Estimation, modeling, and simulation of patterned growth in extreme environments.

PubMed

Strader, B; Schubert, K E; Quintana, M; Gomez, E; Curnutt, J; Boston, P

2011-01-01

In the search for life on Mars and other extraterrestrial bodies or in our attempts to identify biological traces in the most ancient rock record of Earth, one of the biggest problems facing us is how to recognize life or the remains of ancient life in a context very different from our planet's modern biological examples. Specific chemistries or biological properties may well be inapplicable to extraterrestrial conditions or ancient Earth environments. Thus, we need to develop an arsenal of techniques that are of broader applicability. The notion of patterning created in some fashion by biological processes and properties may provide such a generalized property of biological systems no matter what the incidentals of chemistry or environmental conditions. One approach to recognizing these kinds of patterns is to look at apparently organized arrangements created and left by life in extreme environments here on Earth, especially at various spatial scales, different geologies, and biogeochemical circumstances.

Distinct cognitive control mechanisms as revealed by modality-specific conflict adaptation effects.

PubMed

Yang, Guochun; Nan, Weizhi; Zheng, Ya; Wu, Haiyan; Li, Qi; Liu, Xun

2017-04-01

Cognitive control is essential to resolve conflict in stimulus-response compatibility (SRC) tasks. The SRC effect in the current trial is reduced after an incongruent trial as compared with a congruent trial, a phenomenon being termed conflict adaptation (CA). The CA effect is found to be domain-specific , such that it occurs when adjacent trials contain the same type of conflict, but disappears when the conflicts are of different types. Similar patterns have been observed when tasks involve different modalities, but the modality-specific effect may have been confounded by task switching. In the current study, we investigated whether or not cognitive control could transfer across auditory and visual conflicts when task-switching was controlled. Participants were asked to respond to a visual or auditory (Experiments 1A/B) stimulus, with conflict coming from either the same or a different modality. CA effects showed modality-specific patterns. To account for potential confounding effects caused by differences in task-irrelevant properties, we specifically examined the influence of task-irrelevant properties on CA effects within the visual modality (Experiments 2A/B). Significant CA effects were observed across different conflicts from distinct task-irrelevant properties, ruling out that the lack of cross-modal CA effects in Experiments 1A/B resulted from differences in task-irrelevant information. Task-irrelevant properties were further matched in Experiments 3A/B to examine the pure effect of modality. Results replicated Experiments 1A/B showing robust modality-specific CA effects. Taken together, we provide supporting evidences that modality affects cognitive control in conflict resolution, which should be taken into account in theories of cognitive control. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Special Issue: "Functional Dendrimers".

PubMed

Tomalia, Donald A

2016-08-09

This special issue entitled "Functional Dendrimers" focuses on the manipulation of at least six "critical nanoscale design parameters" (CNDPs) of dendrimers including: size, shape, surface chemistry, flexibility/rigidity, architecture and elemental composition. These CNDPs collectively define properties of all "functional dendrimers". This special issue contains many interesting examples describing the manipulation of certain dendrimer CNDPs to create new emerging properties and, in some cases, predictive nanoperiodic property patterns (i.e., dendritic effects). The systematic engineering of CNDPs provides a valuable strategy for optimizing functional dendrimer properties for use in specific applications.

Lithographically Defined Three-dimensional Pore-patterned Carbon with Nitrogen Doping for High-Performance Ultrathin Supercapacitor Applications

PubMed Central

Kang, Da-Young; Moon, Jun Hyuk

2014-01-01

Supercapacitors that exhibit long cycle lives and fast charge/discharge rates are a promising energy-storage technology for next-generation mobile or wearable electronic systems. A great challenge facing the fabrication of ultrathin supercapacitor components, specifically their porous electrodes, is whether such components can be integrated with the fabrication of electronic devices, i.e., semiconductor fabrication processes. Here, we introduce the lithographic fabrication of micrometre-thick, submicrometre-pore-patterned carbon for supercapacitor electrodes. The pore patterns designed by multi-beam interference lithography and direct carbonisation of the photoresist pattern produced pore-patterned carbon films. A facile doping process was subsequently employed to introduce nitrogen atoms into the carbon, which was intended to further enhance the carbon's capacitive properties. Specifically, during these fabrication steps, we developed an approach that uses a supporting shell on the surface of the pore patterns to maintain their structural integrity. The nitrogen-doped, pore-patterned carbon electrodes exhibited an areal specific capacitance of 32.7 mF/cm2 at 0.5 mA/cm2 when used as supercapacitor electrodes, which is approximately 20 times greater than that of commercially available MWCNT films measured under the same conditions. PMID:24953307

Element-specific behaviour and sediment properties modulate transfer and bioaccumulation of trace elements in a highly-contaminated area (Augusta Bay, Central Mediterranean Sea).

PubMed

Signa, Geraldina; Mazzola, Antonio; Di Leonardo, Rossella; Vizzini, Salvatrice

2017-11-01

High sediment contamination in the coastal area of Priolo Bay, adjacent to the highly-polluted Augusta Harbour, poses serious risks for the benthic communities inhabiting the area. Nevertheless, the transfer of trace elements and consequent bioaccumulation in the biota is an overlooked issue. This study aimed to assess the transfer and bioaccumulation patterns of As, Cd, Ni and Hg to the dominant macroalgae and benthic invertebrates of Priolo Bay. Results revealed different patterns among trace elements (TEs), not driven by sediment contamination but rather by element-specific behaviour coupled with sediment physicochemical properties. Specifically, As accumulated in macroalgae but not in invertebrates, indicating bioavailability of dissolved As only, and a lack of effective trophic transfer. Ni was confined to surface sediment and transfer to biota was not highlighted. Cd and Hg showed the highest concentrations in invertebrates and bioaccumulated especially in filter feeders and carnivores, revealing the importance of suspended particulate and diet as transfer pathways. Total organic carbon (TOC), fine-grained sediments and redox potential were the most important sediment features in shaping the sediment contamination spatial patterns as well as those of TE transfer and bioaccumulation. In particular, As and Cd transfer to macroalgae, and especially Hg bioaccumulation in benthic invertebrates was controlled by sediment properties, resulting in limited transfer and accumulation in the most contaminated stations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Oscillations and patterns in a model of simultaneous CO and C2H2 oxidation and NO(x) reduction in a cross-flow reactor.

PubMed

Hadač, Otto; Kohout, Martin; Havlica, Jaromír; Schreiber, Igor

2015-03-07

A model describing simultaneous catalytic oxidation of CO and C2H2 and reduction of NOx in a cross-flow tubular reactor is explored with the aim of relating spatiotemporal patterns to specific pathways in the mechanism. For that purpose, a detailed mechanism proposed for three-way catalytic converters is split into two subsystems, (i) simultaneous oxidation of CO and C2H2, and (ii) oxidation of CO combined with NOx reduction. The ability of these two subsystems to display mechanism-specific dynamical effects is studied initially by neglecting transport phenomena and applying stoichiometric network and bifurcation analyses. We obtain inlet temperature - inlet oxygen concentration bifurcation diagrams, where each region possessing specific dynamics - oscillatory, bistable and excitable - is associated with a dominant reaction pathway. Next, the spatiotemporal behaviour due to reaction kinetics combined with transport processes is studied. The observed spatiotemporal patterns include phase waves, travelling fronts, pulse waves and spatiotemporal chaos. Although these types of pattern occur generally when the kinetic scheme possesses autocatalysis, we find that some of their properties depend on the underlying dominant reaction pathway. The relation of patterns to specific reaction pathways is discussed.

COREPA-M: A MULTI-DIMENSIONAL FORMULATION OF COREPA

EPA Science Inventory

Recently, the COmmon REactivity PAttern (COREPA) approach was developed as a probabilistic classification method which was formalized specifically to advance mechanistic QSAR development by addressing the impact of molecular flexibility on stereoelectronic properties of chemicals...

Altered growth pattern, not altered growth per se, is the hallmark of early lesions preceding cancer development.

PubMed

Doratiotto, S; Marongiu, F; Faedda, S; Pani, P; Laconi, E

2009-01-01

Many human solid cancers arise from focal proliferative lesions that long precede the overt clinical appearance of the disease. The available evidence supports the notion that cancer precursor lesions are clonal in origin, and this notion forms the basis for most of the current theories on the pathogenesis of neoplastic disease. In contrast, far less attention has been devoted to the analysis of the phenotypic property that serves to define these focal lesions, i.e. their altered growth pattern. In fact, the latter is often considered a mere morphological by-product of clonal growth, with no specific relevance in the process. In the following study, evidence will be presented to support the concept that focal growth pattern is an inherent property of altered cells, independent of clonal growth; furthermore, it will be discussed how such a property, far from being merely descriptive, might indeed play a fundamental role in the sequence of events leading to the development of cancer. Within this paradigm, the earliest steps of neoplasia should be considered and analysed as defects in the mechanisms of tissue pattern formation.

Built environment and Property Crime in Seattle, 1998-2000: A Bayesian Analysis.

PubMed

Matthews, Stephen A; Yang, Tse-Chuan; Hayslett-McCall, Karen L; Ruback, R Barry

2010-06-01

The past decade has seen a rapid growth in the use of a spatial perspective in studies of crime. In part this growth has been driven by the availability of georeferenced data, and the tools to analyze and visualize them: geographic information systems (GIS), spatial analysis, and spatial statistics. In this paper we use exploratory spatial data analysis (ESDA) tools and Bayesian models to help better understand the spatial patterning and predictors of property crime in Seattle, Washington for 1998-2000, including a focus on built environment variables. We present results for aggregate property crime data as well as models for specific property crime types: residential burglary, nonresidential burglary, theft, auto theft, and arson. ESDA confirms the presence of spatial clustering of property crime and we seek to explain these patterns using spatial Poisson models implemented in WinBUGS. Our results indicate that built environment variables were significant predictors of property crime, especially the presence of a highway on auto theft and burglary.

Built environment and Property Crime in Seattle, 1998–2000: A Bayesian Analysis

PubMed Central

Matthews, Stephen A.; Yang, Tse-chuan; Hayslett-McCall, Karen L.; Ruback, R. Barry

2014-01-01

The past decade has seen a rapid growth in the use of a spatial perspective in studies of crime. In part this growth has been driven by the availability of georeferenced data, and the tools to analyze and visualize them: geographic information systems (GIS), spatial analysis, and spatial statistics. In this paper we use exploratory spatial data analysis (ESDA) tools and Bayesian models to help better understand the spatial patterning and predictors of property crime in Seattle, Washington for 1998–2000, including a focus on built environment variables. We present results for aggregate property crime data as well as models for specific property crime types: residential burglary, nonresidential burglary, theft, auto theft, and arson. ESDA confirms the presence of spatial clustering of property crime and we seek to explain these patterns using spatial Poisson models implemented in WinBUGS. Our results indicate that built environment variables were significant predictors of property crime, especially the presence of a highway on auto theft and burglary. PMID:24737924

Grammatical gender and inferences about biological properties in german-speaking children.

PubMed

Saalbach, Henrik; Imai, Mutsumi; Schalk, Lennart

2012-01-01

In German, nouns are assigned to one of the three gender classes. For most animal names, however, the assignment is independent of the referent's biological sex. We examined whether German-speaking children understand this independence of grammar from semantics or whether they assume that grammatical gender is mapped onto biological sex when drawing inferences about sex-specific biological properties of animals. Two cross-linguistic studies comparing German-speaking and Japanese-speaking preschoolers were conducted. The results suggest that German-speaking children utilize grammatical gender as a cue for inferences about sex-specific properties of animals. Further, we found that Japanese- and German-speaking children recruit different resources when drawing inferences about sex-specific properties: Whereas Japanese children paralleled their pattern of inference about properties common to all animals, German children relied on the grammatical gender class of the animal. Implications of these findings for studying the relation between language and thought are discussed. Copyright © 2012 Cognitive Science Society, Inc.

Testing key predictions of the associative account of mirror neurons in humans using multivariate pattern analysis.

PubMed

Oosterhof, Nikolaas N; Wiggett, Alison J; Cross, Emily S

2014-04-01

Cook et al. overstate the evidence supporting their associative account of mirror neurons in humans: most studies do not address a key property, action-specificity that generalizes across the visual and motor domains. Multivariate pattern analysis (MVPA) of neuroimaging data can address this concern, and we illustrate how MVPA can be used to test key predictions of their account.

Universal and Language-Specific Patterns in the Acquisition of Verb Argument Structures in German

ERIC Educational Resources Information Center

Leischner, Franziska N.; Weissenborn, Jürgen; Naigles, Letitia R.

2016-01-01

The study investigated the influence of universal and language-specific morpho-syntactic properties (i.e., flexible word order, case) on the acquisition of verb argument structures in German compared with English. To this end, 65 three- to nine-year-old German learning children and adults were asked to act out grammatical ("The sheep…

Spontaneous formation of spiral-like patterns with distinct periodic physical properties by confined electrodeposition of Co-In disks

NASA Astrophysics Data System (ADS)

Golvano-Escobal, Irati; Gonzalez-Rosillo, Juan Carlos; Domingo, Neus; Illa, Xavi; López-Barberá, José Francisco; Fornell, Jordina; Solsona, Pau; Aballe, Lucia; Foerster, Michael; Suriñach, Santiago; Baró, Maria Dolors; Puig, Teresa; Pané, Salvador; Nogués, Josep; Pellicer, Eva; Sort, Jordi

2016-07-01

Spatio-temporal patterns are ubiquitous in different areas of materials science and biological systems. However, typically the motifs in these types of systems present a random distribution with many possible different structures. Herein, we demonstrate that controlled spatio-temporal patterns, with reproducible spiral-like shapes, can be obtained by electrodeposition of Co-In alloys inside a confined circular geometry (i.e., in disks that are commensurate with the typical size of the spatio-temporal features). These patterns are mainly of compositional nature, i.e., with virtually no topographic features. Interestingly, the local changes in composition lead to a periodic modulation of the physical (electric, magnetic and mechanical) properties. Namely, the Co-rich areas show higher saturation magnetization and electrical conductivity and are mechanically harder than the In-rich ones. Thus, this work reveals that confined electrodeposition of this binary system constitutes an effective procedure to attain template-free magnetic, electric and mechanical surface patterning with specific and reproducible shapes.

Authoring and verification of clinical guidelines: a model driven approach.

PubMed

Pérez, Beatriz; Porres, Ivan

2010-08-01

The goal of this research is to provide a framework to enable authoring and verification of clinical guidelines. The framework is part of a larger research project aimed at improving the representation, quality and application of clinical guidelines in daily clinical practice. The verification process of a guideline is based on (1) model checking techniques to verify guidelines against semantic errors and inconsistencies in their definition, (2) combined with Model Driven Development (MDD) techniques, which enable us to automatically process manually created guideline specifications and temporal-logic statements to be checked and verified regarding these specifications, making the verification process faster and cost-effective. Particularly, we use UML statecharts to represent the dynamics of guidelines and, based on this manually defined guideline specifications, we use a MDD-based tool chain to automatically process them to generate the input model of a model checker. The model checker takes the resulted model together with the specific guideline requirements, and verifies whether the guideline fulfils such properties. The overall framework has been implemented as an Eclipse plug-in named GBDSSGenerator which, particularly, starting from the UML statechart representing a guideline, allows the verification of the guideline against specific requirements. Additionally, we have established a pattern-based approach for defining commonly occurring types of requirements in guidelines. We have successfully validated our overall approach by verifying properties in different clinical guidelines resulting in the detection of some inconsistencies in their definition. The proposed framework allows (1) the authoring and (2) the verification of clinical guidelines against specific requirements defined based on a set of property specification patterns, enabling non-experts to easily write formal specifications and thus easing the verification process. Copyright 2010 Elsevier Inc. All rights reserved.

Empirical modeling for intelligent, real-time manufacture control

NASA Technical Reports Server (NTRS)

Xu, Xiaoshu

1994-01-01

Artificial neural systems (ANS), also known as neural networks, are an attempt to develop computer systems that emulate the neural reasoning behavior of biological neural systems (e.g. the human brain). As such, they are loosely based on biological neural networks. The ANS consists of a series of nodes (neurons) and weighted connections (axons) that, when presented with a specific input pattern, can associate specific output patterns. It is essentially a highly complex, nonlinear, mathematical relationship or transform. These constructs have two significant properties that have proven useful to the authors in signal processing and process modeling: noise tolerance and complex pattern recognition. Specifically, the authors have developed a new network learning algorithm that has resulted in the successful application of ANS's to high speed signal processing and to developing models of highly complex processes. Two of the applications, the Weld Bead Geometry Control System and the Welding Penetration Monitoring System, are discussed in the body of this paper.

Design for Verification: Using Design Patterns to Build Reliable Systems

NASA Technical Reports Server (NTRS)

Mehlitz, Peter C.; Penix, John; Koga, Dennis (Technical Monitor)

2003-01-01

Components so far have been mainly used in commercial software development to reduce time to market. While some effort has been spent on formal aspects of components, most of this was done in the context of programming language or operating system framework integration. As a consequence, increased reliability of composed systems is mainly regarded as a side effect of a more rigid testing of pre-fabricated components. In contrast to this, Design for Verification (D4V) puts the focus on component specific property guarantees, which are used to design systems with high reliability requirements. D4V components are domain specific design pattern instances with well-defined property guarantees and usage rules, which are suitable for automatic verification. The guaranteed properties are explicitly used to select components according to key system requirements. The D4V hypothesis is that the same general architecture and design principles leading to good modularity, extensibility and complexity/functionality ratio can be adapted to overcome some of the limitations of conventional reliability assurance measures, such as too large a state space or too many execution paths.

Comments on the use of network structures to analyse commercial companies’ evolution and their impact on economic behaviour

NASA Astrophysics Data System (ADS)

Costea, Carmen

2006-10-01

Network analysis studies the development of the social structure of relationships around a group or an institutional body, and how it affects beliefs and behaviours. Causal constraints require a special and deeper attention to the social structure. The purpose of this paper is to give a new approach to the idea that this reality should be primarily conceived and investigated from the perspective of the properties of relations between and within units, instead of the properties of these units themselves. The relationship may refer to the exchange of products, labour, information and money. By mapping these relationships, network analysis can help to uncover the emergent and informal communication patterns of commercial companies that may be compared to the formal communication structures. These emergent patterns can be used to explain institutional and individuals’ behaviours. Network analysis techniques focus on the communication structure of an organization that can be subdivided and handled with different approaches. Structural features that can be analysed through the use of network analysis techniques are, for example, the (formal and informal) communication patterns in an organization or the identification of specific groups within an organization. Special attention may be given to specific aspects of communication patterns.

The effect of process parameters on Twin Wire Arc spray pattern shape

DOE PAGES

Hall, Aaron Christopher; McCloskey, James Francis; Horner, Allison Lynne

2015-04-20

A design of experiments approach was used to describe process parameter—spray pattern relationships in the Twin Wire Arc process using zinc feed stock in a TAFA 8835 (Praxair, Concord, NH, USA) spray torch. Specifically, the effects of arc current, primary atomizing gas pressure, and secondary atomizing gas pressure on spray pattern size, spray pattern flatness, spray pattern eccentricity, and coating deposition rate were investigated. Process relationships were investigated with the intent of maximizing or minimizing each coating property. It was determined that spray pattern area was most affected by primary gas pressure and secondary gas pressure. Pattern eccentricity was mostmore » affected by secondary gas pressure. Pattern flatness was most affected by primary gas pressure. Lastly, coating deposition rate was most affected by arc current.« less

The effect of process parameters on Twin Wire Arc spray pattern shape

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

Hall, Aaron Christopher; McCloskey, James Francis; Horner, Allison Lynne

A design of experiments approach was used to describe process parameter—spray pattern relationships in the Twin Wire Arc process using zinc feed stock in a TAFA 8835 (Praxair, Concord, NH, USA) spray torch. Specifically, the effects of arc current, primary atomizing gas pressure, and secondary atomizing gas pressure on spray pattern size, spray pattern flatness, spray pattern eccentricity, and coating deposition rate were investigated. Process relationships were investigated with the intent of maximizing or minimizing each coating property. It was determined that spray pattern area was most affected by primary gas pressure and secondary gas pressure. Pattern eccentricity was mostmore » affected by secondary gas pressure. Pattern flatness was most affected by primary gas pressure. Lastly, coating deposition rate was most affected by arc current.« less

Coupled local facilitation and global hydrologic inhibition drive landscape geometry in a patterned peatland

NASA Astrophysics Data System (ADS)

Acharya, S.; Kaplan, D. A.; Casey, S.; Cohen, M. J.; Jawitz, J. W.

2015-05-01

Self-organized landscape patterning can arise in response to multiple processes. Discriminating among alternative patterning mechanisms, particularly where experimental manipulations are untenable, requires process-based models. Previous modeling studies have attributed patterning in the Everglades (Florida, USA) to sediment redistribution and anisotropic soil hydraulic properties. In this work, we tested an alternate theory, the self-organizing-canal (SOC) hypothesis, by developing a cellular automata model that simulates pattern evolution via local positive feedbacks (i.e., facilitation) coupled with a global negative feedback based on hydrology. The model is forced by global hydroperiod that drives stochastic transitions between two patch types: ridge (higher elevation) and slough (lower elevation). We evaluated model performance using multiple criteria based on six statistical and geostatistical properties observed in reference portions of the Everglades landscape: patch density, patch anisotropy, semivariogram ranges, power-law scaling of ridge areas, perimeter area fractal dimension, and characteristic pattern wavelength. Model results showed strong statistical agreement with reference landscapes, but only when anisotropically acting local facilitation was coupled with hydrologic global feedback, for which several plausible mechanisms exist. Critically, the model correctly generated fractal landscapes that had no characteristic pattern wavelength, supporting the invocation of global rather than scale-specific negative feedbacks.

Coupled local facilitation and global hydrologic inhibition drive landscape geometry in a patterned peatland

NASA Astrophysics Data System (ADS)

Acharya, S.; Kaplan, D. A.; Casey, S.; Cohen, M. J.; Jawitz, J. W.

2015-01-01

Self-organized landscape patterning can arise in response to multiple processes. Discriminating among alternative patterning mechanisms, particularly where experimental manipulations are untenable, requires process-based models. Previous modeling studies have attributed patterning in the Everglades (Florida, USA) to sediment redistribution and anisotropic soil hydraulic properties. In this work, we tested an alternate theory, the self-organizing canal (SOC) hypothesis, by developing a cellular automata model that simulates pattern evolution via local positive feedbacks (i.e., facilitation) coupled with a global negative feedback based on hydrology. The model is forced by global hydroperiod that drives stochastic transitions between two patch types: ridge (higher elevation) and slough (lower elevation). We evaluated model performance using multiple criteria based on six statistical and geostatistical properties observed in reference portions of the Everglades landscape: patch density, patch anisotropy, semivariogram ranges, power-law scaling of ridge areas, perimeter area fractal dimension, and characteristic pattern wavelength. Model results showed strong statistical agreement with reference landscapes, but only when anisotropically acting local facilitation was coupled with hydrologic global feedback, for which several plausible mechanisms exist. Critically, the model correctly generated fractal landscapes that had no characteristic pattern wavelength, supporting the invocation of global rather than scale-specific negative feedbacks.

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity

PubMed Central

Jackson, Daniel J.; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M.; Fleck, Claudia

2017-01-01

Abstract Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent “GS” domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. PMID:28961798

Sequentially distant but structurally similar proteins exhibit fold specific patterns based on their biophysical properties.

PubMed

Rajendran, Senthilnathan; Jothi, Arunachalam

2018-05-16

The Three-dimensional structure of a protein depends on the interaction between their amino acid residues. These interactions are in turn influenced by various biophysical properties of the amino acids. There are several examples of proteins that share the same fold but are very dissimilar at the sequence level. For proteins to share a common fold some crucial interactions should be maintained despite insignificant sequence similarity. Since the interactions are because of the biophysical properties of the amino acids, we should be able to detect descriptive patterns for folds at such a property level. In this line, the main focus of our research is to analyze such proteins and to characterize them in terms of their biophysical properties. Protein structures with sequence similarity lesser than 40% were selected for ten different subfolds from three different mainfolds (according to CATH classification) and were used for this analysis. We used the normalized values of the 49 physio-chemical, energetic and conformational properties of amino acids. We characterize the folds based on the average biophysical property values. We also observed a fold specific correlational behavior of biophysical properties despite a very low sequence similarity in our data. We further trained three different binary classification models (Naive Bayes-NB, Support Vector Machines-SVM and Bayesian Generalized Linear Model-BGLM) which could discriminate mainfold based on the biophysical properties. We also show that among the three generated models, the BGLM classifier model was able to discriminate protein sequences coming under all beta category with 81.43% accuracy and all alpha, alpha-beta proteins with 83.37% accuracy. Copyright © 2018 Elsevier Ltd. All rights reserved.

Decoding the neural signatures of emotions expressed through sound.

PubMed

Sachs, Matthew E; Habibi, Assal; Damasio, Antonio; Kaplan, Jonas T

2018-07-01

Effective social functioning relies in part on the ability to identify emotions from auditory stimuli and respond appropriately. Previous studies have uncovered brain regions engaged by the affective information conveyed by sound. But some of the acoustical properties of sounds that express certain emotions vary remarkably with the instrument used to produce them, for example the human voice or a violin. Do these brain regions respond in the same way to different emotions regardless of the sound source? To address this question, we had participants (N = 38, 20 females) listen to brief audio excerpts produced by the violin, clarinet, and human voice, each conveying one of three target emotions-happiness, sadness, and fear-while brain activity was measured with fMRI. We used multivoxel pattern analysis to test whether emotion-specific neural responses to the voice could predict emotion-specific neural responses to musical instruments and vice-versa. A whole-brain searchlight analysis revealed that patterns of activity within the primary and secondary auditory cortex, posterior insula, and parietal operculum were predictive of the affective content of sound both within and across instruments. Furthermore, classification accuracy within the anterior insula was correlated with behavioral measures of empathy. The findings suggest that these brain regions carry emotion-specific patterns that generalize across sounds with different acoustical properties. Also, individuals with greater empathic ability have more distinct neural patterns related to perceiving emotions. These results extend previous knowledge regarding how the human brain extracts emotional meaning from auditory stimuli and enables us to understand and connect with others effectively. Copyright © 2018 Elsevier Inc. All rights reserved.

Symmetries and synchronization in multilayer random networks

NASA Astrophysics Data System (ADS)

Saa, Alberto

2018-04-01

In the light of the recently proposed scenario of asymmetry-induced synchronization (AISync), in which dynamical uniformity and consensus in a distributed system would demand certain asymmetries in the underlying network, we investigate here the influence of some regularities in the interlayer connection patterns on the synchronization properties of multilayer random networks. More specifically, by considering a Stuart-Landau model of complex oscillators with random frequencies, we report for multilayer networks a dynamical behavior that could be also classified as a manifestation of AISync. We show, namely, that the presence of certain symmetries in the interlayer connection pattern tends to diminish the synchronization capability of the whole network or, in other words, asymmetries in the interlayer connections would enhance synchronization in such structured networks. Our results might help the understanding not only of the AISync mechanism itself but also its possible role in the determination of the interlayer connection pattern of multilayer and other structured networks with optimal synchronization properties.

Manipulation of Superparamagnetic Beads on Patterned Exchange-Bias Layer Systems for Biosensing Applications.

PubMed

Ehresmann, Arno; Koch, Iris; Holzinger, Dennis

2015-11-13

A technology platform based on a remotely controlled and stepwise transport of an array arrangement of superparamagnetic beads (SPB) for efficient molecular uptake, delivery and accumulation in the context of highly specific and sensitive analyte molecule detection for the application in lab-on-a-chip devices is presented. The near-surface transport of SPBs is realized via the dynamic transformation of the SPBs' magnetic potential energy landscape above a magnetically stripe patterned Exchange-Bias (EB) thin film layer systems due to the application of sub-mT external magnetic field pulses. In this concept, the SPB velocity is dramatically influenced by the magnitude and gradient of the magnetic field landscape (MFL) above the magnetically stripe patterned EB substrate, the SPB to substrate distance, the magnetic properties of both the SPBs and the EB layer system, respectively, as well as by the properties of the external magnetic field pulses and the surrounding fluid. The focus of this review is laid on the specific MFL design in EB layer systems via light-ion bombardment induced magnetic patterning (IBMP). A numerical approach is introduced for the theoretical description of the MFL in comparison to experimental characterization via scanning Hall probe microscopy. The SPB transport mechanism will be outlined in terms of the dynamic interplay between the EB substrate's MFL and the pulse scheme of the external magnetic field.

Manipulation of Superparamagnetic Beads on Patterned Exchange-Bias Layer Systems for Biosensing Applications

PubMed Central

Ehresmann, Arno; Koch, Iris; Holzinger, Dennis

2015-01-01

A technology platform based on a remotely controlled and stepwise transport of an array arrangement of superparamagnetic beads (SPB) for efficient molecular uptake, delivery and accumulation in the context of highly specific and sensitive analyte molecule detection for the application in lab-on-a-chip devices is presented. The near-surface transport of SPBs is realized via the dynamic transformation of the SPBs’ magnetic potential energy landscape above a magnetically stripe patterned Exchange-Bias (EB) thin film layer systems due to the application of sub-mT external magnetic field pulses. In this concept, the SPB velocity is dramatically influenced by the magnitude and gradient of the magnetic field landscape (MFL) above the magnetically stripe patterned EB substrate, the SPB to substrate distance, the magnetic properties of both the SPBs and the EB layer system, respectively, as well as by the properties of the external magnetic field pulses and the surrounding fluid. The focus of this review is laid on the specific MFL design in EB layer systems via light-ion bombardment induced magnetic patterning (IBMP). A numerical approach is introduced for the theoretical description of the MFL in comparison to experimental characterization via scanning Hall probe microscopy. The SPB transport mechanism will be outlined in terms of the dynamic interplay between the EB substrate’s MFL and the pulse scheme of the external magnetic field. PMID:26580625

Evaluating, Comparing, and Interpreting Protein Domain Hierarchies

PubMed Central

2014-01-01

Abstract Arranging protein domain sequences hierarchically into evolutionarily divergent subgroups is important for investigating evolutionary history, for speeding up web-based similarity searches, for identifying sequence determinants of protein function, and for genome annotation. However, whether or not a particular hierarchy is optimal is often unclear, and independently constructed hierarchies for the same domain can often differ significantly. This article describes methods for statistically evaluating specific aspects of a hierarchy, for probing the criteria underlying its construction and for direct comparisons between hierarchies. Information theoretical notions are used to quantify the contributions of specific hierarchical features to the underlying statistical model. Such features include subhierarchies, sequence subgroups, individual sequences, and subgroup-associated signature patterns. Underlying properties are graphically displayed in plots of each specific feature's contributions, in heat maps of pattern residue conservation, in “contrast alignments,” and through cross-mapping of subgroups between hierarchies. Together, these approaches provide a deeper understanding of protein domain functional divergence, reveal uncertainties caused by inconsistent patterns of sequence conservation, and help resolve conflicts between competing hierarchies. PMID:24559108

Cytometer on a chip

NASA Technical Reports Server (NTRS)

Lynes, Michael A. (Inventor); Fernandez, Salvador M. (Inventor)

2010-01-01

An assay technique for label-free, highly parallel, qualitative and quantitative detection of specific cell populations in a sample and for assessing cell functional status, cell-cell interactions and cellular responses to drugs, environmental toxins, bacteria, viruses and other factors that may affect cell function. The technique includes a) creating a first array of binding regions in a predetermined spatial pattern on a sensor surface capable of specifically binding the cells to be assayed; b) creating a second set of binding regions in specific spatial patterns relative to the first set designed to efficiently capture potential secreted or released products from cells captured on the first set of binding regions; c) contacting the sensor surface with the sample, and d) simultaneously monitoring the optical properties of all the binding regions of the sensor surface to determine the presence and concentration of specific cell populations in the sample and their functional status by detecting released or secreted bioproducts.

Landscape pattern metrics and regional assessment

USGS Publications Warehouse

O'Neill, R. V.; Riitters, K.H.; Wickham, J.D.; Jones, K.B.

1999-01-01

The combination of remote imagery data, geographic information systems software, and landscape ecology theory provides a unique basis for monitoring and assessing large-scale ecological systems. The unique feature of the work has been the need to develop and interpret quantitative measures of spatial pattern-the landscape indices. This article reviews what is known about the statistical properties of these pattern metrics and suggests some additional metrics based on island biogeography, percolation theory, hierarchy theory, and economic geography. Assessment applications of this approach have required interpreting the pattern metrics in terms of specific environmental endpoints, such as wildlife and water quality, and research into how to represent synergystic effects of many overlapping sources of stress.

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity.

PubMed

Jackson, Daniel J; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M; Fleck, Claudia

2017-11-01

Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent "GS" domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The orthographic sensitivity to written Chinese in the occipital-temporal cortex.

PubMed

Liu, Haicheng; Jiang, Yi; Zhang, Bo; Ma, Lifei; He, Sheng; Weng, Xuchu

2013-06-01

Previous studies have identified an area in the left lateral fusiform cortex that is highly responsive to written words and has been named the visual word form area (VWFA). However, there is disagreement on the specific functional role of this area in word recognition. Chinese characters, which are dramatically different from Roman alphabets in the visual form and in the form to phonological mapping, provide a unique opportunity to investigate the properties of the VWFA. Specifically, to clarify the orthographic sensitivity in the mid-fusiform cortex, we compared fMRI response amplitudes (Exp. 1) as well as the spatial patterns of response across multiple voxels (Exp. 2) between Chinese characters and stimuli derived from Chinese characters with different orthographic properties. The fMRI response amplitude results suggest the existence of orthographic sensitivity in the VWFA. The results from multi-voxel pattern analysis indicate that spatial distribution of the responses across voxels in the occipitotemporal cortex contained discriminative information between the different types of character-related stimuli. These results together suggest that the orthographic rules are likely represented in a distributed neural network with the VWFA containing the most specific information regarding a stimulus' orthographic regularity.

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.

Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus

PubMed Central

Jehee, Janneke F. M.; Ballard, Dana H.

2009-01-01

Biphasic neural response properties, where the optimal stimulus for driving a neural response changes from one stimulus pattern to the opposite stimulus pattern over short periods of time, have been described in several visual areas, including lateral geniculate nucleus (LGN), primary visual cortex (V1), and middle temporal area (MT). We describe a hierarchical model of predictive coding and simulations that capture these temporal variations in neuronal response properties. We focus on the LGN-V1 circuit and find that after training on natural images the model exhibits the brain's LGN-V1 connectivity structure, in which the structure of V1 receptive fields is linked to the spatial alignment and properties of center-surround cells in the LGN. In addition, the spatio-temporal response profile of LGN model neurons is biphasic in structure, resembling the biphasic response structure of neurons in cat LGN. Moreover, the model displays a specific pattern of influence of feedback, where LGN receptive fields that are aligned over a simple cell receptive field zone of the same polarity decrease their responses while neurons of opposite polarity increase their responses with feedback. This phase-reversed pattern of influence was recently observed in neurophysiology. These results corroborate the idea that predictive feedback is a general coding strategy in the brain. PMID:19412529

Bulk Properties of Ni3Al(gamma') With Cu and Au Additions

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John

1995-01-01

The BFS method for alloys is applied to the study of 200 alloys obtained from adding Cu and Au impurities to a Ni3Al matrix. We analyze the trends in the bulk properties of these alloys (heat of formation, lattice parameter, and bulk modulus) and detect specific alloy compositions for which these quantities have particular values. A detailed analysis of the atomic interactions that lead to the preferred ordering patterns is presented.

Patterns in hydraulic architecture from roots to branches in six tropical tree species from cacao agroforestry and their relation to wood density and stem growth.

PubMed

Kotowska, Martyna M; Hertel, Dietrich; Rajab, Yasmin Abou; Barus, Henry; Schuldt, Bernhard

2015-01-01

For decades it has been assumed that the largest vessels are generally found in roots and that vessel size and corresponding sapwood area-specific hydraulic conductivity are acropetally decreasing toward the distal twigs. However, recent studies from the perhumid tropics revealed a hump-shaped vessel size distribution. Worldwide tropical perhumid forests are extensively replaced by agroforestry systems often using introduced species of various biogeographical and climatic origins. Nonetheless, it is unknown so far what kind of hydraulic architectural patterns are developed in those agroforestry tree species and which impact this exerts regarding important tree functional traits, such as stem growth, hydraulic efficiency and wood density (WD). We investigated wood anatomical and hydraulic properties of the root, stem and branch wood in Theobroma cacao and five common shade tree species in agroforestry systems on Sulawesi (Indonesia); three of these were strictly perhumid tree species, and the other three tree species are tolerating seasonal drought. The overall goal of our study was to relate these properties to stem growth and other tree functional traits such as foliar nitrogen content and sapwood to leaf area ratio. Our results confirmed a hump-shaped vessel size distribution in nearly all species. Drought-adapted species showed divergent patterns of hydraulic conductivity, vessel density, and relative vessel lumen area between root, stem and branch wood compared to wet forest species. Confirming findings from natural old-growth forests in the same region, WD showed no relationship to specific conductivity. Overall, aboveground growth performance was better predicted by specific hydraulic conductivity than by foliar traits and WD. Our study results suggest that future research on conceptual trade-offs of tree hydraulic architecture should consider biogeographical patterns underlining the importance of anatomical adaptation mechanisms to environment.

Calcium Dynamics in Basal Dendrites of Layer 5A and 5B Pyramidal Neurons Is Tuned to the Cell-Type Specific Physiological Action Potential Discharge

PubMed Central

Krieger, Patrik; de Kock, Christiaan P. J.; Frick, Andreas

2017-01-01

Layer 5 (L5) is a major neocortical output layer containing L5A slender-tufted (L5A-st) and L5B thick-tufted (L5B-tt) pyramidal neurons. These neuron types differ in their in vivo firing patterns, connectivity and dendritic morphology amongst other features, reflecting their specific functional role within the neocortical circuits. Here, we asked whether the active properties of the basal dendrites that receive the great majority of synaptic inputs within L5 differ between these two pyramidal neuron classes. To quantify their active properties, we measured the efficacy with which action potential (AP) firing patterns backpropagate along the basal dendrites by measuring the accompanying calcium transients using two-photon laser scanning microscopy in rat somatosensory cortex slices. For these measurements we used both “artificial” three-AP patterns and more complex physiological AP patterns that were previously recorded in anesthetized rats in L5A-st and L5B-tt neurons in response to whisker stimulation. We show that AP patterns with relatively few APs (3APs) evoke a calcium response in L5B-tt, but not L5A-st, that is dependent on the temporal pattern of the three APs. With more complex in vivo recorded AP patterns, the average calcium response was similar in the proximal dendrites but with a decay along dendrites (measured up to 100 μm) of L5B-tt but not L5A-st neurons. Interestingly however, the whisker evoked AP patterns—although very different for the two cell types—evoke similar calcium responses. In conclusion, although the effectiveness with which different AP patterns evoke calcium transients vary between L5A-st and L5B-tt cell, the calcium influx appears to be tuned such that whisker-evoked calcium transients are within the same dynamic range for both cell types. PMID:28744201

A new bidirectional heteroassociative memory encompassing correlational, competitive and topological properties.

PubMed

Chartier, Sylvain; Giguère, Gyslain; Langlois, Dominic

2009-01-01

In this paper, we present a new recurrent bidirectional model that encompasses correlational, competitive and topological model properties. The simultaneous use of many classes of network behaviors allows for the unsupervised learning/categorization of perceptual patterns (through input compression) and the concurrent encoding of proximities in a multidimensional space. All of these operations are achieved within a common learning operation, and using a single set of defining properties. It is shown that the model can learn categories by developing prototype representations strictly from exposition to specific exemplars. Moreover, because the model is recurrent, it can reconstruct perfect outputs from incomplete and noisy patterns. Empirical exploration of the model's properties and performance shows that its ability for adequate clustering stems from: (1) properly distributing connection weights, and (2) producing a weight space with a low dispersion level (or higher density). In addition, since the model uses a sparse representation (k-winners), the size of topological neighborhood can be fixed, and no longer requires a decrease through time as was the case with classic self-organizing feature maps. Since the model's learning and transmission parameters are independent from learning trials, the model can develop stable fixed points in a constrained topological architecture, while being flexible enough to learn novel patterns.

Fabrication of three dimensional patterns of wide dimensional range using microbes and their applications

NASA Astrophysics Data System (ADS)

Mehta, Sunita; Murugeson, Saravanan; Prakash, Balaji; Deepak

2015-10-01

Inspired by the wound healing property of certain trees, we report a novel microbes based additive process for producing three dimensional patterns, which has a potential of engineering applications in a variety of fields. Imposing a two dimensional pattern of microbes on a gel media and allowing them to grow in the third dimension is known from its use in biological studies. Instead, we have introduced an intermediate porous substrate between the gel media and the microbial growth, which enables three dimensional patterns in specific forms that can be lifted off and used in engineering applications. In order to demonstrate the applicability of this idea in a diverse set of areas, two applications are selected. In one, using this method of microbial growth, we have fabricated microlenses for enhanced light extraction in organic light emitting diodes, where densely packed microlenses of the diameters of hundreds of microns lead to luminance increase by a factor of 1.24X. In another entirely different type of application, braille text patterns are prepared on a normal office paper where the grown microbial colonies serve as braille tactile dots. Braille dot patterns thus prepared meet the standard specifications (size and spacing) for braille books.

Two-phase flow patterns in adiabatic and diabatic corrugated plate gaps

NASA Astrophysics Data System (ADS)

Polzin, A.-E.; Kabelac, S.; de Vries, B.

2016-09-01

Correlations for two-phase heat transfer and pressure drop can be improved considerably, when they are adapted to specific flow patterns. As plate heat exchangers find increasing application as evaporators and condensers, there is a need for flow pattern maps for corrugated plate gaps. This contribution presents experimental results on flow pattern investigations for such a plate heat exchanger background, using an adiabatic visualisation setup as well as a diabatic setup. Three characteristic flow patterns were observed in the considered range of two-phase flow: bubbly flow, film flow and slug flow. The occurrence of these flow patterns is a function of mass flux, void fraction, fluid properties and plate geometry. Two different plate geometries having a corrugation angle of 27° and 63°, respectively and two different fluids (water/air and R365mfc liquid/vapor) have been analysed. A flow pattern map using the momentum flux is presented.

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

Dynamic information routing in complex networks

PubMed Central

Kirst, Christoph; Timme, Marc; Battaglia, Demian

2016-01-01

Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this mechanism specifically for oscillatory dynamics and analyse how individual unit properties, the network topology and external inputs co-act to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine nonlocal network-wide communication. These results help understanding and designing information routing patterns across systems where collective dynamics co-occurs with a communication function. PMID:27067257

3D Printed, Microgroove Pattern-Driven Generation of Oriented Ligamentous Architectures.

PubMed

Park, Chan Ho; Kim, Kyoung-Hwa; Lee, Yong-Moo; Giannobile, William V; Seol, Yang-Jo

2017-09-08

Specific orientations of regenerated ligaments are crucially required for mechanoresponsive properties and various biomechanical adaptations, which are the key interplay to support mineralized tissues. Although various 2D platforms or 3D printing systems can guide cellular activities or aligned organizations, it remains a challenge to develop ligament-guided, 3D architectures with the angular controllability for parallel, oblique or perpendicular orientations of cells required for biomechanical support of organs. Here, we show the use of scaffold design by additive manufacturing for specific topographies or angulated microgroove patterns to control cell orientations such as parallel (0°), oblique (45°) and perpendicular (90°) angulations. These results demonstrate that ligament cells displayed highly predictable and controllable orientations along microgroove patterns on 3D biopolymeric scaffolds. Our findings demonstrate that 3D printed topographical approaches can regulate spatiotemporal cell organizations that offer strong potential for adaptation to complex tissue defects to regenerate ligament-bone complexes.

A host-endoparasite network of Neotropical marine fish: are there organizational patterns?

PubMed

Bellay, Sybelle; Lima, Dilermando P; Takemoto, Ricardo M; Luque, José L

2011-12-01

Properties of ecological networks facilitate the understanding of interaction patterns in host-parasite systems as well as the importance of each species in the interaction structure of a community. The present study evaluates the network structure, functional role of all species and patterns of parasite co-occurrence in a host-parasite network to determine the organization level of a host-parasite system consisting of 170 taxa of gastrointestinal metazoans of 39 marine fish species on the coast of Brazil. The network proved to be nested and modular, with a low degree of connectance. Host-parasite interactions were influenced by host phylogeny. Randomness in parasite co-occurrence was observed in most modules and component communities, although species segregation patterns were also observed. The low degree of connectance in the network may be the cause of properties such as nestedness and modularity, which indicate the presence of a high number of peripheral species. Segregation patterns among parasite species in modules underscore the role of host specificity. Knowledge of ecological networks allows detection of keystone species for the maintenance of biodiversity and the conduction of further studies on the stability of networks in relation to frequent environmental changes.

Stable structural color patterns displayed on transparent insect wings.

PubMed

Shevtsova, Ekaterina; Hansson, Christer; Janzen, Daniel H; Kjærandsen, Jostein

2011-01-11

Color patterns play central roles in the behavior of insects, and are important traits for taxonomic studies. Here we report striking and stable structural color patterns--wing interference patterns (WIPs)--in the transparent wings of small Hymenoptera and Diptera, patterns that have been largely overlooked by biologists. These extremely thin wings reflect vivid color patterns caused by thin film interference. The visibility of these patterns is affected by the way the insects display their wings against various backgrounds with different light properties. The specific color sequence displayed lacks pure red and matches the color vision of most insects, strongly suggesting that the biological significance of WIPs lies in visual signaling. Taxon-specific color patterns are formed by uneven membrane thickness, pigmentation, venation, and hair placement. The optically refracted pattern is also stabilized by microstructures of the wing such as membrane corrugations and spherical cell structures that reinforce the pattern and make it essentially noniridescent over a large range of light incidences. WIPs can be applied to map the micromorphology of wings through direct observation and are useful in several fields of biology. We demonstrate their usefulness as identification patterns to solve cases of cryptic species complexes in tiny parasitic wasps, and indicate their potentials for research on the genetic control of wing development through direct links between the transregulatory wing landscape and interference patterns we observe in Drosophila model species. Some species display sexually dimorphic WIPs, suggesting sexual selection as one of the driving forces for their evolution.

New publicly available chemical query language, CSRML, to support chemotype representations for application to data mining and modeling.

PubMed

Yang, Chihae; Tarkhov, Aleksey; Marusczyk, Jörg; Bienfait, Bruno; Gasteiger, Johann; Kleinoeder, Thomas; Magdziarz, Tomasz; Sacher, Oliver; Schwab, Christof H; Schwoebel, Johannes; Terfloth, Lothar; Arvidson, Kirk; Richard, Ann; Worth, Andrew; Rathman, James

2015-03-23

Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Markup Language (CSRML), and can be encoded not only with connectivity and topology but also with properties of atoms, bonds, electronic systems, or molecules. CSRML has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory, and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper has also been developed and made publicly available in order to enable chemotype searching and fingerprinting against a target structure set. The public ChemoTyper houses the ToxPrint chemotype CSRML dictionary, as well as reference implementation so that the query specifications may be adopted by other chemical structure knowledge systems. The full specifications of the XML-based CSRML standard used to express chemotypes are publicly available to facilitate and encourage the exchange of structural knowledge.

Irregular behavior in an excitatory-inhibitory neuronal network

NASA Astrophysics Data System (ADS)

Park, Choongseok; Terman, David

2010-06-01

Excitatory-inhibitory networks arise in many regions throughout the central nervous system and display complex spatiotemporal firing patterns. These neuronal activity patterns (of individual neurons and/or the whole network) are closely related to the functional status of the system and differ between normal and pathological states. For example, neurons within the basal ganglia, a group of subcortical nuclei that are responsible for the generation of movement, display a variety of dynamic behaviors such as correlated oscillatory activity and irregular, uncorrelated spiking. Neither the origins of these firing patterns nor the mechanisms that underlie the patterns are well understood. We consider a biophysical model of an excitatory-inhibitory network in the basal ganglia and explore how specific biophysical properties of the network contribute to the generation of irregular spiking. We use geometric dynamical systems and singular perturbation methods to systematically reduce the model to a simpler set of equations, which is suitable for analysis. The results specify the dependence on the strengths of synaptic connections and the intrinsic firing properties of the cells in the irregular regime when applied to the subthalamopallidal network of the basal ganglia.

Patterns of muscle activity underlying object-specific grasp by the macaque monkey.

PubMed

Brochier, T; Spinks, R L; Umilta, M A; Lemon, R N

2004-09-01

During object grasp, a coordinated activation of distal muscles is required to shape the hand in relation to the physical properties of the object. Despite the fundamental importance of the grasping action, little is known of the muscular activation patterns that allow objects of different sizes and shapes to be grasped. In a study of two adult macaque monkeys, we investigated whether we could distinguish between EMG activation patterns associated with grasp of 12 differently shaped objects, chosen to evoke a wide range of grasping postures. Each object was mounted on a horizontal shuttle held by a weak spring (load force 1-2 N). Objects were located in separate sectors of a "carousel," and inter-trial rotation of the carousel allowed sequential presentation of the objects in pseudorandom order. EMG activity from 10 to 12 digit, hand, and arm muscles was recorded using chronically implanted electrodes. We show that the grasp of different objects was characterized by complex but distinctive patterns of EMG activation. Cluster analysis shows that these object-related EMG patterns were specific and consistent enough to identify the object unequivocally from the EMG recordings alone. EMG-based object identification required a minimum of six EMGs from simultaneously recorded muscles. EMG patterns were consistent across recording sessions in a given monkey but showed some differences between animals. These results identify the specific patterns of activity required to achieve distinct hand postures for grasping, and they open the way to our understanding of how these patterns are generated by the central motor network.

A Genome-Wide Screen Indicates Correlation between Differentiation and Expression of Metabolism Related Genes

PubMed Central

Shende, Akhilesh; Singh, Anupama; Meena, Anil; Ghosal, Ritika; Ranganathan, Madhav; Bandyopadhyay, Amitabha

2013-01-01

Differentiated tissues may be considered as materials with distinct properties. The differentiation program of a given tissue ensures that it acquires material properties commensurate with its function. It may be hypothesized that some of these properties are acquired through production of tissue-specific metabolites synthesized by metabolic enzymes. To establish correlation between metabolism and organogenesis we have carried out a genome-wide expression study of metabolism related genes by RNA in-situ hybridization. 23% of the metabolism related genes studied are expressed in a tissue-restricted but not tissue-exclusive manner. We have conducted the screen on whole mount chicken (Gallus gallus) embryos from four distinct developmental stages to correlate dynamic changes in expression patterns of metabolic enzymes with spatio-temporally unique developmental events. Our data strongly suggests that unique combinations of metabolism related genes, and not specific metabolic pathways, are upregulated during differentiation. Further, expression of metabolism related genes in well established signaling centers that regulate different aspects of morphogenesis indicates developmental roles of some of the metabolism related genes. The database of tissue-restricted expression patterns of metabolism related genes, generated in this study, should serve as a resource for systematic identification of these genes with tissue-specific functions during development. Finally, comprehensive understanding of differentiation is not possible unless the downstream genes of a differentiation cascade are identified. We propose, metabolic enzymes constitute a significant portion of these downstream target genes. Thus our study should help elucidate different aspects of tissue differentiation. PMID:23717462

A genome-wide screen indicates correlation between differentiation and expression of metabolism related genes.

PubMed

Roy, Priti; Kumar, Brijesh; Shende, Akhilesh; Singh, Anupama; Meena, Anil; Ghosal, Ritika; Ranganathan, Madhav; Bandyopadhyay, Amitabha

2013-01-01

Differentiated tissues may be considered as materials with distinct properties. The differentiation program of a given tissue ensures that it acquires material properties commensurate with its function. It may be hypothesized that some of these properties are acquired through production of tissue-specific metabolites synthesized by metabolic enzymes. To establish correlation between metabolism and organogenesis we have carried out a genome-wide expression study of metabolism related genes by RNA in-situ hybridization. 23% of the metabolism related genes studied are expressed in a tissue-restricted but not tissue-exclusive manner. We have conducted the screen on whole mount chicken (Gallus gallus) embryos from four distinct developmental stages to correlate dynamic changes in expression patterns of metabolic enzymes with spatio-temporally unique developmental events. Our data strongly suggests that unique combinations of metabolism related genes, and not specific metabolic pathways, are upregulated during differentiation. Further, expression of metabolism related genes in well established signaling centers that regulate different aspects of morphogenesis indicates developmental roles of some of the metabolism related genes. The database of tissue-restricted expression patterns of metabolism related genes, generated in this study, should serve as a resource for systematic identification of these genes with tissue-specific functions during development. Finally, comprehensive understanding of differentiation is not possible unless the downstream genes of a differentiation cascade are identified. We propose, metabolic enzymes constitute a significant portion of these downstream target genes. Thus our study should help elucidate different aspects of tissue differentiation.

Network Sampling and Classification:An Investigation of Network Model Representations

PubMed Central

Airoldi, Edoardo M.; Bai, Xue; Carley, Kathleen M.

2011-01-01

Methods for generating a random sample of networks with desired properties are important tools for the analysis of social, biological, and information networks. Algorithm-based approaches to sampling networks have received a great deal of attention in recent literature. Most of these algorithms are based on simple intuitions that associate the full features of connectivity patterns with specific values of only one or two network metrics. Substantive conclusions are crucially dependent on this association holding true. However, the extent to which this simple intuition holds true is not yet known. In this paper, we examine the association between the connectivity patterns that a network sampling algorithm aims to generate and the connectivity patterns of the generated networks, measured by an existing set of popular network metrics. We find that different network sampling algorithms can yield networks with similar connectivity patterns. We also find that the alternative algorithms for the same connectivity pattern can yield networks with different connectivity patterns. We argue that conclusions based on simulated network studies must focus on the full features of the connectivity patterns of a network instead of on the limited set of network metrics for a specific network type. This fact has important implications for network data analysis: for instance, implications related to the way significance is currently assessed. PMID:21666773

Stable structural color patterns displayed on transparent insect wings

PubMed Central

Shevtsova, Ekaterina; Hansson, Christer; Janzen, Daniel H.; Kjærandsen, Jostein

2011-01-01

Color patterns play central roles in the behavior of insects, and are important traits for taxonomic studies. Here we report striking and stable structural color patterns—wing interference patterns (WIPs)—in the transparent wings of small Hymenoptera and Diptera, patterns that have been largely overlooked by biologists. These extremely thin wings reflect vivid color patterns caused by thin film interference. The visibility of these patterns is affected by the way the insects display their wings against various backgrounds with different light properties. The specific color sequence displayed lacks pure red and matches the color vision of most insects, strongly suggesting that the biological significance of WIPs lies in visual signaling. Taxon-specific color patterns are formed by uneven membrane thickness, pigmentation, venation, and hair placement. The optically refracted pattern is also stabilized by microstructures of the wing such as membrane corrugations and spherical cell structures that reinforce the pattern and make it essentially noniridescent over a large range of light incidences. WIPs can be applied to map the micromorphology of wings through direct observation and are useful in several fields of biology. We demonstrate their usefulness as identification patterns to solve cases of cryptic species complexes in tiny parasitic wasps, and indicate their potentials for research on the genetic control of wing development through direct links between the transregulatory wing landscape and interference patterns we observe in Drosophila model species. Some species display sexually dimorphic WIPs, suggesting sexual selection as one of the driving forces for their evolution. PMID:21199954

Effect of post cure time and temperature on the properties of two phenolic-fiber composites

NASA Technical Reports Server (NTRS)

Lucy, M. H.; Price, H. L.

1975-01-01

Some effects of post-cure time and temperature on the physicomechanical properties of a phenolic-asbestos and a phenolic-glass composite are studied. The molding and post-curing procedures are discussed along with physical and mechanical test results. It is found that the specific gravity of the panels tested decreased slightly but the hardness always increased with post cure, and that the mechanical properties had different patterns of response to increasing post-cure time and temperature. For tensile properties, strength decreased, modulus increased, and elongation at break exhibited little change. In general, the phenolic-asbestos showed more positive response to post cure than did the phenolic-glass. Mold venting is found to impart better properties to the composites concerned.

Characterization of craniofacial sutures using the finite element method.

PubMed

Maloul, Asmaa; Fialkov, Jeffrey; Wagner, Diane; Whyne, Cari M

2014-01-03

Characterizing the biomechanical behavior of sutures in the human craniofacial skeleton (CFS) is essential to understand the global impact of these articulations on load transmission, but is challenging due to the complexity of their interdigitated morphology, the multidirectional loading they are exposed to and the lack of well-defined suture material properties. This study aimed to quantify the impact of morphological features, direction of loading and suture material properties on the mechanical behavior of sutures and surrounding bone in the CFS. Thirty-six idealized finite element (FE) models were developed. One additional specimen-specific FE model was developed based on the morphology obtained from a µCT scan to represent the morphological complexity inherent in CFS sutures. Outcome variables of strain energy (SE) and von Mises stress (σvm) were evaluated to characterize the sutures' biomechanical behavior. Loading direction was found to impact the relationship between SE and interdigitation index and yielded varied patterns of σvm in both the suture and surrounding bone. Adding bone connectivity reduced suture strain energy and altered the σvm distribution. Incorporating transversely isotropic material properties was found to reduce SE, but had little impact on stress patterns. High-resolution µCT scanning of the suture revealed a complex morphology with areas of high and low interdigitations. The specimen specific suture model results were reflective of SE absorption and σvm distribution patterns consistent with the simplified FE results. Suture mechanical behavior is impacted by morphologic factors (interdigitation and connectivity), which may be optimized for regional loading within the CFS. © 2013 Elsevier Ltd. All rights reserved.

Sparse Feature Selection Identifies H2A.Z as a Novel, Pattern-Specific Biomarker for Asymmetrically Self-Renewing Distributed Stem Cells

PubMed Central

Huh, Yang Hoon; Noh, Minsoo; Burden, Frank R.; Chen, Jennifer C.; Winkler, David A.; Sherley, James L.

2015-01-01

There is a long-standing unmet clinical need for biomarkers with high specificity for distributed stem cells (DSCs) in tissues, or for use in diagnostic and therapeutic cell preparations (e.g., bone marrow). Although DSCs are essential for tissue maintenance and repair, accurate determination of their numbers for medical applications has been problematic. Previous searches for biomarkers expressed specifically in DSCs were hampered by difficulty obtaining pure DSCs and by the challenges in mining complex molecular expression data. To identify DSC such useful and specific biomarkers, we combined a novel sparse feature selection method with combinatorial molecular expression data focused on asymmetric self-renewal, a conspicuous property of DSCs. The analysis identified reduced expression of the histone H2A variant H2A.Z as a superior molecular discriminator for DSC asymmetric self-renewal. Subsequent molecular expression studies showed H2A.Z to be a novel “pattern-specific biomarker” for asymmetrically self-renewing cells with sufficient specificity to count asymmetrically self-renewing DSCs in vitro and potentially in situ. PMID:25636161

Identifying typical patterns of vulnerability: A 5-step approach based on cluster analysis

NASA Astrophysics Data System (ADS)

Sietz, Diana; Lüdeke, Matthias; Kok, Marcel; Lucas, Paul; Carsten, Walther; Janssen, Peter

2013-04-01

Specific processes that shape the vulnerability of socio-ecological systems to climate, market and other stresses derive from diverse background conditions. Within the multitude of vulnerability-creating mechanisms, distinct processes recur in various regions inspiring research on typical patterns of vulnerability. The vulnerability patterns display typical combinations of the natural and socio-economic properties that shape a systems' vulnerability to particular stresses. Based on the identification of a limited number of vulnerability patterns, pattern analysis provides an efficient approach to improving our understanding of vulnerability and decision-making for vulnerability reduction. However, current pattern analyses often miss explicit descriptions of their methods and pay insufficient attention to the validity of their groupings. Therefore, the question arises as to how do we identify typical vulnerability patterns in order to enhance our understanding of a systems' vulnerability to stresses? A cluster-based pattern recognition applied at global and local levels is scrutinised with a focus on an applicable methodology and practicable insights. Taking the example of drylands, this presentation demonstrates the conditions necessary to identify typical vulnerability patterns. They are summarised in five methodological steps comprising the elicitation of relevant cause-effect hypotheses and the quantitative indication of mechanisms as well as an evaluation of robustness, a validation and a ranking of the identified patterns. Reflecting scale-dependent opportunities, a global study is able to support decision-making with insights into the up-scaling of interventions when available funds are limited. In contrast, local investigations encourage an outcome-based validation. This constitutes a crucial step in establishing the credibility of the patterns and hence their suitability for informing extension services and individual decisions. In this respect, working at the local level provides a clear advantage since, to a large extent, limitations in globally available observational data constrain such a validation on the global scale. Overall, the five steps are outlined in detail in order to facilitate and motivate the application of pattern recognition in other research studies concerned with vulnerability analysis, including future applications to different vulnerability frameworks. Such applications could promote the refinement of mechanisms in specific contexts and advance methodological adjustments. This would further increase the value of identifying typical patterns in the properties of socio-ecological systems for an improved understanding and management of the relation between these systems and particular stresses.

Nucleotide variation in genes invloved in wood formation in two pine species

Treesearch

David Pot; Lisa McMillan; Craig Echt; Gregoire Le Provost; Pauline Garnier-Gere; Sheree Cato; Christophe Plomion

2005-01-01

Nucleotide diversity in eight genes related to wood formation was investigated in two pine species, Pinus pinaster and P. radiata. The nucleotide diversity patterns observed and their properties were compared between the two species according to the specific characteristics of the samples analysed. A lower diversity was observed in P. radiata...

26 CFR 1.482-2A - Determination of taxable income in specific situations.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of this section (except as provided in (b) of this subdivision) until such time as any property... been transferred to Y at that time by virtue of the fact that Y obtained the patent rights to product M..., inventions, formulas, processes, designs, patterns, and other similar items; (b) Copyrights, literary...

The neural response in short-term visual recognition memory for perceptual conjunctions.

PubMed

Elliott, R; Dolan, R J

1998-01-01

Short-term visual memory has been widely studied in humans and animals using delayed matching paradigms. The present study used positron emission tomography (PET) to determine the neural substrates of delayed matching to sample for complex abstract patterns over a 5-s delay. More specifically, the study assessed any differential neural response associated with remembering individual perceptual properties (color only and shape only) compared to conjunction between these properties. Significant activations associated with short-term visual memory (all memory conditions compared to perceptuomotor control) were observed in extrastriate cortex, medial and lateral parietal cortex, anterior cingulate, inferior frontal gyrus, and the thalamus. Significant deactivations were observed throughout the temporal cortex. Although the requirement to remember color compared to shape was associated with subtly different patterns of blood flow, the requirement to remember perceptual conjunctions between these features was not associated with additional specific activations. These data suggest that visual memory over a delay of the order of 5 s is mainly dependent on posterior perceptual regions of the cortex, with the exact regions depending on the perceptual aspect of the stimuli to be remembered.

Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family.

PubMed

Dos Santos, Helena G; Siltberg-Liberles, Jessica

2016-09-19

One of the largest multigene families in Metazoa are the tyrosine kinases (TKs). These are important multifunctional proteins that have evolved as dynamic switches that perform tyrosine phosphorylation and other noncatalytic activities regulated by various allosteric mechanisms. TKs interact with each other and with other molecules, ultimately activating and inhibiting different signaling pathways. TKs are implicated in cancer and almost 30 FDA-approved TK inhibitors are available. However, specific binding is a challenge when targeting an active site that has been conserved in multiple protein paralogs for millions of years. A cassette domain (CD) containing SH3-SH2-Tyrosine Kinase domains reoccurs in vertebrate nonreceptor TKs. Although part of the CD function is shared between TKs, it also presents TK specific features. Here, the evolutionary dynamics of sequence, structure, and phosphorylation across the CD in 17 TK paralogs have been investigated in a large-scale study. We establish that TKs often have ortholog-specific structural disorder and phosphorylation patterns, while secondary structure elements, as expected, are highly conserved. Further, domain-specific differences are at play. Notably, we found the catalytic domain to fluctuate more in certain secondary structure elements than the regulatory domains. By elucidating how different properties evolve after gene duplications and which properties are specifically conserved within orthologs, the mechanistic understanding of protein evolution is enriched and regions supposedly critical for functional divergence across paralogs are highlighted. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Colloidal Inorganic Nanocrystal Based Nanocomposites: Functional Materials for Micro and Nanofabrication

PubMed Central

Ingrosso, Chiara; Panniello, AnnaMaria; Comparelli, Roberto; Curri, Maria Lucia; Striccoli, Marinella

2010-01-01

The unique size- and shape-dependent electronic properties of nanocrystals (NCs) make them extremely attractive as novel structural building blocks for constructing a new generation of innovative materials and solid-state devices. Recent advances in material chemistry has allowed the synthesis of colloidal NCs with a wide range of compositions, with a precise control on size, shape and uniformity as well as specific surface chemistry. By incorporating such nanostructures in polymers, mesoscopic materials can be achieved and their properties engineered by choosing NCs differing in size and/or composition, properly tuning the interaction between NCs and surrounding environment. In this contribution, different approaches will be presented as effective opportunities for conveying colloidal NC properties to nanocomposite materials for micro and nanofabrication. Patterning of such nanocomposites either by conventional lithographic techniques and emerging patterning tools, such as ink jet printing and nanoimprint lithography, will be illustrated, pointing out their technological impact on developing new optoelectronic and sensing devices.

Research Update: Focused ion beam direct writing of magnetic patterns with controlled structural and magnetic properties

NASA Astrophysics Data System (ADS)

Urbánek, Michal; Flajšman, Lukáš; Křižáková, Viola; Gloss, Jonáš; Horký, Michal; Schmid, Michael; Varga, Peter

2018-06-01

Focused ion beam irradiation of metastable Fe78Ni22 thin films grown on Cu(100) substrates is used to create ferromagnetic, body-centered cubic patterns embedded into paramagnetic, face-centered-cubic surrounding. The structural and magnetic phase transformation can be controlled by varying parameters of the transforming gallium ion beam. The focused ion beam parameters such as the ion dose, number of scans, and scanning direction can be used not only to control a degree of transformation but also to change the otherwise four-fold in-plane magnetic anisotropy into the uniaxial anisotropy along a specific crystallographic direction. This change is associated with a preferred growth of specific crystallographic domains. The possibility to create magnetic patterns with continuous magnetization transitions and at the same time to create patterns with periodical changes in magnetic anisotropy makes this system an ideal candidate for rapid prototyping of a large variety of nanostructured samples. Namely, spin-wave waveguides and magnonic crystals can be easily combined into complex devices in a single fabrication step.

Voronoi cell patterns: Theoretical model and applications

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2011-11-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We use our model to describe the Voronoi cell patterns of several systems. Specifically, we study the island nucleation with irreversible attachment, the 1D car-parking problem, the formation of second-level administrative divisions, and the pattern formed by the Paris Métro stations.

Virus-based surface patterning of biological molecules, probes, and inorganic materials.

PubMed

Ahn, Suji; Jeon, Seongho; Kwak, Eun-A; Kim, Jong-Man; Jaworski, Justyn

2014-10-01

An essential requirement for continued technological advancement in many areas of biology, physics, chemistry, and materials science is the growing need to generate custom patterned materials. Building from recent achievements in the site-specific modification of virus for covalent surface tethering, we show in this work that stable 2D virus patterns can be generated in custom geometries over large area glass surfaces to yield templates of biological, biochemical, and inorganic materials in high density. As a nanomaterial building block, filamentous viruses have been extensively used in recent years to produce materials with interesting properties, owing to their ease of genetic and chemical modification. By utilizing un-natural amino acids generated at specific locations on the filamentous fd bacteriophage protein coat, surface immobilization is carried out on APTES patterned glass resulting in precise geometries of covalently linked virus material. This technique facilitated the surface display of a high density of virus that were labeled with biomolecules, fluorescent probes, and gold nanoparticles, thereby opening the possibility of integrating virus as functional components for surface engineering. Copyright © 2014 Elsevier B.V. All rights reserved.

Fabrication of three dimensional patterns of wide dimensional range using microbes and their applications

PubMed Central

Mehta, Sunita; Murugeson, Saravanan; Prakash, Balaji; Deepak

2015-01-01

Inspired by the wound healing property of certain trees, we report a novel microbes based additive process for producing three dimensional patterns, which has a potential of engineering applications in a variety of fields. Imposing a two dimensional pattern of microbes on a gel media and allowing them to grow in the third dimension is known from its use in biological studies. Instead, we have introduced an intermediate porous substrate between the gel media and the microbial growth, which enables three dimensional patterns in specific forms that can be lifted off and used in engineering applications. In order to demonstrate the applicability of this idea in a diverse set of areas, two applications are selected. In one, using this method of microbial growth, we have fabricated microlenses for enhanced light extraction in organic light emitting diodes, where densely packed microlenses of the diameters of hundreds of microns lead to luminance increase by a factor of 1.24X. In another entirely different type of application, braille text patterns are prepared on a normal office paper where the grown microbial colonies serve as braille tactile dots. Braille dot patterns thus prepared meet the standard specifications (size and spacing) for braille books. PMID:26486847

Perceiving environmental structure from optical motion

NASA Technical Reports Server (NTRS)

Lappin, Joseph S.

