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Sample records for contrasting processes revealed

  1. Resource shifts in Malagasy dung beetles: contrasting processes revealed by dissimilar spatial genetic patterns.

    PubMed

    Hanski, Ilkka; Wirta, Helena; Nyman, Toshka; Rahagalala, Pierre

    2008-11-01

    The endemic dung beetle subtribe Helictopleurina has 65 species mostly in wet forests in eastern Madagascar. There are no extant native ungulates in Madagascar, but three Helictopleurus species have shifted to the introduced cattle dung in open habitats in the past 1500 years. Helictopleurus neoamplicollis and Helictopleurus marsyas exhibit very limited cytochrome oxidase subunit 1 haplotype diversity and a single haplotype is present across Madagascar, suggesting that these species shifted to cattle dung in a small region followed by rapid range expansion. In contrast, patterns of molecular diversity in Helictopleurus quadripunctatus indicate a gradual diet shift across most of southern Madagascar, consistent with somewhat broader diet in this species. The three cattle dung-using Helictopleurus species have significantly greater geographical ranges than the forest-dwelling species, apparently because the shift to the currently very abundant new resource relaxed interspecific competition that hinders range expansion in the forest species.

  2. Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions.

    PubMed

    Mongiardino Koch, N; Ceccarelli, F S; Ojanguren-Affilastro, A A; Ramírez, M J

    2017-02-09

    Many palaeontological studies have investigated the evolution of entire body plans, generally relying on discrete character-taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure. We address this question using the scorpion genus Brachistosternus Pocock 1893 as case study. We make use of a time-calibrated multilocus molecular phylogeny, and compile discrete and traditional morphometric data sets, both capturing the overall morphology of the organisms. We find that morphospaces derived from these matrices are significantly different, and that the degree of discordance cannot be replicated by simulations of random character evolution. Moreover, we find strong support for contrasting modes of evolution, with discrete characters being congruent with an 'early burst' scenario whereas morphometric traits suggest species-specific adaptations to have driven morphological evolution. The inferred macroevolutionary dynamics are therefore contingent on the choice of character type. Finally, we confirm that metrics of correlation fail to detect these profound differences given common phylogenetic structure in both data sets, and that methods incorporating a phylogenetic framework and accounting for expected covariance should be favoured.

  3. Recognition memory reveals just how CONTRASTIVE contrastive accenting really is

    PubMed Central

    Fraundorf, Scott H.; Watson, Duane G.; Benjamin, Aaron S.

    2010-01-01

    The effects of pitch accenting on memory were investigated in three experiments. Participants listened to short recorded discourses that contained contrast sets with two items (e.g. British scientists and French scientists); a continuation specified one item from the set. Pitch accenting on the critical word in the continuation was manipulated between non-contrastive (H* in the ToBI system) and contrastive (L+H*). On subsequent recognition memory tests, the L+H* accent increased hits to correct statements and correct rejections of the contrast item (Experiments 1–3), but did not impair memory for other parts of the discourse (Experiment 2). L+H* also did not facilitate correct rejections of lures not in the contrast set (Experiment 3), indicating that contrastive accents do not simply strengthen the representation of the target item. These results suggest comprehenders use pitch accenting to encode and update information about multiple elements in a contrast set. PMID:20835405

  4. Contrasts between deformation accommodated by induced seismic and aseismic processes revealed by combined monitoring of seismicity and surface deformations: Brady Geothermal Field, Nevada, USA

    NASA Astrophysics Data System (ADS)

    Davatzes, N. C.; Ali, S. T.; Mellors, R. J.; Foxall, W.; Wang, H. F.; Feigl, K. L.; Drakos, P. S.; Zemach, E.

    2013-12-01

    Fluid pressure change accompanying pumping in the Brady Geothermal Field is associated with two easily measureable deformation responses: (1) surface deformations and 2) seismic slip. Surface deformation can be imaged by InSAR and appears to correspond to volume change at depth. Seismic slip on fractures is likely induced by either changes in effective normal stress or solid stress with minimal impact to volume. Both responses have potential impact on permeability structure due to dilation or compaction along natural fractures. We present an integrated data set that compares pumping records with these deformation responses to investigate their coupling and to constrain the geometry and rheology of the reservoir and surrounding crust. We also seek to clarify the relationship between induced seismicity and pumping. Currently, the dominant pumping signal is pressure reduction resulting from on-going production since 1992. Surface subsidence extends over a region of approximately 5 km by 2 km with the long axis along the strike of the major normal faults associated with the reservoir. Smaller approximately 1 km length-scale regions of intense subsidence are associated bends or intersections among individual normal fault segments. Modeling of the deformation source indicates that the broader subsidence pattern is consistent with the majority of fluid extraction from a reservoir at a depth of approximately 1 km and extending along the entire length of the mapped Brady normal fault. The more intense subsidence is consistent with fluid extraction along steep conduits from shallower depths that extend to the main reservoir. These results indicate a reservoir much larger than would be expected from the footprint of the production wells. In contrast, seismicity is primarily concentrated along a narrow path between injecting and producing wells, but outside the regions of most intense subsidence. Overall, seismicity represents only a small fraction of the strain energy

  5. Processing of Contrastiveness by Heritage Russian Bilinguals

    ERIC Educational Resources Information Center

    Sekerina, Irina A.; Trueswell, John C.

    2011-01-01

    Two eye-tracking experiments in the Visual World paradigm compared how monolingual Russian (Experiment 1) and heritage Russian-English bilingual (Experiment 2) listeners process contrastiveness online in Russian. Materials were color adjective-noun phrases embedded into the split-constituent construction Krasnuju polozite zvezdovku..."Red put…

  6. Multiscale retinocortical model of contrast processing

    NASA Astrophysics Data System (ADS)

    Moorhead, Ian R.; Haig, Nigel D.

    1996-04-01

    Visual performance models have in the past, typically been empirical, relying on the user to supply numerical values such as target contrast and background luminance to describe the performance of the visual system, when undertaking a specified task. However, it is becoming increasingly easy to obtain computer images using for example digital cameras, scanners, imaging photometers and radiometers. We have therefore been examining the possibility of producing a quantitative model of human vision that is capable of directly processing images in order to provide predictions of performance. We are particularly interested in being able to process images of 'real' scenes. The model is inspired by human vision and the components have analogies with parts of the human visual system but their properties are governed primarily by existing psychophysical data. The first stage of the model generates a multiscale, difference of Gaussian (DoG) representation of the image (Burton, Haig and Moorhead), with a central foveal region of high resolution, and with a resolution that declines with eccentricity as the scale of the filter increases. Incorporated into this stage is a gain control process which ensures that the contrast sensitivity is consistent with the psychophysical data of van Nes and Bouman. The second stage incorporates a model of perceived contrast proposed by Cannon and Fullenkamp. Their model assumes the image is analyzed by oriented (Gabor) filters and produces a representation of the image in terms of perceived contrast.

  7. Processing Polarity Items: Contrastive Licensing Costs

    ERIC Educational Resources Information Center

    Saddy, Douglas; Drenhaus, Heiner; Frisch, Stefan

    2004-01-01

    We describe an experiment that investigated the failure to license polarity items in German using event-related brain potentials (ERPs). The results reveal distinct processing reflexes associated with failure to license positive polarity items in comparison to failure to license negative polarity items. Failure to license both negative and…

  8. Processing Implied Meaning through Contrastive Prosody

    ERIC Educational Resources Information Center

    Dennison, Heeyeon Yoon

    2010-01-01

    Understanding implicature--something meant, implied, or suggested distinct from what is said--is paramount for successful human communication. Yet, it is unclear how our cognitive abilities fill in gaps of unspecified information. This study presents three distinct sets of experiments investigating how people understand implied contrasts conveyed…

  9. The Haikuist's Growth Process Revealed.

    ERIC Educational Resources Information Center

    Frank, Patrick

    1996-01-01

    Views personal growth through long-term work in various literary genres, including haiku-senryu sequencing, as a continuous process. Demonstrates how self-integration can be enhanced through the creative processing of dream material. (SR)

  10. Detection for processing history of seam insertion and contrast enhancement

    NASA Astrophysics Data System (ADS)

    Li, Jianwei; Zhao, Yao; Ni, Rongrong

    2014-11-01

    With the development of manipulations techniques of digital images, digital image forensic technology is becoming more and more necessary. However, the determination of processing history of multi-operation is still a challenge problem. In this paper, we improve the traditional seam insertion algorithm, and propose corresponding detection method. Then an algorithm that focuses on detecting the processing history of seam insertion and contrast enhancement is proposed, which can be widely used in practical image forgery. Based on comprehensive analysis, we have discovered the inherent relationship between seam insertion and contrast enhancement. Different orders of processing make different impacts on images. By using the newly proposed algorithm, both contrast enhancement followed by seam insertion and seam insertion followed by contrast enhancement can be detected correctly. Plenty of experiments have been implemented to prove the accuracy.

  11. Interactive processing of contrastive expressions by Russian children

    PubMed Central

    Sekerina, Irina A.; Trueswell, John C.

    2013-01-01

    Children's ability to interpret color adjective noun phrases (e.g., red butterfly) as contrastive was examined in an eyetracking study with 6-year-old Russian children. Pitch accent placement (on the adjective red, or on the noun butterfly) was compared within a visual context containing two red referents (a butterfly and a fox) when only one of them had a contrast member (a purple butterfly) or when both had a contrast member (a purple butterfly and a grey fox). Contrastiveness was enhanced by the Russian-specific ‘split constituent’ construction (e.g., Red put butterfly . . .) in which a contrastive interpretation of the color term requires pitch accent on the adjective, with the nonsplit sentences serving as control. Regardless of the experimental manipulations, children had to wait until hearing the noun (butterfly) to identify the referent, even in splits. This occurred even under conditions for which the prosody and the visual context allow adult listeners to infer the relevant contrast set and anticipate the referent prior to hearing the noun (accent on the adjective in 1-Contrast scenes). Pitch accent on the adjective did facilitate children's referential processing, but only for the nonsplit constituents. Moreover, visual contexts that encouraged the correct contrast set (1-Contrast) only facilitated referential processing after hearing the noun, even in splits. Further analyses showed that children can anticipate the reference like adults but only when the contrast set is made salient by the preceding supportive discourse, that is, when the inference about the intended contrast set is provided by the preceding utterance. PMID:24465066

  12. Revealing letters in rolled Herculaneum papyri by X-ray phase-contrast imaging

    NASA Astrophysics Data System (ADS)

    Mocella, Vito; Brun, Emmanuel; Ferrero, Claudio; Delattre, Daniel

    2015-01-01

    Hundreds of papyrus rolls, buried by the eruption of Mount Vesuvius in 79 AD and belonging to the only library passed on from Antiquity, were discovered 260 years ago at Herculaneum. These carbonized papyri are extremely fragile and are inevitably damaged or destroyed in the process of trying to open them to read their contents. In recent years, new imaging techniques have been developed to read the texts without unwrapping the rolls. Until now, specialists have been unable to view the carbon-based ink of these papyri, even when they could penetrate the different layers of their spiral structure. Here for the first time, we show that X-ray phase-contrast tomography can reveal various letters hidden inside the precious papyri without unrolling them. This attempt opens up new opportunities to read many Herculaneum papyri, which are still rolled up, thus enhancing our knowledge of ancient Greek literature and philosophy.

  13. Revealing letters in rolled Herculaneum papyri by X-ray phase-contrast imaging.

    PubMed

    Mocella, Vito; Brun, Emmanuel; Ferrero, Claudio; Delattre, Daniel

    2015-01-20

    Hundreds of papyrus rolls, buried by the eruption of Mount Vesuvius in 79 AD and belonging to the only library passed on from Antiquity, were discovered 260 years ago at Herculaneum. These carbonized papyri are extremely fragile and are inevitably damaged or destroyed in the process of trying to open them to read their contents. In recent years, new imaging techniques have been developed to read the texts without unwrapping the rolls. Until now, specialists have been unable to view the carbon-based ink of these papyri, even when they could penetrate the different layers of their spiral structure. Here for the first time, we show that X-ray phase-contrast tomography can reveal various letters hidden inside the precious papyri without unrolling them. This attempt opens up new opportunities to read many Herculaneum papyri, which are still rolled up, thus enhancing our knowledge of ancient Greek literature and philosophy.

  14. Normalized Temperature Contrast Processing in Flash Infrared Thermography

    NASA Technical Reports Server (NTRS)

    Koshti, Ajay M.

    2016-01-01

    The paper presents further development in normalized contrast processing of flash infrared thermography method by the author given in US 8,577,120 B1. The method of computing normalized image or pixel intensity contrast, and normalized temperature contrast are provided, including converting one from the other. Methods of assessing emissivity of the object, afterglow heat flux, reflection temperature change and temperature video imaging during flash thermography are provided. Temperature imaging and normalized temperature contrast imaging provide certain advantages over pixel intensity normalized contrast processing by reducing effect of reflected energy in images and measurements, providing better quantitative data. The subject matter for this paper mostly comes from US 9,066,028 B1 by the author. Examples of normalized image processing video images and normalized temperature processing video images are provided. Examples of surface temperature video images, surface temperature rise video images and simple contrast video images area also provided. Temperature video imaging in flash infrared thermography allows better comparison with flash thermography simulation using commercial software which provides temperature video as the output. Temperature imaging also allows easy comparison of surface temperature change to camera temperature sensitivity or noise equivalent temperature difference (NETD) to assess probability of detecting (POD) anomalies.

  15. The influence of contrast on coherent motion processing in dyslexia.

    PubMed

    Conlon, Elizabeth G; Lilleskaret, Gry; Wright, Craig M; Power, Garry F

    2012-06-01

    The aim of the experiments was to investigate how manipulating the contrast of the signal and noise dots in a random dot kinematogram (RDK), influenced on motion coherence thresholds in adults with dyslexia. In the first of two experiments, coherent motion thresholds were measured when the contrasts of the signal and noise dots in an RDK were manipulated. A significantly greater processing benefit was found for the group with dyslexia than a control group when the signal dots were of higher contrast than the noise dots. However, a significant processing disadvantage was found for the group with dyslexia relative to the control group when the signal dots were of lower contrast than the noise dots. These findings were interpreted as supporting evidence for the noise exclusion hypothesis of dyslexia. In Experiment 2, the effect on coherent motion thresholds of presenting a cue that alerted observers to which stimuli, high or low contrast contained the signals dots was investigated. When the cue directed attention to low contrast signal dots presented in high contrast noise, coherent motion thresholds were only enhanced for the group with dyslexia. This manipulation produced equivalent coherent motion thresholds in the reader groups. In other conditions, the group with dyslexia had significantly higher coherent motion thresholds than the control group. It was concluded that adults with dyslexia who show evidence of a coherent motion deficit (37% of the dyslexia group in each experiment), have a specific difficulty in noise exclusion. This appears to occur as consequence of a sensory processing deficit in the magnocellular or dorsal stream.

  16. Information processing correlates of a size-contrast illusion.

    PubMed

    Gold, Jason M

    2014-01-01

    Perception is often influenced by context. A well-known class of perceptual context effects is perceptual contrast illusions, in which proximate stimulus regions interact to alter the perception of various stimulus attributes, such as perceived brightness, color and size. Although the phenomenal reality of contrast effects is well documented, in many cases the connection between these illusions and how information is processed by perceptual systems is not well understood. Here, we use noise as a tool to explore the information processing correlates of one such contrast effect: the Ebbinghaus-Titchener size-contrast illusion. In this illusion, the perceived size of a central dot is significantly altered by the sizes of a set of surrounding dots, such that the presence of larger surrounding dots tends to reduce the perceived size of the central dot (and vise versa). In our experiments, we first replicated previous results that have demonstrated the subjective reality of the Ebbinghaus-Titchener illusion. We then used visual noise in a detection task to probe the manner in which observers processed information when experiencing the illusion. By correlating the noise with observers' classification decisions, we found that the sizes of the surrounding contextual elements had a direct influence on the relative weight observers assigned to regions within and surrounding the central element. Specifically, observers assigned relatively more weight to the surrounding region and less weight to the central region in the presence of smaller surrounding contextual elements. These results offer new insights into the connection between the subjective experience of size-contrast illusions and their associated information processing correlates.

  17. Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina

    PubMed Central

    Liu, Jian K.; Gollisch, Tim

    2015-01-01

    When visual contrast changes, retinal ganglion cells adapt by adjusting their sensitivity as well as their temporal filtering characteristics. The latter has classically been described by contrast-induced gain changes that depend on temporal frequency. Here, we explored a new perspective on contrast-induced changes in temporal filtering by using spike-triggered covariance analysis to extract multiple parallel temporal filters for individual ganglion cells. Based on multielectrode-array recordings from ganglion cells in the isolated salamander retina, we found that contrast adaptation of temporal filtering can largely be captured by contrast-invariant sets of filters with contrast-dependent weights. Moreover, differences among the ganglion cells in the filter sets and their contrast-dependent contributions allowed us to phenomenologically distinguish three types of filter changes. The first type is characterized by newly emerging features at higher contrast, which can be reproduced by computational models that contain response-triggered gain-control mechanisms. The second type follows from stronger adaptation in the Off pathway as compared to the On pathway in On-Off-type ganglion cells. Finally, we found that, in a subset of neurons, contrast-induced filter changes are governed by particularly strong spike-timing dynamics, in particular by pronounced stimulus-dependent latency shifts that can be observed in these cells. Together, our results show that the contrast dependence of temporal filtering in retinal ganglion cells has a multifaceted phenomenology and that a multi-filter analysis can provide a useful basis for capturing the underlying signal-processing dynamics. PMID:26230927

  18. Cryptic microtextures and geological histories of K-rich alkali feldspars revealed by charge contrast imaging

    NASA Astrophysics Data System (ADS)

    Flude, Stephanie; Lee, Martin R.; Sherlock, Sarah C.; Kelley, Simon P.

    2012-06-01

    Charge contrast imaging in the scanning electron microscope can provide new insights into the scale and composition of alkali feldspar microtextures, and such information helps considerably with the interpretation of their geological histories and results of argon isotope thermochronological analyses. The effectiveness of this technique has been illustrated using potassium-rich alkali feldspars from the Dartmoor granite (UK). These feldspars contain strain-controlled lamellar crypto- and microperthites that are cross-cut by strain-free deuteric microperthites. The constituent albite- and orthoclase-rich phases of both microperthite generations can be readily distinguished by atomic number contrast imaging. The charge contrast results additionally show that sub-micrometre-sized albite `platelets' are commonplace between coarser exsolution lamellae and occur together to make cryptoperthites. Furthermore, charge contrast imaging reveals that the orthoclase-rich feldspar is an intergrowth of two phases, one that is featureless with uniform contrast and another that occurs as cross-cutting veins and grains with the {110} adularia habit. Transmission electron microscopy shows that the featureless feldspar is tweed orthoclase, whereas the veins and euhedral grains are composed of irregular microcline that has formed from orthoclase by `unzipping' during deuteric or hydrothermal alteration. The charge contrast imaging results are especially important in demonstrating that deuteric perthites are far more abundant in alkali feldspars than would be concluded from investigations using conventional microscopy techniques. The unexpected presence of such a high volume of replacement products has significant implications for understanding the origins and geological histories of crustal rocks and the use of alkali feldspars in geo- and thermochronology. Whilst the precise properties of feldspars that generate contrast remain unclear, the similarity between charge contrast images

  19. Contrast Adaptation Implies Two Spatiotemporal Channels but Three Adapting Processes

    ERIC Educational Resources Information Center

    Langley, Keith; Bex, Peter J.

    2007-01-01

    The contrast gain control model of adaptation predicts that the effects of contrast adaptation correlate with contrast sensitivity. This article reports that the effects of high contrast spatiotemporal adaptors are maximum when adapting around 19 Hz, which is a factor of two or more greater than the peak in contrast sensitivity. To explain the…

  20. Contrasting hydrologic processes on semiarid and humid watersheds

    SciTech Connect

    Cundy, T.W.

    1987-12-01

    This seminar compared and contrasted hydrologic processes and the applicability of remote sensing in solving hydrolgic problems on humid and semiarid watersheds. In meeting this goal the seminar also clarified some of the major challenges facing the REFLEX program' a principal one being the ability to utilize remote sensing information and field hydrologic data to move from one spatial scale to another. If REFLEX can provide even a small step toward accomplishing this it would be a major contribution in theoretical and applied hydrology. 2 refs., 4 figs., 1 tab.

  1. Revealing the dual streams of speech processing

    PubMed Central

    Fridriksson, Julius; Yourganov, Grigori; Bonilha, Leonardo; Basilakos, Alexandra; Rorden, Christopher

    2016-01-01

    Several dual route models of human speech processing have been proposed suggesting a large-scale anatomical division between cortical regions that support motor–phonological aspects vs. lexical–semantic aspects of speech processing. However, to date, there is no complete agreement on what areas subserve each route or the nature of interactions across these routes that enables human speech processing. Relying on an extensive behavioral and neuroimaging assessment of a large sample of stroke survivors, we used a data-driven approach using principal components analysis of lesion-symptom mapping to identify brain regions crucial for performance on clusters of behavioral tasks without a priori separation into task types. Distinct anatomical boundaries were revealed between a dorsal frontoparietal stream and a ventral temporal–frontal stream associated with separate components. Collapsing over the tasks primarily supported by these streams, we characterize the dorsal stream as a form-to-articulation pathway and the ventral stream as a form-to-meaning pathway. This characterization of the division in the data reflects both the overlap between tasks supported by the two streams as well as the observation that there is a bias for phonological production tasks supported by the dorsal stream and lexical–semantic comprehension tasks supported by the ventral stream. As such, our findings show a division between two processing routes that underlie human speech processing and provide an empirical foundation for studying potential computational differences that distinguish between the two routes. PMID:27956600

  2. Optical Performance And Process Characterizations Of Several High Contrast Metal-Ion-Free Developer Processes

    NASA Astrophysics Data System (ADS)

    Petersen, John S.; Kozlowski, Alan E.

    1984-05-01

    Projection print quality is dependent upon the response of the resist/developer system to the optically projected image. For this reason, it is critical, during process optimization, to relate final pattern quality to both the chemical and physical contrast terms. One method for doing this is to monitor resist/developer response in the absence and then the presence of diffracted light. These results are then compared to the predicted optical requirements. For best performance, the resist/developer (or chemical) contrast must ex-ceed that of the potential optical (or physical) contrast. To do rapid contrast compari-sons it is convenient to relate the chemical contrast term,r, to the physical contrast term MTF, via the CMTF1: where the CMTF = (1014- 1)/(lol* 1) = (Ethreshold Einitial)/ (Ethreshold Einitial) and the MTF=(Emax Emin)/(Emax + EmiA. Perfect imaging potential occurs chemically when the CMTF = 0, Einitial r-- Ethreshold, and physically when the MTF = 1.0, Emin = 0. As a result, acceptable patterning occurs when the MTF/CMTF ratio is greater than one. This ratio is a comparative, accept/reject test only; final nrocess optimization is done by monitoring the accepted resist/developer systems' performance on projected images. Optimum process latitude is predicted by determining focal tolerances at various mask sizing biases and by measuring linewidth necking over steps. This study demonstrates the dependence of the final print quality on the chemical con-trast. A method is examined for approximating minimum allowable chemical contrast required for adequately printing desired device design sizes. Then chemical contrast results for various metal-ion-free develop processes are shown. Next, the combined resist/developer/ optical performance is optimized by using focal tolerance and linewidth control over steps as process constraints. Finally, it is shown that focal tolerances are dependent on chemical contrast and that the focus budget is tunable.

  3. Eye Movements Reveal Hierarchical Motion Processing

    NASA Technical Reports Server (NTRS)

    Mulligan, Jeffrey B.; Null, Cynthia H. (Technical Monitor)

    1996-01-01

    Purpose: In the analysis of visual motion, local features such as orientation are analyzed early in the cortical processing stream (V1), while integration across orientation and space is thought to occur in higher cortical areas such as MT, MST, etc. If all areas provide inputs to eye movement control centers, we would expect that local properties would drive eye movements with relatively short latencies, while global properties would require longer latencies. When such latencies are observed, they can provide information about when (and where?) various stimulus properties are analyzed. Methods: The stimulus employed was an elliptical Gabor patch with a drifting carrier, in which the orientations of the carrier grating and the contrast window were varied independently. We have previously demonstrated that the directional percepts evoked by this stimulus vary between the "grating direction" (the normal to the grating's orientation) and the "window direction", and that similar effects can be observed in reflexive eye movements. Subjects viewed such a stimulus while attempting to maintain steady fixation on the center of the pattern, and the small reflexive eye movements ("stare OKN") were recorded. In the middle of the trial, the orientation of either the grating or the window was rotated smoothly by 30 degrees. Results: Responses to the shift of both grating orientation and window orientation are seen in the average OKN slow phase velocity. Grating rotations produce a rapid OKN rotation to the grating direction (100 ms latency, 300 ms time constant), followed by a slower rebound to the steady state perceived direction midway between the grating and window directions. Window rotations, on the other hand, evoke a slower response (200 ms latency, 500 ms time constant). Conclusions: The results demonstrate multiple cortical inputs to eye movement control: a fast, early input driven by orientation, and a slower input from higher areas sensitive to global stimulus

  4. Contrasting serpentinization processes in the eastern Central Alps

    USGS Publications Warehouse

    Burkhard, D.J.M.; O'Neil, J.R.

    1988-01-01

    Stable isotope compositions have been determined for serpentinites from between Davos (Arosa-Platta nappe, Switzerland) and the Valmalenco (Italy). ??D and ??18O values (-120 to -60 and 6-10???, respectively) in the Arosa-Platta nappe indicate that serpentinization took place on the continent at relatively low temperatures in the presence of limited amounts of metamorphic fluids that contained a component of meteoric water. One sample of chrysotile has a ??18O value of 13??? providing evidence of high W/R ratios and low formation temperature of lizardite-chrysotile in this area. In contrast, relatively high ??D values (-42 to -34???) and low ??18O values (4.4-7.4???) for serpentine in the eastern part of the Valmalenco suggest a serpentinization process that took place at moderate temperatures in fluids that were dominated by ocean water. The antigorite in the Valmalenco is the first reported example of continental antigorite with an ocean water signature. An amphibole sample from a metasomatically overprinted contact zone to metasediments (??D=-36???) indicates that the metasomatic event also took place in the presence of ocean water. Lower ??D values (-93 to -60???) of serpentines in the western part of the Valmalenco suggest a different alteration history possibly influenced by fluids associated with contact metamorphism. Low water/rock ratios during regional metamorphism (and metasomatism) have to be assumed for both regions. ?? 1988 Springer-Verlag.

  5. The Influence of Contrast on Coherent Motion Processing in Dyslexia

    ERIC Educational Resources Information Center

    Conlon, Elizabeth G.; Lilleskaret, Gry; Wright, Craig M.; Power, Garry F.

    2012-01-01

    The aim of the experiments was to investigate how manipulating the contrast of the signal and noise dots in a random dot kinematogram (RDK), influenced on motion coherence thresholds in adults with dyslexia. In the first of two experiments, coherent motion thresholds were measured when the contrasts of the signal and noise dots in an RDK were…

  6. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    PubMed Central

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  7. Neural Correlates of Contrast and Humor: Processing Common Features of Verbal Irony

    PubMed Central

    Obert, Alexandre; Gierski, Fabien; Calmus, Arnaud; Flucher, Aurélie; Portefaix, Christophe; Pierot, Laurent; Kaladjian, Arthur; Caillies, Stéphanie

    2016-01-01

    Irony is a kind of figurative language used by a speaker to say something that contrasts with the context and, to some extent, lends humor to a situation. However, little is known about the brain regions that specifically support the processing of these two common features of irony. The present study had two main aims: (i) investigate the neural basis of irony processing, by delivering short ironic spoken sentences (and their literal counterparts) to participants undergoing fMRI; and (ii) assess the neural effect of two irony parameters, obtained from normative studies: degree of contrast and humor appreciation. Results revealed activation of the bilateral inferior frontal gyrus (IFG), posterior part of the left superior temporal gyrus, medial frontal cortex, and left caudate during irony processing, suggesting the involvement of both semantic and theory-of-mind networks. Parametric models showed that contrast was specifically associated with the activation of bilateral frontal and subcortical areas, and that these regions were also sensitive to humor, as shown by a conjunction analysis. Activation of the bilateral IFG is consistent with the literature on humor processing, and reflects incongruity detection/resolution processes. Moreover, the activation of subcortical structures can be related to the reward processing of social events. PMID:27851821

  8. Neural Correlates of Contrast and Humor: Processing Common Features of Verbal Irony.

    PubMed

    Obert, Alexandre; Gierski, Fabien; Calmus, Arnaud; Flucher, Aurélie; Portefaix, Christophe; Pierot, Laurent; Kaladjian, Arthur; Caillies, Stéphanie

    2016-01-01

    Irony is a kind of figurative language used by a speaker to say something that contrasts with the context and, to some extent, lends humor to a situation. However, little is known about the brain regions that specifically support the processing of these two common features of irony. The present study had two main aims: (i) investigate the neural basis of irony processing, by delivering short ironic spoken sentences (and their literal counterparts) to participants undergoing fMRI; and (ii) assess the neural effect of two irony parameters, obtained from normative studies: degree of contrast and humor appreciation. Results revealed activation of the bilateral inferior frontal gyrus (IFG), posterior part of the left superior temporal gyrus, medial frontal cortex, and left caudate during irony processing, suggesting the involvement of both semantic and theory-of-mind networks. Parametric models showed that contrast was specifically associated with the activation of bilateral frontal and subcortical areas, and that these regions were also sensitive to humor, as shown by a conjunction analysis. Activation of the bilateral IFG is consistent with the literature on humor processing, and reflects incongruity detection/resolution processes. Moreover, the activation of subcortical structures can be related to the reward processing of social events.

  9. Spatially Explicit Modeling Reveals Cephalopod Distributions Match Contrasting Trophic Pathways in the Western Mediterranean Sea

    PubMed Central

    Puerta, Patricia; Hunsicker, Mary E.; Quetglas, Antoni; Álvarez-Berastegui, Diego; Esteban, Antonio; González, María; Hidalgo, Manuel

    2015-01-01

    Populations of the same species can experience different responses to the environment throughout their distributional range as a result of spatial and temporal heterogeneity in habitat conditions. This highlights the importance of understanding the processes governing species distribution at local scales. However, research on species distribution often averages environmental covariates across large geographic areas, missing variability in population-environment interactions within geographically distinct regions. We used spatially explicit models to identify interactions between species and environmental, including chlorophyll a (Chla) and sea surface temperature (SST), and trophic (prey density) conditions, along with processes governing the distribution of two cephalopods with contrasting life-histories (octopus and squid) across the western Mediterranean Sea. This approach is relevant for cephalopods, since their population dynamics are especially sensitive to variations in habitat conditions and rarely stable in abundance and location. The regional distributions of the two cephalopod species matched two different trophic pathways present in the western Mediterranean Sea, associated with the Gulf of Lion upwelling and the Ebro river discharges respectively. The effects of the studied environmental and trophic conditions were spatially variant in both species, with usually stronger effects along their distributional boundaries. We identify areas where prey availability limited the abundance of cephalopod populations as well as contrasting effects of temperature in the warmest regions. Despite distributional patterns matching productive areas, a general negative effect of Chla on cephalopod densities suggests that competition pressure is common in the study area. Additionally, results highlight the importance of trophic interactions, beyond other common environmental factors, in shaping the distribution of cephalopod populations. Our study presents a valuable

  10. Spatially Explicit Modeling Reveals Cephalopod Distributions Match Contrasting Trophic Pathways in the Western Mediterranean Sea.

    PubMed

    Puerta, Patricia; Hunsicker, Mary E; Quetglas, Antoni; Álvarez-Berastegui, Diego; Esteban, Antonio; González, María; Hidalgo, Manuel

    2015-01-01

    Populations of the same species can experience different responses to the environment throughout their distributional range as a result of spatial and temporal heterogeneity in habitat conditions. This highlights the importance of understanding the processes governing species distribution at local scales. However, research on species distribution often averages environmental covariates across large geographic areas, missing variability in population-environment interactions within geographically distinct regions. We used spatially explicit models to identify interactions between species and environmental, including chlorophyll a (Chla) and sea surface temperature (SST), and trophic (prey density) conditions, along with processes governing the distribution of two cephalopods with contrasting life-histories (octopus and squid) across the western Mediterranean Sea. This approach is relevant for cephalopods, since their population dynamics are especially sensitive to variations in habitat conditions and rarely stable in abundance and location. The regional distributions of the two cephalopod species matched two different trophic pathways present in the western Mediterranean Sea, associated with the Gulf of Lion upwelling and the Ebro river discharges respectively. The effects of the studied environmental and trophic conditions were spatially variant in both species, with usually stronger effects along their distributional boundaries. We identify areas where prey availability limited the abundance of cephalopod populations as well as contrasting effects of temperature in the warmest regions. Despite distributional patterns matching productive areas, a general negative effect of Chla on cephalopod densities suggests that competition pressure is common in the study area. Additionally, results highlight the importance of trophic interactions, beyond other common environmental factors, in shaping the distribution of cephalopod populations. Our study presents a valuable

  11. 30-Year Satellite Record Reveals Contrasting Arctic and Antarctic Decadal Sea Ice Variability

    NASA Technical Reports Server (NTRS)

    Cavalieri, D. J.; Parkinson, C. L.; Vinnikov, K. Y.

    2003-01-01

    A 30-year satellite record of sea ice extents derived mostly from satellite microwave radiometer observations reveals that the Arctic sea ice extent decreased by 0.30+0.03 x 10(exp 6) square kilometers per 10 yr from 1972 through 2002, but by 0.36 plus or minus 0.05 x 10(exp 6) square kilometers per 10yr from 1979 through 2002, indicating an acceleration of 20% in the rate of decrease. In contrast, the Antarctic sea ice extent decreased dramatically over the period 1973-1977, then gradually increased. Over the full 30-year period, the Antarctic ice extent decreased by 0.15 plus or minus 0.08 x 10(exp 6) square kilometers per 10 yr. The trend reversal is attributed to a large positive anomaly in Antarctic sea ice extent in the early 1970's, an anomaly that apparently began in the late 1960's, as observed in early visible and infrared satellite images.

  12. Dynamic full field optical coherence tomography: subcellular metabolic contrast revealed in tissues by interferometric signals temporal analysis

    PubMed Central

    Apelian, Clement; Harms, Fabrice; Thouvenin, Olivier; Boccara, A. Claude

    2016-01-01

    We developed a new endogenous approach to reveal subcellular metabolic contrast in fresh ex vivo tissues taking advantage of the time dependence of the full field optical coherence tomography interferometric signals. This method reveals signals linked with local activity of the endogenous scattering elements which can reveal cells where other OCT-based techniques fail or need exogenous contrast agents. We benefit from the micrometric transverse resolution of full field OCT to image intracellular features. We used this time dependence to identify different dynamics at the millisecond scale on a wide range of organs in normal or pathological conditions. PMID:27446672

  13. New is not always costly: evidence from online processing of topic and contrast in Japanese.

    PubMed

    Wang, Luming; Schumacher, Petra B

    2013-01-01

    Two visual ERP experiments were conducted to investigate topic and contrast assigned by various cues such as discourse context, sentential position, and marker during referential processing in Japanese. Experiment 1 showed that there was no N400-difference for new vs. given noun phrases (NPs) when the new NP was expected (contrastively focused) based on its preceding context and sentential position. Experiment 2 further revealed that the N400 for new NPs can be modulated by the NP's contrastive meaning (exhaustivity) induced from the marker. Both experiments also showed that new NPs engendered an increased Late Positivity. The reduced N400 for new vs. given supports an expectation-based linking mechanism. In addition, costs that were consistently observed for new vs. given entities emerged in a subsequent process, in which the new NP's occurrence requires updating and correcting of the discourse representation built so far, which is indexed by an enhanced Late Positivity. We argue that the overall data pattern should be best explained within a multi-stream model of discourse processing.

  14. New is not always costly: evidence from online processing of topic and contrast in Japanese

    PubMed Central

    Wang, Luming; Schumacher, Petra B.

    2013-01-01

    Two visual ERP experiments were conducted to investigate topic and contrast assigned by various cues such as discourse context, sentential position, and marker during referential processing in Japanese. Experiment 1 showed that there was no N400-difference for new vs. given noun phrases (NPs) when the new NP was expected (contrastively focused) based on its preceding context and sentential position. Experiment 2 further revealed that the N400 for new NPs can be modulated by the NP's contrastive meaning (exhaustivity) induced from the marker. Both experiments also showed that new NPs engendered an increased Late Positivity. The reduced N400 for new vs. given supports an expectation-based linking mechanism. In addition, costs that were consistently observed for new vs. given entities emerged in a subsequent process, in which the new NP's occurrence requires updating and correcting of the discourse representation built so far, which is indexed by an enhanced Late Positivity. We argue that the overall data pattern should be best explained within a multi-stream model of discourse processing. PMID:23825466

  15. Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging.

    PubMed

    Deng, Li; Gregory, Ann; Yilmaz, Suzan; Poulos, Bonnie T; Hugenholtz, Philip; Sullivan, Matthew B

    2012-10-30

    Ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. However, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. We have developed a method called viral tagging (VT), which combines mixtures of host cells and fluorescent viruses with flow cytometry. We investigated multiple viruses which infect each of two model marine bacteria that represent the slow-growing, photoautotrophic genus Synechococcus (Cyanobacteria) and the fast-growing, heterotrophic genus Pseudoalteromonas (Gammaproteobacteria). Overall, viral tagging results for viral infection were consistent with plaque and liquid infection assays for cyanobacterial myo-, podo- and siphoviruses and some (myo- and podoviruses) but not all (four siphoviruses) heterotrophic bacterial viruses. Virus-tagged Pseudoalteromonas organisms were proportional to the added viruses under varied infection conditions (virus-bacterium ratios), while no more than 50% of the Synechococcus organisms were virus tagged even at viral abundances that exceeded (5 to 10×) that of their hosts. Further, we found that host growth phase minimally impacts the fraction of virus-tagged Synechococcus organisms while greatly affecting phage adsorption to Pseudoalteromonas. Together these findings suggest that at least two contrasting viral life strategies exist in the oceans and that they likely reflect adaptation to their host microbes. Looking forward to the point at which the virus-tagging signature is well understood (e.g., for Synechococcus), application to natural communities should begin to provide population genomic data at the proper scale for predictively modeling two of the most abundant biological entities on Earth. Viral study suffers from an inability to link viruses to hosts en

  16. Contrasting General and Process-Specific Slowing in Language Impairment.

    ERIC Educational Resources Information Center

    Windsor, Jennifer

    2002-01-01

    This article compares two theories on why children with language impairment have slower response times when completing linguistic and nonlinguistic tasks. First, the slowing is due to difficulty with a particular cognitive processes and second, the slowing is due to a general cognitive processing limitation. Clinical implications are discussed.…

  17. Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming.

    PubMed

    Aimé, Carla; Laval, Guillaume; Patin, Etienne; Verdu, Paul; Ségurel, Laure; Chaix, Raphaëlle; Hegay, Tatyana; Quintana-Murci, Lluis; Heyer, Evelyne; Austerlitz, Frédéric

    2013-12-01

    Demographic changes are known to leave footprints on genetic polymorphism. Together with the increased availability of large polymorphism data sets, coalescent-based methods allow inferring the past demography of populations from their present-day patterns of genetic diversity. Here, we analyzed both nuclear (20 noncoding regions) and mitochondrial (HVS-I) resequencing data to infer the demographic history of 66 African and Eurasian human populations presenting contrasting lifestyles (nomadic hunter-gatherers, nomadic herders, and sedentary farmers). This allowed us to investigate the relationship between lifestyle and demography and to address the long-standing debate about the chronology of demographic expansions and the Neolithic transition. In Africa, we inferred expansion events for farmers, but constant population sizes or contraction events for hunter-gatherers. In Eurasia, we inferred higher expansion rates for farmers than herders with HVS-I data, except in Central Asia and Korea. Although isolation and admixture processes could have impacted our demographic inferences, these processes alone seem unlikely to explain the contrasted demographic histories inferred in populations with different lifestyles. The small expansion rates or constant population sizes inferred for herders and hunter-gatherers may thus result from constraints linked to nomadism. However, autosomal data revealed contraction events for two sedentary populations in Eurasia, which may be caused by founder effects. Finally, the inferred expansions likely predated the emergence of agriculture and herding. This suggests that human populations could have started to expand in Paleolithic times, and that strong Paleolithic expansions in some populations may have ultimately favored their shift toward agriculture during the Neolithic.

  18. Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs

    PubMed Central

    Krenkel, Martin; Markus, Andrea; Bartels, Matthias; Dullin, Christian; Alves, Frauke; Salditt, Tim

    2015-01-01

    We have performed x-ray phase-contrast tomography on mouse lung tissue. Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view. Thus, macroscopic tissue samples extending over several mm can be studied in sub-cellular-level structural detail. The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel. In combination with suitable phase-retrieval algorithms, challenging radiation-sensitive and low-contrast samples can be reconstructed with minimal artefacts. The dose efficiency of the method is demonstrated by the reconstruction of living macrophages both with and without phagocytized contrast agents. We also used zoom tomography to visualize barium-labelled macrophages in the context of morphological structures in asthmatic and healthy mouse lung tissue one day after intratracheal application. The three-dimensional reconstructions showed that the macrophages predominantly localized to the alveoli, but they were also found in bronchial walls, indicating that these cells might be able to migrate from the lumen of the bronchi through the epithelium. PMID:25966338

  19. Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs

    NASA Astrophysics Data System (ADS)

    Krenkel, Martin; Markus, Andrea; Bartels, Matthias; Dullin, Christian; Alves, Frauke; Salditt, Tim

    2015-05-01

    We have performed x-ray phase-contrast tomography on mouse lung tissue. Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view. Thus, macroscopic tissue samples extending over several mm can be studied in sub-cellular-level structural detail. The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel. In combination with suitable phase-retrieval algorithms, challenging radiation-sensitive and low-contrast samples can be reconstructed with minimal artefacts. The dose efficiency of the method is demonstrated by the reconstruction of living macrophages both with and without phagocytized contrast agents. We also used zoom tomography to visualize barium-labelled macrophages in the context of morphological structures in asthmatic and healthy mouse lung tissue one day after intratracheal application. The three-dimensional reconstructions showed that the macrophages predominantly localized to the alveoli, but they were also found in bronchial walls, indicating that these cells might be able to migrate from the lumen of the bronchi through the epithelium.

  20. Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs.

    PubMed

    Krenkel, Martin; Markus, Andrea; Bartels, Matthias; Dullin, Christian; Alves, Frauke; Salditt, Tim

    2015-05-12

    We have performed x-ray phase-contrast tomography on mouse lung tissue. Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view. Thus, macroscopic tissue samples extending over several mm can be studied in sub-cellular-level structural detail. The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel. In combination with suitable phase-retrieval algorithms, challenging radiation-sensitive and low-contrast samples can be reconstructed with minimal artefacts. The dose efficiency of the method is demonstrated by the reconstruction of living macrophages both with and without phagocytized contrast agents. We also used zoom tomography to visualize barium-labelled macrophages in the context of morphological structures in asthmatic and healthy mouse lung tissue one day after intratracheal application. The three-dimensional reconstructions showed that the macrophages predominantly localized to the alveoli, but they were also found in bronchial walls, indicating that these cells might be able to migrate from the lumen of the bronchi through the epithelium.

  1. Image correction method for the colour contrast effect using inverse processes of the brain.

    PubMed

    Murakoshi, Kazushi; Miura, Mai

    2010-09-01

    In the colour contrast effect, the impression of a colour changes according to the situation; cases occur in which the colour appearance is misunderstood. We propose an image signal processing method for preventing such misperception of colour. Many conventional image improving methods emphasize the contrast of images as same as the brain does. However, by their processes, the colour contrast effect is not canceled; we misunderstand the colour. The objective of this study is to perceive original colour. Therefore, we propose an image correction method using inverse processes of the brain in order to cancel the processes of the brain, the colour contrast effect. We verified whether the proposed method corrected the colour contrast effect by conducting a psychological experiment. The results show that the method succeeds in canceling the colour contrast effect.

  2. Iodinated contrast media electro-degradation: process performance and degradation pathways.

    PubMed

    Del Moro, Guido; Pastore, Carlo; Di Iaconi, Claudio; Mascolo, Giuseppe

    2015-02-15

    The electrochemical degradation of six of the most widely used iodinated contrast media was investigated. Batch experiments were performed under constant current conditions using two DSA® electrodes (titanium coated with a proprietary and patented mixed metal oxide solution of precious metals such as iridium, ruthenium, platinum, rhodium and tantalum). The degradation removal never fell below 85% (at a current density of 64 mA/cm(2) with a reaction time of 150 min) when perchlorate was used as the supporting electrolyte; however, when sulphate was used, the degradation performance was above 80% (at a current density of 64 mA/cm(2) with a reaction time of 150 min) for all of the compounds studied. Three main degradation pathways were identified, namely, the reductive de-iodination of the aromatic ring, the reduction of alkyl aromatic amides to simple amides and the de-acylation of N-aromatic amides to produce aromatic amines. However, as amidotrizoate is an aromatic carboxylate, this is added via the decarboxylation reaction. The investigation did not reveal toxicity except for the lower current density used, which has shown a modest toxicity, most likely for some reaction intermediates that are not further degraded. In order to obtain total removal of the contrast media, it was necessary to employ a current intensity between 118 and 182 mA/cm(2) with energy consumption higher than 370 kWh/m(3). Overall, the electrochemical degradation was revealed to be a reliable process for the treatment of iodinated contrast media that can be found in contaminated waters such as hospital wastewater or pharmaceutical waste-contaminated streams.

  3. Global richness patterns of venomous snakes reveal contrasting influences of ecology and history in two different clades.

    PubMed

    Terribile, Levi Carina; Olalla-Tárraga, Miguel Angel; Morales-Castilla, Ignacio; Rueda, Marta; Vidanes, Rosa M; Rodríguez, Miguel Angel; Diniz-Filho, José Alexandre Felizola

    2009-03-01

    Recent studies addressing broad-scale species richness gradients have proposed two main primary drivers: contemporary climate and evolutionary processes (differential balance between speciation and extinction). Here, we analyze the global richness patterns of two venomous snake clades, Viperidae and Elapidae. We used ordinary least squares multiple regression (OLS) and partial regression analysis to investigate to what extent actual evapotranspiration (AET; summarizing current environmental conditions) and biogeographical regions (representing evolutionary effects) were associated with species richness. For viperids, AET explained 45.6% of the variance in richness whereas the effect of this variable for elapids was almost null (0.5%). On the other hand, biogeographic regions were the best predictors of elapid richness (56.5%), against its relatively small effect (25.9%) in viperid richness. Partial regressions also revealed similar patterns for independent effects of climate and history in both clades. However, the independent historical effect in Elapidae decreased from 45.2 to 17.8% when we excluded Australia from the analyses, indicating that the strong historical effect that had emerged for the global richness pattern was reflecting the historical process of elapid radiation into Australia. Even after excluding Australia, the historical signal in elapid richness in the rest of the globe was still significant and much higher than that observed in viperid richness at a global scale (2.7% after controlling for AET effects). Differences in the evolutionary age of these two clades can be invoked to explain these contrasting results, in that viperids probably had more time for diversification, generating richness responses to environmental gradients, whereas the pattern of distribution of elapid richness can be more directly interpreted in an evolutionary context. Moreover, these results show the importance of starting to adopt deconstructive approaches to species

  4. Regional specificity of MRI contrast parameter changes in normal ageing revealed by voxel-based quantification (VBQ).

    PubMed

    Draganski, B; Ashburner, J; Hutton, C; Kherif, F; Frackowiak, R S J; Helms, G; Weiskopf, N

    2011-04-15

    Normal ageing is associated with characteristic changes in brain microstructure. Although in vivo neuroimaging captures spatial and temporal patterns of age-related changes of anatomy at the macroscopic scale, our knowledge of the underlying (patho)physiological processes at cellular and molecular levels is still limited. The aim of this study is to explore brain tissue properties in normal ageing using quantitative magnetic resonance imaging (MRI) alongside conventional morphological assessment. Using a whole-brain approach in a cohort of 26 adults, aged 18-85years, we performed voxel-based morphometric (VBM) analysis and voxel-based quantification (VBQ) of diffusion tensor, magnetization transfer (MT), R1, and R2* relaxation parameters. We found age-related reductions in cortical and subcortical grey matter volume paralleled by changes in fractional anisotropy (FA), mean diffusivity (MD), MT and R2*. The latter were regionally specific depending on their differential sensitivity to microscopic tissue properties. VBQ of white matter revealed distinct anatomical patterns of age-related change in microstructure. Widespread and profound reduction in MT contrasted with local FA decreases paralleled by MD increases. R1 reductions and R2* increases were observed to a smaller extent in overlapping occipito-parietal white matter regions. We interpret our findings, based on current biophysical models, as a fingerprint of age-dependent brain atrophy and underlying microstructural changes in myelin, iron deposits and water. The VBQ approach we present allows for systematic unbiased exploration of the interaction between imaging parameters and extends current methods for detection of neurodegenerative processes in the brain. The demonstrated parameter-specific distribution patterns offer insights into age-related brain structure changes in vivo and provide essential baseline data for studying disease against a background of healthy ageing.

  5. Ultrastructure of stomatal development in early-divergent angiosperms reveals contrasting patterning and pre-patterning

    PubMed Central

    Rudall, Paula J.; Knowles, Emma V. W.

    2013-01-01

    Background and Aims Angiosperm stomata consistently possess a pair of guard cells, but differ between taxa in the patterning and developmental origin of neighbour cells. Developmental studies of phylogenetically pivotal taxa are essential as comparative yardsticks for understanding the evolution of stomatal development. Methods We present a novel ultrastructural study of developing stomata in leaves of Amborella (Amborellales), Nymphaea and Cabomba (Nymphaeales), and Austrobaileya and Schisandra (Austrobaileyales), representing the three earliest-divergent lineages of extant angiosperms (the ANITA-grade). Key Results Alternative developmental pathways occur in early-divergent angiosperms, resulting partly from differences in pre-patterning and partly from the presence or absence of highly polarized (asymmetric) mitoses in the stomatal cell lineage. Amplifying divisions are absent from ANITA-grade taxa, indicating that ostensible similarities with the stomatal patterning of Arabidopsis are superficial. In Amborella, ‘squared’ pre-patterning occurs in intercostal regions, with groups of four protodermal cells typically arranged in a rectangle; most guard-mother cells are formed by asymmetric division of a precursor cell (the mesoperigenous condition) and are typically triangular or trapezoidal. In contrast, water-lily stomata are always perigenous (lacking asymmetric divisions). Austrobaileya has occasional ‘giant’ stomata. Conclusions Similar mature stomatal phenotypes can result from contrasting morphogenetic factors, although the results suggest that paracytic stomata are invariably the product of at least one asymmetric division. Loss of asymmetric divisions in stomatal development could be a significant factor in land plant evolution, with implications for the diversity of key structural and physiological pathways. PMID:23969762

  6. Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

    PubMed Central

    Lallias, Delphine; Hiddink, Jan G; Fonseca, Vera G; Gaspar, John M; Sung, Way; Neill, Simon P; Barnes, Natalie; Ferrero, Tim; Hall, Neil; Lambshead, P John D; Packer, Margaret; Thomas, W Kelley; Creer, Simon

    2015-01-01

    Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a ‘melting pot' of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model microbial biodiversity are limited for eukaryotes. Although diatoms commonly feature as bioindicator species, additional microbial eukaryotes represent a huge resource for assessing ecosystem health. Of these, meiofaunal communities may represent the optimal compromise between functional diversity that can be assessed using morphology and phenotype–environment interactions as compared with smaller life fractions. Here, using 454 Roche sequencing of the 18S nSSU barcode we investigate which of the local natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of the estuarine ecosystem. In order to investigate potential variation at the ecosystem scale, we compare two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress. The data show that although community turnover is likely to be predictable, taxa are likely to respond to different environmental drivers and, in particular, hydrodynamics, salinity range and granulometry, according to varied life-history characteristics. At the ecosystem level, communities exhibited patterns of estuary-specific similarity within different salinity range habitats, highlighting the environmental sequencing biomonitoring potential of meiofauna, dispersal effects or both. PMID:25423027

  7. Laser speckle contrast reveals cerebral blood flow dynamics evoked by optogenetically controlled neuronal activity

    NASA Astrophysics Data System (ADS)

    Li, Nan; Thakor, Nitish V.; Pelled, Galit

    2013-03-01

    As a critical basis of functional brain imaging, neurovascular coupling describes the link between neuronal and hemodynamic changes. The majority of in vivo neurovascular coupling studies was performed by inducing sensory stimulation via afferent inputs. Unfortunately such an approach results in recruiting of multiple types of cells, which confounds the explanation of neuronal roles in stimulus evoked hemodynamic changes. Recently optogenetics has emerged to provide immediate control of neurons by exciting or inhibiting genetically engineered neurons expressing light sensitive proteins. However, there is a need for optical methods capable of imaging the concurrent hemodynamic changes. We utilize laser speckle contrast imaging (LSCI) to obtain high resolution display of cerebral blood flow (CBF) in the vicinity of the targeted neural population. LSCI is a minimally invasive method for imaging CBF in microvessels through thinned skull, and produces images with high spatiotemporal resolution, wide field of view. In the integrated system light sources with different wavelengths and band-passing/blocking filters were used to allow simultaneous optical manipulation of neuronal activities and optical imaging of corresponding CBF. Experimental studies were carried out in a rodent model expressing channalrhodopsin (ChR2) in excitatory neurons in the somatosensory cortex (S1). The results demonstrated significant increases of CBF in response to ChR2 stimulation (exciting neuronal firing) comparable to the CBF response to contralateral forepaw stimulation. The approach promises to be an exciting minimally invasive method to study neurovascular coupling. The complete system provides a novel approach for broad neuroscience applications.

  8. Unenhanced areas revealed by contrast-enhanced abdominal ultrasonography with Sonazoid™ potentially correspond to colorectal cancer

    PubMed Central

    Tomizawa, Minoru; Togashi, Mizuki; Shinozaki, Fuminobu; Hasegawa, Rumiko; Shirai, Yoshinori; Noritake, Midori; Matsuoka, Yukie; Kainuma, Hiroaki; Iwasaki, Yasuji; Fugo, Kazunori; Motoyoshi, Yasufumi; Sugiyama, Takao; Yamamoto, Shigenori; Kishimoto, Takashi; Ishige, Naoki

    2016-01-01

    The present study investigated the potential utility of contrast-enhanced abdominal ultrasonography (CEUS), using Sonazoid™, in colorectal cancer (CRC). Three patients were subjected to CEUS with Sonazoid™. Surgical specimens were immunostained for CD31. Numbers of blood vessels positive for CD31 were analyzed in each of five fields at ×400 magnification and averaged to determine blood vessel density. Blood vessel density was compared between non-tumorous and tumorous areas. Prior to the administration of Sonazoid™, CRC was illustrated as irregular-shaped wall thickening. One minute after the administration of Sonazoid™, the majority of the thickened wall was enhanced, while some parts of the thickened wall remained unenhanced. Blood vessel densities of non-tumorous and tumorous areas in patient two were 25.2±2.5 and 5.2±1.1 (P<0.0001). Blood vessel densities of non-tumorous and tumorous areas in patient three were 19.0±3.1 and 2.2±0.8 (P<0.0001). Tumorous areas of CRC were not enhanced 1 min after the administration of Sonazoid™. Blood vessel density was lower in tumorous areas compared with non-tumorous areas, as evidenced by immunohistochemistry for CD31. These findings suggest that CEUS may be useful for the determination of the extent of CRC. PMID:28105132

  9. Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations.

    PubMed

    Goldberg, Amy; Günther, Torsten; Rosenberg, Noah A; Jakobsson, Mattias

    2017-03-07

    Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the late Neolithic/Bronze Age migration from the Pontic-Caspian Steppe, can be investigated using patterns of genetic variation among the people who lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome with the autosomes in 20 early Neolithic and 16 late Neolithic/Bronze Age human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic Steppe during the late Neolithic/Bronze Age, however, we estimate a dramatic male bias, with approximately five to 14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

  10. Genetic structure along an elevational gradient in Hawaiian honeycreepers reveals contrasting evolutionary responses to avian malaria

    USGS Publications Warehouse

    Eggert, L.S.; Terwilliger, L.A.; Woodworth, B.L.; Hart, P.J.; Palmer, D.; Fleischer, R.C.

    2008-01-01

    Background. The Hawaiian honeycreepers (Drepanidinae) are one of the best-known examples of an adaptive radiation, but their persistence today is threatened by the introduction of exotic pathogens and their vector, the mosquito Culex quinquefasciatus. Historically, species such as the amakihi (Hemignathus virens), the apapane (Himatione sanguinea), and the iiwi (Vestiaria coccinea) were found from the coastal lowlands to the high elevation forests, but by the late 1800's they had become extremely rare in habitats below 900 m. Recently, however, populations of amakihi and apapane have been observed in low elevation habitats. We used twelve polymorphic microsatellite loci to investigate patterns of genetic structure, and to infer responses of these species to introduced avian malaria along an elevational gradient on the eastern flanks of Mauna Loa and Kilauea volcanoes on the island of Hawaii. Results. Our results indicate that amakihi have genetically distinct, spatially structured populations that correspond with altitude. We detected very few apapane and no iiwi in low-elevation habitats, and genetic results reveal only minimal differentiation between populations at different altitudes in either of these species. Conclusion. Our results suggest that amakihi populations in low elevation habitats have not been recolonized by individuals from mid or high elevation refuges. After generations of strong selection for pathogen resistance, these populations have rebounded and amakihi have become common in regions in which they were previously rare or absent. ?? 2008 Eggert et al; licensee BioMed Central Ltd.

