in patterning the dorsal and lateral regions of the vertebrate CNS, however, the mechanism by which they achieve such patterning has not yet been clearly established. In this report, we examine the mechanisms by which BMPs act on cis-regulatory modules (CRMs) that control localized expression of the Drosophila msh and zebrafish (Danio rerio) msxB in the dorsal central nervous system (CNS). Our analysis suggests that BMPs act differently in these organisms to regulate similar patterns of gene expression in the neuroectoderm: repressing msh expression in Drosophila, while activating msxB expression in the zebrafish. These findings suggest that the mechanisms by which the BMP gradient patterns the dorsal neuroectoderm have reversed since the divergence of these two ancient lineages.

BMPs Regulate msx Gene Expression in the Dorsal Neuroectoderm of Drosophila and Vertebrates by Distinct Mechanisms

PubMed Central

Esteves, Francisco F.; Taylor, Erika; Pyrowolakis, George; Fisher, Shannon; Bier, Ethan

2014-01-01

In a broad variety of bilaterian species the trunk central nervous system (CNS) derives from three primary rows of neuroblasts. The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2.2, ind/gsh and msh/msx in Drosophila melanogaster/vertebrates, which are expressed in corresponding non-overlapping patterns along the dorsal-ventral axis. While this conserved suite of “neural identity” gene expression strongly suggests a common ancestral origin for the patterning systems, it is unclear whether the original regulatory mechanisms establishing these patterns have been similarly conserved during evolution. In Drosophila, genetic evidence suggests that Bone Morphogenetic Proteins (BMPs) act in a dosage-dependent fashion to repress expression of neural identity genes. BMPs also play a dose-dependent role in patterning the dorsal and lateral regions of the vertebrate CNS, however, the mechanism by which they achieve such patterning has not yet been clearly established. In this report, we examine the mechanisms by which BMPs act on cis-regulatory modules (CRMs) that control localized expression of the Drosophila msh and zebrafish (Danio rerio) msxB in the dorsal central nervous system (CNS). Our analysis suggests that BMPs act differently in these organisms to regulate similar patterns of gene expression in the neuroectoderm: repressing msh expression in Drosophila, while activating msxB expression in the zebrafish. These findings suggest that the mechanisms by which the BMP gradient patterns the dorsal neuroectoderm have reversed since the divergence of these two ancient lineages. PMID:25210771

Characterization of traffic-related PM concentration distribution and fluctuation patterns in near-highway urban residential street canyons.

PubMed

Hahn, Intaek; Brixey, Laurie A; Wiener, Russell W; Henkle, Stacy W; Baldauf, Richard

2009-12-01

Analyses of outdoor traffic-related particulate matter (PM) concentration distribution and fluctuation patterns in urban street canyons within a microscale distance of less than 500 m from a highway source are presented as part of the results from the Brooklyn Traffic Real-Time Ambient Pollutant Penetration and Environmental Dispersion (B-TRAPPED) study. Various patterns of spatial and temporal changes in the street canyon PM concentrations were investigated using time-series data of real-time PM concentrations measured during multiple monitoring periods. Concurrent time-series data of local street canyon wind conditions and wind data from the John F. Kennedy (JFK) International Airport National Weather Service (NWS) were used to characterize the effects of various wind conditions on the behavior of street canyon PM concentrations.Our results suggest that wind direction may strongly influence time-averaged mean PM concentration distribution patterns in near-highway urban street canyons. The rooftop-level wind speeds were found to be strongly correlated with the PM concentration fluctuation intensities in the middle sections of the street blocks. The ambient turbulence generated by shifting local wind directions (angles) showed a good correlation with the PM concentration fluctuation intensities along the entire distance of the first and second street blocks only when the wind angle standard deviations were larger than 30 degrees. Within-canyon turbulent shearing, caused by fluctuating local street canyon wind speeds, showed no correlation with PM concentration fluctuation intensities. The time-averaged mean PM concentration distribution along the longitudinal distances of the street blocks when wind direction was mostly constantly parallel to the street was found to be similar to the distribution pattern for the entire monitoring period when wind direction fluctuated wildly. Finally, we showed that two different PM concentration metrics-time-averaged mean concentration and number of concentration peaks above a certain threshold level-can possibly lead to different assessments of spatial concentration distribution patterns.

Carbonate Channel-Levee Systems Influenced by Mass-Transport Deposition, Browse Basin, Australia

NASA Astrophysics Data System (ADS)

Dunlap, D.; Janson, X.; Sanchez-Phelps, C.; Covault, J. A.

2017-12-01

Submarine channels are primary conduits for clastic sediment transport to deep-water basins, thereby controlling the location of marine depocenters and sediment bypass. The evolution and depositional character of submarine channels have broad implications to sediment dispersal, sediment quality, and hydrocarbon exploration potential. Siliciclastic channel systems have been extensively studied in modern environments, seismic and outcrop; however, carbonate channel-levee deposits have only recently been explored. Here we utilize newly released high-resolution (90 Hz) seismic-reflection data from the Australian Browse Basin to document the influence of mass-transport complex (MTC) deposition on the stratigraphic architecture of carbonate channel-levee systems. The 2014 vintage seismic survey is 2500 km2 and hosts numerous large Miocene-age carbonate channel-levee complexes basinward of the shelf edge. Regional horizons and individual channel forms were mapped. Channels range from 200-300 m wide and are bounded by high-relief levee-overbank wedges (>100 ms TWTT). These channels extend across the survey area >70 km. The leveed-channels were sourced from middle and late Miocene slope gullies linked to platform carbonates. Slope-attached and locally derived MTC's are evident throughout the Miocene section likely related to periods of basin inversion and shelf-edge gully incision. We interpret that regionally extensive (>1000 km2) slope-attached MTC's can shut down a channel-levee system and trigger the initiation of a new system, whereas more locally derived (<100 km2) MTC's can promote changes in channel map-view pattern, including avulsion in some cases. The stratigraphic architectures of the carbonate channel-levee systems and their interactions with MTC's are similar to siliciclastic analogs. The similarity in stratigraphic patterns between siliciclastic and carbonate depositional systems suggests similar formative processes related to submarine mass wasting and turbidity currents, which informs depositional models of carbonate slope systems and calls for re-evaluation of the controls on stratigraphic patterns in mixed siliciclastic-carbonate deep-water basins.

Localization of ABCG5 and ABCG8 proteins in human liver, gall bladder and intestine

PubMed Central

Klett, Eric L; Lee, Mi-Hye; Adams, David B; Chavin, Kenneth D; Patel, Shailendra B

2004-01-01

Background The molecular mechanisms that regulate the entry of dietary sterols into the body and their removal via hepatobiliary secretion are now beginning to be defined. These processes are specifically disrupted in the rare autosomal recessive disease, Sitosterolemia (MIM 210250). Mutations in either, but not both, of two genes ABCG5 or ABCG8, comprising the STSL locus, are now known to cause this disease and their protein products are proposed to function as heterodimers. Under normal circumstances cholesterol, but not non-cholesterol sterols, is preferentially absorbed from the diet. Additionally, any small amounts of non-cholesterol sterols that are absorbed are rapidly taken up by the liver and preferentially excreted into bile. Based upon the defects in sitosterolemia, ABCG5 and ABCG8 serve specifically to exclude non-cholesterol sterol entry at the intestinal level and are involved in sterol excretion at the hepatobiliary level. Methods Here we report the biochemical and immuno-localization of ABCG5 and ABCG8 in human liver, gallbladder and intestine using cell fractionation and immunohistochemical analyses. Results We raised peptide antibodies against ABCG5 and ABCG8 proteins. Using human liver samples, cell fractionation studies showed both proteins are found in membrane fractions, but they did not co-localize with caveolin-rafts, ER, Golgi or mitochondrial markers. Although their distribution in the sub-fractions was similar, they were not completely contiguous. Immunohistochemical analyses showed that while both proteins were readily detectable in the liver, ABCG5 was found predominately lining canalicular membranes, whereas ABCG8 was found in association with bile duct epithelia. At the cellular level, ABCG5 appeared to be apically expressed, whereas ABCG8 had a more diffuse expression pattern. Both ABCG5 and ABCG8 appeared to localize apically as shown by co-localization with MRP2. The distribution patterns of ABCG5 and ABCG8 in the gallbladder were very similar to each other. In the small intestine both ABCG5 and ABCG8 appear to line the brush border. However, at the level of the enterocyte, the cellular distribution patterns of ABCG5 and ABCG8 differed, such that ABCG5 was more diffuse, but ABCG8 was principally apical. Using standard deglycosylation methods, ABCG5 and ABCG8 do not appear to be glycosylated, suggesting a difference between human and mouse proteins. Conclusion We report the distribution patterns of ABCG5 and ABCG8 in human tissues. Cell fractionation studies showed that both proteins co-fractionated in general, but could also be found independent of each other. As predicted, they are expressed apically in both intestine and liver, although their intracellular expression patterns are not completely congruent. These studies support the concept of heterodimerization of ABCG5 and ABCG8, but also support the notion that these proteins may have an independent function. PMID:15383151

The variable genomic architecture of isolation between hybridizing species of house mice.

PubMed

Teeter, Katherine C; Thibodeau, Lisa M; Gompert, Zachariah; Buerkle, C Alex; Nachman, Michael W; Tucker, Priscilla K

2010-02-01

Studies of the genetics of hybrid zones can provide insight into the genomic architecture of species boundaries. By examining patterns of introgression of multiple loci across a hybrid zone, it may be possible to identify regions of the genome that have experienced selection. Here, we present a comparison of introgression in two replicate transects through the house mouse hybrid zone through central Europe, using data from 41 single nucleotide markers. Using both genomic and geographic clines, we found many differences in patterns of introgression between the two transects, as well as some similarities. We found that many loci may have experienced the effects of selection at linked sites, including selection against hybrid genotypes, as well as positive selection in the form of genotypes introgressed into a foreign genetic background. We also found many positive associations of conspecific alleles among unlinked markers, which could be caused by epistatic interactions. Different patterns of introgression in the two transects highlight the challenge of using hybrid zones to identify genes underlying isolation and raise the possibility that the genetic basis of isolation between these species may be dependent on the local population genetic make-up or the local ecological setting.

Effect of Charge Patterning on the Phase Behavior of Polymer Coacervates for Charge Driven Self Assembly

NASA Astrophysics Data System (ADS)

Radhakrishna, Mithun; Sing, Charles E.

Oppositely charged polymers can undergo associative liquid-liquid phase separation when mixed under suitable conditions of ionic strength, temperature and pH to form what are known as `polymeric complex coacervates'. Polymer coacervates find use in diverse array of applications like microencapsulation, drug delivery, membrane filtration and underwater adhesives. The similarity between complex coacervate environments and those in biological systems has also found relevance in areas of bio-mimicry. Our previous works have demonstrated how local charge correlations and molecular connectivity can drastically affect the phase behavior of coacervates. The precise location of charges along the chain therefore dramatically influences the local charge correlations, which consequently influences the phase behavior of coacervates. We investigate the effect of charge patterning along the polymer chain on the phase behavior of coacervates in the framework of the Restricted Primitive Model using Gibbs Ensemble Monte Carlo simulations. Our results show that charge patterning dramatically changes the phase behavior of polymer coacervates, which contrasts with the predictions of the classical Voorn-Overbeek theory. This provides the basis for designing new materials through charge driven self assembly by controlling the positioning of the charged monomers along the chain.

Shear wave arrival time estimates correlate with local speckle pattern.

PubMed

Mcaleavey, Stephen A; Osapoetra, Laurentius O; Langdon, Jonathan

2015-12-01

We present simulation and phantom studies demonstrating a strong correlation between errors in shear wave arrival time estimates and the lateral position of the local speckle pattern in targets with fully developed speckle. We hypothesize that the observed arrival time variations are largely due to the underlying speckle pattern, and call the effect speckle bias. Arrival time estimation is a key step in quantitative shear wave elastography, performed by tracking tissue motion via cross-correlation of RF ultrasound echoes or similar methods. Variations in scatterer strength and interference of echoes from scatterers within the tracking beam result in an echo that does not necessarily describe the average motion within the beam, but one favoring areas of constructive interference and strong scattering. A swept-receive image, formed by fixing the transmit beam and sweeping the receive aperture over the region of interest, is used to estimate the local speckle pattern. Metrics for the lateral position of the speckle are found to correlate strongly (r > 0.7) with the estimated shear wave arrival times both in simulations and in phantoms. Lateral weighting of the swept-receive pattern improved the correlation between arrival time estimates and speckle position. The simulations indicate that high RF echo correlation does not equate to an accurate shear wave arrival time estimate-a high correlation coefficient indicates that motion is being tracked with high precision, but the location tracked is uncertain within the tracking beam width. The presence of a strong on-axis speckle is seen to imply high RF correlation and low bias. The converse does not appear to be true-highly correlated RF echoes can still produce biased arrival time estimates. The shear wave arrival time bias is relatively stable with variations in shear wave amplitude and sign (-20 μm to 20 μm simulated) compared with the variation with different speckle realizations obtained along a given tracking vector. We show that the arrival time bias is weakly dependent on shear wave amplitude compared with the variation with axial position/ local speckle pattern. Apertures of f/3 to f/8 on transmit and f/2 and f/4 on receive were simulated. Arrival time error and correlation with speckle pattern are most strongly determined by the receive aperture.

Shear Wave Arrival Time Estimates Correlate with Local Speckle Pattern

PubMed Central

McAleavey, Stephen A.; Osapoetra, Laurentius O.; Langdon, Jonathan

2016-01-01

We present simulation and phantom studies demonstrating a strong correlation between errors in shear wave arrival time estimates and the lateral position of the local speckle pattern in targets with fully developed speckle. We hypothesize that the observed arrival time variations are largely due to the underlying speckle pattern, and call the effect speckle bias. Arrival time estimation is a key step in quantitative shear wave elastography, performed by tracking tissue motion via cross correlation of RF ultrasound echoes or similar methods. Variations in scatterer strength and interference of echoes from scatterers within the tracking beam result in an echo that does not necessarily describe the average motion within the beam, but one favoring areas of constructive interference and strong scattering. A swept-receive image, formed by fixing the transmit beam and sweeping the receive aperture over the region of interest, is used to estimate the local speckle pattern. Metrics for the lateral position of the speckle are found to correlate strongly (r>0.7) with the estimated shear wave arrival times both in simulations and in phantoms. Lateral weighting of the swept-receive pattern improved the correlation between arrival time estimates and speckle position. The simulations indicate that high RF echo correlation does not equate to an accurate shear wave arrival time estimate – a high correlation coefficient indicates that motion is being tracked with high precision, but the location tracked is uncertain within the tracking beam width. The presence of a strong on-axis speckle is seen to imply high RF correlation and low bias. The converse does not appear to be true – highly correlated RF echoes can still produce biased arrival time estimates. The shear wave arrival time bias is relatively stable with variations in shear wave amplitude and sign (−20 μm to 20 μm simulated) compared to the variation with different speckle realizations obtained along a given tracking vector. We show that the arrival time bias is weakly dependent on shear wave amplitude compared to the variation with axial position/local speckle pattern. Apertures of f/3 to f/8 on transmit and f/2 and f/4 on receive were simulated. Arrival time error and correlation with speckle pattern are most strongly determined by the receive aperture. PMID:26670847

Weakly coupled map lattice models for multicellular patterning and collective normalization of abnormal single-cell states

NASA Astrophysics Data System (ADS)

García-Morales, Vladimir; Manzanares, José A.; Mafe, Salvador

2017-04-01

We present a weakly coupled map lattice model for patterning that explores the effects exerted by weakening the local dynamic rules on model biological and artificial networks composed of two-state building blocks (cells). To this end, we use two cellular automata models based on (i) a smooth majority rule (model I) and (ii) a set of rules similar to those of Conway's Game of Life (model II). The normal and abnormal cell states evolve according to local rules that are modulated by a parameter κ . This parameter quantifies the effective weakening of the prescribed rules due to the limited coupling of each cell to its neighborhood and can be experimentally controlled by appropriate external agents. The emergent spatiotemporal maps of single-cell states should be of significance for positional information processes as well as for intercellular communication in tumorigenesis, where the collective normalization of abnormal single-cell states by a predominantly normal neighborhood may be crucial.

Different effects of variation in Xanthium strumarium L. (Compositae) on two insect seed predators.

PubMed

Hare, J Daniel; Futuyma, Douglas J

1978-01-01

To determine the relative importance of variation in several plant characters on susceptibility to herbivores, we examined patterns of seed predation by two monophagous insect species and patterns of variation in ten populations of the cocklebur, Xanthium strumarium. Multiple regression analysis disclosed that one seed predator was most influenced by plant chemical variation, the other was significantly influenced by both chemical and morphological variation, but variation in yet another character, general burr size, was most important in conferring resistance to both insects simultaneously. The plant populations differed most in this character. Although many of the plant characters were correlated with each other, those important in determining susceptibility to each insect species were uncorrelated and independent of those conferring resistance to both insects simultaneously.These results imply that ecological similar herbivores may be influenced by different aspects of plant variation, and that predictions of evolutionary responses of local plant populations to herbivory may require knowledge of the structure of local herbivore communities and the dynamics of their establishment.

LGN plays distinct roles in oral epithelial stratification, filiform papilla morphogenesis and hair follicle development

PubMed Central

Lough, Kendall J.; Patel, Jeet H.; Descovich, Carlos Patiño; Curtis, T. Anthony

2016-01-01

Oral epithelia protect against constant challenges by bacteria, viruses, toxins and injury while also contributing to the formation of ectodermal appendages such as teeth, salivary glands and lingual papillae. Despite increasing evidence that differentiation pathway genes are frequently mutated in oral cancers, comparatively little is known about the mechanisms that regulate normal oral epithelial development. Here, we characterize oral epithelial stratification and describe multiple distinct functions for the mitotic spindle orientation gene LGN (Gpsm2) in promoting differentiation and tissue patterning in the mouse oral cavity. Similar to its function in epidermis, apically localized LGN directs perpendicular divisions that promote stratification of the palatal, buccogingival and ventral tongue epithelia. Surprisingly, however, in dorsal tongue LGN is predominantly localized basally, circumferentially or bilaterally and promotes planar divisions. Loss of LGN disrupts the organization and morphogenesis of filiform papillae but appears to be dispensable for embryonic hair follicle development. Thus, LGN has crucial tissue-specific functions in patterning surface ectoderm and its appendages by controlling division orientation. PMID:27317810

Weakly coupled map lattice models for multicellular patterning and collective normalization of abnormal single-cell states.

PubMed

García-Morales, Vladimir; Manzanares, José A; Mafe, Salvador

2017-04-01

We present a weakly coupled map lattice model for patterning that explores the effects exerted by weakening the local dynamic rules on model biological and artificial networks composed of two-state building blocks (cells). To this end, we use two cellular automata models based on (i) a smooth majority rule (model I) and (ii) a set of rules similar to those of Conway's Game of Life (model II). The normal and abnormal cell states evolve according to local rules that are modulated by a parameter κ. This parameter quantifies the effective weakening of the prescribed rules due to the limited coupling of each cell to its neighborhood and can be experimentally controlled by appropriate external agents. The emergent spatiotemporal maps of single-cell states should be of significance for positional information processes as well as for intercellular communication in tumorigenesis, where the collective normalization of abnormal single-cell states by a predominantly normal neighborhood may be crucial.

Managing an invasive corallimorph at Palmyra Atoll National Wildlife Refuge, Line Islands, Central Pacific

USGS Publications Warehouse

Work, Thierry M.; Aeby, Greta S.; Neal, Benjamin P.; Price, Nichole N.; Conklin, Eric; Pollock, Amanda

2018-01-01

In 2007, a phase shift from corals to corallimorpharians (CM) centered around a shipwreck was documented at Palmyra Atoll, Line Islands. Subsequent surveys revealed CM to be overgrowing the reef benthos, including corals and coralline algae, potentially placing coral ecosystems in the atoll at risk. This prompted the U.S. Fish and Wildlife Service, the lead management agency of the atoll, to remove the shipwreck. Subsequent surveys showed reductions in CM around the ship impact site. We explain patterns of spread of the CM in terms of both life history and local currents and show with a pilot study that pulverized bleach may be an effective tool to eradicate CM on a local scale. If applied strategically, particularly in heavily infested (> 66% cover) areas, active intervention such as this could be an effective management tool to reduce CM impact on localized areas and decrease colonization rate of remaining reefs. This is the first documentation of the response of an invasive cnidarian to shipwreck removal. While this was a singular event in Palmyra, the spatial and temporal patterns of this invasion and the eradications lessons described herein, are useful for anticipating and controlling similar situations elsewhere.

The sexually dimorphic impact of maltreatment on cortical thickness, surface area and gyrification.

PubMed

Kelly, Philip A; Viding, Essi; Puetz, Vanessa B; Palmer, Amy L; Samuel, Sophie; McCrory, Eamon J

2016-09-01

An extensive literature has detailed how maltreatment experience impacts brain structure in children and adolescents. However, there is a dearth of studies on the influence of maltreatment on surface based indices, and to date no study has investigated how sex influences the impact of maltreatment on cortical thickness, surface area and local gyrification. We investigated sex differences in these measures of cortical structure in a large community sample of children aged 10-14 years (n = 122) comprising 62 children with verified maltreatment experience and 60 matched non-maltreated controls. The maltreated group relative to the controls presented with a pattern of decreased cortical thickness within a region of right anterior cingulate, orbitofrontal cortex and superior frontal gyrus; decreased surface area within the right inferior parietal cortex; and increased local gyrification within left superior parietal cortex. This atypical pattern of cortical structure was similar across males and females. An interaction between maltreatment exposure and sex was found only in local gyrification, within two clusters: the right tempo-parietal junction and the left precentral gyrus. These findings suggest that maltreatment impacts cortical structure in brain areas associated with emotional regulation and theory of mind, with few differences between the sexes.

Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe): A new radiomics descriptor.

PubMed

Prasanna, Prateek; Tiwari, Pallavi; Madabhushi, Anant

2016-11-22

In this paper, we introduce a new radiomic descriptor, Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe) for capturing subtle differences between benign and pathologic phenotypes which may be visually indistinguishable on routine anatomic imaging. CoLlAGe seeks to capture and exploit local anisotropic differences in voxel-level gradient orientations to distinguish similar appearing phenotypes. CoLlAGe involves assigning every image voxel an entropy value associated with the co-occurrence matrix of gradient orientations computed around every voxel. The hypothesis behind CoLlAGe is that benign and pathologic phenotypes even though they may appear similar on anatomic imaging, will differ in their local entropy patterns, in turn reflecting subtle local differences in tissue microarchitecture. We demonstrate CoLlAGe's utility in three clinically challenging classification problems: distinguishing (1) radiation necrosis, a benign yet confounding effect of radiation treatment, from recurrent tumors on T1-w MRI in 42 brain tumor patients, (2) different molecular sub-types of breast cancer on DCE-MRI in 65 studies and (3) non-small cell lung cancer (adenocarcinomas) from benign fungal infection (granulomas) on 120 non-contrast CT studies. For each of these classification problems, CoLlAGE in conjunction with a random forest classifier outperformed state of the art radiomic descriptors (Haralick, Gabor, Histogram of Gradient Orientations).

[Geochemical characteristics and sources of atmospheric particulates in Shanghai during dust storm event].

PubMed

Qian, Peng; Zheng, Xiang-min; Zhou, Li-min

2013-05-01

Atmospheric particulates were sampled from three sampling sites of Putuo, Minhang and Qingpu Districts in Shanghai between Oct. , 2009 and Oct. , 2010. In addition, particulate samples were also collected from Nantong, Zhengzhou, Xi'an, and Beijing city where dust storm dust transported along during spring. Element compositions of atmospheric particulates were determined by XRF and ICP-MS. The concentrations of major and trace elements in atmospheric particulates from Putuo, Minhang and Qingpu Districts were similar, indicating their common source. The UCC standardization distribution map showed that the major element composition of dust storm samples was similar to that of loess in northwestern China, indicating that the dust storm dust was mainly derived from Western desert and partly from local area. The REE partition patterns of dust storm dusts among different cities along dust transport route were similar to each other, as well as to those of northern loess, which indicates that the dust storm samples may have the same material source as loess, which mainly comes from crust material. However, the REE partition patterns of non-dust storm particulates were different among the studied cities, and different from those of loess, which suggests that the non-dust storm samples may be mixed with non-crust source material, which is different from dust storm dust and loess. The major element composition and REE partition pattern are effective indicators for source tracing of dust storm dust.

Iron variation within a granitic pluton as determined by near-infrared reflectance

NASA Technical Reports Server (NTRS)

Baird, A. K.

1984-01-01

One-hundred fifty-one previously chemically analyzed samples of tonalite from the Lakeview Mountains pluton, southern California batholith, were analyzed for their iron content using near-infrared spectrophotometry. Compared to the earlier analyses of the same sample set by X-ray fluorescence spectrography, the infrared data have higher analytical variance but clearly define patterns of compositional zonation in the pluton which are closely similar to those patterns obtained from X-ray data; petrogenetic interpretations for the pluton would be the same from either data set. Infrared spectral data can be obtained directly in the field with relatively simple instruments and field measurements can be made to average local heterogeneities that often mask significant plutonic variations.

Comparing Homicide-Suicides in the United States and Sweden.

PubMed

Regoeczi, Wendy C; Granath, Sven; Issa, Rania; Gilson, Thomas; Sturup, Joakim

2016-11-01

Research on homicides followed by suicides has largely relied on very localized samples and relatively short time spans of data. As a result, little is known about the extent to which patterns within cases of homicide-suicides are geographically specific. The current study seeks to help fill this gap by comparing twenty years of homicide-suicide data for Sweden and a large U.S. county. Although some of the underlying patterns in the two countries are similar (e.g., decreasing rates), a number of important differences emerge, particularly with respect to incidence, weapons used, perpetrator age, and relationship of the perpetrator to the victim. © 2016 American Academy of Forensic Sciences.

Speciation on a local geographic scale: the evolution of a rare rock outcrop specialist in Mimulus.

PubMed

Ferris, Kathleen G; Sexton, Jason P; Willis, John H

2014-08-05

Speciation can occur on both large and small geographical scales. In plants, local speciation, where small populations split off from a large-ranged progenitor species, is thought to be the dominant mode, yet there are still few examples to verify speciation has occurred in this manner. A recently described morphological species in the yellow monkey flowers, Mimulus filicifolius, is an excellent candidate for local speciation because of its highly restricted geographical range. Mimulus filicifolius was formerly identified as a population of M. laciniatus due to similar lobed leaf morphology and rocky outcrop habitat. To investigate whether M. filicifolius is genetically divergent and reproductively isolated from M. laciniatus, we examined patterns of genetic diversity in ten nuclear and eight microsatellite loci, and hybrid fertility in M. filicifolius and its purported close relatives: M. laciniatus, M. guttatus and M. nasutus. We found that M. filicifolius is genetically divergent from the other species and strongly reproductively isolated from M. laciniatus. We conclude that M. filicifolius is an independent rock outcrop specialist despite being morphologically and ecologically similar to M. laciniatus, and that its small geographical range nested within other wide-ranging members of the M. guttatus species complex is consistent with local speciation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Evidence for similar patterns of neural activity elicited by picture- and word-based representations of natural scenes.

PubMed

Kumar, Manoj; Federmeier, Kara D; Fei-Fei, Li; Beck, Diane M

2017-07-15

A long-standing core question in cognitive science is whether different modalities and representation types (pictures, words, sounds, etc.) access a common store of semantic information. Although different input types have been shown to activate a shared network of brain regions, this does not necessitate that there is a common representation, as the neurons in these regions could still differentially process the different modalities. However, multi-voxel pattern analysis can be used to assess whether, e.g., pictures and words evoke a similar pattern of activity, such that the patterns that separate categories in one modality transfer to the other. Prior work using this method has found support for a common code, but has two limitations: they have either only examined disparate categories (e.g. animals vs. tools) that are known to activate different brain regions, raising the possibility that the pattern separation and inferred similarity reflects only large scale differences between the categories or they have been limited to individual object representations. By using natural scene categories, we not only extend the current literature on cross-modal representations beyond objects, but also, because natural scene categories activate a common set of brain regions, we identify a more fine-grained (i.e. higher spatial resolution) common representation. Specifically, we studied picture- and word-based representations of natural scene stimuli from four different categories: beaches, cities, highways, and mountains. Participants passively viewed blocks of either phrases (e.g. "sandy beach") describing scenes or photographs from those same scene categories. To determine whether the phrases and pictures evoke a common code, we asked whether a classifier trained on one stimulus type (e.g. phrase stimuli) would transfer (i.e. cross-decode) to the other stimulus type (e.g. picture stimuli). The analysis revealed cross-decoding in the occipitotemporal, posterior parietal and frontal cortices. This similarity of neural activity patterns across the two input types, for categories that co-activate local brain regions, provides strong evidence of a common semantic code for pictures and words in the brain. Copyright © 2017 Elsevier Inc. All rights reserved.

How structure sculpts function: Unveiling the contribution of anatomical connectivity to the brain's spontaneous correlation structure

NASA Astrophysics Data System (ADS)

Bettinardi, R. G.; Deco, G.; Karlaftis, V. M.; Van Hartevelt, T. J.; Fernandes, H. M.; Kourtzi, Z.; Kringelbach, M. L.; Zamora-López, G.

2017-04-01

Intrinsic brain activity is characterized by highly organized co-activations between different regions, forming clustered spatial patterns referred to as resting-state networks. The observed co-activation patterns are sustained by the intricate fabric of millions of interconnected neurons constituting the brain's wiring diagram. However, as for other real networks, the relationship between the connectional structure and the emergent collective dynamics still evades complete understanding. Here, we show that it is possible to estimate the expected pair-wise correlations that a network tends to generate thanks to the underlying path structure. We start from the assumption that in order for two nodes to exhibit correlated activity, they must be exposed to similar input patterns from the entire network. We then acknowledge that information rarely spreads only along a unique route but rather travels along all possible paths. In real networks, the strength of local perturbations tends to decay as they propagate away from the sources, leading to a progressive attenuation of the original information content and, thus, of their influence. Accordingly, we define a novel graph measure, topological similarity, which quantifies the propensity of two nodes to dynamically correlate as a function of the resemblance of the overall influences they are expected to receive due to the underlying structure of the network. Applied to the human brain, we find that the similarity of whole-network inputs, estimated from the topology of the anatomical connectome, plays an important role in sculpting the backbone pattern of time-average correlations observed at rest.

Regional patterns of interannual variability of catchment water balances across the continental U.S.: A Budyko framework

NASA Astrophysics Data System (ADS)

Carmona, Alejandra M.; Sivapalan, Murugesu; Yaeger, Mary A.; Poveda, Germán.

2014-12-01

Patterns of interannual variability of the annual water balance are explored using data from 190 MOPEX catchments across the continental U.S. This analysis has led to the derivation of a quantitative, dimensionless, Budyko-type framework to characterize the observed interannual variability of annual water balances. The resulting model is expressed in terms of a humidity index that measures the competition between water and energy availability at the annual time scale, and a similarity parameter (α) that captures the net effects of other short-term climate features and local landscape characteristics. This application of the model to the 190 study catchments revealed the existence of space-time symmetry between spatial (between-catchment) variability and general trends in the temporal (between-year) variability of the annual water balances. The MOPEX study catchments were classified into eight similar catchment groups on the basis of magnitudes of the similarity parameter α. Interesting regional trends of α across the continental U.S. were brought out through identification of similarities between the spatial positions of the catchment groups with the mapping of distinctive ecoregions that implicitly take into account common climatic and vegetation characteristics. In this context, this study has introduced a deep sense of similarity that is evident in observed space-time variability of water balances that also reflect the codependence and coevolution of climate and landscape properties.

Local adaptation to osmotic environment in killifish, Fundulus heteroclitus, is supported by divergence in swimming performance but not by differences in excess post-exercise oxygen consumption or aerobic scope.

PubMed

Brennan, Reid S; Hwang, Ruth; Tse, Michelle; Fangue, Nann A; Whitehead, Andrew

2016-06-01

Regulation of internal ion homeostasis is essential for fishes inhabiting environments where salinities differ from their internal concentrations. It is hypothesized that selection will reduce energetic costs of osmoregulation in a population's native osmotic habitat, producing patterns of local adaptation. Killifish, Fundulus heteroclitus, occupy estuarine habitats where salinities range from fresh to seawater. Populations inhabiting an environmental salinity gradient differ in physiological traits associated with acclimation to acute salinity stress, consistent with local adaptation. Similarly, metabolic rates differ in populations adapted to different temperatures, but have not been studied in regard to salinity. We investigated evidence for local adaptation between populations of killifish native to fresh and brackish water habitats. Aerobic scope (the difference between minimum and maximum metabolic rates), excess post-exercise oxygen consumption, and swimming performance (time and distance to reach exhaustion) were used as proxies for fitness in fresh and brackish water treatments. Swimming performance results supported local adaptation; fish native to brackish water habitats performed significantly better than freshwater-native fish at high salinity while low salinity performance was similar between populations. However, results from metabolic measures did not support this conclusion; both populations showed an increase in resting metabolic rate and a decrease of aerobic scope in fresh water. Similarly, excess post-exercise oxygen consumption was higher for both populations in fresh than in brackish water. While swimming results suggest that environmentally dependent performance differences may be a result of selection in divergent osmotic environments, the differences between populations are not coupled with divergence in metabolic performance. Copyright © 2016 Elsevier Inc. All rights reserved.

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

Nesterova, E.V.; Bouvier, S.; Bacroix, B.

Transmission electron microscopy (TEM) microstructures of a high-strength dual-phase steel DP800 have been examined after moderate plastic deformations in simple shear and uniaxial tension. Special attention has been paid to the effect of the intergranular hard phase (martensite) on the microstructure evolution in the near-grain boundary regions. Quantitative parameters of dislocation patterning have been determined and compared with the similar characteristics of previously examined single-phase steels. The dislocation patterning in the interiors of the ferrite grains in DP800 steel is found to be similar to that already observed in the single-phase IF (Interstitial Free) steel whereas the martensite-affected zones presentmore » a delay in patterning and display very high gradients of continuous (gradual) disorientations associated with local internal stresses. The above stresses are shown to control the work-hardening of dual-phase materials at moderate strains for monotonic loading and are assumed to influence their microstructure evolution and mechanical behavior under strain-path changes. - Highlights: • The microstructure evolution has been studied by TEM in a DP800 steel. • It is influenced by both martensite and dislocations in the initial state. • The DP800 steel presents a high work-hardening rate due to internal stresses.« less

Surface plasmon quantum cascade lasers as terahertz local oscillators.

PubMed

Hajenius, M; Khosropanah, P; Hovenier, J N; Gao, J R; Klapwijk, T M; Barbieri, S; Dhillon, S; Filloux, P; Sirtori, C; Ritchie, D A; Beere, H E

2008-02-15

We characterize a heterodyne receiver based on a surface-plasmon waveguide quantum cascade laser (QCL) emitting at 2.84 THz as a local oscillator, and an NbN hot electron bolometer as a mixer. We find that the envelope of the far-field pattern of the QCL is diffraction-limited and superimposed onto interference fringes, which are similar to those found in narrow double-metal waveguide QCLs. Compared to the latter, a more directional beam allows for better coupling of the radiation power to the mixer. We obtain a receiver noise temperature of 1050 K when the mixer is at 2 K, which, to our knowledge, is the highest sensitivity reported at frequencies beyond 2.5 THz.

Heavy metal exchange of Ascophyllum nodosum plants in situ

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

Mykestad, S.; Eide, I.; Melsom, S.

In situ experiments with exchange of metals between sea water and plants of the marine alga A. nodosum have been carried out, and the content of zinc, lead, cadmium and mercury determined at different times and in different environments with respect to metal concentration. Plants on small pieces of rock were transferred from one locality to another and anchored with cement. The tissue synthesized in the new growing place had a metal composition similar to the newly synthesized tissue in the native plants from the same locality. The different metals showed somewhat different patterns regarding the metal exchange process. Somemore » possible mechanisms are discussed in relation to results from laboratory investigations.« less

Sorted bedform pattern evolution: Persistence, destruction and self-organized intermittency

NASA Astrophysics Data System (ADS)

Goldstein, Evan B.; Murray, A. Brad; Coco, Giovanni

2011-12-01

We investigate the long-term evolution of inner continental shelf sorted bedform patterns. Numerical modeling suggests that a range of behaviors are possible, from pattern persistence to spatial-temporal intermittency. Sorted bedform persistence results from a robust sorting feedback that operates when the seabed features a sufficient concentration of coarse material. In the absence of storm events, pattern maturation processes such as defect dynamics and pattern migration tend to cause the burial of coarse material and excavation of fine material, leading to the fining of the active layer. Vertical sorting occurs until a critical state of active layer coarseness is reached. This critical state results in the local cessation of the sorting feedback, leading to a self-organized spatially intermittent pattern, a hallmark of observed sorted bedforms. Bedforms in shallow conditions and those subject to high wave climates may be temporally intermittent features as a result of increased wave orbital velocity during storms. Erosion, or deposition of bimodal sediment, similarly leads to a spatially intermittent pattern, with individual coarse domains exhibiting temporal intermittence. Recurring storm events cause coarsening of the seabed (strengthening the sorting feedback) and the development of large wavelength patterns. Cessation of storm events leads to the superposition of storm (large wavelength) and inter-storm (small wavelength) patterns and spatial heterogeneity of pattern modes.

Scalp and Source Power Topography in Sleepwalking and Sleep Terrors: A High-Density EEG Study.

PubMed

Castelnovo, Anna; Riedner, Brady A; Smith, Richard F; Tononi, Giulio; Boly, Melanie; Benca, Ruth M

2016-10-01

To examine scalp and source power topography in sleep arousals disorders (SADs) using high-density EEG (hdEEG). Fifteen adult subjects with sleep arousal disorders (SADs) and 15 age- and gender-matched good sleeping healthy controls were recorded in a sleep laboratory setting using a 256 channel EEG system. Scalp EEG analysis of all night NREM sleep revealed a localized decrease in slow wave activity (SWA) power (1-4 Hz) over centro-parietal regions relative to the rest of the brain in SADs compared to good sleeping healthy controls. Source modelling analysis of 5-minute segments taken from N3 during the first half of the night revealed that the local decrease in SWA power was prominent at the level of the cingulate, motor, and sensori-motor associative cortices. Similar patterns were also evident during REM sleep and wake. These differences in local sleep were present in the absence of any detectable clinical or electrophysiological sign of arousal. Overall, results suggest the presence of local sleep differences in the brain of SADs patients during nights without clinical episodes. The persistence of similar topographical changes in local EEG power during REM sleep and wakefulness points to trait-like functional changes that cross the boundaries of NREM sleep. The regions identified by source imaging are consistent with the current neurophysiological understanding of SADs as a disorder caused by local arousals in motor and cingulate cortices. Persistent localized changes in neuronal excitability may predispose affected subjects to clinical episodes. © 2016 Associated Professional Sleep Societies, LLC.

Rural health care bypass behavior: how community and spatial characteristics affect primary health care selection.

PubMed

Sanders, Scott R; Erickson, Lance D; Call, Vaughn R A; McKnight, Matthew L; Hedges, Dawson W

2015-01-01

(1) To assess the prevalence of rural primary care physician (PCP) bypass, a behavior in which residents travel farther than necessary to obtain health care, (2) To examine the role of community and non-health-care-related characteristics on bypass behavior, and (3) To analyze spatial bypass patterns to determine which rural communities are most affected by bypass. Data came from the Montana Health Matters survey, which gathered self-reported information from Montana residents on their health care utilization, satisfaction with health care services, and community and demographic characteristics. Logistic regression and spatial analysis were used to examine the probability and spatial patterns of bypass. Overall, 39% of respondents bypass local health care. Similar to previous studies, dissatisfaction with local health care was found to increase the likelihood of bypass. Dissatisfaction with local shopping also increases the likelihood of bypass, while the number of friends in a community, and commonality with community reduce the likelihood of bypass. Other significant factors associated with bypass include age, income, health, and living in a highly rural community or one with high commuting flows. Our results suggest that outshopping theory, in which patients bundle services and shopping for added convenience, extends to primary health care selection. This implies that rural health care selection is multifaceted, and that in addition to perceived satisfaction with local health care, the quality of local shopping and levels of community attachment also influence bypass behavior. © 2014 National Rural Health Association.

Exploring children's face-space: a multidimensional scaling analysis of the mental representation of facial identity.

PubMed

Nishimura, Mayu; Maurer, Daphne; Gao, Xiaoqing

2009-07-01

We explored differences in the mental representation of facial identity between 8-year-olds and adults. The 8-year-olds and adults made similarity judgments of a homogeneous set of faces (individual hair cues removed) using an "odd-man-out" paradigm. Multidimensional scaling (MDS) analyses were performed to represent perceived similarity of faces in a multidimensional space. Five dimensions accounted optimally for the judgments of both children and adults, with similar local clustering of faces. However, the fit of the MDS solutions was better for adults, in part because children's responses were more variable. More children relied predominantly on a single dimension, namely eye color, whereas adults appeared to use multiple dimensions for each judgment. The pattern of findings suggests that children's mental representation of faces has a structure similar to that of adults but that children's judgments are influenced less consistently by that overall structure.

Multi-Scale Fractal Analysis of Image Texture and Pattern

NASA Technical Reports Server (NTRS)

Emerson, Charles W.

1998-01-01

Fractals embody important ideas of self-similarity, in which the spatial behavior or appearance of a system is largely independent of scale. Self-similarity is defined as a property of curves or surfaces where each part is indistinguishable from the whole, or where the form of the curve or surface is invariant with respect to scale. An ideal fractal (or monofractal) curve or surface has a constant dimension over all scales, although it may not be an integer value. This is in contrast to Euclidean or topological dimensions, where discrete one, two, and three dimensions describe curves, planes, and volumes. Theoretically, if the digital numbers of a remotely sensed image resemble an ideal fractal surface, then due to the self-similarity property, the fractal dimension of the image will not vary with scale and resolution. However, most geographical phenomena are not strictly self-similar at all scales, but they can often be modeled by a stochastic fractal in which the scaling and self-similarity properties of the fractal have inexact patterns that can be described by statistics. Stochastic fractal sets relax the monofractal self-similarity assumption and measure many scales and resolutions in order to represent the varying form of a phenomenon as a function of local variables across space. In image interpretation, pattern is defined as the overall spatial form of related features, and the repetition of certain forms is a characteristic pattern found in many cultural objects and some natural features. Texture is the visual impression of coarseness or smoothness caused by the variability or uniformity of image tone or color. A potential use of fractals concerns the analysis of image texture. In these situations it is commonly observed that the degree of roughness or inexactness in an image or surface is a function of scale and not of experimental technique. The fractal dimension of remote sensing data could yield quantitative insight on the spatial complexity and information content contained within these data. A software package known as the Image Characterization and Modeling System (ICAMS) was used to explore how fractal dimension is related to surface texture and pattern. The ICAMS software was verified using simulated images of ideal fractal surfaces with specified dimensions. The fractal dimension for areas of homogeneous land cover in the vicinity of Huntsville, Alabama was measured to investigate the relationship between texture and resolution for different land covers.

Pattern Laser Annealing by a Pulsed Laser

NASA Astrophysics Data System (ADS)

Komiya, Yoshio; Hoh, Koichiro; Murakami, Koichi; Takahashi, Tetsuo; Tarui, Yasuo

1981-10-01

Preliminary experiments with contact-type pattern laser annealing were made for local polycrystallization of a-Si, local evaporation of a-Si and local formation of Ni-Si alloy. These experiments showed that the mask patterns can be replicated as annealed regions with a resolution of a few microns on substrates. To overcome shortcomings due to the contact type pattern annealing, a projection type reduction pattern laser annealing system is proposed for resistless low temperature pattern forming processes.

A space oddity: geographic and specific modulation of migration in Eudyptes penguins.

PubMed

Thiebot, Jean-Baptiste; Cherel, Yves; Crawford, Robert J M; Makhado, Azwianewi B; Trathan, Philip N; Pinaud, David; Bost, Charles-André

2013-01-01

Post-breeding migration in land-based marine animals is thought to offset seasonal deterioration in foraging or other important environmental conditions at the breeding site. However the inter-breeding distribution of such animals may reflect not only their optimal habitat, but more subtle influences on an individual's migration path, including such factors as the intrinsic influence of each locality's paleoenvironment, thereby influencing animals' wintering distribution. In this study we investigated the influence of the regional marine environment on the migration patterns of a poorly known, but important seabird group. We studied the inter-breeding migration patterns in three species of Eudyptes penguins (E. chrysolophus, E. filholi and E. moseleyi), the main marine prey consumers amongst the World's seabirds. Using ultra-miniaturized logging devices (light-based geolocators) and satellite tags, we tracked 87 migrating individuals originating from 4 sites in the southern Indian Ocean (Marion, Crozet, Kerguelen and Amsterdam Islands) and modelled their wintering habitat using the MADIFA niche modelling technique. For each site, sympatric species followed a similar compass bearing during migration with consistent species-specific latitudinal shifts. Within each species, individuals breeding on different islands showed contrasting migration patterns but similar winter habitat preferences driven by sea-surface temperatures. Our results show that inter-breeding migration patterns in sibling penguin species depend primarily on the site of origin and secondly on the species. Such site-specific migration bearings, together with similar wintering habitat used by parapatrics, support the hypothesis that migration behaviour is affected by the intrinsic characteristics of each site. The paleo-oceanographic conditions (primarily, sea-surface temperatures) when the populations first colonized each of these sites may have been an important determinant of subsequent migration patterns. Based on previous chronological schemes of taxonomic radiation and geographical expansion of the genus Eudyptes, we propose a simple scenario to depict the chronological onset of contrasting migration patterns within this penguin group.

Estimation of Fractional Plant Lifeform Cover Using Landsat and Airborne LiDAR/hyperspectral Data

NASA Astrophysics Data System (ADS)

Parra, A. S.; Xu, Q.; Dilts, T.; Weisberg, P.; Greenberg, J. A.

2017-12-01

Land-cover change has generally been understood as the result of local, landscape or regional-scale processes with most studies focusing on case-study landscapes or smaller regions. However, as we observe similar types of land-cover change occurring across different biomes worldwide, it becomes clear that global-scale processes such as climate change and CO2 fertilization, in interaction with local influences, are underlying drivers in land-cover change patterns. Prior studies on global land-cover change may not have had a suitable spatial, temporal and thematic resolution for allowing the identification of such patterns. Furthermore, the lack of globally consistent spatial data products also constitutes a limiting factor in evaluating both proximate and ultimate causes of land-cover change. In this study, we derived a global model for broadleaf tree, needleleaf tree, shrub, herbaceous, and "other" fractional cover using Landsat imagery. Combined LiDAR/hyperspectral data sets were used for calibration and validation of the Landsat-derived products. Spatially explicit uncertainties were also created as part of the data products. Our results highlight the potential for large-scale studies that model local and global influences on land-cover transition types and rates at fine thematic, spatial, and temporal resolutions. These spatial data products are relevant for identifying patterns in land-cover change due to underlying global-scale processes and can provide valuable insights into climatic and land-use factors determining vegetation distributions.

Periodic and aperiodic flow patterns around an airfoil with leading-edge protuberances

NASA Astrophysics Data System (ADS)

Cai, Chang; Zuo, Zhigang; Maeda, Takao; Kamada, Yasunari; Li, Qing'an; Shimamoto, Kensei; Liu, Shuhong

2017-11-01

Recently leading-edge protuberances have attracted great attention as a passive method for separation control. In this paper, the effect of multiple leading-edge protuberances on the performance of a two-dimensional airfoil is investigated through experimental measurement of aerodynamic forces, surface tuft visualization, and numerical simulation. In contrast to the sharp stall of the baseline airfoil with large hysteresis effect during AOA (angle of attack) increasing and decreasing, the stall process of the modified airfoil with leading-edge protuberances is gentle and stable. Flow visualization revealed that the flow past each protuberance is periodic and symmetric at small AOAs. Streamwise vortices are generated on the shoulders of the protuberance, leading to a larger separation around the valley sections and a longer attachment along the peak sections. When some critical AOA is exceeded, aperiodic and asymmetric flow patterns occur on the protuberances at different spanwise positions, with leading-edge separation on some of the valley sections and non-stalled condition elsewhere. A combined mechanism, involving both the compartmentalization effect of the slender momentum-enhanced attached flows on the protuberance peaks and the downwash effect of the local stalled region with low circulation, is proposed to explain the generation of the aperiodic flow patterns. The influence of the number of protuberances is also investigated, which shows similar aperiodic flow patterns. The distance between the neighboring local stalled valley sections is found to be in the range of 4-7 times the protuberance wavelength. According to the proposed mechanism, it is speculated that the distance between the neighboring local stalled valley sections is inclined to increase with a smaller protuberance amplitude or at a larger AOA.

More than one way to see it: Individual heuristics in avian visual computation

PubMed Central

Ravignani, Andrea; Westphal-Fitch, Gesche; Aust, Ulrike; Schlumpp, Martin M.; Fitch, W. Tecumseh

2015-01-01

Comparative pattern learning experiments investigate how different species find regularities in sensory input, providing insights into cognitive processing in humans and other animals. Past research has focused either on one species’ ability to process pattern classes or different species’ performance in recognizing the same pattern, with little attention to individual and species-specific heuristics and decision strategies. We trained and tested two bird species, pigeons (Columba livia) and kea (Nestor notabilis, a parrot species), on visual patterns using touch-screen technology. Patterns were composed of several abstract elements and had varying degrees of structural complexity. We developed a model selection paradigm, based on regular expressions, that allowed us to reconstruct the specific decision strategies and cognitive heuristics adopted by a given individual in our task. Individual birds showed considerable differences in the number, type and heterogeneity of heuristic strategies adopted. Birds’ choices also exhibited consistent species-level differences. Kea adopted effective heuristic strategies, based on matching learned bigrams to stimulus edges. Individual pigeons, in contrast, adopted an idiosyncratic mix of strategies that included local transition probabilities and global string similarity. Although performance was above chance and quite high for kea, no individual of either species provided clear evidence of learning exactly the rule used to generate the training stimuli. Our results show that similar behavioral outcomes can be achieved using dramatically different strategies and highlight the dangers of combining multiple individuals in a group analysis. These findings, and our general approach, have implications for the design of future pattern learning experiments, and the interpretation of comparative cognition research more generally. PMID:26113444

Hybrid overlay metrology for high order correction by using CDSEM

NASA Astrophysics Data System (ADS)

Leray, Philippe; Halder, Sandip; Lorusso, Gian; Baudemprez, Bart; Inoue, Osamu; Okagawa, Yutaka

2016-03-01

Overlay control has become one of the most critical issues for semiconductor manufacturing. Advanced lithographic scanners use high-order corrections or correction per exposure to reduce the residual overlay. It is not enough in traditional feedback of overlay measurement by using ADI wafer because overlay error depends on other process (etching process and film stress, etc.). It needs high accuracy overlay measurement by using AEI wafer. WIS (Wafer Induced Shift) is the main issue for optical overlay, IBO (Image Based Overlay) and DBO (Diffraction Based Overlay). We design dedicated SEM overlay targets for dual damascene process of N10 by i-ArF multi-patterning. The pattern is same as device-pattern locally. Optical overlay tools select segmented pattern to reduce the WIS. However segmentation has limit, especially the via-pattern, for keeping the sensitivity and accuracy. We evaluate difference between the viapattern and relaxed pitch gratings which are similar to optical overlay target at AEI. CDSEM can estimate asymmetry property of target from image of pattern edge. CDSEM can estimate asymmetry property of target from image of pattern edge. We will compare full map of SEM overlay to full map of optical overlay for high order correction ( correctables and residual fingerprints).

