ACID RAIN MODELING

EPA Science Inventory

This paper provides an overview of existing statistical methodologies for the estimation of site-specific and regional trends in wet deposition. The interaction of atmospheric processes and emissions tend to produce wet deposition data patterns that show large spatial and tempora...

Which limb is it? Responses to vibrotactile stimulation in early infancy.

PubMed

Somogyi, Eszter; Jacquey, Lisa; Heed, Tobias; Hoffmann, Matej; Lockman, Jeffrey J; Granjon, Lionel; Fagard, Jacqueline; O'Regan, J Kevin

2017-12-11

This study focuses on how the body schema develops during the first months of life, by investigating infants' motor responses to localized vibrotactile stimulation on their limbs. Vibrotactile stimulation was provided by small buzzers that were attached to the infants' four limbs one at a time. Four age groups were compared cross-sectionally (3-, 4-, 5-, and 6-month-olds). We show that before they actually reach for the buzzer, which, according to previous studies, occurs around 7-8 months of age, infants demonstrate emerging knowledge about their body's configuration by producing specific movement patterns associated with the stimulated body area. At 3 months, infants responded with an increase in general activity when the buzzer was placed on the body, independently of the vibrator's location. Differentiated topographical awareness of the body seemed to appear around 5 months, with specific responses resulting from stimulation of the hands emerging first, followed by the differentiation of movement patterns associated with the stimulation of the feet. Qualitative analyses revealed specific movement types reliably associated with each stimulated location by 6 months of age, possibly preparing infants' ability to actually reach for the vibrating target. We discuss this result in relation to newborns' ability to learn specific movement patterns through intersensory contingency. Statement of contribution what is already known on infants' sensorimotor knowledge about their own bodies 3-month-olds readily learn to produce specific limb movements to obtain a desired effect (movement of a mobile). infants detect temporal and spatial correspondences between events involving their own body and visual events. what the present study adds until 4-5 months of age, infants mostly produce general motor responses to localized touch. this is because in the present study, infants could not rely on immediate contingent feedback. we propose a cephalocaudal developmental trend of topographic differentiation of body areas. © 2017 The Authors British Journal of Developmental Psychology published by John Wiley & Sons Ltd on behalf of British Psychological Society.

Combinatorial wetting in colour: an optofluidic nose.

PubMed

Raymond, Kevin P; Burgess, Ian B; Kinney, Mackenzie H; Lončar, Marko; Aizenberg, Joanna

2012-10-07

We present a colourimetric litmus test for simple differentiation of organic liquids based on wetting, which achieves chemical specificity without a significant sacrifice in portability or ease-of-use. Chemical specificity is derived from the combination of colourimetric wetting patterns produced by liquids in an array of inverse opal films, each having a graded wettability, but using different surface groups to define that gradient.

Non-coaxial-based microwave ablation antennas for creating symmetric and asymmetric coagulation zones

NASA Astrophysics Data System (ADS)

Mohtashami, Yahya; Luyen, Hung; Hagness, Susan C.; Behdad, Nader

2018-06-01

We present an investigation of a new class of microwave ablation (MWA) antennas capable of producing axially symmetric or asymmetric heating patterns. The antenna design is based on a dipole fed by a balanced parallel-wire transmission line. The angle and direction of the deployed dipole arms are used to control the heating pattern. We analyzed the specific absorption rate and temperature profiles using electromagnetic and thermal simulations. Two prototypes were fabricated and tested in ex vivo ablation experiments: one was designed to produce symmetric heating patterns and the other was designed to generate asymmetric heating patterns. Both fabricated prototypes exhibited good impedance matching and produced localized coagulation zones as predicted by the simulations. The prototype operating in porcine muscle created an ˜10 cm3 symmetric ablation zone after 10 min of ablation with a power level of 18 W. The prototype operating in egg white created an ˜4 cm3 asymmetric ablation zone with a directionality ratio of 40% after 5 min of ablation with a power level of 25 W. The proposed MWA antenna design shows promise for minimally invasive treatment of tumors in various clinical scenarios where, depending on the situation, a symmetric or an asymmetric heating pattern may be needed.

Patterns for Effectively Documenting Frameworks

NASA Astrophysics Data System (ADS)

Aguiar, Ademar; David, Gabriel

Good design and implementation are necessary but not sufficient pre-requisites for successfully reusing object-oriented frameworks. Although not always recognized, good documentation is crucial for effective framework reuse, and often hard, costly, and tiresome, coming with many issues, especially when we are not aware of the key problems and respective ways of addressing them. Based on existing literature, case studies and lessons learned, the authors have been mining proven solutions to recurrent problems of documenting object-oriented frameworks, and writing them in pattern form, as patterns are a very effective way of communicating expertise and best practices. This paper presents a small set of patterns addressing problems related to the framework documentation itself, here seen as an autonomous and tangible product independent of the process used to create it. The patterns aim at helping non-experts on cost-effectively documenting object-oriented frameworks. In concrete, these patterns provide guidance on choosing the kinds of documents to produce, how to relate them, and which contents to include. Although the focus is more on the documents themselves, rather than on the process and tools to produce them, some guidelines are also presented in the paper to help on applying the patterns to a specific framework.

On Using the Weimer Statistical Model for Real-Time Ionospheric Specifications and Forecasts

NASA Astrophysics Data System (ADS)

Bekerat, H. A.; Schunk, R. W.; Scherliess, L.

2002-12-01

The Weimer statistical model (Weimer, 2001) for the high-latitude convection pattern was tested with regard to its ability to produce real-time convection patterns. This work is being conducted under the polar section of GAIM (Global Assimilation of Ionospheric Measurements). The method adopted involves the comparison of the cross-track ion drift velocities measured by DMSP satellites with those calculated from the Weimer model. Starting with a Weimer pattern obtained using real-time IMF and solar wind data at the time of a DMSP satellite pass in the high-latitude ionosphere, the cross-track ion drift velocities along the DMSP track were calculated from the Weimer convection model and compared to those measured by the DMSP satellite. Then, in order to improve the agreement between the measurement and the model, two of the input parameters to the model, the IMF clock-angle and the solar wind speed, were varied to get the pattern that gives the best agreement with the DMSP satellite measurements. Four months of data (March, July, September, and December 1998) were used to test the Weimer model. The result shows that the agreement between the measurement and the Weimer model is improved by using this procedure. The Weimer model is good in a statistical sense, it was able to produce the large-scale structure in most cases. However, it is not good enough to be used for real-time ionospheric specifications and forecasts because it failed to produce a lot of the mesoscale structure measured along most DMSP satellite passes. Reference Weimer, D. R., J. Geophys. Res., 106, 407,2001

Research Women’s Shirt Production

DTIC Science & Technology

1992-04-17

there was no sense in producing, for fit or wear test, garments which were inherently imprecise due to pattern problems. The resulting discoveries pointed...the approval of additional prototypes, 48 shirts were produced. Detailed garment dimension specification ;charts were provided for future quality...the industry at large, surfaced and were addressed. 14. SUai CRMS IS. NUMHE OR PAGES 25 Apparel manufacturing, women’s shirts C RO’ 17. SECURITY

Segmentally distributed metamorphic changes in neural circuits controlling abdominal bending in the hawk moth Manduca sexta.

PubMed

Lemon, W C; Levine, R B

1997-06-01

During the metamorphosis of Manduca sexta the larval nervous system is reorganized to allow the generation of behaviors that are specific to the pupal and adult stages. In some instances, metamorphic changes in neurons that persist from the larval stage are segment-specific and lead to expression of segment-specific behavior in later stages. At the larval-pupal transition, the larval abdominal bending behavior, which is distributed throughout the abdomen, changes to the pupal gin trap behavior which is restricted to three abdominal segments. This study suggests that the neural circuit that underlies larval bending undergoes segment specific modifications to produce the segmentally restricted gin trap behavior. We show, however, that non-gin trap segments go through a developmental change similar to that seen in gin trap segments. Pupal-specific motor patterns are produced by stimulation of sensory neurons in abdominal segments that do not have gin traps and cannot produce the gin trap behavior. In particular, sensory stimulation in non-gin trap pupal segments evokes a motor response that is faster than the larval response and that displays the triphasic contralateral-ipsilateral-contralateral activity pattern that is typical of the pupal gin trap behavior. Despite the alteration of reflex activity in all segments, developmental changes in sensory neuron morphology are restricted to those segments that form gin traps. In non-gin trap segments, persistent sensory neurons do not expand their terminal arbors, as do sensory neurons in gin trap segments, yet are capable of eliciting gin trap-like motor responses.

Identification of hemolysin BL-producing Bacillus cereus isolates by a discontinuous hemolytic pattern in blood agar.

PubMed Central

Beecher, D J; Wong, A C

1994-01-01

Bacillus cereus causes distinct exotoxin-mediated diarrheal and emetic food poisoning syndromes and a variety of nongastrointestinal infections. Evidence is accumulating that hemolysin BL is a major B. cereus virulence factor. We describe two methods for detection of hemolysin BL in crude samples and on primary culture media. In the first method, the highly unusual discontinuous hemolysis pattern that is characteristic of pure hemolysin BL was produced in sheep and calf blood agar around wells filled with crude culture supernatant from hemolysin BL-producing strains. In the second method, the pattern was formed surrounding colonies of hemolysin BL-producing strains grown on media consisting of nutrient agar, 0.15 M NaCl, 2% calf serum, and sheep or calf blood. Hemolysin BL production was detected with these methods in 41 of 62 (66%) previously identified B. cereus isolates and in 46 of 136 (34%) presumptive B. cereus isolates from soil. All nine isolates tested that were associated with diarrhea or nongastrointestinal illness were positive for hemolysin BL. The methods presented here are specific, simple, inexpensive, and applicable to the screening of large numbers of samples or isolates. Images PMID:8017944

On the role of the reticular formation in vocal pattern generation.

PubMed

Jürgens, Uwe; Hage, Steffen R

2007-09-04

This review is an attempt to localize the brain region responsible for pattern generation of species-specific vocalizations. A catalogue is set up, listing the criteria considered to be essential for a vocal pattern generator. According to this catalogue, a vocal pattern generator should show vocalization-correlated activity, starting before vocal onset and reflecting specific acoustic features of the vocalization. Artificial activation by electrical or glutamatergic stimulation should produce artificially sounding vocalization. Lesioning is expected to have an inhibitory or deteriorating effect on vocalization. Anatomically, a vocal pattern generator can be assumed to have direct or, at least, oligosynaptic connections with all the motoneuron pools involved in phonation. A survey of the literature reveals that the only area meeting all these criteria is a region, reaching from the parvocellular pontine reticular formation just above the superior olive through the lateral reticular formation around the facial nucleus and nucleus ambiguus down to the caudalmost medulla, including the dorsal and ventral reticular nuclei and nucleus retroambiguus. It is proposed that vocal pattern generation takes place within this whole region.

Experimental study of surface pattern effects on the propulsive performance and wake of a bio-inspired pitching panel

NASA Astrophysics Data System (ADS)

King, Justin; Kumar, Rajeev; Green, Melissa

2016-11-01

Force measurements and stereoscopic particle image velocimetry (PIV) were used to characterize the propulsive performance and wake structure of rigid, bio-inspired trapezoidal pitching panels. In the literature, it has been demonstrated that quantities such as thrust coefficient and propulsive efficiency are affected by changes in the surface characteristics of a pitching panel or foil. More specifically, the variation of surface pattern produces significant changes in wake structure and dynamics, especially in the distribution of vorticity in the wake. Force measurements and PIV data were collected for multiple surface patterns chosen to mimic fish surface morphology over a Strouhal number range of 0.17 to 0.56. Performance quantities are compared with the three-dimensional vortex wake structure for both the patterned and smooth panels to determine the nature and magnitude of surface pattern effects in terms of thrust produced, drag reduced, and wake vortices reshaped and reorganized. This work was supported by the Office of Naval Research under ONR Award No. N00014-14-1-0418.

The Role of Frequency in Learning Morphophonological Alternations: Implications for Children With Specific Language Impairment

PubMed Central

Demuth, Katherine; Petocz, Peter

2017-01-01

Purpose The aim of this article was to explore how the type of allomorph (e.g., past tense buzz[d] vs. nod[əd]) influences the ability to perceive and produce grammatical morphemes in children with typical development and with specific language impairment (SLI). Method The participants were monolingual Australian English–speaking children. The SLI group included 13 participants (mean age = 5;7 [years;months]); the control group included 19 children with typical development (mean age = 5;4). Both groups performed a grammaticality judgment and elicited production task with the same set of nonce verbs in third-person singular and past tense forms. Results Five-year-old children are still learning to generalize morphophonological patterns to novel verbs, and syllabic /əz/ and /əd/ allomorphs are significantly more challenging to produce, particularly for the SLI group. The greater phonetic content of these syllabic forms did not enhance perception. Conclusions Acquisition of morphophonological patterns involving low-frequency allomorphs is still underway in 5-year-old children with typical development, and it is even more protracted in SLI populations, despite these patterns being highly predictable. Children with SLI will therefore benefit from targeted intervention with low-frequency allomorphs. PMID:28510615

Fiducial marker for correlating images

DOEpatents

Miller, Lisa Marie [Rocky Point, NY; Smith, Randy J [Wading River, NY; Warren, John B [Port Jefferson, NY; Elliott, Donald [Hampton Bays, NY

2011-06-21

The invention relates to a fiducial marker having a marking grid that is used to correlate and view images produced by different imaging modalities or different imaging and viewing modalities. More specifically, the invention relates to the fiducial marking grid that has a grid pattern for producing either a viewing image and/or a first analytical image that can be overlaid with at least one other second analytical image in order to view a light path or to image different imaging modalities. Depending on the analysis, the grid pattern has a single layer of a certain thickness or at least two layers of certain thicknesses. In either case, the grid pattern is imageable by each imaging or viewing modality used in the analysis. Further, when viewing a light path, the light path of the analytical modality cannot be visualized by viewing modality (e.g., a light microscope objective). By correlating these images, the ability to analyze a thin sample that is, for example, biological in nature but yet contains trace metal ions is enhanced. Specifically, it is desired to analyze both the organic matter of the biological sample and the trace metal ions contained within the biological sample without adding or using extrinsic labels or stains.

Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize.

PubMed

Selinger, D A; Chandler, V L

1999-12-21

The b locus encodes a transcription factor that regulates the expression of genes that produce purple anthocyanin pigment. Different b alleles are expressed in distinct tissues, causing tissue-specific anthocyanin production. Understanding how phenotypic diversity is produced and maintained at the b locus should provide models for how other regulatory genes, including those that influence morphological traits and development, evolve. We have investigated how different levels and patterns of pigmentation have evolved by determining the phenotypic and evolutionary relationships between 18 alleles that represent the diversity of b alleles in Zea mays. Although most of these alleles have few phenotypic differences, five alleles have very distinct tissue-specific patterns of pigmentation. Superimposing the phenotypes on the molecular phylogeny reveals that the alleles with strong and distinctive patterns of expression are closely related to alleles with weak expression, implying that the distinctive patterns have arisen recently. We have identified apparent insertions in three of the five phenotypically distinct alleles, and the fourth has unique upstream restriction fragment length polymorphisms relative to closely related alleles. The insertion in B-Peru has been shown to be responsible for its unique expression and, in the other two alleles, the presence of the insertion correlates with the phenotype. These results suggest that major changes in gene expression are probably the result of large-scale changes in DNA sequence and/or structure most likely mediated by transposable elements.

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.

Patterned corneal collagen crosslinking for astigmatism: Computational modeling study

PubMed Central

Seven, Ibrahim; Roy, Abhijit Sinha; Dupps, William J.

2014-01-01

PURPOSE To test the hypothesis that spatially selective corneal stromal stiffening can alter corneal astigmatism and assess the effects of treatment orientation, pattern, and material model complexity in computational models using patient-specific geometries. SETTING Cornea and Refractive Surgery Service, Academic Eye Institute, Cleveland, Ohio, USA. DESIGN Computational modeling study. METHODS Three-dimensional corneal geometries from 10 patients with corneal astigmatism were exported from a clinical tomography system (Pentacam). Corneoscleral finite element models of each eye were generated. Four candidate treatment patterns were simulated, and the effects of treatment orientation and magnitude of stiffening on anterior curvature and aberrations were studied. The effect of material model complexity on simulated outcomes was also assessed. RESULTS Pretreatment anterior corneal astigmatism ranged from 1.22 to 3.92 diopters (D) in a series that included regular and irregular astigmatic patterns. All simulated treatment patterns oriented on the flat axis resulted in mean reductions in corneal astigmatism and depended on the pattern geometry. The linear bow-tie pattern produced a greater mean reduction in astigmatism (1.08 D ± 0.13 [SD]; range 0.74 to 1.23 D) than other patterns tested under an assumed 2-times increase in corneal stiffness, and it had a nonlinear relationship to the degree of stiffening. The mean astigmatic effect did not change significantly with a fiber- or depth-dependent model, but it did affect the coupling ratio. CONCLUSIONS In silico simulations based on patient-specific geometries suggest that clinically significant reductions in astigmatism are possible with patterned collagen crosslinking. Effect magnitude was dependent on patient-specific geometry, effective stiffening pattern, and treatment orientation. PMID:24767795

Diversity of the Arabidopsis mitochondrial genome occurs via nuclear-controlled recombination activity.

PubMed

Arrieta-Montiel, Maria P; Shedge, Vikas; Davila, Jaime; Christensen, Alan C; Mackenzie, Sally A

2009-12-01

The plant mitochondrial genome is recombinogenic, with DNA exchange activity controlled to a large extent by nuclear gene products. One nuclear gene, MSH1, appears to participate in suppressing recombination in Arabidopsis at every repeated sequence ranging in size from 108 to 556 bp. Present in a wide range of plant species, these mitochondrial repeats display evidence of successful asymmetric DNA exchange in Arabidopsis when MSH1 is disrupted. Recombination frequency appears to be influenced by repeat sequence homology and size, with larger size repeats corresponding to increased DNA exchange activity. The extensive mitochondrial genomic reorganization of the msh1 mutant produced altered mitochondrial transcription patterns. Comparison of mitochondrial genomes from the Arabidopsis ecotypes C24, Col-0, and Ler suggests that MSH1 activity accounts for most or all of the polymorphisms distinguishing these genomes, producing ecotype-specific stoichiometric changes in each line. Our observations suggest that MSH1 participates in mitochondrial genome evolution by influencing the lineage-specific pattern of mitochondrial genetic variation in higher plants.

Cell signals allow the expression of a pre-existent neural pattern in C. elegans.

PubMed

Waring, D A; Wrischnik, L; Kenyon, C

1992-10-01

In C. elegans, a simple pattern develops within a row of epidermal precursor cells, V1-V6. One cell, V5, gives rise to a neuroblast called the postdeirid neuroblast, while the other V cells produce epidermal cells instead. Here we describe experiments suggesting that in order for V5 to produce the postdeirid it must be in close or direct contact with neighboring V cells. Signaling between V cells is required for the formation of the neuroblast; however, which of the V cells can make a postdeirid is not determined by these signals but rather by the action of the homeotic lin-22 and pal-1 genes. These genes prevent V cells in specific body regions from responding to intercellular signals and producing postdeirids. This is a clear example of cell signals playing a permissive rather than an instructive role in neuroblast induction.

The relationship of metabolic burden to productivity levels in CHO cell lines.

PubMed

Zou, Wu; Edros, Raihana; Al-Rubeai, Mohamed

2018-03-01

The growing demand for recombinant therapeutics has driven biotechnologists to develop new production strategies. One such strategy for increasing the expression of heterologous proteins has focused on enhancing cell-specific productivity through environmental perturbations. In this work, the effects of hypothermia, hyperosmolarity, high shear stress, and sodium butyrate treatment on growth and productivity were studied using three (low, medium, and high producing) CHO cell lines that differed in their specific productivities of monoclonal antibody. In all three cell lines, the inhibitory effect of these parameters on proliferation was demonstrated. Additionally, compared to the control, specific productivity was enhanced under all conditions and exhibited a consistent cell line specific pattern, with maximum increases (50-290%) in the low producer, and minimum increases (7-20%) in the high producer. Thus, the high-producing cell line was less responsive to environmental perturbations than the low-producing cell line. We hypothesize that this difference is most likely due to the bottleneck associated with a higher metabolic burden caused by higher antibody expression. Increased recombinant mRNA levels and pyruvate carboxylase activities due to low temperature and hyperosmotic stress were found to be positively associated with the metabolic burden. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

Synthesis in Science.

ERIC Educational Resources Information Center

Horsella, Maria

This paper discusses various techniques that scientists and other professionals can use to keep current in their field despite the large amount of available information, such as consulting abstracts, indexes, reviews, and catalogues. It also examines specific language patterns that are used in the sciences to produce synthesis and abridgement,…

β-Catenin is essential for patterning the maternally specified animal-vegetal axis in the sea urchin embryo

PubMed Central

Wikramanayake, Athula H.; Huang, Ling; Klein, William H.

1998-01-01

In sea urchin embryos, the animal-vegetal axis is specified during oogenesis. After fertilization, this axis is patterned to produce five distinct territories by the 60-cell stage. Territorial specification is thought to occur by a signal transduction cascade that is initiated by the large micromeres located at the vegetal pole. The molecular mechanisms that mediate the specification events along the animal–vegetal axis in sea urchin embryos are largely unknown. Nuclear β-catenin is seen in vegetal cells of the early embryo, suggesting that this protein plays a role in specifying vegetal cell fates. Here, we test this hypothesis and show that β-catenin is necessary for vegetal plate specification and is also sufficient for endoderm formation. In addition, we show that β-catenin has pronounced effects on animal blastomeres and is critical for specification of aboral ectoderm and for ectoderm patterning, presumably via a noncell-autonomous mechanism. These results support a model in which a Wnt-like signal released by vegetal cells patterns the early embryo along the animal–vegetal axis. Our results also reveal similarities between the sea urchin animal–vegetal axis and the vertebrate dorsal–ventral axis, suggesting that these axes share a common evolutionary origin. PMID:9689082

Adult-specific insulin-producing neurons in Drosophila melanogaster.

PubMed

Ohhara, Yuya; Kobayashi, Satoru; Yamakawa-Kobayashi, Kimiko; Yamanaka, Naoki

2018-06-01

Holometabolous insects undergo metamorphosis to reorganize their behavioral and morphological features into adult-specific ones. In the central nervous system (CNS), some larval neurons undergo programmed cell death, whereas others go through remodeling of axonal and dendritic arbors to support functions of re-established adult organs. Although there are multiple neuropeptides that have stage-specific roles in holometabolous insects, the reorganization pattern of the entire neuropeptidergic system through metamorphosis still remains largely unclear. In this study, we conducted a mapping and lineage tracing of peptidergic neurons in the larval and adult CNS by using Drosophila genetic tools. We found that Diuretic hormone 44-producing median neurosecretory cells start expressing Insulin-like peptide 2 in the pharate adult stage. This neuronal cluster projects to the corpora cardiaca and dorsal vessel in both larval and adult stages, and also innervates an adult-specific structure in the digestive tract, the crop. We propose that the adult-specific insulin-producing cells may regulate functions of the digestive system in a stage-specific manner. Our study provides a neuroanatomical basis for understanding remodeling of the neuropeptidergic system during insect development and evolution. © 2018 Wiley Periodicals, Inc.

MapFactory - Towards a mapping design pattern for big geospatial data

NASA Astrophysics Data System (ADS)

Rautenbach, Victoria; Coetzee, Serena

2018-05-01

With big geospatial data emerging, cartographers and geographic information scientists have to find new ways of dealing with the volume, variety, velocity, and veracity (4Vs) of the data. This requires the development of tools that allow processing, filtering, analysing, and visualising of big data through multidisciplinary collaboration. In this paper, we present the MapFactory design pattern that will be used for the creation of different maps according to the (input) design specification for big geospatial data. The design specification is based on elements from ISO19115-1:2014 Geographic information - Metadata - Part 1: Fundamentals that would guide the design and development of the map or set of maps to be produced. The results of the exploratory research suggest that the MapFactory design pattern will help with software reuse and communication. The MapFactory design pattern will aid software developers to build the tools that are required to automate map making with big geospatial data. The resulting maps would assist cartographers and others to make sense of big geospatial data.

Misconceptions regarding the pathogenicity of silicas and silicates.

PubMed

Feigin, D S

1989-01-01

Several inhaled substances, from occupational or other environmental exposure, produce significant pulmonary disease and abnormalities demonstrated by pulmonary imaging. Areas of controversy and misconception relate principally to the extent and nature of both the clinical disease and the imaging abnormalities specific to each substance. The size and shape of the inhaled particles is an important determinant of the nature and severity of the disease produced, with fibrous shapes usually being the most pathogenetic. Fibrogenicity is another important pathogenetic characteristic of talc and kaolin, as well as asbestos. Talc produces four distinct forms of pulmonary disease, depending not only on the other substances with which it is inhaled, but also whether it is inhaled or injected intravenously. When inhaled alone, talc does not appear to produce significant pulmonary fibrosis or malignancy. Kaolin, mica, fuller's earth, zeolite, and fiberglass all vary in disease production according to their shape and fibrogenicity. Silica, diatomaceous earth, and other forms of silica are all highly fibrogenic and thus produce clinically obvious disease with sufficient inhalation. The largest particles usually produce nodular patterns in the upper pulmonary fields, as is typical of silicosis. The fibrous particles are more likely to manifest themselves as interstitial patterns in the lower pulmonary fields.

Embryonic control of epidermal cell patterning in the root and hypocotyl of Arabidopsis.

PubMed

Lin, Y; Schiefelbein, J

2001-10-01

A position-dependent pattern of epidermal cell types is produced during the development of the Arabidopsis seedling root and hypocotyl. To understand the origin and regulation of this patterning mechanism, we have examined the embryonic expression of the GLABRA2 (GL2) gene, which encodes a cell-type-specific transcription factor. Using in situ RNA hybridization and a sensitive GL2::GFP reporter, we discovered that a position-dependent pattern of GL2 expression is established within protodermal cells at the heart stage and is maintained throughout the remainder of embryogenesis. In addition, we show that an exceptional GL2 expression character and epidermal cell pattern arises during development of the root-hypocotyl junction, which represents an anatomical transition zone. Furthermore, we find that two of the genes regulating seedling epidermal patterning, TRANSPARENT TESTA GLABRA (TTG) and WEREWOLF (WER), also control the embryonic GL2 pattern, whereas the CAPRICE (CPC) and GL2 genes are not required to establish this pattern. These results indicate that position-dependent patterning of epidermal cell types begins at an early stage of embryogenesis, before formation of the apical meristems and shortly after the cellular anatomy of the protoderm and outer ground tissue layer is established. Thus, epidermal cell specification in the Arabidopsis seedling relies on the embryonic establishment of a patterning mechanism that is perpetuated postembryonically.

Forces Affecting Educational Decisions.

ERIC Educational Resources Information Center

Sullivan, Neil V.

This speech begins with a discussion of broad social and political patterns and trends that are currently developing and continues to the specific unresolved social issues which will affect the nature and structure of educational systems. Those issues seen by the author is most likely to produce the greatest amount of activity are integration, the…

The Product as Change Agent: The Process of Development.

ERIC Educational Resources Information Center

Bank, Adrianne

Instructional product development--the purpose of which has been to create materials which produce in an identified population of users demonstrable changes in behavior, in accordance with prespecified and specific objectives--generally adheres to a pattern which includes planning, formulating, prototyping measures and materials, field testing,…

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.

Fast fringe pattern phase demodulation using FIR Hilbert transformers

NASA Astrophysics Data System (ADS)

Gdeisat, Munther; Burton, David; Lilley, Francis; Arevalillo-Herráez, Miguel

2016-01-01

This paper suggests the use of FIR Hilbert transformers to extract the phase of fringe patterns. This method is computationally faster than any known spatial method that produces wrapped phase maps. Also, the algorithm does not require any parameters to be adjusted which are dependent upon the specific fringe pattern that is being processed, or upon the particular setup of the optical fringe projection system that is being used. It is therefore particularly suitable for full algorithmic automation. The accuracy and validity of the suggested method has been tested using both computer-generated and real fringe patterns. This novel algorithm has been proposed for its advantages in terms of computational processing speed as it is the fastest available method to extract the wrapped phase information from a fringe pattern.

Revealing the source of the radial flow patterns in proton-proton collisions using hard probes

NASA Astrophysics Data System (ADS)

Ortiz, Antonio; Bencédi, Gyula; Bello, Héctor

2017-06-01

In this work, we propose a tool to reveal the origin of the collective-like phenomena observed in proton-proton collisions. We exploit the fundamental difference between the underlying mechanisms, color reconnection and hydrodynamics, which produce radial flow patterns in Pythia 8 and Epos 3, respectively. Specifically, we proceed by examining the strength of the coupling between the soft and hard components which, by construction, is larger in Pythia 8 than in Epos 3. We study the transverse momentum ({p}{{T}}) distributions of charged pions, kaons and (anti) protons in inelastic pp collisions at \\sqrt{s}=7 TeV produced at mid-rapidity. Specific selections are made on an event-by-event basis as a function of the charged particle multiplicity and the transverse momentum of the leading jet ({p}{{T}}{jet}) reconstructed using the FastJet algorithm at mid-pseudorapidity (| η | < 1). From our studies, quantitative and qualitative differences between Pythia 8 and Epos 3 are found in the {p}{{T}} spectra when (for a given multiplicity class) the leading jet {p}{{T}} is increased. In addition, we show that for low-multiplicity events the presence of jets can produce radial flow-like behavior. Motivated by our findings, we propose to perform a similar analysis using experimental data from RHIC and LHC.

Directional constraint of endpoint force emerges from hindlimb anatomy.

PubMed

Bunderson, Nathan E; McKay, J Lucas; Ting, Lena H; Burkholder, Thomas J

2010-06-15

Postural control requires the coordination of force production at the limb endpoints to apply an appropriate force to the body. Subjected to horizontal plane perturbations, quadruped limbs stereotypically produce force constrained along a line that passes near the center of mass. This phenomenon, referred to as the force constraint strategy, may reflect mechanical constraints on the limb or body, a specific neural control strategy or an interaction among neural controls and mechanical constraints. We used a neuromuscular model of the cat hindlimb to test the hypothesis that the anatomical constraints restrict the mechanical action of individual muscles during stance and constrain the response to perturbations to a line independent of perturbation direction. In a linearized neuromuscular model of the cat hindlimb, muscle lengthening directions were highly conserved across 10,000 different muscle activation patterns, each of which produced an identical, stance-like endpoint force. These lengthening directions were closely aligned with the sagittal plane and reveal an anatomical structure for directionally constrained force responses. Each of the 10,000 activation patterns was predicted to produce stable stance based on Lyapunov stability analysis. In forward simulations of the nonlinear, seven degree of freedom model under the action of 200 random muscle activation patterns, displacement of the endpoint from its equilibrium position produced restoring forces, which were also biased toward the sagittal plane. The single exception was an activation pattern based on minimum muscle stress optimization, which produced destabilizing force responses in some perturbation directions. The sagittal force constraint increased during simulations as the system shifted from an inertial response during the acceleration phase to a viscoelastic response as peak velocity was obtained. These results qualitatively match similar experimental observations and suggest that the force constraint phenomenon may result from the anatomical arrangement of the limb.

Directional constraint of endpoint force emerges from hindlimb anatomy

PubMed Central

Bunderson, Nathan E.; McKay, J. Lucas; Ting, Lena H.; Burkholder, Thomas J.

2010-01-01

Postural control requires the coordination of force production at the limb endpoints to apply an appropriate force to the body. Subjected to horizontal plane perturbations, quadruped limbs stereotypically produce force constrained along a line that passes near the center of mass. This phenomenon, referred to as the force constraint strategy, may reflect mechanical constraints on the limb or body, a specific neural control strategy or an interaction among neural controls and mechanical constraints. We used a neuromuscular model of the cat hindlimb to test the hypothesis that the anatomical constraints restrict the mechanical action of individual muscles during stance and constrain the response to perturbations to a line independent of perturbation direction. In a linearized neuromuscular model of the cat hindlimb, muscle lengthening directions were highly conserved across 10,000 different muscle activation patterns, each of which produced an identical, stance-like endpoint force. These lengthening directions were closely aligned with the sagittal plane and reveal an anatomical structure for directionally constrained force responses. Each of the 10,000 activation patterns was predicted to produce stable stance based on Lyapunov stability analysis. In forward simulations of the nonlinear, seven degree of freedom model under the action of 200 random muscle activation patterns, displacement of the endpoint from its equilibrium position produced restoring forces, which were also biased toward the sagittal plane. The single exception was an activation pattern based on minimum muscle stress optimization, which produced destabilizing force responses in some perturbation directions. The sagittal force constraint increased during simulations as the system shifted from an inertial response during the acceleration phase to a viscoelastic response as peak velocity was obtained. These results qualitatively match similar experimental observations and suggest that the force constraint phenomenon may result from the anatomical arrangement of the limb. PMID:20511528

Contribution to an effective design method for stationary reaction-diffusion patterns.

PubMed

Szalai, István; Horváth, Judit; De Kepper, Patrick

2015-06-01

The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences.

Predispositions to approach and avoid are contextually sensitive and goal dependent.

PubMed

Bamford, Susan; Ward, Robert

2008-04-01

The authors show that predispositions to approach and avoid do not consist simply of specific motor patterns but are more abstract functions that produce a desired environmental effect. It has been claimed that evaluating a visual stimulus as positive or negative evokes a specific motor response, extending the arm to negative stimuli, and contracting to positive stimuli. The authors showed that a large congruency effect (participants were faster to approach pleasant and avoid unpleasant stimuli, than to approach unpleasant and avoid pleasant stimuli) could be produced on a novel touchscreen paradigm (Experiment 1), and that the congruency effect could be reversed by spatial (Experiment 2) and nonspatial (Experiment 3) response effects. Thus, involuntary approach and avoid response activations are not fixed, but sensitive to context, and are specifically based on the desired goal. (Copyright) 2008 APA.

Imitation and Creativity: Beneficial Effects of Propulsion Strategies and Specificity

ERIC Educational Resources Information Center

Mecca, Jensen T.; Mumford, Michael D.

2014-01-01

Prior studies examining imitation of exemplar solutions have produced a mixed pattern of findings with some studies indicating that exemplar imitation contributes to creative problem-solving and other studies indicating that it may inhibit creative problem-solving. In the present effort, it is argued that the effects of exemplar imitation on…

Use of artificial landscapes to isolate controls on burn probability

Treesearch

Marc-Andre Parisien; Carol Miller; Alan A. Ager; Mark A. Finney

2010-01-01

Techniques for modeling burn probability (BP) combine the stochastic components of fire regimes (ignitions and weather) with sophisticated fire growth algorithms to produce high-resolution spatial estimates of the relative likelihood of burning. Despite the numerous investigations of fire patterns from either observed or simulated sources, the specific influence of...

Dysphonia Detected by Pattern Recognition of Spectral Composition.

ERIC Educational Resources Information Center

Leinonen, Lea; And Others

1992-01-01

This study analyzed production of a long vowel sound within Finnish words by normal or dysphonic voices, using the Self-Organizing Map, the artificial neural network algorithm of T. Kohonen which produces two-dimensional representations of speech. The method was found to be both sensitive and specific in the detection of dysphonia. (Author/JDD)

Fabrication of n-type Si nanostructures by direct nanoimprinting with liquid-Si ink

NASA Astrophysics Data System (ADS)

Takagishi, Hideyuki; Masuda, Takashi; Yamazaki, Ken; Shimoda, Tatsuya

2018-01-01

Nanostructures of n-type amorphous silicon (a-Si) and polycrystalline silicon (poly-Si) with a height of 270 nm and line widths of 110-165 nm were fabricated directly onto a substrate through a simple imprinting process that does not require vacuum conditions or photolithography. The n-type Liquid-Si ink was synthesized via photopolymerization of cyclopentasilane (Si5H10) and white phosphorus (P4). By raising the temperature from 160 °C to 200 °C during the nanoimprinting process, well-defined angular patterns were fabricated without any cracking, peeling, or deflections. After the nanoimprinting process, a-Si was produced by heating the nanostructures at 400°C-700 °C, and poly-Si was produced by heating at 800 °C. The dopant P diffuses uniformly in the Si films, and its concentration can be controlled by varying the concentration of P4 in the ink. The specific resistance of the n-type poly-Si pattern was 7.0 × 10-3Ω ṡ cm, which is comparable to the specific resistance of flat n-type poly-Si films.

An Unusual Role for doublesex in Sex Determination in the Dipteran Sciara.

PubMed

Ruiz, María Fernanda; Alvarez, Mercedes; Eirín-López, José M; Sarno, Francesca; Kremer, Leonor; Barbero, José L; Sánchez, Lucas

2015-08-01

The gene doublesex, which is placed at the bottom of the sex-determination gene cascade, plays the ultimate discriminatory role for sex determination in insects. In all insects where this gene has been characterized, the dsx premessenger RNA (pre-mRNA) follows a sex-specific splicing pattern, producing male- and female-specific mRNAs encoding the male-DSXM and female-DSXF proteins, which determine male and female development, respectively. This article reports the isolation and characterization of the gene doublesex of dipteran Sciara insects. The Sciara doublesex gene is constitutively transcribed during development and adult life of males and females. Sciara had no sex-specific doublesex mRNAs but the same transcripts, produced by alternative splicing of its primary transcript, were present in both sexes, although their relative abundance is sex specific. However, only the female DSXF protein, but not the male DSXM protein, was produced at similar amounts in both sexes. An analysis of the expression of female and male Sciara DSX proteins in Drosophila showed that these proteins conserved female and male function, respectively, on the control of Drosophila yolk-protein genes. The molecular evolution of gene doublesex of all insects where this gene has been characterized revealed that Sciara doublesex displays a considerable degree of divergence in its molecular organization and its splicing pattern with respect to the rest of dipterans as suggested by its basal position within the doublesex phylogeny. It is suggested that the doublesex gene is involved in Sciara sex determination although it appears not to play the discriminatory role performed in other insects. Copyright © 2015 by the Genetics Society of America.

ZnO Nanostructure Templates as a Cost-Efficient Mass-Producible Route for the Development of Cellular Networks

PubMed Central

Makarona, Eleni; Peter, Beatrix; Szekacs, Inna; Tsamis, Christos; Horvath, Robert

2016-01-01

The development of artificial surfaces which can regulate or trigger specific functions of living cells, and which are capable of inducing in vivo-like cell behaviors under in vitro conditions has been a long-sought goal over the past twenty years. In this work, an alternative, facile and cost-efficient method for mass-producible cellular templates is presented. The proposed methodology consists of a cost-efficient, two-step, all-wet technique capable of producing ZnO-based nanostructures on predefined patterns on a variety of substrates. ZnO—apart from the fact that it is a biocompatible material—was chosen because of its multifunctional nature which has rendered it a versatile material employed in a wide range of applications. Si, Si3N4, emulated microelectrode arrays and conventional glass cover slips were patterned at the micrometer scale and the patterns were filled with ZnO nanostructures. Using HeLa cells, we demonstrated that the fabricated nanotopographical features could promote guided cellular adhesion on the pre-defined micron-scale patterns only through nanomechanical cues without the need for further surface activation or modification. The basic steps of the micro/nanofabrication are presented and the results from the cell adhesion experiments are discussed, showing the potential of the suggested methodology for creating low-cost templates for engineered cellular networks. PMID:28773382

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.

Sources of and Remedies for Removing Unwanted Reflections in Millimeter Wave Images of Complex SOFI-Covered Space Shuttle Structures

NASA Technical Reports Server (NTRS)

Kharkovsky, S.; Zoughi, R.; Hepburn, Frank L.

2007-01-01

In the recent years, continuous-wave near-field and lens-focused millimeter wave imaging systems have been effectively used to demonstrate their utility for producing high-resolution images of metallic structures covered with spay on foam insulation (SOFI) such as the Space Shuttle external fuel tank. However, for some specific structures a certain interference -pattern may be superimposed on the produced images. There are methods by which the influence of this unwanted interference can be reduced, such as the incorporation of an incidence .angle and the proper use of signal polarization. This paper presents the basics of this problem and describes the use of the methods for reducing this unwanted influence through specific examples.

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

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

Angiocrine functions of organ-specific endothelial cells

PubMed Central

Rafii, Shahin; Butler, Jason M; Ding, Bi-Sen

2016-01-01

Preface Endothelial cells lining blood vessel capillaries are not just passive conduits for delivering blood. Tissue-specific endothelium establish specialized vascular niches that deploy specific sets of growth factors, known as angiocrine factors, which actively participate in inducing, specifying, patterning, and guiding organ regeneration and maintaining homeostasis and metabolism. Angiocrine factors upregulated in response to injury orchestrates self-renewal and differentiation of tissue-specific repopulating resident stem and progenitor cells into functional organs. Uncovering the precise mechanisms whereby physiological-levels of angiocrine factors are spatially and temporally produced, and distributed by organotypic endothelium to repopulating cells, will lay the foundation for driving organ repair without scarring. PMID:26791722

Developmental and communicative factors affecting VOT production in English and Arabic bilingual and monolingual speakers

NASA Astrophysics Data System (ADS)

Khattab, Ghada

2004-05-01

VOT patterns were investigated in the production of three Lebanese-English bilinguals' aged 5, 7, and 10, six aged-matched monolingual controls from the bilinguals' immediate communities, and the parents of bilinguals and monolinguals. The aim was to examine the extent to which children exposed to two languages acquire separate VOT patterns for each language and to determine the factors that affect such acquisition. Results showed that VOT patterns for each bilingual child differed significantly across the two languages. But while the contrast in English resembled a monolingual-like model, that for Arabic exhibited persisting developmental features; explanations were offered in terms of the relationship between input and complexity of voicing lead production. Evidence was used from developmental changes that were noted for two of the bilingual subjects over a period of 18 months. English code-switches produced by the bilinguals during Arabic sessions exhibited different VOT patterns from those produced during English sessions, which underlined the importance of taking the language context into consideration. Finally, results from monolinguals and bilinguals showed that the short lag categories for the two languages were different despite a degree of overlap. Such findings require finer divisions of the three universal VOT categories to account for language-specific patterns.

Recognition of plant parts with problem-specific algorithms

NASA Astrophysics Data System (ADS)

Schwanke, Joerg; Brendel, Thorsten; Jensch, Peter F.; Megnet, Roland

1994-06-01

Automatic micropropagation is necessary to produce cost-effective high amounts of biomass. Juvenile plants are dissected in clean- room environment on particular points on the stem or the leaves. A vision-system detects possible cutting points and controls a specialized robot. This contribution is directed to the pattern- recognition algorithms to detect structural parts of the plant.

Identifying Regulators of the Immune Response to Dying Cells | Center for Cancer Research

Cancer.gov

Cytotoxic T cells are responsible for carrying out antigen-mediated immune responses against virally-infected and malignant cells. In both cases, cytotoxic T cells are stimulated by interacting with antigen presenting cells, such as dendritic cells (DCs). Infected cells produce virus-specific antigens and pathogen associated molecular patterns, which are recognized by DCs and

Analyzing Public Discourse: Using Media Content Analysis to Understand the Policy Process

ERIC Educational Resources Information Center

Saraisky, Nancy Green

2016-01-01

One of the most basic and obvious sources of data for education policy analysis is text. This article discusses content analysis as an important part of the methodological toolbox for elucidating patterns and trends about education policy. Focusing specifically on media, I show how media content analysis can produce nuanced insights about the ways…

Maintaining embryonic stem cell pluripotency with Wnt signaling.

PubMed

Sokol, Sergei Y

2011-10-01

Wnt signaling pathways control lineage specification in vertebrate embryos and regulate pluripotency in embryonic stem (ES) cells, but how the balance between progenitor self-renewal and differentiation is achieved during axis specification and tissue patterning remains highly controversial. The context- and stage-specific effects of the different Wnt pathways produce complex and sometimes opposite outcomes that help to generate embryonic cell diversity. Although the results of recent studies of the Wnt/β-catenin pathway in ES cells appear to be surprising and controversial, they converge on the same conserved mechanism that leads to the inactivation of TCF3-mediated repression.

Neural Correlates of Sexual Orientation in Heterosexual, Bisexual, and Homosexual Men

PubMed Central

Safron, Adam; Sylva, David; Klimaj, Victoria; Rosenthal, A. M.; Li, Meng; Walter, Martin; Bailey, J. Michael

2017-01-01

Studies of subjective and genital sexual arousal in monosexual (i.e. heterosexual and homosexual) men have repeatedly found that erotic stimuli depicting men’s preferred sex produce strong responses, whereas erotic stimuli depicting the other sex produce much weaker responses. Inconsistent results have previously been obtained in bisexual men, who have sometimes demonstrated distinctly bisexual responses, but other times demonstrated patterns more similar to those observed in monosexual men. We used fMRI to investigate neural correlates of responses to erotic pictures and videos in heterosexual, bisexual, and homosexual men, ages 25–50. Sixty participants were included in video analyses, and 62 were included in picture analyses. We focused on the ventral striatum (VS), due to its association with incentive motivation. Patterns were consistent with sexual orientation, with heterosexual and homosexual men showing female-favoring and male-favoring responses, respectively. Bisexual men tended to show less differentiation between male and female stimuli. Consistent patterns were observed in the whole brain, including the VS, and also in additional regions such as occipitotemporal, anterior cingulate, and orbitofrontal cortices. This study extends previous findings of gender-specific neural responses in monosexual men, and provides initial evidence for distinct brain activity patterns in bisexual men. PMID:28145518

Neural Correlates of Sexual Orientation in Heterosexual, Bisexual, and Homosexual Men.

PubMed

Safron, Adam; Sylva, David; Klimaj, Victoria; Rosenthal, A M; Li, Meng; Walter, Martin; Bailey, J Michael

2017-02-01

Studies of subjective and genital sexual arousal in monosexual (i.e. heterosexual and homosexual) men have repeatedly found that erotic stimuli depicting men's preferred sex produce strong responses, whereas erotic stimuli depicting the other sex produce much weaker responses. Inconsistent results have previously been obtained in bisexual men, who have sometimes demonstrated distinctly bisexual responses, but other times demonstrated patterns more similar to those observed in monosexual men. We used fMRI to investigate neural correlates of responses to erotic pictures and videos in heterosexual, bisexual, and homosexual men, ages 25-50. Sixty participants were included in video analyses, and 62 were included in picture analyses. We focused on the ventral striatum (VS), due to its association with incentive motivation. Patterns were consistent with sexual orientation, with heterosexual and homosexual men showing female-favoring and male-favoring responses, respectively. Bisexual men tended to show less differentiation between male and female stimuli. Consistent patterns were observed in the whole brain, including the VS, and also in additional regions such as occipitotemporal, anterior cingulate, and orbitofrontal cortices. This study extends previous findings of gender-specific neural responses in monosexual men, and provides initial evidence for distinct brain activity patterns in bisexual men.

Identification of an Na(+)-dependent transporter associated with saxitoxin-producing strains of the cyanobacterium Anabaena circinalis.

PubMed

Pomati, Francesco; Burns, Brendan P; Neilan, Brett A

2004-08-01

Blooms of the freshwater cyanobacterium Anabaena circinalis are recognized as an important health risk worldwide due to the production of a range of toxins such as saxitoxin (STX) and its derivatives. In this study we used HIP1 octameric-palindrome repeated-sequence PCR to compare the genomic structure of phylogenetically similar Australian isolates of A. circinalis. STX-producing and nontoxic cyanobacterial strains showed different HIP1 (highly iterated octameric palindrome 1) DNA patterns, and characteristic interrepeat amplicons for each group were identified. Suppression subtractive hybridization (SSH) was performed using HIP1 PCR-generated libraries to further identify toxic-strain-specific genes. An STX-producing strain and a nontoxic strain of A. circinalis were chosen as testers in two distinct experiments. The two categories of SSH putative tester-specific sequences were characterized by different families of encoded proteins that may be representative of the differences in metabolism between STX-producing and nontoxic A. circinalis strains. DNA-microarray hybridization and genomic screening revealed a toxic-strain-specific HIP1 fragment coding for a putative Na(+)-dependent transporter. Analysis of this gene demonstrated analogy to the mrpF gene of Bacillus subtilis, whose encoded protein is involved in Na(+)-specific pH homeostasis. The application of this gene as a molecular probe in laboratory and environmental screening for STX-producing A. circinalis strains was demonstrated. The possible role of this putative Na(+)-dependent transporter in the toxic cyanobacterial phenotype is also discussed, in light of recent physiological studies of STX-producing cyanobacteria.

Modeling digits. Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients.

PubMed

Raspopovic, J; Marcon, L; Russo, L; Sharpe, J

2014-08-01

During limb development, digits emerge from the undifferentiated mesenchymal tissue that constitutes the limb bud. It has been proposed that this process is controlled by a self-organizing Turing mechanism, whereby diffusible molecules interact to produce a periodic pattern of digital and interdigital fates. However, the identities of the molecules remain unknown. By combining experiments and modeling, we reveal evidence that a Turing network implemented by Bmp, Sox9, and Wnt drives digit specification. We develop a realistic two-dimensional simulation of digit patterning and show that this network, when modulated by morphogen gradients, recapitulates the expression patterns of Sox9 in the wild type and in perturbation experiments. Our systems biology approach reveals how a combination of growth, morphogen gradients, and a self-organizing Turing network can achieve robust and reproducible pattern formation. Copyright © 2014, American Association for the Advancement of Science.

Assimilation and accommodation patterns in ventral occipitotemporal cortex in learning a second writing system

PubMed Central

Nelson, Jessica R.; Liu, Ying; Fiez, Julie; Perfetti, Charles A.

2017-01-01

Using fMRI, we compared the patterns of fusiform activity produced by viewing English and Chinese for readers who were either English speakers learning Chinese, or Chinese-English bilinguals. The pattern of fusiform activity depended on both the writing system and the reader’s native language. Native Chinese speakers fluent in English recruited bilateral fusiform areas when viewing both Chinese and English. English speakers learning Chinese, however, used heavily left-lateralized fusiform regions when viewing English, but recruited an additional right fusiform region for viewing Chinese. Thus, English learners of Chinese show an accommodation pattern, in which the reading network accommodates the new writing system by adding neural resources that support its specific graphic requirements. Chinese speakers show an assimilation pattern, in which the reading network established for L1 includes procedures sufficient for the graphic demands of L2 without major change. PMID:18381767

Three members of the iodothyronine deiodinase family, dio1, dio2 and dio3, are expressed in spatially and temporally specific patterns during metamorphosis of the flounder, Paralichthys olivaceus.

PubMed

Itoh, Kae; Watanabe, Kohei; Wu, Xiaoming; Suzuki, Tohru

2010-07-01

Flounder metamorphosis, marked by eye migration, lateralized pigmentation, and tissue differentiation in the stomach and skeletal muscle, is stimulated by thyroid hormone (TH). It is known that tri-iodothyronine (T3) produced by iodothyronine deiodinase type-1 (Dio1) from thyroxine (T4) enters the blood, whereas T3 produced by Dio2 penetrates into the nucleus of the Dio2-expressing cells, and then Dio3 inactivates both T4 and T3. To better understand the distinct functions of these three deiodinases in T3 regulation during flounder metamorphosis, we examined the tissue expression patterns of dio1, dio2, and dio3 in larvae of the Japanese flounder, Paralichthys olivaceus, by section in situ hybridization (SISH). We found that each deiodinase is expressed in a spatially and temporally specific pattern. dio1 is expressed in liver parenchymal cells from pro-metamorphosis to early climax, while dio2 is expressed in limited regions of the eyes, tectum, and skeletal muscles from pro-metamorphosis to post-climax. Considering these findings together with reports on other vertebrates, we predict that the liver cells expressing dio1 supply T3 to the blood, and that this systemic T3 synchronizes metamorphosis of differentiating tissues throughout the larval body, whereas the eyes, tectum, and skeletal muscles autonomously produce additional T3 for local tissue differentiation. Finally, dio3 expression is detected in skeletal muscle and gastric gland blastemas, which both undergo marked tissue differentiation at metamorphic climax. We hypothesize that dio3 expression protects these tissues from basal T3 levels early in metamorphosis, ensuring, together with the T3 surge from the liver, the synchronization of tissue differentiation at metamorphic climax.

Illuminating the multifaceted roles of neurotransmission in shaping neuronal circuitry.

PubMed

Okawa, Haruhisa; Hoon, Mrinalini; Yoshimatsu, Takeshi; Della Santina, Luca; Wong, Rachel O L

2014-09-17

Across the nervous system, neurons form highly stereotypic patterns of synaptic connections that are designed to serve specific functions. Mature wiring patterns are often attained upon the refinement of early, less precise connectivity. Much work has led to the prevailing view that many developing circuits are sculpted by activity-dependent competition among converging afferents, which results in the elimination of unwanted synapses and the maintenance and strengthening of desired connections. Studies of the vertebrate retina, however, have recently revealed that activity can play a role in shaping developing circuits without engaging competition among converging inputs that differ in their activity levels. Such neurotransmission-mediated processes can produce stereotypic wiring patterns by promoting selective synapse formation rather than elimination. We discuss how the influence of transmission may also be limited by circuit design and further highlight the importance of transmission beyond development in maintaining wiring specificity and synaptic organization of neural circuits. Copyright © 2014 Elsevier Inc. All rights reserved.

Duodenal Bacteria From Patients With Celiac Disease and Healthy Subjects Distinctly Affect Gluten Breakdown and Immunogenicity.

PubMed

Caminero, Alberto; Galipeau, Heather J; McCarville, Justin L; Johnston, Chad W; Bernier, Steve P; Russell, Amy K; Jury, Jennifer; Herran, Alexandra R; Casqueiro, Javier; Tye-Din, Jason A; Surette, Michael G; Magarvey, Nathan A; Schuppan, Detlef; Verdu, Elena F

2016-10-01

Partially degraded gluten peptides from cereals trigger celiac disease (CD), an autoimmune enteropathy occurring in genetically susceptible persons. Susceptibility genes are necessary but not sufficient to induce CD, and additional environmental factors related to unfavorable alterations in the microbiota have been proposed. We investigated gluten metabolism by opportunistic pathogens and commensal duodenal bacteria and characterized the capacity of the produced peptides to activate gluten-specific T-cells from CD patients. We colonized germ-free C57BL/6 mice with bacteria isolated from the small intestine of CD patients or healthy controls, selected for their in vitro gluten-degrading capacity. After gluten gavage, gliadin amount and proteolytic activities were measured in intestinal contents. Peptides produced by bacteria used in mouse colonizations from the immunogenic 33-mer gluten peptide were characterized by liquid chromatography tandem mass spectrometry and their immunogenic potential was evaluated using peripheral blood mononuclear cells from celiac patients after receiving a 3-day gluten challenge. Bacterial colonizations produced distinct gluten-degradation patterns in the mouse small intestine. Pseudomonas aeruginosa, an opportunistic pathogen from CD patients, exhibited elastase activity and produced peptides that better translocated the mouse intestinal barrier. P aeruginosa-modified gluten peptides activated gluten-specific T-cells from CD patients. In contrast, Lactobacillus spp. from the duodenum of non-CD controls degraded gluten peptides produced by human and P aeruginosa proteases, reducing their immunogenicity. Small intestinal bacteria exhibit distinct gluten metabolic patterns in vivo, increasing or reducing gluten peptide immunogenicity. This microbe-gluten-host interaction may modulate autoimmune risk in genetically susceptible persons and may underlie the reported association of dysbiosis and CD. Copyright © 2016 AGA Institute. Published by Elsevier Inc. All rights reserved.

Patients with impaired verb-tense processing: do they know that yesterday is past?

PubMed

Patterson, Karalyn; Holland, Rachel

2014-01-01

This paper begins with a focus on the task of stem inflection, where participants are given a verb stem and asked to produce the verb's past-tense form, which can produce a neuropsychological double dissociation with respect to regular versus irregular verbs. Two differing theoretical interpretations are outlined: one is based on specifically morphological and separate brain mechanisms for processing regular versus irregular verbs; the other argues that the two sides of the dissociation can arise from one procedure, which is not specifically morphological, and which relies to differing extents on phonological versus semantic information for regular versus irregular verbs. We then present data from a different version of the task, in which patients were given past-tense forms and asked to produce the present-tense or stem forms (talked → talk and ate → eat). This change yielded a very different pattern of performance in four non-fluent aphasic patients as a function of the regular-irregular manipulation, an outcome which is argued to be more compatible with the single- than the dual-mechanism account. Finally, we present a small amount of data from a task in which the patient was asked to judge whether spoken regular and irregular verb stems and past-tense forms indicated actions occurring today or yesterday. This task produced an even more different and intriguing pattern of performance suggesting a deficit in morpho-syntactic knowledge: not how to produce past-tense forms but what such forms mean and how that understanding interacts with verb regularity. The paper concludes with a discussion of how the research field of acquired disorders of tense processing might advance as a result of new approaches, in particular those informed by studies of developmental disorders.

The Influence of Wheelchair Propulsion Hand Pattern on Upper Extremity Muscle Power and Stress

PubMed Central

Slowik, Jonathan S.; Requejo, Philip S.; Mulroy, Sara J.; Neptune, Richard R.

2016-01-01

The hand pattern (i.e., full-cycle hand path) used during manual wheelchair propulsion is frequently classified as one of four distinct hand pattern types: arc, single loop, double loop and semicircular. Current clinical guidelines recommend the use of the semicircular pattern, which is based on advantageous levels of broad biomechanical metrics implicitly related to the demand placed on the upper extremity (e.g., lower cadence). However, an understanding of the influence of hand pattern on specific measures of upper extremity muscle demand (e.g., muscle power and stress) is needed to help make such recommendations, but these quantities are difficult and impractical to measure experimentally. The purpose of this study was to use musculoskeletal modeling and forward dynamics simulations to investigate the influence of the hand pattern used on specific measures of upper extremity muscle demand. The simulation results suggest that the double loop and semicircular patterns produce the most favorable levels of overall muscle stress and total muscle power. The double loop pattern had the lowest full-cycle and recovery-phase upper extremity demand but required high levels of muscle power during the relatively short contact phase. The semicircular pattern had the second-lowest full-cycle levels of overall muscle stress and total muscle power, and demand was more evenly distributed between the contact and recovery phases. These results suggest that in order to decrease upper extremity demand, manual wheelchair users should use either the double loop or semicircular pattern when propelling their wheelchairs at a self-selected speed on level ground. PMID:27062591

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.

Spermatogenic Cell-Specific Gene Mutation in Mice via CRISPR-Cas9.

PubMed

Bai, Meizhu; Liang, Dan; Wang, Yinghua; Li, Qing; Wu, Yuxuan; Li, Jinsong

2016-05-20

Tissue-specific knockout technology enables the analysis of the gene function in specific tissues in adult mammals. However, conventional strategy for producing tissue-specific knockout mice is a time- and labor-consuming process, restricting rapid study of the gene function in vivo. CRISPR-Cas9 system from bacteria is a simple and efficient gene-editing technique, which has enabled rapid generation of gene knockout lines in mouse by direct injection of CRISPR-Cas9 into zygotes. Here, we demonstrate CRISPR-Cas9-mediated spermatogenic cell-specific disruption of Scp3 gene in testes in one step. We first generated transgenic mice by pronuclear injection of a plasmid containing Hspa2 promoter driving Cas9 expression and showed Cas9 specific expression in spermatogenic cells. We then produced transgenic mice carrying Hspa2 promoter driven Cas9 and constitutive expressed sgRNA targeting Scp3 gene. Male founders were infertile due to developmental arrest of spermatogenic cells while female founders could produce progeny normally. Consistently, male progeny from female founders were infertile and females could transmit the transgenes to the next generation. Our study establishes a CRISPR-Cas9-based one-step strategy to analyze the gene function in adult tissues by a temporal-spatial pattern. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer.

PubMed

Petricoin, Emanuel F; Liotta, Lance A

2004-02-01

Proteomics is more than just generating lists of proteins that increase or decrease in expression as a cause or consequence of pathology. The goal should be to characterize the information flow through the intercellular protein circuitry that communicates with the extracellular microenvironment and then ultimately to the serum/plasma macroenvironment. The nature of this information can be a cause, or a consequence, of disease and toxicity-based processes. Serum proteomic pattern diagnostics is a new type of proteomic platform in which patterns of proteomic signatures from high dimensional mass spectrometry data are used as a diagnostic classifier. This approach has recently shown tremendous promise in the detection of early-stage cancers. The biomarkers found by SELDI-TOF-based pattern recognition analysis are mostly low molecular weight fragments produced at the specific tumor microenvironment.

Genetic patterns of Streptococcus uberis isolated from bovine mastitis.

PubMed

Reinoso, Elina B; Lasagno, Mirta C; Odierno, Liliana M

2015-01-01

The aim of this study was to evaluate the genotypic relationships among 40 Streptococcus uberis isolated from bovine mastitis by using pulsed-field gel electrophoresis (PFGE). Additionally, the association between PFGE patterns and virulence profiles was investigated. The isolates exhibited 17 PFGE patterns. Different strains were found within and among herds; however, a low number of isolates within the same herd shared an identical PFGE type. No association between PFGE patterns and virulence profiles was found. However, the detection of specific strains in some herds could indicate that some strains are more virulent than others. Further research needs to be undertaken to elucidate new virulence-associated genes that might contribute to the capability of these strains to produce infection. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Generation of Hepatocytes from Pluripotent Stem Cells for Drug Screening and Developmental Modeling.

PubMed

Gieseck, Richard L; Vallier, Ludovic; Hannan, Nicholas R F

2015-01-01

Hepatocytes produced from the differentiation of human pluripotent stem cells can be used to study human development and liver disease, to investigate the toxicological response of novel drug candidates, and as an alternative source of primary cells for transplantation therapies. Here, we describe a method to produce hepatocytes by differentiating human pluripotent stem cells into definitive endoderm, patterning definitive endoderm into anterior definitive endoderm, specifying anterior definitive endoderm into hepatic endoderm, and differentiating hepatic endoderm into immature hepatocytes. These cells are further matured in either two-dimensional or three-dimensional culture conditions to produce cells capable of metabolizing xenobiotics and generating liver-specific proteins, such as albumin and alpha 1 antitrypsin.

Resistance is not futile: The response of hardwoods to fire-caused wounding

Treesearch

Elaine Kennedy Sutherland; Kevin Smith

2000-01-01

Fires wound trees; but not all of them, and not always. Specific fire behavior and differences among tree species and individual trees produce variable patterns of wounding and wound response. Our work focuses on the relationships between fire behavior and tree biology to better understand how hardwood trees resist injury to the lower stem and either survive or succumb...

Mountain pine beetle voltinism and life history characteristics across latitudinal and elevational gradients in the western United States

Treesearch

Barbara Bentz; James Vandygriff; Camille Jensen; Tom Coleman; Patricia Maloney; Sheri Smith; Amanda Grady; Greta Schen-Langenheim

2014-01-01

Substantial genetic variation in development time is known to exist among mountain pine beetle (Dendroctonus ponderosae Hopkins) populations across the western United States. The effect of this variation on geographic patterns in voltinism (generation time) and thermal requirements to produce specific voltinism pathways have not been investigated. The influence of...

Eliciting naturalistic cortical responses with a sensory prosthesis via optimized microstimulation

NASA Astrophysics Data System (ADS)

Choi, John S.; Brockmeier, Austin J.; McNiel, David B.; von Kraus, Lee M.; Príncipe, José C.; Francis, Joseph T.

2016-10-01

Objective. Lost sensations, such as touch, could one day be restored by electrical stimulation along the sensory neural pathways. Such stimulation, when informed by electronic sensors, could provide naturalistic cutaneous and proprioceptive feedback to the user. Perceptually, microstimulation of somatosensory brain regions produces localized, modality-specific sensations, and several spatiotemporal parameters have been studied for their discernibility. However, systematic methods for encoding a wide array of naturally occurring stimuli into biomimetic percepts via multi-channel microstimulation are lacking. More specifically, generating spatiotemporal patterns for explicitly evoking naturalistic neural activation has not yet been explored. Approach. We address this problem by first modeling the dynamical input-output relationship between multichannel microstimulation and downstream neural responses, and then optimizing the input pattern to reproduce naturally occurring touch responses as closely as possible. Main results. Here we show that such optimization produces responses in the S1 cortex of the anesthetized rat that are highly similar to natural, tactile-stimulus-evoked counterparts. Furthermore, information on both pressure and location of the touch stimulus was found to be highly preserved. Significance. Our results suggest that the currently presented stimulus optimization approach holds great promise for restoring naturalistic levels of sensation.

Analyzing psychotherapy process as intersubjective sensemaking: an approach based on discourse analysis and neural networks.

PubMed

Nitti, Mariangela; Ciavolino, Enrico; Salvatore, Sergio; Gennaro, Alessandro

2010-09-01

The authors propose a method for analyzing the psychotherapy process: discourse flow analysis (DFA). DFA is a technique representing the verbal interaction between therapist and patient as a discourse network, aimed at measuring the therapist-patient discourse ability to generate new meanings through time. DFA assumes that the main function of psychotherapy is to produce semiotic novelty. DFA is applied to the verbatim transcript of the psychotherapy. It defines the main meanings active within the therapeutic discourse by means of the combined use of text analysis and statistical techniques. Subsequently, it represents the dynamic interconnections among these meanings in terms of a "discursive network." The dynamic and structural indexes of the discursive network have been shown to provide a valid representation of the patient-therapist communicative flow as well as an estimation of its clinical quality. Finally, a neural network is designed specifically to identify patterns of functioning of the discursive network and to verify the clinical validity of these patterns in terms of their association with specific phases of the psychotherapy process. An application of the DFA to a case of psychotherapy is provided to illustrate the method and the kinds of results it produces.