1991-01-01

Generally speaking, one of the most important sources of optical information about environmental structure is known to be the deforming optical patterns produced by the movements of the observer (pilot) or environmental objects. As an observer moves through a rigid environment, the projected optical patterns of environmental objects are systematically transformed according to their orientations and positions in 3D space relative to those of the observer. The detailed characteristics of these deforming optical patterns carry information about the 3D structure of the objects and about their locations and orientations relative to those of the observer. The specific geometrical properties of moving images that may constitute visually detected information about the shapes and locations of environmental objects is examined.

Dynamic phases, pinning, and pattern formation for driven dislocation assemblies

DOE PAGES

Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; ...

2015-01-23

We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Lastly, our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation andmore » dynamics in these systems.« less

Analysis of the Raven CPM Subtest Scores for a Sample of Gifted Children.

ERIC Educational Resources Information Center

Kluever, Raymond C.; Green, Kathy E.

The inter-subject/intra-subject subtest patterns (profiles) of the same sample of gifted children were examined based on factors found in a previous study of the Raven Coloured Progressive Matrices Test (CPM) that investigated structural properties with specific application to a sample of gifted children. The sample consisted of 166 children (78…

"Binaural Rivalry": Dichotic Listening as a Tool for the Investigation of the Neural Correlate of Consciousness

ERIC Educational Resources Information Center

Brancucci, Alfredo; Tommasi, Luca

2011-01-01

Since about two decades neuroscientists have systematically faced the problem of consciousness: the aim is to discover the neural activity specifically related to conscious perceptions, i.e. the biological properties of what philosophers call qualia. In this view, a neural correlate of consciousness (NCC) is a precise pattern of brain activity…

26 CFR 1.482-2A - Determination of taxable income in specific situations.

Code of Federal Regulations, 2012 CFR

2012-04-01

... paragraph of this section (except as provided in (b) of this subdivision) until such time as any property... been transferred to Y at that time by virtue of the fact that Y obtained the patent rights to product M..., inventions, formulas, processes, designs, patterns, and other similar items; (b) Copyrights, literary...

26 CFR 1.482-2A - Determination of taxable income in specific situations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... paragraph of this section (except as provided in (b) of this subdivision) until such time as any property... been transferred to Y at that time by virtue of the fact that Y obtained the patent rights to product M..., inventions, formulas, processes, designs, patterns, and other similar items; (b) Copyrights, literary...

26 CFR 1.482-2A - Determination of taxable income in specific situations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... paragraph of this section (except as provided in (b) of this subdivision) until such time as any property... been transferred to Y at that time by virtue of the fact that Y obtained the patent rights to product M..., inventions, formulas, processes, designs, patterns, and other similar items; (b) Copyrights, literary...

Biological Motion Preference in Humans at Birth: Role of Dynamic and Configural Properties

ERIC Educational Resources Information Center

Bardi, Lara; Regolin, Lucia; Simion, Francesca

2011-01-01

The present study addresses the hypothesis that detection of biological motion is an intrinsic capacity of the visual system guided by a non-species-specific predisposition for the pattern of vertebrate movement and investigates the role of global vs. local information in biological motion detection. Two-day-old babies exposed to a biological…

Infants Perceive Human Point-Light Displays as Solid Forms

ERIC Educational Resources Information Center

Moore, Derek G.; Goodwin, Julia E.; George, Rachel; Axelsson, Emma L.; Braddick, Fleur M. B.

2007-01-01

While five-month-old infants show orientation-specific sensitivity to changes in the motion and occlusion patterns of human point-light displays, it is not known whether infants are capable of binding a human representation to these displays. Furthermore, it has been suggested that infants do not encode the same physical properties for humans and…

Applying network theory to animal movements to identify properties of landscape space use.

PubMed

Bastille-Rousseau, Guillaume; Douglas-Hamilton, Iain; Blake, Stephen; Northrup, Joseph M; Wittemyer, George

2018-04-01

Network (graph) theory is a popular analytical framework to characterize the structure and dynamics among discrete objects and is particularly effective at identifying critical hubs and patterns of connectivity. The identification of such attributes is a fundamental objective of animal movement research, yet network theory has rarely been applied directly to animal relocation data. We develop an approach that allows the analysis of movement data using network theory by defining occupied pixels as nodes and connection among these pixels as edges. We first quantify node-level (local) metrics and graph-level (system) metrics on simulated movement trajectories to assess the ability of these metrics to pull out known properties in movement paths. We then apply our framework to empirical data from African elephants (Loxodonta africana), giant Galapagos tortoises (Chelonoidis spp.), and mule deer (Odocoileous hemionus). Our results indicate that certain node-level metrics, namely degree, weight, and betweenness, perform well in capturing local patterns of space use, such as the definition of core areas and paths used for inter-patch movement. These metrics were generally applicable across data sets, indicating their robustness to assumptions structuring analysis or strategies of movement. Other metrics capture local patterns effectively, but were sensitive to specified graph properties, indicating case specific applications. Our analysis indicates that graph-level metrics are unlikely to outperform other approaches for the categorization of general movement strategies (central place foraging, migration, nomadism). By identifying critical nodes, our approach provides a robust quantitative framework to identify local properties of space use that can be used to evaluate the effect of the loss of specific nodes on range wide connectivity. Our network approach is intuitive, and can be implemented across imperfectly sampled or large-scale data sets efficiently, providing a framework for conservationists to analyze movement data. Functions created for the analyses are available within the R package moveNT. © 2018 by the Ecological Society of America.

Alternative mechanisms alter the emergent properties of self-organization in mussel beds

PubMed Central

Liu, Quan-Xing; Weerman, Ellen J.; Herman, Peter M. J.; Olff, Han; van de Koppel, Johan

2012-01-01

Theoretical models predict that spatial self-organization can have important, unexpected implications by affecting the functioning of ecosystems in terms of resilience and productivity. Whether and how these emergent effects depend on specific formulations of the underlying mechanisms are questions that are often ignored. Here, we compare two alternative models of regular spatial pattern formation in mussel beds that have different mechanistic descriptions of the facilitative interactions between mussels. The first mechanism involves a reduced mussel loss rate at high density owing to mutual protection between the mussels, which is the basis of prior studies on the pattern formation in mussels. The second mechanism assumes, based on novel experimental evidence, that mussels feed more efficiently on top of mussel-generated hummocks. Model simulations point out that the second mechanism produces very similar types of spatial patterns in mussel beds. Yet the mechanisms predict a strikingly contrasting effect of these spatial patterns on ecosystem functioning, in terms of productivity and resilience. In the first model, where high mussel densities reduce mussel loss rates, patterns are predicted to strongly increase productivity and decrease the recovery time of the bed following a disturbance. When pattern formation is generated by increased feeding efficiency on hummocks, only minor emergent effects of pattern formation on ecosystem functioning are predicted. Our results provide a warning against predictions of the implications and emergent properties of spatial self-organization, when the mechanisms that underlie self-organization are incompletely understood and not based on the experimental study. PMID:22418256

Prognostic interaction patterns in diabetes mellitus II: A random-matrix-theory relation

NASA Astrophysics Data System (ADS)

Rai, Aparna; Pawar, Amit Kumar; Jalan, Sarika

2015-08-01

We analyze protein-protein interactions in diabetes mellitus II and its normal counterpart under the combined framework of random matrix theory and network biology. This disease is the fifth-leading cause of death in high-income countries and an epidemic in developing countries, affecting around 8 % of the total adult population in the world. Treatment at the advanced stage is difficult and challenging, making early detection a high priority in the cure of the disease. Our investigation reveals specific structural patterns important for the occurrence of the disease. In addition to the structural parameters, the spectral properties reveal the top contributing nodes from localized eigenvectors, which turn out to be significant for the occurrence of the disease. Our analysis is time-efficient and cost-effective, bringing a new horizon in the field of medicine by highlighting major pathways involved in the disease. The analysis provides a direction for the development of novel drugs and therapies in curing the disease by targeting specific interaction patterns instead of a single protein.

Guidance of vascular development: lessons from the nervous system.

PubMed

Larrivée, Bruno; Freitas, Catarina; Suchting, Steven; Brunet, Isabelle; Eichmann, Anne

2009-02-27

The vascular system of vertebrates consists of an organized, branched network of arteries, veins, and capillaries that penetrates all the tissues of the body. One of the most striking features of the vascular system is that its branching pattern is highly stereotyped, with major and secondary branches forming at specific sites and developing highly conserved organ-specific vascular patterns. The factors controlling vascular patterning are not yet completely understood. Recent studies have highlighted the anatomic and structural similarities between blood vessels and nerves. The 2 networks are often aligned, with nerve fibers and blood vessels following parallel routes. Furthermore, both systems require precise control over their guidance and growth. Several molecules with attractive and repulsive properties have been found to modulate the proper guidance of both nerves and blood vessels. These include the Semaphorins, the Slits, and the Netrins and their receptors. In this review, we describe the molecular mechanisms by which blood vessels and axons achieve proper path finding and the molecular cues that are involved in their guidance.

in silico Vascular Modeling for Personalized Nanoparticle Delivery

PubMed Central

Hossain, Shaolie S.; Zhang, Yongjie; Liang, Xinghua; Hussain, Fazle; Ferrari, Mauro; Hughes, Thomas J. R.; Decuzzi, Paolo

2013-01-01

Aims To predict the deposition of nanoparticles in a patient-specific arterial tree as a function of the vascular architecture, flow conditions, receptor surface density, and nanoparticle properties. Materials & methods The patient-specific vascular geometry is reconstructed from CT Angiography images. The Isogeometric Analysis framework integrated with a special boundary condition for the firm wall adhesion of nanoparticles is implemented. A parallel plate flow chamber system is used to validate the computational model in vitro. Results Particle adhesion is dramatically affected by changes in patient-specific attributes, such as branching angle and receptor density. The adhesion pattern correlates well with the spatial and temporal distribution of the wall shear rates. For the case considered, the larger (2.0 μm) particles adhere ≈ 2 times more in the lower branches of the arterial tree, whereas the smaller (0.5 μm) particles deposit more in the upper branches. Conclusion Our computational framework in conjunction with patient specific attributes can be used to rationally select nanoparticle properties to personalize, thus optimize, therapeutic interventions. PMID:23199308

Fourier power spectrum characteristics of face photographs: attractiveness perception depends on low-level image properties.

PubMed

Menzel, Claudia; Hayn-Leichsenring, Gregor U; Langner, Oliver; Wiese, Holger; Redies, Christoph

2015-01-01

We investigated whether low-level processed image properties that are shared by natural scenes and artworks - but not veridical face photographs - affect the perception of facial attractiveness and age. Specifically, we considered the slope of the radially averaged Fourier power spectrum in a log-log plot. This slope is a measure of the distribution of special frequency power in an image. Images of natural scenes and artworks possess - compared to face images - a relatively shallow slope (i.e., increased high spatial frequency power). Since aesthetic perception might be based on the efficient processing of images with natural scene statistics, we assumed that the perception of facial attractiveness might also be affected by these properties. We calculated Fourier slope and other beauty-associated measurements in face images and correlated them with ratings of attractiveness and age of the depicted persons (Study 1). We found that Fourier slope - in contrast to the other tested image properties - did not predict attractiveness ratings when we controlled for age. In Study 2A, we overlaid face images with random-phase patterns with different statistics. Patterns with a slope similar to those in natural scenes and artworks resulted in lower attractiveness and higher age ratings. In Studies 2B and 2C, we directly manipulated the Fourier slope of face images and found that images with shallower slopes were rated as more attractive. Additionally, attractiveness of unaltered faces was affected by the Fourier slope of a random-phase background (Study 3). Faces in front of backgrounds with statistics similar to natural scenes and faces were rated as more attractive. We conclude that facial attractiveness ratings are affected by specific image properties. An explanation might be the efficient coding hypothesis.

Fourier Power Spectrum Characteristics of Face Photographs: Attractiveness Perception Depends on Low-Level Image Properties

PubMed Central

Langner, Oliver; Wiese, Holger; Redies, Christoph

2015-01-01

We investigated whether low-level processed image properties that are shared by natural scenes and artworks – but not veridical face photographs – affect the perception of facial attractiveness and age. Specifically, we considered the slope of the radially averaged Fourier power spectrum in a log-log plot. This slope is a measure of the distribution of special frequency power in an image. Images of natural scenes and artworks possess – compared to face images – a relatively shallow slope (i.e., increased high spatial frequency power). Since aesthetic perception might be based on the efficient processing of images with natural scene statistics, we assumed that the perception of facial attractiveness might also be affected by these properties. We calculated Fourier slope and other beauty-associated measurements in face images and correlated them with ratings of attractiveness and age of the depicted persons (Study 1). We found that Fourier slope – in contrast to the other tested image properties – did not predict attractiveness ratings when we controlled for age. In Study 2A, we overlaid face images with random-phase patterns with different statistics. Patterns with a slope similar to those in natural scenes and artworks resulted in lower attractiveness and higher age ratings. In Studies 2B and 2C, we directly manipulated the Fourier slope of face images and found that images with shallower slopes were rated as more attractive. Additionally, attractiveness of unaltered faces was affected by the Fourier slope of a random-phase background (Study 3). Faces in front of backgrounds with statistics similar to natural scenes and faces were rated as more attractive. We conclude that facial attractiveness ratings are affected by specific image properties. An explanation might be the efficient coding hypothesis. PMID:25835539

Contrasting patterns of structural host specificity of two species of Heligmosomoides nematodes in sympatric rodents.

PubMed

Clough, Dagmar; Råberg, Lars

2014-12-01

Host specificity is a fundamental property of parasites. Whereas most studies focus on measures of specificity on host range, only few studies have considered quantitative aspects such as infection intensity or prevalence. The relative importance of these quantitative aspects is still unclear, mainly because of methodological constraints, yet central to a precise assessment of host specificity. Here, we assessed simultaneously two quantitative measures of host specificity of Heligmosomoides glareoli and Heligmosomoides polygyrus polygyrus infections in sympatric rodent hosts. We used standard morphological techniques as well as real-time quantitative PCR and sequencing of the rDNA ITS2 fragment to analyse parasite infection via faecal sample remains. Although both parasite species are thought to be strictly species-specific, we found morphologically and molecularly validated co- and cross-infections. We also detected contrasting patterns within and between host species with regard to specificity for prevalence and intensity of infection. H. glareoli intensities were twofold higher in bank voles than in yellow-necked mice, but prevalence did not differ significantly between species (33 vs. 18%). We found the opposite pattern in H. polygyrus infections with similar intensity levels between host species but significantly higher prevalence in mouse hosts (56 vs. 10%). Detection rates were higher with molecular tools than morphological methods. Our results emphasize the necessity to consider quantitative aspects of specificity for a full view of a parasites' capacity to replicate and transmit in hosts and present a worked example of how modern molecular tools help to advance our understanding of selective forces in host-parasite ecology and evolution.

Patterns in hydraulic architecture from roots to branches in six tropical tree species from cacao agroforestry and their relation to wood density and stem growth

PubMed Central

Kotowska, Martyna M.; Hertel, Dietrich; Rajab, Yasmin Abou; Barus, Henry; Schuldt, Bernhard

2015-01-01

For decades it has been assumed that the largest vessels are generally found in roots and that vessel size and corresponding sapwood area-specific hydraulic conductivity are acropetally decreasing toward the distal twigs. However, recent studies from the perhumid tropics revealed a hump-shaped vessel size distribution. Worldwide tropical perhumid forests are extensively replaced by agroforestry systems often using introduced species of various biogeographical and climatic origins. Nonetheless, it is unknown so far what kind of hydraulic architectural patterns are developed in those agroforestry tree species and which impact this exerts regarding important tree functional traits, such as stem growth, hydraulic efficiency and wood density (WD). We investigated wood anatomical and hydraulic properties of the root, stem and branch wood in Theobroma cacao and five common shade tree species in agroforestry systems on Sulawesi (Indonesia); three of these were strictly perhumid tree species, and the other three tree species are tolerating seasonal drought. The overall goal of our study was to relate these properties to stem growth and other tree functional traits such as foliar nitrogen content and sapwood to leaf area ratio. Our results confirmed a hump-shaped vessel size distribution in nearly all species. Drought-adapted species showed divergent patterns of hydraulic conductivity, vessel density, and relative vessel lumen area between root, stem and branch wood compared to wet forest species. Confirming findings from natural old-growth forests in the same region, WD showed no relationship to specific conductivity. Overall, aboveground growth performance was better predicted by specific hydraulic conductivity than by foliar traits and WD. Our study results suggest that future research on conceptual trade-offs of tree hydraulic architecture should consider biogeographical patterns underlining the importance of anatomical adaptation mechanisms to environment. PMID:25873922

Factors Related to Spatial Patterns of Rural Land Fragmentation in Texas

NASA Astrophysics Data System (ADS)

Kjelland, Michael E.; Kreuter, Urs P.; Clendenin, George A.; Wilkins, R. Neal; Wu, X. Ben; Afanador, Edith Gonzalez; Grant, William E.

2007-08-01

Fragmentation of family-owned farms and ranches has been identified as the greatest single threat to wildlife habitat, water supply, and the long-term viability of agriculture in Texas. However, an integrative framework for insights into the pathways of land use change has been lacking. The specific objectives of the study are to test the hypotheses that the nonagricultural value (NAV) of rural land is a reliable indicator of trends in land fragmentation and that NAV in Texas is spatially correlated with population density, and to explore the idea that recent changes in property size patterns are better represented by a categorical model than by one that reflects incremental changes. We propose that the State-and-Transition model, developed to describe the dynamics of semi-arid ecosystems, provides an appropriate conceptual framework for characterizing categorical shifts in rural property patterns. Results suggest that changes in population density are spatially correlated with NAV and farm size, and that rural property size is spatially correlated with changes in NAV. With increasing NAV, the proportion of large properties tends to decrease while the area represented by small properties tends to increase. Although a correlation exists between NAV and population density, it is the trend in NAV that appears to be a stronger predictor of land fragmentation. The empirical relationships established herein, viewed within the conceptual framework of the State-and-Transition model, can provide a useful tool for evaluating land use policies for maintaining critical ecosystem services delivered from privately owned land in private land states, such as Texas.

Process-morphology scaling relations quantify self-organization in capillary densified nanofiber arrays.

PubMed

Kaiser, Ashley L; Stein, Itai Y; Cui, Kehang; Wardle, Brian L

2018-02-07

Capillary-mediated densification is an inexpensive and versatile approach to tune the application-specific properties and packing morphology of bulk nanofiber (NF) arrays, such as aligned carbon nanotubes. While NF length governs elasto-capillary self-assembly, the geometry of cellular patterns formed by capillary densified NFs cannot be precisely predicted by existing theories. This originates from the recently quantified orders of magnitude lower than expected NF array effective axial elastic modulus (E), and here we show via parametric experimentation and modeling that E determines the width, area, and wall thickness of the resulting cellular pattern. Both experiments and models show that further tuning of the cellular pattern is possible by altering the NF-substrate adhesion strength, which could enable the broad use of this facile approach to predictably pattern NF arrays for high value applications.

SERENITY Aware System Development Process

NASA Astrophysics Data System (ADS)

Serrano, Daniel; Maña, Antonio; Llarena, Rafael; Crespo, Beatriz Gallego-Nicasio; Li, Keqin

Traditionally, security patterns have successfully been used to describe security and dependability. In the SERENITY Project the notion of security and dependability (S&D) pattern has been extended to exact specifications of re-usable security mechanisms for Ambient Intelligence (AmI) systems. These S&D Patterns include information on the security properties satisfied by the solution and on the context conditions to be fulfilled. This chapter presents the development of applications supported by SERENITY. In the context of SERENITY we refer to these applications as Serenity-aware applications. Firstly, this chapter presents the Serenity-aware application design using S&D Artefacts. Secondly, it proposes a Java Application Programming Interface (API) to be used in the application development. And, finally, it introduces the development of an example Serenity-aware application.

Numerical study on statistical properties of speckle pattern in laser projection display based on human eye model

NASA Astrophysics Data System (ADS)

Cui, Zhe; Wang, Anting; Ma, Qianli; Ming, Hai

2013-12-01

In this paper, the laser speckle pattern on human retina for a laser projection display is simulated. By introducing a specific eye model `Indiana Eye', the statistical properties of the laser speckle are numerical investigated. The results show that the aberrations of human eye (mostly spherical and chromatic) will decrease the speckle contrast felt by people. When the wavelength of the laser source is 550 nm (green), people will feel the strongest speck pattern and the weakest when the wavelength is 450 nm (blue). Myopia and hyperopia will decrease the speckle contrast by introducing large spherical aberrations. Although aberration is good for speckle reduction, but it will degrade the imaging capability of the eye. The results show that laser source (650 nm) will have the best image quality on the retina. At last, we compare the human eye with an aberration-free imaging system. Both the speckle contrast and the image quality appear different behavior in these two imaging systems. The results are useful when a standardized measurement procedure for speckle contrast needs to be built.

Structure-related statistical singularities along protein sequences: a correlation study.

PubMed

Colafranceschi, Mauro; Colosimo, Alfredo; Zbilut, Joseph P; Uversky, Vladimir N; Giuliani, Alessandro

2005-01-01

A data set composed of 1141 proteins representative of all eukaryotic protein sequences in the Swiss-Prot Protein Knowledge base was coded by seven physicochemical properties of amino acid residues. The resulting numerical profiles were submitted to correlation analysis after the application of a linear (simple mean) and a nonlinear (Recurrence Quantification Analysis, RQA) filter. The main RQA variables, Recurrence and Determinism, were subsequently analyzed by Principal Component Analysis. The RQA descriptors showed that (i) within protein sequences is embedded specific information neither present in the codes nor in the amino acid composition and (ii) the most sensitive code for detecting ordered recurrent (deterministic) patterns of residues in protein sequences is the Miyazawa-Jernigan hydrophobicity scale. The most deterministic proteins in terms of autocorrelation properties of primary structures were found (i) to be involved in protein-protein and protein-DNA interactions and (ii) to display a significantly higher proportion of structural disorder with respect to the average data set. A study of the scaling behavior of the average determinism with the setting parameters of RQA (embedding dimension and radius) allows for the identification of patterns of minimal length (six residues) as possible markers of zones specifically prone to inter- and intramolecular interactions.

Inhibition of Shh signalling in the chick wing gives insights into digit patterning and evolution.

PubMed

Pickering, Joseph; Towers, Matthew

2016-10-01

In an influential model of pattern formation, a gradient of Sonic hedgehog (Shh) signalling in the chick wing bud specifies cells with three antero-posterior positional values, which give rise to three morphologically different digits by a self-organizing mechanism with Turing-like properties. However, as four of the five digits of the mouse limb are morphologically similar in terms of phalangeal pattern, it has been suggested that self-organization alone could be sufficient. Here, we show that inhibition of Shh signalling at a specific stage of chick wing development results in a pattern of four digits, three of which can have the same number of phalanges. These patterning changes are dependent on a posterior extension of the apical ectodermal ridge, and this also allows the additional digit to arise from the Shh-producing cells of the polarizing region - an ability lost in ancestral theropod dinosaurs. Our analyses reveal that, if the specification of antero-posterior positional values is curtailed, self-organization can then produce several digits with the same number of phalanges. We present a model that may give important insights into how the number of digits and phalanges has diverged during the evolution of avian and mammalian limbs. © 2016. Published by The Company of Biologists Ltd.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Technical Reports Server (NTRS)

Glass, Christopher E.

1990-01-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Astrophysics Data System (ADS)

Glass, Christopher E.

1990-08-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Relating cell and tissue mechanics: implications and applications.

PubMed

Jakab, Karoly; Damon, Brook; Marga, Françoise; Doaga, Octavian; Mironov, Vladimir; Kosztin, Ioan; Markwald, Roger; Forgacs, Gabor

2008-09-01

The Differential Adhesion Hypothesis (DAH) posits that differences in adhesion provide the driving force for morphogenetic processes. A manifestation of differential adhesion is tissue liquidity and a measure for it is tissue surface tension. In terms of this property, DAH correctly predicts global developmental tissue patterns. However, it provides little information on how these patterns arise from the movement and shape changes of cells. We provide strong qualitative and quantitative support for tissue liquidity both in true developmental context and in vitro assays. We follow the movement and characteristic shape changes of individual cells in the course of specific tissue rearrangements leading to liquid-like configurations. Finally, we relate the measurable tissue-liquid properties to molecular entities, whose direct determination under realistic three-dimensional culture conditions is not possible. Our findings confirm the usefulness of tissue liquidity and provide the scientific underpinning for a novel tissue engineering technology.

From Statistics to Meaning: Infants’ Acquisition of Lexical Categories

PubMed Central

Lany, Jill; Saffran, Jenny R.

2013-01-01

Infants are highly sensitive to statistical patterns in their auditory language input that mark word categories (e.g., noun and verb). However, it is unknown whether experience with these cues facilitates the acquisition of semantic properties of word categories. In a study testing this hypothesis, infants first listened to an artificial language in which word categories were reliably distinguished by statistical cues (experimental group) or in which these properties did not cue category membership (control group). Both groups were then trained on identical pairings between the words and pictures from two categories (animals and vehicles). Only infants in the experimental group learned the trained associations between specific words and pictures. Moreover, these infants generalized the pattern to include novel pairings. These results suggest that experience with statistical cues marking lexical categories sets the stage for learning the meanings of individual words and for generalizing meanings to new category members. PMID:20424058

Subject-specific longitudinal shape analysis by coupling spatiotemporal shape modeling with medial analysis

NASA Astrophysics Data System (ADS)

Hong, Sungmin; Fishbaugh, James; Rezanejad, Morteza; Siddiqi, Kaleem; Johnson, Hans; Paulsen, Jane; Kim, Eun Young; Gerig, Guido

2017-02-01

Modeling subject-specific shape change is one of the most important challenges in longitudinal shape analysis of disease progression. Whereas anatomical change over time can be a function of normal aging, anatomy can also be impacted by disease related degeneration. Anatomical shape change may also be affected by structural changes from neighboring shapes, which may cause non-linear variations in pose. In this paper, we propose a framework to analyze disease related shape changes by coupling extrinsic modeling of the ambient anatomical space via spatiotemporal deformations with intrinsic shape properties from medial surface analysis. We compare intrinsic shape properties of a subject-specific shape trajectory to a normative 4D shape atlas representing normal aging to isolate shape changes related to disease. The spatiotemporal shape modeling establishes inter/intra subject anatomical correspondence, which in turn enables comparisons between subjects and the 4D shape atlas, and also quantitative analysis of disease related shape change. The medial surface analysis captures intrinsic shape properties related to local patterns of deformation. The proposed framework jointly models extrinsic longitudinal shape changes in the ambient anatomical space, as well as intrinsic shape properties to give localized measurements of degeneration. Six high risk subjects and six controls are randomly sampled from a Huntington's disease image database for qualitative and quantitative comparison.

Geometrical and Mechanical Properties Control Actin Filament Organization

PubMed Central

Ennomani, Hajer; Théry, Manuel; Nedelec, Francois; Blanchoin, Laurent

2015-01-01

The different actin structures governing eukaryotic cell shape and movement are not only determined by the properties of the actin filaments and associated proteins, but also by geometrical constraints. We recently demonstrated that limiting nucleation to specific regions was sufficient to obtain actin networks with different organization. To further investigate how spatially constrained actin nucleation determines the emergent actin organization, we performed detailed simulations of the actin filament system using Cytosim. We first calibrated the steric interaction between filaments, by matching, in simulations and experiments, the bundled actin organization observed with a rectangular bar of nucleating factor. We then studied the overall organization of actin filaments generated by more complex pattern geometries used experimentally. We found that the fraction of parallel versus antiparallel bundles is determined by the mechanical properties of actin filament or bundles and the efficiency of nucleation. Thus nucleation geometry, actin filaments local interactions, bundle rigidity, and nucleation efficiency are the key parameters controlling the emergent actin architecture. We finally simulated more complex nucleation patterns and performed the corresponding experiments to confirm the predictive capabilities of the model. PMID:26016478

Retronasal odor representations in the dorsal olfactory bulb of rats

PubMed Central

Gautam, Shree Hari; Verhagen, Justus V.

2012-01-01

Animals perceive their olfactory environment not only from odors originating in the external world (orthonasal route) but also from odors released in the oral cavity while eating food (retronasal route). Retronasal olfaction is crucial for the perception of food flavor in humans. However, little is known about the retronasal stimulus coding in the brain. The most basic question is if and how route affects the odor representations at the level of the olfactory bulb (OB), where odor quality codes originate. We used optical calcium imaging of presynaptic dorsal OB responses to odorants in anesthetized rats to ask whether the rat OB could be activated retronasally, and how these responses compare to orthonasal responses under similar conditions. We further investigated the effects of specific odorant properties on orthoversus retronasal response patterns. We found that at a physiologically relevant flow rate retronasal odorants can effectively reach the olfactory receptor neurons, eliciting glomerular response patterns that grossly overlap with those of orthonasal responses, but differ from the orthonasal patterns in the response amplitude and temporal dynamics. Interestingly, such differences correlated well with specific odorant properties. Less volatile odorants yielded relatively smaller responses retronasally, but volatility did not affect relative temporal profiles. More polar odorants responded with relatively longer onset latency and time to peak retronasally, but polarity did not affect relative response magnitudes. These data provide insight into the early stages of retronasal stimulus coding and establish relationships between ortho- and retronasal odor representations in the rat OB. PMID:22674270

Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus.

PubMed

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

2015-09-24

Hippocampome.org is a comprehensive knowledge base of neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex). Although the hippocampal literature is remarkably information-rich, neuron properties are often reported with incompletely defined and notoriously inconsistent terminology, creating a formidable challenge for data integration. Our extensive literature mining and data reconciliation identified 122 neuron types based on neurotransmitter, axonal and dendritic patterns, synaptic specificity, electrophysiology, and molecular biomarkers. All ∼3700 annotated properties are individually supported by specific evidence (∼14,000 pieces) in peer-reviewed publications. Systematic analysis of this unprecedented amount of machine-readable information reveals novel correlations among neuron types and properties, the potential connectivity of the full hippocampal circuitry, and outstanding knowledge gaps. User-friendly browsing and online querying of Hippocampome.org may aid design and interpretation of both experiments and simulations. This powerful, simple, and extensible neuron classification endeavor is unique in its detail, utility, and completeness.

Bioelectric patterning during oogenesis: stage-specific distribution of membrane potentials, intracellular pH and ion-transport mechanisms in Drosophila ovarian follicles.

PubMed

Krüger, Julia; Bohrmann, Johannes

2015-01-16

Bioelectric phenomena have been found to exert influence on various developmental and regenerative processes. Little is known about their possible functions and the cellular mechanisms by which they might act during Drosophila oogenesis. In developing follicles, characteristic extracellular current patterns and membrane-potential changes in oocyte and nurse cells have been observed that partly depend on the exchange of protons, potassium ions and sodium ions. These bioelectric properties have been supposed to be related to various processes during oogenesis, e. g. pH-regulation, osmoregulation, cell communication, cell migration, cell proliferation, cell death, vitellogenesis and follicle growth. Analysing in detail the spatial distribution and activity of the relevant ion-transport mechanisms is expected to elucidate the roles that bioelectric phenomena play during oogenesis. To obtain an overview of bioelectric patterning along the longitudinal and transversal axes of the developing follicle, the spatial distributions of membrane potentials (Vmem), intracellular pH (pHi) and various membrane-channel proteins were studied systematically using fluorescent indicators, fluorescent inhibitors and antisera. During mid-vitellogenic stages 9 to 10B, characteristic, stage-specific Vmem-patterns in the follicle-cell epithelium as well as anteroposterior pHi-gradients in follicle cells and nurse cells were observed. Corresponding distribution patterns of proton pumps (V-ATPases), voltage-dependent L-type Ca(2+)-channels, amiloride-sensitive Na(+)-channels and Na(+),H(+)-exchangers (NHE) and gap-junction proteins (innexin 3) were detected. In particular, six morphologically distinguishable follicle-cell types are characterized on the bioelectric level by differences concerning Vmem and pHi as well as specific compositions of ion channels and carriers. Striking similarities between Vmem-patterns and activity patterns of voltage-dependent Ca(2+)-channels were found, suggesting a mechanism for transducing bioelectric signals into cellular responses. Moreover, gradients of electrical potential and pH were observed within single cells. Our data suggest that spatial patterning of Vmem, pHi and specific membrane-channel proteins results in bioelectric signals that are supposed to play important roles during oogenesis, e. g. by influencing spatial coordinates, regulating migration processes or modifying the cytoskeletal organization. Characteristic stage-specific changes of bioelectric activity in specialized cell types are correlated with various developmental processes.

Back-Propagation of Physiological Action Potential Output in Dendrites of Slender-Tufted L5A Pyramidal Neurons

PubMed Central

Grewe, Benjamin F.; Bonnan, Audrey; Frick, Andreas

2009-01-01

Pyramidal neurons of layer 5A are a major neocortical output type and clearly distinguished from layer 5B pyramidal neurons with respect to morphology, in vivo firing patterns, and connectivity; yet knowledge of their dendritic properties is scant. We used a combination of whole-cell recordings and Ca2+ imaging techniques in vitro to explore the specific dendritic signaling role of physiological action potential patterns recorded in vivo in layer 5A pyramidal neurons of the whisker-related ‘barrel cortex’. Our data provide evidence that the temporal structure of physiological action potential patterns is crucial for an effective invasion of the main apical dendrites up to the major branch point. Both the critical frequency enabling action potential trains to invade efficiently and the dendritic calcium profile changed during postnatal development. In contrast to the main apical dendrite, the more passive properties of the short basal and apical tuft dendrites prevented an efficient back-propagation. Various Ca2+ channel types contributed to the enhanced calcium signals during high-frequency firing activity, whereas A-type K+ and BKCa channels strongly suppressed it. Our data support models in which the interaction of synaptic input with action potential output is a function of the timing, rate and pattern of action potentials, and dendritic location. PMID:20508744

Specimen-specific modeling of hip fracture pattern and repair.

PubMed

Ali, Azhar A; Cristofolini, Luca; Schileo, Enrico; Hu, Haixiang; Taddei, Fulvia; Kim, Raymond H; Rullkoetter, Paul J; Laz, Peter J

2014-01-22

Hip fracture remains a major health problem for the elderly. Clinical studies have assessed fracture risk based on bone quality in the aging population and cadaveric testing has quantified bone strength and fracture loads. Prior modeling has primarily focused on quantifying the strain distribution in bone as an indicator of fracture risk. Recent advances in the extended finite element method (XFEM) enable prediction of the initiation and propagation of cracks without requiring a priori knowledge of the crack path. Accordingly, the objectives of this study were to predict femoral fracture in specimen-specific models using the XFEM approach, to perform one-to-one comparisons of predicted and in vitro fracture patterns, and to develop a framework to assess the mechanics and load transfer in the fractured femur when it is repaired with an osteosynthesis implant. Five specimen-specific femur models were developed from in vitro experiments under a simulated stance loading condition. Predicted fracture patterns closely matched the in vitro patterns; however, predictions of fracture load differed by approximately 50% due to sensitivity to local material properties. Specimen-specific intertrochanteric fractures were induced by subjecting the femur models to a sideways fall and repaired with a contemporary implant. Under a post-surgical stance loading, model-predicted load sharing between the implant and bone across the fracture surface varied from 59%:41% to 89%:11%, underscoring the importance of considering anatomic and fracture variability in the evaluation of implants. XFEM modeling shows potential as a macro-level analysis enabling fracture investigations of clinical cohorts, including at-risk groups, and the design of robust implants. © 2013 Published by Elsevier Ltd.

Pattern formation in three-dimensional reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Callahan, T. K.; Knobloch, E.

1999-08-01

Existing group theoretic analysis of pattern formation in three dimensions [T.K. Callahan, E. Knobloch, Symmetry-breaking bifurcations on cubic lattices, Nonlinearity 10 (1997) 1179-1216] is used to make specific predictions about the formation of three-dimensional patterns in two models of the Turing instability, the Brusselator model and the Lengyel-Epstein model. Spatially periodic patterns having the periodicity of the simple cubic (SC), face-centered cubic (FCC) or body-centered cubic (BCC) lattices are considered. An efficient center manifold reduction is described and used to identify parameter regimes permitting stable lamellæ, SC, FCC, double-diamond, hexagonal prism, BCC and BCCI states. Both models possess a special wavenumber k* at which the normal form coefficients take on fixed model-independent ratios and both are described by identical bifurcation diagrams. This property is generic for two-species chemical reaction-diffusion models with a single activator and inhibitor.

Rotating non-Boussinesq Rayleigh-Benard convection

NASA Astrophysics Data System (ADS)

Moroz, Vadim Vladimir

This thesis makes quantitative predictions about the formation and stability of hexagonal and roll patterns in convecting system unbounded in horizontal direction. Starting from the Navier-Stokes, heat and continuity equations, the convection problem is then reduced to normal form equations using equivariant bifurcation theory. The relative stabilities of patterns lying on a hexagonal lattice in Fourier space are then determined using appropriate amplitude equations, with coefficients obtained via asymptotic expansion of the governing partial differential equations, with the conducting state being the base state, and the control parameter and the non-Boussinesq effects being small. The software package Mathematica was used to calculate amplitude coefficients of the appropriate coupled Ginzburg-Landau equations for the rigid-rigid and free-free case. A Galerkin code (initial version of which was written by W. Pesch et al.) is used to determine pattern stability further from onset and for strongly non-Boussinesq fluids. Specific predictions about the stability of hexagon and roll patterns for realistic experimental conditions are made. The dependence of the stability of the convective patterns on the Rayleigh number, planform wavenumber and the rotation rate is studied. Long- and shortwave instabilities, both steady and oscillatory, are identified. For small Prandtl numbers oscillatory sideband instabilities are found already very close to onset. A resonant mode interaction in hexagonal patterns arising in non-Boussinesq Rayleigh-Benard convection is studied using symmetry group methods. The lowest-order coupling terms for interacting patterns are identified. A bifurcation analysis of the resulting system of equations shows that the bifurcation is transcritical. Stability properties of resulting patterns are discussed. It is found that for some fluid properties the traditional hexagon convection solution does not exist. Analytical results are supported by numerical solutions of the convection equations using the Galerkin procedure and a Floquet analysis.

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

PubMed Central

Shinbrot, Eve; Henninger, Erin E.; Weinhold, Nils; Covington, Kyle R.; Göksenin, A. Yasemin; Schultz, Nikolaus; Chao, Hsu; Doddapaneni, HarshaVardhan; Muzny, Donna M.; Gibbs, Richard A.; Sander, Chris; Pursell, Zachary F.

2014-01-01

Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication. PMID:25228659

High-performance 193-nm photoresist materials based on ROMA polymers: sub-90-nm contact hole application with resist reflow

NASA Astrophysics Data System (ADS)

Joo, Hyun S.; Seo, Dong C.; Kim, Chang M.; Lim, Young T.; Cho, Seong D.; Lee, Jong B.; Song, Ji Y.; Kim, Kyoung M.; Park, Joo H.; Jung, Jae Chang; Shin, Ki S.; Bok, Cheol Kyu; Moon, Seung C.

2004-05-01

There are numerous methods being explored by lithographers to achieve the patterning of sub-90nm contact hole features. Regarding optical impact on contact imaging, various optical extension techniques such as assist features, focus drilling, phase shift masks, and off-axis illumination are being employed to improve the aerial image. One possible option for improving of the process window in contact hole patterning is resist reflow. We have already reported the resist using a ring opened polymer of maleic anhydride unit(ROMA) during the past two years in this conference. It has several good properties such as UV transmittance, PED stability, solubility and storage stability. The resist using ROMA polymer as a matrix resin showed a good lithographic performance at C/H pattern and one of the best characteristics in a ROMA polymer is the property of thermal shrinkage. It has a specific glass transition temperature(Tg) each polymers, so they made a applying of resist reflow technique to print sub-90nm C/H possible. Recently, we have researched about advanced ROMA polymer(ROMA II), which is composed of cycloolefine derivatives with existing ROMA type polymer(ROMA I), for dry etch resistance increasing, high resolution, and good thermal shrinkage property. In this paper, we will present the structure, thermal shrinkage properties, Tg control, material properties for ROMA II polymer and will show characteristics, the lithographic performance for iso and dense C/H applications of the resist using ROMA II polymer. In addition, we will discuss resist reflow data gained at C/H profile of sub-90nm sizes, which has good process window.

Relative Contributions of Specific Activity Histories and Spontaneous Processes to Size Remodeling of Glutamatergic Synapses

PubMed Central

Dvorkin, Roman; Ziv, Noam E.

2016-01-01

The idea that synaptic properties are defined by specific pre- and postsynaptic activity histories is one of the oldest and most influential tenets of contemporary neuroscience. Recent studies also indicate, however, that synaptic properties often change spontaneously, even in the absence of specific activity patterns or any activity whatsoever. What, then, are the relative contributions of activity history-dependent and activity history-independent processes to changes synapses undergo? To compare the relative contributions of these processes, we imaged, in spontaneously active networks of cortical neurons, glutamatergic synapses formed between the same axons and neurons or dendrites under the assumption that their similar activity histories should result in similar size changes over timescales of days. The size covariance of such commonly innervated (CI) synapses was then compared to that of synapses formed by different axons (non-CI synapses) that differed in their activity histories. We found that the size covariance of CI synapses was greater than that of non-CI synapses; yet overall size covariance of CI synapses was rather modest. Moreover, momentary and time-averaged sizes of CI synapses correlated rather poorly, in perfect agreement with published electron microscopy-based measurements of mouse cortex synapses. A conservative estimate suggested that ~40% of the observed size remodeling was attributable to specific activity histories, whereas ~10% and ~50% were attributable to cell-wide and spontaneous, synapse-autonomous processes, respectively. These findings demonstrate that histories of naturally occurring activity patterns can direct glutamatergic synapse remodeling but also suggest that the contributions of spontaneous, possibly stochastic, processes are at least as great. PMID:27776122

Universal scaling in the branching of the tree of life.

PubMed

Herrada, E Alejandro; Tessone, Claudio J; Klemm, Konstantin; Eguíluz, Víctor M; Hernández-García, Emilio; Duarte, Carlos M

2008-07-23

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.

A Strategic Design of an Opto-Chemical Security Device with Resettable and Reconfigurable Password Based Upon Dual Channel Two-in-One Chemosensor Molecule.

PubMed

Majumdar, Tapas; Haldar, Basudeb; Mallick, Arabinda

2017-02-20

A simple strategy is proposed to design and develop an intelligent device based on dual channel ion responsive spectral properties of a commercially available molecule, harmine (HM). The system can process different sets of opto-chemical inputs generating different patterns as fluorescence outputs at specific wavelengths which can provide an additional level of protection exploiting both password and pattern recognitions. The proposed system could have the potential to come up with highly secured combinatorial locks at the molecular level that could pose valuable real time and on-site applications for user authentication.

Application of optical coherence tomography attenuation imaging for quantification of optical properties in medulloblastoma

NASA Astrophysics Data System (ADS)

Vuong, Barry; Skowron, Patryk; Kiehl, Tim-Rasmus; Kyan, Matthew; Garzia, Livia; Genis, Helen; Sun, Cuiru; Taylor, Michael D.; Yang, Victor X. D.

2015-03-01

The hemodynamic environment is known to play a crucial role in the progression, rupture, and treatment of intracranial aneurysms. Currently there is difficulty assessing and measuring blood flow profiles in vivo. An emerging high resolution imaging modality known as split spectrum Doppler optical coherence tomography (ssDOCT) has demonstrated the capability to quantify hemodynamic patterns as well as arterial microstructural changes. In this study, we present a novel in vitro method to acquire precise blood flow patterns within a patient- specific aneurysm silicone flow models using ssDOCT imaging. Computational fluid dynamics (CFD) models were generated to verify ssDOCT results.

A Strategic Design of an Opto-Chemical Security Device with Resettable and Reconfigurable Password Based Upon Dual Channel Two-in-One Chemosensor Molecule

NASA Astrophysics Data System (ADS)

Majumdar, Tapas; Haldar, Basudeb; Mallick, Arabinda

2017-02-01

A simple strategy is proposed to design and develop an intelligent device based on dual channel ion responsive spectral properties of a commercially available molecule, harmine (HM). The system can process different sets of opto-chemical inputs generating different patterns as fluorescence outputs at specific wavelengths which can provide an additional level of protection exploiting both password and pattern recognitions. The proposed system could have the potential to come up with highly secured combinatorial locks at the molecular level that could pose valuable real time and on-site applications for user authentication.

Using coal inside California for nonelectric applications

NASA Technical Reports Server (NTRS)

Oxley, J. H.

1978-01-01

A review of present energy consumption patterns in the manufacturing, transportation, and residential sectors is presented. The properties of coal that affect its substitution into these market sectors are discussed. Specific needs and concerns of Californians are delineated. Present nonelectric consumptive uses of coal in California are outlined. Current world-wide progress concerning increased industrial use of coal is shown. An overview is given of the options to protect the environment from the direct use of coal, especially from the standpoint of sulfur control; and a time frame for commercialization is projected. Possible desired changes in energy use patterns over the next fifty years are proposed.

Atomic Force Microscopy Mechanical Mapping of Micropatterned Cells Shows Adhesion Geometry-Dependent Mechanical Response on Local and Global Scales

PubMed Central

Rigato, Annafrancesca; Rico, Felix; Eghiaian, Frédéric; Piel, Mathieu; Scheuring, Simon

2015-01-01

In multicellular organisms cell shape and organization are dictated by cell-cell or cell-extracellular matrix adhesion interactions. Adhesion complexes crosstalk with the cytoskeleton enabling cells to sense their mechanical environment. Unfortunately, most of cell biology studies, and cell mechanics studies in particular, are conducted on cultured cells adhering to a hard, homogeneous and unconstrained substrate with non-specific adhesion sites – thus far from physiological and reproducible conditions. Here, we grew cells on three different fibronectin patterns with identical overall dimensions but different geometries (▽, T and Y), and investigated their topography and mechanics by atomic force microscopy (AFM). The obtained mechanical maps were reproducible for cells grown on patterns of the same geometry, revealing pattern-specific subcellular differences. We found that local Young’s moduli variations are related to the cell adhesion geometry. Additionally, we detected local changes of cell mechanical properties induced by cytoskeletal drugs. We thus provide a method to quantitatively and systematically investigate cell mechanics and their variations, and present further evidence for a tight relation between cell adhesion and mechanics. PMID:26013956

An atlas of active enhancers across human cell types and tissues

NASA Astrophysics Data System (ADS)

Andersson, Robin; Gebhard, Claudia; Miguel-Escalada, Irene; Hoof, Ilka; Bornholdt, Jette; Boyd, Mette; Chen, Yun; Zhao, Xiaobei; Schmidl, Christian; Suzuki, Takahiro; Ntini, Evgenia; Arner, Erik; Valen, Eivind; Li, Kang; Schwarzfischer, Lucia; Glatz, Dagmar; Raithel, Johanna; Lilje, Berit; Rapin, Nicolas; Bagger, Frederik Otzen; Jørgensen, Mette; Andersen, Peter Refsing; Bertin, Nicolas; Rackham, Owen; Burroughs, A. Maxwell; Baillie, J. Kenneth; Ishizu, Yuri; Shimizu, Yuri; Furuhata, Erina; Maeda, Shiori; Negishi, Yutaka; Mungall, Christopher J.; Meehan, Terrence F.; Lassmann, Timo; Itoh, Masayoshi; Kawaji, Hideya; Kondo, Naoto; Kawai, Jun; Lennartsson, Andreas; Daub, Carsten O.; Heutink, Peter; Hume, David A.; Jensen, Torben Heick; Suzuki, Harukazu; Hayashizaki, Yoshihide; Müller, Ferenc; Consortium, The Fantom; Forrest, Alistair R. R.; Carninci, Piero; Rehli, Michael; Sandelin, Albin

2014-03-01

Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.

Protein recognition by a pattern-generating fluorescent molecular probe.

PubMed

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

Self-organization and progenitor targeting generate stable patterns in planarian regeneration.

PubMed

Atabay, Kutay Deniz; LoCascio, Samuel A; de Hoog, Thom; Reddien, Peter W

2018-04-27

During animal regeneration, cells must organize into discrete and functional systems. We show that self-organization, along with patterning cues, govern progenitor behavior in planarian regeneration. Surgical paradigms allowed the manipulation of planarian eye regeneration in predictable locations and numbers, generating alternative stable neuroanatomical states for wild-type animals with multiple functional ectopic eyes. We used animals with multiple ectopic eyes and eye transplantation to demonstrate that broad progenitor specification, combined with self-organization, allows anatomy maintenance during regeneration. We propose a model for regenerative progenitors involving (i) migratory targeting cues, (ii) self-organization into existing or regenerating eyes, and (iii) a broad zone, associated with coarse progenitor specification, in which eyes can be targeted by progenitors. These three properties help explain how tissues can be organized during regeneration. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Protein recognition by a pattern-generating fluorescent molecular probe

NASA Astrophysics Data System (ADS)

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M.; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M.; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

[Hormonal and inflammatory impact of different dietetic composition: emphasis on dietary patterns and specific dietary factors].

PubMed

Bressan, Josefina; Hermsdorff, Helen H M; Zulet, María Angeles; Martínez, José Alfredo

2009-07-01

Healthy dietary pattern, characterized by the consumption of fruits, vegetables, white meats, skim dairy products, nuts and moderate intake of vegetable oils and alcohol, is an important factor for a lower risk of chronic disease such as obesity, metabolic syndrome and cardiovascular disease. This beneficial effect can be explained, at least partially, by its modulating role on biomarkers of insulin sensitivity and atherosclerosis as well as of inflammation and endothelial function. On the other hand, the intake of specific dietary factors, such as unsaturated fatty acids (oleic and alpha-linolenic) and micronutrients with antioxidant properties (vitamins A, E and C; selenium, zinc) has been discussed, due to its potential protector action due to chronic disease occurrence and its possible profits in hormonal, metabolic and inflammatory regulations that these dietetic factors can provide within a nutritional treatment to obesity and metabolic syndrome.

[Phylo- and ontogenetic aspects of erect posture and walking in developmental neurology].

PubMed

Berényi, Marianne; Katona, Ferenc; Sanchez, Carmen; Mandujano, Mario

2011-07-30

The group or profile of elementary neuromotor patterns is different from the primitive reflex group which is now called the "primitive reflex profile." All these elementary neuromotor patterns are characterized by a high degree of organization, persistence, and stereotypy. In many regards, these patterns are predecessors or precursors of from them the specific human motor patterns which appear spontaneously later as crawling, creeping, sitting, and walking with erect posture. On the basis of our experiences it can be stated that the elementary neuromotor patterns can be activated in all neonates and young infants as congenital motor functions. With regards to their main properties and functional forms, the normal patterns can be divided into two main groups: (1) One group is characterized by lifting of the head and complex chains of movements which are directed to the verticalization of the body; (2) The other group is characterized by complex movements directed to locomotion and change of body position. The neuromotor patterns can be activated by placing the human infant in specific body positions that trigger the vestibulospinal and the reticulospinal systems, the archicerebellum and the basal gangliae. Most of these systems display early myelinisation and are functioning very soon. Many of the elementary neuromotor patterns reflect the most important - spontaneously developing forms of human movements such as sitting upright in space and head elevation crawling and walking. The majority of the human neuromotor patterns are human specific. When the infant is put in an activating position, crawling, sitting up, and walking begin and last as long as the activating position is maintained. Each elementary neuromotor pattern is a repeated, continuous train of complex movements in response to a special activating position. The brainstem is not sufficient to organize these complex movements, the integrity of the basal ganglia is also necessary. Elementary sensorimotor patterns during human ontogenesis reflect phylogenetic develpoment of species specific human functions. During ontogenesis spontaneous motor development gradually arises from these early specific sensorimotor predecessors.. The regular use of the elementary neuromotor patterns for diagnostic puposes has several distinct advantages. The neuromotor patterns have a natural stereotypy in normal infants and, therefore, deflections from this regular pattern may be detected easily, thus, the activation of the elementary neuromotor pattern is a more suitable method for identifying defects in the motor activity of the neonate or young infant than the assessment of the primitive reflexes. The "stiumulus positions," which activate specific movements according to how the human neonate or young infant is positioned, do not activate such motor patterns in neonate or young primates including apes. The characteristic locomotor pattern in these adult primates, including the apes, is swinging and involves brachiation with an extreme prehensility. This species specific motor activity is reflected in the orangutan and gibbon neonates by an early extensive grasp. However, according to our investigations, no crawling, creeping, elementary walk, or sitting up can be activated in them. Neonates grasp the hair of the mother, a vital function for the survival of the young. In contemporary nonhuman primates including apes, the neonate brain is more mature. Thus, pronounced differences can be observed between early motor ontogenesis in the human and all other primates. The earliest human movements are complex performances rather than simple reflexes. The distinction between primitive reflexes and elementary neuromotor patterns is essential. Primitive reflexes are controlled by the brainstem. All can be activated in primates. These reflexes have short durations and contrary to elementary sensorimotor patterns occur only once in response to one stimulus, e.g., one head drop elicits one abduction-adduction of the upper extremities correlated to adduction and flexion of the lower extremities to a lesser degree with the Moro reflex. Elementary neuromotor patterns are much more complex and most of them including elementary walk may be elicited as early as the 19th-20th gestational week, though less perfectly than later.

Perception of animacy in dogs and humans.

PubMed

Abdai, Judit; Ferdinandy, Bence; Terencio, Cristina Baño; Pogány, Ákos; Miklósi, Ádám

2017-06-01

Humans have a tendency to perceive inanimate objects as animate based on simple motion cues. Although animacy is considered as a complex cognitive property, this recognition seems to be spontaneous. Researchers have found that young human infants discriminate between dependent and independent movement patterns. However, quick visual perception of animate entities may be crucial to non-human species as well. Based on general mammalian homology, dogs may possess similar skills to humans. Here, we investigated whether dogs and humans discriminate similarly between dependent and independent motion patterns performed by geometric shapes. We projected a side-by-side video display of the two patterns and measured looking times towards each side, in two trials. We found that in Trial 1, both dogs and humans were equally interested in the two patterns, but in Trial 2 of both species, looking times towards the dependent pattern decreased, whereas they increased towards the independent pattern. We argue that dogs and humans spontaneously recognized the specific pattern and habituated to it rapidly, but continued to show interest in the 'puzzling' pattern. This suggests that both species tend to recognize inanimate agents as animate relying solely on their motions. © 2017 The Author(s).

Regional Characterization of Soil Properties via a Combination of Methods from Remote Sensing, Geophysics and Geopedology

NASA Astrophysics Data System (ADS)

Meyer, Uwe; Fries, Elke; Frei, Michaela

2016-04-01

Soil is one of the most precious resources on Earth. Preserving, using and enriching soils are most complex processes that fundamentally need a sound regional data base. Many countries lack this sort of extensive data or the existing data must be urgently updated when land use recently changed in major patterns. The project "RECHARBO" (Regional Characterization of Soil Properties) aims at the combination of methods from remote sensing, geophysics and geopedology in order to develop a new system to map soils on a regional scale in a quick and efficient manner. First tests will be performed on existing soil monitoring districts, using newly available sensing systems as well as established techniques. Especially hyperspectral and infrared data measured from satellites or airborne platforms shall be combined. Moreover, a systematic correlation between hyperspectral imagery and gamma-ray spectroscopy shall be established. These recordings will be compared and correlated to measurements upon ground and on soil samples to get hold of properties such as soil moisture, soil density, specific resistance plus analytic properties like clay content, anorganic background, organic matter etc. The goal is to generate a system that enables users to map soil patterns on a regional scale using airborne or satellite data and to fix their characteristics with only a limited number of soil samples.

Electro-Optic Properties of Holographically Patterned, Polymer Stabilized Cholesteric Liquid Crystals (Preprint)

DTIC Science & Technology

2007-01-01

Electro - optic properties of cholesteric liquid crystals with holographically patterned polymer stabilization were examined. It is hypothesized that...enhanced electro - optic properties of the final device. Prior to holographic patterning, polymer stabilization with large elastic memory was generated by way... electro - optic properties appear to stem from a single dimension domain size increase, which allows for a reduction in the LC/polymer interaction.

Cell type-specific expression of FoxP2 in the ferret and mouse retina.

PubMed

Sato, Chihiro; Iwai-Takekoshi, Lena; Ichikawa, Yoshie; Kawasaki, Hiroshi

2017-04-01

Although the anatomical and physiological properties of subtypes of retinal ganglion cells (RGCs) have been extensively investigated, their molecular properties are still unclear. Here, we examined the expression patterns of FoxP2 in the retina of ferrets and mice. We found that FoxP2 was expressed in small subsets of neurons in the adult ferret retina. FoxP2-positive neurons in the ganglion cell layer were divided into two groups. Large FoxP2-positive neurons expressed Brn3a and were retrogradely labeled with cholera toxin subunit B injected into the optic nerve, indicating that they are RGCs. The soma size and the projection pattern of FoxP2-positive RGCs were consistent with those of X cells. Because we previously reported that FoxP2 was selectively expressed in X cells in the ferret lateral geniculate nucleus (LGN), our findings indicate that FoxP2 is specifically expressed in the parvocellular pathway from the retina to the LGN. Small FoxP2-positive neurons were positive for GAD65/67, suggesting that they are GABAergic amacrine cells. Most Foxp2-positive cells were RGCs in the adult mouse retina. Dendritic morphological analyses suggested that Foxp2-positive RGCs included direction-selective RGCs in mice. Thus, our findings suggest that FoxP2 is expressed in specific subtypes of RGCs in the retina of ferrets and mice. Copyright © 2016 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

Layer by Layer Growth of 2D Quantum Superlattices (NBIT III)

DTIC Science & Technology

2017-02-28

building quantum superlatticies using 2D materials as the building blocks. Specifically, we develop methods that allow i) large-scale growth of aligned...superlattice and heterostructures, iii) lateral and clean patterning of 2D materials for atomically-thin circuitry and iv) novel physical properties...high precision and flexibility beyond conventional methods. Moreover, it provides the solutions for current major barrier for 2D materials (e.g

AWARE: Adaptive Software Monitoring and Dynamic Reconfiguration for Critical Infrastructure Protection

DTIC Science & Technology

2015-04-29

in which we applied these adaptation patterns to an adaptive news web server intended to tolerate extremely heavy, unexpected loads. To address...collection of existing models used as benchmarks for OO-based refactoring and an existing web -based repository called REMODD to provide users with model...invariant properties. Specifically, we developed Avida- MDE (based on the Avida digital evolution platform) to support the automatic generation of software

Firing-rate resonances in the peripheral auditory system of the cricket, Gryllus bimaculatus.

PubMed

Rau, Florian; Clemens, Jan; Naumov, Victor; Hennig, R Matthias; Schreiber, Susanne

2015-11-01

In many communication systems, information is encoded in the temporal pattern of signals. For rhythmic signals that carry information in specific frequency bands, a neuronal system may profit from tuning its inherent filtering properties towards a peak sensitivity in the respective frequency range. The cricket Gryllus bimaculatus evaluates acoustic communication signals of both conspecifics and predators. The song signals of conspecifics exhibit a characteristic pulse pattern that contains only a narrow range of modulation frequencies. We examined individual neurons (AN1, AN2, ON1) in the peripheral auditory system of the cricket for tuning towards specific modulation frequencies by assessing their firing-rate resonance. Acoustic stimuli with a swept-frequency envelope allowed an efficient characterization of the cells' modulation transfer functions. Some of the examined cells exhibited tuned band-pass properties. Using simple computational models, we demonstrate how different, cell-intrinsic or network-based mechanisms such as subthreshold resonances, spike-triggered adaptation, as well as an interplay of excitation and inhibition can account for the experimentally observed firing-rate resonances. Therefore, basic neuronal mechanisms that share negative feedback as a common theme may contribute to selectivity in the peripheral auditory pathway of crickets that is designed towards mate recognition and predator avoidance.

The effects of ingested petroleum on the maphthalene-metabolizing properties of the liver tissue in seawater-adapted mallard ducks (Anas platyrhynchos)

USGS Publications Warehouse

Gorsline, J.; Holmes, W.N.; Cronshaw, J.

1981-01-01

Hepatic mixed function oxidase activities were estimated in seawater-adapted mallard ducks (Anas platyrhynchos) that had been consuming food contaminated with one of five different types of crude oil. After 50 days of exposure to contaminated food, enzyme activities of liver microsomal preparations were assessed in terms of their naphthalenemetabolizing properties in vitro. Although dose-dependent increases in the total hepatic enzyme activities (nmole naphthalene metabolized per minute per unit mass body weight) were observed in birds consuming food contaminated with each type of crude oil, three patterns of response were apparent. Crude oils from South Louisiana and Kuwait stimulated large and significant increases in the specific activity of the enzyme system (nmole naphthalene metabolized per minute per unit mass microsomal protein), whereas little or no increase in either microsomal protein content or relative liver weight were observed. In contrast, two crude oils from Santa Barbara, Calif., induced only small increases in specific activity but significant increases occurred in hepatic microsomal protein concentration and relative liver weight. The crude oil from Prudhoe Bay, Ala., evoked intermediate patterns of response. The possible significance of these data is discussed in relation to the survival of seabirds consuming petroleum-contaminated food and drinking water.

Extraordinary Effects in Quasi-Periodic Gold Nanocavities: Enhanced Transmission and Polarization Control of Cavity Modes.

PubMed

Dhama, Rakesh; Caligiuri, Vincenzo; Petti, Lucia; Rashed, Alireza R; Rippa, Massimo; Lento, Raffaella; Termine, Roberto; Caglayan, Humeyra; De Luca, Antonio

2018-01-23

Plasmonic quasi-periodic structures are well-known to exhibit several surprising phenomena with respect to their periodic counterparts, due to their long-range order and higher rotational symmetry. Thanks to their specific geometrical arrangement, plasmonic quasi-crystals offer unique possibilities in tailoring the coupling and propagation of surface plasmons through their lattice, a scenario in which a plethora of fascinating phenomena can take place. In this paper we investigate the extraordinary transmission phenomenon occurring in specifically patterned Thue-Morse nanocavities, demonstrating noticeable enhanced transmission, directly revealed by near-field optical experiments, performed by means of a scanning near-field optical microscope (SNOM). SNOM further provides an intuitive picture of confined plasmon modes inside the nanocavities and confirms that localization of plasmon modes is based on size and depth of nanocavities, while cross talk between close cavities via propagating plasmons holds the polarization response of patterned quasi-crystals. Our performed numerical simulations are in good agreement with the experimental results. Thus, the control on cavity size and incident polarization can be used to alter the intensity and spatial properties of confined cavity modes in such structures, which can be exploited in order to design a plasmonic device with customized optical properties and desired functionalities, to be used for several applications in quantum plasmonics.

Microfabrication of a spider-silk analogue through the liquid rope coiling instability

NASA Astrophysics Data System (ADS)

Gosselin, Frederick P.; Therriault, Daniel; Levesque, Martin

2012-02-01

Spider capture silk outperforms most synthetic materials in terms of specific toughness. We developed a technique to fabricate tough microstructured fibers inspired by the molecular structure of the spider silk protein. To fabricate microfibers (with diameter ˜30μm) with various mechanical properties, we yield the control of their exact geometry to the liquid rope coiling instability. This instability causes a thread of honey to wiggle as it buckles when hitting a surface. Similarly, we flow a filament of viscous polymer solution towards a substrate moving perpendicularly at a slower velocity than the filament flows. The filament buckles repetitively giving rise to periodic meanders and stitch patterns. As the solvent evaporates, the filament solidifies into a fiber with a geometry bestowed by the instability. Microtraction tests performed on fibers show interesting links between the mechanical properties and the instability patterns. Some coiling patterns give rise to high toughness due to the sacrificial bonds created when the viscous filament loops over itself and fuse. The sacrificial bonds in the microstructured fiber play an analogous role to that of the hydrogen bonds present in the molecular structure of the silk protein which give its toughness to spider silk.

Patterns and comparisons of human-induced changes in river flood impacts in cities

NASA Astrophysics Data System (ADS)

Clark, Stephanie; Sharma, Ashish; Sisson, Scott A.

2018-03-01

In this study, information extracted from the first global urban fluvial flood risk data set (Aqueduct) is investigated and visualized to explore current and projected city-level flood impacts driven by urbanization and climate change. We use a novel adaption of the self-organizing map (SOM) method, an artificial neural network proficient at clustering, pattern extraction, and visualization of large, multi-dimensional data sets. Prevalent patterns of current relationships and anticipated changes over time in the nonlinearly-related environmental and social variables are presented, relating urban river flood impacts to socioeconomic development and changing hydrologic conditions. Comparisons are provided between 98 individual cities. Output visualizations compare baseline and changing trends of city-specific exposures of population and property to river flooding, revealing relationships between the cities based on their relative map placements. Cities experiencing high (or low) baseline flood impacts on population and/or property that are expected to improve (or worsen), as a result of anticipated climate change and development, are identified and compared. This paper condenses and conveys large amounts of information through visual communication to accelerate the understanding of relationships between local urban conditions and global processes.

Single-cell vs. bulk activity properties of coastal bacterioplankton over an annual cycle in a temperate ecosystem.

PubMed

Morán, Xosé Anxelu G; Calvo-Díaz, Alejandra

2009-01-01

The connections between single-cell activity properties of heterotrophic planktonic bacteria and whole community metabolism are still poorly understood. Here, we show flow cytometry single-cell analysis of membrane-intact (live), high nucleic acid (HNA) content and actively respiring (CTC+) bacteria with samples collected monthly during 2006 in northern Spain coastal waters. Bulk activity was assessed by measuring 3H-Leucine incorporation and specific growth rates. Consistently, different single-cell relative abundances were found, with 60-100% for live, 30-84% for HNA and 0.2-12% for CTC+ cells. Leucine incorporation rates (2-153 pmol L(-1) h(-1)), specific growth rates (0.01-0.29 day(-1)) and the total and relative abundances of the three single-cell groups showed marked seasonal patterns. Distinct depth distributions during summer stratification and different relations with temperature, chlorophyll and bacterial biovolume suggest the existence of different controlling factors on each single-cell property. Pooled leucine incorporation rates were similarly correlated with the abundance of all physiological groups, while specific growth rates were only substantially explained by the percentage of CTC+ cells. However, the ability to reduce CTC proved notably better than the other two single-cell properties at predicting bacterial bulk rates within seasons, suggesting a tight linkage between bacterial individual respiration and biomass production at the community level.

Soil transference patterns on bras: Image processing and laboratory dragging experiments.

PubMed

Murray, Kathleen R; Fitzpatrick, Robert W; Bottrill, Ralph S; Berry, Ron; Kobus, Hilton

2016-01-01

In a recent Australian homicide, trace soil on the victim's clothing suggested she was initially attacked in her front yard and not the park where her body was buried. However the important issue that emerged during the trial was how soil was transferred to her clothing. This became the catalyst for designing a range of soil transference experiments (STEs) to study, recognise and classify soil patterns transferred onto fabric when a body is dragged across a soil surface. Soil deposits of interest in this murder were on the victim's bra and this paper reports the results of anthropogenic soil transfer to bra-cups and straps caused by dragging. Transfer patterns were recorded by digital photography and photomicroscopy. Eight soil transfer patterns on fabric, specific to dragging as the transfer method, appeared consistently throughout the STEs. The distinctive soil patterns were largely dependent on a wide range of soil features that were measured and identified for each soil tested using X-ray Diffraction and Non-Dispersive Infra-Red analysis. Digital photographs of soil transfer patterns on fabric were analysed using image processing software to provide a soil object-oriented classification of all soil objects with a diameter of 2 pixels and above transferred. Although soil transfer patterns were easily identifiable by naked-eye alone, image processing software provided objective numerical data to support this traditional (but subjective) interpretation. Image software soil colour analysis assigned a range of Munsell colours to identify and compare trace soil on fabric to other trace soil evidence from the same location; without requiring a spectrophotometer. Trace soil from the same location was identified by linking soils with similar dominant and sub-dominant Munsell colour peaks. Image processing numerical data on the quantity of soil transferred to fabric, enabled a relationship to be discovered between soil type, clay mineralogy (smectite), particle size and soil moisture content that would not have been possible otherwise. Soil type (e.g. Anthropogenic, gravelly sandy loam soil or Natural, organic-rich soil), clay mineralogy (smectite) and soil moisture content were the greatest influencing factors in all the dragging soil transference tests (both naked eye and measured properties) to explain the eight categories of soil transference patterns recorded. This study was intended to develop a method for dragging soil transference laboratory experiments and create a baseline of preliminary soil type/property knowledge. Results confirm the need to better understand soil behaviour and properties of clothing fabrics by further testing of a wider range of soil types and clay mineral properties. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Environmental Adaptation Contributes to Gene Polymorphism across the Arabidopsis thaliana Genome

PubMed Central

Lee, Cheng-Ruei

2012-01-01

The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the "environmental relevance" of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study. PMID:22798389

The in vivo plantar soft tissue mechanical property under the metatarsal head: implications of tissues׳ joint-angle dependent response in foot finite element modeling.