  11. Genetic structure along an elevational gradient in Hawaiian honeycreepers reveals contrasting evolutionary responses to avian malaria

    PubMed Central

    2008-01-01

    Background The Hawaiian honeycreepers (Drepanidinae) are one of the best-known examples of an adaptive radiation, but their persistence today is threatened by the introduction of exotic pathogens and their vector, the mosquito Culex quinquefasciatus. Historically, species such as the amakihi (Hemignathus virens), the apapane (Himatione sanguinea), and the iiwi (Vestiaria coccinea) were found from the coastal lowlands to the high elevation forests, but by the late 1800's they had become extremely rare in habitats below 900 m. Recently, however, populations of amakihi and apapane have been observed in low elevation habitats. We used twelve polymorphic microsatellite loci to investigate patterns of genetic structure, and to infer responses of these species to introduced avian malaria along an elevational gradient on the eastern flanks of Mauna Loa and Kilauea volcanoes on the island of Hawaii. Results Our results indicate that amakihi have genetically distinct, spatially structured populations that correspond with altitude. We detected very few apapane and no iiwi in low-elevation habitats, and genetic results reveal only minimal differentiation between populations at different altitudes in either of these species. Conclusion Our results suggest that amakihi populations in low elevation habitats have not been recolonized by individuals from mid or high elevation refuges. After generations of strong selection for pathogen resistance, these populations have rebounded and amakihi have become common in regions in which they were previously rare or absent. PMID:19014596

  12. Molecular phylogenetic relationships reveal contrasting evolutionary patterns in Gorgoniidae (Octocorallia) in the Eastern Pacific.

    PubMed

    Soler-Hurtado, M M; López-González, P J; Machordom, A

    2017-03-24

    The description and delimitation of species in an evolutionary framework is essential for understanding patterns of biodiversity and distribution, and in the assessment of conservation strategies for natural resources. This study seeks to clarify the evolutionary history and genetic variation within and between closely related octocoral species that are fundamental to benthic marine ecosystems for harbouring a high diversity of associated fauna. For our study system, we focused on members of the Gorgoniidae family in the Eastern Pacific, particularly of the Ecuadorian littoral, a less studied marine ecosystem. According to our results, the diagnosis of the genus Pacifigorgia is here amended to include species previously considered in the genus Leptogorgia. The genera Leptogorgia and Eugorgia are included within a single clade, and neither are recovered as monophyletic. In this case, according to the priority rule of the International Code of Zoological Nomenclature (ICZN), our proposal is to include the species considered in these two genera in Leptogorgia. In addition, we found evidence of interesting speciation patterns: morphological differentiation with no apparent genetic differentiation (in Pacifigorgia), and inconsistencies between mitochondrial and nuclear data that suggest a hybridisation phenomenon (in Leptogorgia). In the first case, recent radiation, ancient hybridisation, sympatric speciation, and in the second, reticulate evolution may have contributed to the evolutionary history of the studied taxa. Therefore, incongruences observed between morphological and molecular evidences in these octocorals, and in corals in general, may reveal the types of events/patterns that have influenced their evolution.

  13. The effect of global versus local processing styles on assimilation versus contrast in social judgment.

    PubMed

    Förster, Jens; Liberman, Nira; Kuschel, Stefanie

    2008-04-01

    The authors propose a global/local processing style model (GLOMO) for assimilation and contrast effects in social judgment. GLOMO is based on Schwarz and Bless' (1992, 2007) inclusion-exclusion model, which suggests that when information is included into a category, assimilation occurs, whereas when information is excluded from a category, contrast occurs. According to GLOMO, inclusion versus exclusion should be influenced by whether people process information globally or locally. In 5 experiments, using both disambiguation and social comparison, the authors induced local versus global processing through perceptual tasks and time perspective and showed that global processing produced assimilation, whereas local processing produced contrast. The experiments showed that processing styles elicited in one task can carry over to other tasks and influence social judgments. Furthermore, they found that hemisphere activation and accessibility of judgment-consistent knowledge partially mediated these effects. Implications for current and classic models of social judgment are discussed.

  14. FMRI analysis of contrast polarity processing in face-selective cortex in humans and monkeys

    PubMed Central

    Yue, Xiaomin; Nasr, Shahin; Devaney, Kathryn J.; Holt, Daphne J.; Tootell, Roger B.H.

    2013-01-01

    Recognition is strongly impaired when the normal contrast polarity of faces is reversed. For instance, otherwise-familiar faces become very difficult to recognize when viewed as photographic negatives. Here, we used fMRI to demonstrate related properties in visual cortex: 1) fMRI responses in the human Fusiform Face Area (FFA) decreased strongly (26%) to contrast-reversed faces across a wide range of contrast levels (5.3-100% RMS contrast), in all subjects tested. In a whole brain analysis, this contrast polarity bias was largely confined to the Fusiform Face Area (FFA; p < 0.0001), with possible involvement of a left occipital face-selective region. 2) It is known that reversing facial contrast affects three image properties in parallel (absorbance, shading, and specular reflection). Here, comparison of FFA responses to those in V1 suggests that the contrast polarity bias is produced in FFA only when all three component properties were reversed simultaneously, which suggests a prominent non-linearity in FFA processing. 3) Across a wide range (180°) of illumination source angles, 3D face shapes without texture produced response constancy in FFA, without a contrast polarity bias. 4) Consistent with psychophysics, analogous fMRI biases for normal contrast polarity were not produced by non-face objects, with image statistics similar to the face stimuli. 5) Using fMRI, we also demonstrated a contrast polarity bias in awake behaving macaque monkeys, in the cortical region considered homologous to human FFA. Thus common cortical mechanisms may underlie facial contrast processing across ~ 25 million years of primate evolution. PMID:23518007

  15. Three-dimensional mouse brain cytoarchitecture revealed by laboratory-based x-ray phase-contrast tomography

    NASA Astrophysics Data System (ADS)

    Töpperwien, Mareike; Krenkel, Martin; Vincenz, Daniel; Stöber, Franziska; Oelschlegel, Anja M.; Goldschmidt, Jürgen; Salditt, Tim

    2017-02-01

    Studies of brain cytoarchitecture in mammals are routinely performed by serial sectioning of the specimen and staining of the sections. The procedure is labor-intensive and the 3D architecture can only be determined after aligning individual 2D sections, leading to a reconstructed volume with non-isotropic resolution. Propagation-based x-ray phase-contrast tomography offers a unique potential for high-resolution 3D imaging of intact biological specimen due to the high penetration depth and potential resolution. We here show that even compact laboratory CT at an optimized liquid-metal jet microfocus source combined with suitable phase-retrieval algorithms and a novel tissue preparation can provide cellular and subcellular resolution in millimeter sized samples of mouse brain. We removed water and lipids from entire mouse brains and measured the remaining dry tissue matrix in air, lowering absorption but increasing phase contrast. We present single-cell resolution images of mouse brain cytoarchitecture and show that axons can be revealed in myelinated fiber bundles. In contrast to optical 3D techniques our approach does neither require staining of cells nor tissue clearing, procedures that are increasingly difficult to apply with increasing sample and brain sizes. The approach thus opens a novel route for high-resolution high-throughput studies of brain architecture in mammals.

  16. Three-dimensional mouse brain cytoarchitecture revealed by laboratory-based x-ray phase-contrast tomography

    PubMed Central

    Töpperwien, Mareike; Krenkel, Martin; Vincenz, Daniel; Stöber, Franziska; Oelschlegel, Anja M.; Goldschmidt, Jürgen; Salditt, Tim

    2017-01-01

    Studies of brain cytoarchitecture in mammals are routinely performed by serial sectioning of the specimen and staining of the sections. The procedure is labor-intensive and the 3D architecture can only be determined after aligning individual 2D sections, leading to a reconstructed volume with non-isotropic resolution. Propagation-based x-ray phase-contrast tomography offers a unique potential for high-resolution 3D imaging of intact biological specimen due to the high penetration depth and potential resolution. We here show that even compact laboratory CT at an optimized liquid-metal jet microfocus source combined with suitable phase-retrieval algorithms and a novel tissue preparation can provide cellular and subcellular resolution in millimeter sized samples of mouse brain. We removed water and lipids from entire mouse brains and measured the remaining dry tissue matrix in air, lowering absorption but increasing phase contrast. We present single-cell resolution images of mouse brain cytoarchitecture and show that axons can be revealed in myelinated fiber bundles. In contrast to optical 3D techniques our approach does neither require staining of cells nor tissue clearing, procedures that are increasingly difficult to apply with increasing sample and brain sizes. The approach thus opens a novel route for high-resolution high-throughput studies of brain architecture in mammals. PMID:28240235

  17. Interference Contrast Reveals Debonding

    SciTech Connect

    Boatner, Lynn A; Longmire, Hu Foster; Gray, Allison S

    2007-11-01

    The elastic constants of single crystals can be determined by the high-frequency 'pulse-echo' superposition method, in which a piezoelectric transducer that is bonded to a single crystal sends stress pulses into the sample. The round-trip transit time of these pulses, t, is measured by overlapping the leading cycles of the first two echoes that are reflected back to the transducer. The sound velocity is then found by the relationship V = 2l/t, where l represents the length of the sample. By transmitting the ultrasonic waves along different crystallographic directions, values for the various elastic constants can be calculated by the relationship C = {rho}V{sup 2}.

  18. The evolutionary function of conscious information processing is revealed by its task-dependency in the olfactory system.

    PubMed

    Keller, Andreas

    2014-01-01

    Although many responses to odorous stimuli are mediated without olfactory information being consciously processed, some olfactory behaviors require conscious information processing. I will here contrast situations in which olfactory information is processed consciously to situations in which it is processed non-consciously. This contrastive analysis reveals that conscious information processing is required when an organism is faced with tasks in which there are many behavioral options available. I therefore propose that it is the evolutionary function of conscious information processing to guide behaviors in situations in which the organism has to choose between many possible responses.

  19. Zernike phase contrast cryo-electron microscopy reveals 100 kDa component in a protein complex

    NASA Astrophysics Data System (ADS)

    Wu, Yi-Min; Wang, Chun-Hsiung; Chang, Jen-wei; Chen, Yi-yun; Miyazaki, Naoyuki; Murata, Kazuyoshi; Nagayama, Kuniaki; Chang, Wei-Hau

    2013-12-01

    Cryo-electron microscopy (cryo-EM) has become a powerful technique for obtaining near atomic structures for large protein assemblies or large virus particles, but the application to protein particles smaller than 200-300 kDa has been hampered by the feeble phase contrast obtained for such small samples and the limited number of electrons tolerated by them without incurring excessive radiation damage. By implementing a thin-film quarter-wave phase plate to a cryo-EM, Nagayama, one of the present authors, has recently restored the long-lost very low spatial frequencies, generating in-focus phase contrast superior to that of conventional defocusing phase contrast, and successfully applied the so-called Zernike phase-plate cryo-EM to target various biological samples in native state. Nevertheless, the sought-after goal of using enhanced phase contrast to reveal a native protein as small as 100 kDa waits to be realized. Here, we report a study in which 200 kV Zernike phase-plate cryo-EM with a plate cut-on periodicity of 36 nm was applied to visualize 100 kDa components of various protein complexes, including the small domains on the surface of an icosahedral particle of ˜38 nm derived from the dragon grouper nervous necrosis virus (DGNNV) and the labile sub-complex dissociated from yeast RNA polymerase III of 17 nm. In the former case, we observed a phase contrast reversal phenomenon at the centre of the icosahedral particle and traced its root cause to the near matching of the cut-on size and the particle size. In summary, our work has demonstrated that Zernike phase-plate implementation can indeed expand the size range of proteins that can be successfully investigated by cryo-EM, opening the door for countless proteins. Finally, we briefly discuss the possibility of using a transfer lens system to enlarge the cut-on periodicity without further miniaturizing the plate pinhole.

  20. Dynamic Contrast-Enhanced Magnetic Resonance Imaging Reveals Stress-Induced Angiogenesis in MCF7 Human Breast Tumors

    NASA Astrophysics Data System (ADS)

    Furman-Haran, Edna; Margalit, Raanan; Grobgeld, Dov; Degani, Hadassa

    1996-06-01

    The mechanism of contrast enhancement of tumors using magnetic resonance imaging was investigated in MCF7 human breast cancer implanted in nude mice. Dynamic contrast-enhanced images recorded at high spatial resolution were analyzed by an image analysis method based on a physiological model, which included the blood circulation, the tumor, the remaining tissues, and clearance via the kidneys. This analysis enabled us to map in rapidly enhancing regions within the tumor, the capillary permeability factor (capillary permeability times surface area per voxel volume) and the fraction of leakage space. Correlation of these maps with T2-weighted spin echo images, with histopathology, and with immunohistochemical staining of endothelial cells demonstrated the presence of dense permeable microcapillaries in the tumor periphery and in intratumoral regions that surrounded necrotic loci. The high leakage from the intratumoral permeable capillaries indicated an induction of a specific angiogenic process associated with stress conditions that cause necrosis. This induction was augmented in tumors responding to tamoxifen treatment. Determination of the distribution and extent of this stress-induced angiogenic activity by contrast-enhanced MRI might be of diagnostic and of prognostic value.

  1. Comparison of laser Doppler and laser speckle contrast imaging using a concurrent processing system

    NASA Astrophysics Data System (ADS)

    Sun, Shen; Hayes-Gill, Barrie R.; He, Diwei; Zhu, Yiqun; Huynh, Nam T.; Morgan, Stephen P.

    2016-08-01

    Full field laser Doppler imaging (LDI) and single exposure laser speckle contrast imaging (LSCI) are directly compared using a novel instrument which can concurrently image blood flow using both LDI and LSCI signal processing. Incorporating a commercial CMOS camera chip and a field programmable gate array (FPGA) the flow images of LDI and the contrast maps of LSCI are simultaneously processed by utilizing the same detected optical signals. The comparison was carried out by imaging a rotating diffuser. LDI has a linear response to the velocity. In contrast, LSCI is exposure time dependent and does not provide a linear response in the presence of static speckle. It is also demonstrated that the relationship between LDI and LSCI can be related through a power law which depends on the exposure time of LSCI.

  2. Optical Fourier techniques for medical image processing and phase contrast imaging

    PubMed Central

    Yelleswarapu, Chandra S.; Kothapalli, Sri-Rajasekhar; Rao, D.V.G.L.N.

    2008-01-01

    This paper briefly reviews the basics of optical Fourier techniques (OFT) and applications for medical image processing as well as phase contrast imaging of live biological specimens. Enhancement of microcalcifications in a mammogram for early diagnosis of breast cancer is the main focus. Various spatial filtering techniques such as conventional 4f filtering using a spatial mask, photoinduced polarization rotation in photosensitive materials, Fourier holography, and nonlinear transmission characteristics of optical materials are discussed for processing mammograms. We also reviewed how the intensity dependent refractive index can be exploited as a phase filter for phase contrast imaging with a coherent source. This novel approach represents a significant advance in phase contrast microscopy. PMID:18458764

  3. Direct brain recordings reveal hippocampal rhythm underpinnings of language processing

    PubMed Central

    Anderson, Kristopher L.; Lin, Jack J.; Dewar, Callum; Parvizi, Josef; Dronkers, Nina F.; Knight, Robert T.

    2016-01-01

    Language is classically thought to be supported by perisylvian cortical regions. Here we provide intracranial evidence linking the hippocampal complex to linguistic processing. We used direct recordings from the hippocampal structures to investigate whether theta oscillations, pivotal in memory function, track the amount of contextual linguistic information provided in sentences. Twelve participants heard sentences that were either constrained (“She locked the door with the”) or unconstrained (“She walked in here with the”) before presentation of the final word (“key”), shown as a picture that participants had to name. Hippocampal theta power increased for constrained relative to unconstrained contexts during sentence processing, preceding picture presentation. Our study implicates hippocampal theta oscillations in a language task using natural language associations that do not require memorization. These findings reveal that the hippocampal complex contributes to language in an active fashion, relating incoming words to stored semantic knowledge, a necessary process in the generation of sentence meaning. PMID:27647880

  4. Acting without seeing: eye movements reveal visual processing without awareness.

    PubMed

    Spering, Miriam; Carrasco, Marisa

    2015-04-01

    Visual perception and eye movements are considered to be tightly linked. Diverse fields, ranging from developmental psychology to computer science, utilize eye tracking to measure visual perception. However, this prevailing view has been challenged by recent behavioral studies. Here, we review converging evidence revealing dissociations between the contents of perceptual awareness and different types of eye movement. Such dissociations reveal situations in which eye movements are sensitive to particular visual features that fail to modulate perceptual reports. We also discuss neurophysiological, neuroimaging, and clinical studies supporting the role of subcortical pathways for visual processing without awareness. Our review links awareness to perceptual-eye movement dissociations and furthers our understanding of the brain pathways underlying vision and movement with and without awareness.

  5. Improved motion contrast and processing efficiency in OCT angiography using complex-correlation algorithm

    NASA Astrophysics Data System (ADS)

    Guo, Li; Li, Pei; Pan, Cong; Liao, Rujia; Cheng, Yuxuan; Hu, Weiwei; Chen, Zhong; Ding, Zhihua; Li, Peng

    2016-02-01

    The complex-based OCT angiography (Angio-OCT) offers high motion contrast by combining both the intensity and phase information. However, due to involuntary bulk tissue motions, complex-valued OCT raw data are processed sequentially with different algorithms for correcting bulk image shifts (BISs), compensating global phase fluctuations (GPFs) and extracting flow signals. Such a complicated procedure results in massive computational load. To mitigate such a problem, in this work, we present an inter-frame complex-correlation (CC) algorithm. The CC algorithm is suitable for parallel processing of both flow signal extraction and BIS correction, and it does not need GPF compensation. This method provides high processing efficiency and shows superiority in motion contrast. The feasibility and performance of the proposed CC algorithm is demonstrated using both flow phantom and live animal experiments.

  6. Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis.

    PubMed

    Lowry, David B; Logan, Tierney L; Santuari, Luca; Hardtke, Christian S; Richards, James H; DeRose-Wilson, Leah J; McKay, John K; Sen, Saunak; Juenger, Thomas E

    2013-09-01

    The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression.

  7. [Measuring the contrast resolution limits of human vision based on the modern digital image processing].

    PubMed

    Wang, Zhifang; Liu, Yuhong; Wang, Ying; Li, Hong; Li, Zhangyong; Zhao, Zhiqiang; Xie, Zhengxiang

    2008-10-01

    In the literatures on the human vision physiology and physics, there were reports about space resolution limit of 1' visual angle, frequency resolution limit of 5 nm and time resolution limit of 0.1" of human vision. However, there has been no report about the contrast resolution limit of human vision,especially the report of measuring method and result about the contrast resolution limit of human vision based on the modern digital image processing. Here we report a modern method for measuring the contrast resolution limit of human vision based on computer digital image processing technology, and we present the measured results and their mathematical models. The function relationships of contrast resolution limit varying with background gray in a photopic or a scotopic sights were illuminated respectively. It can be expected that such investigations with regard to human vision will establish the physiological foundation of the theories and techniques in hiding bodies and hiding figures (stealth), in anti-hiding bodies and anti-hiding figures, in the night vision system independent of infrared, as well as in their relative industries.

  8. Low-level processing deficits underlying poor contrast sensitivity for moving plaids in anisometropic amblyopia.

    PubMed

    Tang, Yong; Chen, Linyi; Liu, Zhongjian; Liu, Caiyuan; Zhou, Yifeng

    2012-11-01

    Many studies using random dot kinematograms have indicated a global motion processing deficit originated from extrastriate cortex, specifically middle temporal area (MT) and media superior temporal area (MST), in patients with amblyopia. However, the nature of this deficit remains unclear. To explore whether the ability of motion integration is impaired in amblyopia, contrast sensitivity for moving plaids and their corresponding component gratings were measured over a range of stimulus durations and spatial and temporal frequencies in 10 control subjects and 13 anisometropic amblyopes by using a motion direction discrimination task. The results indicated a significant loss of contrast sensitivity for moving plaids as well as for moving gratings at intermediate and high spatial frequencies in amblyopic eyes (AEs). Additionally, we found that the loss of contrast sensitivity for moving plaids was statistically equivalent to that for moving component gratings in AEs, that is, the former could be almost completely accounted for by the latter. These results suggest that the integration of motion information conveyed by component gratings of moving plaids may be intact in anisometropic amblyopia, and that the apparent deficits in contrast sensitivity for moving plaids in anisometropic amblyopia can be almost completely attributed to those for gratings, that is, low-level processing deficits.

  9. Children processing music: electric brain responses reveal musical competence and gender differences.

    PubMed

    Koelsch, Stefan; Grossmann, Tobias; Gunter, Thomas C; Hahne, Anja; Schröger, Erich; Friederici, Angela D

    2003-07-01

    Numerous studies investigated physiological correlates of the processing of musical information in adults. How these correlates develop during childhood is poorly understood. In the present study, we measured event-related electric brain potentials elicited in 5- and 9-year-old children while they listened to (major-minor tonal) music. Stimuli were chord sequences, infrequently containing harmonically inappropriate chords. Our results demonstrate that the degree of (in)appropriateness of the chords modified the brain responses in both groups according to music-theoretical principles. This suggests that already 5-year-old children process music according to a well-established cognitive representation of the major-minor tonal system and according to music-syntactic regularities. Moreover, we show that, in contrast to adults, an early negative brain response was left predominant in boys, whereas it was bilateral in girls, indicating a gender difference in children processing music, and revealing that children process music with a hemispheric weighting different from that of adults. Because children process, in contrast to adults, music in the same hemispheres as they process language, results indicate that children process music and language more similarly than adults. This finding might support the notion of a common origin of music and language in the human brain, and concurs with findings that demonstrate the importance of musical features of speech for the acquisition of language.

  10. "Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses".

    PubMed

    Eveno, Emmanuelle; Collada, Carmen; Guevara, M Angeles; Léger, Valérie; Soto, Alvaro; Díaz, Luis; Léger, Patrick; González-Martínez, Santiago C; Cervera, M Teresa; Plomion, Christophe; Garnier-Géré, Pauline H

    2008-02-01

    The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed

  11. Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient

    PubMed Central

    Valverde, Angel; Makhalanyane, Thulani P.; Cowan, Don A.

    2014-01-01

    Understanding the relative influence of deterministic and stochastic processes in driving community assembly is a major goal in microbial ecology. Here, we have investigated the influence of these processes on bacterial community assembly in the lateral sediments of a salt pan along a desiccation gradient over a three-year period. We show that the role of deterministic processes increases in communities distant from the water line (shaped by drought), probably as a result of the interplay between abiotic and biotic factors. By contrast, the influence of stochastic processes on bacterial community assembly was higher in the sediments closest to the water line, more likely due to lower levels of abiotic stress. Our results demonstrate that both deterministic and stochastic processes influence bacterial community assembly in salt pan sediments, and that their relative influence varies along a desiccation gradient. PMID:25520714

  12. Catalytic reaction processes revealed by scanning probe microscopy. [corrected].

    PubMed

    Jiang, Peng; Bao, Xinhe; Salmeron, Miquel

    2015-05-19

    Heterogeneous catalysis is of great importance for modern society. About 80% of the chemicals are produced by catalytic reactions. Green energy production and utilization as well as environmental protection also need efficient catalysts. Understanding the reaction mechanisms is crucial to improve the existing catalysts and develop new ones with better activity, selectivity, and stability. Three components are involved in one catalytic reaction: reactant, product, and catalyst. The catalytic reaction process consists of a series of elementary steps: adsorption, diffusion, reaction, and desorption. During reaction, the catalyst surface can change at the atomic level, with roughening, sintering, and segregation processes occurring dynamically in response to the reaction conditions. Therefore, it is imperative to obtain atomic-scale information for understanding catalytic reactions. Scanning probe microscopy (SPM) is a very appropriate tool for catalytic research at the atomic scale because of its unique atomic-resolution capability. A distinguishing feature of SPM, compared to other surface characterization techniques, such as X-ray photoelectron spectroscopy, is that there is no intrinsic limitation for SPM to work under realistic reaction conditions (usually high temperature and high pressure). Therefore, since it was introduced in 1981, scanning tunneling microscopy (STM) has been widely used to investigate the adsorption, diffusion, reaction, and desorption processes on solid catalyst surfaces at the atomic level. STM can also monitor dynamic changes of catalyst surfaces during reactions. These invaluable microscopic insights have not only deepened the understanding of catalytic processes, but also provided important guidance for the development of new catalysts. This Account will focus on elementary reaction processes revealed by SPM. First, we will demonstrate the power of SPM to investigate the adsorption and diffusion process of reactants on catalyst surfaces

  13. Application of image processing techniques for contrast enhancement in dense breast digital mammograms

    NASA Astrophysics Data System (ADS)

    Nunes, Fatima d. L. d. S.; Schiabel, Homero; Benatti, Rodrigo H.

    1999-05-01

    Dense breasts, that usually are characteristic of women less than 40 years old, difficult many times early detection of breast cancer. In this work we present the application of some image processing techniques intended to enhance the contrast in dense breast images, regarding the detection of clustered microcalcifications. The procedure was, firstly, determining in the literature the main techniques used for mammographic images contrast enhancement. The results indicate that, in general: (1) as expected, the overall performance of the CAD scheme for clusters detection decreased when applied exclusively to dense breast images, compared to the application to a set of images without this characteristic; (2) most of the techniques for contrast enhancement used successfully in generic mammography images databases are not able to enhance structures of athirst in databases formed only by dense breasts images, due to the very poor contrast between microcalcifications, for example, and other tissues. These features should stress, therefore, the need of developing a methodology specifically for this type of images in order to provide better conditions to the detection of breast suspicious structures in these group of women.

  14. Wavefront sensing based on phase contrast theory and coherent optical processing

    NASA Astrophysics Data System (ADS)

    Lei, Huang; Qi, Bian; Chenlu, Zhou; Tenghao, Li; Mali, Gong

    2016-07-01

    A novel wavefront sensing method based on phase contrast theory and coherent optical processing is proposed. The wavefront gradient field in the object plane is modulated into intensity distribution in a gang of patterns, making high-density detection available. By applying the method, we have also designed a wavefront sensor. It consists of a classical coherent optical processing system, a CCD detector array, two pieces of orthogonal composite sinusoidal gratings, and a mechanical structure that can perform real-time linear positioning. The simulation results prove and demonstrate the validity of the method and the sensor in high-precision measurement of the wavefront gradient field.

  15. Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions

    PubMed Central

    Santos, Xavier; Felicísimo, Ángel M.

    2016-01-01

    Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks. PMID

  16. The Plasmodium vivax Merozoite Surface Protein 3β Sequence Reveals Contrasting Parasite Populations in Southern and Northwestern Thailand

    PubMed Central

    Kuamsab, Napaporn; Sattabongkot, Jetsumon; Sirichaisinthop, Jeeraphat; Jongwutiwes, Somchai; Cui, Liwang

    2014-01-01

    Background Malaria control efforts have a significant impact on the epidemiology and parasite population dynamics. In countries aiming for malaria elimination, malaria transmission may be restricted to limited transmission hot spots, where parasite populations may be isolated from each other and experience different selection forces. Here we aim to examine the Plasmodium vivax population divergence in geographically isolated transmission zones in Thailand. Methodology We employed the P. vivax merozoite surface protein 3β (PvMSP3β) as a molecular marker for characterizing P. vivax populations based on the extensive diversity of this gene in Southeast Asian parasite populations. To examine two parasite populations with different transmission levels in Thailand, we obtained 45 P. vivax isolates from Tak Province, northwestern Thailand, where the annual parasite incidence (API) was more than 2%, and 28 isolates from Yala and Narathiwat Provinces, southern Thailand, where the API was less than 0.02%. We sequenced the PvMSP3β gene and examined its genetic diversity and molecular evolution between the parasite populations. Principal Findings Of 58 isolates containing single PvMSP3β alleles, 31 sequence types were identified. The overall haplotype diversity was 0.77±0.06 and nucleotide diversity 0.0877±0.0054. The northwestern vivax malaria population exhibited extensive haplotype diversity (HD) of PvMSP3β (HD = 1.0). In contrast, the southern parasite population displayed a single PvMSP3β allele (HD = 0), suggesting a clonal population expansion. This result revealed that the extent of allelic diversity in P. vivax populations in Thailand varies among endemic areas. Conclusion Malaria parasite populations in a given region may vary significantly in genetic diversity, which may be the result of control and influenced by the magnitude of malaria transmission intensity. This is an issue that should be taken into account for the implementation of P. vivax

  17. Laser speckle contrast analysis (LASCA) for blood flow visualization: improved image processing

    NASA Astrophysics Data System (ADS)

    Briers, J. D.; He, Xiao-Wei

    1998-06-01

    LASCA is a single-exposure, full-field technique for mapping flow velocities. The motion of the particles in a fluid flow causes fluctuations in the speckle patten produced when laser light is scattered by the particles. The frequency of these intensity fluctuations increases with increasing velocity. These intensity fluctuations blur the speckle pattern and hence reduce its contrast. With a suitable integration time for the exposure, velocity can be mapped as speckle contrast. The equipment required is very simple. A CCD camera and a framegrabber capture an image of the area of interest. The local speckle contrast is computed and used to produce a false-color map of velocities. LASCA can be used to map capillary blood flow. The results are similar to those obtained by the scanning laser Doppler technique, but are obtained without the need to scan. This reduces the time needed for capturing the image from several minutes to a fraction of a second, already a clinical advantage. Until recently, however, processing the captured image did take several minutes. Improvements in the software have now reduced the processing tome to one second, thus providing a truly real-time method for obtaining a map of capillary blood flow.

  18. Integration of instrumentation and processing software of a laser speckle contrast imaging system

    NASA Astrophysics Data System (ADS)

    Carrick, Jacob J.

    Laser speckle contrast imaging (LSCI) has the potential to be a powerful tool in medicine, but more research in the field is required so it can be used properly. To help in the progression of Michigan Tech's research in the field, a graphical user interface (GUI) was designed in Matlab to control the instrumentation of the experiments as well as process the raw speckle images into contrast images while they are being acquired. The design of the system was successful and is currently being used by Michigan Tech's Biomedical Engineering department. This thesis describes the development of the LSCI GUI as well as offering a full introduction into the history, theory and applications of LSCI.

  19. Initiation process of a thrust fault revealed by analog experiments

    NASA Astrophysics Data System (ADS)

    Yamada, Yasuhiro; Dotare, Tatsuya; Adam, Juergen; Hori, Takane; Sakaguchi, Hide

    2016-04-01

    We conducted 2D (cross-sectional) analog experiments with dry sand using a high resolution digital image correlation (DIC) technique to reveal initiation process of a thrust fault in detail, and identified a number of "weak shear bands" and minor uplift prior to the thrust initiation. The observations suggest that the process can be divided into three stages. Stage 1: characterized by a series of abrupt and short-lived weak shear bands at the location where the thrust will be generated later. Before initiation of the fault, the area to be the hanging wall starts to uplift. Stage 2: defined by the generation of the new thrust and its active displacement. The location of the new thrust seems to be constrained by its associated back-thrust, produced at the foot of the surface slope (by the previous thrust). The activity of the previous thrust turns to zero once the new thrust is generated, but the timing of these two events is not the same. Stage 3: characterized by a constant displacement along the (new) thrust. Similar minor shear bands can be seen in the toe area of the Nankai accretionary prism, SW Japan and we can correlate the along-strike variations in seismic profiles to the model results that show the characteristic features in each thrust development stage.

  20. Prognostic significance of infarct core pathology revealed by quantitative non-contrast in comparison with contrast cardiac magnetic resonance imaging in reperfused ST-elevation myocardial infarction survivors

    PubMed Central

    Carrick, David; Haig, Caroline; Rauhalammi, Sam; Ahmed, Nadeem; Mordi, Ify; McEntegart, Margaret; Petrie, Mark C.; Eteiba, Hany; Hood, Stuart; Watkins, Stuart; Lindsay, Mitchell; Mahrous, Ahmed; Ford, Ian; Tzemos, Niko; Sattar, Naveed; Welsh, Paul; Radjenovic, Aleksandra; Oldroyd, Keith G.; Berry, Colin

    2016-01-01

    Aims To assess the prognostic significance of infarct core tissue characteristics using cardiac magnetic resonance (CMR) imaging in survivors of acute ST-elevation myocardial infarction (STEMI). Methods and results We performed an observational prospective single centre cohort study in 300 reperfused STEMI patients (mean ± SD age 59 ± 12 years, 74% male) who underwent CMR 2 days and 6 months post-myocardial infarction (n = 267). Native T1 was measured in myocardial regions of interest (n = 288). Adverse remodelling was defined as an increase in left ventricular (LV) end-diastolic volume ≥20% at 6 months. All-cause death or first heart failure hospitalization was a pre-specified outcome that was assessed during follow-up (median duration 845 days). One hundred and sixty (56%) patients had a hypo-intense infarct core disclosed by native T1. In multivariable regression, infarct core native T1 was inversely associated with adverse remodelling [odds ratio (95% confidence interval (CI)] per 10 ms reduction in native T1: 0.91 (0.82, 0.00); P = 0.061). Thirty (10.4%) of 288 patients died or experienced a heart failure event and 13 of these events occurred post-discharge. Native T1 values (ms) within the hypo-intense infarct core (n = 160 STEMI patients) were inversely associated with the risk of all-cause death or first hospitalization for heart failure post-discharge (for a 10 ms increase in native T1: hazard ratio 0.730, 95% CI 0.617, 0.863; P < 0.001) including after adjustment for left ventricular ejection fraction, infarct core T2 and myocardial haemorrhage. The prognostic results for microvascular obstruction were similar. Conclusion Infarct core native T1 represents a novel non-contrast CMR biomarker with potential for infarct characterization and prognostication in STEMI survivors. Confirmatory studies are warranted. ClinicalTrials.gov identifier NCT02072850. PMID:26261290

  1. Temporal dynamics of reward processing revealed by magnetoencephalography.

    PubMed

    Doñamayor, Nuria; Marco-Pallarés, Josep; Heldmann, Marcus; Schoenfeld, M Ariel; Münte, Thomas F

    2011-12-01

    Monetary gains and losses in gambling situations are associated with a distinct electroencephalographic signature: in the event-related potentials (ERPs), a mediofrontal feedback-related negativity (FRN) is seen for losses, whereas oscillatory activity shows a burst of in the θ-range for losses and in the β-range for gains. We used whole-head magnetoencephalography to pinpoint the magnetic counterparts of these effects in young healthy adults and explore their evolution over time. On each trial, participants bet on one of two visually presented numbers (25 or 5) by button-press. Both numbers changed color: if the chosen number turned green (red), it indicated a gain (loss) of the corresponding sum in Euro cent. For losses, we found the magnetic correlate of the FRN extending between 230 and 465 ms. Source localization with low-resolution electromagnetic tomography indicated a first generator in posterior cingulate cortex with subsequent activity in the anterior cingulate cortex. Importantly, this effect was sensitive to the magnitude of the monetary loss (25 cent > 5 cent). Later activation was also found in the right insula. Time-frequency analysis revealed a number of oscillatory components in the theta, alpha, and high-beta/low-gamma bands associated to gains, and in the high-beta band, associated to the magnitude of the loss. All together, these effects provide a more fine-grained picture of the temporal dynamics of the processing of monetary rewards and losses in the brain.

  2. Stratification based on reproductive state reveals contrasting patterns of age-related variation in demographic parameters in the kittiwake

    USGS Publications Warehouse

    Cam, E.; Monnat, J.-Y.

    2000-01-01

    Heterogeneity in individual quality can be a major obstacle when interpreting age-specific variation in life-history traits. Heterogeneity is likely to lead to within-generation selection, and patterns observed at the population level may result from the combination of hidden patterns specific to subpopulations. Population-level patterns are not relevant to hypotheses concerning the evolution of age-specific reproductive strategies if they differ from patterns at the individual level. We addressed the influence of age and a variable used as a surrogate of quality (yearly reproductive state) on survival and breeding probability in the kittiwake. We found evidence of an effect of age and quality on both demographic parameters. Patterns observed in breeders are consistent with the selection hypothesis, which predicts age-related increases in survival and traits positively correlated with survival. Our results also reveal unexpected age effects specific to subgroups: the influence of age on survival and future breeding probability is not the same in nonbreeders and breeders. These patterns are observed in higher-quality breeding habitats, where the influence of extrinsic factors on breeding state is the weakest. Moreover, there is slight evidence of an influence of sex on breeding probability (not on survival), but the same overall pattern is observed in both sexes. Our results support the hypothesis that age-related variation in demographic parameters observed at the population level is partly shaped by heterogeneity among individuals. They also suggest processes specific to subpopulations. Recent theoreticaI developments lay emphasis on integration of sources of heterogeneity in optimization models to account for apparently 'sub-optimal' empirical patterns. Incorporation of sources of heterogeneity is also the key to investigation of age-related reproductive strategies in heterogeneous populations. Thwarting 'heterogeneity's ruses' has become a major challenge: for

  3. Anaerobic trophic interactions of contrasting methane-emitting mire soils: processes versus taxa.

    PubMed

    Hunger, Sindy; Gößner, Anita S; Drake, Harold L

    2015-05-01

    Natural wetlands such as mires contribute up to 33% to the global emission of methane. The emission of methane is driven by trophic interactions of anaerobes that collectively degrade biopolymers. The hypothesis of this study was that these interactions in contrasting methane-emitting mire soils are functionally similar but linked to dissimilar taxa. This hypothesis was addressed by evaluating anaerobic processes and microbial taxa of eutrophic, mesotrophic and oligotrophic mire soils. Glucose was fermented to various products (e.g. H2, CO2, butyrate, acetate). Acetoclastic methanogenesis occurred, and acetogenesis and methanogenesis transformed H2-CO2 to acetate and methane, respectively. Although product profiles, cultivable cell numbers and gene copy numbers [mcrA (encodes alpha-subunit of methyl-CoM reductase) and 16S rRNA genes] were similar for all mire soils, only approximately 15% of detected family-level bacteria and species-level methanogens were shared by all mire soils. Approximately, 40% of the detected family-level taxa of each mire soil have no cultured isolates. Acidic conditions appeared to restrict the number of dominant phylotypes. The results indicated (a) that microbial processes which drive methanogenesis are similar but facilitated by dissimilar microbial communities in contrasting mire soils and (b) that mire soils harbor a large number of taxa with no cultured isolates.

  4. Fragmentation process during Ho:YAG laser lithotripsy revealed by time-resolved imaging

    NASA Astrophysics Data System (ADS)

    Beghuin, Didier; Delacretaz, Guy P.; Schmidlin, Franz R.; Rink, Klaus

    1998-01-01

    The stone fragmentation process induced during Ho:YAG laser lithotripsy was observed by time-resolved flash video imaging. Possible acoustic transient occurrence was simultaneously monitored with a PVDF needle hydrophone. We used artificial and cystine kidney stones. We observed that, although the fragmentation process is accompanied with the formation of a cavitation bubble, cavitation has a minimal incidence on stone fragmentation. Fragment ejection is mainly due to a direct laser stone heating and vaporization of stone organic constituents and interstitial water. The minimal effect of the cavitation bubble for fragmentation is confirmed by acoustic transients measurements, which reveal weak pressure transients. This is in contrast with the fragmentation mechanisms induced by laser of shorter pulse duration.

  5. Evolutionary Pets: Offspring Numbers Reveal Speciation Process in Domesticated Chickens

    PubMed Central

    Tiemann, Inga; Rehkämper, Gerd

    2012-01-01

    Since Darwin, the nature of the relationship between evolution and domestication has been debated. Evolution offers different mechanisms of selection that lead to adaptation and may end in the origin of new species as defined by the biological species concept. Domestication has given rise to numerous breeds in almost every domesticated species, including chickens. At the same time, so-called artificial selection seems to exclude mechanisms of sexual selection by the animals themselves. We want to forward the question to the animal itself: With whom do you reproduce successfully? This study focused on the sexual behavior of the domestic chicken Gallus gallus f.dom., particularly the White Crested Polish breed. Experiments on mate choice and the observation of fertilization and hatching rates of mixed-breeding groups revealed breed-specific preferences. In breeding groups containing White Crested Polish and a comparative breed, more purebred chicks hatched than hybrids (number of eggs collected: 1059). Mating was possible in equal shares, but in relation to the number of eggs collected, purebred offspring (62.75%±7.10%, M±SE) hatched to a greater extend compared to hybrid offspring (28.75%±15.32%, M±SE). These data demonstrate that the mechanism of sexual selection is still present in domestic chicken breeds, which includes the alteration of gene frequencies typical for domestication and evolutionary speciation. Due to selection and mate choice we state that breeding in principle can generate new species. Therefore, we see domestication as an evolutionary process that integrates human interests of animal breeding with innate mate choice by the animal. PMID:22879889

  6. Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars

    PubMed Central

    Ma, Jianchao; He, Xiaodong; Bai, Xiaotao; Niu, Zhimin; Duan, Bingbing; Chen, Ningning; Shao, Xuemin; Wan, Dongshi

    2016-01-01

    Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica—which have, respectively, dense and sparse trichomes—to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species. PMID:27916935

  7. Contrasting sedimentary processes along a convergent margin: the Lesser Antilles arc system

    NASA Astrophysics Data System (ADS)

    Picard, Michel; Schneider, Jean-Luc; Boudon, Georges

    2006-12-01

    Sedimentation processes occurring in an active convergent setting are well illustrated in the Lesser Antilles island arc. The margin is related to westward subduction of the North and/or the South America plates beneath the Caribbean plate. From east to west, the arc can be subdivided into several tectono-sedimentary depositional domains: the accretionary prism, the fore-arc basin, the arc platform and inter-arc basin, and the Grenada back-arc basin. The Grenada back-arc basin, the fore-arc basin (Tobago Trough) and the accretionary prism on the east side of the volcanic arc constitute traps for particles derived from the arc platform and the South American continent. The arc is volcanically active, and provides large volumes of volcaniclastic sediments which accumulate mainly in the Grenada basin by volcaniclastic gravity flows (volcanic debris avalanches, debris flows, turbiditic flows) and minor amounts by fallout. By contrast, the eastern side of the margin is fed by ash fallout and minor volcaniclastic turbidites. In this area, the dominant component of the sediments is pelagic in origin, or derived from South America (siliciclastic turbidites). Insular shelves are the locations of carbonate sedimentation, such as large platforms which develop in the Limestone Caribbees in the northern part of the margin. Reworking of carbonate material by turbidity currents also delivers lesser amounts to eastern basins of the margin. This contrasting sedimentation on both sides of the arc platform along the margin is controlled by several interacting factors including basin morphology, volcanic productivity, wind and deep-sea current patterns, and sea-level changes. Basin morphology appears to be the most dominant factor. The western slopes of the arc platform are steeper than the eastern ones, thus favouring gravity flow processes.

  8. What can individual differences reveal about face processing?

    PubMed Central

    Yovel, Galit; Wilmer, Jeremy B.; Duchaine, Brad

    2014-01-01

    Faces are probably the most widely studied visual stimulus. Most research on face processing has used a group-mean approach that averages behavioral or neural responses to faces across individuals and treats variance between individuals as noise. However, individual differences in face processing can provide valuable information that complements and extends findings from group-mean studies. Here we demonstrate that studies employing an individual differences approach—examining associations and dissociations across individuals—can answer fundamental questions about the way face processing operates. In particular these studies allow us to associate and dissociate the mechanisms involved in face processing, tie behavioral face processing mechanisms to neural mechanisms, link face processing to broader capacities and quantify developmental influences on face processing. The individual differences approach we illustrate here is a powerful method that should be further explored within the domain of face processing as well as fruitfully applied across the cognitive sciences. PMID:25191241

  9. Economics of Beaver-Herter extraction process revealed

    SciTech Connect

    Not Available

    1986-09-01

    The Herter process is a surface-mined solvent extraction process which utilizes fatty acids as the solvent. The uniqueness of the Herter process if that it provides a low energy method of separating the fatty acids from the recovered oil for subsequent recycling. The Herter process recovers the fatty acid by saponification, followed by migration of the soap to the aqueous phase, and then desaponification of the resulting soap phase again followed by phase separation. The formation of a hydrocarbon-soap-water emulsion limits the process unless carefully controlled by the addition of an alcohol cosolvent. Addition of the short-chain alcohol limits emulsification and allows a meaningful separation to be accomplished. The modified process is known as the Beaver-Herter process. A bench-scale model of the process has recently been completed and has demonstrated the technical feasibility of the process. A computer model has been designed to evaluate the economic feasibility of the process on a site specific basis. This paper summarizes the process, the site selection (Oklahoma), and the economic analysis.

  10. Orientation enhancement in early visual processing can explain time course of brightness contrast and White's illusion.

    PubMed

    Karmakar, Subhajit; Sarkar, Sandip

    2013-06-01

    Dynamics of orientation tuning in V1 indicates that computational model of V1 should not only comprise of bank of static spatially oriented filters but also include the contribution for dynamical response facilitation or suppression along orientation. Time evolution of orientation response in V1 can emerge due to time- dependent excitation and lateral inhibition in the orientation domain. Lateral inhibition in the orientation domain suggests that Ernst Mach's proposition can be applied for the enhancement of initial orientation distribution that is generated due to interaction of visual stimulus with spatially oriented filters and subcortical temporal filter. Oriented spatial filtering that appears much early (<70 ms) in the sequence of visual information processing can account for many of the brightness illusions observed at steady state. It is therefore expected that time evolution of orientation response might be reflecting in the brightness percept over time. Our numerical study suggests that only spatio-temporal filtering at early phase can explain experimentally observed temporal dynamics of brightness contrast illusion. But, enhancement of orientation response at early phase of visual processing is the key mechanism that can guide visual system to predict the brightness by "Max-rule" or "Winner Takes All" (WTA) estimation and thus producing White's illusions at any exposure.

  11. Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures.

    PubMed

    Johnston, Harvey E; Carter, Matthew J; Cox, Kerry L; Dunscombe, Melanie; Manousopoulou, Antigoni; Townsend, Paul A; Garbis, Spiros D; Cragg, Mark S

    2017-03-01

    Approximately 800,000 leukemia and lymphoma cases are diagnosed worldwide each year. Burkitt's lymphoma (BL) and chronic lymphocytic leukemia (CLL) are examples of contrasting B-cell cancers; BL is a highly aggressive lymphoid tumor, frequently affecting children, whereas CLL typically presents as an indolent, slow-progressing leukemia affecting the elderly. The B-cell-specific overexpression of the myc and TCL1 oncogenes in mice induce spontaneous malignancies modeling BL and CLL, respectively. Quantitative mass spectrometry proteomics and isobaric labeling were employed to examine the biology underpinning contrasting Eμ-myc and Eμ-TCL1 B-cell tumors. Additionally, the plasma proteome was evaluated using subproteome enrichment to interrogate biomarker emergence and the systemic effects of tumor burden. Over 10,000 proteins were identified (q<0.01) of which 8270 cellular and 2095 plasma proteins were quantitatively profiled. A common B-cell tumor signature of 695 overexpressed proteins highlighted ribosome biogenesis, cell-cycle promotion and chromosome segregation. Eμ-myc tumors overexpressed several methylating enzymes and underexpressed many cytoskeletal components. Eμ-TCL1 tumors specifically overexpressed ER stress response proteins and signaling components in addition to both subunits of the interleukin-5 (IL5) receptor. IL5 treatment promoted Eμ-TCL1 tumor proliferation, suggesting an amplification of IL5-induced AKT signaling by TCL1. Tumor plasma contained a substantial tumor lysis signature, most prominent in Eμ-myc plasma, whereas Eμ-TCL1 plasma contained signatures of immune-response, inflammation and microenvironment interactions, with putative biomarkers in early-stage cancer. These findings provide a detailed characterization of contrasting B-cell tumor models, identifying common and specific tumor mechanisms. Integrated plasma proteomics allowed the dissection of a systemic response and a tumor lysis signature present in early- and late

  12. Transcriptome Analysis of Sunflower Genotypes with Contrasting Oxidative Stress Tolerance Reveals Individual- and Combined- Biotic and Abiotic Stress Tolerance Mechanisms

    PubMed Central

    Ramu, Vemanna S.; Paramanantham, Anjugam; Ramegowda, Venkategowda; Mohan-Raju, Basavaiah; Udayakumar, Makarla

    2016-01-01

    In nature plants are often simultaneously challenged by different biotic and abiotic stresses. Although the mechanisms underlying plant responses against single stress have been studied considerably, plant tolerance mechanisms under combined stress is not understood. Also, the mechanism used to combat independently and sequentially occurring many number of biotic and abiotic stresses has also not systematically studied. From this context, in this study, we attempted to explore the shared response of sunflower plants to many independent stresses by using meta-analysis of publically available transcriptome data and transcript profiling by quantitative PCR. Further, we have also analyzed the possible role of the genes so identified in contributing to combined stress tolerance. Meta-analysis of transcriptomic data from many abiotic and biotic stresses indicated the common representation of oxidative stress responsive genes. Further, menadione-mediated oxidative stress in sunflower seedlings showed similar pattern of changes in the oxidative stress related genes. Based on this a large scale screening of 55 sunflower genotypes was performed under menadione stress and those contrasting in oxidative stress tolerance were identified. Further to confirm the role of genes identified in individual and combined stress tolerance the contrasting genotypes were individually and simultaneously challenged with few abiotic and biotic stresses. The tolerant hybrid showed reduced levels of stress damage both under combined stress and few independent stresses. Transcript profiling of the genes identified from meta-analysis in the tolerant hybrid also indicated that the selected genes were up-regulated under individual and combined stresses. Our results indicate that menadione-based screening can identify genotypes not only tolerant to multiple number of individual biotic and abiotic stresses, but also the combined stresses. PMID:27314499

  13. Organic priority substances and microbial processes in river sediments subject to contrasting hydrological conditions.

    PubMed

    Zoppini, Annamaria; Ademollo, Nicoletta; Amalfitano, Stefano; Casella, Patrizia; Patrolecco, Luisa; Polesello, Stefano

    2014-06-15

    Flood and drought events of higher intensity and frequency are expected to increase in arid and semi-arid regions, in which temporary rivers represent both a water resource and an aquatic ecosystem to be preserved. In this study, we explored the variation of two classes of hazardous substances (Polycyclic Aromatic Hydrocarbons and Nonylphenols) and the functioning of the microbial community in river sediments subject to hydrological fluctuations (Candelaro river basin, Italy). Overall, the concentration of pollutants (∑PAHs range 8-275ngg(-1); ∑NPs range 299-4858ngg(-1)) suggests a moderate degree of contamination. The conditions in which the sediments were tested, flow (high/low) and no flow (wet/dry/arid), were associated to significant differences in the chemical and microbial properties. The total organic carbon contribution decreased together with the stream flow reduction, while the contribution of C-PAHs and C-NPs tended to increase. NPs were relatively more concentrated in sediments under high flow, while the more hydrophobic PAHs accumulated under low and no flow conditions. Passing from high to no flow conditions, a gradual reduction of microbial processes was observed, to reach the lowest specific bacterial carbon production rates (0.06fmolCh(-1)cell(-1)), extracellular enzyme activities, and the highest doubling time (40h) in arid sediments. In conclusion, different scenarios for the mobilization of pollutants and microbial processes can be identified under contrasting hydrological conditions: (i) the mobilization of pollutants under high flow and a relatively higher probability for biodegradation; (ii) the accumulation of pollutants during low flow and lower probability for biodegradation; (iii) the drastic reduction of pollutant concentrations under dry and arid conditions, probably independently from the microbial activity (abiotic processes). Our findings let us infer that a multiple approach has to be considered for an appropriate water

  14. Rapid loss of glacial ice reveals stream community assembly processes

    PubMed Central

    Brown, Lee E; Milner, Alexander M

    2012-01-01

    Glacial retreat creates new habitat which is colonized and developed by plants and animals during the process of primary succession. While there has been much debate about the relative role of deterministic and stochastic processes during terrestrial succession, evidence from freshwater ecosystems remains minimal and a general consensus is lacking. Using a unique 27 years record of community assembly following glacial recession in southeast Alaska, we demonstrate significant change in the trait composition of stream invertebrate communities as catchment glacial cover decreased from ∼70% to zero. Functional diversity increased significantly as glacier cover decreased and taxonomic richness increased. Null modelling approaches led to a key finding that niche filtering processes were dominant when glacial cover was extensive, reflecting water temperature and dispersal constraints. Thereafter the community shifted towards co-occurrence of stochastic and deterministic assembly processes. A further novel discovery was that intrinsic functional redundancy developed throughout the study, particularly because new colonizers possessed similar traits to taxa already present. Rapid glacial retreat is occurring in Arctic and alpine environments worldwide and the assembly processes observed in this study provide new fundamental insights into how glacially influenced stream ecosystems will respond. The findings support tolerance as a key primary successional mechanism in this system, and have broader value for developing our understanding of how biological communities in river ecosystems assemble or restructure in response to environmental change.

  15. Laminar microvascular transit time distribution in the mouse somatosensory cortex revealed by Dynamic Contrast Optical Coherence Tomography.

    PubMed

    Merkle, Conrad W; Srinivasan, Vivek J

    2016-01-15

    The transit time distribution of blood through the cerebral microvasculature both constrains oxygen delivery and governs the kinetics of neuroimaging signals such as blood-oxygen-level-dependent functional Magnetic Resonance Imaging (BOLD fMRI). However, in spite of its importance, capillary transit time distribution has been challenging to quantify comprehensively and efficiently at the microscopic level. Here, we introduce a method, called Dynamic Contrast Optical Coherence Tomography (DyC-OCT), based on dynamic cross-sectional OCT imaging of an intravascular tracer as it passes through the field-of-view. Quantitative transit time metrics are derived from temporal analysis of the dynamic scattering signal, closely related to tracer concentration. Since DyC-OCT does not require calibration of the optical focus, quantitative accuracy is achieved even deep in highly scattering brain tissue where the focal spot degrades. After direct validation of DyC-OCT against dilution curves measured using a fluorescent plasma label in surface pial vessels, we used DyC-OCT to investigate the transit time distribution in microvasculature across the entire depth of the mouse somatosensory cortex. Laminar trends were identified, with earlier transit times and less heterogeneity in the middle cortical layers. The early transit times in the middle cortical layers may explain, at least in part, the early BOLD fMRI onset times observed in these layers. The layer-dependencies in heterogeneity may help explain how a single vascular supply manages to deliver oxygen to individual cortical layers with diverse metabolic needs.

  16. Non-Newtonian behavior of magnetized ferrofluids as revealed by high speed x-ray phase contrast imaging

    NASA Astrophysics Data System (ADS)

    Prescod, Joy A.; Cali, A.; Nunez, S.; Smith, R.; Vieira, M.; Trubatch, A. D.; Yecko, P.; Lee, W.-K.

    2011-11-01

    Objects moving through a magnetized ferrofluid experience enhanced drag as a result of the presence of magnetic particles and magnetic particle agglomerations which form due to magnetic attractive forces. The precise impact of an agglomeration on an object depends on the characteristics of the agglomeration, the relative sizes of the object and agglomeration, as well as other control parameters. In this study, high speed phase contrast imaging was used to directly image the impact of long thread-like magnetic particle agglomerations on the rheological properties of ferrofluids. Particularly, numerous types of interactions between these threads and translating objects, including free-falling 500 micron sized solid glass spheres and intermittently rising vapor bubbles were quantified. At these scales, objects may bind to particle threads resulting in momentary re-direction or arrest of the object's trajectory, alluding to a form of yield stress. Therefore, there is a macro-viscosity property in flows of this type, which has a potentially significant impact of the use of ferrofluids in micro-fluidics and drug delivery. Supported by NSF grant no. MPS-1016383.

  17. Thigh muscle function in stroke patients revealed by velocity-encoded cine phase-contrast magnetic resonance imaging.

    PubMed

    Wen, Hongmei; Dou, Zulin; Finni, Taija; Havu, Marko; Kang, Zhuang; Cheng, Shumei; Sipilä, Sarianna; Sinha, Shantanu; Usenius, Jussi-Pekka; Cheng, Sulin

    2008-06-01

    Current methods of clinical assessment of muscle coordination and function after stroke do not provide information on deep muscles. The objective of this study was to examine how stroke affects both superficial and deep muscles' coordination and whether muscle function improves after rehabilitation. Muscle function, coordination, and activity of quadriceps femoris (QF) and hamstrings were evaluated in 10 stroke patients with mild hemiparesis and in 6 controls using velocity-encoded cine phase-contrast magnetic resonance imaging (VE-PC MRI), surface electromyography (sEMG), and maximal voluntary isometric contraction torque (MVC). At baseline, the peak muscle velocity of the rectus femoris (RF) and the ratio between the peak velocities of the RF and vasti were lower in the affected limb (AL) of stroke patients than in controls. Co-contraction of agonists and antagonists was higher in the AL than in controls. Muscle activity measured by sEMG showed similar behavior. After rehabilitation, the activity ratio of hamstrings and adductors to QF decreased slightly toward normal so there were no significant differences between the AL and controls. Impaired biarticular RF muscle function in stroke patients is the limiting factor during knee extension-flexion movements. After rehabilitation, improved functional performance was partly explained by the fact that the activities of the RF and vasti became more synchronized. VE-PC MRI can provide quantitative in vivo measurements of both superficial and deep muscles, and the information acquired after stroke can be utilized to render therapy more efficient and individually tailored.