Automation in clinical microbiology: a new approach to identifying micro-organisms by automated pattern matching of proteins labelled with 35S-methionine.

PubMed Central

Tabaqchali, S; Silman, R; Holland, D

1987-01-01

A new rapid automated method for the identification and classification of microorganisms is described. It is based on the incorporation of 35S-methionine into cellular proteins and subsequent separation of the radiolabelled proteins by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The protein patterns produced were species specific and reproducible, permitting discrimination between the species. A large number of Gram negative and Gram positive aerobic and anaerobic organisms were successfully tested. Furthermore, there were sufficient differences within species between the protein profiles to permit subdivision of the species. New typing schemes for Clostridium difficile, coagulase negative staphylococci, and Staphylococcus aureus, including the methicillin resistant strains, could thus be introduced; this has provided the basis for useful epidemiological studies. To standardise and automate the procedure an automated electrophoresis system and a two dimensional scanner were developed to scan the dried gels directly. The scanner is operated by a computer which also stores and analyses the scan data. Specific histograms are produced for each bacterial species. Pattern recognition software is used to construct databases and to compare data obtained from different gels: in this way duplicate "unknowns" can be identified. Specific small areas showing differences between various histograms can also be isolated and expanded to maximise the differences, thus providing differentiation between closely related bacterial species and the identification of differences within the species to provide new typing schemes. This system should be widely applied in clinical microbiology laboratories in the near future. Images Fig 1 Fig 2 Fig 3 Fig 4 Fig 5 Fig 6 Fig 7 Fig 8 PMID:3312300

Process Mining for Individualized Behavior Modeling Using Wireless Tracking in Nursing Homes

PubMed Central

Fernández-Llatas, Carlos; Benedi, José-Miguel; García-Gómez, Juan M.; Traver, Vicente

2013-01-01

The analysis of human behavior patterns is increasingly used for several research fields. The individualized modeling of behavior using classical techniques requires too much time and resources to be effective. A possible solution would be the use of pattern recognition techniques to automatically infer models to allow experts to understand individual behavior. However, traditional pattern recognition algorithms infer models that are not readily understood by human experts. This limits the capacity to benefit from the inferred models. Process mining technologies can infer models as workflows, specifically designed to be understood by experts, enabling them to detect specific behavior patterns in users. In this paper, the eMotiva process mining algorithms are presented. These algorithms filter, infer and visualize workflows. The workflows are inferred from the samples produced by an indoor location system that stores the location of a resident in a nursing home. The visualization tool is able to compare and highlight behavior patterns in order to facilitate expert understanding of human behavior. This tool was tested with nine real users that were monitored for a 25-week period. The results achieved suggest that the behavior of users is continuously evolving and changing and that this change can be measured, allowing for behavioral change detection. PMID:24225907

Understanding Spatiotemporal Patterns of Biking Behavior by Analyzing Massive Bike Sharing Data in Chicago

PubMed Central

Zhou, Xiaolu

2015-01-01

The growing number of bike sharing systems (BSS) in many cities largely facilitates biking for transportation and recreation. Most recent bike sharing systems produce time and location specific data, which enables the study of travel behavior and mobility of each individual. However, despite a rapid growth of interest, studies on massive bike sharing data and the underneath travel pattern are still limited. Few studies have explored and visualized spatiotemporal patterns of bike sharing behavior using flow clustering, nor examined the station functional profiles based on over-demand patterns. This study investigated the spatiotemporal biking pattern in Chicago by analyzing massive BSS data from July to December in 2013 and 2014. The BSS in Chicago gained more popularity. About 15.9% more people subscribed to this service. Specifically, we constructed bike flow similarity graph and used fastgreedy algorithm to detect spatial communities of biking flows. By using the proposed methods, we discovered unique travel patterns on weekdays and weekends as well as different travel trends for customers and subscribers from the noisy massive amount data. In addition, we also examined the temporal demands for bikes and docks using hierarchical clustering method. Results demonstrated the modeled over-demand patterns in Chicago. This study contributes to offer better knowledge of biking flow patterns, which was difficult to obtain using traditional methods. Given the trend of increasing popularity of the BSS and data openness in different cities, methods used in this study can extend to examine the biking patterns and BSS functionality in different cities. PMID:26445357

Understanding Spatiotemporal Patterns of Biking Behavior by Analyzing Massive Bike Sharing Data in Chicago.

PubMed

Zhou, Xiaolu

2015-01-01

The growing number of bike sharing systems (BSS) in many cities largely facilitates biking for transportation and recreation. Most recent bike sharing systems produce time and location specific data, which enables the study of travel behavior and mobility of each individual. However, despite a rapid growth of interest, studies on massive bike sharing data and the underneath travel pattern are still limited. Few studies have explored and visualized spatiotemporal patterns of bike sharing behavior using flow clustering, nor examined the station functional profiles based on over-demand patterns. This study investigated the spatiotemporal biking pattern in Chicago by analyzing massive BSS data from July to December in 2013 and 2014. The BSS in Chicago gained more popularity. About 15.9% more people subscribed to this service. Specifically, we constructed bike flow similarity graph and used fastgreedy algorithm to detect spatial communities of biking flows. By using the proposed methods, we discovered unique travel patterns on weekdays and weekends as well as different travel trends for customers and subscribers from the noisy massive amount data. In addition, we also examined the temporal demands for bikes and docks using hierarchical clustering method. Results demonstrated the modeled over-demand patterns in Chicago. This study contributes to offer better knowledge of biking flow patterns, which was difficult to obtain using traditional methods. Given the trend of increasing popularity of the BSS and data openness in different cities, methods used in this study can extend to examine the biking patterns and BSS functionality in different cities.

A Data Driven Network Approach to Rank Countries Production Diversity and Food Specialization

PubMed Central

Tu, Chengyi; Carr, Joel

2016-01-01

The easy access to large data sets has allowed for leveraging methodology in network physics and complexity science to disentangle patterns and processes directly from the data, leading to key insights in the behavior of systems. Here we use country specific food production data to study binary and weighted topological properties of the bipartite country-food production matrix. This country-food production matrix can be: 1) transformed into overlap matrices which embed information regarding shared production of products among countries, and or shared countries for individual products, 2) identify subsets of countries which produce similar commodities or subsets of commodities shared by a given country allowing for visualization of correlations in large networks, and 3) used to rank country fitness (the ability to produce a diverse array of products weighted on the type of food commodities) and food specialization (quantified on the number of countries producing a specific food product weighted on their fitness). Our results show that, on average, countries with high fitness produce both low and high specializion food commodities, whereas nations with low fitness tend to produce a small basket of diverse food products, typically comprised of low specializion food commodities. PMID:27832118

A Data Driven Network Approach to Rank Countries Production Diversity and Food Specialization.

PubMed

Tu, Chengyi; Carr, Joel; Suweis, Samir

2016-01-01

The easy access to large data sets has allowed for leveraging methodology in network physics and complexity science to disentangle patterns and processes directly from the data, leading to key insights in the behavior of systems. Here we use country specific food production data to study binary and weighted topological properties of the bipartite country-food production matrix. This country-food production matrix can be: 1) transformed into overlap matrices which embed information regarding shared production of products among countries, and or shared countries for individual products, 2) identify subsets of countries which produce similar commodities or subsets of commodities shared by a given country allowing for visualization of correlations in large networks, and 3) used to rank country fitness (the ability to produce a diverse array of products weighted on the type of food commodities) and food specialization (quantified on the number of countries producing a specific food product weighted on their fitness). Our results show that, on average, countries with high fitness produce both low and high specializion food commodities, whereas nations with low fitness tend to produce a small basket of diverse food products, typically comprised of low specializion food commodities.

Fitting direct covariance structures by the MSTRUCT modeling language of the CALIS procedure.

PubMed

Yung, Yiu-Fai; Browne, Michael W; Zhang, Wei

2015-02-01

This paper demonstrates the usefulness and flexibility of the general structural equation modelling (SEM) approach to fitting direct covariance patterns or structures (as opposed to fitting implied covariance structures from functional relationships among variables). In particular, the MSTRUCT modelling language (or syntax) of the CALIS procedure (SAS/STAT version 9.22 or later: SAS Institute, 2010) is used to illustrate the SEM approach. The MSTRUCT modelling language supports a direct covariance pattern specification of each covariance element. It also supports the input of additional independent and dependent parameters. Model tests, fit statistics, estimates, and their standard errors are then produced under the general SEM framework. By using numerical and computational examples, the following tests of basic covariance patterns are illustrated: sphericity, compound symmetry, and multiple-group covariance patterns. Specification and testing of two complex correlation structures, the circumplex pattern and the composite direct product models with or without composite errors and scales, are also illustrated by the MSTRUCT syntax. It is concluded that the SEM approach offers a general and flexible modelling of direct covariance and correlation patterns. In conjunction with the use of SAS macros, the MSTRUCT syntax provides an easy-to-use interface for specifying and fitting complex covariance and correlation structures, even when the number of variables or parameters becomes large. © 2014 The British Psychological Society.

Pattern of external injuries sustained during bomb blast attacks in Karachi, Pakistan from 2000 to 2007.

PubMed

Surani, Arif Anwar; Ali, Salman; Surani, Asif; Zahid, Sohaib; Shoukat, Akber; Varon, Joseph; Surani, Salim

2015-07-01

To evaluate patterns of external injury resulting from bomb blasts in Karachi, and compare the injury profile resulting from explosions in open versus semi-confined blast environments. The retrospective, cross-sectional study was conducted in Karachi and comprised relevant data from January 2000 to October 2007. Casualty medical records and medico-legal certificates of the victims presented to three large public-sector hospitals were evaluated using a self-designed proforma. SPSS 17 was used for statistical analysis. Of the 1146 victims, data of 481(42%) represented the final study sample. Of these, 306(63.6%) were injured in open spaces and 175(36.4%) in semi-confined spaces. Of the 896 recorded injuries, lacerations were encountered as external injury in 427(47.7%) cases, followed by penetrating wounds in 137(15.3%). Lower and upper extremities were injured in 348(38.8%) and 170(19%) victims respectively. Open and semi-confined blast environments produced specific injury pattern and profile (p<0.001). External injuries sustained during bomb blast attacks in Karachi demonstrated specific injury patterns and profiles. Further studies are required to account for internal injuries and classification of injuries based on standardised scoring systems.

Spontaneous attentional fluctuations in impaired states and pathological conditions: a neurobiological hypothesis.

PubMed

Sonuga-Barke, Edmund J S; Castellanos, F Xavier

2007-01-01

In traditional accounts, fluctuations in sustained and focused attention and associated attentional lapses during task performance are regarded as the result of failures of top-down and effortful higher order processes. The current paper reviews an alternative hypothesis: that spontaneous patterns of very low frequency (<0.1 Hz) coherence within a specific brain network ('default-mode network') thought to support a pattern of generalized task-non-specific cognition during rest, can persist or intrude into periods of active task-specific processing, producing periodic fluctuations in attention that compete with goal-directed activity. We review recent studies supporting the existence of the resting state default network, examine the mechanism underpinning it, describe the consequent temporally distinctive effects on cognition and behaviour of default-mode interference into active processing periods, and suggest some factors that might predispose to it. Finally, we explore the putative role of default-mode interference as a cause of performance variability in attention deficit/hyperactivity disorder.

Reconstitution of the Hepatic Asialoglycoprotein Receptor with Phospholipid Vesicles

NASA Astrophysics Data System (ADS)

Klausner, Richard D.; Bridges, Kenneth; Tsunoo, Hajime; Blumenthal, Robert; Weinstein, John N.; Ashwell, Gilbert

1980-09-01

A solubilized detergent-free preparation of the hepatic binding protein specific for asialoglycoproteins associates spontaneously with small unilamellar lipid vesicles. This process is independent of the phase transition of the lipid and effectively restores the specific binding activity of the receptor protein. The insensitivity of the resulting lipid-protein complex to ionic strength provides evidence for a hydrophobic interaction. There is a perturbation of the lipid phase transition concomitant with addition of the protein. Circular dichroism studies indicate that the protein undergoes a conformational change on association with lipid. Binding of specific ligand produces further physical changes in the receptor as indicated by alterations in the tryptophan fluorescence quenching pattern.

Size, time, and asynchrony matter: the species-area relationship for parasites of freshwater fishes.

PubMed

Zelmer, Derek A

2014-10-01

The tendency to attribute species-area relationships to "island biogeography" effectively bypasses the examination of specific mechanisms that act to structure parasite communities. Positive covariation between fish size and infrapopulation richness should not be examined within the typical extinction-based paradigm, but rather should be addressed from the standpoint of differences in colonization potential among individual hosts. Although most mechanisms producing the aforementioned pattern constitute some variation of passive sampling, the deterministic aspects of the accumulation of parasite individuals by fish hosts makes untenable the suggestion that infracommunities of freshwater fishes are stochastic assemblages. At the component community level, application of extinction-dependent mechanisms might be appropriate, given sufficient time for colonization, but these structuring forces likely act indirectly through their effects on the host community to increase the probability of parasite persistence. At all levels, the passive sampling hypothesis is a relevant null model. The tendency for mechanisms that produce species-area relationships to produce nested subset patterns means that for most systems, the passive sampling hypothesis can be addressed through the application of appropriate null models of nested subset structure.

Asia-Pacific Immigration to the United States. A Conference Report (Honolulu, Hawaii, September 20-25, 1984).

ERIC Educational Resources Information Center

Fawcett, James T.; And Others

This conference report provides the main findings of a meeting whose goal was to produce a state-of-the-art analysis of Asia-Pacific immigration. Five additional, more specific goals of the conference were: (1) To examine the Asia-Pacific situation in relation to global and historical immigration patterns; (2) To analyze immigration in the context…

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

PubMed Central

Baudouin-Gonzalez, Luís; Santos, Marília A; Tempesta, Camille; Sucena, Élio; Roch, Fernando; Tanaka, Kohtaro

2017-01-01

Abstract Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression. PMID:28961967

Oxidation-Specific Epitopes are Danger Associated Molecular Patterns Recognized by Pattern Recognition Receptors of Innate Immunity

PubMed Central

Miller, Yury I.; Choi, Soo-Ho; Wiesner, Philipp; Fang, Longhou; Harkewicz, Richard; Hartvigsen, Karsten; Boullier, Agnès; Gonen, Ayelet; Diehl, Cody J.; Que, Xuchu; Montano, Erica; Shaw, Peter X.; Tsimikas, Sotirios; Binder, Christoph J.; Witztum, Joseph L.

2010-01-01

Oxidation reactions are vital parts of metabolism and signal transduction. However, they also produce reactive oxygen species, which damage lipids, proteins and DNA, generating “oxidation-specific” epitopes. In this review, we will discuss the hypothesis that such common oxidation-specific epitopes are a major target of innate immunity, recognized by a variety of “pattern recognition receptors” (PRRs). By analogy with microbial “pathogen associated molecular patterns” (PAMPs), we postulate that host-derived, oxidation-specific epitopes can be considered to represent “danger (or damage) associated molecular patterns” (DAMPs). We also argue that oxidation-specific epitopes present on apoptotic cells and their cellular debris provided the primary evolutionary pressure for the selection of such PRRs. Further, because many PAMPs on microbes share molecular identity and/or mimicry with oxidation-specific epitopes, such PAMPs provided a strong secondary selecting pressure for the same set of oxidation-specific PRRs as well. Because lipid peroxidation is ubiquitous and a major component of the inflammatory state associated with atherosclerosis, the understanding that oxidation-specific epitopes are DAMPs, and thus the target of multiple arcs of innate immunity, provides novel insights into the pathogenesis of atherosclerosis. As examples, we show that both cellular and soluble PRRs, such as CD36, toll-like receptor-4, natural antibodies, and CRP recognize common oxidation-specific DAMPs, such as oxidized phospholipids and oxidized cholesteryl esters, and mediate a variety of immune responses, from expression of proinflammatory genes to excessive intracellular lipoprotein accumulation to atheroprotective humoral immunity. These insights may lead to improved understanding of inflammation and atherogenesis and suggest new approaches to diagnosis and therapy. PMID:21252151

Cytokine patterns in paediatric patients presenting serious gastrointestinal and respiratory bacterial infections

PubMed Central

Palacios-Martínez, Monika; Rodríguez-Cruz, Leonor; Cortés-Bejar, Consuelo Del Carmen; Valencia-Chavarría, Fernando; Martínez-Gómez, Daniel; González-Torres, María Cristina

2014-01-01

In the adaptive immune response, the types of cytokines produced define whether there is a cellular (T1) or a humoral (T2) response. Specifically, in the T1 response, interleukin 2 (IL-2), interferon γ (IFN-γ) and tumor necrosis factor β (TNF-β) are produced, whereas in the T2 response, IL-4, IL-5, IL- 6, IL-10 and IL-13 are primarily produced. Cytokines are primarily involved in the regulation of immune system cells. The aim of the present study was to evaluate the cytokine patterns (Type 1/Type 2) and TNF-α expression levels in children with severe gastrointestinal and respiratory bacterial infections. The enzyme-linked immunosorbent assay (ELISA) technique was used to identify the cytokines and the infectious agents. The results obtained demonstrated that, in general, children with bacterial infections experienced an increase in IL-2, IFN-γ and IL-4 concentrations and a decrease in TNF-α, IL-5 and IL-6 concentrations when compared to healthy children. Specifically, type 1 cytokines and an increased TNF-α concentration were found in children with gastrointestinal infections. However, patients with respiratory infections showed increased concentrations of both T2 (IL-4, IL-6 and IL-10) and T1 (IL-2 and IFN-γ) components. Thus, it was concluded that children with gastrointestinal infections exclusively developed a T1 response, whereas children with respiratory infections developed a T1/T2 response to fight the infection. PMID:26155128

Carbon Nanotube-Based Structural Health Monitoring Sensors

NASA Technical Reports Server (NTRS)

Wincheski, Russell; Jordan, Jeffrey; Oglesby, Donald; Watkins, Anthony; Patry, JoAnne; Smits, Jan; Williams, Phillip

2011-01-01

Carbon nanotube (CNT)-based sensors for structural health monitoring (SHM) can be embedded in structures of all geometries to monitor conditions both inside and at the surface of the structure to continuously sense changes. These CNTs can be manipulated into specific orientations to create small, powerful, and flexible sensors. One of the sensors is a highly flexible sensor for crack growth detection and strain field mapping that features a very dense and highly ordered array of single-walled CNTs. CNT structural health sensors can be mass-produced, are inexpensive, can be packaged in small sizes (0.5 micron(sup 2)), require less power than electronic or piezoelectric transducers, and produce less waste heat per square centimeter than electronic or piezoelectric transducers. Chemically functionalized lithographic patterns are used to deposit and align the CNTs onto metallic electrodes. This method consistently produces aligned CNTs in the defined locations. Using photo- and electron-beam lithography, simple Cr/Au thin-film circuits are patterned onto oxidized silicon substrates. The samples are then re-patterned with a CNT-attracting, self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) to delineate the desired CNT locations between electrodes. During the deposition of the solution-suspended single- wall CNTs, the application of an electric field to the metallic contacts causes alignment of the CNTs along the field direction. This innovation is a prime candidate for smart skin technologies with applications ranging from military, to aerospace, to private industry.

The aftershock signature of supershear earthquakes.

PubMed

Bouchon, Michel; Karabulut, Hayrullah

2008-06-06

Recent studies show that earthquake faults may rupture at speeds exceeding the shear wave velocity of rocks. This supershear rupture produces in the ground a seismic shock wave similar to the sonic boom produced by a supersonic airplane. This shock wave may increase the destruction caused by the earthquake. We report that supershear earthquakes are characterized by a specific pattern of aftershocks: The fault plane itself is remarkably quiet whereas aftershocks cluster off the fault, on secondary structures that are activated by the supershear rupture. The post-earthquake quiescence of the fault shows that friction is relatively uniform over supershear segments, whereas the activation of off-fault structures is explained by the shock wave radiation, which produces high stresses over a wide zone surrounding the fault.

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.

Polymerizable Supramolecular Approach to Highly Conductive PEDOT:PSS Patterns.

PubMed

Kim, Tae Geun; Ha, Su Ryong; Choi, Hyosung; Uh, Kyungchan; Kundapur, Umesha; Park, Sumin; Lee, Chan Woo; Lee, Sang-Hwa; Kim, Jaeyong; Kim, Jong-Man

2017-06-07

Owing to its high conductivity, solution processability, mechanical flexibility, and transparency, poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) has been extensively explored for use in functional devices including solar cells, sensors, light-emitting diodes, and supercapacitors. The ability to fabricate patterned PEDOT:PSS on a solid substrate is of significant importance to develop practical applications of this conducting polymer. Herein, we describe a new approach to obtain PEDOT:PSS patterns that are based on a polymerizable supramolecular concept. Specifically, we found that UV irradiation of a photopolymerizable diacetylene containing PEDOT:PSS film followed by development in deionized water and subsequent treatment with sulfuric acid (glass and silicon wafer) or formic acid (PET) produces micron-sized PEDOT:PSS patterns on solid substrates. The newly designed photolithographic method, which can be employed to generate highly conductive (>1000 S/cm) PEDOT:PSS patterns, has many advantages including the use of aqueous process conditions, a reduced number of process steps, and no requirement for plasma etching procedures.

A Novel Candidate Gene for Temperature-Dependent Sex Determination in the Common Snapping Turtle.

PubMed

Schroeder, Anthony L; Metzger, Kelsey J; Miller, Alexandra; Rhen, Turk

2016-05-01

Temperature-dependent sex determination (TSD) was described nearly 50 years ago. Researchers have since identified many genes that display differential expression at male- vs. female-producing temperatures. Yet, it is unclear whether these genes (1) are involved in sex determination per se, (2) are downstream effectors involved in differentiation of ovaries and testes, or (3) are thermo-sensitive but unrelated to gonad development. Here we present multiple lines of evidence linking CIRBP to sex determination in the snapping turtle, Chelydra serpentina We demonstrate significant associations between a single nucleotide polymorphism (SNP) (c63A > C) in CIRBP, transcript levels in embryonic gonads during specification of gonad fate, and sex in hatchlings from a thermal regime that produces mixed sex ratios. The A allele was induced in embryos exposed to a female-producing temperature, while expression of the C allele did not differ between female- and male-producing temperatures. In accord with this pattern of temperature-dependent, allele-specific expression, AA homozygotes were more likely to develop ovaries than AC heterozygotes, which, in turn, were more likely to develop ovaries than CC homozygotes. Multiple regression using SNPs in CIRBP and adjacent loci suggests that c63A > C may be the causal variant or closely linked to it. Differences in CIRBP allele frequencies among turtles from northern Minnesota, southern Minnesota, and Texas reflect small and large-scale latitudinal differences in TSD pattern. Finally, analysis of CIRBP protein localization reveals that CIRBP is in a position to mediate temperature effects on the developing gonads. Together, these studies strongly suggest that CIRBP is involved in determining the fate of the bipotential gonad. Copyright © 2016 by the Genetics Society of America.

A Novel Candidate Gene for Temperature-Dependent Sex Determination in the Common Snapping Turtle

PubMed Central

Schroeder, Anthony L.; Metzger, Kelsey J.; Miller, Alexandra; Rhen, Turk

2016-01-01

Temperature-dependent sex determination (TSD) was described nearly 50 years ago. Researchers have since identified many genes that display differential expression at male- vs. female-producing temperatures. Yet, it is unclear whether these genes (1) are involved in sex determination per se, (2) are downstream effectors involved in differentiation of ovaries and testes, or (3) are thermo-sensitive but unrelated to gonad development. Here we present multiple lines of evidence linking CIRBP to sex determination in the snapping turtle, Chelydra serpentina. We demonstrate significant associations between a single nucleotide polymorphism (SNP) (c63A > C) in CIRBP, transcript levels in embryonic gonads during specification of gonad fate, and sex in hatchlings from a thermal regime that produces mixed sex ratios. The A allele was induced in embryos exposed to a female-producing temperature, while expression of the C allele did not differ between female- and male-producing temperatures. In accord with this pattern of temperature-dependent, allele-specific expression, AA homozygotes were more likely to develop ovaries than AC heterozygotes, which, in turn, were more likely to develop ovaries than CC homozygotes. Multiple regression using SNPs in CIRBP and adjacent loci suggests that c63A > C may be the causal variant or closely linked to it. Differences in CIRBP allele frequencies among turtles from northern Minnesota, southern Minnesota, and Texas reflect small and large-scale latitudinal differences in TSD pattern. Finally, analysis of CIRBP protein localization reveals that CIRBP is in a position to mediate temperature effects on the developing gonads. Together, these studies strongly suggest that CIRBP is involved in determining the fate of the bipotential gonad. PMID:26936926

Autism-specific maternal anti-fetal brain autoantibodies are associated with metabolic conditions

PubMed Central

Krakowiak, Paula; Walker, Cheryl K.; Tancredi, Daniel; Hertz-Picciotto, Irva; Van de Water, Judy

2016-01-01

Lay Abstract Approximately 23% of mothers of children with autism spectrum disorder (ASD) produce specific patterns of antibodies to fetal brain tissue that have been detected in only 1% of mothers of typically developing children. However, it is unknown what causes these ASD-specific anti-fetal antibodies to be produced. We examined the relationship between ASD-specific anti-fetal antibodies and metabolic conditions during pregnancy in 227 mothers of 2–5 year old children with ASD, enrolled in the CHARGE (Childhood Autism Risk from Genetics and the Environment) Study, and who had blood samples measured for these anti-fetal brain antibodies after study enrollment. Metabolic conditions included diabetes, hypertensive disorders, and prepregnancy obesity or overweight. The presence of ASD-specific anti-fetal brain antibody patterns was more common among mothers diagnosed with diabetes, hypertensive disorders, or overweight during pregnancy compared to healthy mothers, but these differences did not reach statistical significance. In a subset of 145 mothers whose children exhibited severe ASD symptoms, those diagnosed with type 2 or gestational diabetes were nearly 3 times more likely to have ASD-specific anti-fetal antibodies compared to healthy mothers. Further, those diagnosed with gestational diabetes specifically were over 3 times more likely to have these anti-fetal brain antibodies. In this exploratory study, mothers whose children had severe ASD and who were diagnosed with diabetes were more likely to have anti-fetal brain autoantibodies 2–5 years later. Scientific Abstract Approximately 23% of mothers of children with autism spectrum disorder (ASD) produce specific patterns of autoantibodies to fetal brain proteins that have been detected in only 1% of mothers of typically developing children. The biological mechanisms underlying the development of ASD-specific maternal autoantibodies are poorly understood. We sought to determine whether ASD-specific maternal autoantibodies identified postnatally were associated with metabolic conditions (MCs) during gestation. Participants were 227 mothers of 2–5 year old children with confirmed ASD, enrolled in CHARGE (Childhood Autism Risk from Genetics and the Environment) between January 2003 and April 2008, and from whom blood samples were collected and analyzed for anti-fetal brain autoantibodies (Ab+). MCs included diabetes, hypertensive disorders, and prepregnancy obesity or overweight, ascertained from medical records or structured telephone interviews. Log-linear regression models were performed to estimate prevalence ratios (PR) and 95% confidence intervals (CI) based on robust standard errors. Fifty-six (25%) mothers were Ab+. Ab+ prevalence was higher among mothers with diabetes, hypertensive disorders, or overweight compared to healthy mothers, but differences were not statistically significant. In a subset of 145 mothers whose children exhibited severe ASD (31 Ab+), those diagnosed with type 2 or gestational diabetes were 2.7-fold more likely to be Ab+ (95% CI 1.1, 6.6), controlling for delivery payer and smoking. Gestational diabetes specifically was associated with a 3.2-fold increased Ab+ prevalence (95% CI 1.2, 8.6). In this exploratory study, mothers whose children had severe ASD and who experienced diabetes were more likely to have anti-fetal brain autoantibodies 2–5 years later. PMID:27312731

Whole Genome Analysis of a Wine Yeast Strain

PubMed Central

Hauser, Nicole C.; Fellenberg, Kurt; Gil, Rosario; Bastuck, Sonja; Hoheisel, Jörg D.

2001-01-01

Saccharomyces cerevisiae strains frequently exhibit rather specific phenotypic features needed for adaptation to a special environment. Wine yeast strains are able to ferment musts, for example, while other industrial or laboratory strains fail to do so. The genetic differences that characterize wine yeast strains are poorly understood, however. As a first search of genetic differences between wine and laboratory strains, we performed DNA-array analyses on the typical wine yeast strain T73 and the standard laboratory background in S288c. Our analysis shows that even under normal conditions, logarithmic growth in YPD medium, the two strains have expression patterns that differ significantly in more than 40 genes. Subsequent studies indicated that these differences correlate with small changes in promoter regions or variations in gene copy number. Blotting copy numbers vs. transcript levels produced patterns, which were specific for the individual strains and could be used for a characterization of unknown samples. PMID:18628902

Effects of tributyltin (TBT) on in vitro hormonal and biotransformation responses in Atlantic salmon (Salmo salar).

PubMed

Mortensen, Anne S; Arukwe, Augustine

2009-01-01

The mechanisms by which the biocide tributyltin (TBT) and its metabolites affect the hormonal and xenobiotic biotransformation pathways in aquatic species are not well understood. In this study hepatocytes isolated from salmon were used to evaluate the mechanistical effects of TBT on fish hormonal and xenobiotic biotransformation pathways. Cells were exposed to 0.01, 0.1, 1, or 5 microM TBT and samples were collected at 0, 12, 24, or 48 h following exposure. Gene expression patterns were evaluated using quantitative polymerase chain reaction (PCR), and cytochrome P-450 (CYP)-mediated enzyme activities were evaluated by ethoxyresorufin, benzyloxyresorufin, and pentoxyresorufin O-deethylase (EROD, BROD, and PROD, respectively) activity assays. Generally, exposure of hepatocytes to 1 microM (at 48 h) and 5 microM TBT (at 12, 24, and 48 h) consistently produced reductions in all mRNA species investigated. TBT produced significant decreases of vitellogen (Vtg) expression at 48 h and modified the expression patterns of estrogen receptors (ERalpha and ERbeta) and androgen receptor-beta (ARbeta) that were dependent on time and TBT concentration. In the xenobiotic biotransformation pathway, TBT produced differential expression patterns that were dependent on exposure time and concentration for all salmonid AhR2 isoforms (AhR2alpha, AhR2beta, AhR2delta, and AhR2gamma). For CYP1A1, CYP3A, AhRR, and Arnt mRNA, TBT produced exposure- and time-specific modulations. Catalytic CYP activities showed that BROD activity increased in an apparent concentration-specific manner in cells exposed to TBT for 12 h. Interestingly, EROD activity showed a TBT concentration-dependent increase at 24 h and PROD at 12 and 48 h of exposure. In general our data show that TBT differentially modulated hormonal and biotransformation responses in the salmon in vitro system. The apparent and consistent decrease of the studied responses with time in 1 and 5 microM exposed hepatocytes suggest a possible transcription inhibitory effect of TBT.

Progress in mask replication using jet and flash imprint lithography

NASA Astrophysics Data System (ADS)

Selinidis, Kosta S.; Brooks, Cynthia B.; Doyle, Gary F.; Brown, Laura; Jones, Chris; Imhof, Joseph; LaBrake, Dwayne L.; Resnick, Douglas J.; Sreenivasan, S. V.

2011-04-01

The Jet and Flash Imprint Lithography (J-FILTM) process uses drop dispensing of UV curable resists to assist high resolution patterning for subsequent dry etch pattern transfer. The technology is actively being used to develop solutions for memory markets including Flash memory and patterned media for hard disk drives. It is anticipated that the lifetime of a single template (for patterned media) or mask (for semiconductor) will be on the order of 104 - 105imprints. This suggests that tens of thousands of templates/masks will be required to satisfy the needs of a manufacturing environment. Electron-beam patterning is too slow to feasibly deliver these volumes, but instead can provide a high quality "master" mask which can be replicated many times with an imprint lithography tool. This strategy has the capability to produce the required supply of "working" templates/masks. In this paper, we review the development of the mask form factor, imprint replication tools and processes specifically for semiconductor applications. The requirements needed for semiconductors dictate the need for a well defined form factor for both master and replica masks which is also compatible with the existing mask infrastructure established for the 6025 semi standard, 6" x 6" x 0.25" photomasks. Complying with this standard provides the necessary tooling needed for mask fabrication processes, cleaning, metrology, and inspection. The replica form factor has additional features specific to imprinting such as a pre-patterned mesa. A PerfectaTM MR5000 mask replication tool has been developed specifically to pattern replica masks from an e-beam written master. The system specifications include a throughput of four replicas per hour with an added image placement component of 5nm, 3sigma and a critical dimension uniformity error of less than 1nm, 3sigma. A new process has been developed to fabricate replicas with high contrast alignment marks so that designs for imprint can fit within current device layouts and maximize the usable printed area on the wafer. Initial performance results of this marks are comparable to the baseline fused silica align marks.

Development of Farming Diversification with Implementation Plant Patterns as a Strategy of Economic Strengthening

NASA Astrophysics Data System (ADS)

Anwar, S.; Setyohadi, D. P. S.; Utami, M. M. D.; Damanhuri; Hariono, B.

2018-01-01

Bojonegoro, Tulungagung, and Ponorogo districts are an agrarian area and become one of the leading food crops producers in East Java Province. Diversification of farming in this region is done by applying season-based cropping pattern, which is cultivating various commodities in rotation. Farmers need diversification programs wetland cannot provide an optimal contribution to the income of farmers caused because farmers are not able to cultivate high value-added commodities due to limited capital. This research is to identify the characteristics of farming and to analyse the farming system to know the pattern of planting suggestion and prospect. The research used descriptive method, profit farming analysis, and SWOT. The results showed that each region has a specific planting pattern with rice as the main commodity grown in the rainy season followed by crops and horticultural crops and a suggested planting pattern that needs to be implemented by farmers to increase their income. The prospect of diversification of farming development through the implementation of the proposed planting pattern is very suitable with the character of the region and the market demand.

Carbohydrate conjugation through microwave-assisted functionalization of single-walled carbon nanotubes using perfluorophenyl azides.

PubMed

Kong, Na; Shimpi, Manishkumar R; Ramström, Olof; Yan, Mingdi

2015-03-20

Carbohydrate-functionalized single-walled carbon nanotubes (SWNTs) were synthesized using microwave-assisted reaction of perfluorophenyl azide with the nanotubes. The results showed that microwave radiation provides a rapid and effective means to covalently attach carbohydrates to SWNTs, producing carbohydrate-SWNT conjugates for biorecognition. The carbohydrate-functionalized SWNTs were furthermore shown to interact specifically with cognate carbohydrate-specific proteins (lectins), resulting in predicted recognition patterns. The carbohydrate-presenting SWNTs constitute a new platform for sensitive protein- or cell recognition, which pave the way for glycoconjugated carbon nanomaterials in biorecognition applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

Predicted taxonomic patterns in pheromone production by longhorned beetles

NASA Astrophysics Data System (ADS)

Ray, Ann M.; Lacey, Emerson S.; Hanks, Lawrence M.

2006-11-01

Males of five species of three tribes in the longhorned beetle subfamily Cerambycinae produce volatile pheromones that share a structural motif (hydroxyl or carbonyl groups at carbons two and three in straight-chains of six, eight, or ten carbons). Pheromone gland pores are present on the prothoraces of males, but are absent in females, suggesting that male-specific gland pores could provide a convenient morphological indication that a species uses volatile pheromones. In this article, we assess the taxonomic distribution of gland pores within the Cerambycinae by examining males and females of 65 species in 24 tribes using scanning electron microscopy. Gland pores were present in males and absent in females of 49 species, but absent in both sexes of the remaining 16 species. Pores were confined to indentations in the cuticle. Among the species that had male-specific gland pores were four species already known to produce volatile compounds consistent with the structural motif. These findings support the initial assumption that gland pores are associated with the production of pheromones by males. There were apparently no taxonomic patterns in the presence of gland pores. These findings suggest that volatile pheromones play an important role in reproduction for many species of the Cerambycinae, and that the trait is evolutionarily labile.

Perinatal asphyxia exerts lifelong effects on neuronal responsiveness to stress in specific brain regions in the rat.

PubMed

Salchner, Peter; Engidawork, Ephrem; Hoeger, Harald; Lubec, Barbara; Singewald, Nicolas

2003-09-01

Perinatal asphyxia (PA) causes irreversible damage to the brain of newborns and can produce neurologic and behavioral changes later in life. To identify neuronal substrates underlying the effects of PA, we investigated whether and how neuronal responsiveness to an established stress challenge is affected. We used Fos expression as a marker of neuronal activation and examined the pattern of Fos expression in response to acute swim stress in 24-month-old rats exposed to a 20-minute PA insult. Swim stress produced a similar pattern of Fos expression in control and asphyxiated rats in 34 brain areas. Asphyxiated rats displayed a higher number of stress-induced Fos-positive cells in the nucleus of the solitary tract, parabrachial nucleus, periaqueductal gray, paraventricular hypothalamic nucleus, nucleus accumbens, caudate-putamen, and prelimbic cortex. No differences in the Fos response to stress were observed in other regions, including the locus ceruleus, amygdala, hippocampus, or septum. These data provide functional anatomic evidence that PA has lifelong effects on neuronal communication and leads to an abnormal, augmented neuronal responsiveness to stress in specific brain areas, particularly in the main telencephalic target regions of the mesencephalic dopamine projections, as well as in a functionally related set of brain regions associated with autonomic and neuroendocrine regulation.

Knowing what to respond in the future does not cancel the influence of past events.

PubMed

Tubau, Elisabet; López-Moliner, Joan

2009-05-29

Everyday tasks seldom involve isolate actions but sequences of them. We can see whether previous actions influence the current one by exploring the response time to controlled sequences of stimuli. Specifically, depending on the response-stimulus temporal interval (RSI), different mechanisms have been proposed to explain sequential effects in two-choice serial response tasks. Whereas an automatic facilitation mechanism is thought to produce a benefit for response repetitions at short RSIs, subjective expectancies are considered to replace the automatic facilitation at longer RSIs, producing a cost-benefit pattern: repetitions are faster after other repetitions but they are slower after alternations. However, there is not direct evidence showing the impact of subjective expectancies on sequential effects. By using a fixed sequence, the results of the reported experiment showed that the repetition effect was enhanced in participants who acquired complete knowledge of the order. Nevertheless, a similar cost-benefit pattern was observed in all participants and in all learning blocks. Therefore, results of the experiment suggest that sequential effects, including the cost-benefit pattern, are the consequence of automatic mechanisms which operate independently of (and simultaneously with) explicit knowledge of the sequence or other subjective expectancies.

Shavenbaby Couples Patterning to Epidermal Cell Shape Control

PubMed Central

Fernandes, Isabelle; Roch, Fernando; Payre, François

2006-01-01

It is well established that developmental programs act during embryogenesis to determine animal morphogenesis. How these developmental cues produce specific cell shape during morphogenesis, however, has remained elusive. We addressed this question by studying the morphological differentiation of the Drosophila epidermis, governed by a well-known circuit of regulators leading to a stereotyped pattern of smooth cells and cells forming actin-rich extensions (trichomes). It was shown that the transcription factor Shavenbaby plays a pivotal role in the formation of trichomes and underlies all examined cases of the evolutionary diversification of their pattern. To gain insight into the mechanisms of morphological differentiation, we sought to identify shavenbaby's downstream targets. We show here that Shavenbaby controls epidermal cell shape, through the transcriptional activation of different classes of cellular effectors, directly contributing to the organization of actin filaments, regulation of the extracellular matrix, and modification of the cuticle. Individual inactivation of shavenbaby's targets produces distinct trichome defects and only their simultaneous inactivation prevent trichome formation. Our data show that shavenbaby governs an evolutionarily conserved developmental module consisting of a set of genes collectively responsible for trichome formation, shedding new light on molecular mechanisms acting during morphogenesis and the way they can influence evolution of animal forms. PMID:16933974

A Novel Wounding Device Suitable for Quantitative Biochemical Analysis of Wound Healing and Regeneration of Cultured Epithelium

PubMed Central

Lan, Rongpei; Geng, Hui; Hwang, Yoon; Mishra, Pramod; Skloss, Wayne L.; Sprague, Eugene A.; Saikumar, Pothana; Venkatachalam, Manjeri

2010-01-01

We describe the fabrication and use of an in vitro wounding device that denudes cultured epithelium in patterns designed to leave behind strips or islands of cells sufficiently narrow or small to ensure that all remaining cells become rapidly activated and then migrate, dedifferentiate and proliferate in near synchrony. The design ensures that signals specific to regenerating cells do not become diluted by quiescent differentiated cells that are not affected by wound induced activation. The device consists of a flat circular disk of rubber engraved to produce alternating ridges and grooves in patterns of concentric circles or parallel lines. The disk is mounted at the end of a pneumatically controlled piston assembly. Application of controlled pressure and circular or linear movement of the disk on cultures produced highly reproducible wounding patterns. The near synchronous regenerative activity of cell bands or islands permitted the collection of samples large enough for biochemical studies to sensitively detect alterations involving mRNA for several early response genes and protein phosphorylation in major signaling pathways. The method is versatile, easy to use and reproducible, and should facilitate biochemical, proteomic and genomic studies of wound induced regeneration of cultured epithelium. PMID:20230600

Mold allergy: is it real and what do we do about it?

PubMed

Rudert, Amanda; Portnoy, Jay

2017-08-01

fungi produce substances that contain pathogen-associated molecular patterns (pamps) and damage-associated molecular patterns (damps) which bind to pattern recognition receptors, stimulating innate immune responses in humans. they also produce allergens that induce production of specific ige. Areas covered: In this review we cover both innate and adaptive immune responses to fungi. Some fungal products can activate both innate and adaptive responses and in doing so, cause an intense and complex health effects. Methods of testing for fungal allergy and evidence for clinical treatment including environmental control are also discussed. In addition, we describe controversial issues including the role of Stachybotrys and mycotoxins in adverse health effects. Expert commentary: Concerns about long-term exposure to fungi have led some patients, attorneys and fungus advocates to promote fears about a condition that has been termed toxic mold syndrome. This syndrome is associated with vague symptoms and is believed to be due to exposure to mycotoxins, though this connection has not been proven. Ultimately, more precise methods are needed to measure both fungal exposure and the resulting health effects. Once that such methods become available, much of the speculation will be replaced by knowledge.

Four not six: Revealing culturally common facial expressions of emotion.

PubMed

Jack, Rachael E; Sun, Wei; Delis, Ioannis; Garrod, Oliver G B; Schyns, Philippe G

2016-06-01

As a highly social species, humans generate complex facial expressions to communicate a diverse range of emotions. Since Darwin's work, identifying among these complex patterns which are common across cultures and which are culture-specific has remained a central question in psychology, anthropology, philosophy, and more recently machine vision and social robotics. Classic approaches to addressing this question typically tested the cross-cultural recognition of theoretically motivated facial expressions representing 6 emotions, and reported universality. Yet, variable recognition accuracy across cultures suggests a narrower cross-cultural communication supported by sets of simpler expressive patterns embedded in more complex facial expressions. We explore this hypothesis by modeling the facial expressions of over 60 emotions across 2 cultures, and segregating out the latent expressive patterns. Using a multidisciplinary approach, we first map the conceptual organization of a broad spectrum of emotion words by building semantic networks in 2 cultures. For each emotion word in each culture, we then model and validate its corresponding dynamic facial expression, producing over 60 culturally valid facial expression models. We then apply to the pooled models a multivariate data reduction technique, revealing 4 latent and culturally common facial expression patterns that each communicates specific combinations of valence, arousal, and dominance. We then reveal the face movements that accentuate each latent expressive pattern to create complex facial expressions. Our data questions the widely held view that 6 facial expression patterns are universal, instead suggesting 4 latent expressive patterns with direct implications for emotion communication, social psychology, cognitive neuroscience, and social robotics. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Understanding spatial and temporal patterning of astrocyte calcium transients via interactions between network transport and extracellular diffusion

NASA Astrophysics Data System (ADS)

Shtrahman, E.; Maruyama, D.; Olariu, E.; Fink, C. G.; Zochowski, M.

2017-02-01

Astrocytes form interconnected networks in the brain and communicate via calcium signaling. We investigate how modes of coupling between astrocytes influence the spatio-temporal patterns of calcium signaling within astrocyte networks and specifically how these network interactions promote coordination within this group of cells. To investigate these complex phenomena, we study reduced cultured networks of astrocytes and neurons. We image the spatial temporal patterns of astrocyte calcium activity and quantify how perturbing the coupling between astrocytes influences astrocyte activity patterns. To gain insight into the pattern formation observed in these cultured networks, we compare the experimentally observed calcium activity patterns to the patterns produced by a reduced computational model, where we represent astrocytes as simple units that integrate input through two mechanisms: gap junction coupling (network transport) and chemical release (extracellular diffusion). We examine the activity patterns in the simulated astrocyte network and their dependence upon these two coupling mechanisms. We find that gap junctions and extracellular chemical release interact in astrocyte networks to modulate the spatiotemporal patterns of their calcium dynamics. We show agreement between the computational and experimental findings, which suggests that the complex global patterns can be understood as a result of simple local coupling mechanisms.

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

An evaluation of time-series MODIS 250-meter vegetation index data for crop mapping in the United States Central Great Plains

NASA Astrophysics Data System (ADS)

Wardlow, Brian Douglas

The objectives of this research were to: (1) investigate time-series MODIS (Moderate Resolution Imaging Spectroradiometer) 250-meter EVI (Enhanced Vegetation Index) and NDVI (Normalized Difference Vegetation Index) data for regional-scale crop-related land use/land cover characterization in the U.S. Central Great Plains and (2) develop and test a MODIS-based crop mapping protocol. A pixel-level analysis of the time-series MODIS 250-m VIs for 2,000+ field sites across Kansas found that unique spectral-temporal signatures were detected for the region's major crop types, consistent with the crops' phenology. Intra-class variations were detected in VI data associated with different land use practices, climatic conditions, and planting dates for the crops. The VIs depicted similar seasonal variations and were highly correlated. A pilot study in southwest Kansas found that accurate and detailed cropping patterns could be mapped using the MODIS 250-m VI data. Overall and class-specific accuracies were generally greater than 90% for mapping crop/non-crop, general crops (alfalfa, summer crops, winter wheat, and fallow), summer crops (corn, sorghum, and soybeans), and irrigated/non-irrigated crops using either VI dataset. The classified crop areas also had a high level of agreement (<5% difference) with the USDA reported crop areas. Both VIs produced comparable crop maps with only a 1-2% difference between their classification accuracies and a high level of pixel-level agreement (>90%) between their classified crop patterns. This hierarchical crop mapping protocol was tested for Kansas and produced similar classification results over a larger and more diverse area. Overall and class-specific accuracies were typically between 85% and 95% for the crop maps. At the state level, the maps had a high level of areal agreement (<5% difference) with the USDA crop area figures and their classified patterns were consistent with the state's cropping practices. In general, the protocol's performance was relatively consistent across the state's range of environmental conditions, landscape patterns, and cropping practices. The largest areal differences occurred in eastern Kansas due to the omission of many small cropland areas that were not resolvable at MODIS' 250-m resolution. Notable regional deviations in classified areas also occurred for selected classes due to localized precipitation patterns and specific cropping practices.

Toward robust phase-locking in Melibe swim central pattern generator models

NASA Astrophysics Data System (ADS)

Jalil, Sajiya; Allen, Dane; Youker, Joseph; Shilnikov, Andrey

2013-12-01

Small groups of interneurons, abbreviated by CPG for central pattern generators, are arranged into neural networks to generate a variety of core bursting rhythms with specific phase-locked states, on distinct time scales, which govern vital motor behaviors in invertebrates such as chewing and swimming. These movements in lower level animals mimic motions of organs in higher animals due to evolutionarily conserved mechanisms. Hence, various neurological diseases can be linked to abnormal movement of body parts that are regulated by a malfunctioning CPG. In this paper, we, being inspired by recent experimental studies of neuronal activity patterns recorded from a swimming motion CPG of the sea slug Melibe leonina, examine a mathematical model of a 4-cell network that can plausibly and stably underlie the observed bursting rhythm. We develop a dynamical systems framework for explaining the existence and robustness of phase-locked states in activity patterns produced by the modeled CPGs. The proposed tools can be used for identifying core components for other CPG networks with reliable bursting outcomes and specific phase relationships between the interneurons. Our findings can be employed for identifying or implementing the conditions for normal and pathological functioning of basic CPGs of animals and artificially intelligent prosthetics that can regulate various movements.

Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set.

PubMed

Klimenko, Kyrylo; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

2016-08-22

Curation, standardization and data fusion of the antiviral information present in the ChEMBL public database led to the definition of a robust data set, providing an association of antiviral compounds to seven broadly defined antiviral activity classes. Generative topographic mapping (GTM) subjected to evolutionary tuning was then used to produce maps of the antiviral chemical space, providing an optimal separation of compound families associated with the different antiviral classes. The ability to pinpoint the specific spots occupied (responsibility patterns) on a map by various classes of antiviral compounds opened the way for a GTM-supported search for privileged structural motifs, typical for each antiviral class. The privileged locations of antiviral classes were analyzed in order to highlight underlying privileged common structural motifs. Unlike in classical medicinal chemistry, where privileged structures are, almost always, predefined scaffolds, privileged structural motif detection based on GTM responsibility patterns has the decisive advantage of being able to automatically capture the nature ("resolution detail"-scaffold, detailed substructure, pharmacophore pattern, etc.) of the relevant structural motifs. Responsibility patterns were found to represent underlying structural motifs of various natures-from very fuzzy (groups of various "interchangeable" similar scaffolds), to the classical scenario in medicinal chemistry (underlying motif actually being the scaffold), to very precisely defined motifs (specifically substituted scaffolds).

Improving the discrimination of hand motor imagery via virtual reality based visual guidance.

PubMed

Liang, Shuang; Choi, Kup-Sze; Qin, Jing; Pang, Wai-Man; Wang, Qiong; Heng, Pheng-Ann

2016-08-01

While research on the brain-computer interface (BCI) has been active in recent years, how to get high-quality electrical brain signals to accurately recognize human intentions for reliable communication and interaction is still a challenging task. The evidence has shown that visually guided motor imagery (MI) can modulate sensorimotor electroencephalographic (EEG) rhythms in humans, but how to design and implement efficient visual guidance during MI in order to produce better event-related desynchronization (ERD) patterns is still unclear. The aim of this paper is to investigate the effect of using object-oriented movements in a virtual environment as visual guidance on the modulation of sensorimotor EEG rhythms generated by hand MI. To improve the classification accuracy on MI, we further propose an algorithm to automatically extract subject-specific optimal frequency and time bands for the discrimination of ERD patterns produced by left and right hand MI. The experimental results show that the average classification accuracy of object-directed scenarios is much better than that of non-object-directed scenarios (76.87% vs. 69.66%). The result of the t-test measuring the difference between them is statistically significant (p = 0.0207). When compared to algorithms based on fixed frequency and time bands, contralateral dominant ERD patterns can be enhanced by using the subject-specific optimal frequency and the time bands obtained by our proposed algorithm. These findings have the potential to improve the efficacy and robustness of MI-based BCI applications. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Metabolomic and proteomic biomarkers for III-V semiconductors: chemical-specific porphyrinurias and proteinurias.

PubMed

Fowler, Bruce A; Conner, Elizabeth A; Yamauchi, Hiroshi

2005-08-07

A pressing need exists to develop and validate molecular biomarkers to assess the early effects of chemical agents, both individually and in mixtures. This is particularly true for new and chemically intensive industries such as the semiconductor industry. Previous studies from this laboratory and others have demonstrated element-specific alterations of the heme biosynthetic pathway for the III-V semiconductors gallium arsenide (GaAs) and indium arsenide (InAs) with attendant increased urinary excretion of specific heme precursors. These data represent an example of a metabolomic biomarker to assess chemical effects early, before clinical disease develops. Previous studies have demonstrated that the intratracheal or subcutaneous administration of GaAs and InAs particles to hamsters produces the induction of the major stress protein gene families in renal proximal tubule cells. This was monitored by 35-S methionine labeling of gene products followed by two-dimensional gel electrophoresis after exposure to InAs particles. The present studies examined whether these effects were associated with the development of compound-specific proteinuria after 10 or 30 days following subcutaneous injection of GaAs or InAs particles in hamsters. The results of these studies demonstrated the development of GaAs- and InAs-specific alterations in renal tubule cell protein expression patterns that varied at 10 and 30 days. At the 30-day point, cells in hamsters that received InAs particles showed marked attenuation of protein expression, suggesting inhibition of the stress protein response. These changes were associated with GaAs and InAs proteinuria patterns as monitored by two-dimensional gel electrophoresis and silver staining. The intensity of the protein excretion patterns increased between the 10- and 30-day points and was most pronounced for animals in the 30-day InAs treatment group. No overt morphologic signs of cell death were seen in renal tubule cells of these animals. Western blot analyses of the urines with antibodies to the 32-, 70-, and 90-kDa stress protein families did not show the presence of these molecules, indicating that these proteins were not excreted in the urine samples. These data suggest that the observed proteinuria patterns were not a result of cell death and that the observed chemical-specific proteinurias were produced before marked cellular toxicity. These findings suggest a hypothesis involving GaAs and InAs interference with stress protein chaperoning of reabsorbed proteins for proteosomic degradation and the probable chaperoning of damaged intracellular proteins from renal proximal tubule cells into the urinary filtrate. Overall, the results of these studies provide further information on the nephrotoxicity of these semiconductor compounds. They also suggest the use of two-dimensional gel electrophoresis with silver staining of urinary protein patterns as a potentially useful proteomic approach to renal damage early in relation to intracellular proteotoxicity in kidney tubule cells.

Calmodulin point mutations affect Drosophila development and behavior.

PubMed

Nelson, H B; Heiman, R G; Bolduc, C; Kovalick, G E; Whitley, P; Stern, M; Beckingham, K

1997-12-01

Calmodulin (CAM) is recognized as a major intermediary in intracellular calcium signaling, but as yet little is known of its role in developmental and behavioral processes. We have generated and studied mutations to the endogenous Cam gene of Drosophila melanogaster that change single amino acids within the protein coding region. One of these mutations produces a striking pupal lethal phenotype involving failure of head eversion. Various mutant combinations produce specific patterns of ectopic wing vein formation or melanotic scabs on the cuticle. Anaphase chromosome bridging is also seen as a maternal effect during the early embryonic nuclear divisions. In addition, specific behavioral defects such as poor climbing and flightlessness are detected among these mutants. Comparisons with other Drosophila mutant phenotypes suggests potential CAM targets that may mediate these developmental and behavioral effects, and analysis of the CAM crystal structure suggests the structural consequences of the individual mutations.

Calmodulin Point Mutations Affect Drosophila Development and Behavior

PubMed Central

Nelson, H. B.; Heiman, R. G.; Bolduc, C.; Kovalick, G. E.; Whitley, P.; Stern, M.; Beckingham, K.

1997-01-01

Calmodulin (CAM) is recognized as a major intermediary in intracellular calcium signaling, but as yet little is known of its role in developmental and behavioral processes. We have generated and studied mutations to the endogenous Cam gene of Drosophila melanogaster that change single amino acids within the protein coding region. One of these mutations produces a striking pupal lethal phenotype involving failure of head eversion. Various mutant combinations produce specific patterns of ectopic wing vein formation or melanotic scabs on the cuticle. Anaphase chromosome bridging is also seen as a maternal effect during the early embryonic nuclear divisions. In addition, specific behavioral defects such as poor climbing and flightlessness are detected among these mutants. Comparisons with other Drosophila mutant phenotypes suggests potential CAM targets that may mediate these developmental and behavioral effects, and analysis of the CAM crystal structure suggests the structural consequences of the individual mutations. PMID:9409836

XAP, a program for deconvolution and analysis of complex X-ray spectra

USGS Publications Warehouse

Quick, James E.; Haleby, Abdul Malik

1989-01-01

The X-ray analysis program (XAP) is a spectral-deconvolution program written in BASIC and specifically designed to analyze complex spectra produced by energy-dispersive X-ray analytical systems (EDS). XAP compensates for spectrometer drift, utilizes digital filtering to remove background from spectra, and solves for element abundances by least-squares, multiple-regression analysis. Rather than base analyses on only a few channels, broad spectral regions of a sample are reconstructed from standard reference spectra. The effects of this approach are (1) elimination of tedious spectrometer adjustments, (2) removal of background independent of sample composition, and (3) automatic correction for peak overlaps. Although the program was written specifically to operate a KEVEX 7000 X-ray fluorescence analytical system, it could be adapted (with minor modifications) to analyze spectra produced by scanning electron microscopes, electron microprobes, and probes, and X-ray defractometer patterns obtained from whole-rock powders.

Dorsal and ventral aspects of the most caudal medullary reticular formation have differential roles in modulation and formation of the respiratory motor pattern in rat.

PubMed

Jones, Sarah E; Stanić, Davor; Dutschmann, Mathias

2016-12-01

The respiratory pattern generator of mammals is anatomically organized in lateral respiratory columns (LRCs) within the brainstem. LRC compartments serve specific functions in respiratory pattern and rhythm generation. While the caudal medullary reticular formation (cMRF) has respiratory functions reportedly related to the mediation of expulsive respiratory reflexes, it remains unclear whether neurons of the cMRF functionally belong to the LRC. In the present study we specifically investigated the respiratory functions of the cMRF. Tract tracing shows that the cMRF has substantial connectivity with key compartments of the LRC, particularly the parafacial respiratory group and the Kölliker-Fuse nuclei. These neurons have a loose topography and are located in the ventral and dorsal cMRF. Systematic mapping of the cMRF with glutamate stimulation revealed potent respiratory modulation of the respiratory motor pattern from both dorsal and ventral injection sites. Pharmacological inhibition of the cMRF with the GABA-receptor agonist isoguvacine produced significant and robust changes to the baseline respiratory motor pattern (decreased laryngeal post-inspiratory and abdominal expiratory motor activity, delayed inspiratory off-switch and increased respiratory frequency) after dorsal cMRF injection, while ventral injections had no effect. The present data indicate that the ventral cMRF is not an integral part of the respiratory pattern generator and merely serves as a relay for sensory and/or higher command-related modulation of respiration. On the contrary, the dorsal aspect of the cMRF clearly has a functional role in respiratory pattern formation. These findings revive the largely abandoned concept of a dorsal respiratory group that contributes to the generation of the respiratory motor pattern.

The relationship between articulatory control and improved phonemic accuracy in childhood apraxia of speech: A longitudinal case study

PubMed Central

Grigos, Maria I.; Kolenda, Nicole

2010-01-01

Jaw movement patterns were examined longitudinally in a 3-year-old male with childhood apraxia of speech (CAS) and compared with a typically developing control group. The child with CAS was followed for 8 months, until he began accurately and consistently producing the bilabial phonemes /p/, /b/, and /m/. A movement tracking system was used to study jaw duration, displacement, velocity, and stability. A transcription analysis determined the percentage of phoneme errors and consistency. Results showed phoneme-specific changes which included increases in jaw velocity and stability over time, as well as decreases in duration. Kinematic parameters became more similar to patterns seen in the controls during final sessions where tokens were produced most accurately and consistently. Closing velocity and stability, however, were the only measures to fall within a 95% confidence interval established for the controls across all three target phonemes. These findings suggest that motor processes may differ between children with CAS and their typically developing peers. PMID:20030551

Influences of Deqi on Immediate Analgesia Effect of Needling SP6 (Sanyinjiao) in Patients with Primary Dysmenorrhea in Cold and Dampness Stagnation Pattern: Study Protocol for a Randomized Controlled Trial

PubMed Central

Liu, Yu-qi; Zhang, Peng; Xie, Jie-ping; Ma, Liang-xiao; Yuan, Hong-wen; Li, Jing; Lin, Chi; Wang, Pei; Yang, Guo-yan; Zhu, Jiang

2015-01-01

Deqi, according to traditional Chinese medicine, is a specific needle sensation during the retention of needles at certain acupoints and is considered to be necessary to produce therapeutic effects from acupuncture. Although some modern researches have showed that Deqi is essential for producing acupuncture analgesia and anesthesia, the data are not enough. It is a paper of a multicenter, randomized controlled study protocol, to evaluate the influences of Deqi on acupuncture SP6 in Cold and Dampness Stagnation pattern primary dysmenorrhea patients, in terms of reducing pain and anxiety, and to find out the relationship between Deqi and the temperature changes at SP6 (Sanyinjiao) and CV4 (Guanyuan). The results of this trial will be helpful to explain the role of Deqi in acupuncture analgesia and may provide a new objective index for measuring Deqi in the future study. This trial is registered with ChiCTR-TRC-13003086. PMID:26294921

The evolution of vertebrate Toll-like receptors

USGS Publications Warehouse

Roach, J.C.; Glusman, G.; Rowen, L.; Kaur, A.; Purcell, M.K.; Smith, K.D.; Hood, L.E.; Aderem, A.

2005-01-01

The complete sequences of Takifugu Toll-like receptor (TLR) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis. Strong selective pressure for recognition of and response to pathogen-associated molecular patterns has maintained a largely unchanging TLR recognition in all vertebrates. There are six major families of vertebrate TLRs. This repertoire is distinct from that of invertebrates. TLRs within a family recognize a general class of pathogen-associated molecular patterns. Most vertebrates have exactly one gene ortholog for each TLR family. The family including TLR1 has more species-specific adaptations than other families. A major family including TLR11 is represented in humans only by a pseudogene. Coincidental evolution plays a minor role in TLR evolution. The sequencing phase of this study produced finished genomic sequences for the 12 Takifugu rubripes TLRs. In addition, we have produced > 70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt. ?? 2005 by The National Academy of Sciences of the USA.

Study on Base Management Pattern of Food Producing Enterprise

NASA Astrophysics Data System (ADS)

Zhang, Weibin

When the food producing enterprises often comply with food safety regulations and industry management system passively, we need to consider can they transform their production and business pattern in order to avoid the food safety incidents completely? The answer is yes. The food producing enterprises can develop to the two directions of material planting and products in circulation through base management pattern substituting for the original operation pattern of in-plant processing and outside sales. The food producing enterprises should establish coordination and safe supervision mechanisms in order to achieve the management objectives of unified production, controllable risks and scale magnitude.

Distinct cell-specific expression of homospermidine synthase involved in pyrrolizidine alkaloid biosynthesis in three species of the boraginales.

PubMed

Niemüller, Daniel; Reimann, Andreas; Ober, Dietrich

2012-07-01

Homospermidine synthase (HSS) is the first specific enzyme in pyrrolizidine alkaloid (PA) biosynthesis, a pathway involved in the plant's chemical defense. HSS has been shown to be recruited repeatedly by duplication of a gene involved in primary metabolism. Within the lineage of the Boraginales, only one gene duplication event gave rise to HSS. Here, we demonstrate that the tissue-specific expression of HSS in three boraginaceous species, Heliotropium indicum, Symphytum officinale, and Cynoglossum officinale, is unique with respect to plant organ, tissue, and cell type. Within H. indicum, HSS is expressed exclusively in nonspecialized cells of the lower epidermis of young leaves and shoots. In S. officinale, HSS expression has been detected in the cells of the root endodermis and in leaves directly underneath developing inflorescences. In young roots of C. officinale, HSS is detected only in cells of the endodermis, but in a later developmental stage, additionally in the pericycle. The individual expression patterns are compared with those within the Senecioneae lineage (Asteraceae), where HSS expression is reproducibly found in specific cells of the endodermis and the adjacent cortex parenchyma of the roots. The individual expression patterns within the Boraginales species are discussed as being a requirement for the successful recruitment of HSS after gene duplication. The diversity of HSS expression within this lineage adds a further facet to the already diverse patterns of expression that have been observed for HSS in other PA-producing plant lineages, making this PA-specific enzyme one of the most diverse expressed proteins described in the literature.

Distinct Cell-Specific Expression of Homospermidine Synthase Involved in Pyrrolizidine Alkaloid Biosynthesis in Three Species of the Boraginales1[C][W][OA

PubMed Central

Niemüller, Daniel; Reimann, Andreas; Ober, Dietrich

2012-01-01

Homospermidine synthase (HSS) is the first specific enzyme in pyrrolizidine alkaloid (PA) biosynthesis, a pathway involved in the plant’s chemical defense. HSS has been shown to be recruited repeatedly by duplication of a gene involved in primary metabolism. Within the lineage of the Boraginales, only one gene duplication event gave rise to HSS. Here, we demonstrate that the tissue-specific expression of HSS in three boraginaceous species, Heliotropium indicum, Symphytum officinale, and Cynoglossum officinale, is unique with respect to plant organ, tissue, and cell type. Within H. indicum, HSS is expressed exclusively in nonspecialized cells of the lower epidermis of young leaves and shoots. In S. officinale, HSS expression has been detected in the cells of the root endodermis and in leaves directly underneath developing inflorescences. In young roots of C. officinale, HSS is detected only in cells of the endodermis, but in a later developmental stage, additionally in the pericycle. The individual expression patterns are compared with those within the Senecioneae lineage (Asteraceae), where HSS expression is reproducibly found in specific cells of the endodermis and the adjacent cortex parenchyma of the roots. The individual expression patterns within the Boraginales species are discussed as being a requirement for the successful recruitment of HSS after gene duplication. The diversity of HSS expression within this lineage adds a further facet to the already diverse patterns of expression that have been observed for HSS in other PA-producing plant lineages, making this PA-specific enzyme one of the most diverse expressed proteins described in the literature. PMID:22566491

The spatiotemporal order of signaling events unveils the logic of development signaling.