Regulation of Cell Diameter, For3p Localization, and Cell Symmetry by Fission Yeast Rho-GAP Rga4p

PubMed Central

Das, Maitreyi; Wiley, David J.; Medina, Saskia; Vincent, Helen A.; Larrea, Michelle; Oriolo, Andrea

2007-01-01

Control of cellular dimensions and cell symmetry are critical for development and differentiation. Here we provide evidence that the putative Rho-GAP Rga4p of Schizosaccharomyces pombe controls cellular dimensions. rga4Δ cells are wider in diameter and shorter in length, whereas Rga4p overexpression leads to reduced diameter of the growing cell tip. Consistent with a negative role in cell growth control, Rga4p protein localizes to the cell sides in a “corset” pattern, and to the nongrowing cell tips. Additionally, rga4Δ cells show an altered growth pattern similar to that observed in mutants of the formin homology protein For3p. Consistent with these observations, Rga4p is required for normal localization of For3p and for normal distribution of the actin cytoskeleton. We show that different domains of the Rga4p protein mediate diverse morphological functions. The C-terminal GAP domain mediates For3p localization to the cell tips and maintains cell diameter. Conversely, overexpression of the N-terminal LIM homology domain of Rga4p promotes actin cable formation in a For3p-dependent manner. Our studies indicate that Rga4p functionally interacts with For3p and has a novel function in the control of cell diameter and cell growth. PMID:17377067

What it takes to invade grassland ecosystems: traits, introduction history and filtering processes

PubMed Central

Carboni, Marta; Münkemüller, Tamara; Lavergne, Sébastien; Choler, Philippe; Borgy, Benjamin; Violle, Cyrille; Essl, Franz; Roquet, Cristina; Munoz, François; Consortium, DivGrass; Thuiller, Wilfried

2016-01-01

Whether the success of alien species can be explained by their functional or phylogenetic characteristics remains unresolved because of data limitations, scale issues and weak quantifications of success. Using permanent grasslands across France (50,000 vegetation-plots, 2000 species, 130 aliens) and building on the Rabinowitz’ classification to quantify spread, we showed that phylogenetic and functional similarities to natives were the most important correlates of invasion success compared to intrinsic functional characteristics and introduction history. Results contrasted between spatial scales and components of invasion success. Widespread and common aliens were similar to co-occurring natives at coarse scales (indicating environmental filtering), but dissimilar at finer scales (indicating local competition). In contrast, regionally widespread but locally rare aliens showed patterns of competitive exclusion already at coarse scale. Quantifying trait differences between aliens and natives and distinguishing the components of invasion success improved our ability to understand and potentially predict alien spread at multiple scales. PMID:26689431

Interface proliferation and the growth of labyrinths in a reaction-diffusion system

NASA Astrophysics Data System (ADS)

Goldstein, Raymond E.; Muraki, David J.; Petrich, Dean M.

1996-04-01

In the bistable regime of the FitzHugh-Nagumo model of reaction-diffusion systems, spatially homogeneous patterns may be nonlinearly unstable to the formation of compact "localized states." The formation of space-filling patterns from instabilities of such structures is studied in the context of a nonlocal contour dynamics model for the evolution of boundaries between high and low concentrations of the activator. An earlier heuristic derivation [D. M. Petrich and R. E. Goldstein,

Host specialization in ticks and transmission of tick-borne diseases: a review

PubMed Central

McCoy, Karen D.; Léger, Elsa; Dietrich, Muriel

2013-01-01

Determining patterns of host use, and the frequency at which these patterns change, are of key importance if we are to understand tick population dynamics, the evolution of tick biodiversity, and the circulation and evolution of associated pathogens. The question of whether ticks are typically host specialists or host generalists has been subject to much debate over the last half-century. Indeed, early research proposed that morphological diversity in ticks was linked to host specific adaptations and that most ticks were specialists. Later work disputed this idea and suggested that ticks are largely limited by biogeographic conditions and tend to use all locally available host species. The work presented in this review suggests that the actual answer likely lies somewhere between these two extremes. Although recent observational studies support the view that phylogenetically diverse host species share ticks when found on similar ecological ranges, theory on host range evolution predicts that host specialization should evolve in ticks given their life history characteristics. Contemporary work employing population genetic tools to examine host-associated population structure in several tick systems support this prediction and show that simple species records are not enough to determine whether a parasite is a true host generalist; host specialization does evolve in ticks at local scales, but may not always lead to speciation. Ticks therefore seem to follow a pattern of being global generalists, local specialists. Given this, the notion of host range needs to be modified from an evolutionary perspective, where one simply counts the number of hosts used across the geographic distribution, to a more ecological view, where one considers host use at a local scale, if we are to better understand the circulation of tick-borne pathogens and exposure risks for humans and livestock. PMID:24109592

Host specialization in ticks and transmission of tick-borne diseases: a review.

PubMed

McCoy, Karen D; Léger, Elsa; Dietrich, Muriel

2013-01-01

Determining patterns of host use, and the frequency at which these patterns change, are of key importance if we are to understand tick population dynamics, the evolution of tick biodiversity, and the circulation and evolution of associated pathogens. The question of whether ticks are typically host specialists or host generalists has been subject to much debate over the last half-century. Indeed, early research proposed that morphological diversity in ticks was linked to host specific adaptations and that most ticks were specialists. Later work disputed this idea and suggested that ticks are largely limited by biogeographic conditions and tend to use all locally available host species. The work presented in this review suggests that the actual answer likely lies somewhere between these two extremes. Although recent observational studies support the view that phylogenetically diverse host species share ticks when found on similar ecological ranges, theory on host range evolution predicts that host specialization should evolve in ticks given their life history characteristics. Contemporary work employing population genetic tools to examine host-associated population structure in several tick systems support this prediction and show that simple species records are not enough to determine whether a parasite is a true host generalist; host specialization does evolve in ticks at local scales, but may not always lead to speciation. Ticks therefore seem to follow a pattern of being global generalists, local specialists. Given this, the notion of host range needs to be modified from an evolutionary perspective, where one simply counts the number of hosts used across the geographic distribution, to a more ecological view, where one considers host use at a local scale, if we are to better understand the circulation of tick-borne pathogens and exposure risks for humans and livestock.

Species differences in the localization and number of CNS beta adrenergic receptors: Rat versus guinea pig

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

Booze, R.M.; Crisostomo, E.A.; Davis, J.N.

1989-06-01

The localization and number of beta adrenergic receptors were directly compared in the brains of rats and guinea pigs. The time course of association and saturability of (125I)cyanopindolol (CYP) binding to slide-mounted tissue sections was similar in rats (Kd = 17 pM) and guinea pigs (Kd = 20 pM). The beta-1 and beta-2 receptor subtypes were examined through the use of highly selective unlabeled receptor antagonists, ICI 118,551 (50 nM) and ICI 89,406 (70 nM). Dramatic species differences between rats and guinea pigs were observed in the neuroanatomical regional localization of the beta adrenergic receptor subtypes. For example, in themore » thalamus prominent beta-1 and beta-2 receptor populations were identified in the rat; however, the entire thalamus of the guinea pig had few, if any, beta adrenergic receptors of either subtype. Hippocampal area CA1 had high levels of beta-2 adrenergic receptors in both rats and guinea pigs but was accompanied by a widespread distribution of beta-2 adrenergic receptors only in rats. Quantitative autoradiographic analyses of 25 selected neuroanatomical regions (1) confirmed the qualitative differences in CNS beta adrenergic receptor localization, (2) determined that guinea pigs had significantly lower levels of beta adrenergic receptors than rats and (3) indicated a differential pattern of receptor subtypes between the two species. Knowledge of species differences in receptor patterns may be useful in designing effective experiments as well as in exploring the relationships between receptor and innervation patterns. Collectively, these data suggest caution be used in extrapolation of the relationships of neurotransmitters and receptors from studies of a single species.« less

3D Mechanical Models of Crustal Deformation and the Effect of Erosion on the Strain Pattern in SE Alaska

NASA Astrophysics Data System (ADS)

Barker, A. D.; Koons, P. O.; Upton, P.; Hallet, B.

2008-12-01

Employing 3D mechanical modeling to investigate the susceptibility of strain patterns to distinct erosion conditions we have identified a strong connection between surface erosion and strain localization and vertical motion of crustal material. The specific model geometry and boundary conditions are relevant to the dynamic St. Elias orogen of SE Alaska, but the general results and interpretations are universal. To illustrate the effect of erosion we compare results to a reference model without imposed erosion. We consider the crustal response to boundary conditions representing erosion scenarios: 1) regional erosion (~1 mm a-1 over a region ~600 km on a side) and 2) focused incision (~6 mm a-1 in valleys ~10 km wide and 50-100 km long). Whereas regional erosion mimics broader scale mass wasting and periglacial weathering, focused incision represents efficient erosion confined to valley systems similar to the massive Bering, Malaspina and Bagley glaciers of the St. Elias range. Using these boundary conditions we demonstrate significant localization of strain and crustal uplift beneath the sites of erosion. We also show the strain localization pattern adjusts to spatial shifts in erosion arising from substantial (order of 100km) glacial advance or retreat. The magnitude of the strain is higher in each erosion model compared to the reference model. The difference of the strain magnitude between erosion models and reference model depends on the location of the imposed erosion: crustal strain localize most when the forethrust daylights in the zone being eroded. Sustained focused erosion decreases the overall crustal strength beneath the site of erosion due to thinning of the strong brittle crust. Strain naturally concentrates within the weakened zone. Upward advection of warm crust causes further weakening and thereby leads to a tectonic aneurysm.

Using spatial mark-recapture for conservation monitoring of grizzly bear populations in Alberta.

PubMed

Boulanger, John; Nielsen, Scott E; Stenhouse, Gordon B

2018-03-26

One of the challenges in conservation is determining patterns and responses in population density and distribution as it relates to habitat and changes in anthropogenic activities. We applied spatially explicit capture recapture (SECR) methods, combined with density surface modelling from five grizzly bear (Ursus arctos) management areas (BMAs) in Alberta, Canada, to assess SECR methods and to explore factors influencing bear distribution. Here we used models of grizzly bear habitat and mortality risk to test local density associations using density surface modelling. Results demonstrated BMA-specific factors influenced density, as well as the effects of habitat and topography on detections and movements of bears. Estimates from SECR were similar to those from closed population models and telemetry data, but with similar or higher levels of precision. Habitat was most associated with areas of higher bear density in the north, whereas mortality risk was most associated (negatively) with density of bears in the south. Comparisons of the distribution of mortality risk and habitat revealed differences by BMA that in turn influenced local abundance of bears. Combining SECR methods with density surface modelling increases the resolution of mark-recapture methods by directly inferring the effect of spatial factors on regulating local densities of animals.

Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae)

PubMed Central

Zinck, John W. R.

2016-01-01

Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus) to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD) were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation. PMID:27387485

Plasmodium knowlesi Skeleton-Binding Protein 1 Localizes to the 'Sinton and Mulligan' Stipplings in the Cytoplasm of Monkey and Human Erythrocytes.

PubMed

Lucky, Amuza Byaruhanga; Sakaguchi, Miako; Katakai, Yuko; Kawai, Satoru; Yahata, Kazuhide; Templeton, Thomas J; Kaneko, Osamu

2016-01-01

The malaria parasite, Plasmodium, exports protein products to the infected erythrocyte to introduce modifications necessary for the establishment of nutrient acquisition and surface display of host interaction ligands. Erythrocyte remodeling impacts parasite virulence and disease pathology and is well documented for the human malaria parasite Plasmodium falciparum, but has been less described for other Plasmodium species. For P. falciparum, the exported protein skeleton-binding protein 1 (PfSBP1) is involved in the trafficking of erythrocyte surface ligands and localized to membranous structures within the infected erythrocyte, termed Maurer's clefts. In this study, we analyzed SBP1 orthologs across the Plasmodium genus by BLAST analysis and conserved gene synteny, which were also recently described by de Niz et al. (2016). To evaluate the localization of an SBP1 ortholog, we utilized the zoonotic malaria parasite, Plasmodium knowlesi. Immunofluorescence assay of transgenic P. knowlesi parasites expressing epitope-tagged recombinant PkSBP1 revealed a punctate staining pattern reminiscent of Maurer's clefts, following infection of either monkey or human erythrocytes. The recombinant PkSBP1-positive puncta co-localized with Giemsa-stained structures, known as 'Sinton and Mulligan' stipplings. Immunoelectron microscopy also showed that recombinant PkSBP1 localizes within or on the membranous structures akin to the Maurer's clefts. The recombinant PkSBP1 expressed in P. falciparum-infected erythrocytes co-localized with PfSBP1 at the Maurer's clefts, indicating an analogous trafficking pattern. A member of the P. knowlesi 2TM protein family was also expressed and localized to membranous structures in infected monkey erythrocytes. These results suggest that the trafficking machinery and induced erythrocyte cellular structures of P. knowlesi are similar following infection of both monkey and human erythrocytes, and are conserved with P. falciparum.

The phenetic structure of Aedes albopictus.

PubMed

Morales Vargas, Ronald Enrique; Phumala-Morales, Noppawan; Tsunoda, Takashi; Apiwathnasorn, Chamnan; Dujardin, Jean-Pierre

2013-01-01

The large and recent migrations of the main vector of the Chikungunya virus, Aedes albopictus, raise questions about the epidemiological impact of possible microevolutionary changes in new territories. Quantitative traits are suitable to detect such changes as induced by environmental adaptations, local competition and founder effects. Using landmark-based geometric morphometrics, we compared the size and shape of 22 populations (1572 females) of Ae. albopictus. The collection sites covered five countries around the world, with special emphasis on Asia, which is assumed to be the origin of the vector. Some collections came from places where an important epidemic outbreak of Chikungunya has recently occurred. Quantitative comparisons were based on 18 anatomical landmarks on the wing. To contrast geographic and possible interspecific shape variation, close species were introduced in the sample, namely five Aedes riversi and nine Ae. flavopictus from Japan. The three species had similar size, but they were clearly separated by shape. Within Ae. albopictus, there was general agreement on size variation with the available climatic data. Shape variation was less related to climatic data than to either geography or a known itinerary of past territorial expansion. Thus, two main clusters were distinguished by wing shape variation: the first one composed of the Southeast Asian sample, the second one grouping Japan, Florida, Hawaii and the Reunion Island samples. The Southeast Asian countries, assumed to be at the origin of the geographic expansion of the mosquito, had similar wings and constituted a distinct group where localities clustered into northern and southern localities. Contrasting with this homogeneous group, very distant localities such as United States (US) and Japan shared a common shape pattern. The US Ae. albopictus samples (Hawaii and Florida) were indeed very similar to the Japanese samples, with Florida behaving exactly like a northern Japanese locality, close to Tokyo and Yokohama. Shape proximity among these distant areas could be explained by a common and relatively recent ancestor, as generally suggested in the literature. The three Reunion Island samples conformed a group external to the Southeast Asian countries, loosely connected to the remaining localities. Thus, areas where recent epidemics took place, the Reunion Island and the southernmost localities of Thailand, did not cluster together, but represented separate groups. In sum, the size of the wing was apparently under the influence of climatic factors, while its shape could contribute information on species and geographic differences. Apparent departures from expectations based on geography were explained by known past and present migratory routes. These patterns of shape variation were compatible with genetic drift, suggesting microevolutionary changes probably induced by the expansion of the Ae. albopictus mosquito. Copyright © 2012 Elsevier B.V. All rights reserved.

Dynamical systems proxies of atmospheric predictability and mid-latitude extremes

NASA Astrophysics Data System (ADS)

Messori, Gabriele; Faranda, Davide; Caballero, Rodrigo; Yiou, Pascal

2017-04-01

Extreme weather ocurrences carry enormous social and economic costs and routinely garner widespread scientific and media coverage. Many extremes (for e.g. storms, heatwaves, cold spells, heavy precipitation) are tied to specific patterns of midlatitude atmospheric circulation. The ability to identify these patterns and use them to enhance the predictability of the extremes is therefore a topic of crucial societal and economic value. We propose a novel predictability pathway for extreme events, by building upon recent advances in dynamical systems theory. We use two simple dynamical systems metrics - local dimension and persistence - to identify sets of similar large-scale atmospheric flow patterns which present a coherent temporal evolution. When these patterns correspond to weather extremes, they therefore afford a particularly good forward predictability. We specifically test this technique on European winter temperatures, whose variability largely depends on the atmospheric circulation in the North Atlantic region. We find that our dynamical systems approach provides predictability of large-scale temperature extremes up to one week in advance.

Ecosystem properties self-organize in response to a directional fog-vegetation interaction.

PubMed

Stanton, Daniel E; Armesto, Juan J; Hedin, Lars O

2014-05-01

Feedbacks between vegetation and resource inputs can lead to the local, self-organization of ecosystem properties. In particular, feedbacks in response to directional resources (e.g., coastal fog, slope runoff) can create complex spatial patterns, such as vegetation banding. Although similar feedbacks are thought to be involved in the development of ecosystems, clear empirical examples are rare. We created a simple model of a fog-influenced, temperate rainforest in central Chile, which allows the comparison of natural banding patterns to simulations of various putative mechanisms. We show that only feedbacks between plants and fog were able to replicate the characteristic distributions of vegetation, soil water, and soil nutrients observed in field transects. Other processes, such as rainfall, were unable to match these diagnostic distributions. Furthermore, fog interception by windward trees leads to increased downwind mortality, leading to progressive extinction of the leeward edge. This pattern of ecosystem development and decay through self-organized processes illustrates, on a relatively small spatial and temporal scale, the patterns predicted for ecosystem evolution.

Role of endothelial permeability hotspots and endothelial mitosis in determining age-related patterns of macromolecule uptake by the rabbit aortic wall near branch points.

PubMed

Chooi, K Yean; Comerford, Andrew; Cremers, Stephanie J; Weinberg, Peter D

2016-07-01

Transport of macromolecules between plasma and the arterial wall plays a key role in atherogenesis. Scattered hotspots of elevated endothelial permeability to macromolecules occur in the aorta; a fraction of them are associated with dividing cells. Hotspots occur particularly frequently downstream of branch points, where lesions develop in young rabbits and children. However, the pattern of lesions varies with age, and can be explained by similar variation in the pattern of macromolecule uptake. We investigated whether patterns of hotspots and mitosis also change with age. Evans' Blue dye-labeled albumin was injected intravenously into immature or mature rabbits and its subsequent distribution in the aortic wall around intercostal branch ostia examined by confocal microscopy and automated image analysis. Mitosis was detected by immunofluorescence after adding 5-bromo-2-deoxiuridine to drinking water. Hotspots were most frequent downstream of branches in immature rabbits, but a novel distribution was observed in mature rabbits. Neither pattern was explained by mitosis. Hotspot uptake correlated spatially with the much greater non-hotspot uptake (p < 0.05), and the same pattern was seen when only the largest hotspots were considered. The pattern of hotspots changes with age. The data are consistent with there being a continuum of local permeabilities rather than two distinct mechanisms. The distribution of the dye, which binds to elastin and collagen, was similar to that of non-binding tracers and to lesions apart from a paucity at the lateral margins of branches that can be explained by lower levels of fibrous proteins in those regions. Copyright © 2016. Published by Elsevier Ireland Ltd.

Simultaneously Discovering and Localizing Common Objects in Wild Images.

PubMed

Wang, Zhenzhen; Yuan, Junsong

2018-09-01

Motivated by the recent success of supervised and weakly supervised common object discovery, in this paper, we move forward one step further to tackle common object discovery in a fully unsupervised way. Generally, object co-localization aims at simultaneously localizing objects of the same class across a group of images. Traditional object localization/detection usually trains specific object detectors which require bounding box annotations of object instances, or at least image-level labels to indicate the presence/absence of objects in an image. Given a collection of images without any annotations, our proposed fully unsupervised method is to simultaneously discover images that contain common objects and also localize common objects in corresponding images. Without requiring to know the total number of common objects, we formulate this unsupervised object discovery as a sub-graph mining problem from a weighted graph of object proposals, where nodes correspond to object proposals, and edges represent the similarities between neighbouring proposals. The positive images and common objects are jointly discovered by finding sub-graphs of strongly connected nodes, with each sub-graph capturing one object pattern. The optimization problem can be efficiently solved by our proposed maximal-flow-based algorithm. Instead of assuming that each image contains only one common object, our proposed solution can better address wild images where each image may contain multiple common objects or even no common object. Moreover, our proposed method can be easily tailored to the task of image retrieval in which the nodes correspond to the similarity between query and reference images. Extensive experiments on PASCAL VOC 2007 and Object Discovery data sets demonstrate that even without any supervision, our approach can discover/localize common objects of various classes in the presence of scale, view point, appearance variation, and partial occlusions. We also conduct broad experiments on image retrieval benchmarks, Holidays and Oxford5k data sets, to show that our proposed method, which considers both the similarity between query and reference images and also similarities among reference images, can help to improve the retrieval results significantly.

Long-term direct visualization of passively transferred fluorophore-conjugated antibodies.

PubMed

Schneider, Jeffrey R; Carias, Ann M; Bastian, Arangaserry R; Cianci, Gianguido C; Kiser, Patrick F; Veazey, Ronald S; Hope, Thomas J

2017-11-01

The use of therapeutic antibodies, delivered by intravenous (IV) instillation, is a rapidly expanding area of biomedical treatment for a variety of conditions. However, little is known about how the antibodies are anatomically distributed following infusion and the underlying mechanism mediating therapeutic antibody distribution to specific anatomical sites remains to be elucidated. Current efforts utilize low resolution and sensitivity methods such as ELISA and indirect labeling imaging techniques, which often leads to high background and difficulty in assessing biodistribution. Here, using the in vivo non-human primate model, we demonstrate that it is possible to utilize the fluorophores Cy5 and Cy3 directly conjugated to antibodies for direct visualization and quantification of passively transferred antibodies in plasma, tissue, and in mucosal secretions. Antibodies were formulated with 1-2 fluorophores per antibody to minimally influence antibody function. Fluorophore conjugated Gamunex-C (pooled human IgG) were tested for binding to protein A, via surface plasmon resonance, and showed similar levels of binding when compared to unlabeled Gamunex-C. In order to assess the effect fluorophore labeling has on turnover and localization, rhesus macaques were IV infused with either labeled or unlabeled Gamunex-C. Plasma, vaginal Weck-Cel fluid, cervicovaginal mucus, and vaginal/rectal tissue biopsies were collected up to 8weeks. Similar turnover and biodistribution was observed between labeled and unlabeled antibodies, showing that the labeling process did not have an obvious deleterious effect on localization or turnover. Cy5 and Cy3 labeled antibodies were readily detected in the same pattern regardless of fluorophore. Tissue distribution was measured in macaque vaginal and rectal biopsies. The labeled antibody in macaque biopsies was found to have similar biodistribution pattern to endogenous antibodies in macaque and human tissues. In the vaginal and rectal mucosa, endogenous and infused antibodies were found primarily within the lamina propria. In the mucosal squamous epithelium of the vaginal vault, significant antibody was also observed in a striated pattern in the superficial, nonviable, stratum corneum. Endogenous antibody distribution in both human and macaque squamous tissues exhibited a similar pattern as seen with the labeled and unlabeled antibodies. This proof-of-principle study reveals that the labeled antibody is stable and physiologically similar relative to endogenous antibody setting the stage for future work to better understand the mechanisms of how antibodies reach unique anatomical sites. Direct visualization of fluorophore-conjugated antibodies following passive infusion can be utilized to assess the kinetics of biodistribution of infused antibodies and may be a useful approach to monitor and predict efficacy of therapeutic antibodies. Copyright © 2017 Elsevier B.V. All rights reserved.

SPLASH: structural pattern localization analysis by sequential histograms.

PubMed

Califano, A

2000-04-01

The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that is patterns that occur more frequently than expected, may identify regions that have been preserved by evolution and which may therefore play a key functional or structural role. Sparseness can be important because a handful of non-contiguous residues may play a key role, while others, in between, may be changed without significant loss of function or structure. Similar arguments may be applied to conserved DNA patterns. Available sparse pattern discovery algorithms are either inefficient or impose limitations on the type of patterns that can be discovered. This paper introduces a deterministic pattern discovery algorithm, called Splash, which can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences. Sparse patterns of any length, up to the size of the input sequence, can be discovered without significant loss in performances. Splash is extremely efficient and embarrassingly parallel by nature. Large databases, such as a complete genome or the non-redundant SWISS-PROT database can be processed in a few hours on a typical workstation. Alternatively, a protein family or superfamily, with low overall homology, can be analyzed to discover common functional or structural signatures. Some examples of biologically interesting motifs discovered by Splash are reported for the histone I and for the G-Protein Coupled Receptor families. Due to its efficiency, Splash can be used to systematically and exhaustively identify conserved regions in protein family sets. These can then be used to build accurate and sensitive PSSM or HMM models for sequence analysis. Splash is available to non-commercial research centers upon request, conditional on the signing of a test field agreement. acal@us.ibm.com, Splash main page http://www.research.ibm.com/splash

Stereotyped high-frequency oscillations discriminate seizure onset zones and critical functional cortex in focal epilepsy.

PubMed

Liu, Su; Gurses, Candan; Sha, Zhiyi; Quach, Michael M; Sencer, Altay; Bebek, Nerses; Curry, Daniel J; Prabhu, Sujit; Tummala, Sudhakar; Henry, Thomas R; Ince, Nuri F

2018-01-30

High-frequency oscillations in local field potentials recorded with intracranial EEG are putative biomarkers of seizure onset zones in epileptic brain. However, localized 80-500 Hz oscillations can also be recorded from normal and non-epileptic cerebral structures. When defined only by rate or frequency, physiological high-frequency oscillations are indistinguishable from pathological ones, which limit their application in epilepsy presurgical planning. We hypothesized that pathological high-frequency oscillations occur in a repetitive fashion with a similar waveform morphology that specifically indicates seizure onset zones. We investigated the waveform patterns of automatically detected high-frequency oscillations in 13 epilepsy patients and five control subjects, with an average of 73 subdural and intracerebral electrodes recorded per patient. The repetitive oscillatory waveforms were identified by using a pipeline of unsupervised machine learning techniques and were then correlated with independently clinician-defined seizure onset zones. Consistently in all patients, the stereotypical high-frequency oscillations with the highest degree of waveform similarity were localized within the seizure onset zones only, whereas the channels generating high-frequency oscillations embedded in random waveforms were found in the functional regions independent from the epileptogenic locations. The repetitive waveform pattern was more evident in fast ripples compared to ripples, suggesting a potential association between waveform repetition and the underlying pathological network. Our findings provided a new tool for the interpretation of pathological high-frequency oscillations that can be efficiently applied to distinguish seizure onset zones from functionally important sites, which is a critical step towards the translation of these signature events into valid clinical biomarkers.awx374media15721572971001. © The Author(s) (2018). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Immunolocalization of chloride transporters to gill epithelia of euryhaline teleosts with opposite salinity-induced Na+/K+-ATPase responses.

PubMed

Tang, Cheng-Hao; Hwang, Lie-Yueh; Shen, I-Da; Chiu, Yu-Hui; Lee, Tsung-Han

2011-12-01

Opposite patterns of branchial Na(+)/K(+)-ATPase (NKA) responses were found in euryhaline milkfish (Chanos chanos) and pufferfish (Tetraodon nigroviridis) upon salinity challenge. Because the electrochemical gradient established by NKA is thought to be the driving force for transcellular Cl(-) transport in fish gills, the aim of this study was to explore whether the differential patterns of NKA responses found in milkfish and pufferfish would lead to distinct distribution of Cl(-) transporters in their gill epithelial cells indicating different Cl(-) transport mechanisms. In this study, immunolocalization of various Cl(-) transport proteins, including Na(+)/K(+)/2Cl(-) cotransporter (NKCC), cystic fibrosis transmembrane conductance regulator (CFTR), anion exchanger 1 (AE1), and chloride channel 3 (ClC-3), were double stained with NKA, the basolateral marker of branchial mitochondrion-rich cells (MRCs), to reveal the localization of these transporter proteins in gill MRC of FW- or SW-acclimated milkfish and pufferfish. Confocal microscopic observations showed that the localization of these transport proteins in the gill MRCs of the two studied species were similar. However, the number of gill NKA-immunoreactive (IR) cells in milkfish and pufferfish exhibited to vary with environmental salinities. An increase in the number of NKA-IR cells should lead to the elevation of NKA activity in FW milkfish and SW pufferfish. Taken together, the opposite branchial NKA responses observed in milkfish and pufferfish upon salinity challenge could be attributed to alterations in the number of NKA-IR cells. Furthermore, the localization of these Cl(-) transporters in gill MRCs of the two studied species was identical. It depicted the two studied euryhaline species possess the similar Cl(-) transport mechanisms in gills.

Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space.

PubMed

Stegemann, Björn; Klebe, Gerhard

2012-02-01

Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Copyright © 2011 Wiley Periodicals, Inc.

Testing the enemy release hypothesis: abundance and distribution patterns of helminth communities in grey mullets (Teleostei: Mugilidae) reveal the success of invasive species.

PubMed

Sarabeev, Volodimir; Balbuena, Juan Antonio; Morand, Serge

2017-09-01

The abundance and aggregation patterns of helminth communities of two grey mullet hosts, Liza haematocheilus and Mugil cephalus, were studied across 14 localities in Atlantic and Pacific marine areas. The analysis matched parasite communities of (i) L. haematocheilus across its native and introduced populations (Sea of Japan and Sea of Azov, respectively) and (ii) the introduced population of L. haematocheilus with native populations of M. cephalus (Mediterranean, Azov-Black and Japan Seas). The total mean abundance (TMA), as a feature of the infection level in helminth communities, and slope b of the Taylor's power law, as a measure of parasite aggregation at the infra and component-community levels, were estimated and compared between host species and localities using ANOVA. The TMA of the whole helminth community in the introduced population of L. haematocheilus was over 15 times lower than that of the native population, but the difference was less pronounced for carried (monogeneans) than for acquired (adult and larval digeneans) parasite communities. Similar to the abundance pattern, the species distribution in communities from the invasive population of L. haematocheilus was less aggregated than from its native population for endoparasitic helminths, including adult and larval digeneans, while monogeneans showed a similar pattern of distribution in the compared populations of L. haematocheilus. The aggregation level of the whole helminth community, endoparasitic helminths, adult and larval digeneans was lower in the invasive host species in comparison with native ones as shown by differences in the slope b. An important theoretical implication from this study is that the pattern of parasite aggregation may explain the success of invasive species in ecosystems. Because the effects of parasites on host mortality are likely dose-dependent, the proportion of susceptible host individuals in invasive species is expected to be lower, as the helminth distribution in the invasive host was featured by a higher number of uninfected hosts and a shorter distribution tail when compared with native species. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Dem Local Accuracy Patterns in Land-Use/Land-Cover Classification

NASA Astrophysics Data System (ADS)

Katerji, Wassim; Farjas Abadia, Mercedes; Morillo Balsera, Maria del Carmen

2016-01-01

Global and nation-wide DEM do not preserve the same height accuracy throughout the area of study. Instead of assuming a single RMSE value for the whole area, this study proposes a vario-model that divides the area into sub-regions depending on the land-use / landcover (LULC) classification, and assigns a local accuracy per each zone, as these areas share similar terrain formation and roughness, and tend to have similar DEM accuracies. A pilot study over Lebanon using the SRTM and ASTER DEMs, combined with a set of 1,105 randomly distributed ground control points (GCPs) showed that even though the inputDEMs have different spatial and temporal resolution, and were collected using difierent techniques, their accuracy varied similarly when changing over difierent LULC classes. Furthermore, validating the generated vario-models proved that they provide a closer representation of the accuracy to the validating GCPs than the conventional RMSE, by 94% and 86% for the SRTMand ASTER respectively. Geostatistical analysis of the input and output datasets showed that the results have a normal distribution, which support the generalization of the proven hypothesis, making this finding applicable to other input datasets anywhere around the world.

Competitive aggregation dynamics using phase wave signals.

PubMed

Sakaguchi, Hidetsugu; Maeyama, Satomi

2014-10-21

Coupled equations of the phase equation and the equation of cell concentration n are proposed for competitive aggregation dynamics of slime mold in two dimensions. Phase waves are used as tactic signals of aggregation in this model. Several aggregation clusters are formed initially, and target patterns appear around the localized aggregation clusters. Owing to the competition among target patterns, the number of the localized aggregation clusters decreases, and finally one dominant localized pattern survives. If the phase equation is replaced with the complex Ginzburg-Landau equation, several spiral patterns appear, and n is localized near the center of the spiral patterns. After the competition among spiral patterns, one dominant spiral survives. Copyright © 2014 Elsevier Ltd. All rights reserved.

The pattern of tyrosine phosphorylation in human sperm in response to binding to zona pellucida or hyaluronic acid.

PubMed

Sati, Leyla; Cayli, Sevil; Delpiano, Elena; Sakkas, Denny; Huszar, Gabor

2014-05-01

In mammalian species, acquisition of sperm fertilization competence is dependent on the phenomenon of sperm capacitation. One of the key elements of capacitation is protein tyrosine phosphorylation (TP) in various sperm membrane regions. In previous studies performed, the pattern of TP was examined in human sperm bound to zona pellucida of oocytes. In the present comparative study, TP patterns upon sperm binding to the zona pellucida or hyaluronic acid (HA) were investigated in spermatozoa arising from the same semen samples. Tyrosine phosphorylation, visualized by immunofluorescence, was localized within the acrosomal cap, equatorial head region, neck, and the principal piece. Tyrosine phosphorylation has increased in a time-related manner as capacitation progressed, and the phosphorylation pattern was identical within the principal piece and neck, regardless of the sperm bound to the zona pellucida or HA. Thus, the data demonstrated that the patterns of sperm activation-related TP were similar regardless of the spermatozoa bound to zona pellucida or HA. Further, sperm with incomplete development, as detected by excess cytoplasmic retention, failed to exhibit TP.

The Pattern of Tyrosine Phosphorylation in Human Sperm in Response to Binding to Zona Pellucida or Hyaluronic Acid

PubMed Central

Sati, Leyla; Cayli, Sevil; Delpiano, Elena; Sakkas, Denny

2014-01-01

In mammalian species, acquisition of sperm fertilization competence is dependent on the phenomenon of sperm capacitation. One of the key elements of capacitation is protein tyrosine phosphorylation (TP) in various sperm membrane regions. In previous studies performed, the pattern of TP was examined in human sperm bound to zona pellucida of oocytes. In the present comparative study, TP patterns upon sperm binding to the zona pellucida or hyaluronic acid (HA) were investigated in spermatozoa arising from the same semen samples. Tyrosine phosphorylation, visualized by immunofluorescence, was localized within the acrosomal cap, equatorial head region, neck, and the principal piece. Tyrosine phosphorylation has increased in a time-related manner as capacitation progressed, and the phosphorylation pattern was identical within the principal piece and neck, regardless of the sperm bound to the zona pellucida or HA. Thus, the data demonstrated that the patterns of sperm activation-related TP were similar regardless of the spermatozoa bound to zona pellucida or HA. Further, sperm with incomplete development, as detected by excess cytoplasmic retention, failed to exhibit TP. PMID:24077441

Caterpillars and moths: Part I. Dermatologic manifestations of encounters with Lepidoptera.

PubMed

Hossler, Eric W

2010-01-01

Caterpillars are the larval forms of moths and butterflies and belong to the order Lepidoptera. Caterpillars, and occasionally moths, have evolved defense mechanisms, including irritating hairs, spines, venoms, and toxins that may cause human disease. The pathologic mechanisms underlying reactions to Lepidoptera are poorly understood. Lepidoptera are uncommonly recognized causes of localized stings, eczematous or papular dermatitis, and urticaria. Part I of this two-part series on caterpillars and moths reviews Lepidopteran life cycles, terminology, and the epidemiology of caterpillar and moth envenomation. It also reviews the known pathomechanisms of disease caused by Lepidopteran exposures and how they relate to diagnosis and management. Part II discusses the specific clinical patterns caused by Lepidopteran exposures, with particular emphasis on groups of caterpillars and moths that cause a similar pattern of disease. It also discusses current therapeutic options regarding each pattern of disease.

Alcohol use among Arab Americans: what is the prevalence?

PubMed

Arfken, Cynthia L; Arnetz, Bengt B; Fakhouri, Monty; Ventimiglia, Matthew J; Jamil, Hikmet

2011-08-01

Information is limited on alcohol use among Arab Americans. The purpose of this study was to describe and analyze the alcohol use pattern among Arab Americans by reviewing existing surveys using an acculturation model. Secondary data analysis. Nationally, English-speaking immigrant Arab Americans reported lower rates of lifetime alcohol use (50.8%), past month use (26.4%) and binge drinking (10%) than the White majority group. In a state survey, self-identified English-speaking Arab Americans were less likely to report past month use (45.6%) than the White majority group but reported similar rate of binge drinking (17.0%). Locally, lifetime drinking was reported by 46.2% of the immigrants but only 13.4% of refugees fleeing war. Few databases are available to estimate alcohol use pattern among Arab Americans; the limited data suggest a drinking pattern consistent with acculturation. However, the potential influence of other factors is unknown and needs to be investigated.

Alcohol Use Among Arab Americans: What is the Prevalence?

PubMed Central

Arfken, Cynthia L.; Arnetz, Bengt B.; Fakhouri, Monty; Ventimiglia, Matthew J.; Jamil, Hikmet

2014-01-01

Information is limited on alcohol use among Arab Americans. The purpose of this study was to describe and analyze the alcohol use pattern among Arab Americans by reviewing existing surveys using an acculturation model. Secondary data analysis. Nationally, English-speaking immigrant Arab Americans reported lower rates of lifetime alcohol use (50.8%), past month use (26.4%) and binge drinking (10%) than the White majority group. In a state survey, self-identified English-speaking Arab Americans were less likely to report past month use (45.6%) than the White majority group but reported similar rate of binge drinking (17.0%). Locally, lifetime drinking was reported by 46.2% of the immigrants but only 13.4% of refugees fleeing war. Few databases are available to estimate alcohol use pattern among Arab Americans; the limited data suggest a drinking pattern consistent with acculturation. However, the potential influence of other factors is unknown and needs to be investigated. PMID:21279687

Distribution of the Primary Endosymbiont (Candidatus Uzinura Diaspidicola) Within Host Insects from the Scale Insect Family Diaspididae

PubMed Central

Gruwell, Matthew E.; Flarhety, Meghan; Dittmar, Katharina

2012-01-01

It has long been known that armored scale insects harbor endosymbiotic bacteria inside specialized cells called bacteriocytes. Originally, these endosymbionts were thought to be fungal symbionts but they are now known to be bacterial and have been named Uzinura diaspidicola. Bacteriocyte and endosymbiont distribution patterns within host insects were visualized using in situ hybridization via 16S rRNA specific probes. Images of scale insect embryos, eggs and adult scale insects show patterns of localized bacteriocytes in embryos and randomly distributed bacteriocytes in adults. The symbiont pocket was not found in the armored scale insect eggs that were tested. The pattern of dispersed bacteriocytes in adult scale insects suggest that Uzinura and Blattabacteria may share some homologous traits that coincide with similar life style requirements, such as dispersal in fat bodies and uric acid recycling. PMID:26467959

Green leaf phenology at Landsat resolution: scaling from the plot to satellite

NASA Astrophysics Data System (ADS)

Fisher, J. I.; Mustard, J. F.; Vadeboncour, M.

2005-12-01

Despite the large number of in situ, plot-level phenological measurements and satellite-derived phenological studies, there has been little success to date in merging these records temporally or spatially. In particular, while most phenological patterns and trends derived from satellites appear realistic and coherent, they may not reflect spatial and temporal patterns at the plot level. An obvious explanation is the drastic scale difference from plot-level to most satellite observations. In this research, we bridge this scale gap through higher resolution satellite records (Landsat) and quantify the accuracy of satellite-derived metrics with direct field measurements. We compiled fifty-seven Landsat scenes from southern New England (P12 R51) from 1984 to 2002. Green vegetation areal abundance for each scene was derived from spectral mixture analysis and a single set of endmembers. The leaf area signal was fit with a logistic-growth simulating sigmoid curve to derive phenological markers (half-maximum leaf-onset and offset). Spring leaf-onset dates in homogenous stands of deciduous forests displayed significant and persistent local variability. The local variability was validated with multiple springtime ground observations (r2 = 0.91). The highest degree of verified small-scale variation occurred where contiguous forests displayed leaf-onset gradients of 10-14 days over short distances (<500 m). These dramatic gradients, of a similar magnitude to differences in leaf-onset from MD to MA, occur in of low-relief (<40 m) upland regions. The patterns suggest that microclimates resulting from springtime cold-air drainage may be influential in governing the start of leaf growth. These microclimates may be of crucial importance in interpreting in situ records and interpolating phenology from satellite data. Regional patterns from the Landsat analyses suggest topographic, coastal, and land-use controls on phenology. For example, our results indicate that deciduous forests in the Providence, RI metropolitan area leaf out 5-7 days earlier than comparable rural areas. In preliminary work, we validated the Landsat-derived metrics with similar analyses of MODIS and AVHRR, and demonstrate that aggregating diverse local phenologies into coarse grids may convolute interpretations. Despite these complications, the platform-independent curve-fit methodology may be extended across platforms and field data. The methodologically consistent approach, in tandem with Landsat data, allows us to effectively scale between plot and satellite phenological observations.

Multiscale recurrence quantification analysis of order recurrence plots

NASA Astrophysics Data System (ADS)

Xu, Mengjia; Shang, Pengjian; Lin, Aijing

2017-03-01

In this paper, we propose a new method of multiscale recurrence quantification analysis (MSRQA) to analyze the structure of order recurrence plots. The MSRQA is based on order patterns over a range of time scales. Compared with conventional recurrence quantification analysis (RQA), the MSRQA can show richer and more recognizable information on the local characteristics of diverse systems which successfully describes their recurrence properties. Both synthetic series and stock market indexes exhibit their properties of recurrence at large time scales that quite differ from those at a single time scale. Some systems present more accurate recurrence patterns under large time scales. It demonstrates that the new approach is effective for distinguishing three similar stock market systems and showing some inherent differences.

Microscale vicariance and diversification of Western Balkan caddisflies linked to karstification.

PubMed

Previšić, Ana; Schnitzler, Jan; Kučinić, Mladen; Graf, Wolfram; Ibrahimi, Halil; Kerovec, Mladen; Pauls, Steffen U

2014-03-01

The karst areas in the Dinaric region of the Western Balkan Peninsula are a hotspot of freshwater biodiversity. Many investigators have examined diversification of the subterranean freshwater fauna in these karst systems. However, diversification of surface-water fauna remains largely unexplored. We assessed local and regional diversification of surface-water species in karst systems and asked whether patterns of population differentiation could be explained by dispersal-diversification processes or allopatric diversification following karst-related microscale vicariance. We analyzed mitochondrial cytochrome c oxidase subunit I (mtCOI) sequence data of 4 caddisfly species (genus Drusus ) in a phylogeographic framework to assess local and regional population genetic structure and Pliocene/Pleistocene history. We used BEAST software to assess the timing of intraspecific diversification of the target species. We compared climate envelopes of the study species and projected climatically suitable areas during the last glacial maximum (LGM) to assess differences in the species climatic niches and infer potential LGM refugia. The haplotype distribution of the 4 species (324 individuals from 32 populations) was characterized by strong genetic differentiation with few haplotypes shared among populations (16%) and deep divergence among populations of the 3 endemic species, even at local scales. Divergence among local populations of endemics often exceeded divergence among regional and continental clades of the widespread D. discolor . Major divergences among regional populations dated to 2.0 to 0.5 Mya. Species distribution model projections and genetic structure suggest that the endemic species persisted in situ and diversified locally throughout multiple Pleistocene climate cycles. The pattern for D. discolor was different and consistent with multiple invasions into the region. Patterns of population genetic structure and diversification were similar for the 3 regional endemic Drusus species and consistent with microscale vicariance after the onset of intensified karstification in the Dinaric region. Karstification may induce microscale vicariance of running surface-water habitats and probably promotes allopatric fragmentation of stream insects at small spatial scales.

Regionally coherent, downstream propagating trends of river bed incision and aggradation in glaciated basins of western Washington, USA

NASA Astrophysics Data System (ADS)

Anderson, S. W.; Konrad, C. P.

2016-12-01

Understanding the connections between climate and river bed morphology is relevant both for interpreting the geologic record and understanding modern channel change. Here, we use changing stage-discharge relations at USGS stream-gage sites in western Washington State to infer local bed-elevation changes over the past 50 to 90 years. A network of gages in a large, unregulated basin with active glaciation show decadal periods of aggradation and incision that are strongly correlated when lagged. Best-fit lag times indicate the downstream propagation of single coherent signal at a slope-dependent velocity of 1-4 km/yr. This same pattern of change is observed at the outlets of regional rivers with glaciated headwaters but is absent in unglaciated river systems. Sites high in glaciated river systems also show coherency across basins, suggesting that the similarity in the downstream trends across glaciated basins is the result of the downstream propagation of a regionally coherent headwater signal. Incisional trends emanating from headwaters between 1950 and 1980 match a period when regional glaciers were stable or advancing, but assigning causation is complicated by hydroclimatic trends with similar temporal patterns. The recent trend is aggradational, though current bed elevations are generally similar to those prior to 1950, and are consistent with regional data indicating that sediment production in glaciated basins from 1950 to 1980 was anomalously low relative to conditions over the past several hundred years. Regionally, our results suggest the possibility of forecasting periods of aggradation and increased flood hazards several years to decades in advance in populated downstream settings. More broadly, the methods used in this analysis involve simple calculations on publically available data and provide a low-cost means of assessing local channel change wherever USGS stream-gages have been operated.

Neighborhood binary speckle pattern for deformation measurements insensitive to local illumination variation by digital image correlation.

PubMed

Zhao, Jian; Yang, Ping; Zhao, Yue

2017-06-01

Speckle pattern-based characteristics of digital image correlation (DIC) restrict its application in engineering fields and nonlaboratory environments, since serious decorrelation effect occurs due to localized sudden illumination variation. A simple and efficient speckle pattern adjusting and optimizing approach presented in this paper is aimed at providing a novel speckle pattern robust enough to resist local illumination variation. The new speckle pattern, called neighborhood binary speckle pattern, derived from original speckle pattern, is obtained by means of thresholding the pixels of a neighborhood at its central pixel value and considering the result as a binary number. The efficiency of the proposed speckle pattern is evaluated in six experimental scenarios. Experiment results indicate that the DIC measurements based on neighborhood binary speckle pattern are able to provide reliable and accurate results, even though local brightness and contrast of the deformed images have been seriously changed. It is expected that the new speckle pattern will have more potential value in engineering applications.

Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes.

PubMed

Sommers, Pacifica; Darcy, John L; Gendron, Eli M S; Stanish, Lee F; Bagshaw, Elizabeth A; Porazinska, Dorota L; Schmidt, Steven K

2018-01-01

Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Foxi2 Is an Animally Localized Maternal mRNA in Xenopus, and an Activator of the Zygotic Ectoderm Activator Foxi1e

PubMed Central

Cha, Sang-Wook; McAdams, Meredith; Kormish, Jay; Wylie, Christopher; Kofron, Matthew

2012-01-01

Foxi1e is a zygotic transcription factor that is essential for the expression of early ectodermal genes. It is expressed in a highly specific pattern, only in the deep cell layers of the animal hemisphere, and in a mosaic pattern in which expressing cells are interspersed with non-expressing cells. Previous work has shown that several signals in the blastula control this expression pattern, including nodals, the TGFβ family member Vg1, and Notch. However, these are all inhibitory, which raises the question of what activates Foxi1e. In this work, we show that a related Forkhead family protein, Foxi2, is a maternal activator of Foxi1e. Foxi2 mRNA is maternally encoded, and highly enriched in animal hemisphere cells of the blastula. ChIP assays show that it acts directly on upstream regulatory elements of Foxi1e. Its effect is specific, since animal cells depleted of Foxi2 are able to respond normally to mesoderm inducing signals from vegetal cells. Foxi2 thus acts as a link between the oocyte and the early pathway to ectoderm, in a similar fashion to the vegetally localized VegT acts to initiate endoderm and mesoderm formation. PMID:22848601

Grouping of optic flow stimuli during binocular rivalry is driven by monocular information.

PubMed

Holten, Vivian; Stuit, Sjoerd M; Verstraten, Frans A J; van der Smagt, Maarten J

2016-10-01

During binocular rivalry, perception alternates between two dissimilar images, presented dichoptically. Although binocular rivalry is thought to result from competition at a local level, neighboring image parts with similar features tend to be perceived together for longer durations than image parts with dissimilar features. This simultaneous dominance of two image parts is called grouping during rivalry. Previous studies have shown that this grouping depends on a shared eye-of-origin to a much larger extent than on image content, irrespective of the complexity of a static image. In the current study, we examine whether grouping of dynamic optic flow patterns is also primarily driven by monocular (eye-of-origin) information. In addition, we examine whether image parameters, such as optic flow direction, and partial versus full visibility of the optic flow pattern, affect grouping durations during rivalry. The results show that grouping of optic flow is, as is known for static images, primarily affected by its eye-of-origin. Furthermore, global motion can affect grouping durations, but only under specific conditions. Namely, only when the two full optic flow patterns were presented locally. These results suggest that grouping during rivalry is primarily driven by monocular information even for motion stimuli thought to rely on higher-level motion areas. Copyright © 2016 Elsevier Ltd. All rights reserved.

Oxygen isotope values in bone carbonate and collagen are consistently offset for New World monkeys

PubMed Central

Crowley, Brooke Erin

2014-01-01

Stable oxygen isotopes are increasingly used in ecological research. Here, I present oxygen isotope (δ18O) values for bone carbonate and collagen from howler monkeys (Alouatta palliata), spider monkeys (Ateles geoffroyi) and capuchins (Cebus capucinus) from three localities in Costa Rica. There are apparent differences in δ18Ocarbonate and δ18Ocollagen among species. Monkeys from moist forest have significantly lower isotope values than those from drier localities. Because patterns are similar for both substrates, discrimination (Δ) between δ18Ocarbonate and δ18Ocollagen is relatively consistent among species and localities (17.6 ± 0.9‰). Although this value is larger than that previously obtained for laboratory rats, consistency among species and localities suggests it can be used to compare δ18Ocarbonate and δ18Ocollagen for monkeys, and potentially other medium-bodied mammals. Establishing discrimination for oxygen between these substrates for wild monkeys provides a foundation for future environmental and ecological research on modern and ancient organisms. PMID:25392315

The Neogene genus Streptochilus (Brönnimann and Resig, 1971) from the Gulf of California

USGS Publications Warehouse

Miranda Martínez, A.Y.; Carreño, A.L.; McDougall, Kristin

2017-01-01

Four species of the planktonic foraminiferal genus Streptochilus from key Neogene marine localities are documented in relation to the evolution of the Gulf of California: S. globigerus, S. latus, S. macdougallae sp. nov., and S. inglei sp. nov. Planktonic foraminiferal bioevents and strontium isotopes in the Bouse, Tirabuzón, Carmen and Ojo de Buey lithostratigraphic units constrain the local distribution range between 6 and 5.3 Ma for the last three species, whereas S. globigerus appears locally at 5.5 Ma and disappears between 3.79 and 3.46 Ma in the Imperial and Trinidad Formations. The last occurrence of Streptochilus latus, and the first and last occurrences of S. globigerus in the ancient Gulf of California are correlated with bioevents calibrated in the equatorial Pacific; therefore, they can be used as reliable local biostratigraphic markers. The presence of Streptochilus in the ancient Gulf of California seems to correlate with upwelling, in a pattern similar to that observed in the modern oceans.

Egg buoyancy variability in local populations of Atlantic cod (Gadus morhua).

PubMed

Jung, Kyung-Mi; Folkvord, Arild; Kjesbu, Olav Sigurd; Agnalt, Ann Lisbeth; Thorsen, Anders; Sundby, Svein

2012-01-01

Previous studies have found strong evidences for Atlantic cod ( Gadus morhua ) egg retention in fjords, which are caused by the combination of vertical salinity structure, estuarine circulation, and egg specific gravity, supporting small-scaled geographical differentiations of local populations. Here, we assess the variability in egg specific gravity for selected local populations of this species, that is, two fjord-spawning populations and one coastal-spawning population from Northern Norway (66-71°N/10-25°E). Eggs were naturally spawned by raised broodstocks (March to April 2009), and egg specific gravity was measured by a density-gradient column. The phenotype of egg specific gravity was similar among the three local populations. However, the associated variability was greater at the individual level than at the population level. The noted gradual decrease in specific gravity from gastrulation to hatching with an increase just before hatching could be a generic pattern in pelagic marine fish eggs. This study provides needed input to adequately understand and model fish egg dispersal.

Monitoring and source apportionment of trace elements in PM2.5: Implications for local air quality management.