PubMed

Chen, Wen-Ming; Lee, Sung-Jae; Lee, Peter Vee Sin

2014-12-01

Material properties of the plantar soft tissue have not been well quantified in vivo (i.e., from life subjects) nor for areas other than the heel pad. This study explored an in vivo investigation of the plantar soft tissue material behavior under the metatarsal head (MTH). We used a novel device collecting indentation data at controlled metatarsophalangeal joint angles. Combined with inverse analysis, tissues׳ joint-angle dependent material properties were identified. The results showed that the soft tissue under MTH exhibited joint-angle dependent material responses, and the computed parameters using the Ogden material model were 51.3% and 30.9% larger in the dorsiflexed than in the neutral positions, respectively. Using derived parameters in subject-specific foot finite element models revealed only those models that used tissues׳ joint-dependent responses could reproduce the known plantar pressure pattern under the MTH. It is suggested that, to further improve specificity of the personalized foot finite element models, quantitative mechanical properties of the tissue inclusive of the effects of metatarsophalangeal joint dorsiflexion are needed. Copyright © 2014 Elsevier Ltd. All rights reserved.

An ontology on property for physical, chemical, and biological systems.

PubMed

Dybkaer, René

2004-01-01

Current metrological literature, including the International vocabulary of basic and general terms in metrology (VIM 1993), presents a special language slowly evolved without consistent use of the procedures of terminological work; furthermore, nominal properties are excluded by definition. Both deficiencies create problems in fields, such as laboratory medicine, which have to report results of all types of property, preferably in a unified systematic format. The present text aims at forming a domain ontology around "property", with intensional definitions and systematic terms, mainly using the terminological tools--with some additions--provided by the International Standards ISO 704, 1087-1, and 10241. "System" and "component" are defined, "quantity" is discussed, and the generic concept "property" is given as 'inherent state- or process-descriptive feature of a system including any pertinent components'. Previously, the term 'kind-of-quantity' and quasi-synonyms have been used as primitives; the proposed definition of "kind-of-property" is 'common defining aspect of mutually comparable properties'. "Examination procedure", "examination method", "examination principle", and "examination" are defined, avoiding the term 'test'. The need to distinguish between instances of "characteristic", "property", "type of characteristic", "kind-of-property", and "property value" is emphasized; the latter is defined together with "property value scale". These fundamental concepts are presented in a diagram, and the effect of adding essential characteristics to give expanded definitions is exemplified. Substitution usually leads to unwieldy definitions, but reveals circularity as does exhaustive consecutive listing of defining concepts. The top concept may be generically divided according to many terminological dimensions, especially regarding which operators are allowed among the four sets =, not equal to; <, >; +, -; and x, :. The coordinate concepts defined are termed by the modifiers 'nominal', 'ordinal', 'differential', and 'rational' before '...property'. Other possibilities are given, based on the literature, especially the stepwise division into "nominal property" and "quantity"; "ordinal quantity" and "unitary quantity"; "differential unitary quantity" and "rational unitary quantity". As top concepts, , , , , and are i.a. divided homologously to . The term 'observation' and the modifiers 'qualitative', 'semi-quantitative', and 'quantitative' are avoided. "Metrological unit" and "system of metrological units" are defined together with a number of specific concepts. Some problems with characteristics of "SI unit" are discussed and an alternative system shown. The conceptions of "metrological dimension" are outlined, leading to a definition and specific concepts. The generally accepted IUPAC/IFCC syntax for designations of instantiated properties is 'System (specification)--Component(specification); kind-of-property (specification)', and' 'dedicatedkind-of-property" is defined as 'kind-of-property with given sort of system and any pertinent sorts of component'. The related systematic terms may be generated according to ENV 1614 using generative patterns from ENV 12264. The elements of the appellation and examination result of a singular rational property are diagrammed. Finally, the possibilities of representing properties and their results by the formalisms of relation and function from Set Theory and Object-Oriented Analysis are exemplified.

Influence of surface heterogeneity in electroosmotic flows—Implications in chromatography, fluid mixing, and chemical reactions in microdevices

NASA Astrophysics Data System (ADS)

Adrover, Alessandra; Giona, Massimiliano; Pagnanelli, Francesca; Toro, Luigi

2007-04-01

We analyze the influence of surface heterogeneity, inducing a random ζ-potential at the walls in electroosmotic incompressible flows. Specifically, we focus on how surface heterogeneity modifies the physico-chemical processes (transport, chemical reaction, mixing) occurring in microchannel and microreactors. While the macroscopic short-time features associated with solute transport (e.g. chromatographic patterns) do not depend significantly on ζ-potential heterogeneity, spatial randomness in the surface ζ-potential modifies the spectral properties of the advection-diffusion operator, determining different long-term properties of transport/reaction phenomena compared to the homogeneous case. Examples of physical relevance (chromatography, infinitely fast reactions) are addressed.

Biological robustness.

PubMed

Kitano, Hiroaki

2004-11-01

Robustness is a ubiquitously observed property of biological systems. It is considered to be a fundamental feature of complex evolvable systems. It is attained by several underlying principles that are universal to both biological organisms and sophisticated engineering systems. Robustness facilitates evolvability and robust traits are often selected by evolution. Such a mutually beneficial process is made possible by specific architectural features observed in robust systems. But there are trade-offs between robustness, fragility, performance and resource demands, which explain system behaviour, including the patterns of failure. Insights into inherent properties of robust systems will provide us with a better understanding of complex diseases and a guiding principle for therapy design.

Development of the optimal radiochromic film dosimetry system for measurement of IMRT radiation beams

NASA Astrophysics Data System (ADS)

Baker, Jameson Todd

The complex dose patterns that result in Intensity Modulated Radiation Therapy make the typical QA of a second calculation insufficient for ensuring safe treatment of patients. Many facilities choose to deliver the treatment to film inserted in a phantom and calculate the dose delivered as an additional check of the treatment plan. Radiochromic films allow for measurements without the use of a processor in the current digital age. International Specialty Products developed Gafchromic EBT film, which is a radiochromic film having a useful range of 1 -- 800 cGy. EBT film properties are fully analyzed including studies of uniformity, spectral absorption, exposure sensitivity, energy dependence and post exposure density growth. Dosimetric performance on commercially available digitizers is studied with specific attention on the shortcomings. Finally, a custom designed scanner is built specifically for EBT film and its unique properties. Performance of the EBT digitizer is analyzed and compared against currently available scanners.

Grafting density effects, optoelectrical properties and nano-patterning of poly(para-phenylene) brushes

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

Chen, Jihua; Alonzo, Jose; Yu, Xiang

2013-09-24

Well-defined conjugated polymers in confined geometries are challenging to synthesize and characterize, yet they are potentially useful in a broad range of organic optoelectronic devices such as transistors, light emitting diodes, solar cells, sensors, and nanocircuits. We report a systematic study of optoelectrical properties, grafting density effects, and nanopatterning of a model, end-tethered conjugated polymer system. Specifically, poly(para-phenylene) (PPP) brushes of various grafting density are created in situ by aromatizing well-defined, end-tethered poly(1,3-cyclohexadiene) (PCHD) “precursor brushes”. Furthermore, this novel precursor brush approach provides a convenient way to make and systematically control the grafting density of high molecular weight conjugated polymermore » brushes that would otherwise be insoluble. Finally, this allows us to examine how grafting density impacts the effective conjugation length of the conjugated PPP brushes and to adapt the fabrication method to develop spatially patterned conjugated brush systems, which is important for practical applications of conjugated polymer brushes.« less

Electric organ discharges and near-field spatiotemporal patterns of the electromotive force in a sympatric assemblage of Neotropical electric knifefish.

PubMed

Waddell, Joseph C; Rodríguez-Cattáneo, Alejo; Caputi, Angel A; Crampton, William G R

2016-10-01

Descriptions of the head-to-tail electric organ discharge (ht-EOD) waveform - typically recorded with electrodes at a distance of approximately 1-2 body lengths from the center of the subject - have traditionally been used to characterize species diversity in gymnotiform electric fish. However, even taxa with relatively simple ht-EODs show spatiotemporally complex fields near the body surface that are determined by site-specific electrogenic properties of the electric organ and electric filtering properties of adjacent tissues and skin. In Brachyhypopomus, a pulse-discharging genus in the family Hypopomidae, the regional characteristics of the electric organ and the role that the complex 'near field' plays in communication and/or electrolocation are not well known. Here we describe, compare, and discuss the functional significance of diversity in the ht-EOD waveforms and near-field spatiotemporal patterns of the electromotive force (emf-EODs) among a species-rich sympatric community of Brachyhypopomus from the upper Amazon. Copyright © 2016 Elsevier Ltd. All rights reserved.

Collective chemotaxis and segregation of active bacterial colonies

NASA Astrophysics Data System (ADS)

Amar, M. Ben

2016-02-01

Still recently, bacterial fluid suspensions have motivated a lot of works, both experimental and theoretical, with the objective to understand their collective dynamics from universal and simple rules. Since some species are active, most of these works concern the strong interactions that these bacteria exert on a forced flow leading to instabilities, chaos and turbulence. Here, we investigate the self-organization of expanding bacterial colonies under chemotaxis, proliferation and eventually active-reaction. We propose a simple model to understand and quantify the physical properties of these living organisms which either give cohesion or on the contrary dispersion to the colony. Taking into account the diffusion and capture of morphogens complicates the model since it induces a bacterial density gradient coupled to bacterial density fluctuations and dynamics. Nevertheless under some specific conditions, it is possible to investigate the pattern formation as a usual viscous fingering instability. This explains the similarity and differences of patterns according to the physical bacterial suspension properties and explain the factors which favor compactness or branching.

Theory of Phase Separation and Polarization for Pure Ionic Liquids.

PubMed

Gavish, Nir; Yochelis, Arik

2016-04-07

Room temperature ionic liquids are attractive to numerous applications and particularly, to renewable energy devices. As solvent free electrolytes, they demonstrate a paramount connection between the material morphology and Coulombic interactions: the electrode/RTIL interface is believed to be a product of both polarization and spatiotemporal bulk properties. Yet, theoretical studies have dealt almost exclusively with independent models of morphology and electrokinetics. Introduction of a distinct Cahn-Hilliard-Poisson type mean-field framework for pure molten salts (i.e., in the absence of any neutral component), allows a systematic coupling between morphological evolution and the electrokinetic phenomena, such as transient currents. Specifically, linear analysis shows that spatially periodic patterns form via a finite wavenumber instability and numerical simulations demonstrate that while labyrinthine type patterns develop in the bulk, lamellar structures are favored near charged surfaces. The results demonstrate a qualitative phenomenology that is observed empirically and thus, provide a physically consistent methodology to incorporate phase separation properties into an electrochemical framework.

Usefulness of traditionally defined herbal properties for distinguishing prescriptions of traditional Chinese medicine from non-prescription recipes.

PubMed

Ung, C Y; Li, H; Kong, C Y; Wang, J F; Chen, Y Z

2007-01-03

Traditional Chinese medicine (TCM) has been widely practiced and is considered as an attractive to conventional medicine. Multi-herb recipes have been routinely used in TCM. These have been formulated by using TCM-defined herbal properties (TCM-HPs), the scientific basis of which is unclear. The usefulness of TCM-HPs was evaluated by analyzing the distribution pattern of TCM-HPs of the constituent herbs in 1161 classical TCM prescriptions, which shows patterns of multi-herb correlation. Two artificial intelligence (AI) methods were used to examine whether TCM-HPs are capable of distinguishing TCM prescriptions from non-TCM recipes. Two AI systems were trained and tested by using 1161 TCM prescriptions, 11,202 non-TCM recipes, and two separate evaluation methods. These systems correctly classified 83.1-97.3% of the TCM prescriptions, 90.8-92.3% of the non-TCM recipes. These results suggest that TCM-HPs are capable of separating TCM prescriptions from non-TCM recipes, which are useful for formulating TCM prescriptions and consistent with the expected correlation between TCM-HPs and the physicochemical properties of herbal ingredients responsible for producing the collective pharmacological and other effects of specific TCM prescriptions.

"Machismo," self-esteem, education and high maximum drinking among anglo, black and Mexican-American male drinkers.

PubMed

Neff, J A; Prihoda, T J; Hoppe, S K

1991-09-01

This study seeks to clarify the relevance of machismo to patterns of high maximum drinking among male drinkers. Specifically, the study describes the psychometric properties of a newly developed 7-item machismo measure, compares levels of machismo and self-esteem for a sample of Anglo, black and Mexican-American males, and examines both main and interaction effects of machismo, self-esteem and education as predictors of alcohol use in these racial/ethnic subgroups. Logistic regression analyses document interaction between race/ethnicity, machismo, self-esteem and education, which calls into question the presumed importance of machismo as a cultural element causing heavy drinking patterns among Mexican-American males.

Physiological and morphological characterization of local interneurons in the Drosophila antennal lobe.

PubMed

Seki, Yoichi; Rybak, Jürgen; Wicher, Dieter; Sachse, Silke; Hansson, Bill S

2010-08-01

The Drosophila antennal lobe (AL) has become an excellent model for studying early olfactory processing mechanisms. Local interneurons (LNs) connect a large number of glomeruli and are ideally positioned to increase computational capabilities of odor information processing in the AL. Although the neural circuit of the Drosophila AL has been intensively studied at both the input and the output level, the internal circuit is not yet well understood. An unambiguous characterization of LNs is essential to remedy this lack of knowledge. We used whole cell patch-clamp recordings and characterized four classes of LNs in detail using electrophysiological and morphological properties at the single neuron level. Each class of LN displayed unique characteristics in intrinsic electrophysiological properties, showing differences in firing patterns, degree of spike adaptation, and amplitude of spike afterhyperpolarization. Notably, one class of LNs had characteristic burst firing properties, whereas the others were tonically active. Morphologically, neurons from three classes innervated almost all glomeruli, while LNs from one class innervated a specific subpopulation of glomeruli. Three-dimensional reconstruction analyses revealed general characteristics of LN morphology and further differences in dendritic density and distribution within specific glomeruli between the different classes of LNs. Additionally, we found that LNs labeled by a specific enhancer trap line (GAL4-Krasavietz), which had previously been reported as cholinergic LNs, were mostly GABAergic. The current study provides a systematic characterization of olfactory LNs in Drosophila and demonstrates that a variety of inhibitory LNs, characterized by class-specific electrophysiological and morphological properties, construct the neural circuit of the AL.

Some physical properties of naturally irradiated fluorite

USGS Publications Warehouse

Berman, Robert

1955-01-01

Five samples of purple fluorite found in association with radioactive, materials, and a synthetic colorless control sample were studied and compared.  Before and after heating, observations were made on specific gravity, index of refraction, unit-cell size, breadth of X-ray diffraction lines, and fluorescence.  The purple samples became colorless on heating above 175° C.  During the process, observations were made on color, thermoluminescence, and differential thermal analysis curves.  There were strong correlations between the various physical properties, and it was found possible to arrange the samples in order of increasing difference in their physical properties from the control sample. This order apparently represents increasing structural damage by radiation; if so, it correlates with decreasing specific gravity, increasing index of refraction, broadening of X-ray lines, and increasingly strong exothermic reactions on annealing. The differences between the samples in index of refraction and X-ray pattern are largely eliminated on annealing.  Annealing begins at 1750 C; thermoluminescence at lower temperatures is due to electrons escaping from the metastable potential traps, not the destruction of those traps which takes place on annealing.

Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus

PubMed Central

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

2015-01-01

Hippocampome.org is a comprehensive knowledge base of neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex). Although the hippocampal literature is remarkably information-rich, neuron properties are often reported with incompletely defined and notoriously inconsistent terminology, creating a formidable challenge for data integration. Our extensive literature mining and data reconciliation identified 122 neuron types based on neurotransmitter, axonal and dendritic patterns, synaptic specificity, electrophysiology, and molecular biomarkers. All ∼3700 annotated properties are individually supported by specific evidence (∼14,000 pieces) in peer-reviewed publications. Systematic analysis of this unprecedented amount of machine-readable information reveals novel correlations among neuron types and properties, the potential connectivity of the full hippocampal circuitry, and outstanding knowledge gaps. User-friendly browsing and online querying of Hippocampome.org may aid design and interpretation of both experiments and simulations. This powerful, simple, and extensible neuron classification endeavor is unique in its detail, utility, and completeness. DOI: http://dx.doi.org/10.7554/eLife.09960.001 PMID:26402459

Geomorphometric correlations of vegetation cover properties and topographic karst features based on high-resolution LiDAR DTM of Aggtelek Karst, NE Hungary

NASA Astrophysics Data System (ADS)

Székely, Balázs; Telbisz, Tamás; Koma, Zsófia; Kelemen, Kristóf; Szmorad, Ferenc; Deák, Márton; Látos, Tamás; Standovár, Tibor

2015-04-01

Topography and lithology are two major factors influencing the vegetation cover, its mosaic pattern and lateral transitions. In karstic areas the topography has a high diversity, microtopographic landforms influence the local ecological setting, vegetation structure. Presence of sinkholes of various sizes and geometric arrangements causes rapid lateral variation of the slope, aspect patterns as well as highly modify the soil water balance in time and space. These diversity of factors defines a mosaicked habitat pattern for vegetation assemblages. The World Heritage Site Aggtelek Karst/Slovakian Karst Caves has characteristic natural and environmental properties concerning the geomorphological as well as the ecological values. In order to be able to study the topographic influence on the ecological setting, a high-resolution digital terrain model (DTM) and digital surface model (DSM) have been derived from airborne laser scanning data depicting the karstic micro- and macrotopographic Landscape elements and the envelope surface of the canopy. Additional vegetation parameters like closure and average height have been derived from a normalized digital surface model (nDSM). Extensive mapping of vegetation properties has been carried out: centered on points of a grid array several vegetation-specific data - including composition and structure of tree and shrub layers, herbacesous vegetation and tree regeneration - have been acquired. Various classification patterns - based on trees pecies composition, vertical vegetation structure - have been derived from this data set. The comparison of the vegetation classification data and the geomorphometric DTM derivatives yielded interesting results. Certain vegetation characteristics often correlate with the geomorphometric properties. We interpret this similarity as sensitivity of vegetion to fine-scale variations in geomorphic properties like aspect, illumination conditions and soil properties. However, in many cases the vegetation pattern shows no correlation with natural settings. It may be the result of human impact, which actively formed the local land use in these hilly-low mountain karst area since the Middle Ages. These studies have been financed partly by the following projects: data acquisition: "Hungarian-Slovakian Transnational Cooperation Programme 2007-2013", "Management of World Heritage Aggtelek Karst/Slovakian Karst Caves" (HUSK/1101/221/0180, Aggtelek NP), data evaluation: 'Multipurpose assessment serving forest biodiversity conservation in the Carpathian region of Hungary', Swiss-Hungarian Cooperation Programme (SH/4/13 Project), and Hungarian National Research Fund OTKA NK83400 and OTKA 104811. BS contributed as an Alexander von Humboldt Research Fellow, TT was supported by the János Bolyai Scolarship of the Hungarian Academy of Sciences.

Dry contact transfer printing of aligned carbon nanotube patterns and characterization of their optical properties for diameter distribution and alignment.

PubMed

Pint, Cary L; Xu, Ya-Qiong; Moghazy, Sharief; Cherukuri, Tonya; Alvarez, Noe T; Haroz, Erik H; Mahzooni, Salma; Doorn, Stephen K; Kono, Junichiro; Pasquali, Matteo; Hauge, Robert H

2010-02-23

A scalable and facile approach is demonstrated where as-grown patterns of well-aligned structures composed of single-walled carbon nanotubes (SWNT) synthesized via water-assisted chemical vapor deposition (CVD) can be transferred, or printed, to any host surface in a single dry, room-temperature step using the growth substrate as a stamp. We demonstrate compatibility of this process with multiple transfers for large-scale device and specifically tailored pattern fabrication. Utilizing this transfer approach, anisotropic optical properties of the SWNT films are probed via polarized absorption, Raman, and photoluminescence spectroscopies. Using a simple model to describe optical transitions in the large SWNT species present in the aligned samples, polarized absorption data are demonstrated as an effective tool for accurate assignment of the diameter distribution from broad absorption features located in the infrared. This can be performed on either well-aligned samples or unaligned doped samples, allowing simple and rapid feedback of the SWNT diameter distribution that can be challenging and time-consuming to obtain in other optical methods. Furthermore, we discuss challenges in accurately characterizing alignment in structures of long versus short carbon nanotubes through optical techniques, where SWNT length makes a difference in the information obtained in such measurements. This work provides new insight to the efficient transfer and optical properties of an emerging class of long, large diameter SWNT species typically produced in the CVD process.

Development of compositional and contextual communicable congruence in robots by using dynamic neural network models.

PubMed

Park, Gibeom; Tani, Jun

2015-12-01

The current study presents neurorobotics experiments on acquisition of skills for "communicable congruence" with human via learning. A dynamic neural network model which is characterized by its multiple timescale dynamics property was utilized as a neuromorphic model for controlling a humanoid robot. In the experimental task, the humanoid robot was trained to generate specific sequential movement patterns as responding to various sequences of imperative gesture patterns demonstrated by the human subjects by following predefined compositional semantic rules. The experimental results showed that (1) the adopted MTRNN can achieve generalization by learning in the lower feature perception level by using a limited set of tutoring patterns, (2) the MTRNN can learn to extract compositional semantic rules with generalization in its higher level characterized by slow timescale dynamics, (3) the MTRNN can develop another type of cognitive capability for controlling the internal contextual processes as situated to on-going task sequences without being provided with cues for explicitly indicating task segmentation points. The analysis on the dynamic property developed in the MTRNN via learning indicated that the aforementioned cognitive mechanisms were achieved by self-organization of adequate functional hierarchy by utilizing the constraint of the multiple timescale property and the topological connectivity imposed on the network configuration. These results of the current research could contribute to developments of socially intelligent robots endowed with cognitive communicative competency similar to that of human. Copyright © 2015 Elsevier Ltd. All rights reserved.

How learning might strengthen existing visual object representations in human object-selective cortex.

PubMed

Brants, Marijke; Bulthé, Jessica; Daniels, Nicky; Wagemans, Johan; Op de Beeck, Hans P

2016-02-15

Visual object perception is an important function in primates which can be fine-tuned by experience, even in adults. Which factors determine the regions and the neurons that are modified by learning is still unclear. Recently, it was proposed that the exact cortical focus and distribution of learning effects might depend upon the pre-learning mapping of relevant functional properties and how this mapping determines the informativeness of neural units for the stimuli and the task to be learned. From this hypothesis we would expect that visual experience would strengthen the pre-learning distributed functional map of the relevant distinctive object properties. Here we present a first test of this prediction in twelve human subjects who were trained in object categorization and differentiation, preceded and followed by a functional magnetic resonance imaging session. Specifically, training increased the distributed multi-voxel pattern information for trained object distinctions in object-selective cortex, resulting in a generalization from pre-training multi-voxel activity patterns to after-training activity patterns. Simulations show that the increased selectivity combined with the inter-session generalization is consistent with a training-induced strengthening of a pre-existing selectivity map. No training-related neural changes were detected in other regions. In sum, training to categorize or individuate objects strengthened pre-existing representations in human object-selective cortex, providing a first indication that the neuroanatomical distribution of learning effects depends upon the pre-learning mapping of visual object properties. Copyright © 2015 Elsevier Inc. All rights reserved.

Attention to Distinct Goal-relevant Features Differentially Guides Semantic Knowledge Retrieval.

PubMed

Hanson, Gavin K; Chrysikou, Evangelia G

2017-07-01

A critical aspect of conceptual knowledge is the selective activation of goal-relevant aspects of meaning. Although the contributions of ventrolateral prefrontal and posterior temporal areas to semantic cognition are well established, the precise role of posterior parietal cortex in semantic control remains unknown. Here, we examined whether this region modulates attention to goal-relevant features within semantic memory according to the same principles that determine the salience of task-relevant object properties during visual attention. Using multivoxel pattern analysis, we decoded attentional referents during a semantic judgment task, in which participants matched an object cue to a target according to concrete (i.e., color, shape) or abstract (i.e., function, thematic context) semantic features. The goal-relevant semantic feature participants attended to (e.g., color or shape, function or theme) could be decoded from task-associated cortical activity with above-chance accuracy, a pattern that held for both concrete and abstract semantic features. A Bayesian confusion matrix analysis further identified differential contributions to representing attentional demands toward specific object properties across lateral prefrontal, posterior temporal, and inferior parietal regions, with the dorsolateral pFC supporting distinctions between higher-order properties and the left intraparietal sulcus being the only region supporting distinctions across all semantic features. These results are the first to demonstrate that patterns of neural activity in the parietal cortex are sensitive to which features of a concept are attended to, thus supporting the contributions of posterior parietal cortex to semantic control.

Particle size distribution of rice flour affecting the starch enzymatic hydrolysis and hydration properties.

PubMed

de la Hera, Esther; Gomez, Manuel; Rosell, Cristina M

2013-10-15

Rice flour is becoming very attractive as raw material, but there is lack of information about the influence of particle size on its functional properties and starch digestibility. This study evaluates the degree of dependence of the rice flour functional properties, mainly derived from starch behavior, with the particle size distribution. Hydration properties of flours and gels and starch enzymatic hydrolysis of individual fractions were assessed. Particle size heterogeneity on rice flour significantly affected functional properties and starch features, at room temperature and also after gelatinization; and the extent of that effect was grain type dependent. Particle size heterogeneity on rice flour induces different pattern in starch enzymatic hydrolysis, with the long grain having slower hydrolysis as indicated the rate constant (k). No correlation between starch digestibility and hydration properties or the protein content was observed. It seems that in intact granules interactions with other grain components must be taken into account. Overall, particle size fractionation of rice flour might be advisable for selecting specific physico-chemical properties. Copyright © 2013. Published by Elsevier Ltd.

Low-level image properties in facial expressions.

PubMed

Menzel, Claudia; Redies, Christoph; Hayn-Leichsenring, Gregor U

2018-06-04

We studied low-level image properties of face photographs and analyzed whether they change with different emotional expressions displayed by an individual. Differences in image properties were measured in three databases that depicted a total of 167 individuals. Face images were used either in their original form, cut to a standard format or superimposed with a mask. Image properties analyzed were: brightness, redness, yellowness, contrast, spectral slope, overall power and relative power in low, medium and high spatial frequencies. Results showed that image properties differed significantly between expressions within each individual image set. Further, specific facial expressions corresponded to patterns of image properties that were consistent across all three databases. In order to experimentally validate our findings, we equalized the luminance histograms and spectral slopes of three images from a given individual who showed two expressions. Participants were significantly slower in matching the expression in an equalized compared to an original image triad. Thus, existing differences in these image properties (i.e., spectral slope, brightness or contrast) facilitate emotion detection in particular sets of face images. Copyright © 2018. Published by Elsevier B.V.

Microstructure characterization of multi-phase composites and utilization of phase change materials and recycled rubbers in cementitious materials

NASA Astrophysics Data System (ADS)

Meshgin, Pania

2011-12-01

This research focuses on two important subjects: (1) Characterization of heterogeneous microstructure of multi-phase composites and the effect of microstructural features on effective properties of the material. (2) Utilizations of phase change materials and recycled rubber particles from waste tires to improve thermal properties of insulation materials used in building envelopes. Spatial pattern of multi-phase and multidimensional internal structures of most composite materials are highly random. Quantitative description of the spatial distribution should be developed based on proper statistical models, which characterize the morphological features. For a composite material with multi-phases, the volume fraction of the phases as well as the morphological parameters of the phases have very strong influences on the effective property of the composite. These morphological parameters depend on the microstructure of each phase. This study intends to include the effect of higher order morphological details of the microstructure in the composite models. The higher order statistics, called two-point correlation functions characterize various behaviors of the composite at any two points in a stochastic field. Specifically, correlation functions of mosaic patterns are used in the study for characterizing transport properties of composite materials. One of the most effective methods to improve energy efficiency of buildings is to enhance thermal properties of insulation materials. The idea of using phase change materials and recycled rubber particles such as scrap tires in insulation materials for building envelopes has been studied.

Identification of TLR2/TLR6 signalling lactic acid bacteria for supporting immune regulation.

PubMed

Ren, Chengcheng; Zhang, Qiuxiang; de Haan, Bart J; Zhang, Hao; Faas, Marijke M; de Vos, Paul

2016-10-06

Although many lactic acid bacteria (LAB) influence the consumer's immune status it is not completely understood how this is established. Bacteria-host interactions between bacterial cell-wall components and toll-like receptors (TLRs) have been suggested to play an essential role. Here we investigated the interaction between LABs with reported health effects and TLRs. By using cell-lines expressing single or combination of TLRs, we show that LABs can signal via TLR-dependent and independent pathways. The strains only stimulated and did not inhibit TLRs. We found that several strains such as L. plantarum CCFM634, L. plantarum CCFM734, L. fermentum CCFM381, L. acidophilus CCFM137, and S. thermophilus CCFM218 stimulated TLR2/TLR6. TLR2/TLR6 is essential in immune regulatory processes and of interest for prevention of diseases. Specificity of the TLR2/TLR6 stimulation was confirmed with blocking antibodies. Immunomodulatory properties of LABs were also studied by assessing IL-10 and IL-6 secretion patterns in bacteria-stimulated THP1-derived macrophages, which confirmed species and strain specific effects of the LABs. With this study we provide novel insight in LAB specific host-microbe interactions. Our data demonstrates that interactions between pattern recognition receptors such as TLRs is species and strain specific and underpins the importance of selecting specific strains for promoting specific health effects.

Vacancy and curvature effects on the phonon properties of single wall carbon nanotube

NASA Astrophysics Data System (ADS)

Hossain Howlader, Ashraful; Sherajul Islam, Md.; Tanaka, Satoru; Makino, Takayuki; Hashimoto, Akihiro

2018-02-01

Single wall carbon nanotube (SWCNT) is considered as an ideal candidate for next-generation nanoelectronics owing to its unusual properties. Here we have performed an in-depth theoretical analysis of the effect of vacancy defects and curvature on the phonon properties of (10,0) and (10,10) SWCNTs using the forced vibrational method. We report that Raman active E2g mode softens towards the low-frequency region with increasing vacancies and curvature in both types of CNTs. Vacancy induces some new peaks at low-frequency region of the phonon density of states. Phonon localization properties are also manifested. Our calculated mode pattern and localization length show that optical phonon at Raman D-band frequency is strongly localized in vacancy defected and large curved CNTs. Our findings will be helpful in explaining the thermal conductivity, specific heat capacity, and Raman spectra in vacancy type disordered CNTs, as well as electron transport properties of CNT-based nanoelectronic devices.

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

DOE PAGES

Zhang, Yan; Inouye, Hideyo; Crowley, Michael; ...

2016-10-14

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Junction size dependence of ferroelectric properties in e-beam patterned BaTiO{sub 3} ferroelectric tunnel junctions

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

Singh, A. V.; Gupta, A.; Althammer, M.

We investigate the switching characteristics in BaTiO{sub 3}-based ferroelectric tunnel junctions patterned in a capacitive geometry with circular Ru top electrode with diameters ranging from ∼430 to 2300 nm. Two different patterning schemes, viz., lift-off and ion-milling, have been employed to examine the variations in the ferroelectric polarization, switching, and tunnel electro-resistance resulting from differences in the pattering processes. The values of polarization switching field are measured and compared for junctions of different diameter in the samples fabricated using both patterning schemes. We do not find any specific dependence of polarization switching bias on the size of junctions in both samplemore » stacks. The junctions in the ion-milled sample show up to three orders of resistance change by polarization switching and the polarization retention is found to improve with increasing junction diameter. However, similar switching is absent in the lift-off sample, highlighting the effect of patterning scheme on the polarization retention.« less

Silk protein nanowires patterned using electron beam lithography.

PubMed

Pal, Ramendra K; Yadavalli, Vamsi K

2018-08-17

Nanofabrication approaches to pattern proteins at the nanoscale are useful in applications ranging from organic bioelectronics to cellular engineering. Specifically, functional materials based on natural polymers offer sustainable and environment-friendly substitutes to synthetic polymers. Silk proteins (fibroin and sericin) have emerged as an important class of biomaterials for next generation applications owing to excellent optical and mechanical properties, inherent biocompatibility, and biodegradability. However, the ability to precisely control their spatial positioning at the nanoscale via high throughput tools continues to remain a challenge. In this study electron beam lithography (EBL) is used to provide nanoscale patterning using methacrylate conjugated silk proteins that are photoreactive 'photoresists' materials. Very low energy electron beam radiation can be used to pattern silk proteins at the nanoscale and over large areas, whereby such nanostructure fabrication can be performed without specialized EBL tools. Significantly, using conducting polymers in conjunction with these silk proteins, the formation of protein nanowires down to 100 nm is shown. These wires can be easily degraded using enzymatic degradation. Thus, proteins can be precisely and scalably patterned and doped with conducting polymers and enzymes to form degradable, organic bioelectronic devices.

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

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

Zhang, Yan; Inouye, Hideyo; Crowley, Michael

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

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

Zhang, Yan; Inouye, Hideyo; Crowley, Michael

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Spatial distribution of enzyme driven reactions at micro-scales

NASA Astrophysics Data System (ADS)

Kandeler, Ellen; Boeddinghaus, Runa; Nassal, Dinah; Preusser, Sebastian; Marhan, Sven; Poll, Christian

2017-04-01

Studies of microbial biogeography can often provide key insights into the physiologies, environmental tolerances, and ecological strategies of soil microorganisms that dominate in natural environments. In comparison with aquatic systems, soils are particularly heterogeneous. Soil heterogeneity results from the interaction of a hierarchical series of interrelated variables that fluctuate at many different spatial and temporal scales. Whereas spatial dependence of chemical and physical soil properties is well known at scales ranging from decimetres to several hundred metres, the spatial structure of soil enzymes is less clear. Previous work has primarily focused on spatial heterogeneity at a single analytical scale using the distribution of individual cells, specific types of organisms or collective parameters such as bacterial abundance or total microbial biomass. There are fewer studies that have considered variations in community function and soil enzyme activities. This presentation will give an overview about recent studies focusing on spatial pattern of different soil enzymes in the terrestrial environment. Whereas zymography allows the visualization of enzyme pattern in the close vicinity of roots, micro-sampling strategies followed by MUF analyses clarify micro-scale pattern of enzymes associated to specific microhabitats (micro-aggregates, organo-mineral complexes, subsoil compartments).

Linking suckling biomechanics to the development of the palate

NASA Astrophysics Data System (ADS)

Li, Jingtao; Johnson, Chelsey A.; Smith, Andrew A.; Hunter, Daniel J.; Singh, Gurpreet; Brunski, John B.; Helms, Jill A.

2016-02-01

Skulls are amongst the most informative documents of evolutionary history but a complex geometry, coupled with composite material properties and complicated biomechanics, have made it particularly challenging to identify mechanical principles guiding the skull’s morphogenesis. Despite this challenge, multiple lines of evidence, for example the relationship between masticatory function and the evolution of jaw shape, nonetheless suggest that mechanobiology plays a major role in skull morphogenesis. To begin to tackle this persistent challenge, cellular, molecular and tissue-level analyses of the developing mouse palate were coupled with finite element modeling to demonstrate that patterns of strain created by mammalian-specific oral behaviors produce complementary patterns of chondrogenic gene expression in an initially homogeneous population of cranial neural crest cells. Neural crest cells change from an osteogenic to a chondrogenic fate, leading to the materialization of cartilaginous growth plate-like structures in the palatal midline. These growth plates contribute to lateral expansion of the head but are transient structures; when the strain patterns associated with suckling dissipate at weaning, the growth plates disappear and the palate ossifies. Thus, mechanical cues such as strain appear to co-regulate cell fate specification and ultimately, help drive large-scale morphogenetic changes in head shape.

Human physiological benefits of viewing nature: EEG responses to exact and statistical fractal patterns.

PubMed

Hagerhall, C M; Laike, T; Küller, M; Marcheschi, E; Boydston, C; Taylor, R P

2015-01-01

Psychological and physiological benefits of viewing nature have been extensively studied for some time. More recently it has been suggested that some of these positive effects can be explained by nature's fractal properties. Virtually all studies on human responses to fractals have used stimuli that represent the specific form of fractal geometry found in nature, i.e. statistical fractals, as opposed to fractal patterns which repeat exactly at different scales. This raises the question of whether human responses like preference and relaxation are being driven by fractal geometry in general or by the specific form of fractal geometry found in nature. In this study we consider both types of fractals (statistical and exact) and morph one type into the other. Based on the Koch curve, nine visual stimuli were produced in which curves of three different fractal dimensions evolve gradually from an exact to a statistical fractal. The patterns were shown for one minute each to thirty-five subjects while qEEG was continuously recorded. The results showed that the responses to statistical and exact fractals differ, and that the natural form of the fractal is important for inducing alpha responses, an indicator of a wakefully relaxed state and internalized attention.

Do we really use rainfall observations consistent with reality in hydrological modelling?

NASA Astrophysics Data System (ADS)

Ciampalini, Rossano; Follain, Stéphane; Raclot, Damien; Crabit, Armand; Pastor, Amandine; Moussa, Roger; Le Bissonnais, Yves

2017-04-01

Spatial and temporal patterns in rainfall control how water reaches soil surface and interacts with soil properties (i.e., soil wetting, infiltration, saturation). Once a hydrological event is defined by a rainfall with its spatiotemporal variability and by some environmental parameters such as soil properties (including land use, topographic and anthropic features), the evidence shows that each parameter variation produces different, specific outputs (e.g., runoff, flooding etc.). In this study, we focus on the effect of rainfall patterns because, due to the difficulty to dispose of detailed data, their influence in modelling is frequently underestimated or neglected. A rainfall event affects a catchment non uniformly, it is spatially localized and its pattern moves in space and time. The way and the time how the water reaches the soil and saturates it respect to the geometry of the catchment deeply influences soil saturation, runoff, and then sediment delivery. This research, approaching a hypothetical, simple case, aims to stimulate the debate on the reliability of the rainfall quality used in hydrological / soil erosion modelling. We test on a small catchment of the south of France (Roujan, Languedoc Roussillon) the influence of rainfall variability with the use of a HD hybrid hydrological - soil erosion model, combining a cinematic wave with the St. Venant equation and a simplified "bucket" conceptual model for ground water, able to quantify the effect of different spatiotemporal patterns of a very-high-definition synthetic rainfall. Results indicate that rainfall spatiotemporal patterns are crucial simulating an erosive event: differences between spatially uniform rainfalls, as frequently adopted in simulations, and some hypothetical rainfall patterns here applied, reveal that the outcome of a simulated event can be highly underestimated.

Serotype-dependent transduction efficiencies of recombinant adeno-associated viral vectors in monkey neocortex

PubMed Central

Gerits, Annelies; Vancraeyenest, Pascaline; Vreysen, Samme; Laramée, Marie-Eve; Michiels, Annelies; Gijsbers, Rik; Van den Haute, Chris; Moons, Lieve; Debyser, Zeger; Baekelandt, Veerle; Arckens, Lutgarde; Vanduffel, Wim

2015-01-01

Abstract. Viral vector-mediated expression of genes (e.g., coding for opsins and designer receptors) has grown increasingly popular. Cell-type specific expression is achieved by altering viral vector tropism through crosspackaging or by cell-specific promoters driving gene expression. Detailed information about transduction properties of most recombinant adeno-associated viral vector (rAAV) serotypes in macaque cortex is gradually becoming available. Here, we compare transduction efficiencies and expression patterns of reporter genes in two macaque neocortical areas employing different rAAV serotypes and promoters. A short version of the calmodulin-kinase-II (CaMKIIα0.4) promoter resulted in reporter gene expression in cortical neurons for all tested rAAVs, albeit with different efficiencies for spread: rAAV2/5>>rAAV2/7>rAAV2/8>rAAV2/9>>rAAV2/1 and proportion of transduced cells: rAAV2/1>rAAV2/5>rAAV2/7=rAAV2/9>rAAV2/8. In contrast to rodent studies, the cytomegalovirus (CMV) promoter appeared least efficient in macaque cortex. The human synapsin-1 promoter preceded by the CMV enhancer (enhSyn1) produced homogeneous reporter gene expression across all layers, while two variants of the CaMKIIα promoter resulted in different laminar transduction patterns and cell specificities. Finally, differences in expression patterns were observed when the same viral vector was injected in two neocortical areas. Our results corroborate previous findings that reporter-gene expression patterns and efficiency of rAAV transduction depend on serotype, promoter, cortical layer, and area. PMID:26839901

[Patterns of action potential firing in cortical neurons of neonatal mice and their electrophysiological property].

PubMed

Furong, Liu; Shengtian, L I

2016-05-25

To investigate patterns of action potential firing in cortical heurons of neonatal mice and their electrophysiological properties. The passive and active membrane properties of cortical neurons from 3-d neonatal mice were observed by whole-cell patch clamp with different voltage and current mode. Three patterns of action potential firing were identified in response to depolarized current injection. The effects of action potential firing patterns on voltage-dependent inward and outward current were found. Neurons with three different firing patterns had different thresholds of depolarized current. In the morphology analysis of action potential, the three type neurons were different in rise time, duration, amplitude and threshold of the first action potential evoked by 80 pA current injection. The passive properties were similar in three patterns of action potential firing. These results indicate that newborn cortical neurons exhibit different patterns of action potential firing with different action potential parameters such as shape and threshold.

Spatial patterns of ecohydrologic properties on a hillslope-alluvial fan transect, central New Mexico

USGS Publications Warehouse

Bedford, D.R.; Small, E.E.

2008-01-01

Spatial patterns of soil properties are linked to patchy vegetation in arid and semi-arid landscapes. The patterns of soil properties are generally assumed to be linked to the ecohydrological functioning of patchy dryland vegetation ecosystems. We studied the effects of vegetation canopy, its spatial pattern, and landforms on soil properties affecting overland flow and infiltration in shrublands at the Sevilleta National Wildlife Refuge/LTER in central New Mexico, USA. We studied the patterns of microtopography and saturated conductivity (Ksat), and generally found it to be affected by vegetation canopy and pattern, as well as landform type. On gently sloping alluvial fans, both microtopography and Ksat are high under vegetation canopy and decay with distance from plant center. On steeper hillslope landforms, only microtopography was significantly higher under vegetation canopy, while there was no significant difference in Ksat between vegetation and interspaces. Using geostatistics, we found that the spatial pattern of soil properties was determined by the spatial pattern of vegetation. Most importantly, the effects of vegetation were present in the unvegetated interspaces 2-4 times the extent of vegetation canopy, on the order of 2-3??m. Our results have implications for the understanding the ecohydrologic function of semi-arid ecosystems as well as the parameterization of hydrologic models. ?? 2007 Elsevier B.V. All rights reserved.

Predictability of spatio-temporal patterns in a lattice of coupled FitzHugh–Nagumo oscillators

PubMed Central

Grace, Miriam; Hütt, Marc-Thorsten

2013-01-01

In many biological systems, variability of the components can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In pioneering work in the late 1990s, it was hypothesized that a drift of cellular parameters (along a ‘developmental path’), together with differences in cell properties (‘desynchronization’ of cells on the developmental path) can establish self-organized spatio-temporal patterns (in their example, spiral waves of cAMP in a colony of Dictyostelium discoideum cells) starting from a homogeneous state. Here, we embed a generic model of an excitable medium, a lattice of diffusively coupled FitzHugh–Nagumo oscillators, into a developmental-path framework. In this minimal model of spiral wave generation, we can now study the predictability of spatio-temporal patterns from cell properties as a function of desynchronization (or ‘spread’) of cells along the developmental path and the drift speed of cell properties on the path. As a function of drift speed and desynchronization, we observe systematically different routes towards fully established patterns, as well as strikingly different correlations between cell properties and pattern features. We show that the predictability of spatio-temporal patterns from cell properties contains important information on the pattern formation process as well as on the underlying dynamical system. PMID:23349439

Towards Formal Implementation of PUS Standard

NASA Astrophysics Data System (ADS)

Ilić, D.

2009-05-01

As an effort to promote the reuse of on-board and ground systems ESA developed a standard for packet telemetry and telecommand - PUS. It defines a set of standard service models with the corresponding structures of the associated telemetry and telecommand packets. Various missions then can choose to implement those standard PUS services that best conform to their specific requirements. In this paper we propose a formal development (based on the Event-B method) of reusable service patterns, which can be instantiated for concrete application. Our formal models allow us to formally express and verify specific service properties including various telecommand and telemetry packet structure validation.

Random scalar fields and hyperuniformity

NASA Astrophysics Data System (ADS)

Ma, Zheng; Torquato, Salvatore

2017-06-01

Disordered many-particle hyperuniform systems are exotic amorphous states of matter that lie between crystals and liquids. Hyperuniform systems have attracted recent attention because they are endowed with novel transport and optical properties. Recently, the hyperuniformity concept has been generalized to characterize two-phase media, scalar fields, and random vector fields. In this paper, we devise methods to explicitly construct hyperuniform scalar fields. Specifically, we analyze spatial patterns generated from Gaussian random fields, which have been used to model the microwave background radiation and heterogeneous materials, the Cahn-Hilliard equation for spinodal decomposition, and Swift-Hohenberg equations that have been used to model emergent pattern formation, including Rayleigh-Bénard convection. We show that the Gaussian random scalar fields can be constructed to be hyperuniform. We also numerically study the time evolution of spinodal decomposition patterns and demonstrate that they are hyperuniform in the scaling regime. Moreover, we find that labyrinth-like patterns generated by the Swift-Hohenberg equation are effectively hyperuniform. We show that thresholding (level-cutting) a hyperuniform Gaussian random field to produce a two-phase random medium tends to destroy the hyperuniformity of the progenitor scalar field. We then propose guidelines to achieve effectively hyperuniform two-phase media derived from thresholded non-Gaussian fields. Our investigation paves the way for new research directions to characterize the large-structure spatial patterns that arise in physics, chemistry, biology, and ecology. Moreover, our theoretical results are expected to guide experimentalists to synthesize new classes of hyperuniform materials with novel physical properties via coarsening processes and using state-of-the-art techniques, such as stereolithography and 3D printing.

Neural mechanism of optimal limb coordination in crustacean swimming

PubMed Central

Zhang, Calvin; Guy, Robert D.; Mulloney, Brian; Zhang, Qinghai; Lewis, Timothy J.

2014-01-01

A fundamental challenge in neuroscience is to understand how biologically salient motor behaviors emerge from properties of the underlying neural circuits. Crayfish, krill, prawns, lobsters, and other long-tailed crustaceans swim by rhythmically moving limbs called swimmerets. Over the entire biological range of animal size and paddling frequency, movements of adjacent swimmerets maintain an approximate quarter-period phase difference with the more posterior limbs leading the cycle. We use a computational fluid dynamics model to show that this frequency-invariant stroke pattern is the most effective and mechanically efficient paddling rhythm across the full range of biologically relevant Reynolds numbers in crustacean swimming. We then show that the organization of the neural circuit underlying swimmeret coordination provides a robust mechanism for generating this stroke pattern. Specifically, the wave-like limb coordination emerges robustly from a combination of the half-center structure of the local central pattern generating circuits (CPGs) that drive the movements of each limb, the asymmetric network topology of the connections between local CPGs, and the phase response properties of the local CPGs, which we measure experimentally. Thus, the crustacean swimmeret system serves as a concrete example in which the architecture of a neural circuit leads to optimal behavior in a robust manner. Furthermore, we consider all possible connection topologies between local CPGs and show that the natural connectivity pattern generates the biomechanically optimal stroke pattern most robustly. Given the high metabolic cost of crustacean swimming, our results suggest that natural selection has pushed the swimmeret neural circuit toward a connection topology that produces optimal behavior. PMID:25201976

Adult root structure of Mediterranean shrubs: relationship with post-fire regenerative syndrome.

PubMed

Saura-Mas, S; Lloret, F

2014-01-01

Life-history attributes can impose differences on root system structures and properties related to nutrient and water uptake. Here, we assess whether plants with different post-fire regenerative strategies (resprouters, seeders and seeder-resprouters) differ in the topological and morphological properties of their root systems (external path, altitude, magnitude, topological index, specific root length, root length, root-to-shoot biomass ratio, length of the main axis of the root system and link length). To achieve these objectives, we sampled individuals from eight woody species in a shrubland located in the western Mediterranean Basin. We sampled the adult root systems using manual field excavation with the aid of an air compressor. The results indicate that resprouters have a higher root-to-shoot ratio, confirming their higher ability to store water, starch and nutrients and to invest in the belowground biomass. Moreover, this pattern would allow them to explore deeper parts of the soil layers. Seeder species would benefit from a higher specific root length, pointing to increased relative root growth and water uptake rates. This study confirms that seeders and resprouters may differ in nutrient and water uptake ability according to the characteristics of their root system. Species that can both resprout and establish seedlings after fire had different patterns of root system structure; in particular, root:shoot ratio was more similar to resprouters and specific root length was closer to seeders, supporting the distinct functional performance of this type of species. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

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.

Preliminary analysis of cold stress responsive proteins in Mesocestoides corti larvae.

PubMed

Canclini, Lucía; Esteves, Adriana

2007-07-01

Many parasites undergo sudden changes in environmental conditions at some stage during their life cycle. The molecular response to this variation is characterised by a rapid transcriptional activation of a specific set of genes coding for proteins generically known as stress proteins. They appear to be also involved in various biological processes including cell proliferation and differentiation. The platyhelminth parasite, Mesocestoides corti (Cestoda) presents important properties as a model organism. Under stress conditions, key molecules involved in metabolic pathways as well as in the growth and differentiation of the parasite can be identified. 2D protein expression profile of tetrathyridia of M. corti, submitted to nutritional starvation and cold stress is described, as well as the recovery pattern. A set of specifically expressed proteins was observed in each experimental condition. Quantitative and qualitative differences and stress recovery pattern are also reported. This work makes evident the high plasticity and resistance to extreme environmental conditions of these parasites at the molecular level.

Patterns and determinants of wood physical and mechanical properties across major tree species in China.

PubMed

Zhu, JiangLing; Shi, Yue; Fang, LeQi; Liu, XingE; Ji, ChengJun

2015-06-01

The physical and mechanical properties of wood affect the growth and development of trees, and also act as the main criteria when determining wood usage. Our understanding on patterns and controls of wood physical and mechanical properties could provide benefits for forestry management and bases for wood application and forest tree breeding. However, current studies on wood properties mainly focus on wood density and ignore other wood physical properties. In this study, we established a comprehensive database of wood physical properties across major tree species in China. Based on this database, we explored spatial patterns and driving factors of wood properties across major tree species in China. Our results showed that (i) compared with wood density, air-dried density, tangential shrinkage coefficient and resilience provide more accuracy and higher explanation power when used as the evaluation index of wood physical properties. (ii) Among life form, climatic and edaphic variables, life form is the dominant factor shaping spatial patterns of wood physical properties, climatic factors the next, and edaphic factors have the least effects, suggesting that the effects of climatic factors on spatial variations of wood properties are indirectly induced by their effects on species distribution.

Distributed encoding of spatial and object categories in primate hippocampal microcircuits

PubMed Central

Opris, Ioan; Santos, Lucas M.; Gerhardt, Greg A.; Song, Dong; Berger, Theodore W.; Hampson, Robert E.; Deadwyler, Sam A.

2015-01-01

The primate hippocampus plays critical roles in the encoding, representation, categorization and retrieval of cognitive information. Such cognitive abilities may use the transformational input-output properties of hippocampal laminar microcircuitry to generate spatial representations and to categorize features of objects, images, and their numeric characteristics. Four nonhuman primates were trained in a delayed-match-to-sample (DMS) task while multi-neuron activity was simultaneously recorded from the CA1 and CA3 hippocampal cell fields. The results show differential encoding of spatial location and categorization of images presented as relevant stimuli in the task. Individual hippocampal cells encoded visual stimuli only on specific types of trials in which retention of either, the Sample image, or the spatial position of the Sample image indicated at the beginning of the trial, was required. Consistent with such encoding, it was shown that patterned microstimulation applied during Sample image presentation facilitated selection of either Sample image spatial locations or types of images, during the Match phase of the task. These findings support the existence of specific codes for spatial and numeric object representations in primate hippocampus which can be applied on differentially signaled trials. Moreover, the transformational properties of hippocampal microcircuitry, together with the patterned microstimulation are supporting the practical importance of this approach for cognitive enhancement and rehabilitation, needed for memory neuroprosthetics. PMID:26500473

Functionalization of biomineral reinforcement in crustacean cuticle: Calcite orientation in the partes incisivae of the mandibles of Porcellio scaber and the supralittoral species Tylos europaeus (Oniscidea, Isopoda).

PubMed

Huber, Julia; Griesshaber, Erika; Nindiyasari, Fitriana; Schmahl, Wolfgang W; Ziegler, Andreas

2015-05-01

In arthropods the cuticle forms an exoskeleton with its physical and chemical properties adapted to functions of distinct skeletal elements. The cuticle of the partes incisivae (PI) in mandibles of terrestrial isopods is a composite of chitin-protein fibrils/fibres and minerals. It consists of an unmineralized tip, a middle region with organic fibrils reinforced mainly with amorphous calcium phosphate and a base region mineralized with amorphous calcium carbonate and calcite. In this study we extend our work on the structure and material properties of the incisive cuticle employing electron backscatter diffraction (EBSD), and investigate calcite orientation patterns in the PI of two terrestrial isopod species from different habitats. We trace small-scale differences in texture sharpness and calcite microstructure, and compare calcite organization and orientation patterns in the PI with those in the tergites of the same isopod species. We observe that in the PI calcite orientation, the degree of crystal alignment, and mode of crystalline domain assemblage is highly varied within short length scales. This contrasts to calcite organization in the tergite cuticle, where calcite has only one specific texture pattern. Such a large range in the variation of calcite organization has not been observed in other carbonate biological hard tissues, such as shells and teeth, where one specific texture and microstructure prevails. Thus, the investigated isopod species are able to control crystallization of the amorphous carbonate precursor in a differential way, most probably related to the function of the individual skeletal element and the animals' behavior. Copyright © 2015 Elsevier Inc. All rights reserved.

Patterning of alloy precipitation through external pressure

NASA Astrophysics Data System (ADS)

Franklin, Jack A.

Due to the nature of their microstructure, alloyed components have the benefit of meeting specific design goals across a wide range of electrical, thermal, and mechanical properties. In general by selecting the correct alloy system and applying a proper heat treatment it is possible to create a metallic sample whose properties achieve a unique set of design requirements. This dissertation presents an innovative processing technique intended to control both the location of formation and the growth rates of precipitates within metallic alloys in order to create multiple patterned areas of unique microstructure within a single sample. Specific experimental results for the Al-Cu alloy system will be shown. The control over precipitation is achieved by altering the conventional heat treatment process with an external surface load applied to selected locations during the quench and anneal. It is shown that the applied pressures affect both the rate and directionality of the atomic diffusion in regions close to the loaded surfaces. The control over growth rates is achieved by altering the enthalpic energy required for successful diffusion between lattice sites. Changes in the local chemical free energy required to direct the diffusion of atoms are established by introducing a non-uniform elastic strain energy field within the samples created by the patterned surface pressures. Either diffusion rates or atomic mobility can be selected as the dominating control process by varying the quench rate; with slower quenches having greater control over the mobility of the alloying elements. Results have shown control of Al2Cu precipitation over 100 microns on mechanically polished surfaces. Further experimental considerations presented will address consistency across sample ensembles. This includes repeatable pressure loading conditions and the chemical interaction between any furnace environments and both the alloy sample and metallic pressure loading devices.

A miniaturized multipurpose platform for rapid, label-free, and simultaneous separation, patterning, and in vitro culture of primary and rare cells.

PubMed

Didar, Tohid Fatanat; Bowey, Kristen; Almazan, Guillermina; Tabrizian, Maryam

2014-02-01

Given that current cell isolation techniques are expensive, time consuming, yield low isolation purities, and/or alter target cell properties, a versatile, cost effective, and easy-to-operate microchip with the capability to simultaneously separate, capture, pattern, and culture rare and primary cells in vitro is developed. The platform is based on target cell adhesion onto the micro-fabricated interfaces produced by microcontact printing of cell-specific antibodies. Results show over 95% separation efficiency in less than 10 min for the separation of oligodendrocyte progenitor cells (OPCs) and cardiomyocytes from rat brain and heart mixtures, respectively. Target cell attachment and single cell spreading can be precisely controlled on the basis of the designed patterns. Both cell types can maintain their biofunctionality. Indeed, isolated OPCs can proliferate and differentiate into mature oligodendrocytes, while isolated cardiomyocytes retain their contractile properties on the separation platform. Successful separation of two dissimilar cell types present in varying concentrations in their respective cell mixtures and the demonstration of their integrity after separation open new avenues for time and cost-effective sorting of various cell types using the developed miniaturized platform. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Looking away from faces: influence of high-level visual processes on saccade programming.

PubMed

Morand, Stéphanie M; Grosbras, Marie-Hélène; Caldara, Roberto; Harvey, Monika

2010-03-30

Human faces capture attention more than other visual stimuli. Here we investigated whether such face-specific biases rely on automatic (involuntary) or voluntary orienting responses. To this end, we used an anti-saccade paradigm, which requires the ability to inhibit a reflexive automatic response and to generate a voluntary saccade in the opposite direction of the stimulus. To control for potential low-level confounds in the eye-movement data, we manipulated the high-level visual properties of the stimuli while normalizing their global low-level visual properties. Eye movements were recorded in 21 participants who performed either pro- or anti-saccades to a face, car, or noise pattern, randomly presented to the left or right of a fixation point. For each trial, a symbolic cue instructed the observer to generate either a pro-saccade or an anti-saccade. We report a significant increase in anti-saccade error rates for faces compared to cars and noise patterns, as well as faster pro-saccades to faces and cars in comparison to noise patterns. These results indicate that human faces induce stronger involuntary orienting responses than other visual objects, i.e., responses that are beyond the control of the observer. Importantly, this involuntary processing cannot be accounted for by global low-level visual factors.

Dielectric screening of early differentiation patterns in mesenchymal stem cells induced by steroid hormones.

PubMed

Ron, Amit; Shur, Irena; Daniel, Ramiz; Singh, Ragini Raj; Fishelson, Nick; Croitoru, Nathan; Benayahu, Dafna; Shacham-Diamand, Yosi

2010-06-01

In the framework of this study, target identification and localization of differentiation patterns by means of dielectric spectroscopy is presented. Here, a primary pre-osteoblastic bone marrow-derived MBA-15 cellular system was used to study the variations in the dielectric properties of mesenchymal stem cells while exposed to differentiation regulators. Using the fundamentals of mixed dielectric theories combined with finite numerical tools, the permittivity spectra of MBA-15 cell suspensions have been uniquely analyzed after being activated by steroid hormones to express osteogenic phenotypes. Following the spectral analysis, significant variations were revealed in the dielectric properties of the activated cells in comparison to the untreated populations. Based on the differentiation patterns of MBA-15, the electrical modifications were found to be highly correlated with the activation of specific cellular mechanisms which directly react to the hormonal inductions. In addition, by describing the dielectric dispersion in terms of transfer functions, it is shown that the spectral perturbations are well adapted to variations in the electrical characteristics of the cells. The reported findings vastly emphasize the tight correlation between the cellular and electrical state of the differentiated cells. It therefore emphasizes the vast abilities of impedance-based techniques as potential screening tools for stem cell analysis. Copyright 2009 Elsevier B.V. All rights reserved.

Fractal features of soil particle size distribution under different land-use patterns in the alluvial fans of collapsing gullies in the hilly granitic region of southern China

PubMed Central

Deng, Yusong; Cai, Chongfa; Xia, Dong; Ding, Shuwen; Chen, Jiazhou

2017-01-01

Collapsing gullies are among the most severe soil erosion problems in the tropical and subtropical areas of southern China. However, few studies have examined the relationship of soil particle size distribution (PSD) changes with land-use patterns in the alluvial fans of collapsing gullies. Recently, the fractal method has been applied to estimate soil structure and has proven to be an effective tool in analyzing soil properties and their relationships with other eco-environmental factors. In this study, the soil fractal dimension (D), physico-chemical properties and their relationship with different land-use patterns in alluvial fans were investigated in an experiment that involved seven collapsing gully areas in seven counties of southern China. Our results demonstrated that different land-use patterns of alluvial fans had a significant effect on soil physico-chemical properties. Compared to grasslands and woodlands, farmlands and orchards generally contained more fine soil particles (silt and clay) and fewer coarse particles, whereas significant differences were found in the fractal dimension of soil PSD in different land-use patterns. Specifically, the soil fractal dimension was lower in grasslands and higher in orchards relative to that of other land-use patterns. The average soil fractal dimension of grasslands had a value that was 0.08 lower than that of orchards. Bulk density was lower but porosity was higher in farmlands and orchards. Saturated moisture content was lower in woodlands and grasslands, but saturated hydraulic conductivity was higher in all four land-use patterns. Additionally, the fractal dimension had significant linear relationships with the silt, clay and sand contents and soil properties and exhibited a positive correlation with the clay (R2 = 0.976, P<0.001), silt (R2 = 0.578, P<0.01), organic carbon (R2 = 0.777, P<0.001) and saturated water (R2 = 0.639, P<0.01) contents but a negative correlation with gravel content (R2 = 0.494, P<0.01), coarse sand content (R2 = 0.623, P<0.01) and saturated hydraulic conductivity (R2 = 0.788, P<0.001). However, the fractal dimension exhibited no significant correlation with pH, bulk density or total porosity. Furthermore, the second-degree polynomial equation was found to be more adequate for describing the correlations between soil fractal dimension and particle size distribution. The results of this study demonstrate that a fractal dimension analysis of soil particle size distribution is a useful method for the quantitative description of different land-use patterns in the alluvial fans of collapsing gullies in southern China. PMID:28301524

JPL Electronic Nose: From Sniffing Brain Cancer to Trouble in Space

NASA Technical Reports Server (NTRS)

Homer, Margie L.

2011-01-01

What Is An Electronic Nose? An array of non-specific chemical sensors, controlled and analyzed electronically, which mimics the action of the mammalian nose by recognizing patterns of response. An Enose: (1.) ENose measures background resistance in each sensor and establishes a baseline. (2.) Contaminant comes in contact with sensors on the sensing head. (3.) The sensing films, change physical properties, such as thickness or color, as air composition changes. (4.) Sensor response is recorded by a computer, the change in resistance is computed, and the distributed response pattern of the sensor array is used to identify gases and mixtures of gases. (5. Responses of the sensor array are analyzed and quantified using software developed for the task.

Characterisation of Ductile Prepregs

NASA Astrophysics Data System (ADS)

Pinto, F.; White, A.; Meo, M.

2013-04-01

This study is focused on the analysis of micro-perforated prepregs created from standard, off the shelf prepregs modified by a particular laser process to enhance ductility of prepregs for better formability and drapability. Fibres are shortened through the use of laser cutting in a predetermined pattern intended to maintain alignment, and therefore mechanical properties, yet increase ductility at the working temperature. The increase in ductility allows the product to be more effectively optimised for specific forming techniques. Tensile tests were conducted on several specimens in order to understand the ductility enhancement offered by this process with different micro-perforation patterns over standard prepregs. Furthermore, the effects of forming temperature was also analysed to assess the applicability of this material to hot draping techniques and other heated processes.

The neurogenetic frontier--lessons from misbehaving zebrafish.

PubMed

Burgess, Harold A; Granato, Michael

2008-11-01

One of the central questions in neuroscience is how refined patterns of connectivity in the brain generate and monitor behavior. Genetic mutations can influence neural circuits by disrupting differentiation or maintenance of component neuronal cells or by altering functional patterns of nervous system connectivity. Mutagenesis screens therefore have the potential to reveal not only the molecular underpinnings of brain development and function, but to illuminate the cellular basis of behavior. Practical considerations make the zebrafish an organism of choice for undertaking forward genetic analysis of behavior. The powerful array of experimental tools at the disposal of the zebrafish researcher makes it possible to link molecular function to neuronal properties that underlie behavior. This review focuses on specific challenges to isolating and analyzing behavioral mutants in zebrafish.

The neurogenetic frontier—lessons from misbehaving zebrafish

PubMed Central

Granato, Michael

2008-01-01

One of the central questions in neuroscience is how refined patterns of connectivity in the brain generate and monitor behavior. Genetic mutations can influence neural circuits by disrupting differentiation or maintenance of component neuronal cells or by altering functional patterns of nervous system connectivity. Mutagenesis screens therefore have the potential to reveal not only the molecular underpinnings of brain development and function, but to illuminate the cellular basis of behavior. Practical considerations make the zebrafish an organism of choice for undertaking forward genetic analysis of behavior. The powerful array of experimental tools at the disposal of the zebrafish researcher makes it possible to link molecular function to neuronal properties that underlie behavior. This review focuses on specific challenges to isolating and analyzing behavioral mutants in zebrafish. PMID:18836206

Enzymatic production of defined chitosan oligomers with a specific pattern of acetylation using a combination of chitin oligosaccharide deacetylases

NASA Astrophysics Data System (ADS)

Hamer, Stefanie Nicole; Cord-Landwehr, Stefan; Biarnés, Xevi; Planas, Antoni; Waegeman, Hendrik; Moerschbacher, Bruno Maria; Kolkenbrock, Stephan

2015-03-01

Chitin and chitosan oligomers have diverse biological activities with potentially valuable applications in fields like medicine, cosmetics, or agriculture. These properties may depend not only on the degrees of polymerization and acetylation, but also on a specific pattern of acetylation (PA) that cannot be controlled when the oligomers are produced by chemical hydrolysis. To determine the influence of the PA on the biological activities, defined chitosan oligomers in sufficient amounts are needed. Chitosan oligomers with specific PA can be produced by enzymatic deacetylation of chitin oligomers, but the diversity is limited by the low number of chitin deacetylases available. We have produced specific chitosan oligomers which are deacetylated at the first two units starting from the non-reducing end by the combined use of two different chitin deacetylases, namely NodB from Rhizobium sp. GRH2 that deacetylates the first unit and COD from Vibrio cholerae that deacetylates the second unit starting from the non-reducing end. Both chitin deacetylases accept the product of each other resulting in production of chitosan oligomers with a novel and defined PA. When extended to further chitin deacetylases, this approach has the potential to yield a large range of novel chitosan oligomers with a fully defined architecture.

Arabic morphology in the neural language system.

PubMed

Boudelaa, Sami; Pulvermüller, Friedemann; Hauk, Olaf; Shtyrov, Yury; Marslen-Wilson, William

2010-05-01

There are two views about morphology, the aspect of language concerned with the internal structure of words. One view holds that morphology is a domain of knowledge with a specific type of neurocognitive representation supported by specific brain mechanisms lateralized to left fronto-temporal cortex. The alternate view characterizes morphological effects as being a by-product of the correlation between form and meaning and where no brain area is predicted to subserve morphological processing per se. Here we provided evidence from Arabic that morphemes do have specific memory traces, which differ as a function of their functional properties. In an MMN study, we showed that the abstract consonantal root, which conveys semantic meaning (similarly to monomorphemic content words in English), elicits an MMN starting from 160 msec after the deviation point, whereas the abstract vocalic word pattern, which plays a range of grammatical roles, elicits an MMN response starting from 250 msec after the deviation point. Topographically, the root MMN has a symmetric fronto-central distribution, whereas the word pattern MMN lateralizes significantly to the left, indicating stronger involvement of left peri-sylvian areas. In languages with rich morphologies, morphemic processing seems to be supported by distinct neural networks, thereby providing evidence for a specific neuronal basis for morphology as part of the cerebral language machinery.

Spatial and seasonal patterns in stream water contamination across mountainous watersheds: Linkage with landscape characteristics

NASA Astrophysics Data System (ADS)

Ai, L.; Shi, Z. H.; Yin, W.; Huang, X.

2015-04-01

Landscape characteristics are widely accepted as strongly influencing stream water quality in heterogeneous watersheds. Understanding the relationships between landscape and specific water contaminant can greatly improve the predictability of potential contamination and the assessment of contaminant export. In this work, we examined the combined effects of watershed complexity, in terms of land use and physiography, on specific water contaminant across watersheds close to the Danjiangkou Reservoir. The land use composition, land use pattern, morphometric variables and soil properties were calculated at the watershed scale and considered potential factors of influence. Due to high co-dependence of these watershed characteristics, partial least squares regression was used to elucidate the linkages between some specific water contaminants and the 16 selected watershed characteristic variables. Water contaminant maps revealed spatial and seasonal heterogeneity. The dissolved oxygen values in the dry season were higher than those in the wet season, whereas the other contaminant concentrations displayed the opposite trend. The studied watersheds which are influenced strongly by urbanization, showed higher levels of ammonia nitrogen, total phosphorus, potassium permanganate index and petroleum, and lower levels of dissolved oxygen. The urban land use, largest patch index and the hypsometric integral were the dominant factors affecting specific water contaminant.

A review of visual perception mechanisms that regulate rapid adaptive camouflage in cuttlefish.