PubMed

Zhu, Hao; Owen, Markus R; Mao, Yanlan

2016-08-01

Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. The model is available upon request. hao.zhu@ymail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

The spatiotemporal order of signaling events unveils the logic of development signaling

PubMed Central

Zhu, Hao; Owen, Markus R.; Mao, Yanlan

2016-01-01

Motivation: Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. Results: We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. Availability and implementation: The model is available upon request. Contact: hao.zhu@ymail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153573

Evaporation-induced patterns from droplets containing motile and nonmotile bacteria.

PubMed

Nellimoottil, Tittu Thomas; Rao, Pinjala Nagaraju; Ghosh, Siddhartha Sankar; Chattopadhyay, Arun

2007-08-14

In this letter, we report the observations of specific pattern formation from the evaporation of aqueous droplets containing motile and nonmotile bacteria. We found that when motile bacteria were present the droplet evaporated into disclike patterned deposits of bacteria. However, when the bacteria were made nonmotile by treatment with liquid nitrogen, the droplet evaporated into ringlike deposits. We also observed that bacteria with higher motility produced more uniformly deposited disclike patterns. Furthermore, we propose a model with numerical simulations to explain the mechanism of formation of these patterns. The model is based on the advective fluid flow from the center of the droplet toward the edge due to enhanced evaporation from the edge of the pinned droplet in comparison to that from the free surface. For the case of motile bacteria, we have added another velocity parameter toward the axis of the droplet and directed against the fluid flow in order to account for the disclike pattern formation. The numerical simulations match the experimental observations well. The present work, by qualitative and quantitative understanding of the evaporation of bacteria droplets, demonstrates that the inherent bacterial motility is primarily responsible for the formation of these differential patterns.

Mask replication using jet and flash imprint lithography

NASA Astrophysics Data System (ADS)

Selinidis, Kosta S.; Jones, Chris; Doyle, Gary F.; Brown, Laura; Imhof, Joseph; LaBrake, Dwayne L.; Resnick, Douglas J.; Sreenivasan, S. V.

2011-11-01

The Jet and Flash Imprint Lithography (J-FILTM) process uses drop dispensing of UV curable resists to assist high resolution patterning for subsequent dry etch pattern transfer. The technology is actively being used to develop solutions for memory markets including Flash memory and patterned media for hard disk drives. It is anticipated that the lifetime of a single template (for patterned media) or mask (for semiconductor) will be on the order of 104 - 105imprints. This suggests that tens of thousands of templates/masks will be required to satisfy the needs of a manufacturing environment. Electron-beam patterning is too slow to feasibly deliver these volumes, but instead can provide a high quality "master" mask which can be replicated many times with an imprint lithography tool. This strategy has the capability to produce the required supply of "working" templates/masks. In this paper, we review the development of the mask form factor, imprint replication tools and the semiconductor mask replication process. A PerfectaTM MR5000 mask replication tool has been developed specifically to pattern replica masks from an ebeam written master. Performance results, including image placement, critical dimension uniformity, and pattern transfer are covered in detail.

High performance embedded system for real-time pattern matching

NASA Astrophysics Data System (ADS)

Sotiropoulou, C.-L.; Luciano, P.; Gkaitatzis, S.; Citraro, S.; Giannetti, P.; Dell'Orso, M.

2017-02-01

In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device.

Epigenetic variants of a transgenic petunia line show hypermethylation in transgene DNA: an indication for specific recognition of foreign DNA in transgenic plants.

PubMed

Meyer, P; Heidmann, I

1994-05-25

We analysed de novo DNA methylation occurring in plants obtained from the transgenic petunia line R101-17. This line contains one copy of the maize A1 gene that leads to the production of brick-red pelargonidin pigment in the flowers. Due to its integration into an unmethylated genomic region the A1 transgene is hypomethylated and transcriptionally active. Several epigenetic variants of line 17 were selected that exhibit characteristic and somatically stable pigmentation patterns, displaying fully coloured, marbled or colourless flowers. Analysis of the DNA methylation patterns revealed that the decrease in pigmentation among the epigenetic variants was correlated with an increase in methylation, specifically of the transgene DNA. No change in methylation of the hypomethylated integration region could be detected. A similar increase in methylation, specifically in the transgene region, was also observed among progeny of R101-17del, a deletion derivative of R101-17 that no longer produces pelargonidin pigments due to a deletion in the A1 coding region. Again de novo methylation is specifically directed to the transgene, while the hypomethylated character of neighbouring regions is not affected. Possible mechanisms for transgene-specific methylation and its consequences for long-term use of transgenic material are discussed.

Kinematics, muscular activity and propulsion in gopher snakes

PubMed

Moon; Gans

1998-10-01

Previous studies have addressed the physical principles and muscular activity patterns underlying terrestrial lateral undulation in snakes, but not the mechanism by which muscular activity produces curvature and propulsion. In this study, we used synchronized electromyography and videography to examine the muscular basis and propulsive mechanism of terrestrial lateral undulation in gopher snakes Pituophis melanoleucus affinis. Specifically, we used patch electrodes to record from the semispinalis, longissimus dorsi and iliocostalis muscles in snakes pushing against one or more pegs. Axial bends propagate posteriorly along the body and contact the pegs at or immediately posterior to an inflection of curvature, which then reverses anterior to the peg. The vertebral column bends broadly around a peg, whereas the body wall bends sharply and asymmetrically around the anterior surface of the peg. The epaxial muscles are always active contralateral to the point of contact with a peg; they are activated slightly before or at the point of maximal convexity and deactivated variably between the inflection point and the point of maximal concavity. This pattern is consistent with muscular shortening and the production of axial bends, although variability in the pattern indicates that other muscles may affect the mechanics of the epaxial muscles. The kinematic and motor patterns in snakes crawling against experimentally increased drag indicated that forces are produced largely by muscles that are active in the axial bend around each peg, rather than by distant muscles from which the forces might be transmitted by connective tissues. At each point of force exertion, the propulsive mechanism of terrestrial lateral undulation may be modeled as a type of cam-follower, in which continuous bending of the trunk around the peg produces translation of the snake.

Force-stabilizing synergies in motor tasks involving two actors

PubMed Central

Solnik, Stanislaw; Reschechtko, Sasha; Wu, Yen-Hsun; Zatsiorsky, Vladimir M.; Latash, Mark L.

2015-01-01

We investigated the ability of two persons to produce force-stabilizing synergies in accurate multi-finger force production tasks under visual feedback on the total force only. The subjects produced a time profile of total force (the sum of two hand forces in one-person tasks and the sum of two subject forces in two-person tasks) consisting of a ramp-up, steady-state, and ramp-down segments; the steady-state segment was interrupted in the middle by a quick force pulse. Analyses of the structure of inter-trial finger force variance, motor equivalence, anticipatory synergy adjustments (ASAs), and the unintentional drift of the sharing pattern were performed. The two-person performance was characterized by a dramatically higher amount of inter-trial variance that did not affect total force, higher finger force deviations that did not affect total force (motor equivalent deviations), shorter ASAs, and larger drift of the sharing pattern. The rate of sharing pattern drift correlated with the initial disparity between the forces produced by the two persons (or two hands). The drift accelerated following the quick force pulse. Our observations show that sensory information on the task-specific performance variable is sufficient for the organization of performance-stabilizing synergies. They suggest, however, that two actors are less likely to follow a single optimization criterion as compared to a single performer. The presence of ASAs in the two-person condition might reflect fidgeting by one or both of the subjects. We discuss the characteristics of the drift in the sharing pattern as reflections of different characteristic times of motion within the sub-spaces that affect and do not affect salient performance variables. PMID:26105756

Force-stabilizing synergies in motor tasks involving two actors.

PubMed

Solnik, Stanislaw; Reschechtko, Sasha; Wu, Yen-Hsun; Zatsiorsky, Vladimir M; Latash, Mark L

2015-10-01

We investigated the ability of two persons to produce force-stabilizing synergies in accurate multi-finger force production tasks under visual feedback on the total force only. The subjects produced a time profile of total force (the sum of two hand forces in one-person tasks and the sum of two subject forces in two-person tasks) consisting of a ramp-up, steady-state, and ramp-down segments; the steady-state segment was interrupted in the middle by a quick force pulse. Analyses of the structure of inter-trial finger force variance, motor equivalence, anticipatory synergy adjustments (ASAs), and the unintentional drift of the sharing pattern were performed. The two-person performance was characterized by a dramatically higher amount of inter-trial variance that did not affect total force, higher finger force deviations that did not affect total force (motor equivalent deviations), shorter ASAs, and larger drift of the sharing pattern. The rate of sharing pattern drift correlated with the initial disparity between the forces produced by the two persons (or two hands). The drift accelerated following the quick force pulse. Our observations show that sensory information on the task-specific performance variable is sufficient for the organization of performance-stabilizing synergies. They suggest, however, that two actors are less likely to follow a single optimization criterion as compared to a single performer. The presence of ASAs in the two-person condition might reflect fidgeting by one or both of the subjects. We discuss the characteristics of the drift in the sharing pattern as reflections of different characteristic times of motion within the subspaces that affect and do not affect salient performance variables.

Combination of Fluorescent in situ Hybridization (FISH) and Immunofluorescence Imaging for Detection of Cytokine Expression in Microglia/Macrophage Cells

PubMed Central

Fe Lanfranco, Maria; Loane, David J.; Mocchetti, Italo; Burns, Mark P.; Villapol, Sonia

2017-01-01

Microglia and macrophage cells are the primary producers of cytokines in response to neuroinflammatory processes. But these cytokines are also produced by other glial cells, endothelial cells, and neurons. It is essential to identify the cells that produce these cytokines to target their different levels of activation. We used dual RNAscope® fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) techniques to visualize the mRNA expression pattern of pro- and anti-inflammatory cytokines in microglia/macrophages cells. Using these methods, we can associate one mRNA to specific cell types when combining with different cellular markers by immunofluorescence. Results from RNAscope® probes IL-1β, TNFα, TGFβ, IL-10 or Arg1, showed colocalization with antibodies for microglia/macrophage cells. These target probes showed adequate sensitivity and specificity to detect mRNA expression. New FISH detection techniques combined with immunohistochemical techniques will help to jointly determine the protein and mRNA localization, as well as provide reliable quantification of the mRNA expression levels. PMID:29238736

Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment.

PubMed

Exarchos, Konstantinos P; Exarchos, Themis P; Rigas, Georgios; Papaloukas, Costas; Fotiadis, Dimitrios I

2011-05-10

In peptides and proteins, only a small percentile of peptide bonds adopts the cis configuration. Especially in the case of amide peptide bonds, the amount of cis conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline cis formations (cis-nonPro). In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the cis-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with cis-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between cis-nonPro and trans-nonPro formations. In terms of functional implications, we observe a significant association of cis-nonPro peptide bonds towards ligand/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.

The medial prefrontal and orbitofrontal cortices differentially regulate dopamine system function.

PubMed

Lodge, Daniel J

2011-05-01

The prefrontal cortex (PFC) is essential for top-down control over higher-order executive function. In this study we demonstrate that the medial prefrontal cortex (mPFC) and orbitofrontal cortex (OFC) differentially regulate VTA dopamine neuron activity, and furthermore, the pattern of activity in the PFC drastically alters the dopamine neuron response. Thus, although single-pulse activation of the mPFC either excites or inhibits equivalent numbers of dopamine neurons, activation of the OFC induces a primarily inhibitory response. Moreover, activation of the PFC with a pattern that mimics spontaneous burst firing of pyramidal neurons produces a strikingly different response. Specifically, burst-like activation of the mPFC induces a massive increase in dopamine neuron firing, whereas a similar pattern of OFC activation largely inhibits dopamine activity. Taken together, these data demonstrate that the mPFC and OFC differentially regulate dopamine neuron activity, and that the pattern of cortical activation is critical for determining dopamine system output.

Alternative splicing of the tyrosinase gene transcript in normal human melanocytes and lymphocytes.

PubMed

Fryer, J P; Oetting, W S; Brott, M J; King, R A

2001-11-01

We have identified and isolated ectopically expressed tyrosinase transcripts in normal human melanocytes and lymphocytes and in a human melanoma (MNT-1) cell line to establish a baseline for the expression pattern of this gene in normal tissue. Tyrosinase mRNA from human lymphoblastoid cell lines was reverse transcribed and amplified using specific "nested" primers. This amplification yielded eight identifiable transcripts; five that resulted from alternative splicing patterns arising from the utilization of normal and alternative splice sequences. Identical splicing patterns were found in transcripts from human primary melanocytes in culture and a melanoma cell line, indicating that lymphoblastoid cell lines provide an accurate reflection of transcript processing in melanocytes. Similar splicing patterns have also been found with murine melanocyte tyrosinase transcripts. Our results demonstrate that alternative splicing of human tyrosinase gene transcript produces a number of predictable and identifiable transcripts, and that human lymphoblastoid cell lines provide a source of ectopically expressed transcripts that can be used to study the biology of tyrosinase gene expression in humans.

Shared memories reveal shared structure in neural activity across individuals

PubMed Central

Chen, J.; Leong, Y.C.; Honey, C.J.; Yong, C.H.; Norman, K.A.; Hasson, U.

2016-01-01

Our lives revolve around sharing experiences and memories with others. When different people recount the same events, how similar are their underlying neural representations? Participants viewed a fifty-minute movie, then verbally described the events during functional MRI, producing unguided detailed descriptions lasting up to forty minutes. As each person spoke, event-specific spatial patterns were reinstated in default-network, medial-temporal, and high-level visual areas. Individual event patterns were both highly discriminable from one another and similar between people, suggesting consistent spatial organization. In many high-order areas, patterns were more similar between people recalling the same event than between recall and perception, indicating systematic reshaping of percept into memory. These results reveal the existence of a common spatial organization for memories in high-level cortical areas, where encoded information is largely abstracted beyond sensory constraints; and that neural patterns during perception are altered systematically across people into shared memory representations for real-life events. PMID:27918531

Scattering apodizer for laser beams

DOEpatents

Summers, Mark A.; Hagen, Wilhelm F.; Boyd, Robert D.

1985-01-01

A method is disclosed for apodizing a laser beam to smooth out the production of diffraction peaks due to optical discontinuities in the path of the laser beam, such method comprising introduction of a pattern of scattering elements for reducing the peak intensity in the region of such optical discontinuities, such pattern having smoothly tapering boundaries in which the distribution density of the scattering elements is tapered gradually to produce small gradients in the distribution density, such pattern of scattering elements being effective to reduce and smooth out the diffraction effects which would otherwise be produced. The apodizer pattern may be produced by selectively blasting a surface of a transparent member with fine abrasive particles to produce a multitude of minute pits. In one embodiment, a scattering apodizer pattern is employed to overcome diffraction patterns in a multiple element crystal array for harmonic conversion of a laser beam. The interstices and the supporting grid between the crystal elements are obscured by the gradually tapered apodizer pattern of scattering elements.

Scattering apodizer for laser beams

DOEpatents

Summers, M.A.; Hagen, W.F.; Boyd, R.D.

1984-01-01

A method is disclosed for apodizing a laser beam to smooth out the production of diffraction peaks due to optical discontinuities in the path of the laser beam, such method comprising introduction of a pattern of scattering elements for reducing the peak intensity in the region of such optical discontinuities, such pattern having smoothly tapering boundaries in which the distribution density of the scattering elements is tapered gradually to produce small gradients in the distribution density, such pattern of scattering elements being effective to reduce and smooth out the diffraction effects which would otherwise be produced. The apodizer pattern may be produced by selectively blasting a surface of a transparent member with fine abrasive particles to produce a multitude of minute pits. In one embodiment, a scattering apodizer pattern is employed to overcome diffraction patterns in a multiple element crystal array for harmonic conversion of a laser beam. The interstices and the supporting grid between the crystal elements are obscured by the gradually tapered apodizer pattern of scattering elements.

Methods of biological dosimetry employing chromosome-specific staining

DOEpatents

Gray, Joe W.; Pinkel, Daniel

2000-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Methods And Compositions For Chromosome-Specific Staining

DOEpatents

Gray, Joe W.; Pinkel, Daniel

2003-08-19

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Compositions for chromosome-specific staining

DOEpatents

Gray, Joe W.; Pinkel, Daniel

1998-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Compositions for chromosome-specific staining

DOEpatents

Gray, J.W.; Pinkel, D.

1998-05-26

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. The methods produce staining patterns that can be tailored for specific cytogenetic analyses. The probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. The invention provides for automated means to detect and analyze chromosomal abnormalities. 17 figs.

Cytokinin signalling inhibitory fields provide robustness to phyllotaxis

NASA Astrophysics Data System (ADS)

Besnard, Fabrice; Refahi, Yassin; Morin, Valérie; Marteaux, Benjamin; Brunoud, Géraldine; Chambrier, Pierre; Rozier, Frédérique; Mirabet, Vincent; Legrand, Jonathan; Lainé, Stéphanie; Thévenon, Emmanuel; Farcot, Etienne; Cellier, Coralie; Das, Pradeep; Bishopp, Anthony; Dumas, Renaud; Parcy, François; Helariutta, Ykä; Boudaoud, Arezki; Godin, Christophe; Traas, Jan; Guédon, Yann; Vernoux, Teva

2014-01-01

How biological systems generate reproducible patterns with high precision is a central question in science. The shoot apical meristem (SAM), a specialized tissue producing plant aerial organs, is a developmental system of choice to address this question. Organs are periodically initiated at the SAM at specific spatial positions and this spatiotemporal pattern defines phyllotaxis. Accumulation of the plant hormone auxin triggers organ initiation, whereas auxin depletion around organs generates inhibitory fields that are thought to be sufficient to maintain these patterns and their dynamics. Here we show that another type of hormone-based inhibitory fields, generated directly downstream of auxin by intercellular movement of the cytokinin signalling inhibitor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), is involved in regulating phyllotactic patterns. We demonstrate that AHP6-based fields establish patterns of cytokinin signalling in the meristem that contribute to the robustness of phyllotaxis by imposing a temporal sequence on organ initiation. Our findings indicate that not one but two distinct hormone-based fields may be required for achieving temporal precision during formation of reiterative structures at the SAM, thus indicating an original mechanism for providing robustness to a dynamic developmental system.

Streamflow and sediment dynamics of the Middle Rio Grande Valley, New Mexico, in the context of cottonwood recruitment

USGS Publications Warehouse

Milhous, Robert T.; Wondzell, Mark; Ritter, Amy

1993-01-01

The cottonwood gallery forests of the Middle Rio Grande floodplain in New Mexico provide important habitats for birds and other animals. Over the last century, these forests have changed significantly due to invasion of exotics such as salt cedar and Russian olive, which compete with native cottonwoods, and changes in water use both in the valley and upstream. To successfully germinate and establish, cottonwoods require an adequate water supply, abundant sunlight, and bare, litter-free substrate. Native cottonwoods are adapted to a natural snowmelt hydrograph characterized by spring floods in late May or early June and gradually receding streamflows throughout the remainder of the summer. The natural streamflow pattern has been significantly modified by water management in the Rio Grande basin. The modified pattern is less conducive to establishment of cottonwoods than the natural pattern. In addition, exotic species now compete with native cottonwoods, and the modified flow pattern may favor these exotics. The overall objective of this study was to investigate the possibility of enhancing cottonwood establishment and recruitment along the Middle Rio Grande through streamflow manipulation and reservoir releases. The work integrates concepts of cottonwood establishment, water resources management, and river morphology, and investigates how water management might be used to preserve and enhance cottonwood gallery forests along the river. Specific objectives of the work reported herein were to: (1) develop a technique to calculate flows that will produce channel characteristics necessary to restore and sustain cottonwood gallery forests; (2) develop a model to determine a flow pattern, or sequence of flows, that will improve the potential for cottonwood establishment and recruitment; and (3) determine if the water resources can be managed to produce the desired channel characteristics and flow pattern identified in (1) and (2).

Self-Organized Behavior Generation for Musculoskeletal Robots.

PubMed

Der, Ralf; Martius, Georg

2017-01-01

With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.

Self-Organized Behavior Generation for Musculoskeletal Robots

PubMed Central

Der, Ralf; Martius, Georg

2017-01-01

With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors “waiting” to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics. PMID:28360852

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.

A high-resolution method for the localization of proanthocyanidins in plant tissues

PubMed Central

2011-01-01

Background Histochemical staining of plant tissues with 4-dimethylaminocinnamaldehyde (DMACA) or vanillin-HCl is widely used to characterize spatial patterns of proanthocyanidin accumulation in plant tissues. These methods are limited in their ability to allow high-resolution imaging of proanthocyanidin deposits. Results Tissue embedding techniques were used in combination with DMACA staining to analyze the accumulation of proanthocyanidins in Lotus corniculatus (L.) and Trifolium repens (L.) tissues. Embedding of plant tissues in LR White or paraffin matrices, with or without DMACA staining, preserved the physical integrity of the plant tissues, allowing high-resolution imaging that facilitated cell-specific localization of proanthocyanidins. A brown coloration was seen in proanthocyanidin-producing cells when plant tissues were embedded without DMACA staining and this was likely to have been due to non-enzymatic oxidation of proanthocyanidins and the formation of colored semiquinones and quinones. Conclusions This paper presents a simple, high-resolution method for analysis of proanthocyanidin accumulation in organs, tissues and cells of two plant species with different patterns of proanthocyanidin accumulation, namely Lotus corniculatus (birdsfoot trefoil) and Trifolium repens (white clover). This technique was used to characterize cell type-specific patterns of proanthocyanidin accumulation in white clover flowers at different stages of development. PMID:21595992

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.

Evaluation of photomask flatness compensation for extreme ultraviolet lithography

NASA Astrophysics Data System (ADS)

Ballman, Katherine; Lee, Christopher; Zimmerman, John; Dunn, Thomas; Bean, Alexander

2016-10-01

As the semiconductor industry continues to strive towards high volume manufacturing for EUV, flatness specifications for photomasks have decreased to below 10nm for 2018 production, however the current champion masks being produced report P-V flatness values of roughly 50nm. Write compensation presents the promising opportunity to mitigate pattern placement errors through the use of geometrically adjusted target patterns which counteract the reticle's flatness induced distortions and address the differences in chucking mechanisms between e-beam write and electrostatic clamping during scan. Compensation relies on high accuracy flatness data which provides the critical topographical components of the reticle to the write tool. Any errors included in the flatness data file are translated to the pattern during the write process, which has now driven flatness measurement tools to target a 6σ reproducibility <1nm. Using data collected from a 2011 Sematech study on the Alpha Demo Tool, the proposed methodology for write compensation is validated against printed wafer results. Topographic features which lack compensation capability must then be held to stringent specifications in order to limit their contributions to the final image placement error (IPE) at wafer. By understanding the capabilities and limitations of write compensation, it is then possible to shift flatness requirements towards the "non-correctable" portion of the reticle's profile, potentially relieving polishers from having to adhere to the current single digit flatness specifications.

Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning

PubMed Central

Fakhro, Khalid A.; Choi, Murim; Ware, Stephanie M.; Belmont, John W.; Towbin, Jeffrey A.; Lifton, Richard P.; Khokha, Mustafa K.; Brueckner, Martina

2011-01-01

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10−4). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10−6). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning. PMID:21282601

Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning.

PubMed

Fakhro, Khalid A; Choi, Murim; Ware, Stephanie M; Belmont, John W; Towbin, Jeffrey A; Lifton, Richard P; Khokha, Mustafa K; Brueckner, Martina

2011-02-15

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10(-4)). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10(-6)). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning.

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

Self-organization in a diversity induced thermodynamics.

PubMed

Scirè, Alessandro; Annovazzi-Lodi, Valerio

2017-01-01

In this work we show how global self-organized patterns can come out of a disordered ensemble of point oscillators, as a result of a deterministic, and not of a random, cooperative process. The resulting system dynamics has many characteristics of classical thermodynamics. To this end, a modified Kuramoto model is introduced, by including Euclidean degrees of freedom and particle polarity. The standard deviation of the frequency distribution is the disorder parameter, diversity, acting as temperature, which is both a source of motion and of disorder. For zero and low diversity, robust static phase-synchronized patterns (crystals) appear, and the problem reverts to a generic dissipative many-body problem. From small to moderate diversity crystals display vibrations followed by structure disintegration in a competition of smaller dynamic patterns, internally synchronized, each of which is capable to manage its internal diversity. In this process a huge variety of self-organized dynamic shapes is formed. Such patterns can be seen again as (more complex) oscillators, where the same description can be applied in turn, renormalizing the problem to a bigger scale, opening the possibility of pattern evolution. The interaction functions are kept local because our idea is to build a system able to produce global patterns when its constituents only interact at the bond scale. By further increasing the oscillator diversity, the dynamics becomes erratic, dynamic patterns show short lifetime, and finally disappear for high diversity. Results are neither qualitatively dependent on the specific choice of the interaction functions nor on the shape of the probability function assumed for the frequencies. The system shows a phase transition and a critical behaviour for a specific value of diversity.

Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

PubMed Central

Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

2009-01-01

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming.

PubMed

Couldrey, Christine; Lee, Rita Sf

2010-03-07

Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI). Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1) showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a good predictor of whether the foetus would develop to term or not.

DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

PubMed Central

2010-01-01

Background Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI). Results Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1) showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. Conclusion These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a good predictor of whether the foetus would develop to term or not. PMID:20205951

Divergent phenological response to hydroclimate variability in forested mountain watersheds.

PubMed

Hwang, Taehee; Band, Lawrence E; Miniat, Chelcy F; Song, Conghe; Bolstad, Paul V; Vose, James M; Love, Jason P

2014-08-01

Mountain watersheds are primary sources of freshwater, carbon sequestration, and other ecosystem services. There is significant interest in the effects of climate change and variability on these processes over short to long time scales. Much of the impact of hydroclimate variability in forest ecosystems is manifested in vegetation dynamics in space and time. In steep terrain, leaf phenology responds to topoclimate in complex ways, and can produce specific and measurable shifts in landscape forest patterns. The onset of spring is usually delayed at a specific rate with increasing elevation (often called Hopkins' Law; Hopkins, 1918), reflecting the dominant controls of temperature on greenup timing. Contrary with greenup, leaf senescence shows inconsistent trends along elevation gradients. Here, we present mechanisms and an explanation for this variability and its significance for ecosystem patterns and services in response to climate. We use moderate-resolution imaging spectro-radiometer (MODIS) Normalized Difference Vegetation Index (NDVI) data to derive landscape-induced phenological patterns over topoclimate gradients in a humid temperate broadleaf forest in southern Appalachians. These phenological patterns are validated with different sets of field observations. Our data demonstrate that divergent behavior of leaf senescence with elevation is closely related to late growing season hydroclimate variability in temperature and water balance patterns. Specifically, a drier late growing season is associated with earlier leaf senescence at low elevation than at middle elevation. The effect of drought stress on vegetation senescence timing also leads to tighter coupling between growing season length and ecosystem water use estimated from observed precipitation and runoff generation. This study indicates increased late growing season drought may be leading to divergent ecosystem response between high and low elevation forests. Landscape-induced phenological patterns are easily observed over wide areas and may be used as a unique diagnostic for sources of ecosystem vulnerability and sensitivity to hydroclimate change. © 2014 John Wiley & Sons Ltd.

Functional implications of Major Histocompatibility (MH) variation using estuarine fish populations.

PubMed

Cohen, Sarah; Tirindelli, Joëlle; Gomez-Chiarri, Marta; Nacci, Diane

2006-12-01

Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under strong directional selection by pathogens have revealed fascinating cases of MHC allelic disease linkage. More generally in genetically diverse species, however, these linkages may be hard to find. In this paper, we review approaches for assessing functional variation in MHC and discuss their potential use for discovering smaller-scale intraspecific spatial and temporal patterns of MHC variation. Then, we describe and illustrate an approach using the structural model to produce a population composite of variation in antigen-binding regions by mapping population-specific substitutions onto functional regions of the molecule. We are producing models of variation in major histocompatibility (MH) loci for populations of non-migratory fish (killifish, Fundulus heteroclitus) resident at sites that vary dramatically in environmental quality. We discuss the goal of relating MH population variation to functional differences in disease susceptibility such as those inferred by observations of parasitic infection and direct measurement of bacterial challenges in the laboratory. Our study has focused on relatively well-studied killifish populations, including those resident in a highly disturbed, chemically contaminated estuary and nearby less contaminated sites. Population-specific genetic changes at MHC antigen-binding loci are described, and evidence relevant to functional implications of these changes is reviewed. Population-specific patterns of variation in antigen-binding regions in combination with a range of assessments of immune function will provide a powerful new approach to reveal functional changes in MHC.

Land use and land cover mapping: City of Palm Bay, Florida

NASA Technical Reports Server (NTRS)

Barile, D. D.; Pierce, R.

1977-01-01

Two different computer systems were compared for use in making land use and land cover maps. The Honeywell 635 with the LANDSAT signature development program (LSDP) produced a map depicting general patterns, but themes were difficult to classify as specific land use. Urban areas were unclassified. The General Electric Image 100 produced a map depicting eight land cover categories classifying 68 percent of the total area. Ground truth, LSDP, and Image 100 maps were all made to the same scale for comparison. LSDP agreed with the ground truth 60 percent and 64 percent within the two test areas compared and Image 100 was in agreement 70 percent and 80 percent.

Dissipative inertial transport patterns near coherent Lagrangian eddies in the ocean.

PubMed

Beron-Vera, Francisco J; Olascoaga, María J; Haller, George; Farazmand, Mohammad; Triñanes, Joaquín; Wang, Yan

2015-08-01

Recent developments in dynamical systems theory have revealed long-lived and coherent Lagrangian (i.e., material) eddies in incompressible, satellite-derived surface ocean velocity fields. Paradoxically, observed drifting buoys and floating matter tend to create dissipative-looking patterns near oceanic eddies, which appear to be inconsistent with the conservative fluid particle patterns created by coherent Lagrangian eddies. Here, we show that inclusion of inertial effects (i.e., those produced by the buoyancy and size finiteness of an object) in a rotating two-dimensional incompressible flow context resolves this paradox. Specifically, we obtain that anticyclonic coherent Lagrangian eddies attract (repel) negatively (positively) buoyant finite-size particles, while cyclonic coherent Lagrangian eddies attract (repel) positively (negatively) buoyant finite-size particles. We show how these results explain dissipative-looking satellite-tracked surface drifter and subsurface float trajectories, as well as satellite-derived Sargassum distributions.

Neutron Capture Rates and the r-Process Abundance Pattern in Shocked Neutrino-Driven Winds

NASA Astrophysics Data System (ADS)

Barringer, Daniel; Surman, Rebecca

2009-10-01

The r-process is an important process in nucleosynthesis in which nuclei will undergo rapid neutron captures. Models of the r-process require nuclear data such as neutron capture rates for thousands of individual nuclei, many of which lie far from stability. Among the potential sites for the r-process, and the one that we investigate, is the shocked neutrino-driven wind in core-collapse supernovae. Here we examine the importance of the neutron capture rates of specific, individual nuclei in the second r-process abundance peak occurring at A ˜ 130 for a range of parameterized neutrino-driven wind trajectories. Of specific interest are the nuclei whose capture rates affect the abundances of nuclei outside of the A ˜ 130 peak. We found that increasing the neutron capture rate for a number of nuclei including ^135In, ^132Sn, ^133Sb, ^137Sb, and ^136Te can produce changes in the resulting abundance pattern of up to 13%.

Delineating the Diversity of Spinal Interneurons in Locomotor Circuits.

PubMed

Gosgnach, Simon; Bikoff, Jay B; Dougherty, Kimberly J; El Manira, Abdeljabbar; Lanuza, Guillermo M; Zhang, Ying

2017-11-08

Locomotion is common to all animals and is essential for survival. Neural circuits located in the spinal cord have been shown to be necessary and sufficient for the generation and control of the basic locomotor rhythm by activating muscles on either side of the body in a specific sequence. Activity in these neural circuits determines the speed, gait pattern, and direction of movement, so the specific locomotor pattern generated relies on the diversity of the neurons within spinal locomotor circuits. Here, we review findings demonstrating that developmental genetics can be used to identify populations of neurons that comprise these circuits and focus on recent work indicating that many of these populations can be further subdivided into distinct subtypes, with each likely to play complementary functions during locomotion. Finally, we discuss data describing the manner in which these populations interact with each other to produce efficient, task-dependent locomotion. Copyright © 2017 the authors 0270-6474/17/3710835-07$15.00/0.

Species-specific patterns of hyperostosis in marine teleost fishes

USGS Publications Warehouse

Smith-Vaniz, William F.; Kaufman, L.S.; Glowacki, J.

1995-01-01

The occurrence of swollen or hyperostotic bones in skeletal preparations, preserved museum material or whole fresh specimens of marine teleost fishes was identified in 92 species belonging to 22 families. Patterns of hyperostotic skeletal growth were typically consistent and often species-specific in all individuals larger than a certain size. The taxonomic distribution of hyperostosis in diverse phylogenetic groups suggests that it has arisen independently many times. Selected bones from two species of the family Carangidae, horse-eye jack Caranx latus Agassiz and crevalle jackCaranx hippos (Linnaeus), were examined in detail by light and electron microscopy. Nonhyperostotic bone contained osteoid-producing osteoblasts, resorbing osteoclasts, occasional osteocytes, and a rich vascular network, all characteristics of cellular bone. Thus, these fishes have a spatial juxtaposition of cellular and acellular bone tissues in adjacent and often serially homologous bone sites. The functional significance of hyperostosis is unknown, but it is a predictable manifestation of bone growth and development for the many taxa in which it occurs.

Classification of Thermal Patterns at Karst Springs and Cave Streams

USGS Publications Warehouse

Luhmann, A.J.; Covington, M.D.; Peters, Albert J.; Alexander, S.C.; Anger, C.T.; Green, J.A.; Runkel, Anthony C.; Alexander, E.C.

2011-01-01

Thermal patterns of karst springs and cave streams provide potentially useful information concerning aquifer geometry and recharge. Temperature monitoring at 25 springs and cave streams in southeastern Minnesota has shown four distinct thermal patterns. These patterns can be divided into two types: those produced by flow paths with ineffective heat exchange, such as conduits, and those produced by flow paths with effective heat exchange, such as small fractures and pore space. Thermally ineffective patterns result when water flows through the aquifer before it can equilibrate to the rock temperature. Thermally ineffective patterns can be either event-scale, as produced by rainfall or snowmelt events, or seasonal scale, as produced by input from a perennial surface stream. Thermally effective patterns result when water equilibrates to rock temperature, and the patterns displayed depend on whether the aquifer temperature is changing over time. Shallow aquifers with seasonally varying temperatures display a phase-shifted seasonal signal, whereas deeper aquifers with constant temperatures display a stable temperature pattern. An individual aquifer may display more than one of these patterns. Since karst aquifers typically contain both thermally effective and ineffective routes, we argue that the thermal response is strongly influenced by recharge mode. ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

Additive effects of word frequency and stimulus quality: the influence of trial history and data transformations.

PubMed

Balota, David A; Aschenbrenner, Andrew J; Yap, Melvin J

2013-09-01

A counterintuitive and theoretically important pattern of results in the visual word recognition literature is that both word frequency and stimulus quality produce large but additive effects in lexical decision performance. The additive nature of these effects has recently been called into question by Masson and Kliegl (in press), who used linear mixed effects modeling to provide evidence that the additive effects were actually being driven by previous trial history. Because Masson and Kliegl also included semantic priming as a factor in their study and recent evidence has shown that semantic priming can moderate the additivity of word frequency and stimulus quality (Scaltritti, Balota, & Peressotti, 2012), we reanalyzed data from 3 published studies to determine if previous trial history moderated the additive pattern when semantic priming was not also manipulated. The results indicated that previous trial history did not influence the joint influence of word frequency and stimulus quality. More important, and independent of Masson and Kliegl's conclusions, we also show how a common transformation used in linear mixed effects analyses to normalize the residuals can systematically alter the way in which two variables combine to influence performance. Specifically, using transformed, rather than raw reaction times, consistently produces more underadditive patterns. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Dissemination of IMP-6 metallo-β-lactamase-producing Pseudomonas aeruginosa sequence type 235 in Korea.

PubMed

Seok, Yoonmi; Bae, Il Kwon; Jeong, Seok Hoon; Kim, Soo Hyun; Lee, Hyukmin; Lee, Kyungwon

2011-12-01

To investigate the epidemiological traits of Pseudomonas aeruginosa clinical isolates producing metallo-β-lactamases (MBLs) in Korea. A total of 386 non-duplicate P. aeruginosa clinical isolates were collected from Korea in 2009. Detection of MBL genes was performed by PCR. The genetic organization of class 1 integrons carrying the MBL gene cassette was investigated by PCR mapping and sequencing. The epidemiological relationships of the isolates were investigated by multilocus sequence typing and PFGE. Of 386 P. aeruginosa isolates, 30 (7.8%) isolates carried the bla(IMP-6) gene and 1 (0.3%) isolate carried the bla(VIM-2) gene. A probe specific for the bla(IMP-6) gene was hybridized to an ∼950 kbp I-CeuI-macrorestriction fragment from all 30 isolates and a probe specific for the bla(VIM-2) gene also hybridized to an ∼500 kbp I-CeuI-macrorestriction fragment from 1 isolate (BDC10). All 31 MBL-producing isolates shared an identical sequence type (ST), ST235, and they carried the same bla(OXA-50) allelic type, bla(OXA-50g). All MBL-producing isolates showed similar XbaI-macrorestriction patterns (similarity >85%), irrespective of MBL genotype. P. aeruginosa ST235 carrying the chromosomally located bla(IMP-6) gene is widely disseminated in Korea.

Zymosan-induced immune challenge modifies the stress response of hypoxic air-breathing fish (Anabas testudineus Bloch): Evidence for reversed patterns of cortisol and thyroid hormone interaction, differential ion transporter functions and non-specific immune response.

PubMed

Simi, S; Peter, Valsa S; Peter, M C Subhash

2017-09-15

Fishes have evolved physiological mechanisms to exhibit stress response, where hormonal signals interact with an array of ion transporters and regulate homeostasis. As major ion transport regulators in fish, cortisol and thyroid hormones have been shown to interact and fine-tune the stress response. Likewise, in fishes many interactions have been identified between stress and immune components, but the physiological basis of such interaction has not yet delineated particularly in air-breathing fish. We, therefore, investigated the responses of thyroid hormones and cortisol, ion transporter functions and non-specific immune response of an obligate air-breathing fish Anabas testudineus Bloch to zymosan treatment or hypoxia stress or both, to understand how immune challenge modifies the pattern of stress response in this fish. Induction of experimental peritonitis in these fish by zymosan treatment (200ngg -1 ) for 24h produced rise in respiratory burst and lysozomal activities in head kidney phagocytes. In contrast, hypoxia stress for 30min in immune-challenged fish reversed these non-specific responses of head kidney phagocytes. The decline in plasma cortisol in zymosan-treated fish and its further suppression by hypoxia stress indicate that immune challenge suppresses the cortisol-driven stress response of this fish. Likewise, the decline in plasma T 3 and T 4 after zymosan-treatment and the rise in plasma T 4 after hypoxia stress in immune-challenged fish indicate a critical role for thyroid hormone in immune-stress response due to its differential sensitivity to both immune and stress challenges. Further, analysis of the activity pattern of ion-dependent ATPases viz. Na + /K + -ATPase, H + /K + -ATPase and Na + /NH 4 + -ATPase indicates a functional interaction of ion transport system with the immune response as evident in its differential and spatial modifications after hypoxia stress in immune-challenged fish. The immune-challenge that produced differential pattern of mRNA expression of Na + /K + -ATPase α-subunit isoforms; nkaα1a, nkaα1b and nkaα1c and the shift in nkaα1a and nkaα1b isoforms expression after hypoxia stress in immune-challenged fish, presents transcriptomic evidence for a modified Na + /K + ion transporter system in these fish. Collectively, our data thus provide evidence for an interactive immune-stress response in an air-breathing fish, where the patterns of cortisol-thyroid hormone interaction, the ion transporter functions and the non-specific immune responses are reversed by hypoxia stress in immune-challenged fish. Copyright © 2016 Elsevier Inc. All rights reserved.

Specific expression patterns and cell distribution of ancient and modern PAG in bovine placenta during pregnancy.

PubMed

Touzard, Eve; Reinaud, Pierrette; Dubois, Olivier; Guyader-Joly, Catherine; Humblot, Patrice; Ponsart, Claire; Charpigny, Gilles

2013-10-01

Pregnancy-associated glycoproteins (PAGs) constitute a multigenic family of aspartic proteinases expressed in the trophoblast of the ruminant placenta. In Bos taurus, this family comprises 21 members segregated into ancient and modern phylogenetic groups. Ancient PAGs have been reported to be synthesized throughout the trophoblastic cell layer whereas modern PAGs are produced by binucleate cells of cotyledons. The aim of this study was to investigate modern and ancient PAGs during gestation in cotyledonary and intercotyledonary tissues. To obtain convincing and innovative results despite the high sequence identity shared between PAGs, we designed specific tools such as amplification primers and antibodies. Using real-time RT-PCR, we described the transcript expression of 16 bovine PAGs. Overall, PAGs are characterized by an increase in their expression during gestation. However, we demonstrated a segregation of modern PAGs in cotyledons and of ancient PAGs in the intercotyledonary chorion, except for the ancient PAG2 expressed in cotyledons. By raising specific antibodies against the modern PAG1 and ancient PAG11 and PAG2, we established the expression kinetics of the proteins using western blotting. Immunohistochemistry showed that PAGs were produced by specific cellular populations: PAG1 by binucleate cells in the whole trophoblastic layer, PAG11 was localized in binucleate cells of the intercotyledonary trophoblast and the chorionic plate of the cotyledon, while PAG2 was produced in mononucleate cells of the internal villi of the cotyledon. These results revealed a highly specific regulation of PAG expression and cell localization as a function of their phylogenetic status, suggesting distinct biological functions within placental tissues.

Proteomic analysis of cow, yak, buffalo, goat and camel milk whey proteins: quantitative differential expression patterns.

PubMed

Yang, Yongxin; Bu, Dengpan; Zhao, Xiaowei; Sun, Peng; Wang, Jiaqi; Zhou, Lingyun

2013-04-05

To aid in unraveling diverse genetic and biological unknowns, a proteomic approach was used to analyze the whey proteome in cow, yak, buffalo, goat, and camel milk based on the isobaric tag for relative and absolute quantification (iTRAQ) techniques. This analysis is the first to produce proteomic data for the milk from the above-mentioned animal species: 211 proteins have been identified and 113 proteins have been categorized according to molecular function, cellular components, and biological processes based on gene ontology annotation. The results of principal component analysis showed significant differences in proteomic patterns among goat, camel, cow, buffalo, and yak milk. Furthermore, 177 differentially expressed proteins were submitted to advanced hierarchical clustering. The resulting clustering pattern included three major sample clusters: (1) cow, buffalo, and yak milk; (2) goat, cow, buffalo, and yak milk; and (3) camel milk. Certain proteins were chosen as characterization traits for a given species: whey acidic protein and quinone oxidoreductase for camel milk, biglycan for goat milk, uncharacterized protein (Accession Number: F1MK50 ) for yak milk, clusterin for buffalo milk, and primary amine oxidase for cow milk. These results help reveal the quantitative milk whey proteome pattern for analyzed species. This provides information for evaluating adulteration of specific specie milk and may provide potential directions for application of specific milk protein production based on physiological differences among animal species.

Multiple imputation for handling missing outcome data when estimating the relative risk.

PubMed

Sullivan, Thomas R; Lee, Katherine J; Ryan, Philip; Salter, Amy B

2017-09-06

Multiple imputation is a popular approach to handling missing data in medical research, yet little is known about its applicability for estimating the relative risk. Standard methods for imputing incomplete binary outcomes involve logistic regression or an assumption of multivariate normality, whereas relative risks are typically estimated using log binomial models. It is unclear whether misspecification of the imputation model in this setting could lead to biased parameter estimates. Using simulated data, we evaluated the performance of multiple imputation for handling missing data prior to estimating adjusted relative risks from a correctly specified multivariable log binomial model. We considered an arbitrary pattern of missing data in both outcome and exposure variables, with missing data induced under missing at random mechanisms. Focusing on standard model-based methods of multiple imputation, missing data were imputed using multivariate normal imputation or fully conditional specification with a logistic imputation model for the outcome. Multivariate normal imputation performed poorly in the simulation study, consistently producing estimates of the relative risk that were biased towards the null. Despite outperforming multivariate normal imputation, fully conditional specification also produced somewhat biased estimates, with greater bias observed for higher outcome prevalences and larger relative risks. Deleting imputed outcomes from analysis datasets did not improve the performance of fully conditional specification. Both multivariate normal imputation and fully conditional specification produced biased estimates of the relative risk, presumably since both use a misspecified imputation model. Based on simulation results, we recommend researchers use fully conditional specification rather than multivariate normal imputation and retain imputed outcomes in the analysis when estimating relative risks. However fully conditional specification is not without its shortcomings, and so further research is needed to identify optimal approaches for relative risk estimation within the multiple imputation framework.

Midpoint attractors and species richness: Modelling the interaction between environmental drivers and geometric constraints.

PubMed

Colwell, Robert K; Gotelli, Nicholas J; Ashton, Louise A; Beck, Jan; Brehm, Gunnar; Fayle, Tom M; Fiedler, Konrad; Forister, Matthew L; Kessler, Michael; Kitching, Roger L; Klimes, Petr; Kluge, Jürgen; Longino, John T; Maunsell, Sarah C; McCain, Christy M; Moses, Jimmy; Noben, Sarah; Sam, Katerina; Sam, Legi; Shapiro, Arthur M; Wang, Xiangping; Novotny, Vojtech

2016-09-01

We introduce a novel framework for conceptualising, quantifying and unifying discordant patterns of species richness along geographical gradients. While not itself explicitly mechanistic, this approach offers a path towards understanding mechanisms. In this study, we focused on the diverse patterns of species richness on mountainsides. We conjectured that elevational range midpoints of species may be drawn towards a single midpoint attractor - a unimodal gradient of environmental favourability. The midpoint attractor interacts with geometric constraints imposed by sea level and the mountaintop to produce taxon-specific patterns of species richness. We developed a Bayesian simulation model to estimate the location and strength of the midpoint attractor from species occurrence data sampled along mountainsides. We also constructed midpoint predictor models to test whether environmental variables could directly account for the observed patterns of species range midpoints. We challenged these models with 16 elevational data sets, comprising 4500 species of insects, vertebrates and plants. The midpoint predictor models generally failed to predict the pattern of species midpoints. In contrast, the midpoint attractor model closely reproduced empirical spatial patterns of species richness and range midpoints. Gradients of environmental favourability, subject to geometric constraints, may parsimoniously account for elevational and other patterns of species richness. © 2016 John Wiley & Sons Ltd/CNRS.

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.

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.

Oligonucleotide Array for Identification and Detection of Pythium Species†

PubMed Central

Tambong, J. T.; de Cock, A. W. A. M.; Tinker, N. A.; Lévesque, C. A.

2006-01-01

A DNA array containing 172 oligonucleotides complementary to specific diagnostic regions of internal transcribed spacers (ITS) of more than 100 species was developed for identification and detection of Pythium species. All of the species studied, with the exception of Pythium ostracodes, exhibited a positive hybridization reaction with at least one corresponding species-specific oligonucleotide. Hybridization patterns were distinct for each species. The array hybridization patterns included cluster-specific oligonucleotides that facilitated the recognition of species, including new ones, belonging to groups such as those producing filamentous or globose sporangia. BLAST analyses against 500 publicly available Pythium sequences in GenBank confirmed that species-specific oligonucleotides were unique to all of the available strains of each species, of which there were numerous economically important ones. GenBank entries of newly described species that are not putative synonyms showed no homology to sequences of the spotted species-specific oligonucleotides, but most new species did match some of the cluster-specific oligonucleotides. Further verification of the specificity of the DNA array was done with 50 additional Pythium isolates obtained by soil dilution plating. The hybridization patterns obtained were consistent with the identification of these isolates based on morphology and ITS sequence analyses. In another blind test, total DNA of the same soil samples was amplified and hybridized on the array, and the results were compared to those of 130 Pythium isolates obtained by soil dilution plating and root baiting. The 13 species detected by the DNA array corresponded to the isolates obtained by a combination of soil dilution plating and baiting, except for one new species that was not represented on the array. We conclude that the reported DNA array is a reliable tool for identification and detection of the majority of Pythium species in environmental samples. Simultaneous detection and identification of multiple species of soilborne pathogens such as Pythium species could be a major step forward for epidemiological and ecological studies. PMID:16597974

The Self-Assembly of Nanogold for Optical Metamaterials

NASA Astrophysics Data System (ADS)

Nidetz, Robert A.

2011-12-01

Optical metamaterials are an emerging field that enables manipulation of light like never before. Producing optical metamaterials requires sub-wavelength building blocks. The focus here was to develop methods to produce building blocks for metamaterials from nanogold. Electron-beam lithography was used to define an aminosilane patterned chemical template in order to electrostatically self-assemble citrate-capped gold nanoparticles. Equilibrium self-assembly was achieved in 20 minutes by immersing chemical templates into gold nanoparticle solutions. The number of nanoparticles that self-assembled on an aminosilane dot was controlled by manipulating the diameters of the dots and nanoparticles. Adding salt to the nanoparticle solution enabled the nanoparticles to self-assemble in greater numbers on the same sized dot. However, the preparation of the nanoparticle solution containing salt was sensitive to spikes in the salt concentration which led to aggregation of the nanoparticles and non-specific deposition. Gold nanorods were also electrostatically self-assembled. Polyelectrolyte-coated gold nanorods were patterned with limited success. A polyelectrolyte chemical template also patterned gold nanorods, but the gold nanorods preferred to pattern on the edges of the pattern. Ligand-exchanged gold nanorods displayed the best self-assembly, but suffered from slow kinetics. Self-assembled gold nanoparticles were cross-linked with poly(diallyldimethylammonium chloride). The poly(diallyldimethylammonium chloride) allowed additional nanoparticles to pattern on top of the already patterned nanoparticles. Cross-linked nanoparticles were lifted-off of the substrate by sonication in a sodium hydroxide solution. The presence of van der Waals forces and/or amine bonding prevent the nanogold from lifting-off without sonication. A good-solvent evaporation process was used to self-assemble poly(styrene) coated gold nanoparticles into spherical microbead assemblies. The use of larger nanoparticles and larger poly(styrene) ligands resulted in larger and smaller assemblies, respectively. Stirring the solution resulted in a wider size distribution of microbead assemblies due to the stirring's shear forces. Two undeveloped methods to self-assemble nanogold were investigated. One method used block-copolymer thin films as chemical templates to direct the electrostatic self-assembly of nanogold. Another method used gold nanorods that are passivated with different ligands on different faces. The stability of an alkanethiol ligand in different acids and bases was investigated to determine which materials could be used to produce Janus nanorods.

Mesencephalic basolateral domain specification is dependent on Sonic Hedgehog

PubMed Central

Martinez-Lopez, Jesus E.; Moreno-Bravo, Juan A.; Madrigal, M. Pilar; Martinez, Salvador; Puelles, Eduardo

2015-01-01

In the study of central nervous system morphogenesis, the identification of new molecular markers allows us to identify domains along the antero-posterior and dorso-ventral (DV) axes. In the past years, the alar and basal plates of the midbrain have been divided into different domains. The precise location of the alar-basal boundary is still under discussion. We have identified Barhl1, Nhlh1 and Six3 as appropriate molecular markers to the adjacent domains of this transition. The description of their expression patterns and the contribution to the different mesencephalic populations corroborated their role in the specification of these domains. We studied the influence of Sonic Hedgehog on these markers and therefore on the specification of these territories. The lack of this morphogen produced severe alterations in the expression pattern of Barhl1 and Nhlh1 with consequent misspecification of the basolateral (BL) domain. Six3 expression was apparently unaffected, however its distribution changed leading to altered basal domains. In this study we confirmed the localization of the alar-basal boundary dorsal to the BL domain and demonstrated that the development of the BL domain highly depends on Shh. PMID:25741244

Cations Form Sequence Selective Motifs within DNA Grooves via a Combination of Cation-Pi and Ion-Dipole/Hydrogen Bond Interactions

PubMed Central

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl+) and the polarized first hydration shell waters of divalent cations (Mg2+, Ca2+) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves. PMID:23940752

Contact, Travel, and Transmission: The Impact of Winter Holidays on Influenza Dynamics in the United States

PubMed Central

Ewing, Anne; Lee, Elizabeth C.; Viboud, Cécile

2017-01-01

Abstract Background. The seasonality of influenza is thought to vary according to environmental factors and human behavior. During winter holidays, potential disease-causing contact and travel deviate from typical patterns. We aim to understand these changes on age-specific and spatial influenza transmission. Methods. We characterized the changes to transmission and epidemic trajectories among children and adults in a spatial context before, during, and after the winter holidays among aggregated physician medical claims in the United States from 2001 to 2009 and among synthetic data simulated from a deterministic, age-specific spatial metapopulation model. Results. Winter holidays reduced influenza transmission and delayed the trajectory of influenza season epidemics. The holiday period was marked by a shift in the relative risk of disease from children toward adults. Model results indicated that holidays delayed epidemic peaks and synchronized incidence across locations, and that contact reductions from school closures, rather than age-specific mixing and travel, produced these observed holiday influenza dynamics. Conclusions. Winter holidays delay seasonal influenza epidemic peaks and shift disease risk toward adults because of changes in contact patterns. These findings may inform targeted influenza information and vaccination campaigns during holiday periods. PMID:28031259

Cations form sequence selective motifs within DNA grooves via a combination of cation-pi and ion-dipole/hydrogen bond interactions.

PubMed

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl⁺) and the polarized first hydration shell waters of divalent cations (Mg²⁺, Ca²⁺) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.

Immunoblot analysis of immunoglobulin G response to the Lyme disease agent (Borrelia burgdorferi) in experimentally and naturally exposed dogs.

PubMed Central

Greene, R T; Walker, R L; Nicholson, W L; Heidner, H W; Levine, J F; Burgess, E C; Wyand, M; Breitschwerdt, E B; Berkhoff, H A

1988-01-01

Immunoblots were used to study the immunoglobulin G response to Borrelia burgdorferi in experimentally and naturally exposed dogs. Adsorption studies confirmed that the antibodies were specific for B. burgdorferi. Experimentally exposed dogs were asymptomatic. Naturally exposed dogs included both asymptomatic animals and animals showing signs compatible with Lyme disease. Naturally exposed dogs were from four geographic regions of the country. No differences were detected between immunoblot patterns of naturally exposed symptomatic or asymptomatic dogs from different areas of the country. The immunoblot patterns obtained with sera from experimentally exposed dogs were different from those obtained with sera from naturally exposed dogs and were characterized by reactivity to fewer and different protein bands. Immunoblot analysis using an OspA-protein-producing Escherichia coli recombinant showed that experimentally exposed dogs produced antibodies to OspA, whereas naturally exposed dogs did not. Modifications of the immune response over time, different routes of antigen presentation, and strain variation are factors postulated to account for the observed differences. Images PMID:3366860

Imitated Prosodic Fluency Predicts Reading Comprehension Ability in Good and Poor High School Readers

PubMed Central

Breen, Mara; Kaswer, Lianne; Van Dyke, Julie A.; Krivokapić, Jelena; Landi, Nicole

2016-01-01

Researchers have established a relationship between beginning readers' silent comprehension ability and their prosodic fluency, such that readers who read aloud with appropriate prosody tend to have higher scores on silent reading comprehension assessments. The current study was designed to investigate this relationship in two groups of high school readers: Specifically Poor Comprehenders (SPCs), who have adequate word level and phonological skills but poor reading comprehension ability, and a group of age- and decoding skill-matched controls. We compared the prosodic fluency of the two groups by determining how effectively they produced prosodic cues to syntactic and semantic structure in imitations of a model speaker's production of syntactically and semantically varied sentences. Analyses of pitch and duration patterns revealed that speakers in both groups produced the expected prosodic patterns; however, controls provided stronger durational cues to syntactic structure. These results demonstrate that the relationship between prosodic fluency and reading comprehension continues past the stage of early reading instruction. Moreover, they suggest that prosodically fluent speakers may also generate more fluent implicit prosodic representations during silent reading, leading to more effective comprehension. PMID:27486409

Novel starch based nano scale enteric coatings from soybean meal for colon-specific delivery.

PubMed

Sivapragasam, Nilushni; Thavarajah, Pushparajah; Ohm, Jae-Bom; Ohm, Jae-Bom; Margaret, Khaitsa; Thavarajah, Dil

2014-10-13

Soybean meal was used to isolate resistant starch and produce nanoparticles, which could be potential coating materials for colonic nutrient and drug deliveries. The nanoparticles were in 40 ± 33.2 nm ranges. These nanoparticles were stable under simulated human physiological conditions. The degrees of dissolution in both stomach and intestinal conditions were less than 30%. Furthermore, the nanoparticles were less susceptible to pancreatic enzymatic digestion (20%), which was also evidenced by the co-existence of B-type crystalline pattern. In addition to the dissolution and digestion studies in the upper gastrointestinal tract, the nanoparticles were subjected to in vitro fermentation by Bifidobacterium brevis and Lactobacillus casei. Both species showed an increase in growth and activity, while producing short chain fatty acids: acetate, propionate, and butyrates in varying amounts. Overall this study clearly demonstrated a novel method that can be used for colon-specific delivery of bioactive compounds such as drugs and nutrients. Copyright © 2014 Elsevier Ltd. All rights reserved.

The electrodynamic and hydrodynamic phenomena in magnetically-levitated molten droplets. I - Steady state behavior

NASA Technical Reports Server (NTRS)

Zong, Jin-Ho; Li, Benqiang; Szekely, Julian

1992-01-01

A mathematical formulation is given and computed results are presented describing the behavior of electromagnetically-levitated metal droplets under the conditions of microgravity. In the formulation the electromagnetic force field is calculated using a modification of the volume integral method and these results are then combined with the FIDAP code to calculate the steady state melt velocities. The specific computational results are presented for the conditions corresponding to the planned IML-2 Space Shuttle experiment, using the TEMPUS device, which has separate 'heating' and 'positioning' coils. While the computed results are necessarily specific to the input conditions, some general conclusions may be drawn from this work. These include the fact that for the planned TEMPUS experiments to positioning coils will produce only a weak melt circulation, while the heating coils are like to produce a mildly turbulent recirculating flow pattern within the samples. The computed results also allow us to assess the effect of sample size, material properties and the applied current on these phenomena.

Preparation and characterization of monoclonal antibody against digoxin.

PubMed

Kashanian, S; Rasaee, M J; Paknejad, M; Omidfar, K; Pour-Amir, M; Rajabi, Bazl M

2002-10-01

Mouse-mouse hybridoma cell lines producing stable, highly specific and with good affinity monoclonal antibody (MAb) against the cardiac glycoside digoxin were established. Balb/c mice were immunized via injection of digoxin-3'-bovine serum albumin (BSA). The spleens of which were fused with myeloma cells of SP2/0 origin. Three clones designated as BBA, MBE, and BMG producing good antibodies displayed different patterns of fine specificity for digoxin and low cross-reaction with several digoxin analogues as elucidated by inhibition enzyme-linked immunosorbant assay (ELISA). All three MAbs were of the same class and subclass (IgG(1)). Affinity purification was performed for the selected clone BBA displaying the highest affinity and nearly no cross-reactivity with any of the structurally related molecules. Ultrafiltered concentrated hybrid cell supernatant was also purified by polyethylene glycol (PEG) 6000 precipitation for large-scale preparation and coated onto the wells of microtiter plates. The standard curve was constructed with a sensitivity of 10 pg/well covering up to 10 ng/well.

Acquiring and Producing Sentences: Whether Learners Use Verb-Specific or Verb-General Information Depends on Cue Validity

PubMed Central

Thothathiri, Malathi; Rattinger, Michelle G.

2016-01-01

Learning to produce sentences involves learning patterns that enable the generation of new utterances. Language contains both verb-specific and verb-general regularities that are relevant to this capacity. Previous research has focused on whether one source is more important than the other. We tested whether the production system can flexibly learn to use either source, depending on the predictive validity of different cues in the input. Participants learned new sentence structures in a miniature language paradigm. In three experiments, we manipulated whether individual verbs or verb-general mappings better predicted the structures heard during learning. Evaluation of participants’ subsequent production revealed that they could use either the structural preferences of individual verbs or abstract meaning-to-form mappings to construct new sentences. Further, this choice varied according to cue validity. These results demonstrate flexibility within the production architecture and the importance of considering how language was learned when discussing how language is used. PMID:27047428

Voluntary facial action generates emotion-specific autonomic nervous system activity.

PubMed

Levenson, R W; Ekman, P; Friesen, W V

1990-07-01

Four experiments were conducted to determine whether voluntarily produced emotional facial configurations are associated with differentiated patterns of autonomic activity, and if so, how this might be mediated. Subjects received muscle-by-muscle instructions and coaching to produce facial configurations for anger, disgust, fear, happiness, sadness, and surprise while heart rate, skin conductance, finger temperature, and somatic activity were monitored. Results indicated that voluntary facial activity produced significant levels of subjective experience of the associated emotion, and that autonomic distinctions among emotions: (a) were found both between negative and positive emotions and among negative emotions, (b) were consistent between group and individual subjects' data, (c) were found in both male and female subjects, (d) were found in both specialized (actors, scientists) and nonspecialized populations, (e) were stronger when the voluntary facial configurations most closely resembled actual emotional expressions, and (f) were stronger when experience of the associated emotion was reported. The capacity of voluntary facial activity to generate emotion-specific autonomic activity: (a) did not require subjects to see facial expressions (either in a mirror or on an experimenter's face), and (b) could not be explained by differences in the difficulty of making the expressions or by differences in concomitant somatic activity.

Detection of artifacts from high energy bursts in neonatal EEG.

PubMed

Bhattacharyya, Sourya; Biswas, Arunava; Mukherjee, Jayanta; Majumdar, Arun Kumar; Majumdar, Bandana; Mukherjee, Suchandra; Singh, Arun Kumar

2013-11-01

Detection of non-cerebral activities or artifacts, intermixed within the background EEG, is essential to discard them from subsequent pattern analysis. The problem is much harder in neonatal EEG, where the background EEG contains spikes, waves, and rapid fluctuations in amplitude and frequency. Existing artifact detection methods are mostly limited to detect only a subset of artifacts such as ocular, muscle or power line artifacts. Few methods integrate different modules, each for detection of one specific category of artifact. Furthermore, most of the reference approaches are implemented and tested on adult EEG recordings. Direct application of those methods on neonatal EEG causes performance deterioration, due to greater pattern variation and inherent complexity. A method for detection of a wide range of artifact categories in neonatal EEG is thus required. At the same time, the method should be specific enough to preserve the background EEG information. The current study describes a feature based classification approach to detect both repetitive (generated from ECG, EMG, pulse, respiration, etc.) and transient (generated from eye blinking, eye movement, patient movement, etc.) artifacts. It focuses on artifact detection within high energy burst patterns, instead of detecting artifacts within the complete background EEG with wide pattern variation. The objective is to find true burst patterns, which can later be used to identify the Burst-Suppression (BS) pattern, which is commonly observed during newborn seizure. Such selective artifact detection is proven to be more sensitive to artifacts and specific to bursts, compared to the existing artifact detection approaches applied on the complete background EEG. Several time domain, frequency domain, statistical features, and features generated by wavelet decomposition are analyzed to model the proposed bi-classification between burst and artifact segments. A feature selection method is also applied to select the feature subset producing highest classification accuracy. The suggested feature based classification method is executed using our recorded neonatal EEG dataset, consisting of burst and artifact segments. We obtain 78% sensitivity and 72% specificity as the accuracy measures. The accuracy obtained using the proposed method is found to be about 20% higher than that of the reference approaches. Joint use of the proposed method with our previous work on burst detection outperforms reference methods on simultaneous burst and artifact detection. As the proposed method supports detection of a wide range of artifact patterns, it can be improved to incorporate the detection of artifacts within other seizure patterns and background EEG information as well. © 2013 Elsevier Ltd. All rights reserved.