PubMed

Li, Yueyan; Chang, Miao; Ding, Shanshan; Wang, Shiwen; Ni, Dun; Hu, Hongtao

2017-07-01

Fine particulate matter (PM 2.5 ) samples were collected simultaneously every hour in Beijing between April 2014 and April 2015 at five sites. Thirteen trace elements (TEs) in PM 2.5 were analyzed by online X-ray fluorescence (XRF). The annual average PM 2.5 concentrations ranged from 76.8 to 102.7 μg m -3 . TEs accounted for 5.9%-8.7% of the total PM 2.5 mass with Cl, S, K, and Si as the most dominant elements. Spearman correlation coefficients of PM 2.5 or TE concentrations between the background site and other sites showed that PM 2.5 and some element loadings were affected by regional and local sources, whereas Cr, Si, and Ni were attributed to substantial local emissions. Temporal variations of TEs in PM 2.5 were significant and provided information on source profiles. The PM 2.5 concentrations were highest in autumn and lowest in summer. Mn and Cr showed similar variation. Fe, Ca, Si, and Ti tended to show higher concentrations in spring, whereas concentrations of S peaked in summer. Concentrations of Cl, K, Pb, Zn, Cu, and Ni peaked in winter. PM 2.5 and TE median concentrations were higher on Saturdays than on weekdays. The diurnal pattern of PM 2.5 and TE median concentrations yielded similar bimodal patterns. Five dominant sources of PM 2.5 mass were identified via positive matrix factorization (PMF). These sources included the regional and local secondary aerosols, traffic, coal burning, soil dust, and metal processing. Air quality management strategies, including regional environmental coordination and collaboration, reduction in secondary aerosol precursors, restrictive vehicle emission standards, promotion of public transport, and adoption of clean energy, should be strictly implemented. High time-resolution measurements of TEs provided detailed source profiles, which can greatly improve precision in interpreting source apportionment calculations; the PMF analysis of online XRF data is a powerful tool for local air quality management. Copyright © 2017 Elsevier Ltd. All rights reserved.

Subtle Ecological Gradient in the Tropics Triggers High Species-Turnover in a Local Geographical Scale

PubMed Central

Nguyen, Dinh T.

2016-01-01

Our perception of diversity, including both alpha- and beta-diversity components, depends on spatial scale. Studies of spatial variation of the latter are just starting, with a paucity of research on beta-diversity patterns at smaller scales. Understanding these patterns and the processes shaping the distribution of diversity is critical to describe this diversity, but it is paramount in conservation too. Here, we investigate the diversity and structure of a tropical community of herbivorous beetles at a reduced local scale of some 10 km2, evaluating the effect of a small, gradual ecological change on this structure. We sampled leaf beetles in the Núi Chúa National Park (S Vietnam), studying changes in alpha- and beta-diversity across an elevation gradient up to 500 m, encompassing the ecotone between critically endangered lowland dry deciduous forest and mixed evergreen forest at higher elevations. Leaf beetle diversity was assessed using several molecular tree-based species delimitation approaches (with mtDNA cox1 data), species richness using rarefaction and incidence-based diversity indexes, and beta-diversity was investigated decomposing the contribution of species turnover and nestedness. We documented 155 species in the area explored and species-richness estimates 1.5–2.0x higher. Species diversity was similar in both forest types and changes in alpha-diversity along the elevation gradient showed an expected local increase of diversity in the ecotone. Beta-diversity was high among forest paths (average Sørensen's dissimilarity = 0.694) and, tentatively fixing at 300 m the boundary between otherwise continuous biomes, demonstrated similarly high beta-diversity (Sørensen's dissimilarity = 0.581), with samples clustering according to biome/elevation. Highly relevant considering the local scale of the study, beta-diversity had a high contribution of species replacement among locales (54.8%) and between biomes (79.6%), suggesting environmental heterogeneity as the dominant force shaping diversity at such small scale, directly and indirectly on the plant communities. Protection actions in the Park, especially these addressed at the imperative conservation of dry forest, must ponder the small scale at which processes shape species diversity and community structure for inconspicuous, yet extraordinarily diverse organisms such as the leaf beetles. PMID:27276228

Statistical behavior of the longitudinal variations of daytime electron density in the topside ionosphere at middle latitudes

NASA Astrophysics Data System (ADS)

Su, Fanfan; Wang, Wenbin; Burns, Alan G.; Yue, Xinan; Zhu, Fuying; Lin, Jian

2016-11-01

Electron density in the topside ionosphere has significant variations with latitude, longitude, altitude, local time, season, and solar cycle. This paper focuses on the global and seasonal features of longitudinal structures of daytime topside electron density (Ne) at middle latitudes and their possible causes. We used in situ Ne measured by DEMETER and F2 layer peak height (hmF2) and peak density (NmF2) from COSMIC. The longitudinal variations of the daytime topside Ne show a wave number 2-type structure in the Northern Hemisphere, whereas those in the Southern Hemisphere are dominated by a wave number 1 structure and are much larger than those in the Northern Hemisphere. The patterns around December solstice (DS) in the Northern Hemisphere (winter) are different from other seasons, whereas the patterns in the Southern Hemisphere are similar in each season. Around March equinox (ME), June solstice (JS), and September equinox (SE) in the Northern Hemisphere and around ME, SE, and DS in the Southern Hemisphere, the longitudinal variations of topside Ne have similar patterns to hmF2. Around JS in the Southern Hemisphere (winter), the topside Ne has similar patterns to NmF2 and hmF2 does not change much with longitude. Thus, the topside variations may be explained intuitively in terms of hmF2 and NmF2. This approach works reasonably well in most of the situations except in the northern winter in the topside not too far from the F2 peak. In this sense, understanding variations in hmF2 and NmF2 becomes an important and relevant subject for this topside ionospheric study.

Fluoride availability from natural resources in The Gambia--implications for oral health care.

PubMed

Jordan, Rainer A; Markovic, Ljubisa; Gaengler, Peter

2008-10-01

Changing food patterns in combination with ineffective oral hygiene measures and insufficient bioavailability of fluoride from drinking water and other sources seem to impair the dental health status in developing countries, especially in the younger population. Therefore, preventive programmes in controlling dental caries progression should be based on local conditions. For mapping the drinking water fluoride content throughout The Gambia, samples of water from rural community wells, public water taps, commercial mineral water, and from the Gambia-River were measured. Additionally, fluoride concentrations of locally extracted table salt and green tea were determined. Showed the need for supplementary fluoride intake, because natural dietary fluoride availability is very low. Age-related recommendations for oral health care and for additional fluoride bioavailability are given, taking into account local socio-economic conditions in the Republic of The Gambia and similar developing countries.

Local and global epidemic outbreaks in populations moving in inhomogeneous environments

NASA Astrophysics Data System (ADS)

Buscarino, Arturo; Fortuna, Luigi; Frasca, Mattia; Rizzo, Alessandro

2014-10-01

We study disease spreading in a system of agents moving in a space where the force of infection is not homogeneous. Agents are random walkers that additionally execute long-distance jumps, and the plane in which they move is divided into two regions where the force of infection takes different values. We show the onset of a local epidemic threshold and a global one and explain them in terms of mean-field approximations. We also elucidate the critical role of the agent velocity, jump probability, and density parameters in achieving the conditions for local and global outbreaks. Finally, we show that the results are independent of the specific microscopic rules adopted for agent motion, since a similar behavior is also observed for the distribution of agent velocity based on a truncated power law, which is a model often used to fit real data on motion patterns of animals and humans.

Decomposition and organic matter quality in continental peatlands: The ghost of permafrost past

USGS Publications Warehouse

Turetsky, M.R.

2004-01-01

Permafrost patterning in boreal peatlands contributes to landscape heterogeneity, as peat plateaus, palsas, and localized permafrost mounds are interspersed among unfrozen bogs and fens. The degradation of localized permafrost in peatlands alters local topography, hydrology, thermal regimes, and plant communities, and creates unique peatland features called "internal lawns." I used laboratory incubations to quantify carbon dioxide (CO 2) production in peat formed under different permafrost regimes (with permafrost, without permafrost, melted permafrost), and explored the relationships among proximate organic matter fractions, nutrient concentrations, and decomposition. Peat within each feature (internal lawn, bog, permafrost mound) is more chemically similar than peat collected within the same province (Alberta, Saskatchewan) or within depth intervals (surface, deep). Internal lawn peat produces more CO2 than the other peatland types. Across peatland features, acid-insoluble material (AIM) and AIM/nitrogen are significant predictors of decomposition. However, within each peatland feature, soluble proximate fractions are better predictors of CO2 production. Permafrost stability in peatlands influences plant and soil environments, which control litter inputs, organic matter quality, and decomposition rates. Spatial patterns of permafrost, as well as ecosystem processes within various permafrost features, should be considered when assessing the fate of soil carbon in northern ecosystems. ?? 2004 Springer Science+Business Media, Inc.

LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification.

PubMed

Gonçalves, Joana P; Madeira, Sara C

2014-01-01

Identifying patterns in temporal data is key to uncover meaningful relationships in diverse domains, from stock trading to social interactions. Also of great interest are clinical and biological applications, namely monitoring patient response to treatment or characterizing activity at the molecular level. In biology, researchers seek to gain insight into gene functions and dynamics of biological processes, as well as potential perturbations of these leading to disease, through the study of patterns emerging from gene expression time series. Clustering can group genes exhibiting similar expression profiles, but focuses on global patterns denoting rather broad, unspecific responses. Biclustering reveals local patterns, which more naturally capture the intricate collaboration between biological players, particularly under a temporal setting. Despite the general biclustering formulation being NP-hard, considering specific properties of time series has led to efficient solutions for the discovery of temporally aligned patterns. Notably, the identification of biclusters with time-lagged patterns, suggestive of transcriptional cascades, remains a challenge due to the combinatorial explosion of delayed occurrences. Herein, we propose LateBiclustering, a sensible heuristic algorithm enabling a polynomial rather than exponential time solution for the problem. We show that it identifies meaningful time-lagged biclusters relevant to the response of Saccharomyces cerevisiae to heat stress.

Local breast density assessment using reacquired mammographic images.

PubMed

García, Eloy; Diaz, Oliver; Martí, Robert; Diez, Yago; Gubern-Mérida, Albert; Sentís, Melcior; Martí, Joan; Oliver, Arnau

2017-08-01

The aim of this paper is to evaluate the spatial glandular volumetric tissue distribution as well as the density measures provided by Volpara™ using a dataset composed of repeated pairs of mammograms, where each pair was acquired in a short time frame and in a slightly changed position of the breast. We conducted a retrospective analysis of 99 pairs of repeatedly acquired full-field digital mammograms from 99 different patients. The commercial software Volpara™ Density Maps (Volpara Solutions, Wellington, New Zealand) is used to estimate both the global and the local glandular tissue distribution in each image. The global measures provided by Volpara™, such as breast volume, volume of glandular tissue, and volumetric breast density are compared between the two acquisitions. The evaluation of the local glandular information is performed using histogram similarity metrics, such as intersection and correlation, and local measures, such as statistics from the difference image and local gradient correlation measures. Global measures showed a high correlation (breast volume R=0.99, volume of glandular tissue R=0.94, and volumetric breast density R=0.96) regardless the anode/filter material. Similarly, histogram intersection and correlation metric showed that, for each pair, the images share a high degree of information. Regarding the local distribution of glandular tissue, small changes in the angle of view do not yield significant differences in the glandular pattern, whilst changes in the breast thickness between both acquisition affect the spatial parenchymal distribution. This study indicates that Volpara™ Density Maps is reliable in estimating the local glandular tissue distribution and can be used for its assessment and follow-up. Volpara™ Density Maps is robust to small variations of the acquisition angle and to the beam energy, although divergences arise due to different breast compression conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Scalp and Source Power Topography in Sleepwalking and Sleep Terrors: A High-Density EEG Study

PubMed Central

Castelnovo, Anna; Riedner, Brady A.; Smith, Richard F.; Tononi, Giulio; Boly, Melanie; Benca, Ruth M.

2016-01-01

Study Objectives: To examine scalp and source power topography in sleep arousals disorders (SADs) using high-density EEG (hdEEG). Methods: Fifteen adult subjects with sleep arousal disorders (SADs) and 15 age- and gender-matched good sleeping healthy controls were recorded in a sleep laboratory setting using a 256 channel EEG system. Results: Scalp EEG analysis of all night NREM sleep revealed a localized decrease in slow wave activity (SWA) power (1–4 Hz) over centro-parietal regions relative to the rest of the brain in SADs compared to good sleeping healthy controls. Source modelling analysis of 5-minute segments taken from N3 during the first half of the night revealed that the local decrease in SWA power was prominent at the level of the cingulate, motor, and sensori-motor associative cortices. Similar patterns were also evident during REM sleep and wake. These differences in local sleep were present in the absence of any detectable clinical or electrophysiological sign of arousal. Conclusions: Overall, results suggest the presence of local sleep differences in the brain of SADs patients during nights without clinical episodes. The persistence of similar topographical changes in local EEG power during REM sleep and wakefulness points to trait-like functional changes that cross the boundaries of NREM sleep. The regions identified by source imaging are consistent with the current neurophysiological understanding of SADs as a disorder caused by local arousals in motor and cingulate cortices. Persistent localized changes in neuronal excitability may predispose affected subjects to clinical episodes. Citation: Castelnovo A, Riedner BA, Smith RF, Tononi G, Boly M, Benca RM. Scalp and source power topography in sleepwalking and sleep terrors: a high-density EEG study. SLEEP 2016;39(10):1815–1825. PMID:27568805

Spatial distribution of 12 class B notifiable infectious diseases in China: A retrospective study

PubMed Central

Zhu, Bin; Fu, Yang; Liu, Jinlin

2018-01-01

Background China is the largest developing country with a relatively developed public health system. To further prevent and eliminate the spread of infectious diseases, China has listed 39 notifiable infectious diseases characterized by wide prevalence or great harm, and classified them into classes A, B, and C, with severity decreasing across classes. Class A diseases have been almost eradicated in China, thus making class B diseases a priority in infectious disease prevention and control. In this retrospective study, we analyze the spatial distribution patterns of 12 class B notifiable infectious diseases that remain active all over China. Methods Global and local Moran’s I and corresponding graphic tools are adopted to explore and visualize the global and local spatial distribution of the incidence of the selected epidemics, respectively. Inter-correlations of clustering patterns of each pair of diseases and a cumulative summary of the high/low cluster frequency of the provincial units are also provided by means of figures and maps. Results Of the 12 most commonly notifiable class B infectious diseases, viral hepatitis and tuberculosis show high incidence rates and account for more than half of the reported cases. Almost all the diseases, except pertussis, exhibit positive spatial autocorrelation at the provincial level. All diseases feature varying spatial concentrations. Nevertheless, associations exist between spatial distribution patterns, with some provincial units displaying the same type of cluster features for two or more infectious diseases. Overall, high–low (unit with high incidence surrounded by units with high incidence, the same below) and high–high spatial cluster areas tend to be prevalent in the provincial units located in western and southwest China, whereas low–low and low–high spatial cluster areas abound in provincial units in north and east China. Conclusion Despite the various distribution patterns of 12 class B notifiable infectious diseases, certain similarities between their spatial distributions are present. Substantial evidence is available to support disease-specific, location-specific, and disease-combined interventions. Regarding provinces that show high–high/high–low patterns of multiple diseases, comprehensive interventions targeting different diseases should be established. As to the adjacent provincial units revealing similar patterns, coordinated actions need to be taken across borders. PMID:29621351

The relevance of stress percolation in polycrystalline solids to the deformation of deep earth materials

NASA Astrophysics Data System (ADS)

Burnley, P. C.

2013-12-01

One of the fundamental challenges in characterizing the plastic properties of deep earth materials at relevant length and time scales is that some form of extrapolation will always be required. With increasing computational power, single crystal mechanical properties will probably be accessible to first principles calculations in the not too distant future. If the relationship between single crystal and polycrystal mechanical properties were straightforward, with some ground truthing in the lab, the bulk behavior could be confidently extrapolated to experimentally inaccessible conditions. However, we currently lack a satisfactory paradigm to describe the relationship between single crystal and polycrystalline deformation. Existing mechanical models, including self-consistent models cannot predict or account for the spatial variations in the local stress and strain states observed in real-world materials. Full field models can be constructed so as to explicitly include the spatial relationships between crystals and their neighbors, but in their explicitness they lose the ability to generalize. Using finite element (FEM) simulations of a polycrystalline material (Figure 1a), I show that local variations in stress and strain participate in large-scale patterns, that are a function of the heterogeneity and statistical distribution of elastic and plastic properties across the population of mechanical components (grains and grain boundaries) in the material. The patterns of modulation in the local stress tensor are similar to the patterns of stress distribution observed in granular materials - often referred to as force chains. Force chains are caused by percolation of stress through strong contacts between particles in a granular aggregate. The patterns in stress modulation observed in the FEM simulations are caused by stress percolation through the elastically heterogeneous mechanical elements. Greater degrees of heterogeneity lead to more intense stress concentrations across a less dense pattern (Figure 1b). Lower degrees of elastic heterogeneity lead to a denser pattern of stress transmission that carries smaller modulations (Figure1e). Paralleling the development of shear bands in granular materials, the stress patterns lead directly to shear localization even in the absence of strain softening. The recognition of stress percolation provides a foundation for devising models that link single crystal mechanics and local interactions to bulk behavior. Such rheological models should provide a more robust platform for extrapolating to deep earth conditions including spatial and time scales. Figure 1: Panel a) FE model mesh, inset shows an enlarged region. Properties are assigned to each of 25 grain sets (coded by color). Panels b)-e) Equivalent von Mises stress patterns for models in compression. For b) Young's modulus E of grain sets ranges from 500 to 0 GPa with v=0.1 to 0.4, for c) E= 500 to 0 GPa with v=0.3 for d) E= 200 to 20 GPa with v=0.3 and for e) E =120 to 100 GPa with v=0.3. The maximum value of the equivalent stress in b) is 10 times that found in e).

Monorchiids (Platyhelminthes: Digenea) of chaetodontid fishes (Perciformes): biogeographical patterns in the tropical Indo-West Pacific.

PubMed

McNamara, M K A; Adlard, R D; Bray, R A; Sasal, P; Cribb, T H

2012-06-01

Species richness and biogeography of the monorchiid genus Hurleytrematoides was studied by the examination of 2834 individuals of 45 species of Chaetodontidae at six major sites in the tropical Indo-West Pacific: Heron Island, Lizard Island, Ningaloo (Western Australia), Palau, New Caledonia and Moorea (French Polynesia). In total, 18 species were distributed among six sites; descriptions are provided for eight new species: H. boucheti n. sp., H. combesi n. sp., H. deblocki n. sp., H. dollfusi n. sp., H. euzeti n. sp., H. kulbickii n. sp., H. pasteuri n. sp., and H. planesi n. sp. Overall richness ranged from zero to five Hurleytrematoides species per chaetodontid species. Seven Hurleytrematoides species were found at only one locality and eleven were found at multiple localities. Only one species, H. morandi, was found at all localities. Individual localities had between six (Moorea) and 10 (Heron Island) species; we attribute Moorea's depauperate parasite fauna to its isolation and distance from the Indo-Philippine centre of biological diversity. Using cluster analysis of 18 species of Hurleytrematoides and 45 species of chaetodontids sampled in the Indo-West Pacific, we show that the localities on the Great Barrier Reef (Heron Island and Lizard Island) and New Caledonia have the most similar chaetodontid and parasite fauna of any locality pairs. Cluster analysis results also show that the similarity of the chaetodontid assemblages at five of the six localities is relatively high and that Ningaloo has the most distinct fauna. Similarity values based on sharing of species of Hurleytrematoides are generally lower than those for their hosts; Moorea, Ningaloo and Palau all have low similarity to New Caledonia and Great Barrier Reef sites. We attribute these distinctions to the differential dispersal capability of the fish and their parasites. Chaetodontids have long-lived mobile pelagic larvae, the dispersal of which would be most affected by prominent biogeographical barriers, such as that between the Indian and Pacific Oceans. In contrast, monorchiids have no obvious dispersal stage, and vast distances have the capacity to act as effective barriers to dispersal. We conclude that the present distributions of species of Hurleytrematoides in the Indo-Pacific are driven by historical opportunity and capacity to disperse, and that some disjunct distributions are sculpted by stochasticity. Copyright © 2011. Published by Elsevier Ireland Ltd.

Season-modulated responses of Neotropical bats to forest fragmentation.

PubMed

Ferreira, Diogo F; Rocha, Ricardo; López-Baucells, Adrià; Farneda, Fábio Z; Carreiras, João M B; Palmeirim, Jorge M; Meyer, Christoph F J

2017-06-01

Seasonality causes fluctuations in resource availability, affecting the presence and abundance of animal species. The impacts of these oscillations on wildlife populations can be exacerbated by habitat fragmentation. We assessed differences in bat species abundance between the wet and dry season in a fragmented landscape in the Central Amazon characterized by primary forest fragments embedded in a secondary forest matrix. We also evaluated whether the relative importance of local vegetation structure versus landscape characteristics (composition and configuration) in shaping bat abundance patterns varied between seasons. Our working hypotheses were that abundance responses are species as well as season specific, and that in the wet season, local vegetation structure is a stronger determinant of bat abundance than landscape-scale attributes. Generalized linear mixed-effects models in combination with hierarchical partitioning revealed that relationships between species abundances and local vegetation structure and landscape characteristics were both season specific and scale dependent. Overall, landscape characteristics were more important than local vegetation characteristics, suggesting that landscape structure is likely to play an even more important role in landscapes with higher fragment-matrix contrast. Responses varied between frugivores and animalivores. In the dry season, frugivores responded more to compositional metrics, whereas during the wet season, local and configurational metrics were more important. Animalivores showed similar patterns in both seasons, responding to the same group of metrics in both seasons. Differences in responses likely reflect seasonal differences in the phenology of flowering and fruiting between primary and secondary forests, which affected the foraging behavior and habitat use of bats. Management actions should encompass multiscale approaches to account for the idiosyncratic responses of species to seasonal variation in resource abundance and consequently to local and landscape scale attributes.

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.

PubMed

Xia, Li C; Ai, Dongmei; Cram, Jacob A; Liang, Xiaoyi; Fuhrman, Jed A; Sun, Fengzhu

2015-09-21

Local trend (i.e. shape) analysis of time series data reveals co-changing patterns in dynamics of biological systems. However, slow permutation procedures to evaluate the statistical significance of local trend scores have limited its applications to high-throughput time series data analysis, e.g., data from the next generation sequencing technology based studies. By extending the theories for the tail probability of the range of sum of Markovian random variables, we propose formulae for approximating the statistical significance of local trend scores. Using simulations and real data, we show that the approximate p-value is close to that obtained using a large number of permutations (starting at time points >20 with no delay and >30 with delay of at most three time steps) in that the non-zero decimals of the p-values obtained by the approximation and the permutations are mostly the same when the approximate p-value is less than 0.05. In addition, the approximate p-value is slightly larger than that based on permutations making hypothesis testing based on the approximate p-value conservative. The approximation enables efficient calculation of p-values for pairwise local trend analysis, making large scale all-versus-all comparisons possible. We also propose a hybrid approach by integrating the approximation and permutations to obtain accurate p-values for significantly associated pairs. We further demonstrate its use with the analysis of the Polymouth Marine Laboratory (PML) microbial community time series from high-throughput sequencing data and found interesting organism co-occurrence dynamic patterns. The software tool is integrated into the eLSA software package that now provides accelerated local trend and similarity analysis pipelines for time series data. The package is freely available from the eLSA website: http://bitbucket.org/charade/elsa.

Rainfall-triggered shallow landslides at catchment scale: Threshold mechanics-based modeling for abruptness and localization

NASA Astrophysics Data System (ADS)

von Ruette, J.; Lehmann, P.; Or, D.

2013-10-01

Rainfall-induced shallow landslides may occur abruptly without distinct precursors and could span a wide range of soil mass released during a triggering event. We present a rainfall-induced landslide-triggering model for steep catchments with surfaces represented as an assembly of hydrologically and mechanically interconnected soil columns. The abruptness of failure was captured by defining local strength thresholds for mechanical bonds linking soil and bedrock and adjacent columns, whereby a failure of a single bond may initiate a chain reaction of subsequent failures, culminating in local mass release (a landslide). The catchment-scale hydromechanical landslide-triggering model (CHLT) was applied to results from two event-based landslide inventories triggered by two rainfall events in 2002 and 2005 in two nearby catchments located in the Prealps in Switzerland. Rainfall radar data, surface elevation and vegetation maps, and a soil production model for soil depth distribution were used for hydromechanical modeling of failure patterns for the two rainfall events at spatial and temporal resolutions of 2.5 m and 0.02 h, respectively. The CHLT model enabled systematic evaluation of the effects of soil type, mechanical reinforcement (soil cohesion and lateral root strength), and initial soil water content on landslide characteristics. We compared various landslide metrics and spatial distribution of simulated landslides in subcatchments with observed inventory data. Model parameters were optimized for the short but intense rainfall event in 2002, and the calibrated model was then applied for the 2005 rainfall, yielding reasonable predictions of landslide events and volumes and statistically reproducing localized landslide patterns similar to inventory data. The model provides a means for identifying local hot spots and offers insights into the dynamics of locally resolved landslide hazards in mountainous regions.

Temporal Trends and the Impact of Race, Insurance, and Socioeconomic Status in the Management of Localized Prostate Cancer.

PubMed

Gray, Phillip J; Lin, Chun Chieh; Cooperberg, Matthew R; Jemal, Ahmedin; Efstathiou, Jason A

2017-05-01

Numerous management options exist for patients with prostate cancer; however, recent trends and their influencing factors are not well described. To describe modern patterns of care and factors associated with management choice using the National Cancer Database. Patients with localized prostate cancer diagnosed between 2004 and 2012 were included and grouped according to National Comprehensive Cancer Network guidelines into low, intermediate, or high risk. Trend analyses and multivariate logistic regression was used to identify factors associated with management. There were 598 640 patients who met the study criteria; 36.3% were classified as low risk, 43.8% intermediate risk, and 20.0% high risk. Over the study period, among low-risk patients, observation increased from 9.2% to 21.3%, while radical prostatectomy (RP) increased from 29.5% to 51.1% (p<0.001 for both). In contrast, external beam radiotherapy decreased from 24.3% to 14.5%, while brachytherapy decreased from 31.7% to 11.1%. A similar pattern was seen for patients with intermediate-risk or high-risk disease. Among high-risk patients, RP increased from 25.1% to 43.4% replacing external beam radiotherapy as the dominant therapy. On multivariate analysis, racial minorities, the uninsured, and low-income patients were less likely to receive RP. Low-risk patients in similar subgroups were significantly more likely to be observed. Limitations include potential miscoding or misclassification of variables. Patterns of care in localized prostate cancer are changing rapidly. While use of observation is increasing in low-risk groups, the use of RP is increasing across all risk groups with a concomitant decline in use of radiotherapy. Socioeconomic factors appear to influence management choice. In this report we identify a recent significant increase in the use of radical prostatectomy for prostate cancer patients. Socioeconomic factors such as race, insurance type, and income may affect treatments offered to and received by patients. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Scorpion biodiversity and interslope divergence at "evolution canyon", lower Nahal Oren microsite, Mt. Carmel, Israel.

PubMed

Raz, Shmuel; Retzkin, Sion; Pavlícek, Tomás; Hoffman, Adam; Kimchi, Hagay; Zehavi, Dan; Beiles, Avigdor; Nevo, Eviatar

2009-01-01

Local natural laboratories, designated by us as the "Evolution Canyon" model, are excellent tools to study regional and global ecological dynamics across life. They present abiotic and biotic contrasts locally, permitting the pursuit of observations and experiments across diverse taxa sharing sharp microecological subdivisions. Higher solar radiation received by the "African savannah-like" south-facing slopes (AS) in canyons north of the equator than by the opposite "European maquis-like" north-facing slopes (ES) is associated with higher abiotic stress. Scorpions are a suitable taxon to study interslope biodiversity differences, associated with the differences in abiotic factors (climate, drought), due to their ability to adapt to dry environments. Scorpions were studied by the turning stone method and by UV light methods. The pattern observed in scorpions was contrasted with similar patterns in several other taxa at the same place. As expected, the AS proved to be significantly more speciose regarding scorpions, paralleling the interslope patterns in taxa such as lizards and snakes, butterflies (Rhopalocera), beetles (families Tenebrionidae, Dermestidae, Chrysomelidae), and grasshoppers (Orthoptera). Our results support an earlier conclusion stating that the homogenizing effects of migration and stochasticity are not able to eliminate the interslope intra- and interspecific differences in biodiversity despite an interslope distance of only 100 m at the "EC" valley bottom. In our opinion, the interslope microclimate selection, driven mainly by differences in insolance, could be the primary factor responsible for the observed interslope pattern.

Is the nestedness of metazoan parasite assemblages of marine fishes from the southeastern Pacific coast a pattern associated with the geographical distributional range of the host?

PubMed

González, M T; Oliva, M E

2009-04-01

Nested structure is a pattern originally described in island biogeography to characterize how a set of species is distributed among a set of islands. In parasite communities, nestedness has been intensively studied among individual fish from a locality. However, nested patterns among parasite assemblages from different host populations (localities) have scarcely been investigated. We recorded the occurrence of parasites in 9 fish species widely distributed along the southeastern Pacific coast to determine whether the ecto- and endoparasite assemblages of marine fishes show a nested structure associated with host distributional range. Nestedness was tested using Brualdi-Sanderson index of discrepancy (BR); and 5 null models incorporated in a 'Nestedness' programme (Ulrich, 2006). The ecto- and endoparasite richness do not show similar patterns of latitudinal gradients among fish hosts, with 33-66% of analysed ectoparasite assemblages, and 25-75% of endoparasite assemblages showing nested structures through the host distributional range. For ectoparasites, species richness gradients and nested structure (when present) might be associated with decreased host densities or could reflect negative environmental conditions in the distributional border of the host species, whereas for endoparasites might be caused by geographical breaks of prey or changes in prey availability (intermediate hosts). The sampled extension of the distributional range of the host species, as well as the lack of specificity of some parasites, could influence the detection of nestedness.

The hELENa project - II. Abundance distribution trends of early-type galaxies: from dwarfs to giants

NASA Astrophysics Data System (ADS)

Sybilska, A.; Kuntschner, H.; van de Ven, G.; Vazdekis, A.; Falcón-Barroso, J.; Peletier, R. F.; Lisker, T.

2018-06-01

In this second paper of The role of Environment in shaping Low-mass Early-type Nearby galaxies (hELENa) series we study [Mg/Fe] abundance distribution trends of early-type galaxies (ETGs) observed with the Spectrographic Areal Unit for Research on Optical Nebulae integral field unit, spanning a wide range in mass and local environment densities: 20 low-mass early types (dEs) of Sybilska et al. and 258 massive early types (ETGs) of the ATLAS3D project, all homogeneously reduced and analysed. We show that the [Mg/Fe] ratios scale with velocity dispersion (σ) at fixed [Fe/H] and that they evolve with [Fe/H] along similar paths for all early types, grouped in bins of increasing local and global σ, as well as the second velocity moment Vrms, indicating a common inside-out formation pattern. We then place our dEs on the [Mg/Fe] versus [Fe/H] diagram of Local Group galaxies and show that dEs occupy the same region and show a similar trend line slope in the diagram as the high-metallicity stars of the Milky Way and the Large Magellanic Cloud. This finding extends the similar trend found for dwarf spheroidal versus dwarf irregular galaxies and supports the notion that dEs have evolved from late-type galaxies that have lost their gas at a point of their evolution, which likely coincided with them entering denser environments.

More than one way to see it: Individual heuristics in avian visual computation.

PubMed

Ravignani, Andrea; Westphal-Fitch, Gesche; Aust, Ulrike; Schlumpp, Martin M; Fitch, W Tecumseh

2015-10-01

Comparative pattern learning experiments investigate how different species find regularities in sensory input, providing insights into cognitive processing in humans and other animals. Past research has focused either on one species' ability to process pattern classes or different species' performance in recognizing the same pattern, with little attention to individual and species-specific heuristics and decision strategies. We trained and tested two bird species, pigeons (Columba livia) and kea (Nestor notabilis, a parrot species), on visual patterns using touch-screen technology. Patterns were composed of several abstract elements and had varying degrees of structural complexity. We developed a model selection paradigm, based on regular expressions, that allowed us to reconstruct the specific decision strategies and cognitive heuristics adopted by a given individual in our task. Individual birds showed considerable differences in the number, type and heterogeneity of heuristic strategies adopted. Birds' choices also exhibited consistent species-level differences. Kea adopted effective heuristic strategies, based on matching learned bigrams to stimulus edges. Individual pigeons, in contrast, adopted an idiosyncratic mix of strategies that included local transition probabilities and global string similarity. Although performance was above chance and quite high for kea, no individual of either species provided clear evidence of learning exactly the rule used to generate the training stimuli. Our results show that similar behavioral outcomes can be achieved using dramatically different strategies and highlight the dangers of combining multiple individuals in a group analysis. These findings, and our general approach, have implications for the design of future pattern learning experiments, and the interpretation of comparative cognition research more generally. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Nonrandom community assembly and high temporal turnover promote regional coexistence in tropics but not temperate zone.

PubMed

Freestone, Amy L; Inouye, Brian D

2015-01-01

A persistent challenge for ecologists is understanding the ecological mechanisms that maintain global patterns of biodiversity, particularly the latitudinal diversity gradient of peak species richness in the tropics. Spatial and temporal variation in community composition contribute to these patterns of biodiversity, but how this variation and its underlying processes change across latitude remains unresolved. Using a model system of sessile marine invertebrates across 25 degrees of latitude, from the temperate zone to the tropics, we tested the prediction that spatial and temporal patterns of taxonomic richness and composition, and the community assembly processes underlying these patterns, will differ across latitude. Specifically, we predicted that high beta diversity (spatial variation in composition) and high temporal turnover contribute to the high species richness of the tropics. Using a standardized experimental approach that controls for several confounding factors that hinder interpretation of prior studies, we present results that support our predictions. In the temperate zone, communities were more similar across spatial scales from centimeters to tens of kilometers and temporal scales up to one year than at lower latitudes. Since the patterns at northern latitudes were congruent with a null model, stochastic assembly processes are implicated. In contrast, the communities in the tropics were a dynamic spatial and temporal mosaic, with low similarity even across small spatial scales and high temporal turnover at both local and regional scales. Unlike the temperate zone, deterministic community assembly processes such as predation likely contributed to the high beta diversity in the tropics. Our results suggest that community assembly processes and temporal dynamics vary across latitude and help structure and maintain latitudinal patterns of diversity.

Parasites of a marine benthic fish in the Southwestern Atlantic: searching for geographical recurrent patterns of community structure.

PubMed

Vales, Damián Gustavo; García, Néstor Aníbal; Crespo, Enrique Alberto; Timi, Juan Tomás

2011-02-01

Parasite communities of Raneya brasiliensis are described and its parasites used as biological tags to discriminate its populations. Fish were caught in two zones of the Argentine Sea: one sample from San Jorge Gulf (Patagonian Region) and three samples from off the coast of Buenos Aires (Bonaerense Region). A total of 183 fish were examined for parasites and 11 species were found. Host body size and its ecology are pointed out as drivers of the paucity of taxa found. Multivariate similarity analyses allowed the identification of three stocks: one in the San Jorge Gulf, and two other in the Bonaerense Region. The parasite species that contributed most to the separation of the samples were generally those identified as biological markers in previous studies in the area. Patterns of distance decay in similarity among communities in R. brasiliensis were found; with dissimilarity values between distant localities being higher than between close ones. Whereas the composition and structure of parasite assemblages in Bonaerense waters reflect those of other fish species in this region, being mainly determined by the composition of the compound community, no repeatable patterns were found in the composition of parasites assemblages when R. brasiliensis was compared with other hosts species in Patagonia.

Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere

PubMed Central

Staley, Christopher

2016-01-01

ABSTRACT Recent characterization of the bacterial community structure in beach sands has revealed patterns of biogeography similar to those observed in aquatic environments. Studies to date, however, have mainly focused on subtidal sediments from marine beaches. Here, we investigate the bacterial diversity, using Illumina-based sequencing of the V5-V6 region of the 16S rRNA gene, at 11 beaches representing those next to the Great Lakes, Florida, and the Pacific Ocean. The alpha diversity differed significantly among regions (P < 0.0001), while the within-region diversity was more similar. The beta diversity also differed by region (P < 0.001), where freshwater sands had significantly higher abundances of taxa within the Actinobacteria, Betaproteobacteria, and Verrucomicrobia than marine environments. In contrast, marine sands harbored greater abundances of Gammaproteobacteria and Planctomycetes, and those from Florida had more Deltaproteobacteria and Firmicutes. Marine beaches had significantly different phylogenetic community structures (P ≤ 0.018), but freshwater and Florida beaches showed fewer within-region phylogenetic differences. Furthermore, regionally distinct patterns in taxonomic variation were observed in backshore sands, which had communities distinct from those in nearshore sands (P < 0.001). Sample depth minimally influenced the community composition. The results of this study reveal distinct bacterial community structures in sand on a broad geographic scale but moderate regional similarity and suggest that local variation is primarily related to the distance from the shoreline. This study offers a novel comparison of the bacterial communities in freshwater and marine beach sands and provides an important basis for future comparisons and analyses to elucidate factors affecting microbial ecology in this underexplored environment. IMPORTANCE This study presents a large-scale geographic characterization of the bacterial communities present in beach sands. While previous studies have evaluated how environmental factors influence bacterial community composition, few have evaluated bacterial communities in freshwater sands. Furthermore, the use of a consistent methodology to characterize bacterial communities here allowed a novel comparison of communities across geographic regions. We reveal that while the community composition in sands at individual beaches is distinct, beach sands within the same region harbor similar assemblages of bacteria and these assemblages differ greatly between regions. In addition, moisture, associated with distance from the shoreline, strongly influences the bacteria present in sands and more strongly influences the bacteria present than sample depth does. Thus, the data presented here offer an important basis for a broader characterization of the ecology of bacteria in sands, which may also be relevant to public health and resource management initiatives. PMID:26921429

Combined Loadings and Cross-Dimensional Loadings Timeliness of Presentation of Financial Statements of Local Government

NASA Astrophysics Data System (ADS)

Muda, I.; Dharsuky, A.; Siregar, H. S.; Sadalia, I.

2017-03-01

This study examines the pattern of readiness dimensional accuracy of financial statements of local government in North Sumatra with a routine pattern of two (2) months after the fiscal year ends and patterns of at least 3 (three) months after the fiscal year ends. This type of research is explanatory survey with quantitative methods. The population and the sample used is of local government officials serving local government financial reports. Combined Analysis And Cross-Loadings Loadings are used with statistical tools WarpPLS. The results showed that there was a pattern that varies above dimensional accuracy of the financial statements of local government in North Sumatra.

Physiologically Distributed Loading Patterns Drive the Formation of Zonally Organized Collagen Structures in Tissue-Engineered Meniscus.

PubMed

Puetzer, Jennifer L; Bonassar, Lawrence J

2016-07-01

The meniscus is a dense fibrocartilage tissue that withstands the complex loads of the knee via a unique organization of collagen fibers. Attempts to condition engineered menisci with compression or tensile loading alone have failed to reproduce complex structure on the microscale or anatomic scale. Here we show that axial loading of anatomically shaped tissue-engineered meniscus constructs produced spatial distributions of local strain similar to those seen in the meniscus when the knee is loaded at full extension. Such loading drove formation of tissue with large organized collagen fibers, levels of mechanical anisotropy, and compressive moduli that match native tissue. Loading accelerated the development of native-sized and aligned circumferential and radial collagen fibers. These loading patterns contained both tensile and compressive components that enhanced the major biochemical and functional properties of the meniscus, with loading significantly improved glycosaminoglycan (GAG) accumulation 200-250%, collagen accumulation 40-55%, equilibrium modulus 1000-1800%, and tensile moduli 500-1200% (radial and circumferential). Furthermore, this study demonstrates local changes in mechanical environment drive heterogeneous tissue development and organization within individual constructs, highlighting the importance of recapitulating native loading environments. Loaded menisci developed cartilage-like tissue with rounded cells, a dense collagen matrix, and increased GAG accumulation in the more compressively loaded horns, and fibrous collagen-rich tissue in the more tensile loaded outer 2/3, similar to native menisci. Loaded constructs reached a level of organization not seen in any previous engineered menisci and demonstrate great promise as meniscal replacements.

The effect of local environmental variables on the helminth parasite communities of the pointedbelly frog Leptodactylus podicipinus from ponds in the Pantanal wetlands.

PubMed

Campião, Karla Magalhães; Delatorre, Milena; Rodrigues, Rozangela Batista; da Silva, Reinaldo José; Ferreira, Vanda Lúcia

2012-04-01

Understanding the patterns of species distribution and abundance has been at the core of ecology. In general, these patterns are determined by species dispersion as well as by abiotic and biotic environmental conditions. Similarly, host-parasite relations and the structure of parasite assemblages are also shaped by environmental conditions and landscape composition. Herein, we assessed the influence of environmental variables and parasite species dispersion on the structure of helminth parasites communities in the frog Leptodactylus podicipinus. We sampled 10 ponds and recorded area, depth, altitude, pH, dissolved oxygen, salinity, temperature, and extent of soil, water, and vegetation cover as well as the distances between the ponds. We collected 121 frogs and found 9 helminth taxa; 2 of them were core species (prevalence higher than 50%), which contributed to the relatively high similarity observed among the ponds. Most of the helminths showed some variation in the frequencies of occurrence among communities from different ponds. The change in species composition among ponds was explained by the environmental variables but not by the distance between the ponds. Moreover, the results indicated that local processes (variation in environmental conditions) were more important than the regional processes (species distribution) in determining the structure of parasite communities. The variation in helminth communities among ponds in response to moderate differences in pond environmental characteristics points to the potential of helminth species as indicators of environmental conditions.

Investigating potential transferability of place-based research in land system science

NASA Astrophysics Data System (ADS)

Václavík, Tomáš; Langerwisch, Fanny; Cotter, Marc; Fick, Johanna; Häuser, Inga; Hotes, Stefan; Kamp, Johannes; Settele, Josef; Spangenberg, Joachim H.; Seppelt, Ralf

2016-09-01

Much of our knowledge about land use and ecosystem services in interrelated social-ecological systems is derived from place-based research. While local and regional case studies provide valuable insights, it is often unclear how relevant this research is beyond the study areas. Drawing generalized conclusions about practical solutions to land management from local observations and formulating hypotheses applicable to other places in the world requires that we identify patterns of land systems that are similar to those represented by the case study. Here, we utilize the previously developed concept of land system archetypes to investigate potential transferability of research from twelve regional projects implemented in a large joint research framework that focus on issues of sustainable land management across four continents. For each project, we characterize its project archetype, i.e. the unique land system based on a synthesis of more than 30 datasets of land-use intensity, environmental conditions and socioeconomic indicators. We estimate the transferability potential of project research by calculating the statistical similarity of locations across the world to the project archetype, assuming higher transferability potentials in locations with similar land system characteristics. Results show that areas with high transferability potentials are typically clustered around project sites but for some case studies can be found in regions that are geographically distant, especially when values of considered variables are close to the global mean or where the project archetype is driven by large-scale environmental or socioeconomic conditions. Using specific examples from the local case studies, we highlight the merit of our approach and discuss the differences between local realities and information captured in global datasets. The proposed method provides a blueprint for large research programs to assess potential transferability of place-based studies to other geographical areas and to indicate possible gaps in research efforts.

(Why) Does Evolution Favour Embryogenesis?

PubMed

Rensing, Stefan A

2016-07-01

Complex multicellular organisms typically possess life cycles in which zygotes (formed by gamete fusion) and meiosis occur. Canonical animal embryogenesis describes development from zygote to birth. It involves polarisation of the egg/zygote, asymmetric cell divisions, establishment of axes, symmetry breaking, formation of organs, and parental nutrition (at least in early stages). Similar developmental patterns have independently evolved in other eukaryotic lineages, including land plants and brown algae. The question arises whether embryo-like structures and associated developmental processes recurrently emerge because they are local optima of the evolutionary landscape. To understand which evolutionary principles govern complex multicellularity, we need to analyse why and how similar processes evolve convergently - von Baer's and Haeckel's phylotypic stage revisited in other phyla. Copyright © 2016 Elsevier Ltd. All rights reserved.

A comparison of caveolae and caveolin-1 to folate receptor α in retina and retinal pigment epithelium

PubMed Central

Bridges, Christy C.; El-Sherbeny, Amira; Roon, Penny; Ola, M. Shamsul; Kekuda, Ramesh; Ganapathy, Vadivel; Cameron, Richard S.; Cameron, Patricia L.

2015-01-01

Summary Caveolae are flask-shaped membrane invaginations present in most mammalian cells. They are distinguished by the presence of a striated coat composed of the protein, caveolin. Caveolae have been implicated in numerous cellular processes, including potocytosis in which caveolae are hypothesized to co-localize with folate receptor α and participate in folate uptake. Our laboratory has recently localized folate receptor α to the basolateral surface of the retinal pigment epithelium (RPE). It is present also in many other cells of the retina. In the present study, we asked whether caveolae were present in the RPE, and if so, whether their pattern of distribution was similar to folate receptor α. We also examined the distribution pattern of caveolin-1, which can be a marker of caveolae. Extensive electron microscopical analysis revealed caveolae associated with endothelial cells. However, none were detected in intact or cultured RPE. Laser scanning confocal microscopical analysis of intact RPE localized caveolin-1 to the apical and basal surfaces, a distribution unlike folate receptor α. Western analysis confirmed the presence of caveolin-1 in cultured RPE cells and laser scanning confocal microscopy localized the protein to the basal plasma membrane of the RPE, a distribution like that of folate receptor α. This distribution was confirmed by electron microscopic immunolocalization. The lack of caveolae in the RPE suggests that these structures may not be essential for folate internalization in the RPE. PMID:11508338

Contrasting activity patterns of sympatric and allopatric black and grizzly bears

USGS Publications Warehouse

Schwartz, C.C.; Cain, S.L.; Podruzny, S.; Cherry, S.; Frattaroli, L.

2010-01-01

The distribution of grizzly (Ursus arctos) and American black bears (U. americanus) overlaps in western North America. Few studies have detailed activity patterns where the species are sympatric and no studies contrasted patterns where populations are both sympatric and allopatric. We contrasted activity patterns for sympatric black and grizzly bears and for black bears allopatric to grizzly bears, how human influences altered patterns, and rates of grizzlyblack bear predation. Activity patterns differed between black bear populations, with those sympatric to grizzly bears more day-active. Activity patterns of black bears allopatric with grizzly bears were similar to those of female grizzly bears; both were crepuscular and day-active. Male grizzly bears were crepuscular and night-active. Both species were more night-active and less day-active when ???1 km from roads or developments. In our sympatric study area, 2 of 4 black bear mortalities were due to grizzly bear predation. Our results suggested patterns of activity that allowed for intra- and inter-species avoidance. National park management often results in convergence of locally high human densities in quality bear habitat. Our data provide additional understanding into how bears alter their activity patterns in response to other bears and humans and should help park managers minimize undesirable bearhuman encounters when considering needs for temporal and spatial management of humans and human developments in bear habitats. ?? 2010 The Wildlife Society.

Finger vein recognition using local line binary pattern.

PubMed

Rosdi, Bakhtiar Affendi; Shing, Chai Wuh; Suandi, Shahrel Azmin

2011-01-01

In this paper, a personal verification method using finger vein is presented. Finger vein can be considered more secured compared to other hands based biometric traits such as fingerprint and palm print because the features are inside the human body. In the proposed method, a new texture descriptor called local line binary pattern (LLBP) is utilized as feature extraction technique. The neighbourhood shape in LLBP is a straight line, unlike in local binary pattern (LBP) which is a square shape. Experimental results show that the proposed method using LLBP has better performance than the previous methods using LBP and local derivative pattern (LDP).

On the Local Convergence of Pattern Search

NASA Technical Reports Server (NTRS)

Dolan, Elizabeth D.; Lewis, Robert Michael; Torczon, Virginia; Bushnell, Dennis M. (Technical Monitor)

2000-01-01

We examine the local convergence properties of pattern search methods, complementing the previously established global convergence properties for this class of algorithms. We show that the step-length control parameter which appears in the definition of pattern search algorithms provides a reliable asymptotic measure of first-order stationarity. This gives an analytical justification for a traditional stopping criterion for pattern search methods. Using this measure of first-order stationarity, we analyze the behavior of pattern search in the neighborhood of an isolated local minimizer. We show that a recognizable subsequence converges r-linearly to the minimizer.

Poa secunda local collections and commercial releases: A genotypic evaluation

PubMed Central

Shaw, Alanna N.; Mummey, Daniel L.

2017-01-01

The genetics of native plants influence the success of ecological restoration, yet genetic variability of local seed collections and commercial seed releases remains unclear for most taxa. Poa secunda, a common native grass species in Intermountain West grasslands and a frequent component of restoration seed mixes, is one such species. Here, we evaluate the genetic variation of local Poa secunda collections in the context of wild populations and commercial seed releases. We evaluated AFLP markers for seven Poa secunda collections made over a 4000-hectare area and four commercial releases (High Plains, MT-1, Opportunity, and Sherman). We compare the genetic distance and distribution of genetic variation within and between local collections and commercial releases. The extent and patterns of genetic variation in our local collections indicate subtle site differences with most variation occurring within rather than between collections. Identical genetic matches were usually, but not always, found within 5 m2 collection sites. Our results suggest that the genetic variation in two Poa secunda releases (High Plains and MT-1) is similar to our local collections. Our results affirm that guidelines for Poa secunda seed collection should follow recommendations for selfing species, by collecting from many sites over large individual sites. PMID:28369130

Poa secunda local collections and commercial releases: A genotypic evaluation.

PubMed

Shaw, Alanna N; Mummey, Daniel L

2017-01-01

The genetics of native plants influence the success of ecological restoration, yet genetic variability of local seed collections and commercial seed releases remains unclear for most taxa. Poa secunda, a common native grass species in Intermountain West grasslands and a frequent component of restoration seed mixes, is one such species. Here, we evaluate the genetic variation of local Poa secunda collections in the context of wild populations and commercial seed releases. We evaluated AFLP markers for seven Poa secunda collections made over a 4000-hectare area and four commercial releases (High Plains, MT-1, Opportunity, and Sherman). We compare the genetic distance and distribution of genetic variation within and between local collections and commercial releases. The extent and patterns of genetic variation in our local collections indicate subtle site differences with most variation occurring within rather than between collections. Identical genetic matches were usually, but not always, found within 5 m2 collection sites. Our results suggest that the genetic variation in two Poa secunda releases (High Plains and MT-1) is similar to our local collections. Our results affirm that guidelines for Poa secunda seed collection should follow recommendations for selfing species, by collecting from many sites over large individual sites.

Patterning of magnetic thin films and multilayers using nanostructured tantalum gettering templates.

PubMed

Qiu, Wenlan; Chang, Long; Lee, Dahye; Dannangoda, Chamath; Martirosyan, Karen; Litvinov, Dmitri

2015-03-25

This work demonstrates that a nonmagnetic thin film of cobalt oxide (CoO) sandwiched between Ta seed and capping layers can be effectively reduced to a magnetic cobalt thin film by annealing at 200 °C, whereas CoO does not exhibit ferromagnetic properties at room temperature and is stable at up to ∼400 °C. The CoO reduction is attributed to the thermodynamically driven gettering of oxygen by tantalum, similar to the exothermic reduction-oxidation reaction observed in thermite systems. Similarly, annealing at 200 °C of a nonmagnetic [CoO/Pd]N multilayer thin film sandwiched between Ta seed and Ta capping layers results in the conversion into a magnetic [Co/Pd]N multilayer, a material with perpendicular magnetic anisotropy that is of interest for magnetic data storage applications. A nanopatterning approach is introduced where [CoO/Pd]N multilayers is locally reduced into [Co/Pd]N multilayers to achieve perpendicular magnetic anisotropy nanostructured array. This technique can potentially be adapted to nanoscale patterning of other systems for which thermodynamically favorable combination of oxide and gettering layers can be identified.

Fission-fusion and lineal effect: aspects of the population structure of the Semai Senoi of Malaysia.