  18. Distribution of unresolvable anisotropic microstructures revealed in visibility-contrast images using x-ray Talbot interferometry

    SciTech Connect

    Yashiro, Wataru; Harasse, Sebastien; Kawabata, Katsuyuki; Kuwabara, Hiroaki; Yamazaki, Takashi; Momose, Atsushi

    2011-09-01

    X-ray Talbot interferometry has been widely used as a technique for x-ray phase imaging and tomography. We propose a method using this interferometry for mapping distribution of parameters characterizing anisotropic microstructures, which are typically of the order of {mu}m in size and cannot be resolved by the imaging system, in a sample. The method uses reduction in fringe visibility, which is caused by such unresolvable microstructures, in moire images obtained using an interferometer. We applied the method to a chloroprene rubber sponge sample, which exhibited uniaxial anisotropy of reduced visibility. We measured the dependencies of reduced visibility on both the Talbot order and the orientation of the sample and obtained maps of three parameters and their anisotropies that characterize the unresolvable anisotropic microstructures in the sample. The maps indicated that the anisotropy of the sample's visibility contrast mainly originated from the anisotropy of the microstructure elements' average size. Our method directly provides structural information on unresolvable microstructures in real space, which is only accessible through the ultra-small-angle x-ray scattering measurements in reciprocal space, and is expected to be broadly applied to material, biological, and medical sciences.

  19. Salinity stress in roots of contrasting barley genotypes reveals time-distinct and genotype-specific patterns for defined proteins.

    PubMed

    Witzel, Katja; Matros, Andrea; Strickert, Marc; Kaspar, Stephanie; Peukert, Manuela; Mühling, Karl H; Börner, Andreas; Mock, Hans-Peter

    2014-02-01

    Soil salinity is one of the most severe abiotic stress factors threatening agriculture worldwide. Hence, particular interest exists in unraveling mechanisms leading to salt tolerance and improved crop plant performance on saline soils. Barley is considered to be one of the most salinity-tolerant crops, but varying levels of tolerance are well characterized. A proteomic analysis of the roots of two contrasting cultivars (cv. Steptoe and cv. Morex) is presented. Young plants were exposed to a period of 1, 4, 7, or 10 d at 0, 100, or 150 mM NaCl. The root proteome was analyzed based on two-dimensional gel electrophoresis. A number of cultivar-specific and salinity stress-responsive proteins were identified. Mass spectrometry-based identification was successful for 74 proteins, and a hierarchical clustering analysis grouped these into five clusters based on similarity of expression profile. The rank product method was applied to statistically access the early and late responses, and this delivered a number of new candidate proteins underlying salinity tolerance in barley. Among these were some germin-like proteins, some pathogenesis-related proteins, and numerous as-yet uncharacterized proteins. Notably, proteins involved in detoxification pathways and terpenoid biosynthesis were detected as early responsive to salinity and may function as a means of modulating growth-regulating mechanisms and membrane stability via fine tuning of phytohormone and secondary metabolism in the root.

  20. Processing of subharmonic signals from ultrasound contrast agents to determine ambient pressures.

    PubMed

    Dave, Jaydev K; Halldorsdottir, Valgerdur G; Eisenbrey, John R; Forsberg, Flemming

    2012-04-01

    Subharmonic-aided pressure estimation (SHAPE) is a technique that utilizes the subharmonic emissions, occurring at half the insonation frequency, from ultrasound contrast agents to estimate ambient pressures. The purpose of this work was to compare the performance of different processing techniques for the raw radiofrequency (rf) data acquired for SHAPE. A closed loop flow system was implemented circulating reconstituted Sonazoid (GE Healthcare, Oslo, Norway; 0.2 ml for 750 ml diluent) and the beam-formed unprocessed rf data were obtained from a 4 mm diameter lumen of a Doppler flow phantom (ATS Laboratories, Inc., Bridgeport, CT) using a SonixRP scanner (Ultrasonix, Richmond, BC, Canada). The transmit frequency and incident acoustic pressures were set to 2.5 MHz and 0.22 MPa, respectively, in order to elicit Sonazoid subharmonic emissions that are ambient-pressure sensitive. The time-varying ambient pressures within the flow phantom were recorded by a Millar pressure catheter. Four techniques for extracting the subharmonic amplitude from the rf data were tested along with two noise filtering techniques to process this data. Five filter orders were tested for the noise removing filters. The performance was evaluated based on the least root-mean-square errors reported after linear least-square regression analyses of the subharmonic data and the pressure catheter data and compared using a repeated ANOVA. When the subharmonic amplitudes were extracted as the mean value within a 0.2 MHz bandwidth about 1.25 MHz and when the resulting temporally-varying subharmonic signal was median filtered with an order of 500, the filtered subharmonic signal significantly predicted the ambient pressures (r2 = 0.90; p < 0.001) with the least error. The resulting root mean square and mean absolute errors were 8.16 +/- 0.26 mmHg and 6.70 +/- 0.17 mmHg, respectively. Thus, median processing the subharmonic data extracted as the mean value within a 0.2 MHz bandwidth about the theoretical

  1. European Y-chromosomal lineages in Polynesians: a contrast to the population structure revealed by mtDNA.

    PubMed Central

    Hurles, M E; Irven, C; Nicholson, J; Taylor, P G; Santos, F R; Loughlin, J; Jobling, M A; Sykes, B C

    1998-01-01

    We have used Y-chromosomal polymorphisms to trace paternal lineages in Polynesians by use of samples previously typed for mtDNA variants. A genealogical approach utilizing hierarchical analysis of eight rare-event biallelic polymorphisms, seven microsatellite loci, and internal structural analysis of the hypervariable minisatellite, MSY1, has been used to define three major paternal-lineage clusters in Polynesians. Two of these clusters, both defined by novel MSY1 modular structures and representing 55% of the Polynesians studied, are also found in coastal Papua New Guinea. Reduced Polynesian diversity, relative to that in Melanesians, is illustrated by the presence of several examples of identical MSY1 codes and microsatellite haplotypes within these lineage clusters in Polynesians. The complete lack of Y chromosomes having the M4 base substitution in Polynesians, despite their prevalence (64%) in Melanesians, may also be a result of the multiple bottleneck events during the colonization of this region of the world. The origin of the M4 mutation has been dated by use of two independent methods based on microsatellite-haplotype and minisatellite-code diversity. Because of the wide confidence limits on the mutation rates of these loci, the M4 mutation cannot be conclusively dated relative to the colonization of Polynesia, 3,000 years ago. The other major lineage cluster found in Polynesians, defined by a base substitution at the 92R7 locus, represents 27% of the Polynesians studied and, most probably, originates in Europe. This is the first Y-chromosomal evidence of major European admixture with indigenous Polynesian populations and contrasts sharply with the picture given by mtDNA evidence. PMID:9837833

  2. Orientation processing mechanisms revealed by the plaid tilt illusion

    NASA Technical Reports Server (NTRS)

    Smith, S.; Wenderoth, P.; van der Zwan, R.

    2001-01-01

    The tilt after-effect (TAE) and tilt illusion (TI) have revealed a great deal about the nature of orientation coding of 1-dimensional (1D) lines and gratings. Comparatively little research however has addressed the mechanisms responsible for encoding the orientation of 2-dimensional (2D) plaid stimuli. A multi-stage model of edge detection has recently been proposed [Georgeson, M. A. (1998) Image & Vision Computing, 16(6-7), 389-405] to account for the perceived structure of a plaid stimulus that incorporates extraction of the zero-crossings (ZCs) of the plaid. Data is presented showing that the ZCs of a plaid inducing stimulus can interact with vertical grating test stimulus to induce a standard tilt illusion. However, by considering the second-order structure of a plaid rather than ZCs, it was shown that the perceived orientation of the vertical test grating results from the combination of orientation illusions due to the first- and second-order components of an inducing plaid. The data suggest that the mechanisms encoding the orientation of second-order contours are similar to, and interact directly with, those that encode first-order contours.

  3. Neural measures reveal implicit learning during language processing

    PubMed Central

    Batterink, Laura J.; Cheng, Larry Y.; Paller, Ken A.

    2016-01-01

    Language input is highly variable; phonological, lexical and syntactic features vary systematically across different speakers, geographic regions, and social contexts. Previous evidence shows that language users are sensitive to these contextual changes and that they can rapidly adapt to local regularities. For example, listeners quickly adjust to accented speech, facilitating comprehension. It has been proposed that this type of adaptation is a form of implicit learning. The present study examined a similar type of adaptation, syntactic adaptation, in order to address two issues: (1) whether language comprehenders are sensitive to a subtle probabilistic contingency between an extraneous feature (font color) and syntactic structure, and (2) whether this sensitivity should be attributed to implicit learning. Participants read a large set of sentences, 40% of which were garden-path sentences containing temporary syntactic ambiguities. Critically, but unbeknownst to participants, font color probabilistically predicted the presence of a garden-path structure, with 75% of garden-path sentences (and 25% of normative sentences) appearing in a given font color. Event-related brain potentials (ERPs) were recorded during sentence processing. Almost all participants indicated no conscious awareness of the relationship between font color and sentence structure. Nonetheless, after sufficient time to learn this relationship, ERPs time-locked to the point of syntactic-ambiguity resolution in garden-path sentences differed significantly as a function of font color. End-of-sentence grammaticality judgments were also influenced by font color, suggesting that a match between font color and sentence structure increased processing fluency. Overall, these findings indicate that participants can implicitly detect subtle co-occurrences between physical features of sentences and abstract, syntactic properties, supporting the notion that implicit learning mechanisms are generally operative

  4. Contrasting origins of the upper mantle revealed by hafnium and lead isotopes from the Southeast Indian Ridge.

    PubMed

    Hanan, Barry B; Blichert-Toft, Janne; Pyle, Douglas G; Christie, David M

    2004-11-04

    The origin of the isotopic signature of Indian mid-ocean ridge basalts has remained enigmatic, because the geochemical composition of these basalts is consistent either with pollution from recycled, ancient altered oceanic crust and sediments, or with ancient continental crust or lithosphere. The radiogenic isotopic signature may therefore be the result of contamination of the upper mantle by plumes containing recycled altered ancient oceanic crust and sediments, detachment and dispersal of continental material into the shallow mantle during rifting and breakup of Gondwana, or contamination of the upper mantle by ancient subduction processes. The identification of a process operating on a scale large enough to affect major portions of the Indian mid-ocean ridge basalt source region has been a long-standing problem. Here we present hafnium and lead isotope data from across the Indian-Pacific mantle boundary at the Australian-Antarctic discordance region of the Southeast Indian Ridge, which demonstrate that the Pacific and Indian upper mantle basalt source domains were each affected by different mechanisms. We infer that the Indian upper-mantle isotope signature in this region is affected mainly by lower continental crust entrained during Gondwana rifting, whereas the isotope signature of the Pacific upper mantle is influenced predominantly by ocean floor subduction-related processes.

  5. Contrasting specializations for facial motion within the macaque face-processing system.

    PubMed

    Fisher, Clark; Freiwald, Winrich A

    2015-01-19

    Facial motion transmits rich and ethologically vital information, but how the brain interprets this complex signal is poorly understood. Facial form is analyzed by anatomically distinct face patches in the macaque brain, and facial motion activates these patches and surrounding areas. Yet, it is not known whether facial motion is processed by its own distinct and specialized neural machinery, and if so, what that machinery's organization might be. To address these questions, we used fMRI to monitor the brain activity of macaque monkeys while they viewed low- and high-level motion and form stimuli. We found that, beyond classical motion areas and the known face patch system, moving faces recruited a heretofore unrecognized face patch. Although all face patches displayed distinctive selectivity for face motion over object motion, only two face patches preferred naturally moving faces, while three others preferred randomized, rapidly varying sequences of facial form. This functional divide was anatomically specific, segregating dorsal from ventral face patches, thereby revealing a new organizational principle of the macaque face-processing system.

  6. Contrasting Specializations for Facial Motion Within the Macaque Face-Processing System

    PubMed Central

    Fisher, Clark; Freiwald, Winrich A.

    2014-01-01

    SUMMARY Facial motion transmits rich and ethologically vital information [1, 2], but how the brain interprets this complex signal is poorly understood. Facial form is analyzed by anatomically distinct face patches in the macaque brain [3, 4], and facial motion activates these patches and surrounding areas [5, 6]. Yet it is not known whether facial motion is processed by its own distinct and specialized neural machinery, and if so, what that machinery’s organization might be. To address these questions, we used functional magnetic resonance imaging (fMRI) to monitor the brain activity of macaque monkeys while they viewed low- and high-level motion and form stimuli. We found that, beyond classical motion areas and the known face patch system, moving faces recruited a heretofore-unrecognized face patch. Although all face patches displayed distinctive selectivity for face motion over object motion, only two face patches preferred naturally moving faces, while three others preferred randomized, rapidly varying sequences of facial form. This functional divide was anatomically specific, segregating dorsal from ventral face patches, thereby revealing a new organizational principle of the macaque face-processing system. PMID:25578903

  7. Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp.

    PubMed

    Zhu, Jinyong; Dai, Wenfang; Qiu, Qiongfen; Dong, Chunming; Zhang, Jinjie; Xiong, Jinbo

    2016-11-01

    Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphaproteobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.

  8. Analytical Interference in Serum Iron Determination Reveals Iron Versus Gadolinium Transmetallation With Linear Gadolinium-Based Contrast Agents

    PubMed Central

    Fretellier, Nathalie; Poteau, Nathalie; Factor, Cécile; Mayer, Jean-François; Medina, Christelle; Port, Marc; Idée, Jean-Marc; Corot, Claire

    2014-01-01

    Objectives The purposes of this study were to evaluate the risk for analytical interference with gadolinium-based contrast agents (GBCAs) for the colorimetric measurement of serum iron (Fe3+) and to investigate the mechanisms involved. Materials and Methods Rat serum was spiked with several concentrations of all molecular categories of GBCAs, ligands, or “free” soluble gadolinium (Gd3+). Serum iron concentration was determined by 2 different colorimetric methods at pH 4.0 (with a Vitros DT60 analyzer or a Cobas Integra 400 analyzer). Secondly, the cause of interference was investigated by (a) adding free soluble Gd3+ or Mn2+ to serum in the presence of gadobenic acid or gadodiamide and (b) electrospray ionization mass spectrometry. Results Spurious decrease in serum Fe3+ concentration was observed with all linear GBCAs (only with the Vitros DT60 technique occurring at pH 4.0) but not with macrocyclic GBCAs or with free soluble Gd3+. Spurious hyposideremia was also observed with the free ligands present in the pharmaceutical solutions of the linear GBCAs gadopentetic acid and gadodiamide (ie, diethylene triamine pentaacetic acid and calcium-diethylene triamine pentaacetic acid bismethylamide, respectively), suggesting the formation of Fe-ligand chelate. Gadobenic acid-induced interference was blocked in a concentration-dependent fashion by adding a free soluble Gd3+ salt. Conversely, Mn2+, which has a lower affinity than Gd3+ and Fe3+ for the ligand of gadobenic acid (ie, benzyloxypropionic diethylenetriamine tetraacetic acid), was less effective (interference was only partially blocked), suggesting an Fe3+ versus Gd3+ transmetallation phenomenon at pH 4.0. Similar results were observed with gadodiamide. Mass spectrometry detected the formation of Fe-ligand with all linear GBCAs tested in the presence of Fe3+ and the disappearance of Fe-ligand after the addition of free soluble Gd3+. No Fe-ligand chelate was found in the case of the macrocyclic GBCA gadoteric

  9. Ancient DNA Analyses Reveal Contrasting Phylogeographic Patterns amongst Kiwi (Apteryx spp.) and a Recently Extinct Lineage of Spotted Kiwi

    PubMed Central

    Shepherd, Lara D.; Worthy, Trevor H.; Tennyson, Alan J. D.; Scofield, R. Paul; Ramstad, Kristina M.; Lambert, David M.

    2012-01-01

    The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought. PMID:22876319

  10. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp.) and a recently extinct lineage of spotted kiwi.

    PubMed

    Shepherd, Lara D; Worthy, Trevor H; Tennyson, Alan J D; Scofield, R Paul; Ramstad, Kristina M; Lambert, David M

    2012-01-01

    The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought.

  11. Competing Sound Sources Reveal Spatial Effects in Cortical Processing

    PubMed Central

    Maddox, Ross K.; Billimoria, Cyrus P.; Perrone, Ben P.; Shinn-Cunningham, Barbara G.; Sen, Kamal

    2012-01-01

    Why is spatial tuning in auditory cortex weak, even though location is important to object recognition in natural settings? This question continues to vex neuroscientists focused on linking physiological results to auditory perception. Here we show that the spatial locations of simultaneous, competing sound sources dramatically influence how well neural spike trains recorded from the zebra finch field L (an analog of mammalian primary auditory cortex) encode source identity. We find that the location of a birdsong played in quiet has little effect on the fidelity of the neural encoding of the song. However, when the song is presented along with a masker, spatial effects are pronounced. For each spatial configuration, a subset of neurons encodes song identity more robustly than others. As a result, competing sources from different locations dominate responses of different neural subpopulations, helping to separate neural responses into independent representations. These results help elucidate how cortical processing exploits spatial information to provide a substrate for selective spatial auditory attention. PMID:22563301

  12. Emotion and relative reward processing: an investigation on instrumental successive negative contrast and ultrasonic vocalizations in the rat.

    PubMed

    Binkley, K A; Webber, E S; Powers, D D; Cromwell, H C

    2014-09-01

    Incentive contrast effects include changes in behavioral responses after a reward upshift (positive contrast) or downshift (negative contrast). Proposed influences on these behavioral changes are emotional state reactions after experiencing or anticipating a change in reward outcome. Rat ultrasonic vocalizations have been shown to be indicators of emotional state during behavior and anticipatory periods. The objective of the present study was to monitor rodent ultrasounds during incentive contrast using a classical runway procedure called instrumental successive negative contrast. The procedure is one that has been used often to examine incentive relativity because of its reliability in measuring negative contrast effects. Rats were trained to run in the alleyway to receive a high (12 pellets) or low magnitude (1 pellet) outcome. The high magnitude was then shifted to the low and running speeds in the alleyway for the reward and USV emission were compared. Replicating previous work, a negative contrast effect was observed with postshift running speeds significantly slower in the shifted group compared to the unshifted group. USVs did not follow the same pattern with an apparent lack of significant differences between the groups following the reward downshift. We also tested another group of animals using a visual predictive cue in the same runway test. When visual cues predicted high or low magnitude outcome, no incentive contrast was found for the running speeds following an outcome downshift, but a weak contrast effect was observed for the USV emission. These results demonstrate a separation between USVs and behavioral indicators of incentive contrast suggesting that concomitant shifts in negative affect may not be necessary for anticipatory relative reward processes.

  13. Nucleosome competition reveals processive acetylation by the SAGA HAT module

    PubMed Central

    Ringel, Alison E.; Cieniewicz, Anne M.; Taverna, Sean D.; Wolberger, Cynthia

    2015-01-01

    The Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex hyperacetylates histone tails in vivo in a manner that depends upon histone 3 lysine 4 trimethylation (H3K4me3), a histone mark enriched at promoters of actively transcribed genes. SAGA contains a separable subcomplex known as the histone acetyltransferase (HAT) module that contains the HAT, Gcn5, bound to Sgf29, Ada2, and Ada3. Sgf29 contains a tandem Tudor domain that recognizes H3K4me3-containing peptides and is required for histone hyperacetylation in vivo. However, the mechanism by which H3K4me3 recognition leads to lysine hyperacetylation is unknown, as in vitro studies show no effect of the H3K4me3 modification on histone peptide acetylation by Gcn5. To determine how H3K4me3 binding by Sgf29 leads to histone hyperacetylation by Gcn5, we used differential fluorescent labeling of histones to monitor acetylation of individual subpopulations of methylated and unmodified nucleosomes in a mixture. We find that the SAGA HAT module preferentially acetylates H3K4me3 nucleosomes in a mixture containing excess unmodified nucleosomes and that this effect requires the Tudor domain of Sgf29. The H3K4me3 mark promotes processive, multisite acetylation of histone H3 by Gcn5 that can account for the different acetylation patterns established by SAGA at promoters versus coding regions. Our results establish a model for Sgf29 function at gene promoters and define a mechanism governing crosstalk between histone modifications. PMID:26401015

  14. Revealing plot scale heterogeneity in soil moisture dynamics under contrasting vegetation assemblages using 3D electrical resistivity tomography (ERT) surveys

    NASA Astrophysics Data System (ADS)

    Dick, Jonathan; Tetzlaff, Doerthe; Bradford, John; Soulsby, Chris

    2016-04-01

    Soil moisture is a fundamental component of the water cycle that influences many hydrological processes, such as flooding, solute transport, biogeochemical processes, and land-atmosphere interactions. The relationship between vegetation and soil moisture is complex and reciprocal. Soil moisture may affect vegetation distribution due to its function as the primary source of water, in turn the structure of vegetation canopies regulate water partitioning into interception, throughfall and steam flow. Such spatial differences in inputs, together with complex patterns of water uptake from distributed root networks can create marked heterogeneity in soil moisture dynamics at small scales. Traditional methods of monitoring soil moisture have revolved around limited point measurements, but improved geophysical techniques have facilitated a trend towards more spatially distributed measurements to help understand this heterogeneity. Here, we present a study using 3D ERT surveys in a 3.2km upland catchment in the Scottish Highlands where increasing afforestation (for climate change adaptation, biofuels and conservation) has the potential to increase interception losses and reduce soil moisture storage. The study combined 3D surveys, traditional point measurements and laboratory analysis of soil cores to assess the plot scale soil moisture dynamics in podzolic soils under forest stands of 15m high Scots pine (Pinus sylvestris) and adjacent non-forest plots dominated by heather (Calluna vulgaris) shrubs (<0.5m high). These dominant species are typical of forest and non-forest vegetation communities the Scottish Highlands. Results showed differences in the soil moisture dynamics under the different vegetation types, with heterogeneous patterns in the forested site mainly correlated with canopy cover and mirroring interception losses. Temporal variability in the forested site was greater, probably due to the interception, and increased evapotranspiration losses relative to the

  15. Regions of low density in the contrast-enhanced pituitary gland: normal and pathologic processes

    SciTech Connect

    Chambers, E.F.; Turski, P.A.; LaMasters, D.; Newton, T.H.

    1982-07-01

    The incidence of low-density regions in the contrast-enhanced pituitary gland and the possible causes of these regions were investigated by a retrospective review of computed tomographic (CT) scans of the head in 50 patients and autopsy specimens of the pituitary in 100 other patients. It was found that focal areas of low density within the contrast enhanced pituitary gland can be caused by various normal and pathologic conditions such as pituitary microadenomas, pars intermedia cysts, foci of metastasis, infarcts, epidermoid cysts, and abscesses. Although most focal low-density regions probably represent pituitary microadenomas, careful clinical correlation is needed to establish a diagnosis.

  16. Multivoxel patterns reveal functionally differentiated networks underlying auditory feedback processing of speech.

    PubMed

    Zheng, Zane Z; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N; Munhall, Kevin G; Cusack, Rhodri; Johnsrude, Ingrid S

    2013-03-06

    The everyday act of speaking involves the complex processes of speech motor control. An important component of control is monitoring, detection, and processing of errors when auditory feedback does not correspond to the intended motor gesture. Here we show, using fMRI and converging operations within a multivoxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was used to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during vocalization, compared with during passive listening. One network of regions appears to encode an "error signal" regardless of acoustic features of the error: this network, including right angular gyrus, right supplementary motor area, and bilateral cerebellum, yielded consistent neural patterns across acoustically different, distorted feedback types, only during articulation (not during passive listening). In contrast, a frontotemporal network appears sensitive to the speech features of auditory stimuli during passive listening; this preference for speech features was diminished when the same stimuli were presented as auditory concomitants of vocalization. A third network, showing a distinct functional pattern from the other two, appears to capture aspects of both neural response profiles. Together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple, interactive, functionally differentiated neural systems.

  17. Vortex Image Processing (VIP) package for high-contrast direct imaging

    NASA Astrophysics Data System (ADS)

    Gomez Gonzalez, C.; Absil, O.; Wertz, O.

    2016-05-01

    VIP is a Python instrument-agnostic toolbox featuring a flexible framework for reproducible and robust data reduction. VIP currently supports three high-contrast imaging observational techniques: angular, reference-star and multi-spectral differential imaging. The code can be downloaded from our git repository on Github: http://github.com/vortex-exoplanet/VIP

  18. Perception of Non-Native Consonant Length Contrast: The Role of Attention in Phonetic Processing

    ERIC Educational Resources Information Center

    Porretta, Vincent J.; Tucker, Benjamin V.

    2015-01-01

    The present investigation examines English speakers' ability to identify and discriminate non-native consonant length contrast. Three groups (L1 English No-Instruction, L1 English Instruction, and L1 Finnish control) performed a speeded forced-choice identification task and a speeded AX discrimination task on Finnish non-words (e.g.…

  19. Stimulus intensity affects early sensory processing: visual contrast modulates evoked gamma-band activity in human EEG.

    PubMed

    Schadow, Jeanette; Lenz, Daniel; Thaerig, Stefanie; Busch, Niko A; Fründ, Ingo; Rieger, Jochem W; Herrmann, Christoph S

    2007-10-01

    We studied the effect of different contrast levels on the visual evoked gamma-band response (GBR) in order to investigate whether the GBR is modulated in a similar manner as previously reported for visual evoked potentials. Previous studies showed that the GBR can be modulated by individual characteristics (age) and experimental conditions (task difficulty, attention). However, stimulus properties, such as size and spatial frequency, also have a large impact on the GBR, which necessitates identification and control of relevant stimulus properties for optimal experimental setups. Twenty-one healthy participants were investigated during a forced-choice discrimination task. Sinusoidal gratings were presented at three contrast levels with a constant spatial frequency of 5 cycles per degree visual arc (cpd). The present data replicate the results reported for visual evoked potentials and exhibit a contrast dependent modulation of the GBR. Gamma activity is increased for higher contrast levels. These results demonstrate the importance of stimulus contrast for evoked gamma activity. Thus, it appears meaningful to control the contrast of stimuli in experiments investigating the role of gamma activity in perception and information processing.

  20. Conversational Interaction in the Scanner: Mentalizing during Language Processing as Revealed by MEG

    PubMed Central

    Bögels, Sara; Barr, Dale J.; Garrod, Simon; Kessler, Klaus

    2015-01-01

    Humans are especially good at taking another's perspective—representing what others might be thinking or experiencing. This “mentalizing” capacity is apparent in everyday human interactions and conversations. We investigated its neural basis using magnetoencephalography. We focused on whether mentalizing was engaged spontaneously and routinely to understand an utterance's meaning or largely on-demand, to restore “common ground” when expectations were violated. Participants conversed with 1 of 2 confederate speakers and established tacit agreements about objects' names. In a subsequent “test” phase, some of these agreements were violated by either the same or a different speaker. Our analysis of the neural processing of test phase utterances revealed recruitment of neural circuits associated with language (temporal cortex), episodic memory (e.g., medial temporal lobe), and mentalizing (temporo-parietal junction and ventromedial prefrontal cortex). Theta oscillations (3–7 Hz) were modulated most prominently, and we observed phase coupling between functionally distinct neural circuits. The episodic memory and language circuits were recruited in anticipation of upcoming referring expressions, suggesting that context-sensitive predictions were spontaneously generated. In contrast, the mentalizing areas were recruited on-demand, as a means for detecting and resolving perceived pragmatic anomalies, with little evidence they were activated to make partner-specific predictions about upcoming linguistic utterances. PMID:24904076

  1. Conversational Interaction in the Scanner: Mentalizing during Language Processing as Revealed by MEG.

    PubMed

    Bögels, Sara; Barr, Dale J; Garrod, Simon; Kessler, Klaus

    2015-09-01

    Humans are especially good at taking another's perspective-representing what others might be thinking or experiencing. This "mentalizing" capacity is apparent in everyday human interactions and conversations. We investigated its neural basis using magnetoencephalography. We focused on whether mentalizing was engaged spontaneously and routinely to understand an utterance's meaning or largely on-demand, to restore "common ground" when expectations were violated. Participants conversed with 1 of 2 confederate speakers and established tacit agreements about objects' names. In a subsequent "test" phase, some of these agreements were violated by either the same or a different speaker. Our analysis of the neural processing of test phase utterances revealed recruitment of neural circuits associated with language (temporal cortex), episodic memory (e.g., medial temporal lobe), and mentalizing (temporo-parietal junction and ventromedial prefrontal cortex). Theta oscillations (3-7 Hz) were modulated most prominently, and we observed phase coupling between functionally distinct neural circuits. The episodic memory and language circuits were recruited in anticipation of upcoming referring expressions, suggesting that context-sensitive predictions were spontaneously generated. In contrast, the mentalizing areas were recruited on-demand, as a means for detecting and resolving perceived pragmatic anomalies, with little evidence they were activated to make partner-specific predictions about upcoming linguistic utterances.

  2. Water-Soluble Spinel Ferrites by a Modified Polyol Process as Contrast Agents in MRI

    SciTech Connect

    Basina, Georgia; Tzitzios, Vasilis; Niarchos, Dimitris; Li Wanfeng; Khurshid, Hafsa; Hadjipanayis, George; Mao Hui; Hadjipanayis, Costas

    2010-12-02

    Magnetic nanoparticles have recently been very attractive for biomedical applications. In this study, we have synthesized ferrite nanoparticles for application as contrast agents in MRI experiments. Fe{sub 3}O{sub 4} and MnFe{sub 2}O{sub 4} spinel ferrites with a mean size of 11-12 nm, were prepared by a modified polyol route in commercially available polyethylene glycol with molecular weight 600 (PEG-600). The reaction takes place in the presence of water soluble and non-toxic tri-block copolymer known as Pluronic registered F-127 (PEO{sub 100}-PPO{sub 65}-PEO{sub 100}). The nanoparticles have saturation magnetization values of 52 and 68 emu/g for MnFe{sub 2}O{sub 4} and Fe{sub 3}O{sub 4}, respectively. Both the Fe{sub 3}O{sub 4}, and MnFe{sub 2}O{sub 4} nanoparticles make stable solutions in water known as ferrofluids. Preliminary data demonstrated the capability of these nanoparticles to induce imaging contrast in T{sub 2} weighted MRI experiments, making these materials suitable for biomedical applications such as medical MRI.

  3. Temperature-dependent differences in the nonlinear acoustic behavior of ultrasound contrast agents revealed by high-speed imaging and bulk acoustics.

    PubMed

    Mulvana, Helen; Stride, Eleanor; Tang, Mengxing; Hajnal, Jo V; Eckersley, Robert

    2011-09-01

    Previous work by the authors has established that increasing the temperature of the suspending liquid from 20°C to body temperature has a significant impact on the bulk acoustic properties and stability of an ultrasound contrast agent suspension (SonoVue, Bracco Suisse SA, Manno, Lugano, Switzerland). In this paper the influence of temperature on the nonlinear behavior of microbubbles is investigated, because this is one of the most important parameters in the context of diagnostic imaging. High-speed imaging showed that raising the temperature significantly influences the dynamic behavior of individual microbubbles. At body temperature, microbubbles exhibit greater radial excursion and oscillate less spherically, with a greater incidence of jetting and gas expulsion, and therefore collapse, than they do at room temperature. Bulk acoustics revealed an associated increase in the harmonic content of the scattered signals. These findings emphasize the importance of conducting laboratory studies at body temperature if the results are to be interpreted for in vivo applications.

  4. The Influence of Contextual Contrast on Syntactic Processing: Evidence for Strong-Interaction in Sentence Comprehension

    ERIC Educational Resources Information Center

    Grodner, D.; Gibson, E.; Watson, D.

    2005-01-01

    The present study compares the processing of unambiguous restrictive and non-restrictive relative clauses (RCs) within both a null context and a supportive discourse using a self-paced reading methodology. Individuals read restrictive RCs more slowly than non-restrictive RCs in a null context, but processed restrictive RCs faster than…

  5. Stable isotope signatures in bulk samples from two soils with contrasting characteristics. What do they tell about ongoing pedogenic processes?

    NASA Astrophysics Data System (ADS)

    Jiménez-Morillo, Nicasio T.; dos Anjos Leal, Otávio; Knicker, Heike; Pinheiro Dick, Deborah; González-Vila, Francisco J.; González-Pérez, José A.

    2014-05-01

    Isotopic ratio mass spectrometry (IRMS) has been proven as a promising tool for the monitoring of biogeochemical processes in soil. In this work, stable isotope signatures of light elements δ15N, δ13C, δ18O and δD were determined for two soils with contrasting characteristics in terms of climate, vegetation, land use and management. The studied soils were a Cambisol from a subtropical area (Paraná region, South Brazil) and an Arenosol from a Mediterranean climate (Andalusia, South Spain). A Flash 2000 HT (N, C, S, H and O) elemental analyzer (Thermo Scientific) coupled to a Delta V Advantage IRMS (Thermo Scientific) was used. Isotopic ratios are reported as parts per thousand (o ) deviations from appropriate standards recognized by the international atomic energy agency (IAEA). In a first approach we took advantage of the well-known different δ13C signature between plants using either the C4 or C3 carbon fixation pathway (O'Leary, 1981). The Arenosol (Spain) revealed a δ13C signature which is clearly in the range of C3 plants (-26 to -30 o ). Different plant canopies (tree, shrubs or ferns) caused only slight variations δ13C (STD= 0.98). In contrast, the Cambisol (Brazil) showed less depletion of the heavier carbon isotope corresponding to C4 predominant vegetation. In addition an increase from -19 o in the soil surface (0 - 5 cm) to -16 o in the subsoil (20 - 30 cm) was observed in line with a recent (2 years old) shift of the land use from the predominant C4 grassland to eucalypt (C3) cultivation. Crossplots of δ15N vs. δ18O may provide information about nitrate (NO3-) sources and N cycling (Kendall, 1998). In the Mediterranean Arenosol this signal (δ18O = 30o δ15N = 2o ) was found compatible with a predominant nitrate atmospheric deposition, whereas the signal in the Brazilian Cambisol pointed to the use of a mineral N fertilization with signs of denitrification processes (δ18O = 13o δ15N = 9o ). No conclusive results could be obtained from the

  6. The Question Shapes the Answer: The Neural Correlates of Task Differences Reveal Dynamic Semantic Processing

    ERIC Educational Resources Information Center

    Hargreaves, Ian S.; White, Michelle; Pexman, Penny M.; Pittman, Dan; Goodyear, Brad G.

    2012-01-01

    Task effects in semantic processing were investigated by contrasting the neural activation associated with two semantic categorization tasks (SCT) using event-related fMRI. The two SCTs involved different decision categories: "is it an animal?" vs. "is it a concrete thing?" Participants completed both tasks and, across participants, the same core…

  7. Contrasting amount of fluids along the megathrust ruptured by the 2010 Maule earthquake as revealed by a combined analysis of aftershocks and afterslip

    NASA Astrophysics Data System (ADS)

    Tassara, Andres; Soto, Hugo; Bedford, Jonathan; Moreno, Marcos; Baez, Juan Carlos

    2016-03-01

    We present a novel approach combining time-variable computations of b-value and afterslip to study the postseismic activity following the Mw 8.8 Maule 2010 earthquake. We subdivided the first 392 days after the mainshock into overlapping windows, for which we compared maps of b-value (computed from NEIC seismicity) and afterslip (computed from continuous GPS stations). The correlation between both parameters is weak during the first 2 months when the aftershocks' magnitude of completeness decreases and the number of GPS stations increased. After this early stage, a correlation between both parameters emerges. We interpret this correlated spatiotemporal pattern combining factors proposed to control each parameter separately. This exercise suggests a segmentation of the Maule megathrust. The northern segment is characterized by an increase of afterslip and b-value during the early postseismic phase and then a simultaneous decrease of both parameters, which we interpret as the effect of an ingression of fluids into the megathrust and its subsequent consumption during fault healing. In contrast, the southern segment is characterized by a central region with minimum afterslip and low b-value surrounded by areas that experience mostly seismic afterslip as a consequence of large static stress loaded by the mainshock, suggesting a drier and stronger megathrust where healing was active earlier. Interpreted along with features of the pre- and coseismic phases, our results allow us to propose the existence of two contrasting types of seismic asperities: classical strong stick-slip patches that we link with dry regions of the megathrust, versus weak, wet and conditionally stable frictional patches that could have a range of seismogenic behaviors from creeping and/or locking during the interseismic period, largely contributing with coseismic slip, and concentrating afterslip at their borders. The application of our novel method to other great earthquakes could reveal whether

  8. Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts

    PubMed Central

    Barrios, Shannon L.; Namyst, Anna M.; Lau, Ellen F.; Feldman, Naomi H.; Idsardi, William J.

    2016-01-01

    To attain native-like competence, second language (L2) learners must establish mappings between familiar speech sounds and new phoneme categories. For example, Spanish learners of English must learn that [d] and [ð], which are allophones of the same phoneme in Spanish, can distinguish meaning in English (i.e., /deɪ/ “day” and /ðeɪ/ “they”). Because adult listeners are less sensitive to allophonic than phonemic contrasts in their native language (L1), novel target language contrasts between L1 allophones may pose special difficulty for L2 learners. We investigate whether advanced Spanish late-learners of English overcome native language mappings to establish new phonological relations between familiar phones. We report behavioral and magnetoencepholographic (MEG) evidence from two experiments that measured the sensitivity and pre-attentive processing of three listener groups (L1 English, L1 Spanish, and advanced Spanish late-learners of English) to differences between three nonword stimulus pairs ([idi]-[iði], [idi]-[iɾi], and [iði]-[iɾi]) which differ in phones that play a different functional role in Spanish and English. Spanish and English listeners demonstrated greater sensitivity (larger d' scores) for nonword pairs distinguished by phonemic than by allophonic contrasts, mirroring previous findings. Spanish late-learners demonstrated sensitivity (large d' scores and MMN responses) to all three contrasts, suggesting that these L2 learners may have established a novel [d]-[ð] contrast despite the phonological relatedness of these sounds in the L1. Our results suggest that phonological relatedness influences perceived similarity, as evidenced by the results of the native speaker groups, but may not cause persistent difficulty for advanced L2 learners. Instead, L2 learners are able to use cues that are present in their input to establish new mappings between familiar phones. PMID:27445949

  9. Dominant hydrological processes at three contrasting small permafrost watersheds in changing climate

    NASA Astrophysics Data System (ADS)

    Lebedeva, Liudmila; Semenova, Olga

    2016-04-01

    The most pronounced climatic changes are observed and projected in the Arctic. Large part of the Arctic is influenced by permanently or seasonally frozen ground that controls river runoff generation. The research aims at assessment of observed and projected changes of hydrological regime and identification of dominant hydrological processes at three small watersheds in different landscape and permafrost conditions of Siberia for the last sixty years by data analysis and process-based modelling. Three studied watersheds are located within the Yenisei, Lena and Kolyma river basins. The Graviyka river basin (323 km2) is situated in discontinuous permafrost in transition zone between tundra and taiga ecotones in the lower Yenisei region. Mean annual precipitation is 510 mm/year and air temperature is -8°C (1936-2014). Both air temperature and precipitation have shown significant increase for the last forty years. The Shestakovka river basin (170 km2), a tributary of the Lena river near Yakutsk, is characterized by extremely dry (240 mm/year) and cold (-9.5°C) climate of Central Yakutiya. Larch and pine forests grow on sandy deposits covered by continuous permafrost. Air temperature and river flow have increased for the last thirty years but precipitation have shown no significant changes. The Kontaktovy creek watershed (22 km2) is located in mountains of upper Kolyma river basin. The permafrost is continuous. Main land cover types are bare rocks, mountain tundra and sparse larch forest. Only insignificant changes of air temperature, precipitation and river flow were detected for the last decades. To assess dominant hydrological processes and to project their future changes in each studied watershed the process-based Hydrograph model was applied to historical and future time periods using temperate and extreme climate scenarios. The Hydrograph model does not rely on calibration and the parameters were estimated using all available a-priori information - thematic maps

  10. Contrasted invasion processes imprint the genetic structure of an invasive scale insect across southern Europe

    PubMed Central

    Kerdelhué, C; Boivin, T; Burban, C

    2014-01-01

    Deciphering the colonization processes by which introduced pests invade new areas is essential to limit the risk of further expansion and/or multiple introductions. We here studied the invasion history of the maritime pine bast scale Matsucoccus feytaudi. This host-specific insect does not cause any damage in its native area, but it devastated maritime pine forests of South-Eastern France where it was detected in the 1960s, and since then reached Italy and Corsica. We used population genetic approaches to infer the populations' recent evolutionary history from microsatellite markers and Approximate Bayesian Computation. Consistent with previous mitochondrial data, we showed that the native range is geographically strongly structured, which is probably due to the patchy distribution of the obligate host and the limited dispersal capacity of the scale. Our results show that the invasion history can be described in three successive steps involving different colonization and dispersal processes. During the mid-XXth century, massive introductions occurred from the Landes planted forest to South-Eastern France, probably due to transportation of infested wood material after World War II. Stepping-stone expansion, consistent with natural dispersal, then allowed M. feytaudi to reach the maritime pine forests of Liguria and Tuscany in Italy. The island of Corsica was accidentally colonized in the 1990s, and the most plausible scenario involves the introduction of a limited number of migrants from the forests of South-Eastern France and Liguria, which is consistent with an aerial dispersal due to the dominant winds that blow in spring in this region. PMID:24849170

  11. River temperature processes under contrasting riparian land cover: linking microclimate, heat exchange and water thermal dynamics

    NASA Astrophysics Data System (ADS)

    Hannah, D. M.; Kantola, K.; Malcolm, I.

    2012-12-01

    River temperature influences strongly growth and survival in salmonid fish, which are often the target of river management strategies. Temperature is controlled by transfers of heat and water to/ from the river system, with land and water management modifying exchanges and consequently thermal regime. In the UK, fisheries managers are promoting riparian forest planting as a climate change adaption measure to reduce water temperature extremes. However, scientific understanding lags behind management and policy needs. Specifically, there is an urgent requirement to determine planting strategies that maximise expected benefits of riparian forest in terms of reduction in maximum water temperature. Scientific knowledge is necessary to underpin conceptual and deterministic models to inform management. To address this research gap, this paper analyses high resolution (15 minute) hydrometeorological data collected over a calendar year in the western Scottish Highlands (Loch Ard) to understand the controls and processes determining river temperature dynamics under open moorland (control), semi-natural woodland and commercial forest. The research programme aims: (1) to characterise spatial and temporal variability in riparian microclimate and stream water temperature regime across forest treatments; (2) to identify the hydrological, climatological and site-specific factors affecting stream temperature; (3) to estimate the energy balance at sites representative of each forest treatment and, thus, yield physical process understanding about dominant heat exchanges driving thermal variability; and (4) to use 1-3 to predict stream temperature sensitivity under different forestry and hydroclimatological scenarios. Results indicated that inter-treatment differences in mean and maximum daily water column temperature were ordered open > semi-natural > commercial during summer, but semi-natural > commercial > open during winter. Minimum water temperature was ordered commercial > semi

  12. Identification and characterization of contrasting sunflower genotypes to early leaf senescence process combining molecular and physiological studies (Helianthus annuus L.).

    PubMed

    López Gialdi, A I; Moschen, S; Villán, C S; López Fernández, M P; Maldonado, S; Paniego, N; Heinz, R A; Fernandez, P

    2016-09-01

    Leaf senescence is a complex mechanism ruled by multiple genetic and environmental variables that affect crop yields. It is the last stage in leaf development, is characterized by an active decline in photosynthetic rate, nutrients recycling and cell death. The aim of this work was to identify contrasting sunflower inbred lines differing in leaf senescence and to deepen the study of this process in sunflower. Ten sunflower genotypes, previously selected by physiological analysis from 150 inbred genotypes, were evaluated under field conditions through physiological, cytological and molecular analysis. The physiological measurement allowed the identification of two contrasting senescence inbred lines, R453 and B481-6, with an increase in yield in the senescence delayed genotype. These findings were confirmed by cytological and molecular analysis using TUNEL, genomic DNA gel electrophoresis, flow sorting and gene expression analysis by qPCR. These results allowed the selection of the two most promising contrasting genotypes, which enables future studies and the identification of new biomarkers associated to early senescence in sunflower. In addition, they allowed the tuning of cytological techniques for a non-model species and its integration with molecular variables.

  13. High-resolution functional imaging with ultrasound contrast agents based on RF processing in an in vivo kidney experiment.

    PubMed

    Verbeek, X A; Willigers, J M; Prinzen, F W; Peschar, M; Ledoux, L A; Hoeks, A P

    2001-02-01

    Knowledge of the relative tissue perfusion distribution is valuable in the diagnosis of numerous diseases. Techniques for the assessment of the relative perfusion distribution, based on ultrasound (US) contrast agents, have several advantages compared to established nuclear techniques. These are, among others, a better spatial and temporal resolution, the lack of exposure of the patient to ionizing radiation and the relatively low cost. In the present study, US radiofrequency (RF) image sequences are acquired, containing the signal intensity changes associated with the transit of a bolus contrast agent through the microvasculature of a dog kidney. The primary objective is to explore the feasibility of calculating functional images with high spatial resolution. The functional images characterize the transit of the contrast agent bolus and represent distributions of peak time, peak value, transit time, peak area, wash-in rate and wash-out decay constant. For the evaluation of the method, dog experiments were performed under optimized conditions where motion artefacts were minimized and an IA injection of the contrast agent Levovist was employed. It was demonstrated that processing of RF signals obtained with a 3.5-MHz echo system can provide functional images with a high spatial resolution of 2 mm in axial resolution, 2 to 5 mm in lateral resolution and a slice thickness of 2 mm. The functional images expose several known aspects of kidney perfusion, like perfusion heterogeneity of the kidney cortex and a different peripheral cortical perfusion compared to the inner cortex. Based on the findings of the present study, and given the results of complimentary studies, it is likely that the functional images reflect the relative perfusion distribution of the kidney.

  14. Contrasting suspended covers reveal the impact of an artificial monolayer on heat transfer processes at the interfacial boundary layer.

    PubMed

    Pittaway, P; Martínez-Alvarez, V; Hancock, N

    2015-01-01

    The highly variable performance of artificial monolayers in reducing evaporation from water storages has been attributed to wind speed and wave turbulence. Other factors operating at the interfacial boundary layer have seldom been considered. In this paper, two physical shade covers differing in porosity and reflectivity were suspended over 10 m diameter water tanks to attenuate wind and wave turbulence. The monolayer octadecanol was applied to one of the covered tanks, and micrometeorological conditions above and below the covers were monitored to characterise diurnal variation in the energy balance. A high downward (air-to-water) convective heat flux developed under the black cover during the day, whereas diurnal variation in the heat flux under the more reflective, wind-permeable white cover was much less. Hourly air and water temperature profiles under the covers over 3 days when forced convection was minimal (low wind speed) were selected for analysis. Monolayer application reduced temperature gain in surface water under a downward convective heat flux, and conversely reduced temperature loss under an upward convective heat flux. This 'dual property' may explain why repeat application of an artificial monolayer to retard evaporative loss (reducing latent heat loss) does not inevitably increase water temperature.

  15. Transcranial magnetic stimulation reveals two cortical pathways for visual body processing.

    PubMed

    Urgesi, Cosimo; Calvo-Merino, Beatriz; Haggard, Patrick; Aglioti, Salvatore M

    2007-07-25

    Visual recognition of human bodies is more difficult for upside down than upright presentations. This body inversion effect implies that body perception relies on configural rather than local processing. Although neuroimaging studies indicate that the visual processing of human bodies engages a large fronto-temporo-parietal network, information about the neural underpinnings of configural body processing is meager. Here, we used repetitive transcranial magnetic stimulation (rTMS) to study the causal role of premotor, visual, and parietal areas in configural processing of human bodies. Eighteen participants performed a delayed matching-to-sample task with upright or inverted static body postures. Event-related, dual-pulse rTMS was applied 150 ms after the sample stimulus onset, over left ventral premotor cortex (vPMc), right extrastriate body area (EBA), and right superior parietal lobe (SPL) and, as a control site, over the right primary visual cortex (V1). Interfering stimulation of vPMc significantly reduced accuracy of matching judgments for upright bodies. In contrast, EBA rTMS significantly reduced accuracy for inverted but not for upright bodies. Furthermore, a significant body inversion effect was observed after interfering stimulation of EBA and V1 but not of vPMc and SPL. These results demonstrate an active contribution of the fronto-parietal mirror network to configural processing of bodies and suggest a novel, embodied aspect of visual perception. In contrast, the local processing of the body, possibly based on the form of individual body parts instead of on the whole body unit, appears to depend on EBA. Therefore, we propose two distinct cortical routes for the visual processing of human bodies.

  16. Cross-Linguistic Influence in the Bilingual Mental Lexicon: Evidence of Cognate Effects in the Phonetic Production and Processing of a Vowel Contrast

    PubMed Central

    Amengual, Mark

    2016-01-01

    The present study examines cognate effects in the phonetic production and processing of the Catalan back mid-vowel contrast (/o/-/ɔ/) by 24 early and highly proficient Spanish-Catalan bilinguals in Majorca (Spain). Participants completed a picture-naming task and a forced-choice lexical decision task in which they were presented with either words (e.g., /bɔsk/ “forest”) or non-words based on real words, but with the alternate mid-vowel pair in stressed position (*/bosk/). The same cognate and non-cognate lexical items were included in the production and lexical decision experiments. The results indicate that even though these early bilinguals maintained the back mid-vowel contrast in their productions, they had great difficulties identifying non-words and real words based on the identity of the Catalan mid-vowel. The analyses revealed language dominance and cognate effects: Spanish-dominants exhibited higher error rates than Catalan-dominants, and production and lexical decision accuracy were also affected by cognate status. The present study contributes to the discussion of the organization of early bilinguals' dominant and non-dominant sound systems, and proposes that exemplar theoretic approaches can be extended to include bilingual lexical connections that account for the interactions between the phonetic and lexical levels of early bilingual individuals. PMID:27199849

  17. Proteomic and Metabolomic Analyses Reveal Contrasting Anti-Inflammatory Effects of an Extract of Mucor Racemosus Secondary Metabolites Compared to Dexamethasone

    PubMed Central

    Meier, Samuel M.; Muqaku, Besnik; Ullmann, Ronald; Bileck, Andrea; Kreutz, Dominique; Mader, Johanna C.; Knasmüller, Siegfried; Gerner, Christopher

    2015-01-01

    Classical drug assays are often confined to single molecules and targeting single pathways. However, it is also desirable to investigate the effects of complex mixtures on complex systems such as living cells including the natural multitude of signalling pathways. Evidence based on herbal medicine has motivated us to investigate potential beneficial health effects of Mucor racemosus (M rac) extracts. Secondary metabolites of M rac were collected using a good-manufacturing process (GMP) approved production line and a validated manufacturing process, in order to obtain a stable product termed SyCircue (National Drug Code USA: 10424–102). Toxicological studies confirmed that this product does not contain mycotoxins and is non-genotoxic. Potential effects on inflammatory processes were investigated by treating stimulated cells with M rac extracts and the effects were compared to the standard anti-inflammatory drug dexamethasone on the levels of the proteome and metabolome. Using 2D-PAGE, slight anti-inflammatory effects were observed in primary white blood mononuclear cells, which were more pronounced in primary human umbilical vein endothelial cells (HUVECs). Proteome profiling based on nLC-MS/MS analysis of tryptic digests revealed inhibitory effects of M rac extracts on pro-inflammatory cytoplasmic mediators and secreted cytokines and chemokines in these endothelial cells. This finding was confirmed using targeted proteomics, here treatment of stimulated cells with M rac extracts down-regulated the secretion of IL-6, IL-8, CXCL5 and GROA significantly. Finally, the modulating effects of M rac on HUVECs were also confirmed on the level of the metabolome. Several metabolites displayed significant concentration changes upon treatment of inflammatory activated HUVECs with the M rac extract, including spermine and lysophosphatidylcholine acyl C18:0 and sphingomyelin C26:1, while the bulk of measured metabolites remained unaffected. Interestingly, the effects of M rac

  18. [Value of the technique of intravenous infusion of contrast media for the diagnosis of fluid processes (author's transl)].

    PubMed

    Ramos, L; Marcos, L; Arenas de Pablo, A; Mora, M H; Illanas, M; Paya, F P; Picouto, P P

    1977-01-01

    The study covered 50 patients suffering from hepatic effusions; a solution used in contrast intravenous psychography was administered to them by the intravenous route, at similar doses to those used in intravenous psychography with infusions. This process which we have called Intravenous Viscerogramme, because of the similarity of the images obtained with those of the viscerographic phase of arteriography, has enabled the diagnosis of 35 hydatidiform cysts, one case of cholangiolar hamartoma and an abscess. Owing to the ease with which it can be carried out, we think that it can be used in the diagnosis of tumoral lesions of the liver. When the result is positive, radiological signs are obtained which enable identification of the lesion, thus avoiding resorting to more complex investigations such as angiography.

  19. In-Vivo Imaging of Cell Migration Using Contrast Enhanced MRI and SVM Based Post-Processing.

    PubMed

    Weis, Christian; Hess, Andreas; Budinsky, Lubos; Fabry, Ben

    2015-01-01

    The migration of cells within a living organism can be observed with magnetic resonance imaging (MRI) in combination with iron oxide nanoparticles as an intracellular contrast agent. This method, however, suffers from low sensitivity and specificty. Here, we developed a quantitative non-invasive in-vivo cell localization method using contrast enhanced multiparametric MRI and support vector machines (SVM) based post-processing. Imaging phantoms consisting of agarose with compartments containing different concentrations of cancer cells labeled with iron oxide nanoparticles were used to train and evaluate the SVM for cell localization. From the magnitude and phase data acquired with a series of T2*-weighted gradient-echo scans at different echo-times, we extracted features that are characteristic for the presence of superparamagnetic nanoparticles, in particular hyper- and hypointensities, relaxation rates, short-range phase perturbations, and perturbation dynamics. High detection quality was achieved by SVM analysis of the multiparametric feature-space. The in-vivo applicability was validated in animal studies. The SVM detected the presence of iron oxide nanoparticles in the imaging phantoms with high specificity and sensitivity with a detection limit of 30 labeled cells per mm3, corresponding to 19 μM of iron oxide. As proof-of-concept, we applied the method to follow the migration of labeled cancer cells injected in rats. The combination of iron oxide labeled cells, multiparametric MRI and a SVM based post processing provides high spatial resolution, specificity, and sensitivity, and is therefore suitable for non-invasive in-vivo cell detection and cell migration studies over prolonged time periods.

  20. Niche Divergence versus Neutral Processes: Combined Environmental and Genetic Analyses Identify Contrasting Patterns of Differentiation in Recently Diverged Pine Species

    PubMed Central

    Moreno-Letelier, Alejandra; Ortíz-Medrano, Alejandra; Piñero, Daniel

    2013-01-01

    Background and Aims Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes. PMID:24205167

  1. A comparison of ultrasound-based advanced oxidation processes for the removal of X-ray contrast media.

    PubMed

    Ning, B; Graham, N J D; Lickiss, P D

    2009-01-01

    The degradation of specific iodinated X-ray contrast media (ICM) compounds (viz: diatrizoate, iomeprol, iopromide, and iopamidol) by ultrasound irradiation in aqueous solution, with and without the presence of hydrogen peroxide or ozone, has been studied. Experiments were carried out at a constant ultrasound frequency of 20 kHz, at two power intensity values of 17.6 and 200.1 W cm(-2), and at five power densities up to 0.235 W ml(-1). Zero-order kinetic rate constants for the ICM degradation by ultrasound alone were calculated under certain sonication conditions. Pyrolysis appeared to contribute approximately 30%, and radical attack 70%, of the overall ICM degradation performance. The effect of ultrasound intensity on compound degradation (at a given power density) was found to play a negligible role, whereas ultrasound power density was found to be a major factor controlling the overall oxidation process under these conditions. The compound degradation by ultrasound alone was relatively minor, but the addition of hydrogen peroxide in the sonication process gave some improvement with a doubling in the degradation performance at the greatest applied peroxide concentration. The combination of gaseous ozone and ultrasound was found to be very effective in degrading ICM compounds and an almost complete compound removal could be achieved.

  2. Different hydrodynamic processes regulated on water quality (nutrients, dissolved oxygen, and phytoplankton biomass) in three contrasting waters of Hong Kong.

    PubMed

    Zhou, Weihua; Yuan, Xiangcheng; Long, Aimin; Huang, Hui; Yue, Weizhong

    2014-03-01

    The subtropical Hong Kong (HK) waters are located at the eastern side of the Pearl River Estuary. Monthly changes of water quality, including nutrients, dissolved oxygen (DO), and phytoplankton biomass (Chl-a) were routinely investigated in 2003 by the Hong Kong Environmental Protection Department in three contrasting waters of HK with different prevailing hydrodynamic processes. The western, eastern, and southern waters were mainly dominated by nutrient-replete Pearl River discharge, the nutrient-poor coastal/shelf oceanic waters, and mixtures of estuarine and coastal seawater and sewage effluent of Hong Kong, respectively. Acting in response, the water quality in these three contrasting areas showed apparently spatial–temporal variation pattern. Nutrients usually decreased along western waters to eastern waters. In the dry season, the water column was strongly mixed by monsoon winds and tidal currents, which resulted in relatively low Chl-a (<5 μg l(−1)) and high bottom DO (>4 mg l(−1)), suggesting that mixing enhanced the buffering capacity of eutrophication in HK waters. However, in the wet season, surface Chl-a was generally >10 μg l(−1) in southern waters in summer due to halocline and thermohaline stratification, adequate nutrients, and light availability. Although summer hypoxia (DO <2 mg l(−1)) was episodically observed near sewage effluent site and in southern waters induced by vertical stratification, the eutrophication impacts in HK waters were not as severe as expected owing to P limitation and short water residence time in the wet season.