Bioengineered anterior cruciate ligament

NASA Technical Reports Server (NTRS)

Martin, Ivan (Inventor); Altman, Gregory (Inventor); Kaplan, David (Inventor); Vunjak-Novakovic, Gordana (Inventor)

2001-01-01

The present invention provides a method for producing an anterior cruciate ligament ex vivo. The method comprises seeding pluripotent stem cells in a three dimensional matrix, anchoring the seeded matrix by attachment to two anchors, and culturing the cells within the matrix under conditions appropriate for cell growth and regeneration, while subjecting the matrix to one or more mechanical forces via movement of one or both of the attached anchors. Bone marrow stromal cells are preferably used as the pluripotent cells in the method. Suitable matrix materials are materials to which cells can adhere, such as a gel made from collagen type I. Suitable anchor materials are materials to which the matrix can attach, such as Goinopra coral and also demineralized bone. Optimally, the mechanical forces to which the matrix is subjected mimic mechanical stimuli experienced by an anterior cruciate ligament in vivo. This is accomplished by delivering the appropriate combination of tension, compression, torsion, and shear, to the matrix. The bioengineered ligament which is produced by this method is characterized by a cellular orientation and/or matrix crimp pattern in the direction of the applied mechanical forces, and also by the production of collagen type I, collagen type III, and fibronectin proteins along the axis of mechanical load produced by the mechanical forces. Optimally, the ligament produced has fiber bundles which are arranged into a helical organization. The method for producing an anterior cruciate ligament can be adapted to produce a wide range of tissue types ex vivo by adapting the anchor size and attachment sites to reflect the size of the specific type of tissue to be produced, and also adapting the specific combination of forces applied, to mimic the mechanical stimuli experienced in vivo by the specific type of tissue to be produced. The methods of the present invention can be further modified to incorporate other stimuli experienced in vivo by the particular developing tissue, some examples of the stimuli being chemical stimuli, and electro-magnetic stimuli. Some examples of tissue which can be produced include other ligaments in the body (hand, wrist, elbow, knee), tendon, cartilage, bone, muscle, and blood vessels.

Econometrics and data of the 9 sector Dynamic General Equilibrium Model. Volume III. Final report

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

Berndt, E.R.; Fraumeni, B.M.; Hudson, E.A.

1981-03-01

This report presents the econometrics and data of the 9 sector Dynamic General Equilibrium Model. There are two key components of 9DGEM - the model of household behavior and the model of produconcrneer behavior. The household model is concerned with decisions on consumption, saving, labor supply and the composition of consumption. The producer model is concerned with output price formation and determination of input patterns and purchases for each of the nine producing sectors. These components form the behavioral basis of DGEM. The remaining components are concerned with constraints, balance conditions, accounting, and government revenues and expenditures (these elements aremore » developed in the report on the model specification).« less

On the viewing angle dependence of blazar variability

NASA Astrophysics Data System (ADS)

Eldar, Avigdor; Levinson, Amir

2000-05-01

Internal shocks propagating through an ambient radiation field are subject to a radiative drag that, under certain conditions, can significantly affect their dynamics, and consequently the evolution of the beaming cone of emission produced behind the shocks. The resultant change of the Doppler factor combined with opacity effects leads to a strong dependence on the viewing angle of the variability pattern produced by such systems; specifically, the shape of the light curves and the characteristics of correlated emission. One implication is that objects oriented at relatively large viewing angles to the observer should exhibit a higher level of activity at high synchrotron frequencies (above the self-absorption frequency), and also at gamma-ray energies below the threshold energy of pair production, than at lower (radio/millimetre) frequencies.

A marching-walking hybrid induces step length adaptation and transfers to natural walking

PubMed Central

Long, Andrew W.; Finley, James M.

2015-01-01

Walking is highly adaptable to new demands and environments. We have previously studied adaptation of locomotor patterns via a split-belt treadmill, where subjects learn to walk with one foot moving faster than the other. Subjects learn to adapt their walking pattern by changing the location (spatial) and time (temporal) of foot placement. Here we asked whether we can induce adaptation of a specific walking pattern when one limb does not “walk” but instead marches in place (i.e., marching-walking hybrid). The marching leg's movement is limited during the stance phase, and thus certain sensory signals important for walking may be reduced. We hypothesized that this would produce a spatial-temporal strategy different from that of normal split-belt adaptation. Healthy subjects performed two experiments to determine whether they could adapt their spatial-temporal pattern of step lengths during the marching-walking hybrid and whether the learning transfers to over ground walking. Results showed that the hybrid group did adapt their step lengths, but the time course of adaptation and deadaption was slower than that for the split-belt group. We also observed that the hybrid group utilized a mostly spatial strategy whereas the split-belt group utilized both spatial and temporal strategies. Surprisingly, we found no significant difference between the hybrid and split-belt groups in over ground transfer. Moreover, the hybrid group retained more of the learned pattern when they returned to the treadmill. These findings suggest that physical rehabilitation with this marching-walking paradigm on conventional treadmills may produce changes in symmetry comparable to what is observed during split-belt training. PMID:25867742

A marching-walking hybrid induces step length adaptation and transfers to natural walking.

PubMed

Long, Andrew W; Finley, James M; Bastian, Amy J

2015-06-01

Walking is highly adaptable to new demands and environments. We have previously studied adaptation of locomotor patterns via a split-belt treadmill, where subjects learn to walk with one foot moving faster than the other. Subjects learn to adapt their walking pattern by changing the location (spatial) and time (temporal) of foot placement. Here we asked whether we can induce adaptation of a specific walking pattern when one limb does not "walk" but instead marches in place (i.e., marching-walking hybrid). The marching leg's movement is limited during the stance phase, and thus certain sensory signals important for walking may be reduced. We hypothesized that this would produce a spatial-temporal strategy different from that of normal split-belt adaptation. Healthy subjects performed two experiments to determine whether they could adapt their spatial-temporal pattern of step lengths during the marching-walking hybrid and whether the learning transfers to over ground walking. Results showed that the hybrid group did adapt their step lengths, but the time course of adaptation and deadaption was slower than that for the split-belt group. We also observed that the hybrid group utilized a mostly spatial strategy whereas the split-belt group utilized both spatial and temporal strategies. Surprisingly, we found no significant difference between the hybrid and split-belt groups in over ground transfer. Moreover, the hybrid group retained more of the learned pattern when they returned to the treadmill. These findings suggest that physical rehabilitation with this marching-walking paradigm on conventional treadmills may produce changes in symmetry comparable to what is observed during split-belt training. Copyright © 2015 the American Physiological Society.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

PubMed Central

2013-01-01

Background Butyrate, which is produced by the human microbiome, is essential for a well-functioning colon. Bacteria that produce butyrate are phylogenetically diverse, which hinders their accurate detection based on conventional phylogenetic markers. As a result, reliable information on this important bacterial group is often lacking in microbiome research. Results In this study we describe a gene-targeted approach for 454 pyrotag sequencing and quantitative polymerase chain reaction for the final genes in the two primary bacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). We monitored the establishment and early succession of butyrate-producing communities in four patients with ulcerative colitis who underwent a colectomy with ileal pouch anal anastomosis and compared it with three control samples from healthy colons. All patients established an abundant butyrate-producing community (approximately 5% to 26% of the total community) in the pouch within the 2-month study, but patterns were distinctive among individuals. Only one patient harbored a community profile similar to the healthy controls, in which there was a predominance of but genes that are similar to reference genes from Acidaminococcus sp., Eubacterium sp., Faecalibacterium prausnitzii and Roseburia sp., and an almost complete absence of buk genes. Two patients were greatly enriched in buk genes similar to those of Clostridium butyricum and C. perfringens, whereas a fourth patient displayed abundant communities containing both genes. Most butyrate producers identified in previous studies were detected and the general patterns of taxa found were supported by 16S rRNA gene pyrotag analysis, but the gene-targeted approach provided more detail about the potential butyrate-producing members of the community. Conclusions The presented approach provides quantitative and genotypic insights into butyrate-producing communities and facilitates a more specific functional characterization of the intestinal microbiome. Furthermore, our analysis refines but and buk reference annotations found in central databases. PMID:24451334

Inhibition of cancer cell growth by exposure to a specific time-varying electromagnetic field involves T-type calcium channels.

PubMed

Buckner, Carly A; Buckner, Alison L; Koren, Stan A; Persinger, Michael A; Lafrenie, Robert M

2015-01-01

Electromagnetic field (EMF) exposures affect many biological systems. The reproducibility of these effects is related to the intensity, duration, frequency, and pattern of the EMF. We have shown that exposure to a specific time-varying EMF can inhibit the growth of malignant cells. Thomas-EMF is a low-intensity, frequency-modulated (25-6 Hz) EMF pattern. Daily, 1 h, exposures to Thomas-EMF inhibited the growth of malignant cell lines including B16-BL6, MDA-MB-231, MCF-7, and HeLa cells but did not affect the growth of non-malignant cells. Thomas-EMF also inhibited B16-BL6 cell proliferation in vivo. B16-BL6 cells implanted in syngeneic C57b mice and exposed daily to Thomas-EMF produced smaller tumours than in sham-treated controls. In vitro studies showed that exposure of malignant cells to Thomas-EMF for > 15 min promoted Ca(2+) influx which could be blocked by inhibitors of voltage-gated T-type Ca(2+) channels. Blocking Ca(2+) uptake also blocked Thomas-EMF-dependent inhibition of cell proliferation. Exposure to Thomas-EMF delayed cell cycle progression and altered cyclin expression consistent with the decrease in cell proliferation. Non-malignant cells did not show any EMF-dependent changes in Ca(2+) influx or cell growth. These data confirm that exposure to a specific EMF pattern can affect cellular processes and that exposure to Thomas-EMF may provide a potential anti-cancer therapy.

Inhibition of Cancer Cell Growth by Exposure to a Specific Time-Varying Electromagnetic Field Involves T-Type Calcium Channels

PubMed Central

Buckner, Carly A.; Buckner, Alison L.; Koren, Stan A.; Persinger, Michael A.; Lafrenie, Robert M.

2015-01-01

Electromagnetic field (EMF) exposures affect many biological systems. The reproducibility of these effects is related to the intensity, duration, frequency, and pattern of the EMF. We have shown that exposure to a specific time-varying EMF can inhibit the growth of malignant cells. Thomas-EMF is a low-intensity, frequency-modulated (25-6 Hz) EMF pattern. Daily, 1 h, exposures to Thomas-EMF inhibited the growth of malignant cell lines including B16-BL6, MDA-MB-231, MCF-7, and HeLa cells but did not affect the growth of non-malignant cells. Thomas-EMF also inhibited B16-BL6 cell proliferation in vivo. B16-BL6 cells implanted in syngeneic C57b mice and exposed daily to Thomas-EMF produced smaller tumours than in sham-treated controls. In vitro studies showed that exposure of malignant cells to Thomas-EMF for > 15 min promoted Ca2+ influx which could be blocked by inhibitors of voltage-gated T-type Ca2+ channels. Blocking Ca2+ uptake also blocked Thomas-EMF-dependent inhibition of cell proliferation. Exposure to Thomas-EMF delayed cell cycle progression and altered cyclin expression consistent with the decrease in cell proliferation. Non-malignant cells did not show any EMF-dependent changes in Ca2+ influx or cell growth. These data confirm that exposure to a specific EMF pattern can affect cellular processes and that exposure to Thomas-EMF may provide a potential anti-cancer therapy. PMID:25875081

In the eye of the beholder? Universality and cultural specificity in the expression and perception of emotion.

PubMed

Scherer, Klaus R; Clark-Polner, Elizabeth; Mortillaro, Marcello

2011-12-01

Do members of different cultures express (or "encode") emotions in the same fashion? How well can members of distinct cultures recognize (or "decode") each other's emotion expressions? The question of cultural universality versus specificity in emotional expression has been a hot topic of debate for more than half a century, but, despite a sizeable amount of empirical research produced to date, no convincing answers have emerged. We suggest that this unsatisfactory state of affairs is due largely to a lack of concern with the precise mechanisms involved in emotion expression and perception, and propose to use a modified Brunswikian lens model as an appropriate framework for research in this area. On this basis we provide a comprehensive review of the existing literature and point to research paradigms that are likely to provide the evidence required to resolve the debate on universality vs. cultural specificity of emotional expression. Applying this fresh perspective, our analysis reveals that, given the paucity of pertinent data, no firm conclusions can be drawn on actual expression (encoding) patterns across cultures (although there appear to be more similarities than differences), but that there is compelling evidence for intercultural continuity in decoding, or recognition, ability. We also note a growing body of research on the notion of ingroup advantage due to expression "dialects," above and beyond the general encoding or decoding patterns. We furthermore suggest that these empirical patterns could be explained by both universality in the underlying mechanisms and cultural specificity in the input to, and the regulation of, these expression and perception mechanisms. Overall, more evidence is needed, both to further elucidate these mechanisms and to inventory the patterns of cultural effects. We strongly recommend using more solid conceptual and theoretical perspectives, as well as more ecologically valid approaches, in designing future studies in emotion expression and perception research.

Vascular stents with submicrometer-scale surface patterning realized via titanium deep reactive ion etching

NASA Astrophysics Data System (ADS)

Gott, Shannon C.; Jabola, Benjamin A.; Rao, Masaru P.

2015-08-01

Herein, we report progress towards realization of vascular stents that will eventually provide opportunity for evaluating cellular response to rationally-designed, submicrometer-scale surface patterning in physiologically-relevant contexts, i.e. those that provide exposure to the complex multicellular milieu, flow-induced shear, and tissue-device interactions present in vivo. Specifically, using our novel titanium deep reactive ion etching technique (Ti DRIE), we discuss recent advances that have enabled: (a) fabrication of precisely-defined, grating-based surface patterns on planar Ti foils with minimum feature sizes as small as 0.15 μm (b) creation of cylindrical stents from micromachined planar Ti foils; and (c) integration of these processes to produce the first submicrometer-scale surface-patterned Ti stents that are compatible with conventional balloon catheter deployment techniques. We also discuss results from elastoplastic finite element simulations and preliminary mechanical testing of these devices to assess their mechanical performance. These efforts represent key steps towards our long-term goal of developing a new paradigm in stenting, where rationally-designed surface patterning provides a physical means for facilitating healing, and thus, improving outcomes in vascular intervention applications.

Relationships between in vivo microdamage and the remarkable regional material and strain heterogeneity of cortical bone of adult deer, elk, sheep and horse calcanei

PubMed Central

Skedros, John G; Sybrowsky, Christian L; Anderson, Wm Erick; Chow, Frank

2011-01-01

Natural loading of the calcanei of deer, elk, sheep and horses produces marked regional differences in prevalent/predominant strain modes: compression in the dorsal cortex, shear in medial–lateral cortices, and tension/shear in the plantar cortex. This consistent non-uniform strain distribution is useful for investigating mechanisms that mediate the development of the remarkable regional material variations of these bones (e.g. collagen orientation, mineralization, remodeling rates and secondary osteon morphotypes, size and population density). Regional differences in strain-mode-specific microdamage prevalence and/or morphology might evoke and sustain the remodeling that produces this material heterogeneity in accordance with local strain characteristics. Adult calcanei from 11 animals of each species (deer, elk, sheep and horses) were transversely sectioned and examined using light and confocal microscopy. With light microscopy, 20 linear microcracks were identified (deer: 10; elk: six; horse: four; sheep: none), and with confocal microscopy substantially more microdamage with typically non-linear morphology was identified (deer: 45; elk: 24; horse: 15; sheep: none). No clear regional patterns of strain-mode-specific microdamage were found in the three species with microdamage. In these species, the highest overall concentrations occurred in the plantar cortex. This might reflect increased susceptibility of microdamage in habitual tension/shear. Absence of detectable microdamage in sheep calcanei may represent the (presumably) relatively greater physical activity of deer, elk and horses. Absence of differences in microdamage prevalence/morphology between dorsal, medial and lateral cortices of these bones, and the general absence of spatial patterns of strain-mode-specific microdamage, might reflect the prior emergence of non-uniform osteon-mediated adaptations that reduce deleterious concentrations of microdamage by the adult stage of bone development. PMID:21951210

ChromBiSim: Interactive chromatin biclustering using a simple approach.

PubMed

Noureen, Nighat; Zohaib, Hafiz Muhammad; Qadir, Muhammad Abdul; Fazal, Sahar

2017-10-01

Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis. ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species. ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages. Copyright © 2017 Elsevier Inc. All rights reserved.

Immunocytology on microwave-fixed cells reveals rapid and agonist-specific changes in subcellular accumulation patterns for cAMP or cGMP.

PubMed Central

Barsony, J; Marx, S J

1990-01-01

We developed a method for cAMP and cGMP immunocytology based upon fixation by microwave irradiation. Fixation by microwave irradiation prevented three problems found with other fixation methods: nucleotide loss from cells, nucleotide diffusion within cells, and chemical modification of immunologic epitopes. Six agonists (four that stimulate adenylate cyclase and two that stimulate guanylate cyclase) produced cAMP or cGMP accumulation patterns that were agonist-specific, dose-dependent, detectable at physiologic concentrations of hormone, and time-dependent within 15 sec to 30 min. cAMP accumulation after 1 mM forskolin was greatest in the nucleus. Isoproterenol, prostaglandin E2, or calcitonin caused initial accumulation of cAMP along the plasma membrane, but later accumulation was greater in the cytoplasm. With calcitonin the later accumulation of cAMP was selectively perinuclear and along the nuclear membrane. Sodium nitroprusside stimulated cGMP accumulation diffusely throughout the cytoplasm. Atrial natriuretic peptide initiated cGMP accumulation near the plasma membrane, and cGMP accumulation moved from there into the cytoplasm. In conclusion, microwave irradiation preserved cell structure and allowed visualization of expected as well as unsuspected changes in intracellular accumulation patterns of cAMP and cGMP. Images PMID:2153973

A Bayesian Joint Model of Menstrual Cycle Length and Fecundity

PubMed Central

Lum, Kirsten J.; Sundaram, Rajeshwari; Louis, Germaine M. Buck; Louis, Thomas A.

2015-01-01

Summary Menstrual cycle length (MCL) has been shown to play an important role in couple fecundity, which is the biologic capacity for reproduction irrespective of pregnancy intentions. However, a comprehensive assessment of its role requires a fecundity model that accounts for male and female attributes and the couple’s intercourse pattern relative to the ovulation day. To this end, we employ a Bayesian joint model for MCL and pregnancy. MCLs follow a scale multiplied (accelerated) mixture model with Gaussian and Gumbel components; the pregnancy model includes MCL as a covariate and computes the cycle-specific probability of pregnancy in a menstrual cycle conditional on the pattern of intercourse and no previous fertilization. Day-specific fertilization probability is modeled using natural, cubic splines. We analyze data from the Longitudinal Investigation of Fertility and the Environment Study (the LIFE Study), a couple based prospective pregnancy study, and find a statistically significant quadratic relation between fecundity and menstrual cycle length, after adjustment for intercourse pattern and other attributes, including male semen quality, both partner’s age, and active smoking status (determined by baseline cotinine level 100ng/mL). We compare results to those produced by a more basic model and show the advantages of a more comprehensive approach. PMID:26295923

Different gene-specific mechanisms determine the 'revised-response' memory transcription patterns of a subset of A. thaliana dehydration stress responding genes.

PubMed

Liu, Ning; Ding, Yong; Fromm, Michael; Avramova, Zoya

2014-05-01

Plants that have experienced several exposures to dehydration stress show increased resistance to future exposures by producing faster and/or stronger reactions, while many dehydration stress responding genes in Arabidopsis thaliana super-induce their transcription as a 'memory' from the previous encounter. A previously unknown, rather unusual, memory response pattern is displayed by a subset of the dehydration stress response genes. Despite robustly responding to a first stress, these genes return to their initial, pre-stressed, transcript levels during the watered recovery; surprisingly, they do not respond further to subsequent stresses of similar magnitude and duration. This transcriptional behavior defines the 'revised-response' memory genes. Here, we investigate the molecular mechanisms regulating this transcription memory behavior. Potential roles of abscisic acid (ABA), of transcription factors (TFs) from the ABA signaling pathways (ABF2/3/4 and MYC2), and of histone modifications (H3K4me3 and H3K27me3) as factors in the revised-response transcription memory patterns are elucidated. We identify the TF MYC2 as the critical component for the memory behavior of a specific subset of MYC2-dependent genes. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Variation in motor output and motor performance in a centrally generated motor pattern

PubMed Central

Norris, Brian J.; Doloc-Mihu, Anca; Calabrese, Ronald L.

2014-01-01

Central pattern generators (CPGs) produce motor patterns that ultimately drive motor outputs. We studied how functional motor performance is achieved, specifically, whether the variation seen in motor patterns is reflected in motor performance and whether fictive motor patterns differ from those in vivo. We used the leech heartbeat system in which a bilaterally symmetrical CPG coordinates segmental heart motor neurons and two segmented heart tubes into two mutually exclusive coordination modes: rear-to-front peristaltic on one side and nearly synchronous on the other, with regular side-to-side switches. We assessed individual variability of the motor pattern and the beat pattern in vivo. To quantify the beat pattern we imaged intact adults. To quantify the phase relations between motor neurons and heart constrictions we recorded extracellularly from two heart motor neurons and movement from the corresponding heart segments in minimally dissected leeches. Variation in the motor pattern was reflected in motor performance only in the peristaltic mode, where larger intersegmental phase differences in the motor neurons resulted in larger phase differences between heart constrictions. Fictive motor patterns differed from those in vivo only in the synchronous mode, where intersegmental phase differences in vivo had a larger front-to-rear bias and were more constrained. Additionally, load-influenced constriction timing might explain the amplification of the phase differences between heart segments in the peristaltic mode and the higher variability in motor output due to body shape assumed in this soft-bodied animal. The motor pattern determines the beat pattern, peristaltic or synchronous, but heart mechanics influence the phase relations achieved. PMID:24717348

Thiolated polyethylene oxide as a non-fouling element for nano-patterned bio-devices

NASA Astrophysics Data System (ADS)

Lisboa, Patrícia; Valsesia, Andrea; Colpo, Pascal; Gilliland, Douglas; Ceccone, Giacomo; Papadopoulou-Bouraoui, Andri; Rauscher, Hubert; Reniero, Fabiano; Guillou, Claude; Rossi, François

2007-03-01

This work describes the synthesis of a thiolated polyethylene oxide that self-assembles on gold to create a non-fouling surface. Thiolated polyethylene oxide was synthesised by reacting 16-mercaptohexadecanoic acid with polyethylene glycol mono methyl ether. The coverage of the thiolated polyethylene oxide on gold was studied by cyclic voltammetry, and the modified surfaces were characterised by X-ray photoelectron spectroscopy and ellipsometry. Protein resistance was assessed using quartz crystal microbalance. Results showed a non-fouling character produced by the thiolated polyethylene oxide. The synthesised product was used as the passivation layer on nano-patterned surfaces consisting of arrayed nano-spots, fabricated by plasma based colloidal lithography. The specific adsorption of anti-bovine serum albumin in the mercaptohexadecanoic acid spots was verified by atomic force microscopy.

The effect of flower position on variation and covariation in floral traits in a wild hermaphrodite plant

PubMed Central

2010-01-01

Background Floral traits within plants can vary with flower position or flowering time. Within an inflorescence, sexual allocation of early produced basal flowers is often female-biased while later produced distal flowers are male-biased. Such temporal adjustment of floral resource has been considered one of the potential advantages of modularity (regarding a flower as a module) in hermaphrodites. However, flowers are under constraints of independent evolution of a given trait. To understand flower diversification within inflorescences, here we examine variation and covariation in floral traits within racemes at the individual and the maternal family level respectively in an alpine herb Aconitum gymnandrum (Ranunculaceae). Results We found that floral traits varied significantly with flower position and among families, and position effects were family-specific. Most of the variance of floral traits was among individuals rather than among flowers within individuals or among families. Significant phenotypic correlations between traits were not affected by position, indicating trait integration under shared developmental regulation. In contrast, positive family-mean correlations in floral traits declined gradually from basal to distal flowers (nine significant correlations among floral traits in basal flowers and only three in distal flowers), showing position-specificity. Therefore, the pattern and magnitude of genetic correlations decreased with flower position. Conclusions This finding on covariation pattern in floral reproductive structures within racemes has not been revealed before, providing insights into temporal variation and position effects in floral traits within plants and the potential advantages of modularity in hermaphrodites. PMID:20482889

The effect of flower position on variation and covariation in floral traits in a wild hermaphrodite plant.

PubMed

Zhao, Zhi-Gang; Du, Guo-Zhen; Huang, Shuang-Quan

2010-05-20

Floral traits within plants can vary with flower position or flowering time. Within an inflorescence, sexual allocation of early produced basal flowers is often female-biased while later produced distal flowers are male-biased. Such temporal adjustment of floral resource has been considered one of the potential advantages of modularity (regarding a flower as a module) in hermaphrodites. However, flowers are under constraints of independent evolution of a given trait. To understand flower diversification within inflorescences, here we examine variation and covariation in floral traits within racemes at the individual and the maternal family level respectively in an alpine herb Aconitum gymnandrum (Ranunculaceae). We found that floral traits varied significantly with flower position and among families, and position effects were family-specific. Most of the variance of floral traits was among individuals rather than among flowers within individuals or among families. Significant phenotypic correlations between traits were not affected by position, indicating trait integration under shared developmental regulation. In contrast, positive family-mean correlations in floral traits declined gradually from basal to distal flowers (nine significant correlations among floral traits in basal flowers and only three in distal flowers), showing position-specificity. Therefore, the pattern and magnitude of genetic correlations decreased with flower position. This finding on covariation pattern in floral reproductive structures within racemes has not been revealed before, providing insights into temporal variation and position effects in floral traits within plants and the potential advantages of modularity in hermaphrodites.

Understanding the abstract role of speech in communication at 12 months.

PubMed

Martin, Alia; Onishi, Kristine H; Vouloumanos, Athena

2012-04-01

Adult humans recognize that even unfamiliar speech can communicate information between third parties, demonstrating an ability to separate communicative function from linguistic content. We examined whether 12-month-old infants understand that speech can communicate before they understand the meanings of specific words. Specifically, we test the understanding that speech permits the transfer of information about a Communicator's target object to a Recipient. Initially, the Communicator selectively grasped one of two objects. In test, the Communicator could no longer reach the objects. She then turned to the Recipient and produced speech (a nonsense word) or non-speech (coughing). Infants looked longer when the Recipient selected the non-target than the target object when the Communicator had produced speech but not coughing (Experiment 1). Looking time patterns differed from the speech condition when the Recipient rather than the Communicator produced the speech (Experiment 2), and when the Communicator produced a positive emotional vocalization (Experiment 3), but did not differ when the Recipient had previously received information about the target by watching the Communicator's selective grasping (Experiment 4). Thus infants understand the information-transferring properties of speech and recognize some of the conditions under which others' information states can be updated. These results suggest that infants possess an abstract understanding of the communicative function of speech, providing an important potential mechanism for language and knowledge acquisition. Copyright © 2011 Elsevier B.V. All rights reserved.

Autologous Epstein-Barr virus (EBV)-specific cytotoxic T cells for the treatment of persistent active EBV infection.

PubMed

Savoldo, Barbara; Huls, M Helen; Liu, Zhensheng; Okamura, Takayuki; Volk, Hans-Dieter; Reinke, Petra; Sabat, Robert; Babel, Nina; Jones, James F; Webster-Cyriaque, Jennifer; Gee, Adrian P; Brenner, Malcolm K; Heslop, Helen E; Rooney, Cliona M

2002-12-01

Chronic active Epstein-Barr virus (CAEBV) infection syndrome is a heterogeneous EBV-related disorder characterized by chronic fatigue, fever, lymphadenopathy, and/or hepatosplenomegaly, associated with abnormal patterns of antibody to EBV. CAEBV can range from disabling mild/moderate forms to rapidly lethal disorders. Even patients with mild/moderate disease frequently suffer adverse effects from long-term anti-inflammatory agents and have a quality of life that progressively deteriorates. It is still unknown why these individuals are unable to produce an effective immune response to control EBV, and no effective treatment is currently available. Since ex vivo-expanded EBV-specific cytotoxic T lymphocytes (EBV-CTLs) can safely restore EBV-specific cellular immune responses in immunodeficient patients, we assessed the possibility that adoptive immunotherapy might also effectively treat CAEBV infection. Following stimulation with irradiated EBV-transformed lymphoblastoid cell lines (LCLs), EBV-CTLs were successfully generated from 8 of 8 patients with the mild/moderate form of CAEBV infection. These CTLs were predominantly CD3(+) CD8(+) cells and produced specific killing of the autologous LCLs. There were 5 patients with 1- to 12-year histories of disease who were treated with 1 to 4 injections of EBV-CTLs. Following infusion, there was resolution of fatigue and malaise, disappearance of fever, and regression of lymphadenopathy and splenomegaly. The pattern and titers of anti-EBV antibodies also normalized. No toxicity was observed. There were 4 patients who did not show any relapse of disease within 6 to 36 months follow-up; one patient had recurrence of fatigue and myalgia one year after CTL infusion. We suggest that adoptive immunotherapy with autologous EBV-CTLs may represent a safe and feasible alternative treatment for patients affected with mild/moderate CAEBV infection and that this approach should be evaluated in the more severe forms of the disease.

Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.).

PubMed

Kamenetsky, Rina; Faigenboim, Adi; Shemesh Mayer, Einat; Ben Michael, Tomer; Gershberg, Chen; Kimhi, Sagie; Esquira, Itzhak; Rohkin Shalom, Sarit; Eshel, Dani; Rabinowitch, Haim D; Sherman, Amir

2015-01-22

Garlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not been the subject of either classical breeding or genetic studies. However, recent achievements in fertility restoration in a number of genotypes have led to flowering and seed production, thus enabling genetic studies and breeding in garlic. A transcriptome catalogue of fertile garlic was produced from multiplexed gene libraries, using RNA collected from various plant organs, including inflorescences and flowers. Over 32 million 250-bp paired-end reads were assembled into an extensive transcriptome of 240,000 contigs. An abundant transcriptome assembled separately from 102,000 highly expressed contigs was annotated and analyzed for gene ontology and metabolic pathways. Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers. Analysis of the enriched biological processes and molecular functions revealed characteristic patterns for stress response, flower development and photosynthetic activity. Orthologues of key flowering genes were differentially expressed, not only in reproductive tissues, but also in leaves and bulbs, suggesting their role in flower-signal transduction and the bulbing process. More than 100 variants and isoforms of enzymes involved in organosulfur metabolism were differentially expressed and had organ-specific patterns. In addition to plant genes, viral RNA of at least four garlic viruses was detected, mostly in the roots and cloves, whereas only 1-4% of the reads were found in the foliage leaves. The de novo transcriptome of fertile garlic represents a new resource for research and breeding of this important crop, as well as for the development of effective molecular markers for useful traits, including fertility and seed production, resistance to pests and neutraceutical characteristics.

A Comparison of the Effects of Electrode Implantation and Targeting on Pattern Classification Accuracy for Prosthesis Control

PubMed Central

Farrell, Todd R.; Weir, Richard F. ff.

2011-01-01

The use of surface versus intramuscular electrodes as well as the effect of electrode targeting on pattern-recognition-based multifunctional prosthesis control was explored. Surface electrodes are touted for their ability to record activity from relatively large portions of muscle tissue. Intramuscular electromyograms (EMGs) can provide focal recordings from deep muscles of the forearm and independent signals relatively free of crosstalk. However, little work has been done to compare the two. Additionally, while previous investigations have either targeted electrodes to specific muscles or used untargeted (symmetric) electrode arrays, no work has compared these approaches to determine if one is superior. The classification accuracies of pattern-recognition-based classifiers utilizing surface and intramuscular as well as targeted and untargeted electrodes were compared across 11 subjects. A repeated-measures analysis of variance revealed that when only EMG amplitude information was used from all available EMG channels, the targeted surface, targeted intramuscular, and untargeted surface electrodes produced similar classification accuracies while the untargeted intramuscular electrodes produced significantly lower accuracies. However, no statistical differences were observed between any of the electrode conditions when additional features were extracted from the EMG signal. It was concluded that the choice of electrode should be driven by clinical factors, such as signal robustness/stability, cost, etc., instead of by classification accuracy. PMID:18713689

An experimental test for age-related improvements in reproductive performance in a frog that cares for its young

NASA Astrophysics Data System (ADS)

Dugas, Matthew B.; Moore, Michael P.; Wamelink, Caitlin N.; Richards-Zawacki, Corinne L.; Martin, Ryan A.

2015-10-01

Reproductive performance often increases with age in long-lived iteroparous organisms, a pattern that can result from within-individual increases in effort and/or competence. In free-living populations, it is typically difficult to distinguish these mechanisms or to isolate particular features of reproduction-influencing outcomes. In captive Oophaga pumilio, a frog in which mothers provide extended offspring provisioning via trophic eggs, we experimentally manipulated the age at which females started breeding and then monitored them across repeated reproductive events. This experiment allowed us to decouple age and experience and isolate maternal care as the proximate source of any differences in performance. Younger first-time mothers produced larger broods than older first-time mothers, but did not rear more offspring to independence. Across repeated reproductive events, maternal age was unassociated with any metric of performance. At later reproductive events, however, mothers produced fewer metamorphs, and a lower proportion of individuals in their broods reached independence. These patterns suggest that performance does not improve with age or breeding experience in this frog, and that eventual declines in performance are driven by reproductive activity, not age per se. Broadly, age-specific patterns of reproductive performance may depend on the proximate mechanism by which parents influence offspring fitness and how sensitive these are to effort and competence.

Speckle patterns produced by an optical vortex and its application to surface roughness measurements.

PubMed

Passos, M H M; Lemos, M R; Almeida, S R; Balthazar, W F; da Silva, L; Huguenin, J A O

2017-01-10

In this work, we report on the analysis of speckle patterns produced by illuminating different rough surfaces with an optical vortex, a first-order (l=1) Laguerre-Gaussian beam. The generated speckle patterns were observed in the normal direction exploring four different planes: the diffraction plane, image plane, focal plane, and exact Fourier transform plane. The digital speckle patterns were analyzed using the Hurst exponent of digital images, an interesting tool used to study surface roughness. We show a proof of principle that the Hurst exponent of a digital speckle pattern is more sensitive with respect to the surface roughness when the speckle pattern is produced by an optical vortex and observed at a focal plane. We also show that Hurst exponents are not so sensitive with respect to the topological charge l. These results open news possibilities of investigation into speckle metrology once we have several techniques that use speckle patterns for different applications.

DNA Based Molecular Scale Nanofabrication

DTIC Science & Technology

2015-12-04

structure. We developed a method to produce nanoscale patterns on SAM. (d) Studied the molecular imprinting of DNA origami structure using polymer...to produce nanoscale patterns on SAM. (d) Studied the molecular imprinting of DNA origami structure using polymer substrates. Developed a high... imprinting using DNA nanostructure templates. Soft lithography uses polymeric stamps with certain features to transfer the pattern for printing

Chromosome-specific staining to detect genetic rearrangements

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

2013-04-09

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Gait kinematics and kinetics of 7-year-old children: a comparison to adults using age-specific anthropometric data.

PubMed

Ganley, Kathleen J; Powers, Christopher M

2005-02-01

The purpose of this study was to determine if sagittal plane gait kinematics and kinetics of 7-year-old children differed from those of adults when age-specific anthropometrics were used in the calculations. Joint angles, moments, and power obtained during level walking in 7-year-old children (n=15) were compared to data from adults (n=15). Calculations were performed using age-specific anthropometric data obtained from dual energy X-ray absorptiometry. For most of the variables examined, 7-year-olds were similar to adults, however children demonstrated a diminished peak plantar flexor moment and less peak power absorption and generation at the ankle during late stance. These results provide support for the hypothesis that children lack the neuromuscular maturity, especially at the ankle, to produce an adult-like gait pattern.

Background and stimulus-induced patterns of high metabolic activity in the visual cortex (area 17) of the squirrel and macaque monkey

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

Humphrey, A.L.; Hendrickson, A.E.

1983-02-01

The authors have used 2-deoxy-D-(/sup 14/C)glucose (2-DG) autoradiography and cytochrome oxidase histochemistry to examine background and stimulus-induced patterns of metabolic activity in monkey striate cortex. In squirrel monkeys (Saimiri sciureus) that binocularly or monocularly viewed diffuse white light or binocularly viewed bars of many orientations and spatial frequencies, 2-DG consumption was not uniform across the cortex but consisted of regularly spaced radial zones of high uptake. The cytochrome oxidase stain in these animals also revealed patches of high metabolism which coincided with the 2-DG patches. Squirrel monkeys binocularly viewing vertical stripes showed parallel bands of increased 2-DG uptake in themore » cortex, while the cytochrome label in these animals remained patchy. In macaque (Macaca nemestrina) monkeys, binocular stimulation with many orientations and spatial frequencies produced radial zones of high 2-DG uptake. When viewed tangentially, these zones formed a dots-in-rows pattern with a spacing of 350 X 500 microns; cytochrome oxidase staining produced an identical pattern. Macaca differed from Saimiri in that monocular stimulation labeled alternate rows. These results indicate that there are radial zones of high background metabolism across squirrel and macaque monkey striate cortex. In Saimiri these zones do not appear to be related to an eye dominance system, while in Macaca they do. The presence of these zones of high metabolism may complicate the interpretation of 2-DG autoradiographs that result from specific visual stimuli.« less

Size-Class Effect Contributes to Tree Species Assembly through Influencing Dispersal in Tropical Forests

PubMed Central

Hu, Yue-Hua; Kitching, Roger L.; Lan, Guo-Yu; Zhang, Jiao-Lin; Sha, Li-Qing; Cao, Min

2014-01-01

We have investigated the processes of community assembly using size classes of trees. Specifically our work examined (1) whether point process models incorporating an effect of size-class produce more realistic summary outcomes than do models without this effect; (2) which of three selected models incorporating, respectively environmental effects, dispersal and the joint-effect of both of these, is most useful in explaining species-area relationships (SARs) and point dispersion patterns. For this evaluation we used tree species data from the 50-ha forest dynamics plot in Barro Colorado Island, Panama and the comparable 20 ha plot at Bubeng, Southwest China. Our results demonstrated that incorporating an size-class effect dramatically improved the SAR estimation at both the plots when the dispersal only model was used. The joint effect model produced similar improvement but only for the 50-ha plot in Panama. The point patterns results were not improved by incorporation of size-class effects using any of the three models. Our results indicate that dispersal is likely to be a key process determining both SARs and point patterns. The environment-only model and joint-effects model were effective at the species level and the community level, respectively. We conclude that it is critical to use multiple summary characteristics when modelling spatial patterns at the species and community levels if a comprehensive understanding of the ecological processes that shape species’ distributions is sought; without this results may have inherent biases. By influencing dispersal, the effect of size-class contributes to species assembly and enhances our understanding of species coexistence. PMID:25251538

Cell Patterns Emerge from Coupled Chemical and Physical Fields with Cell Proliferation Dynamics: The Arabidopsis thaliana Root as a Study System

PubMed Central

Barrio, Rafael A.; Romero-Arias, José Roberto; Noguez, Marco A.; Azpeitia, Eugenio; Ortiz-Gutiérrez, Elizabeth; Hernández-Hernández, Valeria; Cortes-Poza, Yuriria; Álvarez-Buylla, Elena R.

2013-01-01

A central issue in developmental biology is to uncover the mechanisms by which stem cells maintain their capacity to regenerate, yet at the same time produce daughter cells that differentiate and attain their ultimate fate as a functional part of a tissue or an organ. In this paper we propose that, during development, cells within growing organs obtain positional information from a macroscopic physical field that is produced in space while cells are proliferating. This dynamical interaction triggers and responds to chemical and genetic processes that are specific to each biological system. We chose the root apical meristem of Arabidopsis thaliana to develop our dynamical model because this system is well studied at the molecular, genetic and cellular levels and has the key traits of multicellular stem-cell niches. We built a dynamical model that couples fundamental molecular mechanisms of the cell cycle to a tension physical field and to auxin dynamics, both of which are known to play a role in root development. We perform extensive numerical calculations that allow for quantitative comparison with experimental measurements that consider the cellular patterns at the root tip. Our model recovers, as an emergent pattern, the transition from proliferative to transition and elongation domains, characteristic of stem-cell niches in multicellular organisms. In addition, we successfully predict altered cellular patterns that are expected under various applied auxin treatments or modified physical growth conditions. Our modeling platform may be extended to explicitly consider gene regulatory networks or to treat other developmental systems. PMID:23658505

Not just black and white: pigment pattern development and evolution in vertebrates

PubMed Central

Mills, Margaret G.; Patterson, Larissa B.

2009-01-01

Animals display diverse colors and patterns that vary within and between species. Similar phenotypes appear in both closely related and widely divergent taxa. Pigment patterns thus provide an opportunity to explore how development is altered to produce differences in form and whether similar phenotypes share a common genetic basis. Understanding the development and evolution of pigment patterns requires knowledge of the cellular interactions and signaling pathways that produce those patterns. These complex traits provide unparalleled opportunities for integrating studies from ecology and behavior to molecular biology and biophysics. PMID:19073271

Patterning of polymer nanofiber meshes by electrospinning for biomedical applications

PubMed Central

Neves, Nuno M; Campos, Rui; Pedro, Adriano; Cunha, José; Macedo, Francisco; Reis, Rui L

2007-01-01

The end-product of the electrospinning process is typically a randomly aligned fiber mesh or membrane. This is a result of the electric field generated between the drop of polymer solution at the needle and the collector. The developed electric field causes the stretching of the fibers and their random deposition. By judicious selection of the collector architecture, it is thus possible to develop other morphologies on the nanofiber meshes. The aim of this work is to prepare fiber meshes using various patterned collectors with specific dimensions and designs and to evaluate how those patterns can affect the properties of the meshes relevant to biomedical applications. This study aims at verifying whether it is possible to control the architecture of the fiber meshes by tailoring the geometry of the collector. Three different metallic collector topographies are used to test this hypothesis. Electrospun nonwoven patterned meshes of polyethylene oxide (PEO) and poly(ε-capro-lactone) (PCL) were successfully prepared. Those fiber meshes were analyzed by scanning electron microscopy (SEM). Both mechanical properties of the meshes and cell contacting experiments were performed to test the effect of the produced patterns over the properties of the meshes relevant for biomedical applications. The present study will evaluate cell adhesion sensitivity to the patterns generated and the effect of those patterns on the tensile properties of the fiber meshes. PMID:18019842

CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA.

PubMed

Xu, Yi-Hua; Manoharan, Herbert T; Pitot, Henry C

2007-09-01

The bisulfite genomic sequencing technique is one of the most widely used techniques to study sequence-specific DNA methylation because of its unambiguous ability to reveal DNA methylation status to the order of a single nucleotide. One characteristic feature of the bisulfite genomic sequencing technique is that a number of sample sequence files will be produced from a single DNA sample. The PCR products of bisulfite-treated DNA samples cannot be sequenced directly because they are heterogeneous in nature; therefore they should be cloned into suitable plasmids and then sequenced. This procedure generates an enormous number of sample DNA sequence files as well as adding extra bases belonging to the plasmids to the sequence, which will cause problems in the final sequence comparison. Finding the methylation status for each CpG in each sample sequence is not an easy job. As a result CpG PatternFinder was developed for this purpose. The main functions of the CpG PatternFinder are: (i) to analyze the reference sequence to obtain CpG and non-CpG-C residue position information. (ii) To tailor sample sequence files (delete insertions and mark deletions from the sample sequence files) based on a configuration of ClustalW multiple alignment. (iii) To align sample sequence files with a reference file to obtain bisulfite conversion efficiency and CpG methylation status. And, (iv) to produce graphics, highlighted aligned sequence text and a summary report which can be easily exported to Microsoft Office suite. CpG PatternFinder is designed to operate cooperatively with BioEdit, a freeware on the internet. It can handle up to 100 files of sample DNA sequences simultaneously, and the total CpG pattern analysis process can be finished in minutes. CpG PatternFinder is an ideal software tool for DNA methylation studies to determine the differential methylation pattern in a large number of individuals in a population. Previously we developed the CpG Analyzer program; CpG PatternFinder is our further effort to create software tools for DNA methylation studies.

Maximizing lipocalin prediction through balanced and diversified training set and decision fusion.

PubMed

Nath, Abhigyan; Subbiah, Karthikeyan

2015-12-01

Lipocalins are short in sequence length and perform several important biological functions. These proteins are having less than 20% sequence similarity among paralogs. Experimentally identifying them is an expensive and time consuming process. The computational methods based on the sequence similarity for allocating putative members to this family are also far elusive due to the low sequence similarity existing among the members of this family. Consequently, the machine learning methods become a viable alternative for their prediction by using the underlying sequence/structurally derived features as the input. Ideally, any machine learning based prediction method must be trained with all possible variations in the input feature vector (all the sub-class input patterns) to achieve perfect learning. A near perfect learning can be achieved by training the model with diverse types of input instances belonging to the different regions of the entire input space. Furthermore, the prediction performance can be improved through balancing the training set as the imbalanced data sets will tend to produce the prediction bias towards majority class and its sub-classes. This paper is aimed to achieve (i) the high generalization ability without any classification bias through the diversified and balanced training sets as well as (ii) enhanced the prediction accuracy by combining the results of individual classifiers with an appropriate fusion scheme. Instead of creating the training set randomly, we have first used the unsupervised Kmeans clustering algorithm to create diversified clusters of input patterns and created the diversified and balanced training set by selecting an equal number of patterns from each of these clusters. Finally, probability based classifier fusion scheme was applied on boosted random forest algorithm (which produced greater sensitivity) and K nearest neighbour algorithm (which produced greater specificity) to achieve the enhanced predictive performance than that of individual base classifiers. The performance of the learned models trained on Kmeans preprocessed training set is far better than the randomly generated training sets. The proposed method achieved a sensitivity of 90.6%, specificity of 91.4% and accuracy of 91.0% on the first test set and sensitivity of 92.9%, specificity of 96.2% and accuracy of 94.7% on the second blind test set. These results have established that diversifying training set improves the performance of predictive models through superior generalization ability and balancing the training set improves prediction accuracy. For smaller data sets, unsupervised Kmeans based sampling can be an effective technique to increase generalization than that of the usual random splitting method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Laser-induced porous graphene films from commercial polymers

NASA Astrophysics Data System (ADS)

Lin, Jian; Peng, Zhiwei; Liu, Yuanyue; Ruiz-Zepeda, Francisco; Ye, Ruquan; Samuel, Errol L. G.; Yacaman, Miguel Jose; Yakobson, Boris I.; Tour, James M.

2014-12-01

The cost effective synthesis and patterning of carbon nanomaterials is a challenge in electronic and energy storage devices. Here we report a one-step, scalable approach for producing and patterning porous graphene films with three-dimensional networks from commercial polymer films using a CO2 infrared laser. The sp3-carbon atoms are photothermally converted to sp2-carbon atoms by pulsed laser irradiation. The resulting laser-induced graphene (LIG) exhibits high electrical conductivity. The LIG can be readily patterned to interdigitated electrodes for in-plane microsupercapacitors with specific capacitances of >4 mF cm-2 and power densities of ~9 mW cm-2. Theoretical calculations partially suggest that enhanced capacitance may result from LIG’s unusual ultra-polycrystalline lattice of pentagon-heptagon structures. Combined with the advantage of one-step processing of LIG in air from commercial polymer sheets, which would allow the employment of a roll-to-roll manufacturing process, this technique provides a rapid route to polymer-written electronic and energy storage devices.

Nonuniform traffic spots (NUTS) in multistage interconnection networks

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

Lang, T.; Kurisaki, L.

1990-09-01

The performance of multistage interconnection networks for multiprocessors is degraded when the traffic pattern produces nonuniform congestion in the blocking switches, that is, when there exist nonuniform traffic spots. For some specific patterns the authors evaluate this degradation in performance and propose modifications to the network organization and operation to reduce the degradation. Successful modifications are the use of diverting switches and the extension of the network with additional links. The use of these modifications makes the network more effective for a larger variety of traffic patterns. The authors also consider the case in which the network carries the superpositionmore » of two types of traffic. One type is the high throughput data and instruction traffic, while the other consists of control and I/O packets which are of low throughput but have severe real-time constraints. The authors conclude that diverting switches and networks with additional links are also suitable for assuring low latency for the real-time traffic, especially when using the displacing mode.« less

Live cell imaging of phosphoinositide dynamics during Legionella infection.

PubMed

Weber, Stephen; Hilbi, Hubert

2014-01-01

The "accidental" pathogen Legionella pneumophila replicates intracellularly in a distinct compartment, the Legionella-containing vacuole (LCV). To form this specific pathogen vacuole, the bacteria translocate via the Icm/Dot type IV secretion system approximately 300 different effector proteins into the host cell. Several of these secreted effectors anchor to the cytoplasmic face of the LCV membrane by binding to phosphoinositide (PI) lipids. L. pneumophila thus largely controls the localization of secreted bacterial effectors and the recruitment of host factors to the LCV through the modulation of the vacuole membrane PI pattern. The LCV PI pattern and its dynamics can be studied in real-time using fluorescently labeled protein probes stably produced by the soil amoeba Dictyostelium discoideum. In this chapter, we describe a protocol to (1) construct and handle amoeba model systems as a tool for observing PIs in live cell imaging, (2) capture rapid changes in membrane PI patterning during uptake events, and (3) observe the dynamics of LCV PIs over the course of a Legionella infection.

Laser-induced porous graphene films from commercial polymers

PubMed Central

Lin, Jian; Peng, Zhiwei; Liu, Yuanyue; Ruiz-Zepeda, Francisco; Ye, Ruquan; Samuel, Errol L. G.; Yacaman, Miguel Jose; Yakobson, Boris I.; Tour, James M.

2014-01-01

Synthesis and patterning of carbon nanomaterials cost effectively is a challenge in electronic and energy storage devices. Here report a one-step, scalable approach for producing and patterning porous graphene films with 3-dimensional networks from commercial polymer films using a CO2 infrared laser. The sp3-carbon atoms are photothermally converted to sp2-carbon atoms by pulsed laser irradiation. The resulting laser-induced graphene (LIG) exhibits high electrical conductivity. The LIG can be readily patterned to interdigitated electrodes for in-plane microsupercapacitors with specific capacitances of >4 mF·cm−2 and power densities of ~9 mW·cm−2. Theoretical calculations partially suggest that enhanced capacitance may result from LIG’s unusual ultra-polycrystalline lattice of pentagon-heptagon structures. Combined with the advantage of one-step processing of LIG in air from commercial polymer sheets, which would allow the employment of a roll-to-roll manufacturing process, this technique provides a rapid route to polymer-written electronic and energy storage devices. PMID:25493446

Metals Electroprocessing in Molten Salts

NASA Technical Reports Server (NTRS)

Sadoway, D. R.

1985-01-01

The present study seeks to explain the poor quality of solid electrodeposits in molten salts through a consideration of the effects of fluid flow of the electrolyte. Transparent cells allow observation of electrolyte circulation by a laser schlieren optical technique during the electrodeposition of solid zinc from the molten salt electrolyte, ZnCl2 - LiCl-KCl. Experimental variables are current, density, electrolyte composition, and cell geometry. Based on the results of earlier electrodeposition studies as well as reports in the literature, these parameters are identified as having the primary influence on cell performance and deposit quality. Experiments are conducted to measure the fluid flow patterns and the electrochemical cell characteristics, and to correlate this information with the morphology of the solid electrodeposit produced. Specifically, cell voltage, cell current, characteristic time for dendrite evolution, and dendrite growth directions are noted. Their relationship to electrolyte flow patterns and the morphology of the resulting electrodeposit are derived. Results to date indicate that laser schlieren imaging is capable of revealing fluid flow patterns in a molten salt electrolyte.

Quadrupedal Robot Locomotion: A Biologically Inspired Approach and Its Hardware Implementation

PubMed Central

Espinal, A.; Rostro-Gonzalez, H.; Carpio, M.; Guerra-Hernandez, E. I.; Ornelas-Rodriguez, M.; Puga-Soberanes, H. J.; Sotelo-Figueroa, M. A.; Melin, P.

2016-01-01

A bioinspired locomotion system for a quadruped robot is presented. Locomotion is achieved by a spiking neural network (SNN) that acts as a Central Pattern Generator (CPG) producing different locomotion patterns represented by their raster plots. To generate these patterns, the SNN is configured with specific parameters (synaptic weights and topologies), which were estimated by a metaheuristic method based on Christiansen Grammar Evolution (CGE). The system has been implemented and validated on two robot platforms; firstly, we tested our system on a quadruped robot and, secondly, on a hexapod one. In this last one, we simulated the case where two legs of the hexapod were amputated and its locomotion mechanism has been changed. For the quadruped robot, the control is performed by the spiking neural network implemented on an Arduino board with 35% of resource usage. In the hexapod robot, we used Spartan 6 FPGA board with only 3% of resource usage. Numerical results show the effectiveness of the proposed system in both cases. PMID:27436997

Quadrupedal Robot Locomotion: A Biologically Inspired Approach and Its Hardware Implementation.

PubMed

Espinal, A; Rostro-Gonzalez, H; Carpio, M; Guerra-Hernandez, E I; Ornelas-Rodriguez, M; Puga-Soberanes, H J; Sotelo-Figueroa, M A; Melin, P

2016-01-01

A bioinspired locomotion system for a quadruped robot is presented. Locomotion is achieved by a spiking neural network (SNN) that acts as a Central Pattern Generator (CPG) producing different locomotion patterns represented by their raster plots. To generate these patterns, the SNN is configured with specific parameters (synaptic weights and topologies), which were estimated by a metaheuristic method based on Christiansen Grammar Evolution (CGE). The system has been implemented and validated on two robot platforms; firstly, we tested our system on a quadruped robot and, secondly, on a hexapod one. In this last one, we simulated the case where two legs of the hexapod were amputated and its locomotion mechanism has been changed. For the quadruped robot, the control is performed by the spiking neural network implemented on an Arduino board with 35% of resource usage. In the hexapod robot, we used Spartan 6 FPGA board with only 3% of resource usage. Numerical results show the effectiveness of the proposed system in both cases.

IgM anti-myeloperoxidase antibody-secreting lymphocytes are present in the peripheral repertoire of lupus mice but rarely differentiate into IgG-producing cells

PubMed Central

Vittecoq, O; Brard, F; Jovelin, F; Le Loet, X; Tron, F; Gilbert, D

1999-01-01

Two IgM, κ anti-myeloperoxidase (MPO) monoclonal antibodies, 6D6 and 9B5, bound to MPO in a solid-phase enzyme-linked immunosorbent assay were derived from the splenocytes of (NZB × NZW) F1 and MRL/lpr-lpr mice, respectively. 6D6 gave a characteristic perinuclear immunofluorescence staining pattern on ethanol-fixed human neutrophils, bound to the native form of MPO by immunoblotting and had a high constant affinity for MPO as demonstrated by real-time specific interaction. 9B5 produced a cytoplasmic immunofluorescence staining pattern, reacted with the heavy chain of MPO and had a low constant affinity for MPO. The heavy-and light-chain variable region genes of monoclonal antibodies (mAb) 6D6 and 9B5 were sequenced and found to be highly homologous to germline genes and to contain negatively charged amino acids in the complementarity determining regions. IgM MPO-binding activity was observed in most BW and MRL/lpr-lpr mouse sera, which may correspond to polyclonal activation of B cells, whereas IgG anti-MPO antibodies could be rarely detected. Thus, this study indicates that (i) BW and MRL/lpr-lpr mice do not delete IgM anti-MPO secreting B cells, do not maintain these B cells in a state of anergy, but most individuals are not able to spontaneously induce the class-switching of this autoantibody population; (ii) IgM anti-MPO antibodies can recognize different epitopes on MPO and produce different immunofluorescence staining pattern on ethanol-fixed human neutrophils, as demonstrated by the immunochemical properties of the two lupus-mouse derived mAb. PMID:10540169

Patterns of Hybrid Loss of Imprinting Reveal Tissue- and Cluster-Specific Regulation

PubMed Central

Wiley, Christopher D.; Matundan, Harry H.; Duselis, Amanda R.; Isaacs, Alison T.; Vrana, Paul B.

2008-01-01

Background Crosses between natural populations of two species of deer mice, Peromyscus maniculatus (BW), and P. polionotus (PO), produce parent-of-origin effects on growth and development. BW females mated to PO males (bw×po) produce growth-retarded but otherwise healthy offspring. In contrast, PO females mated to BW males (PO×BW) produce overgrown and severely defective offspring. The hybrid phenotypes are pronounced in the placenta and include PO×BW conceptuses which lack embryonic structures. Evidence to date links variation in control of genomic imprinting with the hybrid defects, particularly in the PO×BW offspring. Establishment of genomic imprinting is typically mediated by gametic DNA methylation at sites known as gDMRs. However, imprinted gene clusters vary in their regulation by gDMR sequences. Methodology/Principal Findings Here we further assess imprinted gene expression and DNA methylation at different cluster types in order to discern patterns. These data reveal PO×BW misexpression at the Kcnq1ot1 and Peg3 clusters, both of which lose ICR methylation in placental tissues. In contrast, some embryonic transcripts (Peg10, Kcnq1ot1) reactivated the silenced allele with little or no loss of DNA methylation. Hybrid brains also display different patterns of imprinting perturbations. Several cluster pairs thought to use analogous regulatory mechanisms are differentially affected in the hybrids. Conclusions/Significance These data reinforce the hypothesis that placental and somatic gene regulation differs significantly, as does that between imprinted gene clusters and between species. That such epigenetic regulatory variation exists in recently diverged species suggests a role in reproductive isolation, and that this variation is likely to be adaptive. PMID:18958286

Shear-induced endothelial mechanotransduction: the interplay between reactive oxygen species (ROS) and nitric oxide (NO) and the pathophysiological implications

PubMed Central

2014-01-01

Hemodynamic shear stress, the blood flow-generated frictional force acting on the vascular endothelial cells, is essential for endothelial homeostasis under normal physiological conditions. Mechanosensors on endothelial cells detect shear stress and transduce it into biochemical signals to trigger vascular adaptive responses. Among the various shear-induced signaling molecules, reactive oxygen species (ROS) and nitric oxide (NO) have been implicated in vascular homeostasis and diseases. In this review, we explore the molecular, cellular, and vascular processes arising from shear-induced signaling (mechanotransduction) with emphasis on the roles of ROS and NO, and also discuss the mechanisms that may lead to excessive vascular remodeling and thus drive pathobiologic processes responsible for atherosclerosis. Current evidence suggests that NADPH oxidase is one of main cellular sources of ROS generation in endothelial cells under flow condition. Flow patterns and magnitude of shear determine the amount of ROS produced by endothelial cells, usually an irregular flow pattern (disturbed or oscillatory) producing higher levels of ROS than a regular flow pattern (steady or pulsatile). ROS production is closely linked to NO generation and elevated levels of ROS lead to low NO bioavailability, as is often observed in endothelial cells exposed to irregular flow. The low NO bioavailability is partly caused by the reaction of ROS with NO to form peroxynitrite, a key molecule which may initiate many pro-atherogenic events. This differential production of ROS and RNS (reactive nitrogen species) under various flow patterns and conditions modulates endothelial gene expression and thus results in differential vascular responses. Moreover, ROS/RNS are able to promote specific post-translational modifications in regulatory proteins (including S-glutathionylation, S-nitrosylation and tyrosine nitration), which constitute chemical signals that are relevant in cardiovascular pathophysiology. Overall, the dynamic interplay between local hemodynamic milieu and the resulting oxidative and S-nitrosative modification of regulatory proteins is important for ensuing vascular homeostasis. Based on available evidence, it is proposed that a regular flow pattern produces lower levels of ROS and higher NO bioavailability, creating an anti-atherogenic environment. On the other hand, an irregular flow pattern results in higher levels of ROS and yet lower NO bioavailability, thus triggering pro-atherogenic effects. PMID:24410814

Motor Synchronization in Patients With Schizophrenia: Preserved Time Representation With Abnormalities in Predictive Timing.

PubMed

Wilquin, Hélène; Delevoye-Turrell, Yvonne; Dione, Mariama; Giersch, Anne

2018-01-01

Objective: Basic temporal dysfunctions have been described in patients with schizophrenia, which may impact their ability to connect and synchronize with the outer world. The present study was conducted with the aim to distinguish between interval timing and synchronization difficulties and more generally the spatial-temporal organization disturbances for voluntary actions. A new sensorimotor synchronization task was developed to test these abilities. Method: Twenty-four chronic schizophrenia patients matched with 27 controls performed a spatial-tapping task in which finger taps were to be produced in synchrony with a regular metronome to six visual targets presented around a virtual circle on a tactile screen. Isochronous (time intervals of 500 ms) and non-isochronous auditory sequences (alternated time intervals of 300/600 ms) were presented. The capacity to produce time intervals accurately versus the ability to synchronize own actions (tap) with external events (tone) were measured. Results: Patients with schizophrenia were able to produce the tapping patterns of both isochronous and non-isochronous auditory sequences as accurately as controls producing inter-response intervals close to the expected interval of 500 and 900 ms, respectively. However, the synchronization performances revealed significantly more positive asynchrony means (but similar variances) in the patient group than in the control group for both types of auditory sequences. Conclusion: The patterns of results suggest that patients with schizophrenia are able to perceive and produce both simple and complex sequences of time intervals but are impaired in the ability to synchronize their actions with external events. These findings suggest a specific deficit in predictive timing, which may be at the core of early symptoms previously described in schizophrenia.

Electronic characterization of lithographically patterned microcoils for high sensitivity NMR detection.

PubMed

Demas, Vasiliki; Bernhardt, Anthony; Malba, Vince; Adams, Kristl L; Evans, Lee; Harvey, Christopher; Maxwell, Robert S; Herberg, Julie L

2009-09-01

Nuclear magnetic resonance (NMR) offers a non-destructive, powerful, structure-specific analytical method for the identification of chemical and biological systems. The use of radio frequency (RF) microcoils has been shown to increase the sensitivity in mass-limited samples. Recent advances in micro-receiver technology have further demonstrated a substantial increase in mass sensitivity [D.L. Olson, T.L. Peck, A.G. Webb, R.L. Magin, J.V. Sweedler, High-resolution microcoil H-1-NMR for mass-limited, nanoliter-volume samples, Science 270 (5244) (1995) 1967-1970]. Lithographic methods for producing solenoid microcoils possess a level of flexibility and reproducibility that exceeds previous production methods, such as hand winding microcoils. This paper presents electrical characterizations of RF microcoils produced by a unique laser lithography system that can pattern three dimensional surfaces and compares calculated and experimental results to those for wire wound RF microcoils. We show that existing optimization conditions for RF coil design still hold true for RF microcoils produced by lithography. Current lithographic microcoils show somewhat inferior performance to wire wound RF microcoils due to limitations in the existing electroplating technique. In principle, however, when the pitch of the RF microcoil is less than 100mum lithographic coils should show comparable performance to wire wound coils. In the cases of larger pitch, wire cross sections can be significantly larger and resistances lower than microfabricated conductors.

Striation patterns in serrated blade stabs to cartilage.

PubMed

Pounder, Derrick J; Reeder, Francesca D

2011-05-20

Stab wounds were made in porcine cartilage with 13 serrated knives, amongst which 4 were drop-point and 9 straight-spine; 9 coarsely serrated, 3 finely serrated and 1 with mixed pattern serrations. The walls of the stab tracks were cast with dental impression material, and the casts photographed together with the knife blades for comparison. All 13 serrated blades produced an "irregularly regular" pattern of striations on cartilage in all stabbings. Unusual and distinctive blade serration patterns produced equally distinctive wound striation patterns. A reference collection of striation patterns and corresponding blades might prove useful for striation pattern analysis. Drop-point blades produced similar striations to straight-spine blades except that the striations were not parallel but rather fan-shaped, converging towards the wound exit. The fan-shaped striation pattern characteristic of drop-point blades is explained by the initial lateral movement of the blade through the cartilage imposed by the presence of the drop point shape. It appears that the greater the overall angle of the drop point, the shorter the blade length over which the drop point occurs, and the closer the first serration is to the knife tip, the more obvious is the fan-shaped pattern. We anticipate that micro-irregularities producing individualising characteristics in non-serrated drop point blades, provided they were located at the tip opposite the drop point, should also show a fan-shaped pattern indicative of a drop point blade. The examination of the walls of stab wounds to cartilage represents an under-utilised source of forensic information to assist in knife identification. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Electrically induced contraction levels of the quadriceps femoris muscles in healthy men: the effects of three patterns of burst-modulated alternating current and volitional muscle fatigue.

PubMed

Parker, Michael G; Broughton, Alex J; Larsen, Ben R; Dinius, Josh W; Cimbura, Mac J; Davis, Matthew

2011-12-01

The purpose of this study was to compare electrically induced contraction levels produced by three patterns of alternating current in fatigued and nonfatigued skeletal muscles. Eighteen male volunteers without health conditions, with a mean (SD) age of 24.9 (3.4) yrs were randomly exposed to a fatiguing volitional isometric quadriceps contraction and one of three patterns of 2.5-KHz alternating current; two were modulated at 50 bursts per second (10% burst duty cycle with five cycles per burst and 90% burst duty cycle with 45 cycles per burst), and one pattern was modulated at 100 bursts per second (10% burst duty cycle with 2.5 cycles per burst). The electrically induced contraction levels produced by the three patterns of electrical stimulation were compared before and after the fatiguing contraction. The 10% burst duty cycles produced 42.9% (95% confidence interval, 29.1%-56.7%) and 32.1% (95% confidence interval, 18.2%-45.9%) more muscle force (P < 0.001) than did the 90% burst duty cycle pattern. There was no significant interaction effect (P = 0.392) of electrical stimulation patterns and fatigue on the electrically induced contraction levels. The lower burst duty cycle (10%) patterns of electrical stimulation produced stronger muscle contractions. Furthermore, the stimulation patterns had no influence on the difference in muscle force before and after the fatiguing quadriceps contraction. Consequently, for clinical applications in which high forces are desired, the patterns using the 10% burst duty cycle may be helpful.

An experimental design method leading to chemical Turing patterns.