PubMed

Fix, A G

1975-09-01

Analysis of histories and genealogies from seven relatively unacculturated, swidden-farming Semai settlements shows that the composition of local groups fluctuates through time. This instability is similar to a pattern which Neel and his colleagues have suggested is typical of primitive society, the fission-fusion model. In addition, the individuals comprising Semai fission groups are kinsmen which implies that the number of independent genomes represented is markedly less than the number of individual migrants (the lineal effect). Fission groups may form new villages or fuse with an established settlement. In either case, the genetic effects of such migration are more pronounced than would be expected on the basis of founder effect or random migration. Despite several conspicuous differences in social organization between the Semai and the South American Indians (e.g., bilateral vs. unilineal descent) whose population structure provided the empirical basis for the fission-fusion, lineal effect model, the basic similarities are striking. The Semai case thus lends support to the proposition that this pattern may be of some generality in technologically primitive populations.

Variation in the structure of bird nests between northern Manitoba and southeastern Ontario.

PubMed

Crossman, Carla A; Rohwer, Vanya G; Martin, Paul R

2011-04-28

Traits that converge in appearance under similar environmental conditions among phylogenetically independent lineages are thought to represent adaptations to local environments. We tested for convergence in nest morphology and composition of birds breeding in two ecologically different locations in Canada: Churchill in northern Manitoba and Elgin in southeastern Ontario. We examined nests from four families of passerine birds (Turdidae: Turdus, Parulidae: Dendroica, Emberizidae: Passerculus and Fringillidae: Carduelis) where closely related populations or species breed in both locations. Nests of American Robins, Yellow Warblers, and Carduelis finches had heavier nest masses, and tended to have thicker nest-walls, in northern Manitoba compared with conspecifics or congenerics breeding in southeastern Ontario. Together, all species showed evidence for wider internal and external nest-cup diameters in northern Manitoba, while individual species showed varying patterns for internal nest-cup and external nest depths. American Robins, Yellow Warblers, and Carduelis finches in northern Manitoba achieved heavier nest masses in different ways. American Robins increased all materials in similar proportions, and Yellow Warblers and Common Redpolls used greater amounts of select materials. While changes in nest composition vary uniquely for each species, the pattern of larger nests in northern Manitoba compared to southeastern Ontario in three of our four phylogenetically-independent comparisons suggests that birds are adapting to similar selective pressures between locations.

Multivariate Brain Prediction of Heart Rate and Skin Conductance Responses to Social Threat.

PubMed

Eisenbarth, Hedwig; Chang, Luke J; Wager, Tor D

2016-11-23

Psychosocial stressors induce autonomic nervous system (ANS) responses in multiple body systems that are linked to health risks. Much work has focused on the common effects of stress, but ANS responses in different body systems are dissociable and may result from distinct patterns of cortical-subcortical interactions. Here, we used machine learning to develop multivariate patterns of fMRI activity predictive of heart rate (HR) and skin conductance level (SCL) responses during social threat in humans (N = 18). Overall, brain patterns predicted both HR and SCL in cross-validated analyses successfully (r HR = 0.54, r SCL = 0.58, both p < 0.0001). These patterns partly reflected central stress mechanisms common to both responses because each pattern predicted the other signal to some degree (r HR→SCL = 0.21 and r SCL→HR = 0.22, both p < 0.01), but they were largely physiological response specific. Both patterns included positive predictive weights in dorsal anterior cingulate and cerebellum and negative weights in ventromedial PFC and local pattern similarity analyses within these regions suggested that they encode common central stress mechanisms. However, the predictive maps and searchlight analysis suggested that the patterns predictive of HR and SCL were substantially different across most of the brain, including significant differences in ventromedial PFC, insula, lateral PFC, pre-SMA, and dmPFC. Overall, the results indicate that specific patterns of cerebral activity track threat-induced autonomic responses in specific body systems. Physiological measures of threat are not interchangeable, but rather reflect specific interactions among brain systems. We show that threat-induced increases in heart rate and skin conductance share some common representations in the brain, located mainly in the vmPFC, temporal and parahippocampal cortices, thalamus, and brainstem. However, despite these similarities, the brain patterns that predict these two autonomic responses are largely distinct. This evidence for largely output-measure-specific regulation of autonomic responses argues against a common system hypothesis and provides evidence that different autonomic measures reflect distinct, measurable patterns of cortical-subcortical interactions. Copyright © 2016 the authors 0270-6474/16/3611987-12$15.00/0.

77 FR 70381 - General Schedule Locality Pay Areas

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-26

... based on appropriate factors, which may include local labor market patterns, commuting patterns, and the... Implementation The proposed rule will have no effect on existing locality pay area definitions but will prevent...

Image Description with Local Patterns: An Application to Face Recognition

NASA Astrophysics Data System (ADS)

Zhou, Wei; Ahrary, Alireza; Kamata, Sei-Ichiro

In this paper, we propose a novel approach for presenting the local features of digital image using 1D Local Patterns by Multi-Scans (1DLPMS). We also consider the extentions and simplifications of the proposed approach into facial images analysis. The proposed approach consists of three steps. At the first step, the gray values of pixels in image are represented as a vector giving the local neighborhood intensity distrubutions of the pixels. Then, multi-scans are applied to capture different spatial information on the image with advantage of less computation than other traditional ways, such as Local Binary Patterns (LBP). The second step is encoding the local features based on different encoding rules using 1D local patterns. This transformation is expected to be less sensitive to illumination variations besides preserving the appearance of images embedded in the original gray scale. At the final step, Grouped 1D Local Patterns by Multi-Scans (G1DLPMS) is applied to make the proposed approach computationally simpler and easy to extend. Next, we further formulate boosted algorithm to extract the most discriminant local features. The evaluated results demonstrate that the proposed approach outperforms the conventional approaches in terms of accuracy in applications of face recognition, gender estimation and facial expression.

Estimating the Impacts of Local Policy Innovation: The Synthetic Control Method Applied to Tropical Deforestation

PubMed Central

Sills, Erin O.; Herrera, Diego; Kirkpatrick, A. Justin; Brandão, Amintas; Dickson, Rebecca; Hall, Simon; Pattanayak, Subhrendu; Shoch, David; Vedoveto, Mariana; Young, Luisa; Pfaff, Alexander

2015-01-01

Quasi-experimental methods increasingly are used to evaluate the impacts of conservation interventions by generating credible estimates of counterfactual baselines. These methods generally require large samples for statistical comparisons, presenting a challenge for evaluating innovative policies implemented within a few pioneering jurisdictions. Single jurisdictions often are studied using comparative methods, which rely on analysts’ selection of best case comparisons. The synthetic control method (SCM) offers one systematic and transparent way to select cases for comparison, from a sizeable pool, by focusing upon similarity in outcomes before the intervention. We explain SCM, then apply it to one local initiative to limit deforestation in the Brazilian Amazon. The municipality of Paragominas launched a multi-pronged local initiative in 2008 to maintain low deforestation while restoring economic production. This was a response to having been placed, due to high deforestation, on a federal “blacklist” that increased enforcement of forest regulations and restricted access to credit and output markets. The local initiative included mapping and monitoring of rural land plus promotion of economic alternatives compatible with low deforestation. The key motivation for the program may have been to reduce the costs of blacklisting. However its stated purpose was to limit deforestation, and thus we apply SCM to estimate what deforestation would have been in a (counterfactual) scenario of no local initiative. We obtain a plausible estimate, in that deforestation patterns before the intervention were similar in Paragominas and the synthetic control, which suggests that after several years, the initiative did lower deforestation (significantly below the synthetic control in 2012). This demonstrates that SCM can yield helpful land-use counterfactuals for single units, with opportunities to integrate local and expert knowledge and to test innovations and permutations on policies that are implemented in just a few locations. PMID:26173108

Estimating the Impacts of Local Policy Innovation: The Synthetic Control Method Applied to Tropical Deforestation.

PubMed

Sills, Erin O; Herrera, Diego; Kirkpatrick, A Justin; Brandão, Amintas; Dickson, Rebecca; Hall, Simon; Pattanayak, Subhrendu; Shoch, David; Vedoveto, Mariana; Young, Luisa; Pfaff, Alexander

2015-01-01

Quasi-experimental methods increasingly are used to evaluate the impacts of conservation interventions by generating credible estimates of counterfactual baselines. These methods generally require large samples for statistical comparisons, presenting a challenge for evaluating innovative policies implemented within a few pioneering jurisdictions. Single jurisdictions often are studied using comparative methods, which rely on analysts' selection of best case comparisons. The synthetic control method (SCM) offers one systematic and transparent way to select cases for comparison, from a sizeable pool, by focusing upon similarity in outcomes before the intervention. We explain SCM, then apply it to one local initiative to limit deforestation in the Brazilian Amazon. The municipality of Paragominas launched a multi-pronged local initiative in 2008 to maintain low deforestation while restoring economic production. This was a response to having been placed, due to high deforestation, on a federal "blacklist" that increased enforcement of forest regulations and restricted access to credit and output markets. The local initiative included mapping and monitoring of rural land plus promotion of economic alternatives compatible with low deforestation. The key motivation for the program may have been to reduce the costs of blacklisting. However its stated purpose was to limit deforestation, and thus we apply SCM to estimate what deforestation would have been in a (counterfactual) scenario of no local initiative. We obtain a plausible estimate, in that deforestation patterns before the intervention were similar in Paragominas and the synthetic control, which suggests that after several years, the initiative did lower deforestation (significantly below the synthetic control in 2012). This demonstrates that SCM can yield helpful land-use counterfactuals for single units, with opportunities to integrate local and expert knowledge and to test innovations and permutations on policies that are implemented in just a few locations.

Rare earth element mobility in vesicular lava during low-grade metamorphism

NASA Astrophysics Data System (ADS)

Nyström, Jan Olov

1984-12-01

A geochemical comparison of basaltic relicts and spilitic domains from two burial metamorphosed flows in central Chile, of similar original composition and rich and poor in amygdules, respectively, demonstrates a relationship between initial vesicularity and rare earth element (REE) mobility. During spilitization the REE were partly leached from permeable parts of the flows and precipitated in voids, now amygdules and veinlets. The REE (excluding Eu) moved coherently in the highly amygdaloidal flow: spilitic domains and amygdules inherited the basaltic REE pattern. Besides being characterized by a positive Eu anomaly, epidotes separated from amygdules have a REE distribution which mimics that of the basalt; the absolute contents range widely, suggesting local and/or temporal REE variations in the metamorphic fluids. Pumpellyite differs by being strongly enriched in heavy REE. Similar ratios of Th, Hf and Ta in samples as contrasting as relict basalt and a geode are consistent with coherent leaching. Coherent mobility, when established for a rock system, can be used to elucidate, for example, whether minerals in cross-cutting veins were formed by local redistribution or from introduced material.

A Local Fast Marching-Based Diffusion Tensor Image Registration Algorithm by Simultaneously Considering Spatial Deformation and Tensor Orientation

PubMed Central

Xue, Zhong; Li, Hai; Guo, Lei; Wong, Stephen T.C.

2010-01-01

It is a key step to spatially align diffusion tensor images (DTI) to quantitatively compare neural images obtained from different subjects or the same subject at different timepoints. Different from traditional scalar or multi-channel image registration methods, tensor orientation should be considered in DTI registration. Recently, several DTI registration methods have been proposed in the literature, but deformation fields are purely dependent on the tensor features not the whole tensor information. Other methods, such as the piece-wise affine transformation and the diffeomorphic non-linear registration algorithms, use analytical gradients of the registration objective functions by simultaneously considering the reorientation and deformation of tensors during the registration. However, only relatively local tensor information such as voxel-wise tensor-similarity, is utilized. This paper proposes a new DTI image registration algorithm, called local fast marching (FM)-based simultaneous registration. The algorithm not only considers the orientation of tensors during registration but also utilizes the neighborhood tensor information of each voxel to drive the deformation, and such neighborhood tensor information is extracted from a local fast marching algorithm around the voxels of interest. These local fast marching-based tensor features efficiently reflect the diffusion patterns around each voxel within a spherical neighborhood and can capture relatively distinctive features of the anatomical structures. Using simulated and real DTI human brain data the experimental results show that the proposed algorithm is more accurate compared with the FA-based registration and is more efficient than its counterpart, the neighborhood tensor similarity-based registration. PMID:20382233

Mercury sedimentation in lakes in western Whatcom County, Washington, USA and its relation to local industrial and municipal atmospheric sources

USGS Publications Warehouse

Paulson, A.J.; Norton, D.

2008-01-01

Concentrations of mercury (Hg) were measured in six dated cores from four lakes in western Whatcom County, Washington, USA, that were at various bearings from a chlor-alkali plant, two municipal waste incinerators and a municipal sewage sludge incinerator. The importance of atmospheric emissions of Hg from these local municipal and industrial sources was evaluating by comparing the temporal trends in sedimentation of the lake cores with the emission history of each Hg species and by examining the geographical distribution of Hg sedimentation in relation to the region's primary wind pattern. Local municipal and industrial sources of atmospheric Hg were not responsible for the majority of the Hg in the upper layer of sediments of Whatcom County lakes because of (1) the significant enrichment of Hg in lake sediments prior to emissions of local industrial and municipal sources in 1964, (2) smaller increases in Hg concentrations occurred after 1964, (3) the similarity of maximum enrichments found in Whatcom County lakes to those in rural lakes around the world, (4) the inconsistency of the temporal trends in Hg sedimentation with the local emission history, and (5) the inconsistency of the geographic trends in Hg sedimentation with estimated deposition. Maximum enrichment ratios of Hg in lake sediments between 2 and 3 that are similar to rural areas in Alaska, Minnesota, and New England suggest that global sources of Hg were primarily responsible for increases of Hg in Whatcom County lakes beginning about 1900. ?? 2007 GovernmentEmployee: U.S. Government, Department of Interior, U.S. Geological Survey.

Increasing use of radical prostatectomy for locally advanced prostate cancer in the USA and Germany: a comparative population-based study.

PubMed

Hager, B; Kraywinkel, K; Keck, B; Katalinic, A; Meyer, M; Zeissig, S R; Scheufele, R; Wirth, M P; Huber, J

2017-03-01

Current guidelines do not recommend a preferred treatment modality for locally advanced prostate cancer. The aim of the study was to compare treatment patterns found in the USA and Germany and to analyze possible trends over time. We compared 'Surveillance Epidemiology and End Results' (SEER) data (USA) with reports from four German federal epidemiological cancer registries (Eastern Germany, Bavaria, Rhineland-Palatinate, Schleswig-Holstein), both from 2004 to 2012. We defined locally advanced prostate cancer as clinical stage T3 or T4. Exclusion criteria were metastatic disease and age over 79 years. We identified 9127 (USA) and 11 051 (Germany) patients with locally advanced prostate cancer. The share was 2.1% in the USA compared with 6.0% in Germany (P<0.001). In the United States, the utilization of radiotherapy (RT) and radical prostatectomy (RP) was comparably high with 42.0% (RT) and 42.8% (RP). In Germany, the major treatment option was RP with 36.7% followed by RT with 22.1%. During the study period, the use of RP increased in both countries (USA P=0.001 and Germany P=0.003), whereas RT numbers declined (USA P=0.003 and Germany P=0.002). The share of adjuvant RT (aRT) was similar in both countries (USA 21.7% vs Germany 20.7%). We found distinctive differences in treating locally advanced prostate cancer between USA and Germany, but similar trends over time. In the last decade, a growing number of patients underwent RP as a possible first step within a multimodal concept.

Regional variations of organophosphorus flame retardants - Fingerprint of large river basin estuaries/deltas in Europe compared with China.

PubMed

Wolschke, Hendrik; Sühring, Roxana; Massei, Riccardo; Tang, Jianhui; Ebinghaus, Ralf

2018-05-01

This study reports the occurrence and distribution of organophosphorus flame retardants and plasticizer (OPEs) in sediments of eight large river basin estuaries and deltas across Europe. A robust and sensitive OPE analysis method was developed through the application of an in-cell clean-up in an accelerated solvent extraction and the use of an GC-MSMS System for instrumental analyses. OPEs were detected in all sediment samples with sum concentrations of up to 181 ng g -1 dw. A fingerprinting method was used to identify river specific pattern to compare river systems. The estuaries and deltas were chosen to have a conglomerate print of the whole river. The results are showing very similar OPE patterns across Europe with minor differences driven by local industrial input. The European estuary concentrations and patterns were compared with OPEs detected in the Xiaoquing River in China, as an example for a region with other production, usage and legislative regulations. The Chinese fingerprint differed significant from the overall European pattern. Copyright © 2018 Elsevier Ltd. All rights reserved.

Differences in the selection response of serially repeated color pattern characters: standing variation, development, and evolution.

PubMed

Allen, Cerisse E; Beldade, Patrícia; Zwaan, Bas J; Brakefield, Paul M

2008-03-26

There is spectacular morphological diversity in nature but lineages typically display a limited range of phenotypes. Because developmental processes generate the phenotypic variation that fuels natural selection, they are a likely source of evolutionary biases, facilitating some changes and limiting others. Although shifts in developmental regulation are associated with morphological differences between taxa, it is unclear how underlying mechanisms affect the rate and direction of evolutionary change within populations under selection. Here we focus on two ecologically relevant features of butterfly wing color patterns, eyespot size and color composition, which are similarly and strongly correlated across the serially repeated eyespots. Though these two characters show similar patterns of standing variation and covariation within a population, they differ in key features of their underlying development. We targeted pairs of eyespots with artificial selection for coordinated (concerted selection) versus independent (antagonistic selection) change in their color composition and size and compared evolutionary responses of the two color pattern characters. The two characters respond to selection in strikingly different ways despite initially similar patterns of variation in all directions present in the starting population. Size (determined by local properties of a diffusing inductive signal) evolves flexibly in all selected directions. However, color composition (determined by a tissue-level response to the signal concentration gradient) evolves only in the direction of coordinated change. There was no independent evolutionary change in the color composition of two eyespots in response to antagonistic selection. Moreover, these differences in the directions of short-term evolutionary change in eyespot size and color composition within a single species are consistent with the observed wing pattern diversity in the genus. Both characters respond rapidly to selection for coordinated change, but there are striking differences in their response to selection for antagonistic, independent change across eyespots. While many additional factors may contribute to both short- and long-term evolutionary response, we argue that the compartmentalization of developmental processes can influence the diversification of serial repeats such as butterfly eyespots, even under strong selection.

Spatial and temporal analyses of citrus sudden death as a tool to generate hypotheses concerning its etiology.

PubMed

Bassanezi, Renato B; Bergamin Filho, Armando; Amorim, Lilian; Gimenes-Fernandes, Nelson; Gottwald, Tim R; Bové, Joseph M

2003-04-01

ABSTRACT Citrus sudden death (CSD), a new disease of unknown etiology that affects sweet orange grafted on Rangpur lime, was visually monitored for 14 months in 41 groves in Brazil. Ordinary runs analysis of CSD-symptomatic trees indicated a departure from randomness of symptomatic trees status among immediately adjacent trees mainly within rows. The binomial index of dispersion (D) and the intraclass correlation (k) for various quadrat sizes suggested aggregation of CSD-symptomatic trees for almost all plots within the quadrat sizes tested. Estimated parameters of the binary form of Taylor's power law provided an overall measure of aggregation of CSD-symptomatic trees for all quadrat sizes tested. Aggregation in each plot was dependent on disease incidence. Spatial autocorrelation analysis of proximity patterns suggested that aggregation often existed among quadrats of various sizes up to three lag distances; however, significant lag positions discontinuous from main proximity patterns were rare, indicating a lack of spatial association among discrete foci. Some asymmetry was also detected for some spatial autocorrelation proximity patterns, indicating that within-row versus across-row distributions are not necessarily equivalent. These results were interpreted to mean that the cause of the disease was most likely biotic and its dissemination was common within a local area of influence that extended to approximately six trees in all directions, including adjacent trees. Where asymmetry was indicated, this area of influence was somewhat elliptical. Longer-distance patterns were not detected within the confines of the plot sizes tested. Annual rates of CSD progress based on the Gompertz model ranged from 0.37 to 2.02. Numerous similarities were found between the spatial patterns of CSD and Citrus tristeza virus (CTV) described in the literature, both in the presence of the aphid vector, Toxoptera citricida. CSD differs from CTV in that symptoms occur in sweet orange grafted on Rangpur lime. Based on the symptoms of CSD and on its spatial and temporal patterns, our hypothesis is that CSD may be caused by a similar but undescribed pathogen such as a virus and probably vectored by insects such as aphids by similar spatial processes to those affecting CTV.

Finger Vein Recognition Using Local Line Binary Pattern

PubMed Central

Rosdi, Bakhtiar Affendi; Shing, Chai Wuh; Suandi, Shahrel Azmin

2011-01-01

In this paper, a personal verification method using finger vein is presented. Finger vein can be considered more secured compared to other hands based biometric traits such as fingerprint and palm print because the features are inside the human body. In the proposed method, a new texture descriptor called local line binary pattern (LLBP) is utilized as feature extraction technique. The neighbourhood shape in LLBP is a straight line, unlike in local binary pattern (LBP) which is a square shape. Experimental results show that the proposed method using LLBP has better performance than the previous methods using LBP and local derivative pattern (LDP). PMID:22247670

Degeneration of oxidative muscle fibers in HTLV-1 tax transgenic mice.

PubMed

Nerenberg, M I; Wiley, C A

1989-12-01

The HTLV-1 tax gene under control of the HTLV-1 long terminal repeat (LTR) was introduced into transgenic mice. Previously tax protein expression in the muscle and peripheral nerves of three independent mouse lines was reported. Here the localization of this transgenic protein at a cellular and subcellular level is described. Tax protein was expressed in oxidative muscle fibers that developed severe progressive atrophy. It localized to the cytoplasma where it was associated with structures resembling degenerating Z bands. This pattern of muscle fiber involvement is similar to that observed in human retroviral associated myopathy. This transgenic mouse model suggests that preferential expression of the HTLV-1 viral promoter in oxidative muscle fibers may explain the productive infection of these fibers in HTLV-1 myopathy.

Identification of a Group's Physiological Synchronization with Earth's Magnetic Field.

PubMed

Timofejeva, Inga; McCraty, Rollin; Atkinson, Mike; Joffe, Roza; Vainoras, Alfonsas; Alabdulgader, Abdullah A; Ragulskis, Minvydas

2017-09-01

A new analysis technique for the evaluation of the degree of synchronization between the physiological state of a group of people and changes in the Earth's magnetic field based on their cardiac inter-beat intervals was developed and validated. The new analysis method was then used to identify clusters of similar synchronization patterns in a group of 20 individuals over a two-week period. The algorithm for the identification of slow wave dynamics for every person was constructed in order to determine meaningful interrelationships between the participants and the local magnetic field data. The results support the hypothesis that the slow wave rhythms in heart rate variability can synchronize with changes in local magnetic field data, and that the degree of synchronization is affected by the quality of interpersonal relationships.

Reconstructing the migration patterns of late Pleistocene mammals from northern Florida, USA

NASA Astrophysics Data System (ADS)

Hoppe, Kathryn A.; Koch, Paul L.

2007-11-01

We used analyses of the strontium isotope ( 87Sr/ 86Sr) ratios of tooth enamel to reconstruct the migration patterns of fossil mammals collected along the Aucilla River in northern Florida. Specimens date to the late-glacial period and before the last glacial maximum (pre-LGM). Deer and tapir displayed low 87Sr/ 86Sr ratios that were similar to the ratios of Florida environments, which suggest that these taxa did not migrate long distance outside of the Florida region. Mastodons, mammoths, and equids all displayed a wide range of 87Sr/ 86Sr ratios. Some individuals in each taxon displayed low 87Sr/ 86Sr ratios that suggest they ranged locally, while other animals had high 87Sr/ 86Sr ratios that suggest they migrated long distances (> 150 km) outside of the Florida region. Mastodons were the only taxa from this region that provided enough well-dated specimens to compare changes in migration patterns over time. Pre-LGM mastodons displayed significantly lower 87Sr/ 86Sr ratios than late-glacial mastodons, which suggests that late-glacial mastodons from Florida migrated longer distances than their earlier counterparts. This change in movement patterns reflects temporal changes in regional vegetation patterns.

Greenland coastal air temperatures linked to Baffin Bay and Greenland Sea ice conditions during autumn through regional blocking patterns

NASA Astrophysics Data System (ADS)

Ballinger, Thomas J.; Hanna, Edward; Hall, Richard J.; Miller, Jeffrey; Ribergaard, Mads H.; Høyer, Jacob L.

2018-01-01

Variations in sea ice freeze onset and regional sea surface temperatures (SSTs) in Baffin Bay and Greenland Sea are linked to autumn surface air temperatures (SATs) around coastal Greenland through 500 hPa blocking patterns, 1979-2014. We find strong, statistically significant correlations between Baffin Bay freeze onset and SSTs and SATs across the western and southernmost coastal areas, while weaker and fewer significant correlations are found between eastern SATs, SSTs, and freeze periods observed in the neighboring Greenland Sea. Autumn Greenland Blocking Index values and the incidence of meridional circulation patterns have increased over the modern sea ice monitoring era. Increased anticyclonic blocking patterns promote poleward transport of warm air from lower latitudes and local warm air advection onshore from ocean-atmosphere sensible heat exchange through ice-free or thin ice-covered seas bordering the coastal stations. Temperature composites by years of extreme late freeze conditions, occurring since 2006 in Baffin Bay, reveal positive monthly SAT departures that often exceed 1 standard deviation from the 1981-2010 climate normal over coastal areas that exhibit a similar spatial pattern as the peak correlations.

Trends in public perceptions and preferences on energy and environmental policy

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

Farhar, B.C.

1993-02-01

This report presents selected results from a secondary analysis of public opinion surveys, taken at the national and state/local levels, relevant to energy and environmental policy choices. The data base used in the analysis includes about 2000 items from nearly 600 separate surveys conducted between 1979 and 1992. Answers to word-for-word questions were traced over time, permitting trend analysis. Patterns of response were also identified for findings from similarly worded survey items. The analysis identifies changes in public opinion concerning energy during the past 10 to 15 years.

The two-dimensional pattern of metamorphic fluid flow at Mary Kathleen, Australia: Fluid focusing, transverse dispersion, and implications for modeling fluid flow

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

Cartwright, I.

The pattern of [delta][sup 18]O values in layered Corella calc-silicate rocks adjacent to a scapolitized metadolerite dike at Timberu in the Mary Kathleen fold belt illustrates some of the complexities of two-dimensional metamorphic fluid flow. Fluids flowing from the dike ([delta][sup 18]O = 9-10%) into the calc-silicate rocks lowered calcite [delta][sup 18]O values form 19-20% to as low as 10.3%. Time-integrate advectite fluid fluxes varied from 0.72 to > 8.1 m[sup 3]/m[sup 2] over a 4.5-m lateral distance, and there are two distinct channels of higher fluid flux. If the duration of fluid flow was similar across the outcrop, intrinsicmore » permeabilities varied laterally by at least an order of magnitude. Fluid flow was largely focused across lithological layering, with rare excursions parallel to layering, suggesting that (up to 1 m) to those at the isotopic front ([approximately]1.2 m), indicating that the coefficients of transverse and longitudinal dispersion are of similar orders of magnitude. Localities in other terrains probably show similar complex patterns of isotopic resetting that in two dimensions correspond to the predictions of the advective-dispersive transport models, but which are difficult to interpret using a one-dimensional analysis. Transverse dispersion during channeled fluid flow will potentially reset O-isotope ratios adjacent to the channels and cause decoupling of geochemical parameters during advective and dispersive transport. 43 refs., 5 figs., 2 tabs.« less

Experimental studies of high-accuracy RFID localization with channel impairments

NASA Astrophysics Data System (ADS)

Pauls, Eric; Zhang, Yimin D.

2015-05-01

Radio frequency identification (RFID) systems present an incredibly cost-effective and easy-to-implement solution to close-range localization. One of the important applications of a passive RFID system is to determine the reader position through multilateration based on the estimated distances between the reader and multiple distributed reference tags obtained from, e.g., the received signal strength indicator (RSSI) readings. In practice, the achievable accuracy of passive RFID reader localization suffers from many factors, such as the distorted RSSI reading due to channel impairments in terms of the susceptibility to reader antenna patterns and multipath propagation. Previous studies have shown that the accuracy of passive RFID localization can be significantly improved by properly modeling and compensating for such channel impairments. The objective of this paper is to report experimental study results that validate the effectiveness of such approaches for high-accuracy RFID localization. We also examine a number of practical issues arising in the underlying problem that limit the accuracy of reader-tag distance measurements and, therefore, the estimated reader localization. These issues include the variations in tag radiation characteristics for similar tags, effects of tag orientations, and reader RSS quantization and measurement errors. As such, this paper reveals valuable insights of the issues and solutions toward achieving high-accuracy passive RFID localization.

RhoA/ROCK pathway activity is essential for the correct localization of the germ plasm mRNAs in zebrafish embryos.

PubMed

Miranda-Rodríguez, Jerónimo Roberto; Salas-Vidal, Enrique; Lomelí, Hilda; Zurita, Mario; Schnabel, Denhi

2017-01-01

Zebrafish germ plasm is composed of mRNAs such as vasa and nanos and of proteins such as Bucky ball, all of which localize symmetrically in four aggregates at the distal region of the first two cleavage furrows. The coordination of actin microfilaments, microtubules and kinesin is essential for the correct localization of the germ plasm. Rho-GTPases, through their effectors, coordinate cytoskeletal dynamics. We address the participation of RhoA and its effector ROCK in germ plasm localization during the transition from two- to eight-cell embryos. We found that active RhoA is enriched along the cleavage furrow during the first two division cycles, whereas ROCK localizes at the distal region of the cleavage furrows in a similar pattern as the germ plasm mRNAs. Specific inhibition of RhoA and ROCK affected microtubules organization at the cleavage furrow; these caused the incorrect localization of the germ plasm mRNAs. The incorrect localization of the germ plasm led to a dramatic change in the number of germ cells during the blastula and 24hpf embryo stages without affecting any other developmental processes. We demonstrate that the Rho/ROCK pathway is intimately related to the determination of germ cells in zebrafish embryos. Copyright © 2016 Elsevier Inc. All rights reserved.

Weather patterns as a downscaling tool - evaluating their skill in stratifying local climate variables

NASA Astrophysics Data System (ADS)

Murawski, Aline; Bürger, Gerd; Vorogushyn, Sergiy; Merz, Bruno

2016-04-01

The use of a weather pattern based approach for downscaling of coarse, gridded atmospheric data, as usually obtained from the output of general circulation models (GCM), allows for investigating the impact of anthropogenic greenhouse gas emissions on fluxes and state variables of the hydrological cycle such as e.g. on runoff in large river catchments. Here we aim at attributing changes in high flows in the Rhine catchment to anthropogenic climate change. Therefore we run an objective classification scheme (simulated annealing and diversified randomisation - SANDRA, available from the cost733 classification software) on ERA20C reanalyses data and apply the established classification to GCMs from the CMIP5 project. After deriving weather pattern time series from GCM runs using forcing from all greenhouse gases (All-Hist) and using natural greenhouse gas forcing only (Nat-Hist), a weather generator will be employed to obtain climate data time series for the hydrological model. The parameters of the weather pattern classification (i.e. spatial extent, number of patterns, classification variables) need to be selected in a way that allows for good stratification of the meteorological variables that are of interest for the hydrological modelling. We evaluate the skill of the classification in stratifying meteorological data using a multi-variable approach. This allows for estimating the stratification skill for all meteorological variables together, not separately as usually done in existing similar work. The advantage of the multi-variable approach is to properly account for situations where e.g. two patterns are associated with similar mean daily temperature, but one pattern is dry while the other one is related to considerable amounts of precipitation. Thus, the separation of these two patterns would not be justified when considering temperature only, but is perfectly reasonable when accounting for precipitation as well. Besides that, the weather patterns derived from reanalyses data should be well represented in the All-Hist GCM runs in terms of e.g. frequency, seasonality, and persistence. In this contribution we show how to select the most appropriate weather pattern classification and how the classes derived from it are reflected in the GCMs.

Remote sensing image segmentation using local sparse structure constrained latent low rank representation

NASA Astrophysics Data System (ADS)

Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

2016-09-01

Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

Source localization of small sharp spikes: low resolution electromagnetic tomography (LORETA) reveals two distinct cortical sources.

PubMed

Zumsteg, Dominik; Andrade, Danielle M; Wennberg, Richard A

2006-06-01

We have investigated the cortical sources and electroencephalographic (EEG) characteristics of small sharp spikes (SSS) by using statistical non-parametric mapping (SNPM) of low resolution electromagnetic tomography (LORETA). We analyzed 7 SSS patterns (501 individual SSS) in 6 patients who underwent sleep EEG studies with 29 or 23 scalp electrodes. The scalp signals were averaged time-locked to the SSS peak activity and subjected to SNPM of LORETA values. All 7 SSS patterns (mean 72 individual SSS, range 11-200) revealed a very similar and highly characteristic transhemispheric oblique scalp voltage distribution comprising a first negative field maximum over ipsilateral lateral temporal areas, followed by a second negative field maximum over the contralateral subtemporal region approximately 30 ms later. SNPM-LORETA consistently localized the first component into the ipsilateral posterior insular region, and the second component into ipsilateral posterior mesial temporo-occipital structures. SSS comprise an amalgam of two sequential, distinct cortical components, showing a very uniform and peculiar EEG pattern and cortical source solutions. As such, they must be clearly distinguished from interictal epileptiform discharges in patients with epilepsy. The awareness of these peculiar EEG characteristics may increase our ability to differentiate SSS from interictal epileptiform activity. The finding of a posterior insular source might serve as an inspiration for new physiological considerations regarding these enigmatic waveforms.

Role of alveolar topology on acinar flows and convective mixing.

PubMed

Hofemeier, Philipp; Sznitman, Josué

2014-06-01

Due to experimental challenges, computational simulations are often sought to quantify inhaled aerosol transport in the pulmonary acinus. Commonly, these are performed using generic alveolar topologies, including spheres, toroids, and polyhedra, to mimic the complex acinar morphology. Yet, local acinar flows and ensuing particle transport are anticipated to be influenced by the specific morphological structures. We have assessed a range of acinar models under self-similar breathing conditions with respect to alveolar flow patterns, convective flow mixing, and deposition of fine particles (1.3 μm diameter). By tracking passive tracers over cumulative breathing cycles, we find that irreversible flow mixing correlates with the location and strength of the recirculating vortex inside the cavity. Such effects are strongest in proximal acinar generations where the ratio of alveolar to ductal flow rates is low and interalveolar disparities are most apparent. Our results for multi-alveolated acinar ducts highlight that fine 1 μm inhaled particles subject to alveolar flows are sensitive to the alveolar topology, underlining interalveolar disparities in particle deposition patterns. Despite the simplicity of the acinar models investigated, our findings suggest that alveolar topologies influence more significantly local flow patterns and deposition sites of fine particles for upper generations emphasizing the importance of the selected acinar model. In distal acinar generations, however, the alveolar geometry primarily needs to mimic the space-filling alveolar arrangement dictated by lung morphology.

Understanding human activity patterns based on space-time-semantics

NASA Astrophysics Data System (ADS)

Huang, Wei; Li, Songnian

2016-11-01

Understanding human activity patterns plays a key role in various applications in an urban environment, such as transportation planning and traffic forecasting, urban planning, public health and safety, and emergency response. Most existing studies in modeling human activity patterns mainly focus on spatiotemporal dimensions, which lacks consideration of underlying semantic context. In fact, what people do and discuss at some places, inferring what is happening at the places, cannot be simple neglected because it is the root of human mobility patterns. We believe that the geo-tagged semantic context, representing what individuals do and discuss at a place and a specific time, drives a formation of specific human activity pattern. In this paper, we aim to model human activity patterns not only based on space and time but also with consideration of associated semantics, and attempt to prove a hypothesis that similar mobility patterns may have different motivations. We develop a spatiotemporal-semantic model to quantitatively express human activity patterns based on topic models, leading to an analysis of space, time and semantics. A case study is conducted using Twitter data in Toronto based on our model. Through computing the similarities between users in terms of spatiotemporal pattern, semantic pattern and spatiotemporal-semantic pattern, we find that only a small number of users (2.72%) have very similar activity patterns, while the majority (87.14%) show different activity patterns (i.e., similar spatiotemporal patterns and different semantic patterns, similar semantic patterns and different spatiotemporal patterns, or different in both). The population of users that has very similar activity patterns is decreased by 56.41% after incorporating semantic information in the corresponding spatiotemporal patterns, which can quantitatively prove the hypothesis.

Reproducibility of data-driven dietary patterns in two groups of adult Spanish women from different studies.

PubMed

Castelló, Adela; Lope, Virginia; Vioque, Jesús; Santamariña, Carmen; Pedraz-Pingarrón, Carmen; Abad, Soledad; Ederra, Maria; Salas-Trejo, Dolores; Vidal, Carmen; Sánchez-Contador, Carmen; Aragonés, Nuria; Pérez-Gómez, Beatriz; Pollán, Marina

2016-08-01

The objective of the present study was to assess the reproducibility of data-driven dietary patterns in different samples extracted from similar populations. Dietary patterns were extracted by applying principal component analyses to the dietary information collected from a sample of 3550 women recruited from seven screening centres belonging to the Spanish breast cancer (BC) screening network (Determinants of Mammographic Density in Spain (DDM-Spain) study). The resulting patterns were compared with three dietary patterns obtained from a previous Spanish case-control study on female BC (Epidemiological study of the Spanish group for breast cancer research (GEICAM: grupo Español de investigación en cáncer de mama)) using the dietary intake data of 973 healthy participants. The level of agreement between patterns was determined using both the congruence coefficient (CC) between the pattern loadings (considering patterns with a CC≥0·85 as fairly similar) and the linear correlation between patterns scores (considering as fairly similar those patterns with a statistically significant correlation). The conclusions reached with both methods were compared. This is the first study exploring the reproducibility of data-driven patterns from two studies and the first using the CC to determine pattern similarity. We were able to reproduce the EpiGEICAM Western pattern in the DDM-Spain sample (CC=0·90). However, the reproducibility of the Prudent (CC=0·76) and Mediterranean (CC=0·77) patterns was not as good. The linear correlation between pattern scores was statistically significant in all cases, highlighting its arbitrariness for determining pattern similarity. We conclude that the reproducibility of widely prevalent dietary patterns is better than the reproducibility of more population-specific patterns. More methodological studies are needed to establish an objective measurement and threshold to determine pattern similarity.

Over-expression of thymosin β4 in granulomatous lung tissue with active pulmonary tuberculosis.

PubMed

Kang, Yun-Jeong; Jo, Jin-Ok; Ock, Mee Sun; Yoo, Young-Bin; Chun, Bong-Kwon; Oak, Chul-Ho; Cha, Hee-Jae

2014-05-01

Recent studies have shown that thymosin β4 (Tβ4) stimulates angiogenesis by inducing vascular endothelial growth factor (VEGF) expression and stabilizing hypoxia inducible factor-1α (HIF-1α) protein. Pulmonary tuberculosis (TB), a type of granulomatous disease, is accompanied by intense angiogenesis and VEGF levels have been reported to be elevated in serum or tissue inflamed by pulmonary tuberculosis. We investigated the expression of Tβ4 in granulomatous lung tissues at various stages of active pulmonary tuberculosis, and we also examined the expression patterns of VEGF and HIF-1α to compare their Tβ4 expression patterns in patients' tissues and in the tissue microarray of TB patients. Tβ4 was highly expressed in both granulomas and surrounding lymphocytes in nascent granulomatous lung tissue, but was expressed only surrounding tissues of necrotic or caseous necrotic regions. The expression pattern of HIF-1α was similar to that of Tβ4. VEGF was expressed in both granulomas and blood vessels surrounding granulomas. The expression pattern of VEGF co-localized with CD31 (platelet endothelial cell adhesion molecule, PECAM-1), a blood endothelial cell marker, and partially co-localized with Tβ4. However, the expression of Tβ4 did not co-localize with alveolar macrophages. Stained alveolar macrophages were present surrounding regions of granuloma highly expressing Tβ4. We also analyzed mRNA expression in the sputum of 10 normal and 19 pulmonary TB patients. Expression of Tβ4 was significantly higher in patients with pulmonary tuberculosis than in normal controls. These data suggest that Tβ4 is highly expressed in granulomatous lung tissue with active pulmonary TB and is associated with HIF-1α- and VEGF-mediated inflammation and angiogenesis. Furthermore, the expression of Tβ4 in the sputum of pulmonary tuberculosis patients can be used as a potential marker for diagnosis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Plasmodium knowlesi Skeleton-Binding Protein 1 Localizes to the ‘Sinton and Mulligan’ Stipplings in the Cytoplasm of Monkey and Human Erythrocytes

PubMed Central

Lucky, Amuza Byaruhanga; Sakaguchi, Miako; Katakai, Yuko; Kawai, Satoru; Yahata, Kazuhide; Templeton, Thomas J.

2016-01-01

The malaria parasite, Plasmodium, exports protein products to the infected erythrocyte to introduce modifications necessary for the establishment of nutrient acquisition and surface display of host interaction ligands. Erythrocyte remodeling impacts parasite virulence and disease pathology and is well documented for the human malaria parasite Plasmodium falciparum, but has been less described for other Plasmodium species. For P. falciparum, the exported protein skeleton-binding protein 1 (PfSBP1) is involved in the trafficking of erythrocyte surface ligands and localized to membranous structures within the infected erythrocyte, termed Maurer's clefts. In this study, we analyzed SBP1 orthologs across the Plasmodium genus by BLAST analysis and conserved gene synteny, which were also recently described by de Niz et al. (2016). To evaluate the localization of an SBP1 ortholog, we utilized the zoonotic malaria parasite, Plasmodium knowlesi. Immunofluorescence assay of transgenic P. knowlesi parasites expressing epitope-tagged recombinant PkSBP1 revealed a punctate staining pattern reminiscent of Maurer's clefts, following infection of either monkey or human erythrocytes. The recombinant PkSBP1-positive puncta co-localized with Giemsa-stained structures, known as ‘Sinton and Mulligan’ stipplings. Immunoelectron microscopy also showed that recombinant PkSBP1 localizes within or on the membranous structures akin to the Maurer's clefts. The recombinant PkSBP1 expressed in P. falciparum-infected erythrocytes co-localized with PfSBP1 at the Maurer's clefts, indicating an analogous trafficking pattern. A member of the P. knowlesi 2TM protein family was also expressed and localized to membranous structures in infected monkey erythrocytes. These results suggest that the trafficking machinery and induced erythrocyte cellular structures of P. knowlesi are similar following infection of both monkey and human erythrocytes, and are conserved with P. falciparum. PMID:27732628

Moral Reasoning Patterns and Influential Factors in the Context of Environmental Problems

ERIC Educational Resources Information Center

Tuncay, Busra; Yilmaz-Tuzun, Ozgul; Teksoz, Gaye Tuncer

2012-01-01

This study investigated pre-service science teachers' (PSTs') moral reasoning patterns and the factors underlying these reasoning patterns. Local and non-local environmental dilemmas were used to examine moral reasoning patterns. An explanatory design was used with the collection and analysis of quantitative data, which was subsequently refined…

Convergent evolution in the genetic basis of Müllerian mimicry in heliconius butterflies.

PubMed

Baxter, Simon W; Papa, Riccardo; Chamberlain, Nicola; Humphray, Sean J; Joron, Mathieu; Morrison, Clay; ffrench-Constant, Richard H; McMillan, W Owen; Jiggins, Chris D

2008-11-01

The neotropical butterflies Heliconius melpomene and H. erato are Müllerian mimics that display the same warningly colored wing patterns in local populations, yet pattern diversity between geographic regions. Linkage mapping has previously shown convergent red wing phenotypes in these species are controlled by loci on homologous chromosomes. Here, AFLP bulk segregant analysis using H. melpomene crosses identified genetic markers tightly linked to two red wing-patterning loci. These markers were used to screen a H. melpomene BAC library and a tile path was assembled spanning one locus completely and part of the second. Concurrently, a similar strategy was used to identify a BAC clone tightly linked to the locus controlling the mimetic red wing phenotypes in H. erato. A methionine rich storage protein (MRSP) gene was identified within this BAC clone, and comparative genetic mapping shows red wing color loci are in homologous regions of the genome of H. erato and H. melpomene. Subtle differences in these convergent phenotypes imply they evolved independently using somewhat different developmental routes, but are nonetheless regulated by the same switch locus. Genetic mapping of MRSP in a third related species, the "tiger" patterned H. numata, has no association with wing patterning and shows no evidence for genomic translocation of wing-patterning loci.

Cyclophilin A is a new M cell marker of bovine intestinal epithelium.

PubMed

Hondo, Tetsuya; Someya, Shunsuke; Nagasawa, Yuya; Terada, Shunsuke; Watanabe, Hitoshi; Chen, Xiangning; Watanabe, Kouichi; Ohwada, Shyuichi; Kitazawa, Haruki; Rose, Michael T; Nochi, Tomonori; Aso, Hisashi

2016-06-01

Microfold (M) cells in the follicle-associated epithelium (FAE) of Peyer's patches contribute to the mucosal immune response by the transcytosis of microorganisms. The mechanism by which M cells take up microorganisms, and the functional proteins by which they do this, are not clear. In order to explore one such protein, we developed a 2H5-F3 monoclonal antibody (2H5-F3 mAb) through its binding to bovine M cells, and identified the antibody reactive molecule as cyclophilin A (Cyp-A). The localization patterns of Cyp-A were very similar to the localization pattern of cytokeratin (CK) 18-positive M cells. Cyp-A was identified at the luminal surface of CK18-positive M cells in bovine jejunal and ileal FAE. The membranous localization of Cyp-A in the bovine intestinal cell line (BIE cells) increased as cells differentiated toward M cells, as determined by flow cytometry analysis. Additionally, BIE cells released Cyp-A to the extracellular space and the differentiation of BIE cells to M cells increased the secretion of Cyp-A, as determined by western blotting. Accordingly, Cyp-A may be localized in M cells in the small intestinal epithelium of cattle. The rise of the membranous localization and secretion of Cyp-A by differentiation toward M cells indicates that Cyp-A has an important role in the function of M cells. While Cyp-A of the M cell membrane may contribute to the uptake of viruses with peptidyl-prolyl cis-trans isomerase activity, in the extracellular space Cyp-A may work as a chemokine and contribute to the distribution of immuno-competent cells.

Similarities in butterfly emergence dates among populations suggest local adaptation to climate.

PubMed

Roy, David B; Oliver, Tom H; Botham, Marc S; Beckmann, Bjorn; Brereton, Tom; Dennis, Roger L H; Harrower, Colin; Phillimore, Albert B; Thomas, Jeremy A

2015-09-01

Phenology shifts are the most widely cited examples of the biological impact of climate change, yet there are few assessments of potential effects on the fitness of individual organisms or the persistence of populations. Despite extensive evidence of climate-driven advances in phenological events over recent decades, comparable patterns across species' geographic ranges have seldom been described. Even fewer studies have quantified concurrent spatial gradients and temporal trends between phenology and climate. Here we analyse a large data set (~129 000 phenology measures) over 37 years across the UK to provide the first phylogenetic comparative analysis of the relative roles of plasticity and local adaptation in generating spatial and temporal patterns in butterfly mean flight dates. Although populations of all species exhibit a plastic response to temperature, with adult emergence dates earlier in warmer years by an average of 6.4 days per °C, among-population differences are significantly lower on average, at 4.3 days per °C. Emergence dates of most species are more synchronised over their geographic range than is predicted by their relationship between mean flight date and temperature over time, suggesting local adaptation. Biological traits of species only weakly explained the variation in differences between space-temperature and time-temperature phenological responses, suggesting that multiple mechanisms may operate to maintain local adaptation. As niche models assume constant relationships between occurrence and environmental conditions across a species' entire range, an important implication of the temperature-mediated local adaptation detected here is that populations of insects are much more sensitive to future climate changes than current projections suggest. © 2015 The Authors. Global Change Biology published by John Wiley & Sons Ltd.

Medical image classification using spatial adjacent histogram based on adaptive local binary patterns.

PubMed

Liu, Dong; Wang, Shengsheng; Huang, Dezhi; Deng, Gang; Zeng, Fantao; Chen, Huiling

2016-05-01

Medical image recognition is an important task in both computer vision and computational biology. In the field of medical image classification, representing an image based on local binary patterns (LBP) descriptor has become popular. However, most existing LBP-based methods encode the binary patterns in a fixed neighborhood radius and ignore the spatial relationships among local patterns. The ignoring of the spatial relationships in the LBP will cause a poor performance in the process of capturing discriminative features for complex samples, such as medical images obtained by microscope. To address this problem, in this paper we propose a novel method to improve local binary patterns by assigning an adaptive neighborhood radius for each pixel. Based on these adaptive local binary patterns, we further propose a spatial adjacent histogram strategy to encode the micro-structures for image representation. An extensive set of evaluations are performed on four medical datasets which show that the proposed method significantly improves standard LBP and compares favorably with several other prevailing approaches. Copyright © 2016 Elsevier Ltd. All rights reserved.

Defects and spatiotemporal disorder in a pattern of falling liquid columns

NASA Astrophysics Data System (ADS)

Brunet, Philippe; Limat, Laurent

2004-10-01

Disordered regimes of a one-dimensional pattern of liquid columns hanging below an overflowing circular dish are investigated experimentally. The interaction of two basic dynamical modes (oscillations and drift) combined with the occurrence of defects (birth of new columns, disappearances by coalescences of two columns) leads to spatiotemporal chaos. When the flow rate is progressively increased, a continuous transition between transient and permanent chaos is pointed into evidence. We introduce the rate of defects as the sole relevant quantity to quantify this “turbulence” without ambiguity. Statistics on both transient and endlessly chaotic regimes enable to define a critical flow rate around which exponents are extracted. Comparisons are drawn with other interfacial pattern-forming systems, where transition towards chaos follows similar steps. Qualitatively, careful examinations of the global dynamics show that the contamination processes are nonlocal and involve the propagation of blocks of elementary laminar states (such as propagative domains or local oscillations), emitted near the defects, which turn out to be essential ingredients of this self-sustained disorder.

Patterns of particle distribution in multiparticle systems by random walks with memory enhancement and decay

NASA Astrophysics Data System (ADS)

Tan, Zhi-Jie; Zou, Xian-Wu; Huang, Sheng-You; Zhang, Wei; Jin, Zhun-Zhi

2002-07-01

We investigate the pattern of particle distribution and its evolution with time in multiparticle systems using the model of random walks with memory enhancement and decay. This model describes some biological intelligent walks. With decrease in the memory decay exponent α, the distribution of particles changes from a random dispersive pattern to a locally dense one, and then returns to the random one. Correspondingly, the fractal dimension Df,p characterizing the distribution of particle positions increases from a low value to a maximum and then decreases to the low one again. This is determined by the degree of overlap of regions consisting of sites with remanent information. The second moment of the density ρ(2) was introduced to investigate the inhomogeneity of the particle distribution. The dependence of ρ(2) on α is similar to that of Df,p on α. ρ(2) increases with time as a power law in the process of adjusting the particle distribution, and then ρ(2) tends to a stable equilibrium value.

Transdiagnostic differences in the resting-state functional connectivity of the prefrontal cortex in depression and schizophrenia.

PubMed

Chen, Xi; Liu, Chang; He, Hui; Chang, Xin; Jiang, Yuchao; Li, Yingjia; Duan, Mingjun; Li, Jianfu; Luo, Cheng; Yao, Dezhong

2017-08-01

Depression and schizophrenia are two of the most serious psychiatric disorders. They share similar symptoms but the pathology-specific commonalities and differences remain unknown. This study was conducted to acquire a full picture of the functional alterations in schizophrenia and depression patients. The resting-state fMRI data from 20 patients with schizophrenia, 20 patients with depression and 20 healthy control subjects were collected. A data-driven approach that included local functional connectivity density (FCD) analysis combined with multivariate pattern analysis (MVPA) was used to compare the three groups. Based on the results of the MVPA, the local FCD value in the orbitofrontal cortex (OFC) can differentiate depression patients from schizophrenia patients. The patients with depression had a higher local FCD value in the medial and anterior parts of the OFC than the subjects in the other two groups, which suggested altered abstract and reward reinforces processing in depression patients. Subsequent functional connectivity analysis indicated that the connection in the prefrontal cortex was significantly lower in people with schizophrenia compared to people with depression and healthy controls. The systematically different medications for schizophrenia and depression may have different effects on functional connectivity. These results suggested that the resting-state functional connectivity pattern in the prefrontal cortex may be a transdiagnostic difference between depression and schizophrenia patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Patterns and multi-scale drivers of phytoplankton species richness in temperate peri-urban lakes.