PubMed

Chiao, Chuan-Chin; Chubb, Charles; Hanlon, Roger T

2015-09-01

We review recent research on the visual mechanisms of rapid adaptive camouflage in cuttlefish. These neurophysiologically complex marine invertebrates can camouflage themselves against almost any background, yet their ability to quickly (0.5-2 s) alter their body patterns on different visual backgrounds poses a vexing challenge: how to pick the correct body pattern amongst their repertoire. The ability of cuttlefish to change appropriately requires a visual system that can rapidly assess complex visual scenes and produce the motor responses-the neurally controlled body patterns-that achieve camouflage. Using specifically designed visual backgrounds and assessing the corresponding body patterns quantitatively, we and others have uncovered several aspects of scene variation that are important in regulating cuttlefish patterning responses. These include spatial scale of background pattern, background intensity, background contrast, object edge properties, object contrast polarity, object depth, and the presence of 3D objects. Moreover, arm postures and skin papillae are also regulated visually for additional aspects of concealment. By integrating these visual cues, cuttlefish are able to rapidly select appropriate body patterns for concealment throughout diverse natural environments. This sensorimotor approach of studying cuttlefish camouflage thus provides unique insights into the mechanisms of visual perception in an invertebrate image-forming eye.

Uncovering a Dynamic Feature of the Transcriptional Regulatory Network for Anterior-Posterior Patterning in the Drosophila Embryo

PubMed Central

Liu, Junbo; Ma, Jun

2013-01-01

Anterior-posterior (AP) patterning in the Drosophila embryo is dependent on the Bicoid (Bcd) morphogen gradient. However, most target genes of Bcd also require additional inputs to establish their expression domains, reflective of the operation of a cross-regulatory network and contributions of other maternal signals. This is in contrast to hunchback (hb), which has an anterior expression domain driven by an enhancer that appears to respond primarily to the Bcd input. To gain a better understanding of the regulatory logic of the AP patterning network, we perform quantitative studies that specifically investigate the dynamics of hb transcription during development. We show that Bcd-dependent hb transcription, monitored by the intron-containing nascent transcripts near the P2 promoter, is turned off quickly–on the order of a few minutes–upon entering the interphase of nuclear cycle 14A. This shutdown contrasts with earlier cycles during which active hb transcription can persist until the moment when the nucleus enters mitosis. The shutdown takes place at a time when the nuclear Bcd gradient profile in the embryo remains largely intact, suggesting that this is a process likely subject to control of a currently unknown regulatory mechanism. We suggest that this dynamic feature offers a window of opportunity for hb to faithfully interpret, and directly benefit from, Bcd gradient properties, including its scaling properties, to help craft a robust AP patterning outcome. PMID:23646132

A new climate dataset for systematic assessments of climate change impacts as a function of global warming

NASA Astrophysics Data System (ADS)

Heinke, J.; Ostberg, S.; Schaphoff, S.; Frieler, K.; Müller, C.; Gerten, D.; Meinshausen, M.; Lucht, W.

2013-10-01

In the ongoing political debate on climate change, global mean temperature change (ΔTglob) has become the yardstick by which mitigation costs, impacts from unavoided climate change, and adaptation requirements are discussed. For a scientifically informed discourse along these lines, systematic assessments of climate change impacts as a function of ΔTglob are required. The current availability of climate change scenarios constrains this type of assessment to a narrow range of temperature change and/or a reduced ensemble of climate models. Here, a newly composed dataset of climate change scenarios is presented that addresses the specific requirements for global assessments of climate change impacts as a function of ΔTglob. A pattern-scaling approach is applied to extract generalised patterns of spatially explicit change in temperature, precipitation and cloudiness from 19 Atmosphere-Ocean General Circulation Models (AOGCMs). The patterns are combined with scenarios of global mean temperature increase obtained from the reduced-complexity climate model MAGICC6 to create climate scenarios covering warming levels from 1.5 to 5 degrees above pre-industrial levels around the year 2100. The patterns are shown to sufficiently maintain the original AOGCMs' climate change properties, even though they, necessarily, utilise a simplified relationships between ΔTglob and changes in local climate properties. The dataset (made available online upon final publication of this paper) facilitates systematic analyses of climate change impacts as it covers a wider and finer-spaced range of climate change scenarios than the original AOGCM simulations.

A new dataset for systematic assessments of climate change impacts as a function of global warming

NASA Astrophysics Data System (ADS)

Heinke, J.; Ostberg, S.; Schaphoff, S.; Frieler, K.; M{ü}ller, C.; Gerten, D.; Meinshausen, M.; Lucht, W.

2012-11-01

In the ongoing political debate on climate change, global mean temperature change (ΔTglob) has become the yardstick by which mitigation costs, impacts from unavoided climate change, and adaptation requirements are discussed. For a scientifically informed discourse along these lines systematic assessments of climate change impacts as a function of ΔTglob are required. The current availability of climate change scenarios constrains this type of assessment to a~narrow range of temperature change and/or a reduced ensemble of climate models. Here, a newly composed dataset of climate change scenarios is presented that addresses the specific requirements for global assessments of climate change impacts as a function of ΔTglob. A pattern-scaling approach is applied to extract generalized patterns of spatially explicit change in temperature, precipitation and cloudiness from 19 AOGCMs. The patterns are combined with scenarios of global mean temperature increase obtained from the reduced-complexity climate model MAGICC6 to create climate scenarios covering warming levels from 1.5 to 5 degrees above pre-industrial levels around the year 2100. The patterns are shown to sufficiently maintain the original AOGCMs' climate change properties, even though they, necessarily, utilize a simplified relationships betweenΔTglob and changes in local climate properties. The dataset (made available online upon final publication of this paper) facilitates systematic analyses of climate change impacts as it covers a wider and finer-spaced range of climate change scenarios than the original AOGCM simulations.

Sphingolipid hydroxylation in mammals, yeast and plants - An integrated view.

PubMed

Marquês, Joaquim Trigo; Susana Marinho, H; de Almeida, Rodrigo Freire Martins

2018-05-07

This review is focused on sphingolipid backbone hydroxylation, a small but widespread structural feature, with profound impact on membrane biophysical properties. We start by summarizing sphingolipid metabolism in mammalian cells, yeast and plants, focusing on how distinct hydroxylation patterns emerge in different eukaryotic kingdoms. Then, a comparison of the biophysical properties in membrane model systems and cellular membranes from diverse organisms is made. From an integrative perspective, these results can be rationalized considering that superficial hydroxyl groups in the backbone of sphingolipids (by intervening in the H-bond network) alter the balance of favorable interactions between membrane lipids. They may strengthen the bonding or compete with other hydroxyl groups, in particular the one of membrane sterols. Different sphingolipid hydroxylation patterns can stabilize/disrupt specific membrane domains or change whole plasma membrane properties, and therefore be important in the control of protein distribution, function and lateral diffusion and in the formation and overtime stability of signaling platforms. The recent examples explored throughout this review unveil a potentially key role for sphingolipid backbone hydroxylation in both physiological and pathological situations, as they can be of extreme importance for the proper organization of cell membranes in mammalian cells, yeast and, most likely, also in plants. Copyright © 2017. Published by Elsevier Ltd.

Memory. Engram cells retain memory under retrograde amnesia.

PubMed

Ryan, Tomás J; Roy, Dheeraj S; Pignatelli, Michele; Arons, Autumn; Tonegawa, Susumu

2015-05-29

Memory consolidation is the process by which a newly formed and unstable memory transforms into a stable long-term memory. It is unknown whether the process of memory consolidation occurs exclusively through the stabilization of memory engrams. By using learning-dependent cell labeling, we identified an increase of synaptic strength and dendritic spine density specifically in consolidated memory engram cells. Although these properties are lacking in engram cells under protein synthesis inhibitor-induced amnesia, direct optogenetic activation of these cells results in memory retrieval, and this correlates with retained engram cell-specific connectivity. We propose that a specific pattern of connectivity of engram cells may be crucial for memory information storage and that strengthened synapses in these cells critically contribute to the memory retrieval process. Copyright © 2015, American Association for the Advancement of Science.

Engram Cells Retain Memory Under Retrograde Amnesia

PubMed Central

Ryan, Tomás J.; Roy, Dheeraj S.; Pignatelli, Michele; Arons, Autumn; Tonegawa, Susumu

2017-01-01

Memory consolidation is the process by which a newly formed and unstable memory transforms into a stable long-term memory. It is unknown whether the process of memory consolidation occurs exclusively by the stabilization of memory engrams. By employing learning-dependent cell labeling, we identified an increase of synaptic strength and dendritic spine density specifically in consolidated memory engram cells. While these properties are lacking in the engram cells under protein synthesis inhibitor-induced amnesia, direct optogenetic activation of these cells results in memory retrieval, and this correlates with the retained engram cell-specific connectivity. We propose that a specific pattern of connectivity of engram cells may be crucial for memory information storage and that strengthened synapses in these cells critically contribute to the memory retrieval process. PMID:26023136

Objective assessment of chromatic and achromatic pattern adaptation reveals the temporal response properties of different visual pathways.

PubMed

Robson, Anthony G; Kulikowski, Janus J

2012-11-01

The aim was to investigate the temporal response properties of magnocellular, parvocellular, and koniocellular visual pathways using increment/decrement changes in contrast to elicit visual evoked potentials (VEPs). Static achromatic and isoluminant chromatic gratings were generated on a monitor. Chromatic gratings were modulated along red/green (R/G) or subject-specific tritanopic confusion axes, established using a minimum distinct border criterion. Isoluminance was determined using minimum flicker photometry. Achromatic and chromatic VEPs were recorded to contrast increments and decrements of 0.1 or 0.2 superimposed on the static gratings (masking contrast 0-0.6). Achromatic increment/decrement changes in contrast evoked a percept of apparent motion when the spatial frequency was low; VEPs to such stimuli were positive in polarity and largely unaffected by high levels of static contrast, consistent with transient response mechanisms. VEPs to finer achromatic gratings showed marked attenuation as static contrast was increased. Chromatic VEPs to R/G or tritan chromatic contrast increments were of negative polarity and showed progressive attenuation as static contrast was increased, in keeping with increasing desensitization of the sustained responses of the color-opponent visual pathways. Chromatic contrast decrement VEPs were of positive polarity and less sensitive to pattern adaptation. The relative contribution of sustained/transient mechanisms to achromatic processing is spatial frequency dependent. Chromatic contrast increment VEPs reflect the sustained temporal response properties of parvocellular and koniocellular pathways. Cortical VEPs can provide an objective measure of pattern adaptation and can be used to probe the temporal response characteristics of different visual pathways.

Eu3+-doped Gd2O3 nanoparticles as reporters for optical detection and visualization of antibodies patterned by microcontact printing.

PubMed

Nichkova, Mikaela; Dosev, Dosi; Perron, Richard; Gee, Shirley J; Hammock, Bruce D; Kennedy, Ian M

2006-02-01

Lanthanide oxide nanoparticles are promising luminescent probes in bioanalysis, because of their unique spectral properties, photostability, and low-cost synthesis. We report for the first time the application of europium-doped gadolinium oxide (Eu:Gd2O3) nanoparticles to the optical imaging of antibody micropatterns. The nanoparticles were synthesized by spray pyrolysis and coated with antibody (IgG) molecules by physical adsorption. Our experiments showed that the Eu:Gd2O3 is a good biocompatible solid support for antibody immobilization. The antibodies (anti-rabbit IgG) immobilized on the nanoparticles had excellent biological activity in the specific recognition reaction with rabbit IgG patterned in line strips (10 micromx10 microm) on a glass substrate by use of a micro-contact printing technique. The specific immunoreaction was confirmed by two independent microscopic techniques-fluorescence and scanning electron microscopy (SEM). Both microscopic images revealed that the nanoparticles were organized into designated structures as defined by the microcontact printing process with negligible non-specific binding. The nanoparticles can be used as fluorescent markers in a variety of immunosensing applications in a microscale format.

A Resource for Discovering Specific and Universal Biomarkers for Distributed Stem Cells

PubMed Central

Noh, Minsoo; Smith, Janet L.; Huh, Yang Hoon; Sherley, James L.

2011-01-01

Specific and universal biomarkers for distributed stem cells (DSCs) have been elusive. A major barrier to discovery of such ideal DSC biomarkers is difficulty in obtaining DSCs in sufficient quantity and purity. To solve this problem, we used cell lines genetically engineered for conditional asymmetric self-renewal, the defining DSC property. In gene microarray analyses, we identified 85 genes whose expression is tightly asymmetric self-renewal associated (ASRA). The ASRA gene signature prescribed DSCs to undergo asymmetric self-renewal to a greater extent than committed progenitor cells, embryonic stem cells, or induced pluripotent stem cells. This delineation has several significant implications. These include: 1) providing experimental evidence that DSCs in vivo undergo asymmetric self-renewal as individual cells; 2) providing an explanation why earlier attempts to define a common gene expression signature for DSCs were unsuccessful; and 3) predicting that some ASRA proteins may be ideal biomarkers for DSCs. Indeed, two ASRA proteins, CXCR6 and BTG2, and two other related self-renewal pattern associated (SRPA) proteins identified in this gene resource, LGR5 and H2A.Z, display unique asymmetric patterns of expression that have a high potential for universal and specific DSC identification. PMID:21818293

The effect of antiphase boundaries on the elastic properties of Ni-Mn-Ga austenite and premartensite

NASA Astrophysics Data System (ADS)

Seiner, Hanuš; Sedlák, Petr; Bodnárová, Lucie; Drahokoupil, Jan; Kopecký, Vít; Kopeček, Jaromír; Landa, Michal; Heczko, Oleg

2013-10-01

The evolution of elastic properties with temperature and magnetic field was studied in two differently heat-treated single crystals of the Ni-Mn-Ga magnetic shape memory alloy using resonant ultrasound spectroscopy. Quenching and slow furnace cooling were used to obtain different densities of antiphase boundaries. We found that the crystals exhibited pronounced differences in the c‧ elastic coefficient and related shear damping in high-temperature ferromagnetic phases (austenite and premartensite). The difference can be ascribed to the formation of fine magnetic domain patterns and pinning of the magnetic domain walls on antiphase boundaries in the material with a high density of antiphase boundaries due to quenching. The fine domain pattern arising from mutual interactions between antiphase boundaries and ferromagnetic domain walls effectively reduces the magnetocrystalline anisotropy and amplifies the contribution of magnetostriction to the elastic response of the material. As a result, the anomalous elastic softening prior to martensite transformation is significantly enhanced in the quenched sample. Thus, for any comparison of experimental data and theoretical calculations the microstructural changes induced by specific heat treatment must be taken into account.

The effect of antiphase boundaries on the elastic properties of Ni-Mn-Ga austenite and premartensite.

PubMed

Seiner, Hanuš; Sedlák, Petr; Bodnárová, Lucie; Drahokoupil, Jan; Kopecký, Vít; Kopeček, Jaromír; Landa, Michal; Heczko, Oleg

2013-10-23

The evolution of elastic properties with temperature and magnetic field was studied in two differently heat-treated single crystals of the Ni-Mn-Ga magnetic shape memory alloy using resonant ultrasound spectroscopy. Quenching and slow furnace cooling were used to obtain different densities of antiphase boundaries. We found that the crystals exhibited pronounced differences in the c' elastic coefficient and related shear damping in high-temperature ferromagnetic phases (austenite and premartensite). The difference can be ascribed to the formation of fine magnetic domain patterns and pinning of the magnetic domain walls on antiphase boundaries in the material with a high density of antiphase boundaries due to quenching. The fine domain pattern arising from mutual interactions between antiphase boundaries and ferromagnetic domain walls effectively reduces the magnetocrystalline anisotropy and amplifies the contribution of magnetostriction to the elastic response of the material. As a result, the anomalous elastic softening prior to martensite transformation is significantly enhanced in the quenched sample. Thus, for any comparison of experimental data and theoretical calculations the microstructural changes induced by specific heat treatment must be taken into account.

Random Boolean networks for autoassociative memory: Optimization and sequential learning

NASA Astrophysics Data System (ADS)

Sherrington, D.; Wong, K. Y. M.

Conventional neural networks are based on synaptic storage of information, even when the neural states are discrete and bounded. In general, the set of potential local operations is much greater. Here we discuss some aspects of the properties of networks of binary neurons with more general Boolean functions controlling the local dynamics. Two specific aspects are emphasised; (i) optimization in the presence of noise and (ii) a simple model for short-term memory exhibiting primacy and recency in the recall of sequentially taught patterns.

Conduction at the onset of chaos

NASA Astrophysics Data System (ADS)

Baldovin, Fulvio

2017-02-01

After a general discussion of the thermodynamics of conductive processes, we introduce specific observables enabling the connection of the diffusive transport properties with the microscopic dynamics. We solve the case of Brownian particles, both analytically and numerically, and address then whether aspects of the classic Onsager's picture generalize to the non-local non-reversible dynamics described by logistic map iterates. While in the chaotic case numerical evidence of a monotonic relaxation is found, at the onset of chaos complex relaxation patterns emerge.

Magnetic resonance fingerprinting.

PubMed

Ma, Dan; Gulani, Vikas; Seiberlich, Nicole; Liu, Kecheng; Sunshine, Jeffrey L; Duerk, Jeffrey L; Griswold, Mark A

2013-03-14

Magnetic resonance is an exceptionally powerful and versatile measurement technique. The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. Here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (MRF)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. MRF thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. MRF can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. When paired with an appropriate pattern-recognition algorithm, MRF inherently suppresses measurement errors and can thus improve measurement accuracy.

Repetition Is the Feature Behind the Attentional Bias for Recognizing Threatening Patterns.

PubMed

Shabbir, Maryam; Zon, Adelynn M Y; Thuppil, Vivek

2018-01-01

Animals attend to what is relevant in order to behave in an effective manner and succeed in their environments. In several nonhuman species, there is an evolved bias for attending to patterns indicative of threats in the natural environment such as dangerous animals. Because skins of many dangerous animals are typically repetitive, we propose that repetition is the key feature enabling recognition of evolutionarily important threats. The current study consists of two experiments where we measured participants' reactions to pictures of male and female models wearing clothing of various repeating (leopard skin, snakeskin, and floral print) and nonrepeating (camouflage, shiny, and plain) patterns. In Experiment 1, when models wearing patterns were presented side by side with total fixation duration as the measure, the repeating floral pattern was the most provocative, with total fixation duration significantly longer than all other patterns. Leopard and snakeskin patterns had total fixation durations that were significantly longer than the plain pattern. In Experiment 2, we employed a visual-search task where participants were required to find models wearing the various patterns in a setting of a crowded airport terminal. Participants detected leopard skin pattern and repetitive floral pattern significantly faster than two of the nonpatterned clothing styles. Our experimental findings support the hypothesis that repetition of specific visual features might facilitate target detection, especially those characterizing evolutionary important threats. Our findings that intricate, but nonthreatening repeating patterns can have similar attention-grabbing properties to animal skin patterns have important implications for the fashion industry and wildlife trade.

Intrinsic photoluminescence of diatom shells in sensing applications

NASA Astrophysics Data System (ADS)

De Tommasi, E.; Rendina, I.; Rea, I.; De Stefano, M.; Lamberti, A.; De Stefano, L.

2009-05-01

Diatoms are monocellular micro-algae provided with external valves, the frustules, made of amorphous hydrated silica. Frustules present patterns of regular arrays of holes, the areolae, characterized by sub-micrometric dimensions. Frustules from centric diatoms are characterized by a radial disposition of areolae and exhibit several optical properties, such as photoluminescence, lens-like behavior and, in general, photonic-crystal-like behavior as long as confinement of electromagnetic field is concerned. In particular, intrinsic photoluminescence from frustules is strongly influenced by the surrounding atmosphere: on exposure to gases, the induced luminescence changes both in the optical intensity and peaks positions. To give specificity against a target analyte, a key feature for an optical sensor, a biomolecular probe, which naturally recognizes its ligand, can be covalently linked to the diatom surface. We explored the photoluminescence emission properties of frustules of Coscinodiscus wailesii centric species, characterized by a diameter of about 100-200 μm, on exposure to different vapours and in presence of specific bioprobes interacting with target analytes. Very high sensitivities have been observed due to the characteristic morphology of diatoms shells. Particular attention has been devoted to the emission properties of single frustules.

Placing the pieces: Reconstructing the original property mosaic in a warrant and patent watershed

USGS Publications Warehouse

Bain, D.J.; Brush, G.S.

2005-01-01

Recent research shows that land use history is an important determinant of current ecosystem function. In the United States, characterization of land use change following European settlement requires reconstruction of the original property mosaic. However, this task is difficult in unsystematically surveyed areas east of the Appalachian Mountains. The Gwynns Falls watershed (Baltimore, MD) was originally surveyed in the 1600-1700s under a system of warrants and patents (commonly known as 'metes and bounds'). A method for the reconstruction and mapping of warrant and patent properties is presented and used to map the original property mosaic in the Gwynns Falls watershed. Using the mapped mosaic, the persistence of properties and property lines in the current Gwynns Falls landscape is considered. The results of this research indicate that as in agricultural areas, the original property lines in the Gwynns Falls watershed are persistent. At the same time, the results suggest that the property mosaic in heavily urbanized/suburbanized areas is generally 'reset.' Further, trends in surveying technique, parcel size, and settlement patterns cause property line density and property shape complexity to increase in the less urbanized upper watershed. The persistence of original patterns may be damping expression of heterogeneity gradients in this urban landscape. This spatial pattern of complexity in the original mosaic is directly opposite of hypothesized patterns of landscape heterogeneity arising from urbanization. The technique reported here and the resulting observations are important for landscape pattern studies in areas settled under unsystematic survey systems, especially the heavily urbanized areas of the eastern United States. ?? 2004 Kluwer Academic Publishers.

Composite patterning devices for soft lithography

DOEpatents

Rogers, John A.; Menard, Etienne

2007-03-27

The present invention provides methods, devices and device components for fabricating patterns on substrate surfaces, particularly patterns comprising structures having microsized and/or nanosized features of selected lengths in one, two or three dimensions. The present invention provides composite patterning devices comprising a plurality of polymer layers each having selected mechanical properties, such as Young's Modulus and flexural rigidity, selected physical dimensions, such as thickness, surface area and relief pattern dimensions, and selected thermal properties, such as coefficients of thermal expansion, to provide high resolution patterning on a variety of substrate surfaces and surface morphologies.

Neurons with two sites of synaptic integration learn invariant representations.

PubMed

Körding, K P; König, P

2001-12-01

Neurons in mammalian cerebral cortex combine specific responses with respect to some stimulus features with invariant responses to other stimulus features. For example, in primary visual cortex, complex cells code for orientation of a contour but ignore its position to a certain degree. In higher areas, such as the inferotemporal cortex, translation-invariant, rotation-invariant, and even view point-invariant responses can be observed. Such properties are of obvious interest to artificial systems performing tasks like pattern recognition. It remains to be resolved how such response properties develop in biological systems. Here we present an unsupervised learning rule that addresses this problem. It is based on a neuron model with two sites of synaptic integration, allowing qualitatively different effects of input to basal and apical dendritic trees, respectively. Without supervision, the system learns to extract invariance properties using temporal or spatial continuity of stimuli. Furthermore, top-down information can be smoothly integrated in the same framework. Thus, this model lends a physiological implementation to approaches of unsupervised learning of invariant-response properties.

Electrodeposition of Manganese-Nickel Oxide Films on a Graphite Sheet for Electrochemical Capacitor Applications.

PubMed

Lee, Hae-Min; Lee, Kangtaek; Kim, Chang-Koo

2014-01-09

Manganese-nickel (Mn-Ni) oxide films were electrodeposited on a graphite sheet in a bath consisting of manganese acetate and nickel chloride, and the structural, morphological, and electrochemical properties of these films were investigated. The electrodeposited Mn-Ni oxide films had porous structures covered with nanofibers. The X-ray diffractometer pattern revealed the presence of separate manganese oxide (g-MnO₂) and nickel oxide (NiO) in the films. The electrodeposited Mn-Ni oxide electrode exhibited a specific capacitance of 424 F/g in Na₂SO₄ electrolyte. This electrode maintained 86% of its initial specific capacitance over 2000 cycles of the charge-discharge operation, showing good cycling stability.

Tc1 mouse model of trisomy-21 dissociates properties of short- and long-term recognition memory.

PubMed

Hall, Jessica H; Wiseman, Frances K; Fisher, Elizabeth M C; Tybulewicz, Victor L J; Harwood, John L; Good, Mark A

2016-04-01

The present study examined memory function in Tc1 mice, a transchromosomic model of Down syndrome (DS). Tc1 mice demonstrated an unusual delay-dependent deficit in recognition memory. More specifically, Tc1 mice showed intact immediate (30sec), impaired short-term (10-min) and intact long-term (24-h) memory for objects. A similar pattern was observed for olfactory stimuli, confirming the generality of the pattern across sensory modalities. The specificity of the behavioural deficits in Tc1 mice was confirmed using APP overexpressing mice that showed the opposite pattern of object memory deficits. In contrast to object memory, Tc1 mice showed no deficit in either immediate or long-term memory for object-in-place information. Similarly, Tc1 mice showed no deficit in short-term memory for object-location information. The latter result indicates that Tc1 mice were able to detect and react to spatial novelty at the same delay interval that was sensitive to an object novelty recognition impairment. These results demonstrate (1) that novelty detection per se and (2) the encoding of visuo-spatial information was not disrupted in adult Tc1 mice. The authors conclude that the task specific nature of the short-term recognition memory deficit suggests that the trisomy of genes on human chromosome 21 in Tc1 mice impacts on (perirhinal) cortical systems supporting short-term object and olfactory recognition memory. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A gradient-based approach for automated crest-line detection and analysis of sand dune patterns on planetary surfaces

NASA Astrophysics Data System (ADS)

Lancaster, N.; LeBlanc, D.; Bebis, G.; Nicolescu, M.

2015-12-01

Dune-field patterns are believed to behave as self-organizing systems, but what causes the patterns to form is still poorly understood. The most obvious (and in many cases the most significant) aspect of a dune system is the pattern of dune crest lines. Extracting meaningful features such as crest length, orientation, spacing, bifurcations, and merging of crests from image data can reveal important information about the specific dune-field morphological properties, development, and response to changes in boundary conditions, but manual methods are labor-intensive and time-consuming. We are developing the capability to recognize and characterize patterns of sand dunes on planetary surfaces. Our goal is to develop a robust methodology and the necessary algorithms for automated or semi-automated extraction of dune morphometric information from image data. Our main approach uses image processing methods to extract gradient information from satellite images of dune fields. Typically, the gradients have a dominant magnitude and orientation. In many cases, the images have two major dominant gradient orientations, for the sunny and shaded side of the dunes. A histogram of the gradient orientations is used to determine the dominant orientation. A threshold is applied to the image based on gradient orientations which agree with the dominant orientation. The contours of the binary image can then be used to determine the dune crest-lines, based on pixel intensity values. Once the crest-lines have been extracted, the morphological properties can be computed. We have tested our approach on a variety of images of linear and crescentic (transverse) dunes and compared dune detection algorithms with manually-digitized dune crest lines, achieving true positive values of 0.57-0.99; and false positives values of 0.30-0.67, indicating that out approach is generally robust.

Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine

PubMed Central

Pietak, Alexis; Levin, Michael

2016-01-01

Bioelectric cell properties have been revealed as powerful targets for modulating stem cell function, regenerative response, developmental patterning, and tumor reprograming. Spatio-temporal distributions of endogenous resting potential, ion flows, and electric fields are influenced not only by the genome and external signals but also by their own intrinsic dynamics. Ion channels and electrical synapses (gap junctions) both determine, and are themselves gated by, cellular resting potential. Thus, the origin and progression of bioelectric patterns in multicellular tissues is complex, which hampers the rational control of voltage distributions for biomedical interventions. To improve understanding of these dynamics and facilitate the development of bioelectric pattern control strategies, we developed the BioElectric Tissue Simulation Engine (BETSE), a finite volume method multiphysics simulator, which predicts bioelectric patterns and their spatio-temporal dynamics by modeling ion channel and gap junction activity and tracking changes to the fundamental property of ion concentration. We validate performance of the simulator by matching experimentally obtained data on membrane permeability, ion concentration and resting potential to simulated values, and by demonstrating the expected outcomes for a range of well-known cases, such as predicting the correct transmembrane voltage changes for perturbation of single cell membrane states and environmental ion concentrations, in addition to the development of realistic transepithelial potentials and bioelectric wounding signals. In silico experiments reveal factors influencing transmembrane potential are significantly different in gap junction-networked cell clusters with tight junctions, and identify non-linear feedback mechanisms capable of generating strong, emergent, cluster-wide resting potential gradients. The BETSE platform will enable a deep understanding of local and long-range bioelectrical dynamics in tissues, and assist the development of specific interventions to achieve greater control of pattern during morphogenesis and remodeling. PMID:27458581

A Mesoscopic Electromechanical Theory of Ferroelectric Films and Ceramics

NASA Astrophysics Data System (ADS)

Li, Jiangyu; Bhattacharya, Kaushik

2002-08-01

We present a multi-scale modelling framework to predict the effective electromechanical behavior of ferroelectric ceramics and thin films. This paper specifically focuses on the mesoscopic scale and models the effects of domains and domain switching taking into account intergranular constraints. Starting from the properties of the single crystal and the pre-poling granular texture, the theory predicts the domain patterns, the post-poling texture, the saturation polarization, saturation strain and the electromechanical moduli. We demonstrate remarkable agreement with experimental data. The theory also explains the superior electromechanical property of PZT at the morphotropic phase boundary. The paper concludes with the application of the theory to predict the optimal texture for enhanced electromechanical coupling factors and high-strain actuation in selected materials.

Au-Ag-Cu nano-alloys: tailoring of permittivity

NASA Astrophysics Data System (ADS)

Hashimoto, Yoshikazu; Seniutinas, Gediminas; Balčytis, Armandas; Juodkazis, Saulius; Nishijima, Yoshiaki

2016-04-01

Precious metal alloys enables new possibilities to tailor materials for specific optical functions. Here we present a systematic study of the effects of a nanoscale alloying on the permittivity of Au-Ag-Cu metals at 38 different atomic mixing ratios. The permittivity was measured and analyzed numerically by applying the Drude model. X-ray diffraction (XRD) revealed the face centered cubic lattice of the alloys. Both, optical spectra and XRD results point towards an equivalent composition-dependent electron scattering behavior. Correlation between the fundamental structural parameters of alloys and the resulting optical properties is elucidated. Plasmonic properties of the Au-Ag-Cu alloy nanoparticles were investigated by numerical simulations. Guidelines for designing plasmonic response of nano- structures and their patterns are presented from the material science perspective.

The positioning of sustainability within residential property marketing.

PubMed

Kriese, Ulrich; Scholz, Roland W

2011-01-01

This article investigates the evolution of sustainability positioning in residential property marketing to shed light on the specific role and responsibility of housebuilders and housing investors in urban development. To this end, an analysis is made of housing advertisements published in Basel, Switzerland, over a period of more than 100 years. The paper demonstrates how to draw successfully on advertisements to discern sustainability patterns in housing, using criteria situated along the dimensions building, location and people. Cluster analysis allows five clusters of sustainability positioning to be described—namely, good location, green building, comfort living, pre-sustainability and sustainability. Investor and builder types are differently located in these clusters. Location emerges as an issue which, to a large extent, is advertised independently from other sustainability issues.

Multi-layer network utilizing rewarded spike time dependent plasticity to learn a foraging task

PubMed Central

2017-01-01

Neural networks with a single plastic layer employing reward modulated spike time dependent plasticity (STDP) are capable of learning simple foraging tasks. Here we demonstrate advanced pattern discrimination and continuous learning in a network of spiking neurons with multiple plastic layers. The network utilized both reward modulated and non-reward modulated STDP and implemented multiple mechanisms for homeostatic regulation of synaptic efficacy, including heterosynaptic plasticity, gain control, output balancing, activity normalization of rewarded STDP and hard limits on synaptic strength. We found that addition of a hidden layer of neurons employing non-rewarded STDP created neurons that responded to the specific combinations of inputs and thus performed basic classification of the input patterns. When combined with a following layer of neurons implementing rewarded STDP, the network was able to learn, despite the absence of labeled training data, discrimination between rewarding patterns and the patterns designated as punishing. Synaptic noise allowed for trial-and-error learning that helped to identify the goal-oriented strategies which were effective in task solving. The study predicts a critical set of properties of the spiking neuronal network with STDP that was sufficient to solve a complex foraging task involving pattern classification and decision making. PMID:28961245

Predicting atmospheric states from local dynamical properties of the underlying attractor

NASA Astrophysics Data System (ADS)

Faranda, Davide; Rodrigues, David; Alvarez-Castro, M. Carmen; Messori, Gabriele; Yiou, Pascal

2017-04-01

Mid-latitude flows are characterized by a chaotic dynamics and recurring patterns hinting to the existence of an atmospheric attractor. In 1963 Lorenz described this object as: "the collection of all states that the system can assume or approach again and again, as opposed to those that it will ultimately avoid" and analyzed a low dimensional system describing a convective dynamics whose attractor has the shape of a butterfly. Since then, many studies try to find equivalent of the Lorenz butterfly in the complex atmospheric dynamics. Most of the studies where focused to determine the average dimension D of the attractor i.e. the number of degrees of freedom sufficient to describe the atmospheric circulation. However, obtaining reliable estimates of D has proved challenging. Moreover, D does not provide information on transient atmospheric motions, such as those leading to weather extremes. Using recent developments in dynamical systems theory, we show that such motions can be classified through instantaneous rather than average properties of the attractor. The instantaneous properties are uniquely determined by instantaneous dimension and stability. Their extreme values correspond to specific atmospheric patterns, and match extreme weather occurrences. We further show the existence of a significant correlation between the time series of instantaneous stability and dimension and the mean spread of sea-level pressure fields in an operational ensemble weather forecast at lead times of over two weeks. Instantaneous properties of the attractor therefore provide an efficient way of evaluating and informing operational weather forecasts.

In-situ recording of ionic currents in projection neurons and Kenyon cells in the olfactory pathway of the honeybee

PubMed Central

Rössler, Wolfgang

2018-01-01

The honeybee olfactory pathway comprises an intriguing pattern of convergence and divergence: ~60.000 olfactory sensory neurons (OSN) convey olfactory information on ~900 projection neurons (PN) in the antennal lobe (AL). To transmit this information reliably, PNs employ relatively high spiking frequencies with complex patterns. PNs project via a dual olfactory pathway to the mushroom bodies (MB). This pathway comprises the medial (m-ALT) and the lateral antennal lobe tract (l-ALT). PNs from both tracts transmit information from a wide range of similar odors, but with distinct differences in coding properties. In the MBs, PNs form synapses with many Kenyon cells (KC) that encode odors in a spatially and temporally sparse way. The transformation from complex information coding to sparse coding is a well-known phenomenon in insect olfactory coding. Intrinsic neuronal properties as well as GABAergic inhibition are thought to contribute to this change in odor representation. In the present study, we identified intrinsic neuronal properties promoting coding differences between PNs and KCs using in-situ patch-clamp recordings in the intact brain. We found very prominent K+ currents in KCs clearly differing from the PN currents. This suggests that odor coding differences between PNs and KCs may be caused by differences in their specific ion channel properties. Comparison of ionic currents of m- and l-ALT PNs did not reveal any differences at a qualitative level. PMID:29351552

Human uniqueness-self-interest and social cooperation.

PubMed

Okada, Daijiro; Bingham, Paul M

2008-07-21

Humans are unique among all species of terrestrial history in both ecological dominance and individual properties. Many, or perhaps all, of the unique elements of this nonpareil status can be plausibly interpreted as evolutionary and strategic elements and consequences of the unprecedented intensity and scale of our social cooperation. Convincing explanation of this unique human social adaptation remains a central, unmet challenge to the scientific enterprise. We develop a hypothesis for the ancestral origin of expanded cooperative social behavior. Specifically, we present a game theoretic analysis demonstrating that a specific pattern of expanded social cooperation between conspecific individuals with conflicts of interest (including non-kin) can be strategically viable, but only in animals that possess a highly unusual capacity for conspecific violence (credible threat) having very specific properties that dramatically reduce the costs of coercive violence. The resulting reduced costs allow preemptive or compensated coercion to be an instantaneously self-interested behavior under diverse circumstances rather than in rare, idiosyncratic circumstances as in actors (animals) who do not have access to inexpensive coercive threat. Humans are apparently unique among terrestrial organisms in having evolved conspecific coercive capabilities that fulfill these stringent requirements. Thus, our results support the proposal that access to a novel capacity for projection of coercive threat might represent the essential initiating event for the evolution of a human-like pattern of social cooperation and the subsequent evolution of the diverse features of human uniqueness. Empirical evidence indicates that these constraints were, in fact, met only in our evolutionary lineage. The logic for the emergence of uniquely human cooperation suggested by our analysis apparently accounts simply for the human fossil record.

Embracing heterothermic diversity: non-stationary waveform analysis of temperature variation in endotherms.

PubMed

Levesque, Danielle L; Menzies, Allyson K; Landry-Cuerrier, Manuelle; Larocque, Guillaume; Humphries, Murray M

2017-07-01

Recent research is revealing incredible diversity in the thermoregulatory patterns of wild and captive endotherms. As a result of these findings, classic thermoregulatory categories of 'homeothermy', 'daily heterothermy', and 'hibernation' are becoming harder to delineate, impeding our understanding of the physiological and evolutionary significance of variation within and around these categories. However, we lack a generalized analytical approach for evaluating and comparing the complex and diversified nature of the full breadth of heterothermy expressed by individuals, populations, and species. Here we propose a new approach that decomposes body temperature time series into three inherent properties-waveform, amplitude, and period-using a non-stationary technique that accommodates the temporal variability of body temperature patterns. This approach quantifies circadian and seasonal variation in thermoregulatory patterns, and uses the distribution of observed thermoregulatory patterns as a basis for intra- and inter-specific comparisons. We analyse body temperature time series from multiple species, including classical hibernators, tropical heterotherms, and homeotherms, to highlight the approach's general usefulness and the major axes of thermoregulatory variation that it reveals.

Derivation of spatial patterns of soil hydraulic properties based on pedotransfer functions

USDA-ARS?s Scientific Manuscript database

Spatial patterns in soil hydrology are the product of the spatial distribution of soil hydraulic properties. These properties are notorious for the difficulties and high labor costs involved in measuring them. Often, there is a need to resort to estimating these parameters from other, more readily a...

Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.

PubMed

Guo, Yue; Liu, Jing; Zhang, Jiefu; Liu, Shengyi; Du, Jianchang

2017-07-01

It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (K a ) and the rates of synonymous substitution (K s ) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (K a /K s ), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Conveying Movement in Music and Prosody

PubMed Central

Hedger, Stephen C.; Nusbaum, Howard C.; Hoeckner, Berthold

2013-01-01

We investigated whether acoustic variation of musical properties can analogically convey descriptive information about an object. Specifically, we tested whether information from the temporal structure in music interacts with perception of a visual image to form an analog perceptual representation as a natural part of music perception. In Experiment 1, listeners heard music with an accelerating or decelerating temporal pattern, and then saw a picture of a still or moving object and decided whether it was animate or inanimate – a task unrelated to the patterning of the music. Object classification was faster when musical motion matched visually depicted motion. In Experiment 2, participants heard spoken sentences that were accompanied by accelerating or decelerating music, and then were presented with a picture of a still or moving object. When motion information in the music matched motion information in the picture, participants were similarly faster to respond. Fast and slow temporal patterns without acceleration and deceleration, however, did not make participants faster when they saw a picture depicting congruent motion information (Experiment 3), suggesting that understanding temporal structure information in music may depend on specific metaphors about motion in music. Taken together, these results suggest that visuo-spatial referential information can be analogically conveyed and represented by music and can be integrated with speech or influence the understanding of speech. PMID:24146920

Subjective Ratings of Beauty and Aesthetics: Correlations With Statistical Image Properties in Western Oil Paintings

PubMed Central

Lehmann, Thomas; Redies, Christoph

2017-01-01

For centuries, oil paintings have been a major segment of the visual arts. The JenAesthetics data set consists of a large number of high-quality images of oil paintings of Western provenance from different art periods. With this database, we studied the relationship between objective image measures and subjective evaluations of the images, especially evaluations on aesthetics (defined as artistic value) and beauty (defined as individual liking). The objective measures represented low-level statistical image properties that have been associated with aesthetic value in previous research. Subjective rating scores on aesthetics and beauty correlated not only with each other but also with different combinations of the objective measures. Furthermore, we found that paintings from different art periods vary with regard to the objective measures, that is, they exhibit specific patterns of statistical image properties. In addition, clusters of participants preferred different combinations of these properties. In conclusion, the results of the present study provide evidence that statistical image properties vary between art periods and subject matters and, in addition, they correlate with the subjective evaluation of paintings by the participants. PMID:28694958

Lattice-patterned LC-polymer composites containing various nanoparticles as additives

PubMed Central

2012-01-01

In this study, we show the effect of various nanoparticle additives on phase separation behavior of a lattice-patterned liquid crystal [LC]-polymer composite system and on interfacial properties between the LC and polymer. Lattice-patterned LC-polymer composites were fabricated by exposing to UV light a mixture of a prepolymer, an LC, and SiO2 nanoparticles positioned under a patterned photomask. This resulted in the formation of an LC and prepolymer region through phase separation. We found that the incorporation of SiO2 nanoparticles significantly affected the electro-optical properties of the lattice-patterned LC-polymer composites. This effect is a fundamental characteristic of flexible displays. The electro-optical properties depend on the size and surface functional groups of the SiO2 nanoparticles. Compared with untreated pristine SiO2 nanoparticles, which adversely affect the performance of LC molecules surrounded by polymer walls, SiO2 nanoparticles with surface functional groups were found to improve the electro-optical properties of the lattice-patterned LC-polymer composites by increasing the quantity of SiO2 nanoparticles. The surface functional groups of the SiO2 nanoparticles were closely related to the distribution of SiO2 nanoparticles in the LC-polymer composites, and they influenced the electro-optical properties of the LC molecules. It is clear from our work that the introduction of nanoparticles into a lattice-patterned LC-polymer composite provides a method for controlling and improving the composite's electro-optical properties. This technique can be used to produce flexible substrates for various flexible electronic devices. PMID:22222011

An Advanced Electrospinning Method of Fabricating Nanofibrous Patterned Architectures with Controlled Deposition and Desired Alignment

NASA Astrophysics Data System (ADS)

Rasel, Sheikh Md

We introduce a versatile advanced method of electrospinning for fabricating various kinds of nanofibrous patterns along with desired alignment, controlled amount of deposition and locally variable density into the architectures. In this method, we employed multiple electrodes whose potentials have been altered in milliseconds with the help of microprocessor based control system. Therefore, key success of this method was that the electrical field as well as charge carrying fibers could be switched shortly from one electrode's location to another, as a result, electrospun fibers could be deposited on the designated areas with desired alignment. A wide range of nanofibrous patterned architectures were constructed using proper arrangement of multiple electrodes. By controlling the concurrent activation time of two adjacent electrodes, we demonstrated that amount of fibers going into the pattern can be adjusted and desired alignment in electrospun fibers can be obtained. We also revealed that the deposition density of electrospun fibers in different areas of patterned architectures can be varied. We showed that by controlling the deposition time between two adjacent electrodes, a number of functionally graded patterns can be generated with uniaxial alignment. We also demonstrated that this handy method was capable of producing random, aligned, and multidirectional nanofibrous mats by engaging a number of electrodes and switching them in desired patterns. A comprehensive study using finite element method was carried out to understand the effects of electrical field. Simulation results revealed that electrical field strength alters shortly based on electrode control switch patterns. Nanofibrous polyvinyl alcohol (PVA) scaffolds and its composite reinforced with wollastonite and wood flour were fabricated using rotating drum electrospinning technique. Morphological, mechanical, and thermal, properties were characterized on PVA/wollastonite and PVA/wood flour nanocomposites containing 0, 5, 10, and 20 wt % of fillers. Morphological analyses carried out by digital optical microscope, scanning electron microscopy, x-ray computed tomography, and Fourier transform infrared spectroscopy, confirmed the presence and well dispersion of fillers in the composites. In addition, improvement of mechanical properties with increased filler content further emphasized the adhesion between matrix and reinforcement. PVA with 20 wt % wollastonite composite exhibited the highest tensile strength (11.99 MPa) and tensile module (198 MPa) as compared to pure PVA (3.92 MPa and 83 MPa, respectively). Moreover, the thermal tests demonstrated that there is no major deviation in the thermal stability due to the addition of wollastonite in PVA scaffolds. Almost similar trend was observed in PVA/wood flour nanocomposites where tensile strength improved by 228 % for 20 wt % of reinforcement. The PVA/wollastonite and PVA/wood flour fibrous nanocomposite which poses higher mechanical properties might be potentially suitable for many advanced applications such as filtration, tissue engineering, and food processing. We believe this study will contribute to further scientific understanding of the patterning mechanism of electrospun nanofibers and to allow for variety of design of specific patterned nanofibrous architectures with desired functional properties. Therefore, this improved scheme of electrospinning can have significant impact in a broad range of applications including tissue engineering scaffolds, filtrations, and nanoelectronics.

Resemblance of the properties of superimposed volume holograms to the properties of human memory

NASA Astrophysics Data System (ADS)

Orlov, V. V.

2006-09-01

According to current concepts in psychology, a collection of patterns stored in human memory has the property of integrity and contains new information not contained in the individual patterns. It is shown that superimposed volume holograms possess similar properties if the information in them is written by a method that excludes the appearance of crosstalk of the holograms.

Bioprinting for Neural Tissue Engineering.

PubMed

Knowlton, Stephanie; Anand, Shivesh; Shah, Twisha; Tasoglu, Savas

2018-01-01

Bioprinting is a method by which a cell-encapsulating bioink is patterned to create complex tissue architectures. Given the potential impact of this technology on neural research, we review the current state-of-the-art approaches for bioprinting neural tissues. While 2D neural cultures are ubiquitous for studying neural cells, 3D cultures can more accurately replicate the microenvironment of neural tissues. By bioprinting neuronal constructs, one can precisely control the microenvironment by specifically formulating the bioink for neural tissues, and by spatially patterning cell types and scaffold properties in three dimensions. We review a range of bioprinted neural tissue models and discuss how they can be used to observe how neurons behave, understand disease processes, develop new therapies and, ultimately, design replacement tissues. Copyright © 2017 Elsevier Ltd. All rights reserved.

Differential subcellular distribution of ion channels and the diversity of neuronal function.

PubMed

Nusser, Zoltan

2012-06-01

Following the astonishing molecular diversity of voltage-gated ion channels that was revealed in the past few decades, the ion channel repertoire expressed by neurons has been implicated as the major factor governing their functional heterogeneity. Although the molecular structure of ion channels is a key determinant of their biophysical properties, their subcellular distribution and densities on the surface of nerve cells are just as important for fulfilling functional requirements. Recent results obtained with high resolution quantitative localization techniques revealed complex, subcellular compartment-specific distribution patterns of distinct ion channels. Here I suggest that within a given neuron type every ion channel has a unique cell surface distribution pattern, with the functional consequence that this dramatically increases the computational power of nerve cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

Outbreak patterns of the novel avian influenza (H7N9)

NASA Astrophysics Data System (ADS)

Pan, Ya-Nan; Lou, Jing-Jing; Han, Xiao-Pu

2014-05-01

The attack of novel avian influenza (H7N9) in East China caused a serious health crisis and public panic. In this paper, we empirically analyze the onset patterns of human cases of the novel avian influenza and observe several spatial and temporal properties that are similar to other infectious diseases. More specifically, using the empirical analysis and modeling studies, we find that the spatio-temporal network that connects the cities with human cases along the order of outbreak timing emerges two-regime-power-law edge-length distribution, indicating the picture that several islands with higher and heterogeneous risk straggle in East China. The proposed method is applicable to the analysis of the spreading situation in the early stage of disease outbreak using quite limited dataset.

Phonology without universal grammar

PubMed Central

Archangeli, Diana; Pulleyblank, Douglas

2015-01-01

The question of identifying the properties of language that are specific human linguistic abilities, i.e., Universal Grammar, lies at the center of linguistic research. This paper argues for a largely Emergent Grammar in phonology, taking as the starting point that memory, categorization, attention to frequency, and the creation of symbolic systems are all nonlinguistic characteristics of the human mind. The articulation patterns of American English rhotics illustrate categorization and systems; the distribution of vowels in Bantu vowel harmony uses frequencies of particular sequences to argue against Universal Grammar and in favor of Emergent Grammar; prefix allomorphy in Esimbi illustrates the Emergent symbolic system integrating phonological and morphological generalizations. The Esimbi case has been treated as an example of phonological opacity in a Universal Grammar account; the Emergent analysis resolves the pattern without opacity concerns. PMID:26388791

Nano- and Micro-Patterned S-, H-, and X-PDMS for Cell-Based Applications: Comparison of Wettability, Roughness, and Cell-Derived Parameters

PubMed Central

Scharin-Mehlmann, Marina; Häring, Aaron; Rommel, Mathias; Dirnecker, Tobias; Friedrich, Oliver; Frey, Lothar; Gilbert, Daniel F.

2018-01-01

Polydimethylsiloxane (PDMS) is a promising biomaterial for generating artificial extracellular matrix (ECM) like patterned topographies, yet its hydrophobic nature limits its applicability to cell-based approaches. Although plasma treatment can enhance the wettability of PDMS, the surface is known to recover its hydrophobicity within a few hours after exposure to air. To investigate the capability of a novel PDMS-type (X-PDMS) for in vitro based assessment of physiological cell properties, we designed and fabricated plane as well as nano- and micrometer-scaled pillar-patterned growth substrates using the elastomer types S-, H- and X-PDMS, which were fabricated from commercially available components. Most importantly, we compared X-PDMS based growth substrates which have not yet been investigated in this context with H- as well as well-known S-PDMS based substrates. Due to its applicability to fabricating nanometer-sized topographic features with high accuracy and pattern fidelity, this material may be of high relevance for specific biomedical applications. To assess their applicability to cell-based approaches, we characterized the generated surfaces using water contact angle (WCA) measurement and atomic force microscopy (AFM) as indicators of wettability and roughness, respectively. We further assessed cell number, cell area and cellular elongation as indirect measures of cellular viability and adhesion by image cytometry and phenotypic profiling, respectively, using Calcein and Hoechst 33342 stained human foreskin fibroblasts as a model system. We show for the first time that different PDMS types are differently sensitive to plasma treatment. We further demonstrate that surface hydrophobicity changes along with changing height of the pillar-structures. Our data indicate that plane and structured X-PDMS shows cytocompatibility and adhesive properties comparable to the previously described elastomer types S- and H-PDMS. We conclude that nanometer-sized structuring of X-PDMS may serve as a powerful method for altering surface properties toward production of biomedical devices for cell-based applications. PMID:29765941

Understanding spatio-temporal mobility patterns for seniors, child/student and adult using smart card data

NASA Astrophysics Data System (ADS)

Huang, X.; Tan, J.

2014-11-01

Commutes in urban areas create interesting travel patterns that are often stored in regional transportation databases. These patterns can vary based on the day of the week, the time of the day, and commuter type. This study proposes methods to detect underlying spatio-temporal variability among three groups of commuters (senior citizens, child/students, and adults) using data mining and spatial analytics. Data from over 36 million individual trip records collected over one week (March 2012) on the Singapore bus and Mass Rapid Transit (MRT) system by the fare collection system were used. Analyses of such data are important for transportation and landuse designers and contribute to a better understanding of urban dynamics. Specifically, descriptive statistics, network analysis, and spatial analysis methods are presented. Descriptive variables were proposed such as density and duration to detect temporal features of people. A directed weighted graph G ≡ (N , L, W) was defined to analyze the global network properties of every pair of the transportation link in the city during an average workday for all three categories. Besides, spatial interpolation and spatial statistic tools were used to transform the discrete network nodes into structured human movement landscape to understand the role of transportation systems in urban areas. The travel behaviour of the three categories follows a certain degree of temporal and spatial universality but also displays unique patterns within their own specialties. Each category is characterized by their different peak hours, commute distances, and specific locations for travel on weekdays.

Laminar- and Target-Specific Amygdalar Inputs in Rat Primary Gustatory Cortex.

PubMed

Haley, Melissa S; Fontanini, Alfredo; Maffei, Arianna

2016-03-02

The primary gustatory cortex (GC) receives projections from the basolateral nucleus of the amygdala (BLA). Behavioral and electrophysiological studies demonstrated that this projection is involved in encoding the hedonic value of taste and is a source of anticipatory activity in GC. Anatomically, this projection is largest in the agranular portion of GC; however, its synaptic targets and synaptic properties are currently unknown. In vivo electrophysiological recordings report conflicting evidence about BLA afferents either selectively activating excitatory neurons or driving a compound response consistent with the activation of inhibitory circuits. Here we demonstrate that BLA afferents directly activate excitatory neurons and two distinct populations of inhibitory neurons in both superficial and deep layers of rat GC. BLA afferents recruit different proportions of excitatory and inhibitory neurons and show distinct patterns of circuit activation in the superficial and deep layers of GC. These results provide the first circuit-level analysis of BLA inputs to a sensory area. Laminar- and target-specific differences of BLA inputs likely explain the complexity of amygdalocortical interactions during sensory processing. Projections from the basolateral nucleus of the amygdala (BLA) to the cortex convey information about the emotional value and the expectation of a sensory stimulus. Although much work has been done to establish the behavioral role of BLA inputs to sensory cortices, very little is known about the circuit organization of BLA projections. Here we provide the first in-depth analysis of connectivity and synaptic properties of the BLA input to the gustatory cortex. We show that BLA afferents activate excitatory and inhibitory circuits in a layer-specific and pattern-specific manner. Our results provide important new information about how neural circuits establishing the hedonic value of sensory stimuli and driving anticipatory behaviors are organized at the synaptic level. Copyright © 2016 the authors 0270-6474/16/362623-15$15.00/0.

Effects of gel properties produced by chemical reactions on viscous fingering

NASA Astrophysics Data System (ADS)

Ujiie, Tomohiro; Nagatsu, Yuichiro; Ban, Mitsumasa; Iwata, Shuichi; Kato, Yoshihito; Tada, Yutaka

2011-11-01

We have experimentally investigated viscous fingering with chemical reaction producing gel. Here, two systems were employed. In one system, sodium polyacrylate (SPA) solution and ferric ion solution were used as the more and less viscous liquids, respectively. In another system, xthantan gum (XG) solution and the ferric ion solution were used as the more and less viscous liquids, respectively. For high concentration of ferric ion, viscous fingering pattern was changed into spiral pattern in the former system, whereas into fracture pattern in the latter system. We consider that the difference in the change of the patterns in the two systems will be caused by the difference in the properties of the gels. Therefore, we have measured the rheological properties of the gels by means of a rheometer. We have found that the gel in the former case is more elastic. Furthermore, we have discussed the relationship between the measured rheological properties and the observed spiral or fracturing patterns.

Bütschli dynamic droplet system.

PubMed

Armstrong, Rachel; Hanczyc, Martin

2013-01-01

Dynamical oil-water systems such as droplets display lifelike properties and may lend themselves to chemical programming to perform useful work, specifically with respect to the built environment. We present Bütschli water-in-oil droplets as a model for further investigation into the development of a technology with living properties. Otto Bütschli first described the system in 1898, when he used alkaline water droplets in olive oil to initiate a saponification reaction. This simple recipe produced structures that moved and exhibited characteristics that resembled, at least superficially, the amoeba. We reconstructed the Bütschli system and observed its life span under a light microscope, observing chemical patterns and droplet behaviors in nearly three hundred replicate experiments. Self-organizing patterns were observed, and during this dynamic, embodied phase the droplets provided a means of introducing temporal and spatial order in the system with the potential for chemical programmability. The authors propose that the discrete formation of dynamic droplets, characterized by their lifelike behavior patterns, during a variable window of time (from 30 s to 30 min after the addition of alkaline water to the oil phase), qualify this system as an example of living technology. The analysis of the Bütschli droplets suggests that a set of conditions may precede the emergence of lifelike characteristics and exemplifies the richness of this rudimentary chemical system, not only for artificial life investigations but also for possible real-world applications in architectural practice.

Leishmania major survival in selective Phlebotomus papatasi sand fly vector requires a specific SCG-encoded lipophosphoglycan galactosylation pattern.

PubMed

Dobson, Deborah E; Kamhawi, Shaden; Lawyer, Phillip; Turco, Salvatore J; Beverley, Stephen M; Sacks, David L

2010-11-11

Phlebotomine sand flies that transmit the protozoan parasite Leishmania differ greatly in their ability to support different parasite species or strains in the laboratory: while some show considerable selectivity, others are more permissive. In "selective" sand flies, Leishmania binding and survival in the fly midgut typically depends upon the abundant promastigote surface adhesin lipophosphoglycan (LPG), which exhibits species- and strain-specific modifications of the dominant phosphoglycan (PG) repeat units. For the "selective" fly Phlebotomus papatasi PpapJ, side chain galactosyl-modifications (scGal) of PG repeats play key roles in parasite binding. We probed the specificity and properties of this scGal-LPG PAMP (Pathogen Associated Molecular Pattern) through studies of natural isolates exhibiting a wide range of galactosylation patterns, and of a panel of isogenic L. major engineered to express similar scGal-LPG diversity by transfection of SCG-encoded β1,3-galactosyltransferases with different activities. Surprisingly, both 'poly-scGal' and 'null-scGal' lines survived poorly relative to PpapJ-sympatric L. major FV1 and other 'mono-scGal' lines. However, survival of all lines was equivalent in P. duboscqi, which naturally transmit L. major strains bearing 'null-scGal'-LPG PAMPs. We then asked whether scGal-LPG-mediated interactions were sufficient for PpapJ midgut survival by engineering Leishmania donovani, which normally express unsubstituted LPG, to express a 'PpapJ-optimal' scGal-LPG PAMP. Unexpectedly, these "L. major FV1-cloaked" L. donovani-SCG lines remained unable to survive within PpapJ flies. These studies establish that midgut survival of L. major in PpapJ flies is exquisitely sensitive to the scGal-LPG PAMP, requiring a specific 'mono-scGal' pattern. However, failure of 'mono-scGal' L. donovani-SCG lines to survive in selective PpapJ flies suggests a requirement for an additional, as yet unidentified L. major-specific parasite factor(s). The interplay of the LPG PAMP and additional factor(s) with sand fly midgut receptors may determine whether a given sand fly host is "selective" or "permissive", with important consequences to both disease transmission and the natural co-evolution of sand flies and Leishmania.

The effect of flower-like and non-flower-like visual properties on choice of unrewarding patterns by bumblebees

NASA Astrophysics Data System (ADS)

Orbán, Levente L.; Plowright, Catherine M. S.

2013-07-01

How do distinct visual stimuli help bumblebees discover flowers before they have experienced any reward outside of their nest? Two visual floral properties, type of a pattern (concentric vs radial) and its position on unrewarding artificial flowers (central vs peripheral on corolla), were manipulated in two experiments. Both visual properties showed significant effects on floral choice. When pitted against each other, pattern was more important than position. Experiment 1 shows a significant effect of concentric pattern position, and experiment 2 shows a significant preference towards radial patterns regardless of their position. These results show that the presence of markings at the center of a flower are not so important as the presence of markings that will direct bees there.

Biochemical Characterization of Echinococcus multilocularis Antigen B3 Reveals Insight into Adaptation and Maintenance of Parasitic Homeostasis at the Host-Parasite Interface.

PubMed

Ahn, Chun-Seob; Kim, Jeong-Geun; Han, Xiumin; Bae, Young-An; Park, Woo-Jae; Kang, Insug; Wang, Hu; Kong, Yoon

2017-02-03

Alveolar echinococcosis (AE) caused by Echinococcus multilocularis metacestode is frequently associated with deleterious zoonotic helminthiasis. The growth patterns and morphological features of AE, such as invasion of the liver parenchyme and multiplication into multivesiculated masses, are similar to those of malignant tumors. AE has been increasingly detected in several regions of Europe, North America, Central Asia, and northwestern China. An isoform of E. multilocularis antigen B3 (EmAgB3) shows a specific immunoreactivity against patient sera of active-stage AE, suggesting that EmAgB3 might play important roles during adaptation of the parasite to hosts. However, expression patterns and biochemical properties of EmAgB3 remained elusive. The protein profile and nature of component proteins of E. multilocularis hydatid fluid (EmHF) have never been addressed. In this study, we conducted proteome analysis of EmHF of AE cysts harvested from immunocompetent mice. We observed the molecular and biochemical properties of EmAgB3, including differential transcription patterns of paralogous genes, macromolecular protein status by self-assembly, distinct oligomeric states according to individual anatomical compartments of the worm, and hydrophobic ligand-binding protein activity. We also demonstrated tissue expression patterns of EmAgB3 transcript and protein. EmAgB3 might participate in immune response and recruitment of essential host lipids at the host-parasite interface. Our results might contribute to an in depth understanding of the biophysical and biological features of EmAgB3, thus providing insights into the design of novel targets to control AE.

FoxP2 is a Parvocellular-Specific Transcription Factor in the Visual Thalamus of Monkeys and Ferrets

PubMed Central

Iwai, Lena; Ohashi, Yohei; van der List, Deborah; Usrey, William Martin; Miyashita, Yasushi; Kawasaki, Hiroshi

2013-01-01

Although the parallel visual pathways are a fundamental basis of visual processing, our knowledge of their molecular properties is still limited. Here, we uncovered a parvocellular-specific molecule in the dorsal lateral geniculate nucleus (dLGN) of higher mammals. We found that FoxP2 transcription factor was specifically expressed in X cells of the adult ferret dLGN. Interestingly, FoxP2 was also specifically expressed in parvocellular layers 3–6 of the dLGN of adult old world monkeys, providing new evidence for a homology between X cells in the ferret dLGN and parvocellular cells in the monkey dLGN. Furthermore, this expression pattern was established as early as gestation day 140 in the embryonic monkey dLGN, suggesting that parvocellular specification has already occurred when the cytoarchitectonic dLGN layers are formed. Our results should help in gaining a fundamental understanding of the development, evolution, and function of the parallel visual pathways, which are especially prominent in higher mammals. PMID:22791804

A mixed boundary representation to simulate the displacement of a biofluid by a biomaterial in porous media.

PubMed

Widmer, René P; Ferguson, Stephen J

2011-05-01

Characterization of the biomaterial flow through porous bone is crucial for the success of the bone augmentation process in vertebroplasty. The biofluid, biomaterial, and local morphological bone characteristics determine the final shape of the filling, which is important both for the post-treatment mechanical loading and the risk of intraoperative extraosseous leakage. We have developed a computational model that describes the flow of biomaterials in porous bone structures by considering the material porosity, the region-dependent intrinsic permeability of the porous structure, the rheological properties of the biomaterial, and the boundary conditions of the filling process. To simulate the process of the substitution of a biofluid (bone marrow) by a biomaterial (bone cement), we developed a hybrid formulation to describe the evolution of the fluid boundary and properties and coupled it to a modified version of Darcy's law. The apparent rheological properties are derived from a fluid-fluid interface tracking algorithm and a mixed boundary representation. The region- specific intrinsic permeability of the bone is governed by an empirical relationship resulting from a fitting process of experimental data. In a first step, we verified the model by studying the displacement process in spherical domains, where the spreading pattern is known in advance. The mixed boundary model demonstrated, as expected, that the determinants of the spreading pattern are the local intrinsic permeability of the porous matrix and the ratio of the viscosity of the fluids that are contributing to the displacement process. The simulations also illustrate the sensitivity of the mixed boundary representation to anisotropic permeability, which is related to the directional dependent microstructural properties of the porous medium. Furthermore, we compared the nonlinear finite element model to different published experimental studies and found a moderate to good agreement (R(2)=0.9895 for a one-dimensional bone core infiltration test and a 10.94-16.92% relative error for a three-dimensional spreading pattern study, respectively) between computational and experimental results.

Spatial band-pass filtering aids decoding musical genres from auditory cortex 7T fMRI.

PubMed

Sengupta, Ayan; Pollmann, Stefan; Hanke, Michael

2018-01-01

Spatial filtering strategies, combined with multivariate decoding analysis of BOLD images, have been used to investigate the nature of the neural signal underlying the discriminability of brain activity patterns evoked by sensory stimulation -- primarily in the visual cortex. Reported evidence indicates that such signals are spatially broadband in nature, and are not primarily comprised of fine-grained activation patterns. However, it is unclear whether this is a general property of the BOLD signal, or whether it is specific to the details of employed analyses and stimuli. Here we performed an analysis of publicly available, high-resolution 7T fMRI on the response BOLD response to musical genres in primary auditory cortex that matches a previously conducted study on decoding visual orientation from V1.  The results show that the pattern of decoding accuracies with respect to different types and levels of spatial filtering is comparable to that obtained from V1, despite considerable differences in the respective cortical circuitry.

The Art and Science of Polymer Brushes: Recent Developments in Patterning and Characterization Approaches.

PubMed

Panzarasa, Guido

2017-06-28

Polymer brushes are dense arrays of macromolecular chains tethered by one end at a surface. They are at the cutting edge of polymer nanotechnology since the dawn of controlled surface-initiated polymerization techniques unlocked new prospects for the synthesis of polymer brushes with tailorable properties. More recently, thanks to the growing interest in the use of brushes for the generation of functional surfaces, the need for advanced patterning and characterization approaches rapidly increased. Meeting these needs requires the contribution of experts from different disciplines: polymer chemistry, surface science, electrochemistry and particle physics. The focus of this review is to highlight recent developments in the field of polymer brushes, specifically the application of photocatalytic lithography as a versatile patterning strategy, the study of grafted-from polymer brushes by electrochemical methods and, most importantly, the introduction of positron annihilation spectroscopy as a powerful technique for the investigation of the structure of polymer brushes and of their composites with nanoparticles.

Direct growth of single-crystalline III–V semiconductors on amorphous substrates

DOE PAGES

Chen, Kevin; Kapadia, Rehan; Harker, Audrey; ...

2016-01-27

The III–V compound semiconductors exhibit superb electronic and optoelectronic properties. Traditionally, closely lattice-matched epitaxial substrates have been required for the growth of high-quality single-crystal III–V thin films and patterned microstructures. To remove this materials constraint, here we introduce a growth mode that enables direct writing of single-crystalline III–V’s on amorphous substrates, thus further expanding their utility for various applications. The process utilizes templated liquid-phase crystal growth that results in user-tunable, patterned micro and nanostructures of single-crystalline III–V’s of up to tens of micrometres in lateral dimensions. InP is chosen as a model material system owing to its technological importance. Themore » patterned InP single crystals are configured as high-performance transistors and photodetectors directly on amorphous SiO 2 growth substrates, with performance matching state-of-the-art epitaxially grown devices. In conclusion, the work presents an important advance towards universal integration of III–V’s on application-specific substrates by direct growth.« less

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.

Direct growth of single-crystalline III–V semiconductors on amorphous substrates

PubMed Central

Chen, Kevin; Kapadia, Rehan; Harker, Audrey; Desai, Sujay; Seuk Kang, Jeong; Chuang, Steven; Tosun, Mahmut; Sutter-Fella, Carolin M.; Tsang, Michael; Zeng, Yuping; Kiriya, Daisuke; Hazra, Jubin; Madhvapathy, Surabhi Rao; Hettick, Mark; Chen, Yu-Ze; Mastandrea, James; Amani, Matin; Cabrini, Stefano; Chueh, Yu-Lun; Ager III, Joel W.; Chrzan, Daryl C.; Javey, Ali

2016-01-01

The III–V compound semiconductors exhibit superb electronic and optoelectronic properties. Traditionally, closely lattice-matched epitaxial substrates have been required for the growth of high-quality single-crystal III–V thin films and patterned microstructures. To remove this materials constraint, here we introduce a growth mode that enables direct writing of single-crystalline III–V's on amorphous substrates, thus further expanding their utility for various applications. The process utilizes templated liquid-phase crystal growth that results in user-tunable, patterned micro and nanostructures of single-crystalline III–V's of up to tens of micrometres in lateral dimensions. InP is chosen as a model material system owing to its technological importance. The patterned InP single crystals are configured as high-performance transistors and photodetectors directly on amorphous SiO2 growth substrates, with performance matching state-of-the-art epitaxially grown devices. The work presents an important advance towards universal integration of III–V's on application-specific substrates by direct growth. PMID:26813257

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.

Choosing the Rules: Distinct and Overlapping Frontoparietal Representations of Task Rules for Perceptual Decisions

PubMed Central

Kriegeskorte, Nikolaus; Carlin, Johan D.; Rowe, James B.