PubMed

Horváth, Judit; Szalai, István; De Kepper, Patrick

2009-05-08

Chemical reaction-diffusion patterns often serve as prototypes for pattern formation in living systems, but only two isothermal single-phase reaction systems have produced sustained stationary reaction-diffusion patterns so far. We designed an experimental method to search for additional systems on the basis of three steps: (i) generate spatial bistability by operating autoactivated reactions in open spatial reactors; (ii) use an independent negative-feedback species to produce spatiotemporal oscillations; and (iii) induce a space-scale separation of the activatory and inhibitory processes with a low-mobility complexing agent. We successfully applied this method to a hydrogen-ion autoactivated reaction, the thiourea-iodate-sulfite (TuIS) reaction, and noticeably produced stationary hexagonal arrays of spots and parallel stripes of pH patterns attributed to a Turing bifurcation. This method could be extended to biochemical reactions.

Combined mining: discovering informative knowledge in complex data.

PubMed

Cao, Longbing; Zhang, Huaifeng; Zhao, Yanchang; Luo, Dan; Zhang, Chengqi

2011-06-01

Enterprise data mining applications often involve complex data such as multiple large heterogeneous data sources, user preferences, and business impact. In such situations, a single method or one-step mining is often limited in discovering informative knowledge. It would also be very time and space consuming, if not impossible, to join relevant large data sources for mining patterns consisting of multiple aspects of information. It is crucial to develop effective approaches for mining patterns combining necessary information from multiple relevant business lines, catering for real business settings and decision-making actions rather than just providing a single line of patterns. The recent years have seen increasing efforts on mining more informative patterns, e.g., integrating frequent pattern mining with classifications to generate frequent pattern-based classifiers. Rather than presenting a specific algorithm, this paper builds on our existing works and proposes combined mining as a general approach to mining for informative patterns combining components from either multiple data sets or multiple features or by multiple methods on demand. We summarize general frameworks, paradigms, and basic processes for multifeature combined mining, multisource combined mining, and multimethod combined mining. Novel types of combined patterns, such as incremental cluster patterns, can result from such frameworks, which cannot be directly produced by the existing methods. A set of real-world case studies has been conducted to test the frameworks, with some of them briefed in this paper. They identify combined patterns for informing government debt prevention and improving government service objectives, which show the flexibility and instantiation capability of combined mining in discovering informative knowledge in complex data.

The kidney in the pathogenesis of hypertension: the role of renal nerves.

PubMed

DiBona, G F

1985-04-01

The intrinsic efferent innervation of the kidney consists of exclusively noradrenergic fibers that innervate the preglomerular and postgomerular vasculature, all elements of the juxtagomerular apparatus and virtually all segments of the nephron in both cortical and medullo-papillary regions. Increases in efferent renal sympathetic nerve activity produce renal vasoconstriction, release of renin, catecholamines, prostaglandins and other vasoactive substances, and increases in renal tubular sodium reabsorption; these responses are graded and differentiated. The intrinsic afferent innervation of the kidney consists of mechanoreceptors and chemoreceptors which participate in reno-renal and reno-systemic reflexes that modulate sympathetic neural outflow in an organ-specific differentiated pattern. Therefore, alterations in efferent and afferent renal nerve activity produce changes in several important renal functions known to contribute to the development and maintenance of hypertension.

Multicolor microcontact printing of proteins on nanoporous surface for patterned immunoassay

NASA Astrophysics Data System (ADS)

Ng, Elaine; Gopal, Ashwini; Hoshino, Kazunori; Zhang, Xiaojing

2011-07-01

The large scale patterning of therapeutic proteins is a key to the efficient design, characterization, and production of biologics for cost effective, high throughput, and point-of-care detection and analysis system. We demonstrate an efficient method for protein deposition and adsorption on nanoporous silica substrates in specific patterns using a method called "micro-contact printing". Multiple color-tagged proteins can be printed through sequential application of such micro-patterning technique. Two groups of experiments were performed. In the first group, the protein stamp was aligned precisely with the printing sites, where the stamp was applied multiple times. Optimal conditions were identified for protein transfer and adsorption using the pore size of 4 nm and thickness of 30 nm porous silica thin film. In the second group, we demonstrate the patterning of two-color rabbit immunoglobin labeled with fluorescein isothiocyanate and tetramethyl rhodamine iso-thiocyanate on porous silica substrates that have a pore size 4 nm, porosity 57% and thickness of the porous layer 30 nm. A pair of protein stamps, with corresponding alignment markings and coupled patterns, were aligned and used to produce a two-colored stamp pattern of proteins on porous silica. Different colored proteins can be applied to exemplify the diverse protein composition within a sample. This method of multicolor microcontact printing can be used to perform a fluorescence-based patterned enzyme-linked immunosorbent assay to detect the presence of various proteins within a sample.

Evolutionary history of Daphnia drives divergence in grazing selectivity and alters temporal community dynamics of producers.

PubMed

Park, John S; Post, David M

2018-01-01

Consumers with different seasonal life histories encounter different communities of producers during specific seasonal phases. If consumers evolve to prefer the producers that they encounter, then consumers may reciprocally influence the temporal composition of producer communities. Here, we study the keystone consumer Daphnia ambigua, whose seasonal life history has diverged due to intraspecific predator divergence across lakes of New England. We ask whether grazing preferences of Daphnia have diverged also and test whether any grazing differences influence temporal composition patterns of producers. We reared clonal populations of Daphnia from natural populations representing the two diverged life history types for multiple generations. We conducted short-term (24 hr) and long-term (27 days) grazing experiments in equal polycultures consisting of three diatom and two green algae species, treated with no consumer, Daphnia from lakes with anadromous alewife, or from lakes with landlocked alewife. After 24 hr, life history and grazing preference divergence in Daphnia ambigua drove significant differences in producer composition. However, those differences disappeared at the end of the 27-day experiment. Our results illustrate that, despite potentially more complex long-term dynamics, a multitrophic cascade of evolutionary divergence from a predator can influence temporal community dynamics at the producer level.

Direct Harmonic Linear Navier-Stokes Methods for Efficient Simulation of Wave Packets

NASA Technical Reports Server (NTRS)

Streett, C. L.

1998-01-01

Wave packets produced by localized disturbances play an important role in transition in three-dimensional boundary layers, such as that on a swept wing. Starting with the receptivity process, we show the effects of wave-space energy distribution on the development of packets and other three-dimensional disturbance patterns. Nonlinearity in the receptivity process is specifically addressed, including demonstration of an effect which can enhance receptivity of traveling crossflow disturbances. An efficient spatial numerical simulation method is allowing most of the simulations presented to be carried out on a workstation.

Pectinase from Trichoderma reesei QM 9414

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

Haltmeier, T.; Leisola, M.; Ulmer, D.

1983-06-01

The present study was undertaken to determine whether T. reesei produces pectinolytic enzymes and, if so, to determine their action pattern and specificity. The aim was also to find out the practical importance of pectinolytic activity in the hydrolysis of cellulosic materials. It was found that the presence of pectinase does not appear to facilitate the hydrolysis of cellulose in plant material through any cell-separating mechanism. It is concluded that cellulase and xylanase activities are the important activities in the practical hydrolysis of cellulosic materials and that lignin is the real limiting factor. (Refs. 12).

Contact, Travel, and Transmission: The Impact of Winter Holidays on Influenza Dynamics in the United States.

PubMed

Ewing, Anne; Lee, Elizabeth C; Viboud, Cécile; Bansal, Shweta

2017-03-01

The seasonality of influenza is thought to vary according to environmental factors and human behavior. During winter holidays, potential disease-causing contact and travel deviate from typical patterns. We aim to understand these changes on age-specific and spatial influenza transmission. We characterized the changes to transmission and epidemic trajectories among children and adults in a spatial context before, during, and after the winter holidays among aggregated physician medical claims in the United States from 2001 to 2009 and among synthetic data simulated from a deterministic, age-specific spatial metapopulation model. Winter holidays reduced influenza transmission and delayed the trajectory of influenza season epidemics. The holiday period was marked by a shift in the relative risk of disease from children toward adults. Model results indicated that holidays delayed epidemic peaks and synchronized incidence across locations, and that contact reductions from school closures, rather than age-specific mixing and travel, produced these observed holiday influenza dynamics. Winter holidays delay seasonal influenza epidemic peaks and shift disease risk toward adults because of changes in contact patterns. These findings may inform targeted influenza information and vaccination campaigns during holiday periods. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Thermal sensitivity of mitochondrial respiration efficiency and protein phosphorylation in the clam Mercenaria mercenaria.

PubMed

Ulrich, P N; Marsh, A G

2009-01-01

The mitochondria of intertidal invertebrates continue to function when organisms are exposed to rapid substantial shifts in temperature. To test if mitochondrial physiology of the clam Mercenaria mercenaria is compromised under elevated temperatures, we measured mitochondrial respiration efficiency at 15 degrees C, 18 degrees C, and 21 degrees C using a novel, high-throughput, microplate respirometry methodology developed for this study. Though phosphorylating (state 3) and resting (state 4) respiration rates were unaffected over this temperature range, respiratory control ratios (RCRs: ratio of state 3 to state 4 respiration rates) decreased significantly above 18 degrees C (p < 0.05). The drop in RCR was not associated with reduction of phosphorylation efficiency, suggesting that, while aerobic scope of mitochondrial respiration is limited at elevated temperatures, mitochondria continue to efficiently produce adenosine triphosphate. We further investigated the response of clam mitochondria to elevated temperatures by monitoring phosphorylation of mitochondrial protein. Three proteins clearly demonstrated significant time- and temperature-specific phosphorylation patterns. The protein-specific patterns of phosphorylation may suggest that a suite of protein kinases and phosphatases regulate mitochondrial physiology in response to temperature. Thus, while aerobic scope of clam mitochondrial respiration is reduced at moderate temperatures, specific protein phosphorylation responses reflect large shifts in function that are initiated within the organelle at higher temperatures.

Detection of cystic fibrosis mutations in a GeneChip{trademark} assay format

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

Miyada, C.G.; Cronin, M.T.; Kim, S.M.

1994-09-01

We are developing assays for the detection of cystic fibrosis mutations based on DNA hybridization. A DNA sample is amplified by PCR, labeled by incorporating a fluorescein-tagged dNTP, enzymatically treated to produce smaller fragments and hybridized to a series of short (13-16 bases) oligonucleotides synthesized on a glass surface via photolithography. The hybrids are detected by eqifluorescence and mutations are identified by the specific pattern of hybridization. In a GeneChip assay, the chip surface is composed of a series of subarrays, each being specific for a particular mutation. Each subarray is further subdivided into a series of probes (40 total),more » half based on the mutant sequence and the remainder based on the wild-type sequence. For each of the subarrays, there is a redundancy in the number of probes that should hybridize to either a wild-type or a mutant target. The multiple probe strategy provides sequence information for a short five base region overlapping the mutation site. In addition, homozygous wild-type and mutant as well as heterozygous samples are each identified by a specific pattern of hybridization. The small size of each probe feature (250 x 250 {mu}m{sup 2}) permits the inclusion of additional probes required to generate sequence information by hybridization.« less

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.

[Molecular characterization and antimicrobial susceptibility pattern of extended-spectrum β-lactamase-producing Escherichia coli as cause of community acquired urinary tract infection].

PubMed

Galindo-Méndez, Mario

Background Community acquired urinary tract infections (CaUTI) caused by strains of extended-spectrum β-lactamases (ESBL) - producing Escherichia coli, mainly by strains carrying the blaCTX-M-15 gene, is a growing phenomenon worldwide. Aim To determine the antibiotic susceptibility pattern of ESBL-producing E. coli as cause of CaUTI and to identify their molecular pattern. Methods A descriptive study was performed in the city of Oaxaca, Mexico, from where 288 strains of CaUTI-producing strains of E. coli in adults with possible UTI were isolated. The CLSI criteria was followed to determine the antimicrobial susceptibility patterns, and their molecular characterization was performed by using PCR. Results 31.3% of E. coli strains isolated in our population were ESBL producers, which presented higher levels of antibiotic resistance than those of non-producers of these enzymes. 95.6% of the studied strains were carriers of the blaCTX-M gene. Conclusions One-third of the Ca-UTI caused by E. coli in our population are caused by ESBL-producing strains, which present high levels of resistance to the antibiotics widely used in our community. This situation considerably decreases the number of antibiotics available for an empiric treatment against these infections.

Functional significance of the pattern of renal sympathetic nerve activation.

PubMed

Dibona, G F; Sawin, L L

1999-08-01

To assess the renal functional significance of the pattern of renal sympathetic nerve activation, computer-generated stimulus patterns (delivered at constant integrated voltage) were applied to the decentralized renal sympathetic nerve bundle and renal hemodynamic and excretory responses determined in anesthetized rats. When delivered at the same integrated voltage, stimulus patterns resembling those observed in in vivo multifiber recordings of renal sympathetic nerve activity (diamond-wave patterns) produced greater renal vasoconstrictor responses than conventional square-wave patterns. Within diamond-wave patterns, increasing integrated voltage by increasing amplitude produced twofold greater renal vasoconstrictor responses than by increasing duration. With similar integrated voltages that were subthreshold for renal vasoconstriction, neither diamond- nor square-wave pattern altered glomerular filtration rate, whereas diamond- but not square-wave pattern reversibly decreased urinary sodium excretion by 25 +/- 3%. At the same number of pulses per second, intermittent stimulation produced faster and greater renal vasoconstriction than continuous stimulation. At the same number of pulses per second, increases in rest period during intermittent stimulation proportionally augmented the renal vasoconstrictor response compared with that observed with continuous stimulation; the maximum augmentation of 55% occurred at a rest period of 500 ms. These results indicate that the pattern of renal sympathetic nerve stimulation (activity) significantly influences the rapidity, magnitude, and selectivity of the renal vascular and tubular responses.

Microbial Life Driving Low-Temperature Basalt Alteration in the Subsurface: Decoupling Abiotic Processes from Biologically-Mediated Rock Alteration

NASA Astrophysics Data System (ADS)

Moore, R.; Lecoeuvre, A.; Stephant, S.; Dupraz, S.; Ranchou-Peyruse, M.; Ranchou-Peyruse, A.; Gérard, E.; Ménez, B.

2017-12-01

Microorganisms are involved with specific rock alteration processes in the deep subsurface. It is a challenge to link any contribution microbial life may have on rock alteration with specific functions or phyla because many alteration features and secondary minerals produced by metabolic processes can also produce abiotically. Here, two flow-through experiments were designed to mimic the circulation of a CO2-rich fluid through crystalline basalt. In order to identify microbially-mediated alteration and be able to link it with specific metabolisms represented in the subsurface, a relatively fresh crystalline basalt substrate was subsampled, sterilized and used as the substrate for both experiments. In one experiment, the substrate was left sterile, and in the other it was inoculated with an enrichment culture derived from the same aquifer as the rock substrate. Initial results show that the inoculum contained Proteobacteria and Firmicutes, which have diverse metabolic potentials. Fluid and rock analyses before, during, and after the experiments show that mineralogy, fluid chemistry, and dissolution processes differ between the sterile and inoculated systems. In the inoculated experiment iron-rich orthopyroxenes were preferentially dissolved while in the sterile system clinopyroxenes and plagioclases both exhibited a higher degree of dissolution. Additionally, the patterns of CO2 consumption and production over the duration of both experiments is different. This suggest that in a low-temperature basalt system with microorganisms CO2 is either consumed to produce biomass, or that carbonates are produced and then subsequently preserved. This suite of results combined with molecular ecology analyses can be used to conclude that in low-temperature basalts microorganisms play an intrinsic role in rock alteration.

CT differentiation of mucin-producing cystic neoplasms of the liver from solitary bile duct cysts.

PubMed

Kim, Hyoung Jung; Yu, Eun Sil; Byun, Jae Ho; Hong, Seung-Mo; Kim, Kyoung Won; Lee, Jong Seok; Kim, So Yeon

2014-01-01

The purpose of this study was to identify the CT features required for differentiating mucin-producing cystic neoplasms of the liver (mucinous cystic neoplasms and cyst-forming intraductal papillary neoplasms of the bile duct) from solitary bile duct cysts. CT images of pathologically confirmed mucinous cystic neoplasms (n = 15), cyst-forming intraductal papillary neoplasms of the bile duct (n = 16), and solitary bile duct cysts (n = 31) were reviewed. Analysis of the CT findings included shape, presence of septa, location of septa (peripheral vs central), thickness of septa (thin vs thick), mosaic pattern, mural nodules, intracystic debris, calcification, upstream bile duct dilatation, downstream bile duct dilatation, and communication between a cystic lesion and the bile duct. The maximum size of a cystic lesion and the maximum size of the largest mural nodule were measured. The presence of septa, central septa, mural nodules, upstream bile duct dilatation, and downstream bile duct dilatation were found to be significant CT findings for differentiating mucinous cystic neoplasms and cyst-forming intraductal papillary neoplasms of the bile duct from solitary bile duct cysts (p < 0.05 for each finding). When two of these five criteria were used in combination, the sensitivity and specificity for diagnosing mucin-producing cystic neoplasms and cyst-forming intraductal papillary neoplasms of the bile duct were 87% (27 of 31) and 87% (27 of 31), respectively. When two of these five criteria were used in combination, the sensitivity and specificity for diagnosing mucinous cystic neoplasms and cyst-forming intraductal papillary neoplasms of the bile duct were 87% (27 of 31) and 87% (27 of 31), respectively [corrected]. With the use of specific CT criteria, mucin-producing cystic neoplasms of the liver can be differentiated from solitary bile duct cysts with a high degree of accuracy.

Specificity of Esthetic Experience for Artworks: An fMRI Study

PubMed Central

Di Dio, Cinzia; Canessa, Nicola; Cappa, Stefano F.; Rizzolatti, Giacomo

2011-01-01

In a previous functional magnetic resonance imaging (fMRI) study, where we investigated the neural correlates of esthetic experience, we found that observing canonical sculptures, relative to sculptures whose proportions had been modified, produced the activation of a network that included the lateral occipital gyrus, precuneus, prefrontal areas, and, most interestingly, the right anterior insula. We interpreted this latter activation as the neural signature underpinning hedonic response during esthetic experience. With the aim of exploring whether this specific hedonic response is also present during the observation of non-art biological stimuli, in the present fMRI study we compared the activations associated with viewing masterpieces of classical sculpture with those produced by the observation of pictures of young athletes. The two stimulus-categories were matched on various factors, including body postures, proportion, and expressed dynamism. The stimuli were presented in two conditions: observation and esthetic judgment. The two stimulus-categories produced a rather similar global activation pattern. Direct comparisons between sculpture and real-body images revealed, however, relevant differences, among which the activation of right antero-dorsal insula during sculptures viewing only. Along with our previous data, this finding suggests that the hedonic state associated with activation of right dorsal anterior insula underpins esthetic experience for artworks. PMID:22121344

Complex cardiac defects after ethanol exposure during discrete cardiogenic events in zebrafish: Prevention with folic acid

PubMed Central

Sarmah, Swapnalee; Marrs, James A.

2014-01-01

BACKGROUND Fetal alcohol spectrum disorder (FASD) describes a range of birth defects including various congenital heart defects (CHDs). Mechanisms of FASD-associated CHDs are not understood. Whether alcohol interferes with a single critical event or with multiple events in heart formation is not known. RESULTS Our zebrafish embryo experiments showed that ethanol interrupts different cardiac regulatory networks and perturbed multiple steps of cardiogenesis (specification, myocardial migration, looping, chamber morphogenesis and endocardial cushion formation). Ethanol exposure during gastrulation until cardiac specification or during myocardial midline migration did not produce severe or persistent heart development defects. However, exposure comprising gastrulation until myocardial precursor midline fusion or during heart patterning stages produced aberrant heart looping and defective endocardial cushions. Continuous exposure during entire cardiogenesis produced complex cardiac defects leading to severely defective myocardium, endocardium, and endocardial cushions. Supplementation of retinoic acid with ethanol partially rescued early heart developmental defects, but the endocardial cushions did not form correctly. In contrast, supplementation of folic acid rescued normal heart development, including the endocardial cushions. CONCLUSIONS Our results indicate that ethanol exposure interrupted divergent cardiac morphogenesis events causing heart defects. Folic acid supplementation was effective in preventing a wide spectrum of ethanol-induced heart developmental defects. PMID:23832875

Brain modulation of Dufour's gland ester biosynthesis in vitro in the honeybee ( Apis mellifera)

NASA Astrophysics Data System (ADS)

Katzav-Gozansky, Tamar; Hefetz, Abraham; Soroker, Victoria

2007-05-01

Caste-specific pheromone biosynthesis is a prerequisite for reproductive skew in the honeybee. Nonetheless, this process is not hardwired but plastic, in that egg-laying workers produce a queen-like pheromone. Studies with Dufour’s gland pheromone revealed that, in vivo, workers’ gland biosynthesis matches the social status of the worker, i.e., sterile workers showed a worker-like pattern whereas fertile workers showed a queen-like pattern (production of the queen-specific esters). However, when incubated in vitro, the gland spontaneously exhibits the queen-like pattern, irrespective of its original worker type, prompting the notion that ester production in workers is under inhibitory control that is queen-dependent. We tested this hypothesis by exposing queen or worker Dufour’s glands in vitro to brain extracts of queens, queenright (sterile) workers and males. Unexpectedly, worker brain extracts activated the queen-like esters biosynthesis in workers’ Dufour’s gland. This stimulation was gender-specific; queen or worker brains demonstrated a stimulatory activity, but male brains did not. Queen gland could not be further stimulated. Bioassays with heated and filtered extracts indicate that the stimulatory brain factor is below 3,000 Da. We suggest that pheromone production in Dufour’s gland is under dual, negative positive control. Under queenright conditions, the inhibitor is released and blocks ester biosynthesis, whereas under queenless conditions, the activator is released, activating ester biosynthesis in the gland. This is consistent with the hypothesis that queenright workers are unequivocally recognized as non-fertile, whereas queenless workers try to become “false queens” as part of the reproductive competition.

Myosin isoform switching during assembly of the Drosophila flight muscle thick filament lattice.

PubMed

Orfanos, Zacharias; Sparrow, John C

2013-01-01

During muscle development myosin molecules form symmetrical thick filaments, which integrate with the thin filaments to produce the regular sarcomeric lattice. In Drosophila indirect flight muscles (IFMs) the details of this process can be studied using genetic approaches. The weeP26 transgenic line has a GFP-encoding exon inserted into the single Drosophila muscle myosin heavy chain gene, Mhc. The weeP26 IFM sarcomeres have a unique MHC-GFP-labelling pattern restricted to the sarcomere core, explained by non-translation of the GFP exon following alternative splicing. Characterisation of wild-type IFM MHC mRNA confirmed the presence of an alternately spliced isoform, expressed earlier than the major IFM-specific isoform. The two wild-type IFM-specific MHC isoforms differ by the presence of a C-terminal 'tailpiece' in the minor isoform. The sequential expression and assembly of these two MHCs into developing thick filaments suggest a role for the tailpiece in initiating A-band formation. The restriction of the MHC-GFP sarcomeric pattern in weeP26 is lifted when the IFM lack the IFM-specific myosin binding protein flightin, suggesting that it limits myosin dissociation from thick filaments. Studies of flightin binding to developing thick filaments reveal a progressive binding at the growing thick filament tips and in a retrograde direction to earlier assembled, proximal filament regions. We propose that this flightin binding restricts myosin molecule incorporation/dissociation during thick filament assembly and explains the location of the early MHC isoform pattern in the IFM A-band.

Lithographically patterned thin activated carbon films as a new technology platform for on-chip devices.

PubMed

Wei, Lu; Nitta, Naoki; Yushin, Gleb

2013-08-27

Continuous, smooth, visibly defect-free, lithographically patterned activated carbon films (ACFs) are prepared on the surface of silicon wafers. Depending on the synthesis conditions, porous ACFs can either remain attached to the initial substrate or be separated and transferred to another dense or porous substrate of interest. Tuning the activation conditions allows one to change the surface area and porosity of the produced carbon films. Here we utilize the developed thin ACF technology to produce prototypes of functional electrical double-layer capacitor devices. The synthesized thin carbon film electrodes demonstrated very high capacitance in excess of 510 F g(-1) (>390 F cm(-3)) at a slow cyclic voltammetry scan rate of 1 mV s(-1) and in excess of 325 F g(-1) (>250 F cm(-3)) in charge-discharge tests at an ultrahigh current density of 45,000 mA g(-1). Good stability was demonstrated after 10,000 galvanostatic charge-discharge cycles. The high values of the specific and volumetric capacitances of the selected ACF electrodes as well as the capacity retention at high current densities demonstrated great potential of the proposed technology for the fabrication of various on-chip devices, such as micro-electrochemical capacitors.

Tilt aftereffect following adaptation to translational Glass patterns

PubMed Central

Pavan, Andrea; Hocketstaller, Johanna; Contillo, Adriano; Greenlee, Mark W.

2016-01-01

Glass patterns (GPs) consist of randomly distributed dot pairs (dipoles) whose orientations are determined by specific geometric transforms. We assessed whether adaptation to stationary oriented translational GPs suppresses the activity of orientation selective detectors producing a tilt aftereffect (TAE). The results showed that adaptation to GPs produces a TAE similar to that reported in previous studies, though reduced in amplitude. This suggests the involvement of orientation selective mechanisms. We also measured the interocular transfer (IOT) of the GP-induced TAE and found an almost complete IOT, indicating the involvement of orientation selective and binocularly driven units. In additional experiments, we assessed the role of attention in TAE from GPs. The results showed that distraction during adaptation similarly modulates the TAE after adapting to both GPs and gratings. Moreover, in the case of GPs, distraction is likely to interfere with the adaptation process rather than with the spatial summation of local dipoles. We conclude that TAE from GPs possibly relies on visual processing levels in which the global orientation of GPs has been encoded by neurons that are mostly binocularly driven, orientation selective and whose adaptation-related neural activity is strongly modulated by attention. PMID:27005949

Testing the Accuracy of Different A-Axis Types for Measuring the Orientation of Bones in the Archaeological and Paleontological Record

PubMed Central

Domínguez-Rodrigo, Manuel; García-Pérez, Alfonso

2013-01-01

Orientation of archaeological and paleontological materials plays a prominent role in the interpretation of site formation processes. Allochthony and authochthony are frequently assumed from orientation patterns or lack thereof. Although it is still debated to what extent orientation of items can be produced in original depositional contexts, the recent use of GIS tools to measure orientations has highlighted several ways of reproducing A-axes with which to address these taphonomic issues. In the present study, the three most relevant A-axis types are compared to test their accuracy in reproducing water current direction. Although results may be similar in specific bone shapes, differences are important in other shapes. As known in engineering working with wind and fluid mechanics (developing shape optimization), longitudinal symmetrical axes (LSA) are the one that best orient structures against or in the same direction of wind and water. The present work shows that this is also the case for bones (regardless of shape), since LSA produce the most accurate estimates of flow direction. This has important consequences for the interpretation of orientation patterns at sites, since this type of axis is still not properly reproduced by GIS available tools. PMID:23874825

Investigation of protein expression profiles of erythritol-producing Candida magnoliae in response to glucose perturbation.

PubMed

Kim, Hyo Jin; Lee, Hyeong-Rho; Kim, Chang Sup; Jin, Yong-Su; Seo, Jin-Ho

2013-08-15

Protein expression patterns of an erythritol-producing yeast, Candida magnoliae, were analyzed to identify differentially expressed proteins in response to glucose perturbation. Specifically, wild type C. magnoliae was grown under high and low glucose conditions and the cells were harvested at both mid-exponential and erythritol production phases for proteomic studies. In order to analyze intracellular protein abundances from the harvested cells quantitatively, total intracellular proteins were extracted and applied to two-dimensional gel electrophoresis for separation and visualization of individual proteins. Among the proteins distributed in the range of pI 4-7 and molecular weight 29-97kDa, five osmo-responsive proteins were drastically changed in response to glucose perturbation. Hsp60 (Heat-shock protein 60), transaldolase and NADH:quinone oxidoreductase were down-regulated under the high glucose condition and Bro1 (BCK1-like Resistance to Osmotic shock) and Eno1 (enolase1) were up-regulated. These proteins are directly or indirectly related with cellular stress response. Importantly, protein expression patterns of Hsp60, Bro1 and Eno1 were strongly correlated with previous studies identifying the proteins perturbed by osmotic stress for other organisms including Saccharomyces cerevisiae. Copyright © 2013 Elsevier Inc. All rights reserved.

Spatial taxation effects on regional coal economic activities

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

Yang, C.W.; Labys, W.C.

1980-01-01

Spatial taxation effects related to economic activities at the regional level can be directly evaluated using the Kuhn-Tucker system of equations based on a commodity model. In particular, the impacts of a specific tax are predictable within a given set of trade patterns. However, the impacts of an ad valorem tax are difficult to evaluate analytically, mainly because of nonlinearity in the associated response surface. The aspect of spatial-taxation analysis of present relevance for the coal industry related to coal policy, i.e., the share of tax burdens coal producers and consumers are able to bear. Each supplier in a givenmore » market boundary shares the same amount of tax burden, which may eliminate the weakest coal producers, i.e., Southern West Virginia coal mines. The same analogy also applies to the weakest demand region, i.e., Illinois, Wisconsin, and Minnesota utilities. Consequently, a proper policy requires that some preferential tax treatment be given to these regions. Since the taxation effects depend critically on the trade patterns and market boundaries, the successful policy application of present regional energy models will not be possible unless effects of this type are included in the evaluation.« less

The Queen's English: an alternative, biosocial hypothesis for the distinctive features of "gay speech".

PubMed

Rendall, Drew; Vasey, Paul L; McKenzie, Jared

2008-02-01

Popular stereotypes concerning the speech of homosexuals typically attribute speech patterns characteristic of the opposite-sex, i.e., broadly feminized speech in gay men and broadly masculinized speech in lesbian women. A small body of recent empirical research has begun to address the subject more systematically and to consider specific mechanistic hypotheses to account for the potentially distinctive features of homosexual speech. Results do not yet fully endorse the stereotypes but they do not entirely discount them either; nor do they cleanly favor any single mechanistic hypothesis. To contribute to this growing body of research, we report acoustic analyses of 2,875 vowel sounds from a balanced set of 125 speakers representing heterosexual and homosexual individuals of each sex from southern Alberta, Canada. Analyses focused on voice pitch and formant frequencies which together determine the principle perceptual features of vowels. There was no significant difference in mean voice pitch between heterosexual and homosexual men or between heterosexual and homosexual women, but there were significant differences in the formant frequencies of vowels produced by both homosexual groups compared to their heterosexual counterparts. Formant frequency differences were specific to only certain vowel sounds and some could be attributed to basic differences in body size between heterosexual and homosexual speakers. The remaining formant frequency differences were not obviously due to differences in vocal tract anatomy between heterosexual and homosexual speakers, nor did they reflect global feminization or masculinization of vowel production patterns in homosexual men and women, respectively. The vowel-specific differences observed could reflect social modeling processes in which only certain speech patterns of the opposite-sex, or of same-sex homosexuals, are selectively adopted. However, we introduce an alternative biosocial hypothesis, specifically that the distinctive, vowel-specific features of homosexual speakers relative to heterosexual speakers arise incidentally as a product of broader psychobehavioral differences between the two groups that are, in turn, continuous with and flow from the physiological processes that affect sexual orientation to begin with.

Brain Computation Is Organized via Power-of-Two-Based Permutation Logic.

PubMed

Xie, Kun; Fox, Grace E; Liu, Jun; Lyu, Cheng; Lee, Jason C; Kuang, Hui; Jacobs, Stephanie; Li, Meng; Liu, Tianming; Song, Sen; Tsien, Joe Z

2016-01-01

There is considerable scientific interest in understanding how cell assemblies-the long-presumed computational motif-are organized so that the brain can generate intelligent cognition and flexible behavior. The Theory of Connectivity proposes that the origin of intelligence is rooted in a power-of-two-based permutation logic ( N = 2 i -1), producing specific-to-general cell-assembly architecture capable of generating specific perceptions and memories, as well as generalized knowledge and flexible actions. We show that this power-of-two-based permutation logic is widely used in cortical and subcortical circuits across animal species and is conserved for the processing of a variety of cognitive modalities including appetitive, emotional and social information. However, modulatory neurons, such as dopaminergic (DA) neurons, use a simpler logic despite their distinct subtypes. Interestingly, this specific-to-general permutation logic remained largely intact although NMDA receptors-the synaptic switch for learning and memory-were deleted throughout adulthood, suggesting that the logic is developmentally pre-configured. Moreover, this computational logic is implemented in the cortex via combining a random-connectivity strategy in superficial layers 2/3 with nonrandom organizations in deep layers 5/6. This randomness of layers 2/3 cliques-which preferentially encode specific and low-combinatorial features and project inter-cortically-is ideal for maximizing cross-modality novel pattern-extraction, pattern-discrimination and pattern-categorization using sparse code, consequently explaining why it requires hippocampal offline-consolidation. In contrast, the nonrandomness in layers 5/6-which consists of few specific cliques but a higher portion of more general cliques projecting mostly to subcortical systems-is ideal for feedback-control of motivation, emotion, consciousness and behaviors. These observations suggest that the brain's basic computational algorithm is indeed organized by the power-of-two-based permutation logic. This simple mathematical logic can account for brain computation across the entire evolutionary spectrum, ranging from the simplest neural networks to the most complex.

Brain Computation Is Organized via Power-of-Two-Based Permutation Logic

PubMed Central

Xie, Kun; Fox, Grace E.; Liu, Jun; Lyu, Cheng; Lee, Jason C.; Kuang, Hui; Jacobs, Stephanie; Li, Meng; Liu, Tianming; Song, Sen; Tsien, Joe Z.

2016-01-01

There is considerable scientific interest in understanding how cell assemblies—the long-presumed computational motif—are organized so that the brain can generate intelligent cognition and flexible behavior. The Theory of Connectivity proposes that the origin of intelligence is rooted in a power-of-two-based permutation logic (N = 2i–1), producing specific-to-general cell-assembly architecture capable of generating specific perceptions and memories, as well as generalized knowledge and flexible actions. We show that this power-of-two-based permutation logic is widely used in cortical and subcortical circuits across animal species and is conserved for the processing of a variety of cognitive modalities including appetitive, emotional and social information. However, modulatory neurons, such as dopaminergic (DA) neurons, use a simpler logic despite their distinct subtypes. Interestingly, this specific-to-general permutation logic remained largely intact although NMDA receptors—the synaptic switch for learning and memory—were deleted throughout adulthood, suggesting that the logic is developmentally pre-configured. Moreover, this computational logic is implemented in the cortex via combining a random-connectivity strategy in superficial layers 2/3 with nonrandom organizations in deep layers 5/6. This randomness of layers 2/3 cliques—which preferentially encode specific and low-combinatorial features and project inter-cortically—is ideal for maximizing cross-modality novel pattern-extraction, pattern-discrimination and pattern-categorization using sparse code, consequently explaining why it requires hippocampal offline-consolidation. In contrast, the nonrandomness in layers 5/6—which consists of few specific cliques but a higher portion of more general cliques projecting mostly to subcortical systems—is ideal for feedback-control of motivation, emotion, consciousness and behaviors. These observations suggest that the brain’s basic computational algorithm is indeed organized by the power-of-two-based permutation logic. This simple mathematical logic can account for brain computation across the entire evolutionary spectrum, ranging from the simplest neural networks to the most complex. PMID:27895562

Strain-specific transmission in an outbreak of ESBL-producing Enterobacteriaceae in the hemato-oncology care unit: a cohort study.

PubMed

Uemura, Makiko; Imataki, Osamu; Uchida, Shumpei; Nakayama-Imaohji, Haruyuki; Ohue, Yukiko; Matsuka, Harumi; Mori, Hatsune; Dobashi, Hiroaki; Kuwahara, Tomomi; Kadowaki, Norimitsu

2017-01-05

Extended-spectrum β-lactamase (ESBL)-producing bacteria are resistant to several types of antibiotics excluding carbapenems. A transmissibility of ESBL-producing Enterobacteriaceae would be depending on each bacterial property, however, that has not been elucidated in clinical setting. In this study, we attempted to identify the source of an outbreak of ESBL-producing bacteria in a medical oncology and immunology care unit. An ESBL-producing Enterobacteriaceae (ESBL-E) outbreak observed between July 2012 and August 2012 in Kagawa University Hospital was surveyed using various molecular microbiology techniques. We used Pulsed-field gel electrophoresis (PFGE), PCR-based ESBL gene typing, and direct sequence of ESBL gene as molecular microbiology typing method to distinguish each strain. The typical prevalence of ESBL-E isolation in the unit was 7.0 per month (1.7 per week). The prevalence of ESBL-E isolation during the target research period was 20.0 per month (5.0 per week). In total, 19 isolates (11 K. pneumoniae and 8 E. coli) were obtained from clinical samples, including four control strains (two each of both bacteria), that were physically different from those obtained from other inpatient units in our hospital. Pulsed-field gel electrophoresis (PFGE) for K. pneumoniae (digested by XbaI) produced similar patterns excluding one control strain. PCR classification of the ESBL gene for K. pneumoniae revealed that all strains other than the control strain carried SHV and CTX-M-9. This result was reconfirmed by direct DNA sequencing. Although the outbreak of K. pneumoniae was considered to be "clonal," PFGE and PCR classification of the ESBL genes for E. coli uncovered at least six different "non-clonal" strains possessing individual ESBL gene patterns. According to the result of an antibiogram, the pattern of antimicrobial susceptibility was more variable for K. pneumoniae than for E. coli. Typing by PFGE and ESBL gene PCR analysis is practical for discriminating various organisms. In our cohort, two outbreaks were concomitantly spread with different transmission strategies, namely clonal and non-clonal, in the same unit. This might represent clinical evidence that transmissibility differs according to the type of strain. We speculated that patient-to-patient transmission of ESBL-E occurred according to the properties of each individual strain.

Synthesis of metal nanoparticle and patterning in polymeric films induced by electron beam

NASA Astrophysics Data System (ADS)

Yamamoto, Hiroki; Kozawa, Takahiro; Tagawa, Seiichi; Marignier, Jean-Louis; Mostafavi, Mehran; Belloni, Jacqueline

2018-03-01

Using an electron beam, thin polymeric films loaded with metal nanoparticles of silver were prepared by a one-step irradiation-induced reduction of the metal ions embedded in the polymer. The metal nanoparticles were observed by either optical absorption or microscopy. The mechanism of the reduction of metal ions and of the polymer crosslinking were deduced from the average absorbance measurements. In view of realizing specific patterns of high resolution using the electron beam, electron beam produces 200 nm wide lines that can be separated by unexposed spaces of adjustable width, where precursors were dissolved. The resolution of the electron beam has been exploited to demonstrate the achievement of nanopatterning on polymer films using a direct-writing process. This method supplies interesting applications such as masks, replicas, or imprint molds of improved density and contrast.

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia

PubMed Central

Vital, Marius; Gao, Jiarong; Rizzo, Mike; Harrison, Tara; Tiedje, James M

2015-01-01

Butyrate-producing bacteria have an important role in maintaining host health. They are well studied in human and medically associated animal models; however, much less is known for other Vertebrata. We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n=38), Aves (n=8) and Reptilia (n=8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways, namely butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). Most animals exhibit high gene abundances, and clear diet-specific signatures were detected with but genes significantly enriched in omnivores and herbivores compared with carnivores. But dominated the butyrate-producing community in these two groups, whereas buk was more abundant in many carnivorous animals. Clustering of protein sequences (5% cutoff) of the combined communities (but and buk) placed carnivores apart from other diet groups, except for noncarnivorous Carnivora, which clustered together with carnivores. The majority of clusters (but: 5141 and buk: 2924) did not show close relation to any reference sequences from public databases (identity <90%) demonstrating a large ‘unknown diversity'. Each diet group had abundant signature taxa, where buk genes linked to Clostridium perfringens dominated in carnivores and but genes associated with Ruminococcaceae bacterium D16 were specific for herbivores and omnivores. Whereas 16S rRNA gene analysis showed similar overall patterns, it was unable to reveal communities at the same depth and resolution as the functional gene-targeted approach. This study demonstrates that butyrate producers are abundant across vertebrates exhibiting great functional redundancy and that diet is the primary determinant governing the composition of the butyrate-producing guild. PMID:25343515

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.

PubMed

Vital, Marius; Gao, Jiarong; Rizzo, Mike; Harrison, Tara; Tiedje, James M

2015-03-17

Butyrate-producing bacteria have an important role in maintaining host health. They are well studied in human and medically associated animal models; however, much less is known for other Vertebrata. We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n = 38), Aves (n = 8) and Reptilia (n = 8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways, namely butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). Most animals exhibit high gene abundances, and clear diet-specific signatures were detected with but genes significantly enriched in omnivores and herbivores compared with carnivores. But dominated the butyrate-producing community in these two groups, whereas buk was more abundant in many carnivorous animals. Clustering of protein sequences (5% cutoff) of the combined communities (but and buk) placed carnivores apart from other diet groups, except for noncarnivorous Carnivora, which clustered together with carnivores. The majority of clusters (but: 5141 and buk: 2924) did not show close relation to any reference sequences from public databases (identity <90%) demonstrating a large 'unknown diversity'. Each diet group had abundant signature taxa, where buk genes linked to Clostridium perfringens dominated in carnivores and but genes associated with Ruminococcaceae bacterium D16 were specific for herbivores and omnivores. Whereas 16S rRNA gene analysis showed similar overall patterns, it was unable to reveal communities at the same depth and resolution as the functional gene-targeted approach. This study demonstrates that butyrate producers are abundant across vertebrates exhibiting great functional redundancy and that diet is the primary determinant governing the composition of the butyrate-producing guild.

Isolation and characterization of bacteriophages specific to hydrogen-sulfide-producing bacteria.

PubMed

Gong, Chao; Heringa, Spencer; Singh, Randhir; Kim, Jinkyung; Jiang, Xiuping

2013-01-01

The objectives of this study were to isolate and characterize bacteriophages specific to hydrogen-sulfide-producing bacteria (SPB) from raw animal materials, and to develop a SPB-specific bacteriophage cocktail for rendering application. Meat, chicken offal, and feather samples collected from local supermarkets and rendering processing plants were used to isolate SPB (n = 142). Bacteriophages (n = 52) specific to SPB were isolated and purified from the above samples using 18 of those isolated SPB strains as hosts. The host ranges of bacteriophages against 5 selected SPB strains (Escherichia coli, Citrobacter freundii, and Hafnia alvei) were determined. Electron microscopy observation of 9 phages selected for the phage cocktail revealed that 6 phages belonged to the family of Siphoviridae and 3 belonged to the Myoviridae family. Restriction enzyme digestion analysis with endonuclease DraI detected 6 distinguished patterns among the 9 phages. Phage treatment prevented the growth of SPB for up to 10 h with multiplicity of infection ratios of 1, 10, 100, and 1000 in tryptic soy broth at 30 °C, and extended the lag phase of SPB growth for 2 h at 22 °C with multiplicities of infection of 10, 100, and 1000. These results suggest that the selected bacteriophage cocktail has a high potential for phage application to control SPB in raw animal materials destined for the rendering process.

Property Specification Patterns for intelligence building software

NASA Astrophysics Data System (ADS)

Chun, Seungsu

2018-03-01

In this paper, through the property specification pattern research for Modal MU(μ) logical aspects present a single framework based on the pattern of intelligence building software. In this study, broken down by state property specification pattern classification of Dwyer (S) and action (A) and was subdivided into it again strong (A) and weaknesses (E). Through these means based on a hierarchical pattern classification of the property specification pattern analysis of logical aspects Mu(μ) was applied to the pattern classification of the examples used in the actual model checker. As a result, not only can a more accurate classification than the existing classification systems were easy to create and understand the attributes specified.

Evolution and inheritance of early embryonic patterning in D. simulans and D. sechellia

PubMed Central

Lott, Susan E.; Ludwig, Michael Z.; Kreitman, Martin

2010-01-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation which selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth ‘stripe allometry’) in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species D. simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the “margin of error” for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness PMID:21121913

Tools for neuroanatomy and neurogenetics in Drosophila

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

Pfeiffer, Barret D.; Jenett, Arnim; Hammonds, Ann S.

2008-08-11

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayedmore » for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that >80% drive expression patterns in the brain; the observed patterns were, on average, comprised of <100 cells. Our results suggest that the D. melanogaster genome contains >50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.« less

Oligosaccharides from land plants and algae: production and applications in therapeutics and biotechnology.

PubMed

Courtois, Josiane

2009-06-01

Since the past decades, oligosaccharides are considered for their potential biological activities. To exploit them, it was essential to obtain pure molecules in large amounts. Several strategies were developed to produce specific sugar sequences with specific substitution patterns from land plants and algae polysaccharides. Then, pure oligosaccharides were analyzed for their potential biological activities and relations between oligomers structure and function were tackled. First they can be health beneficial molecules when they are added to the diet to enhance the growth of probiotic bacteria, in that case, oligomers that resist to the digestive process are used as specific substrate for the growth of health beneficial bacteria. In other cases, oligomers have to interact with receptors on cells. In this instance, a specific conformation is needed to allow the sugar sequence to establish specific linkages with the receptor. So, to be adapted to the receptor, the oligosaccharides have to present specific groups to the receptor, there, the polymerization degree of oligosaccharides as well as the flexibility of the glycosidic linkages has to be considered.

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.

Dynamic Skin Patterns in Cephalopods

PubMed Central

How, Martin J.; Norman, Mark D.; Finn, Julian; Chung, Wen-Sung; Marshall, N. Justin

2017-01-01

Cephalopods are unrivaled in the natural world in their ability to alter their visual appearance. These mollusks have evolved a complex system of dermal units under neural, hormonal, and muscular control to produce an astonishing variety of body patterns. With parallels to the pixels on a television screen, cephalopod chromatophores can be coordinated to produce dramatic, dynamic, and rhythmic displays, defined collectively here as “dynamic patterns.” This study examines the nature, context, and potential functions of dynamic patterns across diverse cephalopod taxa. Examples are presented for 21 species, including 11 previously unreported in the scientific literature. These range from simple flashing or flickering patterns, to highly complex passing wave patterns involving multiple skin fields. PMID:28674500

Development of an accurate and high-throughput methodology for structural comprehension of chlorophylls derivatives. (I) Phytylated derivatives.

PubMed

Chen, Kewei; Ríos, José Julián; Pérez-Gálvez, Antonio; Roca, María

2015-08-07

Phytylated chlorophyll derivatives undergo specific oxidative reactions through the natural metabolism or during food processing or storage, and consequently pyro-, 13(2)-hydroxy-, 15(1)-hydroxy-lactone chlorophylls, and pheophytins (a and b) are originated. New analytical procedures have been developed here to reproduce controlled oxidation reactions that specifically, and in reasonable amounts, produce those natural target standards. At the same time and under the same conditions, 16 natural chlorophyll derivatives have been analyzed by APCI-HPLC-hrMS(2) and most of them by the first time. The combination of the high-resolution MS mode with powerful post-processing software has allowed the identification of new fragmentation patterns, characterizing specific product ions for some particular standards. In addition, new hypotheses and reaction mechanisms for the established MS(2)-based reactions have been proposed. As a general rule, the main product ions involve the phytyl and the propionic chains but the introduction of oxygenated functional groups at the isocyclic ring produces new and specific productions and at the same time inhibits some particular fragmentations. It is noteworthy that all b derivatives, except 15(1)-hydroxy-lactone compounds, undergo specific CO losses. We propose a new reaction mechanism based in the structural configuration of a and b chlorophyll derivatives that explain the exclusive CO fragmentation in all b series except for 15(1)-hydroxy-lactone b and all a series compounds. Copyright © 2015 Elsevier B.V. All rights reserved.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2002-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nudeic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2008-09-09

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W [San Francisco, CA; Pinkel, Daniel [Lafayette, CA; Kallioniemi, Olli-Pekka [Turku, FI; Kallioniemi, Anne [Tampere, FI; Sakamoto, Masaru [Tokyo, JP

2009-10-06

Methods and compositions for staining based upon nucleic acid sequence that employ .[.nudeic.]. .Iadd.nucleic .Iaddend.acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-Specific Staining To Detect Genetic Rearrangements Associated With Chromosome 3 And/Or Chromosone 17

DOEpatents

Gray; Joe W.; Pinkel; Daniel; Kallioniemi; Olli-Pekka; Kallioniemi; Anne; Sakamoto; Masaru

2002-02-05

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Pre-Service Mathematics Teachers' Pattern Conversion Ability: Generating Figural Patterns Based on Number Patterns

ERIC Educational Resources Information Center

Kiliç, Çigdem

2017-01-01

In that current study, pattern conversion ability of 25 pre-service mathematics teachers (producing figural patterns following number patterns) was investigated. During the study participants were asked to generate figural patterns based on those number patterns. The results of the study indicate that many participants could generate different…

Evolution of aging: individual life history trade-offs and population heterogeneity account for mortality patterns across species.

PubMed

Le Cunff, Y; Baudisch, A; Pakdaman, K

2014-08-01

A broad range of mortality patterns has been documented across species, some even including decreasing mortality over age. Whether there exist a common denominator to explain both similarities and differences in these mortality patterns remains an open question. The disposable soma theory, an evolutionary theory of aging, proposes that universal intracellular trade-offs between maintenance/lifespan and reproduction would drive aging across species. The disposable soma theory has provided numerous insights concerning aging processes in single individuals. Yet, which specific population mortality patterns it can lead to is still largely unexplored. In this article, we propose a model exploring the mortality patterns which emerge from an evolutionary process including only the disposable soma theory core principles. We adapt a well-known model of genomic evolution to show that mortality curves producing a kink or mid-life plateaus derive from a common minimal evolutionary framework. These mortality shapes qualitatively correspond to those of Drosophila melanogaster, Caenorhabditis elegans, medflies, yeasts and humans. Species evolved in silico especially differ in their population diversity of maintenance strategies, which itself emerges as an adaptation to the environment over generations. Based on this integrative framework, we also derive predictions and interpretations concerning the effects of diet changes and heat-shock treatments on mortality patterns. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

A USCLIVAR Project to Assess and Compare the Responses of Global Climate Models to Drought-Related SST Forcing Patterns: Overview and Results

NASA Technical Reports Server (NTRS)

Schubert, Siegfried; Wang, Hailan; Koster, Randal; Weaver, Scott; Gutzler, David; Dai, Aiguo; Delworth, Tom; Deser, Clara; Findell, Kristen; Fu, Rong;

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.

De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination

PubMed Central

Ghiselli, Fabrizio; Milani, Liliana; Chang, Peter L.; Hedgecock, Dennis; Davis, Jonathan P.; Nuzhdin, Sergey V.; Passamonti, Marco

2012-01-01

Males and females share the same genome, thus, phenotypic divergence requires differential gene expression and sex-specific regulation. Accordingly, the analysis of expression patterns is pivotal to the understanding of sex determination mechanisms. Many bivalves are stable gonochoric species, but the mechanism of gonad sexualization and the genes involved are still unknown. Moreover, during the period of sexual rest, a gonad is not present and sex cannot be determined. A mechanism associated with germ line differentiation in some bivalves, including the Manila clam Ruditapes philippinarum, is the doubly uniparental inheritance (DUI) of mitochondria, a variation of strict maternal inheritance. Two mitochondrial lineages are present, one transmitted through eggs and the other through sperm, as well as a mother-dependent sex bias of the progeny. We produced a de novo annotation of 17,186 transcripts from R. philippinarum and compared the transcriptomes of males and females and identified 1,575 genes with strong sex-specific expression and 166 sex-specific single nucleotide polymorphisms, obtaining preliminary information about genes that could be involved in sex determination. Then we compared the transcriptomes between a family producing predominantly females and a family producing predominantly males to identify candidate genes involved in regulation of sex-specific aspects of DUI system, finding a relationship between sex bias and differential expression of several ubiquitination genes. In mammalian embryos, sperm mitochondria are degraded by ubiquitination. A modification of this mechanism is hypothesized to be responsible for the retention of sperm mitochondria in male embryos of DUI species. Ubiquitination can additionally regulate gene expression, playing a role in sex determination of several animals. These data enable us to develop a model that incorporates both the DUI literature and our new findings. PMID:21976711

A Comparison of Component and Factor Patterns: A Monte Carlo Approach.

ERIC Educational Resources Information Center

Velicer, Wayne F.; And Others

1982-01-01

Factor analysis, image analysis, and principal component analysis are compared with respect to the factor patterns they would produce under various conditions. The general conclusion that is reached is that the three methods produce results that are equivalent. (Author/JKS)

Cracking-assisted fabrication of nanoscale patterns for micro/nanotechnological applications

NASA Astrophysics Data System (ADS)

Kim, Minseok; Kim, Dong-Joo; Ha, Dogyeong; Kim, Taesung

2016-05-01

Cracks are frequently observed in daily life, but they are rarely welcome and are considered as a material failure mode. Interestingly, cracks cause critical problems in various micro/nanofabrication processes such as colloidal assembly, thin film deposition, and even standard photolithography because they are hard to avoid or control. However, increasing attention has been given recently to control and use cracks as a facile, low-cost strategy for producing highly ordered nanopatterns. Specifically, cracking is the breakage of molecular bonds and occurs simultaneously over a large area, enabling fabrication of nanoscale patterns at both high resolution and high throughput, which are difficult to obtain simultaneously using conventional nanofabrication techniques. In this review, we discuss various cracking-assisted nanofabrication techniques, referred to as crack lithography, and summarize the fabrication principles, procedures, and characteristics of the crack patterns such as their position, direction, and dimensions. First, we categorize crack lithography techniques into three technical development levels according to the directional freedom of the crack patterns: randomly oriented, unidirectional, or multidirectional. Then, we describe a wide range of novel practical devices fabricated by crack lithography, including bioassay platforms, nanofluidic devices, nanowire sensors, and even biomimetic mechanosensors.

Clinical patterns of cutaneous nontuberculous mycobacterial infections.

PubMed

Bartralot, R; García-Patos, V; Sitjas, D; Rodríguez-Cano, L; Mollet, J; Martín-Casabona, N; Coll, P; Castells, A; Pujol, R M

2005-04-01

Cutaneous nontuberculous mycobacterial infections result from external inoculation, spread of a deeper infection, or haematogenous spread of a disseminated infection. There are two species-specific infections (fish-tank or swimming-pool granuloma, due to Mycobacterium marinum, and Buruli ulcer, caused by M. ulcerans). Most infections, however, produce a nonspecific clinical picture. To define clinical patterns of cutaneous disease in nontuberculous mycobacterial infections. Fifty-one patients with cutaneous nontuberculous mycobacterial infections were reviewed. Clinical and histopathological features of normal hosts and immunosuppressed patients were compared. Two subgroups of immunosuppressed patients were distinguished: patients with cutaneous infection and patients with a disseminated infection and cutaneous involvement. In immunosuppressed patients the number of lesions was significantly higher. Abscesses and ulceration were also more frequently observed. Different species were found in normal hosts and immunosuppressed patients. Several clinical patterns of cutaneous infection were defined: lymphocutaneous or sporotrichoid lesions; nonlymphocutaneous lesions at the site of trauma; folliculitis and furunculosis involving the lower extremities; disseminated lesions on the extremities in immunosuppressed patients. Two patterns were observed in patients with a disseminated infection: localized cutaneous lesions and disseminated cutaneous and mucosal lesions. Cutaneous manifestations of nontuberculous mycobacterial infections may be classified according to criteria such as cutaneous lesions and immune status.

The Effect of Surface Patterning on Corrosion Resistance of Biomedical Devices

NASA Astrophysics Data System (ADS)

Guo, Mengnan; Toloei, Alisina; Rotermund, Harm H.

2016-10-01

In this study, two styles of surface topographies have been created on stainless steel wires to test their corrosion resistance as simulated implanted biomedical devices. Grade 316 LVM stainless steel wire was initially polished to G1500 surface finish before treatment to produce the two different topographies: 1. Unidirectional roughness was created using SiC papers and 2. Various patterns were created with specific hole diameter and inter-hole spacing using focused ion beam (FIB). In order to simulate the environment of implanted biomedical devices, a three-electrode electrochemical cell with 0.9% (by mass) NaCl solution has been used to test the corrosion resistance of the samples by potentiodynamic polarization test method. SEM and EDS analyzed the appearance and chemical composition of different elements including oxygen on the surface. The potential of stable pitting, time related to the initiation of the stable pitting, and the highest corrosion current associated with stable pitting have been compared for samples with the two styles of topography. It was found that surfaces with patterns have a relatively higher pitting potential and it takes longer time to initiate stable pitting than the surface without any patterns.

Image-based spectroscopy for environmental monitoring

NASA Astrophysics Data System (ADS)

Bachmakov, Eduard; Molina, Carolyn; Wynne, Rosalind

2014-03-01

An image-processing algorithm for use with a nano-featured spectrometer chemical agent detection configuration is presented. The spectrometer chip acquired from Nano-Optic DevicesTM can reduce the size of the spectrometer down to a coin. The nanospectrometer chip was aligned with a 635nm laser source, objective lenses, and a CCD camera. The images from a nanospectrometer chip were collected and compared to reference spectra. Random background noise contributions were isolated and removed from the diffraction pattern image analysis via a threshold filter. Results are provided for the image-based detection of the diffraction pattern produced by the nanospectrometer. The featured PCF spectrometer has the potential to measure optical absorption spectra in order to detect trace amounts of contaminants. MATLAB tools allow for implementation of intelligent, automatic detection of the relevant sub-patterns in the diffraction patterns and subsequent extraction of the parameters using region-detection algorithms such as the generalized Hough transform, which detects specific shapes within the image. This transform is a method for detecting curves by exploiting the duality between points on a curve and parameters of that curve. By employing this imageprocessing technique, future sensor systems will benefit from new applications such as unsupervised environmental monitoring of air or water quality.

Spatial patterns of natural hazards mortality in the United States

PubMed Central

Borden, Kevin A; Cutter, Susan L

2008-01-01

Background Studies on natural hazard mortality are most often hazard-specific (e.g. floods, earthquakes, heat), event specific (e.g. Hurricane Katrina), or lack adequate temporal or geographic coverage. This makes it difficult to assess mortality from natural hazards in any systematic way. This paper examines the spatial patterns of natural hazard mortality at the county-level for the U.S. from 1970–2004 using a combination of geographical and epidemiological methods. Results Chronic everyday hazards such as severe weather (summer and winter) and heat account for the majority of natural hazard fatalities. The regions most prone to deaths from natural hazards are the South and intermountain west, but sub-regional county-level mortality patterns show more variability. There is a distinct urban/rural component to the county patterns as well as a coastal trend. Significant clusters of high mortality are in the lower Mississippi Valley, upper Great Plains, and Mountain West, with additional areas in west Texas, and the panhandle of Florida, Significant clusters of low mortality are in the Midwest and urbanized Northeast. Conclusion There is no consistent source of hazard mortality data, yet improvements in existing databases can produce quality data that can be incorporated into spatial epidemiological studies as demonstrated in this paper. It is important to view natural hazard mortality through a geographic lens so as to better inform the public living in such hazard prone areas, but more importantly to inform local emergency practitioners who must plan for and respond to disasters in their community. PMID:19091058

Sexually dimorphic levels of color trait integration and the resolution of sexual conflict in Lake Malawi cichlids.

PubMed

Brzozowski, Frances; Roscoe, Jennifer; Parsons, Kevin; Albertson, Craig

2012-06-01

East African cichlids are renowned for their propensity to radiate, and variation in color patterns accounts for much of endemic cichlid diversity. Sexual dimorphism in color among cichlid species likely represents the outcome of different selective regimes acting on each sex, and is a classic example of sexual conflict. It is generally assumed that this conflict has been mitigated through the evolution of sex-linked color polymorphisms. Here, we propose that the evolution of sex-specific differences in levels of color trait integration may represent an additional mechanism through which sexual conflict has been resolved in this group. Specifically, we predict: (1) that general patterns of integration are influenced by early developmental events and thus conserved across sexes and (2) that male color is less integrated than females, and thus more evolvable in terms of producing an elaborate palette (i.e., in response to sexual selection), whereas female color is more integrated, facilitating wholesale shifts in color for background matching (i.e., in response to natural selection for crypsis). We tested these hypotheses using an F(2) design to compare the segregation of male and female color patterns. Both exploratory methods and hypothesis-driven analyses of integration demonstrate that the covariance structure of color traits in males and females is distinct, and that males are significantly less integrated than females. We suggest that the ability of species to promote different levels, and to a lesser extent patterns, of phenotypic integration between males and females may have contributed to the evolutionary success of this group. © 2012 WILEY PERIODICALS, INC.

Spontaneous long-range calcium waves in developing butterfly wings.

PubMed

Ohno, Yoshikazu; Otaki, Joji M

2015-03-25

Butterfly wing color patterns emerge as the result of a regular arrangement of scales produced by epithelial scale cells at the pupal stage. These color patterns and scale arrangements are coordinated throughout the wing. However, the mechanism by which the development of scale cells is controlled across the entire wing remains elusive. In the present study, we used pupal wings of the blue pansy butterfly, Junonia orithya, which has distinct eyespots, to examine the possible involvement of Ca(2+) waves in wing development. Here, we demonstrate that the developing pupal wing tissue of the blue pansy butterfly displayed spontaneous low-frequency Ca(2+) waves in vivo that propagated slowly over long distances. Some waves appeared to be released from the immediate peripheries of the prospective eyespot and discal spot, though it was often difficult to identify the specific origins of these waves. Physical damage, which is known to induce ectopic eyespots, led to the radiation of Ca(2+) waves from the immediate periphery of the damaged site. Thapsigargin, which is a specific inhibitor of Ca(2+)-ATPases in the endoplasmic reticulum, induced an acute increase in cytoplasmic Ca(2+) levels and halted the spontaneous Ca(2+) waves. Additionally, thapsigargin-treated wings showed incomplete scale development as well as other scale and color pattern abnormalities. We identified a novel form of Ca(2+) waves, spontaneous low-frequency slow waves, which travel over exceptionally long distances. Our results suggest that spontaneous Ca(2+) waves play a critical role in the coordinated development of scale arrangements and possibly in color pattern formation in butterflies.

Silk Gland Gene Expression during Larval-Pupal Transition in the Cotton Leaf Roller Sylepta derogata (Lepidoptera: Pyralidae)

PubMed Central

Su, Honghua; Cheng, Yuming; Wang, Zhongyang; Li, Zhong; Stanley, David; Yang, Yizhong

2015-01-01

The cotton leaf roller, Sylepta derogata, is a silk-producing insect pest. While young larvae feed on the underside of leaves, the older ones roll cotton leaves and feed on the leaf edges, which defoliates cotton plants. The larvae produce silk to stabilize the rolled leaf and to balloon from used to new leaves. Despite the significance of silk in the biology of pest insect species, there is virtually no information on the genes involved in their silk production. This is a substantial knowledge gap because some of these genes may be valuable targets for developing molecular pest management technologies. We addressed the gap by posing the hypothesis that silk gland gene expression changes during the transition from larvae to pupae. We tested our hypothesis using RNA-seq to investigate changes in silk gland gene expression at three developmental stages, 5th instar larvae (silk producing; 15,445,926 clean reads), prepupae (reduced silk producing; 13,758,154) and pupae (beyond silk producing; 16,787,792). We recorded 60,298 unigenes and mapped 50,158 (larvae), 48,415 (prepupae) and 46,623 (pupae) of them to the NCBI database. Most differentially expressed genes in the 5th instar larvae/prepupae libraries were relevant to nucleotide synthesis and maintenance of silk gland function. We identified down-regulated transcriptional factors and several genes involved in silk formation in the three libraries and verified the expression pattern of eight genes by qPCR. The developmental- and tissue-specific expression patterns of the fibroin light chain gene showed it was highly expressed during the larval silk-producing stage. We recorded highest expression of this gene in the larval silk gland, compared to other tissues, including midgut, hindgut, epidermis, Malpighian tubes, hemolymph and fat body. These data are a genetic resource to guide selection of key genes that may be targeted for in planta and other gene-silencing technologies for sustainable cotton agriculture. PMID:26352931

Silk Gland Gene Expression during Larval-Pupal Transition in the Cotton Leaf Roller Sylepta derogata (Lepidoptera: Pyralidae).

PubMed

Su, Honghua; Cheng, Yuming; Wang, Zhongyang; Li, Zhong; Stanley, David; Yang, Yizhong

2015-01-01

The cotton leaf roller, Sylepta derogata, is a silk-producing insect pest. While young larvae feed on the underside of leaves, the older ones roll cotton leaves and feed on the leaf edges, which defoliates cotton plants. The larvae produce silk to stabilize the rolled leaf and to balloon from used to new leaves. Despite the significance of silk in the biology of pest insect species, there is virtually no information on the genes involved in their silk production. This is a substantial knowledge gap because some of these genes may be valuable targets for developing molecular pest management technologies. We addressed the gap by posing the hypothesis that silk gland gene expression changes during the transition from larvae to pupae. We tested our hypothesis using RNA-seq to investigate changes in silk gland gene expression at three developmental stages, 5th instar larvae (silk producing; 15,445,926 clean reads), prepupae (reduced silk producing; 13,758,154) and pupae (beyond silk producing; 16,787,792). We recorded 60,298 unigenes and mapped 50,158 (larvae), 48,415 (prepupae) and 46,623 (pupae) of them to the NCBI database. Most differentially expressed genes in the 5th instar larvae/prepupae libraries were relevant to nucleotide synthesis and maintenance of silk gland function. We identified down-regulated transcriptional factors and several genes involved in silk formation in the three libraries and verified the expression pattern of eight genes by qPCR. The developmental- and tissue-specific expression patterns of the fibroin light chain gene showed it was highly expressed during the larval silk-producing stage. We recorded highest expression of this gene in the larval silk gland, compared to other tissues, including midgut, hindgut, epidermis, Malpighian tubes, hemolymph and fat body. These data are a genetic resource to guide selection of key genes that may be targeted for in planta and other gene-silencing technologies for sustainable cotton agriculture.