  3. Revealing the flux: Using processed Husimi maps to visualize dynamics of bound systems and mesoscopic transport

    NASA Astrophysics Data System (ADS)

    Mason, Douglas J.; Borunda, Mario F.; Heller, Eric J.

    2015-04-01

    We elaborate upon the "processed Husimi map" representation for visualizing quantum wave functions using coherent states as a measurement of the local phase space to produce a vector field related to the probability flux. Adapted from the Husimi projection, the processed Husimi map is mathematically related to the flux operator under certain limits but offers a robust and flexible alternative since it can operate away from these limits and in systems that exhibit zero flux. The processed Husimi map is further capable of revealing the full classical dynamics underlying a quantum wave function since it reverse engineers the wave function to yield the underlying classical ray structure. We demonstrate the capabilities of processed Husimi maps on bound systems with and without electromagnetic fields, as well as on open systems on and off resonance, to examine the relationship between closed system eigenstates and mesoscopic transport.

  4. Clitic pronouns reveal the time course of processing gender and number in a second language.

    PubMed

    Rossi, Eleonora; Kroll, Judith F; Dussias, Paola E

    2014-09-01

    This study investigates grammatical gender and number processing marked on clitic pronouns in native Spanish speakers and in late English-Spanish bilinguals using ERPs. Spanish clitic pronouns were chosen as a critical grammatical structure which is absent in English, and which encodes both grammatical gender and number. Number, but not grammatical gender, is present in English, making this structure a prime one to investigate second language processing. Results reveal a P600 effect in native speakers for violations of both gender and number. Late but relatively proficient English-Spanish bilinguals show a P600 effect only for number violations occurring at the clitic pronoun, but not for gender violations. However a post-hoc analysis reveals that a subset of highly proficient late bilinguals does reveal sensitivity to violations of grammatical gender marked on clitic pronouns. Taken together these results suggest that native-like processing is possible for highly proficient late second language learners for grammatical features that are not present in the speakers' native language, even when those features are encoded on a grammatical morpheme which itself is absent in the speakers' native language.

  5. Clitic pronouns reveal the time course of processing gender and number in a second language

    PubMed Central

    Rossi, Eleonora; Kroll, Judith F.; Dussias, Paola E.

    2014-01-01

    This study investigates grammatical gender and number processing marked on clitic pronouns in native Spanish speakers and in late English-Spanish bilinguals using ERPs. Spanish clitic pronouns were chosen as a critical grammatical structure which is absent in English, and which encodes both grammatical gender and number. Number, but not grammatical gender, is present in English, making this structure a prime one to investigate second language processing. Results reveal a P600 effect in native speakers for violations of both gender and number. Late but relatively proficient English-Spanish bilinguals show a P600 effect only for number violations occurring at the clitic pronoun, but not for gender violations. However a post-hoc analysis reveals that a subset of highly proficient late bilinguals does reveal sensitivity to violations of grammatical gender marked on clitic pronouns. Taken together these results suggest that native-like processing is possible for highly proficient late second language learners for grammatical features that are not present in the speakers' native language, even when those features are encoded on a grammatical morpheme which itself is absent in the speakers' native language. PMID:25036762

  6. Floodplain forest succession reveals fluvial processes: A hydrogeomorphic model for temperate riparian woodlands.

    PubMed

    Egger, Gregory; Politti, Emilio; Lautsch, Erwin; Benjankar, Rohan; Gill, Karen M; Rood, Stewart B

    2015-09-15

    River valley floodplains are physically-dynamic environments where fluvial processes determine habitat gradients for riparian vegetation. These zones support trees and shrubs whose life stages are adapted to specific habitat types and consequently forest composition and successional stage reflect the underlying hydrogeomorphic processes and history. In this study we investigated woodland vegetation composition, successional stage and habitat properties, and compared these with physically-based indicators of hydraulic processes. We thus sought to develop a hydrogeomorphic model to evaluate riparian woodland condition based on the spatial mosaic of successional phases of the floodplain forest. The study investigated free-flowing and dam-impacted reaches of the Kootenai and Flathead Rivers, in Idaho and Montana, USA and British Columbia, Canada. The analyses revealed strong correspondence between vegetation assessments and metrics of fluvial processes indicating morphodynamics (erosion and shear stress), inundation and depth to groundwater. The results indicated that common successional stages generally occupied similar hydraulic environments along the different river segments. Comparison of the spatial patterns between the free-flowing and regulated reaches revealed greater deviation from the natural condition for the braided channel segment than for the meandering segment. This demonstrates the utility of the hydrogeomorphic approach and suggests that riparian woodlands along braided channels could have lower resilience than those along meandering channels and might be more vulnerable to influences such as from river damming or climate change.

  7. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes.

    PubMed

    Wood, Elizabeth T; Stover, Daryn A; Ehret, Christopher; Destro-Bisol, Giovanni; Spedini, Gabriella; McLeod, Howard; Louie, Leslie; Bamshad, Mike; Strassmann, Beverly I; Soodyall, Himla; Hammer, Michael F

    2005-07-01

    To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.

  8. Functional Traits Reveal Processes Driving Natural Afforestation at Large Spatial Scales

    PubMed Central

    Mason, Norman W. H.; Wiser, Susan K.; Richardson, Sarah J.; Thorsen, Michael J.; Holdaway, Robert J.; Dray, Stéphane; Thomson, Fiona J.; Carswell, Fiona E.

    2013-01-01

    An understanding of the processes governing natural afforestation over large spatial scales is vital for enhancing forest carbon sequestration. Models of tree species occurrence probability in non-forest vegetation could potentially identify the primary variables determining natural afforestation. However, inferring processes governing afforestation using tree species occurrence is potentially problematic, since it is impossible to know whether observed occurrences are due to recruitment or persistence of existing trees following disturbance. Plant functional traits have the potential to reveal the processes by which key environmental and land cover variables influence afforestation. We used 10,061 survey plots to identify the primary environmental and land cover variables influencing tree occurrence probability in non-forest vegetation in New Zealand. We also examined how these variables influenced diversity of functional traits linked to plant ecological strategy and dispersal ability. Mean annual temperature was the most important environmental predictor of tree occurrence. Local woody cover and distance to forest were the most important land cover variables. Relationships between these variables and ecological strategy traits revealed a trade-off between ability to compete for light and colonize sites that were marginal for tree occurrence. Biotically dispersed species occurred less frequently with declining temperature and local woody cover, suggesting that abiotic stress limited their establishment and that biotic dispersal did not increase ability to colonize non-woody vegetation. Functional diversity for ecological strategy traits declined with declining temperature and woody cover and increasing distance to forest. Functional diversity for dispersal traits showed the opposite trend. This suggests that low temperatures and woody cover and high distance to forest may limit tree species establishment through filtering on ecological strategy traits, but not on

  9. Functional traits reveal processes driving natural afforestation at large spatial scales.

    PubMed

    Mason, Norman W H; Wiser, Susan K; Richardson, Sarah J; Thorsen, Michael J; Holdaway, Robert J; Dray, Stéphane; Thomson, Fiona J; Carswell, Fiona E

    2013-01-01

    An understanding of the processes governing natural afforestation over large spatial scales is vital for enhancing forest carbon sequestration. Models of tree species occurrence probability in non-forest vegetation could potentially identify the primary variables determining natural afforestation. However, inferring processes governing afforestation using tree species occurrence is potentially problematic, since it is impossible to know whether observed occurrences are due to recruitment or persistence of existing trees following disturbance. Plant functional traits have the potential to reveal the processes by which key environmental and land cover variables influence afforestation. We used 10,061 survey plots to identify the primary environmental and land cover variables influencing tree occurrence probability in non-forest vegetation in New Zealand. We also examined how these variables influenced diversity of functional traits linked to plant ecological strategy and dispersal ability. Mean annual temperature was the most important environmental predictor of tree occurrence. Local woody cover and distance to forest were the most important land cover variables. Relationships between these variables and ecological strategy traits revealed a trade-off between ability to compete for light and colonize sites that were marginal for tree occurrence. Biotically dispersed species occurred less frequently with declining temperature and local woody cover, suggesting that abiotic stress limited their establishment and that biotic dispersal did not increase ability to colonize non-woody vegetation. Functional diversity for ecological strategy traits declined with declining temperature and woody cover and increasing distance to forest. Functional diversity for dispersal traits showed the opposite trend. This suggests that low temperatures and woody cover and high distance to forest may limit tree species establishment through filtering on ecological strategy traits, but not on

  10. Orbital Differential Imaging: a new high-contrast post-processing technique for direct imaging of exoplanets

    NASA Astrophysics Data System (ADS)

    Males, Jared R.; Belikov, Ruslan; Bendek, Eduardo

    2015-09-01

    Current post-processing techniques in high contrast imaging depend on some source of diversity between the exoplanet signal and the residual star light at that location. The two main techniques are angular differential imaging (ADI), which makes use of parallactic sky rotation to separate planet from star light, and spectral differential imaging (SDI), which makes use of differences in the spectrum of planet and star light and the wavelength dependence of the point spread function (PSF). Here we introduce our technique for exploiting another source of diversity: orbital motion. Given repeated observations of an exoplanetary system with sufficiently short orbital periods, the motion of the planets allows us to discriminate them from the PSF. In addition to using powerful PSF subtraction algorithms, such an observing strategy enables temporal filtering. Once an orbit is determined, the planet can be "de-orbited" to further increase the signal-to-noise ratio. We call this collection of techniques Orbital Differential Imaging (ODI). Here we present the motivation for this technique, present a noise model, and present results from simulations. We believe ODI will be an enabling technique for imaging Earth-like planets in the habitable zones of Sun-like stars with dedicated space missions.

  11. The Rational Adolescent: Strategic Information Processing during Decision Making Revealed by Eye Tracking

    PubMed Central

    Kwak, Youngbin; Payne, John W.; Cohen, Andrew L.; Huettel, Scott A.

    2015-01-01

    Adolescence is often viewed as a time of irrational, risky decision-making – despite adolescents' competence in other cognitive domains. In this study, we examined the strategies used by adolescents (N=30) and young adults (N=47) to resolve complex, multi-outcome economic gambles. Compared to adults, adolescents were more likely to make conservative, loss-minimizing choices consistent with economic models. Eye-tracking data showed that prior to decisions, adolescents acquired more information in a more thorough manner; that is, they engaged in a more analytic processing strategy indicative of trade-offs between decision variables. In contrast, young adults' decisions were more consistent with heuristics that simplified the decision problem, at the expense of analytic precision. Collectively, these results demonstrate a counter-intuitive developmental transition in economic decision making: adolescents' decisions are more consistent with rational-choice models, while young adults more readily engage task-appropriate heuristics. PMID:26388664

  12. Degradation of Iodinated Contrast Media in Aquatic Environment by Means of UV, UV/TiO2 Process, and by Activated Sludge.

    PubMed

    Borowska, Ewa; Felis, Ewa; Żabczyński, Sebastian

    Iodinated contrast media (ICM), which are used for radiological visualization of human tissue and cardiovascular system, are poorly biodegradable; hence, new methods of their removal are sought. In this study, the effectiveness of selected X-ray ICM removal by means of UV and UV/TiO2 pretreatment processes from synthetic hospital wastewater was demonstrated. The following compounds were investigated: iodipamide, iohexol, and diatrizoate. The experiments were as follows: (i) estimated susceptibility of the ICM to decay by UV radiation in different aquatic matrices, (ii) determined an optimal retention time of hospital wastewater in the UV reactor, (iii) determined optimum TiO2 concentration to improve the effectiveness of the UV pretreatment, and (iv) investigated removal of ICM by combination of the photochemical and biological treatment methods. The quantum yields of selected ICM decay in deionized water (pH = 7.0) were established as 0.006, 0.004, and 0.029 for iohexol, diatrizoate, and iodipamide, respectively. Furthermore, the experiments revealed that diatrizoate and iohexol removal in the UV/TiO2 process is more efficient than in UV process alone. For diatrizoate, the removal efficiency equaled to 40 and 30 %, respectively, and for iohexol, the efficiency was 38 and 27 %, respectively. No significant increase in iodipamide removal in UV and UV/TiO2 processes was observed (29 and 28 %, respectively). However, highest removal efficiency was demonstrated in synthetic hospital wastewater with the combined photochemical and biological treatment method. The removal of diatrizoate and iohexol increased to at least 90 %, and for iodipamide, to at least 50 %.

  13. Long-Term MR Cell Tracking of Neural Stem Cells Grafted in Immunocompetent Versus Immunodeficient Mice Reveals Distinct Differences in Contrast Between Live and Dead Cells

    PubMed Central

    Berman, Stacey Cromer; Galpoththawela, Chulani; Gilad, Assaf A.; Bulte, Jeff W. M.; Walczak, Piotr

    2011-01-01

    Neural stem cell (NSC)-based therapy is actively being pursued in preclinical and clinical disease models. Magnetic resonance imaging (MRI) cell tracking promises to optimize current cell transplantation paradigms, however, it is limited by dilution of contrast agent during cellular proliferation, transfer of label from dying cells to surrounding endogenous host cells, and/or biodegradation of the label. Here, we evaluated the applicability of magnetic resonance imaging for long-term tracking of transplanted neural stem cells labeled with superparamagnetic iron oxide and transfected with the bioluminescence reporter gene luciferase. Mouse neural stem cells were transplanted into immunodeficient, graft-accepting Rag2 mice or immunocompetent, graft-rejecting Balb/c mice. Hypointense voxel signals and bioluminescence were monitored over a period of 93 days. Unexpectedly, in mice that rejected the cells, the hypointense MR signal persisted throughout the entire time-course, whereas in the nonrejecting mice, the contrast cleared at a faster rate. In immunocompetent, graft-rejecting Balb/c mice, infiltrating leukocytes, and microglia were found surrounding dead cells and internalizing superparamagnetic iron oxide clusters. The present results indicate that live cell proliferation and associated label dilution may dominate contrast clearance as compared with cell death and subsequent transfer and retention of superparamagnetic iron oxide within phagocytes and brain interstitium. Thus, interpretation of signal changes during long-term MR cell tracking is complex and requires caution. PMID:20928883

  14. Non-destructive phase contrast hard x-ray imaging to reveal the three-dimensional microstructure of soft and hard tissues

    NASA Astrophysics Data System (ADS)

    Khimchenko, Anna; Schulz, Georg; Deyhle, Hans; Hieber, Simone E.; Hasan, Samiul; Bikis, Christos; Schulz, Joachim; Costeur, Loïc.; Müller, Bert

    2016-04-01

    X-ray imaging in the absorption contrast mode is an established method of visualising calcified tissues such as bone and teeth. Physically soft tissues such as brain or muscle are often imaged using magnetic resonance imaging (MRI). However, the spatial resolution of MRI is insufficient for identifying individual biological cells within three-dimensional tissue. X-ray grating interferometry (XGI) has advantages for the investigation of soft tissues or the simultaneous three-dimensional visualisation of soft and hard tissues. Since laboratory microtomography (μCT) systems have better accessibility than tomography set-ups at synchrotron radiation facilities, a great deal of effort has been invested in optimising XGI set-ups for conventional μCT systems. In this conference proceeding, we present how a two-grating interferometer is incorporated into a commercially available nanotom m (GE Sensing and Inspection Technologies GmbH) μCT system to extend its capabilities toward phase contrast. We intend to demonstrate superior contrast in spiders (Hogna radiata (Fam. Lycosidae) and Xysticus erraticus (Fam. Thomisidae)), as well as the simultaneous visualisation of hard and soft tissues. XGI is an imaging modality that provides quantitative data, and visualisation is an important part of biomimetics; consequently, hard X-ray imaging provides a sound basis for bioinspiration, bioreplication and biomimetics and allows for the quantitative comparison of biofabricated products with their natural counterparts.

  15. Hemispheric differences in orthographic and semantic processing as revealed by event-related potentials

    PubMed Central

    Dickson, Danielle S.; Federmeier, Kara D.

    2015-01-01

    Differences in how the right and left hemispheres (RH, LH) apprehend visual words were examined using event-related potentials (ERPs) in a repetition paradigm with visual half-field (VF) presentation. In both hemispheres (RH/LVF, LH/RVF), initial presentation of items elicited similar and typical effects of orthographic neighborhood size, with larger N400s for orthographically regular items (words and pseudowords) than for irregular items (acronyms and meaningless illegal strings). However, hemispheric differences emerged on repetition effects. When items were repeated in the LH/RVF, orthographically regular items, relative to irregular items, elicited larger repetition effects on both the N250, a component reflecting processing at the level of visual form (orthography), and on the N400, which has been linked to semantic access. In contrast, in the RH/LVF, repetition effects were biased toward irregular items on the N250 and were similar in size across item types for the N400. The results suggest that processing in the LH is more strongly affected by wordform regularity than in the RH, either due to enhanced processing of familiar orthographic patterns or due to the fact that regular forms can be more readily mapped onto phonology. PMID:25278134

  16. Functional magnetic resonance imaging adaptation reveals the cortical networks for processing grasp-relevant object properties.

    PubMed

    Monaco, Simona; Chen, Ying; Medendorp, W P; Crawford, J D; Fiehler, Katja; Henriques, Denise Y P

    2014-06-01

    Grasping behaviors require the selection of grasp-relevant object dimensions, independent of overall object size. Previous neuroimaging studies found that the intraparietal cortex processes object size, but it is unknown whether the graspable dimension (i.e., grasp axis between selected points on the object) or the overall size of objects triggers activation in that region. We used functional magnetic resonance imaging adaptation to investigate human brain areas involved in processing the grasp-relevant dimension of real 3-dimensional objects in grasping and viewing tasks. Trials consisted of 2 sequential stimuli in which the object's grasp-relevant dimension, its global size, or both were novel or repeated. We found that calcarine and extrastriate visual areas adapted to object size regardless of the grasp-relevant dimension during viewing tasks. In contrast, the superior parietal occipital cortex (SPOC) and lateral occipital complex of the left hemisphere adapted to the grasp-relevant dimension regardless of object size and task. Finally, the dorsal premotor cortex adapted to the grasp-relevant dimension in grasping, but not in viewing, tasks, suggesting that motor processing was complete at this stage. Taken together, our results provide a complete cortical circuit for progressive transformation of general object properties into grasp-related responses.

  17. Contrast Materials

    MedlinePlus

    ... veins of the body, including vessels in the brain, neck, chest, abdomen, pelvis and legs soft tissues of the body, including the muscles, fat and skin brain breast Microbubble Contrast Materials Microbubble contrast materials are ...

  18. Post-contractile BOLD contrast in skeletal muscle at 7 T reveals inter-individual heterogeneity in the physiological responses to muscle contraction.

    PubMed

    Towse, Theodore F; Elder, Christopher P; Bush, Emily C; Klockenkemper, Samuel W; Bullock, Jared T; Dortch, Richard D; Damon, Bruce M

    2016-12-01

    Muscle blood oxygenation-level dependent (BOLD) contrast is greater in magnitude and potentially more influenced by extravascular BOLD mechanisms at 7 T than it is at lower field strengths. Muscle BOLD imaging of muscle contractions at 7 T could, therefore, provide greater or different contrast than at 3 T. The purpose of this study was to evaluate the feasibility of using BOLD imaging at 7 T to assess the physiological responses to in vivo muscle contractions. Thirteen subjects (four females) performed a series of isometric contractions of the calf muscles while being scanned in a Philips Achieva 7 T human imager. Following 2 s maximal isometric plantarflexion contractions, BOLD signal transients ranging from 0.3 to 7.0% of the pre-contraction signal intensity were observed in the soleus muscle. We observed considerable inter-subject variability in both the magnitude and time course of the muscle BOLD signal. A subset of subjects (n = 7) repeated the contraction protocol at two different repetition times (TR : 1000 and 2500 ms) to determine the potential of T1 -related inflow effects on the magnitude of the post-contractile BOLD response. Consistent with previous reports, there was no difference in the magnitude of the responses for the two TR values (3.8 ± 0.9 versus 4.0 ± 0.6% for TR  = 1000 and 2500 ms, respectively; mean ± standard error). These results demonstrate that studies of the muscle BOLD responses to contractions are feasible at 7 T. Compared with studies at lower field strengths, post-contractile 7 T muscle BOLD contrast may afford greater insight into microvascular function and dysfunction.

  19. Dissection of the Process of Brain Metastasis Reveals Targets and Mechanisms for Molecular-based Intervention.

    PubMed

    Weidle, Ulrich H; Birzele, Fabian; Kollmorgen, Gwendlyn; Rüger, Rüdiger

    2016-01-01

    Brain metastases outnumber the incidence of brain tumors by a factor of ten. Patients with brain metastases have a dismal prognosis and current treatment modalities achieve only a modest clinical benefit. We discuss the process of brain metastasis with respect to mechanisms and involved targets to outline options for therapeutic intervention and focus on breast and lung cancer, as well as melanoma. We describe the process of penetration of the blood-brain-barrier (BBB) by disseminated tumor cells, establishment of a metastatic niche, colonization and outgrowth in the brain parenchyma. Furthermore, the role of angiogenesis in colonization of the brain parenchyma, interactions of extravasated tumor cells with microglia and astrocytes, as well as their propensity for neuromimicry, is discussed. We outline targets suitable for prevention of metastasis and summarize targets suitable for treatment of established brain metastases. Finally, we highlight the implications of findings revealing druggable mutations in brain metastases that cannot be identified in matching primary tumors.

  20. Processes affecting oxygen isotope ratios of atmospheric and ecosystem sulfate in two contrasting forest catchments in Central Europe

    SciTech Connect

    Martin Novak; Myron J. Mitchell; Iva Jackova; Frantisek Buzek; Jana Schweigstillova; Lucie Erbanova; Richard Prikryl; Daniela Fottova

    2007-02-15

    Sulfate aerosols are harmful as respirable particles. They also play a role as cloud condensation nuclei and have radiative effects on global climate. A combination of {delta}{sup 18}O-SO{sub 4} data with catchment sulfur mass balances was used to constrain processes affecting S cycling in the atmosphere and spruce forests of the Czech Republic. Extremely high S fluxes via spruce throughfall and runoff were measured at Jezeri (49 and 80 kg S ha{sup -1} yr{sup -1}, respectively). The second catchment, Na Lizu, was 10 times less polluted. In both catchments, {delta}{sup 18}O-SO{sub 4} decreased in the following order: open-area precipitation {gt} throughfall {gt} runoff. The 180-SO{sub 4} values of throughfall exhibited a seasonal pattern at both sites, with maxima in summer and minima in winter. This seasonal pattern paralleled {delta}{sup 18}O-H{sub 2}O values, which were offset by -18{per_thousand}. Sulfate in throughfall was predominantly formed by heterogeneous (aqueous) oxidation of SO{sub 2}. Wet-deposited sulfate in an open area did not show systematic {delta}{sup 18}O-SO{sub 4} trends, suggesting formation by homogeneous (gaseous) oxidation and/or transport from large distances. The percentage of incoming S that is organically cycled in soil was similar under the high and the low pollution. High-temperature {sup 18}O-rich sulfate was not detected, which contrasts with North American industrial sites. 29 refs., 4 figs., 3 tabs.

  1. A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing.

    PubMed

    Bingel-Erlenmeyer, Rouven; Kohler, Rebecca; Kramer, Günter; Sandikci, Arzu; Antolić, Snjezana; Maier, Timm; Schaffitzel, Christiane; Wiedmann, Brigitte; Bukau, Bernd; Ban, Nenad

    2008-03-06

    Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation. The first enzymatic factor that processes nascent chains is peptide deformylase (PDF); it removes this formyl group as polypeptides emerge from the ribosomal tunnel and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase. Bacterial PDFs are metalloproteases sharing a conserved N-terminal catalytic domain. All Gram-negative bacteria, including Escherichia coli, possess class-1 PDFs characterized by a carboxy-terminal alpha-helical extension. Studies focusing on PDF as a target for antibacterial drugs have not revealed the mechanism of its co-translational mode of action despite indications in early work that it co-purifies with ribosomes. Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C-terminal extension. Crystallographic analysis of the complex between the ribosome-interacting helix of PDF and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome-associated chaperone trigger factor.

  2. Gaze data reveal distinct choice processes underlying model-based and model-free reinforcement learning

    PubMed Central

    Konovalov, Arkady; Krajbich, Ian

    2016-01-01

    Organisms appear to learn and make decisions using different strategies known as model-free and model-based learning; the former is mere reinforcement of previously rewarded actions and the latter is a forward-looking strategy that involves evaluation of action-state transition probabilities. Prior work has used neural data to argue that both model-based and model-free learners implement a value comparison process at trial onset, but model-based learners assign more weight to forward-looking computations. Here using eye-tracking, we report evidence for a different interpretation of prior results: model-based subjects make their choices prior to trial onset. In contrast, model-free subjects tend to ignore model-based aspects of the task and instead seem to treat the decision problem as a simple comparison process between two differentially valued items, consistent with previous work on sequential-sampling models of decision making. These findings illustrate a problem with assuming that experimental subjects make their decisions at the same prescribed time. PMID:27511383

  3. Gaze data reveal distinct choice processes underlying model-based and model-free reinforcement learning.

    PubMed

    Konovalov, Arkady; Krajbich, Ian

    2016-08-11

    Organisms appear to learn and make decisions using different strategies known as model-free and model-based learning; the former is mere reinforcement of previously rewarded actions and the latter is a forward-looking strategy that involves evaluation of action-state transition probabilities. Prior work has used neural data to argue that both model-based and model-free learners implement a value comparison process at trial onset, but model-based learners assign more weight to forward-looking computations. Here using eye-tracking, we report evidence for a different interpretation of prior results: model-based subjects make their choices prior to trial onset. In contrast, model-free subjects tend to ignore model-based aspects of the task and instead seem to treat the decision problem as a simple comparison process between two differentially valued items, consistent with previous work on sequential-sampling models of decision making. These findings illustrate a problem with assuming that experimental subjects make their decisions at the same prescribed time.

  4. Gene Expression Reaction Norms Unravel the Molecular and Cellular Processes Underpinning the Plastic Phenotypes of Alternanthera Philoxeroides in Contrasting Hydrological Conditions

    PubMed Central

    Gao, Lexuan; Geng, Yupeng; Yang, Hongxing; Hu, Yonghong; Yang, Ji

    2015-01-01

    Alternanthera philoxeroides is an amphibious invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation. Little is known about the molecular basis underlying environment-induced phenotypic changes. Variation in transcript abundance in A. philoxeroides was characterized throughout the time-courses of pond and upland treatments using RNA-Sequencing. Seven thousand eight hundred and five genes demonstrated variable expression in response to different treatments, forming 11 transcriptionally coordinated gene groups. Functional enrichment analysis of plastically expressed genes revealed pathway changes in hormone-mediated signaling, osmotic adjustment, cell wall remodeling, and programmed cell death, providing a mechanistic understanding of the biological processes underlying the phenotypic changes in A. philoxeroides. Both transcriptional modulation of environmentally sensitive loci and environmentally dependent control of regulatory loci influenced the plastic responses to the environment. Phenotypic responses and gene expression patterns to contrasting hydrological conditions were compared between A. philoxeroides and its alien congener Alternanthera pungens. The terricolous A. pungens displayed limited phenotypic plasticity to different treatments. It was postulated based on gene expression comparison that the interspecific variation in plasticity between A. philoxeroides and A. pungens was not due to environmentally-mediated changes in hormone levels but to variations in the type and relative abundance of different signal transducers and receptors expressed in the target tissue. PMID:26617628

  5. Dual-Task Processing in Younger and Older Adults: Similarities and Differences Revealed by fMRI

    ERIC Educational Resources Information Center

    Hartley, Alan A.; Jonides, John; Sylvester, Ching-Yune C.

    2011-01-01

    fMRI was used to explore age differences in the neural substrate of dual-task processing. Brain activations when there was a 100 ms SOA between tasks, and task overlap was high, were contrasted with activations when there was a 1000 ms SOA, and first task processing was largely complete before the second task began. Younger adults (M = 21 yrs)…

  6. Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes.

    PubMed

    Stöckel, Jana; Welsh, Eric A; Liberton, Michelle; Kunnvakkam, Rangesh; Aurora, Rajeev; Pakrasi, Himadri B

    2008-04-22

    Cyanobacteria are photosynthetic organisms and are the only prokaryotes known to have a circadian lifestyle. Unicellular diazotrophic cyanobacteria such as Cyanothece sp. ATCC 51142 produce oxygen and can also fix atmospheric nitrogen, a process exquisitely sensitive to oxygen. To accommodate such antagonistic processes, the intracellular environment of Cyanothece oscillates between aerobic and anaerobic conditions during a day-night cycle. This is accomplished by temporal separation of the two processes: photosynthesis during the day and nitrogen fixation at night. Although previous studies have examined periodic changes in transcript levels for a limited number of genes in Cyanothece and other unicellular diazotrophic cyanobacteria, a comprehensive study of transcriptional activity in a nitrogen-fixing cyanobacterium is necessary to understand the impact of the temporal separation of photosynthesis and nitrogen fixation on global gene regulation and cellular metabolism. We have examined the expression patterns of nearly 5,000 genes in Cyanothece 51142 during two consecutive diurnal periods. Our analysis showed that approximately 30% of these genes exhibited robust oscillating expression profiles. Interestingly, this set included genes for almost all central metabolic processes in Cyanothece 51142. A transcriptional network of all genes with significantly oscillating transcript levels revealed that the majority of genes encoding enzymes in numerous individual biochemical pathways, such as glycolysis, oxidative pentose phosphate pathway, and glycogen metabolism, were coregulated and maximally expressed at distinct phases during the diurnal cycle. These studies provide a comprehensive picture of how a physiologically relevant diurnal light-dark cycle influences the metabolism in a photosynthetic bacterium.

  7. Skin conductance reveals the early development of the unconscious processing of emotions.

    PubMed

    Nava, Elena; Romano, Daniele; Grassi, Massimo; Turati, Chiara

    2016-11-01

    The ability to rapidly distinguish between positive and negative facial expressions of emotions is critical for adaptive social behaviour. Increasing evidence has shown that emotions can be processed even at an unconscious level in adults. Yet, very little is still known about the early ontogeny of the unconscious processing of emotional signals conveyed by faces. Here, we investigated the processing of subliminally presented face emotional stimuli in infants as young as 3-4 months of age and sought to clarify its neural underpinnings by exploring the role of the autonomic nervous system. Using a visual preference paradigm, Experiment 1 determined the visibility threshold for happy and angry faces and established that infants detected both happy and angry faces at 200- but not at 100 msec. By measuring skin conductance response (SCR), Experiment 2 showed that the autonomic nervous system of infants reacted to both subliminally (100 msec) and supraliminally (200 msec) presented face expressions of emotions, and that SCR were higher for angry than happy facial expressions. Results revealed that 3-4 month-old infants respond to positive and negative emotions even at an unconscious level, but also show that angry faces possess an intrinsic alerting characteristics, suggestive of an adaptive meaning of the physiological response. Findings are discussed in terms of subcortical learning of emotions, and the possibility that the amygdala may be involved in such process.

  8. Brain Signals of Face Processing as Revealed by Event-Related Potentials

    PubMed Central

    Olivares, Ela I.; Iglesias, Jaime; Saavedra, Cristina; Trujillo-Barreto, Nelson J.; Valdés-Sosa, Mitchell

    2015-01-01

    We analyze the functional significance of different event-related potentials (ERPs) as electrophysiological indices of face perception and face recognition, according to cognitive and neurofunctional models of face processing. Initially, the processing of faces seems to be supported by early extrastriate occipital cortices and revealed by modulations of the occipital P1. This early response is thought to reflect the detection of certain primary structural aspects indicating the presence grosso modo of a face within the visual field. The posterior-temporal N170 is more sensitive to the detection of faces as complex-structured stimuli and, therefore, to the presence of its distinctive organizational characteristics prior to within-category identification. In turn, the relatively late and probably more rostrally generated N250r and N400-like responses might respectively indicate processes of access and retrieval of face-related information, which is stored in long-term memory (LTM). New methods of analysis of electrophysiological and neuroanatomical data, namely, dynamic causal modeling, single-trial and time-frequency analyses, are highly recommended to advance in the knowledge of those brain mechanisms concerning face processing. PMID:26160999

  9. Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis.

    PubMed

    Suzuki, Hiroshi I; Young, Richard A; Sharp, Phillip A

    2017-03-09

    Super-enhancers are an emerging subclass of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here, we report that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA (pri-miRNA) processing. Super-enhancers, together with broad H3K4me3 domains, shape a tissue-specific and evolutionarily conserved atlas of miRNA expression and function. CRISPR/Cas9 genomics revealed that super-enhancer constituents act cooperatively and facilitate Drosha/DGCR8 recruitment and pri-miRNA processing to boost cell-specific miRNA production. The BET-bromodomain inhibitor JQ1 preferentially inhibits super-enhancer-directed cotranscriptional pri-miRNA processing. Furthermore, super-enhancers are characterized by pervasive interaction with DGCR8/Drosha and DGCR8/Drosha-regulated mRNA stability control, suggesting unique RNA regulation at super-enhancers. Finally, super-enhancers mark multiple miRNAs associated with cancer hallmarks. This study presents principles underlying miRNA biology in health and disease and an unrecognized higher-order property of super-enhancers in RNA processing beyond transcription.

  10. Contrasts in electron correlations and inelastic scattering between LiFeP and LiFeAs revealed by charge transport

    NASA Astrophysics Data System (ADS)

    Kasahara, S.; Hashimoto, K.; Ikeda, H.; Terashima, T.; Matsuda, Y.; Shibauchi, T.

    2012-02-01

    By using high-quality single crystals, we quantitatively compare the transport properties between LiFeP and LiFeAs superconductors with compensated electron and hole carriers. The low-temperature resistivity follows the Fermi-liquid AT2 dependence with a factor of ˜3 difference in the coefficient A. This highlights weaker electron correlations in LiFeP, which is consistent with its ˜70 times lower upper critical field than that of LiFeAs. Our analysis of the magnetotransport data indicates that in LiFeP, the electron carriers with lighter masses exhibit stronger temperature dependence of inelastic scattering rate than the holes, which is the opposite to the LiFeAs case. This stark difference in the band-dependent inelastic scattering may be relevant to the recently reported contrasting superconducting gap structures in these two superconductors.

  11. Dynamics of respiratory and cardiac CSF motion revealed with real-time simultaneous multi-slice EPI velocity phase contrast imaging.

    PubMed

    Chen, Liyong; Beckett, Alexander; Verma, Ajay; Feinberg, David A

    2015-11-15

    Cerebrospinal fluid (CSF) dynamics have been mostly studied with cardiac-gated phase contrast MRI combining signal from many cardiac cycles to create cine-phase sampling of one time-averaged cardiac cycle. The relative effects of cardiac and respiratory changes on CSF movement are not well understood. There is possible respiration-driven movement of CSF in ventricles, cisterns, and subarachnoid spaces which has not been characterized with velocity measurements. To date, commonly used cine-phase contrast techniques of velocity imaging inherently cannot detect respiratory velocity changes since cardiac-gated data acquired over several minutes randomizes respiratory phase contributions. We have developed an extremely fast, real-time, and quantitative MRI technique to image CSF velocity in simultaneous multi-slice (SMS) echo planar imaging (EPI) acquisitions of 3 or 6 slice levels simultaneously over 30s and observe 3D spatial distributions of CSF velocity. Measurements were made in 10 subjects utilizing a respiratory belt to record respiratory phases and visual cues to instruct subjects on breathing rates. A protocol is able to measure velocity within regions of brain and basal cisterns covered with 24 axial slices in 4 minutes, repeated for 3 velocity directions. These measurements were performed throughout the whole brain, rather than in selected line regions so that a global view of CSF dynamics could be visualized. Observations of cardiac and breathing-driven CSF dynamics show bidirectional respiratory motion occurs primarily along the central axis through the basal cisterns and intraventricular passageways and to a lesser extent in the peripheral Sylvian fissure with little CSF motion present in subarachnoid spaces. During inspiration phase, there is upward (inferior to superior) CSF movement into the cranial cavity and lateral ventricles and a reversal of direction in expiration phase.

  12. Development of a new Sonovue™ contrast-enhanced ultrasound approach reveals temporal and age-related features of muscle microvascular responses to feeding

    PubMed Central

    Mitchell, William Kyle; Phillips, Bethan E; Williams, John P; Rankin, Debbie; Smith, Kenneth; Lund, Jonathan N; Atherton, Philip J

    2013-01-01

    Compromised limb blood flow in aging may contribute to the development of sarcopenia, frailty, and the metabolic syndrome. We developed a novel contrast-enhanced ultrasound technique using Sonovue™ to characterize muscle microvasculature responses to an oral feeding stimulus (15 g essential amino acids) in young (∼20 years) and older (∼70 years) men. Intensity-time replenishment curves were made via an ultrasound probe “fixed” over the quadriceps, with intermittent high mechanical index destruction of microbubbles within muscle vasculature. This permitted real-time measures of microvascular blood volume (MBV), microvascular flow velocity (MFV) and their product, microvascular blood flow (MBF). Leg blood flow (LBF) was measured by Doppler and insulin by enzyme-linked immunosorbent assay. Steady-state contrast concentrations needed for comparison between different physiological states were achieved <150 sec from commencing Sonovue™ infusion, and MFV and MBV measurements were completed <120 sec thereafter. Interindividual coefficients of variation in MBV and MFV were 35–40%, (N = 36). Younger men (N = 6) exhibited biphasic vascular responses to feeding with early increases in MBV (+36%, P < 0.008 45 min post feed) reflecting capillary recruitment, and late increases in MFV (+77%, P < 0.008) and MBF (+130%, P < 0.007 195 min post feed) reflecting more proximal vessel dilatation. Early MBV responses were synchronized with peak insulin but not increased LBF, while later changes in MFV and MBF occurred with insulin at post absorptive values but alongside increased LBF. All circulatory responses were absent in old men (N = 7). Thus, impaired postprandial circulation could impact age-related declines in muscle glucose disposal, protein anabolism, and muscle mass. PMID:24303186

  13. Laser lithotripsy with the Ho:YAG laser: fragmentation process revealed by time-resolved imaging

    NASA Astrophysics Data System (ADS)

    Schmidlin, Franz R.; Beghuin, Didier; Delacretaz, Guy P.; Venzi, Giordano; Jichlinski, Patrice; Rink, Klaus; Leisinger, Hans-Juerg; Graber, Peter

    1998-07-01

    Improvements of endoscopic techniques have renewed the interest of urologists in laser lithotripsy in recent years. Laser energy can be easily transmitted through flexible fibers thereby enabling different surgical procedures such as cutting, coagulating and lithotripsy. The Ho:YAG laser offers multiple medical applications in Urology, among them stone fragmentation. However, the present knowledge of its fragmentation mechanism is incomplete. The objective was therefore to analyze the fragmentation process and to discuss the clinical implications related to the underlying fragmentation mechanism. The stone fragmentation process during Ho:YAG laser lithotripsy was observed by time resolved flash video imaging. Possible acoustic transient occurrence was simultaneously monitored with a PVDF-needle hydrophone. Fragmentation was performed on artificial and cystine kidney stones in water. We observed that though the fragmentation process is accompanied with the formation of a cavitation bubble, cavitation has only a minimal effect on stone fragmentation. Fragment ejection is mainly due to direct laser stone heating leading to vaporization of organic stone constituents and interstitial water. The minimal effect of the cavitation bubble is confirmed by acoustic transients measurements, which reveal weak pressure transients. Stone fragmentation with the Holmium laser is the result of vaporization of interstitial (stone) water and organic stone constituents. It is not due to the acoustic effects of a cavitation bubble or plasma formation. The fragmentation process is strongly related with heat production thereby harboring the risk of undesired thermal damage. Therefore, a solid comprehension of the fragmentation process is needed when using the different clinically available laser types of lithotripsy.

  14. Computational dissection of human episodic memory reveals mental process-specific genetic profiles.

    PubMed

    Luksys, Gediminas; Fastenrath, Matthias; Coynel, David; Freytag, Virginie; Gschwind, Leo; Heck, Angela; Jessen, Frank; Maier, Wolfgang; Milnik, Annette; Riedel-Heller, Steffi G; Scherer, Martin; Spalek, Klara; Vogler, Christian; Wagner, Michael; Wolfsgruber, Steffen; Papassotiropoulos, Andreas; de Quervain, Dominique J-F

    2015-09-01

    Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young adults. We report robust and replicated associations of the amine compound SLC (solute-carrier) transporters gene set with the learning rate, of the collagen formation and transmembrane receptor protein tyrosine kinase activity gene sets with the modulation of memory strength by negative emotional arousal, and of the L1 cell adhesion molecule (L1CAM) interactions gene set with the repetition-based memory improvement. Furthermore, in a large functional MRI sample of 795 subjects we found that the association between L1CAM interactions and memory maintenance revealed large clusters of differences in brain activity in frontal cortical areas. Our findings provide converging evidence that distinct genetic profiles underlie specific mental processes of human episodic memory. They also provide empirical support to previous theoretical and neurobiological studies linking specific neuromodulators to the learning rate and linking neural cell adhesion molecules to memory maintenance. Furthermore, our study suggests additional memory-related genetic pathways, which may contribute to a better understanding of the neurobiology of human memory.

  15. Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program.

    PubMed

    Guo, Xin; Bernard, Allister; Orlando, David A; Haase, Steven B; Hartemink, Alexander J

    2013-03-05

    Due to cell-to-cell variability and asymmetric cell division, cells in a synchronized population lose synchrony over time. As a result, time-series measurements from synchronized cell populations do not reflect the underlying dynamics of cell-cycle processes. Here, we present a branching process deconvolution algorithm that learns a more accurate view of dynamic cell-cycle processes, free from the convolution effects associated with imperfect cell synchronization. Through wavelet-basis regularization, our method sharpens signal without sharpening noise and can remarkably increase both the dynamic range and the temporal resolution of time-series data. Although applicable to any such data, we demonstrate the utility of our method by applying it to a recent cell-cycle transcription time course in the eukaryote Saccharomyces cerevisiae. Our method more sensitively detects cell-cycle-regulated transcription and reveals subtle timing differences that are masked in the original population measurements. Our algorithm also explicitly learns distinct transcription programs for mother and daughter cells, enabling us to identify 82 genes transcribed almost entirely in early G1 in a daughter-specific manner.

  16. Computational dissection of human episodic memory reveals mental process-specific genetic profiles

    PubMed Central

    Luksys, Gediminas; Fastenrath, Matthias; Coynel, David; Freytag, Virginie; Gschwind, Leo; Heck, Angela; Jessen, Frank; Maier, Wolfgang; Milnik, Annette; Riedel-Heller, Steffi G.; Scherer, Martin; Spalek, Klara; Vogler, Christian; Wagner, Michael; Wolfsgruber, Steffen; Papassotiropoulos, Andreas; de Quervain, Dominique J.-F.

    2015-01-01

    Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young adults. We report robust and replicated associations of the amine compound SLC (solute-carrier) transporters gene set with the learning rate, of the collagen formation and transmembrane receptor protein tyrosine kinase activity gene sets with the modulation of memory strength by negative emotional arousal, and of the L1 cell adhesion molecule (L1CAM) interactions gene set with the repetition-based memory improvement. Furthermore, in a large functional MRI sample of 795 subjects we found that the association between L1CAM interactions and memory maintenance revealed large clusters of differences in brain activity in frontal cortical areas. Our findings provide converging evidence that distinct genetic profiles underlie specific mental processes of human episodic memory. They also provide empirical support to previous theoretical and neurobiological studies linking specific neuromodulators to the learning rate and linking neural cell adhesion molecules to memory maintenance. Furthermore, our study suggests additional memory-related genetic pathways, which may contribute to a better understanding of the neurobiology of human memory. PMID:26261317

  17. EEG source reconstruction reveals frontal-parietal dynamics of spatial conflict processing.

    PubMed

    Cohen, Michael X; Ridderinkhof, K Richard

    2013-01-01

    Cognitive control requires the suppression of distracting information in order to focus on task-relevant information. We applied EEG source reconstruction via time-frequency linear constrained minimum variance beamforming to help elucidate the neural mechanisms involved in spatial conflict processing. Human subjects performed a Simon task, in which conflict was induced by incongruence between spatial location and response hand. We found an early (∼200 ms post-stimulus) conflict modulation in stimulus-contralateral parietal gamma (30-50 Hz), followed by a later alpha-band (8-12 Hz) conflict modulation, suggesting an early detection of spatial conflict and inhibition of spatial location processing. Inter-regional connectivity analyses assessed via cross-frequency coupling of theta (4-8 Hz), alpha, and gamma power revealed conflict-induced shifts in cortical network interactions: Congruent trials (relative to incongruent trials) had stronger coupling between frontal theta and stimulus-contrahemifield parietal alpha/gamma power, whereas incongruent trials had increased theta coupling between medial frontal and lateral frontal regions. These findings shed new light into the large-scale network dynamics of spatial conflict processing, and how those networks are shaped by oscillatory interactions.

  18. Genetic dissection of pheromone processing reveals main olfactory system-mediated social behaviors in mice.

    PubMed

    Matsuo, Tomohiko; Hattori, Tatsuya; Asaba, Akari; Inoue, Naokazu; Kanomata, Nobuhiro; Kikusui, Takefumi; Kobayakawa, Reiko; Kobayakawa, Ko

    2015-01-20

    Most mammals have two major olfactory subsystems: the main olfactory system (MOS) and vomeronasal system (VNS). It is now widely accepted that the range of pheromones that control social behaviors are processed by both the VNS and the MOS. However, the functional contributions of each subsystem in social behavior remain unclear. To genetically dissociate the MOS and VNS functions, we established two conditional knockout mouse lines that led to either loss-of-function in the entire MOS or in the dorsal MOS. Mice with whole-MOS loss-of-function displayed severe defects in active sniffing and poor survival through the neonatal period. In contrast, when loss-of-function was confined to the dorsal MOB, sniffing behavior, pheromone recognition, and VNS activity were maintained. However, defects in a wide spectrum of social behaviors were observed: attraction to female urine and the accompanying ultrasonic vocalizations, chemoinvestigatory preference, aggression, maternal behaviors, and risk-assessment behaviors in response to an alarm pheromone. Functional dissociation of pheromone detection and pheromonal induction of behaviors showed the anterior olfactory nucleus (AON)-regulated social behaviors downstream from the MOS. Lesion analysis and neural activation mapping showed pheromonal activation in multiple amygdaloid and hypothalamic nuclei, important regions for the expression of social behavior, was dependent on MOS and AON functions. Identification of the MOS-AON-mediated pheromone pathway may provide insights into pheromone signaling in animals that do not possess a functional VNS, including humans.

  19. Contextual effects on preattentive processing of sound motion as revealed by spatial MMN.

    PubMed

    Shestopalova, L B; Petropavlovskaia, E A; Vaitulevich, S Ph; Nikitin, N I

    2015-04-01

    The magnitude of spatial distance between sound stimuli is critically important for their preattentive discrimination, yet the effect of stimulus context on auditory motion processing is not clear. This study investigated the effects of acoustical change and stimulus context on preattentive spatial change detection. Auditory event-related potentials (ERPs) were recorded for stationary midline noises and two patterns of sound motion produced by linear or abrupt changes of interaural time differences. Each of the three types of stimuli was used as standard or deviant in different blocks. Context effects on mismatch negativity (MMN) elicited by stationary and moving sound stimuli were investigated by reversing the role of standard and deviant stimuli, while the acoustical stimulus parameters were kept the same. That is, MMN amplitudes were calculated by subtracting ERPs to identical stimuli presented as standard in one block and deviant in another block. In contrast, effects of acoustical change on MMN amplitudes were calculated by subtracting ERPs of standards and deviants presented within the same block. Preattentive discrimination of moving and stationary sounds indexed by MMN was strongly dependent on the stimulus context. Higher MMNs were produced in oddball configurations where deviance represented increments of the sound velocity, as compared to configurations with velocity decrements. The effect of standard-deviant reversal was more pronounced with the abrupt sound displacement than with gradual sound motion.

  20. FMRI reveals abnormal central processing of sensory and pain stimuli in ill Gulf War veterans.

    PubMed

    Gopinath, Kaundinya; Gandhi, Parina; Goyal, Aman; Jiang, Lei; Fang, Yan; Ouyang, Luo; Ganji, Sandeepkumar; Buhner, David; Ringe, Wendy; Spence, Jeffrey; Biggs, Melanie; Briggs, Richard; Haley, Robert

    2012-06-01

    Many veterans chronically ill from the 1991 Gulf War exhibit symptoms of altered sensation, including chronic pain. In this study of 55 veterans of a Construction Battalion previously examined in 1995-1996 and 1997-1998, brain activation to innocuous and noxious heat stimuli was assessed in 2008-2009 with a quantitative sensory testing fMRI protocol in control veterans and groups representing three syndrome variants. Testing outside the scanner revealed no significant differences in warm detection or heat pain threshold among the four groups. In the fMRI study, Syndrome 1 and Syndrome 2, but not Syndrome 3, exhibited hypo-activation to innocuous heat and hyper-activation to noxious heat stimuli compared to controls. The results indicate abnormal central processing of sensory and painful stimuli in 2 of 3 variants of Gulf War illness and call for a more comprehensive study with a larger, representative sample of veterans.

  1. Action potential processing in a detailed Purkinje cell model reveals a critical role for axonal compartmentalization

    PubMed Central

    Masoli, Stefano; Solinas, Sergio; D'Angelo, Egidio

    2015-01-01

    The Purkinje cell (PC) is among the most complex neurons in the brain and plays a critical role for cerebellar functioning. PCs operate as fast pacemakers modulated by synaptic inputs but can switch from simple spikes to complex bursts and, in some conditions, show bistability. In contrast to original works emphasizing dendritic Ca-dependent mechanisms, recent experiments have supported a primary role for axonal Na-dependent processing, which could effectively regulate spike generation and transmission to deep cerebellar nuclei (DCN). In order to account for the numerous ionic mechanisms involved (at present including Nav1.6, Cav2.1, Cav3.1, Cav3.2, Cav3.3, Kv1.1, Kv1.5, Kv3.3, Kv3.4, Kv4.3, KCa1.1, KCa2.2, KCa3.1, Kir2.x, HCN1), we have elaborated a multicompartmental model incorporating available knowledge on localization and gating of PC ionic channels. The axon, including initial segment (AIS) and Ranvier nodes (RNs), proved critical to obtain appropriate pacemaking and firing frequency modulation. Simple spikes initiated in the AIS and protracted discharges were stabilized in the soma through Na-dependent mechanisms, while somato-dendritic Ca channels contributed to sustain pacemaking and to generate complex bursting at high discharge regimes. Bistability occurred only following Na and Ca channel down-regulation. In addition, specific properties in RNs K currents were required to limit spike transmission frequency along the axon. The model showed how organized electroresponsive functions could emerge from the molecular complexity of PCs and showed that the axon is fundamental to complement ionic channel compartmentalization enabling action potential processing and transmission of specific spike patterns to DCN. PMID:25759640

  2. Contrastive Lexicology.

    ERIC Educational Resources Information Center

    Hartmann, R. R. K.

    This paper deals with the relation between etymologically related words in different languages. A survey is made of seven stages in the development of contrastive lexicology. These are: prelinguistic word studies, semantics, lexicography, translation, foreign language learning, bilingualism, and finally contrastive analysis. Concerning contrastive…

  3. Contrastive Analysis.

    ERIC Educational Resources Information Center

    James, Carl

    Contrastive analysis is viewed as an interlinguistic, bidirectional phenomenon which is concerned with both the form and function of language. As such, contrastive analysis must view language psycholinguistically and sociolinguistically as a system to be both described and acquired. Due to the need for a psychological component in the analysis,…

  4. Voltage contrast X-ray photoelectron spectroscopy reveals graphene-substrate interaction in graphene devices fabricated on the C- and Si- faces of SiC

    SciTech Connect

    Aydogan, Pinar; Suzer, Sefik; Arslan, Engin; Cakmakyapan, Semih; Ozbay, Ekmel; Strupinski, Wlodek

    2015-09-21

    We report on an X-ray photoelectron spectroscopy (XPS) study of two graphene based devices that were analyzed by imposing a significant current under +3 V bias. The devices were fabricated as graphene layers(s) on hexagonal SiC substrates, either on the C- or Si-terminated faces. Position dependent potential distributions (IR-drop), as measured by variations in the binding energy of a C1s peak are observed to be sporadic for the C-face graphene sample, but very smooth for the Si-face one, although the latter is less conductive. We attribute these sporadic variations in the C-face device to the incomplete electrical decoupling between the graphene layer(s) with the underlying buffer and/or substrate layers. Variations in the Si2p and O1s peaks of the underlayer(s) shed further light into the electrical interaction between graphene and other layers. Since the potential variations are amplified only under applied bias (voltage-contrast), our methodology gives unique, chemically specific electrical information that is difficult to obtain by other techniques.

  5. Assessing Precipitation Isotope Variations during Atmospheric River Events to Reveal Dominant Atmospheric/Hydrologic Processes

    NASA Astrophysics Data System (ADS)

    McCabe-Glynn, S. E.; Johnson, K. R.; Yoshimura, K.; Buenning, N. H.; Welker, J. M.

    2015-12-01

    Extreme precipitation events across the Western US commonly associated with atmospheric rivers (ARs), whereby extensive fluxes of moisture are transported from the subtropics, can result in major damage and are projected by most climate models to increase in frequency and severity. However, they are difficult to project beyond ~ten days and the location of landfall and topographically induced precipitation is even more uncertain. Water isotopes, often used to reconstruct past rainfall variability, are useful natural tracers of atmospheric hydrologic processes. Because of the typical tropical and sub-tropical origins, ARs can carry unique water isotope (δ18O and δ2H, d-excess) signatures that can be utilized to provide source and process information that can lead to improving AR predictions. Recent analysis of the top 10 weekly precipitation total samples from Sequoia National Park, CA, of which 9 contained AR events, shows a high variability in the isotopic values. NOAA Hysplit back trajectory analyses reveals a variety of trajectories and varying latitudinal source regions contributed to moisture delivered to this site, which may explain part of the high variability (δ2H = -150.03 to -49.52 ‰, δ18O = -19.27 to -7.20 ‰, d-excess = 4.1 to 25.8). Here we examine the top precipitation totals occurring during AR events and the associated isotopic composition of precipitation samples from several sites across the Western US. We utilize IsoGSM, an isotope-enabled atmospheric general circulation model, to characterize the hydrologic processes and physical dynamics contributing to the observed isotopic variations. We investigate isotopic influences from moisture source location, AR speed, condensation height, and associated temperature. We explore the dominant controls on spatial and temporal variations of the isotopic composition of AR precipitation which highlights different physical processes for different AR events.

  6. Neogene depositional processes on the Texas-Louisiana continental slope revealed by high-resolution seismic studies

    SciTech Connect

    Damuth, J.E.; Olson, H.C. ); Twichell, D.C. )

    1991-03-01

    Systematic interpretation of high-resolution seismic profiles (3.5-10 kHz echograms and 100 Hz air gun) from the continental slope and rise of offshore Texas and Louisiana from the shelf break across the highly deformed zone of salt diapirs, folds, and intraslope basins to water depths greater than 3,500 m seaward of the Sigsbee Escarpment reveals the geometries, scales, distributions, and depositional processes of deep-water deposits in this region. The 3.5-10 kHz data indicate that redistribution of sediment by mass-transport processes a ubiquitous, and a wide spectrum of slumps, slide blocks, and debris flows are observed from small, isolated deposits in intraslope basins to large, complex deposits covering hundreds of kilometers. The reflection character (echo character) of many intraslope basin and canyon floors indicates sand-rich deposits; however, aggradational leveed-channel systems, characteristic of deep-sea fans, are not observed in the steep-walled intraslope basins. In contrast, some large submarine-fan channel-levee complexes do extend seaward from the mouths of these large canyons and basins at the base of the Sigsbee Escarpment to form one or more large deep-sea fans on the continental rise. Apparently, large quantities of terrigenous sediments can be transported by turbidity flows through the intricate network of rugged intraslope basins and canyons to feed these fans. Evidence of sediment redistribution by bottom currents (contour currents) is also observed in the form of sediment waves and drift deposits across a large area of the continental rise seaward of the southeastern base of the Sigsbee Escarpment.

  7. Mixing behavior and bioavailability of dissolved organic matter in two contrasting subterranean estuaries as revealed by fluorescence spectroscopy and parallel factor analysis

    NASA Astrophysics Data System (ADS)

    Yang, Liyang; Chen, Chen-Tung Arthur; Hong, Huasheng; Chang, Yu-Chang; Lui, Hon-Kit

    2015-12-01

    Groundwater discharge represents a potentially important source of dissolved organic matter (DOM) for the coastal ocean, but the mixing behavior and bioavailability of DOM in subterranean estuaries are poorly known. This study examined the concentration, chemical composition and bioavailability of DOM in two subterranean estuaries of southwest Taiwan with contrasting pollution degrees, using dissolved organic carbon (DOC) and excitation emission matrix fluorescence spectroscopy-parallel factor analysis. The DOC and fluorescent components were non-conservative and very dynamic in both subterranean estuaries. In the less-polluted Longquanwan (LQW) subterranean estuary, the levels of DOC and fluorescence components were generally low, and the humic-like fluorescent components received significant additions during mixing between freshwater and seawater. In the highly-polluted Sizihwan (SZW) subterranean estuary, the DOC and fluorescence intensities were high in the freshwater end but were subject to active additions and removals during estuarine mixing. The humification index (HIX) and the autochthonous index (BIX) were 1.0-13.4 and 0.73-1.01 for all groundwater samples. The HIX were elevated in the low-to-mid salinity zone of the LQW subterranean estuary in March and increased with salinity in the SZW subterranean estuary. The BIX decreased with salinity in both subterranean estuaries. These results suggested that subterranean estuaries are important zones where both the level and the chemical composition of groundwater DOM change notably. In addition, the DOC, fluorescent intensities, HIX and BIX in groundwater showed limited changes in microbial incubation experiments (≤20%) in 28 days, which suggested low bioavailability of groundwater DOM.