2013-01-01

Behavior is governed by rules that associate stimuli with responses and outcomes. Human and monkey studies have shown that rule-specific information is widely represented in the frontoparietal cortex. However, it is not known how establishing a rule under different contexts affects its neural representation. Here, we use event-related functional MRI (fMRI) and multivoxel pattern classification methods to investigate the human brain's mechanisms of establishing and maintaining rules for multiple perceptual decision tasks. Rules were either chosen by participants or specifically instructed to them, and the fMRI activation patterns representing rule-specific information were compared between these contexts. We show that frontoparietal regions differ in the properties of their rule representations during active maintenance before execution. First, rule-specific information maintained in the dorsolateral and medial frontal cortex depends on the context in which it was established (chosen vs specified). Second, rule representations maintained in the ventrolateral frontal and parietal cortex are independent of the context in which they were established. Furthermore, we found that the rule-specific coding maintained in anticipation of stimuli may change with execution of the rule: representations in context-independent regions remain invariant from maintenance to execution stages, whereas rule representations in context-dependent regions do not generalize to execution stage. The identification of distinct frontoparietal systems with context-independent and context-dependent task rule representations, and the distinction between anticipatory and executive rule representations, provide new insights into the functional architecture of goal-directed behavior. PMID:23864675

Feasibility of e-paper made with cellulose

NASA Astrophysics Data System (ADS)

Yoo, K. H.; Han, K. J.; Chen, Yi; Kang, K. S.; Kim, Jaehwan

2008-03-01

Cellulose is a beneficial material that has low cost, light weight, high compatibility, and biodegradability. Recently electro-active paper (EAPap) composed with cellulose was discovered as a smart material for application to variety industrial fields such as smart wall-paper, actuator, and magic carpet. It also exhibited actuator property through ion migration and piezoelectric effect. Since cellulose acetate (CA) film has optically transparent property, we focused on optical field application, such as electronic paper, prismsheet, and polarized film. Since CA can be easily dissolved in variety of organic solvent, various weight % (from 1 to 25 wt. %) of CA solution in acetone was prepared. Polydimethylsilane (PDMS) master pattern was fabricated on the silicone wafer. CA solution was poured to the master mold and dried using spin-coating or tape casting method. Various shape and height patterns, such as circle, honeycomb, and rectangular patterns were fabricated using 12 wt. % CA solution. The resulting pattern showed uniform size in the large area without defect. These patterns can be utilized as a substrate and cell pattern for the electronic paper. To investigate saponification (SA) effect to convert CA to regenerated cellulose, CA film was immersed into the sodium methoxide solution in methanol for various times. The fabricated CA films were stretched and immersed into the sodium methoxide solution in methanol to desubstitute the acetate group. These regenerated cellulose films have larger mechanical strength than CA films. Although the UV-visible transmittance was decreased as increasing SA time, the transmittance of the further SA process and stretched film backed up near untreated CA film. Although the cross-sectional image of the saponified and unstretched CA film did not have specific directional structure, the cross-sectional FESEM image of the saponified and stretched CA film had one directional fiber structure. The fiber was aligned to the stretched direction. Most of the compositions were one directional ordered nanofibers having diameter of approximately 30nm.

Electrophysiological Correlates of Second-Language Syntactic Processes Are Related to Native and Second Language Distance Regardless of Age of Acquisition

PubMed Central

Díaz, Begoña; Erdocia, Kepa; de Menezes, Robert F.; Mueller, Jutta L.; Sebastián-Gallés, Núria; Laka, Itziar

2016-01-01

In the present study, we investigate how early and late L2 learners process L2 grammatical traits that are either present or absent in their native language (L1). Thirteen early (AoA = 4 years old) and 13 late (AoA = 18 years old) Spanish learners of Basque performed a grammatical judgment task on auditory Basque sentences while their event-related brain potentials (ERPs) were recorded. The sentences contained violations of a syntactic property specific to participants' L2, i.e., ergative case, or violations of a syntactic property present in both of the participants' languages, i.e., verb agreement. Two forms of verb agreement were tested: subject agreement, found in participants' L1 and L2, and object agreement, present only in participants' L2. Behaviorally, early bilinguals were more accurate in the judgment task than late L2 learners. Early bilinguals showed native-like ERPs for verb agreement, which differed from the late learners' ERP pattern. Nonetheless, approximation to native-likeness was greater for the subject-verb agreement processing, the type of verb-agreement present in participants' L1, compared to object-verb agreement, the type of verb-agreement present only in participants' L2. For the ergative argument alignment, unique to L2, the two non-native groups showed similar ERP patterns which did not correspond to the natives' ERP pattern. We conclude that non-native syntactic processing approximates native processing for early L2 acquisition and high proficiency levels when the syntactic property is common to the L1 and L2. However, syntactic traits that are not present in the L1 do not rely on native-like processing, despite early AoA and high proficiency. PMID:26903930

Electrophysiological and morphological properties of neurons in the prepositus hypoglossi nucleus that express both ChAT and VGAT in a double-transgenic rat model.

PubMed

Saito, Yasuhiko; Zhang, Yue; Yanagawa, Yuchio

2015-04-01

Although it has been proposed that neurons that contain both acetylcholine (ACh) and γ-aminobutyric acid (GABA) are present in the prepositus hypoglossi nucleus (PHN), these neurons have not been characterized because of the difficulty in identifying them. In the present study, PHN neurons that express both choline acetyltransferase and the vesicular GABA transporter (VGAT) were identified using double-transgenic rats, in which the cholinergic and inhibitory neurons express the fluorescent proteins tdTomato and Venus, respectively. To characterize the neurons that express both tdTomato and Venus (D+ neurons), the afterhyperpolarization (AHP) profiles and firing patterns of these neurons were investigated via whole-cell recordings of brainstem slice preparations. Regarding the three AHP profiles and four firing patterns that the D+ neurons exhibited, an AHP with an afterdepolarization and a firing pattern that exhibited a delay in the generation of the first spike were the preferential properties of these neurons. In the three morphological types classified, the multipolar type that exhibited radiating dendrites was predominant among the D+ neurons. Immunocytochemical analysis revealed that the VGAT-immunopositive axonal boutons that expressed tdTomato were primarily located in the dorsal cap of inferior olive (IO) and the PHN. Although the PHN receives cholinergic inputs from the pedunculopontine tegmental nucleus and laterodorsal tegmental nucleus, D+ neurons were absent from these brain areas. Together, these results suggest that PHN neurons that co-express ACh and GABA exhibit specific electrophysiological and morphological properties, and innervate the dorsal cap of the IO and the PHN. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Stripe-patterned thermo-responsive cell culture dish for cell separation without cell labeling.

PubMed

Kumashiro, Yoshikazu; Ishihara, Jun; Umemoto, Terumasa; Itoga, Kazuyoshi; Kobayashi, Jun; Shimizu, Tatsuya; Yamato, Masayuki; Okano, Teruo

2015-02-11

A stripe-patterned thermo-responsive surface is prepared to enable cell separation without labeling. The thermo-responsive surface containing a 3 μm striped pattern exhibits various cell adhesion and detachment properties. A mixture of three cell types is separated on the patterned surface based on their distinct cell-adhesion properties, and the composition of the cells is analyzed by flow cytometry. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular modeling.

PubMed

Pichert, Annelie; Samsonov, Sergey A; Theisgen, Stephan; Thomas, Lars; Baumann, Lars; Schiller, Jürgen; Beck-Sickinger, Annette G; Huster, Daniel; Pisabarro, M Teresa

2012-01-01

The interactions between glycosaminoglycans (GAGs), important components of the extracellular matrix, and proteins such as growth factors and chemokines play critical roles in cellular regulation processes. Therefore, the design of GAG derivatives for the development of innovative materials with bio-like properties in terms of their interaction with regulatory proteins is of great interest for tissue engineering and regenerative medicine. Previous work on the chemokine interleukin-8 (IL-8) has focused on its interaction with heparin and heparan sulfate, which regulate chemokine function. However, the extracellular matrix contains other GAGs, such as hyaluronic acid (HA), dermatan sulfate (DS) and chondroitin sulfate (CS), which have so far not been characterized in terms of their distinct molecular recognition properties towards IL-8 in relation to their length and sulfation patterns. NMR and molecular modeling have been in great part the methods of choice to study the structural and recognition properties of GAGs and their protein complexes. However, separately these methods have challenges to cope with the high degree of similarity and flexibility that GAGs exhibit. In this work, we combine fluorescence spectroscopy, NMR experiments, docking and molecular dynamics simulations to study the configurational and recognition properties of IL-8 towards a series of HA and CS derivatives and DS. We analyze the effects of GAG length and sulfation patterns in binding strength and specificity, and the influence of GAG binding on IL-8 dimer formation. Our results highlight the importance of combining experimental and theoretical approaches to obtain a better understanding of the molecular recognition properties of GAG-protein systems.

Machine learning reveals cyclic changes in seismic source spectra in Geysers geothermal field.

PubMed

Holtzman, Benjamin K; Paté, Arthur; Paisley, John; Waldhauser, Felix; Repetto, Douglas

2018-05-01

The earthquake rupture process comprises complex interactions of stress, fracture, and frictional properties. New machine learning methods demonstrate great potential to reveal patterns in time-dependent spectral properties of seismic signals and enable identification of changes in faulting processes. Clustering of 46,000 earthquakes of 0.3 < M L < 1.5 from the Geysers geothermal field (CA) yields groupings that have no reservoir-scale spatial patterns but clear temporal patterns. Events with similar spectral properties repeat on annual cycles within each cluster and track changes in the water injection rates into the Geysers reservoir, indicating that changes in acoustic properties and faulting processes accompany changes in thermomechanical state. The methods open new means to identify and characterize subtle changes in seismic source properties, with applications to tectonic and geothermal seismicity.

Longitudinal development of cortical thickness, folding, and fiber density networks in the first 2 years of life.

PubMed

Nie, Jingxin; Li, Gang; Wang, Li; Shi, Feng; Lin, Weili; Gilmore, John H; Shen, Dinggang

2014-08-01

Quantitatively characterizing the development of cortical anatomical networks during the early stage of life plays an important role in revealing the relationship between cortical structural connection and high-level functional development. The development of correlation networks of cortical-thickness, cortical folding, and fiber-density is systematically analyzed in this article to study the relationship between different anatomical properties during the first 2 years of life. Specifically, longitudinal MR images of 73 healthy subjects from birth to 2 year old are used. For each subject at each time point, its measures of cortical thickness, cortical folding, and fiber density are projected to its cortical surface that has been partitioned into 78 cortical regions. Then, the correlation matrices for cortical thickness, cortical folding, and fiber density at each time point can be constructed, respectively, by computing the inter-regional Pearson correlation coefficient (of any pair of ROIs) across all 73 subjects. Finally, the presence/absence pattern (i.e., binary pattern) of the connection network is constructed from each inter-regional correlation matrix, and its statistical and anatomical properties are adopted to analyze the longitudinal development of anatomical networks. The results show that the development of anatomical network could be characterized differently by using different anatomical properties (i.e., using cortical thickness, cortical folding, or fiber density). Copyright © 2013 Wiley Periodicals, Inc.

The Spatial Scaling of Global Rainfall Extremes

NASA Astrophysics Data System (ADS)

Devineni, N.; Xi, C.; Lall, U.; Rahill-Marier, B.

2013-12-01

Floods associated with severe storms are a significant source of risk for property, life and supply chains. These property losses tend to be determined as much by the duration of flooding as by the depth and velocity of inundation. High duration floods are typically induced by persistent rainfall (upto 30 day duration) as seen recently in Thailand, Pakistan, the Ohio and the Mississippi Rivers, France, and Germany. Events related to persistent and recurrent rainfall appear to correspond to the persistence of specific global climate patterns that may be identifiable from global, historical data fields, and also from climate models that project future conditions. A clear understanding of the space-time rainfall patterns for events or for a season will enable in assessing the spatial distribution of areas likely to have a high/low inundation potential for each type of rainfall forcing. In this paper, we investigate the statistical properties of the spatial manifestation of the rainfall exceedances. We also investigate the connection of persistent rainfall events at different latitudinal bands to large-scale climate phenomena such as ENSO. Finally, we present the scaling phenomena of contiguous flooded areas as a result of large scale organization of long duration rainfall events. This can be used for spatially distributed flood risk assessment conditional on a particular rainfall scenario. Statistical models for spatio-temporal loss simulation including model uncertainty to support regional and portfolio analysis can be developed.

Modifications of Ti-6Al-4V surfaces by direct-write laser machining of linear grooves

NASA Astrophysics Data System (ADS)

Ulerich, Joseph P.; Ionescu, Lara C.; Chen, Jianbo; Soboyejo, Winston O.; Arnold, Craig B.

2007-02-01

As patients who receive orthopedic implants live longer and opt for surgery at a younger age, the need to extend the in vivo lifetimes of these implants has grown. One approach is to pattern implant surfaces with linear grooves, which elicit a cellular response known as contact guidance. Lasers provide a unique method of generating these surface patterns because they are capable of modifying physical and chemical properties over multiple length scales. In this paper we explore the relationship between surface morphology and laser parameters such as fluence, pulse overlap (translation distance), number of passes, and machining environment. We find that using simple procedures involving multiple passes it is possible to manipulate groove properties such as depth, shape, sub-micron roughness, and chemical composition of the Ti-6Al-4V oxide layer. Finally, we demonstrate this procedure by machining several sets of grooves with the same primary groove parameters but varied secondary characteristics. The significance of the secondary groove characteristics is demonstrated by preliminary cell studies indicating that the grooves exhibit basic features of contact guidance and that the cell proliferation in these grooves are significantly altered despite their similar primary characteristics. With further study it will be possible to use specific laser parameters during groove formation to create optimal physical and chemical properties for improved osseointegration.

Direct generation of superhydrophobic microstructures in metals by UV laser sources in the nanosecond regime

NASA Astrophysics Data System (ADS)

Ocaña, Jose L.; Jagdheesh, R.; García-Ballesteros, J. J.

2016-02-01

The current availability of new advanced fiber and DPSS lasers with characteristic pulse lengths ranging from ns to fs has provided a unique frame in which the development of laser-generated microstructures has been made possible for very diverse kinds of materials and applications. At the same time, the development of the appropriate laser-processing workstations granting the appropriate precision and repeatability of the respective laser interaction processes in line with the characteristic dimension features required in the microstructured samples has definitively consolidated laser surface microstructuring as a reference domain, nowadays, unavoidable for the design and manufacturing of current use microsystem: MEMSs, fluidic devices, advanced sensors, biomedical devices and instruments, etc., are all among the most well-known developments of the micromanufacturing technology. Completing the broad spectrum of applications developed mostly involving the generation of geometrical features on a subtrate with specific functional purposes, a relatively new, emerging class of laser-microstructuring techniques is finding an important niche of application in the generation of physically structured surfaces (particularly of metallic materials) with specific contact, friction, and wear functionalities, for whose generation the concourse of different types of laser sources is being found as an appropriate tool. In this paper, the application of laser sources with emission in the UV and at ns time regime to the surface structuration of metal surfaces (specifically Al) for the modification of their wettability properties is described as an attractive application basis for the generation of self-cleaning properties of extended functional surfaces. Flat aluminum sheets of thickness 100 μm were laser machined with ultraviolet laser pulses of 30 ns with different laser parameters to optimize the process parameters. The samples produced at the optimum conditions with respect to contact angle measurement were subjected to microstructure and chemical analysis. The wetting properties were evaluated by static contact angle measurements on the laser-patterned surface. The laser-patterned microstructures exhibited superhydrophobicity with a maximum contact angle of 180° for the droplet volumes in the range of 8-12 μl.

Lytic and latent antigens of the human gammaherpesviruses Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus induce T-cell responses with similar functional properties and memory phenotypes.

PubMed

Bihl, Florian; Narayan, Murli; Chisholm, John V; Henry, Leah M; Suscovich, Todd J; Brown, Elizabeth E; Welzel, Tania M; Kaufmann, Daniel E; Zaman, Tauheed M; Dollard, Sheila; Martin, Jeff N; Wang, Fred; Scadden, David T; Kaye, Kenneth M; Brander, Christian

2007-05-01

The cellular immunity against Kaposi's sarcoma-associated herpesvirus (KSHV) is poorly characterized and has not been compared to T-cell responses against other human herpesviruses. Here, novel and dominant targets of KSHV-specific cellular immunity are identified and compared to T cells specific for lytic and latent antigens in a second human gammaherpesvirus, Epstein-Barr virus. The data identify a novel HLA-B57- and HLA-B58-restricted epitope in the Orf57 protein and show consistently close parallels in immune phenotypes and functional response patterns between cells targeting lytic or latent KSHV- and EBV-encoded antigens, suggesting common mechanisms in the induction of these responses.

Coherent light depolarization by multiple scattering media and tissues: some fundamentals and applications

NASA Astrophysics Data System (ADS)

Zimnyakov, Dmitry A.; Tuchin, Valery V.; Yodh, Arjun G.; Mishin, Alexey A.; Peretochkin, Igor S.

1998-04-01

Relationships between decorrelation and depolarization of coherent light scattered by disordered media are examined by using the conception of the photon paths distribution functions. Analysis of behavior of the autocorrelation functions of the scattered field fluctuations and their polarization properties allows us to introduce generalized parameter of scattering media such as specific correlation time. Determination of specific correlation time has been carried out for phantom scattering media (water suspensions of polystyrene spheres). Results of statistical, correlation and polarization analysis of static and dynamic speckle patterns carried out in the experiments with human sclera with artificially controlled optical transmittance are presented. Some possibilities of applications of such polarization- correlation technique for monitoring and visualization of non- single scattering tissue structures are discussed.

Distributional properties of relative phase in bimanual coordination.

PubMed

James, Eric; Layne, Charles S; Newell, Karl M

2010-10-01

Studies of bimanual coordination have typically estimated the stability of coordination patterns through the use of the circular standard deviation of relative phase. The interpretation of this statistic depends upon the assumption of a von Mises distribution. The present study tested this assumption by examining the distributional properties of relative phase in three bimanual coordination patterns. There were significant deviations from the von Mises distribution due to differences in the kurtosis of distributions. The kurtosis depended upon the relative phase pattern performed, with leptokurtic distributions occurring in the in-phase and antiphase patterns and platykurtic distributions occurring in the 30° pattern. Thus, the distributional assumptions needed to validly and reliably use the standard deviation are not necessarily present in relative phase data though they are qualitatively consistent with the landscape properties of the intrinsic dynamics.

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

Neural dynamics based on the recognition of neural fingerprints

PubMed Central

Carrillo-Medina, José Luis; Latorre, Roberto

2015-01-01

Experimental evidence has revealed the existence of characteristic spiking features in different neural signals, e.g., individual neural signatures identifying the emitter or functional signatures characterizing specific tasks. These neural fingerprints may play a critical role in neural information processing, since they allow receptors to discriminate or contextualize incoming stimuli. This could be a powerful strategy for neural systems that greatly enhances the encoding and processing capacity of these networks. Nevertheless, the study of information processing based on the identification of specific neural fingerprints has attracted little attention. In this work, we study (i) the emerging collective dynamics of a network of neurons that communicate with each other by exchange of neural fingerprints and (ii) the influence of the network topology on the self-organizing properties within the network. Complex collective dynamics emerge in the network in the presence of stimuli. Predefined inputs, i.e., specific neural fingerprints, are detected and encoded into coexisting patterns of activity that propagate throughout the network with different spatial organization. The patterns evoked by a stimulus can survive after the stimulation is over, which provides memory mechanisms to the network. The results presented in this paper suggest that neural information processing based on neural fingerprints can be a plausible, flexible, and powerful strategy. PMID:25852531

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.

Au-Ag-Cu nano-alloys: tailoring of permittivity

PubMed Central

Hashimoto, Yoshikazu; Seniutinas, Gediminas; Balčytis, Armandas; Juodkazis, Saulius; Nishijima, Yoshiaki

2016-01-01

Precious metal alloys enables new possibilities to tailor materials for specific optical functions. Here we present a systematic study of the effects of a nanoscale alloying on the permittivity of Au-Ag-Cu metals at 38 different atomic mixing ratios. The permittivity was measured and analyzed numerically by applying the Drude model. X-ray diffraction (XRD) revealed the face centered cubic lattice of the alloys. Both, optical spectra and XRD results point towards an equivalent composition-dependent electron scattering behavior. Correlation between the fundamental structural parameters of alloys and the resulting optical properties is elucidated. Plasmonic properties of the Au-Ag-Cu alloy nanoparticles were investigated by numerical simulations. Guidelines for designing plasmonic response of nano- structures and their patterns are presented from the material science perspective. PMID:27118459

The immunomodulatory properties of the CD5 lymphocyte receptor in health and disease

PubMed Central

Soldevila, Gloria; Raman, Chander; Lozano, Francisco

2011-01-01

Summary CD5 is a scavenger-like receptor expressed in association with the antigen-specific receptors on T and B-1a lymphocytes. Recent studies reveal a broader biology for CD5 that includes its role as regulator of cell death and as a receptor for pathogen associated molecular patterns, in addition to its previously described function as an inhibitory receptor. These findings shed new light into the mechanistic role of CD5 in leukemias and effector cells to exogenous (infectious) or endogenous (autoimmune, tumoral) antigens. The newly identified properties make this receptor a potential candidate to be targeted for therapeutic intervention as well as immune modulation. This review describes the current knowledge on the function of CD5 as an immunomodulatory receptor both in health and disease. PMID:21482089

Role of autofluorescence in inflammatory/infective diseases of the retina and choroid.

PubMed

Samy, Ahmed; Lightman, Sue; Ismetova, Filis; Talat, Lazha; Tomkins-Netzer, Oren

2014-01-01

Fundus autofluorescence (FAF) has recently emerged as a novel noninvasive imaging technique that uses the fluorescent properties of innate fluorophores accumulated in the retinal pigment epithelium (RPE) to assess the health and viability of the RPE/photoreceptor complex. Recent case reports suggest FAF as a promising tool for monitoring eyes with posterior uveitis helping to predict final visual outcome. In this paper we review the published literature on FAF in these disorders, specifically patterns in infectious and noninfectious uveitis, and illustrate some of these with short case histories.

Ear Deformations Give Bats a Physical Mechanism for Fast Adaptation of Ultrasonic Beam Patterns

NASA Astrophysics Data System (ADS)

Gao, Li; Balakrishnan, Sreenath; He, Weikai; Yan, Zhen; Müller, Rolf

2011-11-01

A large number of mammals, including humans, have intricate outer ear shapes that diffract incoming sound in a direction- and frequency-specific manner. Through this physical process, the outer ear shapes encode sound-source information into the sensory signals from each ear. Our results show that horseshoe bats could dynamically control these diffraction processes through fast nonrigid ear deformations. The bats’ ear shapes can alter between extreme configurations in about 100 ms and thereby change their acoustic properties in ways that would suit different acoustic sensing tasks.

NDRAM: nonlinear dynamic recurrent associative memory for learning bipolar and nonbipolar correlated patterns.

PubMed

Chartier, Sylvain; Proulx, Robert

2005-11-01

This paper presents a new unsupervised attractor neural network, which, contrary to optimal linear associative memory models, is able to develop nonbipolar attractors as well as bipolar attractors. Moreover, the model is able to develop less spurious attractors and has a better recall performance under random noise than any other Hopfield type neural network. Those performances are obtained by a simple Hebbian/anti-Hebbian online learning rule that directly incorporates feedback from a specific nonlinear transmission rule. Several computer simulations show the model's distinguishing properties.

Atomistic insight into the adsorption site selectivity of stepped Au(111) surfaces

NASA Astrophysics Data System (ADS)

Gaspari, Roberto; Pignedoli, Carlo A.; Fasel, Roman; Treier, Matthias; Passerone, Daniele

2010-07-01

Using classical and ab initio simulations, we study the interplay between the Au(111) surface reconstruction and monoatomic steps on a vicinal face. The experimentally observed discommensuration line patterns on a specific vicinal are reproduced and explained, and a complete description of the structure is given. An unusual atomic arrangement is shown to be responsible for the lower reactivity of hcp segments of step edges compared to the one of fcc segments. Our results provide an unprecedented understanding of the electronic and geometric properties of the complex Au(111) surface.

Supramolecular structure of polymer binders and composites: targeted control based on the hierarchy

NASA Astrophysics Data System (ADS)

Matveeva, Larisa; Belentsov, Yuri

2017-10-01

The article discusses the problem of targeted control over properties by modifying the supramolecular structure of polymer binders and composites based on their hierarchy. Control over the structure formation of polymers and introduction of modifying additives should be tailored to the specific hierarchical structural levels. Characteristics of polymer materials are associated with structural defects, which also display a hierarchical pattern. Classification of structural defects in polymers is presented. The primary structural level (nano level) of supramolecular formations is of great importance to the reinforcement and regulation of strength characteristics.

An anisotropically and heterogeneously aligned patterned electrospun scaffold with tailored mechanical property and improved bioactivity for vascular tissue engineering.

PubMed

Xu, He; Li, Haiyan; Ke, Qinfei; Chang, Jiang

2015-04-29

The development of vascular scaffolds with controlled mechanical properties and stimulatory effects on biological activities of endothelial cells still remains a significant challenge to vascular tissue engineering. In this work, we reported an innovative approach to prepare a new type of vascular scaffolds with anisotropically and heterogeneously aligned patterns using electrospinning technique with unique wire spring templates, and further investigated the structural effects of the patterned electrospun scaffolds on mechanical properties and angiogenic differentiation of human umbilical vein endothelial cells (HUVECs). Results showed that anisotropically aligned patterned nanofibrous structure was obtained by depositing nanofibers on template in a structurally different manner, one part of nanofibers densely deposited on the embossments of wire spring and formed cylindrical-like structures in the transverse direction, while others loosely suspended and aligned along the longitudinal direction, forming a three-dimensional porous microstructure. We further found that such structures could efficiently control the mechanical properties of electrospun vascular scaffolds in both longitudinal and transverse directions by altering the interval distances between the embossments of patterned scaffolds. When HUVECs were cultured on scaffolds with different microstructures, the patterned scaffolds distinctively promoted adhesion of HUVECs at early stage and proliferation during the culture period. Most importantly, cells experienced a large shape change associated with cell cytoskeleton and nuclei remodeling, leading to a stimulatory effect on angiogenesis differentiation of HUVECs by the patterned microstructures of electrospun scaffolds, and the scaffolds with larger distances of intervals showed a higher stimulatory effect. These results suggest that electrospun scaffolds with the anisotropically and heterogeneously aligned patterns, which could efficiently control the mechanical properties and bioactivities of the scaffolds, might have great potential in vascular tissue engineering application.

Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

NASA Astrophysics Data System (ADS)

Kathrin Hassler, Sibylle; Weiler, Markus; Blume, Theresa

2018-01-01

Transpiration is a key process in the hydrological cycle, and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation and evaluation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology and soils, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls.We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites across a 290 km2 catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocity and derived sap flow patterns of these 61 trees, and we determined the importance of the different controls.Results indicate that a combination of mainly tree- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, geology and aspect. For sap flow we included only the stand- and site-specific predictors in the models to ensure variable independence. Of those, geology and aspect were most important. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, are correlated to the temporal dynamics of potential evaporation. We conclude that transpiration estimates on the landscape scale would benefit from not only consideration of hydro-meteorological drivers, but also tree, stand and site characteristics in order to improve the spatial and temporal representation of transpiration for hydrological and soil-vegetation-atmosphere transfer models.

Selective and Efficient Neural Coding of Communication Signals Depends on Early Acoustic and Social Environment

PubMed Central

Amin, Noopur; Gastpar, Michael; Theunissen, Frédéric E.

2013-01-01

Previous research has shown that postnatal exposure to simple, synthetic sounds can affect the sound representation in the auditory cortex as reflected by changes in the tonotopic map or other relatively simple tuning properties, such as AM tuning. However, their functional implications for neural processing in the generation of ethologically-based perception remain unexplored. Here we examined the effects of noise-rearing and social isolation on the neural processing of communication sounds such as species-specific song, in the primary auditory cortex analog of adult zebra finches. Our electrophysiological recordings reveal that neural tuning to simple frequency-based synthetic sounds is initially established in all the laminae independent of patterned acoustic experience; however, we provide the first evidence that early exposure to patterned sound statistics, such as those found in native sounds, is required for the subsequent emergence of neural selectivity for complex vocalizations and for shaping neural spiking precision in superficial and deep cortical laminae, and for creating efficient neural representations of song and a less redundant ensemble code in all the laminae. Our study also provides the first causal evidence for ‘sparse coding’, such that when the statistics of the stimuli were changed during rearing, as in noise-rearing, that the sparse or optimal representation for species-specific vocalizations disappeared. Taken together, these results imply that a layer-specific differential development of the auditory cortex requires patterned acoustic input, and a specialized and robust sensory representation of complex communication sounds in the auditory cortex requires a rich acoustic and social environment. PMID:23630587

Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

NASA Astrophysics Data System (ADS)

Hassler, Sibylle; Markus, Weiler; Theresa, Blume

2017-04-01

Transpiration is a key process in the hydrological cycle and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls. We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites spread over a 290 km2-catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocities of these 61 trees and determined the importance of the different predictors. Results indicate that a combination of tree-, stand- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, the stand density, geology and aspect. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, are correlated to the temporal dynamics of potential evaporation. Thus, transpiration estimates at the landscape scale would benefit from not only considering hydro-meteorological drivers, but also including tree, stand and site characteristics in order to improve the spatial representation of transpiration for hydrological and soil-vegetation-atmosphere transfer models.

Evaluation of Vertical Lacunarity Profiles in Forested Areas Using Airborne Laser Scanning Point Clouds

NASA Astrophysics Data System (ADS)

Székely, B.; Kania, A.; Standovár, T.; Heilmeier, H.

2016-06-01

The horizontal variation and vertical layering of the vegetation are important properties of the canopy structure determining the habitat; three-dimensional (3D) distribution of objects (shrub layers, understory vegetation, etc.) is related to the environmental factors (e.g., illumination, visibility). It has been shown that gaps in forests, mosaic-like structures are essential to biodiversity; various methods have been introduced to quantify this property. As the distribution of gaps in the vegetation is a multi-scale phenomenon, in order to capture it in its entirety, scale-independent methods are preferred; one of these is the calculation of lacunarity. We used Airborne Laser Scanning point clouds measured over a forest plantation situated in a former floodplain. The flat topographic relief ensured that the tree growth is independent of the topographic effects. The tree pattern in the plantation crops provided various quasi-regular and irregular patterns, as well as various ages of the stands. The point clouds were voxelized and layers of voxels were considered as images for two-dimensional input. These images calculated for a certain vicinity of reference points were taken as images for the computation of lacunarity curves, providing a stack of lacunarity curves for each reference points. These sets of curves have been compared to reveal spatial changes of this property. As the dynamic range of the lacunarity values is very large, the natural logarithms of the values were considered. Logarithms of lacunarity functions show canopy-related variations, we analysed these variations along transects. The spatial variation can be related to forest properties and ecology-specific aspects.

Visual Attention to Global and Local Stimulus Properties in 6-Month-Old Infants: Individual Differences and Event-Related Potentials

ERIC Educational Resources Information Center

Guy, Maggie W.; Reynolds, Greg D.; Zhang, Dantong

2013-01-01

Event-related potentials (ERPs) were utilized in an investigation of 21 six-month-olds' attention to and processing of global and local properties of hierarchical patterns. Overall, infants demonstrated an advantage for processing the overall configuration (i.e., global properties) of local features of hierarchical patterns; however,…

The calcination temperature dependence of microstructural, vibrational spectra and magnetic properties of nanocrystalline Mn0.5Zn0.5Fe2O4

NASA Astrophysics Data System (ADS)

Indrayana, I. P. T.; Siregar, N.; Suharyadi, E.; Kato, T.; Iwata, S.

2016-11-01

Effect of calcination temperature on microstructural, vibrational, and magnetic properties of Mn0.5Zn0.5Fe2O4 nanoparticles have been successfully investigated. The nanoparticles were synthesized via coprecipitation method and calcined at different temperatures varying from 400, 600, 800, and 1000°C. The X-ray diffraction (XRD) pattern confirmed the formation of cubic spinel structure Mn0.5Zn0.5Fe2O4 with crystallite size ranging from 18.3 nm to 24.8 nm. The TEM micrograph showed the morphology of nanoparticles change from nearly spherical to cubic form after calcination. The FTIR spectra confirmed the existence of vibrations at 416.6 cm-1 - 455.2 cm-1 and 555.5 cm-1 -578.6 cm-1 which corresponds to the intrinsic stretching vibration of metal-oxygen at octahedral and tetrahedral sites, respectively. The maximum specific magnetization and coercivity increase with increasing calcination temperature. The maximum specific magnetization value of 54.7emu/gram was obtained for sample calcined at 1000°C. The results showed that calcination treatment will facilitate the tunability of microstructural and magnetic properties of nanoparticles for expanding the field of application.

Stiffness Customization and Patterning for Property Modulation of Silicone-Based Soft Pneumatic Actuators.

PubMed

Sun, Yi; Yap, Hong Kai; Liang, Xinquan; Guo, Jin; Qi, Peng; Ang, Marcelo H; Yeow, Chen-Hua

2017-09-01

Soft pneumatic actuators (SPAs), as novel types of motion drivers for robotic devices, excel in many applications, such as rehabilitation and biomimicry, which demand compliance and softness. To further expand their scope of utilization, the SPAs should be customizable to meet the distinctive requirements of different applications. This article proposes a novel perspective on the SPA working mechanism based on stiffness distribution and then presents a versatile method called stiffness customization and patterning (SCP) for SPA body stiffness layout as a novel attempt to customize SPAs with distinctive properties. We fabricated a hybrid type of material combining unstretchable material and silicone with customizable aggregated elasticity. The tensile results showed that embedding unstretchable material directly increases the stiffness of the hybrid material sample, and our stress-strain model for SCP is able to adequately predict the elasticity of hybrid samples with specific material ratios. By applying this approach to bending-type SPAs, we are able to mitigate SPA buckling, a main failure mode of SPAs, and improve the SPA tip force by using hybrid material with globally increased stiffness. We also diversify bending modalities with different stiffness configurations in the hybrid material. SCP offers numerous ways to engineer SPAs for more applications.

Uninformative memories will prevail: the storage of correlated representations and its consequences.

PubMed

Kropff, Emilio; Treves, Alessandro

2007-11-01

Autoassociative networks were proposed in the 80's as simplified models of memory function in the brain, using recurrent connectivity with Hebbian plasticity to store patterns of neural activity that can be later recalled. This type of computation has been suggested to take place in the CA3 region of the hippocampus and at several levels in the cortex. One of the weaknesses of these models is their apparent inability to store correlated patterns of activity. We show, however, that a small and biologically plausible modification in the "learning rule" (associating to each neuron a plasticity threshold that reflects its popularity) enables the network to handle correlations. We study the stability properties of the resulting memories (in terms of their resistance to the damage of neurons or synapses), finding a novel property of autoassociative networks: not all memories are equally robust, and the most informative are also the most sensitive to damage. We relate these results to category-specific effects in semantic memory patients, where concepts related to "non-living things" are usually more resistant to brain damage than those related to "living things," a phenomenon suspected to be rooted in the correlation between representations of concepts in the cortex.

Fluorophore labeling of a cell-penetrating peptide induces differential effects on its cellular distribution and affects cell viability.

PubMed

Birch, Ditlev; Christensen, Malene Vinther; Staerk, Dan; Franzyk, Henrik; Nielsen, Hanne Mørck

2017-12-01

Cell-penetrating peptides constitute efficient delivery vectors, and studies of their uptake and mechanism of translocation typically involve fluorophore-labeled conjugates. In the present study, the influence of a number of specific fluorophores on the physico-chemical properties and uptake-related characteristics of penetratin were studied. An array of seven fluorophores belonging to distinct structural classes was examined, and the impact of fluorophore labeling on intracellular distribution and cytotoxicity was correlated to the physico-chemical properties of the conjugates. Exposure of several mammalian cell types to fluorophore-penetratin conjugates revealed a strong structure-dependent reduction in viability (1.5- to 20-fold lower IC 50 values as compared to those of non-labeled penetratin). Also, the degree of less severe effects on membrane integrity, as well as intracellular distribution patterns differed among the conjugates. Overall, neutral hydrophobic fluorophores or negatively charged fluorophores conferred less cytotoxicity as compared to the effect exerted by positively charged, hydrophobic fluorophores. The latter conjugates, however, exhibited less membrane association and more clearly defined intracellular distribution patterns. Thus, selection of the appropriate flurophore is critical. Copyright © 2017 Elsevier B.V. All rights reserved.

Robust curb detection with fusion of 3D-Lidar and camera data.

PubMed

Tan, Jun; Li, Jian; An, Xiangjing; He, Hangen

2014-05-21

Curb detection is an essential component of Autonomous Land Vehicles (ALV), especially important for safe driving in urban environments. In this paper, we propose a fusion-based curb detection method through exploiting 3D-Lidar and camera data. More specifically, we first fuse the sparse 3D-Lidar points and high-resolution camera images together to recover a dense depth image of the captured scene. Based on the recovered dense depth image, we propose a filter-based method to estimate the normal direction within the image. Then, by using the multi-scale normal patterns based on the curb's geometric property, curb point features fitting the patterns are detected in the normal image row by row. After that, we construct a Markov Chain to model the consistency of curb points which utilizes the continuous property of the curb, and thus the optimal curb path which links the curb points together can be efficiently estimated by dynamic programming. Finally, we perform post-processing operations to filter the outliers, parameterize the curbs and give the confidence scores on the detected curbs. Extensive evaluations clearly show that our proposed method can detect curbs with strong robustness at real-time speed for both static and dynamic scenes.

Structure and Dynamics of Water Confined in Imogolite Nanotubes.

PubMed

Scalfi, Laura; Fraux, Guillaume; Boutin, Anne; Coudert, François-Xavier

2018-06-12

We have studied the properties of water adsorbed inside nanotubes of hydrophilic imogolite, an aluminum silicate clay mineral, by means of molecular simulations. We used a classical force field to describe the water and the flexible imogolite nanotube and validated it against the data obtained from first-principles molecular dynamics. With it, we observe a strong structuration of the water confined in the nanotube, with specific adsorption sites and a distribution of hydrogen bond patterns. The combination of number of adsorption sites, their geometry, and the preferential tetrahedral hydrogen bonding pattern of water leads to frustration and disorder. We further characterize the dynamics of the water, as well as the hydrogen bonds formed between water molecules and the nanotube, which is found to be more than 1 order of magnitude longer than water-water hydrogen bonds.

The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx

PubMed Central

Stenseth, Nils Chr.; Ehrich, Dorothee; Rueness, Eli Knispel; Lingjærde, Ole Chr.; Chan, Kung-Sik; Boutin, Stan; O'Donoghue, Mark; Robinson, David A.; Viljugrein, Hildegunn; Jakobsen, Kjetill S.

2004-01-01

The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the “climate forcing of ecological and evolutionary patterns” model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics. PMID:15067131

Experimental study on nonlinear vibrating of aluminum foam using electronic speckle pattern interferometry

NASA Astrophysics Data System (ADS)

Yang, Fujun; Ma, Yinhang; Tao, Nan; He, Xiaoyuan

2017-06-01

Due to its multi properties, including excellent stiffness-to-weight and strength-to-weight ratios, closed-cell aluminum and its alloy foams become candidate materials for use in many high-technology industries, such as the automotive and aerospace industries. For the efficient use of closed-cell foams in structural applications, it is necessary and important to detailly understand their mechanical characteristics. In this paper, the nonlinear vibration responses of the cantilever beams of closed-cell aluminum foams were investigated by use of electronic speckle pattern interferometry (ESPI). The nonlinear resonant mode shapes of testing specimens under harmonic excitation were measured. It is first time to obtain from the experimental results that there exist super-harmonic responses when the cantilever beams of closed-cell aluminum foam were forced to vibrate, which was caused by its specific cellular structures.

Machine learning reveals cyclic changes in seismic source spectra in Geysers geothermal field

PubMed Central

Paisley, John

2018-01-01

The earthquake rupture process comprises complex interactions of stress, fracture, and frictional properties. New machine learning methods demonstrate great potential to reveal patterns in time-dependent spectral properties of seismic signals and enable identification of changes in faulting processes. Clustering of 46,000 earthquakes of 0.3 < ML < 1.5 from the Geysers geothermal field (CA) yields groupings that have no reservoir-scale spatial patterns but clear temporal patterns. Events with similar spectral properties repeat on annual cycles within each cluster and track changes in the water injection rates into the Geysers reservoir, indicating that changes in acoustic properties and faulting processes accompany changes in thermomechanical state. The methods open new means to identify and characterize subtle changes in seismic source properties, with applications to tectonic and geothermal seismicity. PMID:29806015

Synthesis of heparan sulfate with cyclophilin B-binding properties is determined by cell type-specific expression of sulfotransferases.

PubMed

Deligny, Audrey; Denys, Agnès; Marcant, Adeline; Melchior, Aurélie; Mazurier, Joël; van Kuppevelt, Toin H; Allain, Fabrice

2010-01-15

Cyclophilin B (CyPB) induces migration and adhesion of T lymphocytes via a mechanism that requires interaction with 3-O-sulfated heparan sulfate (HS). HS biosynthesis is a complex process with many sulfotransferases involved. N-Deacetylases/N-sulfotransferases are responsible for N-sulfation, which is essential for subsequent modification steps, whereas 3-O-sulfotransferases (3-OSTs) catalyze the least abundant modification. These enzymes are represented by several isoforms, which differ in term of distribution pattern, suggesting their involvement in making tissue-specific HS. To elucidate how the specificity of CyPB binding is determined, we explored the relationships between the expression of these sulfotransferases and the generation of HS motifs with CyPB-binding properties. We demonstrated that high N-sulfate density and the presence of 2-O- and 3-O-sulfates determine binding of CyPB, as evidenced by competitive experiments with heparin derivatives, soluble HS, and anti-HS antibodies. We then showed that target cells, i.e. CD4+ lymphocyte subsets, monocytes/macrophages, and related cell lines, specifically expressed high levels of NDST2 and 3-OST3 isoforms. Silencing the expression of NDST1, NDST2, 2-OST, and 3-OST3 by RNA interference efficiently decreased binding and activity of CyPB, thus confirming their involvement in the biosynthesis of binding sequences for CyPB. Moreover, we demonstrated that NDST1 was able to partially sulfate exogenous substrate in the absence of NDST2 but not vice versa, suggesting that both isoenzymes do not have redundant activities but do have rather complementary activities in making N-sulfated sequences with CyPB-binding properties. Altogether, these results suggest a regulatory mechanism in which cell type-specific expression of certain HS sulfotransferases determines the specific binding of CyPB to target cells.

Synthesis of Heparan Sulfate with Cyclophilin B-binding Properties Is Determined by Cell Type-specific Expression of Sulfotransferases*

PubMed Central

Deligny, Audrey; Denys, Agnès; Marcant, Adeline; Melchior, Aurélie; Mazurier, Joël; van Kuppevelt, Toin H.; Allain, Fabrice

2010-01-01

Cyclophilin B (CyPB) induces migration and adhesion of T lymphocytes via a mechanism that requires interaction with 3-O-sulfated heparan sulfate (HS). HS biosynthesis is a complex process with many sulfotransferases involved. N-Deacetylases/N-sulfotransferases are responsible for N-sulfation, which is essential for subsequent modification steps, whereas 3-O-sulfotransferases (3-OSTs) catalyze the least abundant modification. These enzymes are represented by several isoforms, which differ in term of distribution pattern, suggesting their involvement in making tissue-specific HS. To elucidate how the specificity of CyPB binding is determined, we explored the relationships between the expression of these sulfotransferases and the generation of HS motifs with CyPB-binding properties. We demonstrated that high N-sulfate density and the presence of 2-O- and 3-O-sulfates determine binding of CyPB, as evidenced by competitive experiments with heparin derivatives, soluble HS, and anti-HS antibodies. We then showed that target cells, i.e. CD4+ lymphocyte subsets, monocytes/macrophages, and related cell lines, specifically expressed high levels of NDST2 and 3-OST3 isoforms. Silencing the expression of NDST1, NDST2, 2-OST, and 3-OST3 by RNA interference efficiently decreased binding and activity of CyPB, thus confirming their involvement in the biosynthesis of binding sequences for CyPB. Moreover, we demonstrated that NDST1 was able to partially sulfate exogenous substrate in the absence of NDST2 but not vice versa, suggesting that both isoenzymes do not have redundant activities but do have rather complementary activities in making N-sulfated sequences with CyPB-binding properties. Altogether, these results suggest a regulatory mechanism in which cell type-specific expression of certain HS sulfotransferases determines the specific binding of CyPB to target cells. PMID:19940140

Linear Look-Ahead in Conjunctive Cells: An Entorhinal Mechanism for Vector-Based Navigation

PubMed Central

Kubie, John L.; Fenton, André A.

2012-01-01

The crisp organization of the “firing bumps” of entorhinal grid cells and conjunctive cells leads to the notion that the entorhinal cortex may compute linear navigation routes. Specifically, we propose a process, termed “linear look-ahead,” by which a stationary animal could compute a series of locations in the direction it is facing. We speculate that this computation could be achieved through learned patterns of connection strengths among entorhinal neurons. This paper has three sections. First, we describe the minimal grid cell properties that will be built into our network. Specifically, the network relies on “rigid modules” of neurons, where all members have identical grid scale and orientation, but differ in spatial phase. Additionally, these neurons must be densely interconnected with synapses that are modifiable early in the animal’s life. Second, we investigate whether plasticity during short bouts of locomotion could induce patterns of connections amongst grid cells or conjunctive cells. Finally, we run a simulation to test whether the learned connection patterns can exhibit linear look-ahead. Our results are straightforward. A simulated 30-min walk produces weak strengthening of synapses between grid cells that do not support linear look-ahead. Similar training in a conjunctive cell module produces a small subset of very strong connections between cells. These strong pairs have three properties: the pre- and post-synaptic cells have similar heading direction. The cell pairs have neighboring grid bumps. Finally, the spatial offset of firing bumps of the cell pair is in the direction of the common heading preference. Such a module can produce strong and accurate linear look-ahead starting in any location and extending in any direction. We speculate that this process may: (1) compute linear paths to goals; (2) update grid cell firing during navigation; and (3) stabilize the rigid modules of grid cells and conjunctive cells. PMID:22557948

Individual-level movement bias leads to the formation of higher-order social structure in a mobile group of baboons.

PubMed

Bonnell, Tyler R; Clarke, Parry M; Henzi, S Peter; Barrett, Louise

2017-07-01

In mobile social groups, influence patterns driving group movement can vary between democratic and despotic. The arrival at any single pattern of influence is thought to be underpinned by both environmental factors and group composition. To identify the specific patterns of influence driving travel decision-making in a chacma baboon troop, we used spatially explicit data to extract patterns of individual movement bias. We scaled these estimates of individual-level bias to the level of the group by constructing an influence network and assessing its emergent structural properties. Our results indicate that there is heterogeneity in movement bias: individual animals respond consistently to particular group members, and higher-ranking animals are more likely to influence the movement of others. This heterogeneity resulted in a group-level network structure that consisted of a single core and two outer shells. Here, the presence of a core suggests that a set of highly interdependent animals drove routine group movements. These results suggest that heterogeneity at the individual level can lead to group-level influence structures, and that movement patterns in mobile social groups can add to the exploration of both how these structures develop (i.e. mechanistic aspects) and what consequences they have for individual- and group-level outcomes (i.e. functional aspects).

The representation of order information in auditory-verbal short-term memory.

PubMed

Kalm, Kristjan; Norris, Dennis

2014-05-14

Here we investigate how order information is represented in auditory-verbal short-term memory (STM). We used fMRI and a serial recall task to dissociate neural activity patterns representing the phonological properties of the items stored in STM from the patterns representing their order. For this purpose, we analyzed fMRI activity patterns elicited by different item sets and different orderings of those items. These fMRI activity patterns were compared with the predictions made by positional and chaining models of serial order. The positional models encode associations between items and their positions in a sequence, whereas the chaining models encode associations between successive items and retain no position information. We show that a set of brain areas in the postero-dorsal stream of auditory processing store associations between items and order as predicted by a positional model. The chaining model of order representation generates a different pattern similarity prediction, which was shown to be inconsistent with the fMRI data. Our results thus favor a neural model of order representation that stores item codes, position codes, and the mapping between them. This study provides the first fMRI evidence for a specific model of order representation in the human brain. Copyright © 2014 the authors 0270-6474/14/346879-08$15.00/0.

Individual-level movement bias leads to the formation of higher-order social structure in a mobile group of baboons

PubMed Central

Clarke, Parry M.; Henzi, S. Peter; Barrett, Louise

2017-01-01

In mobile social groups, influence patterns driving group movement can vary between democratic and despotic. The arrival at any single pattern of influence is thought to be underpinned by both environmental factors and group composition. To identify the specific patterns of influence driving travel decision-making in a chacma baboon troop, we used spatially explicit data to extract patterns of individual movement bias. We scaled these estimates of individual-level bias to the level of the group by constructing an influence network and assessing its emergent structural properties. Our results indicate that there is heterogeneity in movement bias: individual animals respond consistently to particular group members, and higher-ranking animals are more likely to influence the movement of others. This heterogeneity resulted in a group-level network structure that consisted of a single core and two outer shells. Here, the presence of a core suggests that a set of highly interdependent animals drove routine group movements. These results suggest that heterogeneity at the individual level can lead to group-level influence structures, and that movement patterns in mobile social groups can add to the exploration of both how these structures develop (i.e. mechanistic aspects) and what consequences they have for individual- and group-level outcomes (i.e. functional aspects). PMID:28791140

Evaluation of the effect scan pattern has on the trueness and precision of six intraoral digital impression systems.

PubMed

Mennito, Anthony S; Evans, Zachary P; Lauer, Abigail W; Patel, Ravi B; Ludlow, Mark E; Renne, Walter G

2018-03-01

Clinicians have been slow to adopt digital impression technologies due possibly to perceived technique sensitivities involved in data acquisition. This research has two aims: determine whether scan pattern and sequence affects the accuracy of the three-dimensional (3D) model created from this digital impression and to compare the 5 imaging systems with regards to their scanning accuracy for sextant impressions. Six digital intraoral impression systems were used to scan a typodont sextant with optical properties similar to natural teeth. The impressions were taken using five different scan patterns and the resulting digital models were overlayed on a master digital model to determine the accuracy of each scanner performing each scan pattern. Furthermore, regardless of scan pattern, each digital impression system was evaluated for accuracy to the other systems in this same manner. No differences of significance were noted in the accuracy of 3D models created using six distinct scan patterns with one exception involving the CEREC Omnicam. Planmeca Planscan was determined to be the truest scanner while 3Shape Trios was determined to be the most precise for sextant impression making. Scan pattern does not significantly affect the accuracy of the resulting digital model for sextant scanning. Companies who make digital impression systems often recommend a scan pattern specific for their system. However, every clinical scanning scenario is different and may require a different approach. Knowing how important scan pattern is with regards to accuracy would be helpful for guiding a growing number of practitioners who are utilizing this technology. © 2018 Wiley Periodicals, Inc.

Effect of long real space flight on the whole genome mRNA expression properties in medaka Oryzias latipes

NASA Astrophysics Data System (ADS)

Kozlova, Olga; Gusev, Oleg; Levinskikh, Margarita; Sychev, Vladimir; Poddubko, Svetlana

The current study is addressed to the complex analysis of whole genome mRNA expression profile and properties of splicing variants formation in different organs of medaka fish exposed to prolonged space flight in the frame of joint Russia-Japan research program “Aquarium-AQH”. The fish were kept in the AQH joint-aquariums system in October-December 2013, followed by fixation in RNA-preserving buffers and freezing during the space flight. The samples we returned to the Earth frozen in March 2013 and mRNAs from four fish were sequenced in organ-specific manner using HiSeq Illumina sequencing platform. The ground group fish treated in the same way was used as a control. The comparison between the groups revealed space group-specific specific mRNA expression pattern. More than 50 genes (including several types of myosins) were down-regulated in the space group. Moreover, we found an evidence for formation of space group-specific splicing variants of mRNA. Taking together, the data suggest that in spite of aquatic environment, space flight-associated factors have a strong effect on the activity of fish genome. This work was supported in part by subsidy of the Russian Government to support the Program of competitive growth of Kazan Federal University among world class academic centres and universities.

Light-Directed Particle Patterning by Evaporative Optical Marangoni Assembly.

PubMed

Varanakkottu, Subramanyan Namboodiri; Anyfantakis, Manos; Morel, Mathieu; Rudiuk, Sergii; Baigl, Damien

2016-01-13

Controlled particle deposition on surfaces is crucial for both exploiting collective properties of particles and their integration into devices. Most available methods depend on intrinsic properties of either the substrate or the particles to be deposited making them difficult to apply to complex, naturally occurring or industrial formulations. Here we describe a new strategy to pattern particles from an evaporating drop, regardless of inherent particle characteristics and suspension composition. We use light to generate Marangoni surface stresses resulting in flow patterns that accumulate particles at predefined positions. Using projected images, we generate a broad variety of complex patterns, including multiple spots, lines and letters. Strikingly, this method, which we call evaporative optical Marangoni assembly (eOMA), allows us to pattern particles regardless of their size or surface properties, in model suspensions as well as in complex, real-world formulations such as commercial coffee.

The Halophile protein database.

PubMed

Sharma, Naveen; Farooqi, Mohammad Samir; Chaturvedi, Krishna Kumar; Lal, Shashi Bhushan; Grover, Monendra; Rai, Anil; Pandey, Pankaj

2014-01-01

Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/ © The Author(s) 2014. Published by Oxford University Press.

The auditory and non-auditory brain areas involved in tinnitus. An emergent property of multiple parallel overlapping subnetworks

PubMed Central

Vanneste, Sven; De Ridder, Dirk

2012-01-01

Tinnitus is the perception of a sound in the absence of an external sound source. It is characterized by sensory components such as the perceived loudness, the lateralization, the tinnitus type (pure tone, noise-like) and associated emotional components, such as distress and mood changes. Source localization of quantitative electroencephalography (qEEG) data demonstrate the involvement of auditory brain areas as well as several non-auditory brain areas such as the anterior cingulate cortex (dorsal and subgenual), auditory cortex (primary and secondary), dorsal lateral prefrontal cortex, insula, supplementary motor area, orbitofrontal cortex (including the inferior frontal gyrus), parahippocampus, posterior cingulate cortex and the precuneus, in different aspects of tinnitus. Explaining these non-auditory brain areas as constituents of separable subnetworks, each reflecting a specific aspect of the tinnitus percept increases the explanatory power of the non-auditory brain areas involvement in tinnitus. Thus, the unified percept of tinnitus can be considered an emergent property of multiple parallel dynamically changing and partially overlapping subnetworks, each with a specific spontaneous oscillatory pattern and functional connectivity signature. PMID:22586375

Preschool physics: Using the invisible property of weight in causal reasoning tasks

PubMed Central

Williamson, Rebecca A.; Meltzoff, Andrew N.

2018-01-01

Causal reasoning is an important aspect of scientific thinking. Even young human children can use causal reasoning to explain observations, make predictions, and design actions to bring about specific outcomes in the physical world. Weight is an interesting type of cause because it is an invisible property. Here, we tested preschool children with causal problem-solving tasks that assessed their understanding of weight. In an experimental setting, 2- to 5-year-old children completed three different tasks in which they had to use weight to produce physical effects—an object displacement task, a balance-scale task, and a tower-building task. The results showed that the children’s understanding of how to use object weight to produce specific object-to-object causal outcomes improved as a function of age, with 4- and 5-year-olds showing above-chance performance on all three tasks. The younger children’s performance was more variable. The pattern of results provides theoretical insights into which aspects of weight processing are particularly difficult for preschool children and why they find it difficult. PMID:29561840

Preschool physics: Using the invisible property of weight in causal reasoning tasks.

PubMed

Wang, Zhidan; Williamson, Rebecca A; Meltzoff, Andrew N

2018-01-01

Causal reasoning is an important aspect of scientific thinking. Even young human children can use causal reasoning to explain observations, make predictions, and design actions to bring about specific outcomes in the physical world. Weight is an interesting type of cause because it is an invisible property. Here, we tested preschool children with causal problem-solving tasks that assessed their understanding of weight. In an experimental setting, 2- to 5-year-old children completed three different tasks in which they had to use weight to produce physical effects-an object displacement task, a balance-scale task, and a tower-building task. The results showed that the children's understanding of how to use object weight to produce specific object-to-object causal outcomes improved as a function of age, with 4- and 5-year-olds showing above-chance performance on all three tasks. The younger children's performance was more variable. The pattern of results provides theoretical insights into which aspects of weight processing are particularly difficult for preschool children and why they find it difficult.

Light-induced quantitative microprinting of biomolecules

NASA Astrophysics Data System (ADS)

Strale, Pierre-Olivier; Azioune, Ammar; Bugnicourt, Ghislain; Lecomte, Yohan; Chahid, Makhlad; Studer, Vincent

2017-02-01

Printing of biomolecules on substrates has developed tremendously in the past few years. The existing methods either rely on slow serial writing processes or on parallelized photolithographic techniques where cumbersome mask alignment procedures usually impair the ability to generate multi-protein patterns. We recently developed a new technology allowing for high resolution multi protein micro-patterning. This technology named "Light-Induced Molecular Adsorption of Proteins (LIMAP)" is based on a water-soluble photo-initiator able to reverse the antifouling property of polymer brushes when exposed to UV light. We developed a wide-field pattern projection system based on a DMD coupled to a conventional microscope which permits to generate arbitrary grayscale patterns of UV light at the micron scale. Interestingly, the density of adsorbed molecules scales with the dose of UV light thus allowing the quantitative patterning of biomolecules. The very low non specific background of biomolecules outside of the UV-exposed areas allows for the sequential printing of multiple proteins without alignment procedures. Protein patterns ranging from 500 nm up to 1 mm can be performed within seconds, as well as gradients of arbitrary shapes. The range of applications of the LIMAP approach extends from the single molecule up to the multicellular scale with an exquisite control over local protein density. We show that it can be used to generate complex protein landscapes useful to study protein-protein, cell-cell and cell-matrix interactions.

Simulation program for estimating statistical power of Cox's proportional hazards model assuming no specific distribution for the survival time.

PubMed

Akazawa, K; Nakamura, T; Moriguchi, S; Shimada, M; Nose, Y

1991-07-01

Small sample properties of the maximum partial likelihood estimates for Cox's proportional hazards model depend on the sample size, the true values of regression coefficients, covariate structure, censoring pattern and possibly baseline hazard functions. Therefore, it would be difficult to construct a formula or table to calculate the exact power of a statistical test for the treatment effect in any specific clinical trial. The simulation program, written in SAS/IML, described in this paper uses Monte-Carlo methods to provide estimates of the exact power for Cox's proportional hazards model. For illustrative purposes, the program was applied to real data obtained from a clinical trial performed in Japan. Since the program does not assume any specific function for the baseline hazard, it is, in principle, applicable to any censored survival data as long as they follow Cox's proportional hazards model.

Array-based sensing using nanoparticles: an alternative approach for cancer diagnostics.

PubMed

Le, Ngoc D B; Yazdani, Mahdieh; Rotello, Vincent M

2014-07-01

Array-based sensing using nanoparticles (NPs) provides an attractive alternative to specific biomarker-focused strategies for cancer diagnosis. The physical and chemical properties of NPs provide both the recognition and transduction capabilities required for biosensing. Array-based sensors utilize a combined response from the interactions between sensors and analytes to generate a distinct pattern (fingerprint) for each analyte. These interactions can be the result of either the combination of multiple specific biomarker recognition (specific binding) or multiple selective binding responses, known as chemical nose sensing. The versatility of the latter array-based sensing using NPs can facilitate the development of new personalized diagnostic methodologies in cancer diagnostics, a necessary evolution in the current healthcare system to better provide personalized treatments. This review will describe the basic principle of array-based sensors, along with providing examples of both invasive and noninvasive samples used in cancer diagnosis.

Morphometry Based on Effective and Accurate Correspondences of Localized Patterns (MEACOLP)

PubMed Central

Wang, Hu; Ren, Yanshuang; Bai, Lijun; Zhang, Wensheng; Tian, Jie

2012-01-01

Local features in volumetric images have been used to identify correspondences of localized anatomical structures for brain morphometry. However, the correspondences are often sparse thus ineffective in reflecting the underlying structures, making it unreliable to evaluate specific morphological differences. This paper presents a morphometry method (MEACOLP) based on correspondences with improved effectiveness and accuracy. A novel two-level scale-invariant feature transform is used to enhance the detection repeatability of local features and to recall the correspondences that might be missed in previous studies. Template patterns whose correspondences could be commonly identified in each group are constructed to serve as the basis for morphometric analysis. A matching algorithm is developed to reduce the identification errors by comparing neighboring local features and rejecting unreliable matches. The two-sample t-test is finally adopted to analyze specific properties of the template patterns. Experiments are performed on the public OASIS database to clinically analyze brain images of Alzheimer's disease (AD) and normal controls (NC). MEACOLP automatically identifies known morphological differences between AD and NC brains, and characterizes the differences well as the scaling and translation of underlying structures. Most of the significant differences are identified in only a single hemisphere, indicating that AD-related structures are characterized by strong anatomical asymmetry. In addition, classification trials to differentiate AD subjects from NC confirm that the morphological differences are reliably related to the groups of interest. PMID:22540000

Computational advances towards linking BOLD and behavior.

PubMed

Serences, John T; Saproo, Sameer

2012-03-01

Traditionally, fMRI studies have focused on analyzing the mean response amplitude within a cortical area. However, the mean response is blind to many important patterns of cortical modulation, which severely limits the formulation and evaluation of linking hypotheses between neural activity, BOLD responses, and behavior. More recently, multivariate pattern classification analysis (MVPA) has been applied to fMRI data to evaluate the information content of spatially distributed activation patterns. This approach has been remarkably successful at detecting the presence of specific information in targeted brain regions, and provides an extremely flexible means of extracting that information without a precise generative model for the underlying neural activity. However, this flexibility comes at a cost: since MVPA relies on pooling information across voxels that are selective for many different stimulus attributes, it is difficult to infer how specific sub-sets of tuned neurons are modulated by an experimental manipulation. In contrast, recently developed encoding models can produce more precise estimates of feature-selective tuning functions, and can support the creation of explicit linking hypotheses between neural activity and behavior. Although these encoding models depend on strong - and often untested - assumptions about the response properties of underlying neural generators, they also provide a unique opportunity to evaluate population-level computational theories of perception and cognition that have previously been difficult to assess using either single-unit recording or conventional neuroimaging techniques. Copyright © 2011. Published by Elsevier Ltd.

Axial mesendoderm refines rostrocaudal pattern in the chick nervous system.

PubMed

Rowan, A M; Stern, C D; Storey, K G

1999-07-01

There has long been controversy concerning the role of the axial mesoderm in the induction and rostrocaudal patterning of the vertebrate nervous system. Here we investigate the neural inducing and regionalising properties of defined rostrocaudal regions of head process/prospective notochord in the chick embryo by juxtaposing these tissues with extraembryonic epiblast or neural plate explants. We localise neural inducing signals to the emerging head process and using a large panel of region-specific neural markers, show that different rostrocaudal levels of the head process derived from headfold stage embryos can induce discrete regions of the central nervous system. However, we also find that rostral and caudal head process do not induce expression of any of these molecular markers in explants of the neural plate. During normal development the head process emerges beneath previously induced neural plate, which we show has already acquired some rostrocaudal character. Our findings therefore indicate that discrete regions of axial mesendoderm at headfold stages are not normally responsible for the establishment of rostrocaudal pattern in the neural plate. Strikingly however, we do find that caudal head process inhibits expression of rostral genes in neural plate explants. These findings indicate that despite the ability to induce specific rostrocaudal regions of the CNS de novo, signals provided by the discrete regions of axial mesendoderm do not appear to establish regional differences, but rather refine the rostrocaudal character of overlying neuroepithelium.

Aggrecan-based extracellular matrix shows unique cortical features and conserved subcortical principles of mammalian brain organization in the Madagascan lesser hedgehog tenrec (Echinops telfairi Martin, 1838).

PubMed

Morawski, M; Brückner, G; Jäger, C; Seeger, G; Künzle, H; Arendt, T

2010-02-03

The Madagascan tenrecs (Afrotheria), an ancient mammalian clade, are characterized by unique brain anatomy. Striking features are an expanded paleocortex but a small and poorly differentiated neocortex devoid of a distinct granular layer IV. To investigate the organization of cortical areas we analyzed extracellular matrix components in perineuronal nets (PNs) using antibodies to aggrecan, lectin staining and hyaluronan-binding protein. Selected subcortical regions were studied to correlate the cortical patterns with features in evolutionary conserved systems. In the neocortex, paleocortex and hippocampus PNs were associated with nonpyramidal neurons. Quantitative analysis in the cerebral cortex revealed area-specific proportions and laminar distribution patterns of neurons ensheathed by PNs. Cortical PNs showed divergent structural phenotypes. Diffuse PNs forming a cotton wool-like perisomatic rim were characteristic of the paleocortex. These PNs were associated with a dense pericellular plexus of calretinin-immunoreactive fibres. Clearly contoured PNs were devoid of a calretinin-positive plexus and predominated in the neocortex and hippocampus. The organization of the extracellular matrix in subcortical nuclei followed the widely distributed mammalian type. We conclude that molecular properties of the aggrecan-based extracellular matrix are conserved during evolution of mammals; however, the matrix scaffold is adapted to specific wiring patterns of cortical and subcortical neuronal networks. Copyright 2010 IBRO. Published by Elsevier Ltd. All rights reserved.

Imbalanced pattern completion vs. separation in cognitive disease: network simulations of synaptic pathologies predict a personalized therapeutics strategy.

PubMed

Hanson, Jesse E; Madison, Daniel V

2010-08-13

Diverse Mouse genetic models of neurodevelopmental, neuropsychiatric, and neurodegenerative causes of impaired cognition exhibit at least four convergent points of synaptic malfunction: 1) Strength of long-term potentiation (LTP), 2) Strength of long-term depression (LTD), 3) Relative inhibition levels (Inhibition), and 4) Excitatory connectivity levels (Connectivity). To test the hypothesis that pathological increases or decreases in these synaptic properties could underlie imbalances at the level of basic neural network function, we explored each type of malfunction in a simulation of autoassociative memory. These network simulations revealed that one impact of impairments or excesses in each of these synaptic properties is to shift the trade-off between pattern separation and pattern completion performance during memory storage and recall. Each type of synaptic pathology either pushed the network balance towards intolerable error in pattern separation or intolerable error in pattern completion. Imbalances caused by pathological impairments or excesses in LTP, LTD, inhibition, or connectivity, could all be exacerbated, or rescued, by the simultaneous modulation of any of the other three synaptic properties. Because appropriate modulation of any of the synaptic properties could help re-balance network function, regardless of the origins of the imbalance, we propose a new strategy of personalized cognitive therapeutics guided by assay of pattern completion vs. pattern separation function. Simulated examples and testable predictions of this theorized approach to cognitive therapeutics are presented.

Mechanical Testing of Polymeric Composites for Aircraft Applications: Standards, Requirements and Limitations

NASA Astrophysics Data System (ADS)

Chinchan, Levon; Shevtsov, Sergey; Soloviev, Arcady; Shevtsova, Varvara; Huang, Jiun-Ping

The high-loaded parts of modern aircrafts and helicopters are often produced from polymeric composite materials. Such materials consist of reinforcing fibers, packed by layers with the different angles, and resin, which uniformly distributes the structural stresses between fibers. These composites should have an orthotropic symmetry of mechanical properties to obtain the desirable spatial distribution of elastic moduli consistent to the external loading pattern. Main requirements to the aircraft composite materials are the specified elastic properties (9 for orthotropic composite), long-term strength parameters, high resistance against the environmental influences, low thermal expansion to maintain the shape stability. These properties are ensured by an exact implementation of technological conditions and many testing procedures performed with the fibers, resin, prepregs and ready components. Most important mechanical testing procedures are defined by ASTM, SACMA and other standards. However in each case the wide diversity of components (dimensions and lay-up of fibers, rheological properties of thermosetting resins) requires a specific approach to the sample preparation, testing, and numerical processing of the testing results to obtain the veritable values of tested parameters. We pay the special attention to the cases where the tested specimens are cut not from the plates recommended by standards, but from the ready part manufactured with the specific lay-up, tension forces on the reinforcing fiber at the filament winding, and curing schedule. These tests can provide most useful information both for the composite structural design and to estimate a quality of the ready parts. We consider an influence of relation between specimen dimensions and pattern of the fibers winding (or lay-up) on the results of mechanical testing for determination of longitudinal, transverse and in-plane shear moduli, an original numerical scheme for reconstruction of in-plane shear modulus measured by the modified Iosipescu method which use finite element based numerical processing and indicative data preliminary obtained by the short-beam test. The sensitivity and ability to decoupling the values of in-plane and interlaminar shear moduli obtained by the sample twisting test is studied and discussed.

Trail networks formed by populations of immune cells

NASA Astrophysics Data System (ADS)

Yang, Taeseok Daniel; Kwon, Tae Goo; Park, Jin-sung; Lee, Kyoung J.