High intensity portable fluorescent light

NASA Technical Reports Server (NTRS)

Kendall, F. B.

1972-01-01

Eight high intensity portable fluorescent lights were produced. Three prototype lights were also produced, two of which were subsequently updated to the physical and operational configuration of the qualification and flight units. Positioning of lamp apertures and reflectors in these lights is such that the light is concentrated and intensified in a specific pattern rather than widely diffused. Indium amalgam control of mercury vapor pressure in the lamp gives high output at lamp ambient temperatures up to 105 C. A small amount of amalgam applied to each electrode stem helps to obtain fast warm-up. Shrinking a Teflon sleeve on the tube and potting metal caps on each end of the lamp minimizes dispersion of mercury vapor and glass particles in the event of accidental lamp breakage. Operation at 20 kHz allows the lamps to consume more power than at low frequency, thus increasing their light output and raising their efficiency. When used to expose color photographic film, light from the lamps produces results approximately equal to sunlight.

Ontogenetic Tooth Reduction in Stenopterygius quadriscissus (Reptilia: Ichthyosauria): Negative Allometry, Changes in Growth Rate, and Early Senescence of the Dental Lamina

PubMed Central

Dick, Daniel G.; Maxwell, Erin E.

2015-01-01

We explore the functional, developmental, and evolutionary processes which are argued to produce tooth reduction in the extinct marine reptile Stenopterygius quadriscissus (Reptilia: Ichthyosauria). We analyze the relationship between mandible growth and tooth size, shape, and count, to establish an ontogenetic trend. The pattern in S. quadriscissus is consistent with hypotheses of tooth size reduction by neutral selection, and this unusual morphology (a functionally edentulous rostrum) was produced by a series of different evolutionary developmental changes that are known for other taxa showing tooth reduction and loss. Specifically, this species evolved functional edentulism by evolutionary changes in the growth allometry of the dentition and by altering growth rates through ontogeny. This observation supports previous hypotheses that S. quadriscissus underwent ontogenetic tooth reduction. Tooth reduction in S. quadriscissus may be caused by unique selective pressures resulting from prey choice and feeding behavior, expanding our current understanding of the mechanisms producing tooth reduction. PMID:26579712

Ontogenetic Tooth Reduction in Stenopterygius quadriscissus (Reptilia: Ichthyosauria): Negative Allometry, Changes in Growth Rate, and Early Senescence of the Dental Lamina.

PubMed

Dick, Daniel G; Maxwell, Erin E

2015-01-01

We explore the functional, developmental, and evolutionary processes which are argued to produce tooth reduction in the extinct marine reptile Stenopterygius quadriscissus (Reptilia: Ichthyosauria). We analyze the relationship between mandible growth and tooth size, shape, and count, to establish an ontogenetic trend. The pattern in S. quadriscissus is consistent with hypotheses of tooth size reduction by neutral selection, and this unusual morphology (a functionally edentulous rostrum) was produced by a series of different evolutionary developmental changes that are known for other taxa showing tooth reduction and loss. Specifically, this species evolved functional edentulism by evolutionary changes in the growth allometry of the dentition and by altering growth rates through ontogeny. This observation supports previous hypotheses that S. quadriscissus underwent ontogenetic tooth reduction. Tooth reduction in S. quadriscissus may be caused by unique selective pressures resulting from prey choice and feeding behavior, expanding our current understanding of the mechanisms producing tooth reduction.

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.

A 3D Monte Carlo model of radiation affecting cells, and its application to neuronal cells and GCR irradiation

NASA Astrophysics Data System (ADS)

Ponomarev, Artem; Sundaresan, Alamelu; Kim, Angela; Vazquez, Marcelo E.; Guida, Peter; Kim, Myung-Hee; Cucinotta, Francis A.

A 3D Monte Carlo model of radiation transport in matter is applied to study the effect of heavy ion radiation on human neuronal cells. Central nervous system effects, including cognitive impairment, are suspected from the heavy ion component of galactic cosmic radiation (GCR) during space missions. The model can count, for instance, the number of direct hits from ions, which will have the most affect on the cells. For comparison, the remote hits, which are received through δ-rays from the projectile traversing space outside the volume of the cell, are also simulated and their contribution is estimated. To simulate tissue effects from irradiation, cellular matrices of neuronal cells, which were derived from confocal microscopy, were simulated in our model. To produce this realistic model of the brain tissue, image segmentation was used to identify cells in the images of cells cultures. The segmented cells were inserted pixel by pixel into the modeled physical space, which represents a volume of interacting cells with periodic boundary conditions (PBCs). PBCs were used to extrapolate the model results to the macroscopic tissue structures. Specific spatial patterns for cell apoptosis are expected from GCR, as heavy ions produce concentrated damage along their trajectories. The apoptotic cell patterns were modeled based on the action cross sections for apoptosis, which were estimated from the available experimental data. The cell patterns were characterized with an autocorrelation function, which values are higher for non-random cell patterns, and the values of the autocorrelation function were compared for X rays and Fe ion irradiations. The autocorrelation function indicates the directionality effects present in apoptotic neuronal cells from GCR.

High community faecal carriage rates of CTX-M ESBL-producing Escherichia coli in a specific population group in Birmingham, UK.

PubMed

Wickramasinghe, Nimal H; Xu, Li; Eustace, Andrew; Shabir, Sahida; Saluja, Tranprit; Hawkey, Peter M

2012-05-01

To determine the proportion of E. coli carrying specific CTX-M extended-spectrum β-lactamase (ESBL) genotypes in a community population of East and North Birmingham. General practice and outpatient stool samples from 732 individuals submitted for examination for faecal pathogens in 2010 were screened for ESBL-producing E. coli using chromogenic agar. Multiplex PCR, denaturing HPLC, DNA sequencing and PFGE were used to determine the CTX-M genotype and clonal subtype. Isolates from people were assigned to 'Europe', 'Middle East/South Asia' (MESA) or 'uncategorized' groups using software to determine probable global origin based on the subject's full name. Prevalence of CTX-M carriage in the sample population was 11.3%. There was a statistically significant difference (P < 0.001) between carriage in the Europe group (8.1%) and the MESA group (22.8%). There was also a higher rate of carriage of CTX-M-15-producing E. coli (P < 0.001) in MESA subjects. The high community carriage rate and the significant difference in carriage between the Europe and MESA subjects may have important consequences for therapy. If the rising trend in carriage of bacteria producing ESBLs continues, guidelines for empirical therapy for patients presenting from the community may need to be modified. The findings also raise the concern that the pattern and routes of spread of CTX-M-15 may be replicated in the future by broader-spectrum β-lactamases, such as New Delhi metallo-β-lactamase ('NDM-1').

An agent-based model of dialect evolution in killer whales.

PubMed

Filatova, Olga A; Miller, Patrick J O

2015-05-21

The killer whale is one of the few animal species with vocal dialects that arise from socially learned group-specific call repertoires. We describe a new agent-based model of killer whale populations and test a set of vocal-learning rules to assess which mechanisms may lead to the formation of dialect groupings observed in the wild. We tested a null model with genetic transmission and no learning, and ten models with learning rules that differ by template source (mother or matriline), variation type (random errors or innovations) and type of call change (no divergence from kin vs. divergence from kin). The null model without vocal learning did not produce the pattern of group-specific call repertoires we observe in nature. Learning from either mother alone or the entire matriline with calls changing by random errors produced a graded distribution of the call phenotype, without the discrete call types observed in nature. Introducing occasional innovation or random error proportional to matriline variance yielded more or less discrete and stable call types. A tendency to diverge from the calls of related matrilines provided fast divergence of loose call clusters. A pattern resembling the dialect diversity observed in the wild arose only when rules were applied in combinations and similar outputs could arise from different learning rules and their combinations. Our results emphasize the lack of information on quantitative features of wild killer whale dialects and reveal a set of testable questions that can draw insights into the cultural evolution of killer whale dialects. Copyright © 2015 Elsevier Ltd. All rights reserved.

Remote Sensing the Patterns of Vector-borne Disease in El Nino and non-El Nino Years

NASA Technical Reports Server (NTRS)

Wood, B. L.; Chang, J.; Lobitz, B.; Beck, L.; DAntoni, Hector (Technical Monitor)

1997-01-01

The relationship between El Nino and non-El Nino and the patterns of vector-borne disease can be viewed at a variety of spatial and temporal scales. At one extreme are long term predictions of changing precipitation and temperature patterns at continental and global scales. At the opposite extreme are the local or site specific ecological changes associated with the long term events. In order to understand and address the human health consequences of El Nino events, especially the patterns of vector-borne diseases, it is necessary to combine both scales of observation. At a local or regional scale the patterns of vector-borne diseases are determined by temperature, precipitation, and habitat availability. These factors, as well as disease incidence can be altered by El Nino events. Remote sensing data such as that acquired by the NOAA AVHRR and Landsat TM sensors can be used to characterize and monitor changing ecological conditions and therefore predict vector-borne disease patterns. The authors present the results of preliminary work on the analysis of historical AVHRR and TM data acquired during El Nino and nonfatal Nino years to characterize ecological conditions in Peru on a monthly basis. This information will then be combined with disease data to determine the relationship between changes in ecological conditions and disease incidence. Our goal is to produce a sequence of remotely sensed images which can be used to show the ecological and disease patterns associated with long term El Nino events and predictions.

Dietary intake in midlife and associations with standard of living, education and nutrition literacy.

PubMed

Wall, Catherine L; Gearry, Richard B; Pearson, John; Parnell, Winsome; Skidmore, Paula M L

2014-07-04

Cardiovascular disease is a leading cause of death in New Zealand, but risk factors may be decreased by consuming a heart healthy diet. This pilot study investigated whether participants met the guidelines for a heart healthy diet and whether a novel heart healthy dietary pattern could be identified using principal components analysis (PCA). The second aim of this project was to assess if higher education, standard of living and nutrition literacy are associated with a heart healthy dietary pattern. This exploratory study was undertaken using data from the first participants enrolled in the Canterbury Health Ageing and Lifecourse study: an observational study of 50 year olds in the Canterbury District Health Board region. Eighty-two people were selected from the General and Maori electoral role and interviewed prior to the 22 February 2011 Christchurch Earthquake. PCA was conducted to identify dietary patterns, based on intake of specific nutrients as indicated by the New Zealand and international heart healthy dietary guidelines. 62 participants completed questionnaires and an estimated food record. No participants met all five of the heart healthy dietary guidelines. One dietary pattern was produced by PCA: a "higher CVD risk" pattern. Regression analysis indicated that higher standard of living, education and nutrition literacy were inversely associated with a "higher CVD risk" pattern. Higher standard of living, education and nutrition literacy were associated with a healthier dietary eating pattern. However, as no participants met all the dietary recommendations more education and support is needed to help people meet these.

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

Multi-Bandwidth Frequency Selective Surfaces for Near Infrared Filtering: Design and Optimization

NASA Technical Reports Server (NTRS)

Cwik, Tom; Fernandez, Salvador; Ksendzov, A.; LaBaw, Clayton C.; Maker, Paul D.; Muller, Richard E.

1999-01-01

Frequency selective surfaces are widely used in the microwave and millimeter wave regions of the spectrum for filtering signals. They are used in telecommunication systems for multi-frequency operation or in instrument detectors for spectroscopy. The frequency selective surface operation depends on a periodic array of elements resonating at prescribed wavelengths producing a filter response. The size of the elements is on the order of half the electrical wavelength, and the array period is typically less than a wavelength for efficient operation. When operating in the optical region, diffraction gratings are used for filtering. In this regime the period of the grating may be several wavelengths producing multiple orders of light in reflection or transmission. In regions between these bands (specifically in the infrared band) frequency selective filters consisting of patterned metal layers fabricated using electron beam lithography are beginning to be developed. The operation is completely analogous to surfaces made in the microwave and millimeter wave region except for the choice of materials used and the fabrication process. In addition, the lithography process allows an arbitrary distribution of patterns corresponding to resonances at various wavelengths to be produced. The design of sub-millimeter filters follows the design methods used in the microwave region. Exacting modal matching, integral equation or finite element methods can be used for design. A major difference though is the introduction of material parameters and thicknesses tha_ may not be important in longer wavelength designs. This paper describes the design of multi-bandwidth filters operating in the I-5 micrometer wavelength range. This work follows on previous design [1,2]. In this paper extensions based on further optimization and an examination of the specific shape of the element in the periodic cell will be reported. Results from the design, manufacture and test of linear wedge filters built using micro-lithographic techniques and used ir spectral imaging applications will be presented.

Multi-Bandwidth Frequency Selective Surfaces for Near Infrared Filtering: Design and Optimization

NASA Technical Reports Server (NTRS)

Cwik, Tom; Fernandez, Salvador; Ksendzov, A.; LaBaw, Clayton C.; Maker, Paul D.; Muller, Richard E.

1998-01-01

Frequency selective surfaces are widely used in the microwave and millimeter wave regions of the spectrum for filtering signals. They are used in telecommunication systems for multi-frequency operation or in instrument detectors for spectroscopy. The frequency selective surface operation depends on a periodic array of elements resonating at prescribed wavelengths producing a filter response. The size of the elements is on the order of half the electrical wavelength, and the array period is typically less than a wavelength for efficient operation. When operating in the optical region, diffraction gratings are used for filtering. In this regime the period of the grating may be several wavelengths producing multiple orders of light in reflection or transmission. In regions between these bands (specifically in the infrared band) frequency selective filters consisting of patterned metal layers fabricated using electron beam lithography are beginning to be developed. The operation is completely analogous to surfaces made in the microwave and millimeter wave region except for the choice of materials used and the fabrication process. In addition, the lithography process allows an arbitrary distribution of patterns corresponding to resonances at various wavelengths to be produced. The design of sub-millimeter filters follows the design methods used in the microwave region. Exacting modal matching, integral equation or finite element methods can be used for design. A major difference though is the introduction of material parameters and thicknesses that may not be important in longer wavelength designs. This paper describes the design of multi- bandwidth filters operating in the 1-5 micrometer wavelength range. This work follows on a previous design. In this paper extensions based on further optimization and an examination of the specific shape of the element in the periodic cell will be reported. Results from the design, manufacture and test of linear wedge filters built using microlithographic techniques and used in spectral imaging applications will be presented.

Evidence for the contribution of multiple mechanisms in the feeding pattern of rats exposed to p-chloro-diphenyl diselenide-supplemented diets.

PubMed

Bortolatto, Cristiani F; Heck, Suélen O; Zborowski, Vanessa A; Gai, Bibiana M; Neto, José S S; Nogueira, Cristina W

2015-11-01

Preliminary findings suggest that food intake reduction induced by p-chloro-diphenyl diselenide [(p-ClPhSe)2] in rats is mediated by a satiating action; however, additional experiments are necessary to clarify its actions. The purpose of this study was to investigate the effects of diets supplemented with (p-ClPhSe)2 on feeding behavior of rats as well as the (p-ClPhSe)2 effectiveness in producing aversive reactions or specific flavor. The results demonstrated that behavioral satiety sequence (BSS) was preserved in animals exposed to (p-ClPhSe)2-supplemented diets (0.01 and 0.1%) and associated with a shift of the onset of resting to the left indicating a satiating action at the first contact. In addition, the frequency, the mean duration and the mean size of meals were decreased in rats exposed to a 0.1% (p-ClPhSe)2 diet. Alternatively, a second contact with a 0.01% (p-ClPhSe)2 diet caused disruption of BSS and pronounced changes in the meal pattern, suggesting that it produces aversiveness. In fact, rats developed a significant taste aversion to the saccharin solution after receiving the administration of (p-ClPhSe)2 (1 and 10mg/kg; i.p.). Lastly, a diet containing 0.1% of (p-ClPhSe)2 seems to alter the palatability of food given that rats had a preference for the control diet. The findings of the present study suggest that (p-ClPhSe)2 reduced the food intake of rats by inducing a satiating action at the first contact, but it also produced aversive reactions when rats were re-exposed to it. A specific flavor seems also to contribute to (p-ClPhSe)2 suppressant effects on feeding. Copyright © 2015 Elsevier Inc. All rights reserved.

Boltushka: A Homemade Amphetamine-Type Stimulant and HIV Risk in Odessa, Ukraine

PubMed Central

Chintalova-Dallas, Repsina; Case, Patricia; Kitsenko, Nataliya; Lazzarini, Zita

2009-01-01

Background Homemade amphetamine-type stimulants (ATSs) have been reported in Russia and Eastern Europe for decades. Recipes differ geographically and over time producing differing active ingredients. Vint and jeff (active ingredients methamphetamine and methcathinone, respectively) are two such homemade ATSs originally produced from over-the-counter cold medications and household chemicals. Methods During a Rapid Policy Assessment and Responses (RPAR) project in Odessa, Ukraine, researchers found use of boltushka, a novel homemade ATS. Fourteen supplemental qualitative interviews were conducted, including ten interviews with boltushka injectors and four interviews with pharmacists. We report patterns of boltushka use among local injection drug users (IDUs) as well as the role of laws, regulations, and current pharmacy practices. Results Legal restrictions on over-the-counter cold medicines in Ukraine led to products containing phenypropanolamine (PPA), which oxidized with KMnO4 (potassium permanganate), produces a weak ATS, cathinone, called boltushka. Boltushka’s ingredients are easily available in pharmacies or on the black market. IDUs reported a mean age at first use of 16 years old (range 12–21). While published data are scant, anecdotal evidence reported here include amphetamine-like effects on energy and appetite, binging patterns of use, and some reports of shaking and other neurological damage consistent with earlier reports from exposure to KMnO4. Users reported sharing syringes and other non-sterile injection practices. No users reported specific treatment or prevention programs for boltushka users. Conclusions Although Ukrainian government regulations have limited access to precursor chemicals, IDUs have continued to make and use boltushka. The actual extent and demographics of boltushka use are unknown. Besides risk of bloodborne disease, the health effects of injected homemade ATSs and their constituent chemicals are poorly documented. Interventions beyond available harm reduction efforts may be required. Education/treatment specific to boltushka users and screening for other physical harms are critical interventions. PMID:18976896

Investigation occurrences of turing pattern in Schnakenberg and Gierer-Meinhardt equation

NASA Astrophysics Data System (ADS)

Nurahmi, Annisa Fitri; Putra, Prama Setia; Nuraini, Nuning

2018-03-01

There are several types of animals with unusual, varied patterns on their skin. The skin pigmentation system influences this in the animal. On the other side, in 1950 Alan Turing formulated the mathematical theory of morphogenesis, where this model can bring up a spatial pattern or so-called Turing pattern. This research discusses the identification of Turing's model that can produce animal skin pattern. Investigations conducted on two types of equations: Schnakenberg (1979), and Gierer-Meinhardt (1972). In this research, parameters were explored to produce Turing's patter on that both equation. The numerical simulation in this research done using Neumann Homogeneous and Dirichlet Homogeneous boundary condition. The investigation of Schnakenberg equation yielded poison dart frog (Andinobates dorisswansonae) and ladybird (Coccinellidae septempunctata) pattern while skin fish pattern was showed by Gierer-Meinhardt equation.

Hearing Lips and Seeing Voices: How Cortical Areas Supporting Speech Production Mediate Audiovisual Speech Perception

PubMed Central

Skipper, Jeremy I.; van Wassenhove, Virginie; Nusbaum, Howard C.; Small, Steven L.

2009-01-01

Observing a speaker’s mouth profoundly influences speech perception. For example, listeners perceive an “illusory” “ta” when the video of a face producing /ka/ is dubbed onto an audio /pa/. Here, we show how cortical areas supporting speech production mediate this illusory percept and audiovisual (AV) speech perception more generally. Specifically, cortical activity during AV speech perception occurs in many of the same areas that are active during speech production. We find that different perceptions of the same syllable and the perception of different syllables are associated with different distributions of activity in frontal motor areas involved in speech production. Activity patterns in these frontal motor areas resulting from the illusory “ta” percept are more similar to the activity patterns evoked by AV/ta/ than they are to patterns evoked by AV/pa/ or AV/ka/. In contrast to the activity in frontal motor areas, stimulus-evoked activity for the illusory “ta” in auditory and somatosensory areas and visual areas initially resembles activity evoked by AV/pa/ and AV/ka/, respectively. Ultimately, though, activity in these regions comes to resemble activity evoked by AV/ta/. Together, these results suggest that AV speech elicits in the listener a motor plan for the production of the phoneme that the speaker might have been attempting to produce, and that feedback in the form of efference copy from the motor system ultimately influences the phonetic interpretation. PMID:17218482

Comparative jet wake structure and swimming performance of salps.

PubMed

Sutherland, Kelly R; Madin, Laurence P

2010-09-01

Salps are barrel-shaped marine invertebrates that swim by jet propulsion. Morphological variations among species and life-cycle stages are accompanied by differences in swimming mode. The goal of this investigation was to compare propulsive jet wakes and swimming performance variables among morphologically distinct salp species (Pegea confoederata, Weelia (Salpa) cylindrica, Cyclosalpa sp.) and relate swimming patterns to ecological function. Using a combination of in situ dye visualization and particle image velocimetry (PIV) measurements, we describe properties of the jet wake and swimming performance variables including thrust, drag and propulsive efficiency. Locomotion by all species investigated was achieved via vortex ring propulsion. The slow-swimming P. confoederata produced the highest weight-specific thrust (T=53 N kg(-1)) and swam with the highest whole-cycle propulsive efficiency (eta(wc)=55%). The fast-swimming W. cylindrica had the most streamlined body shape but produced an intermediate weight-specific thrust (T=30 N kg(-1)) and swam with an intermediate whole-cycle propulsive efficiency (eta(wc)=52%). Weak swimming performance variables in the slow-swimming C. affinis, including the lowest weight-specific thrust (T=25 N kg(-1)) and lowest whole-cycle propulsive efficiency (eta(wc)=47%), may be compensated by low energetic requirements. Swimming performance variables are considered in the context of ecological roles and evolutionary relationships.

Two-stage fluid flow and element transfers in shear zones during collision burial-exhumation cycle: Insights from the Mont Blanc Crystalline Massif (Western Alps)

NASA Astrophysics Data System (ADS)

Rolland, Y.; Rossi, M.

2016-11-01

The Mont-Blanc Massif was intensely deformed during the Alpine orogenesis: in a first stage of prograde underthrusting at c. 30 Ma and in a second stage of uplift and exhumation at 22-11 Ma. Mid-crustal shear zones of 1 mm-50 m size, neighbouring episyenites (quartz-dissolved altered granite) and alpine veins, have localised intense fluid flow, which produced substantial changes in mineralogy and whole-rock geochemistry. Four main metamorphic zones are oriented parallel to the strike of the massif: (i) epidote, (ii) chlorite, (iii) actinolite-muscovite ± biotite and (iv) muscovite ± biotite. In addition, phlogopite-bearing shear zones occur in the chlorite zone, and calcite-bearing shear zones are locally found in the muscovite zone. The initial chemical composition of the granitic protolith is relatively constant at massif scale, which allows investigating compositional changes related to shear zone activity, and subsequent volume change and elements mobility. The variations of whole-rock composition and mineral chemistry in shear zones reflect variations in fluid/rock ratios and fluid's chemistry, which have produced specific mineral reactions. Estimated time-integrated fluid fluxes are of the order of 106 m3/m2. The mineral assemblages that crystallised upon these fluid-P-T conditions are responsible for specific major and trace element enrichments. The XFe (Fe/Fe + Mg) pattern of shear zone phyllosilicates and the δ13C pattern of vein calcite both show a bell-type pattern across the massif with high values on the massif rims and low values in the centre of the massif. These low XFe and δ13C values are explained by down temperature up-flow of a Fe-Mg-CO2-rich and silica-depleted fluid during stage 1, while the massif was underthrusting. These produced phlogopite, chlorite and actinolite precipitation and quartz hydrolysis, resulting in strong volume losses. In contrast, during stage 2 (uplift), substantial volume gains occurred on the massif rims due to the precipitation of quartz, epidote and muscovite from a local fluid hosted in the Helvetic cover. These two fluids advocate for the presence of an upper-crustal scaled fluid convection cell, with up-going fluids through the lower crust and likely down-going fluids in the 15 km upper crust.

Biomineralization, life-time of odontogenic cells and differential expression of the two homeobox genes MSX-1 and DLX-2 in transgenic mice.

PubMed

Lézot, F; Thomas, B; Hotton, D; Forest, N; Orestes-Cardoso, S; Robert, B; Sharpe, P; Berdal, A

2000-03-01

Msx and Dlx homeobox genes encode for transcription factors that control early morphogenesis. More specifically, Msx-1, Msx-2, and Dlx-2 homeobox genes contribute to the initial patterning of the dentition. The present study is devoted to the potential role of those homeobox genes during the late formation of mineralized tissues, using the rodent incisor as an experimental system. The continuously erupting mandibular incisor allows (1) the coinvestigation of the whole sequences of amelogenesis and dentinogenesis, aligned along the main dental axis in a single sample in situ and (2) the differential characterization of transcripts generated by epithelial and ectomesenchymal odontogenic cells. Northern blot experiments on microdissected cells showed the continuing expression of Msx-2 and Dlx-2 in the later stages of dental biomineralization, differentially in epithelial and ectomesenchymal compartments. Transgenic mice produced with LacZ reporter constructs for Dlx-2 and Msx-1 were used to detect different components of the gene expression patterns with the sensitive beta-galactosidase histoenzymology. The results show a prominent epithelial involvement of Dlx-2, with stage-specific variations in the cells involved in enamel formation. Quantitative analyses identified specific modulations of Dlx-2 expression in ameloblasts depending on the anatomical sites of the incisor, showing more specifically an inverse linear relationship between the Dlx-2 promoter activity level and enamel thickness. This investigation extends the role of homeoproteins to postmitotic stages, which would control secretory cell activity, in a site-specific manner as shown here for Dlx-2.

A physical interaction between viral replicase and capsid protein is required for genome-packaging specificity in an RNA virus.

PubMed

Seo, Jang-Kyun; Kwon, Sun-Jung; Rao, A L N

2012-06-01

Genome packaging is functionally coupled to replication in RNA viruses pathogenic to humans (Poliovirus), insects (Flock house virus [FHV]), and plants (Brome mosaic virus [BMV]). However, the underlying mechanism is not fully understood. We have observed previously that in FHV and BMV, unlike ectopically expressed capsid protein (CP), packaging specificity results from RNA encapsidation by CP that has been translated from mRNA produced from replicating genomic RNA. Consequently, we hypothesize that a physical interaction with replicase increases the CP specificity for packaging viral RNAs. We tested this hypothesis by evaluating the molecular interaction between replicase protein and CP using a FHV-Nicotiana benthamiana system. Bimolecular fluorescence complementation in conjunction with fluorescent cellular protein markers and coimmunoprecipitation assays demonstrated that FHV replicase (protein A) and CP physically interact at the mitochondrial site of replication and that this interaction requires the N-proximal region from either amino acids 1 to 31 or amino acids 32 to 50 of the CP. In contrast to the mitochondrial localization of CP derived from FHV replication, ectopic expression displayed a characteristic punctate pattern on the endoplasmic reticulum (ER). This pattern was altered to relocalize the CP throughout the cytoplasm when the C-proximal hydrophobic domain was deleted. Analysis of the packaging phenotypes of the CP mutants defective either in protein A-CP interactions or ER localization suggested that synchronization between protein A-CP interaction and its subcellular localization is imperative to confer packaging specificity.

A Physical Interaction between Viral Replicase and Capsid Protein Is Required for Genome-Packaging Specificity in an RNA Virus

PubMed Central

Seo, Jang-Kyun; Kwon, Sun-Jung

2012-01-01

Genome packaging is functionally coupled to replication in RNA viruses pathogenic to humans (Poliovirus), insects (Flock house virus [FHV]), and plants (Brome mosaic virus [BMV]). However, the underlying mechanism is not fully understood. We have observed previously that in FHV and BMV, unlike ectopically expressed capsid protein (CP), packaging specificity results from RNA encapsidation by CP that has been translated from mRNA produced from replicating genomic RNA. Consequently, we hypothesize that a physical interaction with replicase increases the CP specificity for packaging viral RNAs. We tested this hypothesis by evaluating the molecular interaction between replicase protein and CP using a FHV-Nicotiana benthamiana system. Bimolecular fluorescence complementation in conjunction with fluorescent cellular protein markers and coimmunoprecipitation assays demonstrated that FHV replicase (protein A) and CP physically interact at the mitochondrial site of replication and that this interaction requires the N-proximal region from either amino acids 1 to 31 or amino acids 32 to 50 of the CP. In contrast to the mitochondrial localization of CP derived from FHV replication, ectopic expression displayed a characteristic punctate pattern on the endoplasmic reticulum (ER). This pattern was altered to relocalize the CP throughout the cytoplasm when the C-proximal hydrophobic domain was deleted. Analysis of the packaging phenotypes of the CP mutants defective either in protein A-CP interactions or ER localization suggested that synchronization between protein A-CP interaction and its subcellular localization is imperative to confer packaging specificity. PMID:22438552

Detection of Coconut cadang-cadang viroid (CCCVd) in oil palm by reverse transcription loop-mediated isothermal amplification (RT-LAMP).

PubMed

Thanarajoo, Sathis Sri; Kong, Lih Ling; Kadir, Jugah; Lau, Wei Hongi; Vadamalai, Ganesan

2014-06-01

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) detected Coconut cadang-cadang viroid (CCCVd) within 60 min at 60 °C in total nucleic acid extracted from oil palm leaves infected with CCCVd. Positive reactions showed colour change from orange to green in the reaction mix after the addition of fluorescent reagent, and a laddering pattern band on 2% agarose gel electrophoresis. Conventional RT-PCR with LAMP primers produced amplicons with a sequence identical to the 297-nt CCCVd oil palm variant with the primers being specific for CCCVd and not for other viroids such as PSTVd and CEVd. RT-LAMP was found to be rapid and specific for detecting oil palm CCCVd. Copyright © 2014 Elsevier B.V. All rights reserved.

Fabrication of ordered arrays of micro- and nanoscale features with control over their shape and size via templated solid-state dewetting.

PubMed

Ye, Jongpil

2015-05-08

Templated solid-state dewetting of single-crystal films has been shown to be used to produce regular patterns of various shapes. However, the materials for which this patterning method is applicable, and the size range of the patterns produced are still limited. Here, it is shown that ordered arrays of micro- and nanoscale features can be produced with control over their shape and size via solid-state dewetting of patches patterned from single-crystal palladium and nickel films of different thicknesses and orientations. The shape and size characteristics of the patterns are found to be widely controllable with varying the shape, width, thickness, and orientation of the initial patches. The morphological evolution of the patches is also dependent on the film material, with different dewetting behaviors observed in palladium and nickel films. The mechanisms underlying the pattern formation are explained in terms of the influence on Rayleigh-like instability of the patch geometry and the surface energy anisotropy of the film material. This mechanistic understanding of pattern formation can be used to design patches for the precise fabrication of micro- and nanoscale structures with the desired shapes and feature sizes.

Fabrication of ordered arrays of micro- and nanoscale features with control over their shape and size via templated solid-state dewetting

PubMed Central

Ye, Jongpil

2015-01-01

Templated solid-state dewetting of single-crystal films has been shown to be used to produce regular patterns of various shapes. However, the materials for which this patterning method is applicable, and the size range of the patterns produced are still limited. Here, it is shown that ordered arrays of micro- and nanoscale features can be produced with control over their shape and size via solid-state dewetting of patches patterned from single-crystal palladium and nickel films of different thicknesses and orientations. The shape and size characteristics of the patterns are found to be widely controllable with varying the shape, width, thickness, and orientation of the initial patches. The morphological evolution of the patches is also dependent on the film material, with different dewetting behaviors observed in palladium and nickel films. The mechanisms underlying the pattern formation are explained in terms of the influence on Rayleigh-like instability of the patch geometry and the surface energy anisotropy of the film material. This mechanistic understanding of pattern formation can be used to design patches for the precise fabrication of micro- and nanoscale structures with the desired shapes and feature sizes. PMID:25951816

Sequence-specific "gene signatures" can be obtained by PCR with single specific primers at low stringency.

PubMed Central

Pena, S D; Barreto, G; Vago, A R; De Marco, L; Reinach, F C; Dias Neto, E; Simpson, A J

1994-01-01

Low-stringency single specific primer PCR (LSSP-PCR) is an extremely simple PCR-based technique that detects single or multiple mutations in gene-sized DNA fragments. A purified DNA fragment is subjected to PCR using high concentrations of a single specific oligonucleotide primer, large amounts of Taq polymerase, and a very low annealing temperature. Under these conditions the primer hybridizes specifically to its complementary region and nonspecifically to multiple sites within the fragment, in a sequence-dependent manner, producing a heterogeneous set of reaction products resolvable by electrophoresis. The complex banding pattern obtained is significantly altered by even a single-base change and thus constitutes a unique "gene signature." Therefore LSSP-PCR will have almost unlimited application in all fields of genetics and molecular medicine where rapid and sensitive detection of mutations and sequence variations is important. The usefulness of LSSP-PCR is illustrated by applications in the study of mutants of smooth muscle myosin light chain, analysis of a family with X-linked nephrogenic diabetes insipidus, and identity testing using human mitochondrial DNA. Images PMID:8127912

The Arabidopsis translatome cell-specific mRNA atlas: Mining suberin and cutin lipid monomer biosynthesis genes as an example for data application.

PubMed

Mustroph, Angelika; Bailey-Serres, Julia

2010-03-01

Plants consist of distinct cell types distinguished by position, morphological features and metabolic activities. We recently developed a method to extract cell-type specific mRNA populations by immunopurification of ribosome-associated mRNAs. Microarray profiles of 21 cell-specific mRNA populations from seedling roots and shoots comprise the Arabidopsis Translatome dataset. This gene expression atlas provides a new tool for the study of cell-specific processes. Here we provide an example of how genes involved in a pathway limited to one or few cell-types can be further characterized and new candidate genes can be predicted. Cells of the root endodermis produce suberin as an inner barrier between the cortex and stele, whereas the shoot epidermal cells form cutin as a barrier to the external environment. Both polymers consist of fatty acid derivates, and share biosynthetic origins. We use the Arabidopsis Translatome dataset to demonstrate the significant cell-specific expression patterns of genes involved in those biosynthetic processes and suggest new candidate genes in the biosynthesis of suberin and cutin.

Beef cow-calf production.

PubMed

Feuz, Dillon M; Umberger, Wendy J

2003-07-01

Cow-calf production occurs in all 50 states over varied resource bases and under vastly different environmental conditions. Multiple breeds exist and management styles and objectives are as numerous as the number of cow-calf producers. There is not one area of the country, one breed of cattle, or one management style that is most profitable for producing cows and calves. There are, however, some common strategies that can be employed by cow-calf producers to enhance profitability. Costs need to be controlled without jeopardizing cow herd productivity or net returns. It appears that the cost associated with purchased and harvested feeds varies considerably across operations. Understanding cyclic and seasonal price patterns, weight-price slides, cattle shrink, and other marketing costs can help producers enhance their profit by marketing (and not by just selling) their cattle. Producers with superior cattle genetics can become part of a specific alliance or, at a minimum, document the performance of their cattle so that they can get paid for the superior genetics. The beef industry is changing and will likely continue to change. Cow-calf producers will need to examine their own management practices to determine whether they are optimal for the current industry. Those producers who are most adept at matching their management abilities to their cattle type, their resource base, and the appropriate market outlet will be the most successful in the future.

Fluoro-Jade and TUNEL staining as useful tools to identify ischemic brain damage following moderate extradural compression of sensorimotor cortex.

PubMed

Kundrotiene, Jurgita; Wägner, Anna; Liljequist, Sture

2004-01-01

Cerebral ischemia was produced by moderate compression for 30 min of a specific brain area in the sensorimotor cortex of Sprague-Dawley rats. On day 1, that is 24 h after the transient sensorimotor compression, ischemia-exposed animals displayed a marked focal neurological deficit documented as impaired beam walking performance. This functional disturbance was mainly due to contralateral fore- and hind-limb paresis. As assessed by daily beam walking tests it was shown that there was a spontaneous recovery of motor functions over a period of five to seven days after the ischemic event. Using histopathological analysis (Nissl staining) we have previously reported that the present experimental paradigm does not produce pannecrosis (tissue cavitation) despite the highly reproducible focal neurological deficit. We now show how staining with fluorescent markers for neuronal death, that is Fluoro-Jade and TUNEL, respectively, identifies regional patterns of selective neuronal death. These observations add further support to the working hypothesis that the brain damage caused by cortical compression-induced ischemia consists of scattered, degenerating neurons in specific brain regions. Postsurgical administration of the AMPA receptor specific antagonist, LY326325 (30 mg/kg; i.p., 70 min after compression), not only improved beam walking performance on day 1 to 3, respectively but also significantly reduced the number of Fluoro-Jade stained neurons on day 5. These results suggest that enhanced AMPA/glutamate receptor activity is at least partially responsible for the ischemia-produced brain damage detected by the fluorescent marker Fluoro-Jade.

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.

The bioelectric code: An ancient computational medium for dynamic control of growth and form.

PubMed

Levin, Michael; Martyniuk, Christopher J

2018-02-01

What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity. All cells, not only nerves and muscles, produce and sense electrical signals; in vivo, these processes form bioelectric circuits that harness individual cell behaviors toward specific anatomical endpoints. We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering. Copyright © 2017 Elsevier B.V. All rights reserved.

Manipulation of Nano-/Micro Particles Using Light-Actuated Marangoni Tweezers

NASA Astrophysics Data System (ADS)

Lu, Cunjing; Varanakkottu, Subramanyan; Hardt, Steffen; Nano-; Microfluidics, Center of Smart Interfaces, TU Darmstadt Team

2015-11-01

The ability to manipulate and produce patterns of nano-/micro objects has been of great interest from both a fundamental and an application point of view. Here we demonstrate particle patterning using an optical landscape and optical nanoparticle manipulation based on light-actuated Marangoni tweezers. A liquid film with a photosurfactant which exists in two isomeric states (cis and trans) is employed for that purpose. Under multiple laser spots created by diffractive optical elements from a He-Cd laser, cis-rich regions with higher surface tension than unexposed trans-rich regions are created, resulting in converging Marangoni flows directing particles attached to the liquid surface toward the irradiated area. 10 μm polystyrene particles and 600 nm λ-DNA molecules distributed over the liquid surface move to the nearest laser spot and can be arranged in specific patterns. Furthermore, 100 nm polystyrene particles and 20 nm quantum dots can also be trapped, and the 100 nm particles can be driven along quite complex trajectories. Compared to conventional optical tweezers, the corresponding power requirements are much lower.

Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study.

PubMed

Srinivas, Goundla; Swope, William C; Pitera, Jed W

2007-12-13

The lamellar and cylindrical phases of block copolymers have a number of technological applications, particularly when they occur in supported thin films. One such application is block copolymer lithography, the use of these materials to subdivide or enhance submicrometer patterns defined by optical or electron beam methods. A key parameter of all lithographic methods is the line edge roughness (LER), because the electronic or optical activities of interest are sensitive to small pattern variations. While mean-field models provide a partial picture of the LER and interfacial width expected for the block interface in a diblock copolymer, these models lack chemical detail. To complement mean-field approaches, we have carried out coarse-grain molecular dynamics simulations on model poly(ethyleneoxide)-poly(ethylethylene) (PEO-PEE) lamellae, exploring the influence of chain length and hypothetical chemical modifications on the observed line edge roughness. As expected, our simulations show that increasing chi (the Flory-Huggins parameter) is the most direct route to decreased roughness, although the addition of strong specific interactions at the block interface can also produce smoother patterns.

Reaction-diffusion systems and external morphogen gradients: the two-dimensional case, with an application to skeletal pattern formation.

PubMed

Glimm, Tilmann; Zhang, Jianying; Shen, Yun-Qiu; Newman, Stuart A

2012-03-01

We investigate a reaction-diffusion system consisting of an activator and an inhibitor in a two-dimensional domain. There is a morphogen gradient in the domain. The production of the activator depends on the concentration of the morphogen. Mathematically, this leads to reaction-diffusion equations with explicitly space-dependent terms. It is well known that in the absence of an external morphogen, the system can produce either spots or stripes via the Turing bifurcation. We derive first-order expansions for the possible patterns in the presence of an external morphogen and show how both stripes and spots are affected. This work generalizes previous one-dimensional results to two dimensions. Specifically, we consider the quasi-one-dimensional case of a thin rectangular domain and the case of a square domain. We apply the results to a model of skeletal pattern formation in vertebrate limbs. In the framework of reaction-diffusion models, our results suggest a simple explanation for some recent experimental findings in the mouse limb which are much harder to explain in positional-information-type models.

Foundations for Streaming Model Transformations by Complex Event Processing.

PubMed

Dávid, István; Ráth, István; Varró, Dániel

2018-01-01

Streaming model transformations represent a novel class of transformations to manipulate models whose elements are continuously produced or modified in high volume and with rapid rate of change. Executing streaming transformations requires efficient techniques to recognize activated transformation rules over a live model and a potentially infinite stream of events. In this paper, we propose foundations of streaming model transformations by innovatively integrating incremental model query, complex event processing (CEP) and reactive (event-driven) transformation techniques. Complex event processing allows to identify relevant patterns and sequences of events over an event stream. Our approach enables event streams to include model change events which are automatically and continuously populated by incremental model queries. Furthermore, a reactive rule engine carries out transformations on identified complex event patterns. We provide an integrated domain-specific language with precise semantics for capturing complex event patterns and streaming transformations together with an execution engine, all of which is now part of the Viatra reactive transformation framework. We demonstrate the feasibility of our approach with two case studies: one in an advanced model engineering workflow; and one in the context of on-the-fly gesture recognition.

The organization of the lateral geniculate nucleus and of the geniculocortical pathway that develops without retinal afferents.

PubMed

Guillery, R W; Ombrellaro, M; LaMantia, A L

1985-06-01

The fine structure and cortical connections of the dorsal lateral geniculate nucleus have been studied in postnatal (3.5-14-month-old) ferrets in which all retinal afferents had been removed prenatally at the time these fibers are first starting to invade the nucleus. The synaptic profiles in the mature nucleus show the cytological characteristics and arrangements that would remain if the retinal afferents were removed, with no significant compensatory ingrowth of foreign specific afferents. The nucleus is reduced in overall volume, but the geniculocortical and corticogeniculate interconnections show an essentially normal topography. Although in these experiments the geniculocortical projections can establish a normal topographic pattern in the absence of retinal afferents an accompanying paper shows that this topographic pattern can also be modified in the presence of abnormal retinogeniculate inputs. We conclude that two separate mechanisms contribute to the formation of retinal maps within the geniculocortical pathways and that different interactions between these two mechanisms produce the different patterns of abnormal geniculocortical pathways that have been described in pigment-deficient cats, mink and ferrets.

Evaluation of Sex-Specific Movement Patterns in Judo Using Probabilistic Neural Networks.

PubMed

Miarka, Bianca; Sterkowicz-Przybycien, Katarzyna; Fukuda, David H

2017-10-01

The purpose of the present study was to create a probabilistic neural network to clarify the understanding of movement patterns in international judo competitions by gender. Analysis of 773 male and 638 female bouts was utilized to identify movements during the approach, gripping, attack (including biomechanical designations), groundwork, defense, and pause phases. Probabilistic neural network and chi-square (χ 2 ) tests modeled and compared frequencies (p ≤ .05). Women (mean [interquartile range]: 9.9 [4; 14]) attacked more than men (7.0 [3; 10]) while attempting a greater number of arm/leg lever (women: 2.7 [1; 6]; men: 4.0 [0; 4]) and trunk/leg lever (women: 0.8 [0; 1]; men: 2.4 [0; 4]) techniques but fewer maximal length-moment arm techniques (women: 0.7 [0; 1]; men: 1.0 [0; 2]). Male athletes displayed one-handed gripping of the back and sleeve, whereas female athletes executed a greater number of groundwork techniques. An optimized probabilistic neural network model, using patterns from the gripping, attack, groundwork, and pause phases, produced an overall prediction accuracy of 76% for discrimination between men and women.

Developmental patterns of jicama (Pachyrhizus erosus (L.) Urban) plant and the chemical constituents of roots grown in Sonora, Mexico.

PubMed

Fernandez, M V; Warid, W A; Loaiza, J M; Montiel, A

1997-01-01

The developmental pattern of jicama (Pachyrhizus erosus (L.) Urban) was studied by sampling plants aged 20 to 36 weeks at weekly intervals. There was an increase in all characteristics of foliage: fresh and dry weight, number of leaves per plant, main stem length, number of leaves, nodes and internodes of the main stem; and in all root characteristics: fresh and dry weight, diameter and length. The chemical analysis was determined for roots at different plant ages. The range values for dry matter were 16.19-22.28%, protein 1.11-1.62%, fat 0.553-0.867%, crude fiber 0.3048-0.3943%, and ash 0.669-1.089%. The chemical constituents fluctuated with age but without specific trends. These values are considered the first record of roots produced by plants grown in Mexico.

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

Multiplex analysis of DNA

DOEpatents

Church, George M.; Kieffer-Higgins, Stephen

1992-01-01

This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

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.

Ribosomal Alterations Controlling Alkaline Phosphatase Isozymes in Escherichia coli

PubMed Central

Piggot, P. J.; Sklar, M. D.; Gorini, L.

1972-01-01

Different patterns of isozymes were obtained by starch-gel electrophoresis of alkaline phosphatase from Escherichia coli strains differing only by strA or ram mutations, or both, in the 30S ribosomal subunit. The isozyme spread was reduced in strA and increased in ram strains; this strictly parallels the restriction and enhancement of translational ambiguity produced by these mutations. Streptomycin present during growth had an effect similar to ram on both isozymes and ambiguity. The three isozymes analyzed have different N-terminal residues: aspartic acid, valine, and threonine. Different patterns of isozymes were also obtained in a wild-type strain through the specific action of exogenous arginine. A link between the mechanism of the effect of arginine and that of the ribosome is not obvious. The possibility is discussed that in both cases, although by different mechanisms, N-terminals are formed with different sensitivity to limited degradative attack. Images PMID:4552993

Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models

PubMed Central

Do, Catherine; Xing, Zhuo; Yu, Y Eugene; Tycko, Benjamin

2017-01-01

An important line of postgenomic research seeks to understand how genetic factors can influence epigenetic patterning. Here we review epigenetic effects of chromosomal aneuploidies, focusing on findings in Down syndrome (DS, trisomy 21). Recent work in human DS and mouse models has shown that the extra chromosome 21 acts in trans to produce epigenetic changes, including differential CpG methylation (DS-DM), in specific sets of downstream target genes, mostly on other chromosomes. Mechanistic hypotheses emerging from these data include roles of chromosome 21-linked methylation pathway genes (DNMT3L and others) and transcription factor genes (RUNX1, OLIG2, GABPA, ERG and ETS2) in shaping the patterns of DS-DM. The findings may have broader implications for trans-acting epigenetic effects of chromosomal and subchromosomal aneuploidies in other human developmental and neuropsychiatric disorders, and in cancers. PMID:27911079

Characterizing Tityus discrepans scorpion venom from a fractal perspective: Venom complexity, effects of captivity, sexual dimorphism, differences among species.

PubMed

D'Suze, Gina; Sandoval, Moisés; Sevcik, Carlos

2015-12-15

A characteristic of venom elution patterns, shared with many other complex systems, is that many their features cannot be properly described with statistical or euclidean concepts. The understanding of such systems became possible with Mandelbrot's fractal analysis. Venom elution patterns were produced using the reversed phase high performance liquid chromatography (HPLC) with 1 mg of venom. One reason for the lack of quantitative analyses of the sources of venom variability is parametrizing the venom chromatograms' complexity. We quantize this complexity by means of an algorithm which estimates the contortedness (Q) of a waveform. Fractal analysis was used to compare venoms and to measure inter- and intra-specific venom variability. We studied variations in venom complexity derived from gender, seasonal and environmental factors, duration of captivity in the laboratory, technique used to milk venom. Copyright © 2015 Elsevier Ltd. All rights reserved.

Method for Accurately Calibrating a Spectrometer Using Broadband Light

NASA Technical Reports Server (NTRS)

Simmons, Stephen; Youngquist, Robert

2011-01-01

A novel method has been developed for performing very fine calibration of a spectrometer. This process is particularly useful for modern miniature charge-coupled device (CCD) spectrometers where a typical factory wavelength calibration has been performed and a finer, more accurate calibration is desired. Typically, the factory calibration is done with a spectral line source that generates light at known wavelengths, allowing specific pixels in the CCD array to be assigned wavelength values. This method is good to about 1 nm across the spectrometer s wavelength range. This new method appears to be accurate to about 0.1 nm, a factor of ten improvement. White light is passed through an unbalanced Michelson interferometer, producing an optical signal with significant spectral variation. A simple theory can be developed to describe this spectral pattern, so by comparing the actual spectrometer output against this predicted pattern, errors in the wavelength assignment made by the spectrometer can be determined.

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.

Spine Patterning Is Guided by Segmentation of the Notochord Sheath.

PubMed

Wopat, Susan; Bagwell, Jennifer; Sumigray, Kaelyn D; Dickson, Amy L; Huitema, Leonie F A; Poss, Kenneth D; Schulte-Merker, Stefan; Bagnat, Michel

2018-02-20

The spine is a segmented axial structure made of alternating vertebral bodies (centra) and intervertebral discs (IVDs) assembled around the notochord. Here, we show that, prior to centra formation, the outer epithelial cell layer of the zebrafish notochord, the sheath, segments into alternating domains corresponding to the prospective centra and IVD areas. This process occurs sequentially in an anteroposterior direction via the activation of Notch signaling in alternating segments of the sheath, which transition from cartilaginous to mineralizing domains. Subsequently, osteoblasts are recruited to the mineralized domains of the notochord sheath to form mature centra. Tissue-specific manipulation of Notch signaling in sheath cells produces notochord segmentation defects that are mirrored in the spine. Together, our findings demonstrate that notochord sheath segmentation provides a template for vertebral patterning in the zebrafish spine. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Novel PCR-Restriction Fragment Length Polymorphism Method for Determining Serotypes or Serogroups of Streptococcus pneumoniae Isolates

PubMed Central

Batt, Sarah L.; Charalambous, Bambos M.; McHugh, Timothy D.; Martin, Siobhan; Gillespie, Stephen H.

2005-01-01

Serotyping Streptococcus pneumoniae is a technique generally confined to reference laboratories, as purchasing pneumococcal antisera is a huge investment. Many attempts have been made to modify serological agglutination techniques to make them more accessible, and more recently developments in serotyping have focused on molecular techniques. This paper describes a PCR assay which amplifies the entire capsulation locus between dexB and aliA. Amplicons are digested to produce serotype-specific patterns. We have shown, using 81 epidemiologically unrelated strains representing 46 different serotypes, that the patterns correlate with a 90 to 100% similarity range for the same serotype or serogroup. Prospective testing of 73 isolates of unknown serotype confirmed reliable serotype attribution, and serotype profiles are reproducible on repeated testing. Once our database contains all 90 serotypes, this technique should be fully portable, cost-effective, and useful in any laboratory with sufficient molecular experience. PMID:15956380

Karyotype Analysis of Four Vicia Species using In Situ Hybridization with Repetitive Sequences

PubMed Central

NAVRÁTILOVÁ, ALICE; NEUMANN, PAVEL; MACAS, JIŘÍ

2003-01-01

Mitotic chromosomes of four Vicia species (V. sativa, V. grandiflora, V. pannonica and V. narbonensis) were subjected to in situ hybridization with probes derived from conserved plant repetitive DNA sequences (18S–25S and 5S rDNA, telomeres) and genus‐specific satellite repeats (VicTR‐A and VicTR‐B). Numbers and positions of hybridization signals provided cytogenetic landmarks suitable for unambiguous identification of all chromosomes, and establishment of the karyotypes. The VicTR‐A and ‐B sequences, in particular, produced highly informative banding patterns that alone were sufficient for discrimination of all chromosomes. However, these patterns were not conserved among species and thus could not be employed for identification of homologous chromosomes. This fact, together with observed variations in positions and numbers of rDNA loci, suggests considerable divergence between karyotypes of the species studied. PMID:12770847

Identifying Regulators of the Immune Response to Dying Cells | Center for Cancer Research

Cancer.gov

Cytotoxic T cells are responsible for carrying out antigen-mediated immune responses against virally-infected and malignant cells. In both cases, cytotoxic T cells are stimulated by interacting with antigen presenting cells, such as dendritic cells (DCs). Infected cells produce virus-specific antigens and pathogen associated molecular patterns, which are recognized by DCs and lead to robust T cell activation. Dead or dying uninfected cells, on the other hand, release damage associated molecular patterns, but their release does not always appear to be sufficient to induce cytotoxic T cell activity. Tim Greten, M.D., of CCR’s Medical Oncology Branch, and a group of international collaborators set out to understand how immune responses against dying cancer cells are regulated. These processes are likely to be important for improving the efficacy of cancer treatment vaccines, which induce an immune reaction against a patient’s cancer cells.

2D spatially controlled polymer micro patterning for cellular behavior studies

NASA Astrophysics Data System (ADS)

Dinca, V.; Palla-Papavlu, A.; Paraico, I.; Lippert, T.; Wokaun, A.; Dinescu, M.

2011-04-01

A simple and effective method to functionalize glass surfaces that enable polymer micropatterning and subsequent spatially controlled adhesion of cells is reported in this paper. The method involves the application of laser induced forward transfer (LIFT) to achieve polymer patterning in a single step onto cell repellent substrates (i.e. polyethyleneglycol (PEG)). This approach was used to produce micron-size polyethyleneimine (PEI)-patterns alternating with cell-repellent areas. The focus of this work is the ability of SH-SY5Y human neuroblastoma cells to orient, migrate, and produce organized cellular arrangements on laser generated PEI patterns.

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.

Sterols in spermatogenesis and sperm maturation

PubMed Central

Keber, Rok; Rozman, Damjana; Horvat, Simon

2013-01-01

Mammalian spermatogenesis is a complex developmental program in which a diploid progenitor germ cell transforms into highly specialized spermatozoa. One intriguing aspect of sperm production is the dynamic change in membrane lipid composition that occurs throughout spermatogenesis. Cholesterol content, as well as its intermediates, differs vastly between the male reproductive system and nongonadal tissues. Accumulation of cholesterol precursors such as testis meiosis-activating sterol and desmosterol is observed in testes and spermatozoa from several mammalian species. Moreover, cholesterogenic genes, especially meiosis-activating sterol-producing enzyme cytochrome P450 lanosterol 14α-demethylase, display stage-specific expression patterns during spermatogenesis. Discrepancies in gene expression patterns suggest a complex temporal and cell-type specific regulation of sterol compounds during spermatogenesis, which also involves dynamic interactions between germ and Sertoli cells. The functional importance of sterol compounds in sperm production is further supported by the modulation of sterol composition in spermatozoal membranes during epididymal transit and in the female reproductive tract, which is a prerequisite for successful fertilization. However, the exact role of sterols in male reproduction is unknown. This review discusses sterol dynamics in sperm maturation and describes recent methodological advances that will help to illuminate the complexity of sperm formation and function. PMID:23093550

Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.

PubMed

Rua, Cintia P J; de Oliveira, Louisi S; Froes, Adriana; Tschoeke, Diogo A; Soares, Ana Carolina; Leomil, Luciana; Gregoracci, Gustavo B; Coutinho, Ricardo; Hajdu, Eduardo; Thompson, Cristiane C; Berlinck, Roberto G S; Thompson, Fabiano L

2018-03-15

Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.

Biological cell classification by multiangle light scattering

DOEpatents

Salzman, G.C.; Crowell, J.M.; Mullaney, P.F.

1975-06-03

The specification is directed to an apparatus and method for detecting light scattering from a biological cell. Light, preferably from a coherent source of radiation, intercepts an individual biological cell in a stream of cells passing through the beam. Light scattered from the cell is detected at a selected number of angles between 0 and 90/sup 0/ to the longitudinal axis of the beam with a circular array of light responsive elements which produce signals representative of the intensity of light incident thereon. Signals from the elements are processed to determine the light-scattering pattern of the cell and therefrom its identity.

Method for detecting pathogens attached to specific antibodies

DOEpatents

Miles, Robin R.; Venkateswaran, Kodumudi S.; Fuller, Christopher K.

2005-01-25

The use of impedance measurements to detect the presence of pathogens attached to antibody-coated beads. In a fluidic device antibodies are immobilized on a surface of a patterned interdigitated electrode. Pathogens in a sample fluid streaming past the electrode attach to the immobilized antibodies, which produces a change in impedance between two adjacent electrodes, which impedance change is measured and used to detect the presence of a pathogen. To amplify the signal, beads coated with antibodies are introduced and the beads would stick to the pathogen causing a greater change in impedance between the two adjacent electrodes.

Golgi Compartmentation and Identity

PubMed Central

Papanikou, Effrosyni; Glick, Benjamin S.

2014-01-01

Recent work supports the idea that cisternae of the Golgi apparatus can be assigned to three classes, which correspond to discrete stages of cisternal maturation. Each stage has a unique pattern of membrane traffic. At the first stage, cisternae form in association with the ER at multifunctional membrane assembly stations. At the second stage, cisternae synthesize carbohydrates while exchanging material via COPI vesicles. At the third stage, cisternae of the trans-Golgi network segregate into domains and produce transport carriers with the aid of specific lipids and the actin cytoskeleton. These processes are coordinated by cascades of Rab and Arf/Arl GTPases. PMID:24840895

Chemical fingerprinting and source tracing of obsidian: the central Mediterranean trade in black gold.

PubMed

Tykot, Robert H

2002-08-01

Chemical fingerprinting using major or trace element composition is used to characterize the Mediterranean island sources of obsidian and can even differentiate as many as nine flows in the Monte Arci region of Sardinia. Analysis of significant numbers of obsidian artifacts from Neolithic sites in the central Mediterranean reveals specific patterns of source exploitation and suggests particular trade mechanisms and routes. The use of techniques such as X-ray fluorescence, the electron microprobe, neutron activation analysis, and laser ablation ICP mass spectrometry are emphasized in order to produce quantitative results while minimizing damage to valuable artifacts.

Ultrafast electron diffraction optimized for studying structural dynamics in thin films and monolayers

PubMed Central

Badali, D. S.; Gengler, R. Y. N.; Miller, R. J. D.

2016-01-01

A compact electron source specifically designed for time-resolved diffraction studies of free-standing thin films and monolayers is presented here. The sensitivity to thin samples is achieved by extending the established technique of ultrafast electron diffraction to the “medium” energy regime (1–10 kV). An extremely compact design, in combination with low bunch charges, allows for high quality diffraction in a lensless geometry. The measured and simulated characteristics of the experimental system reveal sub-picosecond temporal resolution, while demonstrating the ability to produce high quality diffraction patterns from atomically thin samples. PMID:27226978

Heterogeneous genetic diversity pattern in Plasmodium vivax genes encoding merozoite surface proteins (MSP) -7E, -7F and -7L.

PubMed

Garzón-Ospina, Diego; Forero-Rodríguez, Johanna; Patarroyo, Manuel A

2014-12-13

The msp-7 gene has become differentially expanded in the Plasmodium genus; Plasmodium vivax has the highest copy number of this gene, several of which encode antigenic proteins in merozoites. DNA sequences from thirty-six Colombian clinical isolates from P. vivax (pv) msp-7E, -7F and -7L genes were analysed for characterizing and studying the genetic diversity of these pvmsp-7 members which are expressed during the intra-erythrocyte stage; natural selection signals producing the variation pattern so observed were evaluated. The pvmsp-7E gene was highly polymorphic compared to pvmsp-7F and pvmsp-7L which were seen to have limited genetic diversity; pvmsp-7E polymorphism was seen to have been maintained by different types of positive selection. Even though these copies seemed to be species-specific duplications, a search in the Plasmodium cynomolgi genome (P. vivax sister taxon) showed that both species shared the whole msp-7 repertoire. This led to exploring the long-term effect of natural selection by comparing the orthologous sequences which led to finding signatures for lineage-specific positive selection. The results confirmed that the P. vivax msp-7 family has a heterogeneous genetic diversity pattern; some members are highly conserved whilst others are highly diverse. The results suggested that the 3'-end of these genes encode MSP-7 proteins' functional region whilst the central region of pvmsp-7E has evolved rapidly. The lineage-specific positive selection signals found suggested that mutations occurring in msp-7s genes during host switch may have succeeded in adapting the ancestral P. vivax parasite population to humans.

DNA methyl transferases are differentially expressed in the human anterior eye segment.

PubMed

Bonnin, Nicolas; Belville, Corinne; Chiambaretta, Frédéric; Sapin, Vincent; Blanchon, Loïc

2014-08-01

DNA methylation is an epigenetic mark involved in the control of genes expression. Abnormal epigenetic events have been reported in human pathologies but weakly documented in eye diseases. The purpose of this study was to establish DNMT mRNA and protein expression levels in the anterior eye segment tissues and their related (primary or immortalized) cell cultures as a first step towards future in vivo and in vitro methylomic studies. Total mRNA was extracted from human cornea, conjunctiva, anterior lens capsule, trabeculum and related cell cultures (cornea epithelial, trabecular meshwork, keratocytes for primary cells; and HCE, Chang, B-3 for immortalized cells). cDNA was quantified by real-time PCR using specific primers for DNMT1, 2, 3A, 3B and 3L. Immunolocalization assays were carried out on human cornea using specific primary antibodies for DNMT1, 2 and 3A, 3B and 3L. All DNMT transcripts were detected in human cornea, conjunctiva, anterior lens capsule, trabeculum and related cells but showed statistically different expression patterns between tissues and cells. DNMT2 protein presented a specific and singular expression pattern in corneal endothelium. This study produced the first inventory of the expression patterns of DNMTs in human adult anterior eye segment. Our research highlights that DNA methylation cannot be ruled out as a way to bring new insights into well-known ocular diseases. In addition, future DNA methylation studies using various cells as experimental models need to be conducted with attention to approach the results analysis from a global tissue perspective. © 2014 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Occurrence Frequencies of Acoustic Patterns of Vocal Fry in American English Speakers.

PubMed

Abdelli-Beruh, Nassima B; Drugman, Thomas; Red Owl, R H

2016-11-01

The goal of this study was to analyze the occurrence frequencies of three individual acoustic patterns (A, B, C) and of vocal fry overall (A + B + C) as a function of gender, word position in the sentence (Not Last Word vs. Last Word), and sentence length (number of words in a sentence). This is an experimental design. Twenty-five male and 29 female American English (AE) speakers read the Grandfather Passage. The recordings were processed by a Matlab toolbox designed for the analysis and detection of creaky segments, automatically identified using the Kane-Drugman algorithm. The experiment produced subsamples of outcomes, three that reflect a single, discrete acoustic pattern (A, B, or C) and the fourth that reflects the occurrence frequency counts of Vocal Fry Overall without regard to any specific pattern. Zero-truncated Poisson regression analyses were conducted with Gender and Word Position as predictors and Sentence Length as a covariate. The results of the present study showed that the occurrence frequencies of the three acoustic patterns and vocal fry overall (A + B + C) are greatest at the end of sentences but are unaffected by sentence length. The findings also reveal that AE female speakers exhibit Pattern C significantly more frequently than Pattern B, and the converse holds for AE male speakers. Future studies are needed to confirm such outcomes, assess the perceptual salience of these acoustic patterns, and determine the physiological correlates of these acoustic patterns. The findings have implications for the design of new excitation models of vocal fry. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

EXO70A1-mediated vesicle trafficking is critical for tracheary element development in Arabidopsis.

PubMed

Li, Shipeng; Chen, Min; Yu, Dali; Ren, Shichao; Sun, Shufeng; Liu, Linde; Ketelaar, Tijs; Emons, Anne-Mie C; Liu, Chun-Ming

2013-05-01

Exocysts are highly conserved octameric complexes that play an essential role in the tethering of Golgi-derived vesicles to target membranes in eukaryotic organisms. Genes encoding the EXO70 subunit are highly duplicated in plants. Based on expression analyses, we proposed previously that individual EXO70 members may provide the exocyst with functional specificity to regulate cell type- or cargo-specific exocytosis, although direct evidence is not available. Here, we show that, as a gene expressed primarily during tracheary element (TE) development, EXO70A1 regulates vesicle trafficking in TE differentiation in Arabidopsis thaliana. Mutations of EXO70A1 led to aberrant xylem development, producing dwarfed and nearly sterile plants with very low fertility, reduced cell expansion, and decreased water potential and hydraulic transport. Grafting of a mutant shoot onto wild-type rootstock rescued most of these aboveground phenotypes, while grafting of a wild-type shoot to the mutant rootstock did not rescue the short root hair phenotype, consistent with the role of TEs in hydraulic transport from roots to shoots. Histological analyses revealed an altered pattern of secondary cell wall thickening and accumulation of large membrane-bound compartments specifically in developing TEs of the mutant. We thus propose that EXO70A1 functions in vesicle trafficking in TEs to regulate patterned secondary cell wall thickening.