  8. Analysis of Phosphorus Use Efficiency Traits in Coffea Genotypes Reveals Coffea arabica and Coffea canephora Have Contrasting Phosphorus Uptake and Utilization Efficiencies

    PubMed Central

    Neto, Ana P.; Favarin, José L.; Hammond, John P.; Tezotto, Tiago; Couto, Hilton T. Z.

    2016-01-01

    Background and Aims: Phosphate (Pi) is one of the most limiting nutrients for agricultural production in Brazilian soils due to low soil Pi concentrations and rapid fixation of fertilizer Pi by adsorption to oxidic minerals and/or precipitation by iron and aluminum ions. The objectives of this study were to quantify phosphorus (P) uptake and use efficiency in cultivars of the species Coffea arabica L. and Coffea canephora L., and group them in terms of efficiency and response to Pi availability. Methods: Plants of 21 cultivars of C. arabica and four cultivars of C. canephora were grown under contrasting soil Pi availabilities. Biomass accumulation, tissue P concentration and accumulation and efficiency indices for P use were measured. Key Results: Coffee plant growth was significantly reduced under low Pi availability, and P concentration was higher in cultivars of C. canephora. The young leaves accumulated more P than any other tissue. The cultivars of C. canephora had a higher root/shoot ratio and were significantly more efficient in P uptake, while the cultivars of C. arabica were more efficient in P utilization. Agronomic P use efficiency varied among coffee cultivars and E16 Shoa, E22 Sidamo, Iêmen and Acaiá cultivars were classified as the most efficient and responsive to Pi supply. A positive correlation between P uptake efficiency and root to shoot ratio was observed across all cultivars at low Pi supply. These data identify Coffea genotypes better adapted to low soil Pi availabilities, and the traits that contribute to improved P uptake and use efficiency. These data could be used to select current genotypes with improved P uptake or utilization efficiencies for use on soils with low Pi availability and also provide potential breeding material and targets for breeding new cultivars better adapted to the low Pi status of Brazilian soils. This could ultimately reduce the use of Pi fertilizers in tropical soils, and contribute to more sustainable coffee

  9. Nanoscale assembly processes revealed in the nacroprismatic transition zone of Pinna nobilis mollusc shells

    NASA Astrophysics Data System (ADS)

    Hovden, Robert; Wolf, Stephan E.; Holtz, Megan E.; Marin, Frédéric; Muller, David A.; Estroff, Lara A.

    2015-12-01

    Intricate biomineralization processes in molluscs engineer hierarchical structures with meso-, nano- and atomic architectures that give the final composite material exceptional mechanical strength and optical iridescence on the macroscale. This multiscale biological assembly inspires new synthetic routes to complex materials. Our investigation of the prism-nacre interface reveals nanoscale details governing the onset of nacre formation using high-resolution scanning transmission electron microscopy. A wedge-polishing technique provides unprecedented, large-area specimens required to span the entire interface. Within this region, we find a transition from nanofibrillar aggregation to irregular early-nacre layers, to well-ordered mature nacre suggesting the assembly process is driven by aggregation of nanoparticles (~50-80 nm) within an organic matrix that arrange in fibre-like polycrystalline configurations. The particle number increases successively and, when critical packing is reached, they merge into early-nacre platelets. These results give new insights into nacre formation and particle-accretion mechanisms that may be common to many calcareous biominerals.

  10. Nanoscale assembly processes revealed in the nacroprismatic transition zone of Pinna nobilis mollusc shells.

    PubMed

    Hovden, Robert; Wolf, Stephan E; Holtz, Megan E; Marin, Frédéric; Muller, David A; Estroff, Lara A

    2015-12-03

    Intricate biomineralization processes in molluscs engineer hierarchical structures with meso-, nano- and atomic architectures that give the final composite material exceptional mechanical strength and optical iridescence on the macroscale. This multiscale biological assembly inspires new synthetic routes to complex materials. Our investigation of the prism-nacre interface reveals nanoscale details governing the onset of nacre formation using high-resolution scanning transmission electron microscopy. A wedge-polishing technique provides unprecedented, large-area specimens required to span the entire interface. Within this region, we find a transition from nanofibrillar aggregation to irregular early-nacre layers, to well-ordered mature nacre suggesting the assembly process is driven by aggregation of nanoparticles (∼50-80 nm) within an organic matrix that arrange in fibre-like polycrystalline configurations. The particle number increases successively and, when critical packing is reached, they merge into early-nacre platelets. These results give new insights into nacre formation and particle-accretion mechanisms that may be common to many calcareous biominerals.

  11. Nanoscale assembly processes revealed in the nacroprismatic transition zone of Pinna nobilis mollusc shells

    PubMed Central

    Hovden, Robert; Wolf, Stephan E.; Holtz, Megan E.; Marin, Frédéric; Muller, David A.; Estroff, Lara A.

    2015-01-01

    Intricate biomineralization processes in molluscs engineer hierarchical structures with meso-, nano- and atomic architectures that give the final composite material exceptional mechanical strength and optical iridescence on the macroscale. This multiscale biological assembly inspires new synthetic routes to complex materials. Our investigation of the prism–nacre interface reveals nanoscale details governing the onset of nacre formation using high-resolution scanning transmission electron microscopy. A wedge-polishing technique provides unprecedented, large-area specimens required to span the entire interface. Within this region, we find a transition from nanofibrillar aggregation to irregular early-nacre layers, to well-ordered mature nacre suggesting the assembly process is driven by aggregation of nanoparticles (∼50–80 nm) within an organic matrix that arrange in fibre-like polycrystalline configurations. The particle number increases successively and, when critical packing is reached, they merge into early-nacre platelets. These results give new insights into nacre formation and particle-accretion mechanisms that may be common to many calcareous biominerals. PMID:26631940

  12. Diffusion Modelling Reveals the Decision Making Processes Underlying Negative Judgement Bias in Rats.

    PubMed

    Hales, Claire A; Robinson, Emma S J; Houghton, Conor J

    2016-01-01

    Human decision making is modified by emotional state. Rodents exhibit similar biases during interpretation of ambiguous cues that can be altered by affective state manipulations. In this study, the impact of negative affective state on judgement bias in rats was measured using an ambiguous-cue interpretation task. Acute treatment with an anxiogenic drug (FG7142), and chronic restraint stress and social isolation both induced a bias towards more negative interpretation of the ambiguous cue. The diffusion model was fit to behavioural data to allow further analysis of the underlying decision making processes. To uncover the way in which parameters vary together in relation to affective state manipulations, independent component analysis was conducted on rate of information accumulation and distances to decision threshold parameters for control data. Results from this analysis were applied to parameters from negative affective state manipulations. These projected components were compared to control components to reveal the changes in decision making processes that are due to affective state manipulations. Negative affective bias in rodents induced by either FG7142 or chronic stress is due to a combination of more negative interpretation of the ambiguous cue, reduced anticipation of the high reward and increased anticipation of the low reward.

  13. Crystal structure of human CD1e reveals a groove suited for lipid-exchange processes.

    PubMed

    Garcia-Alles, Luis F; Giacometti, Gaelle; Versluis, Cees; Maveyraud, Laurent; de Paepe, Diane; Guiard, Julie; Tranier, Samuel; Gilleron, Martine; Prandi, Jacques; Hanau, Daniel; Heck, Albert J R; Mori, Lucia; De Libero, Gennaro; Puzo, Germain; Mourey, Lionel; de la Salle, Henri

    2011-08-09

    CD1e is the only human CD1 protein existing in soluble form in the late endosomes of dendritic cells, where it facilitates the processing of glycolipid antigens that are ultimately recognized by CD1b-restricted T cells. The precise function of CD1e remains undefined, thus impeding efforts to predict the participation of this protein in the presentation of other antigens. To gain insight into its function, we determined the crystal structure of recombinant CD1e expressed in human cells at 2.90-Å resolution. The structure revealed a groove less intricate than in other CD1 proteins, with a significantly wider portal characterized by a 2 Å-larger spacing between the α1 and α2 helices. No electron density corresponding to endogenous ligands was detected within the groove, despite the presence of ligands unequivocally established by native mass spectrometry in recombinant CD1e. Our structural data indicate that the water-exposed CD1e groove could ensure the establishment of loose contacts with lipids. In agreement with this possibility, lipid association and dissociation processes were found to be considerably faster with CD1e than with CD1b. Moreover, CD1e was found to mediate in vitro the transfer of lipids to CD1b and the displacement of lipids from stable CD1b-antigen complexes. Altogether, these data support that CD1e could have evolved to mediate lipid-exchange/editing processes with CD1b and point to a pathway whereby the repertoire of lipid antigens presented by human dendritic cells might be expanded.

  14. The development of control processes supporting source memory discrimination as revealed by event-related potentials.

    PubMed

    de Chastelaine, Marianne; Friedman, David; Cycowicz, Yael M

    2007-08-01

    Improvement in source memory performance throughout childhood is thought to be mediated by the development of executive control. As postretrieval control processes may be better time-locked to the recognition response rather than the retrieval cue, the development of processes underlying source memory was investigated with both stimulus- and response-locked event-related potentials (ERPs). These were recorded in children, adolescents, and adults during a recognition memory exclusion task. Green- and red-outlined pictures were studied, but were tested in black outline. The test requirement was to endorse old items shown in one study color ("targets") and to reject new items along with old items shown in the alternative study color ("nontargets"). Source memory improved with age. All age groups retrieved target and nontarget memories as reflected by reliable parietal episodic memory (EM) effects, a stimulus-locked ERP correlate of recollection. Response-locked ERPs to targets and nontargets diverged in all groups prior to the response, although this occurred at an increasingly earlier time point with age. We suggest these findings reflect the implementation of attentional control mechanisms to enhance target memories and facilitate response selection with the greatest and least success, respectively, in adults and children. In adults only, response-locked ERPs revealed an early-onsetting parietal negativity for nontargets, but not for targets. This was suggested to reflect adults' ability to consistently inhibit prepotent target responses for nontargets. The findings support the notion that the development of source memory relies on the maturation of control processes that serve to enhance accurate selection of task-relevant memories.

  15. Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes

    SciTech Connect

    Stockel, Jana; Welsh, Eric A.; Liberton, Michelle L.; Kunnavakkam, Rangesh V.; Aurora, Rajeev; Pakrasi, Himadri B.

    2008-04-22

    Cyanobacteria are oxygenic photosynthetic organisms, and the only prokaryotes known to have a circadian cycle. Unicellular diazotrophic cyanobacteria such as Cyanothece 51142 can fix atmospheric nitrogen, a process exquisitely sensitive to oxygen. Thus, the intracellular environment of Cyanothece oscillates between aerobic and anaerobic conditions during a day-night cycle. This is accomplished by temporal separation of two processes: photosynthesis during the day, and nitrogen fixation at night. While previous studies have examined periodic changes transcript levels for a limited number of genes in Cyanothece and other unicellular diazotrophic cyanobacteria, a comprehensive study of transcriptional activity in a nitrogen-fixing cyanobacterium is necessary to understand the impact of the temporal separation of photosynthesis and nitrogen fixation on global gene regulation and cellular metabolism. We have examined the expression patterns of nearly 5000 genes in Cyanothece 51142 during two consecutive diurnal periods. We found that ~30% of these genes exhibited robust oscillating expression profiles. Interestingly, this set included genes for almost all central metabolic processes in Cyanothece. A transcriptional network of all genes with significantly oscillating transcript levels revealed that the majority of genes in numerous individual pathways, such as glycolysis, pentose phosphate pathway and glycogen metabolism, were co-regulated and maximally expressed at distinct phases during the diurnal cycle. Our analyses suggest that the demands of nitrogen fixation greatly influence major metabolic activities inside Cyanothece cells and thus drive various cellular activities. These studies provide a comprehensive picture of how a physiologically relevant diurnal light-dark cycle influences the metabolism in a photosynthetic bacterium

  16. Five years investigation of female and male genotypes in Périgord black truffle (Tuber melanosporum Vittad.) revealed contrasted reproduction strategies.

    PubMed

    De la Varga, Herminia; Le Tacon, François; Lagoguet, Mélanie; Todesco, Flora; Varga, Torda; Miquel, Igor; Barry-Etienne, Dominique; Robin, Christophe; Halkett, Fabien; Martin, Francis; Murat, Claude

    2017-03-29

    The Périgord black truffle (Tuber melanosporum Vittad.) is a heterothallic ascomycete that establishes ectomycorrhizal symbiosis with trees and shrubs. Small-scale genetic structures of female genotypes in truffle orchards are known, but it has not yet been studied in male genotypes. In this study, our aim was to characterize the small-scale genetic structure of both male and female genotypes over five years in an orchard to better understand the T. melanosporum sexual reproduction strategy, male genotype dynamics, and origins. Two-hundred forty-one ascocarps, 475 ectomycorrhizas, and 20 soil cores were harvested and genotyped using microsatellites and mating type genes. Isolation by distance analysis revealed pronounced small-scale genetic structures for both female and male genotypes. The genotypic diversity was higher for male than female genotypes with numerous small size genotypes suggesting an important turnover due to ascospore recruitment. Larger and perennial female and male genotypes were also detected. Only three genotypes (1.5%) were found as both female and male genotypes (hermaphrodites) while most were detected only as female or male genotype (dioecy). Our results suggest that germinating ascospores act as male genotypes, but we also proposed that soil mycelium could be a reservoir of male genotypes. This article is protected by copyright. All rights reserved.

  17. Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene

    PubMed Central

    Cernadas, Raul A.; Doyle, Erin L.; Niño-Liu, David O.; Wilkins, Katherine E.; Bancroft, Timothy; Wang, Li; Schmidt, Clarice L.; Caldo, Rico; Yang, Bing; White, Frank F.; Nettleton, Dan; Wise, Roger P.; Bogdanove, Adam J.

    2014-01-01

    Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s) via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S) genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting. PMID:24586171

  18. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.

    PubMed

    Cernadas, Raul A; Doyle, Erin L; Niño-Liu, David O; Wilkins, Katherine E; Bancroft, Timothy; Wang, Li; Schmidt, Clarice L; Caldo, Rico; Yang, Bing; White, Frank F; Nettleton, Dan; Wise, Roger P; Bogdanove, Adam J

    2014-02-01

    Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s) via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S) genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting.

  19. Fault zone hydrogeologic properties and processes revealed by borehole temperature monitoring

    NASA Astrophysics Data System (ADS)

    Fulton, P. M.; Brodsky, E. E.

    2015-12-01

    High-resolution borehole temperature monitoring can provide valuable insight into the hydrogeologic structure of fault zones and transient processes that affect fault zone stability. Here we report on results from a subseafloor temperature observatory within the Japan Trench plate boundary fault. In our efforts to interpret this unusual dataset, we have developed several new methods for probing hydrogeologic properties and processes. We illustrate how spatial variations in the thermal recovery of the borehole after drilling and other spectral characteristics provide a measure of the subsurface permeability architecture. More permeable zones allow for greater infiltration of cool drilling fluids, are more greatly thermally disturbed, and take longer to recover. The results from the JFAST (Japan Trench Fast Drilling Project) observatory are consistent with geophysical logs, core data, and other hydrologic observations and suggest a permeable damage zone consisting of steeply dipping faults and fractures overlays a low-permeability clay-rich plate boundary fault. Using high-resolution time series data, we have also developed methods to map out when and where fluid advection occurs in the subsurface over time. In the JFAST data, these techniques reveal dozens of transient earthquake-driven fluid pulses that are spatially correlated and consistently located around inferred permeable areas of the fault damage zone. These observations are suspected to reflect transient fluid flow driven by pore pressure changes in response to dynamic and/or static stresses associated with nearby earthquakes. This newly recognized hydrologic phenomenon has implications for understanding subduction zone heat and chemical transport as well as the redistribution of pore fluid pressure which influences fault stability and can trigger other earthquakes.

  20. Proteomic Profile of Cryptococcus neoformans Biofilm Reveals Changes in Metabolic Processes

    PubMed Central

    2015-01-01

    Cryptococcus neoformans, a pathogenic yeast, causes meningoencephalitis, especially in immunocompromised patients, leading in some cases to death. Microbes in biofilms can cause persistent infections, which are harder to treat. Cryptococcal biofilms are becoming common due to the growing use of brain valves and other medical devices. Using shotgun proteomics we determine the differences in protein abundance between biofilm and planktonic cells. Applying bioinformatic tools, we also evaluated the metabolic pathways involved in biofilm maintenance and protein interactions. Our proteomic data suggest general changes in metabolism, protein turnover, and global stress responses. Biofilm cells show an increase in proteins related to oxidation–reduction, proteolysis, and response to stress and a reduction in proteins related to metabolic process, transport, and translation. An increase in pyruvate-utilizing enzymes was detected, suggesting a shift from the TCA cycle to fermentation-derived energy acquisition. Additionally, we assign putative roles to 33 proteins previously categorized as hypothetical. Many changes in metabolic enzymes were identified in studies of bacterial biofilm, potentially revealing a conserved strategy in biofilm lifestyle. PMID:24467693

  1. Proteomic profile of Cryptococcus neoformans biofilm reveals changes in metabolic processes.

    PubMed

    Santi, Lucélia; Beys-da-Silva, Walter O; Berger, Markus; Calzolari, Diego; Guimarães, Jorge A; Moresco, James J; Yates, John R

    2014-03-07

    Cryptococcus neoformans, a pathogenic yeast, causes meningoencephalitis, especially in immunocompromised patients, leading in some cases to death. Microbes in biofilms can cause persistent infections, which are harder to treat. Cryptococcal biofilms are becoming common due to the growing use of brain valves and other medical devices. Using shotgun proteomics we determine the differences in protein abundance between biofilm and planktonic cells. Applying bioinformatic tools, we also evaluated the metabolic pathways involved in biofilm maintenance and protein interactions. Our proteomic data suggest general changes in metabolism, protein turnover, and global stress responses. Biofilm cells show an increase in proteins related to oxidation-reduction, proteolysis, and response to stress and a reduction in proteins related to metabolic process, transport, and translation. An increase in pyruvate-utilizing enzymes was detected, suggesting a shift from the TCA cycle to fermentation-derived energy acquisition. Additionally, we assign putative roles to 33 proteins previously categorized as hypothetical. Many changes in metabolic enzymes were identified in studies of bacterial biofilm, potentially revealing a conserved strategy in biofilm lifestyle.

  2. EEG reveals an early influence of social conformity on visual processing in group pressure situations.

    PubMed

    Trautmann-Lengsfeld, Sina Alexa; Herrmann, Christoph Siegfried

    2013-01-01

    Humans are social beings and often have to perceive and perform within groups. In conflict situations, this puts them under pressure to either adhere to the group opinion or to risk controversy with the group. Psychological experiments have demonstrated that study participants adapt to erroneous group opinions in visual perception tasks, which they can easily solve correctly when performing on their own. Until this point, however, it is unclear whether this phenomenon of social conformity influences early stages of perception that might not even reach awareness or later stages of conscious decision-making. Using electroencephalography, this study has revealed that social conformity to the wrong group opinion resulted in a decrease of the posterior-lateral P1 in line with a decrease of the later centro-parietal P3. These results suggest that group pressure situations impact early unconscious visual perceptual processing, which results in a later diminished stimulus discrimination and an adaptation even to the wrong group opinion. These findings might have important implications for understanding social behavior in group settings and are discussed within the framework of social influence on eyewitness testimony.

  3. Awake fMRI reveals a specialized region in dog temporal cortex for face processing

    PubMed Central

    Dilks, Daniel D.; Cook, Peter; Weiller, Samuel K.; Berns, Helen P.; Spivak, Mark

    2015-01-01

    Recent behavioral evidence suggests that dogs, like humans and monkeys, are capable of visual face recognition. But do dogs also exhibit specialized cortical face regions similar to humans and monkeys? Using functional magnetic resonance imaging (fMRI) in six dogs trained to remain motionless during scanning without restraint or sedation, we found a region in the canine temporal lobe that responded significantly more to movies of human faces than to movies of everyday objects. Next, using a new stimulus set to investigate face selectivity in this predefined candidate dog face area, we found that this region responded similarly to images of human faces and dog faces, yet significantly more to both human and dog faces than to images of objects. Such face selectivity was not found in dog primary visual cortex. Taken together, these findings: (1) provide the first evidence for a face-selective region in the temporal cortex of dogs, which cannot be explained by simple low-level visual feature extraction; (2) reveal that neural machinery dedicated to face processing is not unique to primates; and (3) may help explain dogs’ exquisite sensitivity to human social cues. PMID:26290784

  4. Neuter is not common in Dutch: eye movements reveal asymmetrical gender processing.

    PubMed

    Loerts, Hanneke; Wieling, Martijn; Schmid, Monika S

    2013-12-01

    Native speakers of languages with transparent gender systems can use gender cues to anticipate upcoming words. To examine whether this also holds true for a non-transparent two-way gender system, i.e. Dutch, eye movements were monitored as participants followed spoken instructions to click on one of four displayed items on a screen (e.g., Klik op [Formula: see text] rode appel [Formula: see text], 'Click on the[Formula: see text] red apple[Formula: see text]'). The items contained the target, a colour- and/or gender-matching competitor, and two unrelated distractors. A mixed-effects regression analysis revealed that the presence of a colour-matching and/or gender-matching competitor significantly slowed the process of finding the target. The gender effect, however, was only observed for common nouns, reflecting the fact that neuter gender-marking cannot disambiguate as all Dutch nouns become neuter when used as diminutives. The gender effect for common nouns occurred before noun onset, suggesting that gender information is, at least partially, activated automatically before encountering the noun.

  5. Contrast lipocryolysis

    PubMed Central

    Pinto, Hernán; Melamed, Graciela

    2014-01-01

    Alternative crystal structures are possible for all lipids and each different crystal structure is called a polymorphic form. Inter-conversion between polymorphisms would imply the possibility of leaning crystal formation toward the most effective polymorphism for adipocyte destruction. Food industry has been tempering lipids for decades. Tempering technology applied to lipocryolysis gave birth to “contrast lipocryolysis”, which involves pre- and post-lipocryolysis fat layer heating as part of a specific tempering protocol. In this study, we evaluated the skinfold thickness of 10 subjects after a single contrast lipocryolysis session and witnessed important and fast reductions. PMID:25068088

  6. Harmonic and frequency modulated ultrasonic vocalizations reveal differences in conditioned and unconditioned reward processing.

    PubMed

    Garcia, Erik J; McCowan, Talus J; Cain, Mary E

    2015-01-01

    Novelty and sensation seeking (NSS) and ultrasonic vocalizations (USVs) are both used as measures of individual differences in reward sensitivity in rodent models. High responders in the inescapable novelty screen have a greater response to low doses of amphetamine and acquire self-administration more rapidly, while the novelty place preference screen is positively correlated with compulsive drug seeking. These screens are uncorrelated and implicated in separate drug abuse models. 50 kHz USVs measure affective state in rats and are evoked by positive stimuli. NSS and USVs are each implicated in drug response, self-administration, and reveal differences in individual behavior, yet their relationship with each other is not understood. The present study screened rats for their response to novelty and measured USVs of all call types in response to heterospecific play to determine the relationships between these individual difference traits. Generally, we hypothesized that 50k Hz USVs would be positively correlated with the NPP screen, and that 22 kHz would be positively correlated with the IEN screen. Results indicate none of the screens were correlated indicating they are measuring different individual difference traits. However, examination of the subtypes of USVs indicated harmonic USVs and the novelty place preference were positively correlated. Harmonic 50 kHz USVs increased in response to reward associated context, suggesting animals conditioned to the heterospecific tickle arena and anticipated rewarding stimuli, while FM only increased in response to tickling. USV subtypes can be used to elucidate differences in attribution of incentive value across conditioned stimuli and receipt of rewarding stimuli. These data provide strong support that harmonic and FM USVs can be used to understand reward processing in addition to NSS.

  7. Contrasting hydrological processes of meteoric water incursion during magmatic-hydrothermal ore deposition: An oxygen isotope study by ion microprobe

    NASA Astrophysics Data System (ADS)

    Fekete, Szandra; Weis, Philipp; Driesner, Thomas; Bouvier, Anne-Sophie; Baumgartner, Lukas; Heinrich, Christoph A.

    2016-10-01

    Meteoric water convection has long been recognized as an efficient means to cool magmatic intrusions in the Earth's upper crust. This interplay between magmatic and hydrothermal activity thus exerts a primary control on the structure and evolution of volcanic, geothermal and ore-forming systems. Incursion of meteoric water into magmatic-hydrothermal systems has been linked to tin ore deposition in granitic plutons. In contrast, evidence from porphyry copper ore deposits suggests that crystallizing subvolcanic magma bodies are only affected by meteoric water incursion in peripheral zones and during late post-ore stages. We apply high-resolution secondary ion mass spectrometry (SIMS) to analyze oxygen isotope ratios of individual growth zones in vein quartz crystals, imaged by cathodo-luminescence microscopy (SEM-CL). Existing microthermometric information from fluid inclusions enables calculation of the oxygen isotope composition of the fluid from which the quartz precipitated, constraining the relative timing of meteoric water input into these two different settings. Our results confirm that incursion of meteoric water directly contributes to cooling of shallow granitic plutons and plays a key role in concurrent tin mineralization. By contrast, data from two porphyry copper deposits suggest that downward circulating meteoric water is counteracted by up-flowing hot magmatic fluids. Our data show that porphyry copper ore deposition occurs close to a magmatic-meteoric water interface, rather than in a purely magmatic fluid plume, confirming recent hydrological modeling. On a larger scale, the expulsion of magmatic fluids against the meteoric water interface can shield plutons from rapid convective cooling, which may aid the build-up of large magma chambers required for porphyry copper ore formation.

  8. Multiscale Processes of Hurricane Sandy (2012) as Revealed by the CAMVis-MAP

    NASA Astrophysics Data System (ADS)

    Shen, B.; Li, J. F.; Cheung, S.

    2013-12-01

    filter period windows, the PEEMD achieves a speedup of over 100 times as compared to the original EEMD. The advanced GMM, 4D visualizations and PEEMD method are being used to examine the multiscale processes of Sandy and its environmental flows that may contribute to the extended lead-time predictability of Hurricane Sandy. Figure 1: Evolution of Hurricane Sandy (2012) as revealed by the advanced visualization.

  9. Disruption of Fixation Reveals Latent Sensorimotor Processes in the Superior Colliculus

    PubMed Central

    Gandhi, Neeraj J.

    2016-01-01

    Executive control of voluntary movements is a hallmark of the mammalian brain. In the gaze-control network, this function is thought to be mediated by a critical balance between neurons responsible for generating movements and those responsible for fixating or suppressing movements, but the nature of this balance between the relevant elements—saccade-generating and fixation-related neurons—remains unclear. Specifically, it has been debated whether the two functions are necessarily coupled (i.e., push-and-pull) or independently controlled. Here we show that behavioral perturbation of ongoing fixation with the trigeminal blink reflex in monkeys (Macaca mulatta) alters the effective balance between fixation and saccade-generating neurons in the superior colliculus (SC) and can lead to premature gaze shifts reminiscent of compromised inhibitory control. The shift in balance is primarily driven by an increase in the activity of visuomovement neurons in the caudal SC, and the extent to which fixation-related neurons in the rostral SC play a role seems to be linked to the animal's propensity to make microsaccades. The perturbation also reveals a hitherto unknown feature of sensorimotor integration: the presence of a hidden visual response in canonical movement neurons. These findings offer new insights into the latent functional interactions, or lack thereof, between components of the gaze-control network, suggesting that the perturbation technique used here may prove to be a useful tool for probing the neural mechanisms of movement generation in executive function and dysfunction. SIGNIFICANCE STATEMENT Eye movements are an integral part of how we explore the environment. Although we know a great deal about where sensorimotor transformations leading to saccadic eye movements are implemented in the brain, less is known about the functional interactions between neurons that maintain gaze fixation and neurons that program saccades. In this study, we used a novel

  10. Covert contrast in velar fronting: An acoustic and ultrasound study

    PubMed Central

    Byun, Tara McAllister; Buchwald, Adam; Mizoguchi, Ai

    2016-01-01

    There is growing evidence that speech sound acquisition is a gradual process, with instrumental measures frequently revealing covert contrast in errors perceived to involve phonemic substitution. Ultrasound imaging has the potential to expand our understanding of covert contrast by showing whether a child uses different tongue shapes while producing sounds that are perceived as neutralized. This study used an ultrasound measure (Dorsum Excursion Index) and acoustic measures (VOT and spectral moments of the burst) to investigate overt and covert contrast between velar and alveolar stops in child speech. Participants were two children who produced a perceptually overt velar-alveolar contrast and two children who neutralized the contrast via velar fronting. Both acoustic and ultrasound measures revealed significant differences between perceptually distinct velar and alveolar targets. One child with velar fronting demonstrated covert contrast in one acoustic and one ultrasound measure; the other showed no evidence of contrast. Clinical implications are discussed. PMID:26325303

  11. Power relations and contrasting conceptions of evidence in patient-involvement processes used to inform health funding decisions in Australia.

    PubMed

    Lopes, Edilene; Carter, Drew; Street, Jackie

    2015-06-01

    We collected and analysed views of key stakeholders on the processes used to involve patient organisations in health care funding decision making in Australia. We conducted 12 semi-structured interviews with patient organisation representatives and members of Advisory Committees that provide advice to the Australian Department of Health and employ Health Technology Assessment (HTA) as an evaluation framework. Using two theoretical frameworks, we analysed structural and contextual elements pertaining to the involvement processes. The findings reported in this article relate to interviewees' perspectives on contextual elements, analysed using a Foucauldian lens. These elements include: the perspectives of marginalised voices; the diversity of views on what ought to be considered valid evidence in a HTA setting; and the relationships between stakeholders, along with how these relationships impact on involvement processes and the outcomes of those processes. The findings demonstrate that the involvement processes currently used are deemed inadequate by both patient organisation representatives and Advisory Committee members, but for different reasons connected to how different stakeholders conceptualise evidence. Advisory Committee members viewed evidence as encompassing clinical outcomes and patient preferences, whereas patient organisation representatives tended to view evidence as encompassing aspects not directly related to a disease entity, such as the social and emotional aspects of patients' experiences in living with illness. Patient organisation representatives reported interacting with other stakeholders (especially industry) to increase the influence of their conception of evidence on decision making. The use of this strategy by interviewees illustrates how power struggles occur in government decision-making processes which involve both medical expertise and patients' accounts. Such struggles, and the power differentials they reflect, need to be considered

  12. Geologically Controlled Isotope-Time Patterns Reveal Early Differentiation and Crust Formation Processes

    NASA Astrophysics Data System (ADS)

    Bennett, V. C.; Nutman, A. P.

    2014-12-01

    The mechanisms of continental crust production and evolution in the early Earth remain controversial, as are questions of the relative roles of early differentiation versus subsequent tectonic procssing in creating Earth's chemical signatures. Here we present geologic observations integrated with whole rock major, trace element and Sm-Nd isotopic signatures and combined with U-Pb and Lu-Hf isotopic compositions of zircon populations from the same rocks, from the most extensive early rock record comprising the 3.9 Ga to 3.6 Ga terranes of southwest Greenland. These data reveal repeated patterns of formation of juvenile TTG crust and associated mafic and ultramafic rocks in convergent margin settings followed by formation of more evolved granites [1]. Our new zircon Lu-Hf data from rare 3.6-3.7 Ga tonalites within the Itsaq Gneiss Complex, obtained from single component, non-migmatitic gneisses with simple zircon populations, limited within sample Hf isotopic variability and accurate U-Pb ages, now document extraction of juvenile tonalites from a near chondritic mantle source between 3.9 Ga and 3.6 Ga. The more evolved, granitic rocks in each area show slightly negative initial ɛHf in accord with crustal reworking of the older (3.8-3.9 Ga) gniesses. There is no evidence for Hadean material in the sources of the granitoids. The Hf isotope-time patterns are consistent with juvenile crust production from a mantle source that experienced only modest amounts of prior crustal extraction. They are distinct from those predicted by reprocessing of an enriched Hadean mafic crust, as has been proposed for this region [2] and for the source of the Hadean Jack Hills zircons [3]. The well-documented, time decreasing, positive 142Nd anomalies [e.g., 4] from these rocks are further evidence of crustal derivation from a convecting mantle source, rather than reworking of an enriched mafic lithosphere. The 143Nd isotopic -time patterns are more complex, reflecting the interplay

  13. Impacts of climate and land use changes on the hydrological and erosion processes of two contrasting Mediterranean catchments.

    PubMed

    Serpa, D; Nunes, J P; Santos, J; Sampaio, E; Jacinto, R; Veiga, S; Lima, J C; Moreira, M; Corte-Real, J; Keizer, J J; Abrantes, N

    2015-12-15

    The impacts of climate and land use changes on streamflow and sediment export were evaluated for a humid (São Lourenço) and a dry (Guadalupe) Mediterranean catchment, using the SWAT model. SWAT was able to produce viable streamflow and sediment export simulations for both catchments, which provided a baseline for investigating climate and land use changes under the A1B and B1 emission scenarios for 2071-2100. Compared to the baseline scenario (1971-2000), climate change scenarios showed a decrease in annual rainfall for both catchments (humid: -12%; dry: -8%), together with strong increases in rainfall during winter. Land use changes were derived from a socio-economic storyline in which traditional agriculture is replaced by more profitable land uses (i.e. corn and commercial forestry at the humid site; sunflower at the dry site). Climate change projections showed a decrease in streamflow for both catchments, whereas sediment export decreased only for the São Lourenço catchment. Land use changes resulted in an increase in streamflow, but the erosive response differed between catchments. The combination of climate and land use change scenarios led to a reduction in streamflow for both catchments, suggesting a domain of the climatic response. As for sediments, contrasting results were observed for the humid (A1B: -29%; B1: -22%) and dry catchment (A1B: +222%; B1: +5%), which is mainly due to differences in the present-day and forecasted vegetation types. The results highlight the importance of climate-induced land-use change impacts, which could be similar to or more severe than the direct impacts of climate change alone.

  14. Factors influencing real time internal structural visualization and dynamic process monitoring in plants using synchrotron-based phase contrast X-ray imaging

    PubMed Central

    Karunakaran, Chithra; Lahlali, Rachid; Zhu, Ning; Webb, Adam M.; Schmidt, Marina; Fransishyn, Kyle; Belev, George; Wysokinski, Tomasz; Olson, Jeremy; Cooper, David M. L.; Hallin, Emil

    2015-01-01

    Minimally invasive investigation of plant parts (root, stem, leaves, and flower) has good potential to elucidate the dynamics of plant growth, morphology, physiology, and root-rhizosphere interactions. Laboratory based absorption X-ray imaging and computed tomography (CT) systems are extensively used for in situ feasibility studies of plants grown in natural and artificial soil. These techniques have challenges such as low contrast between soil pore space and roots, long X-ray imaging time, and low spatial resolution. In this study, the use of synchrotron (SR) based phase contrast X-ray imaging (PCI) has been demonstrated as a minimally invasive technique for imaging plants. Above ground plant parts and roots of 10 day old canola and wheat seedlings grown in sandy clay loam soil were successfully scanned and reconstructed. Results confirmed that SR-PCI can deliver good quality images to study dynamic and real time processes such as cavitation and water-refilling in plants. The advantages of SR-PCI, effect of X-ray energy, and effective pixel size to study plant samples have been demonstrated. The use of contrast agents to monitor physiological processes in plants was also investigated and discussed. PMID:26183486

  15. Factors influencing real time internal structural visualization and dynamic process monitoring in plants using synchrotron-based phase contrast X-ray imaging.

    PubMed

    Karunakaran, Chithra; Lahlali, Rachid; Zhu, Ning; Webb, Adam M; Schmidt, Marina; Fransishyn, Kyle; Belev, George; Wysokinski, Tomasz; Olson, Jeremy; Cooper, David M L; Hallin, Emil

    2015-07-17

    Minimally invasive investigation of plant parts (root, stem, leaves, and flower) has good potential to elucidate the dynamics of plant growth, morphology, physiology, and root-rhizosphere interactions. Laboratory based absorption X-ray imaging and computed tomography (CT) systems are extensively used for in situ feasibility studies of plants grown in natural and artificial soil. These techniques have challenges such as low contrast between soil pore space and roots, long X-ray imaging time, and low spatial resolution. In this study, the use of synchrotron (SR) based phase contrast X-ray imaging (PCI) has been demonstrated as a minimally invasive technique for imaging plants. Above ground plant parts and roots of 10 day old canola and wheat seedlings grown in sandy clay loam soil were successfully scanned and reconstructed. Results confirmed that SR-PCI can deliver good quality images to study dynamic and real time processes such as cavitation and water-refilling in plants. The advantages of SR-PCI, effect of X-ray energy, and effective pixel size to study plant samples have been demonstrated. The use of contrast agents to monitor physiological processes in plants was also investigated and discussed.

  16. Factors influencing real time internal structural visualization and dynamic process monitoring in plants using synchrotron-based phase contrast X-ray imaging

    NASA Astrophysics Data System (ADS)

    Karunakaran, Chithra; Lahlali, Rachid; Zhu, Ning; Webb, Adam M.; Schmidt, Marina; Fransishyn, Kyle; Belev, George; Wysokinski, Tomasz; Olson, Jeremy; Cooper, David M. L.; Hallin, Emil

    2015-07-01

    Minimally invasive investigation of plant parts (root, stem, leaves, and flower) has good potential to elucidate the dynamics of plant growth, morphology, physiology, and root-rhizosphere interactions. Laboratory based absorption X-ray imaging and computed tomography (CT) systems are extensively used for in situ feasibility studies of plants grown in natural and artificial soil. These techniques have challenges such as low contrast between soil pore space and roots, long X-ray imaging time, and low spatial resolution. In this study, the use of synchrotron (SR) based phase contrast X-ray imaging (PCI) has been demonstrated as a minimally invasive technique for imaging plants. Above ground plant parts and roots of 10 day old canola and wheat seedlings grown in sandy clay loam soil were successfully scanned and reconstructed. Results confirmed that SR-PCI can deliver good quality images to study dynamic and real time processes such as cavitation and water-refilling in plants. The advantages of SR-PCI, effect of X-ray energy, and effective pixel size to study plant samples have been demonstrated. The use of contrast agents to monitor physiological processes in plants was also investigated and discussed.

  17. Skin age testing criteria: characterization of human skin structures by 500 MHz MRI multiple contrast and image processing.

    PubMed

    Sharma, Rakesh

    2010-07-21

    Ex vivo magnetic resonance microimaging (MRM) image characteristics are reported in human skin samples in different age groups. Human excised skin samples were imaged using a custom coil placed inside a 500 MHz NMR imager for high-resolution microimaging. Skin MRI images were processed for characterization of different skin structures. Contiguous cross-sectional T1-weighted 3D spin echo MRI, T2-weighted 3D spin echo MRI and proton density images were compared with skin histopathology and NMR peaks. In all skin specimens, epidermis and dermis thickening and hair follicle size were measured using MRM. Optimized parameters TE and TR and multicontrast enhancement generated better MRI visibility of different skin components. Within high MR signal regions near to the custom coil, MRI images with short echo time were comparable with digitized histological sections for skin structures of the epidermis, dermis and hair follicles in 6 (67%) of the nine specimens. Skin % tissue composition, measurement of the epidermis, dermis, sebaceous gland and hair follicle size, and skin NMR peaks were signatures of skin type. The image processing determined the dimensionality of skin tissue components and skin typing. The ex vivo MRI images and histopathology of the skin may be used to measure the skin structure and skin NMR peaks with image processing may be a tool for determining skin typing and skin composition.

  18. Skin age testing criteria: characterization of human skin structures by 500 MHz MRI multiple contrast and image processing

    NASA Astrophysics Data System (ADS)

    Sharma, Rakesh

    2010-07-01

    Ex vivo magnetic resonance microimaging (MRM) image characteristics are reported in human skin samples in different age groups. Human excised skin samples were imaged using a custom coil placed inside a 500 MHz NMR imager for high-resolution microimaging. Skin MRI images were processed for characterization of different skin structures. Contiguous cross-sectional T1-weighted 3D spin echo MRI, T2-weighted 3D spin echo MRI and proton density images were compared with skin histopathology and NMR peaks. In all skin specimens, epidermis and dermis thickening and hair follicle size were measured using MRM. Optimized parameters TE and TR and multicontrast enhancement generated better MRI visibility of different skin components. Within high MR signal regions near to the custom coil, MRI images with short echo time were comparable with digitized histological sections for skin structures of the epidermis, dermis and hair follicles in 6 (67%) of the nine specimens. Skin % tissue composition, measurement of the epidermis, dermis, sebaceous gland and hair follicle size, and skin NMR peaks were signatures of skin type. The image processing determined the dimensionality of skin tissue components and skin typing. The ex vivo MRI images and histopathology of the skin may be used to measure the skin structure and skin NMR peaks with image processing may be a tool for determining skin typing and skin composition.

  19. Contrast cystography.

    PubMed

    Essman, Stephanie C

    2005-02-01

    Cystography is a radiographic study performed to aid in evaluation of the urinary bladder for extramural, mural, or intraluminal lesions. These lesions may primarily involve the urinary bladder or may be an extension of disease from adjacent organs. Cystography is easy to perform with relatively few complications. Different types of cystography (positive versus negative contrast) may be used depending on the type of information that the clinician hopes to obtain. Although a valuable technique, it is important to correlate the findings on cystography with other clinical information to arrive at the final diagnosis.

  20. Microbial community in anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454 pyrosequencing analysis.

    PubMed

    Ning, Xinqiang; Qiao, Wenwen; Zhang, Lei; Gao, Xu

    2014-12-01

    Modification of the anoxic-oxic (AO) process by inserting a sludge holding tank (SHT) into the sludge return line forms an anoxic-oxic-settling-anaerobic (A+OSA) process that can achieve a 48.98% sludge reduction rate. The 454 pyrosequencing method was used to obtain the microbial communities of the AO and A+OSA processes. Results showed that the microbial community structures of the 2 processes were different as a result of the SHT insertion. Bacteria assigned to the phyla Proteobacteria and Bacteroidetes commonly existed and dominated the microbial populations of the 2 processes. However, the relative abundance of these populations shifted in the presence of SHT. The relative abundance of Proteobacteria decreased during the A+OSA process. A specific comparison at the class level showed that Sphingobacteria was enriched in the A+OSA process. The result suggested that the fermentative bacteria Sphingobacteria may have key functions in reducing the sludge from the A+OSA process. Uncultured Nitrosomonadaceae gradually became the dominant ammonia-oxidizing bacteria, and the nitrite-oxidizing bacterium Nitrospira was enriched in the A+OSA process. Both occurrences were favorable for stabilized nitrogen removal. The known denitrifying species in the A+OSA process were similar to those in the AO process; however, their relative abundance also decreased.

  1. Experience-dependent hemispheric specialization of letters and numbers is revealed in early visual processing.

    PubMed

    Park, Joonkoo; Chiang, Crystal; Brannon, Elizabeth M; Woldorff, Marty G

    2014-10-01

    Recent fMRI research has demonstrated that letters and numbers are preferentially processed in distinct regions and hemispheres in the visual cortex. In particular, the left visual cortex preferentially processes letters compared with numbers, whereas the right visual cortex preferentially processes numbers compared with letters. Because letters and numbers are cultural inventions and are otherwise physically arbitrary, such a double dissociation is strong evidence for experiential effects on neural architecture. Here, we use the high temporal resolution of ERPs to investigate the temporal dynamics of the neural dissociation between letters and numbers. We show that the divergence between ERP traces to letters and numbers emerges very early in processing. Letters evoked greater N1 waves (latencies 140-170 msec) than did numbers over left occipital channels, whereas numbers evoked greater N1s than letters over the right, suggesting letters and numbers are preferentially processed in opposite hemispheres early in visual encoding. Moreover, strings of letters, but not single letters, elicited greater P2 ERP waves (starting around 250 msec) than numbers did over the left hemisphere, suggesting that the visual cortex is tuned to selectively process combinations of letters, but not numbers, further along in the visual processing stream. Additionally, the processing of both of these culturally defined stimulus types differentiated from similar but unfamiliar visual stimulus forms (false fonts) even earlier in the processing stream (the P1 at 100 msec). These findings imply major cortical specialization processes within the visual system driven by experience with reading and mathematics.

  2. Event-Related Brain Potentials Reveal Anomalies in Temporal Processing of Faces in Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    McPartland, James; Dawson, Geraldine; Webb, Sara J.; Panagiotides, Heracles; Carver, Leslie J.

    2004-01-01

    Background: Individuals with autism exhibit impairments in face recognition, and neuroimaging studies have shown that individuals with autism exhibit abnormal patterns of brain activity during face processing. The current study examined the temporal characteristics of face processing in autism and their relation to behavior. Method: High-density…

  3. New Levels of Language Processing Complexity and Organization Revealed by Granger Causation

    PubMed Central

    Gow, David W.; Caplan, David N.

    2012-01-01

    Granger causation analysis of high spatiotemporal resolution reconstructions of brain activation offers a new window on the dynamic interactions between brain areas that support language processing. Premised on the observation that causes both precede and uniquely predict their effects, this approach provides an intuitive, model-free means of identifying directed causal interactions in the brain. It requires the analysis of all non-redundant potentially interacting signals, and has shown that even “early” processes such as speech perception involve interactions of many areas in a strikingly large network that extends well beyond traditional left hemisphere perisylvian cortex that play out over hundreds of milliseconds. In this paper we describe this technique and review several general findings that reframe the way we think about language processing and brain function in general. These include the extent and complexity of language processing networks, the central role of interactive processing dynamics, the role of processing hubs where the input from many distinct brain regions are integrated, and the degree to which task requirements and stimulus properties influence processing dynamics and inform our understanding of “language-specific” localized processes. PMID:23293611

  4. Mystery Montage: A Holistic, Visual, and Kinesthetic Process for Expanding Horizons and Revealing the Core of a Teaching Philosophy

    ERIC Educational Resources Information Center

    Ennis, Kim; Priebe, Carly; Sharipova, Mayya; West, Kim

    2012-01-01

    Revealing the core of a teaching philosophy is the key to a concise and meaningful philosophy statement, but it can be an elusive goal. This paper offers a visual, kinesthetic, and holistic process for expanding the horizons of self-reflection, self-analysis, and self-knowledge. Mystery montage, a variation of visual mapping, storyboarding, and…

  5. Contrasting effects of hemiparasites on ecosystem processes: can positive litter effects offset the negative effects of parasitism?

    PubMed Central

    Suding, Katharine N.

    2010-01-01

    Hemiparasites are known to influence community structure and ecosystem functioning, but the underlying mechanisms are not well studied. Variation in the impacts of hemiparasites on diversity and production could be due to the difference in the relative strength of two interacting pathways: direct negative effects of parasitism and positive effects on N availability via litter. Strong effects of parasitism should result in substantial changes in diversity and declines in productivity. Conversely, strong litter effects should result in minor changes in diversity and increased productivity. We conducted field-based surveys to determine the association of Castillejaoccidentalis with diversity and productivity in the alpine tundra. To examine litter effects, we compared the decomposition of Castilleja litter with litter of four other abundant plant species, and examined the decomposition of those four species when mixed with Castilleja. Castilleja was associated with minor changes in diversity but almost a twofold increase in productivity and greater foliar N in co-occurring species. Our decomposition trials suggest litter effects are due to both the rapid N loss of Castilleja litter and the effects of mixing Castilleja litter with co-occurring species. Castilleja produces litter that accelerates decomposition in the alpine tundra, which could accelerate the slow N cycle and boost productivity. We speculate that these positive effects of litter outweigh the effects of parasitism in nutrient-poor systems with long-lived hemiparasites. Determining the relative importance of parasitism and litter effects of this functional group is crucial to understand the strong but variable roles hemiparasites play in affecting community structure and ecosystem processes. PMID:20658151

  6. GREENER CHEMICAL PROCESS DESIGN ALTERNATIVES ARE REVEALED USING THE WASTE REDUCTION DECISION SUPPORT SYSTEM (WAR DSS)

    EPA Science Inventory

    The Waste Reduction Decision Support System (WAR DSS) is a Java-based software product providing comprehensive modeling of potential adverse environmental impacts (PEI) predicted to result from newly designed or redesigned chemical manufacturing processes. The purpose of this so...

  7. Dynamic information processing states revealed through neurocognitive models of object semantics

    PubMed Central

    Clarke, Alex

    2015-01-01

    Recognising objects relies on highly dynamic, interactive brain networks to process multiple aspects of object information. To fully understand how different forms of information about objects are represented and processed in the brain requires a neurocognitive account of visual object recognition that combines a detailed cognitive model of semantic knowledge with a neurobiological model of visual object processing. Here we ask how specific cognitive factors are instantiated in our mental processes and how they dynamically evolve over time. We suggest that coarse semantic information, based on generic shared semantic knowledge, is rapidly extracted from visual inputs and is sufficient to drive rapid category decisions. Subsequent recurrent neural activity between the anterior temporal lobe and posterior fusiform supports the formation of object-specific semantic representations – a conjunctive process primarily driven by the perirhinal cortex. These object-specific representations require the integration of shared and distinguishing object properties and support the unique recognition of objects. We conclude that a valuable way of understanding the cognitive activity of the brain is though testing the relationship between specific cognitive measures and dynamic neural activity. This kind of approach allows us to move towards uncovering the information processing states of the brain and how they evolve over time. PMID:25745632

  8. Temporal lobe abnormalities in semantic processing by criminal psychopaths as revealed by functional magnetic resonance imaging.

    PubMed

    Kiehl, Kent A; Smith, Andra M; Mendrek, Adrianna; Forster, Bruce B; Hare, Robert D; Liddle, Peter F

    2004-04-30

    We tested the hypothesis that psychopathy is associated with abnormalities in semantic processing of linguistic information. Functional magnetic resonance imaging (fMRI) was used to elucidate and characterize the neural architecture underlying lexico-semantic processes in criminal psychopathic individuals and in a group of matched control participants. Participants performed a lexical decision task in which blocks of linguistic stimuli alternated with a resting baseline condition. In each lexical decision block, the stimuli were either concrete words and pseudowords or abstract words and pseudowords. Consistent with our hypothesis, psychopathic individuals, relative to controls, showed poorer behavioral performance for processing abstract words. Analysis of the fMRI data for both groups indicated that processing of word stimuli, compared with the resting baseline condition, was associated with neural activation in bilateral fusiform gyrus, anterior cingulate, left middle temporal gyrus, right posterior superior temporal gyrus, and left and right inferior frontal gyrus. Analyses confirmed our prediction that psychopathic individuals would fail to show the appropriate neural differentiation between abstract and concrete stimuli in the right anterior temporal gyrus and surrounding cortex. The results are consistent with other studies of semantic processing in psychopathy and support the theory that psychopathy is associated with right hemisphere abnormalities for processing conceptually abstract material.

  9. Temporal lobe abnormalities in semantic processing by criminal psychopaths as revealed by functional magnetic resonance imaging.

    PubMed

    Kiehl, Kent A; Smith, Andra M; Mendrek, Adrianna; Forster, Bruce B; Hare, Robert D; Liddle, Peter F

    2004-01-15

    We tested the hypothesis that psychopathy is associated with abnormalities in semantic processing of linguistic information. Functional magnetic resonance imaging (fMRI) was used to elucidate and characterize the neural architecture underlying lexico-semantic processes in criminal psychopathic individuals and in a group of matched control participants. Participants performed a lexical decision task in which blocks of linguistic stimuli alternated with a resting baseline condition. In each lexical decision block, the stimuli were either concrete words and pseudowords or abstract words and pseudowords. Consistent with our hypothesis, psychopathic individuals, relative to controls, showed poorer behavioral performance for processing abstract words. Analysis of the fMRI data for both groups indicated that processing of word stimuli, compared with the resting baseline condition, was associated with neural activation in bilateral fusiform gyrus, anterior cingulate, left middle temporal gyrus, right posterior superior temporal gyrus, and left and right inferior frontal gyrus. Analyses confirmed our prediction that psychopathic individuals would fail to show the appropriate neural differentiation between abstract and concrete stimuli in the right anterior temporal gyrus and surrounding cortex. The results are consistent with other studies of semantic processing in psychopathy and support the theory that psychopathy is associated with right hemisphere abnormalities for processing conceptually abstract material.

  10. Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity.

    PubMed

    Knott, Brandon C; Crowley, Michael F; Himmel, Michael E; Ståhlberg, Jerry; Beckham, Gregg T

    2014-06-18

    Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.

  11. Transcriptomic comparison of Drosophila snRNP biogenesis mutants reveals mutant-specific changes in pre-mRNA processing: implications for spinal muscular atrophy.

    PubMed

    Garcia, Eric L; Wen, Ying; Praveen, Kavita; Matera, A Gregory

    2016-08-01

    Survival motor neuron (SMN) functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) that catalyze pre-mRNA splicing. Here, we used disruptions in Smn and two additional snRNP biogenesis genes, Phax and Ars2, to classify RNA processing differences as snRNP-dependent or gene-specific in Drosophila Phax and Smn mutants exhibited comparable reductions in snRNAs, and comparison of their transcriptomes uncovered shared sets of RNA processing changes. In contrast, Ars2 mutants displayed only small decreases in snRNA levels, and RNA processing changes in these mutants were generally distinct from those identified in Phax and Smn animals. Instead, RNA processing changes in Ars2 mutants support the known interaction of Ars2 protein with the cap-binding complex, as splicing changes showed a clear bias toward the first intron. Bypassing disruptions in snRNP biogenesis, direct knockdown of spliceosomal proteins caused similar changes in the splicing of snRNP-dependent events. However, these snRNP-dependent events were largely unaltered in three Smn mutants expressing missense mutations that were originally identified in human spinal muscular atrophy (SMA) patients. Hence, findings here clarify the contributions of Phax, Smn, and Ars2 to snRNP biogenesis in Drosophila, and loss-of-function mutants for these proteins reveal differences that help disentangle cause and effect in SMA model flies.

  12. Soil infrastructure evolution and its effect on water transfer processes under contrasted tillage systems with preliminary results

    NASA Astrophysics Data System (ADS)

    Parvin, Nargish; Degré, Aurore; Chélin, Marie; Hiel, Marie-Pierre; Garré, Sarah; Bodson, Bernard

    2014-05-01

    The heterogeneity of soil structure and porosity are highly influenced by external factors like tillage systems and other land management approaches. The aim of this project is to investigate the effect of soil tillage along with residue management on the changing pattern of soil structure. This investigation will help to emphasize the different water flow dynamics especially the preferential flow processes through the soil that are influenced by the changes in structural distribution in the soil profile. Mostly the preferential flow of water is addressed by the apparent velocity through the soil but this study will focus on soil structure along with soil moisture dynamics at pedon scale or more specifically at aggregate scale. The experimentation has been started from June 2013 in the research field known as Solcouvert (objects: strip-till (ST) versus winter ploughing (WP)) and Solresidus (objects: no-till with organic matter restitution (NI) versus no-till without organic matter restitution (NO)). Soil profile description has been carried out in the four objects of land management. Soil sampling has been done in different depths of soil according to the soil profile description. Soil samples will be used for the measurement of water retention capacity (done), hydraulic conductivity and x-ray microtomography. The assessment of soil water retention curves with pressure plate technique show significantly (p<0.05) higher water retention (Hwr) in WP than ST at 9.8 to 98 hPa, Hwr in WP than NI at 39 to 14710 hPa, Hwr in ST than NI at 294 to 14710 hPa and Hwr in WP than NO at 69 to 98 hPa. There was no significant difference in the water retention between NO and NI and ST and NO. Since, tillage practices generally increase soil porosity, the correlation between soil hydraulics and porosity distribution would expect to be different for different tillage systems. In our study, WP retains more water due to the increase of macroporosity than ST, NI and NO. As the changes in

  13. Unconscious Processing of Negative Animals and Objects: Role of the Amygdala Revealed by fMRI

    PubMed Central

    Fang, Zhiyong; Li, Han; Chen, Gang; Yang, JiongJiong

    2016-01-01

    Previous studies have shown that emotional stimuli can be processed through the amygdala without conscious awareness. The amygdala is also involved in processing animate and social information. However, it is unclear whether different categories of pictures (e.g., animals, objects) elicit different activity in the amygdale and other regions without conscious awareness. The objective of this study was to explore whether the factors of category, emotion and picture context modulate brain activation for unconscious processing. Pictures denoting different nonhuman animals and objects in negative and neutral emotional valences were presented using a sandwich-masking paradigm. Half of them were presented with human-related information in the contexts, and half were not. Our results showed significant interaction among category, emotion and context in the amygdala and subcortical regions. Specifically, negative animals elicited stronger activation in these regions than negative objects, especially with human contexts. In addition, there were different correlation patterns between the amygdala and cortical regions according to whether they included human context. There were limited activations in cortical category-related networks. These results suggest that the amygdala and subcortical regions dominantly process negative animals, and contextual information modulates their activities, making threatening stimuli that are most relevant to human survival preferentially processed without conscious awareness. PMID:27092067

  14. Oligomerization process of Bcl-2 associated X protein revealed from intermediate structures in solution.

    PubMed

    Shih, Orion; Yeh, Yi-Qi; Liao, Kuei-Fen; Sung, Tai-Ching; Chiang, Yun-Wei; Jeng, U-Ser

    2017-03-15

    Upon apoptotic stress, Bcl-2 associated X (BAX) protein undergoes conformational changes and oligomerizes, leading to the mitochondrial membrane permeabilization and cell death. While structures of the resultant oligomer have been extensively studied, little is known about the intermediates that describe the reaction pathway from the inactive monomers to activated oligomers. Here we characterize the intermediate structures of BAX using combined small-angle X-ray scattering (SAXS) with on-line gel-filtration and electron spin resonance (ESR). The intermediates, including monomers, dimers, and tetramers, are reconstructed via integrating the SAXS-envelopes and ESR-determined skeleton structures. The hence revealed structures suggest a linear oligomerization of BAX utilizing the extended dimers with the two flexible α6 chains protruded out as ditopic ligands. The results of molecular dynamics simulation also support the ditopic dimer conformation with mobile α6. The ditopic dimers could further wind into a helical rod structure with three dimers in one helical turn. Our results not only reveal the on-pathway intermediates, but also suggest a ditopic oligomerization mechanism that may bridge the observed intermediate structures in solution to the large BAX assemblies lately observed on mitochondria.