2014-02-01

Populations of biological cells that communicate with each other can organize themselves to generate large-scale patterns. Examples can be found in diverse systems, ranging from developing embryos, cardiac tissues, chemotaxing ameba and swirling bacteria. The similarity, often shared by the patterns, suggests the existence of some general governing principle. On the other hand, rich diversity and system-specific properties are exhibited, depending on the type of involved cells and the nature of their interactions. The study on the similarity and the diversity constitutes a rapidly growing field of research. Here, we introduce a new class of self-organized patterns of cell populations that we term as ‘cellular trail networks’. They were observed with populations of rat microglia, the immune cells of the brain and the experimental evidence suggested that haptotaxis is the key element responsible for them. The essential features of the observed patterns are well captured by the mathematical model cells that actively crawl and interact with each other through a decomposing but non-diffusing chemical attractant laid down by the cells. Our finding suggests an unusual mechanism of socially cooperative long-range signaling for the crawling immune cells.

The neural basis of visual word form processing: a multivariate investigation.

PubMed

Nestor, Adrian; Behrmann, Marlene; Plaut, David C

2013-07-01

Current research on the neurobiological bases of reading points to the privileged role of a ventral cortical network in visual word processing. However, the properties of this network and, in particular, its selectivity for orthographic stimuli such as words and pseudowords remain topics of significant debate. Here, we approached this issue from a novel perspective by applying pattern-based analyses to functional magnetic resonance imaging data. Specifically, we examined whether, where and how, orthographic stimuli elicit distinct patterns of activation in the human cortex. First, at the category level, multivariate mapping found extensive sensitivity throughout the ventral cortex for words relative to false-font strings. Secondly, at the identity level, the multi-voxel pattern classification provided direct evidence that different pseudowords are encoded by distinct neural patterns. Thirdly, a comparison of pseudoword and face identification revealed that both stimulus types exploit common neural resources within the ventral cortical network. These results provide novel evidence regarding the involvement of the left ventral cortex in orthographic stimulus processing and shed light on its selectivity and discriminability profile. In particular, our findings support the existence of sublexical orthographic representations within the left ventral cortex while arguing for the continuity of reading with other visual recognition skills.

Establishment of embryonic neuroepithelial cell lines exhibiting an epiplastic expression pattern of region specific markers.

PubMed

Nardelli, Jeannette; Catala, Martin; Charnay, Patrick

2003-09-15

Neuroepithelial b2T cells were derived from the hindbrain and the spinal cord of mouse transgenic embryos, which expressed SV40 T antigen under the control of a Hoxb2 enhancer. Strikingly, b2T cell lines of either origin exhibit a very similar gene expression pattern, including markers of the hindbrain and the spinal cord, such as Hox genes, but not of more anterior cephalic regions. In addition, the broad expression pattern of b2T cells, probably linked to culture conditions, appeared to be appropriately modulated when the cells were reimplanted at different longitudinal levels into chick host embryos, suggesting that these cells are responsive to exogenous signalling mechanisms. Further support for these allegations was obtained by culturing b2T cells in defined medium and by assessing the expression of Krox20, an odd-numbered rhombomere marker, which appeared to be modulated by a complex interplay between FGF, retinoic acid (RA), and noggin. With respect to these as yet unique properties, b2T cells constitute an original alternative tool to in vivo models for the analysis of molecular pathways involved in the patterning of the neural tube. Copyright 2003 Wiley-Liss, Inc.

Endogenous Sequential Cortical Activity Evoked by Visual Stimuli

PubMed Central

Miller, Jae-eun Kang; Hamm, Jordan P.; Jackson, Jesse; Yuste, Rafael

2015-01-01

Although the functional properties of individual neurons in primary visual cortex have been studied intensely, little is known about how neuronal groups could encode changing visual stimuli using temporal activity patterns. To explore this, we used in vivo two-photon calcium imaging to record the activity of neuronal populations in primary visual cortex of awake mice in the presence and absence of visual stimulation. Multidimensional analysis of the network activity allowed us to identify neuronal ensembles defined as groups of cells firing in synchrony. These synchronous groups of neurons were themselves activated in sequential temporal patterns, which repeated at much higher proportions than chance and were triggered by specific visual stimuli such as natural visual scenes. Interestingly, sequential patterns were also present in recordings of spontaneous activity without any sensory stimulation and were accompanied by precise firing sequences at the single-cell level. Moreover, intrinsic dynamics could be used to predict the occurrence of future neuronal ensembles. Our data demonstrate that visual stimuli recruit similar sequential patterns to the ones observed spontaneously, consistent with the hypothesis that already existing Hebbian cell assemblies firing in predefined temporal sequences could be the microcircuit substrate that encodes visual percepts changing in time. PMID:26063915

Calcium spikes, waves and oscillations in a large, patterned epithelial tissue

PubMed Central

Balaji, Ramya; Bielmeier, Christina; Harz, Hartmann; Bates, Jack; Stadler, Cornelia; Hildebrand, Alexander; Classen, Anne-Kathrin

2017-01-01

While calcium signaling in excitable cells, such as muscle or neurons, is extensively characterized, calcium signaling in epithelial tissues is little understood. Specifically, the range of intercellular calcium signaling patterns elicited by tightly coupled epithelial cells and their function in the regulation of epithelial characteristics are little explored. We found that in Drosophila imaginal discs, a widely studied epithelial model organ, complex spatiotemporal calcium dynamics occur. We describe patterns that include intercellular waves traversing large tissue domains in striking oscillatory patterns as well as spikes confined to local domains of neighboring cells. The spatiotemporal characteristics of intercellular waves and oscillations arise as emergent properties of calcium mobilization within a sheet of gap-junction coupled cells and are influenced by cell size and environmental history. While the in vivo function of spikes, waves and oscillations requires further characterization, our genetic experiments suggest that core calcium signaling components guide actomyosin organization. Our study thus suggests a possible role for calcium signaling in epithelia but importantly, introduces a model epithelium enabling the dissection of cellular mechanisms supporting the initiation, transmission and regeneration of long-range intercellular calcium waves and the emergence of oscillations in a highly coupled multicellular sheet. PMID:28218282

Climate-soil Interactions: Global Change, Local Properties, and Ecological Sites

USDA-ARS?s Scientific Manuscript database

Global climate change is predicted to alter historic patterns of precipitation and temperature in rangelands globally. Vegetation community response to altered weather patterns will be mediated at the site level by local-scale properties that govern ecological potential, including geology, topograph...

Zebra finches are able to learn affixation-like patterns.

PubMed

Chen, Jiani; Jansen, Naomi; ten Cate, Carel

2016-01-01

Adding an affix to transform a word is common across the world languages, with the edges of words more likely to carry out such a function. However, detecting affixation patterns is also observed in learning tasks outside the domain of language, suggesting that the underlying mechanism from which affixation patterns have arisen may not be language or even human specific. We addressed whether a songbird, the zebra finch, is able to discriminate between, and generalize, affixation-like patterns. Zebra finches were trained and tested in a Go/Nogo paradigm to discriminate artificial song element sequences resembling prefixed and suffixed 'words.' The 'stems' of the 'words,' consisted of different combinations of a triplet of song elements, to which a fourth element was added as either a 'prefix' or a 'suffix.' After training, the birds were tested with novel stems, consisting of either rearranged familiar element types or novel element types. The birds were able to generalize the affixation patterns to novel stems with both familiar and novel element types. Hence, the discrimination resulting from the training was not based on memorization of individual stimuli, but on a shared property among Go or Nogo stimuli, i.e., affixation patterns. Remarkably, birds trained with suffixation as Go pattern showed clear evidence of using both prefix and suffix, while those trained with the prefix as the Go stimulus used primarily the prefix. This finding illustrates that an asymmetry in attending to different affixations is not restricted to human languages.

Peripheral mechanisms for vocal production in birds - differences and similarities to human speech and singing.

PubMed

Riede, Tobias; Goller, Franz

2010-10-01

Song production in songbirds is a model system for studying learned vocal behavior. As in humans, bird phonation involves three main motor systems (respiration, vocal organ and vocal tract). The avian respiratory mechanism uses pressure regulation in air sacs to ventilate a rigid lung. In songbirds sound is generated with two independently controlled sound sources, which reside in a uniquely avian vocal organ, the syrinx. However, the physical sound generation mechanism in the syrinx shows strong analogies to that in the human larynx, such that both can be characterized as myoelastic-aerodynamic sound sources. Similarities include active adduction and abduction, oscillating tissue masses which modulate flow rate through the organ and a layered structure of the oscillating tissue masses giving rise to complex viscoelastic properties. Differences in the functional morphology of the sound producing system between birds and humans require specific motor control patterns. The songbird vocal apparatus is adapted for high speed, suggesting that temporal patterns and fast modulation of sound features are important in acoustic communication. Rapid respiratory patterns determine the coarse temporal structure of song and maintain gas exchange even during very long songs. The respiratory system also contributes to the fine control of airflow. Muscular control of the vocal organ regulates airflow and acoustic features. The upper vocal tract of birds filters the sounds generated in the syrinx, and filter properties are actively adjusted. Nonlinear source-filter interactions may also play a role. The unique morphology and biomechanical system for sound production in birds presents an interesting model for exploring parallels in control mechanisms that give rise to highly convergent physical patterns of sound generation. More comparative work should provide a rich source for our understanding of the evolution of complex sound producing systems. Copyright © 2009 Elsevier Inc. All rights reserved.

Multiphase flow modeling in centrifugal partition chromatography.

PubMed

Adelmann, S; Schwienheer, C; Schembecker, G

2011-09-09

The separation efficiency in Centrifugal Partition Chromatography (CPC) depends on selection of a suitable biphasic solvent system (distribution ratio, selectivity factor, sample solubility) and is influenced by hydrodynamics in the chambers. Especially the stationary phase retention, the interfacial area for mass transfer and the flow pattern (backmixing) are important parameters. Their relationship with physical properties, operating parameters and chamber geometry is not completely understood and predictions are hardly possible. Experimental flow visualization is expensive and two-dimensional only. Therefore we simulated the flow pattern using a volume-of-fluid (VOF) method, which was implemented in OpenFOAM®. For the three-dimensional simulation of a rotating FCPC®-chamber, gravitational centrifugal and Coriolis forces were added to the conservation equation. For experimental validation the flow pattern of different solvent systems was visualized with an optical measurement system. The amount of mobile phase in a chamber was calculated from gray scale values of videos recorded by an image processing routine in ImageJ®. To visualize the flow of the stationary phase polyethylene particles were used to perform a qualitative particle image velocimetry (PIV) analysis. We found a good agreement between flow patterns and velocity profiles of experiments and simulations. By using the model we found that increasing the chamber depth leads to higher specific interfacial area. Additionally a circular flow in the stationary phase was identified that lowers the interfacial area because it pushes the jet of mobile phase to the chamber wall. The Coriolis force alone gives the impulse for this behavior. As a result the model is easier to handle than experiments and allows 3D prediction of hydrodynamics in the chamber. Additionally it can be used for optimizing geometry and operating parameters for given physical properties of solvent systems. Copyright © 2011 Elsevier B.V. All rights reserved.

Introducing nuclei scatterer patterns into histology based intravascular ultrasound simulation framework

NASA Astrophysics Data System (ADS)

Kraft, Silvan; Karamalis, Athanasios; Sheet, Debdoot; Drecoll, Enken; Rummeny, Ernst J.; Navab, Nassir; Noël, Peter B.; Katouzian, Amin

2013-03-01

Medical ultrasonic grayscale images are formed from acoustic waves following their interactions with distributed scatterers within tissues media. For accurate simulation of acoustic wave propagation, a reliable model describing unknown parameters associated with tissues scatterers such as distribution, size and acoustic properties is essential. In this work, we introduce a novel approach defining ultrasonic scatterers by incorporating a distribution of cellular nuclei patterns in biological tissues to simulate ultrasonic response of atherosclerotic tissues in intravascular ultrasound (IVUS). For this reason, a virtual phantom is generated through manual labeling of different tissue types (fibrotic, lipidic and calcified) on histology sections. Acoustic properties of each tissue type are defined by assuming that the ultrasound signal is primarily backscattered by the nuclei of the organic cells within the intima and media of the vessel wall. This resulting virtual phantom is subsequently used to simulate ultrasonic wave propagation through the tissue medium computed using finite difference estimation. Subsequently B-mode images for a specific histological section are processed from the simulated radiofrequency (RF) data and compared with the original IVUS of the same tissue section. Real IVUS RF signals for these histological sections were obtained using a single-element mechanically rotating 40MHz transducer. Evaluation is performed by trained reviewers subjectively assessing both simulated and real B-mode IVUS images. Our simulation platform provides a high image quality with a very promising correlation to the original IVUS images. This will facilitate to better understand progression of such a chronic disease from micro-level and its integration into cardiovascular disease-specific models.

An analysis of current source density profiles activated by local stimulation in the mouse auditory cortex in vitro.

PubMed

Yamamura, Daiki; Sano, Ayaka; Tateno, Takashi

2017-03-15

To examine local network properties of the mouse auditory cortex in vitro, we recorded extracellular spatiotemporal laminar profiles driven by short electric local stimulation on a planar multielectrode array substrate. The recorded local field potentials were subsequently evaluated using current source density (CSD) analysis to identify sources and sinks. Current sinks are thought to be an indicator of net synaptic current in the small volume of cortex surrounding the recording site. Thus, CSD analysis combined with multielectrode arrays enabled us to compare mean synaptic activity in response to small current stimuli on a layer-by-layer basis. We also used senescence-accelerated mice (SAM), some strains of which show earlier onset of age-related hearing loss, to examine the characteristic spatiotemporal CSD profiles stimulated by electrodes in specific cortical layers. Thus, the CSD patterns were classified into several clusters based on stimulation sites in the cortical layers. We also found some differences in CSD patterns between the two SAM strains in terms of aging according to principle component analysis with dimension reduction. For simultaneous two-site stimulation, we modeled the obtained CSD profiles as a linear superposition of the CSD profiles to individual single-site stimulation. The model analysis indicated the nonlinearity of spatiotemporal integration over stimulus-driven activity in a layer-specific manner. Finally, on the basis of these results, we discuss the auditory cortex local network properties and the effects of aging on these mouse strains. Copyright © 2017 Elsevier B.V. All rights reserved.

An image-processing methodology for extracting bloodstain pattern features.

PubMed

Arthur, Ravishka M; Humburg, Philomena J; Hoogenboom, Jerry; Baiker, Martin; Taylor, Michael C; de Bruin, Karla G

2017-08-01

There is a growing trend in forensic science to develop methods to make forensic pattern comparison tasks more objective. This has generally involved the application of suitable image-processing methods to provide numerical data for identification or comparison. This paper outlines a unique image-processing methodology that can be utilised by analysts to generate reliable pattern data that will assist them in forming objective conclusions about a pattern. A range of features were defined and extracted from a laboratory-generated impact spatter pattern. These features were based in part on bloodstain properties commonly used in the analysis of spatter bloodstain patterns. The values of these features were consistent with properties reported qualitatively for such patterns. The image-processing method developed shows considerable promise as a way to establish measurable discriminating pattern criteria that are lacking in current bloodstain pattern taxonomies. Copyright © 2017 Elsevier B.V. All rights reserved.

Magnetic hyperthermia properties of iron oxide nanoparticles: The effect of concentration

NASA Astrophysics Data System (ADS)

Ebrahimisadr, Saeid; Aslibeiki, Bagher; Asadi, Reza

2018-06-01

We investigated the effect of concentration on magnetic hyperthermia properties of Fe3O4 nanoparticles (NPs). The NPs were synthesized by co-precipitation method at 80 °C. Scanning electron microscope image showed that the mean diameter of NPs is about 18 nm. The XRD pattern indicated that the sample is pure Fe3O4 with spinel structure and the FT-IR spectroscopy confirmed formation of metal-oxygen bonds in the octahedral and tetrahedral spinel sub-lattice which further confirmed crystalline structure of the sample. The hyperthermia property of Fe3O4 NPs was investigated via an induction heater generating alternating magnetic field with frequency of 92 kHz. The temperature rise (ΔT) of suspension in the AC magnetic field was studied on different concentrations of NPs and the specific absorption rate (SAR) was obtained from Box-Lucas equation and linear fitting of ΔT-time curve. The results showed that the ΔT sharply increases with increasing the NPs concentration while the SAR remains almost constant.

A unified nonlocal strain gradient plate model for nonlinear axial instability of functionally graded porous micro/nano-plates reinforced with graphene platelets

NASA Astrophysics Data System (ADS)

Sahmani, Saeid; Aghdam, Mohammad Mohammadi; Rabczuk, Timon

2018-04-01

By gradually changing of the porosity across a specific direction, functionally graded porous materials (FGPMs) are produced which can impart desirable mechanical properties. To enhance these properties, it is common to reinforce FGPMs with nanofillers. The main aim of the current study is to investigate the size-dependent nonlinear axial postbuckling characteristics of FGPM micro/nano-plates reinforced with graphene platelets. For this purpose, the theory of nonlocal strain gradient elasticity incorporating the both stiffness reduction and stiffness enhancement mechanisms of size effects is applied to the refined exponential shear deformation plate theory. Three different patterns of porosity dispersion across the plate thickness in conjunction with the uniform one are assumed for FGPM as an open-cell metal foam is utilized associated with the coefficients of the relative density and porosity. With the aid of the virtual work’s principle, the non-classical governing differential equations are constructed. Thereafter, an improved perturbation technique is employed to capture the size dependencies in the nonlinear load-deflection and load-shortening responses of the reinforced FGPM micro/nano-plates with and without initial geometric imperfection. It is indicated that by increasing the value of porosity coefficient, the size-dependent critical buckling loads of reinforced FGPM micro/nano-plates with all types of porosity dispersion pattern reduce, but the associated shortening may increase or decrease which depends on the type of dispersion pattern.

Gaze holding deficits discriminate early from late onset cerebellar degeneration.

PubMed

Tarnutzer, Alexander A; Weber, K P; Schuknecht, B; Straumann, D; Marti, S; Bertolini, G

2015-08-01

The vestibulo-cerebellum calibrates the output of the inherently leaky brainstem neural velocity-to-position integrator to provide stable gaze holding. In healthy humans small-amplitude centrifugal nystagmus is present at extreme gaze-angles, with a non-linear relationship between eye-drift velocity and eye eccentricity. In cerebellar degeneration this calibration is impaired, resulting in pathological gaze-evoked nystagmus (GEN). For cerebellar dysfunction, increased eye drift may be present at any gaze angle (reflecting pure scaling of eye drift found in controls) or restricted to far-lateral gaze (reflecting changes in shape of the non-linear relationship) and resulting eyed-drift patterns could be related to specific disorders. We recorded horizontal eye positions in 21 patients with cerebellar neurodegeneration (gaze-angle = ±40°) and clinically confirmed GEN. Eye-drift velocity, linearity and symmetry of drift were determined. MR-images were assessed for cerebellar atrophy. In our patients, the relation between eye-drift velocity and gaze eccentricity was non-linear, yielding (compared to controls) significant GEN at gaze-eccentricities ≥20°. Pure scaling was most frequently observed (n = 10/18), followed by pure shape-changing (n = 4/18) and a mixed pattern (n = 4/18). Pure shape-changing patients were significantly (p = 0.001) younger at disease-onset compared to pure scaling patients. Atrophy centered around the superior/dorsal vermis, flocculus/paraflocculus and dentate nucleus and did not correlate with the specific drift behaviors observed. Eye drift in cerebellar degeneration varies in magnitude; however, it retains its non-linear properties. With different drift patterns being linked to age at disease-onset, we propose that the gaze-holding pattern (scaling vs. shape-changing) may discriminate early- from late-onset cerebellar degeneration. Whether this allows a distinction among specific cerebellar disorders remains to be determined.

Promotion of Testa Rupture during Garden Cress Germination Involves Seed Compartment-Specific Expression and Activity of Pectin Methylesterases1[OPEN

PubMed Central

Scheler, Claudia; Weitbrecht, Karin; Pearce, Simon P.; Hampstead, Anthony; Büttner-Mainik, Annette; Lee, Kieran J.D.; Voegele, Antje; Oracz, Krystyna; Dekkers, Bas J.W.; Wang, Xiaofeng; Wood, Andrew T.A.; Bentsink, Leónie; King, John R.; Knox, J. Paul; Holdsworth, Michael J.; Müller, Kerstin; Leubner-Metzger, Gerhard

2015-01-01

Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR. Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination. PMID:25429110

Within-individual variation in bullfrog vocalizations: implications for a vocally mediated social recognition system.

PubMed

Bee, Mark A

2004-12-01

Acoustic signals provide a basis for social recognition in a wide range of animals. Few studies, however, have attempted to relate the patterns of individual variation in signals to behavioral discrimination thresholds used by receivers to discriminate among individuals. North American bullfrogs (Rana catesbeiana) discriminate among familiar and unfamiliar individuals based on individual variation in advertisement calls. The sources, patterns, and magnitudes of variation in eight acoustic properties of multiple-note advertisement calls were examined to understand how patterns of within-individual variation might either constrain, or provide additional cues for, vocal recognition. Six of eight acoustic properties exhibited significant note-to-note variation within multiple-note calls. Despite this source of within-individual variation, all call properties varied significantly among individuals, and multivariate analyses indicated that call notes were individually distinct. Fine-temporal and spectral call properties exhibited less within-individual variation compared to gross-temporal properties and contributed most toward statistically distinguishing among individuals. Among-individual differences in the patterns of within-individual variation in some properties suggest that within-individual variation could also function as a recognition cue. The distributions of among-individual and within-individual differences were used to generate hypotheses about the expected behavioral discrimination thresholds of receivers.

Multicomponent patterned ultrathin carbon nanomembranes by laser ablation

NASA Astrophysics Data System (ADS)

Frese, Natalie; Scherr, Julian; Beyer, André; Terfort, Andreas; Gölzhäuser, Armin; Hampp, Norbert; Rhinow, Daniel

2018-01-01

Carbon nanomembranes (CNMs) are a class of two-dimensional materials, which are obtained by electron beam-induced crosslinking of aromatic self-assembled monolayers (SAMs) on solid substrates. CNMs made from a single type of precursor molecule are uniform with homogeneous chemical and physical properties. We have developed a method for the fabrication of internally patterned CNMs resembling a key feature of biological membranes. Direct laser patterning is used to obtain multicomponent patterned SAMs on gold, which are subsequently crosslinked by electron irradiation. We demonstrate that the structure of internally patterned CNMs is preserved upon transfer to different substrates. The method enables rapid fabrication of patterned 2D materials with local variations in chemical and physical properties on the micrometer to centimeter scale.

Lytic and Latent Antigens of the Human Gammaherpesviruses Kaposi's Sarcoma-Associated Herpesvirus and Epstein-Barr Virus Induce T-Cell Responses with Similar Functional Properties and Memory Phenotypes▿

PubMed Central

Bihl, Florian; Narayan, Murli; Chisholm, John V.; Henry, Leah M.; Suscovich, Todd J.; Brown, Elizabeth E.; Welzel, Tania M.; Kaufmann, Daniel E.; Zaman, Tauheed M.; Dollard, Sheila; Martin, Jeff N.; Wang, Fred; Scadden, David T.; Kaye, Kenneth M.; Brander, Christian

2007-01-01

The cellular immunity against Kaposi's sarcoma-associated herpesvirus (KSHV) is poorly characterized and has not been compared to T-cell responses against other human herpesviruses. Here, novel and dominant targets of KSHV-specific cellular immunity are identified and compared to T cells specific for lytic and latent antigens in a second human gammaherpesvirus, Epstein-Barr virus. The data identify a novel HLA-B57- and HLA-B58-restricted epitope in the Orf57 protein and show consistently close parallels in immune phenotypes and functional response patterns between cells targeting lytic or latent KSHV- and EBV-encoded antigens, suggesting common mechanisms in the induction of these responses. PMID:17329344

Architected cellular ceramics with tailored stiffness via direct foam writing

NASA Astrophysics Data System (ADS)

Muth, Joseph T.; Dixon, Patrick G.; Woish, Logan; Gibson, Lorna J.; Lewis, Jennifer A.

2017-02-01

Hierarchical cellular structures are ubiquitous in nature because of their low-density, high-specific properties, and multifunctionality. Inspired by these systems, we created lightweight ceramic architectures composed of closed-cell porous struts patterned in the form of hexagonal and triangular honeycombs by direct foam writing. The foam ink contains bubbles stabilized by attractive colloidal particles suspended in an aqueous solution. The printed and sintered ceramic foam honeycombs possess low relative density (˜6%). By tailoring their microstructure and geometry, we created honeycombs with different modes of deformation, exceptional specific stiffness, and stiffness values that span over an order of magnitude. This capability represents an important step toward the scalable fabrication of hierarchical porous materials for applications, including lightweight structures, thermal insulation, tissue scaffolds, catalyst supports, and electrodes.

Architected cellular ceramics with tailored stiffness via direct foam writing

PubMed Central

Muth, Joseph T.; Dixon, Patrick G.; Woish, Logan; Gibson, Lorna J.; Lewis, Jennifer A.

2017-01-01

Hierarchical cellular structures are ubiquitous in nature because of their low-density, high-specific properties, and multifunctionality. Inspired by these systems, we created lightweight ceramic architectures composed of closed-cell porous struts patterned in the form of hexagonal and triangular honeycombs by direct foam writing. The foam ink contains bubbles stabilized by attractive colloidal particles suspended in an aqueous solution. The printed and sintered ceramic foam honeycombs possess low relative density (∼6%). By tailoring their microstructure and geometry, we created honeycombs with different modes of deformation, exceptional specific stiffness, and stiffness values that span over an order of magnitude. This capability represents an important step toward the scalable fabrication of hierarchical porous materials for applications, including lightweight structures, thermal insulation, tissue scaffolds, catalyst supports, and electrodes. PMID:28179570

Cryptically Patterned Moths Perceive Bark Structure When Choosing Body Orientations That Match Wing Color Pattern to the Bark Pattern

PubMed Central

Kang, Chang-ku; Moon, Jong-yeol; Lee, Sang-im; Jablonski, Piotr G.

2013-01-01

Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i) whether a choice of resting orientation by moths depends on the properties of natural background, and ii) what sensory cues moths use. We studied moths’ behavior on natural (a tree log) and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature). We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel) to achieve crypticity in another sensory modality (visual). This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis. PMID:24205118

Cryptically patterned moths perceive bark structure when choosing body orientations that match wing color pattern to the bark pattern.

PubMed

Kang, Chang-Ku; Moon, Jong-Yeol; Lee, Sang-Im; Jablonski, Piotr G

2013-01-01

Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i) whether a choice of resting orientation by moths depends on the properties of natural background, and ii) what sensory cues moths use. We studied moths' behavior on natural (a tree log) and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature). We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel) to achieve crypticity in another sensory modality (visual). This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis.

Relative importance of modularity and other morphological attributes on different types of lithic point weapons: assessing functional variations.

PubMed

González-José, Rolando; Charlin, Judith

2012-01-01

The specific using of different prehistoric weapons is mainly determined by its physical properties, which provide a relative advantage or disadvantage to perform a given, particular function. Since these physical properties are integrated to accomplish that function, examining design variables and their pattern of integration or modularity is of interest to estimate the past function of a point. Here we analyze a composite sample of lithic points from southern Patagonia likely formed by arrows, thrown spears and hand-held points to test if they can be viewed as a two-module system formed by the blade and the stem, and to evaluate the degree in which shape, size, asymmetry, blade: stem length ratio, and tip angle explain the observed variance and differentiation among points supposedly aimed to accomplish different functions. To do so we performed a geometric morphometric analysis on 118 lithic points, departing from 24 two-dimensional landmark and semi landmarks placed on the point's contour. Klingenberg's covariational modularity tests were used to evaluate different modularity hypotheses, and a composite PCA including shape, size, asymmetry, blade: stem length ratio, and tip angle was used to estimate the importance of each attribute to explaining variation patterns. Results show that the blade and the stem can be seen as "near decomposable units" in the points integrating the studied sample. However, this modular pattern changes after removing the effects of reduction. Indeed, a resharpened point tends to show a tip/rest of the point modular pattern. The composite PCA analyses evidenced three different patterns of morphometric attributes compatible with arrows, thrown spears, and hand-held tools. Interestingly, when analyzed independently, these groups show differences in their modular organization. Our results indicate that stone tools can be approached as flexible designs, characterized by a composite set of interacting morphometric attributes, and evolving on a modular way.

Relative Importance of Modularity and Other Morphological Attributes on Different Types of Lithic Point Weapons: Assessing Functional Variations

PubMed Central

González-José, Rolando; Charlin, Judith

2012-01-01

The specific using of different prehistoric weapons is mainly determined by its physical properties, which provide a relative advantage or disadvantage to perform a given, particular function. Since these physical properties are integrated to accomplish that function, examining design variables and their pattern of integration or modularity is of interest to estimate the past function of a point. Here we analyze a composite sample of lithic points from southern Patagonia likely formed by arrows, thrown spears and hand-held points to test if they can be viewed as a two-module system formed by the blade and the stem, and to evaluate the degree in which shape, size, asymmetry, blade: stem length ratio, and tip angle explain the observed variance and differentiation among points supposedly aimed to accomplish different functions. To do so we performed a geometric morphometric analysis on 118 lithic points, departing from 24 two-dimensional landmark and semi landmarks placed on the point's contour. Klingenberg's covariational modularity tests were used to evaluate different modularity hypotheses, and a composite PCA including shape, size, asymmetry, blade: stem length ratio, and tip angle was used to estimate the importance of each attribute to explaining variation patterns. Results show that the blade and the stem can be seen as “near decomposable units” in the points integrating the studied sample. However, this modular pattern changes after removing the effects of reduction. Indeed, a resharpened point tends to show a tip/rest of the point modular pattern. The composite PCA analyses evidenced three different patterns of morphometric attributes compatible with arrows, thrown spears, and hand-held tools. Interestingly, when analyzed independently, these groups show differences in their modular organization. Our results indicate that stone tools can be approached as flexible designs, characterized by a composite set of interacting morphometric attributes, and evolving on a modular way. PMID:23094104

Detection of Anomalies in Hydrometric Data Using Artificial Intelligence Techniques

NASA Astrophysics Data System (ADS)

Lauzon, N.; Lence, B. J.

2002-12-01

This work focuses on the detection of anomalies in hydrometric data sequences, such as 1) outliers, which are individual data having statistical properties that differ from those of the overall population; 2) shifts, which are sudden changes over time in the statistical properties of the historical records of data; and 3) trends, which are systematic changes over time in the statistical properties. For the purpose of the design and management of water resources systems, it is important to be aware of these anomalies in hydrometric data, for they can induce a bias in the estimation of water quantity and quality parameters. These anomalies may be viewed as specific patterns affecting the data, and therefore pattern recognition techniques can be used for identifying them. However, the number of possible patterns is very large for each type of anomaly and consequently large computing capacities are required to account for all possibilities using the standard statistical techniques, such as cluster analysis. Artificial intelligence techniques, such as the Kohonen neural network and fuzzy c-means, are clustering techniques commonly used for pattern recognition in several areas of engineering and have recently begun to be used for the analysis of natural systems. They require much less computing capacity than the standard statistical techniques, and therefore are well suited for the identification of outliers, shifts and trends in hydrometric data. This work constitutes a preliminary study, using synthetic data representing hydrometric data that can be found in Canada. The analysis of the results obtained shows that the Kohonen neural network and fuzzy c-means are reasonably successful in identifying anomalies. This work also addresses the problem of uncertainties inherent to the calibration procedures that fit the clusters to the possible patterns for both the Kohonen neural network and fuzzy c-means. Indeed, for the same database, different sets of clusters can be established with these calibration procedures. A simple method for analyzing uncertainties associated with the Kohonen neural network and fuzzy c-means is developed here. The method combines the results from several sets of clusters, either from the Kohonen neural network or fuzzy c-means, so as to provide an overall diagnosis as to the identification of outliers, shifts and trends. The results indicate an improvement in the performance for identifying anomalies when the method of combining cluster sets is used, compared with when only one cluster set is used.

Leishmania major Survival in Selective Phlebotomus papatasi Sand Fly Vector Requires a Specific SCG-Encoded Lipophosphoglycan Galactosylation Pattern

PubMed Central

Dobson, Deborah E.; Kamhawi, Shaden; Lawyer, Phillip; Turco, Salvatore J.; Beverley, Stephen M.; Sacks, David L.

2010-01-01

Phlebotomine sand flies that transmit the protozoan parasite Leishmania differ greatly in their ability to support different parasite species or strains in the laboratory: while some show considerable selectivity, others are more permissive. In “selective” sand flies, Leishmania binding and survival in the fly midgut typically depends upon the abundant promastigote surface adhesin lipophosphoglycan (LPG), which exhibits species- and strain-specific modifications of the dominant phosphoglycan (PG) repeat units. For the “selective” fly Phlebotomus papatasi PpapJ, side chain galactosyl-modifications (scGal) of PG repeats play key roles in parasite binding. We probed the specificity and properties of this scGal-LPG PAMP (Pathogen Associated Molecular Pattern) through studies of natural isolates exhibiting a wide range of galactosylation patterns, and of a panel of isogenic L. major engineered to express similar scGal-LPG diversity by transfection of SCG-encoded β1,3-galactosyltransferases with different activities. Surprisingly, both ‘poly-scGal’ and ‘null-scGal’ lines survived poorly relative to PpapJ-sympatric L. major FV1 and other ‘mono-scGal’ lines. However, survival of all lines was equivalent in P. duboscqi, which naturally transmit L. major strains bearing ‘null-scGal’-LPG PAMPs. We then asked whether scGal-LPG-mediated interactions were sufficient for PpapJ midgut survival by engineering Leishmania donovani, which normally express unsubstituted LPG, to express a ‘PpapJ-optimal’ scGal-LPG PAMP. Unexpectedly, these “L. major FV1-cloaked” L. donovani-SCG lines remained unable to survive within PpapJ flies. These studies establish that midgut survival of L. major in PpapJ flies is exquisitely sensitive to the scGal-LPG PAMP, requiring a specific ‘mono-scGal’ pattern. However, failure of ‘mono-scGal’ L. donovani-SCG lines to survive in selective PpapJ flies suggests a requirement for an additional, as yet unidentified L. major-specific parasite factor(s). The interplay of the LPG PAMP and additional factor(s) with sand fly midgut receptors may determine whether a given sand fly host is “selective” or “permissive”, with important consequences to both disease transmission and the natural co-evolution of sand flies and Leishmania. PMID:21085609

Practical 3-D Beam Pattern Based Channel Modeling for Multi-Polarized Massive MIMO Systems.

PubMed

Aghaeinezhadfirouzja, Saeid; Liu, Hui; Balador, Ali

2018-04-12

In this paper, a practical non-stationary three-dimensional (3-D) channel models for massive multiple-input multiple-output (MIMO) systems, considering beam patterns for different antenna elements, is proposed. The beam patterns using dipole antenna elements with different phase excitation toward the different direction of travels (DoTs) contributes various correlation weights for rays related towards/from the cluster, thus providing different elevation angle of arrivals (EAoAs) and elevation angle of departures (EAoDs) for each antenna element. These include the movements of the user that makes our channel to be a non-stationary model of clusters at the receiver (RX) on both the time and array axes. In addition, their impacts on 3-D massive MIMO channels are investigated via statistical properties including received spatial correlation. Additionally, the impact of elevation/azimuth angles of arrival on received spatial correlation is discussed. Furthermore, experimental validation of the proposed 3-D channel models on azimuth and elevation angles of the polarized antenna are specifically evaluated and compared through simulations. The proposed 3-D generic models are verified using relevant measurement data.

Practical 3-D Beam Pattern Based Channel Modeling for Multi-Polarized Massive MIMO Systems †

PubMed Central

Aghaeinezhadfirouzja, Saeid; Liu, Hui

2018-01-01

In this paper, a practical non-stationary three-dimensional (3-D) channel models for massive multiple-input multiple-output (MIMO) systems, considering beam patterns for different antenna elements, is proposed. The beam patterns using dipole antenna elements with different phase excitation toward the different direction of travels (DoTs) contributes various correlation weights for rays related towards/from the cluster, thus providing different elevation angle of arrivals (EAoAs) and elevation angle of departures (EAoDs) for each antenna element. These include the movements of the user that makes our channel to be a non-stationary model of clusters at the receiver (RX) on both the time and array axes. In addition, their impacts on 3-D massive MIMO channels are investigated via statistical properties including received spatial correlation. Additionally, the impact of elevation/azimuth angles of arrival on received spatial correlation is discussed. Furthermore, experimental validation of the proposed 3-D channel models on azimuth and elevation angles of the polarized antenna are specifically evaluated and compared through simulations. The proposed 3-D generic models are verified using relevant measurement data. PMID:29649177

Learning Midlevel Auditory Codes from Natural Sound Statistics.

PubMed

Młynarski, Wiktor; McDermott, Josh H

2018-03-01

Interaction with the world requires an organism to transform sensory signals into representations in which behaviorally meaningful properties of the environment are made explicit. These representations are derived through cascades of neuronal processing stages in which neurons at each stage recode the output of preceding stages. Explanations of sensory coding may thus involve understanding how low-level patterns are combined into more complex structures. To gain insight into such midlevel representations for sound, we designed a hierarchical generative model of natural sounds that learns combinations of spectrotemporal features from natural stimulus statistics. In the first layer, the model forms a sparse convolutional code of spectrograms using a dictionary of learned spectrotemporal kernels. To generalize from specific kernel activation patterns, the second layer encodes patterns of time-varying magnitude of multiple first-layer coefficients. When trained on corpora of speech and environmental sounds, some second-layer units learned to group similar spectrotemporal features. Others instantiate opponency between distinct sets of features. Such groupings might be instantiated by neurons in the auditory cortex, providing a hypothesis for midlevel neuronal computation.

Voronoi Cell Patterns: theoretical model and application to submonolayer growth

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2012-02-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We apply our model to describe the Voronoi cell patterns of island nucleation for critical island sizes i=0,1,2,3. Experimental results for the Voronoi cells of InAs/GaAs quantum dots are also described by our model.

Atomic Force Microscopy Mechanical Mapping of Micropatterned Cells Shows Adhesion Geometry-Dependent Mechanical Response on Local and Global Scales.

PubMed

Rigato, Annafrancesca; Rico, Felix; Eghiaian, Frédéric; Piel, Mathieu; Scheuring, Simon

2015-06-23

In multicellular organisms, cell shape and organization are dictated by cell-cell or cell-extracellular matrix adhesion interactions. Adhesion complexes crosstalk with the cytoskeleton enabling cells to sense their mechanical environment. Unfortunately, most of cell biology studies, and cell mechanics studies in particular, are conducted on cultured cells adhering to a hard, homogeneous, and unconstrained substrate with nonspecific adhesion sites, thus far from physiological and reproducible conditions. Here, we grew cells on three different fibronectin patterns with identical overall dimensions but different geometries (▽, T, and Y), and investigated their topography and mechanics by atomic force microscopy (AFM). The obtained mechanical maps were reproducible for cells grown on patterns of the same geometry, revealing pattern-specific subcellular differences. We found that local Young's moduli variations are related to the cell adhesion geometry. Additionally, we detected local changes of cell mechanical properties induced by cytoskeletal drugs. We thus provide a method to quantitatively and systematically investigate cell mechanics and their variations, and present further evidence for a tight relation between cell adhesion and mechanics.

Judgments relative to patterns: how temporal sequence patterns affect judgments and memory.

PubMed

Kusev, Petko; Ayton, Peter; van Schaik, Paul; Tsaneva-Atanasova, Krasimira; Stewart, Neil; Chater, Nick

2011-12-01

Six experiments studied relative frequency judgment and recall of sequentially presented items drawn from 2 distinct categories (i.e., city and animal). The experiments show that judged frequencies of categories of sequentially encountered stimuli are affected by certain properties of the sequence configuration. We found (a) a first-run effect whereby people overestimated the frequency of a given category when that category was the first repeated category to occur in the sequence and (b) a dissociation between judgments and recall; respondents may judge 1 event more likely than the other and yet recall more instances of the latter. Specifically, the distribution of recalled items does not correspond to the frequency estimates for the event categories, indicating that participants do not make frequency judgments by sampling their memory for individual items as implied by other accounts such as the availability heuristic (Tversky & Kahneman, 1973) and the availability process model (Hastie & Park, 1986). We interpret these findings as reflecting the operation of a judgment heuristic sensitive to sequential patterns and offer an account for the relationship between memory and judged frequencies of sequentially encountered stimuli.

Basic Research of Intrinsic Tamper Indication Markings Defined by Pulsed Laser Irradiation (Quad Chart).

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

Moody, Neville R.

Objective: We will research how short (ns) and ultrashort (fs) laser pulses interact with the surfaces of various materials to create complex color layers and morphological patterns. Method: We are investigating the site-specific, formation of microcolor features. Also, research includes a fundamental study of the physics underlying periodic ripple formation during femtosecond laser irradiation. Status of effort: Laser induced color markings were demonstrated on an increased number of materials (including metal thin films) and investigated for optical properties and microstructure. Technology that allows for marking curved surfaces (and large areas) has been implemented. We have used electro-magnetic solvers to modelmore » light-solid interactions leading to periodic surface ripple patterns. This includes identifying the roles of surface plasmon polaritons. Goals/Milestones: Research corrosion resistance of oxide color markings (salt spray, fog, polarization tests); Through modeling, investigate effects of multi-source scattering and interference on ripple patterns; Investigate microspectrophotometry for mapping color; and Investigate new methods for laser color marking curved surfaces and large areas.« less

Genetically increased cell-intrinsic excitability enhances neuronal integration into adult brain circuits

PubMed Central

Lin, Chia-Wei; Sim, Shuyin; Ainsworth, Alice; Okada, Masayoshi; Kelsch, Wolfgang; Lois, Carlos

2009-01-01

New neurons are added to the adult brain throughout life, but only half ultimately integrate into existing circuits. Sensory experience is an important regulator of the selection of new neurons but it remains unknown whether experience provides specific patterns of synaptic input, or simply a minimum level of overall membrane depolarization critical for integration. To investigate this issue, we genetically modified intrinsic electrical properties of adult-generated neurons in the mammalian olfactory bulb. First, we observed that suppressing levels of cell-intrinsic neuronal activity via expression of ESKir2.1 potassium channels decreases, whereas enhancing activity via expression of NaChBac sodium channels increases survival of new neurons. Neither of these modulations affects synaptic formation. Furthermore, even when neurons are induced to fire dramatically altered patterns of action potentials, increased levels of cell-intrinsic activity completely blocks cell death triggered by NMDA receptor deletion. These findings demonstrate that overall levels of cell-intrinsic activity govern survival of new neurons and precise firing patterns are not essential for neuronal integration into existing brain circuits. PMID:20152111

Individual Biases, Cultural Evolution, and the Statistical Nature of Language Universals: The Case of Colour Naming Systems

PubMed Central

Baronchelli, Andrea; Loreto, Vittorio; Puglisi, Andrea

2015-01-01

Language universals have long been attributed to an innate Universal Grammar. An alternative explanation states that linguistic universals emerged independently in every language in response to shared cognitive or perceptual biases. A computational model has recently shown how this could be the case, focusing on the paradigmatic example of the universal properties of colour naming patterns, and producing results in quantitative agreement with the experimental data. Here we investigate the role of an individual perceptual bias in the framework of the model. We study how, and to what extent, the structure of the bias influences the corresponding linguistic universal patterns. We show that the cultural history of a group of speakers introduces population-specific constraints that act against the pressure for uniformity arising from the individual bias, and we clarify the interplay between these two forces. PMID:26018391

Improved method for predicting protein fold patterns with ensemble classifiers.

PubMed

Chen, W; Liu, X; Huang, Y; Jiang, Y; Zou, Q; Lin, C

2012-01-27

Protein folding is recognized as a critical problem in the field of biophysics in the 21st century. Predicting protein-folding patterns is challenging due to the complex structure of proteins. In an attempt to solve this problem, we employed ensemble classifiers to improve prediction accuracy. In our experiments, 188-dimensional features were extracted based on the composition and physical-chemical property of proteins and 20-dimensional features were selected using a coupled position-specific scoring matrix. Compared with traditional prediction methods, these methods were superior in terms of prediction accuracy. The 188-dimensional feature-based method achieved 71.2% accuracy in five cross-validations. The accuracy rose to 77% when we used a 20-dimensional feature vector. These methods were used on recent data, with 54.2% accuracy. Source codes and dataset, together with web server and software tools for prediction, are available at: http://datamining.xmu.edu.cn/main/~cwc/ProteinPredict.html.

The Spanish version of the Self-Determination Inventory Student Report: application of item response theory to self-determination measurement.

PubMed

Mumbardó-Adam, C; Guàrdia-Olmos, J; Giné, C; Raley, S K; Shogren, K A

2018-04-01

A new measure of self-determination, the Self-Determination Inventory: Student Report (Spanish version), has recently been adapted and empirically validated in Spanish language. As it is the first instrument intended to measure self-determination in youth with and without disabilities, there is a need to further explore and strengthen its psychometric analysis based on item response patterns. Through item response theory approach, this study examined item observed distributions across the essential characteristics of self-determination. The results demonstrated satisfactory to excellent item functioning patterns across characteristics, particularly within agentic action domains. Increased variability across items was also found within action-control beliefs dimensions, specifically within the self-realisation subdomain. These findings further support the instrument's psychometric properties and outline future research directions. © 2017 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Lead zirconate titanate nanoscale patterning by ultraviolet-based lithography lift-off technique for nano-electromechanical system applications.

PubMed

Guillon, Samuel; Saya, Daisuke; Mazenq, Laurent; Costecalde, Jean; Rèmiens, Denis; Soyer, Caroline; Nicu, Liviu

2012-09-01

The advantage of using lead zirconate titanate (PbZr(0.54)Ti(0.46)O(3)) ceramics as an active material in nanoelectromechanical systems (NEMS) comes from its relatively high piezoelectric coefficients. However, its integration within a technological process is limited by the difficulty of structuring this material with submicrometer resolution at the wafer scale. In this work, we develop a specific patterning method based on optical lithography coupled with a dual-layer resist process. The main objective is to obtain sub-micrometer features by lifting off a 100-nm-thick PZT layer while preserving the material's piezoelectric properties. A subsequent result of the developed method is the ability to stack several layers with a lateral resolution of few tens of nanometers, which is mandatory for the fabrication of NEMS with integrated actuation and read-out capabilities.

Electrospun nanofibers: Work for medicine?

NASA Astrophysics Data System (ADS)

Liao, Susan; Chan, Casey K.; Ramakrishna, S.

2010-03-01

Attempts have been made to fabricate nanofibrous scaffolds to mimic the chemical composition and structural properties of the extracellular matrix (ECM) for tissue/organ replacement. Nanofiber scaffolds with various patterns have been successfully produced from synthetic and natural polymers through a relatively simple technique of electrospinning. The resulting patterns can mimic some of the diverse tissue-specific orientation and three-dimensional (3D) fibrous structures. Studies on cell-nanofiber interactions, including studies on stem cells, have revealed the importance of nanotopography on cell adhesion, proliferation and differentiation. Furthermore, clinical application of electrospun nanofibers including wound healing, tissue regeneration, drug delivery and stem cell therapy are highly feasible due to the ease and flexibility of fabrication of making nanofiber with this cost-effective method using electrospinning. In this review, we have highlighted the current state of the art and provided future perspectives on electrospun nanofiber in medical applications.

Baseline assessment of physical characteristics, aquatic biota, and selected water-quality properties at the reach and mesohabitat scale for reaches of Big Cypress, Black Cypress, and Little Cypress Bayous, Big Cypress Basin, northeastern Texas, 2010–11

USGS Publications Warehouse

Braun, Christopher L.; Moring, James B.

2013-01-01

In the absence of flow during fall 2011, the reach at Black Cypress was reduced to four isolated pools, and the reach at Little Cypress was reduced to three isolated pools. Dissolved oxygen, temperature, pH, and specific conductance data were collected from the pools because it was hypothesized that these conditions would be the most limiting with respect to aquatic life. Dissolved oxygen concentrations ranged from 0.58 milligrams per liter (mg/L) to 4.79 mg/L at Black Cypress and from 0.24 mg/L to 5.33 mg/L at Little Cypress; both sites exhibited a stratified pattern in dissolved oxygen concentrations along transect lines, but the pattern was less pronounced at Black Cypress.

Self-similar conductance patterns in graphene Cantor-like structures.

PubMed

García-Cervantes, H; Gaggero-Sager, L M; Díaz-Guerrero, D S; Sotolongo-Costa, O; Rodríguez-Vargas, I

2017-04-04

Graphene has proven to be an ideal system for exotic transport phenomena. In this work, we report another exotic characteristic of the electron transport in graphene. Namely, we show that the linear-regime conductance can present self-similar patterns with well-defined scaling rules, once the graphene sheet is subjected to Cantor-like nanostructuring. As far as we know the mentioned system is one of the few in which a self-similar structure produces self-similar patterns on a physical property. These patterns are analysed quantitatively, by obtaining the scaling rules that underlie them. It is worth noting that the transport properties are an average of the dispersion channels, which makes the existence of scale factors quite surprising. In addition, that self-similarity be manifested in the conductance opens an excellent opportunity to test this fundamental property experimentally.

Prediction limits of mobile phone activity modelling

NASA Astrophysics Data System (ADS)

Kondor, Dániel; Grauwin, Sebastian; Kallus, Zsófia; Gódor, István; Sobolevsky, Stanislav; Ratti, Carlo

2017-02-01

Thanks to their widespread usage, mobile devices have become one of the main sensors of human behaviour and digital traces left behind can be used as a proxy to study urban environments. Exploring the nature of the spatio-temporal patterns of mobile phone activity could thus be a crucial step towards understanding the full spectrum of human activities. Using 10 months of mobile phone records from Greater London resolved in both space and time, we investigate the regularity of human telecommunication activity on urban scales. We evaluate several options for decomposing activity timelines into typical and residual patterns, accounting for the strong periodic and seasonal components. We carry out our analysis on various spatial scales, showing that regularity increases as we look at aggregated activity in larger spatial units with more activity in them. We examine the statistical properties of the residuals and show that it can be explained by noise and specific outliers. Also, we look at sources of deviations from the general trends, which we find to be explainable based on knowledge of the city structure and places of attractions. We show examples how some of the outliers can be related to external factors such as specific social events.

The compelling case for indentation as a functional exploratory and characterization tool

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

Tandon, Rajan; Marshall, David B.; Cook, Robert F.

The utility of indentation testing for characterizing a wide range of mechanical properties of brittle materials is highlighted in light of recent articles questioning its validity, specifically in relation to the measurement of toughness. Contrary to assertion by some critics, indentation fracture theory is fundamentally founded in Griffith–Irwin fracture mechanics, based on model crack systems evolving within inhomogeneous but well-documented elastic and elastic–plastic contact stress fields. Notwithstanding some numerical uncertainty in associated stress intensity factor relations, the technique remains an unrivalled quick, convenient and economical means for comparative, site-specific toughness evaluation. Most importantly, indentation patterns are unique fingerprints of mechanicalmore » behavior and thereby afford a powerful functional tool for exploring the richness of material diversity. At the same time, it is cautioned that unconditional usage without due attention to the conformation of the indentation patterns can lead to overstated toughness values. Limitations of an alternative, more engineering approach to fracture evaluation, that of propagating a precrack through a “standard” machined specimen, are also outlined. Thus misconceptions in the critical literature concerning the fundamental nature of crack equilibrium and stability within contact and other inhomogeneous stress fields are discussed.« less

The compelling case for indentation as a functional exploratory and characterization tool

DOE PAGES

Tandon, Rajan; Marshall, David B.; Cook, Robert F.; ...

2015-07-30

The utility of indentation testing for characterizing a wide range of mechanical properties of brittle materials is highlighted in light of recent articles questioning its validity, specifically in relation to the measurement of toughness. Contrary to assertion by some critics, indentation fracture theory is fundamentally founded in Griffith–Irwin fracture mechanics, based on model crack systems evolving within inhomogeneous but well-documented elastic and elastic–plastic contact stress fields. Notwithstanding some numerical uncertainty in associated stress intensity factor relations, the technique remains an unrivalled quick, convenient and economical means for comparative, site-specific toughness evaluation. Most importantly, indentation patterns are unique fingerprints of mechanicalmore » behavior and thereby afford a powerful functional tool for exploring the richness of material diversity. At the same time, it is cautioned that unconditional usage without due attention to the conformation of the indentation patterns can lead to overstated toughness values. Limitations of an alternative, more engineering approach to fracture evaluation, that of propagating a precrack through a “standard” machined specimen, are also outlined. Thus misconceptions in the critical literature concerning the fundamental nature of crack equilibrium and stability within contact and other inhomogeneous stress fields are discussed.« less

On the determination of the origin of linear anomaly in the macrostructure of VPPA welded 2219-T87 aluminum alloy

NASA Technical Reports Server (NTRS)

Jemian, W. A.

1986-01-01

The objective was to determine the cause and significance of the weld radiograph enigma, which is a linear anomaly in the features of the X-ray film. By observing features on available radiographs and in studying published reports of similar features it was possible to conclude that there are many manifestations of the enigma, and that they are all specific features of fine structure in radiographs due to natural processes connected with welding and to specific X-ray absorption and diffraction phenomena. These processes include the thermal distribution and liquid metal flow in welding, the development of microstructure, morpohology, second phase particles and porosity due to the solidification process and to the pattern of residual stresses after the weld metal has cooled to the ambient temperature. Microdensitometer traces were made across weld radiographs of standard and enigmatic types. Similar patterns were produced by computer simulation. These show that the enigma is a relatively low contrast feature compared to real weld defects, such as undercuts or centerline cracks. The enigma can be distinguished from weld defects by these microdensitometer traces. The enigma effect on weld properties is not known but is expected to be minor.

On the determination of the origin of linear anomaly in the macrostructure of VPPA welded 2219-T87 aluminum alloy: Preliminary report

NASA Technical Reports Server (NTRS)

Jemian, W. A.

1986-01-01

The cause and significance of the weld radiograph enigma, which is a linear anomaly in the features of the X-ray film is examined. By observing features on available radiographs and in studying published reports of similar features, it was possible to conclude that there are many manifestations of the enigma, and that they are all specific features of fine structure in radiographs due to natural processes connected with welding and to specific X-ray absorption and diffraction phenomena. These processes include the thermal distribution and liquid metal flow in welding, the development of microstructure, morphology, second phase particles and porosity due to the solidification process, and to the pattern of residual stresses after the weld metal has cooled to the ambient temperature. Microdensitometer traces were made across weld radiographs of standard enigmatic types. Similar patterns were produced by computer simulation. These show that the enigma is a relatively low contrast feature compared to real weld defects, such as undercuts or centerline cracks. The enigma can be distinguished from weld defects by these microdensitometer traces. The enigma effect on weld properties is not known but is expected to be minor.

Prediction limits of mobile phone activity modelling.

PubMed

Kondor, Dániel; Grauwin, Sebastian; Kallus, Zsófia; Gódor, István; Sobolevsky, Stanislav; Ratti, Carlo

2017-02-01

Thanks to their widespread usage, mobile devices have become one of the main sensors of human behaviour and digital traces left behind can be used as a proxy to study urban environments. Exploring the nature of the spatio-temporal patterns of mobile phone activity could thus be a crucial step towards understanding the full spectrum of human activities. Using 10 months of mobile phone records from Greater London resolved in both space and time, we investigate the regularity of human telecommunication activity on urban scales. We evaluate several options for decomposing activity timelines into typical and residual patterns, accounting for the strong periodic and seasonal components. We carry out our analysis on various spatial scales, showing that regularity increases as we look at aggregated activity in larger spatial units with more activity in them. We examine the statistical properties of the residuals and show that it can be explained by noise and specific outliers. Also, we look at sources of deviations from the general trends, which we find to be explainable based on knowledge of the city structure and places of attractions. We show examples how some of the outliers can be related to external factors such as specific social events.

Identification of avian wax synthases

PubMed Central

2012-01-01

Background Bird species show a high degree of variation in the composition of their preen gland waxes. For instance, galliform birds like chicken contain fatty acid esters of 2,3-alkanediols, while Anseriformes like goose or Strigiformes like barn owl contain wax monoesters in their preen gland secretions. The final biosynthetic step is catalyzed by wax synthases (WS) which have been identified in pro- and eukaryotic organisms. Results Sequence similarities enabled us to identify six cDNAs encoding putative wax synthesizing proteins in chicken and two from barn owl and goose. Expression studies in yeast under in vivo and in vitro conditions showed that three proteins from chicken performed WS activity while a sequence from chicken, goose and barn owl encoded a bifunctional enzyme catalyzing both wax ester and triacylglycerol synthesis. Mono- and bifunctional WS were found to differ in their substrate specificities especially with regard to branched-chain alcohols and acyl-CoA thioesters. According to the expression patterns of their transcripts and the properties of the enzymes, avian WS proteins might not be confined to preen glands. Conclusions We provide direct evidence that avian preen glands possess both monofunctional and bifunctional WS proteins which have different expression patterns and WS activities with different substrate specificities. PMID:22305293

Robustness of sensory-evoked excitation is increased by inhibitory inputs to distal apical tuft dendrites

PubMed Central

Egger, Robert; Schmitt, Arno C.; Wallace, Damian J.; Sakmann, Bert; Oberlaender, Marcel; Kerr, Jason N. D.

2015-01-01

Cortical inhibitory interneurons (INs) are subdivided into a variety of morphologically and functionally specialized cell types. How the respective specific properties translate into mechanisms that regulate sensory-evoked responses of pyramidal neurons (PNs) remains unknown. Here, we investigated how INs located in cortical layer 1 (L1) of rat barrel cortex affect whisker-evoked responses of L2 PNs. To do so we combined in vivo electrophysiology and morphological reconstructions with computational modeling. We show that whisker-evoked membrane depolarization in L2 PNs arises from highly specialized spatiotemporal synaptic input patterns. Temporally L1 INs and L2–5 PNs provide near synchronous synaptic input. Spatially synaptic contacts from L1 INs target distal apical tuft dendrites, whereas PNs primarily innervate basal and proximal apical dendrites. Simulations of such constrained synaptic input patterns predicted that inactivation of L1 INs increases trial-to-trial variability of whisker-evoked responses in L2 PNs. The in silico predictions were confirmed in vivo by L1-specific pharmacological manipulations. We present a mechanism—consistent with the theory of distal dendritic shunting—that can regulate the robustness of sensory-evoked responses in PNs without affecting response amplitude or latency. PMID:26512104

[Adaptive specific features of energy metabolism in fish ontogenesis].

PubMed

Ozerniuk, N D

2011-01-01

A review of data on the pattern of change of the intensity of oxygen consumption during early ontogenesis of different fish species (rainbow trout, loach, zebrafish, carp, and grass carp) is provided. It has a similar pattern: this index increases in the period of embryonic and larval development and, after passing of larvae to an active feeding, it begins to gradually decline. This dynamics is determined by specific features of an increase in the rate of oxygen uptake and body weight in the course of early stages of fish ontogenesis. For determining optimal temperature conditions of development, a method of total (for a definite stage of development) oxygen uptake was suggested, which makes it possible to determine minimal energy expenditures necessary for the process of a particular stage of embryogenesis to take place. Analysis of temperature dependence of kinetic properties of enzymes with reference to the Michaelis constant (Km) for lactate dehydrogenase demonstrated that minimal Km, corresponding to maximal enzyme-substrate affinity, for embryos of different fish species differs in correspondence with differences in temperature conditions of development of these species in nature. For embryos of one species developing at changing temperature conditions (salmonids), this index changes in accordance with a temperature drift in nature.

Incorporating geologic information into hydraulic tomography: A general framework based on geostatistical approach

NASA Astrophysics Data System (ADS)

Zha, Yuanyuan; Yeh, Tian-Chyi J.; Illman, Walter A.; Onoe, Hironori; Mok, Chin Man W.; Wen, Jet-Chau; Huang, Shao-Yang; Wang, Wenke

2017-04-01

Hydraulic tomography (HT) has become a mature aquifer test technology over the last two decades. It collects nonredundant information of aquifer heterogeneity by sequentially stressing the aquifer at different wells and collecting aquifer responses at other wells during each stress. The collected information is then interpreted by inverse models. Among these models, the geostatistical approaches, built upon the Bayesian framework, first conceptualize hydraulic properties to be estimated as random fields, which are characterized by means and covariance functions. They then use the spatial statistics as prior information with the aquifer response data to estimate the spatial distribution of the hydraulic properties at a site. Since the spatial statistics describe the generic spatial structures of the geologic media at the site rather than site-specific ones (e.g., known spatial distributions of facies, faults, or paleochannels), the estimates are often not optimal. To improve the estimates, we introduce a general statistical framework, which allows the inclusion of site-specific spatial patterns of geologic features. Subsequently, we test this approach with synthetic numerical experiments. Results show that this approach, using conditional mean and covariance that reflect site-specific large-scale geologic features, indeed improves the HT estimates. Afterward, this approach is applied to HT surveys at a kilometer-scale-fractured granite field site with a distinct fault zone. We find that by including fault information from outcrops and boreholes for HT analysis, the estimated hydraulic properties are improved. The improved estimates subsequently lead to better prediction of flow during a different pumping test at the site.

A framework for grouping nanoparticles based on their measurable characteristics.

PubMed

Sayes, Christie M; Smith, P Alex; Ivanov, Ivan V

2013-01-01

There is a need to take a broader look at nanotoxicological studies. Eventually, the field will demand that some generalizations be made. To begin to address this issue, we posed a question: are metal colloids on the nanometer-size scale a homogeneous group? In general, most people can agree that the physicochemical properties of nanomaterials can be linked and related to their induced toxicological responses. The focus of this study was to determine how a set of selected physicochemical properties of five specific metal-based colloidal materials on the nanometer-size scale - silver, copper, nickel, iron, and zinc - could be used as nanodescriptors that facilitate the grouping of these metal-based colloids. The example of the framework pipeline processing provided in this paper shows the utility of specific statistical and pattern recognition techniques in grouping nanoparticles based on experimental data about their physicochemical properties. Interestingly, the results of the analyses suggest that a seemingly homogeneous group of nanoparticles could be separated into sub-groups depending on interdependencies observed in their nanodescriptors. These particles represent an important category of nanomaterials that are currently mass produced. Each has been reputed to induce toxicological and/or cytotoxicological effects. Here, we propose an experimental methodology coupled with mathematical and statistical modeling that can serve as a prototype for a rigorous framework that aids in the ability to group nanomaterials together and to facilitate the subsequent analysis of trends in data based on quantitative modeling of nanoparticle-specific structure-activity relationships. The computational part of the proposed framework is rather general and can be applied to other groups of nanomaterials as well.

Complete Genome Sequence of a Yersinia enterocolitica “Old World” (3/O:9) Strain and Comparison with the “New World” (1B/O:8) Strain▿†

PubMed Central

Wang, Xin; Li, Yang; Jing, Huaiqi; Ren, Yan; Zhou, Zhemin; Wang, Shaojing; Kan, Biao; Xu, Jianguo; Wang, Lei

2011-01-01

Yersinia enterocolitica is a heterogeneous bacterial species with a wide range of animal reservoirs through which human intestinal illness can be facilitated. In contrast to the epidemiological pattern observed in the United States, infections in China present a pattern similar to those in European countries and Japan, wherein “Old World” strains (biotypes 2 to 5) are prevalent. To gain insights into the evolution of Y. enterocolitica and pathogenic properties toward human hosts, we sequenced the genome of a biotype 3 strain, 105.5R(r) (O:9), obtained from a Chinese patient. Comparative genome sequence analysis with strain 8081 (1B/O:8) revealed new insights into Y. enterocolitica. Both strains have more than 14% specific genes. In strain 105.5R(r), putative virulence factors were found in strain-specific genomic pathogenicity islands that comprised a novel type III secretion system and rtx-like genes. Many of the loci representing ancestral clusters, which are believed to contribute to enteric survival and pathogenesis, are present in strain 105.5R(r) but lost in strain 8081. Insertion elements in 105.5R(r) have a pattern distinct from those in strain 8081 and were exclusively located in a strain-specific region. In summary, our comparative genome analysis indicates that these two strains may have attained their pathogenicity by completely separate evolutionary events, and the 105.5R(r) strain, a representative of the Old World biogroup, lies in a branch of Y. enterocolitica that is distinct from the “New World” 8081 strain. PMID:21325549

A Systematic Survey of Expression and Function of Zebrafish frizzled Genes

PubMed Central

Nikaido, Masataka; Law, Edward W. P.; Kelsh, Robert N.

2013-01-01

Wnt signaling is crucial for the regulation of numerous processes in development. Consistent with this, the gene families for both the ligands (Wnts) and receptors (Frizzleds) are very large. Surprisingly, while we have a reasonable understanding of the Wnt ligands likely to mediate specific Wnt-dependent processes, the corresponding receptors usually remain to be elucidated. Taking advantage of the zebrafish model's excellent genomic and genetic properties, we undertook a comprehensive analysis of the expression patterns of frizzled (fzd) genes in zebrafish. To explore their functions, we focused on testing their requirement in several developmental events known to be regulated by Wnt signaling, convergent extension movements of gastrulation, neural crest induction, and melanocyte specification. We found fourteen distinct fzd genes in the zebrafish genome. Systematic analysis of their expression patterns between 1-somite and 30 hours post-fertilization revealed complex, dynamic and overlapping expression patterns. This analysis demonstrated that only fzd3a, fzd9b, and fzd10 are expressed in the dorsal neural tube at stages corresponding to the timing of melanocyte specification. Surprisingly, however, morpholino knockdown of these, alone or in combination, gave no indication of reduction of melanocytes, suggesting the important involvement of untested fzds or another type of Wnt receptor in this process. Likewise, we found only fzd7b and fzd10 expressed at the border of the neural plate at stages appropriate for neural crest induction. However, neural crest markers were not reduced by knockdown of these receptors. Instead, these morpholino knockdown studies showed that fzd7a and fzd7b work co-operatively to regulate convergent extension movement during gastrulation. Furthermore, we show that the two fzd7 genes function together with fzd10 to regulate epiboly movements and mesoderm differentiation. PMID:23349976

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.

Interlocked Photo-degradable Macrocycles Allow One-Off Photo-triggerable Gelation of Organo- and Hydrogelators.

PubMed

Tung, Shun-Te; Cheng, Hung-Te; Inthasot, Alex; Hsueh, Fang-Che; Gu, Ting-Jia; Yan, Pei-Cong; Lai, Chien-Chen; Chiu, Sheng-Hsien

2018-02-01

[2]Rotaxanes displaying one-off photo-triggerable gelation properties have been synthesized through the "clipping" of photo-degradable macrocycles around the amide or urea functionalities of organo- and hydrogelators. Irradiation with UV-light cleaved the photo-labile macrocyclic components from the [2]rotaxanes, resulting in the free gelators being released into solution and, thereafter, forming gels. When the rate of gelation was sufficiently rapid, selective gelation of specific regions of the solution-and, indeed, photo-patterning of the solution-was possible. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Numerical simulation of forced convection in a duct subjected to microwave heating

NASA Astrophysics Data System (ADS)

Zhu, J.; Kuznetsov, A. V.; Sandeep, K. P.

2007-01-01

In this paper, forced convection in a rectangular duct subjected to microwave heating is investigated. Three types of non-Newtonian liquids flowing through the duct are considered, specifically, apple sauce, skim milk, and tomato sauce. A finite difference time domain method is used to solve Maxwell’s equations simulating the electromagnetic field. The three-dimensional temperature field is determined by solving the coupled momentum, energy, and Maxwell’s equations. Numerical results show that the heating pattern strongly depends on the dielectric properties of the fluid in the duct and the geometry of the microwave heating system.

Versatile digital micromirror device-based method for the recording of multilevel optical diffractive elements in photosensitive chalcogenide layers (AMTIR-1).

PubMed

Joerg, Alexandre; Vignaux, Mael; Lumeau, Julien

2016-08-01

A new alternative and versatile method for the production of diffractive optical elements (DOEs) with up to four phase levels in AMTIR-1 (Ge₃₃As₁₂Se₅₅) layers is demonstrated. The developed method proposes the use of the photosensitive properties of the layers and a specific in situ optical monitoring coupled with a reverse engineering algorithm to control the trigger points of the writing of the different diffractive patterns. Examples of various volume DOEs are presented.

Morphological properties of vestibulospinal neurons in primates

NASA Technical Reports Server (NTRS)

Boyle, Richard; Johanson, Curt

2003-01-01

The lateral and medial vestibulospinal tracts constitute the major descending pathways controlling extensor musculature of the body. We examined the axon morphology and synaptic input patterns and targets in the cervical spinal segments from these tract cells using intracellular recording and biocytin labeling in the squirrel monkey. Lumbosacral projecting cells represent a private, and mostly rapid, communication pathway between the dorsal Deiters' nucleus and the motor circuits controlling the lower limbs and tail. The cervical projecting cells provide both redundant and variable synaptic input to spinal cell groups, suggesting both general and specific control of the head and neck reflexes.

Patterned gallium surfaces as molecular mirrors.

PubMed

Bossi, Alessandra; Rivetti, Claudio; Mangiarotti, Laura; Whitcombe, Michael J; Turner, Anthony P F; Piletsky, Sergey A

2007-09-30

An entirely new means of printing molecular information on a planar film, involving casting nanoscale impressions of the template protein molecules in molten gallium, is presented here for the first time. The metallic imprints not only replicate the shape and size of the proteins used as template. They also show specific binding for the template species. Such a simple approach to the creation of antibody-like properties in metallic mirrors can lead to applications in separations, microfluidic devices, and the development of new optical and electronic sensors, and will be of interest to chemists, materials scientists, analytical specialists, and electronic engineers.