Genes involved in convergent evolution of eusociality in bees

PubMed Central

Woodard, S. Hollis; Fischman, Brielle J.; Venkat, Aarti; Hudson, Matt E.; Varala, Kranthi; Cameron, Sydney A.; Clark, Andrew G.; Robinson, Gene E.

2011-01-01

Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living in small colonies with overt conflict over reproduction to species in which colonies contain hundreds of thousands of highly specialized sterile workers produced by one or a few queens. Although the evolution of eusociality has been intensively studied, the genetic changes involved in the evolution of eusociality are relatively unknown. We examined patterns of molecular evolution across three independent origins of eusociality by sequencing transcriptomes of nine socially diverse bee species and combining these data with genome sequence from the honey bee Apis mellifera to generate orthologous sequence alignments for 3,647 genes. We found a shared set of 212 genes with a molecular signature of accelerated evolution across all eusocial lineages studied, as well as unique sets of 173 and 218 genes with a signature of accelerated evolution specific to either highly or primitively eusocial lineages, respectively. These results demonstrate that convergent evolution can involve a mosaic pattern of molecular changes in both shared and lineage-specific sets of genes. Genes involved in signal transduction, gland development, and carbohydrate metabolism are among the most prominent rapidly evolving genes in eusocial lineages. These findings provide a starting point for linking specific genetic changes to the evolution of eusociality. PMID:21482769

Patterned titania nanostructures produced by electrochemical anodization of titanium sheet

NASA Astrophysics Data System (ADS)

Dong, Junzhe; Ariyanti, Dessy; Gao, Wei; Niu, Zhenjiang; Weil, Emeline

2017-07-01

A two-step anodization method has been used to produce patterned arrays of TiO2 on the surface of Ti sheet. Hexagonal ripples were created on Ti substrate after removing the TiO2 layer produced by first-step anodization. The shallow concaves were served as an ideal position for the subsequent step anodization due to their low electrical resistance, resulting in novel hierarchical nanostructures with small pits inside the original ripples. The mechanism of morphology evolution during patterned anodization was studied through changing the anodizing voltages and duration time. This work provides a new idea for controlling nanostructures and thus tailoring the photocatalytic property and wettability of anodic TiO2.

Modeling the role of back-arc spreading in controlling 3-D circulation and temperature patterns in subduction zones

NASA Astrophysics Data System (ADS)

Kincaid, C.

2005-12-01

Subduction of oceanic lithosphere provides a dominant driving force for mantle dynamics and plate tectonics, and strongly modulates the thermal evolution of the mantle. Magma generation in arc environments is related to slab temperatures, slab dehydration/wedge hydration processes and circulation patterns in the mantle wedge. A series of laboratory experiments is used to model three-dimensional aspects of flow in subduction zones, and the consequent temperature variations in the slab and overlying mantle wedge. The experiments utilize a tank of glucose syrup to simulate the mantle and a Phenolic plate to represent subducting oceanic lithosphere. Different modes of plate sinking are produced using hydraulic pistons. The effects of longitudinal, rollback and slab-steepening components of slab motions are considered, along with different thicknesses of the over-riding lithosphere. Models look specifically at how distinct modes of back-arc spreading alter subduction zone temperatures and flow in the mantle wedge. Results show remarkably different temperature and circulation patterns when spreading is produced by rollback of the trench-slab-arc relative to a stationary overriding back-arc plate versus spreading due to motion of the overriding plate away from a fixed trench location. For rollback-induced spreading, flow trajectories in the wedge are shallow (e.g., limited upwelling), both the sub-arc and back-arc regions are supplied by material flowing around the receding slab. Flow lines in the sub-arc wedge are strongly trench-parallel. In these cases, strong lateral variations in slab surface temperature (SST) are recorded (hot at plate center, cool at plate edge). When the trench is fixed in space and spreading is produced by motion of the overriding plate, strong vertical flow velocities are recorded in the wedge, both the shallow sub-arc and back-arc regions are supplied by flow from under the overriding plate producing strong vertical shear. In these cases SSTs are nearly uniform across the plate. Results have implications for geochemical and seismic models of 3-D flow in subduction zones influenced by back-arc spreading, such as the Marianas.

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.

Motion processing with two eyes in three dimensions.

PubMed

Rokers, Bas; Czuba, Thaddeus B; Cormack, Lawrence K; Huk, Alexander C

2011-02-11

The movement of an object toward or away from the head is perhaps the most critical piece of information an organism can extract from its environment. Such 3D motion produces horizontally opposite motions on the two retinae. Little is known about how or where the visual system combines these two retinal motion signals, relative to the wealth of knowledge about the neural hierarchies involved in 2D motion processing and binocular vision. Canonical conceptions of primate visual processing assert that neurons early in the visual system combine monocular inputs into a single cyclopean stream (lacking eye-of-origin information) and extract 1D ("component") motions; later stages then extract 2D pattern motion from the cyclopean output of the earlier stage. Here, however, we show that 3D motion perception is in fact affected by the comparison of opposite 2D pattern motions between the two eyes. Three-dimensional motion sensitivity depends systematically on pattern motion direction when dichoptically viewing gratings and plaids-and a novel "dichoptic pseudoplaid" stimulus provides strong support for use of interocular pattern motion differences by precluding potential contributions from conventional disparity-based mechanisms. These results imply the existence of eye-of-origin information in later stages of motion processing and therefore motivate the incorporation of such eye-specific pattern-motion signals in models of motion processing and binocular integration.

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.

Evolution and inheritance of early embryonic patterning in Drosophila simulans and D. sechellia.

PubMed

Lott, Susan E; Ludwig, Michael Z; Kreitman, Martin

2011-05-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation that selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth "stripe allometry") in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species Drosophila simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the "margin of error" for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems.

PubMed

Woolley, Thomas E; Baker, Ruth E; Gaffney, Eamonn A; Maini, Philip K; Seirin-Lee, Sungrim

2012-05-01

Cellular gene expression is a complex process involving many steps, including the transcription of DNA and translation of mRNA; hence the synthesis of proteins requires a considerable amount of time, from ten minutes to several hours. Since diffusion-driven instability has been observed to be sensitive to perturbations in kinetic delays, the application of Turing patterning mechanisms to the problem of producing spatially heterogeneous differential gene expression has been questioned. In deterministic systems a small delay in the reactions can cause a large increase in the time it takes a system to pattern. Recently, it has been observed that in undelayed systems intrinsic stochasticity can cause pattern initiation to occur earlier than in the analogous deterministic simulations. Here we are interested in adding both stochasticity and delays to Turing systems in order to assess whether stochasticity can reduce the patterning time scale in delayed Turing systems. As analytical insights to this problem are difficult to attain and often limited in their use, we focus on stochastically simulating delayed systems. We consider four different Turing systems and two different forms of delay. Our results are mixed and lead to the conclusion that, although the sensitivity to delays in the Turing mechanism is not completely removed by the addition of intrinsic noise, the effects of the delays are clearly ameliorated in certain specific cases.

The Sterol Methyltransferases SMT1, SMT2, and SMT3 Influence Arabidopsis Development through Nonbrassinosteroid Products1[W][OA

PubMed Central

Carland, Francine; Fujioka, Shozo; Nelson, Timothy

2010-01-01

Plant sterols are structural components of cell membranes that provide rigidity, permeability, and regional identity to membranes. Sterols are also the precursors to the brassinosteroid signaling molecules. Evidence is accumulating that specific sterols have roles in pattern formation during development. COTYLEDON VASCULAR PATTERNING1 (CVP1) encodes C-24 STEROL METHYLTRANSFERASE2 (SMT2), one of three SMTs in Arabidopsis (Arabidopsis thaliana). SMT2 and SMT3, which also encodes a C-24 SMT, catalyze the reaction that distinguishes the synthesis of structural sterols from signaling brassinosteroid derivatives and are highly regulated. The deficiency of SMT2 in the cvp1 mutant results in moderate developmental defects, including aberrant cotyledon vein patterning, serrated floral organs, and reduced stature, but plants are viable, suggesting that SMT3 activity can substitute for the loss of SMT2. To test the distinct developmental roles of SMT2 and SMT3, we identified a transcript null smt3 mutant. Although smt3 single mutants appear wild type, cvp1 smt3 double mutants show enhanced defects relative to cvp1 mutants, such as discontinuous cotyledon vein pattern, and produce novel phenotypes, including defective root growth, loss of apical dominance, sterility, and homeotic floral transformations. These phenotypes are correlated with major alterations in the profiles of specific sterols but without significant alterations to brassinosteroid profiles. The alterations to sterol profiles in cvp1 mutants affect auxin response, demonstrated by weak auxin insensitivity, enhanced axr1 auxin resistance, ectopically expressed DR5:β-glucuronidase in developing embryos, and defective response to auxin-inhibited PIN2-green fluorescent protein endocytosis. We discuss the developmental roles of sterols implied by these results. PMID:20421456

Differential regional expression patterns of α-synuclein, TNF-α, and IL-1β; and variable status of dopaminergic neurotoxicity in mouse brain after Paraquat treatment

PubMed Central

2011-01-01

Background Paraquat (1, 1-dimethyl-4, 4-bipyridium dichloride; PQ) causes neurotoxicity, especially dopaminergic neurotoxicity, and is a supposed risk factor for Parkinson's disease (PD). However, the cellular and molecular mechanisms of PQ-induced neurodegeneration are far from clear. Previous studies have shown that PQ induces neuroinflammation and dopaminergic cell loss, but the prime cause of those events is still in debate. Methods We examined the neuropathological effects of PQ not only in substantia nigra (SN) but also in frontal cortex (FC) and hippocampus of the progressive mouse (adult Swiss albino) model of PD-like neurodegeneration, using immunohistochemistry, western blots, and histological and biochemical analyses. Results PQ caused differential patterns of changes in cellular morphology and expression of proteins related to PD and neuroinflammation in the three regions examined (SN, FC and hippocampus). Coincident with behavioral impairment and brain-specific ROS generation, there was differential immunolocalization and decreased expression levels of tyrosine hydroxylase (TH) in the three regions, whereas α-synuclein immunopositivity increased in hippocampus, increased in FC and decreased in SN. PQ-induced neuroinflammation was characterized by area-specific changes in localization and appearances of microglial cells with or without activation and increment in expression patterns of tumor necrosis factor-α in the three regions of mouse brain. Expression of interleukin-1β was increased in FC and hippocampus but not significantly changed in SN. Conclusion The present study demonstrates that PQ induces ROS production and differential α-synuclein expression that promotes neuroinflammation in microglia-dependent or -independent manners, and produces different patterns of dopaminergic neurotoxicity in three different regions of mouse brain. PMID:22112368

The influence of reservoirs, climate, land use and hydrologic conditions on loads and chemical quality of dissolved organic carbon in the Colorado River

USGS Publications Warehouse

Miller, Matthew P.

2012-01-01

Longitudinal patterns in dissolved organic carbon (DOC) loads and chemical quality were identified in the Colorado River from the headwaters in the Rocky Mountains to the United States-Mexico border from 1994 to 2011. Watershed- and reach-scale climate, land use, river discharge and hydrologic modification conditions that contribute to patterns in DOC were also identified. Principal components analysis (PCA) identified site-specific precipitation and reach-scale discharge as being correlated with sites in the upper basin, where there were increases in DOC load from the upstream to downstream direction. In the lower basin, where DOC load decreased from upstream to downstream, sites were correlated with site-specific temperature and reach-scale population, urban land use and hydrologic modification. In the reaches containing Lakes Powell and Mead, the two largest reservoirs in the United States, DOC quantity decreased, terrestrially derived aromatic DOC was degraded and/or autochthonous less aromatic DOC was produced. Taken together, these results suggest that longitudinal patterns in the relatively unregulated upper basin are influenced by watershed inputs of water and DOC, whereas DOC patterns in the lower basin are reflective of a balance between watershed contribution of water and DOC to the river and loss of water and DOC due to hydrologic modification and/or biogeochemical processes. These findings suggest that alteration of constituent fluxes in rivers that are highly regulated may overshadow watershed processes that would control fluxes in comparable unregulated rivers. Further, these results provide a foundation for detailed assessments of factors controlling the transport and chemical quality of DOC in the Colorado River.

A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure

PubMed Central

Nampally, Malathi; Rajulu, M. B. Govinda; Gillet, Dominique; Suryanarayanan, T. S.; Moerschbacher, Bruno B.

2015-01-01

Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs) have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering. PMID:26273652

A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure.

PubMed

Nampally, Malathi; Rajulu, M B Govinda; Gillet, Dominique; Suryanarayanan, T S; Moerschbacher, Bruno B

2015-01-01

Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs) have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering.

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.

Burst Firing in Bee Gustatory Neurons Prevents Adaptation.

PubMed

Miriyala, Ashwin; Kessler, Sébastien; Rind, F Claire; Wright, Geraldine A

2018-05-01

Animals detect changes in the environment using modality-specific, peripheral sensory neurons. The insect gustatory system encodes tastant identity and concentration through the independent firing of gustatory receptor neurons (GRNs) that spike rapidly at stimulus onset and quickly adapt. Here, we show the first evidence that concentrated sugar evokes a temporally structured burst pattern of spiking involving two GRNs within the gustatory sensilla of bumblebees. Bursts of spikes resulted when a sucrose-activated GRN was inhibited by another GRN at a frequency of ∼22 Hz during the first 1 s of stimulation. Pharmacological blockade of gap junctions abolished bursting, indicating that bee GRNs have electrical synapses that produce a temporal pattern of spikes when one GRN is activated by a sugar ligand. Bursting permitted bee GRNs to maintain a high rate of spiking and to exhibit the slowest rate of adaptation of any insect species. Feeding bout duration correlated with coherent bursting; only sugar concentrations that produced bursting evoked the bumblebee's feeding reflex. Volume of solution imbibed was a direct function of time in contact with food. We propose that gap junctions among GRNs enable a sustained rate of GRN spiking that is necessary to drive continuous feeding by the bee proboscis. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Control Theory Model of Smoking

PubMed Central

Bobashev, Georgiy; Holloway, John; Solano, Eric; Gutkin, Boris

2017-01-01

We present a heuristic control theory model that describes smoking under restricted and unrestricted access to cigarettes. The model is based on the allostasis theory and uses a formal representation of a multiscale opponent process. The model simulates smoking behavior of an individual and produces both short-term (“loading up” after not smoking for a while) and long-term smoking patterns (e.g., gradual transition from a few cigarettes to one pack a day). By introducing a formal representation of withdrawal- and craving-like processes, the model produces gradual increases over time in withdrawal- and craving-like signals associated with abstinence and shows that after 3 months of abstinence, craving disappears. The model was programmed as a computer application allowing users to select simulation scenarios. The application links images of brain regions that are activated during the binge/intoxication, withdrawal, or craving with corresponding simulated states. The model was calibrated to represent smoking patterns described in peer-reviewed literature; however, it is generic enough to be adapted to other drugs, including cocaine and opioids. Although the model does not mechanistically describe specific neurobiological processes, it can be useful in prevention and treatment practices as an illustration of drug-using behaviors and expected dynamics of withdrawal and craving during abstinence. PMID:28868531

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.

Nitric oxide-mediated intersegmental modulation of cycle frequency in the crayfish swimmeret system.

PubMed

Yoshida, Misaki; Nagayama, Toshiki; Newland, Philip

2018-05-21

Crayfish swimmerets are paired appendages located on the ventral side of each abdominal segment that show rhythmic beating during forward swimming produced by central pattern generators in most abdominal segments. For animals with multiple body segments and limbs, intersegmental coordination of central pattern generators in each segment is crucial for the production of effective movements. Here we develop a novel pharmacological approach to analyse intersegmental modulation of swimmeret rhythm by selectively elevating nitric oxide levels and reducing them with pharmacological agents, in specific ganglia. Bath application of L-arginine, the substrate NO synthesis, increased the cyclical spike responses of the power-stroke motor neurons. By contrast the NOS inhibitor, L-NAME decreased them. To determine the role of the different local centres in producing and controlling the swimmeret rhythm, these two drugs were applied locally to two separate ganglia following bath application of carbachol. Results revealed that there was both ascending and descending intersegmental modulation of cycle frequency of the swimmeret rhythm in the abdominal ganglia and that synchrony of cyclical activity between segments of segments was maintained. We also found that there were gradients in the strength effectiveness in modulation, that ascending modulation of the swimmeret rhythm was stronger than descending modulation. © 2018. Published by The Company of Biologists Ltd.

ERP profiles for face and word recognition are based on their status in semantic memory not their stimulus category.

PubMed

Nie, Aiqing; Griffin, Michael; Keinath, Alexander; Walsh, Matthew; Dittmann, Andrea; Reder, Lynne

2014-04-04

Previous research has suggested that faces and words are processed and remembered differently as reflected by different ERP patterns for the two types of stimuli. Specifically, face stimuli produced greater late positive deflections for old items in anterior compared to posterior regions, while word stimuli produced greater late positive deflections in posterior compared to anterior regions. Given that words have existing representations in subjects׳ long-term memories (LTM) and that face stimuli used in prior experiments were of unknown individuals, we conducted an ERP study that crossed face and letter stimuli with the presence or absence of a prior (stable or existing) memory representation. During encoding, subjects judged whether stimuli were known (famous face or real word) or not known (unknown person or pseudo-word). A surprise recognition memory test required subjects to distinguish between stimuli that appeared during the encoding phase and stimuli that did not. ERP results were consistent with previous research when comparing unknown faces and words; however, the late ERP pattern for famous faces was more similar to that for words than for unknown faces. This suggests that the critical ERP difference is mediated by whether there is a prior representation in LTM, and not whether the stimulus involves letters or faces. Published by Elsevier B.V.

The bouquet of grapevine (Vitis vinifera L. cv. Cabernet Sauvignon) flowers arises from the biosynthesis of sesquiterpene volatiles in pollen grains

PubMed Central

Martin, Diane M.; Toub, Omid; Chiang, Angela; Lo, Bernard C.; Ohse, Sebastian; Lund, Steven T.; Bohlmann, Jörg

2009-01-01

Terpenoid volatiles are important information molecules that enable pollinators to locate flowers and may protect reproductive tissues against pathogens or herbivores. Inflorescences of grapevine (Vitis vinifera L.) are composed of tiny green flowers that produce an abundance of sesquiterpenoid volatiles. We demonstrate that male flower parts of grapevines are responsible for sesquiterpenoid floral scent formation. We describe temporal and spatial patterns of biosynthesis and release of floral volatiles throughout the blooming of V. vinifera L. cv. Cabernet Sauvignon. The biosynthesis of sesquiterpene volatiles, which are emitted with a light-dependent diurnal pattern early in the morning at prebloom and bloom, is localized to anthers and, more specifically, within the developing pollen grains. Valencene synthase (VvValCS) enzyme activity, which produces the major sesquiterpene volatiles of grapevine flowers, is present in anthers. VvValCS transcripts are most abundant in flowers at prebloom stages. Western blot analysis identified VvValCS protein in anthers, and in situ immunolabeling located VvValCS protein in pollen grains during bloom. Histochemical staining, as well as immunolabeling analysis by fluorescent microscopy and transmission electron microscopy, indicated that VvValCS localizes close to lipid bodies within the maturing microspore. PMID:19359488

The tymbal muscle of cicada has flight muscle-type sarcomeric architecture and protein expression.

PubMed

Iwamoto, Hiroyuki

2017-01-01

The structural and biochemical features of the tymbal (sound-producing) muscle of cicadas were studied by X-ray diffraction and immunochemistry, and compared with those of flight muscles from the same species. The X-ray diffraction pattern of the tymbal muscle was very similar to that of the dorsal longitudinal flight muscle: In both muscles, the 2,0 equatorial reflection is much more intense than the 1,1, indicating that both muscles have a flight muscle-type myofilament lattice. In rigor, the first myosin/actin layer line reflection was finely lattice-sampled, indicating that the contractile proteins are arranged with a crystalline regularity as in asynchronous flight muscles. In contrast, the diffraction pattern from the tensor muscle, which modulates the sound by stressing the tymbal, did not show signs of such high regularity or flight muscle-type filament lattice. Electrophoretic patterns of myofibrillar proteins were also very similar in the tymbal muscle and flight muscles, but distinct from those from the tensor or leg muscles. The antibody raised against the flight muscle-specific troponin-I isoform reacted with an 80-kDa band from both tymbal and flight muscles, but with none of the bands from the tensor or leg muscles. The close similarities of the structural and biochemical profiles between the tymbal and the flight muscles suggest the possibility that a set of flight muscle-specific proteins is diverted to the tymbal muscle to meet its demand for fast, repetitive contractions.

Linear and branched perfluorooctane sulfonate (PFOS) isomer patterns differ among several tissues and blood of polar bears.

PubMed

Greaves, Alana K; Letcher, Robert J

2013-09-01

Perfluorooctane sulfonate (PFOS) is a globally distributed persistent organic pollutant that has been found to bioaccumulate and biomagnify in aquatic food webs. Although principally in its linear isomeric configuration, 21-35% of the PFOS manufactured via electrochemical fluorination is produced as a branched structural isomer. PFOS isomer patterns were investigated in multiple tissues of polar bears (Ursus maritimus) from East Greenland. The liver (n = 9), blood (n = 19), brain (n = 16), muscle (n = 5), and adipose (n = 5) were analyzed for linear PFOS (n-PFOS), as well as multiple mono- and di-trifluoromethyl-substituted branched isomers. n-PFOS accounted for 93.0 ± 0.5% of Σ-PFOS isomer concentrations in the liver, whereas the proportion was significantly lower (p<0.05) in the blood (85.4 ± 0.5%). Branched isomers were quantifiable in the liver and blood, but not in the brain, muscle, or adipose. In both the liver and blood, 6-perfluoromethylheptane sulfonate (P6MHpS) was the dominant branched isomer (2.61 ± 0.10%, and 3.26 ± 0.13% of Σ-PFOS concentrations, respectively). No di-trifluoromethyl-substituted isomers were detectable in any of the tissues analyzed. These tissue-specific isomer patterns suggest isomer-specific pharmacokinetics, perhaps due to differences in protein affinities, and thus differences in protein interactions, as well transport, absorption, and/or metabolism in the body. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Oral candidosis in relation to oral immunity.

PubMed

Feller, L; Khammissa, R A G; Chandran, R; Altini, M; Lemmer, J

2014-09-01

Symptomatic oral infection with Candida albicans is characterized by invasion of the oral epithelium by virulent hyphae that cause tissue damage releasing the inflammatory mediators that initiate and sustain local inflammation. Candida albicans triggers pattern-recognition receptors of keratinocytes, macrophages, monocytes and dendritic cells, stimulating the production of IL-1β, IL-6 and IL-23. These cytokines induce the differentiation of Th17 cells and the generation of IL-17- and/or IL-22-mediated antifungal protective immuno-inflammatory responses in infected mucosa. Some immune cells including NKT cells, γδ T cells and lymphoid cells that are innate to the oral mucosa have the capacity to produce large quantities of IL-17 in response to C. albicans, sufficient to mediate effective protective immunity against C. albicans. On the other hand, molecular structures of commensal C. albicans blastoconidia, although detected by pattern-recognition receptors, are avirulent, do not invade the oral epithelium, do not elicit inflammatory responses in a healthy host, but induce regulatory immune responses that maintain tissue tolerance to the commensal fungi. The type, specificity and sensitivity of the protective immune response towards C. albicans is determined by the outcome of the integrated interactions between the intracellular signalling pathways of specific combinations of activated pattern-recognition receptors (TLR2, TLR4, Dectin-1 and Dectin-2). IL-17-mediated protective immune response is essential for oral mucosal immunity to C. albicans infection. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest.

PubMed

Mangan, Scott A; Schnitzer, Stefan A; Herre, Edward A; Mack, Keenan M L; Valencia, Mariana C; Sanchez, Evelyn I; Bever, James D

2010-08-05

The accumulation of species-specific enemies around adults is hypothesized to maintain plant diversity by limiting the recruitment of conspecific seedlings relative to heterospecific seedlings. Although previous studies in forested ecosystems have documented patterns consistent with the process of negative feedback, these studies are unable to address which classes of enemies (for example, pathogens, invertebrates, mammals) exhibit species-specific effects strong enough to generate negative feedback, and whether negative feedback at the level of the individual tree is sufficient to influence community-wide forest composition. Here we use fully reciprocal shade-house and field experiments to test whether the performance of conspecific tree seedlings (relative to heterospecific seedlings) is reduced when grown in the presence of enemies associated with adult trees. Both experiments provide strong evidence for negative plant-soil feedback mediated by soil biota. In contrast, above-ground enemies (mammals, foliar herbivores and foliar pathogens) contributed little to negative feedback observed in the field. In both experiments, we found that tree species that showed stronger negative feedback were less common as adults in the forest community, indicating that susceptibility to soil biota may determine species relative abundance in these tropical forests. Finally, our simulation models confirm that the strength of local negative feedback that we measured is sufficient to produce the observed community-wide patterns in tree-species relative abundance. Our findings indicate that plant-soil feedback is an important mechanism that can maintain species diversity and explain patterns of tree-species relative abundance in tropical forests.

Distribution of health-related social surplus in pharmaceuticals: an estimation of consumer and producer surplus in the management of high blood lipids and COPD.

PubMed

Refoios Camejo, Rodrigo; Camejo, Rodrigo Refoios; McGrath, Clare; Miraldo, Marisa; Rutten, Frans

2014-05-01

Following suggestions that developers should be allowed to capture a defined share of the total value generated by their technologies, the amount of surplus accruing to the pharmaceutical industry has become an important concept when discussing policies to encourage innovation in healthcare. Observational clinical and market data spanning over a period of 20 years were applied in order to estimate the social surplus generated by pharmaceuticals used in the management of high cholesterol and chronic obstructive pulmonary disease (COPD). The distribution of social surplus between consumers and producers was also computed and the dynamics of rent extraction examined. Health-related social surplus increased consistently over time for both disease areas, mostly due to the launch of more effective technologies and a greater number of patients being treated for the conditions. However, the growth rate of social surplus differed for each disease and dissimilar patterns of distribution between consumer and producer surplus emerged across the years. For lipid-lowering therapies, yearly consumer surplus reaches 85 % of total health-related social surplus after the loss of exclusivity of major molecules, whilst for COPD it ranges from 54 to 69 %. Average producer surplus is approximately 25 % of total health-related social surplus in the lipid-lowering market between 1990 and 2010, and 37 % for COPD between 2001 and 2010. The share of surplus captured by non-innovative generic producers also varies differently across periods for both markets, reaching 11.12 % in the case of lipid-lowering therapies but just 1.55 % in the case of COPD. A considerable amount of the value may be recouped by consumers only towards the end of the lifecycle. Elements affecting the distribution of social surplus vary across disease areas and include the market pricing structure and the pattern of clinical effectiveness observed over time. The application of a longer-term disease specific perspective may be required when assessing the cost-effectiveness of health technologies at launch.

Influence of culture medium composition on relative mRNA abundances in domestic cat embryos.

PubMed

Hribal, R; Jewgenow, K; Braun, B C; Comizzoli, P

2013-04-01

Different culture conditions have been used to produce domestic cat embryos. As part of the in vitro procedures, the medium composition significantly affects the quality of the embryo development also. Quality assessments based on cleavage kinetics and blastomere symmetry are useful, but embryos also can differ in their relative gene expression patterns despite similar morphological characteristics. The aim of this study was to compare cat embryos produced with two different in vitro culture systems routinely used in two different laboratories [Smithsonian Conservation Biology Institute, Washington D.C., USA (SCBI) and Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (IZW)]. Specifically, relative mRNA expression patterns of critical genes for pre-implantation embryo development were assessed in both conditions. Embryos were produced in parallel in both culture systems by IVF using frozen-thawed ejaculated semen in the United States and fresh epididymal sperm in Germany. Success of embryo development in vitro was recorded as well as relative mRNA abundances [DNA methyltransferases 1 and 3A (DNMT1, DNMT3A), gap junction protein alpha 1 (GJA1), octamer-binding transcription factor 4 [OCT4], insulin-like growth factors 1 and 2 receptors (IGF1R, IGF2R), beta-actin (ACTB)] in pools of days 4-5 morulae by semi-quantitative RT-PCR assay. Percentages of cleaved embryos were similar (p > 0.05) between both culture systems, regardless of the location. OCT4 mRNA abundance was higher (p < 0.05) in embryos derived in the SCBI culture system compared with those from the IZW system when epididymal sperm was used for IVF. No clear correlation between the expression pattern and the culture system could be found for all other genes. It is suggested that OCT4 expression might be affected by the media composition in some conditions and can be the indicator of a better embryo quality. © 2012 Blackwell Verlag GmbH.

Diversity of fish sound types in the Pearl River Estuary, China

PubMed Central

Wang, Zhi-Tao; Nowacek, Douglas P.; Akamatsu, Tomonari; Liu, Jian-Chang; Duan, Guo-Qin; Cao, Han-Jiang

2017-01-01

Background Repetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species. Methods Underwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1,408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine. Results We identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2,600 Hz and a majority of the energy below 4,000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1 + 1 and 1 + N10 might belong to big-snout croaker (Johnius macrorhynus), and 1 + N19 might be produced by Belanger’s croaker (J. belangerii). Discussion Categorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin (Sousa chinensis) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed. PMID:29085746

Diversity of fish sound types in the Pearl River Estuary, China.

PubMed

Wang, Zhi-Tao; Nowacek, Douglas P; Akamatsu, Tomonari; Wang, Ke-Xiong; Liu, Jian-Chang; Duan, Guo-Qin; Cao, Han-Jiang; Wang, Ding

2017-01-01

Repetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species. Underwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1,408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine. We identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2,600 Hz and a majority of the energy below 4,000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1 + 1 and 1 + N 10 might belong to big-snout croaker ( Johnius macrorhynus ), and 1 + N 19 might be produced by Belanger's croaker ( J. belangerii ). Categorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin ( Sousa chinensis ) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed.

Morphological Diversity of the Colony Produced by Bacteria Proteus mirabilis

NASA Astrophysics Data System (ADS)

Nakahara, Akio; Shimada, Yuji; Wakita, Jun-ichi; Matsushita, Mitsugu; Matsuyama, Tohey

1996-08-01

Morphological changes of colonies have been investigatedfor a bacterial strain of Proteus mirabilis, which is a famous speciesfor producing concentric-ring-like colonies. It was found that colony patterns can be classified into three types,i.e., cyclic spreading, diffusion-limited growth (DLA-like)and three-dimensional growth (inside the agar medium) patterns. Cyclic spreading patterns can further be classifiedinto three subgroups, i.e., concentric-ring, homogeneous and spatiotemporal patterns. These subgroups were classified by examining the development of colony structure after colonies spread all over petri-dishes. Comparison of the results with thoseof another bacterial species Bacillus subtilis is also discussed.

The Virtual Teacher (VT) Paradigm: Learning New Patterns of Interpersonal Coordination Using the Human Dynamic Clamp

PubMed Central

2015-01-01

The Virtual Teacher paradigm, a version of the Human Dynamic Clamp (HDC), is introduced into studies of learning patterns of inter-personal coordination. Combining mathematical modeling and experimentation, we investigate how the HDC may be used as a Virtual Teacher (VT) to help humans co-produce and internalize new inter-personal coordination pattern(s). Human learners produced rhythmic finger movements whilst observing a computer-driven avatar, animated by dynamic equations stemming from the well-established Haken-Kelso-Bunz (1985) and Schöner-Kelso (1988) models of coordination. We demonstrate that the VT is successful in shifting the pattern co-produced by the VT-human system toward any value (Experiment 1) and that the VT can help humans learn unstable relative phasing patterns (Experiment 2). Using transfer entropy, we find that information flow from one partner to the other increases when VT-human coordination loses stability. This suggests that variable joint performance may actually facilitate interaction, and in the long run learning. VT appears to be a promising tool for exploring basic learning processes involved in social interaction, unraveling the dynamics of information flow between interacting partners, and providing possible rehabilitation opportunities. PMID:26569608

The effects of morphine on fixed-interval patterning and temporal discrimination.

PubMed Central

Odum, A L; Schaal, D W

2000-01-01

Changes produced by drugs in response patterns under fixed-interval schedules of reinforcement have been interpreted to result from changes in temporal discrimination. To examine this possibility, this experiment determined the effects of morphine on the response patterning of 4 pigeons during a fixed-interval 1-min schedule of food delivery with interpolated temporal discrimination trials. Twenty of the 50 total intervals were interrupted by choice trials. Pecks to one key color produced food if the interval was interrupted after a short time (after 2 or 4.64 s). Pecks to another key color produced food if the interval was interrupted after a long time (after 24.99 or 58 s). Morphine (1.0 to 10.0 mg/kg) decreased the index of curvature (a measure of response patterning) during fixed intervals and accuracy during temporal discrimination trials. Accuracy was equally disrupted following short and long sample durations. Although morphine disrupted temporal discrimination in the context of a fixed-interval schedule, these effects are inconsistent with interpretations of the disruption of response patterning as a selective overestimation of elapsed time. The effects of morphine may be related to the effects of more conventional external stimuli on response patterning. PMID:11029024

The Virtual Teacher (VT) Paradigm: Learning New Patterns of Interpersonal Coordination Using the Human Dynamic Clamp.

PubMed

Kostrubiec, Viviane; Dumas, Guillaume; Zanone, Pier-Giorgio; Kelso, J A Scott

2015-01-01

The Virtual Teacher paradigm, a version of the Human Dynamic Clamp (HDC), is introduced into studies of learning patterns of inter-personal coordination. Combining mathematical modeling and experimentation, we investigate how the HDC may be used as a Virtual Teacher (VT) to help humans co-produce and internalize new inter-personal coordination pattern(s). Human learners produced rhythmic finger movements whilst observing a computer-driven avatar, animated by dynamic equations stemming from the well-established Haken-Kelso-Bunz (1985) and Schöner-Kelso (1988) models of coordination. We demonstrate that the VT is successful in shifting the pattern co-produced by the VT-human system toward any value (Experiment 1) and that the VT can help humans learn unstable relative phasing patterns (Experiment 2). Using transfer entropy, we find that information flow from one partner to the other increases when VT-human coordination loses stability. This suggests that variable joint performance may actually facilitate interaction, and in the long run learning. VT appears to be a promising tool for exploring basic learning processes involved in social interaction, unraveling the dynamics of information flow between interacting partners, and providing possible rehabilitation opportunities.

Identification of nuclear weapons

DOEpatents

Mihalczo, J.T.; King, W.T.

1987-04-10

A method and apparatus for non-invasively indentifying different types of nuclear weapons is disclosed. A neutron generator is placed against the weapon to generate a stream of neutrons causing fissioning within the weapon. A first detects the generation of the neutrons and produces a signal indicative thereof. A second particle detector located on the opposite side of the weapon detects the fission particles and produces signals indicative thereof. The signals are converted into a detected pattern and a computer compares the detected pattern with known patterns of weapons and indicates which known weapon has a substantially similar pattern. Either a time distribution pattern or noise analysis pattern, or both, is used. Gamma-neutron discrimination and a third particle detector for fission particles adjacent the second particle detector are preferably used. The neutrons are generated by either a decay neutron source or a pulled neutron particle accelerator.

Primary prevention research: a preliminary review of program outcome studies.

PubMed

Schaps, E; Churgin, S; Palley, C S; Takata, B; Cohen, A Y

1980-07-01

This article reviews 35 drug abuse prevention program evaluations employing drug-specific outcome measures. Many of these evaluations assessed the effects of "new generation" prevention strategies: affective, peer-oriented, and multidimensional approaches. Only 14 studies evaluated purely informational programs. Evaluations were analyzed to ascertain (1) characteristics of the programs under study, (2) characteristics of the research designs, and (3) patterns among findings. This review provides some evidence that the newer prevention strategies may produce more positive and fewer negative outcomes than did older drug information approaches. Over 70% of the programs using the newer strategies produced some positive effects; only 29% showed negative effects. In contrast, 46% of informational programs showed positive effects; 46% showed negative effects. These findings must be approached with great caution, since the research was frequently scientifically inadequate, and since rigor of research was negatively correlated with intensity and duration of program services.

Atypical prosody in Asperger syndrome: perceptual and acoustic measurements.

PubMed

Filipe, Marisa G; Frota, Sónia; Castro, São Luís; Vicente, Selene G

2014-08-01

It is known that individuals with Asperger syndrome (AS) may show no problems with regard to what is said (e.g., lexical content) but tend to have difficulties in how utterances are produced, i.e., they may show prosodic impairments. In the present study, we focus on the use of prosodic features to express grammatical meaning. Specifically, we explored the sentence type difference between statements and questions that is conveyed by intonation, using perceptual and acoustic measurements. Children aged 8 and 9 years with AS (n = 12) were matched according to age and nonverbal intelligence with typically developing peers (n = 17). Although children with AS could produce categorically accurate prosodic patterns, their prosodic contours were perceived as odd by adult listeners, and acoustic measurements showed alterations in duration and pitch. Additionally, children with AS had greater variability in fundamental frequency contours compared to typically developing peers.

Emotional modulation of body-selective visual areas.

PubMed

Peelen, Marius V; Atkinson, Anthony P; Andersson, Frederic; Vuilleumier, Patrik

2007-12-01

Emotionally expressive faces have been shown to modulate activation in visual cortex, including face-selective regions in ventral temporal lobe. Here, we tested whether emotionally expressive bodies similarly modulate activation in body-selective regions. We show that dynamic displays of bodies with various emotional expressions vs neutral bodies, produce significant activation in two distinct body-selective visual areas, the extrastriate body area and the fusiform body area. Multi-voxel pattern analysis showed that the strength of this emotional modulation was related, on a voxel-by-voxel basis, to the degree of body selectivity, while there was no relation with the degree of selectivity for faces. Across subjects, amygdala responses to emotional bodies positively correlated with the modulation of body-selective areas. Together, these results suggest that emotional cues from body movements produce topographically selective influences on category-specific populations of neurons in visual cortex, and these increases may implicate discrete modulatory projections from the amygdala.

Optical nose based on porous silicon photonic crystal infiltrated with ionic liquids.

PubMed

Zhang, Haijuan; Lin, Leimiao; Liu, Dong; Chen, Qiaofen; Wu, Jianmin

2017-02-08

A photonic-nose for the detection and discrimination of volatile organic compounds (VOCs) was constructed. Each sensing element on the photonic sensor array was formed by infiltrating a specific type of ionic liquid (IL) into the pore channel of a patterned porous silicon (PSi) chip. Upon exposure to VOC, the density of IL dramatically decreased due to the nano-confinement effect. As a result, the IL located in pore channel expanded its volume and protrude out of the pore channel, leading to the formation of microdroplets on the PSi surface. These VOC-stimulated microdroplets could scatter the light reflected from the PSi rugate filter, thereby producing an optical response to VOC. The intensity of the optical response produced by IL/PSi sensor mainly depends on the size and shape of microdroplets, which is related to the concentration of VOC and the physi-chemical propertied of ILs. For ethanol vapor, the optical response has linear relationship with its relative vapor pressure within 0-60%. The LOD of the IL/PSi sensor for ethanol detection is calculated to be 1.3 ppm. It takes around 30 s to reach a full optical response, while the time for recovery is less than 1 min. In addition, the sensor displayed good stability and reproducibility. Owing to the different molecular interaction between IL and VOC, the ILs/PSi sensor array can generate a unique cross-reactive "fingerprint" in response to a specific type of VOC analyte. With the assistance of image technologies and principle components analysis (PCA), rapid discrimination of VOC analyte could be achieved based on the pattern recognition of photonic sensor array. The technology established in this work allows monitoring in-door air pollution in a visualized way. Copyright © 2016 Elsevier B.V. All rights reserved.

Atmospheric circulation patterns and phenological anomalies of grapevine in Italy

NASA Astrophysics Data System (ADS)

Cola, Gabriele; Alilla, Roberta; Dal Monte, Giovanni; Epifani, Chiara; Mariani, Luigi; Parisi, Simone Gabriele

2014-05-01

Grapevine (Vitis vinifera L.) is a fundamental crop for Italian agriculture as testified by the first place of Italy in the world producers ranking. This justify the importance of quantitative analyses referred to this crucial crop and aimed to quantify meteorological resources and limitations to development and production. Phenological rhythms of grapevine are strongly affected by surface fields of air temperature which in their turn are affected by synoptic circulation. This evidence highlights the importance of an approach based on dynamic climatology in order to detect and explain phenological anomalies that can have relevant effects on quantity and quality of grapevine production. In this context, this research is aimed to study the existing relation among the 850 hPa circulation patterns over the Euro-Mediterranean area from NOAA Ncep dataset and grapevine phenological fields for Italy over the period 2006-2013, highlighting the main phenological anomalies and analyzing synoptic determinants. This work is based on phenological fields with a standard pixel of 2 km routinely produced from 2006 by the Iphen project (Italian Phenological network) on the base of phenological observations spatialized by means of a specific algorithm based on cumulated thermal resources expressed as Normal Heat Hours (NHH). Anomalies have been evaluated with reference to phenological normal fields defined for the Italian area on the base of phenological observations and Iphen model. Results show that relevant phenological anomalies observed over the reference period are primarily associated with long lasting blocking systems driving cold air masses (Arctic or Polar-Continental) or hot ones (Sub-Tropical) towards the Italian area. Specific cases are presented for some years like 2007 and 2011.

Thermographic image analysis for classification of ACL rupture disease, bone cancer, and feline hyperthyroid, with Gabor filters

NASA Astrophysics Data System (ADS)

Alvandipour, Mehrdad; Umbaugh, Scott E.; Mishra, Deependra K.; Dahal, Rohini; Lama, Norsang; Marino, Dominic J.; Sackman, Joseph

2017-05-01

Thermography and pattern classification techniques are used to classify three different pathologies in veterinary images. Thermographic images of both normal and diseased animals were provided by the Long Island Veterinary Specialists (LIVS). The three pathologies are ACL rupture disease, bone cancer, and feline hyperthyroid. The diagnosis of these diseases usually involves radiology and laboratory tests while the method that we propose uses thermographic images and image analysis techniques and is intended for use as a prescreening tool. Images in each category of pathologies are first filtered by Gabor filters and then various features are extracted and used for classification into normal and abnormal classes. Gabor filters are linear filters that can be characterized by the two parameters wavelength λ and orientation θ. With two different wavelength and five different orientations, a total of ten different filters were studied. Different combinations of camera views, filters, feature vectors, normalization methods, and classification methods, produce different tests that were examined and the sensitivity, specificity and success rate for each test were produced. Using the Gabor features alone, sensitivity, specificity, and overall success rates of 85% for each of the pathologies was achieved.

Physiotherapy for functional motor disorders: a consensus recommendation

PubMed Central

Nielsen, Glenn; Stone, Jon; Matthews, Audrey; Brown, Melanie; Sparkes, Chris; Farmer, Ross; Masterton, Lindsay; Duncan, Linsey; Winters, Alisa; Daniell, Laura; Lumsden, Carrie; Carson, Alan; David, Anthony S; Edwards, Mark

2015-01-01

Background Patients with functional motor disorder (FMD) including weakness and paralysis are commonly referred to physiotherapists. There is growing evidence that physiotherapy is an effective treatment, but the existing literature has limited explanations of what physiotherapy should consist of and there are insufficient data to produce evidence-based guidelines. We aim to address this issue by presenting recommendations for physiotherapy treatment. Methods A meeting was held between physiotherapists, neurologists and neuropsychiatrists, all with extensive experience in treating FMD. A set of consensus recommendations were produced based on existing evidence and experience. Results We recommend that physiotherapy treatment is based on a biopsychosocial aetiological framework. Treatment should address illness beliefs, self-directed attention and abnormal habitual movement patterns through a process of education, movement retraining and self-management strategies within a positive and non-judgemental context. We provide specific examples of these strategies for different symptoms. Conclusions Physiotherapy has a key role in the multidisciplinary management of patients with FMD. There appear to be specific physiotherapy techniques which are useful in FMD and which are amenable to and require prospective evaluation. The processes involved in referral, treatment and discharge from physiotherapy should be considered carefully as a part of a treatment package. PMID:25433033

Sampling methods to the statistical control of the production of blood components.

PubMed

Pereira, Paulo; Seghatchian, Jerard; Caldeira, Beatriz; Santos, Paula; Castro, Rosa; Fernandes, Teresa; Xavier, Sandra; de Sousa, Gracinda; de Almeida E Sousa, João Paulo

2017-12-01

The control of blood components specifications is a requirement generalized in Europe by the European Commission Directives and in the US by the AABB standards. The use of a statistical process control methodology is recommended in the related literature, including the EDQM guideline. The control reliability is dependent of the sampling. However, a correct sampling methodology seems not to be systematically applied. Commonly, the sampling is intended to comply uniquely with the 1% specification to the produced blood components. Nevertheless, on a purely statistical viewpoint, this model could be argued not to be related to a consistent sampling technique. This could be a severe limitation to detect abnormal patterns and to assure that the production has a non-significant probability of producing nonconforming components. This article discusses what is happening in blood establishments. Three statistical methodologies are proposed: simple random sampling, sampling based on the proportion of a finite population, and sampling based on the inspection level. The empirical results demonstrate that these models are practicable in blood establishments contributing to the robustness of sampling and related statistical process control decisions for the purpose they are suggested for. Copyright © 2017 Elsevier Ltd. All rights reserved.

Polyclonal Antisera To Distinguish Strains and Form Variants of Photorhabdus (Xenorhabdus) luminescens

PubMed Central

Gerritsen, L.; van der Wolf, J. M.; van Vuurde, J.; Ehlers, R.; Krasomil-Osterfel..., K. C.; Smits, P. H.

1995-01-01

In this study antisera against Photorhabdus luminescens strains were prepared for the first time. P. luminescens is a bacterial symbiont of entomopathogenic nematodes belonging to the genus Heterorhabditis. To characterize P. luminescens strains and form variants, we produced polyclonal antisera against P. luminescens PE (obtained from nematode strain NLH-E87.3) and against the primary and secondary forms of P. luminescens PSH (obtained from nematode strain DH-SH1). In double-diffusion tests all form variants of strain PE reacted with the antiserum against the primary form, but each variant produced a different diffusion pattern. The primary and secondary forms of strain PSH were also serologically different. Antiserum 9226 reacted with almost all P. luminescens strains tested, but it reacted differently with each strain in the double-diffusion test, showing that the strains were serologically different. The specificity of the antisera was increased by cross-absorption. After cross-absorption the antiserum against the strain PSH primary or secondary form was specific for that form and did not react with the other form. Using the cross-absorbed antisera in immunofluorescence cell-staining tests, we could distinguish primary and secondary form cells in a mixed strain PSH culture. PMID:16534911

Profiling agricultural land cover change in the North Central U.S. using ten years of the Cropland Data Layer

NASA Astrophysics Data System (ADS)

Sandborn, A.; Ebinger, L.

2016-12-01

The Cropland Data Layer (CDL), produced by the USDA/National Agricultural Statistics Service, provides annual, georeferenced crop specific land cover data over the contiguous United States. Several analyses were performed on ten years (2007-2016) of CDL data in order to visualize and quantify agricultural change over the North Central region (North Dakota, South Dakota, and Minnesota). Crop masks were derived from the CDL and layered to produce a ten-year time stack of corn, soybeans, and spring wheat at 30m spatial resolution. Through numerous image analyses, a temporal profile of each crop type was compiled and portrayed cartographically. For each crop, analyses included calculating the mean center of crop area over the ten year sequence, identifying the first and latest year the crop was grown on each pixel, and distinguishing crop rotation patterns and replacement statistics. Results show a clear north-western expansion trend for corn and soybeans, and a western migration trend for spring wheat. While some change may be due to commonly practiced crop rotation, this analysis shows that crop footprints have extended into areas that were previously other crops, idle cropland, and pasture/rangeland. Possible factors contributing to this crop migration pattern include profit advantages of row crops over small grains, improved crop genetics, climate change, and farm management program changes. Identifying and mapping these crop planting differences will better inform agricultural best practices, help to monitor the latest crop migration patterns, and present researchers with a way to quantitatively measure and forecast future agricultural trends.

Exploiting Human Resource Requirements to Infer Human Movement Patterns for Use in Modelling Disease Transmission Systems: An Example from Eastern Province, Zambia.

PubMed

Alderton, Simon; Noble, Jason; Schaten, Kathrin; Welburn, Susan C; Atkinson, Peter M

2015-01-01

In this research, an agent-based model (ABM) was developed to generate human movement routes between homes and water resources in a rural setting, given commonly available geospatial datasets on population distribution, land cover and landscape resources. ABMs are an object-oriented computational approach to modelling a system, focusing on the interactions of autonomous agents, and aiming to assess the impact of these agents and their interactions on the system as a whole. An A* pathfinding algorithm was implemented to produce walking routes, given data on the terrain in the area. A* is an extension of Dijkstra's algorithm with an enhanced time performance through the use of heuristics. In this example, it was possible to impute daily activity movement patterns to the water resource for all villages in a 75 km long study transect across the Luangwa Valley, Zambia, and the simulated human movements were statistically similar to empirical observations on travel times to the water resource (Chi-squared, 95% confidence interval). This indicates that it is possible to produce realistic data regarding human movements without costly measurement as is commonly achieved, for example, through GPS, or retrospective or real-time diaries. The approach is transferable between different geographical locations, and the product can be useful in providing an insight into human movement patterns, and therefore has use in many human exposure-related applications, specifically epidemiological research in rural areas, where spatial heterogeneity in the disease landscape, and space-time proximity of individuals, can play a crucial role in disease spread.

Computer simulation of flagellar movement VIII: coordination of dynein by local curvature control can generate helical bending waves.

PubMed

Brokaw, Charles J

2002-10-01

Computer simulations have been carried out with a model flagellum that can bend in three dimensions. A pattern of dynein activation in which regions of dynein activity propagate along each doublet, with a phase shift of approximately 1/9 wavelength between adjacent doublets, will produce a helical bending wave. This pattern can be termed "doublet metachronism." The simulations show that doublet metachronism can arise spontaneously in a model axoneme in which activation of dyneins is controlled locally by the curvature of each outer doublet microtubule. In this model, dyneins operate both as sensors of curvature and as motors. Doublet metachronism and the chirality of the resulting helical bending pattern are regulated by the angular difference between the direction of the moment and sliding produced by dyneins on a doublet and the direction of the controlling curvature for that doublet. A flagellum that is generating a helical bending wave experiences twisting moments when it moves against external viscous resistance. At high viscosities, helical bending will be significantly modified by twist unless the twist resistance is greater than previously estimated. Spontaneous doublet metachronism must be modified or overridden in order for a flagellum to generate the planar bending waves that are required for efficient propulsion of spermatozoa. Planar bending can be achieved with the three-dimensional flagellar model by appropriate specification of the direction of the controlling curvature for each doublet. However, experimental observations indicate that this "hard-wired" solution is not appropriate for real flagella. Copyright 2002 Wiley-Liss, Inc.

[Function of glutamate in pattern-gene-rating network is modified by nitric oxide NO].

PubMed

D'iakonova, T L; D'iakonova, V E

2007-03-01

In previous study on the terrestrial snail Helix pomatia, it has been shown that responsiveness of certain neurons to glutamate is controlled by NO; specifically, the donors of NO produced transformation of inhibitory responses to excitatory ones. Here, we extend this study to buccal neurons related to feeding behavior of the pond snail L. stagnalis. Glutamate is known to operate in the standard three-phase feeding pattern as a phase transmitter which mediates the effects of the second phase interneuron N2v. In isolated CNS, we recorded motor neuron B4 that was inhibited during firing of glutamatergic N2v, but expressed excitatory glutamate receptors as well. In some preparations (n = 17), bath application of 0.1 mM glutamate resulted in profound hyperpolarization of, and cessation of synaptic inputs to, the B4. Following treatment for 10-15 min with the NO donor sodium nitroprusside (n = 9), glutamate effect on B4 became excitatory, and a peculiar, sustained two-phase rhythmic activity of the pattern-generating network appeared. In other non-treated preparations (n = 12), 0.1 mM glutamate produced depolarization and excitation of B4, supplemented, in 8 cases, with emergence of the above mentioned two-phase rhythmic activity. Pretreatment for 10-20 min with the NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (n = 7) abolished these effects of glutamate. Our results suggest that 1) glutamate role in buccal rhythm generation depends on NO level, and 2) this mechanism is involved in modification of the feeding behavior in Lymnaea.

COMPARISON OF SPATIAL PATTERNS OF POLLUTANT DISTRIBUTION WITH CMAQ PREDICTIONS

EPA Science Inventory

One indication of model performance is the comparison of spatial patterns of pollutants, either as concentration or deposition, predicted by the model with spatial patterns derived from measurements. If the spatial patterns produced by the model are similar to the observations i...

Morphology and histochemistry of the "C" cells of guinea pig thyroid gland after treatment with STH preparation: Part II--young animals.

PubMed

Sawicki, B

1977-01-01

Investigations were carried out on 32 male guinea pigs 2 to 3 months of age. The STH (produced by BIOMED, Warszawa, Poland) was administered intramuscularly every other day, in 7 injections of 20 Evans's units (E. U.) or 100 E. U./kg body weight each. Thyroid gland sections were stained with heamatoxylin and eosin and with the Azan method. The C cells were detected with the modified silver method of Grimelius and with the HCl-toluidine blue and HCl-lead haemotoxylin techniques. Moreover, reactions were performed for succinate and alpha-glycerophosphate dehydrogenases and also for non-specific esterases and non-specific acetylcholinesterase. STH evoked proliferation of the C cells, changed their morphology and activity pattern of the enzymes present therein, probably testifying to an enhanced secretory activity of these cells.

High-speed duetting - latency times of the female acoustic response within the bush-cricket genera Leptophyes and Andreiniimon (Orthoptera, Phaneropteridae).

PubMed

Heller, Klaus-Gerhard; Korsunovskaya, Olga; Massa, Bruno; Iorgu, Ionuț Ștefan

2018-01-01

To find a mate, male and female bush-crickets of the family Phaneropteridae typically engage in duets. The male sings and the female responds. For mutual recognition, the amplitude pattern of the male song and the species-specific timing of the female response have been shown to be very important. In the seven studied species, belonging to the genera Leptophyes and Andreiniimon , these duets are extremely fast and nearly completely in the ultrasonic range. The females produce very short sounds by fast closing movements of the tegmina. They respond with species-specific delays of 20 to 150 ms after the beginning of the male song. The different latency times are probably not important for species recognition, since in sympatric species they are quite similar.

Method of detecting genetic translocations identified with chromosomal abnormalities

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas

2001-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Method of detecting genetic deletions identified with chromosomal abnormalities

DOEpatents

Gray, Joe W; Pinkel, Daniel; Tkachuk, Douglas

2013-11-26

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acids probes are typically of a complexity greater tha 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particlularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar ut genetically different diseases, and for many prognostic and diagnostic applications.

High-speed duetting – latency times of the female acoustic response within the bush-cricket genera Leptophyes and Andreiniimon (Orthoptera, Phaneropteridae)

PubMed Central

Heller, Klaus-Gerhard; Korsunovskaya, Olga; Massa, Bruno; Iorgu, Ionuț Ștefan

2018-01-01

Abstract To find a mate, male and female bush-crickets of the family Phaneropteridae typically engage in duets. The male sings and the female responds. For mutual recognition, the amplitude pattern of the male song and the species-specific timing of the female response have been shown to be very important. In the seven studied species, belonging to the genera Leptophyes and Andreiniimon, these duets are extremely fast and nearly completely in the ultrasonic range. The females produce very short sounds by fast closing movements of the tegmina. They respond with species-specific delays of 20 to 150 ms after the beginning of the male song. The different latency times are probably not important for species recognition, since in sympatric species they are quite similar. PMID:29692644

Development of Instrumental Techniques for Color Assessment of Camouflage Patterns

ERIC Educational Resources Information Center

Fang, Gang

2012-01-01

Camouflage fabrics are produced on a large scale for use in the US military and other applications. One of the highest volume camouflage fabrics is known as the Universal Camouflage Pattern (UCP) which is produced for the US Department of Defense. At present, no standard measurement-based color quality control method exists for camouflage…

Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals

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

Polikanov, Yury S.; Moore, Peter B.

2015-09-26

The diffuse scattering pattern produced by frozen crystals of the 70S ribosome fromThermus thermophilusis as highly structured as it would be if it resulted entirely from domain-scale motions within these particles. However, the qualitative properties of the scattering pattern suggest that acoustic displacements of the crystal lattice make a major contribution to it.

Tree Leaf Shadows to the Sun's Density: A Surprising Route

ERIC Educational Resources Information Center

Mallmann, A. James

2013-01-01

Rays of sunlight that strike raindrops produce rainbows that provide information about the spectrum of sunlight. Rays of sunlight that strike airborne ice crystals produce halos, sun pillars, and many other patterns of light and color in the sky. Analysis of those patterns makes it possible to determine the types and orientations of the ice…

A Drosophila protein family implicated in pheromone perception is related to Tay-Sachs GM2-activator protein.

PubMed

Starostina, Elena; Xu, Aiguo; Lin, Heping; Pikielny, Claudio W

2009-01-02

Low volatility, lipid-like cuticular hydrocarbon pheromones produced by Drosophila melanogaster females play an essential role in triggering and modulating mating behavior, but the chemosensory mechanisms involved remain poorly understood. Recently, we showed that the CheB42a protein, which is expressed in only 10 pheromone-sensing taste hairs on the front legs of males, modulates progression to late stages of male courtship behavior in response to female-specific cuticular hydrocarbons. Here we report that expression of all 12 genes in the CheB gene family is predominantly or exclusively gustatory-specific, and occurs in many different, often non-overlapping patterns. Only the Gr family of gustatory receptor genes displays a comparable variety of gustatory-specific expression patterns. Unlike Grs, however, expression of all but one CheB gene is sexually dimorphic. Like CheB42a, other CheBs may therefore function specifically in gustatory perception of pheromones. We also show that CheBs belong to the ML superfamily of lipid-binding proteins, and are most similar to human GM2-activator protein (GM2-AP). In particular, GM2-AP residues involved in ligand binding are conserved in CheBs but not in other ML proteins. Finally, CheB42a is specifically secreted into the inner lumen of pheromone-sensing taste hairs, where pheromones interact with membrane-bound receptors. We propose that CheB proteins interact directly with lipid-like Drosophila pheromones and modulate their detection by the gustatory signal transduction machinery. Furthermore, as loss of GM2-AP in Tay-Sachs disease prevents degradation of GM2 gangliosides and results in neurodegeneration, the function of CheBs in pheromone response may involve biochemical mechanisms critical for lipid metabolism in human neurons.

The mechanisms underlying the production of discontinuous gas exchange cycles in insects.

PubMed

Matthews, Philip G D

2018-03-01

This review examines the control of gas exchange in insects, specifically examining what mechanisms could explain the emergence of discontinuous gas exchange cycles (DGCs). DGCs are gas exchange patterns consisting of alternating breath-hold periods and bouts of gas exchange. While all insects are capable of displaying a continuous pattern of gas exchange, this episodic pattern is known to occur within only some groups of insects and then only sporadically or during certain phases of their life cycle. Investigations into DGCs have tended to emphasise the role of chemosensory thresholds in triggering spiracle opening as critical for producing these gas exchange patterns. However, a chemosensory basis for episodic breathing also requires an as-of-yet unidentified hysteresis between internal respiratory stimuli, chemoreceptors, and the spiracles. What has been less appreciated is the role that the insect's central nervous system (CNS) might play in generating episodic patterns of ventilation. The active ventilation displayed by many insects during DGCs suggests that this pattern could be the product of directed control by the CNS rather than arising passively as a result of self-sustaining oscillations in internal oxygen and carbon dioxide levels. This paper attempts to summarise what is currently known about insect gas exchange regulation, examining the location and control of ventilatory pattern generators in the CNS, the influence of chemoreceptor feedback in the form of O 2 and CO 2 /pH fluctuations in the haemolymph, and the role of state-dependent changes in CNS activity on ventilatory control. This information is placed in the context of what is currently known regarding the production of discontinuous gas exchange patterns.

Method for extreme ultraviolet lithography

DOEpatents

Felter, T. E.; Kubiak, Glenn D.

1999-01-01

A method of producing a patterned array of features, in particular, gate apertures, in the size range 0.4-0.05 .mu.m using projection lithography and extreme ultraviolet (EUV) radiation. A high energy laser beam is used to vaporize a target material in order to produce a plasma which in turn, produces extreme ultraviolet radiation of a characteristic wavelength of about 13 nm for lithographic applications. The radiation is transmitted by a series of reflective mirrors to a mask which bears the pattern to be printed. The demagnified focused mask pattern is, in turn, transmitted by means of appropriate optics and in a single exposure, to a substrate coated with photoresists designed to be transparent to EUV radiation and also satisfy conventional processing methods.

Method for extreme ultraviolet lithography

DOEpatents

Felter, T. E.; Kubiak, G. D.

2000-01-01

A method of producing a patterned array of features, in particular, gate apertures, in the size range 0.4-0.05 .mu.m using projection lithography and extreme ultraviolet (EUV) radiation. A high energy laser beam is used to vaporize a target material in order to produce a plasma which in turn, produces extreme ultraviolet radiation of a characteristic wavelength of about 13 nm for lithographic applications. The radiation is transmitted by a series of reflective mirrors to a mask which bears the pattern to be printed. The demagnified focused mask pattern is, in turn, transmitted by means of appropriate optics and in a single exposure, to a substrate coated with photoresists designed to be transparent to EUV radiation and also satisfy conventional processing methods.

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

PubMed Central

Pandey, Shivendra; Gultepe, Evin; Gracias, David H.

2013-01-01

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two dimensional (2D) structures. These technologies are mature, offer high precision and many of them can be implemented in a high-throughput manner. We leverage the advantages of planar lithography and combine them with self-folding methods1-20 wherein physical forces derived from surface tension or residual stress, are used to curve or fold planar structures into three dimensional (3D) structures. In doing so, we make it possible to mass produce precisely patterned static and reconfigurable particles that are challenging to synthesize. In this paper, we detail visualized experimental protocols to create patterned particles, notably, (a) permanently bonded, hollow, polyhedra that self-assemble and self-seal due to the minimization of surface energy of liquefied hinges21-23 and (b) grippers that self-fold due to residual stress powered hinges24,25. The specific protocol described can be used to create particles with overall sizes ranging from the micrometer to the centimeter length scales. Further, arbitrary patterns can be defined on the surfaces of the particles of importance in colloidal science, electronics, optics and medicine. More generally, the concept of self-assembling mechanically rigid particles with self-sealing hinges is applicable, with some process modifications, to the creation of particles at even smaller, 100 nm length scales22, 26 and with a range of materials including metals21, semiconductors9 and polymers27. With respect to residual stress powered actuation of reconfigurable grasping devices, our specific protocol utilizes chromium hinges of relevance to devices with sizes ranging from 100 μm to 2.5 mm. However, more generally, the concept of such tether-free residual stress powered actuation can be used with alternate high-stress materials such as heteroepitaxially deposited semiconductor films5,7 to possibly create even smaller nanoscale grasping devices. PMID:23407436

Genomics of Mature and Immature Olfactory Sensory Neurons

PubMed Central

Nickell, Melissa D.; Breheny, Patrick; Stromberg, Arnold J.; McClintock, Timothy S.

2014-01-01

The continuous replacement of neurons in the olfactory epithelium provides an advantageous model for investigating neuronal differentiation and maturation. By calculating the relative enrichment of every mRNA detected in samples of mature mouse olfactory sensory neurons (OSNs), immature OSNs, and the residual population of neighboring cell types, and then comparing these ratios against the known expression patterns of >300 genes, enrichment criteria that accurately predicted the OSN expression patterns of nearly all genes were determined. We identified 847 immature OSN-specific and 691 mature OSN-specific genes. The control of gene expression by chromatin modification and transcription factors, and neurite growth, protein transport, RNA processing, cholesterol biosynthesis, and apoptosis via death domain receptors, were overrepresented biological processes in immature OSNs. Ion transport (ion channels), presynaptic functions, and cilia-specific processes were overrepresented in mature OSNs. Processes overrepresented among the genes expressed by all OSNs were protein and ion transport, ER overload response, protein catabolism, and the electron transport chain. To more accurately represent gradations in mRNA abundance and identify all genes expressed in each cell type, classification methods were used to produce probabilities of expression in each cell type for every gene. These probabilities, which identified 9,300 genes expressed in OSNs, were 96% accurate at identifying genes expressed in OSNs and 86% accurate at discriminating genes specific to mature and immature OSNs. This OSN gene database not only predicts the genes responsible for the major biological processes active in OSNs, but also identifies thousands of never before studied genes that support OSN phenotypes. PMID:22252456

Multiplex PCR identification of Taenia spp. in rodents and carnivores.