  15. Revealing Defect-State Photoluminescence in Monolayer WS2 by Cryogenic Laser Processing.

    PubMed

    He, Zhengyu; Wang, Xiaochen; Xu, Wenshuo; Zhou, Yingqiu; Sheng, Yuewen; Rong, Youmin; Smith, Jason M; Warner, Jamie H

    2016-06-28

    Understanding the stability of monolayer transition metal dichalcogenides in atmospheric conditions has important consequences for their handling, life-span, and utilization in applications. We show that cryogenic photoluminescence spectroscopy (PL) is a highly sensitive technique to the detection of oxidation induced degradation of monolayer tungsten disulfide (WS2) caused by exposure to ambient conditions. Although long-term exposure to atmospheric conditions causes massive degradation from oxidation that is optically visible, short-term exposure produces no obvious changes to the PL or Raman spectra measured at either room temperature or even cryogenic environment. Laser processing was employed to remove the surface adsorbents, which enables the defect states to be detected via cryogenic PL spectroscopy. Thermal cycling to room temperature and back down to 77 K shows the process is reversible. We also monitor the degradation process of WS2 using this method, which shows that the defect related peak can be observed after one month aging in ambient conditions.

  16. Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

    NASA Astrophysics Data System (ADS)

    Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

    2016-04-01

    Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3- concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

  17. Seeing the Light: Adapting Luminance Reveals Low-Level Visual Processes in the Attentional Blink

    ERIC Educational Resources Information Center

    Giesbrecht, Barry; Bischof, Walter F.; Kingstone, Alan

    2004-01-01

    It is widely assumed that high-level visual processes subserve the attentional blink (AB). Recent evidence from studies of visual masking during the AB that were designed to directly test the contributions of high-level masking effects, however, have failed to provide empirical support for this position.The implication is that low-level visual…

  18. Conceptual processing in music as revealed by N400 effects on words and musical targets.

    PubMed

    Daltrozzo, Jérôme; Schön, Daniele

    2009-10-01

    The cognitive processing of concepts, that is, abstract general ideas, has been mostly studied with language. However, other domains, such as music, can also convey concepts. Koelsch et al. [Koelsch, S., Kasper, E., Sammler, D., Schulze, K., Gunter, T., & Friederici, A. D. Music, language and meaning: Brain signatures of semantic processing. Nature Neuroscience, 7, 302-307, 2004] showed that 10 sec of music can influence the semantic processing of words. However, the length of the musical excerpts did not allow the authors to study the effect of words on musical targets. In this study, we decided to replicate Koelsch et al. findings using 1-sec musical excerpts (Experiment 1). This allowed us to study the reverse influence, namely, of a linguistic context on conceptual processing of musical excerpts (Experiment 2). In both experiments, we recorded behavioral and electrophysiological responses while participants were presented 50 related and 50 unrelated pairs (context/target). Experiments 1 and 2 showed a larger N400 component of the event-related brain potentials to targets following a conceptually unrelated compared to a related context. The presence of an N400 effect with musical targets suggests that music may convey concepts. The relevance of these results for the comprehension of music as a structured set of conceptual units and for the domain specificity of the mechanisms underlying N400 effects are discussed.

  19. Using Regression to Measure Holistic Face Processing Reveals a Strong Link with Face Recognition Ability

    ERIC Educational Resources Information Center

    DeGutis, Joseph; Wilmer, Jeremy; Mercado, Rogelio J.; Cohan, Sarah

    2013-01-01

    Although holistic processing is thought to underlie normal face recognition ability, widely discrepant reports have recently emerged about this link in an individual differences context. Progress in this domain may have been impeded by the widespread use of subtraction scores, which lack validity due to their contamination with control condition…

  20. Revealing the Principal's Role in the Induction Process: Novice Teachers Telling Their Stories

    ERIC Educational Resources Information Center

    Bickmore, Steven T.; Bickmore, Dana L.

    2010-01-01

    As part of a larger study of two middle-grade schools, we interviewed novice teachers, their mentors, and administrators to determine their perceptions of various aspects of a multifaceted induction program. During the initial analysis, stories repeatedly surfaced about the administrator's role in the induction process. Reanalysis of the data…

  1. Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms.

    PubMed

    Giglione, C; Serero, A; Pierre, M; Boisson, B; Meinnel, T

    2000-11-01

    The N-terminal protein processing pathway is an essential mechanism found in all organisms. However, it is widely believed that deformylase, a key enzyme involved in this process in bacteria, does not exist in eukaryotes, thus making it a target for antibacterial agents such as actinonin. In an attempt to define this process in higher eukaryotes we have used Arabidopsis thaliana as a model organism. Two deformylase cDNAs, the first identified in any eukaryotic system, and six distinct methionine aminopeptidase cDNAs were cloned. The corresponding proteins were characterized in vivo and in vitro. Methionine aminopeptidases were found in the cytoplasm and in the organelles, while deformylases were localized in the organelles only. Our work shows that higher plants have a much more complex machinery for methionine removal than previously suspected. We were also able to identify deformylase homologues from several animals and clone the corresponding cDNA from human cells. Our data provide the first evidence that lower and higher eukaryotes, as well as bacteria, share a similar N-terminal protein processing machinery, indicating universality of this system.

  2. Low Frequency Fluctuations Reveal Integrated and Segregated Processing among the Cerebral Hemispheres

    PubMed Central

    Gee, Dylan G.; Biswal, Bharat B.; Kelly, Clare; Stark, David E.; Margulies, Daniel S.; Shehzad, Zarrar; Uddin, Lucina Q.; Klein, Donald F.; Banich, Marie T.; Castellanos, F. Xavier; Milham, Michael P.

    2011-01-01

    Resting-state functional magnetic resonance imaging (fMRI) has provided a novel approach for examining interhemispheric interaction, demonstrating a high degree of functional connectivity between homotopic regions in opposite hemispheres. However, heterotopic resting state functional connectivity (RSFC) remains relatively uncharacterized. In the present study, we examine non-homotopic regions, characterizing heterotopic RSFC and comparing it to intrahemispheric RSFC, to examine the impact of hemispheric separation on the integration and segregation of processing in the brain. Resting-state fMRI scans were acquired from 59 healthy participants to examine interregional correlations in spontaneous low frequency fluctuations in BOLD signal. Using a probabilistic atlas, we correlated probability-weighted time series from 112 regions (56 per hemisphere) distributed throughout the entire cerebrum. We compared RSFC for pairings of non-homologous regions located in different hemispheres (heterotopic connectivity) to RSFC for the same pairings when located within hemisphere (intrahemispheric connectivity). For positive connections, connectivity strength was greater within each hemisphere, consistent with integrated intrahemispheric processing. However, for negative connections, RSFC strength was greater between the hemispheres, consistent with segregated interhemispheric processing. These patterns were particularly notable for connections involving frontal and heteromodal regions. The distribution of positive and negative connectivity was nearly identical within and between the hemispheres, though we demonstrated detailed regional variation in distribution. We discuss implications for leading models of interhemispheric interaction. The future application of our analyses may provide important insight into impaired interhemispheric processing in clinical and aging populations. PMID:20570737

  3. Constructive Processes in Linear Order Problems Revealed by Sentence Study Times

    ERIC Educational Resources Information Center

    Mynatt, Barbee T.; Smith, Kirk H.

    1977-01-01

    This research was a further test of the theory of constructive processes proposed by Foos, Smith, Sabol, and Mynatt (1976) to account for differences among presentation orders in the construction of linear orders. This theory is composed of different series of mental operations that must be performed when an order relationship is integrated with…

  4. Temporally and functionally dissociable retrieval processing operations revealed by event-related potentials.

    PubMed

    Cruse, Damian; Wilding, Edward L

    2011-06-01

    In a pair of recent studies, frontally distributed event-related potential (ERP) indices of two distinct post-retrieval processes were identified. It has been proposed that one of these processes operates over any kinds of task relevant information in service of task demands, while the other operates selectively over recovered contextual (episodic) information. The experiment described here was designed to test this account, by requiring retrieval of different kinds of contextual information to that required in previous relevant studies. Participants heard words spoken in either a male or female voice at study and ERPs were acquired at test where all words were presented visually. Half of the test words had been spoken at study. Participants first made an old/new judgment, distinguishing via key press between studied and unstudied words. For words judged 'old', participants indicated the voice in which the word had been spoken at study, and their confidence (high/low) in the voice judgment. There was evidence for only one of the two frontal old/new effects that had been identified in the previous studies. One possibility is that the ERP effect in previous studies that was tied specifically to recollection reflects processes operating over only some kinds of contextual information. An alternative is that the index reflects processes that are engaged primarily when there are few contextual features that distinguish between studied stimuli.

  5. Event-Related Potentials Reveal Anomalous Morphosyntactic Processing in Developmental Dyslexia

    ERIC Educational Resources Information Center

    Cantiani, Chiara; Lorusso, Maria Luisa; Perego, Paolo; Molteni, Massimo; Guasti, Maria Teresa

    2013-01-01

    In the light of the literature describing oral language difficulties in developmental dyslexia (DD), event-related potentials were used in order to compare morphosyntactic processing in 16 adults with DD (aged 20-28 years) and unimpaired controls. Sentences including subject-verb agreement violations were presented auditorily, with grammaticality…

  6. Terahertz radiation from bacteriorhodopsin reveals correlated primary electron and proton transfer processes.

    PubMed

    Groma, G I; Hebling, J; Kozma, I Z; Váró, G; Hauer, J; Kuhl, J; Riedle, E

    2008-05-13

    The kinetics of electrogenic events associated with the different steps of the light-induced proton pump of bacteriorhodopsin is well studied in a wide range of time scales by direct electric methods. However, the investigation of the fundamental primary charge translocation phenomena taking place in the functional energy conversion process of this protein, and in other biomolecular assemblies using light energy, has remained experimentally unfeasible because of the lack of proper detection technique operating in the 0.1- to 20-THz region. Here, we show that extending the concept of the familiar Hertzian dipole emission into the extreme spatial and temporal range of intramolecular polarization processes provides an alternative way to study ultrafast electrogenic events on naturally ordered biological systems. Applying a relatively simple experimental arrangement based on this idea, we were able to observe light-induced coherent terahertz radiation from bacteriorhodopsin with femtosecond time resolution. The detected terahertz signal was analyzed by numerical simulation in the framework of different models for the elementary polarization processes. It was found that the principal component of the terahertz emission can be well described by excited-state intramolecular electron transfer within the retinal chromophore. An additional slower process is attributed to the earliest phase of the proton pump, probably occurring by the redistribution of a H bond near the retinal. The correlated electron and proton translocation supports the concept, assigning a functional role to the light-induced sudden polarization in retinal proteins.

  7. Altered Evoked Gamma-Band Responses Reveal Impaired Early Visual Processing in ADHD Children

    ERIC Educational Resources Information Center

    Lenz, Daniel; Krauel, Kerstin; Flechtner, Hans-Henning; Schadow, Jeanette; Hinrichs, Hermann; Herrmann, Christoph S.

    2010-01-01

    Neurophysiological studies yield contrary results whether attentional problems of patients with attention-deficit/hyperactivity disorder (ADHD) are related to early visual processing deficits or not. Evoked gamma-band responses (GBRs), being among the first cortical responses occurring as early as 90 ms after visual stimulation in human EEG, have…

  8. Differences in the Processing of Prefixes and Suffixes Revealed by a Letter-Search Task

    ERIC Educational Resources Information Center

    Beyersmann, Elisabeth; Ziegler, Johannes C.; Grainger, Jonathan

    2015-01-01

    A letter-search task was used to test the hypothesis that affixes are chunked during morphological processing and that such chunking might operate differently for prefixes and suffixes. Participants had to detect a letter target that was embedded either in a prefix or suffix (e.g., "R" in "propoint" or "filmure") or…

  9. Microarray analysis reveals novel features of the muscle aging process in men and women.

    PubMed

    Liu, Dongmei; Sartor, Maureen A; Nader, Gustavo A; Pistilli, Emidio E; Tanton, Leah; Lilly, Charles; Gutmann, Laurie; IglayReger, Heidi B; Visich, Paul S; Hoffman, Eric P; Gordon, Paul M

    2013-09-01

    To develop a global view of muscle transcriptional differences between older men and women and sex-specific aging, we obtained muscle biopsies from the biceps brachii of young and older men and women and profiled the whole-genome gene expression using microarray. A logistic regression-based method in combination with an intensity-based Bayesian moderated t test was used to identify significant sex- and aging-related gene functional groups. Our analysis revealed extensive sex differences in the muscle transcriptome of older individuals and different patterns of transcriptional changes with aging in men and women. In older women, we observed a coordinated transcriptional upregulation of immune activation, extracellular matrix remodeling, and lipids storage; and a downregulation of mitochondrial biogenesis and function and muscle regeneration. The effect of aging results in sexual dimorphic alterations in the skeletal muscle transcriptome, which may modify the risk for developing musculoskeletal and metabolic diseases in men and women.

  10. Microarray Analysis Reveals Novel Features of the Muscle Aging Process in Men and Women

    PubMed Central

    2013-01-01

    To develop a global view of muscle transcriptional differences between older men and women and sex-specific aging, we obtained muscle biopsies from the biceps brachii of young and older men and women and profiled the whole-genome gene expression using microarray. A logistic regression-based method in combination with an intensity-based Bayesian moderated t test was used to identify significant sex- and aging-related gene functional groups. Our analysis revealed extensive sex differences in the muscle transcriptome of older individuals and different patterns of transcriptional changes with aging in men and women. In older women, we observed a coordinated transcriptional upregulation of immune activation, extracellular matrix remodeling, and lipids storage; and a downregulation of mitochondrial biogenesis and function and muscle regeneration. The effect of aging results in sexual dimorphic alterations in the skeletal muscle transcriptome, which may modify the risk for developing musculoskeletal and metabolic diseases in men and women. PMID:23418191

  11. Eddy-Kuroshio interaction processes revealed by mooring observations off Taiwan and Luzon

    NASA Astrophysics Data System (ADS)

    Tsai, Cheng-Ju; Andres, Magdalena; Jan, Sen; Mensah, Vigan; Sanford, Thomas B.; Lien, Ren-Chieh; Lee, Craig M.

    2015-10-01

    The influence and fate of westward propagating eddies that impinge on the Kuroshio were observed with pressure sensor-equipped inverted echo sounders (PIESs) deployed east of Taiwan and northeast of Luzon. Zero lag correlations between PIES-measured acoustic travel times and satellite-measured sea surface height anomalies (SSHa), which are normally negative, have lower magnitude toward the west, suggesting the eddy-influence is weakened across the Kuroshio. The observational data reveal that impinging eddies lead to seesaw-like SSHa and pycnocline depth changes across the Kuroshio east of Taiwan, whereas analogous responses are not found in the Kuroshio northeast of Luzon. Anticyclones intensify sea surface and pycnocline slopes across the Kuroshio, while cyclones weaken these slopes, particularly east of Taiwan. During the 6 month period of overlap between the two PIES arrays, only one anticyclone affected the pycnocline depth first at the array northeast of Luzon and 21 days later in the downstream Kuroshio east of Taiwan.

  12. Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo.

    PubMed

    Yang, Helen H; St-Pierre, François; Sun, Xulu; Ding, Xiaozhe; Lin, Michael Z; Clandinin, Thomas R

    2016-06-30

    A mechanistic understanding of neural computation requires determining how information is processed as it passes through neurons and across synapses. However, it has been challenging to measure membrane potential changes in axons and dendrites in vivo. We use in vivo, two-photon imaging of novel genetically encoded voltage indicators, as well as calcium imaging, to measure sensory stimulus-evoked signals in the Drosophila visual system with subcellular resolution. Across synapses, we find major transformations in the kinetics, amplitude, and sign of voltage responses to light. We also describe distinct relationships between voltage and calcium signals in different neuronal compartments, a substrate for local computation. Finally, we demonstrate that ON and OFF selectivity, a key feature of visual processing across species, emerges through the transformation of membrane potential into intracellular calcium concentration. By imaging voltage and calcium signals to map information flow with subcellular resolution, we illuminate where and how critical computations arise.

  13. Genome sequencing of normal cells reveals developmental lineages and mutational processes

    PubMed Central

    Behjati, Sam; Wedge, David C; Tamuri, Asif U; Martincorena, Inigo; Petljak, Mia; Alexandrov, Ludmil B; Gundem, Gunes; Tarpey, Patrick S; Roerink, Sophie; Blokker, Joyce; Maddison, Mark; Mudie, Laura; Robinson, Ben; Nik-Zainal, Serena; Campbell, Peter; Goldman, Nick; van de Wetering, Marc; Cuppen, Edwin; Clevers, Hans; Stratton, Michael R

    2014-01-01

    The somatic mutations present in the genome of a cell have been accumulated over the lifetime of a multicellular organism. These mutations can provide insights into the developmental lineage tree1, the number of divisions each cell has undergone and the mutational processes that have been operative2. Here, we conducted whole genome sequencing of clonal lines3 derived from multiple tissues of healthy mice. Using somatic base substitutions, we reconstructed the early cell divisions of each animal demonstrating the contributions of embryonic cells to adult tissues. Differences were observed between tissues in the numbers and types of mutations accumulated by each cell, which likely reflect differences in the number of cell divisions they have undergone and varying contributions of different mutational processes. If somatic mutation rates are similar to those in mice, the results indicate that precise insights into development and mutagenesis of normal human cells will be possible. PMID:25043003

  14. Temporal Accumulation and Decision Processes in the Duration Bisection Task Revealed by Contingent Negative Variation

    PubMed Central

    Ng, Kwun Kei; Tobin, Simon; Penney, Trevor B.

    2011-01-01

    The duration bisection paradigm is a classic task used to examine how humans and other animals perceive time. Typically, participants first learn short and long anchor durations and are subsequently asked to classify probe durations as closer to the short or long anchor duration. However, the specific representations of time and the decision rules applied in this task remain the subject of debate. For example, researchers have questioned whether participants actually use representations of the short and long anchor durations in the decision process rather than merely a response threshold that is derived from those anchor durations. Electroencephalographic (EEG) measures, like the contingent negative variation (CNV), can provide information about the perceptual and cognitive processes that occur between the onset of the timing stimulus and the motor response. The CNV has been implicated as an electrophysiological marker of interval timing processes such as temporal accumulation, representation of the target duration, and the decision that the target duration has been attained. We used the CNV to investigate which durations are involved in the bisection categorization decision. The CNV increased in amplitude up to the value of the short anchor, remained at a constant level until about the geometric mean (GM) of the short and long anchors, and then began to resolve. These results suggest that the short anchor and the GM of the short and long anchors are critical target durations used in the bisection categorization decision process. In addition, larger mean N1P2 amplitude differences were associated with larger amplitude CNVs, which may reflect the participant’s precision in initiating timing on each trial across a test session. Overall, the results demonstrate the value of using scalp-recorded EEG to address basic questions about interval timing. PMID:22144952

  15. Single cell analysis reveals the stochastic phase of reprogramming to pluripotency is an ordered probabilistic process.

    PubMed

    Chung, Kyung-Min; Kolling, Frederick W; Gajdosik, Matthew D; Burger, Steven; Russell, Alexander C; Nelson, Craig E

    2014-01-01

    Despite years of research, the reprogramming of human somatic cells to pluripotency remains a slow, inefficient process, and a detailed mechanistic understanding of reprogramming remains elusive. Current models suggest reprogramming to pluripotency occurs in two-phases: a prolonged stochastic phase followed by a rapid deterministic phase. In this paradigm, the early stochastic phase is marked by the random and gradual expression of pluripotency genes and is thought to be a major rate-limiting step in the successful generation of induced Pluripotent Stem Cells (iPSCs). Recent evidence suggests that the epigenetic landscape of the somatic cell is gradually reset during a period known as the stochastic phase, but it is known neither how this occurs nor what rate-limiting steps control progress through the stochastic phase. A precise understanding of gene expression dynamics in the stochastic phase is required in order to answer these questions. Moreover, a precise model of this complex process will enable the measurement and mechanistic dissection of treatments that enhance the rate or efficiency of reprogramming to pluripotency. Here we use single-cell transcript profiling, FACS and mathematical modeling to show that the stochastic phase is an ordered probabilistic process with independent gene-specific dynamics. We also show that partially reprogrammed cells infected with OSKM follow two trajectories: a productive trajectory toward increasingly ESC-like expression profiles or an alternative trajectory leading away from both the fibroblast and ESC state. These two pathways are distinguished by the coordinated expression of a small group of chromatin modifiers in the productive trajectory, supporting the notion that chromatin remodeling is essential for successful reprogramming. These are the first results to show that the stochastic phase of reprogramming in human fibroblasts is an ordered, probabilistic process with gene-specific dynamics and to provide a precise

  16. Network analysis of postharvest senescence process in citrus fruits revealed by transcriptomic and metabolomic profiling.

    PubMed

    Ding, Yuduan; Chang, Jiwei; Ma, Qiaoli; Chen, Lingling; Liu, Shuzhen; Jin, Shuai; Han, Jingwen; Xu, Rangwei; Zhu, Andan; Guo, Jing; Luo, Yi; Xu, Juan; Xu, Qiang; Zeng, YunLiu; Deng, Xiuxin; Cheng, Yunjiang

    2015-05-01

    Citrus (Citrus spp.), a nonclimacteric fruit, is one of the most important fruit crops in global fruit industry. However, the biological behavior of citrus fruit ripening and postharvest senescence remains unclear. To better understand the senescence process of citrus fruit, we analyzed data sets from commercial microarrays, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry and validated physiological quality detection of four main varieties in the genus Citrus. Network-based approaches of data mining and modeling were used to investigate complex molecular processes in citrus. The Citrus Metabolic Pathway Network and correlation networks were constructed to explore the modules and relationships of the functional genes/metabolites. We found that the different flesh-rind transport of nutrients and water due to the anatomic structural differences among citrus varieties might be an important factor that influences fruit senescence behavior. We then modeled and verified the citrus senescence process. As fruit rind is exposed directly to the environment, which results in energy expenditure in response to biotic and abiotic stresses, nutrients are exported from flesh to rind to maintain the activity of the whole fruit. The depletion of internal substances causes abiotic stresses, which further induces phytohormone reactions, transcription factor regulation, and a series of physiological and biochemical reactions.

  17. Doing arithmetic by hand: hand movements during exact arithmetic reveal systematic, dynamic spatial processing.

    PubMed

    Marghetis, Tyler; Núñez, Rafael; Bergen, Benjamin K

    2014-01-01

    Mathematics requires precise inferences about abstract objects inaccessible to perception. How is this possible? One proposal is that mathematical reasoning, while concerned with entirely abstract objects, nevertheless relies on neural resources specialized for interacting with the world-in other words, mathematics may be grounded in spatial or sensorimotor systems. Mental arithmetic, for instance, could involve shifts in spatial attention along a mental "number-line", the product of cultural artefacts and practices that systematically spatialize number and arithmetic. Here, we investigate this hypothesized spatial processing during exact, symbolic arithmetic (e.g., 4 + 3 = 7). Participants added and subtracted single-digit numbers and selected the exact solution from responses in the top corners of a computer monitor. While they made their selections using a computer mouse, we recorded the movement of their hand as indexed by the streaming x, y coordinates of the computer mouse cursor. As predicted, hand movements during addition and subtraction were systematically deflected toward the right and the left, respectively, as if calculation involved simultaneously simulating motion along a left-to-right mental number-line. This spatial-arithmetical bias, moreover, was distinct from-but correlated with-individuals' spatial-numerical biases (i.e., spatial-numerical association of response codes, SNARC, effect). These results are the first evidence that exact, symbolic arithmetic prompts systematic spatial processing associated with mental calculation. We discuss the possibility that mathematical calculation relies, in part, on an integrated system of spatial processes.

  18. Network analysis of corticocortical connections reveals ventral and dorsal processing streams in mouse visual cortex

    PubMed Central

    Wang, Quanxin; Sporns, Olaf; Burkhalter, Andreas

    2012-01-01

    Much of the information used for visual perception and visually guided actions is processed in complex networks of connections within the cortex. To understand how this works in the normal brain and to determine the impact of disease, mice are promising models. In primate visual cortex, information is processed in a dorsal stream specialized for visuospatial processing and guided action and a ventral stream for object recognition. Here, we traced the outputs of 10 visual areas and used quantitative graph analytic tools of modern network science to determine, from the projection strengths in 39 cortical targets, the community structure of the network. We found a high density of the cortical graph that exceeded that previously shown in monkey. Each source area showed a unique distribution of projection weights across its targets (i.e. connectivity profile) that was well-fit by a lognormal function. Importantly, the community structure was strongly dependent on the location of the source area: outputs from medial/anterior extrastriate areas were more strongly linked to parietal, motor and limbic cortex, whereas lateral extrastriate areas were preferentially connected to temporal and parahippocampal cortex. These two subnetworks resemble dorsal and ventral cortical streams in primates, demonstrating that the basic layout of cortical networks is conserved across species. PMID:22457489

  19. Immediate relativity: EEG reveals early engagement of comparison in social information processing.

    PubMed

    Ohmann, Katharina; Stahl, Jutta; Mussweiler, Thomas; Kedia, Gayannée

    2016-11-01

    A wide array of social decisions relies on social comparisons. As such, these decisions require fast access to relative information. Therefore, we expect that signatures of the comparative process should be observable in electrophysiological components at an early stage of information processing. However, to date, little is known about the neural time course of social target comparisons. Therefore, we tested this hypothesis in 2 electroencephalography (EEG) studies using a social distance effect paradigm. The distance effect capitalizes on the fact that stimuli close on a certain dimension take longer to compare than stimuli clearly differing on this dimension. Here, we manipulated the distance of face characteristics regarding their levels of attractiveness (Study 1) and trustworthiness (Study 2), 2 essential social dimensions. In both studies, size comparisons served as a nonsocial control condition. In Study 1, distance related effects were apparent 170 ms (vertex positive potential, VPP) and 200 ms (N2) after stimulus onset for attractiveness comparisons. In Study 2, trustworthiness comparisons took effect already after 100 ms (N1) and likewise carried over to an event-related N2. Remarkably, we observed a similar temporal pattern for social (attractiveness, trustworthiness) and nonsocial (size) dimensions. These results speak in favor of an early encoding of comparative information and emphasize the primary role of comparison in social information processing. (PsycINFO Database Record

  20. Virtual head rotation reveals a process of route reconstruction from human vestibular signals.

    PubMed

    Day, Brian L; Fitzpatrick, Richard C

    2005-09-01

    The vestibular organs can feed perceptual processes that build a picture of our route as we move about in the world. However, raw vestibular signals do not define the path taken because, during travel, the head can undergo accelerations unrelated to the route and also be orientated in any direction to vary the signal. This study investigated the computational process by which the brain transforms raw vestibular signals for the purpose of route reconstruction. We electrically stimulated the vestibular nerves of human subjects to evoke a virtual head rotation fixed in skull co-ordinates and measure its perceptual effect. The virtual head rotation caused subjects to perceive an illusory whole-body rotation that was a cyclic function of head-pitch angle. They perceived whole-body yaw rotation in one direction with the head pitched forwards, the opposite direction with the head pitched backwards, and no rotation with the head in an intermediate position. A model based on vector operations and the anatomy and firing properties of semicircular canals precisely predicted these perceptions. In effect, a neural process computes the vector dot product between the craniocentric vestibular vector of head rotation and the gravitational unit vector. This computation yields the signal of body rotation in the horizontal plane that feeds our perception of the route travelled.

  1. How the Thatcher illusion reveals evolutionary differences in the face processing of primates.

    PubMed

    Weldon, Kimberly B; Taubert, Jessica; Smith, Carolynn L; Parr, Lisa A

    2013-09-01

    Face recognition in humans is a complex cognitive skill that requires sensitivity to unique configurations of eyes, mouth, and other facial features. The Thatcher illusion has been used to demonstrate the importance of orientation when processing configural information within faces. Transforming an upright face so that the eyes and mouth are inverted renders the face grotesque; however, when this "Thatcherized" face is inverted, the effect disappears. Due to the use of primate models in social cognition research, it is important to determine the extent to which specialized cognitive functions like face processing occur across species. To date, the Thatcher illusion has been explored in only a few species with mixed results. Here, we used computerized tasks to examine whether nonhuman primates perceive the Thatcher illusion. Chimpanzees and rhesus monkeys were required to discriminate between Thatcherized and unaltered faces presented upright and inverted. Our results confirm that chimpanzees perceived the Thatcher illusion, but rhesus monkeys did not, suggesting species differences in the importance of configural information in face processing. Three further experiments were conducted to understand why our results differed from previously published accounts of the Thatcher illusion in rhesus monkeys.

  2. Atypical Asymmetry for Processing Human and Robot Faces in Autism Revealed by fNIRS

    PubMed Central

    Jung, Corinne E.; Strother, Lars; Feil-Seifer, David J.; Hutsler, Jeffrey J.

    2016-01-01

    Deficits in the visual processing of faces in autism spectrum disorder (ASD) individuals may be due to atypical brain organization and function. Studies assessing asymmetric brain function in ASD individuals have suggested that facial processing, which is known to be lateralized in neurotypical (NT) individuals, may be less lateralized in ASD. Here we used functional near-infrared spectroscopy (fNIRS) to first test this theory by comparing patterns of lateralized brain activity in homologous temporal-occipital facial processing regions during observation of faces in an ASD group and an NT group. As expected, the ASD participants showed reduced right hemisphere asymmetry for human faces, compared to the NT participants. Based on recent behavioral reports suggesting that robots can facilitate increased verbal interaction over human counterparts in ASD, we also measured responses to faces of robots to determine if these patterns of activation were lateralized in each group. In this exploratory test, both groups showed similar asymmetry patterns for the robot faces. Our findings confirm existing literature suggesting reduced asymmetry for human faces in ASD and provide a preliminary foundation for future testing of how the use of categorically different social stimuli in the clinical setting may be beneficial in this population. PMID:27389017

  3. Speech processing asymmetry revealed by dichotic listening and functional brain imaging.

    PubMed

    Hugdahl, Kenneth; Westerhausen, René

    2016-12-01

    In this article, we review research in our laboratory from the last 25 to 30 years on the neuronal basis for laterality of speech perception focusing on the upper, posterior parts of the temporal lobes, and its functional and structural connections to other brain regions. We review both behavioral and brain imaging data, with a focus on dichotic listening experiments, and using a variety of imaging modalities. The data have come in most parts from healthy individuals and from studies on normally functioning brain, although we also review a few selected clinical examples. We first review and discuss the structural model for the explanation of the right-ear advantage (REA) and left hemisphere asymmetry for auditory language processing. A common theme across many studies have been our interest in the interaction between bottom-up, stimulus-driven, and top-down, instruction-driven, aspects of hemispheric asymmetry, and how perceptual factors interact with cognitive factors to shape asymmetry of auditory language information processing. In summary, our research have shown laterality for the initial processing of consonant-vowel syllables, first observed as a behavioral REA when subjects are required to report which syllable of a dichotic syllable-pair they perceive. In subsequent work we have corroborated the REA with brain imaging, and have shown that the REA is modulated through both bottom-up manipulations of stimulus properties, like sound intensity, and top-down manipulations of cognitive properties, like attention focus.

  4. Torque measurements reveal large process differences between materials during high solid enzymatic hydrolysis of pretreated lignocellulose

    PubMed Central

    2012-01-01

    Background A common trend in the research on 2nd generation bioethanol is the focus on intensifying the process and increasing the concentration of water insoluble solids (WIS) throughout the process. However, increasing the WIS content is not without problems. For example, the viscosity of pretreated lignocellulosic materials is known to increase drastically with increasing WIS content. Further, at elevated viscosities, problems arise related to poor mixing of the material, such as poor distribution of the enzymes and/or difficulties with temperature and pH control, which results in possible yield reduction. Achieving good mixing is unfortunately not without cost, since the power requirements needed to operate the impeller at high viscosities can be substantial. This highly important scale-up problem can easily be overlooked. Results In this work, we monitor the impeller torque (and hence power input) in a stirred tank reactor throughout high solid enzymatic hydrolysis (< 20% WIS) of steam-pretreated Arundo donax and spruce. Two different process modes were evaluated, where either the impeller speed or the impeller power input was kept constant. Results from hydrolysis experiments at a fixed impeller speed of 10 rpm show that a very rapid decrease in impeller torque is experienced during hydrolysis of pretreated arundo (i.e. it loses its fiber network strength), whereas the fiber strength is retained for a longer time within the spruce material. This translates into a relatively low, rather WIS independent, energy input for arundo whereas the stirring power demand for spruce is substantially larger and quite WIS dependent. By operating the impeller at a constant power input (instead of a constant impeller speed) it is shown that power input greatly affects the glucose yield of pretreated spruce whereas the hydrolysis of arundo seems unaffected. Conclusions The results clearly highlight the large differences between the arundo and spruce materials, both in terms of

  5. The microbiota of marketed processed edible insects as revealed by high-throughput sequencing.

    PubMed

    Garofalo, Cristiana; Osimani, Andrea; Milanović, Vesna; Taccari, Manuela; Cardinali, Federica; Aquilanti, Lucia; Riolo, Paola; Ruschioni, Sara; Isidoro, Nunzio; Clementi, Francesca

    2017-04-01

    Entomophagy has been linked to nutritional, economic, social and ecological benefits. However, scientific studies on the potential safety risks in eating edible insects need to be carried out for legislators, markets and consumers. In this context, the microbiota of edible insects deserves to be deeply investigated. The aim of this study was to elucidate the microbial species occurring in some processed marketed edible insects, namely powdered small crickets, whole dried small crickets (Acheta domesticus), whole dried locusts (Locusta migratoria), and whole dried mealworm larvae (Tenebrio molitor), through culture-dependent (classical microbiological analyses) and -independent methods (pyrosequencing). A great bacterial diversity and variation among insects was seen. Relatively low counts of total mesophilic aerobes, Enterobacteriaceae, lactic acid bacteria, Clostridium perfringens spores, yeasts and moulds in all of the studied insect batches were found. Furthermore, the presence of several gut-associated bacteria, some of which may act as opportunistic pathogens in humans, were found through pyrosequencing. Food spoilage bacteria were also identified, as well as Spiroplasma spp. in mealworm larvae, which has been found to be related to neurodegenerative diseases in animals and humans. Although viable pathogens such as Salmonella spp. and Listeria monocytogenes were not detected, the presence of Listeria spp., Staphylococcus spp., Clostridium spp. and Bacillus spp. (with low abundance) was also found through pyrosequencing. The results of this study contribute to the elucidation of the microbiota associated with edible insects and encourage further studies aimed to evaluate the influence of rearing and processing conditions on that microbiota.

  6. Vibrotactile masking experiments reveal accelerated somatosensory processing in congenitally blind braille readers.

    PubMed

    Bhattacharjee, Arindam; Ye, Amanda J; Lisak, Joy A; Vargas, Maria G; Goldreich, Daniel

    2010-10-27

    Braille reading is a demanding task that requires the identification of rapidly varying tactile patterns. During proficient reading, neighboring characters impact the fingertip at ∼100 ms intervals, and adjacent raised dots within a character at 50 ms intervals. Because the brain requires time to interpret afferent sensorineural activity, among other reasons, tactile stimuli separated by such short temporal intervals pose a challenge to perception. How, then, do proficient Braille readers successfully interpret inputs arising from their fingertips at such rapid rates? We hypothesized that somatosensory perceptual consolidation occurs more rapidly in proficient Braille readers. If so, Braille readers should outperform sighted participants on masking tasks, which demand rapid perceptual processing, but would not necessarily outperform the sighted on tests of simple vibrotactile sensitivity. To investigate, we conducted two-interval forced-choice vibrotactile detection, amplitude discrimination, and masking tasks on the index fingertips of 89 sighted and 57 profoundly blind humans. Sighted and blind participants had similar unmasked detection (25 ms target tap) and amplitude discrimination (compared with 100 μm reference tap) thresholds, but congenitally blind Braille readers, the fastest readers among the blind participants, exhibited significantly less masking than the sighted (masker, 50 Hz, 50 μm; target-masker delays, ±50 and ±100 ms). Indeed, Braille reading speed correlated significantly and specifically with masking task performance, and in particular with the backward masking decay time constant. We conclude that vibrotactile sensitivity is unchanged but that perceptual processing is accelerated in congenitally blind Braille readers.

  7. Revealing action representation processes in audio perception using fractal EEG analysis.

    PubMed

    Hadjidimitriou, Stelios K; Zacharakis, Asteris I; Doulgeris, Panagiotis C; Panoulas, Konstantinos J; Hadjileontiadis, Leontios J; Panas, Stavros M

    2011-04-01

    Electroencephalogram (EEG) recordings, and especially the Mu-rhythm over the sensorimotor cortex that relates to the activation of the mirror neuron system (MNS), were acquired from two subject groups (orchestral musicians and nonmusicians), in order to explore action representation processes involved in the perception and performance of musical pieces. Two types of stimuli were used, i.e., an auditory one consisting of an excerpt of Beethoven's fifth symphony and a visual one presenting a conductor directing an orchestra performing the same excerpt of the piece. Three tasks were conducted including auditory stimulation, audiovisual stimulation, and visual stimulation only, and the acquired signals were processed using fractal [time-dependent fractal dimension (FD) estimation] and statistical analysis (analysis of variance, Mann-Whitney). Experimental results showed significant differences between the two groups while desychronization of the Mu-rhythm, which can be linked to MNS activation, was observed during all tasks for the musicians' group, as opposed to the nonmusicians' group who exhibited similar response only when the visual stimulus was present. The mobility of the conductor was also correlated to the estimated FD signals, showing significantly higher correlation for the case of musicians compared to nonmusicians' one. The present study sheds light upon the difference in action representation in auditory perception between musicians and nonmusicians and paves the way for better comprehension of the underlying mechanisms of the MNS.

  8. Electrophysiology reveals semantic priming at a short SOA irrespective of depth of prime processing.

    PubMed

    Küper, Kristina; Heil, Martin

    2009-04-03

    The otherwise robust behavioral semantic priming effect is reduced to the point of being absent when a letter search has to be performed on the prime word. As a result the automaticity of semantic activation has been called into question. It is unclear, however, in how far automatic processes are even measurable in the letter search priming paradigm as the prime task necessitates a long prime-probe stimulus-onset asynchrony (SOA). In a modified procedure, a short SOA can be realized by delaying the prime task response until after participants have made a lexical decision on the probe. While the absence of lexical decision priming has already been demonstrated in this design it seems premature to draw any definite conclusions from this purely behavioral result since event related potential (ERP) measures have been shown to be a more sensitive index of semantic activation. Using the modified paradigm we thus recorded ERP in addition to lexical decision times. Stimuli were presented at two different SOAs (240 ms vs. 840 ms) and participants performed either a grammatical discrimination (Experiment 1) or a letter search (Experiment 2) on the prime. Irrespective of prime task, the modulation of the N400, the ERP correlate of semantic activation, provided clear-cut evidence of semantic processing at the short SOA. Implications for theories of semantic activation as well as the constraints of the delayed prime task procedure are discussed.

  9. Adaptation to real motion reveals direction-selective interactions between real and implied motion processing.

    PubMed

    Lorteije, Jeannette A M; Kenemans, J Leon; Jellema, Tjeerd; van der Lubbe, Rob H J; Lommers, Marjolein W; van Wezel, Richard J A

    2007-08-01

    Viewing static pictures of running humans evokes neural activity in the dorsal motion-sensitive cortex. To establish whether this response arises from direction-selective neurons that are also involved in real motion processing, we measured the visually evoked potential to implied motion following adaptation to static or moving random dot patterns. The implied motion response was defined as the difference between evoked potentials to pictures with and without implied motion. Interaction between real and implied motion was found as a modulation of this difference response by the preceding motion adaptation. The amplitude of the implied motion response was significantly reduced after adaptation to motion in the same direction as the implied motion, compared to motion in the opposite direction. At 280 msec after stimulus onset, the average difference in amplitude reduction between opposite and same adapted direction was 0.5 muV on an average implied motion amplitude of 2.0 muV. These results indicate that the response to implied motion arises from direction-selective motion-sensitive neurons. This is consistent with interactions between real and implied motion processing at a neuronal level.

  10. Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing.

    PubMed

    Goldfarb, Katherine C; Cech, Thomas R

    2017-01-01

    MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR-Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor-analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing-implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation.

  11. Nanoscopic characterization of the water vapor-salt interfacial layer reveals a unique biphasic adsorption process

    PubMed Central

    Yang, Liu; He, Jianfeng; Shen, Yi; Li, Xiaowei; Sun, Jielin; Czajkowsky, Daniel M.; Shao, Zhifeng

    2016-01-01

    Our quantitative understanding of water adsorption onto salt surfaces under ambient conditions is presently quite poor owing to the difficulties in directly characterizing this interfacial layer under these conditions. Here we determine the thickness of the interfacial layer on NaCl at different relative humidities (RH) based on a novel application of atomic force spectroscopy and capillary condensation theory. In particular, we take advantage of the microsecond-timescale of the capillary condensation process to directly resolve the magnitude of its contribution in the tip-sample interaction, from which the interfacial water thickness is determined. Further, to correlate this thickness with salt dissolution, we also measure surface conductance under similar conditions. We find that below 30% RH, there is essentially only the deposition of water molecules onto this surface, typical of conventional adsorption onto solid surfaces. However, above 30% RH, adsorption is simultaneous with the dissolution of ions, unlike conventional adsorption, leading to a rapid increase of surface conductance. Thus, water adsorption on NaCl is an unconventional biphasic process in which the interfacial layer not only exhibits quantitative differences in thickness but also qualitative differences in composition. PMID:27527905

  12. Analysis of variance components reveals the contribution of sample processing to transcript variation.

    PubMed

    van der Veen, Douwe; Oliveira, José Miguel; van den Berg, Willy A M; de Graaff, Leo H

    2009-04-01

    The proper design of DNA microarray experiments requires knowledge of biological and technical variation of the studied biological model. For the filamentous fungus Aspergillus niger, a fast, quantitative real-time PCR (qPCR)-based hierarchical experimental design was used to determine this variation. Analysis of variance components determined the contribution of each processing step to total variation: 68% is due to differences in day-to-day handling and processing, while the fermentor vessel, cDNA synthesis, and qPCR measurement each contributed equally to the remainder of variation. The global transcriptional response to d-xylose was analyzed using Affymetrix microarrays. Twenty-four statistically differentially expressed genes were identified. These encode enzymes required to degrade and metabolize D-xylose-containing polysaccharides, as well as complementary enzymes required to metabolize complex polymers likely present in the vicinity of D-xylose-containing substrates. These results confirm previous findings that the d-xylose signal is interpreted by the fungus as the availability of a multitude of complex polysaccharides. Measurement of a limited number of transcripts in a defined experimental setup followed by analysis of variance components is a fast and reliable method to determine biological and technical variation present in qPCR and microarray studies. This approach provides important parameters for the experimental design of batch-grown filamentous cultures and facilitates the evaluation and interpretation of microarray data.

  13. Functional MRI reveals compromised neural integrity of the face processing network in congenital prosopagnosia.

    PubMed

    Avidan, Galia; Behrmann, Marlene

    2009-07-14

    The summed activity of multiple nodes of a distributed cortical network supports face recognition in humans, including "core" ventral occipitotemporal cortex (VOTC) regions, and "extended" regions outside VOTC. Many individuals with congenital prosopagnosia-an impairment in face processing-exhibit normal blood oxygenation level-dependent (BOLD) activation in the core VOTC regions. These individuals evince a reduction in the structural integrity of the white matter tracts connecting VOTC to anterior temporal and frontal cortices, part of the "extended" face network. The impairment in congenital prosopagnosia may arise, therefore, not from a dysfunction of the core VOTC areas but from a failure to propagate signals between the intact VOTC and the extended nodes of the network. Using the fMR adaptation paradigm with famous and unknown faces, we show that individuals with congenital prosopagnosia evince normal adaptation effects in VOTC, indicating sensitivity to facial identity, but show no differential activation for familiar versus unknown faces outside VOTC, particularly in the precuneus/posterior cingulate cortex and the anterior paracingulate cortex. Normal BOLD activation in VOTC is thus insufficient to subserve intact face recognition, and disrupted information propagation between VOTC and the extended face processing network may explain the functional impairment in congenital prosopagnosia.

  14. Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes

    PubMed Central

    2009-01-01

    Background Thiomonas strains are ubiquitous in arsenic-contaminated environments. Differences between Thiomonas strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five Thiomonas strains, that are interesting in terms of arsenic metabolism were selected: T. arsenivorans, Thiomonas spp. WJ68 and 3As are able to oxidise As(III), while Thiomonas sp. Ynys1 and T. perometabolis are not. Moreover, T. arsenivorans and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor. Results The metabolism of carbon and arsenic was compared in the five Thiomonas strains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/rpoA gene phylogeny, especially regarding arsenic metabolism. Physiologically, T. perometabolis and Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack the aox arsenic-oxidising genes and carried only a single ars arsenic resistance operon. Thiomonas arsenivorans belonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that in T. arsenivorans, the rbc/cbb genes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed in Thiomonas sp. 3As. Conclusion Taken together, these results show that these closely related bacteria differ substantially in their response to arsenic, amongst other factors, and suggest different relationships between carbon assimilation and arsenic metabolism. PMID:19549320

  15. Diversity of Orientia tsutsugamushi clinical isolates in Cambodia reveals active selection and recombination process.

    PubMed

    Duong, Veasna; Blassdell, Kim; May, Thinh Thi Xuan; Sreyrath, Lay; Gavotte, Laurent; Morand, Serge; Frutos, Roger; Buchy, Philippe

    2013-04-01

    Orientia tsutsugamushi, the causative agent of scrub typhus in South East Asia and Pacific, is an obligate intracellular bacterium closely related to the Rickettsia. The pathogen is transmitted to humans through the bites of infected larvae of trombiculid mites of the genus Leptotrombidium in which is maintained trough vertical transmission mechanism. The infection in rodents has been described in over 20 species. Scrub typhus is commonly confused with other tropical fevers and late diagnosis and treatment can lead to severe organ failures and a strain-dependent mortality rate of up to 50%. A MLST scheme associating seven core function genes: adk, lepB, lipA, lipB, secY, sodB and sucA was developed and validated on seven Cambodian strains detected in patients and two complete reference genomes from Korea and Japan. Sequence data were analyzed both with respect to sequence type (ST) diversity and DNA polymorphism. Differing trends were revealed. DNA polymorphism and phylogeny of individual gene loci indicated a significant level of recombination and genetic diversity. However, the ST distribution is clearly clonal and the clinical situation can be summarized by the formula: one patient, one strain, one ST. This contradiction is only apparent and is most likely the consequence of the unique life cycle of O. tsutsugamushi. The quasi exclusive vertical transmission mode in mites generates repeated bottlenecks and small-size populations and strongly limits genetic diversity. O. tsutsugamushi has developed specific mechanisms for generating genetic diversity which include recombination, duplication and conjugation. Recombination and other mechanisms for increasing genetic diversity are likely to occur in rodents which can act as maintenance hosts, although occurrence in mites cannot be excluded. Consequences for the epidemiology of scrub typhus are discussed.

  16. Endoscopy imaging intelligent contrast improvement.

    PubMed

    Sheraizin, S; Sheraizin, V

    2005-01-01

    In this paper, we present a medical endoscopy video contrast improvement method that provides intelligent automatic adaptive contrast control. The method fundamentals are video data clustering and video data histogram modification. The video data clustering allows an effective use the low noise two channel contrast enhancement processing. The histogram analysis permitted to determine the video exposure type for simple and complicated contrast distribution. We determined the needed gamma value for automatic local area contrast improvement for the following exposure types: dark, normal, light, dark light, dark normal etc. The experimental results of medical endoscopy video processing allow defining the automatic gamma control range from 0.5 to 2.0.

  17. Acetylome analysis reveals the involvement of lysine acetylation in diverse biological processes in Phytophthora sojae.

    PubMed

    Li, Delong; Lv, Binna; Tan, Lingling; Yang, Qianqian; Liang, Wenxing

    2016-07-14

    Lysine acetylation is a dynamic and highly conserved post-translational modification that plays an important regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Phytophthora sojae is one of the most important plant pathogens due to its huge economic impact. However, to date, little is known about the functions of lysine acetylation in this Phytopthora. Here, we conducted a lysine acetylome in P. sojae. Overall, 2197 lysine acetylation sites in 1150 proteins were identified. The modified proteins are involved in diverse biological processes and are localized to multiple cellular compartments. Importantly, 7 proteins involved in the pathogenicity or the secretion pathway of P. sojae were found to be acetylated. These data provide the first comprehensive view of the acetylome of P. sojae and serve as an important resource for functional analysis of lysine acetylation in plant pathogens.

  18. Acetylome analysis reveals the involvement of lysine acetylation in diverse biological processes in Phytophthora sojae

    PubMed Central

    Li, Delong; Lv, Binna; Tan, Lingling; Yang, Qianqian; Liang, Wenxing

    2016-01-01

    Lysine acetylation is a dynamic and highly conserved post-translational modification that plays an important regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Phytophthora sojae is one of the most important plant pathogens due to its huge economic impact. However, to date, little is known about the functions of lysine acetylation in this Phytopthora. Here, we conducted a lysine acetylome in P. sojae. Overall, 2197 lysine acetylation sites in 1150 proteins were identified. The modified proteins are involved in diverse biological processes and are localized to multiple cellular compartments. Importantly, 7 proteins involved in the pathogenicity or the secretion pathway of P. sojae were found to be acetylated. These data provide the first comprehensive view of the acetylome of P. sojae and serve as an important resource for functional analysis of lysine acetylation in plant pathogens. PMID:27412925

  19. The Physical Processes of Eruptive Flares Revealed By An Extremely-Long-Duration Event

    NASA Astrophysics Data System (ADS)

    Zhang, Jie; Zhou, Zhenjun

    2016-05-01

    In this work, we report the physical processes of eruptive flares inferred from an extremely- long-duration event occurred on June 21, 2011. The flare, peaked at C7.7 level, had a two-hour-long rise time in soft X-rays emission; this rise time is much longer than the typical rise time of solar flares that last for only about ten minutes. Combining the fact that the flare occurred near the disk center as seen by SDO, but near the limbs as seen by STEREO A and B, we are able to track the evolution of the eruption in 3-D as well as in a rare slow-motion manner. The time sequence of temperature maps, constructed from six corona-temperature passbands of AIA, clearly shows process of how the highly-twisted sigmoid structure prior to the eruption is transformed into a near-potential post-eruption loop arcade. The observed sigmoid is likely to be the structure of a twisted magnetic flux rope, which reached a height of about 60 Mm at the onset of the eruption. The onset is likely triggered by the torus instability (or loss of equilibrium) of the flux rope as indicated by the slow rise motion prior to the impulsive phase. We also find that the complex evolution of footprints of the eruption as seen from AIA transition region images is consistent with the magnetic evolution in the corona, which is the consequence of the combined effects of the expansion of the magnetic flux rope and the magnetic reconnection of surrounding magnetic fields.

  20. Auditory N1 reveals planning and monitoring processes during music performance.

    PubMed

    Mathias, Brian; Gehring, William J; Palmer, Caroline

    2017-02-01

    The current study investigated the relationship between planning processes and feedback monitoring during music performance, a complex task in which performers prepare upcoming events while monitoring their sensory outcomes. Theories of action planning in auditory-motor production tasks propose that the planning of future events co-occurs with the perception of auditory feedback. This study investigated the neural correlates of planning and feedback monitoring by manipulating the contents of auditory feedback during music performance. Pianists memorized and performed melodies at a cued tempo in a synchronization-continuation task while the EEG was recorded. During performance, auditory feedback associated with single melody tones was occasionally substituted with tones corresponding to future (next), present (current), or past (previous) melody tones. Only future-oriented altered feedback disrupted behavior: Future-oriented feedback caused pianists to slow down on the subsequent tone more than past-oriented feedback, and amplitudes of the auditory N1 potential elicited by the tone immediately following the altered feedback were larger for future-oriented than for past-oriented or noncontextual (unrelated) altered feedback; larger N1 amplitudes were associated with greater slowing following altered feedback in the future condition only. Feedback-related negativities were elicited in all altered feedback conditions. In sum, behavioral and neural evidence suggests that future-oriented feedback disrupts performance more than past-oriented feedback, consistent with planning theories that posit similarity-based interference between feedback and planning contents. Neural sensory processing of auditory feedback, reflected in the N1 ERP, may serve as a marker for temporal disruption caused by altered auditory feedback in auditory-motor production tasks.

  1. Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales.

    PubMed

    Luza, André Luís; Gonçalves, Gislene Lopes; Hartz, Sandra Maria

    2015-02-01

    The relative roles of historical processes, environmental filtering, and ecological interactions in the organization of species assemblages vary depending on the spatial scale. We evaluated the phylogenetic and morphological relationships between species and individuals (i.e., inter- and intraspecific variability) of Neotropical nonvolant small mammals coexisting in grassland-forest ecotones, in landscapes and in regions, that is, three different scales. We used a phylogenetic tree to infer evolutionary relationships, and morphological traits as indicators of performance and niche similarities between species and individuals. Subsequently, we applied phylogenetic and morphologic indexes of diversity and distance between species to evaluate small mammal assemblage structures on the three scales. The results indicated a repulsion pattern near forest edges, showing that phylogenetically similar species coexisted less often than expected by chance. The strategies for niche differentiation might explain the phylogenetic repulsion observed at the edge. Phylogenetic and morphological clustering in the grassland and at the forest interior indicated the coexistence of closely related and ecologically similar species and individuals. Coexistence patterns were similar whether species-trait values or individual values were used. At the landscape and regional scales, assemblages showed a predominant pattern of phylogenetic and morphological clustering. Environmental filters influenced the coexistence patterns at three scales, showing the importance of phylogenetically conserved ecological tolerances in enabling taxa co-occurrence. Evidence of phylogenetic repulsion in one region indicated that other processes beyond environmental filtering are important for community assembly at broad scales. Finally, ecological interactions and environmental filtering seemed important at the local scale, while environmental filtering and historical colonization seemed important for community

  2. Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales

    PubMed Central

    Luza, André Luís; Gonçalves, Gislene Lopes; Hartz, Sandra Maria

    2015-01-01

    The relative roles of historical processes, environmental filtering, and ecological interactions in the organization of species assemblages vary depending on the spatial scale. We evaluated the phylogenetic and morphological relationships between species and individuals (i.e., inter- and intraspecific variability) of Neotropical nonvolant small mammals coexisting in grassland-forest ecotones, in landscapes and in regions, that is, three different scales. We used a phylogenetic tree to infer evolutionary relationships, and morphological traits as indicators of performance and niche similarities between species and individuals. Subsequently, we applied phylogenetic and morphologic indexes of diversity and distance between species to evaluate small mammal assemblage structures on the three scales. The results indicated a repulsion pattern near forest edges, showing that phylogenetically similar species coexisted less often than expected by chance. The strategies for niche differentiation might explain the phylogenetic repulsion observed at the edge. Phylogenetic and morphological clustering in the grassland and at the forest interior indicated the coexistence of closely related and ecologically similar species and individuals. Coexistence patterns were similar whether species-trait values or individual values were used. At the landscape and regional scales, assemblages showed a predominant pattern of phylogenetic and morphological clustering. Environmental filters influenced the coexistence patterns at three scales, showing the importance of phylogenetically conserved ecological tolerances in enabling taxa co-occurrence. Evidence of phylogenetic repulsion in one region indicated that other processes beyond environmental filtering are important for community assembly at broad scales. Finally, ecological interactions and environmental filtering seemed important at the local scale, while environmental filtering and historical colonization seemed important for community

  3. The Physical Processes of Eruptive Flares Revealed By An Extremely-Long-Duration Event

    NASA Astrophysics Data System (ADS)

    Zhou, Zhenjun; Zhang, Jie; Chintzoglou, Georgios

    2015-04-01

    In this work, we report the physical processes of eruptive flares inferred from an extremely- long-duration event occurred on June 21, 2011. The flare, peaked at C7.5 level, had a two-hour-long rise time in soft X-rays; this rise time is much longer than the usual rise time of solar flares that last for only about ten minutes. Combining the fact that the flare occurred near the disk center as seen by SDO, but near the limbs as seen by STEREO A and B, we are able to track the evolution of the eruption in 3-D as well as in a rare slow-motion manner. The time sequence of temperature maps, constructed from six corona-temperature passbands of AIA, clearly shows process of how the highly-twisted sigmoid structure prior to the eruption is transformed into a near-potential post-eruption loop arcade. The observed sigmoid is likely to be the structure of a twisted magnetic flux rope, which reached a height of about 60 Mm at the onset of the eruption. The onset is likely triggered by the instability (or loss of equilibrium) of the flux rope as indicated by the slow rise motion prior to the impulsive phase. We also find that the complex evolution of footprints of the eruption as seen from AIA transition region images is consistent with the magnetic evolution in the corona, which is the consequence of the combined effects of the expansion of the magnetic flux rope and the magnetic reconnection of surrounding magnetic fields. The 3-D magnetic structure inferred from NLFFF extrapolation will be compared with that inferred from observations. ​

  4. Visual motion processing in migraine: Enhanced motion after-effects are related to display contrast, visual symptoms, visual triggers and attack frequency.