PubMed

Catherine, Arnaud; Selma, Maloufi; Mouillot, David; Troussellier, Marc; Bernard, Cécile

2016-07-15

Local species richness (SR) is a key characteristic affecting ecosystem functioning. Yet, the mechanisms regulating phytoplankton diversity in freshwater ecosystems are not fully understood, especially in peri-urban environments where anthropogenic pressures strongly impact the quality of aquatic ecosystems. To address this issue, we sampled the phytoplankton communities of 50 lakes in the Paris area (France) characterized by a large gradient of physico-chemical and catchment-scale characteristics. We used large phytoplankton datasets to describe phytoplankton diversity patterns and applied a machine-learning algorithm to test the degree to which species richness patterns are potentially controlled by environmental factors. Selected environmental factors were studied at two scales: the lake-scale (e.g. nutrients concentrations, water temperature, lake depth) and the catchment-scale (e.g. catchment, landscape and climate variables). Then, we used a variance partitioning approach to evaluate the interaction between lake-scale and catchment-scale variables in explaining local species richness. Finally, we analysed the residuals of predictive models to identify potential vectors of improvement of phytoplankton species richness predictive models. Lake-scale and catchment-scale drivers provided similar predictive accuracy of local species richness (R(2)=0.458 and 0.424, respectively). Both models suggested that seasonal temperature variations and nutrient supply strongly modulate local species richness. Integrating lake- and catchment-scale predictors in a single predictive model did not provide increased predictive accuracy; therefore suggesting that the catchment-scale model probably explains observed species richness variations through the impact of catchment-scale variables on in-lake water quality characteristics. Models based on catchment characteristics, which include simple and easy to obtain variables, provide a meaningful way of predicting phytoplankton species richness in temperate lakes. This approach may prove useful and cost-effective for the management and conservation of aquatic ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

The role of local sea surface temperature pattern changes in shaping climate change in the North Atlantic sector

NASA Astrophysics Data System (ADS)

Hand, Ralf; Keenlyside, Noel S.; Omrani, Nour-Eddine; Bader, Jürgen; Greatbatch, Richard J.

2018-03-01

Beside its global effects, climate change is manifested in many regionally pronounced features mainly resulting from changes in the oceanic and atmospheric circulation. Here we investigate the influence of the North Atlantic SST on shaping the winter-time response to global warming. Our results are based on a long-term climate projection with the Max Planck Institute Earth System Model (MPI-ESM) to investigate the influence of North Atlantic sea surface temperature pattern changes on shaping the atmospheric climate change signal. In sensitivity experiments with the model's atmospheric component we decompose the response into components controlled by the local SST structure and components controlled by global/remote changes. MPI-ESM simulates a global warming response in SST similar to other climate models: there is a warming minimum—or "warming hole"—in the subpolar North Atlantic, and the sharp SST gradients associated with the Gulf Stream and the North Atlantic Current shift northward by a few a degrees. Over the warming hole, global warming causes a relatively weak increase in rainfall. Beyond this, our experiments show more localized effects, likely resulting from future SST gradient changes in the North Atlantic. This includes a significant precipitation decrease to the south of the Gulf Stream despite increased underlying SSTs. Since this region is characterised by a strong band of precipitation in the current climate, this is contrary to the usual case that wet regions become wetter and dry regions become drier in a warmer climate. A moisture budget analysis identifies a complex interplay of various processes in the region of modified SST gradients: reduced surface winds cause a decrease in evaporation; and thermodynamic, modified atmospheric eddy transports, and coastal processes cause a change in the moisture convergence. The changes in the the North Atlantic storm track are mainly controlled by the non-regional changes in the forcing. The impact of the local SST pattern changes on regions outside the North Atlantic is small in our setup.

Extreme plasticity in thermoregulatory behaviors of free-ranging black-tailed prairie dogs

USGS Publications Warehouse

Lehmer, E.M.; Savage, L.T.; Antolin, M.F.; Biggins, D.E.

2006-01-01

In the natural environment, hibernating sciurids generally remain dormant during winter and enter numerous deep torpor bouts from the time of first immergence in fall until emergence in spring. In contrast, black-tailed prairie dogs (Cynomys ludovicianus) remain active throughout winter but periodically enter short and shallow bouts of torpor. While investigating body temperature (Tb) patterns of black-tailed prairie dogs from six separate colonies in northern Colorado, we observed one population that displayed torpor patterns resembling those commonly seen in hibernators. Five individuals in this population experienced multiple torpor bouts in immediate succession that increased in length and depth as winter progressed, whereas 16 prairie dogs in five neighboring colonies remained euthermic for the majority of winter and entered shallow bouts of torpor infrequently. Our results suggest that these differences in torpor patterns did not result from differences in the physiological indicators that we measured because the prairie dogs monitored had similar body masses and concentrations of stored lipids across seasons. Likewise, our results did not support the idea that differences in overwinter Tb patterns between prairie dogs in colonies with differing torpor patterns resulted from genetic differences between populations; genetic analyses of prairie dog colonies revealed high genetic similarity between the populations and implied that individuals regularly disperse between colonies. Local environmental conditions probably played a role in the unusual T b patterns experienced by prairie dogs in the colony where hibernation-like patterns were observed; this population received significantly less rainfall than neighboring colonies during the summer growing seasons before, during, and after the year of the winter in which they hibernated. Our study provides a rare example of extreme plasticity in thermoregulatory behaviors of free-ranging prairie dogs and provides evidence contrary to models that propose a clear delineation between homeothermy, facultative torpor, and hibernation. ?? 2006 by The University of Chicago. All rights reserved.

Oxygen isotope values in bone carbonate and collagen are consistently offset for New World monkeys.

PubMed

Crowley, Brooke Erin

2014-11-01

Stable oxygen isotopes are increasingly used in ecological research. Here, I present oxygen isotope (δ(18)O) values for bone carbonate and collagen from howler monkeys (Alouatta palliata), spider monkeys (Ateles geoffroyi) and capuchins (Cebus capucinus) from three localities in Costa Rica. There are apparent differences in δ(18)Ocarbonate and δ(18)Ocollagen among species. Monkeys from moist forest have significantly lower isotope values than those from drier localities. Because patterns are similar for both substrates, discrimination (Δ) between δ(18)Ocarbonate and δ(18)Ocollagen is relatively consistent among species and localities (17.6 ± 0.9‰). Although this value is larger than that previously obtained for laboratory rats, consistency among species and localities suggests it can be used to compare δ(18)Ocarbonate and δ(18)Ocollagen for monkeys, and potentially other medium-bodied mammals. Establishing discrimination for oxygen between these substrates for wild monkeys provides a foundation for future environmental and ecological research on modern and ancient organisms. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

The neglected nonlocal effects of deforestation

NASA Astrophysics Data System (ADS)

Winckler, Johannes; Reick, Christian; Pongratz, Julia

2017-04-01

Deforestation changes surface temperature locally via biogeophysical effects by changing the water, energy and momentum balance. Adding to these locally induced changes (local effects), deforestation at a given location can cause changes in temperature elsewhere (nonlocal effects). Most previous studies have not considered local and nonlocal effects separately, but investigated the total (local plus nonlocal) effects, for which global deforestation was found to cause a global mean cooling. Recent modeling and observational studies focused on the isolated local effects: The local effects are relevant for local living conditions, and they can be obtained from in-situ and satellite observations. Observational studies suggest that the local effects of potential deforestation cause a warming when averaged globally. This contrast between local warming and total cooling indicates that the nonlocal effects of deforestation are causing a cooling and thus counteract the local effects. It is still unclear how the nonlocal effects depend on the spatial scale of deforestation, and whether they still compensate the local warming in a more realistic spatial distribution of deforestation. To investigate this, we use a fully coupled climate model and separate local and nonlocal effects of deforestation in three steps: Starting from a forest world, we simulate deforestation in one out of four grid boxes using a regular spatial pattern and increase the number of deforestation grid boxes step-wise up to three out of four boxes in subsequent simulations. To compare these idealized spatial distributions of deforestation to a more realistic case, we separate local and nonlocal effects in a simulation where deforestation is applied in regions where it occurred historically. We find that the nonlocal effects scale nearly linearly with the number of deforested grid boxes, and the spatial distribution of the nonlocal effects is similar for the regular spatial distribution of deforestation and the more realistic pattern. Globally averaged, the deforestation-induced warming of the local effects is counteracted by the nonlocal effects, which are about three times as strong as the local effects (up to 0.1K local warming versus -0.3K nonlocal cooling). Thus, the nonlocal effects are more cooling than the local effects are warming, and this is valid not only for idealized simulations of large-scale deforestation, but also for a more realistic deforestation scenario. We conclude that the local effects of deforestation only yield an incomplete picture of the total climate effects by biogeophysical pathways. While the local effects capture the direct climatic response at the site of deforestation, the nonlocal effects have to be included if the biogeophysical effects of deforestation are considered for an implementation in climate policies.

Scorpion Biodiversity and Interslope Divergence at “Evolution Canyon”, Lower Nahal Oren Microsite, Mt. Carmel, Israel

PubMed Central

Raz, Shmuel; Retzkin, Sion; Pavlíček, Tomáš; Hoffman, Adam; Kimchi, Hagay; Beiles, Avigdor; Nevo, Eviatar

2009-01-01

Background Local natural laboratories, designated by us as the “Evolution Canyon” model, are excellent tools to study regional and global ecological dynamics across life. They present abiotic and biotic contrasts locally, permitting the pursuit of observations and experiments across diverse taxa sharing sharp microecological subdivisions. Higher solar radiation received by the “African savannah-like” south-facing slopes (AS) in canyons north of the equator than by the opposite “European maquis-like” north-facing slopes (ES) is associated with higher abiotic stress. Scorpions are a suitable taxon to study interslope biodiversity differences, associated with the differences in abiotic factors (climate, drought), due to their ability to adapt to dry environments. Methodology/Principal Findings Scorpions were studied by the turning stone method and by UV light methods. The pattern observed in scorpions was contrasted with similar patterns in several other taxa at the same place. As expected, the AS proved to be significantly more speciose regarding scorpions, paralleling the interslope patterns in taxa such as lizards and snakes, butterflies (Rhopalocera), beetles (families Tenebrionidae, Dermestidae, Chrysomelidae), and grasshoppers (Orthoptera). Conclusions/Significance Our results support an earlier conclusion stating that the homogenizing effects of migration and stochasticity are not able to eliminate the interslope intra- and interspecific differences in biodiversity despite an interslope distance of only 100 m at the “EC” valley bottom. In our opinion, the interslope microclimate selection, driven mainly by differences in insolance, could be the primary factor responsible for the observed interslope pattern. PMID:19357787

The glycoprotein character of multiple forms of Aspergillus polygalacturonase.

PubMed

Stratilová, E; Mislovicová, D; Kacuráková, M; Machová, E; Kolarová, N; Markovic, O; Jörnvall, H

1998-02-01

Comparisons of known primary structures of polygalacturonases show that extent and localization of potential N-glycosylation sites differ. Some sites are similar in position and adjacent to strictly conserved residues at the potential active site. The presence of N-acetylglucosamine and mannose in the molecules of two homogeneous, major Aspergillus sp. polygalacturonase forms was confirmed by IR spectroscopy. The purification method, based on interaction of the carbohydrate part with concanavalin A immobilized on chlorotriazine bead cellulose, was optimized. Deglycosylation with N-glycosidase F under denaturating and nondenaturating conditions led to molecular mass decreases followed by complete inactivation of the polygalacturonase enzyme activity. These results show the importance of glycosylation in these protein forms, while the comparative patterns establish both variability and some similarities in overall glycosylation architectures.

Sedimentology and preservation of aeolian sediments on steep terrains: Incipient sand ramps on the Atacama coast (northern Chile)

NASA Astrophysics Data System (ADS)

Ventra, Dario; Rodríguez-López, Juan Pedro; de Boer, Poppe L.

2017-05-01

The origin of topographically controlled aeolian landforms in high-relief settings is difficult to synthesize under general models, given the dependence of such accumulations on local morphology. Quaternary sand ramps have been linked to palaeoclimate, regional geomorphology and wind patterns; however, controls on the early development and preservation of such landforms are poorly known. This study describes the morphology and sedimentology of complex sedimentary aprons along steep coastal slopes in the Atacama Desert (Chile). Direct slope accessibility and continuous stratigraphic exposures enable comparisons between active processes and stratigraphic signatures. Stratigraphic facies distribution and its links with patterns of aeolian deposition show that the preservation of wind-laid sediments depends on the morphology and processes of specific slope sectors. The spatial organization of runoff depends on bedrock configuration and directly controls the permanence or erosion of aeolian sediment. The occurrence of either water or mass flows depends on the role of aeolian fines in the rheology of flash floods. In turn, the establishment of a rugged surface topography controlled by patterns of mass-flow deposition creates local accommodation for aeolian fines, sustaining the initial aggradation of a colluvial-aeolian system. By contrast, slopes subject to runoff develop a thin, extensive aeolian mantle whose featureless surface is subject mostly to sediment bypass down- and across-slope; the corresponding stratigraphic record comprises almost exclusively thin debris-flow and sheetflood deposits. Slope morphology and processes are fundamental in promoting or inhibiting aeolian aggradation in mountain settings. Long-term sand-ramp construction depends on climate and regional topography, but the initial development is probably controlled by local geomorphic factors. The observed interactions between wind and topography in the study area may also represent a process analogue for the interpretation of similar geomorphic features on Mars.

Airflow in Tracheobronchial Tree of Subjects with Tracheal Bronchus Simulated Using CT Image Based Models and CFD Method.

PubMed

Qi, Shouliang; Zhang, Baihua; Yue, Yong; Shen, Jing; Teng, Yueyang; Qian, Wei; Wu, Jianlin

2018-03-01

Tracheal Bronchus (TB) is a rare congenital anomaly characterized by the presence of an abnormal bronchus originating from the trachea or main bronchi and directed toward the upper lobe. The airflow pattern in tracheobronchial trees of TB subjects is critical, but has not been systemically studied. This study proposes to simulate the airflow using CT image based models and the computational fluid dynamics (CFD) method. Six TB subjects and three health controls (HC) are included. After the geometric model of tracheobronchial tree is extracted from CT images, the spatial distribution of velocity, wall pressure, wall shear stress (WSS) is obtained through CFD simulation, and the lobar distribution of air, flow pattern and global pressure drop are investigated. Compared with HC subjects, the main bronchus angle of TB subjects and the variation of volume are large, while the cross-sectional growth rate is small. High airflow velocity, wall pressure, and WSS are observed locally at the tracheal bronchus, but the global patterns of these measures are still similar to those of HC. The ratio of airflow into the tracheal bronchus accounts for 6.6-15.6% of the inhaled airflow, decreasing the ratio to the right upper lobe from 15.7-21.4% (HC) to 4.9-13.6%. The air into tracheal bronchus originates from the right dorsal near-wall region of the trachea. Tracheal bronchus does not change the global pressure drop which is dependent on multiple variables. Though the tracheobronchial trees of TB subjects present individualized features, several commonalities on the structural and airflow characteristics can be revealed. The observed local alternations might provide new insight into the reason of recurrent local infections, cough and acute respiratory distress related to TB.

Gene Expression and Metabolite Profiling of Developing Highbush Blueberry Fruit Indicates Transcriptional Regulation of Flavonoid Metabolism and Activation of Abscisic Acid Metabolism1[W][OA

PubMed Central

Zifkin, Michael; Jin, Alena; Ozga, Jocelyn A.; Zaharia, L. Irina; Schernthaner, Johann P.; Gesell, Andreas; Abrams, Suzanne R.; Kennedy, James A.; Constabel, C. Peter

2012-01-01

Highbush blueberry (Vaccinium corymbosum) fruits contain substantial quantities of flavonoids, which are implicated in a wide range of health benefits. Although the flavonoid constituents of ripe blueberries are known, the molecular genetics underlying their biosynthesis, localization, and changes that occur during development have not been investigated. Two expressed sequence tag libraries from ripening blueberry fruit were constructed as a resource for gene identification and quantitative real-time reverse transcription-polymerase chain reaction primer design. Gene expression profiling by quantitative real-time reverse transcription-polymerase chain reaction showed that flavonoid biosynthetic transcript abundance followed a tightly regulated biphasic pattern, and transcript profiles were consistent with the abundance of the three major classes of flavonoids. Proanthocyanidins (PAs) and corresponding biosynthetic transcripts encoding anthocyanidin reductase and leucoanthocyanidin reductase were most concentrated in young fruit and localized predominantly to the inner fruit tissue containing the seeds and placentae. Mean PA polymer length was seven to 8.5 subunits, linked predominantly via B-type linkages, and was relatively constant throughout development. Flavonol accumulation and localization patterns were similar to those of the PAs, and the B-ring hydroxylation pattern of both was correlated with flavonoid-3′-hydroxylase transcript abundance. By contrast, anthocyanins accumulated late in maturation, which coincided with a peak in flavonoid-3-O-glycosyltransferase and flavonoid-3′5′-hydroxylase transcripts. Transcripts of VcMYBPA1, which likely encodes an R2R3-MYB transcriptional regulator of PA synthesis, were prominent in both phases of development. Furthermore, the initiation of ripening was accompanied by a substantial rise in abscisic acid, a growth regulator that may be an important component of the ripening process and contribute to the regulation of blueberry flavonoid biosynthesis. PMID:22086422

Gene expression and metabolite profiling of developing highbush blueberry fruit indicates transcriptional regulation of flavonoid metabolism and activation of abscisic acid metabolism.

PubMed

Zifkin, Michael; Jin, Alena; Ozga, Jocelyn A; Zaharia, L Irina; Schernthaner, Johann P; Gesell, Andreas; Abrams, Suzanne R; Kennedy, James A; Constabel, C Peter

2012-01-01

Highbush blueberry (Vaccinium corymbosum) fruits contain substantial quantities of flavonoids, which are implicated in a wide range of health benefits. Although the flavonoid constituents of ripe blueberries are known, the molecular genetics underlying their biosynthesis, localization, and changes that occur during development have not been investigated. Two expressed sequence tag libraries from ripening blueberry fruit were constructed as a resource for gene identification and quantitative real-time reverse transcription-polymerase chain reaction primer design. Gene expression profiling by quantitative real-time reverse transcription-polymerase chain reaction showed that flavonoid biosynthetic transcript abundance followed a tightly regulated biphasic pattern, and transcript profiles were consistent with the abundance of the three major classes of flavonoids. Proanthocyanidins (PAs) and corresponding biosynthetic transcripts encoding anthocyanidin reductase and leucoanthocyanidin reductase were most concentrated in young fruit and localized predominantly to the inner fruit tissue containing the seeds and placentae. Mean PA polymer length was seven to 8.5 subunits, linked predominantly via B-type linkages, and was relatively constant throughout development. Flavonol accumulation and localization patterns were similar to those of the PAs, and the B-ring hydroxylation pattern of both was correlated with flavonoid-3'-hydroxylase transcript abundance. By contrast, anthocyanins accumulated late in maturation, which coincided with a peak in flavonoid-3-O-glycosyltransferase and flavonoid-3'5'-hydroxylase transcripts. Transcripts of VcMYBPA1, which likely encodes an R2R3-MYB transcriptional regulator of PA synthesis, were prominent in both phases of development. Furthermore, the initiation of ripening was accompanied by a substantial rise in abscisic acid, a growth regulator that may be an important component of the ripening process and contribute to the regulation of blueberry flavonoid biosynthesis.

Correlations between ventricular enlargement and gray and white matter volumes of cortex, thalamus, striatum, and internal capsule in schizophrenia.

PubMed

Horga, Guillermo; Bernacer, Javier; Dusi, Nicola; Entis, Jonathan; Chu, Kingwai; Hazlett, Erin A; Haznedar, M Mehmet; Kemether, Eileen; Byne, William; Buchsbaum, Monte S

2011-10-01

Ventricular enlargement is one of the most consistent abnormal structural brain findings in schizophrenia and has been used to infer brain shrinkage. However, whether ventricular enlargement is related to local overlying cortex and/or adjacent subcortical structures or whether it is related to brain volume change globally has not been assessed. We systematically assessed interrelations of ventricular volumes with gray and white matter volumes of 40 Brodmann areas (BAs), the thalamus and its medial dorsal nucleus and pulvinar, the internal capsule, caudate and putamen. We acquired structural MRI ( patients with schizophrenia (n = 64) and healthy controls (n = 56)) and diffusion tensor fractional anisotropy (FA) (untreated schizophrenia n = 19, controls n = 32). Volumes were assessed by manual tracing of central structures and a semi-automated parcellation of BAs. Patients with schizophrenia had increased ventricular size associated with decreased cortical gray matter volumes widely across the brain; a similar but less pronounced pattern was seen in normal controls; local correlations (e.g. temporal horn with temporal lobe volume) were not appreciably higher than non-local correlations (e.g. temporal horn with prefrontal volume). White matter regions adjacent to the ventricles similarly did not reveal strong regional relationships. FA and center of mass of the anterior limb of the internal capsule also appeared differentially influenced by ventricular volume but findings were similarly not regional. Taken together, these findings indicate that ventricular enlargement is globally interrelated with gray matter volume diminution but not directly correlated with volume loss in the immediately adjacent caudate, putamen, or internal capsule.

Localized-atlas-based segmentation of breast MRI in a decision-making framework.

PubMed

Fooladivanda, Aida; Shokouhi, Shahriar B; Ahmadinejad, Nasrin

2017-03-01

Breast-region segmentation is an important step for density estimation and Computer-Aided Diagnosis (CAD) systems in Magnetic Resonance Imaging (MRI). Detection of breast-chest wall boundary is often a difficult task due to similarity between gray-level values of fibroglandular tissue and pectoral muscle. This paper proposes a robust breast-region segmentation method which is applicable for both complex cases with fibroglandular tissue connected to the pectoral muscle, and simple cases with high contrast boundaries. We present a decision-making framework based on geometric features and support vector machine (SVM) to classify breasts in two main groups, complex and simple. For complex cases, breast segmentation is done using a combination of intensity-based and atlas-based techniques; however, only intensity-based operation is employed for simple cases. A novel atlas-based method, that is called localized-atlas, accomplishes the processes of atlas construction and registration based on the region of interest (ROI). Atlas-based segmentation is performed by relying on the chest wall template. Our approach is validated using a dataset of 210 cases. Based on similarity between automatic and manual segmentation results, the proposed method achieves Dice similarity coefficient, Jaccard coefficient, total overlap, false negative, and false positive values of 96.3, 92.9, 97.4, 2.61 and 4.77%, respectively. The localization error of the breast-chest wall boundary is 1.97 mm, in terms of averaged deviation distance. The achieved results prove that the suggested framework performs the breast segmentation with negligible errors and efficient computational time for different breasts from the viewpoints of size, shape, and density pattern.

Wildlife uses and hunting patterns in rural communities of the Yucatan Peninsula, Mexico.

PubMed

Santos-Fita, Dídac; Naranjo, Eduardo J; Rangel-Salazar, José Luis

2012-10-02

Subsistence hunting is a traditional practice providing food and many other goods for households in the Yucatan Peninsula, southeast Mexico. Economic, demographic, and cultural change in this region drive wildlife habitat loss and local extinctions. Improving our understanding about current practices of wildlife use may support better management strategies for conserving game species and their habitat. We aimed to evaluate if wildlife use remained relevant for the subsistence of rural residents of the Yucatan Peninsula, as well as if local hunting practices were related to environmental, geographical, and cultural factors. Fieldwork was done between March 2010 and March 2011. Information was obtained through conversations, interviews, and participant observation. Record forms allowed recording animals hunted, biomass extracted, distance intervals to hunting sites, habitat types and seasonality of wildlife harvests. Data were analyzed using one-way Analysis of Variance, and Generalized Linear Models. Forty-six terrestrial vertebrate species were used for obtaining food, medicine, tools, adornments, pets, ritual objects, and for sale and mitigating damage. We recorded 968 animals taken in 664 successful hunting events. The Great Curassow, Ocellated Turkey, paca, white-tailed deer, and collared peccary were the top harvested species, providing 80.7% of biomass (10,190 kg). The numbers of animals hunted and biomass extracted declined as hunting distances increased from villages. Average per capita consumption was 4.65 ± 2.7 kg/person/year. Hunting frequencies were similar in forested and agricultural areas. Wildlife use, hunting patterns, and technologies observed in our study sites were similar to those recorded in previous studies for rural Mayan and mestizo communities in the Yucatan Peninsula and other Neotropical sites. The most heavily hunted species were those providing more products and by-products for residents. Large birds such as the Great Curassow and the Ocellated Turkey were extremely important for local hunters, representing around 40% of total prey taken. Our results suggest that hunting is frequent in our study areas. Low human densities allow low hunting pressure on most game species and favor conservation of the tropical forest. We suggest that co-management may help regulating hunting, prioritizing cultural practices of sustainable use and conservation for benefiting local users and animal populations.

Local and global evaluation for remote sensing image segmentation

NASA Astrophysics Data System (ADS)

Su, Tengfei; Zhang, Shengwei

2017-08-01

In object-based image analysis, how to produce accurate segmentation is usually a very important issue that needs to be solved before image classification or target recognition. The study for segmentation evaluation method is key to solving this issue. Almost all of the existent evaluation strategies only focus on the global performance assessment. However, these methods are ineffective for the situation that two segmentation results with very similar overall performance have very different local error distributions. To overcome this problem, this paper presents an approach that can both locally and globally quantify segmentation incorrectness. In doing so, region-overlapping metrics are utilized to quantify each reference geo-object's over and under-segmentation error. These quantified error values are used to produce segmentation error maps which have effective illustrative power to delineate local segmentation error patterns. The error values for all of the reference geo-objects are aggregated through using area-weighted summation, so that global indicators can be derived. An experiment using two scenes of very different high resolution images showed that the global evaluation part of the proposed approach was almost as effective as other two global evaluation methods, and the local part was a useful complement to comparing different segmentation results.

A Local Agreement Pattern Measure Based on Hazard Functions for Survival Outcomes

PubMed Central

Dai, Tian; Guo, Ying; Peng, Limin; Manatunga, Amita K.

2017-01-01

Summary Assessing agreement is often of interest in biomedical and clinical research when measurements are obtained on the same subjects by different raters or methods. Most classical agreement methods have been focused on global summary statistics, which cannot be used to describe various local agreement patterns. The objective of this work is to study the local agreement pattern between two continuous measurements subject to censoring. In this paper, we propose a new agreement measure based on bivariate hazard functions to characterize the local agreement pattern between two correlated survival outcomes. The proposed measure naturally accommodates censored observations, fully captures the dependence structure between bivariate survival times and provides detailed information on how the strength of agreement evolves over time. We develop a nonparametric estimation method for the proposed local agreement pattern measure and study theoretical properties including strong consistency and asymptotical normality. We then evaluate the performance of the estimator through simulation studies and illustrate the method using a prostate cancer data example. PMID:28724196

A local agreement pattern measure based on hazard functions for survival outcomes.

PubMed

Dai, Tian; Guo, Ying; Peng, Limin; Manatunga, Amita K

2018-03-01

Assessing agreement is often of interest in biomedical and clinical research when measurements are obtained on the same subjects by different raters or methods. Most classical agreement methods have been focused on global summary statistics, which cannot be used to describe various local agreement patterns. The objective of this work is to study the local agreement pattern between two continuous measurements subject to censoring. In this article, we propose a new agreement measure based on bivariate hazard functions to characterize the local agreement pattern between two correlated survival outcomes. The proposed measure naturally accommodates censored observations, fully captures the dependence structure between bivariate survival times and provides detailed information on how the strength of agreement evolves over time. We develop a nonparametric estimation method for the proposed local agreement pattern measure and study theoretical properties including strong consistency and asymptotical normality. We then evaluate the performance of the estimator through simulation studies and illustrate the method using a prostate cancer data example. © 2017, The International Biometric Society.

Rethinking pattern formation in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Halatek, J.; Frey, E.

2018-05-01

The present theoretical framework for the analysis of pattern formation in complex systems is mostly limited to the vicinity of fixed (global) equilibria. Here we present a new theoretical approach to characterize dynamical states arbitrarily far from (global) equilibrium. We show that reaction-diffusion systems that are driven by locally mass-conserving interactions can be understood in terms of local equilibria of diffusively coupled compartments. Diffusive coupling generically induces lateral redistribution of the globally conserved quantities, and the variable local amounts of these quantities determine the local equilibria in each compartment. We find that, even far from global equilibrium, the system is well characterized by its moving local equilibria. We apply this framework to in vitro Min protein pattern formation, a paradigmatic model for biological pattern formation. Within our framework we can predict and explain transitions between chemical turbulence and order arbitrarily far from global equilibrium. Our results reveal conceptually new principles of self-organized pattern formation that may well govern diverse dynamical systems.

Box-Counting Dimension Revisited: Presenting an Efficient Method of Minimizing Quantization Error and an Assessment of the Self-Similarity of Structural Root Systems

PubMed Central

Bouda, Martin; Caplan, Joshua S.; Saiers, James E.

2016-01-01

Fractal dimension (FD), estimated by box-counting, is a metric used to characterize plant anatomical complexity or space-filling characteristic for a variety of purposes. The vast majority of published studies fail to evaluate the assumption of statistical self-similarity, which underpins the validity of the procedure. The box-counting procedure is also subject to error arising from arbitrary grid placement, known as quantization error (QE), which is strictly positive and varies as a function of scale, making it problematic for the procedure's slope estimation step. Previous studies either ignore QE or employ inefficient brute-force grid translations to reduce it. The goals of this study were to characterize the effect of QE due to translation and rotation on FD estimates, to provide an efficient method of reducing QE, and to evaluate the assumption of statistical self-similarity of coarse root datasets typical of those used in recent trait studies. Coarse root systems of 36 shrubs were digitized in 3D and subjected to box-counts. A pattern search algorithm was used to minimize QE by optimizing grid placement and its efficiency was compared to the brute force method. The degree of statistical self-similarity was evaluated using linear regression residuals and local slope estimates. QE, due to both grid position and orientation, was a significant source of error in FD estimates, but pattern search provided an efficient means of minimizing it. Pattern search had higher initial computational cost but converged on lower error values more efficiently than the commonly employed brute force method. Our representations of coarse root system digitizations did not exhibit details over a sufficient range of scales to be considered statistically self-similar and informatively approximated as fractals, suggesting a lack of sufficient ramification of the coarse root systems for reiteration to be thought of as a dominant force in their development. FD estimates did not characterize the scaling of our digitizations well: the scaling exponent was a function of scale. Our findings serve as a caution against applying FD under the assumption of statistical self-similarity without rigorously evaluating it first. PMID:26925073

Metazoan fish parasites of Macrourus berglax Lacepède, 1801 and other macrourids of the North Atlantic: Invasion of the deep sea from the continental shelf

NASA Astrophysics Data System (ADS)

Palm, H. W.; Klimpel, S.

2008-01-01

Between 2001 and 2003, a total of 105 Macrourus berglax Lacepède, 1801 were collected from Irminger Sea, at depths between 250 and 450 m, and were studied for parasites. Twenty-four different parasite species were identified. Nematodes (eight spp.) and digeneans (six spp.) were the most species rich, followed by crustaceans (four spp.), cestodes (three spp.), acanthocephalans (two spp.) and monogeneans (one sp.). Core species included the digenean Gonocerca phycidis (maximum 62.9% prevalence), the nematodes Anisakis sp. (62.9%), Capillaria gracilis (65.8%), Hysterothylacium aduncum (60.0%), Neoascarophis macrouri (88.6%), Spinitectus oviflagellis (82.9%), and the acanthocephalan Echinorhynchus gadi (97.1%). M. berglax was the final host for most of the parasites, and was infested with only a few larval forms. The species composition, diversity as well as the prevalence and intensity of infestation for most parasite species collected, were similar in the different years, indicating no distinct interannual variation at this deep-sea locality. Comparisons of the parasite fauna of M. berglax with macrourids belonging to the genera Macrourus, Coryphaenoides, Coelorhynchus and Nezumia revealed a similar infestation pattern amongst these deep-sea fish, consisting of the same or closely related species. This observation suggests that the parasite life-cycles in these benthopelagic deep-sea fishes follow similar pathways independent of geographical location. A similar habitat and food preference of macrourids results in a similar parasite fauna. The host specificity of some of the parasites is low, with most species (nine) infesting Teleostei, Gadiformes (six), Macrouridae (two), Macrourus spp. (one) and specifically M. berglax (five). Overlapping infestation patterns of M. berglax parasites with phylogenetically related gadiform fish from the continental shelf region suggest that the deep-sea parasite fauna in macrourids has evolved along with their hosts from parasite generalists that originated from the continental shelf. We propose that the parasite fauna of macrourids from the Mid-Atlantic Ridge harbours a similar parasite fauna and infestation pattern than that of macrourids from other parts of the world Oceans.

Metonymy as Referential Dependency: Psycholinguistic and Neurolinguistic Arguments for a Unified Linguistic Treatment.

PubMed

Piñango, Maria M; Zhang, Muye; Foster-Hanson, Emily; Negishi, Michiro; Lacadie, Cheryl; Constable, R Todd

2017-03-01

We examine metonymy at psycho- and neurolinguistic levels, seeking to adjudicate between two possible processing implementations (one- vs. two-mechanism). We compare highly conventionalized systematic metonymy (producer-for-product: "All freshmen read O'Connell") to lesser-conventionalized circumstantial metonymy ("[a waitress says to another:] 'Table 2 asked for more coffee."'). Whereas these two metonymy types differ in terms of contextual demands, they each reveal a similar dependency between the named and intended conceptual entities (e.g., Jackendoff, 1997; Nunberg, 1979, 1995). We reason that if each metonymy yields a distinct processing time course and substantially non-overlapping preferential localization pattern, it would not only support a two-mechanism view (one lexical, one pragmatic) but would suggest that conventionalization acts as a linguistic categorizer. By contrast, a similar behavior in time course and localization would support a one-mechanism view and the inference that conventionalization acts instead as a modulator of contextual felicitousness, and that differences in interpretation introduced by conventionalization are of degree, not of kind. Results from three paradigms: self-paced reading (SPR), event-related potentials (ERP), and functional magnetic resonance imaging (fMRI), reveal the following: no main effect by condition (metonymy vs. matched literal control) for either metonymy type immediately after the metonymy trigger, and a main effect for only the Circumstantial metonymy one word post-trigger (SPR); a N400 effect across metonymy types and a late positivity for Circumstantial metonymy (ERP); and a highly overlapping activation connecting the left ventrolateral prefrontal cortex and the left dorsolateral prefrontal cortex (fMRI). Altogether, the pattern observed does not reach the threshold required to justify a two-mechanism system. Instead, the pattern is more naturally (and conservatively) understood as resulting from the implementation of a generalized referential dependency mechanism, modulated by degree of context dependence/conventionalization, thus supporting architectures of language whereby "lexical" and "pragmatic" meaning relations are encoded along a cline of contextual underspecification. Copyright © 2016 Cognitive Science Society, Inc.

Quantifying spatial and temporal trends in beach-dune volumetric changes using spatial statistics

NASA Astrophysics Data System (ADS)

Eamer, Jordan B. R.; Walker, Ian J.

2013-06-01

Spatial statistics are generally underutilized in coastal geomorphology, despite offering great potential for identifying and quantifying spatial-temporal trends in landscape morphodynamics. In particular, local Moran's Ii provides a statistical framework for detecting clusters of significant change in an attribute (e.g., surface erosion or deposition) and quantifying how this changes over space and time. This study analyzes and interprets spatial-temporal patterns in sediment volume changes in a beach-foredune-transgressive dune complex following removal of invasive marram grass (Ammophila spp.). Results are derived by detecting significant changes in post-removal repeat DEMs derived from topographic surveys and airborne LiDAR. The study site was separated into discrete, linked geomorphic units (beach, foredune, transgressive dune complex) to facilitate sub-landscape scale analysis of volumetric change and sediment budget responses. Difference surfaces derived from a pixel-subtraction algorithm between interval DEMs and the LiDAR baseline DEM were filtered using the local Moran's Ii method and two different spatial weights (1.5 and 5 m) to detect statistically significant change. Moran's Ii results were compared with those derived from a more spatially uniform statistical method that uses a simpler student's t distribution threshold for change detection. Morphodynamic patterns and volumetric estimates were similar between the uniform geostatistical method and Moran's Ii at a spatial weight of 5 m while the smaller spatial weight (1.5 m) consistently indicated volumetric changes of less magnitude. The larger 5 m spatial weight was most representative of broader site morphodynamics and spatial patterns while the smaller spatial weight provided volumetric changes consistent with field observations. All methods showed foredune deflation immediately following removal with increased sediment volumes into the spring via deposition at the crest and on lobes in the lee, despite erosion on the stoss slope and dune toe. Generally, the foredune became wider by landward extension and the seaward slope recovered from erosion to a similar height and form to that of pre-restoration despite remaining essentially free of vegetation.

fMRI activation patterns in an analytic reasoning task: consistency with EEG source localization

NASA Astrophysics Data System (ADS)

Li, Bian; Vasanta, Kalyana C.; O'Boyle, Michael; Baker, Mary C.; Nutter, Brian; Mitra, Sunanda

2010-03-01

Functional magnetic resonance imaging (fMRI) is used to model brain activation patterns associated with various perceptual and cognitive processes as reflected by the hemodynamic (BOLD) response. While many sensory and motor tasks are associated with relatively simple activation patterns in localized regions, higher-order cognitive tasks may produce activity in many different brain areas involving complex neural circuitry. We applied a recently proposed probabilistic independent component analysis technique (PICA) to determine the true dimensionality of the fMRI data and used EEG localization to identify the common activated patterns (mapped as Brodmann areas) associated with a complex cognitive task like analytic reasoning. Our preliminary study suggests that a hybrid GLM/PICA analysis may reveal additional regions of activation (beyond simple GLM) that are consistent with electroencephalography (EEG) source localization patterns.

Patterns of Adherence of Helicobacter pylori Clinical Isolates to Epithelial Cells, and its Association with Disease and with Virulence Factors.

PubMed

Vázquez-Jiménez, Flor Elizabeth; Torres, Javier; Flores-Luna, Lourdes; Cerezo, Silvia Giono; Camorlinga-Ponce, Margarita

2016-02-01

Adherence to the gastric epithelium is one of the most important steps of Helicobacter pylori to remain and cause disease. The aim of this study was to analyze whether H. pylori isolates from patients with different gastroduodenal diseases present differences in the pattern of adherence to gastric epithelial cells (AGS), in the ability to induce IL-8, and in the presence of virulence genes. We tested 75 H. pylori strains isolated from nonatrophic gastritis, gastric cancer, and duodenal ulcer patients. The adhesion pattern and IL-8 induction were determined in AGS cells, and invasion of AGS cells was studied using a gentamicin protection assay. The IL-8 levels induced were determined by ELISA. Helicobacter pylori strains presented diffuse adherence (DA) and localized (LA) adherence patterns, similar to those described for enteropathogenic E. coli (EPEC), were observed in AGS cells. A DA pattern was observed in 57% and LA in 43% of the strains, and DA was more frequent in isolates from patients with gastric cancer (p = 0.044). Strains with a LA pattern induced higher levels of IL-8 (p = 0.042) in AGS cells. The adherence pattern was not associated with neither invasiveness nor with the presence of virulence genes. Our study shows that H. pylori strains present adherence patterns to AGS cells resembling those observed in EPEC and that these patterns may be associated with disease and with activity on AGS cells. © 2015 John Wiley & Sons Ltd.

Intrinsic physiological properties of rat retinal ganglion cells with a comparative analysis.

PubMed

Wong, Raymond C S; Cloherty, Shaun L; Ibbotson, Michael R; O'Brien, Brendan J

2012-10-01

Mammalian retina contains 15-20 different retinal ganglion cell (RGC) types, each of which is responsible for encoding different aspects of the visual scene. The encoding is defined by a combination of RGC synaptic inputs, the neurotransmitter systems used, and their intrinsic physiological properties. Each cell's intrinsic properties are defined by its morphology and membrane characteristics, including the complement and localization of the ion channels expressed. In this study, we examined the hypothesis that the intrinsic properties of individual RGC types are conserved among mammalian species. To do so, we measured the intrinsic properties of 16 morphologically defined rat RGC types and compared these data with cat RGC types. Our data demonstrate that in the rat different morphologically defined RGC types have distinct patterns of intrinsic properties. Variation in these properties across cell types was comparable to that found for cat RGC types. When presumed morphological homologs in rat and cat retina were compared directly, some RGC types had very similar properties. The rat A2 cell exhibited patterns of intrinsic properties nearly identical to the cat alpha cell. In contrast, rat D2 cells (ON-OFF directionally selective) had a very different pattern of intrinsic properties than the cat iota cell. Our data suggest that the intrinsic properties of RGCs with similar morphology and suspected visual function may be subject to variation due to the behavioral needs of the species.

Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms.

PubMed

Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

2017-01-01

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the "elements of metacommunity structure" analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.

Phenotypic Mismatches Reveal Escape from Arms-Race Coevolution

PubMed Central

Hanifin, Charles T; Brodie, Edmund D; Brodie, Edmund D

2008-01-01

Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race. PMID:18336073

TrackCC: A Practical Wireless Indoor Localization System Based on Less-Expensive Chips

PubMed Central

Li, Xiaolong; Zheng, Yan; Cai, Jun; Yi, Yunfei

2017-01-01

This paper aims at proposing a new wireless indoor localization system (ILS), called TrackCC, based on a commercial type of low-power system-on-chip (SoC), nRF24LE1. This type of chip has only l output power levels and acute fluctuation for a received minimum power level in operation, which give rise to many practical challenges for designing localization algorithms. In order to address these challenges, we exploit the Markov theory to construct a (l+1)×(l+1) -sized state transition matrix to remove the fluctuation, and then propose a priority-based pattern matching algorithm to search for the most similar match in the signal map to estimate the real position of unknown nodes. The experimental results show that, compared to two existing wireless ILSs, LANDMARC and SAIL, which have meter level positioning accuracy, the proposed TrackCC can achieve the decimeter level accuracy on average in both line-of-sight (LOS) and non-line-of-sight (NLOS) senarios. PMID:28617313

Fibrillatory conduction in branching atrial tissue--Insight from volumetric and monolayer computer models.

PubMed

Wieser, L; Fischer, G; Nowak, C N; Tilg, B

2007-05-01

Increased local load in branching atrial tissue (muscle fibers and bundle insertions) influences wave propagation during atrial fibrillation (AF). This computer model study reveals two principal phenomena: if the branching is distant from the driving rotor (>19 mm), the load causes local slowing of conduction or wavebreaks. If the driving rotor is close to the branching, the increased load causes first a slow drift of the rotor towards the branching. Finally, the rotor anchors, and a stable, repeatable pattern of activation can be observed. Variation of the bundle geometry from a cylindrical, volumetric structure to a flat strip of a comparable load in a monolayer model changed the local activation sequence in the proximity of the bundle. However, the global behavior and the basic effects are similar in all models. Wavebreaks in branching tissue contribute to the chaotic nature of AF (fibrillatory conduction). The stabilization (anchoring) of driving rotors by branching tissue might contribute to maintain sustained AF.

Quantum dot immunocytochemical localization of somatostatin in somatostatinoma by Widefield Epifluorescence, super-resolution light, and immunoelectron microscopy.

PubMed

Killingsworth, Murray C; Lai, Ken; Wu, Xiaojuan; Yong, Jim L C; Lee, C Soon

2012-11-01

Quantum dot nanocrystal probes (QDs) have been used for detection of somatostatin hormone in secretory granules of somatostatinoma tumor cells by immunofluorescence light microscopy, super-resolution light microscopy, and immunoelectron microscopy. Immunostaining for all modalities was done using sections taken from an epoxy resin-embedded tissue specimen and a similar labeling protocol. This approach allowed assessment of labeling at light microscopy level before examination at super-resolution and electron microscopy level and was a significant aid in interpretation. Etching of ultrathin sections with saturated sodium metaperiodate was a critical step presumably able to retrieve some tissue antigenicity masked by processing in epoxy resin. Immunofluorescence microscopy of QD-immunolabeled sections showed somatostatin hormone localization in cytoplasmic granules. Some variable staining of tumor gland-like structures appeared related to granule maturity and dispersal of granule contents within the tumor cell cytoplasm. Super-resolution light microscopy demonstrated localization of somatostatin within individual secretory granules to be heterogeneous, and this staining pattern was confirmed by immunoelectron microscopy.

Rolling Tobacco in Banana Leaves, Newspaper, or Copybook Paper Associated With Significant Reduction in Lung Function in Vanuatu.

PubMed

Weitz, Charles A; Olszowy, Kathryn M; Dancause, Kelsey N; Sun, Cheng; Pomer, Alysa; Silverman, Howard; Lee, G; Tarivonda, Len; Chan, Chim W; Kaneko, Akira; Lum, J K; Garruto, Ralph M

2017-04-01

In addition to the widespread availability of packaged cigarettes, the inhabitants of island nations of the Southwest Pacific frequently smoke commercially available loose tobacco using manufactured rolling papers, as well as locally grown tobacco rolled in manufactured rolling paper or wrapped in leaves, copybook paper, and newspaper. In this study, Vanuatu men who smoked local tobacco rolled in leaves, copybook paper, or newspaper showed significantly lower forced vital capacity (FVC), forced expiratory volume in 1 second (FEV 1 ), and FEV 1 /FVC ratios than men who smoked packaged cigarettes, store-bought tobacco rolled in manufactured rolling paper, or who smoked locally grown tobacco rolled in manufactured rolling papers. The addition of toxins from these unusual tobacco-wrapping media produces lung function deficits similar to the pattern noted among tobacco smokers who also inhale smoke from burning biomass. Thus, public health initiatives should consider including strategies addressing the use of wrapping media among smokers in South Pacific island societies.

Kinesiology tape mediates soccer-simulated and local peroneal fatigue in soccer players.

PubMed

Farquharson, Claire; Greig, Matt

2017-01-01

To investigate the efficacy of kinesiology taping in mediating the influence of fatigue on ankle sprain risk, 12 male soccer players completed single-leg dynamic balance trials pre- and post-exercise (soccer-specific protocol, isokinetic ankle inversion/eversion protocol) in each of three counter-balanced taping conditions (no tape, zinc oxide tape ZO, kinesiology tape KT). Balance was quantified as the overall stability index (OSI) and directional stability indices of platform deflection. Soccer-specific fatigue only increased OSI in the no tape condition (p = 0.03), with ZO and KT trials negating a fatigue affect. Localized fatigue increased OSI in the no tape (p = 0.01) and ZO (p = 0.05) trials, with no increase in the KT trial. A similar pattern was observed in medio-lateral and anterio-posterior balance indices. KT mediates soccer-simulated and local peroneal fatigue, with practical implications for epidemiological observations of increased injury risk during the latter stages of match play.

Selectivity of harvesting differs between local and foreign roe deer hunters: trophy stalkers have the first shot at the right place

PubMed Central

Mysterud, Atle; Tryjanowski, Piotr; Panek, Marek

2006-01-01

Harvesting represents a major source of mortality in many deer populations. The extent to which harvesting is selective for specific traits is important in order to understand contemporary evolutionary processes. In addition, since such data are frequently used in life-history studies, it is important to know the pattern of selectivity as a source of bias. Recently, it was demonstrated that different hunting methods were selected for different weights in red deer (Cervus elaphus), but little insight was offered into why this occurs. In this study, we show that foreign trophy stalkers select for larger antlers when hunting roe deer (Capreolus capreolus) than local hunters, but that close to half of the difference in selectivity was due to foreigners hunting earlier in the season and in locations with larger males. The relationship between antler size and age was nevertheless fairly similar based on whether deer was shot by foreign or local hunters. PMID:17148307

Quantum Dot Immunocytochemical Localization of Somatostatin in Somatostatinoma by Widefield Epifluorescence, Super-resolution Light, and Immunoelectron Microscopy

PubMed Central

Lai, Ken; Wu, Xiaojuan; Yong, Jim L. C.; Lee, C. Soon

2012-01-01

Quantum dot nanocrystal probes (QDs) have been used for detection of somatostatin hormone in secretory granules of somatostatinoma tumor cells by immunofluorescence light microscopy, super-resolution light microscopy, and immunoelectron microscopy. Immunostaining for all modalities was done using sections taken from an epoxy resin-embedded tissue specimen and a similar labeling protocol. This approach allowed assessment of labeling at light microscopy level before examination at super-resolution and electron microscopy level and was a significant aid in interpretation. Etching of ultrathin sections with saturated sodium metaperiodate was a critical step presumably able to retrieve some tissue antigenicity masked by processing in epoxy resin. Immunofluorescence microscopy of QD-immunolabeled sections showed somatostatin hormone localization in cytoplasmic granules. Some variable staining of tumor gland-like structures appeared related to granule maturity and dispersal of granule contents within the tumor cell cytoplasm. Super-resolution light microscopy demonstrated localization of somatostatin within individual secretory granules to be heterogeneous, and this staining pattern was confirmed by immunoelectron microscopy. PMID:22899862

Are the Stress Drops of Small Earthquakes Good Predictors of the Stress Drops of Larger Earthquakes?

NASA Astrophysics Data System (ADS)

Hardebeck, J.

2017-12-01

Uncertainty in PSHA could be reduced through better estimates of stress drop for possible future large earthquakes. Studies of small earthquakes find spatial variability in stress drop; if large earthquakes have similar spatial patterns, their stress drops may be better predicted using the stress drops of small local events. This regionalization implies the variance with respect to the local mean stress drop may be smaller than the variance with respect to the global mean. I test this idea using the Shearer et al. (2006) stress drop catalog for M1.5-3.1 events in southern California. I apply quality control (Hauksson, 2015) and remove near-field aftershocks (Wooddell & Abrahamson, 2014). The standard deviation of the distribution of the log10 stress drop is reduced from 0.45 (factor of 3) to 0.31 (factor of 2) by normalizing each event's stress drop by the local mean. I explore whether a similar variance reduction is possible when using the Shearer catalog to predict stress drops of larger southern California events. For catalogs of moderate-sized events (e.g. Kanamori, 1993; Mayeda & Walter, 1996; Boyd, 2017), normalizing by the Shearer catalog's local mean stress drop does not reduce the standard deviation compared to the unmodified stress drops. I compile stress drops of larger events from the literature, and identify 15 M5.5-7.5 earthquakes with at least three estimates. Because of the wide range of stress drop estimates for each event, and the different techniques and assumptions, it is difficult to assign a single stress drop value to each event. Instead, I compare the distributions of stress drop estimates for pairs of events, and test whether the means of the distributions are statistically significantly different. The events divide into 3 categories: low, medium, and high stress drop, with significant differences in mean stress drop between events in the low and the high stress drop categories. I test whether the spatial patterns of the Shearer catalog stress drops can predict the categories of the 15 events. I find that they cannot, rather the large event stress drops are uncorrelated with the local mean stress drop from the Shearer catalog. These results imply that the regionalization of stress drops of small events does not extend to the larger events, at least with current standard techniques of stress drop estimation.

Small-scale polygons on Mars

NASA Technical Reports Server (NTRS)

Lucchitta, B. K.

1984-01-01

Polygonal-fracture patterns on the martian surface were discovered on Viking Orbiter images. The polygons are 2-20 km in diameter, much larger than those of known patterned ground on Earth. New observations show, however, that polygons exist on Mars that have diameters similar to those of ice-wedge polygons on Earth (generally a few meters to more than 100 m). Various explanations for the origin of these crustal features are examined; seasonal desiccation and thermal-contraction cracking in ice-rich ground. It is difficult to ascertain whether the polygons are forming today or are relics from the past. The crispness of some crack suggests a recent origin. On the other hand the absence of upturned edges (indicating actively forming ice wedges), the locally disintegrating ground, and a few possible superposed rayed craters indicate that the polygons are not forming at the present.

Sampling of the Diurnal Cycle of Precipitation using TRMM

NASA Technical Reports Server (NTRS)

Negri, Andrew J.; Bell, Thomas L.; Xu, Li-Ming; Starr, David OC. (Technical Monitor)

2001-01-01

We examine the temporal sampling of tropical regions using observations from the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) and Precipitation Radar (PR). We conclude that PR estimates at any one hour, even using three years of data, are inadequate to describe the diurnal cycle of precipitation over regions smaller than 12 degrees, due to high spatial variability in sampling. We show that the optimum period of accumulation is four hours. Diurnal signatures display half as much sampling error when averaged over four hours of local time. A similar pattern of sampling variability is found in the TMI data, despite the TMI's wider swath and increased sampling. These results are verified using an orbital model. The sensitivity of the sampling to satellite altitude is presented, as well as sampling patterns at the new TRMM altitude of 402.5 km.