PubMed

Al-Sabi, Mohammad N S; Kapel, Christian M O

2011-11-01

The genus Taenia includes several species of veterinary and public health importance, but diagnosis of the etiological agent in definitive and intermediate hosts often relies on labor intensive and few specific morphometric criteria, especially in immature worms and underdeveloped metacestodes. In the present study, a multiplex PCR, based on five primers targeting the 18S rDNA and ITS2 sequences, produced a species-specific banding patterns for a range of Taenia spp. Species typing by the multiplex PCR was compared to morphological identification and sequencing of cox1 and/or 12S rDNA genes. As compared to sequencing, the multiplex PCR identified 31 of 32 Taenia metacestodes from rodents, whereas only 14 cysts were specifically identified by morphology. Likewise, the multiplex PCR identified 108 of 130 adult worms, while only 57 were identified to species by morphology. The tested multiplex PCR system may potentially be used for studies of Taenia spp. transmitted between rodents and carnivores.

Effect of acute acid-base disturbances on ErbB1/2 tyrosine phosphorylation in rabbit renal proximal tubules.

PubMed

Skelton, Lara A; Boron, Walter F

2013-12-15

The renal proximal tubule (PT) is a major site for maintaining whole body pH homeostasis and is responsible for reabsorbing ∼80% of filtered HCO3(-), the major plasma buffer, into the blood. The PT adapts its rate of HCO3(-) reabsorption (JHCO3(-)) in response to acute acid-base disturbances. Our laboratory previously showed that single isolated perfused PTs adapt JHCO3(-) in response to isolated changes in basolateral (i.e., blood side) CO2 and HCO3(-) concentrations but, surprisingly, not to pH. The response to CO2 concentration can be blocked by the ErbB family tyrosine kinase inhibitor PD-168393. In the present study, we exposed enriched rabbit PT suspensions to five acute acid-base disturbances for 5 and 20 min using a panel of phosphotyrosine (pY)-specific antibodies to determine the influence of each disturbance on pan-pY, ErbB1-specific pY (four sites), and ErbB2-specific pY (two sites). We found that each acid-base treatment generated a distinct temporal pY pattern. For example, the summated responses of the individual ErbB1/2-pY sites to each disturbance showed that metabolic acidosis (normal CO2 concentration and reduced HCO3(-) concentration) produced a transient summated pY decrease (5 vs. 20 min), whereas metabolic alkalosis produced a transient increase. Respiratory acidosis (normal HCO3(-) concentration and elevated CO2 concentration) had little effect on summated pY at 5 min but produced an elevation at 20 min, whereas respiratory alkalosis produced a reduction at 20 min. Our data show that ErbB1 and ErbB2 in the PT respond to acute acid-base disturbances, consistent with the hypothesis that they are part of the signaling cascade.

Effect of acute acid-base disturbances on ErbB1/2 tyrosine phosphorylation in rabbit renal proximal tubules

PubMed Central

Skelton, Lara A.

2013-01-01

The renal proximal tubule (PT) is a major site for maintaining whole body pH homeostasis and is responsible for reabsorbing ∼80% of filtered HCO3−, the major plasma buffer, into the blood. The PT adapts its rate of HCO3− reabsorption (JHCO3−) in response to acute acid-base disturbances. Our laboratory previously showed that single isolated perfused PTs adapt JHCO3− in response to isolated changes in basolateral (i.e., blood side) CO2 and HCO3− concentrations but, surprisingly, not to pH. The response to CO2 concentration can be blocked by the ErbB family tyrosine kinase inhibitor PD-168393. In the present study, we exposed enriched rabbit PT suspensions to five acute acid-base disturbances for 5 and 20 min using a panel of phosphotyrosine (pY)-specific antibodies to determine the influence of each disturbance on pan-pY, ErbB1-specific pY (four sites), and ErbB2-specific pY (two sites). We found that each acid-base treatment generated a distinct temporal pY pattern. For example, the summated responses of the individual ErbB1/2-pY sites to each disturbance showed that metabolic acidosis (normal CO2 concentration and reduced HCO3− concentration) produced a transient summated pY decrease (5 vs. 20 min), whereas metabolic alkalosis produced a transient increase. Respiratory acidosis (normal HCO3− concentration and elevated CO2 concentration) had little effect on summated pY at 5 min but produced an elevation at 20 min, whereas respiratory alkalosis produced a reduction at 20 min. Our data show that ErbB1 and ErbB2 in the PT respond to acute acid-base disturbances, consistent with the hypothesis that they are part of the signaling cascade. PMID:24133121

Cloning, expression and characterization of a ι-carrageenase from marine bacterium Wenyingzhuangia fucanilytica: A biocatalyst for producing ι-carrageenan oligosaccharides.

PubMed

Shen, Jingjing; Chang, Yaoguang; Dong, Shujun; Chen, Feng

2017-10-10

ι-Carrageenan is an algal polysaccharide widely applied in the food industry. Specific glycoside hydrolases are valuable tools for modifying polysaccharides and producing oligosaccharides. In this study, the gene of a novel GH82 family ι-carrageenase was cloned from the genome of marine bacterium Wenyingzhuangia fucanilytica. The ι-carrageenase designated as Cgi82A was expressed in Escherichia coli, and its biochemical properties, kinetic constants and hydrolysis pattern were characterized. The enzyme could reach its highest activity at 25°C, which is lower than all hitherto reported GH82 ι-carrageenases. It was an endo-acting hydrolase, and could be utilized as a potential biocatalyst for producing ι-carrageenan oligosaccharides with different polymerization degrees. Cgi82A possessed relatively high substrate-binding affinity and catalysis efficiency indicated by its kinetic constants (K m , 1.12μM;K cat , 560.75s -1 ). Its major end product was ι-carrageenan tetrasaccharide. The acquiring of this novel enzyme would facilitate the future application of ι-carrageenan and its oligosaccharides. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

COMMUNICATION Designing a somatosensory neural prosthesis: percepts evoked by different patterns of thalamic stimulation

NASA Astrophysics Data System (ADS)

Heming, Ethan; Sanden, Andrew; Kiss, Zelma H. T.

2010-12-01

Although major advances have been made in the development of motor prostheses, fine motor control requires intuitive somatosensory feedback. Here we explored whether a thalamic site for a somatosensory neural prosthetic could provide natural somatic sensation to humans. Different patterns of electrical stimulation (obtained from thalamic spike trains) were applied in patients undergoing deep brain stimulation surgery. Changes in pattern produced different sensations, while preserving somatotopic representation. While most percepts were reported as 'unnatural', some stimulations produced more 'natural' sensations than others. However, the additional patterns did not elicit more 'natural' percepts than high-frequency (333 Hz) electrical stimulation. These features suggest that despite some limitations, the thalamus may be a feasible site for a somatosensory neural prosthesis and different stimulation patterns may be useful in its development.

Transducer model produces facilitation from opposite-sign flanks

NASA Technical Reports Server (NTRS)

Solomon, J. A.; Watson, A. B.; Morgan, M. J.

1999-01-01

Small spots, lines and Gabor patterns can be easier to detect when they are superimposed upon similar spots, lines and Gabor patterns. Traditionally, such facilitation has been understood to be a consequence of nonlinear contrast transduction. Facilitation has also been reported to arise from non-overlapping patterns with opposite sign. We point out that this result does not preclude the traditional explanation for superimposed targets. Moreover, we find that facilitation from opposite-sign flanks is weaker than facilitation from same-sign flanks. Simulations with a transducer model produce opposite-sign facilitation.

Comparison of three GIS-based models for predicting rockfall runout zones at a regional scale

NASA Astrophysics Data System (ADS)

Dorren, Luuk K. A.; Seijmonsbergen, Arie C.

2003-11-01

Site-specific information about the level of protection that mountain forests provide is often not available for large regions. Information regarding rockfalls is especially scarce. The most efficient way to obtain information about rockfall activity and the efficacy of protection forests at a regional scale is to use a simulation model. At present, it is still unknown which forest parameters could be incorporated best in such models. Therefore, the purpose of this study was to test and evaluate a model for rockfall assessment at a regional scale in which simple forest stand parameters, such as the number of trees per hectare and the diameter at breast height, are incorporated. Therefore, a newly developed Geographical Information System (GIS)-based distributed model is compared with two existing rockfall models. The developed model is the only model that calculates the rockfall velocity on the basis of energy loss due to collisions with trees and on the soil surface. The two existing models calculate energy loss over the distance between two cell centres, while the newly developed model is able to calculate multiple bounces within a pixel. The patterns of rockfall runout zones produced by the three models are compared with patterns of rockfall deposits derived from geomorphological field maps. Furthermore, the rockfall velocities modelled by the three models are compared. It is found that the models produced rockfall runout zone maps with rather similar accuracies. However, the developed model performs best on forested hillslopes and it also produces velocities that match best with field estimates on both forested and nonforested hillslopes irrespective of the slope gradient.

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.

The organ-specific expression of terpene synthase genes contributes to the terpene hydrocarbon composition of chamomile essential oils.

PubMed

Irmisch, Sandra; Krause, Sandra T; Kunert, Grit; Gershenzon, Jonathan; Degenhardt, Jörg; Köllner, Tobias G

2012-06-08

The essential oil of chamomile, one of the oldest and agronomically most important medicinal plant species in Europe, has significant antiphlogistic, spasmolytic and antimicrobial activities. It is rich in chamazulene, a pharmaceutically active compound spontaneously formed during steam distillation from the sesquiterpene lactone matricine. Chamomile oil also contains sesquiterpene alcohols and hydrocarbons which are produced by the action of terpene synthases (TPS), the key enzymes in constructing terpene carbon skeletons. Here, we present the identification and characterization of five TPS enzymes contributing to terpene biosynthesis in chamomile (Matricaria recutita). Four of these enzymes were exclusively expressed in above-ground organs and produced the common terpene hydrocarbons (-)-(E)-β-caryophyllene (MrTPS1), (+)-germacrene A (MrTPS3), (E)-β-ocimene (MrTPS4) and (-)-germacrene D (MrTPS5). A fifth TPS, the multiproduct enzyme MrTPS2, was mainly expressed in roots and formed several Asteraceae-specific tricyclic sesquiterpenes with (-)-α-isocomene being the major product. The TPS transcript accumulation patterns in different organs of chamomile were consistent with the abundance of the corresponding TPS products isolated from these organs suggesting that the spatial regulation of TPS gene expression qualitatively contribute to terpene composition. The terpene synthases characterized in this study are involved in the organ-specific formation of essential oils in chamomile. While the products of MrTPS1, MrTPS2, MrTPS4 and MrTPS5 accumulate in the oils without further chemical alterations, (+)-germacrene A produced by MrTPS3 accumulates only in trace amounts, indicating that it is converted into another compound like matricine. Thus, MrTPS3, but also the other TPS genes, are good markers for further breeding of chamomile cultivars rich in pharmaceutically active essential oils.

Differential developmental ability of embryos cloned from tissue-specific stem cells.

PubMed

Inoue, Kimiko; Noda, Shinichi; Ogonuki, Narumi; Miki, Hiromi; Inoue, Shinichi; Katayama, Kazufumi; Mekada, Kazuyuki; Miyoshi, Hiroyuki; Ogura, Atsuo

2007-05-01

Although cloning animals by somatic cell nuclear transfer is generally inefficient, the use of certain nuclear donor cell types may significantly improve or deteriorate outcomes. We evaluated whether two multipotent stem cell lines produced in vitro--neural stem cells (NSCs) and mesenchymal stem cells (MSCs)--could serve as nuclear donors for nuclear transfer cloning. Most (76%) NSC-derived embryos survived the two-cell-to-four-cell transition, the stage when the major zygotic gene activation occurs. Consistent with this observation, the expression patterns of zygotically active genes were better in NSC-derived embryos than in fibroblast clone embryos, which arrested at the two-cell stage more frequently. Embryo transfer experiments demonstrated that at least some of these NSC embryos had the ability to develop to term fetuses (1.6%, 3/189). In contrast, embryos reconstructed using MSCs showed a low rate of in vitro development and never underwent implantation in vivo. Chromosomal analysis of the donor MSCs revealed very frequent aneuploidy, which probably impaired the potential for development of their derived clones. This is the first demonstration that tissue-specific multipotent stem cells produced in vitro can serve as donors of nuclei for cloning mice; however, these cells may be prone to chromosomal aberrations, leading to high embryonic death rates. We found previously that hematopoietic stem cells (HSCs) are very inefficient donor cells because of their failure to activate the genes essential for embryonic development. Taken together, our data led us to conclude that tissue-specific stem cells in mice, namely NSCs, MSCs, and HSCs, exhibited marked variations in the ability to produce cloned offspring and that this ability varies according to both the epigenetic and genetic status of the original genomes. Disclosure of potential conflicts of interest is found at the end of this article.

Process for Making Ceramic Mold

NASA Technical Reports Server (NTRS)

Buck, Gregory M. (Inventor); Vasquez, Peter (Inventor)

2001-01-01

An improved process for slip casting molds that can be more economically automated and that also exhibits greater dimensional stability is disclosed. The process involves subjecting an investment pattern, preferably made from wax, to successive cycles of wet-dipping in a slurry of colloidal, silica-based binder and dry powder-coating, or stuccoing with plaster of Paris or calcium sulfate mixtures to produce a multi-layer shell over the pattern. The invention as claimed entails applying a primary and a secondary coating to the investment pattern. At least two wet-dipping on in a primary slurry and dry-stuccoing cycles provide the primary coating, and an additional two wet-dippings and dry-stuccoing cycles provide the secondary, or back-up, coating. The primary and secondary coatings produce a multi-layered shell pattern. The multi-layered shell pattern is placed in a furnace first to cure and harden, and then to vaporize the investment pattern, leaving a detailed, high precision shell mold.

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.

Tile Patterns with LOGO--Part II: Tile Patterns from Rep Tiles Using LOGO.

ERIC Educational Resources Information Center

Clason, Robert G.

1991-01-01

Described is a recursive LOGO method for dissecting polygons into congruent parts (rep tiles) similar to the original polygon, thereby producing unexpected patterns. A list of descriptions for such dissections is included along with suggestions for modifications that allow extended student explorations into tile patterns. (JJK)

A USCLVAR Multi-Model Assessment of the Impact of SST Anomalies and Land-Atmosphere Feedbacks on Drought

NASA Technical Reports Server (NTRS)

Schubert, Siegfried

2009-01-01

The USCLIVAR working group on drought recently initiated a series of global climate model simulations forced with idealized SST anomaly patterns, designed to address a number of uncertainties regarding the impact of SST forcing and the role of land-atmosphere feedbacks on regional drought. Specific questions that the runs are designed to address include, What are the mechanisms that maintain drought across the seasonal cycle and from one year to the next? What is the role of the leading patterns of SST variability, and what are the physical mechanisms linking the remote SST forcing to regional drought, including the role of land-atmosphere coupling? The runs were carried out with five different atmospheric general circulation models (AGCMs), and one coupled atmosphere-ocean model in which the model was continuously nudged to the imposed SST forcing. This talk provides an overview of the experiments and some initial results focusing on the responses to the leading patterns of annual mean SST variability consisting of a Pacific El Nino/Southern Oscillation (ENSO)-like pattern, a pattern that resembles the Atlantic Multi-decadal Oscillation (AMO), and a global trend pattern. One of the key findings is that all the AGCMs produce broadly similar (though different in detail) precipitation responses to the Pacific forcing pattern, with a cold Pacific leading to reduced precipitation and a warm Pacific leading to enhanced precipitation over most of the United States. While the response to the Atlantic pattern is less robust, there is general agreement among the models that the largest precipitation response over the U.S. tends to occur when the two oceans have anomalies of opposite sign. That is, a cold Pacific and warm Atlantic tend to produce the largest precipitation reductions, whereas a warm Pacific and cold Atlantic tend to produce the greatest precipitation enhancements. Further analysis of the response over the U.S. to the Pacific forcing highlights a number of noteworthy and to some extent unexpected results. These include a seasonal dependence of the precipitation response that is characterized by signal-to-noise ratios that peak in spring, and surface temperature signal-to-noise ratios that are both lower and show less agreement among the models than those found for the precipitation response. Another interesting result concerns what appears to be a substantially different character in the surface temperature response over the U.S. to the Pacific forcing by the only model examined here that was developed for use in numerical weather prediction. The response to the positive SST trend forcing pattern is an overall surface warming over the world's land areas with substantial regional variations that are in part reproduced in runs forced with a globally uniform SST trend forcing. The precipitation response to the trend forcing is weak in all the models. It is hoped that these early results will serve to stimulate further analysis of these simulations, as well as suggest new research on the physical mechanisms contributing to hydroclimatic variability and change throughout the world.

Patterns of light interference produced by damaged cuticle cells in human hair.

PubMed

Gamez-Garcia, Manuel; Lu, Yuan

2007-01-01

Colorful patterns of light interference have been observed to occur in human hair cuticle cells. The light interference phenomenon has been analyzed by optical microscopy. The strong patterns of light interference appeared only in cuticle cells that had been damaged either mechanically or by thermal stresses. Cuticle cells that were not damaged did not produce this phenomenon. The zones of light interference on the hair surface were seen to extend to cuticle sheath areas whose damage was not apparent when analyzed under the Scanning Electron Microscope. The presence of oils and other hydrophobic materials in the hair had a strong effect in the appearance or disappearance of the interference patterns.

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.

Frequency and time pattern differences in acoustic signals produced by Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae) and Sitophilus zeamais (Motschulsky) (Coleoptera: Curculionidae) in stored maize

USDA-ARS?s Scientific Manuscript database

The acoustic signals emitted by the last stage larval instars and adults of Prostephanus truncatus and Sitophilus zeamais in stored maize were investigated. Analyses were performed to identify brief, 1-10-ms broadband sound impulses of five different frequency patterns produced by larvae and adults,...

Structure, dynamics and movement patterns of the Australian pig industry.

PubMed

East, I J; Davis, J; Sergeant, E S G; Garner, M G

2014-03-01

To assess management practices and movement patterns that could influence the establishment and spread of exotic animal diseases (EAD) in pigs in Australia. A literature review of published information and a telephone survey of 370 pig producers owning >10 pigs who were registered with the PigPass national vendor declaration scheme. The movement and marketing patterns of Australian pig producers interviewed were divided into two groups based predominantly on the size of the herd. Major pig producers maintain closed herds, use artificial insemination and market direct to abattoirs. Smaller producers continue to purchase from saleyards and market to other farms, abattoirs and through saleyards in an apparently opportunistic fashion. The role of saleyards in the Australian pig industry continues to decline, with 92% of all pigs marketed directly from farm to abattoir. This survey described movement patterns that will assist in modelling the potential spread of EAD in the Australian pig industry. Continued movement towards vertical integration and closed herds in the Australian pig industry effectively divides the industry into a number of compartments that mitigate against the widespread dissemination of disease to farms adopting these practices. © 2014 Australian Veterinary Association.

Lip movements affect infants' audiovisual speech perception.

PubMed

Yeung, H Henny; Werker, Janet F

2013-05-01

Speech is robustly audiovisual from early in infancy. Here we show that audiovisual speech perception in 4.5-month-old infants is influenced by sensorimotor information related to the lip movements they make while chewing or sucking. Experiment 1 consisted of a classic audiovisual matching procedure, in which two simultaneously displayed talking faces (visual [i] and [u]) were presented with a synchronous vowel sound (audio /i/ or /u/). Infants' looking patterns were selectively biased away from the audiovisual matching face when the infants were producing lip movements similar to those needed to produce the heard vowel. Infants' looking patterns returned to those of a baseline condition (no lip movements, looking longer at the audiovisual matching face) when they were producing lip movements that did not match the heard vowel. Experiment 2 confirmed that these sensorimotor effects interacted with the heard vowel, as looking patterns differed when infants produced these same lip movements while seeing and hearing a talking face producing an unrelated vowel (audio /a/). These findings suggest that the development of speech perception and speech production may be mutually informative.

Patterns produced when soil is transferred to bras by placing and dragging actions: The application of digital photography and image processing to support visible observations.

PubMed

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

2017-07-01

A series of soil transference experiments (STEs) were undertaken to determine whether patterns identified in laboratory experiments could also be recognised at a simulated crime scene in the field. A clothed 55kg human rescue dummy dressed in a padded bra was either dragged or merely placed on a soil surface at sites with natural and anthropogenic soil types under both wet and dry soil conditions. Transfer patterns produced by dragging compared favourably with those of laboratory experiments. Twelve patterns were identified when a clothed human rescue dummy was dragged across the two soil types in the field. This expanded the original set of eight soil transfer patterns identified from dragging weighted fabric across soil samples in the laboratory. Soil transferred by placing the human rescue dummy resulted in a set of six transfer patterns that were different to those produced by dragging. By comparing trace soil patterns transferred to bras using each transfer method, it was revealed that certain transfer patterns on bras could indicate how the fabric had made contact with a soil surface. A photographic method was developed for crime scene examiners to capture this often subtle soil evidence before a body is transported or the clothing removed. This improved understanding of the dynamics of soil transference to bras and related clothing fabric may assist forensic investigators reconstruct the circumstances of a variety of forensic events. Copyright © 2017 Elsevier B.V. All rights reserved.

Sources of Error in Substance Use Prevalence Surveys

PubMed Central

Johnson, Timothy P.

2014-01-01

Population-based estimates of substance use patterns have been regularly reported now for several decades. Concerns with the quality of the survey methodologies employed to produce those estimates date back almost as far. Those concerns have led to a considerable body of research specifically focused on understanding the nature and consequences of survey-based errors in substance use epidemiology. This paper reviews and summarizes that empirical research by organizing it within a total survey error model framework that considers multiple types of representation and measurement errors. Gaps in our knowledge of error sources in substance use surveys and areas needing future research are also identified. PMID:27437511

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

The Interactions of Human Neutrophils with Shiga Toxins and Related Plant Toxins: Danger or Safety?

PubMed Central

Brigotti, Maurizio

2012-01-01

Shiga toxins and ricin are well characterized similar toxins belonging to quite different biological kingdoms. Plant and bacteria have evolved the ability to produce these powerful toxins in parallel, while humans have evolved a defense system that recognizes molecular patterns common to foreign molecules through specific receptors expressed on the surface of the main actors of innate immunity, namely monocytes and neutrophils. The interactions between these toxins and neutrophils have been widely described and have stimulated intense debate. This paper is aimed at reviewing the topic, focusing particularly on implications for the pathogenesis and diagnosis of hemolytic uremic syndrome. PMID:22741061

LEAFY blossoms.

PubMed

Moyroud, Edwige; Kusters, Elske; Monniaux, Marie; Koes, Ronald; Parcy, François

2010-06-01

The LEAFY (LFY) gene of Arabidopsis and its homologs in other angiosperms encode a unique plant-specific transcription factor that assigns the floral fate of meristems and plays a key role in the patterning of flowers, probably since the origin of flowering plants. LFY-like genes are also found in gymnosperms, ferns and mosses that do not produce flowers, but their role in these plants is poorly understood. Here, we review recent findings explaining how the LFY protein works and how it could have evolved throughout land plant history. We propose that LFY homologs have an ancestral role in regulating cell division and arrangement, and acquired novel functions in seed plants, such as activating reproductive gene networks.

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

Bartolo, Nicola; Guzzetti, Maria Chiara; Liguori, Michele

We investigate the potential for the LISA space-based interferometer to detect the stochastic gravitational wave background produced from different mechanisms during inflation. Focusing on well-motivated scenarios, we study the resulting contributions from particle production during inflation, inflationary spectator fields with varying speed of sound, effective field theories of inflation with specific patterns of symmetry breaking and models leading to the formation of primordial black holes. The projected sensitivities of LISA are used in a model-independent way for various detector designs and configurations. We demonstrate that LISA is able to probe these well-motivated inflationary scenarios beyond the irreducible vacuum tensor modesmore » expected from any inflationary background.« less

Porous silicon ring resonator for compact, high sensitivity biosensing applications

DOE PAGES

Rodriguez, Gilberto A.; Hu, Shuren; Weiss, Sharon M.

2015-01-01

A ring resonator is patterned on a porous silicon slab waveguide to produce a compact, high quality factor biosensor with a large internal surface area available for enhanced recognition of biological and chemical molecules. The porous nature of the ring resonator allows molecules to directly interact with the guided mode. Quality factors near 10,000 were measured for porous silicon ring resonators with a radius of 25 μm. A bulk detection sensitivity of 380 nm/RIU was measured upon exposure to salt water solutions. Specific detection of nucleic acid molecules was demonstrated with a surface detection sensitivity of 4 pm/nM.

Categorization of multiple sclerosis relapse subtypes by B cell profiling in the blood.

PubMed

Hohmann, Christopher; Milles, Bianca; Schinke, Michael; Schroeter, Michael; Ulzheimer, Jochen; Kraft, Peter; Kleinschnitz, Christoph; Lehmann, Paul V; Kuerten, Stefanie

2014-09-16

B cells are attracting increasing attention in the pathogenesis of multiple sclerosis (MS). B cell-targeted therapies with monoclonal antibodies or plasmapheresis have been shown to be successful in a subset of patients. Here, patients with either relapsing-remitting (n = 24) or secondary progressive (n = 6) MS presenting with an acute clinical relapse were screened for their B cell reactivity to brain antigens and were re-tested three to nine months later. Enzyme-linked immunospot technique (ELISPOT) was used to identify brain-reactive B cells in peripheral blood mononuclear cells (PBMC) directly ex vivo and after 96 h of polyclonal stimulation. Clinical severity of symptoms was determined using the Expanded Disability Status Scale (EDSS). Nine patients displayed B cells in the blood producing brain-specific antibodies directly ex vivo. Six patients were classified as B cell positive donors only after polyclonal B cell stimulation. In 15 patients a B cell response to brain antigens was absent. Based on the autoreactive B cell response we categorized MS relapses into three different patterns. Patients who displayed brain-reactive B cell responses both directly ex vivo and after polyclonal stimulation (pattern I) were significantly younger than patients in whom only memory B cell responses were detectable or entirely absent (patterns II and III; p = 0.003). In one patient a conversion to a positive B cell response as measured directly ex vivo and subsequently also after polyclonal stimulation was associated with the development of a clinical relapse. The evaluation of the predictive value of a brain antigen-specific B cell response showed that seven of eight patients (87.5%) with a pattern I response encountered a clinical relapse during the observation period of 10 months, compared to two of five patients (40%) with a pattern II and three of 14 patients (21.4%) with a pattern III response (p = 0.0005; hazard ratio 6.08 (95% confidence interval 1.87-19.77). Our data indicate actively ongoing B cell-mediated immunity against brain antigens in a subset of MS patients that may be causative of clinical relapses and provide new diagnostic and therapeutic options for a subset of patients.

Peptides for functionalization of InP semiconductors.

PubMed

Estephan, Elias; Saab, Marie-belle; Larroque, Christian; Martin, Marta; Olsson, Fredrik; Lourdudoss, Sebastian; Gergely, Csilla

2009-09-15

The challenge is to achieve high specificity in molecular sensing by proper functionalization of micro/nano-structured semiconductors by peptides that reveal specific recognition for these structures. Here we report on surface modification of the InP semiconductors by adhesion peptides produced by the phage display technique. An M13 bacteriophage library has been used to screen 10(10) different peptides against the InP(001) and the InP(111) surfaces to finally isolate specific peptides for each orientation of the InP. MALDI-TOF/TOF mass spectrometry has been employed to study real affinity of the peptide towards the InP surfaces. The peptides serve for controlled placement of biotin onto InP to bind then streptavidin. Our Atomic Force Microscopy study revealed a total surface coverage of molecules when the InP surface was functionalized by its specific biotinylated peptide (YAIKGPSHFRPS). Finally, fluorescence microscopy has been employed to demonstrate the preferential attachment of the peptide onto a micro-patterned InP surface. Use of substrate specific peptides could present an alternative solution for the problems encountered in the actually existing sensing methods and molecular self-assembly due to the unwanted unspecific interactions.

Diffractive optical devices produced by light-assisted trapping of nanoparticles.

PubMed

Muñoz-Martínez, J F; Jubera, M; Matarrubia, J; García-Cabañes, A; Agulló-López, F; Carrascosa, M

2016-01-15

One- and two-dimensional diffractive optical devices have been fabricated by light-assisted trapping and patterning of nanoparticles. The method is based on the dielectrophoretic forces appearing in the vicinity of a photovoltaic crystal, such as Fe:LiNbO3, during or after illumination. By illumination with the appropriate light distribution, the nanoparticles are organized along patterns designed at will. One- and two-dimensional diffractive components have been achieved on X- and Z-cut Fe:LiNbO3 crystals, with their polar axes parallel and perpendicular to the crystal surface, respectively. Diffraction gratings with periods down to around a few micrometers have been produced using metal (Al, Ag) nanoparticles with radii in the range of 70-100 nm. Moreover, several 2D devices, such as Fresnel zone plates, have been also produced showing the potential of the method. The diffractive particle patterns remain stable when light is removed. A method to transfer the diffractive patterns to other nonphotovoltaic substrates, such as silica glass, has been also reported.

Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls

PubMed Central

Leininger, Elizabeth C.; Kelley, Darcy B.

2013-01-01

Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the calling brain and vocal organ (larynx) in two species that independently evolved simplified calls. We find that each species uses distinct neural and neuromuscular strategies to produce the simplified calls. Isolated  Xenopus borealis brains produce fictive vocal patterns that match temporal patterns of actual male calls; the larynx converts nerve activity faithfully into muscle contractions and single clicks. In contrast, fictive patterns from isolated Xenopus boumbaensis brains are short bursts of nerve activity; the isolated larynx requires stimulus bursts to produce a single click of sound. Thus, unlike X. borealis, the output of the X. boumbaensis hindbrain vocal pattern generator is an ancestral burst-type pattern, transformed by the larynx into single clicks. Temporally simple advertisement calls in genetically distant species of Xenopus have thus arisen independently via reconfigurations of central and peripheral vocal neuroeffectors. PMID:23407829

Density patterns in metal films produced by laser interference.

PubMed

Peláez, R J; Afonso, C N; Škereň, M; Bulíř, J

2015-01-26

Fringed periodic patterns have been produced by laser interference at 193 nm in an almost continuous 9.5 nm-thick Ag film that exhibits a number density of ≈189 μm(-2) holes. Patterns with four periods in the range of 1.8-10.2 μm were produced by changing the projection optics. At high fluences, the film breaks up into nanostructures around the regions exposed to intensity maxima due to laser-induced melting. At low fluences, a new process is observed that is triggered at the initial holes of the film by solid-state dewetting. Once the fluence is high enough to prevent the temperature balance across the pattern, mass transport from cold to hot regions is observed, leading to film densification in regions around intensity maxima sites. The novel patterns are thus formed by fringes of material that is more/less dense than the as-grown film, each of which is located at intensity maxima/minima sites, and have negligible topography. Comparing the present results to earlier reports in the literature shows that the thermal gradient across the pattern is influenced by the initial film microstructure, rather than by the thickness. The existence of a minimum period, which is achievable depending on the thermal continuity of the film, is also discussed.

Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls.

PubMed

Leininger, Elizabeth C; Kelley, Darcy B

2013-04-07

Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the calling brain and vocal organ (larynx) in two species that independently evolved simplified calls. We find that each species uses distinct neural and neuromuscular strategies to produce the simplified calls. Isolated Xenopus borealis brains produce fictive vocal patterns that match temporal patterns of actual male calls; the larynx converts nerve activity faithfully into muscle contractions and single clicks. In contrast, fictive patterns from isolated Xenopus boumbaensis brains are short bursts of nerve activity; the isolated larynx requires stimulus bursts to produce a single click of sound. Thus, unlike X. borealis, the output of the X. boumbaensis hindbrain vocal pattern generator is an ancestral burst-type pattern, transformed by the larynx into single clicks. Temporally simple advertisement calls in genetically distant species of Xenopus have thus arisen independently via reconfigurations of central and peripheral vocal neuroeffectors.

Anomalous Accretionary Margin Topography Formed By Repeated Earthquakes

NASA Astrophysics Data System (ADS)

Furlong, Kevin P.

2014-05-01

It has long been recognized that accretionary margins of major subduction zones undergo substantial deformation. However even with the large amounts of shortening accommodated within the margin, for most subduction zones, there is an extended submarine portion to the accretionary, highly-deformed upper-plate between the trench and the coast. This is a vexing situation since this submarine section typically overlies the actual locked or coupled patch of the plate interface. The result of this is added difficulty in directly observing processes related to the plate interface coupling - such processes as micro-seismicity and the actual patterns of plate coupling. There are a few locations globally in which there are sub-aerially exposed terranes that lie closer to the trench and overlie the inferred coupled or seismogenic portion of the plate interface. Such regions have taken on significance in subduction zone studies as they provide locations to observe the plate interface coupling effects in the near-field. In particular the Pacific coast of Costa Rica provides such a location, and there has been substantial geologic, geophysical, and geodetic research exploiting the positions of these near-trench peninsulas (Nicoya, Osa, and Burica). These sites provide near-field access to plate-interface processes, but whether they represent typical subduction zone behavior remains an open question as the deformational processes or inherited structures that have produced this anomalous topography are not well constrained. Simply put, if the existence of these sub-aerial, near-trench terranes is a result of anomalous behavior on the plate interface (as has been suggested), then their utility in providing high-fidelity near-field insight into the plate interface properties and processes is substantially reduced. Here we propose a new mechanism that could be responsible for the formation of both the Nicoya and Osa Peninsulas in the past, and is currently producing a third peninsula - the Burica Peninsula at the intersection of the Panama fracture zone and the margin. Specifically we propose that the anomalous topography along the Pacific coast of Costa Rica has been produced by repeated, great subduction earthquakes that have ruptured across the boundary separating the Cocos and Nazca plates - the subducted continuation of the Panama fracture zone. The pattern of upper-plate shortening generated by such a process (documented in the 2007 Mw 8.1 Solomon Islands earthquake, which produced co-seismic localized uplift above the subducted transform plate boundary) convolved with the migration history of the Panama triple junction (PTJ) is proposed as the mechanism to produce substantial along-margin, long-lived accretionary margin topography. Specifically we argue that repeated great subduction earthquakes that rupture across fundamental plate boundary structures can produce substantial, long-lived upper plate deformation above the inter-seismically coupled plate interface.

Greek PDO saffron authentication studies using species specific molecular markers.

PubMed

Bosmali, I; Ordoudi, S A; Tsimidou, M Z; Madesis, P

2017-10-01

Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C. sativus L. from the cultivation area of "Krokos Kozanis" as well as the potential differences with the band pattern produced by other Crocus species. Then, species-specific markers were developed taking advantage of an advanced molecular technique such as the HRM analysis coupled with universal DNA barcoding regions (trnL) (Bar-HRM) and applied to saffron admixtures with some of the most common plant adulterants (Calendula officinalis, Carthamus tinctorius, Gardenia jasminoides, Zea mays and Curcuma longa). The sensitivity of the procedure was tested for turmeric as a case study whereas HPLC-fluorescence determination of secondary metabolites was also employed for comparison. The overall results indicated that the Bar-HRM approach is quite effective in terms of specificity and sensitivity. Its effectiveness regarding the detection of turmeric was comparable to that of a conventional HPLC method (0.5% vs 1.0%, w/w). Yet, the proposed DNA-based method is much faster, cost-effective and can be used even by non-geneticists, in any laboratory having access to an HRM-capable real-time PCR instrumentation. It can be, thus, regarded as a strong analytical tool in saffron authentication studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

GABAB-receptor activation alters the firing pattern of dopamine neurons in the rat substantia nigra.

PubMed

Engberg, G; Kling-Petersen, T; Nissbrandt, H

1993-11-01

Previous electrophysiological experiments have emphasized the importance of the firing pattern for the functioning of midbrain dopamine (DA) neurons. In this regard, excitatory amino acid receptors appear to constitute an important modulatory control mechanism. In the present study, extracellular recording techniques were used to investigate the significance of GABAB-receptor activation for the firing properties of DA neurons in the substantia nigra (SN) in the rat. Intravenous administration of the GABAB-receptor agonist baclofen (1-16 mg/kg) was associated with a dose-dependent regularization of the firing pattern, concomitant with a reduction in burst firing. At higher doses (16-32 mg/kg), the firing rate of the DA neurons was dose-dependently decreased. Also, microiontophoretic application of baclofen regularized the firing pattern of nigral DA neurons, including a reduction of burst firing. Both the regularization of the firing pattern and inhibition of firing rate produced by systemic baclofen administration was antagonized by the GABAB-receptor antagonist CGP 35348 (200 mg/kg, i.v.). The GABAA-receptor agonist muscimol produced effects on the firing properties of DA neurons that were opposite to those observed following baclofen, i.e., an increase in firing rate accompanied by a decreased regularity. The NMDA receptor antagonist MK 801 (0.4-3.2 mg/kg, i.v.) produced a moderate, dose-dependent increase in the firing rate of the nigral DA neurons as well as a slightly regularized firing pattern. Pretreatment with MK 801 (3.2 mg/kg, i.v., 3-10 min) did neither promote nor prevent the regularization of the firing pattern or inhibition of firing rate on the nigral DA neurons produced by baclofen. The present results clearly show that GABAB-receptors can alter the firing pattern of nigral DA neurons, hereby counterbalancing the previously described ability of glutamate to induce burst firing activity on these neurons.

Multiple cis-acting sequence elements are required for efficient splicing of simian virus 40 small-t antigen pre-mRNA.

PubMed Central

Fu, X Y; Colgan, J D; Manley, J L

1988-01-01

We have determined the effects of a number of mutations in the small-t antigen mRNA intron on the alternative splicing pattern of the simian virus 40 early transcript. Expansion of the distance separating the small-t pre-mRNA lariat branch point and the shared large T-small t 3' splice site from 18 to 29 nucleotides (nt) resulted in a relative enhancement of small-t splicing in vivo. This finding, coupled with the observation that large-T pre-RNA splicing in vitro was not affected by this expansion, suggests that small-t splicing is specifically constrained by a short branch point-3' splice site distance. Similarly, the distance separating the 5' splice site and branch point (48 nt) was found to be at or near a minimum for small-t splicing, because deletions in this region as small as 2 nt dramatically reduced the ratio of small-t to large-T mRNA that accumulated in transfected cells. Finally, a specific sequence within the small-t intron, encompassing the upstream branch sites used in large-T splicing, was found to be an important element in the cell-specific pattern of early alternative splicing. Substitutions within this region reduced the ratio of small-t to large-T mRNA produced in HeLa cells but had only minor effects in human 293 cells. Images PMID:2851720

ASIC or PIC? Implantable stimulators based on semi-custom CMOS technology or low-power microcontroller architecture.

PubMed

Salmons, S; Gunning, G T; Taylor, I; Grainger, S R; Hitchings, D J; Blackhurst, J; Jarvis, J C

2001-01-01

To gain a better understanding of the effects of chronic stimulation on mammalian muscles we needed to generate patterns of greater variety and complexity than simple constant-frequency or burst patterns. We describe here two approaches to the design of implantable neuromuscular stimulators that can satisfy these requirements. Devices of both types were developed and used in long-term experiments. The first device was based on a semi-custom Application Specific Integrated Circuit (ASIC). This approach has the advantage that the circuit can be completely tested at every stage of development and production, assuring a high degree of reliability. It has the drawback of inflexibility: the patterns are produced by state machines implemented in silicon, so each new set of patterns requires a fresh production run, which is costly and time-consuming. The second device was based on a commercial microcontroller (Microchip PIC16C84). The functionality of this type of circuit is specified in software rather than in silicon hardware, allowing a single device to be programmed for different functions. With the use of features designed to improve fault-tolerance we found this approach to be as reliable as that based on ASICs. The encapsulated devices can easily be accommodated subcutaneously on the flank of a rabbit and a recent version is small enough to implant into the peritoneal cavity of rats. The current devices are programmed with a predetermined set of 12 patterns before assembly; the desired pattern is selected after implantation with an electronic flash gun. The operating current drain is less than 40 microA.

Pathogenic mechanisms of intracellular bacteria.

PubMed

Niller, Hans Helmut; Masa, Roland; Venkei, Annamária; Mészáros, Sándor; Minarovits, Janos

2017-06-01

We wished to overview recent data on a subset of epigenetic changes elicited by intracellular bacteria in human cells. Reprogramming the gene expression pattern of various host cells may facilitate bacterial growth, survival, and spread. DNA-(cytosine C5)-methyltransferases of Mycoplasma hyorhinis targeting cytosine-phosphate-guanine (CpG) dinucleotides and a Mycobacterium tuberculosis methyltransferase targeting non-CpG sites methylated the host cell DNA and altered the pattern of gene expression. Gene silencing by CpG methylation and histone deacetylation, mediated by cellular enzymes, also occurred in M. tuberculosis-infected macrophages. M. tuberculosis elicited cell type-specific epigenetic changes: it caused increased DNA methylation in macrophages, but induced demethylation, deposition of euchromatic histone marks and activation of immune-related genes in dendritic cells. A secreted transposase of Acinetobacter baumannii silenced a cellular gene, whereas Mycobacterium leprae altered the epigenotype, phenotype, and fate of infected Schwann cells. The 'keystone pathogen' oral bacterium Porphyromonas gingivalis induced local DNA methylation and increased the level of histone acetylation in host cells. These epigenetic changes at the biofilm-gingiva interface may contribute to the development of periodontitis. Epigenetic regulators produced by intracellular bacteria alter the epigenotype and gene expression pattern of host cells and play an important role in pathogenesis.

Closely related dermatophyte species produce different patterns of secreted proteins.

PubMed

Giddey, Karin; Favre, Bertrand; Quadroni, Manfredo; Monod, Michel

2007-02-01

Dermatophytes are the most common infectious agents responsible for superficial mycosis in humans and animals. Various species in this group of fungi show overlapping characteristics. We investigated the possibility that closely related dermatophyte species with different behaviours secrete distinct proteins when grown in the same culture medium. Protein patterns from culture filtrates of several strains of the same species were very similar. In contrast, secreted protein profiles from various species were different, and so a specific signature could be associated with each of the six analysed species. In particular, protein patterns were useful to distinguish Trichophyton tonsurans from Trichophyton equinum, which cannot be differentiated by ribosomal DNA sequencing. The secreted proteases Sub2, Sub6 and Sub7 of the subtilisin family, as well as Mep3 and Mep4 of the fungalisin family were identified. SUB6, SUB7, MEP3 and MEP4 genes were cloned and sequenced. Although the protein sequence of each protease was highly conserved across species, their level of secretion by the various species was not equivalent. These results suggest that a switch of habitat could be related to a differential expression of genes encoding homologous secreted proteins.

Bayesian Ising approximation for learning dictionaries of multispike timing patterns in premotor neurons

NASA Astrophysics Data System (ADS)

Hernandez Lahme, Damian; Sober, Samuel; Nemenman, Ilya

Important questions in computational neuroscience are whether, how much, and how information is encoded in the precise timing of neural action potentials. We recently demonstrated that, in the premotor cortex during vocal control in songbirds, spike timing is far more informative about upcoming behavior than is spike rate (Tang et al, 2014). However, identification of complete dictionaries that relate spike timing patterns with the controled behavior remains an elusive problem. Here we present a computational approach to deciphering such codes for individual neurons in the songbird premotor area RA, an analog of mammalian primary motor cortex. Specifically, we analyze which multispike patterns of neural activity predict features of the upcoming vocalization, and hence are important codewords. We use a recently introduced Bayesian Ising Approximation, which properly accounts for the fact that many codewords overlap and hence are not independent. Our results show which complex, temporally precise multispike combinations are used by individual neurons to control acoustic features of the produced song, and that these code words are different across individual neurons and across different acoustic features. This work was supported, in part, by JSMF Grant 220020321, NSF Grant 1208126, NIH Grant NS084844 and NIH Grant 1 R01 EB022872.

Opportunities for Fluid Dynamics Research in the Forensic Discipline of Bloodstain Pattern Analysis

NASA Astrophysics Data System (ADS)

Attinger, Daniel; Moore, Craig; Donaldson, Adam; Jafari, Arian; Stone, Howard

2013-11-01

This review [Forensic Science International, vol. 231, pp. 375-396, 2013] highlights research opportunities for fluid dynamics (FD) studies related to the forensic discipline of bloodstain pattern analysis (BPA). The need for better integrating FD and BPA is mentioned in a 2009 report by the US National Research Council, entitled ``Strengthening Forensic Science in the United States: A Path Forward''. BPA aims for practical answers to specific questions of the kind: ``How did a bloodletting incident happen?'' FD, on the other hand, aims to quantitatively describe the transport of fluids and the related causes, with general equations. BPA typically solves the indirect problem of inspecting stains in a crime scene to infer the most probable bloodletting incident that produced these patterns. FD typically defines the initial and boundary conditions of a fluid system and from there describe how the system evolves in time and space, most often in a deterministic manner. We review four topics in BPA with strong connections to FD: the generation of drops, their flight, their impact and the formation of stains. Future research on these topics would deliver new quantitative tools and methods for BPA, and present new multiphase flow problems for FD.

Genetics and evolution of Yersinia pseudotuberculosis O-specific polysaccharides: a novel pattern of O-antigen diversity

PubMed Central

Kenyon, Johanna J.; Cunneen, Monica M.

2017-01-01

Abstract O-antigen polysaccharide is a major immunogenic feature of the lipopolysaccharide of Gram-negative bacteria, and most species produce a large variety of forms that differ substantially from one another. There are 18 known O-antigen forms in the Yersinia pseudotuberculosis complex, which are typical in being composed of multiple copies of a short oligosaccharide called an O unit. The O-antigen gene clusters are located between the hemH and gsk genes, and are atypical as 15 of them are closely related, each having one of five downstream gene modules for alternative main-chain synthesis, and one of seven upstream modules for alternative side-branch sugar synthesis. As a result, many of the genes are in more than one gene cluster. The gene order in each module is such that, in general, the earlier a gene product functions in O-unit synthesis, the closer the gene is to the 5΄ end for side-branch modules or the 3΄ end for main-chain modules. We propose a model whereby natural selection could generate the observed pattern in gene order, a pattern that has also been observed in other species. PMID:28364730

A face versus non-face context influences amygdala responses to masked fearful eye whites.

PubMed

Kim, M Justin; Solomon, Kimberly M; Neta, Maital; Davis, F Caroline; Oler, Jonathan A; Mazzulla, Emily C; Whalen, Paul J

2016-12-01

The structure of the mask stimulus is crucial in backward masking studies and we recently demonstrated such an effect when masking faces. Specifically, we showed that activity of the amygdala is increased to fearful facial expressions masked with neutral faces and decreased to fearful expressions masked with a pattern mask-but critically both masked conditions discriminated fearful expressions from happy expressions. Given this finding, we sought to test whether masked fearful eye whites would produce a similar profile of amygdala response in a face vs non-face context. During functional magnetic resonance imaging scanning sessions, 30 participants viewed fearful or happy eye whites masked with either neutral faces or pattern images. Results indicated amygdala activity was increased to fearful vs happy eye whites in the face mask condition, but decreased to fearful vs happy eye whites in the pattern mask condition-effectively replicating and expanding our previous report. Our data support the idea that the amygdala is responsive to fearful eye whites, but that the nature of this activity observed in a backward masking design depends on the mask stimulus. © The Author (2016). Published by Oxford University Press.

Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids.

PubMed

Wang, Jianlin; Tian, Lu; Madlung, Andreas; Lee, Hyeon-Se; Chen, Meng; Lee, Jinsuk J; Watson, Brian; Kagochi, Trevor; Comai, Luca; Chen, Z Jeffrey

2004-08-01

Polyploidization is an abrupt speciation mechanism for eukaryotes and is especially common in plants. However, little is known about patterns and mechanisms of gene regulation during early stages of polyploid formation. Here we analyzed differential expression patterns of the progenitors' genes among successive selfing generations and independent lineages. The synthetic Arabidopsis allotetraploid lines were produced by a genetic cross between A. thaliana and A. arenosa autotetraploids. We found that some progenitors' genes are differentially expressed in early generations, whereas other genes are silenced in late generations or among different siblings within a selfing generation, suggesting that the silencing of progenitors' genes is rapidly and/or stochastically established. Moreover, a subset of genes is affected in autotetraploid and multiple independent allotetraploid lines and in A. suecica, a natural allotetraploid derived from A. thaliana and A. arenosa, indicating locus-specific susceptibility to ploidy-dependent gene regulation. The role of DNA methylation in silencing progenitors' genes is tested in DNA-hypomethylation transgenic lines of A. suecica using RNA interference (RNAi). Two silenced genes are reactivated in both ddm1- and met1-RNAi lines, consistent with the demethylation of centromeric repeats and gene-specific regions in the genome. A rapid and stochastic process of differential gene expression is reinforced by epigenetic regulation during polyploid formation and evolution. Copyright 2004 Genetics Society of America

Unique cell-type-specific patterns of DNA methylation in the root meristem.

PubMed

Kawakatsu, Taiji; Stuart, Tim; Valdes, Manuel; Breakfield, Natalie; Schmitz, Robert J; Nery, Joseph R; Urich, Mark A; Han, Xinwei; Lister, Ryan; Benfey, Philip N; Ecker, Joseph R

2016-04-29

DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base-resolution whole-genome DNA methylomes, mRNA transcriptomes and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell-type-specific patterns of DNA methylation, especially in the CHH sequence context, where H is A, C or T. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized so far. It is hypermethylated within transposable elements (TEs), accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24-nt small RNAs (smRNAs). The absence of the nucleosome remodeller DECREASED DNA METHYLATION 1 (DDM1), required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests that a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing an excess of 24-nt smRNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types.

Regional dialect variation in the vowel systems of typically developing children

PubMed Central

Jacewicz, Ewa; Fox, Robert Allen; Salmons, Joseph

2015-01-01

Purpose To investigate regional dialect variation in the vowel systems of normally developing 8–12 years-old children. Method Thirteen vowels in isolated h_d words were produced by 94 children and 93 adults, males and females. All participants spoke American English and were born and raised in one of three distinct dialect regions in the United States: western North Carolina (Southern dialect), central Ohio (Midland) and southeastern Wisconsin (Northern Midwestern dialect). Acoustic analysis included formant frequencies (F1 and F2) measured at five equidistant time points in a vowel and formant movement (trajectory length). Results Children’s productions showed many dialect-specific features comparable to those in adult speakers, both in terms of vowel dispersion patterns and formant movement. Different features were also found including systemic vowel changes, significant monophthongization of selected vowels and greater formant movement in diphthongs. Conclusions The acoustic results provide evidence for regional distinctiveness in children’s vowel systems. Children acquire not only the systemic relations among vowels but also their dialect-specific patterns of formant dynamics. Directing attention to the regional variation in the production of American English vowels, this work may prove helpful in better understanding and interpretation of the development of vowel categories and vowel systems in children. PMID:20966384

Steroid profiling reveals widespread local regulation of glucocorticoid levels during mouse development.

PubMed

Taves, Matthew D; Plumb, Adam W; Sandkam, Benjamin A; Ma, Chunqi; Van Der Gugten, Jessica Grace; Holmes, Daniel T; Close, David A; Abraham, Ninan; Soma, Kiran K

2015-02-01

Glucocorticoids (GCs) are produced by the adrenal glands and circulate in the blood to coordinate organismal physiology. In addition, different tissues may independently regulate their local GC levels via local GC synthesis. Here, we find that in the mouse, endogenous GCs show tissue-specific developmental patterns, rather than mirroring GCs in the blood. Using solid-phase extraction, HPLC, and specific immunoassays, we quantified endogenous steroids and found that in tissues of female and male mice, (1) local GC levels can be much higher than systemic GC levels, (2) local GCs follow age-related patterns different from those of systemic GCs, and (3) local GCs have identities different from those of systemic GCs. For example, whereas corticosterone is the predominant circulating adrenal GC in mice, high concentrations of cortisol were measured in neonatal thymus, bone marrow, and heart. The presence of cortisol was confirmed with liquid chromatography-tandem mass spectrometry. In addition, gene expression of steroidogenic enzymes was detected across multiple tissues, consistent with local GC production. Our results demonstrate that local GCs can differ from GCs in circulating blood. This finding suggests that steroids are widely used as local (paracrine or autocrine) signals, in addition to their classic role as systemic (endocrine) signals. Local GC regulation may even be the norm, rather than the exception, especially during development.

Identification of input variables for feature based artificial neural networks-saccade detection in EOG recordings.

PubMed

Tigges, P; Kathmann, N; Engel, R R

1997-07-01

Though artificial neural networks (ANN) are excellent tools for pattern recognition problems when signal to noise ratio is low, the identification of decision relevant features for ANN input data is still a crucial issue. The experience of the ANN designer and the existing knowledge and understanding of the problem seem to be the only links for a specific construction. In the present study a backpropagation ANN based on modified raw data inputs showed encouraging results. Investigating the specific influences of prototypical input patterns on a specially designed ANN led to a new sparse and efficient input data presentation. This data coding obtained by a semiautomatic procedure combining existing expert knowledge and the internal representation structures of the raw data based ANN yielded a list of feature vectors, each representing the relevant information for saccade identification. The feature based ANN produced a reduction of the error rate of nearly 40% compared with the raw data ANN. An overall correct classification of 92% of so far unknown data was realized. The proposed method of extracting internal ANN knowledge for the production of a better input data representation is not restricted to EOG recordings, and could be used in various fields of signal analysis.

Using the Leitz LMS 2000 for monitoring and improvement of an e-beam

NASA Astrophysics Data System (ADS)

Blaesing-Bangert, Carola; Roeth, Klaus-Dieter; Ogawa, Yoichi

1994-11-01

Kaizen--a continuously improving--is a philosophy lived in Japan which is also becoming more and more important in Western companies. To implement this philosophy in the semiconductor industry, a high performance metrology tool is essential to determine the status of production quality periodically. An important prerequisite for statistical process control is the high stability of the metrology tool over several months or years; the tool-induced shift should be as small as possible. The pattern placement metrology tool Leitz LMS 2000 has been used in a major European mask house for several years now to qualify masks within the tightest specifications and to monitor the MEBES III and its cassettes. The mask shop's internal specification for the long term repeatability of the pattern placement metrology tool is 19 nm instead of 42 nm as specified by the supplier of the tool. Then the process capability of the LMS 2000 over 18 months is represented by an average cpk value of 2.8 for orthogonality, 5.2 for x-scaling, and 3.0 for y-scaling. The process capability of the MEBES III and its cassettes was improved in the past years. For instance, 100% of the masks produced with a process tolerance of +/- 200 nm are now within this limit.

Applying Data Mining Techniques to Extract Hidden Patterns about Breast Cancer Survival in an Iranian Cohort Study.

PubMed

Khalkhali, Hamid Reza; Lotfnezhad Afshar, Hadi; Esnaashari, Omid; Jabbari, Nasrollah

2016-01-01

Breast cancer survival has been analyzed by many standard data mining algorithms. A group of these algorithms belonged to the decision tree category. Ability of the decision tree algorithms in terms of visualizing and formulating of hidden patterns among study variables were main reasons to apply an algorithm from the decision tree category in the current study that has not studied already. The classification and regression trees (CART) was applied to a breast cancer database contained information on 569 patients in 2007-2010. The measurement of Gini impurity used for categorical target variables was utilized. The classification error that is a function of tree size was measured by 10-fold cross-validation experiments. The performance of created model was evaluated by the criteria as accuracy, sensitivity and specificity. The CART model produced a decision tree with 17 nodes, 9 of which were associated with a set of rules. The rules were meaningful clinically. They showed in the if-then format that Stage was the most important variable for predicting breast cancer survival. The scores of accuracy, sensitivity and specificity were: 80.3%, 93.5% and 53%, respectively. The current study model as the first one created by the CART was able to extract useful hidden rules from a relatively small size dataset.

A deceptive pollination system targeting drosophilids through olfactory mimicry of yeast.

PubMed

Stökl, Johannes; Strutz, Antonia; Dafni, Amots; Svatos, Ales; Doubsky, Jan; Knaden, Markus; Sachse, Silke; Hansson, Bill S; Stensmyr, Marcus C

2010-10-26

In deceptive pollination, insects are bamboozled into performing nonrewarded pollination. A prerequisite for the evolutionary stability in such systems is that the plants manage to generate a perfect sensory impression of a desirable object in the insect nervous system [1]. The study of these plants can provide important insights into sensory preference of their visiting insects. Here, we present the first description of a deceptive pollination system that specifically targets drosophilid flies. We show that the examined plant (Arum palaestinum) accomplishes its deception through olfactory mimicry of fermentation, a strategy that represents a novel pollination syndrome. The lily odor is composed of volatiles characteristic of yeast, and produces in Drosophila melanogaster an antennal detection pattern similar to that elicited by a range of fermentation products. By functional imaging, we show that the lily odors target a specific subset of odorant receptors (ORs), which include the most conserved OR genes in the drosophilid olfactome. Furthermore, seven of eight visiting drosophilid species show a congruent olfactory response pattern to the lily, in spite of comprising species pairs separated by ∼40 million years [2], showing that the lily targets a basal function of the fly nose, shared by species with similar ecological preference. Copyright © 2010 Elsevier Ltd. All rights reserved.

Microgenomic analysis reveals cell type-specific gene expression patterns between ray and fusiform initials within the cambial meristem of Populus.

PubMed

Goué, Nadia; Lesage-Descauses, Marie-Claude; Mellerowicz, Ewa J; Magel, Elisabeth; Label, Philippe; Sundberg, Björn

2008-01-01

The vascular cambium is the meristem in trees that produce wood. This meristem consists of two types of neighbouring initials: fusiform cambial cells (FCCs), which give rise to the axial cell system (i.e. fibres and vessel elements), and ray cambial cells (RCCs), which give rise to rays. There is little molecular information on the mechanisms whereby the differing characteristics of these neighbouring cells are maintained. A microgenomic approach was adopted in which the transcriptomes of FCCs and RCCs dissected out from the cambial meristem of poplar (Populus trichocarpa x Populus deltoïdes var. Boelare) were analysed, and a transcriptional database for these two cell types established. Photosynthesis genes were overrepresented in RCCs, providing molecular support for the presence of photosynthetic systems in rays. Genes that putatively encode transporters (vesicle, lipid and metal ion transporters and aquaporins) in RCCs were also identified. In addition, many cell wall-related genes showed cell type-specific expression patterns. Notably, genes involved in pectin metabolism and xyloglucan metabolism were overrepresented in RCCs and FCCs, respectively. The results demonstrate the use of microgenomics to reveal differences in biological processes in neighbouring meristematic cells, and to identify key genes involved in these processes.

A spatiotemporal profile of visual system activation revealed by current source density analysis in the awake macaque.

PubMed

Schroeder, C E; Mehta, A D; Givre, S J

1998-01-01

We investigated the spatiotemporal activation pattern, produced by one visual stimulus, across cerebral cortical regions in awake monkeys. Laminar profiles of postsynaptic potentials and action potentials were indexed with current source density (CSD) and multiunit activity profiles respectively. Locally, we found contrasting activation profiles in dorsal and ventral stream areas. The former, like V1 and V2, exhibit a 'feedforward' profile, with excitation beginning at the depth of Lamina 4, followed by activation of the extragranular laminae. The latter often displayed a multilaminar/columnar profile, with initial responses distributed across the laminae and reflecting modulation rather than excitation; CSD components were accompanied by either no changes or by suppression of action potentials. System-wide, response latencies indicated a large dorsal/ventral stream latency advantage, which generalizes across a wide range of methods. This predicts a specific temporal ordering of dorsal and ventral stream components of visual analysis, as well as specific patterns of dorsal-ventral stream interaction. Our findings support a hierarchical model of cortical organization that combines serial and parallel elements. Critical in such a model is the recognition that processing within a location typically entails multiple temporal components or 'waves' of activity, driven by input conveyed over heterogeneous pathways from the retina.

Gut microbiota, diet, and obesity-related disorders-The good, the bad, and the future challenges.

PubMed

Portune, Kevin J; Benítez-Páez, Alfonso; Del Pulgar, Eva Maria Gomez; Cerrudo, Victor; Sanz, Yolanda

2017-01-01

Diet has been shown to be a major factor in modulating the structure of the mammalian gut microbiota by providing specific nutrient sources and inducing environmental changes (pH, bile acids) in the gut ecosystem. Long-term dietary patterns and short-term interventions have been shown to induce changes in gut microbiota structure and function, with several studies revealing metabolic changes likely resulting from the host microbiota cross-talk, which ultimately could influence host physiology. However, a more precise identification of the specific dietary patterns and food constituents that effectively modulate the gut microbiota and bring a predictable benefit to the host metabolic phenotype is needed to establish microbiome-based dietary recommendations. Here, we briefly review the existing data regarding gut microbiota changes induced by different macronutrients and the resulting metabolites produced via their respective fermentation, including their potential effects on obesity and associated metabolic disorders. We also discuss major limitations of current dietary intervention studies as well as future needs of applying cutting-edge "omic" techniques and of progressing in functional microbiota gene discovery to establish robust causal relationships between the dietary microbiota induced changes and metabolic health or disease. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Soft lithographic functionalization and patterning oxide-free silicon and germanium.

PubMed

Bowers, Carleen M; Toone, Eric J; Clark, Robert L; Shestopalov, Alexander A

2011-12-16

The development of hybrid electronic devices relies in large part on the integration of (bio)organic materials and inorganic semiconductors through a stable interface that permits efficient electron transport and protects underlying substrates from oxidative degradation. Group IV semiconductors can be effectively protected with highly-ordered self-assembled monolayers (SAMs) composed of simple alkyl chains that act as impervious barriers to both organic and aqueous solutions. Simple alkyl SAMs, however, are inert and not amenable to traditional patterning techniques. The motivation for immobilizing organic molecular systems on semiconductors is to impart new functionality to the surface that can provide optical, electronic, and mechanical function, as well as chemical and biological activity. Microcontact printing (μCP) is a soft-lithographic technique for patterning SAMs on myriad surfaces. Despite its simplicity and versatility, the approach has been largely limited to noble metal surfaces and has not been well developed for pattern transfer to technologically important substrates such as oxide-free silicon and germanium. Furthermore, because this technique relies on the ink diffusion to transfer pattern from the elastomer to substrate, the resolution of such traditional printing is essentially limited to near 1 μm. In contrast to traditional printing, inkless μCP patterning relies on a specific reaction between a surface-immobilized substrate and a stamp-bound catalyst. Because the technique does not rely on diffusive SAM formation, it significantly expands the diversity of patternable surfaces. In addition, the inkless technique obviates the feature size limitations imposed by molecular diffusion, facilitating replication of very small (<200 nm) features. However, up till now, inkless μCP has been mainly used for patterning relatively disordered molecular systems, which do not protect underlying surfaces from degradation. Here, we report a simple, reliable high-throughput method for patterning passivated silicon and germanium with reactive organic monolayers and demonstrate selective functionalization of the patterned substrates with both small molecules and proteins. The technique utilizes a preformed NHS-reactive bilayered system on oxide-free silicon and germanium. The NHS moiety is hydrolyzed in a pattern-specific manner with a sulfonic acid-modified acrylate stamp to produce chemically distinct patterns of NHS-activated and free carboxylic acids. A significant limitation to the resolution of many μCP techniques is the use of PDMS material which lacks the mechanical rigidity necessary for high fidelity transfer. To alleviate this limitation we utilized a polyurethane acrylate polymer, a relatively rigid material that can be easily functionalized with different organic moieties. Our patterning approach completely protects both silicon and germanium from chemical oxidation, provides precise control over the shape and size of the patterned features, and gives ready access to chemically discriminated patterns that can be further functionalized with both organic and biological molecules. The approach is general and applicable to other technologically-relevant surfaces.

Unexpected Patterns in Snow and Dirt

ERIC Educational Resources Information Center

Ackerson, Bruce J.

2018-01-01

For more than 30 years, Albert A. Bartlett published "Thermal patterns in the snow" in this journal. These are patterns produced by heat sources underneath the snow. Bartlett's articles encouraged me to pay attention to patterns in snow and to understanding them. At winter's end the last snow becomes dirty and is heaped into piles. This…

Background and stimulus-induced patterns of high metabolic activity in the visual cortex (area 17) of the squirrel and macaque monkey

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

Humphrey, A.L.; Hendrickson, A.E.

1983-02-01

We have used 2-deoxy-D-(/sup 14/C)glucose (2-DG) autoradiography and cytochrome oxidase histochemistry to examine background and stimulus-induced patterns of metabolic activity in monkey striate cortex. In squirrel monkeys (Saimiri sciureus) that binocularly or monocularly viewed diffuse white light or binocularly viewed bars of many orientations and spatial frequencies, 2-DG consumption was not uniform across the cortex but consisted of regularly spaced radial zones of high uptake. The zones extended through all laminae except IVc beta and, when viewed tangentially, formed separate patches 500 microns apart. The cytochrome oxidase stain in these animals also revealed patches of high metabolism which coincided withmore » the 2-DG patches. Squirrel monkeys binocularly viewing vertical stripes showed parallel bands of increased 2-DG uptake in the cortex, while the cytochrome label in these animals remained patchy. When monkeys were kept in the dark during 2-DG exposure, 2-DG-labeled patches were not seen but cytochrome oxidase-positive patches remained. In macaque (Macaca nemestrina) monkeys, binocular stimulation with many orientations and spatial frequencies produced radial zones of high 2-DG uptake in layers I to IVa and VI. When viewed tangentially, these zones formed a dots-in-rows pattern with a spacing of 350 X 500 microns; cytochrome oxidase staining produced an identical pattern. Macaca differed from Saimiri in that monocular stimulation labeled alternate rows. These results indicate that there are radial zones of high background metabolism across squirrel and macaque monkey striate cortex. In Saimiri these zones do not appear to be related to an eye dominance system, while in Macaca they do. The presence of these zones of high metabolism may complicate the interpretation of 2-DG autoradiographs that result from specific visual stimuli.« less