    PubMed

    Shepherd, Alex J; Joly-Mascheroni, Ramiro M

    2017-04-01

    Background Visual after-effects are illusions that occur after prolonged viewing of visual displays. The motion after-effect (MAE), for example, is an illusory impression of motion after viewing moving displays: subsequently, stationary displays appear to drift in the opposite direction. After-effects have been used extensively in basic vision research and in clinical settings, and are enhanced in migraine. Objective The objective of this article is to assess associations between ( 1 ) MAE duration and visual symptoms experienced during/between migraine/headache attacks, and ( 2 ) visual stimuli reported as migraine/headache triggers. Methods The MAE was elicited after viewing motion for 45 seconds. MAE duration was tested for three test contrast displays (high, medium, low). Participants also completed a headache questionnaire that included migraine/headache triggers. Results For each test contrast, the MAE was prolonged in migraine. MAE duration was associated with photophobia; visual triggers (flicker, striped patterns); and migraine or headache frequency. Conclusions Group differences on various visual tasks have been attributed to abnormal cortical processing in migraine, such as hyperexcitability, heightened responsiveness and/or a lack of intra-cortical inhibition. The results are not consistent with hyperexcitability simply from a general lack of inhibition. Alternative multi-stage models are discussed and suggestions for further research are recommended, including visual tests in clinical assessments/clinical trials.

  5. How does climate change influence demographic processes of widespread species? Lessons from the comparative analysis of contrasted populations of roe deer.

    PubMed

    Gaillard, Jean-Michel; Hewison, A J Mark; Klein, François; Plard, Floriane; Douhard, Mathieu; Davison, Raziel; Bonenfant, Christophe

    2013-05-01

    How populations respond to climate change depends on the interplay between life history, resource availability, and the intensity of the change. Roe deer are income breeders, with high levels of allocation to reproduction, and are hence strongly constrained by the availability of high quality resources during spring. We investigated how recent climate change has influenced demographic processes in two populations of this widespread species. Spring began increasingly earlier over the study, allowing us to identify 2 periods with contrasting onset of spring. Both populations grew more slowly when spring was early. As expected for a long-lived and iteroparous species, adult survival had the greatest potential impact on population growth. Using perturbation analyses, we measured the relative contribution of the demographic parameters to observed variation in population growth, both within and between periods and populations. Within periods, the identity of the critical parameter depended on the variance in growth rate, but variation in recruitment was the main driver of observed demographic change between periods of contrasting spring earliness. Our results indicate that roe deer in forest habitats cannot currently cope with increasingly early springs. We hypothesise that they should shift their distribution to richer, more heterogeneous landscapes to offset energetic requirements during the critical rearing stage.

  6. The effect of interocular phase difference on perceived contrast.

    PubMed

    Baker, Daniel H; Wallis, Stuart A; Georgeson, Mark A; Meese, Tim S

    2012-01-01

    Binocular vision is traditionally treated as two processes: the fusion of similar images, and the interocular suppression of dissimilar images (e.g. binocular rivalry). Recent work has demonstrated that interocular suppression is phase-insensitive, whereas binocular summation occurs only when stimuli are in phase. But how do these processes affect our perception of binocular contrast? We measured perceived contrast using a matching paradigm for a wide range of interocular phase offsets (0-180°) and matching contrasts (2-32%). Our results revealed a complex interaction between contrast and interocular phase. At low contrasts, perceived contrast reduced monotonically with increasing phase offset, by up to a factor of 1.6. At higher contrasts the pattern was non-monotonic: perceived contrast was veridical for in-phase and antiphase conditions, and monocular presentation, but increased a little at intermediate phase angles. These findings challenge a recent model in which contrast perception is phase-invariant. The results were predicted by a binocular contrast gain control model. The model involves monocular gain controls with interocular suppression from positive and negative phase channels, followed by summation across eyes and then across space. Importantly, this model--applied to conditions with vertical disparity--has only a single (zero) disparity channel and embodies both fusion and suppression processes within a single framework.

  7. Regional tomography reveals mantle traces of tectonic processes in the Circum-Arctic region

    NASA Astrophysics Data System (ADS)

    Koulakov, I.; Dobretsov, N. L.; Jakovlev, A.; Bushenkova, N.

    2012-04-01

    Studying the deep seismic structure beneath the Circum-Arctic region is important to understand the mechanisms of recent tectonic evolution. However, poor coverage of the region with seismic networks makes it difficult applying common tomography schemes. We propose using the travel time data from global seismological catalogues which correspond to seismicity located in the study region and recorded by worldwide stations at any epicentral distances. Another possibility to study "blank" areas is using travel times of PP rays having reflection points in the study area. Using more than 50 years of the ISC catalogue data, we have computed a seismic model in the upper mantle down to 700 km depth beneath the Arctic region. Based on this model, we confirm the existence of thick lithosphere (up to 300 km) beneath Greenland, Canadian and Baltic shield and the Siberian craton. The orogenic areas of Alaska, Chukotka and Yakutia coincide with low-velocity seismic anomalies which indicate the existence of relatively thin lithosphere that can be easily deformed due to tectonic displacements. In the oceanic segments corresponding to the Northern part of the Atlantic ocean and beneath Bering and Baffin seas we observe strong low-velocity anomalies indicating to the anomalously hot mantle. At the same time, beneath central basins of Arctic, the tomographic model does not reveal any significant perturbations. We propose that opening of the oceanic basins in Central Arctic is caused by passive rifting due to relative displacement of Eurasia and America. Beneath Chukotka, below 300 km depth we observe high-velocity anomaly whose origin is actively debated. It might be the trace of an old subduction zone which took place close to the Arctic coast of Chukotka. On the other hand, this positive anomaly might be a continuation of the Aleutian slab which moves horizontally along the transition zone between 410 km and 670 km depth. Besides the Arctic features we clearly observe well known

  8. Metamorphic records for subduction erosion and subsequent underplating processes revealed by garnet-staurolite-muscovite schists in central Qiangtang, Tibet

    NASA Astrophysics Data System (ADS)

    Zhang, Xiu-Zheng; Dong, Yong-Sheng; Wang, Qiang; Dan, Wei; Zhang, Chunfu; Xu, Wang; Huang, Ming-Liang

    2017-01-01

    Subduction erosion is confirmed as a crucial geodynamic process of crustal recycling based on geological, geochemical, and geophysical observations at modern convergent plate margins. So far, not a single metamorphic record has been used for constraining a general tectonic evolution for subduction erosion. Here we first revealed metamorphic records for a subduction erosion process based on our study of the Late Paleozoic garnet-staurolite-muscovite schists in the central Qiangtang block, Tibet. Provenance analyses suggest that the protoliths of garnet-staurolite-muscovite schists have the Northern Qiangtang-affinity and were deposited in an active continental margin setting. Mineral inclusion data show that the early metamorphic stage (M1) recorded blueschist facies pressure-temperature (P-T) conditions of 0.8-1.1 GPa and 402-441°C, indicating that a part of the material from the overriding plate had been abraded into the subduction channel and undergone high-pressure/low-temperature metamorphism. The peak metamorphic stage (M2) recorded amphibolite facies P-T conditions of 0.3-0.5 GPa and 470-520°C. The 40Ar/39Ar cooling ages (263-259 Ma) yielded from muscovite suggest the amphibolite facies metamorphism (>263 Ma) occurred at oceanic subduction stage. The distinctly staged metamorphism defines a clockwise and warming decompression P-T-t path which reveals an underplating process following the early subduction erosion. During the tectonic process, the eroded low-density material escaped from the cold subduction channel and rise upward into the warm middle-lower crust of the upper plate, undergoing amphibolite facies metamorphism. Our new results revealed a complete evolutional process from the early subduction erosion to the subsequent underplating during the northward subduction of the Paleo-Tethys Ocean.

  9. The molecular signature of AML mesenchymal stromal cells reveals candidate genes related to the leukemogenic process.

    PubMed

    Binato, Renata; de Almeida Oliveira, Nathalia Correa; Du Rocher, Barbara; Abdelhay, Eliana

    2015-12-01

    Acute myeloid leukemia (AML) is a heterogeneous disease characterized by myeloid precursor proliferation in the bone marrow, apoptosis reduction and differentiation arrest. Although there are several studies in this field, events related to disease initiation and progression remain unknown. The malignant transformation of hematopoietic stem cells (HSC) is thought to generate leukemic stem cells, and this transformation could be related to changes in mesenchymal stromal cell (hMSC) signaling. Thus, the aim of this work was to analyze the gene expression profile of hMSC from AML patients (hMSC-AML) compared to healthy donors hMSCs (hMSC-HD). The results showed a common molecular signature for all hMSC-AML. Other assays were performed with a large number of patients and the results confirmed a molecular signature that is capable of distinguishing hMSC-AML from hMSC-HD. Moreover, CCL2 and BMP4 genes encode secreted proteins that could affect HSCs. To verify whether these proteins are differentially expressed in AML patients, ELISA was performed with plasma samples. CCL2 and BMP4 proteins are differentially expressed in AML patients, indicating changes in hMSC-AML signaling. Altogether, hMSCs-AML signaling alterations could be an important factor in the leukemic transformation process.

  10. Carbon isotope fractionation reveals distinct process of CH4 emission from different compartments of paddy ecosystem

    NASA Astrophysics Data System (ADS)

    Zhang, Guangbin; Yu, Haiyang; Fan, Xianfang; Ma, Jing; Xu, Hua

    2016-06-01

    Carbon isotopic fractionations in the processes of CH4 emission from paddy field remain poorly understood. The δ13C-values of CH4 in association with production, oxidation and transport of CH4 in different pools of a paddy field were determined, and the stable carbon isotope fractionations were calibrated to assess relative contribution of acetate to CH4 production (fac) and fraction of CH4 oxidized (fox) by different pathways. The apparent isotope fractionation for CO2 conversion to CH4 (αapp) was 1.041–1.056 in the soil and 1.046–1.080 on the roots, indicating that fac was 10–60% and 0–50%, respectively. Isotope fractionation associated with CH4 oxidation (αox) was 1.021 ± 0.007 in the soil and 1.013 ± 0.005 on the roots, and the transport fractionation (εtransport) by rice plants was estimated to be ‑16.7‰ ~ ‑11.1‰. Rhizospheric fox was about 30–100%, and it was more important at the beginning but decreased fast towards the end of season. Large value of fox was also observed at the soil-water interface and soil and roots surfaces, respectively. The results demonstrate that carbon isotopic fractionations which might be different in different conditions were sensitive to the estimations of fac and fox in paddy field.

  11. Spectrotemporal resolution tradeoff in auditory processing as revealed by human auditory brainstem responses and psychophysical indices.

    PubMed

    Bidelman, Gavin M; Syed Khaja, Ameenuddin

    2014-06-20

    Auditory filter theory dictates a physiological compromise between frequency and temporal resolution of cochlear signal processing. We examined neurophysiological correlates of these spectrotemporal tradeoffs in the human auditory system using auditory evoked brain potentials and psychophysical responses. Temporal resolution was assessed using scalp-recorded auditory brainstem responses (ABRs) elicited by paired clicks. The inter-click interval (ICI) between successive pulses was parameterized from 0.7 to 25 ms to map ABR amplitude recovery as a function of stimulus spacing. Behavioral frequency difference limens (FDLs) and auditory filter selectivity (Q10 of psychophysical tuning curves) were obtained to assess relations between behavioral spectral acuity and electrophysiological estimates of temporal resolvability. Neural responses increased monotonically in amplitude with increasing ICI, ranging from total suppression (0.7 ms) to full recovery (25 ms) with a temporal resolution of ∼3-4 ms. ABR temporal thresholds were correlated with behavioral Q10 (frequency selectivity) but not FDLs (frequency discrimination); no correspondence was observed between Q10 and FDLs. Results suggest that finer frequency selectivity, but not discrimination, is associated with poorer temporal resolution. The inverse relation between ABR recovery and perceptual frequency tuning demonstrates a time-frequency tradeoff between the temporal and spectral resolving power of the human auditory system.

  12. A flash-drag effect in random motion reveals involvement of preattentive motion processing.

    PubMed

    Fukiage, Taiki; Whitney, David; Murakami, Ikuya

    2011-11-11

    The flash-drag (FDE) effect refers to the phenomenon in which the position of a stationary flashed object in one location appears shifted in the direction of nearby motion. Over the past decade, it has been debated how bottom-up and top-down processes contribute to this illusion. In this study, we demonstrate that randomly phase-shifting gratings can produce the FDE. In the random motion sequence we used, the FDE inducer (a sinusoidal grating) jumped to a random phase every 125 ms and stood still until the next jump. Because this random sequence could not be tracked attentively, it was impossible for the observer to discern the jump direction at the time of the flash. By sorting the data based on the flash's onset time relative to each jump time in the random motion sequence, we found that a large FDE with a broad temporal tuning occurred around 50 to 150 ms before the jump and that this effect was not correlated with any other jumps in the past or future. These results suggest that as few as two frames of unpredictable apparent motion can preattentively cause the FDE with a broad temporal tuning.

  13. The dynamics of the epileptic brain reveal long-memory processes.

    PubMed

    Cook, Mark J; Varsavsky, Andrea; Himes, David; Leyde, Kent; Berkovic, Samuel Frank; O'Brien, Terence; Mareels, Iven

    2014-01-01

    The pattern of epileptic seizures is often considered unpredictable and the interval between events without correlation. A number of studies have examined the possibility that seizure activity respects a power-law relationship, both in terms of event magnitude and inter-event intervals. Such relationships are found in a variety of natural and man-made systems, such as earthquakes or Internet traffic, and describe the relationship between the magnitude of an event and the number of events. We postulated that human inter-seizure intervals would follow a power-law relationship, and furthermore that evidence for the existence of a long-memory process could be established in this relationship. We performed a post hoc analysis, studying eight patients who had long-term (up to 2 years) ambulatory intracranial EEG data recorded as part of the assessment of a novel seizure prediction device. We demonstrated that a power-law relationship could be established in these patients (β = - 1.5). In five out of the six subjects whose data were sufficiently stationary for analysis, we found evidence of long memory between epileptic events. This memory spans time scales from 30 min to 40 days. The estimated Hurst exponents range from 0.51 to 0.77 ± 0.01. This finding may provide evidence of phase-transitions underlying the dynamics of epilepsy.

  14. Carbon isotope fractionation reveals distinct process of CH4 emission from different compartments of paddy ecosystem

    PubMed Central

    Zhang, Guangbin; Yu, Haiyang; Fan, Xianfang; Ma, Jing; Xu, Hua

    2016-01-01

    Carbon isotopic fractionations in the processes of CH4 emission from paddy field remain poorly understood. The δ13C-values of CH4 in association with production, oxidation and transport of CH4 in different pools of a paddy field were determined, and the stable carbon isotope fractionations were calibrated to assess relative contribution of acetate to CH4 production (fac) and fraction of CH4 oxidized (fox) by different pathways. The apparent isotope fractionation for CO2 conversion to CH4 (αapp) was 1.041–1.056 in the soil and 1.046–1.080 on the roots, indicating that fac was 10–60% and 0–50%, respectively. Isotope fractionation associated with CH4 oxidation (αox) was 1.021 ± 0.007 in the soil and 1.013 ± 0.005 on the roots, and the transport fractionation (εtransport) by rice plants was estimated to be −16.7‰ ~ −11.1‰. Rhizospheric fox was about 30–100%, and it was more important at the beginning but decreased fast towards the end of season. Large value of fox was also observed at the soil-water interface and soil and roots surfaces, respectively. The results demonstrate that carbon isotopic fractionations which might be different in different conditions were sensitive to the estimations of fac and fox in paddy field. PMID:27251886

  15. A "concrete view" of aging: event related potentials reveal age-related changes in basic integrative processes in language.

    PubMed

    Huang, Hsu-Wen; Meyer, Aaron M; Federmeier, Kara D

    2012-01-01

    Normal aging is accompanied by changes in both structural and functional cerebral organization. Although verbal knowledge seems to be relatively stable across the lifespan, there are age-related changes in the rapid use of that knowledge during on-line language processing. In particular, aging has been linked to reduce effectiveness in preparing for upcoming words and building an integrated sentence-level representation. The current study assessed whether such age-related changes extend even to much simpler language units, such as modification relations between a centrally presented adjective and a lateralized noun. Adjectives were used to elicit concrete and abstract meanings of the same, polysemous lexical items (e.g., "green book" vs. "interesting book"). Consistent with findings that lexical information is preserved with age, older adults, like younger adults, exhibited concreteness effects at the adjectives, with more negative responses to concrete adjectives over posterior (300-500 ms; N400) and frontal (300-900 ms) channels. However, at the noun, younger adults exhibited concreteness-based predictability effects linked to left hemisphere processing and imagery effects linked to right hemisphere processing, contingent on whether the adjectives and nouns formed a cohesive conceptual unit. In contrast, older adults showed neither effect, suggesting that they were less able to rapidly link the adjective-noun meaning to form an integrated conceptual representation. Age-related changes in language processing may thus be more pervasive than previously realized.

  16. Empirical evidence for musical syntax processing? Computer simulations reveal the contribution of auditory short-term memory

    PubMed Central

    Bigand, Emmanuel; Delbé, Charles; Poulin-Charronnat, Bénédicte; Leman, Marc; Tillmann, Barbara

    2014-01-01

    During the last decade, it has been argued that (1) music processing involves syntactic representations similar to those observed in language, and (2) that music and language share similar syntactic-like processes and neural resources. This claim is important for understanding the origin of music and language abilities and, furthermore, it has clinical implications. The Western musical system, however, is rooted in psychoacoustic properties of sound, and this is not the case for linguistic syntax. Accordingly, musical syntax processing could be parsimoniously understood as an emergent property of auditory memory rather than a property of abstract processing similar to linguistic processing. To support this view, we simulated numerous empirical studies that investigated the processing of harmonic structures, using a model based on the accumulation of sensory information in auditory memory. The simulations revealed that most of the musical syntax manipulations used with behavioral and neurophysiological methods as well as with developmental and cross-cultural approaches can be accounted for by the auditory memory model. This led us to question whether current research on musical syntax can really be compared with linguistic processing. Our simulation also raises methodological and theoretical challenges to study musical syntax while disentangling the confounded low-level sensory influences. In order to investigate syntactic abilities in music comparable to language, research should preferentially use musical material with structures that circumvent the tonal effect exerted by psychoacoustic properties of sounds. PMID:24936174

  17. Pupil size reveals preparatory processes in the generation of pro-saccades and anti-saccades.

    PubMed

    Wang, Chin-An; Brien, Donald C; Munoz, Douglas P

    2015-04-01

    The ability to generate flexible behaviors to accommodate changing goals in response to identical sensory stimuli is a signature that is inherited in humans and higher-level animals. In the oculomotor system, this function has often been examined with the anti-saccade task, in which subjects are instructed, prior to stimulus appearance, to either automatically look at the peripheral stimulus (pro-saccade) or to suppress the automatic response and voluntarily look in the opposite direction from the stimulus (anti-saccade). Distinct neural preparatory activity between the pro-saccade and anti-saccade conditions has been well documented, particularly in the superior colliculus (SC) and the frontal eye field (FEF), and this has shown higher inhibition-related fixation activity in preparation for anti-saccades than in preparation for pro-saccades. Moreover, the level of preparatory activity related to motor preparation is negatively correlated with reaction times. We hypothesised that preparatory signals may be reflected in pupil size through a link between the SC and the pupil control circuitry. Here, we examined human pupil dynamics during saccade preparation prior to the execution of pro-saccades and anti-saccades. Pupil size was larger in preparation for correct anti-saccades than in preparation for correct pro-saccades and erroneous pro-saccades made in the anti-saccade condition. Furthermore, larger pupil dilation prior to stimulus appearance accompanied saccades with faster reaction times, with a trial-by-trial correlation between dilation size and anti-saccade reaction times. Overall, our results demonstrate that pupil size is modulated by saccade preparation, and neural activity in the SC, together with the FEF, supports these findings, providing unique insights into the neural substrate coordinating cognitive processing and pupil diameter.

  18. Differentiation processes in FeO-rich asteroids revealed by the achondrite Lewis Cliff 88763

    NASA Astrophysics Data System (ADS)

    Day, James M. D.; Corder, Christopher A.; Rumble, Douglas; Assayag, Nelly; Cartigny, Pierre; Taylor, Lawrence A.

    2015-10-01

    Olivine-dominated (70-80 modal %) achondrite meteorite Lewis Cliff (LEW) 88763 originated from metamorphism and limited partial melting of a FeO-rich parent body. The meteorite experienced some alteration on Earth, evident from subchondritic Re/Os, and redistribution of rhenium within the sample. LEW 88763 is texturally similar to winonaites, has a Δ17O value of -1.19 ± 0.10‰, and low bulk-rock Mg/(Mg+Fe) (0.39), similar to the FeO-rich cumulate achondrite Northwest Africa (NWA) 6693. The similar bulk-rock major-, minor-, and trace-element abundances of LEW 88763, relative to some carbonaceous chondrites, including ratios of Pd/Os, Pt/Os, Ir/Os, and 187Os/188Os (0.1262), implies a FeO- and volatile-rich precursor composition. Lack of fractionation of the rare earth elements, but a factor of approximately two lower highly siderophile element abundances in LEW 88763, compared with chondrites, implies limited loss of Fe-Ni-S melts during metamorphism and anatexis. These results support the generation of high Fe/Mg, sulfide, and/or metal-rich partial melts from FeO-rich parent bodies during partial melting. In detail, however, LEW 88763 cannot be a parent composition to any other meteorite sample, due to highly limited silicate melt loss (0 to <<5%). As such, LEW 88763 represents the least-modified FeO-rich achondrite source composition recognized to date and is distinct from all other meteorites. LEW 88763 should be reclassified as an anomalous achondrite that experienced limited Fe,Ni-FeS melt loss. Lewis Cliff 88763, combined with a growing collection of FeO-rich meteorites, such as brachinites, brachinite-like achondrites, the Graves Nunataks (GRA) 06128/9 meteorites, NWA 6693, and Tafassasset, has important implications for understanding the initiation of planetary differentiation. Specifically, regardless of precursor compositions, partial melting and differentiation processes appear to be similar on asteroidal bodies spanning a range of initial oxidation

  19. Processive action of cellobiohydrolase Cel7A from Trichoderma reesei is revealed as ‘burst’ kinetics on fluorescent polymeric model substrates

    PubMed Central

    2004-01-01

    Reaction conditions for the reducing-end-specific derivatization of cellulose substrates with the fluorogenic compound, anthranilic acid, have been established. Hydrolysis of fluorescence-labelled celluloses by cellobiohydrolase Cel7A from Trichoderma reesei was consistent with the active-site titration kinetics (burst kinetics), which allowed the quantification of the processivity of the enzyme. The processivity values of 88±10, 42±10 and 34±2.0 cellobiose units were found for Cel7A acting on labelled bacterial cellulose, bacterial microcrystalline cellulose and endoglucanase-pretreated bacterial cellulose respectively. The anthranilic acid derivatization also provides an alternative means for estimating the average degree of polymerization of cellulose and, furthermore, allows the quantitative monitoring of the production of reducing end groups on solid cellulose on hydrolysis by cellulases. Hydrolysis of bacterial cellulose by cellulases from T. reesei revealed that, by contrast with endoglucanase Cel5A, neither cellobiohydrolases Cel7A nor Cel6A produced detectable amounts of new reducing end groups on residual cellulose. PMID:15362979

  20. Earthquake-triggered Tsaoling landslide mechanics and dynamic process revealed by discrete element method

    NASA Astrophysics Data System (ADS)

    Chang, K.-J.; Chen, R.-F.; Chan, Y.-C.; Kuo, C.-Y.; Weng, C.-H.

    2012-04-01

    transported debris was about 30 - 90 m thick, covered on the preexisting debris deposit hill and around the river channel. The debris formed a dammed lake, with a maximum volume of 45 Mm3. Based on DTMs data sets, field observations, the discrete element method - PFC3D is adapts to analyze the triggering mechanism and sling dynamic process. The presence and the coupling effect from the strong ground excitation and high pore water pressure is the essential factor to triggering the landslide event. The results shows that the best fit between the deposit topography of the post-event DTM and numerical simulations, the fictional coefficient of the sliding surface is as low as 0.087. The maximum sliding speed is as high as 87.2 m/s, the result coincide with the seismic record from the nearby strong motion seismic record.

  1. Reach tracking reveals dissociable processes underlying inhibitory control in 5- to 10-year-olds and adults.

    PubMed

    Erb, Christopher D; Moher, Jeff; Song, Joo-Hyun; Sobel, David M

    2017-02-24

    Researchers have proposed that two processes featuring distinct types of inhibition support inhibitory control: a response threshold adjustment process involving the global inhibition of motor output and a conflict resolution process involving competitive inhibition among co-active response alternatives. To target the development of these processes, we measured the reaching behavior of 5- to 10-year-olds (Experiment 1) and adults (Experiment 2) as they performed an Eriksen flanker task. This method provided two key measures: initiation time (the time elapsed between stimulus onset and movement onset) and reach curvature (the degree to which a movement deviates from a direct path to the selected target). We suggest that initiation time reflects the response threshold adjustment process by indexing the degree of motoric stopping experienced before a movement is started, while reach curvature reflects the conflict resolution process by indexing the degree of co-activation between response alternatives over the course of a movement. Our results support this claim, revealing different patterns effects in initiation time and curvature, and divergent developmental trajectories between childhood and adulthood. These findings provide behavioral evidence for the dissociation between global and competitive inhibition, and offer new insight into the development of inhibitory control.

  2. The distribution process of traffic contamination on roadside surface and the influence of meteorological conditions revealed by magnetic monitoring.

    PubMed

    Ma, Mingming; Hu, Shouyun; Wang, Longsheng; Appel, Erwin

    2016-11-01

    With the increasing number of vehicles and the development of transport systems, traffic contamination has become an important source of current environmental pollution. The study of roadside distribution patterns of traffic-related contaminants and its influencing factors can contribute to assess the scope and distribution process of the contaminants. A large number of works confirmed that magnetic methods which are fast and economic can be used to indicate the traffic-related pollution. Based on the previous study, we installed two new monitoring sites and conducted repeated in situ measurements of magnetic susceptibility (κ). From these data, we calculated the accumulation amount and accumulation rate of κ to reveal the detailed distribution process of traffic contaminants on the roadside surface over time. In addition, we collected daily meteorological data (rainfall and wind direction) and conducted a correlation analysis between the accumulation rate of κ and the meteorological data. The results show that the accumulation rate of traffic contaminants on the roadside surface is lower in periods of higher rainfall, and that the winds influence the distribution pattern of contaminants through changing their transmission path. The results confirm that magnetic methods can be used to reveal the detailed distribution process of traffic-related contaminants and its influencing factors.

  3. Major, trace and REE geochemistry in contrasted chlorite schist weathering profiles from southern Cameroon: Influence of the Nyong and Dja Rivers water table fluctuations in geochemical evolution processes

    NASA Astrophysics Data System (ADS)

    Onana, Vincent Laurent; Ntouala, Roger Firmin Donald; Tang, Sylvie Noa; Effoudou, Estelle Ndome; Kamgang, Veronique Kabeyene; Ekodeck, Georges Emmanuel

    2016-12-01

    Three weathering profiles developed on chlorite schists, formations on which little studies have been conducted, were chosen to understand the weathering processes prevailing downslope in Southern Cameroon. The materials nearest to Nyong River at Ayos weather under the influence of the fluctuations of groundwater table and acid rain, while those from Bengbis and Mbalmayo weather under the influence of acid rain. The result is the thickening of materials and weathering profiles, without formation of a nodular ferruginous horizon at Ayos. The Ayos weathered materials (CIA ∼ 92) are the most altered and the least lateritised (IOL ∼ 32). The most stable systems are Hf - U - Nb - Ti - Zr - Mo - W (Bengbis), Yb - U - Nb - Ti - Zr - Hf - Mo - W - Th (Mbalmayo) and Th - Nb - Zr - Hf - Mo - Ta (Ayos). Molybdenum accumulations are important in the studied materials. Uranium accumulations are found only in Mbalmayo. Coarse saprolitic materials at Ayos are the most depleted and fractionated in REE ((La/Yb)N = 0.07, Ce/Ce* = 2.24), while superficial clayey materials are less fractionated. This process is reversed at Bengbis and Mbalmayo. By contrast, weathered materials at Ayos do not show any Eu anomalies (as in Bengbis and Mbalmayo). Weathered materials from Bengbis, nearest to the Dja River, have (La/Yb)N < 1 ratios, indicating the relative immobility of HREE relative to LREE due to xenotime abnormally rich in HREE (HREE-PO4). Weak Ce anomalies (1.05-2.24) are ubiquitous in all the studied materials.

  4. Phonological abilities in literacy-impaired children: Brain potentials reveal deficient phoneme discrimination, but intact prosodic processing.

    PubMed

    Männel, Claudia; Schaadt, Gesa; Illner, Franziska K; van der Meer, Elke; Friederici, Angela D

    2017-02-01

    Intact phonological processing is crucial for successful literacy acquisition. While individuals with difficulties in reading and spelling (i.e., developmental dyslexia) are known to experience deficient phoneme discrimination (i.e., segmental phonology), findings concerning their prosodic processing (i.e., suprasegmental phonology) are controversial. Because there are no behavior-independent studies on the underlying neural correlates of prosodic processing in dyslexia, these controversial findings might be explained by different task demands. To provide an objective behavior-independent picture of segmental and suprasegmental phonological processing in impaired literacy acquisition, we investigated event-related brain potentials during passive listening in typically and poor-spelling German school children. For segmental phonology, we analyzed the Mismatch Negativity (MMN) during vowel length discrimination, capturing automatic auditory deviancy detection in repetitive contexts. For suprasegmental phonology, we analyzed the Closure Positive Shift (CPS) that automatically occurs in response to prosodic boundaries. Our results revealed spelling group differences for the MMN, but not for the CPS, indicating deficient segmental, but intact suprasegmental phonological processing in poor spellers. The present findings point towards a differential role of segmental and suprasegmental phonology in literacy disorders and call for interventions that invigorate impaired literacy by utilizing intact prosody in addition to training deficient phonemic awareness.

  5. The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing

    SciTech Connect

    Jackson, R.N.; Robinson, H.; Klauer, A. A.; Hintze, B. J.; van Hoof, A.; Johnson, S. J.

    2010-07-01

    The essential RNA helicase, Mtr4, performs a critical role in RNA processing and degradation as an activator of the nuclear exosome. The molecular basis for this vital function is not understood and detailed analysis is significantly limited by the lack of structural data. In this study, we present the crystal structure of Mtr4. The structure reveals a new arch-like domain that is specific to Mtr4 and Ski2 (the cytosolic homologue of Mtr4). In vivo and in vitro analyses demonstrate that the Mtr4 arch domain is required for proper 5.8S rRNA processing, and suggest that the arch functions independently of canonical helicase activity. In addition, extensive conservation along the face of the putative RNA exit site highlights a potential interface with the exosome. These studies provide a molecular framework for understanding fundamental aspects of helicase function in exosome activation, and more broadly define the molecular architecture of Ski2-like helicases.

  6. Ways of making-sense: Local gamma synchronization reveals differences between semantic processing induced by music and language.

    PubMed

    Barraza, Paulo; Chavez, Mario; Rodríguez, Eugenio

    2016-01-01

    Similar to linguistic stimuli, music can also prime the meaning of a subsequent word. However, it is so far unknown what is the brain dynamics underlying the semantic priming effect induced by music, and its relation to language. To elucidate these issues, we compare the brain oscillatory response to visual words that have been semantically primed either by a musical excerpt or by an auditory sentence. We found that semantic violation between music-word pairs triggers a classical ERP N400, and induces a sustained increase of long-distance theta phase synchrony, along with a transient increase of local gamma activity. Similar results were observed after linguistic semantic violation except for gamma activity, which increased after semantic congruence between sentence-word pairs. Our findings indicate that local gamma activity is a neural marker that signals different ways of semantic processing between music and language, revealing the dynamic and self-organized nature of the semantic processing.

  7. Double vibronic process in the quantum spin ice candidate Tb2Ti2O7 revealed by terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

    Constable, E.; Ballou, R.; Robert, J.; Decorse, C.; Brubach, J.-B.; Roy, P.; Lhotel, E.; Del-Rey, L.; Simonet, V.; Petit, S.; deBrion, S.

    2017-01-01

    The origin of quantum fluctuations responsible for the spin liquid state in Tb2Ti2O7 has remained a long-standing problem. By synchrotron-based terahertz measurements, we show evidence of strong coupling between the magnetic and lattice degrees of freedom that provides a path to the quantum melting process. As revealed by hybrid crystal electric field-phonon excitations that appear at 0.67 THz below 200 K, and around 0.42 THz below 50 K, the double vibronic process is unique for Tb3 + in the titanate family due to adequate energy matching and strong quadrupolar moments. The results suggest that lattice motion can indeed be the driving force behind spin flips within the hybridized ground and first excited states, promoting quantum terms in the effective Hamiltonian that describes Tb2Ti2O7 .

  8. Early activation of Broca's area in grammar processing as revealed by the syntactic mismatch negativity and distributed source analysis.

    PubMed

    Hanna, Jeff; Mejias, Sandrine; Schelstraete, Marie-Anne; Pulvermüller, Friedemann; Shtyrov, Yury; Van der Lely, Heather K J

    2014-01-01

    Though activation of Broca's region in the combinatorial processing of symbols (language, music) has been revealed by neurometabolic studies, most previous neurophysiological research found the earliest grammar indices in the temporal cortex, with inferior-frontal generators becoming active at relatively late stages. We use the attention- and task-free syntactic mismatch negativity (sMMN) event-related potential (ERP) to measure rapid and automatic sensitivity of the human brain to grammatical information in participants' native language (French). Further, sources underlying the MMN were estimated by applying the Parametrical Empirical Bayesian (PEB) approach, with the Multiple Sparse Priors (MSP) technique. Results showed reliable grammar-related activation focused on Broca's region already in the 150-190 ms time window, providing robust documentation of its involvement in the first stages of syntactic processing.

  9. Atypical category processing and hemispheric asymmetries in high-functioning children with autism: revealed through high-density EEG mapping.

    PubMed

    Fiebelkorn, Ian C; Foxe, John J; McCourt, Mark E; Dumas, Kristina N; Molholm, Sophie

    2013-05-01

    Behavioral evidence for an impaired ability to group objects based on similar physical or semantic properties in autism spectrum disorders (ASD) has been mixed. Here, we recorded brain activity from high-functioning children with ASD as they completed a visual-target detection task. We then assessed the extent to which object-based selective attention automatically generalized from targets to non-target exemplars from the same well-known object class (e.g., dogs). Our results provide clear electrophysiological evidence that children with ASD (N=17, aged 8-13 years) process the similarity between targets (e.g., a specific dog) and same-category non-targets (SCNT) (e.g., another dog) to a lesser extent than do their typically developing (TD) peers (N=21). A closer examination of the data revealed striking hemispheric asymmetries that were specific to the ASD group. These findings align with mounting evidence in the autism literature of anatomic underconnectivity between the cerebral hemispheres. Years of research in individuals with TD have demonstrated that the left hemisphere (LH) is specialized toward processing local (or featural) stimulus properties and the right hemisphere (RH) toward processing global (or configural) stimulus properties. We therefore propose a model where a lack of communication between the hemispheres in ASD, combined with typical hemispheric specialization, is a root cause for impaired categorization and the oft-observed bias to process local over global stimulus properties.

  10. Extroversion-related differences in speed of premotor and motor processing as revealed by lateralized readiness potentials.

    PubMed

    Stahl, Jutta; Rammsayer, Thomas

    2008-03-01

    To further elucidate extroversion-related differences in speed of sensorimotor processing, the authors obtained behavioral and psychophysiological measures as participants (16 introverts and 16 extroverts) performed a visual go/no-go task. Although no extroversion-related differences in reaction time emerged, introverts showed faster premotor processing but slower central and peripheral motor processing--as indicated by latencies of the lateralized readiness potential (LRP) and electromyographic (EMG) data, respectively--than extroverts did. Additional regression analyses revealed that stimulus-locked LRP latency, response-locked LRP latency, and Nl EMG amplitude accounted for 40% of overall variability in individual extroversion scores. On the basis of the present results, the authors introduce a compensation hypothesis that accounts for the common failure of researchers to demonstrate extroversion-related differences in reaction time. The present results challenge J. Brebner and C. Cooper's (1985) model of extroversion in which stimulus analysis is not slower in introverts than in extroverts. However, the present findings support the assumption of faster motor processing in extroverts.

  11. Process-Based Species Pools Reveal the Hidden Signature of Biotic Interactions Amid the Influence of Temperature Filtering.

    PubMed

    Lessard, Jean-Philippe; Weinstein, Ben G; Borregaard, Michael K; Marske, Katharine A; Martin, Danny R; McGuire, Jimmy A; Parra, Juan L; Rahbek, Carsten; Graham, Catherine H

    2016-01-01

    A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations, and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature-but not precipitation or dispersal limitation-acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.

  12. Sources and processes affecting the spatio-temporal distribution of pharmaceuticals and X-ray contrast media in the water resources of the Lower Jordan Valley, Jordan.

    PubMed

    Zemann, Moritz; Wolf, Leif; Pöschko, Antje; Schmidt, Natalie; Sawarieh, Ali; Seder, Nayef; Tiehm, Andreas; Hötzl, Heinz; Goldscheider, Nico

    2014-08-01

    The closed basin of the Lower Jordan Valley with the Dead Sea as final sink features high evapotranspiration rates and almost complete reuse of treated wastewater for irrigation farming. This study focuses on the water transfer schemes and the presence, spreading, and potential accumulation of pharmaceutical residues in the local water resources based on findings of a five-year monitoring program. Overall 16 pharmaceuticals and 9 iodinated X-ray contrast media were monitored in groundwater, surface water, and treated wastewater. A total of 95 samples were taken to cover all geographical settings and flow paths from origin (wastewater) to target (groundwater). Nine substances were detected in groundwater, with concentrations ranging between 11 ng/L and 33,000 ng/L. Sometimes, detection rates were higher than in comparable studies: Diatrizoic acid 75%, iopamidol 42%, iopromide 19%, iomeprol 11%, carbamazepine and iohexol 8%, ibuprofen 6%, and fenofibrate and iothalamic acid 3%. Concentrations in groundwater generally increase from north to south depending on the application of treated wastewater for irrigation. Almost all substances occurred most frequently and with highest concentrations in treated wastewater, followed by surface water and groundwater. As exception, diatrizoic acid was found more frequently in groundwater than in treated wastewater, with concentrations being similar. This indicates the persistence of diatrizoic acid with long residence times in local groundwater systems, but may also reflect changing prescription patterns, which would be in accordance with increasing iopamidol findings and surveys at local hospitals. Trend analyses confirm this finding and indicate a high probability of increasing iopamidol concentrations, while other substances did not reveal any trends. However, no proof of evaporative enrichment could be found. The high spatial and temporal variability of the concentrations measured calls for further systematic studies to assess

  13. Finding of low-contrast formations in the solar corona using a low contrast method

    NASA Astrophysics Data System (ADS)

    Kuznetsova, S. M.; Krissinel, B. B.; Obukhov, A. G.; Prosovetsky, D. V.; Smolkov, G. Ya.

    2009-12-01

    Coronal holes, bright coronal points, filaments, and prominences are among the initial factors responsible for variability of the space weather conditions. Radioheliographic data on low-contrast formations contain valuable information necessary for studying conditions of origination, peculiarities of evolution, and prediction of solar-terrestrial relations. It is important to identify these formations on the solar disk when physical properties of coronal holes are revealed. The algorithm based on the Wiener-Tikhonov filter modification with controlled parameters and a high-frequency contrast filter was developed in order to isolate low-contrast formations in the solar corona brightness distributions obtained at a wavelength of 5.2 cm from the Siberian solar radio telescope observations. In this case low-contrast sources are isolated in two main stages: (1) HF noise smoothing based on an evolutionary filter with controlled parameters and (2) contrasting of sources using an HF filter. The evolutionary filter regularization parameters and the dimensions of an HF contrast filter mask are selected depending on the signal-to-noise ratio and dimensions of the studied region based on the results of preliminary data processing. The corresponding software has been developed in order to identify low-contrast objects on the Sun’s radio images using this method. The algorithm is used to isolate filaments and coronal holes and the results of this usage are presented in this work.

  14. TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level

    PubMed Central

    2014-01-01

    Background The TGF-β signaling pathway is a fundamental pathway in the living cell, which plays a key role in many central cellular processes. The complex and sometimes contradicting mechanisms by which TGF-β yields phenotypic effects are not yet completely understood. In this study we investigated and compared the transcriptional response profile of TGF-β1 stimulation in different cell types. For this purpose, extensive experiments are performed and time-course microarray data are generated in human and mouse parenchymal liver cells, human mesenchymal stromal cells and mouse hematopoietic progenitor cells at different time points. We applied a panel of bioinformatics methods on our data to uncover common patterns in the dynamic gene expression response in respective cells. Results Our analysis revealed a quite variable and multifaceted transcriptional response profile of TGF-β1 stimulation, which goes far beyond the well-characterized classical TGF-β1 signaling pathway. Nonetheless, we could identify several commonly affected processes and signaling pathways across cell types and species. In addition our analysis suggested an important role of the transcription factor EGR1, which appeared to have a conserved influence across cell-types and species. Validation via an independent dataset on A549 lung adenocarcinoma cells largely confirmed our findings. Network analysis suggested explanations, how TGF-β1 stimulation could lead to the observed effects. Conclusions The analysis of dynamical transcriptional response to TGF-β treatment experiments in different human and murine cell systems revealed commonly affected biological processes and pathways, which could be linked to TGF-β1 via network analysis. This helps to gain insights about TGF-β pathway activities in these cell systems and its conserved interactions between the species and tissue types. PMID:24886091

  15. Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis

    PubMed Central

    Huang, Shu; Wang, Jun; Yue, Wucheng; Chen, Jiao; Gaughan, Sarah; Lu, Weiqun; Lu, Guoqing; Wang, Chenghui

    2015-01-01

    Molting is a critical developmental process for crustaceans, yet the underlying molecular mechanism is unknown. In this study, we used RNA-Seq to investigate transcriptomic profiles of the hepatopancreas and identified differentially expressed genes at four molting stages of Chinese mitten crab (Eriocheir sinensis). A total of 97,398 transcripts were assembled, with 31,900 transcripts annotated. Transcriptomic comparison revealed 1,189 genes differentially expressed amongst different molting stages. We observed a pattern associated with energy metabolism and physiological responses during a molting cycle. In specific, differentially expressed genes enriched in postmolt were linked to energy consumption whereas genes enriched in intermolt were related to carbohydrates, lipids metabolic and biosynthetic processes. In premolt, a preparation stage for upcoming molting and energy consumption, highly expressed genes were enriched in response to steroid hormone stimulus and immune system development. The expression profiles of twelve functional genes detected via RNA-Seq were corroborated through real-time RT-PCR assay. Together, our results, including assembled transcriptomes, annotated functional elements and enriched differentially expressed genes amongst different molting stages, provide novel insights into the functions of the hepatopancreas in energy metabolism and biological processes pertaining to molting in crustaceans. PMID:26369734

  16. Looking at the evidence in visual world: eye-movements reveal how bilingual and monolingual Turkish speakers process grammatical evidentiality

    PubMed Central

    Arslan, Seçkin; Bastiaanse, Roelien; Felser, Claudia

    2015-01-01

    This study presents pioneering data on how adult early bilinguals (heritage speakers) and late bilingual speakers of Turkish and German process grammatical evidentiality in a visual world setting in comparison to monolingual speakers of Turkish. Turkish marks evidentiality, the linguistic reference to information source, through inflectional affixes signaling either direct (-DI) or indirect (-mIş) evidentiality. We conducted an eye-tracking-during-listening experiment where participants were given access to visual ‘evidence’ supporting the use of either a direct or indirect evidential form. The behavioral results indicate that the monolingual Turkish speakers comprehended direct and indirect evidential scenarios equally well. In contrast, both late and early bilinguals were less accurate and slower to respond to direct than to indirect evidentials. The behavioral results were also reflected in the proportions of looks data. That is, both late and early bilinguals fixated less frequently on the target picture in the direct than in the indirect evidential condition while the monolinguals showed no difference between these conditions. Taken together, our results indicate reduced sensitivity to the semantic and pragmatic function of direct evidential forms in both late and early bilingual speakers, suggesting a simplification of the Turkish evidentiality system in Turkish heritage grammars. We discuss our findings with regard to theories of incomplete acquisition and first language attrition. PMID:26441762

  17. Looking at the evidence in visual world: eye-movements reveal how bilingual and monolingual Turkish speakers process grammatical evidentiality.

    PubMed

    Arslan, Seçkin; Bastiaanse, Roelien; Felser, Claudia

    2015-01-01

    This study presents pioneering data on how adult early bilinguals (heritage speakers) and late bilingual speakers of Turkish and German process grammatical evidentiality in a visual world setting in comparison to monolingual speakers of Turkish. Turkish marks evidentiality, the linguistic reference to information source, through inflectional affixes signaling either direct (-DI) or indirect (-mIş) evidentiality. We conducted an eye-tracking-during-listening experiment where participants were given access to visual 'evidence' supporting the use of either a direct or indirect evidential form. The behavioral results indicate that the monolingual Turkish speakers comprehended direct and indirect evidential scenarios equally well. In contrast, both late and early bilinguals were less accurate and slower to respond to direct than to indirect evidentials. The behavioral results were also reflected in the proportions of looks data. That is, both late and early bilinguals fixated less frequently on the target picture in the direct than in the indirect evidential condition while the monolinguals showed no difference between these conditions. Taken together, our results indicate reduced sensitivity to the semantic and pragmatic function of direct evidential forms in both late and early bilingual speakers, suggesting a simplification of the Turkish evidentiality system in Turkish heritage grammars. We discuss our findings with regard to theories of incomplete acquisition and first language attrition.

  18. Genome-wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics.

    PubMed

    Yant, Levi

    2012-02-01

    How does evolution forge adaptive responses? Are many changes required or few? Just how complex are the transcriptional networks that control development? Diverse questions like these are being newly addressed by next-generation sequencing-based techniques. Facilitating a mechanistic understanding, these approaches reveal the direct in vivo interactions between transcription factors and their physical targets, combined with genome-scale readouts to comprehensively map adaptive gene regulatory networks (GRNs). Here I focus on pioneering work from the last 3 years that has leveraged these data to investigate diverse aspects of GRN circuitry controlling the reproductive transition in plants. These approaches have revealed surprising new functions for long-investigated key players in developmental programs and laid bare the basis for pleiotropy in many others, suggesting widespread process integration at the transcriptional level. Evolutionary questions begged by the recent deluge of GRN mapping data are being assessed anew, both by emerging work outside Arabidopsis thaliana and novel analyses within. These studies have swiftly exposed the distinctive power and adaptability of genome-wide GRN mapping and illustrate that this unique data type holds tremendous promise for plant biology.

  19. RAP-PCR fingerprinting reveals time-dependent expression of development-related genes following differentiation process of Bacillus thuringiensis.

    PubMed

    Huang, Tianpei; Yu, Xiaomin; Gelbič, Ivan; Guan, Xiong

    2015-09-01

    Gene expression profiles are important data to reveal the functions of genes putatively involved in crucial biological processes. RNA arbitrarily primed polymerase chain reaction (RAP-PCR) and specifically primed reverse transcription polymerase chain reaction (RT-PCR) were combined to screen differentially expressed genes following development of a commercial Bacillus thuringiensis subsp. kurstaki strain 8010 (serotype 3a3b). Six differentially expressed transcripts (RAP1 to RAP6) were obtained. RAP1 encoded a putative triple helix repeat-containing collagen or an exosporium protein H related to spore pathogenicity. RAP2 was homologous to a ClpX protease and an ATP-dependent protease La (LonB), which likely acted as virulence factors. RAP3 was homologous to a beta subunit of propionyl-CoA carboxylase required for the development of Myxococcus xanthus. RAP4 had homology to a quinone oxidoreductase involved in electron transport and ATP formation. RAP5 showed significant homology to a uridine kinase that mediates phosphorylation of uridine and azauridine. RAP6 shared high sequence identity with 3-methyl-2-oxobutanoate-hydroxymethyltransferase (also known as ketopantoate hydroxymethyltransferase or PanB) involved in the operation of the tricarboxylic acid cycle. The findings described here would help to elucidate the molecular mechanisms underlying the differentiation process of B. thuringiensis and unravel novel pathogenic genes.

  20. Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing.

    PubMed

    Mizrachi, Eshchar; Verbeke, Lieven; Christie, Nanette; Fierro, Ana C; Mansfield, Shawn D; Davis, Mark F; Gjersing, Erica; Tuskan, Gerald A; Van Montagu, Marc; Van de Peer, Yves; Marchal, Kathleen; Myburg, Alexander A

    2017-01-31

    As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.

  1. Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

    DOE PAGES

    Mizrachi, Eshchar; Verbeke, Lieven; Christie, Nanette; ...

    2017-01-17

    As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We havemore » applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. Furthermore, a more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.« less

  2. Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

    PubMed Central

    Mizrachi, Eshchar; Christie, Nanette; Fierro, Ana C.; Mansfield, Shawn D.; Davis, Mark F.; Gjersing, Erica; Tuskan, Gerald A.; Van Montagu, Marc; Van de Peer, Yves; Marchal, Kathleen; Myburg, Alexander A.

    2017-01-01

    As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy. PMID:28096391

  3. Degradation mechanisms and kinetic studies for the treatment of X-ray contrast media compounds by advanced oxidation/reduction processes.

    PubMed

    Jeong, Joonseon; Jung, Jinyoung; Cooper, William J; Song, Weihua

    2010-08-01

    The presence of iodinated X-ray contrast media compounds (ICM) in surface and ground waters has been reported. This is likely due to their biological inertness and incomplete removal in wastewater treatment processes. The present study reports partial degradation mechanisms based on elucidating the structures of major reaction by-products using gamma-irradiation and LC-MS. Studies conducted at concentrations higher than observed in natural waters is necessary to elucidate the reaction by-product structures and to develop destruction mechanisms. To support these mechanistic studies, the bimolecular rate constants for the reaction of OH and e(-)(aq) with one ionic ICM (diatrizoate), four non-ionic ICM (iohexol, iopromide, iopamidol, and iomeprol), and the several analogues of diatrizoate were determined. The absolute bimolecular reaction rate constants for diatrizoate, iohexol, iopromide, iopamidol, and iomeprol with OH were (9.58 +/- 0.23)x10(8), (3.20 +/- 0.13)x10(9), (3.34 +/- 0.14)x10(9), (3.42 +/- 0.28)x10(9), and (2.03 +/- 0.13) x 10(9) M(-1) s(-1), and with e(-)(aq) were (2.13 +/- 0.03)x10(10), (3.35 +/- 0.03)x10(10), (3.25 +/- 0.05)x10(10), (3.37 +/- 0.05)x10(10), and (3.47 +/- 0.02) x 10(10) M(-1) s(-1), respectively. Transient spectra for the intermediates formed by the reaction of OH were also measured over the time period of 1-100 micros to better understand the stability of the radicals and for evaluation of reaction rate constants. Degradation efficiencies for the OH and e(-)(aq) reactions with the five ICM were determined using steady-state gamma-radiolysis. Collectively, these data will form the basis of kinetic models for application of advanced oxidation/reduction processes for treating water containing these compounds.

  4. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing

    PubMed Central

    Tang, Thean Hock; Rozhdestvensky, Timofey S.; d’Orval, Béatrice Clouet; Bortolin, Marie-Line; Huber, Harald; Charpentier, Bruno; Branlant, Christiane; Bachellerie, Jean-Pierre; Brosius, Jürgen; Hüttenhofer, Alexander

    2002-01-01

    The bulge–helix–bulge (BHB) motif recognised by the archaeal splicing endonuclease is also found in the long processing stems of archaeal rRNA precursors in which it is cleaved to generate pre-16S and pre-23S rRNAs. We show that in two species, Archaeoglobus fulgidus and Sulfolobus solfataricus, representatives from the two major archaeal kingdoms Euryarchaeota and Crenarchaeota, respectively, the pre-rRNA spacers cleaved at the BHB motifs surrounding pre-16S and pre-23S rRNAs subsequently become ligated. In addition, we present evidence that this is accompanied by circularisation of ribosomal pre-16S and pre-23S rRNAs in both species. These data reveal a further link between intron splicing and pre-rRNA processing in Archaea, which might reflect a common evolutionary origin of the two processes. One spliced RNA species designated 16S-D RNA, resulting from religation at the BHB motif of 16S pre-rRNA, is a highly abundant and stable RNA which folds into a three-stem structure interrupted by two single-stranded regions as assessed by chemical probing. It spans a region of the pre-rRNA 5′ external transcribed spacer exhibiting a highly conserved folding pattern in Archaea. Surprisingly, 16S-D RNA contains structural motifs found in archaeal C/D box small RNAs and binds to the L7Ae protein, a core component of archaeal C/D box RNPs. This supports the notion that it might have an important but still unknown role in pre-rRNA biogenesis or might even target RNA molecules other than rRNA. PMID:11842103

  5. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    PubMed

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2015-11-20

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments.

  6. Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves.

    PubMed

    Xu, Wenying; Yang, Rendong; Li, Meina; Xing, Zhuo; Yang, Wenqiang; Chen, Guang; Guo, Han; Gong, Xiaojie; Du, Zhou; Zhang, Zhenhai; Hu, Xingming; Wang, Dong; Qian, Qian; Wang, Tai; Su, Zhen; Xue, Yongbiao

    2011-03-02

    Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological

  7. Analysis of gene expression dynamics revealed delayed and abnormal epidermal repair process in aged compared to young skin.

    PubMed

    Sextius, Peggy; Marionnet, Claire; Tacheau, Charlotte; Bon, François-Xavier; Bastien, Philippe; Mauviel, Alain; Bernard, Bruno A; Bernerd, Françoise; Dubertret, Louis

    2015-05-01

    With aging, epidermal homeostasis and barrier function are disrupted. In a previous study, we analyzed the transcriptomic response of young skin epidermis after stratum corneum removal, and obtained a global kinetic view of the molecular processes involved in barrier function recovery. In the present study, the same analysis was performed in aged skin in order to better understand the defects which occur with aging. Thirty healthy male volunteers (67 ± 4 years old) were involved. Tape-strippings were carried out on the inner face of one forearm, the other unstripped forearm serving as control. At 2, 6, 18, 30 and 72 h after stripping, TEWL measurements were taken, and epidermis samples were collected. Total RNA was extracted and analyzed using DermArray(®) cDNA microarrays. The results highlighted that barrier function recovery and overall kinetics of gene expression were delayed following stripping in aged skin. Indeed, the TEWL measurements showed that barrier recovery in the young group appeared to be dramatically significant during the overall kinetics, while there were no significant evolution in the aged group until 30 h. Moreover, gene expression analysis revealed that the number of modulated genes following tape stripping increased as a function of time and reached a peak at 6 h after tape stripping in young skin, while it was at 30 h in aged skin, showing that cellular activity linked to the repair process may be engaged earlier in young epidermis than in aged epidermis. A total of 370 genes were modulated in the young group. In the aged group, 382 genes were modulated, whose 184 were also modulated in the young group. Only eight genes that were modulated in both groups were significantly differently modulated. The characterization of these genes into 15 functional families helped to draw a scenario for the aging process affecting epidermal repair capacity.

  8. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis

    PubMed Central

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela

    2015-01-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. PMID:26590278

  9. Inactivation of the Anterior Cingulate Reveals Enhanced Reliance on Cortical Networks for Remote Spatial Memory Retrieval after Sequential Memory Processing

    PubMed Central

    Wartman, Brianne C.; Gabel, Jennifer; Holahan, Matthew R.