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.

Structure-Property Characterization of the Crinkle-Leaf Peach Wood Phenotype: A Future Model System for Wood Properties Research?

NASA Astrophysics Data System (ADS)

Wiedenhoeft, Alex C.; Arévalo, Rafael; Ledbetter, Craig; Jakes, Joseph E.

2016-09-01

Nearly 400 million years of evolution and field-testing by the natural world has given humans thousands of wood types, each with unique structure-property relationships to study, exploit, and ideally, to manipulate, but the slow growth of trees makes them a recalcitrant experimental system. Variations in wood features of two genotypes of peach ( Prunus persica L.) trees, wild-type and crinkle-leaf, were examined to elucidate the nature of weak wood in crinkle-leaf trees. Crinkle-leaf is a naturally-occurring mutation in which wood strength is altered in conjunction with an easily observed `crinkling' of the leaves' surface. Trees from three vigor classes (low growth rate, average growth rate, and high growth rate) of each genotype were sampled. No meaningful tendency of dissimilarities among the different vigor classes was found, nor any pattern in features in a genotype-by-vigor analysis. Wild-type trees exhibited longer vessels and fibers, wider rays, and slightly higher specific gravity. Neither cell wall mechanical properties measured with nanoindentation nor cell wall histochemical properties were statistically or observably different between crinkle-leaf and wild-type wood. The crinkle-leaf mutant has the potential to be a useful model system for wood properties investigation and manipulation if it can serve as a field-observable vegetative marker for altered wood properties.

Increased endothelial cell adhesion and elongation on micron-patterned nano-rough poly(dimethylsiloxane) films.

PubMed

Ranjan, Ashwini; Webster, Thomas J

2009-07-29

The success of synthetic vascular grafts is largely determined by their ability to promote vital endothelial cell functions such as adhesion, alignment, proliferation, and extracellular matrix (ECM) deposition. Developing such biomaterials requires the design and fabrication of materials that mimic select properties of native extracellular matrices. Furthermore, cells of the native endothelium have elongated and aligned morphology in the direction of blood flow, yet few materials promote this type of morphology initially, but rather rely on blood flow to orient endothelial cells. Therefore, the objective of this in vitro study was to design a biomaterial that mimics the conditions of the micro- and nano-environment of vascular intima tissue suitable for endothelial cell adhesion and elongation to improve the efficacy of small synthetic vascular grafts. Towards this end, patterned poly(dimethylsiloxane) (PDMS) films consisting of periodic arrays of nano-grooves (500 nm), with spacings ranging from 22 to 80 microm, and alternating nano- and micron roughness were fabricated using a novel electron beam physical vapor deposition method followed by polymer casting. By varying pattern spacing, the area of micron- and nano-rough surface was controlled. In vitro rat aortic endothelial cell adhesion and elongation studies indicated that endothelial cell function was enhanced on patterned PDMS surfaces with the widest spacing and greatest surface area of nano-roughness, as compared to more narrow pattern spacings and non-patterned PDMS surfaces. Specifically, endothelial cells adherent on PDMS patterned films of the widest spacing (greatest nano-rough area) displayed almost twice as much elongation as cells on non-patterned surfaces. For these reasons, the present study highlighted design criteria (the use of micron patterns of nano-features on PDMS) that may contribute to the intelligent design of new-generation vascular grafts.

The substance use risk profile scale: a scale measuring traits linked to reinforcement-specific substance use profiles.

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

Woicik, P.A.; Stewart, S.H.; Pihl, R.O.

The Substance Use Risk Profile Scale (SURPS) is based on a model of personality risk for substance abuse in which four personality dimensions (hopelessness, anxiety sensitivity, impulsivity, and sensation seeking) are hypothesized to differentially relate to specific patterns of substance use. The current series of studies is a preliminary exploration of the psychometric properties of the SURPS in two populations (undergraduate and high school students). In study 1, an analysis of the internal structure of two versions of the SURPS shows that the abbreviated version best reflects the 4-factor structure. Concurrent, discriminant, and incremental validity of the SURPS is supportedmore » by convergent/divergent relationships between the SURPS subscales and other theoretically relevant personality and drug use criterion measures. In Study 2, the factorial structure of the SURPS is confirmed and evidence is provided for its test-retest reliability and validity with respect to measuring personality vulnerability to reinforcement-specific substance use patterns. In Study 3, the SURPS was administered in a more youthful population to test its sensitivity in identifying younger problematic drinkers. The results from the current series of studies demonstrate support for the reliability and construct validity of the SURPS, and suggest that four personality dimensions may be linked to substance-related behavior through different reinforcement processes. This brief assessment tool may have important implications for clinicians and future research.« less

The Substance Use Risk Profile Scale: a scale measuring traits linked to reinforcement-specific substance use profiles.

PubMed

Woicik, Patricia A; Stewart, Sherry H; Pihl, Robert O; Conrod, Patricia J

2009-12-01

The Substance Use Risk Profile Scale (SURPS) is based on a model of personality risk for substance abuse in which four personality dimensions (hopelessness, anxiety sensitivity, impulsivity, and sensation seeking) are hypothesized to differentially relate to specific patterns of substance use. The current series of studies is a preliminary exploration of the psychometric properties of the SURPS in two populations (undergraduate and high school students). In study 1, an analysis of the internal structure of two versions of the SURPS shows that the abbreviated version best reflects the 4-factor structure. Concurrent, discriminant, and incremental validity of the SURPS is supported by convergent/divergent relationships between the SURPS subscales and other theoretically relevant personality and drug use criterion measures. In Study 2, the factorial structure of the SURPS is confirmed and evidence is provided for its test-retest reliability and validity with respect to measuring personality vulnerability to reinforcement-specific substance use patterns. In Study 3, the SURPS was administered in a more youthful population to test its sensitivity in identifying younger problematic drinkers. The results from the current series of studies demonstrate support for the reliability and construct validity of the SURPS, and suggest that four personality dimensions may be linked to substance-related behavior through different reinforcement processes. This brief assessment tool may have important implications for clinicians and future research.

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors.

PubMed

Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

2012-03-01

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

E6D25E, HPV16 Asian variant shows specific proteomic pattern correlating in cells transformation and suppressive innate immune response

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

Chopjitt, Peechanika; Pientong, Chamsai; Sunthamala, Nuchsupha

HPV16 Asian variant (HPV16As) containing E6D25E oncogene, is commonly associated with cervical cancers of Asian populations. To explore a mechanism of E6D25E oncoprotein in carcinogenesis, we compared protein profiles in human keratinocytes expressing E6D25E with E6 of HPV16 prototype (E6Pro). A human cervical keratinocyte cell line, HCK1T, was transduced with retroviruses containing E6D25E or E6Pro genes. Biological properties of E6D25E or E6Pro transduced HCK1T cells were characterized. Protein profiles of the transduced HCK1T cells were analyzed using 2D-PAGE and characterized by mass spectrometry and western blotting. Reactomes of modulated proteins were analyzed by using the Reactome Knowledgebase. The E6D25E andmore » E6Pro oncoproteins were comparable for their abilities to degrade p53 and suppress the induction of p21, and induce cell proliferation. Interestingly, the protein profiles of the HCK1T cells transduced with E6D25E showed specific proteomic patterns different from those with E6Pro. Among altered proteins, more than 1.5-fold up- or down- regulation was observed in E6D25E-expressing cells for gp96 and keratin7 which involved in activation of TLR signaling and transformation of squamocolumnar junction cells, respectively. This report describes new cellular proteins specifically targeted by E6D25E oncoprotein that may contribute to impair immune response against viral infection and cell transformation associated with oncogenic property of HPV16As variant. - Highlights: • E6D25E HPV16 specifically modulates protein profile of human keratinocytes. • E6D25E HPV16 modulates protein profile which involves in TLR signalling and transformation of squamocolumnar junction cells. • E6D25E oncoprotein may correlate to impair of immune response against viral infection and cells transformation.« less

On the influence of surface patterning on tissue self-assembly and mechanics.

PubMed

Coppola, Valerio; Ventre, Maurizio; Natale, Carlo F; Rescigno, Francesca; Netti, Paolo A

2018-04-28

Extracellular matrix assembly and composition influence the biological and mechanical functions of tissues. Developing strategies to control the spatial arrangement of cells and matrix is of central importance for tissue engineering-related approaches relying on self-assembling and scaffoldless processes. Literature reports demonstrated that signals patterned on material surfaces are able to control cell positioning and matrix orientation. However, the mechanisms underlying the interactions between material signals and the structure of the de novo synthesized matrix are far from being thoroughly understood. In this work, we investigated the ordering effect provided by nanoscale topographic patterns on the assembly of tissue sheets grown in vitro. We stimulated MC3T3-E1 preosteoblasts to produce and assemble a collagen-rich matrix on substrates displaying patterns with long- or short-range order. Then, we investigated microstructural features and mechanical properties of the tissue in uniaxial tension. Our results demonstrate that patterned material surfaces are able to control the initial organization of cells in close contact to the surface; then cell-generated contractile forces profoundly remodel tissue structure towards mechanically stable spatial patterns. Such a remodelling effect acts both locally, as it affects cell and nuclear shape and globally, by affecting the gross mechanical response of the tissue. Such an aspect of dynamic interplay between cells and the surrounding matrix must be taken into account when designing material platform for the in vitro generation of tissue with specific microstructural assemblies. Copyright © 2018 John Wiley & Sons, Ltd.

Neuromusculoskeletal models based on the muscle synergy hypothesis for the investigation of adaptive motor control in locomotion via sensory-motor coordination.

PubMed

Aoi, Shinya; Funato, Tetsuro

2016-03-01

Humans and animals walk adaptively in diverse situations by skillfully manipulating their complicated and redundant musculoskeletal systems. From an analysis of measured electromyographic (EMG) data, it appears that despite complicated spatiotemporal properties, muscle activation patterns can be explained by a low dimensional spatiotemporal structure. More specifically, they can be accounted for by the combination of a small number of basic activation patterns. The basic patterns and distribution weights indicate temporal and spatial structures, respectively, and the weights show the muscle sets that are activated synchronously. In addition, various locomotor behaviors have similar low dimensional structures and major differences appear in the basic patterns. These analysis results suggest that neural systems use muscle group combinations to solve motor control redundancy problems (muscle synergy hypothesis) and manipulate those basic patterns to create various locomotor functions. However, it remains unclear how the neural system controls such muscle groups and basic patterns through neuromechanical interactions in order to achieve adaptive locomotor behavior. This paper reviews simulation studies that explored adaptive motor control in locomotion via sensory-motor coordination using neuromusculoskeletal models based on the muscle synergy hypothesis. Herein, the neural mechanism in motor control related to the muscle synergy for adaptive locomotion and a potential muscle synergy analysis method including neuromusculoskeletal modeling for motor impairments and rehabilitation are discussed. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

High-Si content BARC for dual-BARC systems such as trilayer patterning

NASA Astrophysics Data System (ADS)

Kennedy, Joseph; Xie, Song-Yuan; Wu, Ze-Yu; Katsanes, Ron; Flanigan, Kyle; Lee, Kevin; Slezak, Mark; Liu, Zhi; Lin, Shang-Ho

2009-03-01

This work discusses the requirements and performance of Honeywell's middle layer material, UVAS, for tri-layer patterning. UVAS is a high Si content polymer synthesized directly from Si containing starting monomer components. The monomers are selected to produce a film that meets the requirements as a middle layer for tri-layer patterning (TLP) and gives us a level of flexibility to adjust the properties of the film to meet the customer's specific photoresist and patterning requirements. Results of simulations of the substrate reflectance versus numerical aperture, UVAS thickness, and under layer film are presented. ArF photoresist line profiles and process latitude versus UVAS bake at temperatures as low as 150ºC are presented and discussed. Immersion lithographic patterning of ArF photoresist line space and contact hole features will be presented. A sequence of SEM images detailing the plasma etch transfer of line space photoresist features through the middle and under layer films comprising the TLP film stack will be presented. Excellent etch selectivity between the UVAS and the organic under layer film exists as no edge erosion or faceting is observed as a result of the etch process. A detailed study of the impact of a PGMEA solvent photoresist rework process on the lithographic process window of a TLP film stack was performed with the results indicating that no degradation to the UVAS film occurs.

Microstructure and Mechanical Properties of Additively Manufactured Parts with Staircase Feature

NASA Astrophysics Data System (ADS)

Keya, Tahmina

This thesis focuses on a part with staircase feature that is made of Inconel 718 and fabricated by SLM process. The objective of the study was to observe build height effect on the microstructure and mechanical properties of the part. Due to the nature of SLM, there is possibility of different microstructure and mechanical properties in different locations depending on the design of the part. The objective was to compare microstructure and mechanical properties from different location and four comparison groups were considered: 1. Effect of thermal cycle; 2. External and internal surfaces; 3. Build height effect and 4. Bottom surfaces. To achieve the goals of this research, standard metallurgical procedure has been performed to prepare samples. Etching was done to reveal the microstructure of SLM processed Inconel 718 parts. Young's modulus and hardness were measured using nanoindentation technique. FEM analysis was performed to simulate nanoindentation. The conclusions drawn from this research are: 1. The microstructure of front and side surface of SLM processed Inconel 718 consists of arc shaped cut ends of melt pools with intermetallic phase at the border of the melt pool; 2. On top surface, melted tracks and scanning patterns can be observed and the average width of melted tracks is 100-150 microm; 3. The microstructure looks similar at different build height; 4. Microstructure on the top of a stair is more defined and organized than the internal surface; 5. The mechanical properties are highest at the bottom. OM images revealed slight difference in microstructure in terms of build height for this specific part, but mechanical properties seem to be vary noticeably. This is something to be kept in mind while designing or determining build orientation. External and internal surfaces of a stair at the same height showed difference in both microstructure and mechanical properties. To minimize that effect and to make it more uniform, gradual elevation can be considered when suitable as far as design modification is concerned. Above all, this study reveals important information about the pattern of microstructure, thus heat transfer mechanism inside a part which is useful to understand the SLM process.

Properties of Fructan:Fructan 1-Fructosyltransferases from Chicory and Globe Thistle, Two Asteracean Plants Storing Greatly Different Types of Inulin1

PubMed Central

Vergauwen, Rudy; Van Laere, André; Van den Ende, Wim

2003-01-01

Remarkably, within the Asteraceae, a species-specific fructan pattern can be observed. Some species such as artichoke (Cynara scolymus) and globe thistle (Echinops ritro) store fructans with a considerably higher degree of polymerization than the one observed in chicory (Cichorium intybus) and Jerusalem artichoke (Helianthus tuberosus). Fructan:fructan 1-fructosyltransferase (1-FFT) is the enzyme responsible for chain elongation of inulin-type fructans. 1-FFTs were purified from chicory and globe thistle. A comparison revealed that chicory 1-FFT has a high affinity for sucrose (Suc), fructose (Fru), and 1-kestose as acceptor substrate. This makes redistribution of Fru moieties from large to small fructans very likely during the period of active fructan synthesis in the root when import and concentration of Suc can be expected to be high. In globe thistle, this problem is avoided by the very low affinity of 1-FFT for Suc, Fru, and 1-kestose and the higher affinity for inulin as acceptor substrate. Therefore, the 1-kestose formed by Suc:Suc 1-fructosyltransferase is preferentially used for elongation of inulin molecules, explaining why inulins with a much higher degree of polymerization accumulate in roots of globe thistle. Inulin patterns obtained in vitro from 1-kestose and the purified 1-FFTs from both species closely resemble the in vivo inulin patterns. Therefore, we conclude that the species-specific fructan pattern within the Asteraceae can be explained by the different characteristics of their respective 1-FFTs. Although 1-FFT and bacterial levansucrases clearly differ in their ability to use Suc as a donor substrate, a kinetic analysis suggests that 1-FFT also works via a ping-pong mechanism. PMID:12970504

Propagation of tau pathology: hypotheses, discoveries, and yet unresolved questions from experimental and human brain studies.

PubMed

Lewis, Jada; Dickson, Dennis W

2016-01-01

Tau is a microtubule-associated protein and a key regulator of microtubule stabilization as well as the main component of neurofibrillary tangles-a principle neuropathological hallmark of Alzheimer's disease (AD)-as well as pleomorphic neuronal and glial inclusions in neurodegenerative tauopathies. Cross-sectional studies of neurofibrillary pathology in AD reveal a stereotypic spatiotemporal pattern of neuronal vulnerability that correlates with disease severity; however, the relationship of this pattern to disease progression is less certain and exceptions to the typical pattern have been described in a subset of AD patients. The basis for the selective vulnerability of specific populations of neurons to tau pathology and cell death is largely unknown, although there have been a number of hypotheses based upon shared properties of vulnerable neurons (e.g., degree of axonal myelination or synaptic plasticity). A recent hypothesis for selective vulnerability takes into account the emerging science of functional connectivity based upon resting state functional magnetic resonance imaging, where subsets of neurons that fire synchronously define patterns of degeneration similar to specific neurodegenerative disorders, including various tauopathies. In the past 6 years, the concept of tau propagation has emerged from numerous studies in cell and animal models suggesting that tau moves from cell-to-cell and that this may trigger aggregation and region-to-region spread of tau pathology within the brain. How the spread of tau pathology relates to functional connectivity is an area of active investigation. Observations of templated folding and propagation of tau have prompted comparisons of tau to prions, the pathogenic proteins in transmissible spongiform encephalopathies. In this review, we discuss the most compelling studies in the field, discuss their shortcomings and consider their implications with respect to human tauopathies as well as the controversy that tauopathies may be prion-like disorders.

Event Perception and Pattern Perception in Early Infancy.

ERIC Educational Resources Information Center

Vurpillot, Eliane

Human infants are sensitive from birth to some intrinsic properties of objects; they are also sensitive to position. During the first weeks of life, pertinent dimensions of differentiation between objects are relative to global properties of the entire object or pattern. Position is defined by the direction of a displacement: the trajectory…

Multiscale analysis of surface soil moisture dynamics in a mesoscale catchment utilizing an integrated ecohydrological model

NASA Astrophysics Data System (ADS)

Korres, W.; Reichenau, T. G.; Schneider, K.

2012-12-01

Soil moisture is one of the fundamental variables in hydrology, meteorology and agriculture, influencing the partitioning of solar energy into latent and sensible heat flux as well as the partitioning of precipitation into runoff and percolation. Numerous studies have shown that in addition to natural factors (rainfall, soil, topography etc.) agricultural management is one of the key drivers for spatio-temporal patterns of soil moisture in agricultural landscapes. Interactions between plant growth, soil hydrology and soil nitrogen transformation processes are modeled by using a dynamically coupled modeling approach. The process-based ecohydrological model components of the integrated decision support system DANUBIA are used to identify the important processes and feedbacks determining soil moisture patterns in agroecosystems. Integrative validation of plant growth and surface soil moisture dynamics serves as a basis for a spatially distributed modeling analysis of surface soil moisture patterns in the northern part of the Rur catchment (1100 sq km), Western Germany. An extensive three year dataset (2007-2009) of surface soil moisture-, plant- (LAI, organ specific biomass and N) and soil- (texture, N, C) measurements was collected. Plant measurements were carried out biweekly for winter wheat, maize, and sugar beet during the growing season. Soil moisture was measured with three FDR soil moisture stations. Meteorological data was measured with an eddy flux station. The results of the model validation showed a very good agreement between the modeled plant parameters (biomass, green LAI) and the measured parameters with values between 0.84 and 0.98 (Willmotts index of agreement). The modeled surface soil moisture (0 - 20 cm) showed also a very favorable agreement with the measurements for winter wheat and sugar beet with an RMSE between 1.68 and 3.45 Vol.-%. For maize, the RMSE was less favorable particularly in the 1.5 months prior to harvest. The modeled soil moisture remained in contrast to the measurements very responsive to precipitation with high soil moisture after precipitation events. This behavior indicates that the soil properties might have changed due to the formation of a surface crust or seal towards the end of the growing season. Spatial soil moisture patterns were investigated using a grid resolution of 150 meter. Spatial autocorrelation was computed on a daily basis using patterns of soil texture as well as transpiration and precipitation indices as co-variables. Spatial patterns of surface soil moisture are mostly determined by the structure of the soil properties (soil type) during winter, early growing season and after harvest of all crops. Later in the growing season, after establishment of a closed canopy the dependence of the soil moisture patterns on soil texture patterns becomes smaller and diminishes quickly after precipitation events, due to differences of the transpiration rate of the different crops. When changing the spatial scale of the analysis, the highest autocorrelation values can be found on a grid cell size between 450 and 1200 meters. Thus, small scale variability of transpiration induced by the land use pattern almost averages out, leaving the larger scale structure of soil properties to explain the soil moisture patterns.

Predicting and Detecting Emerging Cyberattack Patterns Using StreamWorks

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

Chin, George; Choudhury, Sutanay; Feo, John T.

2014-06-30

The number and sophistication of cyberattacks on industries and governments have dramatically grown in recent years. To counter this movement, new advanced tools and techniques are needed to detect cyberattacks in their early stages such that defensive actions may be taken to avert or mitigate potential damage. From a cybersecurity analysis perspective, detecting cyberattacks may be cast as a problem of identifying patterns in computer network traffic. Logically and intuitively, these patterns may take on the form of a directed graph that conveys how an attack or intrusion propagates through the computers of a network. Such cyberattack graphs could providemore » cybersecurity analysts with powerful conceptual representations that are natural to express and analyze. We have been researching and developing graph-centric approaches and algorithms for dynamic cyberattack detection. The advanced dynamic graph algorithms we are developing will be packaged into a streaming network analysis framework known as StreamWorks. With StreamWorks, a scientist or analyst may detect and identify precursor events and patterns as they emerge in complex networks. This analysis framework is intended to be used in a dynamic environment where network data is streamed in and is appended to a large-scale dynamic graph. Specific graphical query patterns are decomposed and collected into a graph query library. The individual decomposed subpatterns in the library are continuously and efficiently matched against the dynamic graph as it evolves to identify and detect early, partial subgraph patterns. The scalable emerging subgraph pattern algorithms will match on both structural and semantic network properties.« less

Convergence of marine megafauna movement patterns in coastal and open oceans.

PubMed

Sequeira, A M M; Rodríguez, J P; Eguíluz, V M; Harcourt, R; Hindell, M; Sims, D W; Duarte, C M; Costa, D P; Fernández-Gracia, J; Ferreira, L C; Hays, G C; Heupel, M R; Meekan, M G; Aven, A; Bailleul, F; Baylis, A M M; Berumen, M L; Braun, C D; Burns, J; Caley, M J; Campbell, R; Carmichael, R H; Clua, E; Einoder, L D; Friedlaender, Ari; Goebel, M E; Goldsworthy, S D; Guinet, C; Gunn, J; Hamer, D; Hammerschlag, N; Hammill, M; Hückstädt, L A; Humphries, N E; Lea, M-A; Lowther, A; Mackay, A; McHuron, E; McKenzie, J; McLeay, L; McMahon, C R; Mengersen, K; Muelbert, M M C; Pagano, A M; Page, B; Queiroz, N; Robinson, P W; Shaffer, S A; Shivji, M; Skomal, G B; Thorrold, S R; Villegas-Amtmann, S; Weise, M; Wells, R; Wetherbee, B; Wiebkin, A; Wienecke, B; Thums, M

2018-03-20

The extent of increasing anthropogenic impacts on large marine vertebrates partly depends on the animals' movement patterns. Effective conservation requires identification of the key drivers of movement including intrinsic properties and extrinsic constraints associated with the dynamic nature of the environments the animals inhabit. However, the relative importance of intrinsic versus extrinsic factors remains elusive. We analyze a global dataset of ∼2.8 million locations from >2,600 tracked individuals across 50 marine vertebrates evolutionarily separated by millions of years and using different locomotion modes (fly, swim, walk/paddle). Strikingly, movement patterns show a remarkable convergence, being strongly conserved across species and independent of body length and mass, despite these traits ranging over 10 orders of magnitude among the species studied. This represents a fundamental difference between marine and terrestrial vertebrates not previously identified, likely linked to the reduced costs of locomotion in water. Movement patterns were primarily explained by the interaction between species-specific traits and the habitat(s) they move through, resulting in complex movement patterns when moving close to coasts compared with more predictable patterns when moving in open oceans. This distinct difference may be associated with greater complexity within coastal microhabitats, highlighting a critical role of preferred habitat in shaping marine vertebrate global movements. Efforts to develop understanding of the characteristics of vertebrate movement should consider the habitat(s) through which they move to identify how movement patterns will alter with forecasted severe ocean changes, such as reduced Arctic sea ice cover, sea level rise, and declining oxygen content.

Predicting spiral wave patterns from cell properties in a model of biological self-organization.

PubMed

Geberth, Daniel; Hütt, Marc-Thorsten

2008-09-01

In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

The importance of stress percolation patterns in rocks and other polycrystalline materials.

PubMed

Burnley, P C

2013-01-01

A new framework for thinking about the deformation behavior of rocks and other heterogeneous polycrystalline materials is proposed, based on understanding the patterns of stress transmission through these materials. Here, using finite element models, I show that stress percolates through polycrystalline materials that have heterogeneous elastic and plastic properties of the same order as those found in rocks. The pattern of stress percolation is related to the degree of heterogeneity in and statistical distribution of the elastic and plastic properties of the constituent grains in the aggregate. The development of these stress patterns leads directly to shear localization, and their existence provides insight into the formation of rhythmic features such as compositional banding and foliation in rocks that are reacting or dissolving while being deformed. In addition, this framework provides a foundation for understanding and predicting the macroscopic rheology of polycrystalline materials based on single-crystal elastic and plastic mechanical properties.

The importance of stress percolation patterns in rocks and other polycrystalline materials

PubMed Central

Burnley, P.C.

2013-01-01

A new framework for thinking about the deformation behavior of rocks and other heterogeneous polycrystalline materials is proposed, based on understanding the patterns of stress transmission through these materials. Here, using finite element models, I show that stress percolates through polycrystalline materials that have heterogeneous elastic and plastic properties of the same order as those found in rocks. The pattern of stress percolation is related to the degree of heterogeneity in and statistical distribution of the elastic and plastic properties of the constituent grains in the aggregate. The development of these stress patterns leads directly to shear localization, and their existence provides insight into the formation of rhythmic features such as compositional banding and foliation in rocks that are reacting or dissolving while being deformed. In addition, this framework provides a foundation for understanding and predicting the macroscopic rheology of polycrystalline materials based on single-crystal elastic and plastic mechanical properties. PMID:23823992

Predicting spiral wave patterns from cell properties in a model of biological self-organization

NASA Astrophysics Data System (ADS)

Geberth, Daniel; Hütt, Marc-Thorsten

2008-09-01

In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

3D-QSPR Method of Computational Technique Applied on Red Reactive Dyes by Using CoMFA Strategy

PubMed Central

Mahmood, Uzma; Rashid, Sitara; Ali, S. Ishrat; Parveen, Rasheeda; Zaheer-ul-Haq; Ambreen, Nida; Khan, Khalid Mohammed; Perveen, Shahnaz; Voelter, Wolfgang

2011-01-01

Cellulose fiber is a tremendous natural resource that has broad application in various productions including the textile industry. The dyes, which are commonly used for cellulose printing, are “reactive dyes” because of their high wet fastness and brilliant colors. The interaction of various dyes with the cellulose fiber depends upon the physiochemical properties that are governed by specific features of the dye molecule. The binding pattern of the reactive dye with cellulose fiber is called the ligand-receptor concept. In the current study, the three dimensional quantitative structure property relationship (3D-QSPR) technique was applied to understand the red reactive dyes interactions with the cellulose by the Comparative Molecular Field Analysis (CoMFA) method. This method was successfully utilized to predict a reliable model. The predicted model gives satisfactory statistical results and in the light of these, it was further analyzed. Additionally, the graphical outcomes (contour maps) help us to understand the modification pattern and to correlate the structural changes with respect to the absorptivity. Furthermore, the final selected model has potential to assist in understanding the charachteristics of the external test set. The study could be helpful to design new reactive dyes with better affinity and selectivity for the cellulose fiber. PMID:22272108

Determining quantitative immunophenotypes and evaluating their implications

NASA Astrophysics Data System (ADS)

Redelman, Douglas; Hudig, Dorothy; Berner, Dave; Castell, Linda M.; Roberts, Don; Ensign, Wayne

2002-05-01

Quantitative immunophenotypes varied widely among > 100 healthy young males but were maintained at characteristic levels within individuals. The initial results (SPIE Proceedings 4260:226) that examined cell numbers and the quantitative expression of adhesion and lineage-specific molecules, e.g., CD2 and CD14, have now been confirmed and extended to include the quantitative expression of inducible molecules such as HLA-DR and perforin (Pf). Some properties, such as the ratio of T helper (Th) to T cytotoxic/suppressor (Tc/s) cells, are known to be genetically determined. Other properties, e.g., the T:B cell ratio, the amount of CD19 per B cell, etc., behaved similarly and may also be inherited traits. Since some patterns observed in these healthy individuals resembled those found in pathological situations we tested whether the patterns could be associated with the occurrence of disease. The current studies shows that there were associations between quantitative immunophenotypes and the subsequent incidence and severity of disease. For example, individuals with characteristically low levels of HLA-DR or B cells or reduced numbers of Pf+ Tc/s cells had more frequent and/or more severe upper respiratory infections. Quantitative immunophenotypes will be more widely measured if the necessary standards are available and if appropriate procedures are made more accessible.

Marrow-derived mesenchymal stem cells: role in epithelial tumor cell determination.

PubMed

Fierro, Fernando A; Sierralta, Walter D; Epuñan, Maria J; Minguell, José J

2004-01-01

Marrow stroma represents an advantageous environment for development of micrometastatic cells. Within the cellular structure of marrow stroma, mesenchymal stem cells (MSC) have been postulated as an interacting target for disseminated cancer cells. The studies reported here were performed to gain more information on the interaction of the human breast cancer cell line MCF-7 with human bone marrow-derived MSC cells and to investigate whether this interaction affects tumor cell properties. The results showed that after co-culture with MSC, changes were detected in the morphology, proliferative capacity and aggregation pattern of MCF-7 cells, but these parameters were not affected after the co-culture of MSC cells with a non-tumorigenic breast epithelial cell line, MCF-10. Since the indirect culture of MCF-7 with MSC or its products also resulted in functional changes in the tumor cells, we evaluated whether these effects could be attributed to growth factors produced by MSC cells. It was found that VEGF and IL-6 mimic the effects produced by MSC or its products on the proliferation and aggregation properties of MCF-7, cells, respectively. Thus, it seems that after entry of disseminated tumor cells into the marrow space, their proliferative and morphogenetic organization patterns are modified after interaction with distinct stromal cells and/or with specific signals from the marrow microenvironment.

Robust Curb Detection with Fusion of 3D-Lidar and Camera Data

PubMed Central

Tan, Jun; Li, Jian; An, Xiangjing; He, Hangen

2014-01-01

Curb detection is an essential component of Autonomous Land Vehicles (ALV), especially important for safe driving in urban environments. In this paper, we propose a fusion-based curb detection method through exploiting 3D-Lidar and camera data. More specifically, we first fuse the sparse 3D-Lidar points and high-resolution camera images together to recover a dense depth image of the captured scene. Based on the recovered dense depth image, we propose a filter-based method to estimate the normal direction within the image. Then, by using the multi-scale normal patterns based on the curb's geometric property, curb point features fitting the patterns are detected in the normal image row by row. After that, we construct a Markov Chain to model the consistency of curb points which utilizes the continuous property of the curb, and thus the optimal curb path which links the curb points together can be efficiently estimated by dynamic programming. Finally, we perform post-processing operations to filter the outliers, parameterize the curbs and give the confidence scores on the detected curbs. Extensive evaluations clearly show that our proposed method can detect curbs with strong robustness at real-time speed for both static and dynamic scenes. PMID:24854364

Evolving spiking neural networks: a novel growth algorithm exhibits unintelligent design

NASA Astrophysics Data System (ADS)

Schaffer, J. David

2015-06-01

Spiking neural networks (SNNs) have drawn considerable excitement because of their computational properties, believed to be superior to conventional von Neumann machines, and sharing properties with living brains. Yet progress building these systems has been limited because we lack a design methodology. We present a gene-driven network growth algorithm that enables a genetic algorithm (evolutionary computation) to generate and test SNNs. The genome for this algorithm grows O(n) where n is the number of neurons; n is also evolved. The genome not only specifies the network topology, but all its parameters as well. Experiments show the algorithm producing SNNs that effectively produce a robust spike bursting behavior given tonic inputs, an application suitable for central pattern generators. Even though evolution did not include perturbations of the input spike trains, the evolved networks showed remarkable robustness to such perturbations. In addition, the output spike patterns retain evidence of the specific perturbation of the inputs, a feature that could be exploited by network additions that could use this information for refined decision making if required. On a second task, a sequence detector, a discriminating design was found that might be considered an example of "unintelligent design"; extra non-functional neurons were included that, while inefficient, did not hamper its proper functioning.

Selectively reflective transparent sheets

NASA Astrophysics Data System (ADS)

Waché, Rémi; Florescu, Marian; Sweeney, Stephen J.; Clowes, Steven K.

2015-08-01

We investigate the possibility to selectively reflect certain wavelengths while maintaining the optical properties on other spectral ranges. This is of particular interest for transparent materials, which for specific applications may require high reflectivity at pre-determined frequencies. Although there exist currently techniques such as coatings to produce selective reflection, this work focuses on new approaches for mass production of polyethylene sheets which incorporate either additives or surface patterning for selective reflection between 8 to 13 μ m. Typical additives used to produce a greenhouse effect in plastics include particles such as clays, silica or hydroxide materials. However, the absorption of thermal radiation is less efficient than the decrease of emissivity as it can be compared with the inclusion of Lambertian materials. Photonic band gap engineering by the periodic structuring of metamaterials is known in nature for producing the vivid bright colors in certain organisms via strong wavelength-selective reflection. Research to artificially engineer such structures has mainly focused on wavelengths in the visible and near infrared. However few studies to date have been carried out to investigate the properties of metastructures in the mid infrared range even though the patterning of microstructure is easier to achieve. We present preliminary results on the diffuse reflectivity using FDTD simulations and analyze the technical feasibility of these approaches.

Effects and mode of action of chitosan and ivy fruit saponins on the microbiome, fermentation and methanogenesis in the rumen simulation technique.

PubMed

Belanche, Alejandro; Pinloche, Eric; Preskett, David; Newbold, C Jamie

2016-01-01

This study investigates the effects of supplementing a control diet (CON) with chitosan (CHI) or ivy fruit saponins (IVY) as natural feed additives. Both additives had similar abilities to decrease rumen methanogenesis (-42% and -40%, respectively) using different mechanisms: due to its antimicrobial and nutritional properties CHI promoted a shift in the fermentation pattern towards propionate production which explained about two thirds of the decrease in methanogenesis. This shift was achieved by a simplification of the structure in the bacterial community and a substitution of fibrolytic (Firmicutes and Fibrobacteres) by amylolytic bacteria (Bacteroidetes and Proteobacteria) which led to greater amylase activity, lactate and microbial protein yield with no detrimental effect on feed digestibility. Contrarily, IVY had negligible nutritional properties promoting minor changes in the fermentation pattern and on the bacterial community. Instead, IVY modified the structure of the methanogen community and decreased its diversity. This specific antimicrobial effect of IVY against methanogens was considered its main antimethanogenic mechanism. IVY had however a negative impact on microbial protein synthesis. Therefore, CHI and IVY should be further investigated in vivo to determine the optimum doses which maintain low methanogenesis but prevent negative effects on the rumen fermentation and animal metabolism. © FEMS 2015.

Effects and mode of action of chitosan and ivy fruit saponins on the microbiome, fermentation and methanogenesis in the rumen simulation technique

PubMed Central

Belanche, Alejandro; Pinloche, Eric; Preskett, David; Newbold, C. Jamie

2015-01-01

This study investigates the effects of supplementing a control diet (CON) with chitosan (CHI) or ivy fruit saponins (IVY) as natural feed additives. Both additives had similar abilities to decrease rumen methanogenesis (–42% and –40%, respectively) using different mechanisms: due to its antimicrobial and nutritional properties CHI promoted a shift in the fermentation pattern towards propionate production which explained about two thirds of the decrease in methanogenesis. This shift was achieved by a simplification of the structure in the bacterial community and a substitution of fibrolytic (Firmicutes and Fibrobacteres) by amylolytic bacteria (Bacteroidetes and Proteobacteria) which led to greater amylase activity, lactate and microbial protein yield with no detrimental effect on feed digestibility. Contrarily, IVY had negligible nutritional properties promoting minor changes in the fermentation pattern and on the bacterial community. Instead, IVY modified the structure of the methanogen community and decreased its diversity. This specific antimicrobial effect of IVY against methanogens was considered its main antimethanogenic mechanism. IVY had however a negative impact on microbial protein synthesis. Therefore, CHI and IVY should be further investigated in vivo to determine the optimum doses which maintain low methanogenesis but prevent negative effects on the rumen fermentation and animal metabolism. PMID:26676056

The Graphic Pattern Generation Test in Healthy Aging and Alzheimer's Disease: Psychometric Properties and Normative Data

PubMed Central

Sunderaraman, Preeti; Sokolov, Elisaveta; Cines, Sarah; Sullo, Elizabeth; Orly, Aidan; Lerer, Bianca; Karlawish, Jason; Huey, Edward; Cosentino, Stephanie

2015-01-01

Design fluency tests, commonly used in both clinical and research contexts to evaluate nonverbal concept generation, have the potential to offer useful information in the differentiation of healthy versus pathological aging. While normative data for older adults are available for multiple timed versions of this test, similar data have been unavailable for a previously published untimed task, the Graphic Pattern Generation Task (GPG). Time constraints common to almost all of the available design fluency tests may cloud interpretation of higher level executive abilities, for example in individuals with slow processing speed. The current study examined the psychometric properties of the GPG and presents normative data in a sample of 167 healthy older adults (OAs) and 110 individuals diagnosed with Alzheimer's disease (AD). Results suggest that a brief version of the GPG can be administered reliably, and that this short form has high test-retest and inter-rater reliability. Number of perseverations was higher in individuals with AD as compared to OAs. A cut-off score of 4 or more perseverations showed a moderate degree of sensitivity (76%) and specificity (37%) in distinguishing individuals with AD and OAs. Finally, perseverations were associated with nonmemory indices, underscoring the nonverbal nature of this error in OAs and individuals with AD. PMID:25679880

Design of a QA method to characterize submillimeter-sized PBS beam properties using a 2D ionization chamber array

NASA Astrophysics Data System (ADS)

Lin, Yuting; Bentefour, Hassan; Flanz, Jacob; Kooy, Hanne; Clasie, Benjamin

2018-05-01

Pencil beam scanning (PBS) periodic quality assurance (QA) programs ensure the beam delivered to patients is within technical specifications. Two critical specifications for PBS delivery are the beam width and position. The aim of this study is to investigate whether a 2D ionization chamber array, such as the MatriXX detector (IBA Dosimetry, Schwarzenbruck, Germany), can be used to characterize submillimeter-sized PBS beam properties. The motivation is to use standard equipment, which may have pixel spacing coarser than the pencil beam size, and simplify QA workflow. The MatriXX pixels are cylindrical in shape with 4.5 mm diameter and are spaced 7.62 mm from center to center. Two major effects limit the ability of using the MatriXX to measure the spot position and width accurately. The first effect is that too few pixels sample the Gaussian shaped pencil beam profile and the second effect is volume averaging of the Gaussian profile over the pixel sensitive volumes. We designed a method that overcomes both limitations and hence enables the use of the MatriXX to characterize sub-millimeter-sized PBS beam properties. This method uses a cross-like irradiation pattern that is designed to increase the number of sampling data points and a modified Gaussian fitting technique to correct for volume averaging effects. Detector signals were calculated in this study and random noise and setup errors were added to simulate measured data. With the techniques developed in this work, the MatriXX detector can be used to characterize the position and width of sub-millimeter, σ  =  0.7 mm, sized pencil beams with uncertainty better than 3% relative to σ. With the irradiation only covering 60% of the MatriXX, the position and width of σ  =  0.9 mm sized pencil beams can be determined with uncertainty better than 3% relative to σ. If one were to not use a cross-like irradiation pattern, then the position and width of σ  =  3.6 mm sized pencil beams can be determined with uncertainty better than 3% relative to σ. If one were to not use a cross-like pattern nor volume averaging corrections, then the position and width of σ  =  5.0 mm sized pencil beams can be determined with uncertainty better than 3% relative to σ. This work helps to simplify periodic QA in proton therapy because more routinely used ionization chamber arrays can be used to characterize narrow pencil beam properties.

Design of a QA method to characterize submillimeter-sized PBS beam properties using a 2D ionization chamber array.

PubMed

Lin, Yuting; Bentefour, Hassan; Flanz, Jacob; Kooy, Hanne; Clasie, Benjamin

2018-05-15

Pencil beam scanning (PBS) periodic quality assurance (QA) programs ensure the beam delivered to patients is within technical specifications. Two critical specifications for PBS delivery are the beam width and position. The aim of this study is to investigate whether a 2D ionization chamber array, such as the MatriXX detector (IBA Dosimetry, Schwarzenbruck, Germany), can be used to characterize submillimeter-sized PBS beam properties. The motivation is to use standard equipment, which may have pixel spacing coarser than the pencil beam size, and simplify QA workflow. The MatriXX pixels are cylindrical in shape with 4.5 mm diameter and are spaced 7.62 mm from center to center. Two major effects limit the ability of using the MatriXX to measure the spot position and width accurately. The first effect is that too few pixels sample the Gaussian shaped pencil beam profile and the second effect is volume averaging of the Gaussian profile over the pixel sensitive volumes. We designed a method that overcomes both limitations and hence enables the use of the MatriXX to characterize sub-millimeter-sized PBS beam properties. This method uses a cross-like irradiation pattern that is designed to increase the number of sampling data points and a modified Gaussian fitting technique to correct for volume averaging effects. Detector signals were calculated in this study and random noise and setup errors were added to simulate measured data. With the techniques developed in this work, the MatriXX detector can be used to characterize the position and width of sub-millimeter, σ  =  0.7 mm, sized pencil beams with uncertainty better than 3% relative to σ. With the irradiation only covering 60% of the MatriXX, the position and width of σ  =  0.9 mm sized pencil beams can be determined with uncertainty better than 3% relative to σ. If one were to not use a cross-like irradiation pattern, then the position and width of σ  =  3.6 mm sized pencil beams can be determined with uncertainty better than 3% relative to σ. If one were to not use a cross-like pattern nor volume averaging corrections, then the position and width of σ  =  5.0 mm sized pencil beams can be determined with uncertainty better than 3% relative to σ. This work helps to simplify periodic QA in proton therapy because more routinely used ionization chamber arrays can be used to characterize narrow pencil beam properties.

Coupled in silico platform: Computational fluid dynamics (CFD) and physiologically-based pharmacokinetic (PBPK) modelling.

PubMed

Vulović, Aleksandra; Šušteršič, Tijana; Cvijić, Sandra; Ibrić, Svetlana; Filipović, Nenad

2018-02-15

One of the critical components of the respiratory drug delivery is the manner in which the inhaled aerosol is deposited in respiratory tract compartments. Depending on formulation properties, device characteristics and breathing pattern, only a certain fraction of the dose will reach the target site in the lungs, while the rest of the drug will deposit in the inhalation device or in the mouth-throat region. The aim of this study was to link the Computational fluid dynamics (CFD) with physiologically-based pharmacokinetic (PBPK) modelling in order to predict aerolisolization of different dry powder formulations, and estimate concomitant in vivo deposition and absorption of amiloride hydrochloride. Drug physicochemical properties were experimentally determined and used as inputs for the CFD simulations of particle flow in the generated 3D geometric model of Aerolizer® dry powder inhaler (DPI). CFD simulations were used to simulate air flow through Aerolizer® inhaler and Discrete Phase Method (DPM) was used to simulate aerosol particles deposition within the fluid domain. The simulated values for the percent emitted dose were comparable to the values obtained using Andersen cascade impactor (ACI). However, CFD predictions indicated that aerosolized DPI have smaller particle size and narrower size distribution than assumed based on ACI measurements. Comparison with the literature in vivo data revealed that the constructed drug-specific PBPK model was able to capture amiloride absorption pattern following oral and inhalation administration. The PBPK simulation results, based on the CFD generated particle distribution data as input, illustrated the influence of formulation properties on the expected drug plasma concentration profiles. The model also predicted the influence of potential changes in physiological parameters on the extent of inhaled amiloride absorption. Overall, this study demonstrated the potential of the combined CFD-PBPK approach to model inhaled drug bioperformance, and suggested that CFD generated results might serve as input for the prediction of drug deposition pattern in vivo. Copyright © 2017 Elsevier B.V. All rights reserved.

The inconsistency in adsorption properties and powder XRD data of MOF-5 is rationalized by framework interpenetration and the presence of organic and inorganic species in the nanocavities.

PubMed

Hafizovic, Jasmina; Bjørgen, Morten; Olsbye, Unni; Dietzel, Pascal D C; Bordiga, Silvia; Prestipino, Carmelo; Lamberti, Carlo; Lillerud, Karl Petter

2007-03-28

MOF-5 is the archetype metal-organic framework and has been subjected to numerous studies the past few years. The focal point of this report is the pitfalls related to the MOF-5 phase identification based on powder XRD data. A broad set of conditions and procedures have been reported for MOF-5 synthesis. These variations have led to materials with substantially different adsorption properties (specific surface areas in the range 700 to 3400 m(2)/g). The relatively low weight loss observed for some as synthesized samples upon solvent removal is also indicative of a low pore volume. Regrettably, these materials have all been described as MOF-5 without any further comments. Furthermore, the reported powder XRD patterns hint at structural differences: The variations in surface area are accompanied by peak splitting phenomena and rather pronounced changes in the relative peak intensities in the powder XRD patterns. In this work, we use single-crystal XRD to investigate structural differences between low and high surface area MOF-5. The low surface area MOF-5 sample had two different classes of crystals. For the dominant phase, Zn(OH)2 species partly occupied the cavities. The presence of Zn species makes the hosting cavity and possibly also adjacent cavities inaccessible and thus efficiently reduces the pore volume of the material. Furthermore, the minor phase consisted of doubly interpenetrated MOF-5 networks, which lowers the adsorption capacity. The presence of Zn species and lattice interpenetration changes the symmetry from cubic to trigonal and explains the peak splitting observed in the powder XRD patterns. Pore-filling effects from the Zn species (and partly the solvent molecules) are also responsible for the pronounced variations in powder XRD peak intensities. This latter conclusion is particularly useful for predicting the adsorption properties of a MOF-5-type material from powder XRD.

Pattern Visual Evoked Potentials Elicited by Organic Electroluminescence Screen

PubMed Central

Matsumoto, Celso Soiti; Shinoda, Kei; Matsumoto, Harue; Funada, Hideaki; Minoda, Haruka

2014-01-01

Purpose. To determine whether organic electroluminescence (OLED) screens can be used as visual stimulators to elicit pattern-reversal visual evoked potentials (p-VEPs). Method. Checkerboard patterns were generated on a conventional cathode-ray tube (S710, Compaq Computer Co., USA) screen and on an OLED (17 inches, 320 × 230 mm, PVM-1741, Sony, Tokyo, Japan) screen. The time course of the luminance changes of each monitor was measured with a photodiode. The p-VEPs elicited by these two screens were recorded from 15 eyes of 9 healthy volunteers (22.0 ± 0.8 years). Results. The OLED screen had a constant time delay from the onset of the trigger signal to the start of the luminescence change. The delay during the reversal phase from black to white for the pattern was 1.0 msec on the cathode-ray tube (CRT) screen and 0.5 msec on the OLED screen. No significant differences in the amplitudes of P100 and the implicit times of N75 and P100 were observed in the p-VEPs elicited by the CRT and the OLED screens. Conclusion. The OLED screen can be used as a visual stimulator to elicit p-VEPs; however the time delay and the specific properties in the luminance change must be taken into account. PMID:25197652

Pattern visual evoked potentials elicited by organic electroluminescence screen.

PubMed

Matsumoto, Celso Soiti; Shinoda, Kei; Matsumoto, Harue; Funada, Hideaki; Sasaki, Kakeru; Minoda, Haruka; Iwata, Takeshi; Mizota, Atsushi

2014-01-01

To determine whether organic electroluminescence (OLED) screens can be used as visual stimulators to elicit pattern-reversal visual evoked potentials (p-VEPs). Checkerboard patterns were generated on a conventional cathode-ray tube (S710, Compaq Computer Co., USA) screen and on an OLED (17 inches, 320 × 230 mm, PVM-1741, Sony, Tokyo, Japan) screen. The time course of the luminance changes of each monitor was measured with a photodiode. The p-VEPs elicited by these two screens were recorded from 15 eyes of 9 healthy volunteers (22.0 ± 0.8 years). The OLED screen had a constant time delay from the onset of the trigger signal to the start of the luminescence change. The delay during the reversal phase from black to white for the pattern was 1.0 msec on the cathode-ray tube (CRT) screen and 0.5 msec on the OLED screen. No significant differences in the amplitudes of P100 and the implicit times of N75 and P100 were observed in the p-VEPs elicited by the CRT and the OLED screens. The OLED screen can be used as a visual stimulator to elicit p-VEPs; however the time delay and the specific properties in the luminance change must be taken into account.

Mechanochemical pattern formation in simple models of active viscoelastic fluids and solids

NASA Astrophysics Data System (ADS)

Alonso, Sergio; Radszuweit, Markus; Engel, Harald; Bär, Markus

2017-11-01

The cytoskeleton of the organism Physarum polycephalum is a prominent example of a complex active viscoelastic material wherein stresses induce flows along the organism as a result of the action of molecular motors and their regulation by calcium ions. Experiments in Physarum polycephalum have revealed a rich variety of mechanochemical patterns including standing, traveling and rotating waves that arise from instabilities of spatially homogeneous states without gradients in stresses and resulting flows. Herein, we investigate simple models where an active stress induced by molecular motors is coupled to a model describing the passive viscoelastic properties of the cellular material. Specifically, two models for viscoelastic fluids (Maxwell and Jeffrey model) and two models for viscoelastic solids (Kelvin-Voigt and Standard model) are investigated. Our focus is on the analysis of the conditions that cause destabilization of spatially homogeneous states and the related onset of mechano-chemical waves and patterns. We carry out linear stability analyses and numerical simulations in one spatial dimension for different models. In general, sufficiently strong activity leads to waves and patterns. The primary instability is stationary for all active fluids considered, whereas all active solids have an oscillatory primary instability. All instabilities found are of long-wavelength nature reflecting the conservation of the total calcium concentration in the models studied.

Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

PubMed Central

2010-01-01

Background The zona limitans intrathalamica (ZLI) and the isthmus organizer (IsO) are two major secondary organizers of vertebrate brain development. These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively). To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians. Results In this paper, we identified a conserved sequence motif (Fezf box) in all bilaterians. We report the expression pattern of Fezf in amphioxus and Drosophila and compare it with those of Gbx, Otx and Irx. We found that the relative expression patterns of these genes in vertebrates are fully conserved in amphioxus and flies, indicating that the genetic subdivisions defining the location of both secondary organizers in early vertebrate brain development were probably present in the last common ancestor of extant bilaterians. However, in contrast to vertebrates, we found that Irx-defective flies do not show an affected Fezf expression pattern. Conclusions The absence of expression of the corresponding morphogens from cells at these conserved genetic boundaries in invertebrates suggests that the organizing properties might have evolved specifically in the vertebrate lineage by the recruitment of key morphogens to these conserved genetic locations. PMID:20849572

Higher Dimensional Meta-State Analysis Reveals Reduced Resting fMRI Connectivity Dynamism in Schizophrenia Patients.

PubMed

Miller, Robyn L; Yaesoubi, Maziar; Turner, Jessica A; Mathalon, Daniel; Preda, Adrian; Pearlson, Godfrey; Adali, Tulay; Calhoun, Vince D

2016-01-01

Resting-state functional brain imaging studies of network connectivity have long assumed that functional connections are stationary on the timescale of a typical scan. Interest in moving beyond this simplifying assumption has emerged only recently. The great hope is that training the right lens on time-varying properties of whole-brain network connectivity will shed additional light on previously concealed brain activation patterns characteristic of serious neurological or psychiatric disorders. We present evidence that multiple explicitly dynamical properties of time-varying whole-brain network connectivity are strongly associated with schizophrenia, a complex mental illness whose symptomatic presentation can vary enormously across subjects. As with so much brain-imaging research, a central challenge for dynamic network connectivity lies in determining transformations of the data that both reduce its dimensionality and expose features that are strongly predictive of important population characteristics. Our paper introduces an elegant, simple method of reducing and organizing data around which a large constellation of mutually informative and intuitive dynamical analyses can be performed. This framework combines a discrete multidimensional data-driven representation of connectivity space with four core dynamism measures computed from large-scale properties of each subject's trajectory, ie., properties not identifiable with any specific moment in time and therefore reasonable to employ in settings lacking inter-subject time-alignment, such as resting-state functional imaging studies. Our analysis exposes pronounced differences between schizophrenia patients (Nsz = 151) and healthy controls (Nhc = 163). Time-varying whole-brain network connectivity patterns are found to be markedly less dynamically active in schizophrenia patients, an effect that is even more pronounced in patients with high levels of hallucinatory behavior. To the best of our knowledge this is the first demonstration that high-level dynamic properties of whole-brain connectivity, generic enough to be commensurable under many decompositions of time-varying connectivity data, exhibit robust and systematic differences between schizophrenia patients and healthy controls.

Higher Dimensional Meta-State Analysis Reveals Reduced Resting fMRI Connectivity Dynamism in Schizophrenia Patients

PubMed Central

Miller, Robyn L.; Yaesoubi, Maziar; Turner, Jessica A.; Mathalon, Daniel; Preda, Adrian; Pearlson, Godfrey; Adali, Tulay; Calhoun, Vince D.

2016-01-01

Resting-state functional brain imaging studies of network connectivity have long assumed that functional connections are stationary on the timescale of a typical scan. Interest in moving beyond this simplifying assumption has emerged only recently. The great hope is that training the right lens on time-varying properties of whole-brain network connectivity will shed additional light on previously concealed brain activation patterns characteristic of serious neurological or psychiatric disorders. We present evidence that multiple explicitly dynamical properties of time-varying whole-brain network connectivity are strongly associated with schizophrenia, a complex mental illness whose symptomatic presentation can vary enormously across subjects. As with so much brain-imaging research, a central challenge for dynamic network connectivity lies in determining transformations of the data that both reduce its dimensionality and expose features that are strongly predictive of important population characteristics. Our paper introduces an elegant, simple method of reducing and organizing data around which a large constellation of mutually informative and intuitive dynamical analyses can be performed. This framework combines a discrete multidimensional data-driven representation of connectivity space with four core dynamism measures computed from large-scale properties of each subject’s trajectory, ie., properties not identifiable with any specific moment in time and therefore reasonable to employ in settings lacking inter-subject time-alignment, such as resting-state functional imaging studies. Our analysis exposes pronounced differences between schizophrenia patients (Nsz = 151) and healthy controls (Nhc = 163). Time-varying whole-brain network connectivity patterns are found to be markedly less dynamically active in schizophrenia patients, an effect that is even more pronounced in patients with high levels of hallucinatory behavior. To the best of our knowledge this is the first demonstration that high-level dynamic properties of whole-brain connectivity, generic enough to be commensurable under many decompositions of time-varying connectivity data, exhibit robust and systematic differences between schizophrenia patients and healthy controls. PMID:26981625

Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families.

PubMed

Dimitrieva, Slavica; Anisimova, Maria

2014-01-01

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To evaluate the extent and the nature of site-specific selection on synonymous codons, we computed the site-to-site synonymous rate variation (SRV) and identified gene properties that make SRV more likely in a large database of protein-coding gene families and protein domains. To our knowledge, this is the first study that explores the determinants and patterns of the SRV in real data. We show that the SRV is widespread in the evolution of protein-coding sequences, putting in doubt the validity of the synonymous rate as a standard neutral proxy. While protein domains rarely undergo adaptive evolution, the SRV appears to play important role in optimizing the domain function at the level of DNA. In contrast, protein families are more likely to evolve by positive selection, but are less likely to exhibit SRV. Stronger SRV was detected in genes with stronger codon bias and tRNA reusage, those coding for proteins with larger number of interactions or forming larger number of structures, located in intracellular components and those involved in typically conserved complex processes and functions. Genes with extreme SRV show higher expression levels in nearly all tissues. This indicates that codon bias in a gene, which often correlates with gene expression, may often be a site-specific phenomenon regulating the speed of translation along the sequence, consistent with the co-translational folding hypothesis. Strikingly, genes with SRV were strongly overrepresented for metabolic pathways and those associated with several genetic diseases, particularly cancers and diabetes.

Bacteria in the vaginal microbiome alter the innate immune response and barrier properties of the human vaginal epithelia in a species-specific manner.

PubMed

Doerflinger, Sylvie Y; Throop, Andrea L; Herbst-Kralovetz, Melissa M

2014-06-15

Bacterial vaginosis increases the susceptibility to sexually transmitted infections and negatively affects women's reproductive health. To investigate host-vaginal microbiota interactions and the impact on immune barrier function, we colonized 3-dimensional (3-D) human vaginal epithelial cells with 2 predominant species of vaginal microbiota (Lactobacillus iners and Lactobacillus crispatus) or 2 prevalent bacteria associated with bacterial vaginosis (Atopobium vaginae and Prevotella bivia). Colonization of 3-D vaginal epithelial cell aggregates with vaginal microbiota was observed with direct attachment to host cell surface with no cytotoxicity. A. vaginae infection yielded increased expression membrane-associated mucins and evoked a robust proinflammatory, immune response in 3-D vaginal epithelial cells (ie, expression of CCL20, hBD-2, interleukin 1β, interleukin 6, interleukin 8, and tumor necrosis factor α) that can negatively affect barrier function. However, P. bivia and L. crispatus did not significantly upregulate pattern-recognition receptor-signaling, mucin expression, antimicrobial peptides/defensins, or proinflammatory cytokines in 3-D vaginal epithelial cell aggregates. Notably, L. iners induced pattern-recognition receptor-signaling activity, but no change was observed in mucin expression or secretion of interleukin 6 and interleukin 8. We identified unique species-specific immune signatures from vaginal epithelial cells elicited by colonization with commensal and bacterial vaginosis-associated bacteria. A. vaginae elicited a signature that is consistent with significant disruption of immune barrier properties, potentially resulting in enhanced susceptibility to sexually transmitted infections during bacterial vaginosis. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Nanoamplifiers synthesized from gadolinium and gold nanocomposites for magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Tian, Xiumei; Shao, Yuanzhi; He, Haoqiang; Liu, Huan; Shen, Yingying; Huang, Wenlin; Li, Li

2013-03-01

We have synthesized an efficient and highly sensitive nanoamplifier composed of gadolinium-doped silica nanoparticles and gold nanoparticles (AuNPs). Magnetic resonance imaging (MRI) in vitro and in vivo assays revealed enhancement of signal sensitivity, which may be explained by electron transfer between water and gadolinium-doped nanoparticles, apparent in the presence of gold. In vitro and in vivo evaluation demonstrated nanoamplifier incurred minimal cytotoxicity and immunotoxicity, increased stability, and gradual excretion patterns. Tumor targeted properties were preliminarily determined when the nanoamplifier was injected into mouse models of colon cancer liver metastasis. Furthermore, although AuNPs departed from the nanoamplifiers in specific mice tissues, optical and magnetic resonance imaging was efficient, especially in metastatic tumors. These assays validate our nanoamplifier as an effective MRI signal enhancer with sensitive cancer diagnosis potential.We have synthesized an efficient and highly sensitive nanoamplifier composed of gadolinium-doped silica nanoparticles and gold nanoparticles (AuNPs). Magnetic resonance imaging (MRI) in vitro and in vivo assays revealed enhancement of signal sensitivity, which may be explained by electron transfer between water and gadolinium-doped nanoparticles, apparent in the presence of gold. In vitro and in vivo evaluation demonstrated nanoamplifier incurred minimal cytotoxicity and immunotoxicity, increased stability, and gradual excretion patterns. Tumor targeted properties were preliminarily determined when the nanoamplifier was injected into mouse models of colon cancer liver metastasis. Furthermore, although AuNPs departed from the nanoamplifiers in specific mice tissues, optical and magnetic resonance imaging was efficient, especially in metastatic tumors. These assays validate our nanoamplifier as an effective MRI signal enhancer with sensitive cancer diagnosis potential. Electronic supplementary information (ESI) available: Protocols for the characterization, immunotoxicity and pharmacokinetics analyses. Additional supporting figures. See DOI: 10.1039/c3nr00170a

Large-Scale Constraint-Based Pattern Mining

ERIC Educational Resources Information Center

Zhu, Feida

2009-01-01

We studied the problem of constraint-based pattern mining for three different data formats, item-set, sequence and graph, and focused on mining patterns of large sizes. Colossal patterns in each data formats are studied to discover pruning properties that are useful for direct mining of these patterns. For item-set data, we observed robustness of…

Hydraulic properties of fronds from palms of varying height and habitat.

PubMed

Renninger, Heidi J; Phillips, Nathan

2011-12-01

Because palms grow in highly varying climates and reach considerable heights, they present a unique opportunity to evaluate how environment and plant size impact hydraulic function. We studied hydraulic properties of petioles from palms of varying height from three species: Iriartea deltoidea, a tropical rainforest species; Mauritia flexuosa, a tropical rainforest, swamp species; and Washingtonia robusta, a subtropical species. We measured leaf areas, petiole cross-sectional areas, specific conductivity (K(S)), petiole anatomical properties, vulnerability to embolism and leaf water potentials and calculated petiole Huber values and leaf-specific conductivities (K(L)). Leaf and petiole cross-sectional areas varied widely with height. However, hydraulic properties including Huber values, K(S) and K(L), remained constant. The two palmate species, M. flexuosa and W. robusta, had larger Huber values than I. deltoidea, a pinnately-compound species which exhibited the highest K(S). Metaxylem vessel diameters and vascular bundle densities varied with height in opposing patterns to maintain petiole conductivities. I. deltoidea and W. robusta petioles had similar P(50) values (the point at which 50% of hydraulic conductivity is lost) averaged over all crown heights, but W. robusta exhibited more negative P(50) values in taller palms. Comparison of P (50) values with transpiring midday leaf water potentials, as well as a double-dye staining experiment in a 1-m-tall palm, suggested that a fairly significant amount of embolisms were occurring and refilled on a diurnal basis. Therefore, across palms differing widely in height and growing environments, we found convergence in water transport per unit leaf area (K(L)) with individuals exhibiting differing strategies for achieving this.

"Land-Cover Conversion in Amazonia, The Role of ENV" Ironment and Substrate composition in Modifying SOI

NASA Technical Reports Server (NTRS)

Roberts, Dar A.; Chadwick, Oliver A.; Batista, Getulio T.

2003-01-01

LBA research from the first phase of LBA focused on three broad categories: 1) mapping land cover and quantifying rates of change, persistence of pasture, and area of recovering forest; 2) evaluating the role of environmental factors and land-use history on soil biogeochemistry; and 3) quantifying the natural and human controls on stream nutrient concentrations. The focus of the research was regional, concentrating primarily in the state of RondBnia, but also included land-cover mapping in the vicinity of Maraba, Para, and Manaus, Amazonas. Remote sensing analysis utilized Landsat Thematic Mapper (TM) and Multispectral Scanner (MS S) data to map historical patterns of land-cover change. Specific questions addressed by the remote sensing component of the research included: 1) what is the areal extent of dominant land-cover classes? 2) what are the rates of change of dominant land cover through processes of deforestation, disturbance and regeneration? and 3) what are the dynamic properties of each class that characterize temporal variability, duration, and frequency of repeat disturbance? Biogeochemical analysis focused on natural variability and impacts of land-use/land-cover changes on soil and stream biogeochemical properties at the regional scale. An emphasis was given to specific soil properties considered to be primary limiting factors regionally, including phosphorus, nitrogen, base cations and cation-exchange properties. Stream sampling emphasized the relative effects of the rates and timing of land-cover change on stream nutrients, demonstrating that vegetation conversion alone does not impact nutrients as much as subsequent land use and urbanization.

Calculation of spin-densities within the context of density functional theory. The crucial role of the correlation functional

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2005-09-01

It is demonstrated that the LYP correlation functional is not suited to be used for the calculation of electron spin resonance hyperfine structure (HFS) constants, nuclear magnetic resonance spin-spin coupling constants, magnetic, shieldings and other properties that require a balanced account of opposite- and equal-spin correlation, especially in the core region. In the case of the HFS constants of alkali atoms, LYP exaggerates opposite-spin correlation effects thus invoking too strong in-out correlation effects, an exaggerated spin-polarization pattern in the core shells of the atoms, and, consequently, too large HFS constants. Any correlation functional that provides a balanced account of opposite- and equal-spin correlation leads to improved HFS constants, which is proven by comparing results obtained with the LYP and the PW91 correlation functional. It is suggested that specific response properties are calculated with the PW91 rather than the LYP correlation functional.

Stable aqueous based Cu nanoparticle ink for printing well-defined highly conductive features on a plastic substrate.

PubMed

Jeong, Sunho; Song, Hae Chun; Lee, Won Woo; Lee, Sun Sook; Choi, Youngmin; Son, Wonil; Kim, Eui Duk; Paik, Choon Hoon; Oh, Seok Heon; Ryu, Beyong-Hwan

2011-03-15

With the aim of inkjet printing highly conductive and well-defined Cu features on plastic substrates, aqueous based Cu ink is prepared for the first time using water-soluble Cu nanoparticles with a very thin surface oxide layer. Owing to the specific properties, high surface tension and low boiling point, of water, the aqueous based Cu ink endows a variety of advantages over conventional Cu inks based on organic solvents in printing narrow conductive patterns without irregular morphologies. It is demonstrated how the design of aqueous based ink affects the basic properties of printed conductive features such as surface morphology, microstructure, conductivity, and line width. The long-term stability of aqueous based Cu ink against oxidation is analyzed through an X-ray photoelectron spectroscopy (XPS) based investigation on the evolution of the surface oxide layer in the aqueous based ink.

Crystalline metamaterials for topological properties at subwavelength scales

PubMed Central

Yves, Simon; Fleury, Romain; Berthelot, Thomas; Fink, Mathias; Lemoult, Fabrice; Lerosey, Geoffroy

2017-01-01

The exciting discovery of topological condensed matter systems has lately triggered a search for their photonic analogues, motivated by the possibility of robust backscattering-immune light transport. However, topological photonic phases have so far only been observed in photonic crystals and waveguide arrays, which are inherently physically wavelength scaled, hindering their application in compact subwavelength systems. In this letter, we tackle this problem by patterning the deep subwavelength resonant elements of metamaterials onto specific lattices, and create crystalline metamaterials that can develop complex nonlocal properties due to multiple scattering, despite their very subwavelength spatial scale that usually implies to disregard their structure. These spatially dispersive systems can support subwavelength topological phases, as we demonstrate at microwaves by direct field mapping. Our approach gives a straightforward tabletop platform for the study of photonic topological phases, and allows to envision applications benefiting the compactness of metamaterials and the amazing potential of topological insulators. PMID:28719573

Advances in imaging and quantification of electrical properties at the nanoscale using Scanning Microwave Impedance Microscopy (sMIM)

NASA Astrophysics Data System (ADS)

Friedman, Stuart; Yang, Yongliang; Amster, Oskar

2015-03-01

Scanning Microwave Impedance Microscopy (sMIM) is a mode for Atomic Force Microscopy (AFM) enabling imaging of unique contrast mechanisms and measurement of local permittivity and conductivity at the 10's of nm length scale. Recent results will be presented illustrating high-resolution electrical features such as sub 15 nm Moire' patterns in Graphene, carbon nanotubes of various electrical states and ferro-electrics. In addition to imaging, the technique is suited to a variety of metrology applications where specific physical properties are determined quantitatively. We will present research activities on quantitative measurements using multiple techniques to determine dielectric constant (permittivity) and conductivity (e.g. dopant concentration) for a range of materials. Examples include bulk dielectrics, low-k dielectric thin films, capacitance standards and doped semiconductors. Funded in part by DOE SBIR DE-SC0009586.

Food quality inspection by speckle decorrelation properties of bacteria colonies

NASA Astrophysics Data System (ADS)

Bianco, V.; Mandracchia, B.; Nazzaro, F.; Marchesano, V.; Gennari, O.; Paturzo, M.; Grilli, S.; Ferraro, P.