Systemic and local gut-specific antibody responses in preruminant calves sensitive to soya.

PubMed

Lallès, J P; Dréau, D; Huet, A; Toullec, R

1995-07-01

The systemic and local (gut) patterns of antibodies against various proteins from soyabean were analysed in preruminant calves fed milk substitutes based on skim milk powder (SMP) or heated soyabean flour (HSF) as the main protein sources. The titres of IgM, IgA, IgG1 and IgG2 antibodies were determined against feed extracts and purified soyabean proteins by dot-blotting in plasma after three months and jejunal mucous secretions after six months of feeding the experimental diets. The calves fed HSF had higher levels of circulating IgA, IgG1 and IgG2 antibodies against raw or heated soya extracts and purified proteins including alpha-conglycinin, beta-conglycinin, Bowman-Birk protease inhibitors and lectins than the calves fed SMP. In contrast, the differences between the IgM titres of the groups were most often not significant. The patterns of specific antibodies present in the jejunum were broadly similar to those observed in the blood, although the differences between the groups of calves more often reached significance for IgG2 and IgM than for IgA and IgG1, when the purified soyabean proteins were considered.

Brain activity across the development of automatic categorization: A comparison of categorization tasks using multi-voxel pattern analysis

PubMed Central

Soto, Fabian A.; Waldschmidt, Jennifer G.; Helie, Sebastien; Ashby, F. Gregory

2013-01-01

Previous evidence suggests that relatively separate neural networks underlie initial learning of rule-based and information-integration categorization tasks. With the development of automaticity, categorization behavior in both tasks becomes increasingly similar and exclusively related to activity in cortical regions. The present study uses multi-voxel pattern analysis to directly compare the development of automaticity in different categorization tasks. Each of three groups of participants received extensive training in a different categorization task: either an information-integration task, or one of two rule-based tasks. Four training sessions were performed inside an MRI scanner. Three different analyses were performed on the imaging data from a number of regions of interest (ROIs). The common patterns analysis had the goal of revealing ROIs with similar patterns of activation across tasks. The unique patterns analysis had the goal of revealing ROIs with dissimilar patterns of activation across tasks. The representational similarity analysis aimed at exploring (1) the similarity of category representations across ROIs and (2) how those patterns of similarities compared across tasks. The results showed that common patterns of activation were present in motor areas and basal ganglia early in training, but only in the former later on. Unique patterns were found in a variety of cortical and subcortical areas early in training, but they were dramatically reduced with training. Finally, patterns of representational similarity between brain regions became increasingly similar across tasks with the development of automaticity. PMID:23333700

Serbia within the European context: An analysis of premature mortality.

PubMed

Santric Milicevic, Milena; Bjegovic, Vesna; Terzic, Zorica; Vukovic, Dejana; Kocev, Nikola; Marinkovic, Jelena; Vasic, Vladimir

2009-08-05

Based on the global predictions majority of deaths will be collectively caused by cancer, cardiovascular diseases, and traffic accidents over the coming 25 years. In planning future national health policy actions, inter - regional assessments play an important role. The purpose of the study was to analyze similarities and differences in premature mortality between Serbia, EURO A, EURO B, and EURO C regions in 2000. Mortality and premature mortality patterns were analysed according to cause of death, by gender and seven age intervals. The study results are presented in relative (%) and absolute terms (age-specific and age-standardized death rates per 100,000 population, and age-standardized rates of years of life lost - YLL per 1,000). Direct standardization of rates was undertaken using the standard population of Europe. The inter-regional comparison was based on a calculation of differences in YLL structures and with a ratio of age-standardized YLL rates per 1,000. A multivariate generalized linear model was used to explore mortality of Serbia and Europe sub-regions with ln age-specific death rates. The dissimilarity was achieved with a p

Local and Global Auditory Processing: Behavioral and ERP Evidence

PubMed Central

Sanders, Lisa D.; Poeppel, David

2007-01-01

Differential processing of local and global visual features is well established. Global precedence effects, differences in event-related potentials (ERPs) elicited when attention is focused on local versus global levels, and hemispheric specialization for local and global features all indicate that relative scale of detail is an important distinction in visual processing. Observing analogous differential processing of local and global auditory information would suggest that scale of detail is a general organizational principle of the brain. However, to date the research on auditory local and global processing has primarily focused on music perception or on the perceptual analysis of relatively higher and lower frequencies. The study described here suggests that temporal aspects of auditory stimuli better capture the local-global distinction. By combining short (40 ms) frequency modulated tones in series to create global auditory patterns (500 ms), we independently varied whether pitch increased or decreased over short time spans (local) and longer time spans (global). Accuracy and reaction time measures revealed better performance for global judgments and asymmetric interference that were modulated by amount of pitch change. ERPs recorded while participants listened to identical sounds and indicated the direction of pitch change at the local or global levels provided evidence for differential processing similar to that found in ERP studies employing hierarchical visual stimuli. ERP measures failed to provide evidence for lateralization of local and global auditory perception, but differences in distributions suggest preferential processing in more ventral and dorsal areas respectively. PMID:17113115

Strong influence of regional species pools on continent-wide structuring of local communities.

PubMed

Lessard, Jean-Philippe; Borregaard, Michael K; Fordyce, James A; Rahbek, Carsten; Weiser, Michael D; Dunn, Robert R; Sanders, Nathan J

2012-01-22

There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.

Effectiveness of Radiotherapy in Myxoid Sarcomas Is Associated With a Dense Vascular Pattern

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

Vreeze, Ronald S.A. de; Jong, Daphne de; Haas, Rick L.

2008-12-01

Purpose: Surgery and adjuvant radiotherapy (RT) have long been the standard treatment for most deep-seated sarcomas; however, since the randomized trial from the National Cancer Institute of Canada, which described similar local control for pre- vs. postoperative RT, both modalities are now widely accepted. As a group, sarcomas are classified as radiation resistant. The subgroup of myxoid liposarcoma (MLS), a sarcoma with a typical vascular crow's feet pattern, is highly radiosensitive, but a mechanism for this phenomenon is unknown. Here we describe our results with preoperative RT and propose a mechanism explaining the high sensitivity based on the distinctive vascularizationmore » pattern of MLS. Methods and Materials: Between 2002 and 2006, 31 sarcoma patients, including 10 with MLS, underwent preoperative RT at our institute. Resected specimens were histologically evaluated, focusing on classification, grade, and vascularization patterns. Results: Twenty sarcomas showed more than 80% pathologic response after preoperative RT. A pathologic complete response was found in all 'pure' MLS specimens after preoperative RT (n = 8). There were no pathologic complete responses in the remaining sarcoma patients (n = 23), although 12 showed 80% to 90% pathologic response. In contrast to the remaining RT-resistant sarcomas, the highly responding specimens contained branching vasculature, partial thrombus formation and inflammation of medium sized arterioles, similar to the vascular changes in MLS. Conclusions: Both MLS and sarcomas with MLS-like vasculature are highly radiosensitive. Radiation sensitivity may be explained by changes in medium-sized arterioles, obstructing the specific crow's feet vascularization and inducing hypoxia with secondary tumor cell death.« less

Contrasting patterns of historical colonization in white oaks (Quercus spp.) in California and Europe.

PubMed

Grivet, Delphine; Deguilloux, Marie-France; Petit, Remy J; Sork, Victoria L

2006-11-01

Phylogeography allows the inference of evolutionary processes that have shaped the current distribution of genealogical lineages across a landscape. In this perspective, comparative phylogeographical analyses are useful in detecting common historical patterns by either comparing different species within the same area within a continent or by comparing similar species in different areas. Here, we analyse one taxon (the white oak, genus Quercus, subgenus Quercus, section Quercus) that is widespread worldwide, and we evaluate its phylogeographical pattern on two different continents: western North America and Western Europe. The goals of the present study are: (i) to compare the chloroplast genetic diversity found in one California oak species vs. that found in the extensively studied European oak species (in France and the Iberian Peninsula); (ii) to contrast the geographical structure of haplotypes between these two taxa and test for a phylogeographical structure for the California species. For this purpose, we used the same six maternally inherited chloroplast microsatellite markers and a similar sampling strategy. The haplotype diversity within site as well as the differentiation among sites was alike in both taxa, but the Californian species has higher allelic richness with a greater number of haplotypes (39 vs. 11 in the European white oak complex). Furthermore, in California these 39 haplotypes are distributed locally in patches while in the European oaks haplotypes are distributed into lineages partitioned longitudinally. These contrasted patterns could indicate that gene movement in California oak populations have been more stable in response to past climatic and geological events, in contrast to their European counterparts.

LOCAL VS. REGIONAL EFFECTS ON FISH DIVERSITY AS MEDIATED BY STREAMFLOW DISTURBANCE REGIME

EPA Science Inventory

abstract

The interplay of local and regional processes on fish diversity is poorly understood, especially related to patterns of streamflow disturbance regime. Articulation of the relationship between flow disturbance patterns and river fishes across local to regional scal...

Application of local binary pattern and human visual Fibonacci texture features for classification different medical images

NASA Astrophysics Data System (ADS)

Sanghavi, Foram; Agaian, Sos

2017-05-01

The goal of this paper is to (a) test the nuclei based Computer Aided Cancer Detection system using Human Visual based system on the histopathology images and (b) Compare the results of the proposed system with the Local Binary Pattern and modified Fibonacci -p pattern systems. The system performance is evaluated using different parameters such as accuracy, specificity, sensitivity, positive predictive value, and negative predictive value on 251 prostate histopathology images. The accuracy of 96.69% was observed for cancer detection using the proposed human visual based system compared to 87.42% and 94.70% observed for Local Binary patterns and the modified Fibonacci p patterns.

Palm Vein Verification Using Multiple Features and Locality Preserving Projections

PubMed Central

Bu, Wei; Wu, Xiangqian; Zhao, Qiushi

2014-01-01

Biometrics is defined as identifying people by their physiological characteristic, such as iris pattern, fingerprint, and face, or by some aspects of their behavior, such as voice, signature, and gesture. Considerable attention has been drawn on these issues during the last several decades. And many biometric systems for commercial applications have been successfully developed. Recently, the vein pattern biometric becomes increasingly attractive for its uniqueness, stability, and noninvasiveness. A vein pattern is the physical distribution structure of the blood vessels underneath a person's skin. The palm vein pattern is very ganglion and it shows a huge number of vessels. The attitude of the palm vein vessels stays in the same location for the whole life and its pattern is definitely unique. In our work, the matching filter method is proposed for the palm vein image enhancement. New palm vein features extraction methods, global feature extracted based on wavelet coefficients and locality preserving projections (WLPP), and local feature based on local binary pattern variance and locality preserving projections (LBPV_LPP) have been proposed. Finally, the nearest neighbour matching method has been proposed that verified the test palm vein images. The experimental result shows that the EER to the proposed method is 0.1378%. PMID:24693230

Palm vein verification using multiple features and locality preserving projections.

PubMed

Al-Juboori, Ali Mohsin; Bu, Wei; Wu, Xiangqian; Zhao, Qiushi

2014-01-01

Biometrics is defined as identifying people by their physiological characteristic, such as iris pattern, fingerprint, and face, or by some aspects of their behavior, such as voice, signature, and gesture. Considerable attention has been drawn on these issues during the last several decades. And many biometric systems for commercial applications have been successfully developed. Recently, the vein pattern biometric becomes increasingly attractive for its uniqueness, stability, and noninvasiveness. A vein pattern is the physical distribution structure of the blood vessels underneath a person's skin. The palm vein pattern is very ganglion and it shows a huge number of vessels. The attitude of the palm vein vessels stays in the same location for the whole life and its pattern is definitely unique. In our work, the matching filter method is proposed for the palm vein image enhancement. New palm vein features extraction methods, global feature extracted based on wavelet coefficients and locality preserving projections (WLPP), and local feature based on local binary pattern variance and locality preserving projections (LBPV_LPP) have been proposed. Finally, the nearest neighbour matching method has been proposed that verified the test palm vein images. The experimental result shows that the EER to the proposed method is 0.1378%.

Thermal motion of a nonlinear localized pattern in a quasi-one-dimensional system.

PubMed

Dessup, Tommy; Coste, Christophe; Saint Jean, Michel

2016-07-01

We study the dynamics of localized nonlinear patterns in a quasi-one-dimensional many-particle system near a subcritical pitchfork bifurcation. The normal form at the bifurcation is given and we show that these patterns can be described as solitary-wave envelopes. They are stable in a large temperature range and can diffuse along the chain of interacting particles. During their displacements the particles are continually redistributed on the envelope. This change of particle location induces a small modulation of the potential energy of the system, with an amplitude that depends on the transverse confinement. At high temperature, this modulation is irrelevant and the thermal motion of the localized patterns displays all the characteristics of a free quasiparticle diffusion with a diffusion coefficient that may be deduced from the normal form. At low temperature, significant physical effects are induced by the modulated potential. In particular, the localized pattern may be trapped at very low temperature. We also exhibit a series of confinement values for which the modulation amplitudes vanishes. For these peculiar confinements, the mean-square displacement of the localized patterns also evidences free-diffusion behavior at low temperature.

Local search to improve coordinate-based task mapping

DOE PAGES

Balzuweit, Evan; Bunde, David P.; Leung, Vitus J.; ...

2015-10-31

We present a local search strategy to improve the coordinate-based mapping of a parallel job’s tasks to the MPI ranks of its parallel allocation in order to reduce network congestion and the job’s communication time. The goal is to reduce the number of network hops between communicating pairs of ranks. Our target is applications with a nearest-neighbor stencil communication pattern running on mesh systems with non-contiguous processor allocation, such as Cray XE and XK Systems. Utilizing the miniGhost mini-app, which models the shock physics application CTH, we demonstrate that our strategy reduces application running time while also reducing the runtimemore » variability. Furthermore, we further show that mapping quality can vary based on the selected allocation algorithm, even between allocation algorithms of similar apparent quality.« less

Innate immune memory in plants.

PubMed

Reimer-Michalski, Eva-Maria; Conrath, Uwe

2016-08-01

The plant innate immune system comprises local and systemic immune responses. Systemic plant immunity develops after foliar infection by microbial pathogens, upon root colonization by certain microbes, or in response to physical injury. The systemic plant immune response to localized foliar infection is associated with elevated levels of pattern-recognition receptors, accumulation of dormant signaling enzymes, and alterations in chromatin state. Together, these systemic responses provide a memory to the initial infection by priming the remote leaves for enhanced defense and immunity to reinfection. The plant innate immune system thus builds immunological memory by utilizing mechanisms and components that are similar to those employed in the trained innate immune response of jawed vertebrates. Therefore, there seems to be conservation, or convergence, in the evolution of innate immune memory in plants and vertebrates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Patterning of leaf vein networks by convergent auxin transport pathways.

PubMed

Sawchuk, Megan G; Edgar, Alexander; Scarpella, Enrico

2013-01-01

The formation of leaf vein patterns has fascinated biologists for centuries. Transport of the plant signal auxin has long been implicated in vein patterning, but molecular details have remained unclear. Varied evidence suggests a central role for the plasma-membrane (PM)-localized PIN-FORMED1 (PIN1) intercellular auxin transporter of Arabidopsis thaliana in auxin-transport-dependent vein patterning. However, in contrast to the severe vein-pattern defects induced by auxin transport inhibitors, pin1 mutant leaves have only mild vein-pattern defects. These defects have been interpreted as evidence of redundancy between PIN1 and the other four PM-localized PIN proteins in vein patterning, redundancy that underlies many developmental processes. By contrast, we show here that vein patterning in the Arabidopsis leaf is controlled by two distinct and convergent auxin-transport pathways: intercellular auxin transport mediated by PM-localized PIN1 and intracellular auxin transport mediated by the evolutionarily older, endoplasmic-reticulum-localized PIN6, PIN8, and PIN5. PIN6 and PIN8 are expressed, as PIN1 and PIN5, at sites of vein formation. pin6 synthetically enhances pin1 vein-pattern defects, and pin8 quantitatively enhances pin1pin6 vein-pattern defects. Function of PIN6 is necessary, redundantly with that of PIN8, and sufficient to control auxin response levels, PIN1 expression, and vein network formation; and the vein pattern defects induced by ectopic PIN6 expression are mimicked by ectopic PIN8 expression. Finally, vein patterning functions of PIN6 and PIN8 are antagonized by PIN5 function. Our data define a new level of control of vein patterning, one with repercussions on other patterning processes in the plant, and suggest a mechanism to select cell files specialized for vascular function that predates evolution of PM-localized PIN proteins.

Similarity of Cortical Activity Patterns Predicts generalization Behavior

PubMed Central

Engineer, Crystal T.; Perez, Claudia A.; Carraway, Ryan S.; Chang, Kevin Q.; Roland, Jarod L.; Sloan, Andrew M.; Kilgard, Michael P.

2013-01-01

Humans and animals readily generalize previously learned knowledge to new situations. Determining similarity is critical for assigning category membership to a novel stimulus. We tested the hypothesis that category membership is initially encoded by the similarity of the activity pattern evoked by a novel stimulus to the patterns from known categories. We provide behavioral and neurophysiological evidence that activity patterns in primary auditory cortex contain sufficient information to explain behavioral categorization of novel speech sounds by rats. Our results suggest that category membership might be encoded by the similarity of the activity pattern evoked by a novel speech sound to the patterns evoked by known sounds. Categorization based on featureless pattern matching may represent a general neural mechanism for ensuring accurate generalization across sensory and cognitive systems. PMID:24147140

Spatial variation in egg size of a top predator: Interplay of body size and environmental factors?

NASA Astrophysics Data System (ADS)

Louzao, Maite; Igual, José M.; Genovart, Meritxell; Forero, Manuela G.; Hobson, Keith A.; Oro, Daniel

2008-09-01

It is expected that nearby populations are constrained by the same ecological features shaping in turn similarity in their ecological traits. Here, we studied the spatio-temporal variability in egg size among local populations of the critically endangered Balearic shearwater Puffinus mauretanicus, a top marine predator endemic to the western Mediterranean region. Specifically we assessed whether this trait was influenced by maternal body size, as an indicator of a genetic component, and feeding ecology (through stable-carbon and nitrogen-isotope measurements), as an indicator of environmental factors. We found that egg size varied among local populations, an unexpected result at such a small spatial scale. Body size differences at the local population level only partially explained such differences. Blood isotope measurements also differed among local populations. Values of δ 15N suggested inter-population differences in trophic level, showing a similar general pattern with egg size, and suggesting a nutritional link between them whereby egg size was affected by differences in feeding resources and/or behaviour. Values of δ 13C suggested that local populations did not differ in foraging habits with respect to benthic- vs. pelagic-based food-webs. Egg size did not vary among years as did breeding performance, suggesting that a differential temporal window could affect both breeding parameters in relation to food availability. The absence of a relationship between breeding performance and egg size suggested that larger eggs might only confer an advantage during harsh conditions. Alternatively parental quality could greatly affect breeding performance. We showed that inter-population differences in egg size could be influenced by both body size and environmental factors.

Waterfalls drive parallel evolution in a freshwater goby

PubMed Central

Kano, Yuichi; Nishida, Shin; Nakajima, Jun

2012-01-01

Waterfalls may affect fish distribution and genetic structure within drainage networks even to the extent of leading evolutionary events. Here, parallel evolution was studied by focusing on waterfall and the landlocked freshwater goby Rhinogobius sp. YB (YB), which evolved from amphidromous R. brunneus (BR). The fish fauna was surveyed at 30 sites in 11 rivers on Iriomote Island, Japan, the geography of which was characterized by terraces/tablelands with many waterfalls. We found that all YB individuals were distributed only above waterfalls (height 6.8–58.7 m), whereas BR, and other fishes, were mostly distributed below waterfalls. Mitochondrial DNA analysis showed that every YB local population above the waterfall was independently evolved from BR. In contrast, cluster analysis of nine morphological characters, such as fin color and body pattern, showed that the morphology of YB individuals held a similarity beyond the genetic divergence, suggesting parallel evolution has occurred relating to their morphology. Genetic distance between each YB local population and BR was significantly correlated with waterfall height (r2 = 0.94), suggesting that the waterfalls have been heightened due to the constant geological erosion and that their height represents the isolation period of YB local populations from BR (ca. 11,000–88,000 years). Each local population of BR was once landlocked in upstream by waterfall formation, consequently evolving to YB in each site. Although the morphology of YB had a high degree of similarity among local populations, finer scale analysis showed that the morphology of YB was significantly correlated with the genetic distance from BR. Consequently, there could be simultaneous multiple phases of allopatric/parallel evolution of the goby due to variations in waterfall height on this small island. PMID:22957183

A coarse-to-fine kernel matching approach for mean-shift based visual tracking

NASA Astrophysics Data System (ADS)

Liangfu, L.; Zuren, F.; Weidong, C.; Ming, J.

2009-03-01

Mean shift is an efficient pattern match algorithm. It is widely used in visual tracking fields since it need not perform whole search in the image space. It employs gradient optimization method to reduce the time of feature matching and realize rapid object localization, and uses Bhattacharyya coefficient as the similarity measure between object template and candidate template. This thesis presents a mean shift algorithm based on coarse-to-fine search for the best kernel matching. This paper researches for object tracking with large motion area based on mean shift. To realize efficient tracking of such an object, we present a kernel matching method from coarseness to fine. If the motion areas of the object between two frames are very large and they are not overlapped in image space, then the traditional mean shift method can only obtain local optimal value by iterative computing in the old object window area, so the real tracking position cannot be obtained and the object tracking will be disabled. Our proposed algorithm can efficiently use a similarity measure function to realize the rough location of motion object, then use mean shift method to obtain the accurate local optimal value by iterative computing, which successfully realizes object tracking with large motion. Experimental results show its good performance in accuracy and speed when compared with background-weighted histogram algorithm in the literature.

Geographical genetics of Pseudoplatystoma punctifer (Castelnau, 1855) (Siluriformes, Pimelodidae) in the Amazon Basin.

PubMed

Telles, M P C; Collevatti, R G; Braga, R S; Guedes, L B S; Castro, T G; Costa, M C; Silva-Júnior, N J; Barthem, R B; Diniz-Filho, J A F

2014-05-09

Geographical genetics allows the evaluation of evolutionary processes underlying genetic variation within and among local populations and forms the basis for establishing more effective strategies for biodiversity conservation at the population level. In this study, we used explicit spatial analyses to investigate molecular genetic variation (estimated using 7 microsatellite markers) of Pseudoplatystoma punctifer, by using samples obtained from 15 localities along the Madeira River and Solimões, Amazon Basin. A high genetic diversity was observed associated with a relatively low FST (0.057; P < 0.001), but pairwise FST values ranged from zero up to 0.21 when some pairs of populations were compared. These FST values have a relatively low correlation with geographic distances (r = 0.343; P = 0.074 by Mantel test), but a Mantel correlogram revealed that close populations (up to 80 km) tended to be more similar than expected by chance (r = 0.360; P = 0.015). The correlogram also showed a exponential-like decrease of genetic similarity with distance, with a patch-size of around 200 km, compatible with isolation-by-distance and analogous processes related to local constraints of dispersal and spatially structured levels of gene flow. The pattern revealed herein has important implications for establishing strategies to maintain genetic diversity in the species, especially considering the threats due to human impacts caused by building large dams in this river system.

Cholera and shigellosis in Bangladesh: similarities and differences in population dynamics under climate forcing

NASA Astrophysics Data System (ADS)

Pascual, M.; Cash, B.; Reiner, R.; King, A.; Emch, M.; Yunus, M.; Faruque, A. S.

2012-12-01

The influence of climate variability on the population dynamics of infectious diseases is considered a large scale, regional, phenomenon, and as such, has been previously addressed for cholera with temporal models that do not incorporate fine-scale spatial structure. In our previous work, evidence for a role of ENSO (El Niño Southern Oscillation) on cholera in Bangladesh was elucidated, and shown to influence the regional climate through precipitation. With a probabilistic spatial model for cholera dynamics in the megacity of Dhaka, we found that the action of climate variability (ENSO and flooding) is localized: there is a climate-sensitive urban core that acts to propagate risk to the rest of the city. Here, we consider long-term surveillance data for shigellosis, another diarrheal disease that coexists with cholera in Bangladesh. We compare the patterns of association with climate variables for these two diseases in a rural setting, as well as the spatial structure in their spatio-temporal dynamics in an urban one. Evidence for similar patterns is presented, and discussed in the context of the differences in the routes of transmission of the two diseases and the proposed role of an environmental reservoir in cholera. The similarities provide evidence for a more general influence of hydrology and of socio-economic factors underlying human susceptibility and sanitary conditions.

A modeling comparison of projection neuron- and neuromodulator-elicited oscillations in a central pattern generating network.

PubMed

Kintos, Nickolas; Nusbaum, Michael P; Nadim, Farzan

2008-06-01

Many central pattern generating networks are influenced by synaptic input from modulatory projection neurons. The network response to a projection neuron is sometimes mimicked by bath applying the neuronally-released modulator, despite the absence of network interactions with the projection neuron. One interesting example occurs in the crab stomatogastric ganglion (STG), where bath applying the neuropeptide pyrokinin (PK) elicits a gastric mill rhythm which is similar to that elicited by the projection neuron modulatory commissural neuron 1 (MCN1), despite the absence of PK in MCN1 and the fact that MCN1 is not active during the PK-elicited rhythm. MCN1 terminals have fast and slow synaptic actions on the gastric mill network and are presynaptically inhibited by this network in the STG. These local connections are inactive in the PK-elicited rhythm, and the mechanism underlying this rhythm is unknown. We use mathematical and biophysically-realistic modeling to propose potential mechanisms by which PK can elicit a gastric mill rhythm that is similar to the MCN1-elicited rhythm. We analyze slow-wave network oscillations using simplified mathematical models and, in parallel, develop biophysically-realistic models that account for fast, action potential-driven oscillations and some spatial structure of the network neurons. Our results illustrate how the actions of bath-applied neuromodulators can mimic those of descending projection neurons through mathematically similar but physiologically distinct mechanisms.

Variation in the Structure of Bird Nests between Northern Manitoba and Southeastern Ontario

PubMed Central

Crossman, Carla A.; Rohwer, Vanya G.; Martin, Paul R.

2011-01-01

Traits that converge in appearance under similar environmental conditions among phylogenetically independent lineages are thought to represent adaptations to local environments. We tested for convergence in nest morphology and composition of birds breeding in two ecologically different locations in Canada: Churchill in northern Manitoba and Elgin in southeastern Ontario. We examined nests from four families of passerine birds (Turdidae: Turdus, Parulidae: Dendroica, Emberizidae: Passerculus and Fringillidae: Carduelis) where closely related populations or species breed in both locations. Nests of American Robins, Yellow Warblers, and Carduelis finches had heavier nest masses, and tended to have thicker nest-walls, in northern Manitoba compared with conspecifics or congenerics breeding in southeastern Ontario. Together, all species showed evidence for wider internal and external nest-cup diameters in northern Manitoba, while individual species showed varying patterns for internal nest-cup and external nest depths. American Robins, Yellow Warblers, and Carduelis finches in northern Manitoba achieved heavier nest masses in different ways. American Robins increased all materials in similar proportions, and Yellow Warblers and Common Redpolls used greater amounts of select materials. While changes in nest composition vary uniquely for each species, the pattern of larger nests in northern Manitoba compared to southeastern Ontario in three of our four phylogenetically-independent comparisons suggests that birds are adapting to similar selective pressures between locations. PMID:21552515

Genealogical correspondence of a forebrain centre implies an executive brain in the protostome–deuterostome bilaterian ancestor

PubMed Central

2016-01-01

Orthologous genes involved in the formation of proteins associated with memory acquisition are similarly expressed in forebrain centres that exhibit similar cognitive properties. These proteins include cAMP-dependent protein kinase A catalytic subunit (PKA-Cα) and phosphorylated Ca2+/calmodulin-dependent protein kinase II (pCaMKII), both required for long-term memory formation which is enriched in rodent hippocampus and insect mushroom bodies, both implicated in allocentric memory and both possessing corresponding neuronal architectures. Antibodies against these proteins resolve forebrain centres, or their equivalents, having the same ground pattern of neuronal organization in species across five phyla. The ground pattern is defined by olfactory or chemosensory afferents supplying systems of parallel fibres of intrinsic neurons intersected by orthogonal domains of afferent and efferent arborizations with local interneurons providing feedback loops. The totality of shared characters implies a deep origin in the protostome–deuterostome bilaterian ancestor of elements of a learning and memory circuit. Proxies for such an ancestral taxon are simple extant bilaterians, particularly acoels that express PKA-Cα and pCaMKII in discrete anterior domains that can be properly referred to as brains. PMID:26598732

Dealing with gene expression missing data.

PubMed

Brás, L P; Menezes, J C

2006-05-01

Compared evaluation of different methods is presented for estimating missing values in microarray data: weighted K-nearest neighbours imputation (KNNimpute), regression-based methods such as local least squares imputation (LLSimpute) and partial least squares imputation (PLSimpute) and Bayesian principal component analysis (BPCA). The influence in prediction accuracy of some factors, such as methods' parameters, type of data relationships used in the estimation process (i.e. row-wise, column-wise or both), missing rate and pattern and type of experiment [time series (TS), non-time series (NTS) or mixed (MIX) experiments] is elucidated. Improvements based on the iterative use of data (iterative LLS and PLS imputation--ILLSimpute and IPLSimpute), the need to perform initial imputations (modified PLS and Helland PLS imputation--MPLSimpute and HPLSimpute) and the type of relationships employed (KNNarray, LLSarray, HPLSarray and alternating PLS--APLSimpute) are proposed. Overall, it is shown that data set properties (type of experiment, missing rate and pattern) affect the data similarity structure, therefore influencing the methods' performance. LLSimpute and ILLSimpute are preferable in the presence of data with a stronger similarity structure (TS and MIX experiments), whereas PLS-based methods (MPLSimpute, IPLSimpute and APLSimpute) are preferable when estimating NTS missing data.

Tilt aftereffect following adaptation to translational Glass patterns

PubMed Central

Pavan, Andrea; Hocketstaller, Johanna; Contillo, Adriano; Greenlee, Mark W.

2016-01-01

Glass patterns (GPs) consist of randomly distributed dot pairs (dipoles) whose orientations are determined by specific geometric transforms. We assessed whether adaptation to stationary oriented translational GPs suppresses the activity of orientation selective detectors producing a tilt aftereffect (TAE). The results showed that adaptation to GPs produces a TAE similar to that reported in previous studies, though reduced in amplitude. This suggests the involvement of orientation selective mechanisms. We also measured the interocular transfer (IOT) of the GP-induced TAE and found an almost complete IOT, indicating the involvement of orientation selective and binocularly driven units. In additional experiments, we assessed the role of attention in TAE from GPs. The results showed that distraction during adaptation similarly modulates the TAE after adapting to both GPs and gratings. Moreover, in the case of GPs, distraction is likely to interfere with the adaptation process rather than with the spatial summation of local dipoles. We conclude that TAE from GPs possibly relies on visual processing levels in which the global orientation of GPs has been encoded by neurons that are mostly binocularly driven, orientation selective and whose adaptation-related neural activity is strongly modulated by attention. PMID:27005949

The pollination biology of a pavement plain: pollinator visitation patterns.

PubMed

O'Brien, Mary H

1980-01-01

The pollination biology of the 20 plant species of a treeless, pavement plain in the San Bernardino Mountains of southern California was studied throughout one flowering season.Several patterns of pollinator activity recorded during the season underline the necessity for noting the activity of all insect pollinators whether specialized, non-specialized, regular, or occasional: 1) Occasional insect visitors were a feature of the visitation to nine of the twelve entomophilous plant species and were the sole pollinators for three of these twelve species. 2) The eight entomophilous plant species which had open, generalized flower morphologies received the heaviest pollinator visitation, while three of the four entomophilous species with specialized flower morphologies received little visitation. 3) Most regular flower visitors, whether bees, flies, or wasps, appeared to be similar with respect to number of plant species visited regularly, purity of pollen load, length of residence and localization of activity on the site. The question is raised as to whether such similarity of behavior as pollen vectors is a function of the low plant diversity or a feature commonly found when the pollen loads and behavior of different pollinator types are actually monitored.

Polysensory response characteristics of dorsal root ganglion neurones that may serve sensory functions during myocardial ischaemia.

PubMed

Huang, M H; Horackova, M; Negoescu, R M; Wolf, S; Armour, J A

1996-09-01

To determine the response characteristics of dorsal root ganglion neurones that may serve sensory functions during myocardial ischaemia. Extracellular recordings were made from 54 spontaneously active and 5 normally quiescent dorsal root ganglion neurones (T2-T5) in 22 anaesthetized open-chest dogs under control conditions and during epicardial mechanical or chemical stimulation and myocardial ischaemia. The activity of 78% of spontaneously active and all quiescent neurones with left ventricular sensory fields was modified by left ventricular ischaemia. Forty-six spontaneously active neurones (85%) were polysensory with respect to mechanical and chemical stimuli. The 5 quiescent neurones responded only to chemical stimuli. Spontaneously active neurones associated with left ventricular mechanosensory endings (37 neurones) generated four different activity patterns in response to similar mechanical stimuli (high or low pressure active, high-low pressure active, high-low pressure inactive). A fifth group generated activity which was not related to chamber dynamics. Adenosine, adenosine 5'-triphosphate, substance P and bradykinin modified 72, 61, 65 and 63% of the spontaneously active neurones, respectively. Maximum local mechanical or chemical stimuli enhanced activity to similar degrees, as did ischaemia. Each ischaemia-sensitive neurone displayed unique activity patterns in response to similar mechanical or chemical stimuli. Most myocardial ischemia-sensitive dorsal root ganglion neurones associated with epicardial neurites sense mechanical and multiple chemical stimuli, a small population sensing only mechanical or chemical stimuli. Activity patterns generated by these neurones depend on their primary sensory characteristics or those of other neurones that may converge on them, as well as the type and magnitude of the stimuli that impinge upon their sensory fields, both normally and during ischaemia.

Seeing the order in a mess: optical signature of periodicity in a cloud of plasmonic nanowires.

PubMed

Natarov, Denys M; Marciniak, Marian; Sauleau, Ronan; Nosich, Alexander I

2014-11-17

We consider the two-dimensional (2-D) problem of the H-polarized plane wave scattering by a linear chain of silver nanowires in a cloud of similar pseudo-randomly located wires, in the visible range. Numerical solution uses the field expansions in local coordinates and addition theorems for cylindrical functions and has a guaranteed convergence. The total scattering cross-sections and near- and far-zone field patterns are presented. The observed resonance effects are studied and compared with their counterparts in the scattering by the same linear chain of wires in free space.

A new species of Rhadinella (Serpentes: Colubridae) from the Pacific versant of Oaxaca, Mexico.

PubMed

Campbell, Jonathan A

2015-02-12

I describe a new species of Rhadinella from the Pacific versant of Oaxaca, Mexico, a region where the genus was previously unknown. This diminutive snake is a member of a group of snakes that have dark dorsal coloration, which mostly or completely obfuscates a pattern of longitudinal striping characteristic of most species of Rhadinella. The closest relative of the new species, on the basis of morphological similarities, appears to be Rhadinella pilonaorum which occurs to the east of the Isthmus of Tehuantepec about 800 km from the type-locality of the new species.

UDOF direct improvement by modulating mask absorber thickness

NASA Astrophysics Data System (ADS)

Yu, Tuan-Yen; Lio, En Chuan; Chen, Po Tsang; Wei, Chih I.; Chen, Yi Ting; Peng, Ming Chun; Chou, William; Yu, Chun Chi

2016-10-01

As the process generation migrate to advanced and smaller dimension or pitch, the mask and resist 3D effects will impact the lithography focus common window severely because of both individual depth-of-focus (iDOF) range decrease and center mismatch. Furthermore, some chemical or thermal factors, such as PEB (Post Exposure Bake) also worsen the usable depth-of-focus (uDOF) performance. So the mismatch of thru-pitch iDOF center should be considered as a lithography process integration issue, and more complicated to partition the 3D effects induced by optical or chemical factors. In order to reduce the impact of 3D effects induced by both optical and chemical issues, and improve iDOF center mismatch, we would like to propose a mask absorber thickness offset approach, which is directly to compensate the iDOF center bias by adjusting mask absorber thickness, for iso, semi-iso or dense characteristics in line, space or via patterns to enlarge common process window, i.e uDOF, which intends to provide similar application as Flexwave[1] (ASML trademark). By the way, since mask absorber thickness offset approach is similar to focus tuning or change on wafer lithography process, it could be acted as the process tuning method of photoresist (PR) profile optimization locally, PR scum improvement in specific patterns or to modulate etching bias to meet process integration request. For mass production consideration, and available material, current att-PSM blank, quartz, MoSi with chrome layer as hard-mask in reticle process, will be implemented in this experiment, i.e. chrome will be kept remaining above partial thru-pitch patterns, and act as the absorber thickness bias in different patterns. And then, from the best focus offset of thru-pitch patterns, the iDOF center shifts could be directly corrected and to enlarge uDOF by increasing the overlap of iDOF. Finally, some negative tone development (NTD) result in line patterns will be demonstrated as well.

78 FR 5115 - General Schedule Locality Pay Areas

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-24

... contains regulatory documents #0;having general applicability and legal effect, most of which are keyed #0... appropriate factors, which may include local labor market patterns, commuting patterns, and the practices of... any changes. Impact The rule has no effect on existing locality pay area definitions but prevents any...

Mapping Informative Clusters in a Hierarchial Framework of fMRI Multivariate Analysis

PubMed Central

Xu, Rui; Zhen, Zonglei; Liu, Jia

2010-01-01

Pattern recognition methods have become increasingly popular in fMRI data analysis, which are powerful in discriminating between multi-voxel patterns of brain activities associated with different mental states. However, when they are used in functional brain mapping, the location of discriminative voxels varies significantly, raising difficulties in interpreting the locus of the effect. Here we proposed a hierarchical framework of multivariate approach that maps informative clusters rather than voxels to achieve reliable functional brain mapping without compromising the discriminative power. In particular, we first searched for local homogeneous clusters that consisted of voxels with similar response profiles. Then, a multi-voxel classifier was built for each cluster to extract discriminative information from the multi-voxel patterns. Finally, through multivariate ranking, outputs from the classifiers were served as a multi-cluster pattern to identify informative clusters by examining interactions among clusters. Results from both simulated and real fMRI data demonstrated that this hierarchical approach showed better performance in the robustness of functional brain mapping than traditional voxel-based multivariate methods. In addition, the mapped clusters were highly overlapped for two perceptually equivalent object categories, further confirming the validity of our approach. In short, the hierarchical framework of multivariate approach is suitable for both pattern classification and brain mapping in fMRI studies. PMID:21152081

Influence of atmospheric transport patterns on xenon detections at the CTBTO radionuclide network

NASA Astrophysics Data System (ADS)

Krysta, Monika; Kusmierczyk-Michulec, Jolanta

2016-04-01

In order to fulfil its task of monitoring for signals emanating from nuclear explosions, Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO) operates global International Monitoring System (IMS) comprising seismic, infrasound, hydroacoustic and radionuclide measurement networks. At present, 24 among 80 radionuclide stations foreseen by the Comprehensive Nuclear-Test-Ban Treaty (CTBT) are equipped with certified noble gas measurement systems. Over a past couple of years these systems collected a rich set of measurements of radioactive isotopes of xenon. Atmospheric transport modelling simulations are crucial to an assessment of the origin of xenon detected at the IMS stations. Numerous studies undertaken in the past enabled linking these detections to non Treaty-relevant activities and identifying main contributors. Presence and quantity of xenon isotopes at the stations is hence a result of an interplay of emission patterns and atmospheric circulation. In this presentation we analyse the presence or absence of radioactive xenon at selected stations from an angle of such an interplay. We attempt to classify the stations according to similarity of detection patterns, examine seasonality in those patterns and link them to large scale or local meteorological phenomena. The studies are undertaken using crude hypotheses on emission patterns from known sources and atmospheric transport modelling simulations prepared with the FLEXPART model.

Cognitive and affective theory of mind share the same local patterns of activity in posterior temporal but not medial prefrontal cortex

PubMed Central

Hofstetter, Christoph; Vuilleumier, Patrik

2014-01-01

Understanding emotions in others engages specific brain regions in temporal and medial prefrontal cortices. These activations are often attributed to more general cognitive ‘mentalizing’ functions, associated with theory of mind and also necessary to represent people’s non-emotional mental states, such as beliefs or intentions. Here, we directly investigated whether understanding emotional feelings recruit similar or specific brain systems, relative to other non-emotional mental states. We used functional magnetic resonance imaging with multivoxel pattern analysis in 46 volunteers to compare activation patterns in theory-of-mind tasks for emotions, relative to beliefs or somatic states accompanied with pain. We found a striking dissociation between the temporoparietal cortex, that exhibited a remarkable voxel-by-voxel pattern overlap between emotions and beliefs (but not pain), and the dorsomedial prefrontal cortex, that exhibited distinct (and yet nearby) patterns of activity during the judgment of beliefs and emotions in others. Pain judgment was instead associated with activity in the supramarginal gyrus, middle cingulate cortex and middle insular cortex. Our data reveal for the first time a functional dissociation within brain networks sub-serving theory of mind for different mental contents, with a common recruitment for cognitive and affective states in temporal regions, and distinct recruitment in prefrontal areas. PMID:23770622

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

PubMed Central

De La Vega, Francisco M.; Isaac, Hadar; Collins, Andrew; Scafe, Charles R.; Halldórsson, Bjarni V.; Su, Xiaoping; Lippert, Ross A.; Wang, Yu; Laig-Webster, Marion; Koehler, Ryan T.; Ziegle, Janet S.; Wogan, Lewis T.; Stevens, Junko F.; Leinen, Kyle M.; Olson, Sheri J.; Guegler, Karl J.; You, Xiaoqing; Xu, Lily H.; Hemken, Heinz G.; Kalush, Francis; Itakura, Mitsuo; Zheng, Yi; de Thé, Guy; O'Brien, Stephen J.; Clark, Andrew G.; Istrail, Sorin; Hunkapiller, Michael W.; Spier, Eugene G.; Gilbert, Dennis A.

2005-01-01

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies. PMID:15781572

Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes

PubMed Central

Huang, Yongjie; Mrázek, Jan

2014-01-01

Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented. Representation of patterns that promote Z-DNA and intrinsic DNA curvature increases with increasing optimal growth temperature (OGT), and decreases with increasing oxygen requirement. Additionally, representations of close direct repeats, palindromes and inverted repeats exhibit clear negative trends with increasing OGT. The observed relationships with environmental characteristics, particularly OGT, suggest possible evolutionary scenarios of structural adaptation of DNA to particular environmental niches. PMID:24408877

Deinterlacing using modular neural network

NASA Astrophysics Data System (ADS)

Woo, Dong H.; Eom, Il K.; Kim, Yoo S.

2004-05-01

Deinterlacing is the conversion process from the interlaced scan to progressive one. While many previous algorithms that are based on weighted-sum cause blurring in edge region, deinterlacing using neural network can reduce the blurring through recovering of high frequency component by learning process, and is found robust to noise. In proposed algorithm, input image is divided into edge and smooth region, and then, to each region, one neural network is assigned. Through this process, each neural network learns only patterns that are similar, therefore it makes learning more effective and estimation more accurate. But even within each region, there are various patterns such as long edge and texture in edge region. To solve this problem, modular neural network is proposed. In proposed modular neural network, two modules are combined in output node. One is for low frequency feature of local area of input image, and the other is for high frequency feature. With this structure, each modular neural network can learn different patterns with compensating for drawback of counterpart. Therefore it can adapt to various patterns within each region effectively. In simulation, the proposed algorithm shows better performance compared with conventional deinterlacing methods and single neural network method.

Bet-hedging as a complex interaction among developmental instability, environmental heterogeneity, dispersal, and life-history strategy.

PubMed

Scheiner, Samuel M

2014-02-01

One potential evolutionary response to environmental heterogeneity is the production of randomly variable offspring through developmental instability, a type of bet-hedging. I used an individual-based, genetically explicit model to examine the evolution of developmental instability. The model considered both temporal and spatial heterogeneity alone and in combination, the effect of migration pattern (stepping stone vs. island), and life-history strategy. I confirmed that temporal heterogeneity alone requires a threshold amount of variation to select for a substantial amount of developmental instability. For spatial heterogeneity only, the response to selection on developmental instability depended on the life-history strategy and the form and pattern of dispersal with the greatest response for island migration when selection occurred before dispersal. Both spatial and temporal variation alone select for similar amounts of instability, but in combination resulted in substantially more instability than either alone. Local adaptation traded off against bet-hedging, but not in a simple linear fashion. I found higher-order interactions between life-history patterns, dispersal rates, dispersal patterns, and environmental heterogeneity that are not explainable by simple intuition. We need additional modeling efforts to understand these interactions and empirical tests that explicitly account for all of these factors.

Long-term community dynamics of small landbirds with and without exposure to extensive disturbance from military training activities.

PubMed

Rivers, James W; Gipson, Philip S; Althoff, Donald P; Pontius, Jeffrey S

2010-02-01

Military training activities are known to impact individual species, yet our understanding of how such activities influence animal communities is limited. In this study, we used long-term data in a case study approach to examine the extent to which the local small landbird community differed between a site in northeast Kansas that experienced intensive disturbance from military training activities (Ft. Riley Military Installation) and a similar, nearby site that experienced minimal human disturbance (Konza Prairie Biological Station). In addition, we characterized how the regional pool of potential colonizers influenced local community dynamics using Breeding Bird Survey data. From 1991 to 2001, most species of small terrestrial landbirds (73%) recorded during breeding surveys were found at both sites and the mean annual richness at Ft. Riley (39.0 +/- 2.86 [SD]) was very similar to that of Konza Prairie (39.4 +/- 2.01). Richness was maintained at relatively constant levels despite compositional changes because colonizations compensated local extinctions at both sites. These dynamics were driven primarily by woodland species that exhibited stochastic losses and gains and were present at a low local and regional abundance. Our results suggest that military training activities may mimic natural disturbances for some species in this area because the small landbird community did not differ markedly between sites with and sites without extensive human disturbance. Although our results suggest that military training is not associated with large changes in the avian community, additional studies are needed to determine if this pattern is found in other ecological communities.

Fractal nematic colloids

NASA Astrophysics Data System (ADS)

Hashemi, S. M.; Jagodič, U.; Mozaffari, M. R.; Ejtehadi, M. R.; Muševič, I.; Ravnik, M.

2017-01-01

Fractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and numerical modelling. Explicit generation of topological defect pairs is found, with the number of defects following exponential-law dependence and reaching few 100 already at fractal iteration four. This work demonstrates a route for generation of fractal topological defect states in responsive soft matter.

Earthquake potential in California-Nevada implied by correlation of strain rate and seismicity

USGS Publications Warehouse

Zeng, Yuehua; Petersen, Mark D.; Shen, Zheng-Kang

2018-01-01

Rock mechanics studies and dynamic earthquake simulations show that patterns of seismicity evolve with time through (1) accumulation phase, (2) localization phase, and (3) rupture phase. We observe a similar pattern of changes in seismicity during the past century across California and Nevada. To quantify these changes, we correlate GPS strain rates with seismicity. Earthquakes of M > 6.5 are collocated with regions of highest strain rates. By contrast, smaller magnitude earthquakes of M ≥ 4 show clear spatiotemporal changes. From 1933 to the late 1980s, earthquakes of M ≥ 4 were more diffused and broadly distributed in both high and low strain rate regions (accumulation phase). From the late 1980s to 2016, earthquakes were more concentrated within the high strain rate areas focused on the major fault strands (localization phase). In the same time period, the rate of M > 6.5 events also increased significantly in the high strain rate areas. The strong correlation between current strain rate and the later period of seismicity indicates that seismicity is closely related to the strain rate. The spatial patterns suggest that before the late 1980s, the strain rate field was also broadly distributed because of the stress shadows from previous large earthquakes. As the deformation field evolved out of the shadow in the late 1980s, strain has refocused on the major fault systems and we are entering a period of increased risk for large earthquakes in California.

Earthquake Potential in California-Nevada Implied by Correlation of Strain Rate and Seismicity

NASA Astrophysics Data System (ADS)

Zeng, Yuehua; Petersen, Mark D.; Shen, Zheng-Kang

2018-02-01

Rock mechanics studies and dynamic earthquake simulations show that patterns of seismicity evolve with time through (1) accumulation phase, (2) localization phase, and (3) rupture phase. We observe a similar pattern of changes in seismicity during the past century across California and Nevada. To quantify these changes, we correlate GPS strain rates with seismicity. Earthquakes of M > 6.5 are collocated with regions of highest strain rates. By contrast, smaller magnitude earthquakes of M ≥ 4 show clear spatiotemporal changes. From 1933 to the late 1980s, earthquakes of M ≥ 4 were more diffused and broadly distributed in both high and low strain rate regions (accumulation phase). From the late 1980s to 2016, earthquakes were more concentrated within the high strain rate areas focused on the major fault strands (localization phase). In the same time period, the rate of M > 6.5 events also increased significantly in the high strain rate areas. The strong correlation between current strain rate and the later period of seismicity indicates that seismicity is closely related to the strain rate. The spatial patterns suggest that before the late 1980s, the strain rate field was also broadly distributed because of the stress shadows from previous large earthquakes. As the deformation field evolved out of the shadow in the late 1980s, strain has refocused on the major fault systems and we are entering a period of increased risk for large earthquakes in California.

Biofilm three-dimensional architecture influences in situ pH distribution pattern on the human enamel surface

PubMed Central

Xiao, Jin; Hara, Anderson T; Kim, Dongyeop; Zero, Domenick T; Koo, Hyun; Hwang, Geelsu

2017-01-01

To investigate how the biofilm three-dimensional (3D) architecture influences in situ pH distribution patterns on the enamel surface. Biofilms were formed on human tooth enamel in the presence of 1% sucrose or 0.5% glucose plus 0.5% fructose. At specific time points, biofilms were exposed to a neutral pH buffer to mimic the buffering of saliva and subsequently pulsed with 1% glucose to induce re-acidification. Simultaneous 3D pH mapping and architecture of intact biofilms was performed using two-photon confocal microscopy. The enamel surface and mineral content characteristics were examined successively via optical profilometry and microradiography analyses. Sucrose-mediated biofilm formation created spatial heterogeneities manifested by complex networks of bacterial clusters (microcolonies). Acidic regions (pH<5.5) were found only in the interior of microcolonies, which impedes rapid neutralization (taking more than 120 min for neutralization). Glucose exposure rapidly re-created the acidic niches, indicating formation of diffusion barriers associated with microcolonies structure. Enamel demineralization (white spots), rougher surface, deeper lesion and more mineral loss appeared to be associated with the localization of these bacterial clusters at the biofilm-enamel interface. Similar 3D architecture was observed in plaque-biofilms formed in vivo in the presence of sucrose. The formation of complex 3D architectures creates spatially heterogeneous acidic microenvironments in close proximity of enamel surface, which might correlate with the localized pattern of the onset of carious lesions (white spot like) on teeth. PMID:28452377

Regional patterns of mercury content in snowpack, sphagnum, and fish in northeastern North America

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

Haines, T.; Mower, B.; Perry, R.

1995-12-31

High levels of mercury have been found in fish from lakes throughout the northeastern US and eastern Canada, in waters with no known local mercury source. If this mercury originates from anthropogenic emissions to the atmosphere, deposition should be higher near population centers or other point sources. The authors surveyed the mercury content of late-season snowpack, sphagnum moss, and fish at locations from southwestern Connecticut to northern Newfoundland to determine if such a pattern existed. Mercury in snow ranged 1.5 to 20 ng/L, and in sphagnum < 24 to 289 ng/g dry wt. Concentrations were generally highest at southwestern sitesmore » and lowest at northeastern sites with some exceptions. The highest concentrations in both media were at locations in Rhode Island and New Hampshire, and may reflect local source emissions. Excluding these sites, the range in concentration from south to north is only a factor of two or three. These values are similar to those reported in other areas and reflect the long atmospheric residence time of gaseous elemental mercury. Mercury concentration in fish ranged 0.1 to 1.0 ug/g wet wt. and showed no regional pattern. Rather, fish mercury concentration was affected by fish species and size, being highest in large predatory species such as smallmouth bass (Micropterus dolomieu), and lowest in small nonpredatory species such as yellow perch (Perca flavescens) and brook trout (Salvelinus fontinalis).« less

Symbiotic specificity, association patterns, and function determine community responses to global changes: defining critical research areas for coral-Symbiodinium symbioses.

PubMed

Fabina, Nicholas S; Putnam, Hollie M; Franklin, Erik C; Stat, Michael; Gates, Ruth D

2013-11-01

Climate change-driven stressors threaten the persistence of coral reefs worldwide. Symbiotic relationships between scleractinian corals and photosynthetic endosymbionts (genus Symbiodinium) are the foundation of reef ecosystems, and these associations are differentially impacted by stress. Here, we couple empirical data from the coral reefs of Moorea, French Polynesia, and a network theoretic modeling approach to evaluate how patterns in coral-Symbiodinium associations influence community stability under climate change. To introduce the effect of climate perturbations, we simulate local 'extinctions' that represent either the loss of coral species or the ability to engage in symbiotic interactions. Community stability is measured by determining the duration and number of species that persist through the simulated extinctions. Our results suggest that four factors greatly increase coral-Symbiodinium community stability in response to global changes: (i) the survival of generalist hosts and symbionts maximizes potential symbiotic unions; (ii) elevated symbiont diversity provides redundant or complementary symbiotic functions; (iii) compatible symbiotic assemblages create the potential for local recolonization; and (iv) the persistence of certain traits associate with symbiotic diversity and redundancy. Symbiodinium may facilitate coral persistence through novel environmental regimes, but this capacity is mediated by symbiotic specificity, association patterns, and the functional performance of the symbionts. Our model-based approach identifies general trends and testable hypotheses in coral-Symbiodinium community responses. Future studies should consider similar methods when community size and/or environmental complexity preclude experimental approaches. © 2013 John Wiley & Sons Ltd.

Patterns of human local cerebral glucose metabolism during epileptic seizures

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

Engel, J. Jr.; Kuhl, D.E.; Phelps, M.E.

1982-10-01

Ictal patterns of local cerebral metabolic rate have been studied in epileptic patients by positron computed tomography with /sup 18/F-labeled 2-fluoro-2-deoxy-D-glucose. Partial seizures were associated with activation of anatomic structures unique to each patient studied. Ictal increases and decreases in local cerebral metabolism were observed. Scans performed during generalized convulsions induced by electroshock demonstrated a diffuse ictal increase and postictal decrease in cerebral metabolism. Petit mal absences were associated with a diffuse increase in cerebral metabolic rate. The ictal fluorodeoxyglucose patterns obtained from patients do not resemble autoradiographic patterns obtained from common experimental animal models of epilepsy.

Research applications of ecosystem patterns

Treesearch

Robert G. Bailey

2009-01-01

This article discusses the origins of natural ecosystem patterns from global to local scales. It describes how understanding these patterns can help scientists and managers in two ways. First, the local systems are shown within the context of larger systems. This perspective can be applied in assessing the connections between action at one scale and effect at another,...

Global Patterns of the Isotopic Composition of Soil and Plant Nitrogen

NASA Astrophysics Data System (ADS)

Amundson, R.; Yoo, K.

2014-12-01

From a societal perspective, soil N follows only soil C in the importance of soil to 21st century environmental issues. Amundson et al (2003) developed a mass balance model for soil N and the ratio of 15N/14N, and provided the first global projections of the spatial patterns of soil and plant δ15N values. It was hypothesized that state factors, particularly climate, should drive broad patterns of soil and plant δ15N values in a manner analogous to the known patterns of total soil N (e.g. Post et al., 1984). At that time, the N isotope data available to explore the effect of individual factors was modest. In the past decade, numerous papers from a broad spectrum of locations have created a rich database that can be used to further refine the initial projections made more than a decade ago. In this paper, hundreds of published measurements will be used to more deeply examine the climatic impacts on soil and plant δ15N values. Additionally, we will focus on the local controls of topography on ecosystem N cycling, which can create local isotopic variation that is similar in magnitude to the global effects of climate. The adoption of process-based models from the hillslope geomorphology community appears to be a powerful tool for explaining some existing data from toposequences, designing new studies of topographic controls on biogeochemistry, and particularly for parameterization in global models. Amundson, R., A.T. Austin, E.A.G. Schuur, K. Yoo, V. Matzek, C. Kendall, A. Uebersax, D. Brenner, and W.T. Baisden. 2003. Global Biogeochemical Cycles 17(1):1031.

Perceptions of Community Benefits from Two Wild and Scenic Rivers

NASA Astrophysics Data System (ADS)

Smith, Jordan W.; Moore, Roger L.

2011-05-01

Wild and Scenic Rivers provide a host of psychological, social, ecological, and economic benefits to local communities. In this study, we use data collected from recreational users of two Wild and Scenic Rivers to examine perceptions of the benefits provided by the rivers to local communities. Our purposes are (1) to determine if similar perceptions of community benefits exist across the two rivers, (2) to determine if individuals' proximity to the rivers are related to the benefits they perceive, (3) to determine if individuals' prior recreation experience on the river is related to variations in perceived benefits, (4) to determine if users' sociodemographic characteristics are related to perceived community benefits, and (5) to determine if the influence of these characteristics on perceived community benefits is similar across the two resource areas. Perceived benefits were found to be analogous across both rivers as individuals consistently ranked ecological/affective benefits as well as tangible benefits similarly. Recreationists living further from the river ranked ecological and affective benefits as significantly less important than those individuals living closer to the river. Women perceived the community benefits produced by the resource areas to be significantly more important when compared to men. Significant relationships were also found between perceived benefits and recreationists' previous use of the river, their age, and their level of education. With the exception of resource proximity and prior use history, the effects of user characteristics on perceived community benefits were not statistically different across the two rivers. These findings imply similar patterns of perceived community benefits exist across distinct resource areas and that the relationships between user characteristics and perceived benefits are also similar across the study rivers.

The evolution of sexual size dimorphism in the house finch. II. Population divergence in relation to local selection.

PubMed

Badyaev, A V; Hill, G E; Stoehr, A M; Nolan, P M; McGraw, K J

2000-12-01

Recent colonization of ecologically distinct areas in North America by the house finch (Carpodacus mexicanus) was accompanied by strong population divergence in sexual size dimorphism. Here we examined whether this divergence was produced by population differences in local selection pressures acting on each sex. In a long-term study of recently established populations in Alabama, Michigan, and Montana, we examined three selection episodes for each sex: selection for pairing success, overwinter survival, and within-season fecundity. Populations varied in intensity of these selection episodes, the contribution of each episode to the net selection, and in the targets of selection. Direction and intensity of selection strongly differed between sexes, and different selection episodes often favored opposite changes in morphological traits. In each population, current net selection for sexual dimorphism was highly concordant with observed sexual dimorphism--in each population, selection for dimorphism was the strongest on the most dimorphic traits. Strong directional selection on sexually dimorphic traits, and similar intensities of selection in both sexes, suggest that in each of the recently established populations, both males and females are far from their local fitness optimum, and that sexual dimorphism has arisen from adaptive responses in both sexes. Population differences in patterns of selection on dimorphism, combined with both low levels of ontogenetic integration in heritable sexually dimorphic traits and sexual dimorphism in growth patterns, may account for the close correspondence between dimorphism in selection and observed dimorphism in morphology across house finch populations.

Endogenous contributions to egg protein formation in lesser scaup Aythya affinis

USGS Publications Warehouse

Cutting, Kyle A.; Hobson, Keith A.; Rotella, Jay J.; Warren, Jeffrey M.; Wainwright-de la Cruz, Susan E.; Takekawa, John Y.

2011-01-01

Lesser scaup Aythya affinis populations have declined throughout the North American continent for the last three decades. It has been hypothesized that the loss and degradation of staging habitats has resulted in reduced female body condition on the breeding grounds and a concomitant decline in productivity. We explored the importance of body (endogenous) reserves obtained prior to arrival on the breeding ground in egg protein formation in southwestern Montana during 2006–2008 using stable-carbon (δ13C) and nitrogen (δ15N) isotope analyses of scaup egg components, female tissue, and local prey items. From arrival on the breeding grounds through the egg-laying period, δ15N values of scaup red blood cells decreased while δ13C values became less variable; a pattern consistent with endogenous tissues equilibrating with local (freshwater) dietary sources. In 2006 and 2008, isotopic values for egg albumen and yolk protein indicated that most (>90%) protein used to produce these components was obtained on the breeding grounds. However, in 2007, a year with an exceptionally warm and dry spring, endogenous reserves contributed on average 41% of yolk and 29% of albumen. Results from this study suggest that female scaup can meet the protein needs of egg production largely from local dietary food sources. This highlights the importance of providing high-quality breeding habitats for scaup. Whether this pattern holds in areas with similar breeding season lengths but longer migration routes, such as those found in the western boreal forest, should be investigated.

Local overfishing may be avoided by examining parameters of a spatio-temporal model

PubMed Central

Shackell, Nancy; Mills Flemming, Joanna

2017-01-01

Spatial erosion of stock structure through local overfishing can lead to stock collapse because fish often prefer certain locations, and fisheries tend to focus on those locations. Fishery managers are challenged to maintain the integrity of the entire stock and require scientific approaches that provide them with sound advice. Here we propose a Bayesian hierarchical spatio-temporal modelling framework for fish abundance data to estimate key parameters that define spatial stock structure: persistence (similarity of spatial structure over time), connectivity (coherence of temporal pattern over space), and spatial variance (variation across the seascape). The consideration of these spatial parameters in the stock assessment process can help identify the erosion of structure and assist in preventing local overfishing. We use Atlantic cod (Gadus morhua) in eastern Canada as a case study an examine the behaviour of these parameters from the height of the fishery through its collapse. We identify clear signals in parameter behaviour under circumstances of destructive stock erosion as well as for recovery of spatial structure even when combined with a non-recovery in abundance. Further, our model reveals the spatial pattern of areas of high and low density persists over the 41 years of available data and identifies the remnant patches. Models of this sort are crucial to recovery plans if we are to identify and protect remaining sources of recolonization for Atlantic cod. Our method is immediately applicable to other exploited species. PMID:28886179

Local overfishing may be avoided by examining parameters of a spatio-temporal model.

PubMed

Carson, Stuart; Shackell, Nancy; Mills Flemming, Joanna

2017-01-01

Spatial erosion of stock structure through local overfishing can lead to stock collapse because fish often prefer certain locations, and fisheries tend to focus on those locations. Fishery managers are challenged to maintain the integrity of the entire stock and require scientific approaches that provide them with sound advice. Here we propose a Bayesian hierarchical spatio-temporal modelling framework for fish abundance data to estimate key parameters that define spatial stock structure: persistence (similarity of spatial structure over time), connectivity (coherence of temporal pattern over space), and spatial variance (variation across the seascape). The consideration of these spatial parameters in the stock assessment process can help identify the erosion of structure and assist in preventing local overfishing. We use Atlantic cod (Gadus morhua) in eastern Canada as a case study an examine the behaviour of these parameters from the height of the fishery through its collapse. We identify clear signals in parameter behaviour under circumstances of destructive stock erosion as well as for recovery of spatial structure even when combined with a non-recovery in abundance. Further, our model reveals the spatial pattern of areas of high and low density persists over the 41 years of available data and identifies the remnant patches. Models of this sort are crucial to recovery plans if we are to identify and protect remaining sources of recolonization for Atlantic cod. Our method is immediately applicable to other exploited species.

RELATIONSHIPS BETWEEN FLUID VORTICITY, KINETIC HELICITY, AND MAGNETIC FIELD ON SMALL-SCALES (QUIET-NETWORK) ON THE SUN

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

Sangeetha, C. R.; Rajaguru, S. P., E-mail: crsangeetha@iiap.res.in

We derive horizontal fluid motions on the solar surface over large areas covering the quiet-Sun magnetic network from local correlation tracking of convective granules imaged in continuum intensity and Doppler velocity by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory . From these we calculate the horizontal divergence, the vertical component of vorticity, and the kinetic helicity of fluid motions. We study the correlations between fluid divergence and vorticity, and between vorticity (kinetic helicity) and the magnetic field. We find that the vorticity (kinetic helicity) around small-scale fields exhibits a hemispherical pattern (in sign) similar tomore » that followed by the magnetic helicity of large-scale active regions (containing sunspots). We identify this pattern to be a result of the Coriolis force acting on supergranular-scale flows (both the outflows and inflows), consistent with earlier studies using local helioseismology. Furthermore, we show that the magnetic fields cause transfer of vorticity from supergranular inflow regions to outflow regions, and that they tend to suppress the vortical motions around them when magnetic flux densities exceed about 300 G (from HMI). We also show that such an action of the magnetic fields leads to marked changes in the correlations between fluid divergence and vorticity. These results are speculated to be of importance to local dynamo action (if present) and to the dynamical evolution of magnetic helicity at the small-scale.« less

Icelandic inclusion, German hesitation and American fear: A cross-cultural comparison of mental-health stigma and the media.

PubMed

Manago, Bianca; Pescosolido, Bernice A; Olafsdottir, Sigrun

2018-03-01

Quantitative survey research findings reveal that Western countries have lower rates of public stigma surrounding mental illness than other nations. However, qualitative media research across selected Western countries reports differences in stigmatising messages. Here, we take an in-depth look at country-level data exploring both similarities and differences in this stigma across three countries. Specifically, we use previous findings on global differences in public stigma and media to examine whether there is a correspondence between themes in newspaper reporting and variations in attitudes across seven stigma dimensions. The Stigma in Global Context - Mental Health Study provides nationally representative data from Iceland ( N=1033; response rate=71%), Germany ( N=1255; response rate=63.16%) and the USA ( N=1425; response rate=67.31%). We limit analyses to respondents who received a vignette describing an individual meeting clinical criterion for schizophrenia or depression. Exploratory data analyses are used to examine overall patterns and cross-national differences. Graphical analyses show patterned similarities, especially for more individuals endorsing social distance as contact becomes more intimate. However, results also corroborate cross-national differences documented in media research. More Americans endorse evaluations of dangerousness, to both self and others. Fewer Icelanders report exclusionary tendencies, whilst Germans report the most consistently moderate levels of stigma. While Western nations tend to report similar, lower levels of stigma globally, they each have unique areas of concern. Anti-stigma programs must take note of both similarities and differences to tailor their efforts to the local context.

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

Devpura, S; Li, H; Liu, C

Purpose: To correlate dose distributions computed using six algorithms for recurrent early stage non-small cell lung cancer (NSCLC) patients treated with stereotactic body radiotherapy (SBRT), with outcome (local failure). Methods: Of 270 NSCLC patients treated with 12Gyx4, 20 were found to have local recurrence prior to the 2-year time point. These patients were originally planned with 1-D pencil beam (1-D PB) algorithm. 4D imaging was performed to manage tumor motion. Regions of local failures were determined from follow-up PET-CT scans. Follow-up CT images were rigidly fused to the planning CT (pCT), and recurrent tumor volumes (Vrecur) were mapped to themore » pCT. Dose was recomputed, retrospectively, using five algorithms: 3-D PB, collapsed cone convolution (CCC), anisotropic analytical algorithm (AAA), AcurosXB, and Monte Carlo (MC). Tumor control probability (TCP) was computed using the Marsden model (1,2). Patterns of failure were classified as central, in-field, marginal, and distant for Vrecur ≥95% of prescribed dose, 95–80%, 80–20%, and ≤20%, respectively (3). Results: Average PTV D95 (dose covering 95% of the PTV) for 3-D PB, CCC, AAA, AcurosXB, and MC relative to 1-D PB were 95.3±2.1%, 84.1±7.5%, 84.9±5.7%, 86.3±6.0%, and 85.1±7.0%, respectively. TCP values for 1-D PB, 3-D PB, CCC, AAA, AcurosXB, and MC were 98.5±1.2%, 95.7±3.0, 79.6±16.1%, 79.7±16.5%, 81.1±17.5%, and 78.1±20%, respectively. Patterns of local failures were similar for 1-D and 3D PB plans, which predicted that the majority of failures occur in centraldistal regions, with only ∼15% occurring distantly. However, with convolution/superposition and MC type algorithms, the majority of failures (65%) were predicted to be distant, consistent with the literature. Conclusion: Based on MC and convolution/superposition type algorithms, average PTV D95 and TCP were ∼15% lower than the planned 1-D PB dose calculation. Patterns of failure results suggest that MC and convolution/superposition type algorithms predict different outcomes for patterns of failure relative to PB algorithms. Work supported in part by Varian Medical Systems, Palo Alto, CA.« less

Pulmonary tuberculosis in Asian elephants (Elephas maximus): histologic lesions with correlation to local immune responses.

PubMed

Landolfi, J A; Terio, K A; Miller, M; Junecko, B F; Reinhart, T

2015-05-01

Although Mycobacterium tuberculosis infection is an important health concern for Asian elephants (Elephas maximus), no studies have evaluated the associated local immune responses or histologic lesions. In primates including humans, latent tuberculosis is distinguished by well-organized granulomas with TH1 cytokine expression, whereas active disease is characterized by poorly organized inflammation and local imbalance in TH1/TH2 cytokines. This study examined archival, formalin-fixed, paraffin-embedded lung samples from 5 tuberculosis-negative and 9 tuberculosis-positive Asian elephants. Lesions were assessed by light microscopy, and lymphoid infiltrates were characterized by CD3 and CD20 immunolabeling. Expression of TH1 (interferon [IFN]-γ, tumor necrosis factor [TNF]-α) and TH2 (interleukin [IL]-4, IL-10, transforming growth factor [TGF]-β) cytokines was determined using in situ hybridization. In 6 of 9 samples, inflammation was similar to the pattern of primate active disease with low to moderate numbers of lymphocytes, most of which were CD20 positive. In 1 sample, inflammation was most similar to latent tuberculosis in primates with numerous CD3-positive lymphocytes. Expression of IFN-γ was detected in 3 of 8 tuberculosis-positive samples. Expression of TNF-α was detected in 3 of 8 positive samples, including the one with latent morphology. Low-level expression of IL-4 was present in 4 of 8 positive samples. Only single positive samples displayed expression of IL-10 and TGF-β. Tuberculosis-negative samples generally lacked cytokine expression. Results showed heterogeneity in lesions of elephant tuberculosis similar to those of latent and active disease in primates, with variable expression of both TH1 and TH2 cytokines. © The Author(s) 2014.

2D DOST based local phase pattern for face recognition

NASA Astrophysics Data System (ADS)

Moniruzzaman, Md.; Alam, Mohammad S.

2017-05-01

A new two dimensional (2-D) Discrete Orthogonal Stcokwell Transform (DOST) based Local Phase Pattern (LPP) technique has been proposed for efficient face recognition. The proposed technique uses 2-D DOST as preliminary preprocessing and local phase pattern to form robust feature signature which can effectively accommodate various 3D facial distortions and illumination variations. The S-transform, is an extension of the ideas of the continuous wavelet transform (CWT), is also known for its local spectral phase properties in time-frequency representation (TFR). It provides a frequency dependent resolution of the time-frequency space and absolutely referenced local phase information while maintaining a direct relationship with the Fourier spectrum which is unique in TFR. After utilizing 2-D Stransform as the preprocessing and build local phase pattern from extracted phase information yield fast and efficient technique for face recognition. The proposed technique shows better correlation discrimination compared to alternate pattern recognition techniques such as wavelet or Gabor based face recognition. The performance of the proposed method has been tested using the Yale and extended Yale facial database under different environments such as illumination variation and 3D changes in facial expressions. Test results show that the proposed technique yields better performance compared to alternate time-frequency representation (TFR) based face recognition techniques.

Metastatic pancreatic cancer presenting as linitis plastica of the stomach.

PubMed

Garg, Shivani; Mulki, Ramzi; Sher, Daniel

2016-03-08

Metastatic disease from pancreatic carcinoma involving the stomach is an unusual event, and the pattern of spread in the form of linitis plastica, to our knowledge, has not been reported previously. Local recurrence after curative resection for pancreatic cancer is the most common pattern of disease. We report a case of metastatic pancreatic adenocarcinoma presenting as linitis plastica of the stomach 4 years after curative resection. A 52-year-old man presented with epigastric pain and melaena 4 years after undergoing a Whipple's procedure for a poorly-differentiated pancreatic adenocarcinoma, stage IB; T2N0M0. CT imaging of the abdomen revealed thickening of the gastric wall, and subsequent oesophagogastroduodenoscopy (OGD) revealed diffuse friable erythaematous tissue. The biopsy specimen obtained during the OGD revealed a poorly differentiated adenocarcinoma, with similar appearance to the prior specimen obtained from the pancreas. 2016 BMJ Publishing Group Ltd.

Immunohistochemical distribution of collagens type I, III, IV and VI, of undulin and of tenascin in oral fibrous hyperplasia.

PubMed

Becker, J; Schuppan, D; Müller, S

1993-11-01

The distribution of collagens type I, IV and VI, of procollagen type III, of undulin and of tenascin was studied in 10 lesions which were clinically and histologically diagnosed as localized oral fibrous hyperplasias. The immunohistochemical distribution of these proteins was similar to that observed for normal oral mucosa. Undulin showed a pattern of parallel fibers throughout. Collagen type VI was pronounced in the subepithelial connective tissue, whereas the collagen fiber bundles were equally reactive for collagens type I and III. Tenascin was observed close to the subepithelial basement membrane and in proximity to collagen fiber bundles in the upper connective tissue. The present findings indicate that oral fibrous hyperplasias that are probably caused by inflammation or chronic irritation show the differentiated and ordered pattern of extracellular matrix proteins characteristic of normal oral mucosa.

Substance P binding sites in the nucleus tractus solitarius of the cat

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

Maley, B.E.; Sasek, C.A.; Seybold, V.S.

1988-11-01

Substance P binding sites in the nucleus tractus solitarius were visualized with receptor autoradiography using Bolton-Hunter (/sup 125/I)substance P. Substance P binding sites were found to have distinct patterns within the cat nucleus tractus solitarius. The majority of substance P binding sites were present in the medial, intermediate and the peripheral rim of the parvocellular subdivisions. Lower amounts of substance P binding sites were present in the commissural, ventrolateral, interstitial and dorsolateral subdivisions. No substance P binding sites were present in the central region of the parvocellular subdivision or the solitary tract. The localization of substance P binding sites inmore » the nucleus tractus solitarius is very similar to the patterns of substance P immunoreactive fibers previously described for this region. Results of this study add further support for a functional role of substance P in synaptic circuits of the nucleus tractus solitarius.« less

The Temporal Signature of Memories: Identification of a General Mechanism for Dynamic Memory Replay in Humans

PubMed Central

Michelmann, Sebastian; Bowman, Howard; Hanslmayr, Simon

2016-01-01

Reinstatement of dynamic memories requires the replay of neural patterns that unfold over time in a similar manner as during perception. However, little is known about the mechanisms that guide such a temporally structured replay in humans, because previous studies used either unsuitable methods or paradigms to address this question. Here, we overcome these limitations by developing a new analysis method to detect the replay of temporal patterns in a paradigm that requires participants to mentally replay short sound or video clips. We show that memory reinstatement is accompanied by a decrease of low-frequency (8 Hz) power, which carries a temporal phase signature of the replayed stimulus. These replay effects were evident in the visual as well as in the auditory domain and were localized to sensory-specific regions. These results suggest low-frequency phase to be a domain-general mechanism that orchestrates dynamic memory replay in humans. PMID:27494601

Comparing and modelling land use organization in cities

PubMed Central

Lenormand, Maxime; Picornell, Miguel; Cantú-Ros, Oliva G.; Louail, Thomas; Herranz, Ricardo; Barthelemy, Marc; Frías-Martínez, Enrique; San Miguel, Maxi; Ramasco, José J.

2015-01-01

The advent of geolocated information and communication technologies opens the possibility of exploring how people use space in cities, bringing an important new tool for urban scientists and planners, especially for regions where data are scarce or not available. Here we apply a functional network approach to determine land use patterns from mobile phone records. The versatility of the method allows us to run a systematic comparison between Spanish cities of various sizes. The method detects four major land use types that correspond to different temporal patterns. The proportion of these types, their spatial organization and scaling show a strong similarity between all cities that breaks down at a very local scale, where land use mixing is specific to each urban area. Finally, we introduce a model inspired by Schelling's segregation, able to explain and reproduce these results with simple interaction rules between different land uses. PMID:27019730

Similarity indices based on link weight assignment for link prediction of unweighted complex networks

NASA Astrophysics Data System (ADS)

Liu, Shuxin; Ji, Xinsheng; Liu, Caixia; Bai, Yi

2017-01-01

Many link prediction methods have been proposed for predicting the likelihood that a link exists between two nodes in complex networks. Among these methods, similarity indices are receiving close attention. Most similarity-based methods assume that the contribution of links with different topological structures is the same in the similarity calculations. This paper proposes a local weighted method, which weights the strength of connection between each pair of nodes. Based on the local weighted method, six local weighted similarity indices extended from unweighted similarity indices (including Common Neighbor (CN), Adamic-Adar (AA), Resource Allocation (RA), Salton, Jaccard and Local Path (LP) index) are proposed. Empirical study has shown that the local weighted method can significantly improve the prediction accuracy of these unweighted similarity indices and that in sparse and weakly clustered networks, the indices perform even better.

Along fault friction and fluid pressure effects on the spatial distribution of fault-related fractures

NASA Astrophysics Data System (ADS)

Maerten, Laurent; Maerten, Frantz; Lejri, Mostfa

2018-03-01

Whatever the processes involved in the natural fracture development in the subsurface, fracture patterns are often affected by the local stress field during propagation. This homogeneous or heterogeneous local stress field can be of mechanical and/or tectonic origin. In this contribution, we focus on the fracture-pattern development where active faults perturb the stress field, and are affected by fluid pressure and sliding friction along the faults. We analyse and geomechanically model two fractured outcrops in UK (Nash Point) and in France (Les Matelles). We demonstrate that the observed local radial joint pattern is best explained by local fluid pressure along the faults and that observed fracture pattern can only be reproduced when fault friction is very low (μ < 0.2). Additionally, in the case of sub-vertical faults, we emphasize that the far field horizontal stress ratio does not affect stress trajectories, or fracture patterns, unless fault normal displacement (dilation or contraction) is relatively large.

Modelling control of epidemics spreading by long-range interactions.

PubMed

Dybiec, Bartłomiej; Kleczkowski, Adam; Gilligan, Christopher A

2009-10-06

We have studied the spread of epidemics characterized by a mixture of local and non-local interactions. The infection spreads on a two-dimensional lattice with the fixed nearest neighbour connections. In addition, long-range dynamical links are formed by moving agents (vectors). Vectors perform random walks, with step length distributed according to a thick-tail distribution. Two distributions are considered in this paper, an alpha-stable distribution describing self-similar vector movement, yet characterized by an infinite variance and an exponential power characterized by a large but finite variance. Such long-range interactions are hard to track and make control of epidemics very difficult. We also allowed for cryptic infection, whereby an infected individual on the lattice can be infectious prior to showing any symptoms of infection or disease. To account for such cryptic spread, we considered a control strategy in which not only detected, i.e. symptomatic, individuals but also all individuals within a certain control neighbourhood are treated upon the detection of disease. We show that it is possible to eradicate the disease by using such purely local control measures, even in the presence of long-range jumps. In particular, we show that the success of local control and the choice of the optimal strategy depend in a non-trivial way on the dispersal patterns of the vectors. By characterizing these patterns using the stability index of the alpha-stable distribution to change the power-law behaviour or the exponent characterizing the decay of an exponential power distribution, we show that infection can be successfully contained using relatively small control neighbourhoods for two limiting cases for long-distance dispersal and for vectors that are much more limited in their dispersal range.

Clustering change patterns using Fourier transformation with time-course gene expression data.

PubMed

Kim, Jaehee

2011-01-01

To understand the behavior of genes, it is important to explore how the patterns of gene expression change over a period of time because biologically related gene groups can share the same change patterns. In this study, the problem of finding similar change patterns is induced to clustering with the derivative Fourier coefficients. This work is aimed at discovering gene groups with similar change patterns which share similar biological properties. We developed a statistical model using derivative Fourier coefficients to identify similar change patterns of gene expression. We used a model-based method to cluster the Fourier series estimation of derivatives. We applied our model to cluster change patterns of yeast cell cycle microarray expression data with alpha-factor synchronization. It showed that, as the method clusters with the probability-neighboring data, the model-based clustering with our proposed model yielded biologically interpretable results. We expect that our proposed Fourier analysis with suitably chosen smoothing parameters could serve as a useful tool in classifying genes and interpreting possible biological change patterns.

Holographic Reconstruction of Photoelectron Diffraction and Its Circular Dichroism for Local Structure Probing

NASA Astrophysics Data System (ADS)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

The local atomic structure around a specific element atom can be recorded as a photoelectron diffraction pattern. Forward focusing peaks and diffraction rings around them indicate the directions and distances from the photoelectron emitting atom to the surrounding atoms. The state-of-the-art holography reconstruction algorithm enables us to image the local atomic arrangement around the excited atom in a real space. By using circularly polarized light as an excitation source, the angular momentum transfer from the light to the photoelectron induces parallax shifts in these diffraction patterns. As a result, stereographic images of atomic arrangements are obtained. These diffraction patterns can be used as atomic-site-resolved probes for local electronic structure investigation in combination with spectroscopy techniques. Direct three-dimensional atomic structure visualization and site-specific electronic property analysis methods are reviewed. Furthermore, circular dichroism was also found in valence photoelectron and Auger electron diffraction patterns. The investigation of these new phenomena provides hints for the development of new techniques for local structure probing.

Global/local processing of hierarchical visual stimuli in a conflict-choice task by capuchin monkeys (Sapajus spp.).

PubMed

Truppa, Valentina; Carducci, Paola; De Simone, Diego Antonio; Bisazza, Angelo; De Lillo, Carlo

2017-03-01

In the last two decades, comparative research has addressed the issue of how the global and local levels of structure of visual stimuli are processed by different species, using Navon-type hierarchical figures, i.e. smaller local elements that form larger global configurations. Determining whether or not the variety of procedures adopted to test different species with hierarchical figures are equivalent is of crucial importance to ensure comparability of results. Among non-human species, global/local processing has been extensively studied in tufted capuchin monkeys using matching-to-sample tasks with hierarchical patterns. Local dominance has emerged consistently in these New World primates. In the present study, we assessed capuchins' processing of hierarchical stimuli with a method frequently adopted in studies of global/local processing in non-primate species: the conflict-choice task. Different from the matching-to-sample procedure, this task involved processing local and global information retained in long-term memory. Capuchins were trained to discriminate between consistent hierarchical stimuli (similar global and local shape) and then tested with inconsistent hierarchical stimuli (different global and local shapes). We found that capuchins preferred the hierarchical stimuli featuring the correct local elements rather than those with the correct global configuration. This finding confirms that capuchins' local dominance, typically observed using matching-to-sample procedures, is also expressed as a local preference in the conflict-choice task. Our study adds to the growing body of comparative studies on visual grouping functions by demonstrating that the methods most frequently used in the literature on global/local processing produce analogous results irrespective of extent of the involvement of memory processes.

The problem and promise of scale dependency in community phylogenetics.

PubMed

Swenson, Nathan G; Enquist, Brian J; Pither, Jason; Thompson, Jill; Zimmerman, Jess K

2006-10-01

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Influence of climate on the presence of colour polymorphism in two montane reptile species

PubMed Central

Broennimann, Olivier; Ursenbacher, Sylvain; Meyer, Andreas; Golay, Philippe; Monney, Jean-Claude; Schmocker, Hans; Guisan, Antoine; Dubey, Sylvain

2014-01-01

The coloration of ectotherms plays an important role in thermoregulation processes. Dark individuals should heat up faster and be able to reach a higher body temperature than light individuals and should therefore have benefits in cool areas. In central Europe, montane local populations of adder (Vipera berus) and asp viper (Vipera aspis) exhibit a varying proportion of melanistic individuals. We tested whether the presence of melanistic V. aspis and V. berus could be explained by climatic conditions. We measured the climatic niche position and breadth of monomorphic (including strictly patterned individuals) and polymorphic local populations, calculated their niche overlap and tested for niche equivalency and similarity. In accordance with expectations, niche overlap between polymorphic local populations of both species is high, and even higher than that of polymorphic versus monomorphic montane local populations of V. aspis, suggesting a predominant role of melanism in determining the niche of ectothermic vertebrates. However, unexpectedly, the niche of polymorphic local populations of both species is narrower than that of monomorphic ones, indicating that colour polymorphism does not always enable the exploitation of a greater variability of resources, at least at the intraspecific level. Overall, our results suggest that melanism might be present only when the thermoregulatory benefit is higher than the cost of predation. PMID:25392313

Mercury in mosses Hylocomium splendens (Hedw.) B.S.G. and Pleurozium schreberi (Brid.) Mitt. from Poland and Alaska: Understanding the origin of pollution sources

USGS Publications Warehouse

Migaszewski, Z.M.; Galuszka, A.; Dole, ogonekgowska S.; Crock, J.G.; Lamothe, P.J.

2010-01-01

This report shows baseline concentrations of mercury in the moss species Hylocomium splendens and Pleurozium schreberi from the Kielce area and the remaining Holy Cross Mountains (HCM) region (south-central Poland), and Wrangell-Saint Elias National Park and Preserve (Alaska) and Denali National Park and Preserve (Alaska). Like mosses from many European countries, Polish mosses were distinctly elevated in Hg, bearing a signature of cross-border atmospheric transport combined with local point sources. In contrast, Alaskan mosses showed lower Hg levels, reflecting mostly the underlying geology. Compared to HCM, Alaskan and Kielce mosses exhibited more uneven spatial distribution patterns of Hg. This variation is linked to topography and location of local point sources (Kielce) and underlying geology (Alaska). Both H. splendens and P. schreberi showed similar bioaccumulative capabilities of Hg in all four study areas. ?? 2010 Elsevier Inc.

Community Near-Port Modeling System (C-PORT): Briefing for ...

EPA Pesticide Factsheets

What C-PORT is: Screening level tool for assessing port activities and exploring the range of potential impacts that changes to port operations might have on local air quality; Analysis of decision alternatives through mapping of the likely pattern of potential pollutant dispersion and an estimated change in pollutant concentrations for user-designated scenarios; Designed primarily to evaluate the local air quality impacts of proposed port expansion or modernization, as well as to identify options for mitigating any impacts; Currently includes data from 21 US seaports and features a map-based interface similar to the widely used Google Earth; Still under development, C-PORT is designed as an easy-to-use computer modeling tool for users, such as state air quality managers and planners. This is part of our product outreach prior to model public release and to solicit for additional beta testers.

Moiré-Modulated Conductance of Hexagonal Boron Nitride Tunnel Barriers.

PubMed

Summerfield, Alex; Kozikov, Aleksey; Cheng, Tin S; Davies, Andrew; Cho, Yong-Jin; Khlobystov, Andrei N; Mellor, Christopher J; Foxon, C Thomas; Watanabe, Kenji; Taniguchi, Takashi; Eaves, Laurence; Novoselov, Kostya S; Novikov, Sergei V; Beton, Peter H

2018-06-27

Monolayer hexagonal boron nitride (hBN) tunnel barriers investigated using conductive atomic force microscopy reveal moiré patterns in the spatial maps of their tunnel conductance consistent with the formation of a moiré superlattice between the hBN and an underlying highly ordered pyrolytic graphite (HOPG) substrate. This variation is attributed to a periodc modulation of the local density of states and occurs for both exfoliated hBN barriers and epitaxially grown layers. The epitaxial barriers also exhibit enhanced conductance at localized subnanometer regions which are attributed to exposure of the substrate to a nitrogen plasma source during the high temperature growth process. Our results show clearly a spatial periodicity of tunnel current due to the formation of a moiré superlattice and we argue that this can provide a mechanism for elastic scattering of charge carriers for similar interfaces embedded in graphene/hBN resonant tunnel diodes.

Is fast fiber innervation responsible for increased acetylcholinesterase activity in reinnervating soleus muscles?

NASA Technical Reports Server (NTRS)

Misulis, K. E.; Dettbarn, W. D.

1985-01-01

An investigation was conducted as to whether the predominantly slow SOL, which is low in AChE activity, is initially reinnervated by axons that originally innervated fast muscle fibers with high AChE activity, such as those of the EDL. Local denervation of the SOL in the guinea pig was performed because this muscle is composed solely of slow (type I) fibers; thereby virtually eliminating the possibility of homologous muscle fast fiber innervation. The overshoot in this preparation was qualitatively similar to that seen with distal denervation in the guinea pig and local and distal denervation in the rat. Thus, initial fast fiber innvervation is not responsible for the patterns of change in AChE activity seen with reinnervation in the SOL. It is concluded that the neural control of AChe is different in these two muscles and may reflect specific differences in the characteristics of AChE regulation in fast and slow muscle.

Local Generation and Propagation of Ripples along the Septotemporal Axis of the Hippocampus

PubMed Central

Patel, Jagdish; Schomburg, Erik W.; Berényi, Antal; Fujisawa, Shigeyoshi

2013-01-01

A topographical relationship exists between the septotemporal segments of the hippocampus and their entorhinal–neocortical targets, but the physiological organization of activity along the septotemporal axis is poorly understood. We recorded sharp-wave ripple patterns in rats during sleep from the entire septotemporal axis of the CA1 pyramidal layer. Qualitatively similar ripples emerged at all levels. From the local seed, ripples traveled septally or temporally at a speed of ∼0.35 m/s, and the spatial spread depended on ripple magnitude. Ripples propagated smoothly across the septal and intermediate segments of the hippocampus, but ripples in the temporal segment often remained isolated. These findings show that ripples can combine information from the septal and intermediate hippocampus and transfer integrated signals downstream. In contrast, ripples that emerged in the temporal pole broadcast largely independent information to their cortical and subcortical targets. PMID:24155307

Perceptual and conceptual information processing in schizophrenia and depression.

PubMed

Dreben, E K; Fryer, J H; McNair, D M

1995-04-01

Schizophrenic patients (n = 20), depressive patients (n = 20), and normal adults (n = 20) were compared on global vs local analyses of perceptual information using tachistoscopic tasks and on top-down vs bottom-up conceptual processing using card-sort tasks. The schizophrenic group performed more poorly on tasks requiring either global analyses (counting lines when distracting circles were present) or top-down conceptual processing (rule learning) than they did on tasks requiring local analyses (counting heterogeneous lines) or bottom-up processing (attribute identification). The schizophrenic group appeared not to use conceptually guided processing. Normal adults showed the reverse pattern. The depressive group performed similarly to the schizophrenic group on perceptual tasks but closer to the normal group on conceptual tasks, thereby appearing to be less dependent on a particular information-processing strategy. These deficits in organizational strategy may be related to the use of available processing resources as well as the allocation of attention.

Local Conjecturing Process in the Solving of Pattern Generalization Problem

ERIC Educational Resources Information Center

Sutarto; Nusantara, Toto; Subanji; Sisworo

2016-01-01

This aim of this study is to describe the process of local conjecturing in generalizing patterns based on Action, Process, Object, Schema (APOS) theory. The subjects were 16 grade 8 students from a junior high school. Data collection used Pattern Generalization Problem (PGP) and interviews. In the first stage, students completed PGP; in the second…

Regional homogeneity and functional connectivity patterns in major depressive disorder, cognitive vulnerability to depression and healthy subjects.

PubMed

Sun, Hui; Luo, Lizhu; Yuan, Xinru; Zhang, Lu; He, Yini; Yao, Shuqiao; Wang, Jiaojian; Xiao, Jing

2018-08-01

Cognitive vulnerability to depression (CVD) is a high risk for depressive disorder. Recent studies focus on individuals with CVD to determine the neural basis of major depressive disorder (MDD) neuropathology. However, whether CVD showed specific or similar brain functional activity and connectivity patterns, compared to MDD, remain largely unknown. Here, using resting-state functional magnetic resonance imaging in subjects with CVD, healthy controls (HC) and MDD, regional homogeneity (ReHo) and resting-state functional connectivity (R-FC) analyses were conducted to assess local synchronization and changes in functional connectivity patterns. Significant ReHo differences were found in right posterior lobe of cerebellum (PLC), left lingual gyrus (LG) and precuneus. Compared to HC, CVD subjects showed increased ReHo in the PLC, which was similar to the difference found between MDD and HC. Compared to MDD patients, CVD subjects showed decreased ReHo in PLC, LG, and precuneus. R-FC analyses found increased functional connections between LG and left inferior parietal lobule, posterior cingulate cortex, and dorsolateral prefrontal cortex in CVD compared to both HC and MDD. Moreover, Regional mean ReHo values were positively correlated with Center for Epidemiologic Studies Depression Scale scores. These analyses revealed that PLC and functional connections between LG and left inferior parietal lobule, posterior cingulate cortex, and dorsolateral prefrontal cortex may be a potential marker for CVD. Copyright © 2018 Elsevier B.V. All rights reserved.

Reentrant Information Flow in Electrophysiological Rat Default Mode Network.

PubMed

Jing, Wei; Guo, Daqing; Zhang, Yunxiang; Guo, Fengru; Valdés-Sosa, Pedro A; Xia, Yang; Yao, Dezhong

2017-01-01

Functional MRI (fMRI) studies have demonstrated that the rodent brain shows a default mode network (DMN) activity similar to that in humans, offering a potential preclinical model both for physiological and pathophysiological studies. However, the neuronal mechanism underlying rodent DMN remains poorly understood. Here, we used electrophysiological data to analyze the power spectrum and estimate the directed phase transfer entropy (dPTE) within rat DMN across three vigilance states: wakeful rest (WR), slow-wave sleep (SWS), and rapid-eye-movement sleep (REMS). We observed decreased gamma powers during SWS compared with WR in most of the DMN regions. Increased gamma powers were found in prelimbic cortex, cingulate cortex, and hippocampus during REMS compared with WR, whereas retrosplenial cortex showed a reverse trend. These changed gamma powers are in line with the local metabolic variation of homologous brain regions in humans. In the analysis of directional interactions, we observed well-organized anterior-to-posterior patterns of information flow in the delta band, while opposite patterns of posterior-to-anterior flow were found in the theta band. These frequency-specific opposite patterns were only observed in WR and REMS. Additionally, most of the information senders in the delta band were also the receivers in the theta band, and vice versa. Our results provide electrophysiological evidence that rat DMN is similar to its human counterpart, and there is a frequency-dependent reentry loop of anterior-posterior information flow within rat DMN, which may offer a mechanism for functional integration, supporting conscious awareness.

Lung respiratory rhythm and pattern generation in the bullfrog: role of neurokinin-1 and mu-opioid receptors.

PubMed

Davies, B L; Brundage, C M; Harris, M B; Taylor, B E

2009-07-01

Location of the lung respiratory rhythm generator (RRG) in the bullfrog brainstem was investigated by examining neurokinin-1 and mu-opioid receptor (NK1R, muOR) colocalization by immunohistochemistry and characterizing the role of these receptors in lung rhythm and episodic pattern generation. NK1R and muOR occurred in brainstems from all developmental stages. In juvenile bullfrogs a distinct area of colocalization was coincident with high-intensity fluorescent labeling of muOR; high-intensity labeling of muOR was not distinctly and consistently localized in tadpole brainstems. NK1R labeling intensity did not change with development. Similarity in colocalization is consistent with similarity in responses to substance P (SP, NK1R agonist) and DAMGO (muOR agonist) when bath applied to bullfrog brainstems of different developmental stages. In early stage tadpoles and juvenile bullfrogs, SP increased and DAMGO decreased lung burst frequency. In juvenile bullfrogs, SP increased lung burst frequency, episode frequency, but decreased number of lung bursts per episode and lung burst duration. In contrast, DAMGO decreased lung burst frequency and burst cycle frequency, episode frequency, and number of lung bursts per episode but increased all other lung burst parameters. Based on these results, we hypothesize that NK1R and muOR colocalization together with a metamorphosis-related increase in muOR intensity marks the location of the lung RRG but not necessarily the lung episodic pattern generator.

Total levels, localization patterns, and proportions of sperm exhibiting phospholipase C zeta are significantly correlated with fertilization rates after intracytoplasmic sperm injection.

PubMed

Yelumalai, Suseela; Yeste, Marc; Jones, Celine; Amdani, Siti N; Kashir, Junaid; Mounce, Ginny; Da Silva, Sarah J Martins; Barratt, Christopher L; McVeigh, Enda; Coward, Kevin

2015-09-01

To study the relationship of total levels, localization patterns, and proportions of sperm exhibiting phospholipase C zeta, with fertilization rates after in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). Laboratory study; controls vs. patients after IVF (n = 27) or ICSI (n = 17) treatment. Fertility center. A total of 44 semen samples, subjected to either IVF or ICSI treatment. Oocyte collection, ICSI or IVF, determination of sperm concentration and motility, and immunocytochemical analyses of phospholipase C zeta (PLCζ). None. Percentages of sperm exhibiting PLCζ. Significant positive correlation between ICSI fertilization rates and total levels, localization patterns, and the proportion (percentage) of sperm exhibiting PLCζ. Total levels, localization patterns, and the proportion of sperm exhibiting PLCζ are correlated with fertilization rates for ICSI, but not for IVF. Evaluating total levels, localization patterns, and proportions of PLCζ may represent a useful diagnostic tool for clinical purposes in men for whom IVF is not advised or has previously failed. This clinical study further supports the fundamental role of PLCζ in the oocyte activation process. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Mammalian Biogeography and the Latitudinal Climatic Gradient in Western North America During the Paleocene Evolutionary Radiation of Mammals (Invited)

NASA Astrophysics Data System (ADS)

Fox, D. L.; Rose, P.

2010-12-01

We use the middle Paleocene (ca. 63-58) mammalian fossil record of western North America to examine the latitudinal gradients in both species richness and body size of mammals during their evolutionary radiation following the Cretaceous-Paleogene mass extinction. Decreasing species richness with latitude is a biogeographic pattern common to most clades today, including mammals, and is linked to climatic gradients; an inverse relationship between body size and environmental temperature (Bergmann’s rule) is well-known both within and among species of living endothermic vertebrates, including diverse clades of mammals. Despite the frequency among mammals of these patterns today, their long-term histories in the fossil record is not well documented. We compiled mammalian taxonomic occurrence data from published literature, online museum collection databases, and the Paleobiology Database for roughly 160 Torrejonian (To, ca. 63-60 Ma) and Tiffanian (Ti, ca. 60-58 Ma) North American Land Mammal Age fossil localities in western North America from Texas to Alberta. These localities were binned into nine geographic regions based on paleolatitude, and the centroids of the regions span ca. 28° of latitude. For the faunas from these regions, we compiled body size data from the literature for 170 Paleocene (Torrejonian and Tiffanian) mammal species, using lower first molar area (m1 LxW) as a proxy for body mass. The phosphate oxygen isotope composition of teeth from species of a single clade of herbivorous mammals (Phenacodontidae) indicates that mid-Paleocene latitudinal climate gradients were broadly similar to modern gradients in the region, so we treat paleolatitude as a proxy for temperature. Slopes of separate least squares linear regressions of rarefied To and Ti species richness on paleolatitude are not significantly different from zero, and the regressions explain only a small fraction of the variances in richness. For all species, m1 area has a statistically significant negative relationship with paleolatitude. For both analyses, results are similar at the genus levels. In eight species that occur in four or more regions, none demonstrate a statistically significant increase in m1 area with latitude. Thus, despite climatic gradients in the mid-Paleocene that were similar to modern gradients, mammals in the region during the Paleocene appear to violate two essentially canonical biogeographic patterns seen in modern mammals and diverse other organisms, potentially ruling out climate as a long-term control on these patterns. The contrasts between the biogeography of modern and mid-Paleocene mammals in the region could result from distinct community ecology of faunas dominated by extinct “archaic” clades of mammals, ongoing ecological recovery after the Cretaceous-Paleogene extinction, and/or the modern biogeographic patterns being geologically recent or episodic phenomenon and not long-term characteristics of the geographic distribution of mammalian species richness or body size.

Climate network analysis of regional precipitation extremes: The true story told by event synchronization

NASA Astrophysics Data System (ADS)

Odenweller, Adrian; Donner, Reik V.

2017-04-01

Over the last decade, complex network methods have been frequently used for characterizing spatio-temporal patterns of climate variability from a complex systems perspective, yielding new insights into time-dependent teleconnectivity patterns and couplings between different components of the Earth climate. Among the foremost results reported, network analyses of the synchronicity of extreme events as captured by the so-called event synchronization have been proposed to be powerful tools for disentangling the spatio-temporal organization of particularly extreme rainfall events and anticipating the timing of monsoon onsets or extreme floodings. Rooted in the analysis of spike train synchrony analysis in the neurosciences, event synchronization has the great advantage of automatically classifying pairs of events arising at two distinct spatial locations as temporally close (and, thus, possibly statistically - or even dynamically - interrelated) or not without the necessity of selecting an additional parameter in terms of a maximally tolerable delay between these events. This consideration is conceptually justified in case of the original application to spike trains in electroencephalogram (EEG) recordings, where the inter-spike intervals show relatively narrow distributions at high temporal sampling rates. However, in case of climate studies, precipitation extremes defined by daily precipitation sums exceeding a certain empirical percentile of their local distribution exhibit a distinctively different type of distribution of waiting times between subsequent events. This raises conceptual concerns if event synchronization is still appropriate for detecting interlinkages between spatially distributed precipitation extremes. In order to study this problem in more detail, we employ event synchronization together with an alternative similarity measure for event sequences, event coincidence rates, which requires a manual setting of the tolerable maximum delay between two events to be considered potentially related. Both measures are then used to generate climate networks from parts of the satellite-based TRMM precipitation data set at daily resolution covering the Indian and East Asian monsoon domains, respectively, thereby reanalysing previously published results. The obtained spatial patterns of degree densities and local clustering coefficients exhibit marked differences between both similarity measures. Specifically, we demonstrate that there exists a strong relationship between the fraction of extremes occurring at subsequent days and the degree density in the event synchronization based networks, suggesting that the spatial patterns obtained using this approach are strongly affected by the presence of serial dependencies between events. Given that a manual selection of the maximally tolerable delay between two events can be guided by a priori climatological knowledge and even used for systematic testing of different hypotheses on climatic processes underlying the emergence of spatio-temporal patterns of extreme precipitation, our results provide evidence that event coincidence rates are a more appropriate statistical characteristic for similarity assessment and network construction for climate extremes, while results based on event synchronization need to be interpreted with great caution.

Parallel and competitive processes in hierarchical analysis: perceptual grouping and encoding of closure.

PubMed

Han, S; Humphreys, G W; Chen, L

1999-10-01

The role of perceptual grouping and the encoding of closure of local elements in the processing of hierarchical patterns was studied. Experiments 1 and 2 showed a global advantage over the local level for 2 tasks involving the discrimination of orientation and closure, but there was a local advantage for the closure discrimination task relative to the orientation discrimination task. Experiment 3 showed a local precedence effect for the closure discrimination task when local element grouping was weakened by embedding the stimuli from Experiment 1 in a background made up of cross patterns. Experiments 4A and 4B found that dissimilarity of closure between the local elements of hierarchical stimuli and the background figures could facilitate the grouping of closed local elements and enhanced the perception of global structure. Experiment 5 showed that the advantage for detecting the closure of local elements in hierarchical analysis also held under divided- and selective-attention conditions. Results are consistent with the idea that grouping between local elements takes place in parallel and competes with the computation of closure of local elements in determining the selection between global and local levels of hierarchical patterns for response.

Complex Patterns of Local Adaptation in Teosinte

PubMed Central

Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

2013-01-01

Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

Nanoscale observation of local bound charges of patterned protein arrays by scanning force microscopy

NASA Astrophysics Data System (ADS)

Oh, Y. J.; Jo, W.; Kim, S.; Park, S.; Kim, Y. S.

2008-09-01

A protein patterned surface using micro-contact printing methods has been investigated by scanning force microscopy. Electrostatic force microscopy (EFM) was utilized for imaging the topography and detecting the electrical properties such as the local bound charge distribution of the patterned proteins. It was found that the patterned IgG proteins are arranged down to 1 µm, and the 90° rotation of patterned anti-IgG proteins was successfully undertaken. Through the estimation of the effective areas, it was possible to determine the local bound charges of patterned proteins which have opposite electrostatic force behaviors. Moreover, we studied the binding probability between IgG and anti-IgG in a 1 µm2 MIMIC system by topographic and electrostatic signals for applicable label-free detections. We showed that the patterned proteins can be used for immunoassay of proteins on the functional substrate, and that they can also be used for bioelectronics device application, indicating distinct advantages with regard to accuracy and a label-free detection.