2017-06-01

The development of tools for rapid food quality inspection is a highly pursued goal. These could be valuable devices to be used by food producers in factories or the customers themselves in specific installations at the marketplace. Here we show how speckle patterns in coherent imaging systems can be can be employed as indicators of the presence of bacteria colonies contaminating food or water. Speckle decorrelation is induced by the self-propelling movement of these organisms when they interact with coherent light. Hence, their presence can be detected using a simple setup in a condition in which the single element cannot be imaged, but the properties of the ensemble can be exploited. Thanks to the small magnification factor we set, our system can inspect a large Field-of-View (FoV). We show the possibility to discriminate between fresh and contaminated food, thus paving the way to the rapid food quality testing by consumers at the marketplace.

Sub-micron scale patterning of fluorescent silver nanoclusters using low-power laser.

PubMed

Kunwar, Puskal; Hassinen, Jukka; Bautista, Godofredo; Ras, Robin H A; Toivonen, Juha

2016-04-05

Noble metal nanoclusters are ultrasmall nanomaterials with tunable properties and huge application potential; however, retaining their enhanced functionality is difficult as they readily lose their properties without stabilization. Here, we demonstrate a facile synthesis of highly photostable silver nanoclusters in a polymer thin film using visible light photoreduction. Furthermore, the different stages of the nanocluster formation are investigated in detail using absorption and fluorescence spectroscopy, fluorescence microscopy, and atomic force microscopy. A cost-effective fabrication of photostable micron-sized fluorescent silver nanocluster barcode is demonstrated in silver-impregnated polymer films using a low-power continuous-wave laser diode. It is shown that a laser power of as low as 0.75 mW is enough to write fluorescent structures, corresponding to the specifications of a commercially available laser pointer. The as-formed nanocluster-containing microstructures can be useful in direct labeling applications such as authenticity marking and fluorescent labeling.

Controlled nanostructrures formation by ultra fast laser pulses for color marking.

PubMed

Dusser, B; Sagan, Z; Soder, H; Faure, N; Colombier, J P; Jourlin, M; Audouard, E

2010-02-01

Precise nanostructuration of surface and the subsequent upgrades in material properties is a strong outcome of ultra fast laser irradiations. Material characteristics can be designed on mesoscopic scales, carrying new optical properties. We demonstrate in this work, the possibility of achieving material modifications using ultra short pulses, via polarization dependent structures generation, that can generate specific color patterns. These oriented nanostructures created on the metal surface, called ripples, are typically smaller than the laser wavelength and in the range of visible spectrum. In this way, a complex colorization process of the material, involving imprinting, calibration and reading, has been performed to associate a priori defined colors. This new method based on the control of the laser-driven nanostructure orientation allows cumulating high quantity of information in a minimal surface, proposing new applications for laser marking and new types of identifying codes.

Cannabinoid receptor CB1 mRNA is highly expressed in the rat ciliary body: implications for the antiglaucoma properties of marihuana.

PubMed

Porcella, A; Casellas, P; Gessa, G L; Pani, L

1998-07-15

We used RT-PCR to measure relative differences in cannabinoid receptor (CB) mRNAs in the rat eye, comparing CB1 or CB2 transcripts to that of the normalizing reference gene beta2 microglobulin (beta2m). Significantly higher levels of CB1 mRNA levels were found in the ciliary body (0.84+/-0.05% of beta2m) than in the iris, (0.34+/-0.04% of beta2m), retina (0.07+/-0.005% of beta2m) and choroid (0.06+/-0.005% of beta2m). CB2 mRNA was undetectable. This expression pattern supports a specific role for the CB1 receptor in controlling intraocular pressure, helping to explain the antiglaucoma property of cannabinoids. Copyright 1998 Elsevier Science B.V. All rights reserved.

Paleo-tribology: development of wear measurement techniques and a three-dimensional model revealing how grinding dentitions self-wear to enable functionality

NASA Astrophysics Data System (ADS)

Erickson, Gregory M.; Sidebottom, Mark A.; Curry, John F.; Kay, David Ian; Kuhn-Hendricks, Stephen; Norell, Mark A.; Sawyer, W. Gregory; Krick, Brandon A.

2016-06-01

In most mammals and a rare few reptilian lineages the evolution of precise dental occlusion led to the capacity to form functional chewing surfaces due to pressures generated while feeding. The complex dental architectures of such teeth and the biomechanics of their self-wearing nature are poorly understood. Our research team composed of paleontologists, evolutionary biologists, and engineers have developed a protocol to: (1) determine the histological make-up of grinding dentitions in extant and fossil taxa; (2) ascertain wear-relevant material properties of the tissues; (3) determine how those properties relate to inter-tissue-biomechanics leading the dental functionality using a three-dimensional Archard’s wear model developed specifically for dental applications; (4) analyze those data in phylogenetic contexts to infer evolutionary patterns as they relate to feeding. Finally we discuss industrial applications that are emerging from our paleontologically-inspired research.

Crystalline metamaterials for topological properties at subwavelength scales

NASA Astrophysics Data System (ADS)

Yves, Simon; Fleury, Romain; Berthelot, Thomas; Fink, Mathias; Lemoult, Fabrice; Lerosey, Geoffroy

2017-07-01

The exciting discovery of topological condensed matter systems has lately triggered a search for their photonic analogues, motivated by the possibility of robust backscattering-immune light transport. However, topological photonic phases have so far only been observed in photonic crystals and waveguide arrays, which are inherently physically wavelength scaled, hindering their application in compact subwavelength systems. In this letter, we tackle this problem by patterning the deep subwavelength resonant elements of metamaterials onto specific lattices, and create crystalline metamaterials that can develop complex nonlocal properties due to multiple scattering, despite their very subwavelength spatial scale that usually implies to disregard their structure. These spatially dispersive systems can support subwavelength topological phases, as we demonstrate at microwaves by direct field mapping. Our approach gives a straightforward tabletop platform for the study of photonic topological phases, and allows to envision applications benefiting the compactness of metamaterials and the amazing potential of topological insulators.

Indications for quantum computation requirements from comparative brain analysis

NASA Astrophysics Data System (ADS)

Bernroider, Gustav; Baer, Wolfgang

2010-04-01

Whether or not neuronal signal properties can engage 'non-trivial', i.e. functionally significant, quantum properties, is the subject of an ongoing debate. Here we provide evidence that quantum coherence dynamics can play a functional role in ion conduction mechanism with consequences on the shape and associative character of classical membrane signals. In particular, these new perspectives predict that a specific neuronal topology (e.g. the connectivity pattern of cortical columns in the primate brain) is less important and not really required to explain abilities in perception and sensory-motor integration. Instead, this evidence is suggestive for a decisive role of the number and functional segregation of ion channel proteins that can be engaged in a particular neuronal constellation. We provide evidence from comparative brain studies and estimates of computational capacity behind visual flight functions suggestive for a possible role of quantum computation in biological systems.

Human oocyte developmental potential is predicted by mechanical properties within hours after fertilization

PubMed Central

Yanez, Livia Z.; Han, Jinnuo; Behr, Barry B.; Pera, Renee A. Reijo; Camarillo, David B.

2016-01-01

The causes of embryonic arrest during pre-implantation development are poorly understood. Attempts to correlate patterns of oocyte gene expression with successful embryo development have been hampered by the lack of reliable and nondestructive predictors of viability at such an early stage. Here we report that zygote viscoelastic properties can predict blastocyst formation in humans and mice within hours after fertilization, with >90% precision, 95% specificity and 75% sensitivity. We demonstrate that there are significant differences between the transcriptomes of viable and non-viable zygotes, especially in expression of genes important for oocyte maturation. In addition, we show that low-quality oocytes may undergo insufficient cortical granule release and zona-hardening, causing altered mechanics after fertilization. Our results suggest that embryo potential is largely determined by the quality and maturation of the oocyte before fertilization, and can be predicted through a minimally invasive mechanical measurement at the zygote stage. PMID:26904963

A Window into the Brain: Advances in Psychiatric fMRI

PubMed Central

Zhan, Xiaoyan

2015-01-01

Functional magnetic resonance imaging (fMRI) plays a key role in modern psychiatric research. It provides a means to assay differences in brain systems that underlie psychiatric illness, treatment response, and properties of brain structure and function that convey risk factor for mental diseases. Here we review recent advances in fMRI methods in general use and progress made in understanding the neural basis of mental illness. Drawing on concepts and findings from psychiatric fMRI, we propose that mental illness may not be associated with abnormalities in specific local regions but rather corresponds to variation in the overall organization of functional communication throughout the brain network. Future research may need to integrate neuroimaging information drawn from different analysis methods and delineate spatial and temporal patterns of brain responses that are specific to certain types of psychiatric disorders. PMID:26413531

The evolution of filamin – A protein domain repeat perspective

PubMed Central

Light, Sara; Sagit, Rauan; Ithychanda, Sujay S.; Qin, Jun; Elofsson, Arne

2013-01-01

Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. PMID:22414427

The evolution of filamin-a protein domain repeat perspective.

PubMed

Light, Sara; Sagit, Rauan; Ithychanda, Sujay S; Qin, Jun; Elofsson, Arne

2012-09-01

Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. Copyright © 2012 Elsevier Inc. All rights reserved.

The effect of adriamycin exposure on the notochord of mouse embryos.

PubMed

Hajduk, Piotr; May, Alison; Puri, Prem; Murphy, Paula

2012-04-01

The notochord has important structural and signaling properties during vertebrate development with key roles in patterning surrounding tissues, including the foregut. The adriamycin mouse model is an established model of foregut anomalies where exposure of embryos in utero to the drug adriamycin leads to malformations including oesophageal atresia and tracheoesophageal fistula. In addition to foregut abnormalities, treatment also causes branching, displacement, and hypertrophy of the notochord. Here, we explore the hypothesis that the notochord may be a primary target of disruption leading to abnormal patterning of the foregut by examining notochord position and structure in early embryos following adriamycin exposure. Treated (n = 46) and control (n = 30) embryos were examined during the crucial period when the notochord normally delaminates away from the foregut endoderm (6-28 somite pairs). Transverse sections were derived from the anterior foregut and analyzed by confocal microscopy following immunodetection of extracellular matrix markers E-cadherin and Laminin. In adriamycin-treated embryos across all stages, the notochord was abnormally displaced ventrally with prolonged attachment to the foregut endoderm. While E-cadherin was normally detected in the foregut endoderm with no expression in the notochord of control embryos, treated embryos up to 24 somites showed ectopic notochordal expression indicating a change in characteristics of the tissue; specifically an increase in intracellular adhesiveness, which may be instrumental in structural changes, affecting mechanical and signaling properties. This is consistent with disruption of the notochord leading to altered signaling to the foregut causing abnormal patterning and congenital foregut malformations. © 2012 Wiley Periodicals, Inc.

Climate and landscape influence on indicators of lake carbon cycling through spatial patterns in dissolved organic carbon.

PubMed

Lapierre, Jean-Francois; Seekell, David A; Del Giorgio, Paul A

2015-12-01

Freshwater ecosystems are strongly influenced by both climate and the surrounding landscape, yet the specific pathways connecting climatic and landscape drivers to the functioning of lake ecosystems are poorly understood. Here, we hypothesize that the links that exist between spatial patterns in climate and landscape properties and the spatial variation in lake carbon (C) cycling at regional scales are at least partly mediated by the movement of terrestrial dissolved organic carbon (DOC) in the aquatic component of the landscape. We assembled a set of indicators of lake C cycling (bacterial respiration and production, chlorophyll a, production to respiration ratio, and partial pressure of CO2 ), DOC concentration and composition, and landscape and climate characteristics for 239 temperate and boreal lakes spanning large environmental and geographic gradients across seven regions. There were various degrees of spatial structure in climate and landscape features that were coherent with the regionally structured patterns observed in lake DOC and indicators of C cycling. These different regions aligned well, albeit nonlinearly along a mean annual temperature gradient; whereas there was a considerable statistical effect of climate and landscape properties on lake C cycling, the direct effect was small and the overall effect was almost entirely overlapping with that of DOC concentration and composition. Our results suggest that key climatic and landscape signals are conveyed to lakes in part via the movement of terrestrial DOC to lakes and that DOC acts both as a driver of lake C cycling and as a proxy for other external signals. © 2015 John Wiley & Sons Ltd.

The effect of measured and estimated soil hydraulic properties on simulated water regime in the analysis of grapevine adaptability to future climate

NASA Astrophysics Data System (ADS)

Bonfante, Antonello; Alfieri, Silvia Maria; Agrillo, Antonietta; Dragonetti, Giovanna; Mileti, Antonio; Monaco, Eugenia; De Lorenzi, Francesca

2013-04-01

In the last years many research works have been addressed to evaluate the impact of future climate on crop productivity and plant water use at different spatial scales (global, regional, field) by means of simulation models of agricultural crop systems. Most of these approaches use estimated soil hydraulic properties, through pedotransfer functions (PTF). This choice is related to soil data availability: soil data bases lack measured soil hydraulic properties, but generally they contain information that allow the application of PTF . Although the reliability of the predicted future climate scenarios cannot be immediately validated, we address to evaluate the effects of a simplification of the soil system by using PTF. Thus we compare simulations performed with measured soil hydraulic properties versus simulations carried out with estimated properties. The water regimes resulting from the two procedures are evaluated with respect to crop adaptability to future climate. In particular we will examine if the two procedures bring about different seasonal and spatial variations in the soil water regime patterns, and if these patterns influence adaptation options. The present case study uses the agro-hydrological model SWAP (soil-water-atmosphere and plant) and studies future adaptability of grapevine. The study area is a viticultural area of Southern Italy (Valle Telesina, BN) devoted to the production of high quality wines (DOC and DOCG), and characterized by a complex geomorphology and pedology. The future climate scenario (2021-2050) was constructed applying statistical downscaling techniques to GCMs scenarios. The moisture regime for 25 soils of the selected study area was calculated by means of SWAP model, using both measured and estimated soil hydraulic properties. In the simulation, the upper boundary conditions were derived from the regional climate scenarios. Unit gradient in soil water potential was set as lower boundary condition. Crop-specific input data and model parameters were estimated on the basis of scientific literature and assumed to be generically representative of the species. From the output of the simulation runs, the relative evapotranspiration deficit (or Crop Water Stress Index - CWSI) of the soil units was calculated. Since CWSI is considered an important indicator of the qualitative grapevine responses, its pattern in both simulation procedures has been evaluated. The work was carried out within the Italian national project AGROSCENARI funded by the Ministry for Agricultural, Food and Forest Policies (MIPAAF, D.M. 8608/7303/2008)

Statistical mechanics of high-density bond percolation

NASA Astrophysics Data System (ADS)

Timonin, P. N.

2018-05-01

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

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian B.; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2016-03-08

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2017-12-26

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

Learning optimal features for visual pattern recognition

NASA Astrophysics Data System (ADS)

Labusch, Kai; Siewert, Udo; Martinetz, Thomas; Barth, Erhardt

2007-02-01

The optimal coding hypothesis proposes that the human visual system has adapted to the statistical properties of the environment by the use of relatively simple optimality criteria. We here (i) discuss how the properties of different models of image coding, i.e. sparseness, decorrelation, and statistical independence are related to each other (ii) propose to evaluate the different models by verifiable performance measures (iii) analyse the classification performance on images of handwritten digits (MNIST data base). We first employ the SPARSENET algorithm (Olshausen, 1998) to derive a local filter basis (on 13 × 13 pixels windows). We then filter the images in the database (28 × 28 pixels images of digits) and reduce the dimensionality of the resulting feature space by selecting the locally maximal filter responses. We then train a support vector machine on a training set to classify the digits and report results obtained on a separate test set. Currently, the best state-of-the-art result on the MNIST data base has an error rate of 0,4%. This result, however, has been obtained by using explicit knowledge that is specific to the data (elastic distortion model for digits). We here obtain an error rate of 0,55% which is second best but does not use explicit data specific knowledge. In particular it outperforms by far all methods that do not use data-specific knowledge.

Analysis of shear wave propagation derived from MR elastography in 3D thigh skeletal muscle using subject specific finite element model.

PubMed

Dao, Tien Tuan; Pouletaut, Philippe; Charleux, Fabrice; Tho, Marie-Christine Ho Ba; Bensamoun, Sabine

2014-01-01

The purpose of this study was to develop a subject specific finite element model derived from MRI images to numerically analyze the MRE (magnetic resonance elastography) shear wave propagation within skeletal thigh muscles. A sagittal T2 CUBE MRI sequence was performed on the 20-cm thigh segment of a healthy male subject. Skin, adipose tissue, femoral bone and 11 muscles were manually segmented in order to have 3D smoothed solid and meshed models. These tissues were modeled with different constitutive laws. A transient modal dynamics analysis was applied to simulate the shear wave propagation within the thigh tissues. The effects of MRE experimental parameters (frequency, force) and the muscle material properties (shear modulus: C10) were analyzed through the simulated shear wave displacement within the vastus medialis muscle. The results showed a plausible range of frequencies (from 90Hz to 120 Hz), which could be used for MRE muscle protocol. The wave amplitude increased with the level of the force, revealing the importance of the boundary condition. Moreover, different shear displacement patterns were obtained as a function of the muscle mechanical properties. The present study is the first to analyze the shear wave propagation in skeletal muscles using a 3D subject specific finite element model. This study could be of great value to assist the experimenters in the set-up of MRE protocols.

A descriptive analysis of temporal and spatial patterns of variability in Puget Sound oceanographic properties

Treesearch

Stephanie Moore; Nathan J. Mantua; Jan A. Newton; Mitsuhiro Kawase; Mark J. Warner; Jonathan P. Kellogg

2008-01-01

Temporal and spatial patterns of variability in Puget Sound's oceanographic properties are determined using continuous vertical profile data from two long-term monitoring programs; monthly observations at 16 stations from 1993 to 2002, and biannual observations at 40 stations from 1998 to 2003. Climatological monthly means of temperature, salinity, and density...

Magnetic antenna excitation of whistler modes. IV. Receiving antennas and reciprocity

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

Stenzel, R. L., E-mail: stenzel@physics.ucla.edu; Urrutia, J. M.

Antenna radiation patterns are an important property of antennas. Reciprocity holds in free space and the radiation patterns for exciting and receiving antennas are the same. In anisotropic plasmas, radiation patterns are complicated by the fact that group and phase velocities differ and certain wave properties like helicity depend on the direction of wave propagation with respect to the background magnetic field B{sub 0}. Interference and wave focusing effects are different than in free space. Reciprocity does not necessarily hold in a magnetized plasma. The present work considers the properties of various magnetic antennas used for receiving whistler modes. Itmore » is based on experimental data from exciting low frequency whistler modes in a large uniform laboratory plasma. By superposition of linear waves from different antennas, the radiation patterns of antenna arrays are derived. Plane waves are generated and used to determine receiving radiation patterns of different receiving antennas. Antenna arrays have radiation patterns with narrow lobes, whose angular position can be varied by physical rotation or electronic phase shifting. Reciprocity applies to broadside antenna arrays but not to end fire arrays which can have asymmetric lobes with respect to B{sub 0}. The effect of a relative motion between an antenna and the plasma has been modeled by the propagation of a short wave packet moving along a linear antenna array. An antenna moving across B{sub 0} has a radiation pattern characterized by an oscillatory “whistler wing.” A receiving antenna in motion can detect any plane wave within the group velocity resonance cone. The radiation pattern also depends on loop size relative to the wavelength. Motional effects prevent reciprocity. The concept of the radiation pattern loses its significance for wave packets since the received signal does not only depend on the antenna but also on the properties of the wave packet. The present results are of fundamental interest and of relevance to loop antennas in space.« less

Clinical applicability of quantitative nailfold capillaroscopy in differential diagnosis of connective tissue diseases with Raynaud's phenomenon.

PubMed

Wu, Po-Chang; Huang, Min-Nung; Kuo, Yu-Min; Hsieh, Song-Chou; Yu, Chia-Li

2013-08-01

Nailfold capillaroscopy is a useful tool to distinguish primary from secondary Raynaud's phenomenon (RP) by examining the morphology of nailfold capillaries but its role in disease diagnosis is not clearly established. The purpose of this study was to evaluate the roles of quantitative nailfold capillaroscopy in differential diagnosis of connective tissue diseases (CTDs) with RP. The data between the year 2005 and 2009 were retrieved from the nailfold capillaroscopic database of National Taiwan University Hospital (NTUH). Only the data from the patients with RP were analyzed. The criteria for interpretation of capillaroscopic findings were predefined. The final diagnoses of the patients were based on the American College of Rheumatology classification criteria for individual diseases, independent of nailfold capillaroscopic findings. The sensitivity and the specificity of each capillaroscopic pattern to the diseases were determined. The data from a total of 67 patients were qualified for the current study. We found the sensitivity and specificity of scleroderma pattern for systemic sclerosis (SSc) were 89.47% and 80%, and the specificity of the early, active, and late scleroderma patterns for SSc reached 87.5%, 97.5%, and 95%, respectively. The sensitivity/specificity of systemic lupus erythematosus (SLE) pattern for SLE and polymyositis/dermatomyositis (PM/DM) pattern for PM/DM were 33.33%/95.45% and 60%/96.3%, respectively. The sensitivity/specificity of mixed connective tissue disease (MCTD) pattern for MCTD were 20%/100%. The nailfold capillaroscopic (NC) patterns may be useful in the differential diagnosis of CTDs with RP. The NC patterns for SSc and PM/DM are both sensitive and specific to the diseases, while the SLE and MCTD patterns exhibit high specificity but relatively low sensitivity. Copyright © 2012. Published by Elsevier B.V.

Exploring the interaction of physical exercise load and pattern recall performance in female handball players.

PubMed

Schapschröer, M; Baker, J; Schorer, J

2016-06-01

Studies examining experts' superiority within domain-specific structured pattern recall tasks have typically had athletes perform them at rest, which is far different from how they are executed in their sport. The aim of this study was to investigate whether performing these tasks under different physical exercise intensities influenced pattern recall results of experts, advanced and novices. In two experiments, 68 participants (experiment 1: n = 33; experiment 2: n = 35) were tested using a handball-specific pattern recall task both at rest and during physical exercise. Physical exercises of 60 % heart rate reserve (constant workload: experiment 1) and of 86.5-90 % HRmax (handball-specific interval load: experiment 2) were induced. Results of both experiments revealed significant group differences with experts recalling patterns more accurately than novices but no significant within-subject differences for the two conditions and no interaction between both factors. Our findings replicate prior research concerning perceptual-cognitive expertise in structured specific pattern recall tasks. However, the lack of intergroup differences between the two conditions or interactions was surprising, suggesting sport-specific pattern recall skill is robust to changes in exercise stimuli. Future work is needed to further examine the impact of "physiological specificity" on perceptual-cognitive expertise.

Three-dimensional structure-activity relationship modeling of cocaine binding to two monoclonal antibodies by comparative molecular field analysis.

PubMed

Paula, Stefan; Tabet, Michael R; Keenan, Susan M; Welsh, William J; Ball, W James

2003-01-17

Successful immunotherapy of cocaine addiction and overdoses requires cocaine-binding antibodies with specific properties, such as high affinity and selectivity for cocaine. We have determined the affinities of two cocaine-binding murine monoclonal antibodies (mAb: clones 3P1A6 and MM0240PA) for cocaine and its metabolites by [3H]-radioligand binding assays. mAb 3P1A6 (K(d) = 0.22 nM) displayed a 50-fold higher affinity for cocaine than mAb MM0240PA (K(d) = 11 nM) and also had a greater specificity for cocaine. For the systematic exploration of both antibodies' binding specificities, we used a set of approximately 35 cocaine analogues as structural probes by determining their relative binding affinities (RBAs) using an enzyme-linked immunosorbent competition assay. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models on the basis of comparative molecular field analysis (CoMFA) techniques correlated the binding data with structural features of the ligands. The analysis indicated that despite the mAbs' differing specificities for cocaine, the relative contributions of the steric (approximately 80%) and electrostatic (approximately 20%) field interactions to ligand-binding were similar. Generated three-dimensional CoMFA contour plots then located the specific regions about cocaine where the ligand/receptor interactions occurred. While the overall binding patterns of the two mAbs had many features in common, distinct differences were observed about the phenyl ring and the methylester group of cocaine. Furthermore, using previously published data, a 3D-QSAR model was developed for cocaine binding to the dopamine reuptake transporter (DAT) that was compared to the mAb models. Although the relative steric and electrostatic field contributions were similar to those of the mAbs, the DAT cocaine-binding site showed a preference for negatively charged ligands. Besides establishing molecular level insight into the interactions that govern cocaine binding specificity by biopolymers, the three-dimensional images obtained reflect the properties of the mAbs binding pockets and provide the initial information needed for the possible design of novel antibodies with properties optimized for immunotherapy. Copyright 2003 Elsevier Science Ltd.

Dendritic Cells Program Non-Immunogenic Prostate-Specific T Cell Responses Beginning at Early Stages of Prostate Tumorigenesis

PubMed Central

Mihalyo, Marianne A.; Hagymasi, Adam T.; Slaiby, Aaron M.; Nevius, Erin E.; Adler, Adam J.

2010-01-01

BACKGROUND Prostate cancer promotes the development of T cell tolerance towards prostatic antigens, potentially limiting the efficacy of prostate cancer vaccines targeting these antigens. Here, we sought to determine the stage of disease progression when T cell tolerance develops, as well as the role of steady state dendritic cells (DC) and CD4+CD25+ T regulatory cells (Tregs) in programming tolerance. METHODS The response of naïve HA-specific CD4+ T cells were analyzed following adoptive transfer into Pro-HA × TRAMP transgenic mice harboring variably-staged HA-expressing prostate tumors on two genetic backgrounds that display different patterns and kinetics of tumorigenesis. The role of DC and Tregs in programming HA-specific CD4 cell responses were assessed via depletion. RESULTS HA-specific CD4 cells underwent non-immunogenic responses at all stages of tumorigenesis in both genetic backgrounds. These responses were completely dependent on DC, but not appreciably influenced by Tregs. CONCLUSIONS These results suggest that tolerogenicity is an early and general property of prostate tumors. PMID:17221844

ROKU: a novel method for identification of tissue-specific genes.

PubMed

Kadota, Koji; Ye, Jiazhen; Nakai, Yuji; Terada, Tohru; Shimizu, Kentaro

2006-06-12

One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes. We describe a method, ROKU, which selects tissue-specific patterns from gene expression data for many tissues and thousands of genes. ROKU ranks genes according to their overall tissue specificity using Shannon entropy and detects tissues specific to each gene if any exist using an outlier detection method. We evaluated the capacity for the detection of various specific expression patterns using synthetic and real data. We observed that ROKU was superior to a conventional entropy-based method in its ability to rank genes according to overall tissue specificity and to detect genes whose expression pattern are specific only to objective tissues. ROKU is useful for the detection of various tissue-specific expression patterns. The framework is also directly applicable to the selection of diagnostic markers for molecular classification of multiple classes.

Assembly Properties of Divergent Tubulin Isotypes and Altered Tubulin Polypeptides in Vivo

NASA Astrophysics Data System (ADS)

Gu, Wei

1990-01-01

Mbeta1 is one of the closely related (though distinct) gene products termed isotypes encoded by the mouse beta-tubulin multigene family. These isotypes typically share 95%-98% homology at the amino acid level. However, Mbeta 1 is unusual in its relatively high degree of divergence compared to other beta-tubulin isotypes; furthermore, its tissue-restricted pattern of expression (Mbeta1 is only expressed in hematopoietic tissue) led to speculation that this isotype might be specialized for assembly into unique microtubule structures (such as the marginal band in some erythropoietic cell types). To test if this isotype is capable of coassembly into microtubules in cell types other than those in which it is normally expressed, a method was developed for the generation of an anti-Mbeta1 specific antibody. The Mbeta1 tubulin isotype was introduced into tissue culture cells by transfection and its expression and assembly properties were studied in both transiently transfected cells and stable cell lines using the anti -Mbeta1 specific antibody. The successful expression and coassembly of a 'foreign' tubulin isotype into microtubules in tissue culture cells and the generation of an antibody that can specifically recognize this isotype provided an approach to study the properties of altered beta-tubulin polypeptides in vivo. beta-tubulin synthesis in eukaryotic cells is autoregulated by a posttranscriptional mechanism in which the first four amino acids are responsible for determining the stability of beta -tubulin mRNA. To test if the beta -tubulin amino-terminal regulatory domain also contributes to the capacity of the tubulin monomer to polymerize into microtubules, altered sequences encoding Mbeta 1 but containing deletions encompassing amino acids 2-5 were expressed in HeLa cells. Stable cell lines expressing the altered Mbeta1 isotype were also generated. The assembly properties and stability of these altered Mbeta1 tubulin polypeptides were tested using the anti-Mbeta1 specific antibody. The data suggest that the first four amino acids of beta-tubulin play a regulatory rather than a structural role.

Three-dimensionally patterned energy absorptive material and method of fabrication

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

Duoss, Eric; Frank, James M.; Kuntz, Joshua

A three-dimensionally patterned energy absorptive material and fabrication method having multiple layers of patterned filaments extrusion-formed from a curable pre-cursor material and stacked and cured in a three-dimensionally patterned architecture so that the energy absorptive material produced thereby has an engineered bulk property associated with the three-dimensionally patterned architecture.

A petal-specific InMYB1 promoter from Japanese morning glory: a useful tool for molecular breeding of floricultural crops.

PubMed

Azuma, Mirai; Morimoto, Reina; Hirose, Mana; Morita, Yasumasa; Hoshino, Atsushi; Iida, Shigeru; Oshima, Yoshimi; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Shiratake, Katsuhiro

2016-01-01

Production of novel transgenic floricultural crops with altered petal properties requires transgenes that confer a useful trait and petal-specific promoters. Several promoters have been shown to control transgenes in petals. However, all suffer from inherent drawbacks such as low petal specificity and restricted activity during the flowering stage. In addition, the promoters were not examined for their ability to confer petal-specific expression in a wide range of plant species. Here, we report the promoter of InMYB1 from Japanese morning glory as a novel petal-specific promoter for molecular breeding of floricultural crops. First, we produced stable InMYB1_1kb::GUS transgenic Arabidopsis and Eustoma plants and characterized spatial and temporal expression patterns under the control of the InMYB1 promoter by histochemical β-glucuronidase (GUS) staining. GUS staining patterns were observed only in petals. This result showed that the InMYB1 promoter functions as a petal-specific promoter. Second, we transiently introduced the InMYB1_1 kb::GUS construct into Eustoma, chrysanthemum, carnation, Japanese gentian, stock, rose, dendrobium and lily petals by particle bombardment. GUS staining spots were observed in Eustoma, chrysanthemum, carnation, Japanese gentian and stock. These results showed that the InMYB1 promoter functions in most dicots. Third, to show the InMYB1 promoter utility in molecular breeding, a MIXTA-like gene function was suppressed or enhanced under the control of InMYB1 promoter in Arabidopsis. The transgenic plant showed a conspicuous morphological change only in the form of wrinkled petals. Based on these results, the InMYB1 promoter can be used as a petal-specific promoter in molecular breeding of floricultural crops. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Modelling the perceptual similarity of facial expressions from image statistics and neural responses.

PubMed

Sormaz, Mladen; Watson, David M; Smith, William A P; Young, Andrew W; Andrews, Timothy J

2016-04-01

The ability to perceive facial expressions of emotion is essential for effective social communication. We investigated how the perception of facial expression emerges from the image properties that convey this important social signal, and how neural responses in face-selective brain regions might track these properties. To do this, we measured the perceptual similarity between expressions of basic emotions, and investigated how this is reflected in image measures and in the neural response of different face-selective regions. We show that the perceptual similarity of different facial expressions (fear, anger, disgust, sadness, happiness) can be predicted by both surface and feature shape information in the image. Using block design fMRI, we found that the perceptual similarity of expressions could also be predicted from the patterns of neural response in the face-selective posterior superior temporal sulcus (STS), but not in the fusiform face area (FFA). These results show that the perception of facial expression is dependent on the shape and surface properties of the image and on the activity of specific face-selective regions. Copyright © 2016 Elsevier Inc. All rights reserved.

Predicting the Stochastic Properties of the Shallow Subsurface for Improved Geophysical Modeling

NASA Astrophysics Data System (ADS)

Stroujkova, A.; Vynne, J.; Bonner, J.; Lewkowicz, J.

2005-12-01

Strong ground motion data from numerous explosive field experiments and from moderate to large earthquakes show significant variations in amplitude and waveform shape with respect to both azimuth and range. Attempts to model these variations using deterministic models have often been unsuccessful. It has been hypothesized that a stochastic description of the geological medium is a more realistic approach. To estimate the stochastic properties of the shallow subsurface, we use Measurement While Drilling (MWD) data, which are routinely collected by mines in order to facilitate design of blast patterns. The parameters, such as rotation speed of the drill, torque, and penetration rate, are used to compute the rock's Specific Energy (SE), which is then related to a blastability index. We use values of SE measured at two different mines and calibrated to laboratory measurements of rock properties to determine correlation lengths of the subsurface rocks in 2D, needed to obtain 2D and 3D stochastic models. The stochastic models are then combined with the deterministic models and used to compute synthetic seismic waveforms.

Socioemotional selectivity in older adults: Evidence from the subjective experience of angry memories.

PubMed

Uzer, Tugba; Gulgoz, Sami

2015-01-01

Few studies have compared the phenomenological properties of younger and older adults' memories for emotional events. Some studies suggest that younger adults remember negative information more vividly than positive information whereas other studies suggest that positive emotion yields phenomenologically richer memories than negative emotion for both younger and older adults. One problem with previous studies is a tendency to treat emotion as a dichotomous variable. In contrast, emotional richness demands inclusion of assessments beyond just a positive and negative dimension (e.g., assessing specific emotions like anger, fear and happiness). The present study investigated different properties of autobiographical remembering as a function of discrete emotions and age. Thirty-two younger and thirty-one older adults participated by recalling recent and remote memories associated with six emotional categories and completed the Memory Characteristics Questionnaire for each. Results demonstrated that older adults' angry memories received lower ratings on some phenomenological properties than other emotional memories whereas younger adults' angry memories did not show this same pattern. These results are discussed within the context of socioemotional selectivity theory.

Improving of the electrical and magnetic properties of BiFeO{sub 3} by doping with yttrium

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

Ilić, Nikola I., E-mail: niksentije@gmail.com; Bobić, Jelena D.; Stojadinović, Bojan S.

2016-05-15

Bismuth ferrite is one of the most promising multiferroic materials, and the main barriers for exploiting all of its specific properties are difficulties in obtaining pure, high resistive material with nanosized grains. Doping of BiFeO{sub 3} with different transition metals and rare earth elements is often used way for overcoming these obstacles. Yttrium doped bismuth ferrite, Bi{sub 1−x}Y{sub x}FeO{sub 3} (x = 0; 0.01; 0.03; 0.05; 0.1), was prepared by auto-combustion method. X-ray diffraction patterns and Raman results showed that partial phase transition from rhombohedral to orthorhombic structure took place at around 10 mol% of Y. Effect of Y dopingmore » on microstructure was studied from SEM micrographies, showing the reduction of grain size in doped samples. Electrical measurements showed continuous improvement of resistivity with Y doping, whereas the values of saturation and remnant polarizations exhibit maximums at around 5 mol% of Y. Yttrium doping also enhanced magnetic properties, leading to weak ferromagnetism.« less

Differential roles of nonsynaptic and synaptic plasticity in operant reward learning-induced compulsive behavior.

PubMed

Sieling, Fred; Bédécarrats, Alexis; Simmers, John; Prinz, Astrid A; Nargeot, Romuald

2014-05-05

Rewarding stimuli in associative learning can transform the irregularly and infrequently generated motor patterns underlying motivated behaviors into output for accelerated and stereotyped repetitive action. This transition to compulsive behavioral expression is associated with modified synaptic and membrane properties of central neurons, but establishing the causal relationships between cellular plasticity and motor adaptation has remained a challenge. We found previously that changes in the intrinsic excitability and electrical synapses of identified neurons in Aplysia's central pattern-generating network for feeding are correlated with a switch to compulsive-like motor output expression induced by in vivo operant conditioning. Here, we used specific computer-simulated ionic currents in vitro to selectively replicate or suppress the membrane and synaptic plasticity resulting from this learning. In naive in vitro preparations, such experimental manipulation of neuronal membrane properties alone increased the frequency but not the regularity of feeding motor output found in preparations from operantly trained animals. On the other hand, changes in synaptic strength alone switched the regularity but not the frequency of feeding output from naive to trained states. However, simultaneously imposed changes in both membrane and synaptic properties reproduced both major aspects of the motor plasticity. Conversely, in preparations from trained animals, experimental suppression of the membrane and synaptic plasticity abolished the increase in frequency and regularity of the learned motor output expression. These data establish direct causality for the contributions of distinct synaptic and nonsynaptic adaptive processes to complementary facets of a compulsive behavior resulting from operant reward learning. Copyright © 2014 Elsevier Ltd. All rights reserved.

Distinct signalling properties of insulin receptor substrate (IRS)-1 and IRS-2 in mediating insulin/IGF-1 action.

PubMed

Rabiee, Atefeh; Krüger, Marcus; Ardenkjær-Larsen, Jacob; Kahn, C Ronald; Emanuelli, Brice

2018-07-01

Insulin/IGF-1 action is driven by a complex and highly integrated signalling network. Loss-of-function studies indicate that the major insulin/IGF-1 receptor substrate (IRS) proteins, IRS-1 and IRS-2, mediate different biological functions in vitro and in vivo, suggesting specific signalling properties despite their high degree of homology. To identify mechanisms contributing to the differential signalling properties of IRS-1 and IRS-2 in the mediation of insulin/IGF-1 action, we performed comprehensive mass spectrometry (MS)-based phosphoproteomic profiling of brown preadipocytes from wild type, IRS-1 -/- and IRS-2 -/- mice in the basal and IGF-1-stimulated states. We applied stable isotope labeling by amino acids in cell culture (SILAC) for the accurate quantitation of changes in protein phosphorylation. We found ~10% of the 6262 unique phosphorylation sites detected to be regulated by IGF-1. These regulated sites included previously reported substrates of the insulin/IGF-1 signalling pathway, as well as novel substrates including Nuclear Factor I X and Semaphorin-4B. In silico prediction suggests the protein kinase B (PKB), protein kinase C (PKC), and cyclin-dependent kinase (CDK) as the main mediators of these phosphorylation events. Importantly, we found preferential phosphorylation patterns depending on the presence of either IRS-1 or IRS-2, which was associated with specific sets of kinases involved in signal transduction downstream of these substrates such as PDHK1, MAPK3, and PKD1 for IRS-1, and PIN1 and PKC beta for IRS-2. Overall, by generating a comprehensive phosphoproteomic profile from brown preadipocyte cells in response to IGF-1 stimulation, we reveal both common and distinct insulin/IGF-1 signalling events mediated by specific IRS proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Use of regional mechanical properties of abdominal aortic aneurysms to advance finite element modeling of rupture risk.

PubMed

Tierney, Áine P; Callanan, Anthony; McGloughlin, Timothy M

2012-02-01

To investigate the use of regional variations in the mechanical properties of abdominal aortic aneurysms (AAA) in finite element (FE) modeling of AAA rupture risk, which has heretofore assumed homogeneous mechanical tissue properties. Electrocardiogram-gated computed tomography scans from 3 male patients with known infrarenal AAA were used to characterize the behavior of the aneurysm in 4 different segments (posterior, anterior, and left and right lateral) at maximum diameter and above the infrarenal aorta. The elasticity of the aneurysm (circumferential cyclic strain, compliance, and the Hudetz incremental modulus) was calculated for each segment and the aneurysm as a whole. The FE analysis inclusive of prestress (pre-existing tensile stress) produced a detailed stress pattern on each of the aneurysm models under pressure loading. The 4 largest areas of stress in each region were considered in conjunction with the local regional properties of the segment to define a specific regional prestress rupture index (RPRI). In terms of elasticity, there were average reductions of 68% in circumferential cyclic strain and 63% in compliance, with a >5-fold increase in incremental modulus, between the healthy and the aneurysmal aorta for each patient. There were also regional variations in all elastic properties in each individual patient. The average difference in total stress inclusive of prestress was 59%, 67%, and 15%, respectively, for the 3 patients. Comparing the strain from FE models with the CT scans revealed an average difference in strain of 1.55% for the segmented models and 3.61% for the homogeneous models, which suggests that the segmented models more accurately reflect in vivo behavior. RPRI values were calculated for each segment for all patients. A greater understanding of the local material properties and their use in FE models is essential for greater accuracy in rupture prediction. Quantifying the regional behavior will yield insight into the changes in patient-specific aneurysms and increase understanding about the progression of aneurysmal disease.

Porosity and Variations in Microgravity Aerogel Nano-Structures. 2; New Laser Speckle Characterization Methods

NASA Technical Reports Server (NTRS)

Hunt, A. J.; Ayers, M. R.; Sibille, L.; Smith, D. D.

2001-01-01

The transition from sol to gel is a process that is critical to the properties of engineered nanomaterials, but one with few available techniques for observing the dynamic processes occurring during the evolution of the gel network. Specifically, the observation of various cluster aggregation models, such as diffusion-limited and reaction-limited cluster growth can be quite difficult. This can be rather important as the actual aggregation model can dramatically influence the mechanical properties of gels, and is significantly affected by the presence of convective flows, or their absence in microgravity. We have developed two new non-intrusive optical methods for observing the aggregation processes within gels in real time. These make use of the dynamic behavior of laser speckle patterns produced when an intense laser source is passed through a gelling sol. The first method is a simplified time-correlation measurement, where the speckle pattern is observed using a CCD camera and information on the movement of the scattering objects is readily apparent. This approach is extremely sensitive to minute variations in the flow field as the observed speckle pattern is a diffraction-based image, and is therefore sensitive to motions within the sol on the order of the wavelength of the probing light. Additionally, this method has proven useful in determining a precise time for the gel-point, an event often difficult to measure. Monitoring the evolution of contrast within the speckle field is another method that has proven useful for studying aeration. In this case, speckle contrast is dependent upon the size (correlation length) and number of scattering centers, increasing with increasing size, and decreasing with increasing numbers. The dynamic behavior of cluster growth in gels causes both of these to change simultaneously with time, the exact rate of which is determined by the specific aggregation model involved. Actual growth processes can now be observed, and the effects of varying gravity fields on the growth processes qualitatively described. Results on preliminary ground-based measurements have been obtained.

Graphene electron cannon: High-current edge emission from aligned graphene sheets

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

Liu, Jianlong; Li, Nannan; Guo, Jing

2014-01-13

High-current field emitters are made by graphene paper consist of aligned graphene sheets. Field emission luminance pattern shows that their electron beams can be controlled by rolling the graphene paper from sheet to cylinder. These specific electron beams would be useful to vacuum devices and electron beam lithograph. To get high-current emission, the graphene paper is rolled to array and form graphene cannon. Due to aligned emission array, graphene cannon have high emission current. Besides high emission current, the graphene cannon is also tolerable with excellent emission stability. With good field emission properties, these aligned graphene emitters bring application insight.

Antenna design for microwave hepatic ablation using an axisymmetric electromagnetic model

PubMed Central

Bertram, John M; Yang, Deshan; Converse, Mark C; Webster, John G; Mahvi, David M

2006-01-01

Background An axisymmetric finite element method (FEM) model was employed to demonstrate important techniques used in the design of antennas for hepatic microwave ablation (MWA). To effectively treat deep-seated hepatic tumors, these antennas should produce a highly localized specific absorption rate (SAR) pattern and be efficient radiators at approved generator frequencies. Methods and results As an example, a double slot choked antenna for hepatic MWA was designed and implemented using FEMLAB™ 3.0. Discussion This paper emphasizes the importance of factors that can affect simulation accuracy, which include boundary conditions, the dielectric properties of liver tissue, and mesh resolution. PMID:16504153

Effect of ternary addition and gamma-irradiation on the characteristics of rapidly solidified Pb-base alloys

NASA Astrophysics Data System (ADS)

Abd El-Khalek, A. M.

The properties of a series of rapidly solidified Pb-Sb-3-Sn-x alloys ( x =0-2.5 wt.%) irradiated with gamma-rays were studied. Variations in the internal friction, Q(-1) , thermal diffusivity D th and dynamic Young's modulus Y were traced before and after irradiation by applying the resonance technique. Variations of specific heat C-p were obtained from DTA thermograms. Structure parameters were obtained from the X-rays diffraction patterns. A marked change in the behaviour of the measured parameters was observed at 1.5 wt.% Sn addition. Besides, irradiation induced defects increased the level of the measured hardening parameters.

Sectoral transitions - modeling the development from agrarian to service economies

NASA Astrophysics Data System (ADS)

Lutz, Raphael; Spies, Michael; Reusser, Dominik E.; Kropp, Jürgen P.; Rybski, Diego

2013-04-01

We consider the sectoral composition of a country's GDP, i.e the partitioning into agrarian, industrial, and service sectors. Exploring a simple system of differential equations we characterise the transfer of GDP shares between the sectors in the course of economic development. The model fits for the majority of countries providing 4 country-specific parameters. Relating the agrarian with the industrial sector, a data collapse over all countries and all years supports the applicability of our approach. Depending on the parameter ranges, country development exhibits different transfer properties. Most countries follow 3 of 8 characteristic paths. The types are not random but show distinct geographic and development patterns.

Origin of steps in magnetization loops of martensitic Ni-Mn-Ga films on MgO(001)

NASA Astrophysics Data System (ADS)

Laptev, Aleksej; Lebecki, Kristof; Welker, Gesa; Luo, Yuansu; Samwer, Konrad; Fonin, Mikhail

2016-09-01

We study the temperature dependent magnetization properties of (010)-oriented Ni-Mn-Ga epitaxial films on MgO(001) substrates. In the martensitic phase, we observe pronounced abrupt slope changes in the magnetization loops for all studied samples. Our experimental findings are discussed in conjunction with the micromagnetic simulations, revealing that the characteristic magnetization behavior is governed solely by the magnetization switching within the specific martensitic variant pattern, and no reorientation of twin variants is involved in the process. Our study emphasizes the important role of the magnetostatic interactions in the magnetization behavior of magnetic shape memory alloy thin films.

Plasma-Assisted Dry Etching of Ferroelectric Capacitor Modules and Application to a 32M Ferroelectric Random Access Memory Devices with Submicron Feature Sizes

NASA Astrophysics Data System (ADS)

Lee, Sang-Woo; Joo, Suk-Ho; Cho, Sung Lae; Son, Yoon-Ho; Lee, Kyu-Mann; Nam, Sang-Don; Park, Kun-Sang; Lee, Yong-Tak; Seo, Jung-Suk; Kim, Young-Dae; An, Hyeong-Geun; Kim, Hyoung-Joon; Jung, Yong-Ju; Heo, Jang-Eun; Lee, Moon-Sook; Park, Soon-Oh; Chung, U-In; Moon, Joo-Tae

2002-11-01

In the manufacturing of a 32M ferroelectric random access memory (FRAM) device on the basis of 0.25 design rule (D/R), one of the most difficult processes is to pattern a submicron capacitor module while retaining good ferroelectric properties. In this paper, we report the ferroelectric property of patterned submicron capacitor modules with a stack height of 380 nm, where the 100 nm-thick Pb(Zr, Ti)O3 (PZT) films were prepared by the sol-gel method. After patterning, overall sidewall slope was approximately 70° and cell-to-cell node separation was made to be 80 nm to prevent possible twin-bit failure in the device. Finally, several heat treatment conditions were investigated to retain the ferroelectric property of the patterned capacitor. It was found that rapid thermal processing (RTP) treatment yields better properties than conventional furnace annealing. This result is directly related to the near-surface chemistry of the PZT films, as confirmed by X-ray photoelectron spectroscopy (XPS) analysis. The resultant switching polarization value of the submicron capacitor was approximately 30 μC/cm2 measured at 3 V.

Quantitative assessment of soft tissue deformation using digital speckle pattern interferometry: studies on phantom breast models.

PubMed

Karuppanan, Udayakumar; Unni, Sujatha Narayanan; Angarai, Ganesan R

2017-01-01

Assessment of mechanical properties of soft matter is a challenging task in a purely noninvasive and noncontact environment. As tissue mechanical properties play a vital role in determining tissue health status, such noninvasive methods offer great potential in framing large-scale medical screening strategies. The digital speckle pattern interferometry (DSPI)-based image capture and analysis system described here is capable of extracting the deformation information from a single acquired fringe pattern. Such a method of analysis would be required in the case of the highly dynamic nature of speckle patterns derived from soft tissues while applying mechanical compression. Soft phantoms mimicking breast tissue optical and mechanical properties were fabricated and tested in the DSPI out of plane configuration set up. Hilbert transform (HT)-based image analysis algorithm was developed to extract the phase and corresponding deformation of the sample from a single acquired fringe pattern. The experimental fringe contours were found to correlate with numerically simulated deformation patterns of the sample using Abaqus finite element analysis software. The extracted deformation from the experimental fringe pattern using the HT-based algorithm is compared with the deformation value obtained using numerical simulation under similar conditions of loading and the results are found to correlate with an average %error of 10. The proposed method is applied on breast phantoms fabricated with included subsurface anomaly mimicking cancerous tissue and the results are analyzed.

Wood specific gravity variation among five important hardwood species of Kashmir Himalaya.

PubMed

Wani, Bilal Ahmad; Bodha, R H; Khan, Amina

2014-02-01

Wood Specific Gravity (SG) is a measure of the amount of structural material a tree species allocates to support and strength. In the present study, specific gravity varied among the five different woods at three different sites from 0.40 in Populus nigra at site III (Shopian) to 0.80 in Parrotiopsis jacquemontiana at site II (Surasyar). Among the three different sites, specific gravity varied from 0.73 to 0.80 in Parroptiosis jacquemontiana; in Robinia pseudoacacia it varied from 0.71 to 0.79; in Salix alba, it varied from 0.42 to 0.48; In Populus nigra it varied from 0.40 to 0.48 and in Juglans regia it varied from 0.59 to 0.66. On the basis of the specific gravity variation patterns these woods were categorized as light (Salix alba, Populus nigra) moderately heavy (Juglans regia) and moderately heavy to heavy (Robinia pseudoacacia, Parrotiopsis jacquemontiana) which predicts their properties like strength, dimensional stability with moisture content change, ability to retain paint, fiber yield per unit volume, suitability for making particleboard and related wood composite materials and suitability as a raw material for making paper.

Cancer Stratification by Molecular Imaging

PubMed Central

Weber, Justus; Haberkorn, Uwe; Mier, Walter

2015-01-01

The lack of specificity of traditional cytotoxic drugs has triggered the development of anticancer agents that selectively address specific molecular targets. An intrinsic property of these specialized drugs is their limited applicability for specific patient subgroups. Consequently, the generation of information about tumor characteristics is the key to exploit the potential of these drugs. Currently, cancer stratification relies on three approaches: Gene expression analysis and cancer proteomics, immunohistochemistry and molecular imaging. In order to enable the precise localization of functionally expressed targets, molecular imaging combines highly selective biomarkers and intense signal sources. Thus, cancer stratification and localization are performed simultaneously. Many cancer types are characterized by altered receptor expression, such as somatostatin receptors, folate receptors or Her2 (human epidermal growth factor receptor 2). Similar correlations are also known for a multitude of transporters, such as glucose transporters, amino acid transporters or hNIS (human sodium iodide symporter), as well as cell specific proteins, such as the prostate specific membrane antigen, integrins, and CD20. This review provides a comprehensive description of the methods, targets and agents used in molecular imaging, to outline their application for cancer stratification. Emphasis is placed on radiotracers which are used to identify altered expression patterns of cancer associated markers. PMID:25749472

A GRAPH PARTITIONING APPROACH TO PREDICTING PATTERNS IN LATERAL INHIBITION SYSTEMS

PubMed Central

RUFINO FERREIRA, ANA S.; ARCAK, MURAT

2017-01-01

We analyze spatial patterns on networks of cells where adjacent cells inhibit each other through contact signaling. We represent the network as a graph where each vertex represents the dynamics of identical individual cells and where graph edges represent cell-to-cell signaling. To predict steady-state patterns we find equitable partitions of the graph vertices and assign them into disjoint classes. We then use results from monotone systems theory to prove the existence of patterns that are structured in such a way that all the cells in the same class have the same final fate. To study the stability properties of these patterns, we rely on the graph partition to perform a block decomposition of the system. Then, to guarantee stability, we provide a small-gain type criterion that depends on the input-output properties of each cell in the reduced system. Finally, we discuss pattern formation in stochastic models. With the help of a modal decomposition we show that noise can enhance the parameter region where patterning occurs. PMID:29225552

Dynamical Properties of Transient Spatio-Temporal Patterns in Bacterial Colony of Proteus mirabilis

NASA Astrophysics Data System (ADS)

Watanabe, Kazuhiko; Wakita, Jun-ichi; Itoh, Hiroto; Shimada, Hirotoshi; Kurosu, Sayuri; Ikeda, Takemasa; Yamazaki, Yoshihiro; Matsuyama, Tohey; Matsushita, Mitsugu

2002-02-01

Spatio-temporal patterns emerged inside a colony of bacterial species Proteus mirabilis on the surface of nutrient-rich semisolid agar medium have been investigated. We observed various patterns composed of the following basic types: propagating stripe, propagating stripe with fixed dislocation, expanding and shrinking target, and rotating spiral. The remarkable point is that the pattern changes immediately when we alter the position for observation, but it returns to the original if we restore the observing position within a few minutes. We further investigated mesoscopic and microscopic properties of the spatio-temporal patterns. It turned out that whenever the spatio-temporal patterns are observed in a colony, the areas are composed of two superimposed monolayers of elongated bacterial cells. In each area they are aligned almost parallel with each other like a two-dimensional nematic liquid crystal, and move collectively and independently of another layer. It has been found that the observed spatio-temporal patterns are explained as the moiré effect.

Impacts of salt marsh plants on tidal channel initiation and inheritance

NASA Astrophysics Data System (ADS)

Schwarz, Christian; Ye, Qinghua; van der Wal, Daphne; Zhang, Liquan; Ysebaert, Tom; Herman, Peter MJ

2013-04-01

Tidal channel networks are the most prominent and striking features visible in tidal wetlands. They serve as major pathways for the exchange of water, sediments, nutrients and contaminants between the wetland and the adjacent open water body. Previous studies identified topography guided sheet flows, as the predominate process for tidal channel initiation. Guided through differences in local topography, sheet flows are able to locally exceed bottom shear stress thresholds, initiating scouring and incision of tidal channels, which then further grow through head ward erosion. The fate of these channels after plant colonization is described in literature as being inherited into the salt marsh through vegetation induced bank stabilization (further referred to as vegetation stabilized channel inheritance). In this study we present a combination of flume experiments and modelling simulations elucidating the impact of vegetation on tidal channel initiation. We first studied the impact of plant properties (stiff: Spartina alterniflora versus flexible: Scirpus mariqueter) on local sediment transport utilizing a flume experiment. Then a coupled hydrodynamic morphodynamic plant growth model was set up to simulate plant colonization by these two different species in the pioneer zone at the mudflat - salt marsh transition. Based on the model we investigated the ramifications of interactions between vegetation, sediment and flow on tidal channel initiation. We specifically compared the effect of vegetation properties (such as stiffness, growth velocity and stress tolerance) on emerging channel patterns, hypothesizing that vegetation mediated channel incision (vegetation induced flow routing and differential sedimentation/erosion patterns leading to tidal channel incision) plays an active role in intertidal landscape evolution. We finally extended our model simulation by imposing pre-existing mudflat channels with different maximum depths, to investigate the impact of existing channels on vegetation mediated channel incision. This simulated landscape development was then compared to aerial photographs from the Scheldt estuary (the Netherlands) and the Yangtze estuary (China). Our results suggest a significant impact of plant properties on tidal channel network emergence, specifically in respect to network drainage density and channel width. This emphasizes the repercussions of vegetation mediated channel incision on estuarine landscape development. Further do our results point to the existence of a threshold in pre-existing mudflat channel depth favoring either vegetation stabilized channel inheritance or vegetation mediated channel incision processes. Increasing depth in mudflat channels favors flow routing via these channels, leaving less flow and momentum remaining for the interaction between vegetation, sediment and flow and therefore vegetation mediated channel incision. This threshold will be influenced by field specific parameters such as hydrodynamics (tidal range, waves, and flow), sediments and predominant plant species. Hence our study not only demonstrates to importance of plant properties on landscape development it also shows that vegetation stabilized channel inheritance or vegetation mediated channel incision are two occurring mechanisms depending on ecosystem properties, adding important information for salt marsh management and conservation.

Tomographical imaging using uniformly redundant arrays

NASA Technical Reports Server (NTRS)

Cannon, T. M.; Fenimore, E. E.

1979-01-01

An investigation is conducted of the behavior of two types of uniformly redundant array (URA) when used for close-up imaging. One URA pattern is a quadratic residue array whose characteristics for imaging planar sources have been simulated by Fenimore and Cannon (1978), while the second is based on m sequences that have been simulated by Gunson and Polychronopulos (1976) and by MacWilliams and Sloan (1976). Close-up imaging is necessary in order to obtain depth information for tomographical purposes. The properties of the two URA patterns are compared with a random array of equal open area. The goal considered in the investigation is to determine if a URA pattern exists which has the desirable defocus properties of the random array while maintaining artifact-free image properties for in-focus objects.

Rapid Long-Range Disynaptic Inhibition Explains the Formation of Cortical Orientation Maps

PubMed Central

Antolík, Ján

2017-01-01

Competitive interactions are believed to underlie many types of cortical processing, ranging from memory formation, attention and development of cortical functional organization (e.g., development of orientation maps in primary visual cortex). In the latter case, the competitive interactions happen along the cortical surface, with local populations of neurons reinforcing each other, while competing with those displaced more distally. This specific configuration of lateral interactions is however in stark contrast with the known properties of the anatomical substrate, i.e., excitatory connections (mediating reinforcement) having longer reach than inhibitory ones (mediating competition). No satisfactory biologically plausible resolution of this conflict between anatomical measures, and assumed cortical function has been proposed. Recently a specific pattern of delays between different types of neurons in cat cortex has been discovered, where direct mono-synaptic excitation has approximately the same delay, as the combined delays of the disynaptic inhibitory interactions between excitatory neurons (i.e., the sum of delays from excitatory to inhibitory and from inhibitory to excitatory neurons). Here we show that this specific pattern of delays represents a biologically plausible explanation for how short-range inhibition can support competitive interactions that underlie the development of orientation maps in primary visual cortex. We demonstrate this statement analytically under simplifying conditions, and subsequently show using network simulations that development of orientation maps is preserved when long-range excitation, direct inhibitory to inhibitory interactions, and moderate inequality in the delays between excitatory and inhibitory pathways is added. PMID:28408869

Genetic Programming and Frequent Itemset Mining to Identify Feature Selection Patterns of iEEG and fMRI Epilepsy Data

PubMed Central

Smart, Otis; Burrell, Lauren

2014-01-01

Pattern classification for intracranial electroencephalogram (iEEG) and functional magnetic resonance imaging (fMRI) signals has furthered epilepsy research toward understanding the origin of epileptic seizures and localizing dysfunctional brain tissue for treatment. Prior research has demonstrated that implicitly selecting features with a genetic programming (GP) algorithm more effectively determined the proper features to discern biomarker and non-biomarker interictal iEEG and fMRI activity than conventional feature selection approaches. However for each the iEEG and fMRI modalities, it is still uncertain whether the stochastic properties of indirect feature selection with a GP yield (a) consistent results within a patient data set and (b) features that are specific or universal across multiple patient data sets. We examined the reproducibility of implicitly selecting features to classify interictal activity using a GP algorithm by performing several selection trials and subsequent frequent itemset mining (FIM) for separate iEEG and fMRI epilepsy patient data. We observed within-subject consistency and across-subject variability with some small similarity for selected features, indicating a clear need for patient-specific features and possible need for patient-specific feature selection or/and classification. For the fMRI, using nearest-neighbor classification and 30 GP generations, we obtained over 60% median sensitivity and over 60% median selectivity. For the iEEG, using nearest-neighbor classification and 30 GP generations, we obtained over 65% median sensitivity and over 65% median selectivity except one patient. PMID:25580059

Direct laser interference patterning of magnetic thin films

NASA Astrophysics Data System (ADS)

Aktag, Aliekber

Recently, patterned magnetic thin films have attracted much attention for a variety of applications such as high density magnetic recording, magnetoresistive sensing, and magnetic random access memories. In the case of magnetic recording, one scheme calls for the films to be patterned into single domain "dots", where every dot represents a thermally stable bit. In this thesis, we extended a technique called direct laser interference patterning (DLIP), originally developed by Polushkin and co-workers, to pattern and locally modify the materials properties of magnetic thin films. In this technique, a high-intensity Nd:YAG pulse laser beam was split into two, three, or four beams, which are then recombined to interfere on a sample surface. The interference intensity maxima can modify the local materials properties of the film through local "annealing" or, more drastically, by ablation. We carried out some preliminary investigations of the DLIP process in several films including co-sputtered Co-C, amorphous Dy/Co:SiO2 multilayers, and Co/SiO2 multilayers in order to refine our techniques. We successfully produced regular arrays of lines, dots, or antidots formed by ablation of the thin film. The preliminary studies also showed that, in the regime of more modest pulse energies, it is possible to modify the magnetic properties of the films without noticeably changing the film topography. We then prepared perpendicular magnetic anisotropy Co/Pt multilayers with a SiO x passivation layer and applied DLIP at fairly modest intensities to pattern the film. We then studied the structural and magnetic changes that occurred in some detail. X-ray diffraction scans showed the Co/Pt:SiO x multilayer films to be nanocrystalline before and after patterning. Atomic force microscopy images showed no evidence for topographic changes of the Co/Pt:SiOx during patterning. In contrast, magnetic force microscopy showed regular periodic dot arrays, indicating that the local magnetic properties were significantly affected by the patterning process. Alternating-gradient-force magnetometry and magneto-optic measurements also showed that the magnetic properties were markedly changed by the DLIP process. Our results offer strong evidence that local heating causes the moments to change from perpendicular to in-plane, with the consequent formation of an "anisotropy lattice": dots of in-plane magnetization within a matrix of perpendicular magnetization. We also carried out some optical interference calculations to predict the light intensity distributions for two, three, and four interfering beams of light. We found that the patterns could be controlled by varying the angles of incidence, the polarizations of the beams, and the wavelength and intensity of the beams, and that a wide variety of patterns are possible. The predicted patterns were in quite good agreement with those observed experimentally.

New database for improving virtual system “body-dress”

NASA Astrophysics Data System (ADS)

Yan, J. Q.; Zhang, S. C.; Kuzmichev, V. E.; Adolphe, D. C.

2017-10-01

The aim of this exploration is to develop a new database of solid algorithms and relations between the dress fit and the fabric mechanical properties, the pattern block construction for improving the reality of virtual system “body-dress”. In virtual simulation, the system “body-clothing” sometimes shown distinct results with reality, especially when important changes in pattern block and fabrics were involved. In this research, to enhance the simulation process, diverse fit parameters were proposed: bottom height of dress, angle of front center contours, air volume and its distribution between dress and dummy. Measurements were done and optimized by ruler, camera, 3D body scanner image processing software and 3D modeling software. In the meantime, pattern block indexes were measured and fabric properties were tested by KES. Finally, the correlation and linear regression equations between indexes of fabric properties, pattern blocks and fit parameters were investigated. In this manner, new database could be extended in programming modules of virtual design for more realistic results.

A general model to explore complex dominance patterns in plant sporophytic self-incompatibility systems.

PubMed

Billiard, Sylvain; Castric, Vincent; Vekemans, Xavier

2007-03-01

We developed a general model of sporophytic self-incompatibility under negative frequency-dependent selection allowing complex patterns of dominance among alleles. We used this model deterministically to investigate the effects on equilibrium allelic frequencies of the number of dominance classes, the number of alleles per dominance class, the asymmetry in dominance expression between pollen and pistil, and whether selection acts on male fitness only or both on male and on female fitnesses. We show that the so-called "recessive effect" occurs under a wide variety of situations. We found emerging properties of finite population models with several alleles per dominance class such as that higher numbers of alleles are maintained in more dominant classes and that the number of dominance classes can evolve. We also investigated the occurrence of homozygous genotypes and found that substantial proportions of those can occur for the most recessive alleles. We used the model for two species with complex dominance patterns to test whether allelic frequencies in natural populations are in agreement with the distribution predicted by our model. We suggest that the model can be used to test explicitly for additional, allele-specific, selective forces.

A pattern recognition approach to transistor array parameter variance

NASA Astrophysics Data System (ADS)

da F. Costa, Luciano; Silva, Filipi N.; Comin, Cesar H.

2018-06-01

The properties of semiconductor devices, including bipolar junction transistors (BJTs), are known to vary substantially in terms of their parameters. In this work, an experimental approach, including pattern recognition concepts and methods such as principal component analysis (PCA) and linear discriminant analysis (LDA), was used to experimentally investigate the variation among BJTs belonging to integrated circuits known as transistor arrays. It was shown that a good deal of the devices variance can be captured using only two PCA axes. It was also verified that, though substantially small variation of parameters is observed for BJT from the same array, larger variation arises between BJTs from distinct arrays, suggesting the consideration of device characteristics in more critical analog designs. As a consequence of its supervised nature, LDA was able to provide a substantial separation of the BJT into clusters, corresponding to each transistor array. In addition, the LDA mapping into two dimensions revealed a clear relationship between the considered measurements. Interestingly, a specific mapping suggested by the PCA, involving the total harmonic distortion variation expressed in terms of the average voltage gain, yielded an even better separation between the transistor array clusters. All in all, this work yielded interesting results from both semiconductor engineering and pattern recognition perspectives.

Deterministic Nanopatterning of Diamond Using Electron Beams.

PubMed

Bishop, James; Fronzi, Marco; Elbadawi, Christopher; Nikam, Vikram; Pritchard, Joshua; Fröch, Johannes E; Duong, Ngoc My Hanh; Ford, Michael J; Aharonovich, Igor; Lobo, Charlene J; Toth, Milos

2018-03-27

Diamond is an ideal material for a broad range of current and emerging applications in tribology, quantum photonics, high-power electronics, and sensing. However, top-down processing is very challenging due to its extreme chemical and physical properties. Gas-mediated electron beam-induced etching (EBIE) has recently emerged as a minimally invasive, facile means to dry etch and pattern diamond at the nanoscale using oxidizing precursor gases such as O 2 and H 2 O. Here we explain the roles of oxygen and hydrogen in the etch process and show that oxygen gives rise to rapid, isotropic etching, while the addition of hydrogen gives rise to anisotropic etching and the formation of topographic surface patterns. We identify the etch reaction pathways and show that the anisotropy is caused by preferential passivation of specific crystal planes. The anisotropy can be controlled by the partial pressure of hydrogen and by using a remote RF plasma source to radicalize the precursor gas. It can be used to manipulate the geometries of topographic surface patterns as well as nano- and microstructures fabricated by EBIE. Our findings constitute a comprehensive explanation of the anisotropic etch process and advance present understanding of electron-surface interactions.

Sound production patterns from humpback whales in a high latitude foraging area

NASA Astrophysics Data System (ADS)

Stimpert, Alison K.; Wiley, David N.; Barton, Kira L.; Johnson, Mark P.; Lammers, Marc O.; Au, Whitlow W. L.

2005-09-01

Numerous studies have been conducted on humpback whale song, but substantially fewer have focused on the acoustic properties of non-song sound production (i.e., feeding and social sounds). Non-invasive digital acoustic recording tags (DTAGS) were attached to humpback whales on the western North Atlantics Great South Channel feeding grounds during July 2004. Acoustic records totaling 48.4 data hours from four of these attachments were aurally analyzed for temporal trends in whale signal production. A custom automatic detection function was also used to identify occurrences of specific signals and evaluate their temporal consistency. Patterns in sound usage varied by stage of foraging dive and by time of day. Amount of time with signals present was greater at the bottom of dives than during surface periods, indicating that sounds are probably related to foraging at depth. For the two tags that recorded at night, signals were present during a greater proportion of daylight hours than night hours. These results will be compared with previously published trends describing diel patterns in male humpback whale song chorusing on the breeding grounds. Data from the continuation of this research during the summer of 2005 will also be included.

Adaptation to implied tilt: extensive spatial extrapolation of orientation gradients

PubMed Central

Roach, Neil W.; Webb, Ben S.

2013-01-01

To extract the global structure of an image, the visual system must integrate local orientation estimates across space. Progress is being made toward understanding this integration process, but very little is known about whether the presence of structure exerts a reciprocal influence on local orientation coding. We have previously shown that adaptation to patterns containing circular or radial structure induces tilt-aftereffects (TAEs), even in locations where the adapting pattern was occluded. These spatially “remote” TAEs have novel tuning properties and behave in a manner consistent with adaptation to the local orientation implied by the circular structure (but not physically present) at a given test location. Here, by manipulating the spatial distribution of local elements in noisy circular textures, we demonstrate that remote TAEs are driven by the extrapolation of orientation structure over remarkably large regions of visual space (more than 20°). We further show that these effects are not specific to adapting stimuli with polar orientation structure, but require a gradient of orientation change across space. Our results suggest that mechanisms of visual adaptation exploit orientation gradients to predict the local pattern content of unfilled regions of space. PMID:23882243