Self-similar grid patterns in free-space shuffle-exchange networks

NASA Astrophysics Data System (ADS)

Haney, Michael W.

1993-12-01

Self-similar grid patterns are proposed as an alternative to rectangular grid, array optoelectronic sources, and detectors of smart pixels. For shuffle based multistage interconnection networks, it is suggested that smart pixel should not be arrayed on a rectangular grid and that smart pixel unit cell should be the kernel of a self-similar grid pattern.

Neural Pattern Similarity in the Left IFG and Fusiform Is Associated with Novel Word Learning

PubMed Central

Qu, Jing; Qian, Liu; Chen, Chuansheng; Xue, Gui; Li, Huiling; Xie, Peng; Mei, Leilei

2017-01-01

Previous studies have revealed that greater neural pattern similarity across repetitions is associated with better subsequent memory. In this study, we used an artificial language training paradigm and representational similarity analysis to examine whether neural pattern similarity across repetitions before training was associated with post-training behavioral performance. Twenty-four native Chinese speakers were trained to learn a logographic artificial language for 12 days and behavioral performance was recorded using the word naming and picture naming tasks. Participants were scanned while performing a passive viewing task before training, after 4-day training and after 12-day training. Results showed that pattern similarity in the left pars opercularis (PO) and fusiform gyrus (FG) before training was negatively associated with reaction time (RT) in both word naming and picture naming tasks after training. These results suggest that neural pattern similarity is an effective neurofunctional predictor of novel word learning in addition to word memory. PMID:28878640

Hydroclimatic variability in the Lake Mondsee region and its relationships with large-scale climate anomaly patterns

NASA Astrophysics Data System (ADS)

Rimbu, Norel; Ionita, Monica; Swierczynski, Tina; Brauer, Achim; Kämpf, Lucas; Czymzik, Markus

2017-04-01

Flood triggered detrital layers in varved sediments of Lake Mondsee, located at the northern fringe of the European Alps (47°48'N,13°23'E), provide an important archive of regional hydroclimatic variability during the mid- to late Holocene. To improve the interpretation of the flood layer record in terms of large-scale climate variability, we investigate the relationships between observational hydrological records from the region, like the Mondsee lake level, the runoff of the lake's main inflow Griesler Ache, with observed precipitation and global climate patterns. The lake level shows a strong positive linear trend during the observational period in all seasons. Additionally, lake level presents important interannual to multidecadal variations. These variations are associated with distinct seasonal atmospheric circulation patterns. A pronounced anomalous anticyclonic center over the Iberian Peninsula is associated with high lake levels values during winter. This center moves southwestward during spring, summer and autumn. In the same time, a cyclonic anomaly center is recorded over central and western Europe. This anomalous circulation extends southwestward from winter to autumn. Similar atmospheric circulation patterns are associated with river runoff and precipitation variability from the region. High lake levels are associated with positive local precipitation anomalies in all seasons as well as with negative local temperature anomalies during spring, summer and autumn. A correlation analysis reveals that lake level, runoff and precipitation variability is related to large-scale sea surface temperature anomaly patterns in all seasons suggesting a possible impact of large-scale climatic modes, like the North Atlantic Oscillation and Atlantic Multidecadal Oscillation on hydroclimatic variability in the Lake Mondsee region. The results presented in this study can be used for a more robust interpretation of the long flood layer record from Lake Mondsee sediments in terms of regional and large-scale climate variability during the past.

Intraspecific karyotypic polymorphism is highly concordant with allozyme variation in Lysimachia mauritiana (Primulaceae: Myrsinoideae) in Taiwan: implications for the colonization history and dispersal patterns of coastal plants

PubMed Central

Kono, Yoshiko; Chung, Kuo-Fang; Chen, Chih-Hui; Hoshi, Yoshikazu; Setoguchi, Hiroaki; Chou, Chang-Hung; Oginuma, Kazuo; Peng, Ching-I

2012-01-01

Background and Aims Investigating intraspecific karyotypic and genetic variations jointly can provide unique insights into how historical, ecological and cytogenetic factors influence microevolution. A coastal herb, Lysimachia mauritiana, exhibits extensive karyotypic polymorphism and displays a complex cytogeographic pattern across the Ryukyus. To explore whether a similar degree of chromosomal variation exists south of the Ryukyus, and in an attempt to ascertain the mechanisms that may have generated the patterns, comprehensive sampling was conducted in Taiwan. Methods Karyotypes were analysed at mitotic metaphase for 550 individuals from 42 populations throughout Taiwan Proper and its adjacent islands. In addition, genetic variation was estimated using 12 allozymes (21 loci) of 314 individuals sampled from 12 localities. Key Results Four chromosome numbers and eight cytotypes, including four endemic cytotypes, were detected. Cytotype distributions were highly structured geographically, with single cytotypes present in most populations and four major cytotypes dominating the north, east and south of Taiwan and the Penghu Archipelago. Allozyme variation was very low and F-statistics indicated an extremely high level of population differentiation, implying limited gene flow among populations. Cluster analysis of allozyme variation uncovered four geographic groups, each corresponding perfectly to the four dominant cytotypes. The geographic structure of cytotype distribution and allozyme variation probably resulted from severe genetic drift triggered by genetic bottlenecks, suggesting that Taiwanese populations were likely to be derived from four independent founder events. In the few localities with multiple cytotypes, cytogeographic patterns and inferences of chromosomal evolution revealed a trend of northward dispersal, consistent with the course of the Kuroshio Current that has been influential in shaping the coastal biota of the region. Conclusions The data elucidate the patterns of colonization and the effects of the Kuroshio Current on the distribution of L. mauritiana in Taiwan. These inferences are highly relevant to other coastal plant species in the region and will stimulate further studies. PMID:23022678

Accumulation of PCB congeners in nestling tree swallows (Tachycineta bicolor) on the Hudson River, New York

USGS Publications Warehouse

Echols, Kathy R.; Tillitt, Donald E.; Nichols, John W.; Secord, Anne L.; McCarty, John P.

2004-01-01

Tree swallows (Tachycineta bicolor) were used as a sentinel species to monitor the contamination and bioavailability of polychlorinated biphenyls (PCBs) in the Hudson River watershed. Several tree swallow nest box colonies around and downstream from Hudson Falls, NY, were studied. Tree swallow eggs, adults, and 5-, 10-, and 15-day-old nestlings were collected and analyzed for 103 PCB congeners. Emergent insects collected by net (primarily Odonata) or as a food bolus (primarily Diptera) taken from the mouths of adult tree swallows returning to the nest were analyzed in the same manner. Total PCB concentrations (wet weight) in eggs from two contaminated sites ranged from 9000 to 25 000 ng/g and accumulated to 32 000 and 96 000 ng/g in 15-day-old nestling at two contaminated sites. The congener patterns of PCBs in eggs, nestlings, and adults were compared to those found in emergent insects (Odonata and Diptera) using principal components analysis. The PCB patterns of the biota differed from that of Aroclor technical mixtures. PCB patterns in adult tree swallows were similar to those in eggs, while the patterns in dietary insects were similar to nestling tree swallows. Uptake rate constants were determined for tree swallow nestlings and compared between the two contaminated sites. The estimated PCB congener uptake rate constants were 0.008-0.02 d-1 based on uptake in nestlings until day 15 post-hatch. The rate constants were comparable between the two study areas and may be used to predict nestling contamination at other locations. Our studies confirm the utility of nestling tree swallows to evaluate localized PCB contamination.

Diversification patterns in cosmopolitan earthworms: similar mode but different tempo.

PubMed

Fernández, Rosa; Novo, Marta; Marchán, Daniel F; Díaz Cosín, Darío J

2016-01-01

Comparative phylogeography of widespread species that span the same geographic areas can elucidate the influence of historical events on current patterns of biodiversity, identify patterns of co-vicariance, and therefore aid the understanding of general evolutionary processes. Soil-dwelling animals present characteristics that make them suitable for testing the effect of the palaeogeographical events on their distribution and diversification, such as their low vagility and population structure. In this study, we shed light on the spatial lineage diversification and cladogenesis of two widely-distributed cosmopolitan and invasive earthworms (Aporrectodea rosea and A. trapezoides) in their putative ancestral area of origin, the Western Palearctic, and a few populations in North America. Molecular analyses were conducted on mitochondrial and nuclear markers from 220 (A. rosea) and 198 (A. trapezoides) individuals collected in 56 and 57 localities, respectively. We compared the lineage diversification pattern, genetic variability and cladogenesis in both species. Our findings showed that both species underwent a similar diversification from the Western Mediterranean plates to (i) Northern Europe and (ii) the Iberian Peninsula, establishing their two main lineages. Their diversification was in concordance with the main palaeogeographical events in the Iberian Peninsula and Western Mediterranean, followed by a later colonization of North America from individuals derived exclusively from the Eurosiberian lineage. Their diversification occurred at different times, with the diversification of A. rosea being potentially more ancient. Cladogenesis in both species seems to have been modelled only by the Mediterranean plate shifts, ignoring historical climatic oscillations such as the Messinian salinity crisis. Their high genetic variability, strong population structure, lack of gene flow and stepping-stone-like cladogenesis suggest the existence of different cryptic lineages. Our results may indicate a recurrent event in invasive earthworms within their ancestral distribution areas in the Western Palearctic. Copyright © 2015 Elsevier Inc. All rights reserved.

HOTS: A Hierarchy of Event-Based Time-Surfaces for Pattern Recognition.

PubMed

Lagorce, Xavier; Orchard, Garrick; Galluppi, Francesco; Shi, Bertram E; Benosman, Ryad B

2017-07-01

This paper describes novel event-based spatio-temporal features called time-surfaces and how they can be used to create a hierarchical event-based pattern recognition architecture. Unlike existing hierarchical architectures for pattern recognition, the presented model relies on a time oriented approach to extract spatio-temporal features from the asynchronously acquired dynamics of a visual scene. These dynamics are acquired using biologically inspired frameless asynchronous event-driven vision sensors. Similarly to cortical structures, subsequent layers in our hierarchy extract increasingly abstract features using increasingly large spatio-temporal windows. The central concept is to use the rich temporal information provided by events to create contexts in the form of time-surfaces which represent the recent temporal activity within a local spatial neighborhood. We demonstrate that this concept can robustly be used at all stages of an event-based hierarchical model. First layer feature units operate on groups of pixels, while subsequent layer feature units operate on the output of lower level feature units. We report results on a previously published 36 class character recognition task and a four class canonical dynamic card pip task, achieving near 100 percent accuracy on each. We introduce a new seven class moving face recognition task, achieving 79 percent accuracy.This paper describes novel event-based spatio-temporal features called time-surfaces and how they can be used to create a hierarchical event-based pattern recognition architecture. Unlike existing hierarchical architectures for pattern recognition, the presented model relies on a time oriented approach to extract spatio-temporal features from the asynchronously acquired dynamics of a visual scene. These dynamics are acquired using biologically inspired frameless asynchronous event-driven vision sensors. Similarly to cortical structures, subsequent layers in our hierarchy extract increasingly abstract features using increasingly large spatio-temporal windows. The central concept is to use the rich temporal information provided by events to create contexts in the form of time-surfaces which represent the recent temporal activity within a local spatial neighborhood. We demonstrate that this concept can robustly be used at all stages of an event-based hierarchical model. First layer feature units operate on groups of pixels, while subsequent layer feature units operate on the output of lower level feature units. We report results on a previously published 36 class character recognition task and a four class canonical dynamic card pip task, achieving near 100 percent accuracy on each. We introduce a new seven class moving face recognition task, achieving 79 percent accuracy.

Association mining of dependency between time series

NASA Astrophysics Data System (ADS)

Hafez, Alaaeldin

2001-03-01

Time series analysis is considered as a crucial component of strategic control over a broad variety of disciplines in business, science and engineering. Time series data is a sequence of observations collected over intervals of time. Each time series describes a phenomenon as a function of time. Analysis on time series data includes discovering trends (or patterns) in a time series sequence. In the last few years, data mining has emerged and been recognized as a new technology for data analysis. Data Mining is the process of discovering potentially valuable patterns, associations, trends, sequences and dependencies in data. Data mining techniques can discover information that many traditional business analysis and statistical techniques fail to deliver. In this paper, we adapt and innovate data mining techniques to analyze time series data. By using data mining techniques, maximal frequent patterns are discovered and used in predicting future sequences or trends, where trends describe the behavior of a sequence. In order to include different types of time series (e.g. irregular and non- systematic), we consider past frequent patterns of the same time sequences (local patterns) and of other dependent time sequences (global patterns). We use the word 'dependent' instead of the word 'similar' for emphasis on real life time series where two time series sequences could be completely different (in values, shapes, etc.), but they still react to the same conditions in a dependent way. In this paper, we propose the Dependence Mining Technique that could be used in predicting time series sequences. The proposed technique consists of three phases: (a) for all time series sequences, generate their trend sequences, (b) discover maximal frequent trend patterns, generate pattern vectors (to keep information of frequent trend patterns), use trend pattern vectors to predict future time series sequences.

Local control of globally competing patterns in coupled Swift-Hohenberg equations

NASA Astrophysics Data System (ADS)

Becker, Maximilian; Frenzel, Thomas; Niedermayer, Thomas; Reichelt, Sina; Mielke, Alexander; Bär, Markus

2018-04-01

We present analytical and numerical investigations of two anti-symmetrically coupled 1D Swift-Hohenberg equations (SHEs) with cubic nonlinearities. The SHE provides a generic formulation for pattern formation at a characteristic length scale. A linear stability analysis of the homogeneous state reveals a wave instability in addition to the usual Turing instability of uncoupled SHEs. We performed weakly nonlinear analysis in the vicinity of the codimension-two point of the Turing-wave instability, resulting in a set of coupled amplitude equations for the Turing pattern as well as left- and right-traveling waves. In particular, these complex Ginzburg-Landau-type equations predict two major things: there exists a parameter regime where multiple different patterns are stable with respect to each other and that the amplitudes of different patterns interact by local mutual suppression. In consequence, different patterns can coexist in distinct spatial regions, separated by localized interfaces. We identified specific mechanisms for controlling the position of these interfaces, which distinguish what kinds of patterns the interface connects and thus allow for global pattern selection. Extensive simulations of the original SHEs confirm our results.

Characterizing the correlations between local phase fractions of gas-liquid two-phase flow with wire-mesh sensor.

PubMed

Tan, C; Liu, W L; Dong, F

2016-06-28

Understanding of flow patterns and their transitions is significant to uncover the flow mechanics of two-phase flow. The local phase distribution and its fluctuations contain rich information regarding the flow structures. A wire-mesh sensor (WMS) was used to study the local phase fluctuations of horizontal gas-liquid two-phase flow, which was verified through comparing the reconstructed three-dimensional flow structure with photographs taken during the experiments. Each crossing point of the WMS is treated as a node, so the measurement on each node is the phase fraction in this local area. An undirected and unweighted flow pattern network was established based on connections that are formed by cross-correlating the time series of each node under different flow patterns. The structure of the flow pattern network reveals the relationship of the phase fluctuations at each node during flow pattern transition, which is then quantified by introducing the topological index of the complex network. The proposed analysis method using the WMS not only provides three-dimensional visualizations of the gas-liquid two-phase flow, but is also a thorough analysis for the structure of flow patterns and the characteristics of flow pattern transition. This article is part of the themed issue 'Supersensing through industrial process tomography'. © 2016 The Author(s).

Characterizing the correlations between local phase fractions of gas–liquid two-phase flow with wire-mesh sensor

PubMed Central

Liu, W. L.; Dong, F.

2016-01-01

Understanding of flow patterns and their transitions is significant to uncover the flow mechanics of two-phase flow. The local phase distribution and its fluctuations contain rich information regarding the flow structures. A wire-mesh sensor (WMS) was used to study the local phase fluctuations of horizontal gas–liquid two-phase flow, which was verified through comparing the reconstructed three-dimensional flow structure with photographs taken during the experiments. Each crossing point of the WMS is treated as a node, so the measurement on each node is the phase fraction in this local area. An undirected and unweighted flow pattern network was established based on connections that are formed by cross-correlating the time series of each node under different flow patterns. The structure of the flow pattern network reveals the relationship of the phase fluctuations at each node during flow pattern transition, which is then quantified by introducing the topological index of the complex network. The proposed analysis method using the WMS not only provides three-dimensional visualizations of the gas–liquid two-phase flow, but is also a thorough analysis for the structure of flow patterns and the characteristics of flow pattern transition. This article is part of the themed issue ‘Supersensing through industrial process tomography’. PMID:27185959

SpolSimilaritySearch - A web tool to compare and search similarities between spoligotypes of Mycobacterium tuberculosis complex.

PubMed

Couvin, David; Zozio, Thierry; Rastogi, Nalin

2017-07-01

Spoligotyping is one of the most commonly used polymerase chain reaction (PCR)-based methods for identification and study of genetic diversity of Mycobacterium tuberculosis complex (MTBC). Despite its known limitations if used alone, the methodology is particularly useful when used in combination with other methods such as mycobacterial interspersed repetitive units - variable number of tandem DNA repeats (MIRU-VNTRs). At a worldwide scale, spoligotyping has allowed identification of information on 103,856 MTBC isolates (corresponding to 98049 clustered strains plus 5807 unique isolates from 169 countries of patient origin) contained within the SITVIT2 proprietary database of the Institut Pasteur de la Guadeloupe. The SpolSimilaritySearch web-tool described herein (available at: http://www.pasteur-guadeloupe.fr:8081/SpolSimilaritySearch) incorporates a similarity search algorithm allowing users to get a complete overview of similar spoligotype patterns (with information on presence or absence of 43 spacers) in the aforementioned worldwide database. This tool allows one to analyze spread and evolutionary patterns of MTBC by comparing similar spoligotype patterns, to distinguish between widespread, specific and/or confined patterns, as well as to pinpoint patterns with large deleted blocks, which play an intriguing role in the genetic epidemiology of M. tuberculosis. Finally, the SpolSimilaritySearch tool also provides with the country distribution patterns for each queried spoligotype. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biological pattern formation: from basic mechanisms to complex structures

NASA Astrophysics Data System (ADS)

Koch, A. J.; Meinhardt, H.

1994-10-01

The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns? Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of Drosophila and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

Social interactions elicit rapid shifts in functional connectivity in the social decision-making network of zebrafish

PubMed Central

Teles, Magda C.; Almeida, Olinda; Lopes, João S.; Oliveira, Rui F.

2015-01-01

According to the social decision-making (SDM) network hypothesis, SDM is encoded in a network of forebrain and midbrain structures in a distributed and dynamic fashion, such that the expression of a given social behaviour is better reflected by the overall profile of activation across the different loci rather than by the activity of a single node. This proposal has the implicit assumption that SDM relies on integration across brain regions, rather than on regional specialization. Here we tested the occurrence of functional localization and of functional connectivity in the SDM network. For this purpose we used zebrafish to map different social behaviour states into patterns of neuronal activity, as indicated by the expression of the immediate early genes c-fos and egr-1, across the SDM network. The results did not support functional localization, as some loci had similar patterns of activity associated with different social behaviour states, and showed socially driven changes in functional connectivity. Thus, this study provides functional support to the SDM network hypothesis and suggests that the neural context in which a given node of the network is operating (i.e. the state of its interconnected areas) is central to its functional relevance. PMID:26423839

Social interactions elicit rapid shifts in functional connectivity in the social decision-making network of zebrafish.

PubMed

Teles, Magda C; Almeida, Olinda; Lopes, João S; Oliveira, Rui F

2015-10-07

According to the social decision-making (SDM) network hypothesis, SDM is encoded in a network of forebrain and midbrain structures in a distributed and dynamic fashion, such that the expression of a given social behaviour is better reflected by the overall profile of activation across the different loci rather than by the activity of a single node. This proposal has the implicit assumption that SDM relies on integration across brain regions, rather than on regional specialization. Here we tested the occurrence of functional localization and of functional connectivity in the SDM network. For this purpose we used zebrafish to map different social behaviour states into patterns of neuronal activity, as indicated by the expression of the immediate early genes c-fos and egr-1, across the SDM network. The results did not support functional localization, as some loci had similar patterns of activity associated with different social behaviour states, and showed socially driven changes in functional connectivity. Thus, this study provides functional support to the SDM network hypothesis and suggests that the neural context in which a given node of the network is operating (i.e. the state of its interconnected areas) is central to its functional relevance. © 2015 The Author(s).

Characterising an intense PM pollution episode in March 2015 in France from multi-site approach and near real time data: Climatology, variabilities, geographical origins and model evaluation

NASA Astrophysics Data System (ADS)

Petit, J.-E.; Amodeo, T.; Meleux, F.; Bessagnet, B.; Menut, L.; Grenier, D.; Pellan, Y.; Ockler, A.; Rocq, B.; Gros, V.; Sciare, J.; Favez, O.

2017-04-01

During March 2015, a severe and large-scale particulate matter (PM) pollution episode occurred in France. Measurements in near real-time of the major chemical composition at four different urban background sites across the country (Paris, Creil, Metz and Lyon) allowed the investigation of spatiotemporal variabilities during this episode. A climatology approach showed that all sites experienced clear unusual rain shortage, a pattern that is also found on a longer timescale, highlighting the role of synoptic conditions over Wester-Europe. This episode is characterized by a strong predominance of secondary pollution, and more particularly of ammonium nitrate, which accounted for more than 50% of submicron aerosols at all sites during the most intense period of the episode. Pollution advection is illustrated by similar variabilities in Paris and Creil (distant of around 100 km), as well as trajectory analyses applied on nitrate and sulphate. Local sources, especially wood burning, are however found to contribute to local/regional sub-episodes, notably in Metz. Finally, simulated concentrations from Chemistry-Transport model CHIMERE were compared to observed ones. Results highlighted different patterns depending on the chemical components and the measuring site, reinforcing the need of such exercises over other pollution episodes and sites.

Declining Dioxin concentrations in the Rhone River, France, attest to the effectiveness of emissions controls

USGS Publications Warehouse

Van Metre, Peter C.; Babut, Marc; Mourier, Brice; Mahler, Barbara J.; Roux, Gwenaelle; Desmet, Marc

2015-01-01

Emission-control policies have been implemented in Europe and North America since the 1990s for polychlorodibenzodioxins (PCDDs) and furans (PCDFs). To assess the effect of these policies on temporal trends and spatial patterns for these compounds in a large European river system, sediment cores were collected in seven depositional areas along the Rhone River in France, dated, and analyzed for PCDDs and PCDFs. Results show concentrations increase in the downstream direction and have decreased temporally at all sites during the last two decades, with an average decrease of 83% from 1992 to 2010. The time for a 50% decrease in concentrations (t1/2) averaged 6.9 ± 2.6 and 9.1 ± 2.9 years for the sum of measured PCDDs and PCDFs, respectively. Congener patterns are similar among cores and indicate dominance of regional atmospheric deposition and possibly weathered local sources. Local sources are clearly indicated at the most downstream site, where concentrations of the most toxic dioxin, TCDD, are about 2 orders of magnitude higher than at the other six sites. The relatively steep downward trends attest to the effects of the dioxin emissions reduction policy in Europe and suggest that risks posed to aquatic life in the Rhone River basin from dioxins and furans have been greatly reduced.

Buffer kinetics shape the spatiotemporal patterns of IP3-evoked Ca2+ signals

PubMed Central

Dargan, Sheila L; Parker, Ian

2003-01-01

Ca2+ liberation through inositol 1,4,5-trisphosphate receptors (IP3Rs) plays a universal role in cell regulation, and specificity of cell signalling is achieved through the spatiotemporal patterning of Ca2+ signals. IP3Rs display Ca2+-induced Ca2+ release (CICR), but are grouped in clusters so that regenerative Ca2+ signals may remain localized to individual clusters, or propagate globally between clusters by successive cycles of Ca2+ diffusion and CICR. We used confocal microscopy and photoreleased IP3 in Xenopus oocytes to study how these properties are modulated by mobile cytosolic Ca2+ buffers. EGTA (a buffer with slow ‘on-rate’) speeded Ca2+ signals and ‘balkanized’ Ca2+ waves by dissociating them into local signals. In contrast, BAPTA (a fast buffer with similar affinity) slowed Ca2+ responses and promoted ‘globalization’ of spatially uniform Ca2+ signals. These actions are likely to arise through differential effects on Ca2+ feedback within and between IP3R clusters, because Ca2+ signals evoked by influx through voltage-gated channels were little affected. We propose that cell-specific expression of Ca2+-binding proteins with distinct kinetics may shape the time course and spatial distribution of IP3-evoked Ca2+ signals for specific physiological roles. PMID:14555715

Community Detection in Complex Networks via Clique Conductance.

PubMed

Lu, Zhenqi; Wahlström, Johan; Nehorai, Arye

2018-04-13

Network science plays a central role in understanding and modeling complex systems in many areas including physics, sociology, biology, computer science, economics, politics, and neuroscience. One of the most important features of networks is community structure, i.e., clustering of nodes that are locally densely interconnected. Communities reveal the hierarchical organization of nodes, and detecting communities is of great importance in the study of complex systems. Most existing community-detection methods consider low-order connection patterns at the level of individual links. But high-order connection patterns, at the level of small subnetworks, are generally not considered. In this paper, we develop a novel community-detection method based on cliques, i.e., local complete subnetworks. The proposed method overcomes the deficiencies of previous similar community-detection methods by considering the mathematical properties of cliques. We apply the proposed method to computer-generated graphs and real-world network datasets. When applied to networks with known community structure, the proposed method detects the structure with high fidelity and sensitivity. When applied to networks with no a priori information regarding community structure, the proposed method yields insightful results revealing the organization of these complex networks. We also show that the proposed method is guaranteed to detect near-optimal clusters in the bipartition case.

Quantification of DNA cleavage specificity in Hi-C experiments.

PubMed

Meluzzi, Dario; Arya, Gaurav

2016-01-08

Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonuclease. Although this cleavage should happen specifically at the enzyme's recognition sequence, an unknown proportion of cleavage events may involve other sequences, owing to the enzyme's star activity or to random DNA breakage. A quantitative estimation of these non-specific cleavages may enable simulating realistic Hi-C read pairs for validation of downstream analyses, monitoring the reproducibility of experimental conditions and investigating biophysical properties that correlate with DNA cleavage patterns. Here we describe a computational method for analyzing Hi-C read pairs to estimate the fractions of cleavages at different possible targets. The method relies on expressing an observed local target distribution downstream of aligned reads as a linear combination of known conditional local target distributions. We validated this method using Hi-C read pairs obtained by computer simulation. Application of the method to experimental Hi-C datasets from murine cells revealed interesting similarities and differences in patterns of cleavage across the various experiments considered. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Inferring species roles in metacommunity structure from species co-occurrence networks

PubMed Central

Borthagaray, Ana I.; Arim, Matías; Marquet, Pablo A.

2014-01-01

A long-standing question in community ecology is what determines the identity of species that coexist across local communities or metacommunity assembly. To shed light upon this question, we used a network approach to analyse the drivers of species co-occurrence patterns. In particular, we focus on the potential roles of body size and trophic status as determinants of metacommunity cohesion because of their link to resource use and dispersal ability. Small-sized individuals at low-trophic levels, and with limited dispersal potential, are expected to form highly linked subgroups, whereas large-size individuals at higher trophic positions, and with good dispersal potential, will foster the spatial coupling of subgroups and the cohesion of the whole metacommunity. By using modularity analysis, we identified six modules of species with similar responses to ecological conditions and high co-occurrence across local communities. Most species either co-occur with species from a single module or are connectors of the whole network. Among the latter are carnivorous species of intermediate body size, which by virtue of their high incidence provide connectivity to otherwise isolated communities playing the role of spatial couplers. Our study also demonstrates that the incorporation of network tools to the analysis of metacommunity ecology can help unveil the mechanisms underlying patterns and processes in metacommunity assembly. PMID:25143039

International Airport Impacts to Air Quality: Size and Related Properties of Large Increases in Ultrafine Particle Number Concentrations.

PubMed

Hudda, N; Fruin, S A

2016-04-05

We measured particle size distributions and spatial patterns of particle number (PN) and particle surface area concentrations downwind from the Los Angeles International Airport (LAX) where large increases (over local background) in PN concentrations routinely extended 18 km downwind. These elevations were mostly comprised of ultrafine particles smaller than 40 nm. For a given downwind distance, the greatest increases in PN concentrations, along with the smallest mean sizes, were detected at locations under the landing jet trajectories. The smaller size of particles in the impacted area, as compared to the ambient urban aerosol, increased calculated lung deposition fractions to 0.7-0.8 from 0.5-0.7. A diffusion charging instrument (DiSCMini), that simulates alveolar lung deposition, measured a fivefold increase in alveolar-lung deposited surface area concentrations 2-3 km downwind from the airport (over local background), decreasing steadily to a twofold increase 18 km downwind. These ratios (elevated lung-deposited surface area over background) were lower than the corresponding ratios for elevated PN concentrations, which decreased from tenfold to twofold over the same distance, but the spatial patterns of elevated concentrations were similar. It appears that PN concentration can serve as a nonlinear proxy for lung deposited surface area downwind of major airports.

A Study of the Response of the Human Cadaver Head to Impact

PubMed Central

Hardy, Warren N.; Mason, Matthew J.; Foster, Craig D.; Shah, Chirag S.; Kopacz, James M.; Yang, King H.; King, Albert I.; Bishop, Jennifer; Bey, Michael; Anderst, William; Tashman, Scott

2008-01-01

High-speed biplane x-ray and neutral density targets were used to examine brain displacement and deformation during impact. Relative motion, maximum principal strain, maximum shear strain, and intracranial pressure were measured in thirty-five impacts using eight human cadaver head and neck specimens. The effect of a helmet was evaluated. During impact, local brain tissue tends to keep its position and shape with respect to the inertial frame, resulting in relative motion between the brain and skull and deformation of the brain. The local brain motions tend to follow looping patterns. Similar patterns are observed for impact in different planes, with some degree of posterior-anterior and right-left symmetry. Peak coup pressure and pressure rate increase with increasing linear acceleration, but coup pressure pulse duration decreases. Peak average maximum principal strain and maximum shear are on the order of 0.09 for CFC 60 Hz data for these tests. Peak average maximum principal strain and maximum shear increase with increasing linear acceleration, coup pressure, and coup pressure rate. Linear and angular acceleration of the head are reduced with use of a helmet, but strain increases. These results can be used for the validation of finite element models of the human head. PMID:18278591

Spatial reconstruction of single-cell gene expression data.

PubMed

Satija, Rahul; Farrell, Jeffrey A; Gennert, David; Schier, Alexander F; Regev, Aviv

2015-05-01

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

Spatial reconstruction of single-cell gene expression

PubMed Central

Satija, Rahul; Farrell, Jeffrey A.; Gennert, David; Schier, Alexander F.; Regev, Aviv

2015-01-01

Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems. PMID:25867923

Convolution Comparison Pattern: An Efficient Local Image Descriptor for Fingerprint Liveness Detection

PubMed Central

Gottschlich, Carsten

2016-01-01

We present a new type of local image descriptor which yields binary patterns from small image patches. For the application to fingerprint liveness detection, we achieve rotation invariant image patches by taking the fingerprint segmentation and orientation field into account. We compute the discrete cosine transform (DCT) for these rotation invariant patches and attain binary patterns by comparing pairs of two DCT coefficients. These patterns are summarized into one or more histograms per image. Each histogram comprises the relative frequencies of pattern occurrences. Multiple histograms are concatenated and the resulting feature vector is used for image classification. We name this novel type of descriptor convolution comparison pattern (CCP). Experimental results show the usefulness of the proposed CCP descriptor for fingerprint liveness detection. CCP outperforms other local image descriptors such as LBP, LPQ and WLD on the LivDet 2013 benchmark. The CCP descriptor is a general type of local image descriptor which we expect to prove useful in areas beyond fingerprint liveness detection such as biological and medical image processing, texture recognition, face recognition and iris recognition, liveness detection for face and iris images, and machine vision for surface inspection and material classification. PMID:26844544

Input-Specific Gain Modulation by Local Sensory Context Shapes Cortical and Thalamic Responses to Complex Sounds.

PubMed

Williamson, Ross S; Ahrens, Misha B; Linden, Jennifer F; Sahani, Maneesh

2016-07-20

Sensory neurons are customarily characterized by one or more linearly weighted receptive fields describing sensitivity in sensory space and time. We show that in auditory cortical and thalamic neurons, the weight of each receptive field element depends on the pattern of sound falling within a local neighborhood surrounding it in time and frequency. Accounting for this change in effective receptive field with spectrotemporal context improves predictions of both cortical and thalamic responses to stationary complex sounds. Although context dependence varies among neurons and across brain areas, there are strong shared qualitative characteristics. In a spectrotemporally rich soundscape, sound elements modulate neuronal responsiveness more effectively when they coincide with sounds at other frequencies, and less effectively when they are preceded by sounds at similar frequencies. This local-context-driven lability in the representation of complex sounds-a modulation of "input-specific gain" rather than "output gain"-may be a widespread motif in sensory processing. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

The effects of dispersal patterns on marine reserves: does the tail wag the dog?

PubMed

Lockwood, Dale R; Hastings, Alan; Botsford, Louis W

2002-05-01

The concept of marine reserves as a method of improving management of fisheries is gaining momentum. While the list of benefits from reserves is frequently promoted, precise formulations of theory to support reserve design are not fully developed. To determine the size of reserves and the distances between reserves an understanding of the requirements for persistence of local populations is required. Unfortunately, conditions for persistence are poorly characterized, as are the larval dispersal patterns on which persistence depends. With the current paucity of information regarding meroplanktonic larval transport processes, understanding the robustness of theoretical results to larval dispersal is of key importance. From this formulation a broad range of dispersal patterns are analyzed. Larval dispersal is represented by a probability distribution that defines the fraction of successful settlers from an arbitrary location, the origin of the distribution, to any other location along the coast. While the effects of specific dispersal patterns have been investigated for invasion processes, critical habitat size and persistence issues have generally been addressed with only one or two dispersal types. To that end, we formulate models based on integrodifference equations that are spatially continuous and temporally discrete. We consider a range of dispersal distributions from leptokurtic to platykurtic. The effect of different dispersal patterns is considered for a single isolated reserve of varying size receiving no external larvae, as well as multiple reserves with varying degrees of connectivity. While different patterns result in quantitative differences in persistence, qualitatively similar effects across all patterns are seen in both single- and multiple reserve models. Persistence in an isolated reserve requires a size that is approximately twice the mean dispersal distance and regardless of the dispersal pattern the population in a patch is not persistent if the reserve size is reduced to just the mean dispersal distance. With an idealized coastline structure consisting of an infinite line of equally spaced reserves separated by regions of coastline in which reproduction is nil, the relative settlement as a function of the fraction of coastline and size of reserve is qualitatively very similar over a broad range of dispersal patterns. The upper limit for the minimum fraction of coastline held in reserve is about 40%. As the fraction of coastline is reduced, the minimum size of reserve becomes no more than 1.25 times the mean dispersal distance.

Effects of Aging on Cortical Neural Dynamics and Local Sleep Homeostasis in Mice

PubMed Central

Fisher, Simon P.; Cui, Nanyi; Peirson, Stuart N.; Foster, Russell G.

2018-01-01

Healthy aging is associated with marked effects on sleep, including its daily amount and architecture, as well as the specific EEG oscillations. Neither the neurophysiological underpinnings nor the biological significance of these changes are understood, and crucially the question remains whether aging is associated with reduced sleep need or a diminished capacity to generate sufficient sleep. Here we tested the hypothesis that aging may affect local cortical networks, disrupting the capacity to generate and sustain sleep oscillations, and with it the local homeostatic response to sleep loss. We performed chronic recordings of cortical neural activity and local field potentials from the motor cortex in young and older male C57BL/6J mice, during spontaneous waking and sleep, as well as during sleep after sleep deprivation. In older animals, we observed an increase in the incidence of non-rapid eye movement sleep local field potential slow waves and their associated neuronal silent (OFF) periods, whereas the overall pattern of state-dependent cortical neuronal firing was generally similar between ages. Furthermore, we observed that the response to sleep deprivation at the level of local cortical network activity was not affected by aging. Our data thus suggest that the local cortical neural dynamics and local sleep homeostatic mechanisms, at least in the motor cortex, are not impaired during healthy senescence in mice. This indicates that powerful protective or compensatory mechanisms may exist to maintain neuronal function stable across the life span, counteracting global changes in sleep amount and architecture. SIGNIFICANCE STATEMENT The biological significance of age-dependent changes in sleep is unknown but may reflect either a diminished sleep need or a reduced capacity to generate deep sleep stages. As aging has been linked to profound disruptions in cortical sleep oscillations and because sleep need is reflected in specific patterns of cortical activity, we performed chronic electrophysiological recordings of cortical neural activity during waking, sleep, and after sleep deprivation from young and older mice. We found that all main hallmarks of cortical activity during spontaneous sleep and recovery sleep after sleep deprivation were largely intact in older mice, suggesting that the well-described age-related changes in global sleep are unlikely to arise from a disruption of local network dynamics within the neocortex. PMID:29581380

Effects of Aging on Cortical Neural Dynamics and Local Sleep Homeostasis in Mice.

PubMed

McKillop, Laura E; Fisher, Simon P; Cui, Nanyi; Peirson, Stuart N; Foster, Russell G; Wafford, Keith A; Vyazovskiy, Vladyslav V

2018-04-18

Healthy aging is associated with marked effects on sleep, including its daily amount and architecture, as well as the specific EEG oscillations. Neither the neurophysiological underpinnings nor the biological significance of these changes are understood, and crucially the question remains whether aging is associated with reduced sleep need or a diminished capacity to generate sufficient sleep. Here we tested the hypothesis that aging may affect local cortical networks, disrupting the capacity to generate and sustain sleep oscillations, and with it the local homeostatic response to sleep loss. We performed chronic recordings of cortical neural activity and local field potentials from the motor cortex in young and older male C57BL/6J mice, during spontaneous waking and sleep, as well as during sleep after sleep deprivation. In older animals, we observed an increase in the incidence of non-rapid eye movement sleep local field potential slow waves and their associated neuronal silent (OFF) periods, whereas the overall pattern of state-dependent cortical neuronal firing was generally similar between ages. Furthermore, we observed that the response to sleep deprivation at the level of local cortical network activity was not affected by aging. Our data thus suggest that the local cortical neural dynamics and local sleep homeostatic mechanisms, at least in the motor cortex, are not impaired during healthy senescence in mice. This indicates that powerful protective or compensatory mechanisms may exist to maintain neuronal function stable across the life span, counteracting global changes in sleep amount and architecture. SIGNIFICANCE STATEMENT The biological significance of age-dependent changes in sleep is unknown but may reflect either a diminished sleep need or a reduced capacity to generate deep sleep stages. As aging has been linked to profound disruptions in cortical sleep oscillations and because sleep need is reflected in specific patterns of cortical activity, we performed chronic electrophysiological recordings of cortical neural activity during waking, sleep, and after sleep deprivation from young and older mice. We found that all main hallmarks of cortical activity during spontaneous sleep and recovery sleep after sleep deprivation were largely intact in older mice, suggesting that the well-described age-related changes in global sleep are unlikely to arise from a disruption of local network dynamics within the neocortex. Copyright © 2018 McKillop et al.

Restoring Consistency In Subjective Information For Groundwater Driven Health Risk Assessment

NASA Astrophysics Data System (ADS)

Ozbek, M. M.; Pinder, G. F.

2004-12-01

In an earlier work (Ozbek and Pinder, 2003), we constructed a fuzzy rule-based knowledge base that uses subjective expert opinion to calculate risk-based design constraints (i.e., dose and pattern of exposure) to sustain the groundwater-driven individual health risk at a desired level. Ideally, our system must be capable to produce for any individual a meaningful risk result or for any given risk a meaningful design constraint, in the sense that the result is neither the empty set nor the whole domain of the variable of interest. Otherwise we consider our system as inconsistent. We present a method based on fuzzy similarity relations to restore consistency in our implicative fuzzy rule based system used for the risk-based groundwater remediation design problem. Both a global and a local approach are considered. Even though straightforward and computationally less demanding, the global approach can affect pieces of knowledge negatively by inducing unwarranted imprecision into the knowledge base. On the other hand, the local approach, given a family of parameterized similarity relations, determines a parameter for each inference such that consistent results are computed which may not be feasible in real time applications of our knowledge base. Several scenarios are considered for comparing the two approaches that suggest that for specific applications one or several approaches ranging from a completely global to a completely local one will be more suitable than others while calculating the design constraints.

Localization, Concentration, and Transmission Efficiency of Banana bunchy top virus in Four Asexual Lineages of Pentalonia aphids

PubMed Central

Watanabe, Shizu; Greenwell, April M.; Bressan, Alberto

2013-01-01

Banana bunchy top virus (BBTV) is the most destructive pathogenic virus of banana plants worldwide. The virus is transmitted in a circulative non-propagative manner by the banana aphid, Pentalonia nigronervosa Coquerel. In this work, we examined the localization, accumulation, and transmission efficiency of BBTV in four laboratory-established lineages of Pentalonia aphids derived from four different host plants: taro (Colocasia esculenta), heliconia (Heliconia spp.), red ginger (Alpinia purpurata), and banana (Musa sp.). Mitochondrial sequencing identified three and one lineages as Pentalonia caladii van der Goot, a recently proposed species, and P. nigronervosa, respectively. Microsatellite analysis separated the aphid lineages into four distinct genotypes. The transmission of BBTV was tested using leaf disk and whole-plant assays, both of which showed that all four lineages are competent vectors of BBTV, although the P. caladii from heliconia transmitted BBTV to the leaf disks at a significantly lower rate than did P. nigronervosa. The concentration of BBTV in dissected guts, haemolymph, and salivary glands was quantified by real-time PCR. The BBTV titer reached similar concentrations in the guts, haemolymph, and salivary glands of aphids from all four lineages tested. Furthermore, immunofluorescence assays showed that BBTV antigens localized to the anterior midguts and the principal salivary glands, demonstrating a similar pattern of translocations across the four lineages. The results reported in this study showed for the first time that P. caladii is a competent vector of BBTV. PMID:23435241

Localization, concentration, and transmission efficiency of Banana bunchy top virus in four asexual lineages of Pentalonia aphids.

PubMed

Watanabe, Shizu; Greenwell, April M; Bressan, Alberto

2013-02-22

Banana bunchy top virus (BBTV) is the most destructive pathogenic virus of banana plants worldwide. The virus is transmitted in a circulative non-propagative manner by the banana aphid, Pentalonia nigronervosa Coquerel. In this work, we examined the localization, accumulation, and transmission efficiency of BBTV in four laboratory-established lineages of Pentalonia aphids derived from four different host plants: taro (Colocasia esculenta), heliconia (Heliconia spp.), red ginger (Alpinia purpurata), and banana (Musa sp.). Mitochondrial sequencing identified three and one lineages as Pentalonia caladii van der Goot, a recently proposed species, and P. nigronervosa, respectively. Microsatellite analysis separated the aphid lineages into four distinct genotypes. The transmission of BBTV was tested using leaf disk and whole-plant assays, both of which showed that all four lineages are competent vectors of BBTV, although the P. caladii from heliconia transmitted BBTV to the leaf disks at a significantly lower rate than did P. nigronervosa. The concentration of BBTV in dissected guts, haemolymph, and salivary glands was quantified by real-time PCR. The BBTV titer reached similar concentrations in the guts, haemolymph, and salivary glands of aphids from all four lineages tested. Furthermore, immunofluorescence assays showed that BBTV antigens localized to the anterior midguts and the principal salivary glands, demonstrating a similar pattern of translocations across the four lineages. The results reported in this study showed for the first time that P. caladii is a competent vector of BBTV.

Multiplex Competition, Collaboration, and Funding Networks Among Health and Social Organizations: Toward Organization-based HIV Interventions for Young Men Who Have Sex With Men.

PubMed

Fujimoto, Kayo; Wang, Peng; Kuhns, Lisa M; Ross, Michael W; Williams, Mark L; Garofalo, Robert; Klovdahl, Alden S; Laumann, Edward O; Schneider, John A

2017-02-01

Young men who have sex with men (YMSM) have the highest rates of human immunodeficiency virus (HIV) infection in the United States. Decades into the HIV epidemic, the relationships that YMSM-serving health and social organizations have with one another has not been studied in depth. The aim of this study was to examine the competition, collaboration, and funding source structures of multiplex organization networks and the mechanisms that promote fruitful relationships among these organizations. The study data collection method was a survey of health and social organizations from 2013-2014 in 2 cities, Chicago, IL and Houston, TX. Study participants were representatives from 138 health and social organizations. Responses to survey questions were used to reconstruct competition, collaboration, and combined competition-collaboration networks. While taking into consideration the collaborative relationships among organizations, we provide statistical evidence that organizations of similar type, similar social media use patterns, comparable patterns of funding, and similar network contexts tended to compete with one another. This competition was less likely to be accompanied by any sort of collaboration if the organizations shared common funding sources. Competition that excludes potential collaboration may be detrimental to mobilizing the collective efforts that serve local YMSM communities. System-level interventions may provide promising approaches to scaling-up HIV prevention and treatment efforts so as to encourage organizations to form partnerships with otherwise competing providers.

Multiplex competition, collaboration, and funding networks among health and social organizations: Towards organization-based HIV interventions for young men who have sex with men

PubMed Central

Fujimoto, Kayo; Wang, Peng; Kuhns, Lisa; Ross, Michael W; Williams, Mark L.; Garofalo, Robert; Klovdahl, Alden S.; Laumann, Edward O.; Schneider, John A.

2016-01-01

Background Young men who have sex with men (YMSM) have the highest rates of HIV infection in the United States. Decades into the HIV epidemic, the relationships that YMSM-serving health and social organizations have with one another has not been studied in depth. Objectives The aim of this study was to examine the competition, collaboration and funding source structures of multiplex organization networks and the mechanisms that promote fruitful relationships among these organizations. Research Design The study data collection method was a survey of health and social organizations from 2013–2014 in two cities, Chicago IL, and Houston TX. Subjects Study participants were representatives from 138 health and social organizations. Measures Responses to survey questions were used to reconstruct competition, collaboration and combined competition-collaboration networks. Results While taking into consideration the collaborative relationships among organizations, we provide solid statistical evidence that organizations of similar type, similar social media use patterns, comparable patterns of funding, and similar network contexts tended to compete with one another. This competition was less likely to be accompanied by any sort of collaboration if the organizations shared common funding sources. Conclusions Competition that excludes potential collaboration may be detrimental to mobilizing the collective efforts that serve local YMSM communities. System-level interventions may provide promising approaches to scaling-up HIV prevention and treatment efforts so as to encourage organizations to form partnerships with otherwise competing providers. PMID:27676400

Trace metals in fugitive dust from unsurfaced roads in the Viburnum Trend resource mining District of Missouri--implementation of a direct-suspension sampling methodology.

PubMed

Witt, Emitt C; Wronkiewicz, David J; Pavlowsky, Robert T; Shi, Honglan

2013-09-01

Fugitive dust from 18 unsurfaced roadways in Missouri were sampled using a novel cyclonic fugitive dust collector that was designed to obtain suspended bulk samples for analysis. The samples were analyzed for trace metals, Fe and Al, particle sizes, and mineralogy to characterize the similarities and differences between roadways. Thirteen roads were located in the Viburnum Trend (VT) mining district, where there has been a history of contaminant metal loading of local soils; while the remaining five roads were located southwest of the VT district in a similar rural setting, but without any mining or industrial process that might contribute to trace metal enrichment. Comparison of these two groups shows that trace metal concentration is higher for dusts collected in the VT district. Lead is the dominant trace metal found in VT district dusts representing on average 79% of the total trace metal concentration, and was found moderately to strongly enriched relative to unsurfaced roads in the non-VT area. Fugitive road dust concentrations calculated for the VT area substantially exceed the 2008 Federal ambient air standard of 0.15μgm(-3) for Pb. The pattern of trace metal contamination in fugitive dust from VT district roads is similar to trace metal concentrations patterns observed for soils measured more than 40years ago indicating that Pb contamination in the region is persistent as a long-term soil contaminant. Published by Elsevier Ltd.

Brain regions with abnormal network properties in severe epilepsy of Lennox-Gastaut phenotype: Multivariate analysis of task-free fMRI.

PubMed

Pedersen, Mangor; Curwood, Evan K; Archer, John S; Abbott, David F; Jackson, Graeme D

2015-11-01

Lennox-Gastaut syndrome, and the similar but less tightly defined Lennox-Gastaut phenotype, describe patients with severe epilepsy, generalized epileptic discharges, and variable intellectual disability. Our previous functional neuroimaging studies suggest that abnormal diffuse association network activity underlies the epileptic discharges of this clinical phenotype. Herein we use a data-driven multivariate approach to determine the spatial changes in local and global networks of patients with severe epilepsy of the Lennox-Gastaut phenotype. We studied 9 adult patients and 14 controls. In 20 min of task-free blood oxygen level-dependent functional magnetic resonance imaging data, two metrics of functional connectivity were studied: Regional homogeneity or local connectivity, a measure of concordance between each voxel to a focal cluster of adjacent voxels; and eigenvector centrality, a global connectivity estimate designed to detect important neural hubs. Multivariate pattern analysis of these data in a machine-learning framework was used to identify spatial features that classified disease subjects. Multivariate pattern analysis was 95.7% accurate in classifying subjects for both local and global connectivity measures (22/23 subjects correctly classified). Maximal discriminating features were the following: increased local connectivity in frontoinsular and intraparietal areas; increased global connectivity in posterior association areas; decreased local connectivity in sensory (visual and auditory) and medial frontal cortices; and decreased global connectivity in the cingulate cortex, striatum, hippocampus, and pons. Using a data-driven analysis method in task-free functional magnetic resonance imaging, we show increased connectivity in critical areas of association cortex and decreased connectivity in primary cortex. This supports previous findings of a critical role for these association cortical regions as a final common pathway in generating the Lennox-Gastaut phenotype. Abnormal function of these areas is likely to be important in explaining the intellectual problems characteristic of this disorder. Wiley Periodicals, Inc. © 2015 International League Against Epilepsy.

Mapping air quality zones for coastal urban centers.

PubMed

Freeman, Brian; Gharabaghi, Bahram; Thé, Jesse; Munshed, Mohammad; Faisal, Shah; Abdullah, Meshal; Al Aseed, Athari

2017-05-01

This study presents a new method that incorporates modern air dispersion models allowing local terrain and land-sea breeze effects to be considered along with political and natural boundaries for more accurate mapping of air quality zones (AQZs) for coastal urban centers. This method uses local coastal wind patterns and key urban air pollution sources in each zone to more accurately calculate air pollutant concentration statistics. The new approach distributes virtual air pollution sources within each small grid cell of an area of interest and analyzes a puff dispersion model for a full year's worth of 1-hr prognostic weather data. The difference of wind patterns in coastal and inland areas creates significantly different skewness (S) and kurtosis (K) statistics for the annually averaged pollutant concentrations at ground level receptor points for each grid cell. Plotting the S-K data highlights grouping of sources predominantly impacted by coastal winds versus inland winds. The application of the new method is demonstrated through a case study for the nation of Kuwait by developing new AQZs to support local air management programs. The zone boundaries established by the S-K method were validated by comparing MM5 and WRF prognostic meteorological weather data used in the air dispersion modeling, a support vector machine classifier was trained to compare results with the graphical classification method, and final zones were compared with data collected from Earth observation satellites to confirm locations of high-exposure-risk areas. The resulting AQZs are more accurate and support efficient management strategies for air quality compliance targets effected by local coastal microclimates. A novel method to determine air quality zones in coastal urban areas is introduced using skewness (S) and kurtosis (K) statistics calculated from grid concentrations results of air dispersion models. The method identifies land-sea breeze effects that can be used to manage local air quality in areas of similar microclimates.

Impact of Local Resources on Hospitalization Patterns of Medicare Beneficiaries and Propensity to Travel outside Local Markets

ERIC Educational Resources Information Center

Basu, Jayasree; Mobley, Lee R.

2010-01-01

Purpose: To examine how local health care resources impact travel patterns of patients age 65 and older across the rural urban continuum. Methods: Information on inpatient hospital discharges was drawn from complete 2004 hospital discharge files from the Healthcare Cost and Utilization Project (HCUP) State Inpatient Databases (SID) for New York,…