    2014-01-01

    One system consolidation model suggests that as time passes, ensembles of cortical neurons form strong connections to represent remote memories. In this model, the anterior cingulate cortex (ACC) serves as a cortical region that represents remote memories. However, there is debate as to whether remote spatial memories go through this systems consolidation process and come to rely on the ACC. The present experiment examined whether increasing the processing demand on the hippocampus, by sequential training on two spatial tasks, would more fully engage the ACC during retrieval of a remote spatial memory. In this scenario, inactivation of the ACC at a remote time point was hypothesized to produce a severe memory deficit if rats had been trained on two, sequential spatial tasks. Rats were trained on a water maze (WM) task only or a WM task followed by a radial arm maze task. A WM probe test was given recently or remotely to all rats. Prior to the probe test, rats received an injection of saline or muscimol into the ACC. A subtle deficit in probe performance was found at the remote time point in the group trained on only one spatial task and treated with muscimol. In the group trained on two spatial tasks and treated with muscimol, a subtle deficit in probe performance was noted at the recent time point and a substantial deficit in probe performance was observed at the remote time point. c-Fos labeling in the hippocampus revealed more labeling in the CA1 region in all remotely tested groups than recently tested groups. Findings suggest that spatial remote memories come to rely more fully on the ACC when hippocampal processing requirements are increased. Results also suggest continued involvement of the hippocampus in spatial memory retrieval along with a progressive strengthening of cortical connections as time progresses. PMID:25279556

  10. Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions

    PubMed Central

    2011-01-01

    Background Infection processes consist of a sequence of steps, each critical for the interaction between host and parasite. Studies of host-parasite interactions rarely take into account the fact that different steps might be influenced by different factors and might, therefore, make different contributions to shaping coevolution. We designed a new method using the Daphnia magna - Pasteuria ramosa system, one of the rare examples where coevolution has been documented, in order to resolve the steps of the infection and analyse the factors that influence each of them. Results Using the transparent Daphnia hosts and fluorescently-labelled spores of the bacterium P. ramosa, we identified a sequence of infection steps: encounter between parasite and host; activation of parasite dormant spores; attachment of spores to the host; and parasite proliferation inside the host. The chances of encounter had been shown to depend on host genotype and environment. We tested the role of genetic and environmental factors in the newly described activation and attachment steps. Hosts of different genotypes, gender and species were all able to activate endospores of all parasite clones tested in different environments; suggesting that the activation cue is phylogenetically conserved. We next established that parasite attachment occurs onto the host oesophagus independently of host species, gender and environmental conditions. In contrast to spore activation, attachment depended strongly on the combination of host and parasite genotypes. Conclusions Our results show that different steps are influenced by different factors. Host-type-independent spore activation suggests that this step can be ruled out as a major factor in Daphnia-Pasteuria coevolution. On the other hand, we show that the attachment step is crucial for the pronounced genetic specificities of this system. We suggest that this one step can explain host population structure and could be a key force behind coevolutionary

  11. Anisotropic contrast optical microscope.

    PubMed

    Peev, D; Hofmann, T; Kananizadeh, N; Beeram, S; Rodriguez, E; Wimer, S; Rodenhausen, K B; Herzinger, C M; Kasputis, T; Pfaunmiller, E; Nguyen, A; Korlacki, R; Pannier, A; Li, Y; Schubert, E; Hage, D; Schubert, M

    2016-11-01

    An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. These images are obtained from sets of multiple images obtained under various polarizer, analyzer, and compensator settings. Up to 16 independent Mueller matrix images can be obtained, while our current setup is limited to 11 images normalized by the unpolarized intensity. We demonstrate the anisotropic contrast optical microscope by measuring lithographically defined micro-patterned anisotropic filters, and we quantify the adsorption of an organic self-assembled monolayer film onto the anisotropic filter. Comparison with an isotropic glass slide demonstrates the image enhancement obtained by our method over microscopy without the use of an anisotropic filter. In our current instrument, we estimate the limit of detection for organic volumetric mass within the object plane of ≈49 fg within ≈7 × 7 μm(2) object surface area. Compared to a quartz crystal microbalance with dissipation instrumentation, where contemporary limits require a total load of ≈500 pg for detection, the instrumentation demonstrated here improves

  12. Anisotropic contrast optical microscope

    NASA Astrophysics Data System (ADS)

    Peev, D.; Hofmann, T.; Kananizadeh, N.; Beeram, S.; Rodriguez, E.; Wimer, S.; Rodenhausen, K. B.; Herzinger, C. M.; Kasputis, T.; Pfaunmiller, E.; Nguyen, A.; Korlacki, R.; Pannier, A.; Li, Y.; Schubert, E.; Hage, D.; Schubert, M.

    2016-11-01

    An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. These images are obtained from sets of multiple images obtained under various polarizer, analyzer, and compensator settings. Up to 16 independent Mueller matrix images can be obtained, while our current setup is limited to 11 images normalized by the unpolarized intensity. We demonstrate the anisotropic contrast optical microscope by measuring lithographically defined micro-patterned anisotropic filters, and we quantify the adsorption of an organic self-assembled monolayer film onto the anisotropic filter. Comparison with an isotropic glass slide demonstrates the image enhancement obtained by our method over microscopy without the use of an anisotropic filter. In our current instrument, we estimate the limit of detection for organic volumetric mass within the object plane of ≈49 fg within ≈7 × 7 μm2 object surface area. Compared to a quartz crystal microbalance with dissipation instrumentation, where contemporary limits require a total load of ≈500 pg for detection, the instrumentation demonstrated here improves

  13. A two-step ICT process for solvatochromic betaine pyridinium revealed by ultrafast spectroscopy, multivariate curve resolution, and TDDFT calculations.

    PubMed

    Aloïse, Stéphane; Pawlowska, Zuzanna; Ruckebusch, Cyril; Sliwa, Michel; Dubois, Julien; Poizat, Olivier; Buntinx, Guy; Perrier, Aurélie; Maurel, François; Jacques, Patrice; Malval, Jean-Pierre; Poisson, Lionel; Piani, Giovanni; Abe, Jiro

    2012-02-14

    This work deals with the photophysics of a pyridinium betaine, 2-pyridin-1-yl-1H-benzimidazole (SBPa), based on a combination of steady-state, femtosecond photoionization (gas phase) and femtosecond transient absorption (solution) spectroscopic measurements, supported by (LR)-PCM-(TD)DFT calculations. Preliminary and new electrochemical results have revealed a strongly negative solvatochromic charge transfer (CT) absorption due to a S(0) → S(2) vertical transition and a weakly-solvatochromic emission due to S(1) → S(0) transition. Advanced TDDFT optimizations of the Franck-Condon states S(2)(FC) and S(1)(FC) led to two additional CT levels with planar geometry, S(2)(CT) and S(1)(CT), respectively, allowing prediction of a two-step photoinduced ICT process, i.e., S(0) → S(2)(FC) and S(2)(CT) → S(1)(CT), separated by a S(2)(FC) → S(2)(CT) back charge transfer relaxation. While the pyridinium ring is the acceptor group in both steps, two different donor groups, the benzene ring and the imidazole bridge, are involved in the excitation and internal conversion processes, respectively. Femtosecond transient absorption experiments supported by MCR-ALS decomposition confirmed indeed the contribution of two distinct CT states in the photophysics of SBPa: following excitation to the S(2)(CT) state, ultrafast production of the emissive S(1) state (the only channel observable in the gas phase) was observed to occur in competition with a further ICT process toward the S(1)(CT) state, with a time constant ranging from 300 fs to 20 ps depending on the solvent. While in aprotic media this ICT process was found to be purely solvent controlled (double polarity and viscosity dependency), in protic solvents, the influence of the hydrogen bond network has to be taken into account. Comparison with data obtained for a pre-twisted SBPa analogue led us to exclude the presence of any large-amplitude geometrical change during ICT. Analyzing the solvent dependency using the power law

  14. Polychromatic diffraction contrast tomography

    SciTech Connect

    King, A.; Reischig, P.; Adrien, J.; Peetermans, S.; Ludwig, W.

    2014-11-15

    This tutorial review introduces the use of polychromatic radiation for 3D grain mapping using X-ray diffraction contrast tomography. The objective is to produce a 3D map of the grain shapes and orientations within a bulk, millimeter-sized polycrystalline sample. The use of polychromatic radiation enables the standard synchrotron X-ray technique to be applied in a wider range of contexts: 1) Using laboratory X-ray sources allows a much wider application of the diffraction contrast tomography technique. 2) Neutron sources allow large samples, or samples containing high Z elements to be studied. 3) Applied to synchrotron sources, smaller samples may be treated, or faster measurements may be possible. Challenges and particularities in the data acquisition and processing, and the limitations of the different variants, are discussed. - Highlights: • We present a tutorial review of polychromatic diffraction contrast tomography techniques. • The use of polychromatic radiation allows the standard synchrotron DCT technique to be extended to a range of other sources. • The characteristics and limitations of all variants of the techniques are derived, discussed and compared. • Examples using laboratory X-ray and cold neutron radiation are presented. • Suggestions for the future development of these techniques are presented.

  15. Comparative transcriptome analysis reveals a global insight into molecular processes regulating citrate accumulation in sweet orange (Citrus sinensis).

    PubMed

    Lu, Xiaopeng; Cao, Xiongjun; Li, Feifei; Li, Jing; Xiong, Jiang; Long, Guiyou; Cao, Shangyin; Xie, Shenxi

    2016-12-01

    Citrate, the predominant organic acid in citrus, determines the taste of these fruits. However, little is known about the synergic molecular processes regulating citrate accumulation. Using 'Dahongtiancheng' (Citrus sinensis) and 'Bingtangcheng' (C. sinensis) with significant difference in citrate, the objectives of this study were to understand the global mechanisms of high-citrate accumulation in sweet orange. 'Dahongtiancheng' and 'Bingtangcheng' exhibit significantly different patterns in citrate accumulation throughout fruit development, with the largest differences observed at 50-70 days after full bloom (DAFB). Comparative transcriptome profiling was performed for the endocarps of both cultivars at 50 and 70 DAFB. Over 34.5 million clean reads per library were successfully mapped to the reference database and 670-2630 differentially expressed genes (DEGs) were found in four libraries. Among the genes, five transcription factors were ascertained to be the candidates regulating citrate accumulation. Functional assignments of the DEGs indicated that photosynthesis, the citrate cycle and amino acid metabolism were significantly altered in 'Dahongtiancheng'. Physiological and molecular analyses suggested that high photosynthetic efficiency and partial impairment of citrate catabolism were crucial for the high-citrate trait, and amino acid biosynthesis was one of the important directions for citrate flux. The results reveal a global insight into the gene expression changes in a high-citrate compared with a low-citrate sweet orange. High accumulating efficiency and impaired degradation of citrate may be associated with the high-citrate trait of 'Dahongtiancheng'. Findings in this study increase understanding of the molecular processes regulating citrate accumulation in sweet orange.

  16. An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination.

    PubMed

    Wei, Ting; He, Zilong; Tan, XinYu; Liu, Xue; Yuan, Xiao; Luo, Yingfeng; Hu, Songnian

    2015-08-14

    Seed germination is a crucial stage for plant development and agricultural production. To investigate its complex regulation process, the RNA-Seq study of rice embryo was conducted at three time points of 0, 12 and 48 h post imbibition (HPI). Dynamic transcriptional alterations were observed, especially in the early stage (0-12 HPI). Seed related genes, especially those encoding desiccation inducible proteins and storage reserves in embryo, decreased drastically after imbibition. The expression profiles of phytohormone related genes indicated distinct roles of abscisic acid (ABA), gibberellin (GA) and brassinosteroid (BR) in germination. Moreover, network analysis revealed the importance of protein phosphorylation in phytohormone interactions. Network and gene ontology (GO) analyses suggested that transcription factors (TFs) played a regulatory role in functional transitions during germination, and the enriched TF families at 0 HPI implied a regulation of epigenetic modification in dry seeds. In addition, 35 germination-specific TF genes in embryo were identified and seven genes were verified by qRT-PCR. Besides, enriched TF binding sites (TFBSs) supported physiological changes in germination. Overall, this study expands our comprehensive knowledge of multiple regulation factors underlying rice seed germination.

  17. Origin and Depositional Processes of Coastal Sands Revealed by Grain-Size Analysis (golfe du Lion, Mediterranean Sea, France)

    NASA Astrophysics Data System (ADS)

    Barusseau, J. P.; Braud, R.

    2014-12-01

    The study focused on the lower beach and nearshore zone of the Golfe du Lion (northwestern Mediterranean Sea -France). We looked at grain-size distribution in the berm, collision zone, inner and outer bars, lower shoreface applying parametric methods, grain-size modal analysis and a deconvolution program (LNDoGS).Results indicate a mixture of three recognizable sedimentary types (ST1 - ST3 - ST4) and explain grain-size distribution (GSD) of the sands in both multimodal and apparently unimodal GSDs. ST1 flows from the River Rhone, ST3 and 4 are local components originating from either fluvial input or nearshore reworking of Quaternary sediments.A fourth component (ST2), derived in situ from ST1, is found far from the overwhelming footprint of the Rhone river sands, westward in the lower shoreface.The mixing process entails significant variations in grain-size indices and skewness appears as a very sensitive and meaningful parameter. Skewness and bimodality, generated in all zones, are two aspects of the mixing process, depending on the relative proportions of STs.Using LNDoGS makes deciphering the STs a lot easier. It also reveals that some GSDs can result from a combination of 3 sedimentary variants (SVs) belonging to the same ST (monotype grain-size distributions). Monotype mixtures are very abundant on the lower shoreface, significantly present on the berm and inner bar but rare in the most dynamic zones. On the berm they tend towards a lognormal model for only bedload is present in the swash. This trend towards a lognormal model can also be observed on the lower shoreface, possibly indicating the occurrence of suspension as a dominant process.Thus, each segment of the nearshore - foreshore profile can be characterized using coarseness, skewness sign, the presence of locally generated ST2, abundance of bimodalities, occurrence of SVs. Finally, a more detailed description of the spatial properties of grain-size distributions could help explore possible mechanisms

  18. A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing.

    PubMed

    Kremsky, Isaac; Bellora, Nicolás; Eyras, Eduardo

    2015-01-01

    High-throughput sequencing, and genome-based datasets in general, are often represented as profiles centered at reference points to study the association of protein binding and other signals to particular regulatory mechanisms. Although these profiles often provide compelling evidence of these associations, they do not provide a quantitative assessment of the enrichment, which makes the comparison between signals and conditions difficult. In addition, a number of biases can confound profiles, but are rarely accounted for in the tools currently available. We present a novel computational method, ProfileSeq, for the quantitative assessment of biological profiles to provide an exact, nonparametric test that specific regions of the test profile have higher or lower signal densities than a control set. The method is applicable to high-throughput sequencing data (ChIP-Seq, GRO-Seq, CLIP-Seq, etc.) and to genome-based datasets (motifs, etc.). We validate ProfileSeq by recovering and providing a quantitative assessment of several results reported before in the literature using independent datasets. We show that input signal and mappability have confounding effects on the profile results, but that normalizing the signal by input reads can eliminate these biases while preserving the biological signal. Moreover, we apply ProfileSeq to ChIP-Seq data for transcription factors, as well as for motif and CLIP-Seq data for splicing factors. In all examples considered, the profiles were robust to biases in mappability of sequencing reads. Furthermore, analyses performed with ProfileSeq reveal a number of putative relationships between transcription factor binding to DNA and splicing factor binding to pre-mRNA, adding to the growing body of evidence relating chromatin and pre-mRNA processing. ProfileSeq provides a robust way to quantify genome-wide coordinate-based signal. Software and documentation are freely available for academic use at https://bitbucket.org/regulatorygenomicsupf/profileseq/.

  19. High-frequency monitoring reveals nutrient sources and transport processes in an agriculture-dominated lowland water system

    NASA Astrophysics Data System (ADS)

    van der Grift, Bas; Broers, Hans Peter; Berendrecht, Wilbert; Rozemeijer, Joachim; Osté, Leonard; Griffioen, Jasper

    2016-05-01

    Many agriculture-dominated lowland water systems worldwide suffer from eutrophication caused by high nutrient loads. Insight in the hydrochemical functioning of embanked polder catchments is highly relevant for improving the water quality in such areas or for reducing export loads to downstream water bodies. This paper introduces new insights in nutrient sources and transport processes in a polder in the Netherlands situated below sea level using high-frequency monitoring technology at the outlet, where the water is pumped into a higher situated lake, combined with a low-frequency water quality monitoring programme at six locations within the drainage area. Seasonal trends and short-scale temporal dynamics in concentrations indicated that the NO3 concentration at the pumping station originated from N loss from agricultural lands. The NO3 loads appear as losses via tube drains after intensive rainfall events during the winter months due to preferential flow through the cracked clay soil. Transfer function-noise modelling of hourly NO3 concentrations reveals that a large part of the dynamics in NO3 concentrations during the winter months can be related to rainfall. The total phosphorus (TP) concentration and turbidity almost doubled during operation of the pumping station, which points to resuspension of particulate P from channel bed sediments induced by changes in water flow due to pumping. Rainfall events that caused peaks in NO3 concentrations did not results in TP concentration peaks. The rainfall induced and NO3 enriched quick interflow, may also be enriched in TP but retention of TP due to sedimentation of particulate P then results in the absence of rainfall induced TP concentration peaks. Increased TP concentrations associated with run-off events is only observed during a rainfall event at the end of a freeze-thaw cycle. All these observations suggest that the P retention potential of polder water systems is primarily due to the artificial pumping regime

  20. High-frequency monitoring reveals nutrient sources and transport processes in an agriculture-dominated lowland water system

    NASA Astrophysics Data System (ADS)

    van der Grift, B.; Broers, H. P.; Berendrecht, W. L.; Rozemeijer, J. C.; Osté, L. A.; Griffioen, J.

    2015-08-01

    Many agriculture-dominated lowland water systems worldwide suffer from eutrophication caused by high nutrient loads. Insight in the hydrochemical functioning of embanked polder catchments is highly relevant for improving the water quality in such areas. This paper introduces new insights in nutrient sources and transport processes in a low elevated polder in the Netherlands using high-frequency monitoring technology at the outlet, where the water is pumped into a higher situated lake, combined with a low-frequency water quality monitoring program at six locations within the drainage area. Seasonal trends and short scale temporal dynamics in concentrations indicated that the NO3 concentration at the pumping station originated from N-loss from agricultural lands. The NO3 loads appear as losses with drain water discharge after intensive rainfall events during the winter months due to preferential flow through the cracked clay soil. Transfer function-noise modelling of hourly NO3 concentrations reveals that a large part of the dynamics in NO3 concentrations during the winter months can be related to rainfall. The total phosphorus (TP) concentration almost doubled during operation of the pumping station which points to resuspension of particulate P from channel bed sediments induced by changes in water flow due to pumping. Rainfall events that caused peaks in NO3 concentrations did not results in TP concentration peaks. The by rainfall induced and NO3 enriched quick interflow, may also be enriched in TP but this is then buffered in the water system due to sedimentation of particulate P. Increased TP concentrations associated with run-off events is only observed during a rainfall event at the end of a freeze-thaw cycle. All these observations suggest that the P retention potential of polder water systems is highly due to the artificial pumping regime that buffers high flows. As the TP concentration is affected by operation of the pumping station, timing of sampling

  1. Source Rupture Process of the 2008 Iwate-Miyagi Nairiku, Japan, Earthquake Revealed from Near Fault Strong Motion Records

    NASA Astrophysics Data System (ADS)

    Suzuki, W.; Aoi, S.; Sekiguchi, H.

    2008-12-01

    We reveal the source rupture process of the 2008 Iwate-Miyagi Nairiku earthquake through the waveform inversion of the near fault strong motion records. At 8:43, June 14, 2008 (JST), a M7.2 shallow inland crustal earthquake struck Iwate and Miyagi Prefectures, northeast Japan. This earthquake, the 2008 Iwate-Miyagi Nairiku earthquake, is a reverse fault event, whose fault plane strikes to the southwest and dips to the northwest according to moment tensor solutions, aftershock distribution, and surface fault break. Strong motion networks, K-NET and KiK-net, operated by the National Research Institute for Earth Science and Disaster Prevention (NIED) obtained lots of the strong motion records at the near source region, which provide the information of the detailed source rupture process. We employ the multi-time-window linear waveform inversion method (Hartzell and Heaton, 1983). S-wave portion of the velocity waveforms (0.1-1 Hz) are used for the inversion. We use mainly borehole data at KiK- net stations. Green's functions are calculated using the discrete wavenumber method (Bouchon, 1981) and reflection/transmission coefficient matrix method (Kennett and Kerry, 1979) on the assumption of 1-D layered velocity structure. The rupture propagation effect within the subfault is included in the Green's function following Sekiguchi et al. (2002). Some stations are located on thick sediment. In order to take into account their effect on the observed waveforms, we construct the velocity structure model for each station referring to a 3-D subsurface structure model compiled for strong motion evaluation of whole Japan (Fujiwara et al., 2006). Validity of the assumed velocity structure is confirmed by simulating the aftershock records. The rupture starting point is set on the hypocenter relocated by Sekine et al. (2008) using double-difference method (Waldhauser and Ellsworth, 2000). Assumed fault plane covers a space of 40 km × 18 km. Its strike angle is 209° referring to F

  2. The Contrastive Analysis Hypothesis

    ERIC Educational Resources Information Center

    Wardhaugh, Ronald

    1970-01-01

    Discusses the strong contrastive analysis hypothesis, which claims predictive powers for contrastive analysis, and the weak hypothesis, which claims only that contrastive analysis can help account for observed difficulties in second language learning. The strong hypothesis is found untenable, and difficulties with the weak hypothesis are discussed…

  3. Continental-Margin Processes Recorded in Shelf and Canyon Sediments Documenting Fine-Sediment Import and Export for Two Contrasting Mesotidal Flats

    DTIC Science & Technology

    2008-01-01

    are the foundation for understanding and interpreting sedimentary processes and seabed stratigraphy . To investigate the relationship between... Sedimentological Congress, Fukuoka (2006). T.M. Drexler, C.A. Nittrouer, A.S. Ogston, P. Puig, Sediment record on the Rhone prodelta and processes controlling

  4. Metabolomics reveals the mechanisms for the cardiotoxicity of Pinelliae Rhizoma and the toxicity-reducing effect of processing

    NASA Astrophysics Data System (ADS)

    Su, Tao; Tan, Yong; Tsui, Man-Shan; Yi, Hua; Fu, Xiu-Qiong; Li, Ting; Chan, Chi Leung; Guo, Hui; Li, Ya-Xi; Zhu, Pei-Li; Tse, Anfernee Kai Wing; Cao, Hui; Lu, Ai-Ping; Yu, Zhi-Ling

    2016-10-01

    Pinelliae Rhizoma (PR) is a commonly used Chinese medicinal herb, but it has been frequently reported about its toxicity. According to the traditional Chinese medicine theory, processing can reduce the toxicity of the herbs. Here, we aim to determine if processing reduces the toxicity of raw PR, and to explore the underlying mechanisms of raw PR-induced toxicities and the toxicity-reducing effect of processing. Biochemical and histopathological approaches were used to evaluate the toxicities of raw and processed PR. Rat serum metabolites were analyzed by LC-TOF-MS. Ingenuity pathway analysis of the metabolomics data highlighted the biological pathways and network functions involved in raw PR-induced toxicities and the toxicity-reducing effect of processing, which were verified by molecular approaches. Results showed that raw PR caused cardiotoxicity, and processing reduced the toxicity. Inhibition of mTOR signaling and activation of the TGF-β pathway contributed to raw PR-induced cardiotoxicity, and free radical scavenging might be responsible for the toxicity-reducing effect of processing. Our data shed new light on the mechanisms of raw PR-induced cardiotoxicity and the toxicity-reducing effect of processing. This study provides scientific justifications for the traditional processing theory of PR, and should help in optimizing the processing protocol and clinical combinational application of PR.

  5. Metabolomics reveals the mechanisms for the cardiotoxicity of Pinelliae Rhizoma and the toxicity-reducing effect of processing

    PubMed Central

    Su, Tao; Tan, Yong; Tsui, Man-Shan; Yi, Hua; Fu, Xiu-Qiong; Li, Ting; Chan, Chi Leung; Guo, Hui; Li, Ya-Xi; Zhu, Pei-Li; Tse, Anfernee Kai Wing; Cao, Hui; Lu, Ai-Ping; Yu, Zhi-Ling

    2016-01-01

    Pinelliae Rhizoma (PR) is a commonly used Chinese medicinal herb, but it has been frequently reported about its toxicity. According to the traditional Chinese medicine theory, processing can reduce the toxicity of the herbs. Here, we aim to determine if processing reduces the toxicity of raw PR, and to explore the underlying mechanisms of raw PR-induced toxicities and the toxicity-reducing effect of processing. Biochemical and histopathological approaches were used to evaluate the toxicities of raw and processed PR. Rat serum metabolites were analyzed by LC-TOF-MS. Ingenuity pathway analysis of the metabolomics data highlighted the biological pathways and network functions involved in raw PR-induced toxicities and the toxicity-reducing effect of processing, which were verified by molecular approaches. Results showed that raw PR caused cardiotoxicity, and processing reduced the toxicity. Inhibition of mTOR signaling and activation of the TGF-β pathway contributed to raw PR-induced cardiotoxicity, and free radical scavenging might be responsible for the toxicity-reducing effect of processing. Our data shed new light on the mechanisms of raw PR-induced cardiotoxicity and the toxicity-reducing effect of processing. This study provides scientific justifications for the traditional processing theory of PR, and should help in optimizing the processing protocol and clinical combinational application of PR. PMID:27698376

  6. A Pattern of Perseveration in Cocaine Addiction May Reveal Neurocognitive Processes Implicit in the Wisconsin Card Sorting Test

    ERIC Educational Resources Information Center

    Woicik, Patricia A.; Urban, Catherine; Alia-Klein, Nelly; Henry, Ashley; Maloney, Thomas; Telang, Frank; Wang, Gene-Jack; Volkow, Nora D.; Goldstein, Rita Z.

    2011-01-01

    The ability to adapt behavior in a changing environment is necessary for humans to achieve their goals and can be measured in the lab with tests of rule-based switching. Disease models, such as cocaine addiction, have revealed that alterations in dopamine interfere with adaptive set switching, culminating in perseveration. We explore perseverative…

  7. Characterizing growth patterns in longitudinal MRI using image contrast

    NASA Astrophysics Data System (ADS)

    Vardhan, Avantika; Prastawa, Marcel; Vachet, Clement; Piven, Joseph; Gerig, Guido

    2014-03-01

    Understanding the growth patterns of the early brain is crucial to the study of neuro-development. In the early stages of brain growth, a rapid sequence of biophysical and chemical processes take place. A crucial component of these processes, known as myelination, consists of the formation of a myelin sheath around a nerve fiber, enabling the effective transmission of neural impulses. As the brain undergoes myelination, there is a subsequent change in the contrast between gray matter and white matter as observed in MR scans. In this work, gray-white matter contrast is proposed as an effective measure of appearance which is relatively invariant to location, scanner type, and scanning conditions. To validate this, contrast is computed over various cortical regions for an adult human phantom. MR (Magnetic Resonance) images of the phantom were repeatedly generated using different scanners, and at different locations. Contrast displays less variability over changing conditions of scan compared to intensity-based measures, demonstrating that it is less dependent than intensity on external factors. Additionally, contrast is used to analyze longitudinal MR scans of the early brain, belonging to healthy controls and Down's Syndrome (DS) patients. Kernel regression is used to model subject-specific trajectories of contrast changing with time. Trajectories of contrast changing with time, as well as time-based biomarkers extracted from contrast modeling, show large differences between groups. The preliminary applications of contrast based analysis indicate its future potential to reveal new information not covered by conventional volumetric or deformation-based analysis, particularly for distinguishing between normal and abnormal growth patterns.

  8. Application of Hoffman modulation contrast microscopy coupled with three-wavelength two-beam interferometry to the in situ direct observation of the growth process of a crystal in microgravity

    NASA Technical Reports Server (NTRS)

    Tsukamoto, Katsuo

    1988-01-01

    Direct visualization of three dimensional transfer process of both heat and mass around a growing crystal and mono-molecular growth layers on the surface is possible in situ by means of high resolution Hoffman modulation contrast microscopy coupled with three wavelength two beam Mach-Zehnder interferometry. This in situ observation is very suitable for the verification of the growth mechanism of a crystal in a solution or a melt in microgravity.

  9. Unexpected bismuth concentration profiles in metal-organic vapor phase epitaxy-grown Ga(As{sub 1−x}Bi{sub x})/GaAs superlattices revealed by Z-contrast scanning transmission electron microscopy imaging

    SciTech Connect

    Wood, A. W.; Babcock, S. E.; Guan, Y.; Forghani, K.; Anand, A.; Kuech, T. F.

    2015-03-01

    A set of GaAs{sub 1−x}Bi{sub x}/GaAs multilayer quantum-well structures was deposited by metal-organic vapor phase epitaxy at 390 °C and 420 °C. The precursor fluxes were introduced with the intent of growing discrete and compositionally uniform GaAs{sub 1−x}Bi{sub x} well and GaAs barrier layers in the epitaxial films. High-resolution high-angle annular-dark-field (or “Z-contrast”) scanning transmission electron microscopy imaging revealed concentration profiles that were periodic in the growth direction, but far more complicated in shape than the intended square wave. The observed composition profiles could explain various reports of physical properties measurements that suggest compositional inhomogeneity in GaAs{sub 1−x}Bi{sub x} alloys as they currently are grown.

  10. Individual Differences in Skilled Adult Readers Reveal Dissociable Patterns of Neural Activity Associated with Component Processes of Reading

    ERIC Educational Resources Information Center

    Welcome, Suzanne E.; Joanisse, Marc F.

    2012-01-01

    We used fMRI to examine patterns of brain activity associated with component processes of visual word recognition and their relationships to individual differences in reading skill. We manipulated both the judgments adults made on written stimuli and the characteristics of the stimuli. Phonological processing led to activation in left inferior…

  11. Cognitive Objectives Revealed by Classroom Questions in "Process-Oriented" and "Content-Oriented" Secondary Social Studies Programs.

    ERIC Educational Resources Information Center

    Tinsley, Drew C.; And Others

    This study investigates the cognitive nature of teacher-pupil questions in "process oriented" and "content oriented" secondary social studies programs. Subjects were five classes selected from a program viewed by both teachers and pupils as process-oriented; five from a program viewed by both teachers and pupils as content…

  12. Striatal and Hippocampal Entropy and Recognition Signals in Category Learning: Simultaneous Processes Revealed by Model-Based fMRI

    ERIC Educational Resources Information Center

    Davis, Tyler; Love, Bradley C.; Preston, Alison R.

    2012-01-01

    Category learning is a complex phenomenon that engages multiple cognitive processes, many of which occur simultaneously and unfold dynamically over time. For example, as people encounter objects in the world, they simultaneously engage processes to determine their fit with current knowledge structures, gather new information about the objects, and…

  13. Indicators of Early and Late Processing Reveal the Importance of Within-Trial-Time for Theories of Associative Learning

    PubMed Central

    Lachnit, Harald; Thorwart, Anna; Schultheis, Holger; Lotz, Anja; Koenig, Stephan; Uengoer, Metin

    2013-01-01

    In four human learning experiments (Pavlovian skin conductance, causal learning, speeded classification task), we evaluated several associative learning theories that assume either an elemental (modified unique cue model and Harris’ model) or a configural (Pearce’s configural theory and an extension of it) form of stimulus processing. The experiments used two modified patterning problems (A/B/C+, AB/BC/AC+ vs. ABC-; A+, BC+ vs. ABC-). Pearce’s configural theory successfully predicted all of our data reflecting early stimulus processing, while the predictions of the elemental theories were in accord with all of our data reflecting later stages of stimulus processing. Our results suggest that the form of stimulus representation depends on the amount of time available for stimulus processing. Our findings highlight the necessity to investigate stimulus processing during conditioning on a finer time scale than usually done in contemporary research. PMID:23826092

  14. The unmasking of 'junk' RNA reveals novel sRNAs: from processed RNA fragments to marooned riboswitches.

    PubMed

    De Lay, Nicholas R; Garsin, Danielle A

    2016-04-01

    While the notion that RNAs can function as regulators dates back to early molecular studies of gene regulation of the lac operon, it is only over the last decade that the ubiquity and diversity of regulatory RNAs are being realized. Advancements in high throughput sequencing and the adoption of these approaches to rapidly sequence genomes and transcriptomes and to examine gene expression and RNA binding protein specificity have revealed an ever-expanding RNA world. In this review, we focus on recent studies revealing that RNA fragments cleaved from larger coding or noncoding RNAs can have regulatory functions. Additionally, we discuss examples of riboswitches that function in trans as mRNA or protein-binding sRNAs, upending the traditional thinking that these are exclusively cis-acting elements.

  15. In situ observation of fracture processes in high-strength concretes and limestone using high-speed X-ray phase-contrast imaging

    NASA Astrophysics Data System (ADS)

    Parab, Niranjan D.; Guo, Zherui; Hudspeth, Matthew; Claus, Benjamin; Lim, Boon Him; Sun, Tao; Xiao, Xianghui; Fezzaa, Kamel; Chen, Weinong W.

    2017-01-01

    The mechanical properties and fracture mechanisms of geomaterials and construction materials such as concrete are reported to be dependent on the loading rates. However, the in situ cracking inside such specimens cannot be visualized using traditional optical imaging methods since the materials are opaque. In this study, the in situ sub-surface failure/damage mechanisms in Cor-Tuf (a reactive powder concrete), a high-strength concrete (HSC) and Indiana limestone under dynamic loading were investigated using high-speed synchrotron X-ray phase-contrast imaging. Dynamic compressive loading was applied using a modified Kolsky bar and fracture images were recorded using a synchronized high-speed synchrotron X-ray imaging set-up. Three-dimensional synchrotron X-ray tomography was also performed to record the microstructure of the specimens before dynamic loading. In the Cor-Tuf and HSC specimens, two different modes of cracking were observed: straight cracking or angular cracking with respect to the direction of loading. In limestone, cracks followed the grain boundaries and voids, ultimately fracturing the specimen. Cracks in HSC were more tortuous than the cracks in Cor-Tuf specimens. The effects of the microstructure on the observed cracking behaviour are discussed. This article is part of the themed issue 'Experimental testing and modelling of brittle materials at high strain rates'.

  16. Clouds of high contrast on Uranus.

    PubMed

    Karkoschka, E

    1998-04-24

    Near-infrared images of Uranus taken with the Hubble Space Telescope in July and October 1997 revealed discrete clouds with contrasts exceeding 10 times the highest contrast observed before with other techniques. At visible wavelengths, these 10 clouds had lower contrasts than clouds seen by Voyager 2 in 1986. Uranus' rotational rates for southern latitudes were identical in 1986 and 1997. Clouds in northern latitudes rotate slightly more slowly than clouds in opposite southern latitudes.

  17. Earlier timbre processing of instrumental tones compared to equally complex spectrally rotated sounds as revealed by the mismatch negativity.

    PubMed

    Christmann, Corinna A; Lachmann, Thomas; Berti, Stefan

    2014-10-03

    Harmonically rich sounds have been shown to be processed more efficiently by the human brain compared to single sinusoidal tones. To control for stimulus complexity as a potentially confounding factor, tones and equally complex spectrally rotated sounds, have been used in the present study to investigate the role of the overtone series in sensory auditory processing in non-musicians. Timbre differences in instrumental tones with equal pitch elicited a MMN which was earlier compared to that elicited by the spectrally rotated sounds, indicating that harmonically rich tones are processed faster compared to non-musical sounds without an overtone series, even when pitch is not the relevant information.

  18. To What Extent Do We Hear Phonemic Contrasts in a Non-Native Regional Variety? Tracking the Dynamics of Perceptual Processing with EEG

    ERIC Educational Resources Information Center

    Dufour, Sophie; Brunelliere, Angele; Nguyen, Noel

    2013-01-01

    This combined ERP and behavioral experiment explores the dynamics of processing during the discrimination of vowels in a non-native regional variety. Southern listeners were presented with three word forms, two of which are encountered in both Standard and Southern French ([kot] and [kut]), whereas the third one exists in Standard but not Southern…

  19. Contrasting pyroclast density spectra from subaerial and submarine silicic eruptions in the Kermadec arc: implications for eruption processes and dredge sampling

    NASA Astrophysics Data System (ADS)

    Barker, Simon J.; Rotella, Melissa D.; Wilson, Colin J. N.; Wright, Ian C.; Wysoczanski, Richard J.

    2012-08-01

    Pyroclastic deposits from four caldera volcanoes in the Kermadec arc have been sampled from subaerial sections (Raoul and Macauley) and by dredging from the submerged volcano flanks (Macauley, Healy, and the newly discovered Raoul SW). Suites of 16-32 mm sized clasts have been analyzed for density and shape, and larger clasts have been analyzed for major element compositions. Density spectra for subaerial dry-type eruptions on Raoul Island have narrow unimodal distributions peaking at vesicularities of 80-85%, whereas ingress of external water (wet-type eruption) or extended timescales for degassing generate broader distributions, including denser clasts. Submarine-erupted pyroclasts show two different patterns. Healy and Raoul SW dredge samples and Macauley Island subaerial-emplaced samples are dominated by modes at ~80-85%, implying that submarine explosive volcanism at high eruption rates can generate clasts with similar vesicularities to their subaerial counterparts. A minor proportion of Healy and Raoul SW clasts also show a pink oxidation color, suggesting that hot clasts met air despite 0.5 to >1 km of intervening water. In contrast, Macauley dredged samples have a bimodal density spectrum dominated by clasts formed in a submarine-eruptive style that is not highly explosive. Macauley dredged pyroclasts are also the mixed products of multiple eruptions, as shown by pumice major-element chemistry, and the sea-floor deposits reflect complex volcanic and sedimentation histories. The Kermadec calderas are composite features, and wide dispersal of pumice does not require large single eruptions. When coupled with chemical constraints and textural observations, density spectra are useful for interpreting both eruptive style and the diversity of samples collected from the submarine environment.

  20. Quantifying the uncertainty of eddy covariance fluxes due to the use of different software packages and combinations of processing steps in two contrasting ecosystems

    NASA Astrophysics Data System (ADS)

    Mammarella, Ivan; Peltola, Olli; Nordbo, Annika; Järvi, Leena; Rannik, Üllar

    2016-10-01

    We have carried out an inter-comparison between EddyUH and EddyPro®, two public software packages for post-field processing of eddy covariance data. Datasets including carbon dioxide, methane and water vapour fluxes measured over 2 months at a wetland in southern Finland and carbon dioxide and water vapour fluxes measured over 3 months at an urban site in Helsinki were processed and analysed. The purpose was to estimate the flux uncertainty due to the use of different software packages and to evaluate the most critical processing steps, determining the largest deviations in the calculated fluxes. Turbulent fluxes calculated with a reference combination of processing steps were in good agreement, the systematic difference between the two software packages being up to 2.0 and 6.7 % for half-hour and cumulative sum values, respectively. The raw data preparation and processing steps were consistent between the software packages, and most of the deviations in the estimated fluxes were due to the flux corrections. Among the different calculation procedures analysed, the spectral correction had the biggest impact for closed-path latent heat fluxes, reaching a nocturnal median value of 15 % at the wetland site. We found up to a 43 % median value of deviation (with respect to the run with all corrections included) if the closed-path carbon dioxide flux is calculated without the dilution correction, while the methane fluxes were up to 10 % lower without both dilution and spectroscopic corrections. The Webb-Pearman-Leuning (WPL) and spectroscopic corrections were the most critical steps for open-path systems. However, we found also large spectral correction factors for the open-path methane fluxes, due to the sensor separation effect.

  1. Multiscale regression modeling in mouse supraspinatus tendons reveals that dynamic processes act as mediators in structure-function relationships.

    PubMed

    Connizzo, Brianne K; Adams, Sheila M; Adams, Thomas H; Jawad, Abbas F; Birk, David E; Soslowsky, Louis J

    2016-06-14

    Recent advances in technology have allowed for the measurement of dynamic processes (re-alignment, crimp, deformation, sliding), but only a limited number of studies have investigated their relationship with mechanical properties. The overall objective of this study was to investigate the role of composition, structure, and the dynamic response to load in predicting tendon mechanical properties in a multi-level fashion mimicking native hierarchical collagen structure. Multiple linear regression models were investigated to determine the relationships between composition/structure, dynamic processes, and mechanical properties. Mediation was then used to determine if dynamic processes mediated structure-function relationships. Dynamic processes were strong predictors of mechanical properties. These predictions were location-dependent, with the insertion site utilizing all four dynamic responses and the midsubstance responding primarily with fibril deformation and sliding. In addition, dynamic processes were moderately predicted by composition and structure in a regionally-dependent manner. Finally, dynamic processes were partial mediators of the relationship between composition/structure and mechanical function, and results suggested that mediation is likely shared between multiple dynamic processes. In conclusion, the mechanical properties at the midsubstance of the tendon are controlled primarily by fibril structure and this region responds to load via fibril deformation and sliding. Conversely, the mechanical function at the insertion site is controlled by many other important parameters and the region responds to load via all four dynamic mechanisms. Overall, this study presents a strong foundation on which to design future experimental and modeling efforts in order to fully understand the complex structure-function relationships present in tendon.

  2. Speech Perception in Tones and Noise via Cochlear Implants Reveals Influence of Spectral Resolution on Temporal Processing

    PubMed Central

    Kreft, Heather A.

    2014-01-01

    Under normal conditions, human speech is remarkably robust to degradation by noise and other distortions. However, people with hearing loss, including those with cochlear implants, often experience great difficulty in understanding speech in noisy environments. Recent work with normal-hearing listeners has shown that the amplitude fluctuations inherent in noise contribute strongly to the masking of speech. In contrast, this study shows that speech perception via a cochlear implant is unaffected by the inherent temporal fluctuations of noise. This qualitative difference between acoustic and electric auditory perception does not seem to be due to differences in underlying temporal acuity but can instead be explained by the poorer spectral resolution of cochlear implants, relative to the normally functioning ear, which leads to an effective smoothing of the inherent temporal-envelope fluctuations of noise. The outcome suggests an unexpected trade-off between the detrimental effects of poorer spectral resolution and the beneficial effects of a smoother noise temporal envelope. This trade-off provides an explanation for the long-standing puzzle of why strong correlations between speech understanding and spectral resolution have remained elusive. The results also provide a potential explanation for why cochlear-implant users and hearing-impaired listeners exhibit reduced or absent masking release when large and relatively slow temporal fluctuations are introduced in noise maskers. The multitone maskers used here may provide an effective new diagnostic tool for assessing functional hearing loss and reduced spectral resolution. PMID:25315376

  3. Speech perception in tones and noise via cochlear implants reveals influence of spectral resolution on temporal processing.

    PubMed

    Oxenham, Andrew J; Kreft, Heather A

    2014-10-13

    Under normal conditions, human speech is remarkably robust to degradation by noise and other distortions. However, people with hearing loss, including those with cochlear implants, often experience great difficulty in understanding speech in noisy environments. Recent work with normal-hearing listeners has shown that the amplitude fluctuations inherent in noise contribute strongly to the masking of speech. In contrast, this study shows that speech perception via a cochlear implant is unaffected by the inherent temporal fluctuations of noise. This qualitative difference between acoustic and electric auditory perception does not seem to be due to differences in underlying temporal acuity but can instead be explained by the poorer spectral resolution of cochlear implants, relative to the normally functioning ear, which leads to an effective smoothing of the inherent temporal-envelope fluctuations of noise. The outcome suggests an unexpected trade-off between the detrimental effects of poorer spectral resolution and the beneficial effects of a smoother noise temporal envelope. This trade-off provides an explanation for the long-standing puzzle of why strong correlations between speech understanding and spectral resolution have remained elusive. The results also provide a potential explanation for why cochlear-implant users and hearing-impaired listeners exhibit reduced or absent masking release when large and relatively slow temporal fluctuations are introduced in noise maskers. The multitone maskers used here may provide an effective new diagnostic tool for assessing functional hearing loss and reduced spectral resolution.

  4. Molecular Diversity of Eukaryotes in Municipal Wastewater Treatment Processes as Revealed by 18S rRNA Gene Analysis

    PubMed Central

    Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

    2014-01-01

    Eukaryotic communities involved in sewage treatment processes have been investigated by morphological identification, but have not yet been well-characterized using molecular approaches. In the present study, eukaryotic communities were characterized by constructing 18S rRNA gene clone libraries. The phylogenetic affiliations of a total of 843 clones were Alveolata, Fungi, Rhizaria, Euglenozoa, Stramenopiles, Amoebozoa, and Viridiplantae as protozoans and Rotifera, Gastrotricha, and Nematoda as metazoans. Sixty percent of the clones had <97% sequence identity to described eukaryotes, indicating the greater diversity of eukaryotes than previously recognized. A core OTU closely related to Epistylis chrysemydis was identified, and several OTUs were shared by 4–8 libraries. Members of the uncultured lineage LKM11 in Cryptomycota were predominant fungi in sewage treatment processes. This comparative study represents an initial step in furthering understanding of the diversity and role of eukaryotes in sewage treatment processes. PMID:25491751

  5. Molecular diversity of eukaryotes in municipal wastewater treatment processes as revealed by 18S rRNA gene analysis.

    PubMed

    Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

    2014-01-01

    Eukaryotic communities involved in sewage treatment processes have been investigated by morphological identification, but have not yet been well-characterized using molecular approaches. In the present study, eukaryotic communities were characterized by constructing 18S rRNA gene clone libraries. The phylogenetic affiliations of a total of 843 clones were Alveolata, Fungi, Rhizaria, Euglenozoa, Stramenopiles, Amoebozoa, and Viridiplantae as protozoans and Rotifera, Gastrotricha, and Nematoda as metazoans. Sixty percent of the clones had <97% sequence identity to described eukaryotes, indicating the greater diversity of eukaryotes than previously recognized. A core OTU closely related to Epistylis chrysemydis was identified, and several OTUs were shared by 4-8 libraries. Members of the uncultured lineage LKM11 in Cryptomycota were predominant fungi in sewage treatment processes. This comparative study represents an initial step in furthering understanding of the diversity and role of eukaryotes in sewage treatment processes.

  6. Striatal and Hippocampal Entropy and Recognition Signals in Category Learning: Simultaneous Processes Revealed by Model-Based fMRI

    PubMed Central

    Davis, Tyler; Love, Bradley C.; Preston, Alison R.

    2012-01-01

    Category learning is a complex phenomenon that engages multiple cognitive processes, many of which occur simultaneously and unfold dynamically over time. For example, as people encounter objects in the world, they simultaneously engage processes to determine their fit with current knowledge structures, gather new information about the objects, and adjust their representations to support behavior in future encounters. Many techniques that are available to understand the neural basis of category learning assume that the multiple processes that subserve it can be neatly separated between different trials of an experiment. Model-based functional magnetic resonance imaging offers a promising tool to separate multiple, simultaneously occurring processes and bring the analysis of neuroimaging data more in line with category learning’s dynamic and multifaceted nature. We use model-based imaging to explore the neural basis of recognition and entropy signals in the medial temporal lobe and striatum that are engaged while participants learn to categorize novel stimuli. Consistent with theories suggesting a role for the anterior hippocampus and ventral striatum in motivated learning in response to uncertainty, we find that activation in both regions correlates with a model-based measure of entropy. Simultaneously, separate subregions of the hippocampus and striatum exhibit activation correlated with a model-based recognition strength measure. Our results suggest that model-based analyses are exceptionally useful for extracting information about cognitive processes from neuroimaging data. Models provide a basis for identifying the multiple neural processes that contribute to behavior, and neuroimaging data can provide a powerful test bed for constraining and testing model predictions. PMID:22746951

  7. Linear and Circular Polarisation Vision in Stomatopod Crustaceans: Information Processing and Signals to the Brain, Secret Signals Between Animals and Contrast Enhancement

    DTIC Science & Technology

    2009-11-27

    ANNUAL REPORT Grant Number AOARD-07-4086 “Linear and Circular Polarisation Vision in Stomatopod Crustaceans : Information...FInal 3. DATES COVERED 22-08-2007 to 14-11-2009 4. TITLE AND SUBTITLE Linear and circular polarisation vision in stomatopod crustaceans 5a...communication in stomatopod crustaceans . Specifically, determine if there are polarization connection pathways in the neural processing systems, and

  8. Genome-Wide Screen Reveals Rhythmic Regulation of Genes Involved in Odor Processing in the Olfactory Epithelium.

    PubMed

    Saleh, Manjana; Jürchott, Karsten; Oberland, Sonja; Neuhaus, Eva M; Kramer, Achim; Abraham, Ute

    2015-12-01

    Odor discrimination behavior displays circadian fluctuations in mice, indicating that mammalian olfactory function is under control of the circadian system. This is further supported by the facts that odor discrimination rhythms depend on the presence of clock genes and that olfactory tissues contain autonomous circadian clocks. However, the molecular link between circadian function and olfactory processing is still unknown. To elucidate the molecular mechanisms underlying this link, we focused on the olfactory epithelium (OE), the primary target of odors and the site of the initial events in olfactory processing. We asked whether olfactory sensory neurons (OSNs) within the OE possess an autonomous circadian clock and whether olfactory pathways are under circadian control. Employing clock gene-driven bioluminescence reporter assays and time-dependent immunohistochemistry on OE samples, we found robust circadian rhythms of core clock genes and their proteins in OSNs, suggesting that the OE indeed contains an autonomous circadian clock. Furthermore, we performed a circadian transcriptome analysis and identified several OSN-specific components that are under circadian control, including those with putative roles in circadian olfactory processing, such as KIRREL2-an established factor involved in short-term OSN activation. The spatiotemporal expression patterns of our candidate proteins suggest that they are involved in short-term anabolic processes to rhythmically prepare the cell for peak performances and to promote circadian function of OSNs.

  9. The Neural Correlates of Implicit and Explicit Sequence Learning: Interacting Networks Revealed by the Process Dissociation Procedure

    ERIC Educational Resources Information Center

    Laureys, Steven; Degueldre, Christian; Del Fiore, Guy; Aerts, Joel; Luxen, Andre; Van Der Linden, Martial; Cleeremans, Axel; Maquet, Pierre; Destrebecqz, Arnaud; Peigneux, Philippe

    2005-01-01

    In two H[subscript 2] [superscript 15]O PET scan experiments, we investigated the cerebral correlates of explicit and implicit knowledge in a serial reaction time (SRT) task. To do so, we used a novel application of the Process Dissociation Procedure, a behavioral paradigm that makes it possible to separately assess conscious and unconscious…

  10. Eye-tracking reveals a slowdown of social context processing during intention attribution in patients with schizophrenia

    PubMed Central

    Roux, Paul; Brunet-Gouet, Eric; Passerieux, Christine; Ramus, Franck

    2016-01-01

    Background Schizophrenia is associated with poor theory of mind (ToM), particularly in the attribution of intentions to others. It is also associated with abnormal gaze behaviours and contextual processing. This study investigated to what extent impaired ToM in patients with schizophrenia is related to abnormal processing of social context. Methods We evaluated ToM using a nonverbal intention attribution task based on comic strips depicting social/nonsocial and contextual/noncontextual events while eye movements were recorded. Eye-tracking was used to assess processing time dedicated to visual cues contained in regions of interest identified in a pilot study. We measured cognitive contextual control on a separate task. Results We tested 29 patients with schizophrenia and 29 controls. Compared with controls, patients were slower in intention attribution but not in physical reasoning. They looked longer than controls at contextual cues displayed in the first 2 context pictures of the comic strips, and this difference was greater for intention attribution than for physical reasoning. We found no group difference in time spent looking at noncontextual cues. Patients’ impairment in contextual control did not explain their increased reaction time and gaze duration on contextual cues during intention attribution. Limitations Difficulty may not have been equivalent between intention attribution and physical reasoning conditions. Conclusion Overall, schizophrenia was characterized by a delay in intention attribution related to a slowdown of social context processing that was not explained by worse executive contextual control. PMID:26836621

  11. Shades of Emotion: What the Addition of Sunglasses or Masks to Faces Reveals about the Development of Facial Expression Processing

    ERIC Educational Resources Information Center

    Roberson, Debi; Kikutani, Mariko; Doge, Paula; Whitaker, Lydia; Majid, Asifa

    2012-01-01

    Three studies investigated developmental changes in facial expression processing, between 3 years-of-age and adulthood. For adults and older children, the addition of sunglasses to upright faces caused an equivalent decrement in performance to face inversion. However, younger children showed "better" classification of expressions of faces wearing…

  12. Using a Process of Collective Biography Writing in Higher Education to Develop an Ability to Explore, Reveal and Critically Reflect

    ERIC Educational Resources Information Center

    Wihlborg, Monne

    2013-01-01

    Teaching and learning are frequently treated as processes that are separate from each other, while teachers and learners are considered as disembodied entities with a neutral position towards the content which is negotiated. In collective biography writing (CBW), a very different approach is taken. Writing, reading and learning are seen as an…

  13. Neural Decoding Reveals Impaired Face Configural Processing in the Right Fusiform Face Area of Individuals with Developmental Prosopagnosia

    PubMed Central

    Zhang, Jiedong; Liu, Jia

    2015-01-01

    Most of human daily social interactions rely on the ability to successfully recognize faces. Yet ∼2% of the human population suffers from face blindness without any acquired brain damage [this is also known as developmental prosopagnosia (DP) or congenital prosopagnosia]). Despite the presence of severe behavioral face recognition deficits, surprisingly, a majority of DP individuals exhibit normal face selectivity in the right fusiform face area (FFA), a key brain region involved in face configural processing. This finding, together with evidence showing impairments downstream from the right FFA in DP individuals, has led some to argue that perhaps the right FFA is largely intact in DP individuals. Using fMRI multivoxel pattern analysis, here we report the discovery of a neural impairment in the right FFA of DP individuals that may play a critical role in mediating their face-processing deficits. In seven individuals with DP, we discovered that, despite the right FFA's preference for faces and it showing decoding for the different face parts, it exhibited impaired face configural decoding and did not contain distinct neural response patterns for the intact and the scrambled face configurations. This abnormality was not present throughout the ventral visual cortex, as normal neural decoding was found in an adjacent object-processing region. To our knowledge, this is the first direct neural evidence showing impaired face configural processing in the right FFA in individuals with DP. The discovery of this neural impairment provides a new clue to our understanding of the neural basis of DP. PMID:25632131

  14. Neural decoding reveals impaired face configural processing in the right fusiform face area of individuals with developmental prosopagnosia.

    PubMed

    Zhang, Jiedong; Liu, Jia; Xu, Yaoda

    2015-01-28

    Most of human daily social interactions rely on the ability to successfully recognize faces. Yet ∼2% of the human population suffers from face blindness without any acquired brain damage [this is also known as developmental prosopagnosia (DP) or congenital prosopagnosia]). Despite the presence of severe behavioral face recognition deficits, surprisingly, a majority of DP individuals exhibit normal face selectivity in the right fusiform face area (FFA), a key brain region involved in face configural processing. This finding, together with evidence showing impairments downstream from the right FFA in DP individuals, has led some to argue that perhaps the right FFA is largely intact in DP individuals. Using fMRI multivoxel pattern analysis, here we report the discovery of a neural impairment in the right FFA of DP individuals that may play a critical role in mediating their face-processing deficits. In seven individuals with DP, we discovered that, despite the right FFA's preference for faces and it showing decoding for the different face parts, it exhibited impaired face configural decoding and did not contain distinct neural response patterns for the intact and the scrambled face configurations. This abnormality was not present throughout the ventral visual cortex, as normal neural decoding was found in an adjacent object-processing region. To our knowledge, this is the first direct neural evidence showing impaired face configural processing in the right FFA in individuals with DP. The discovery of this neural impairment provides a new clue to our understanding of the neural basis of DP.

  15. Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process

    NASA Astrophysics Data System (ADS)

    Iacovache, Ioan; de Carlo, Sacha; Cirauqui, Nuria; Dal Peraro, Matteo; van der Goot, F. Gisou; Zuber, Benoît

    2016-07-01

    Owing to their pathogenical role and unique ability to exist both as soluble proteins and transmembrane complexes, pore-forming toxins (PFTs) have been a focus of microbiologists and structural biologists for decades. PFTs are generally secreted as water-soluble monomers and subsequently bind the membrane of target cells. Then, they assemble into circular oligomers, which undergo conformational changes that allow membrane insertion leading to pore formation and potentially cell death. Aerolysin, produced by the human pathogen Aeromonas hydrophila, is the founding member of a major PFT family found throughout all kingdoms of life. We report cryo-electron microscopy structures of three conformational intermediates and of the final aerolysin pore, jointly providing insight into the conformational changes that allow pore formation. Moreover, the structures reveal a protein fold consisting of two concentric β-barrels, tightly kept together by hydrophobic interactions. This fold suggests a basis for the prion-like ultrastability of aerolysin pore and its stoichiometry.

  16. Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes

    PubMed Central

    Tausta, S. Lori; Li, Pinghua; Si, Yaqing; Gandotra, Neeru; Liu, Peng; Sun, Qi; Brutnell, Thomas P.; Nelson, Timothy

    2014-01-01

    The comparison of the cell-specific transcriptomes of bundle sheath (BS) and mesophyll (M) cells from successive developmental stages of maize (Zea mays) leaves reveals that the number of genes preferentially transcribed in one cell type or the other varies considerably from the sink–source transition to mature photosynthetic stages. The number of differentially expressed (DE) genes is maximal at a stage well before full maturity, including those that encode key functions for C4 photosynthesis. The developmental dynamics of BS/M differential expression can be used to identify candidates for other C4-related functions and to simplify the identification of specific pathways members from otherwise complex gene families. A significant portion of the candidates for C4-related transcription factors identified with this developmental DE strategy overlap with those identified in studies using alternative strategies, thus providing independent support for their potential importance. PMID:24790109

  17. The role of fluids in rock layering development: a pressure solution self-organized process revealed by laboratory experiments

    NASA Astrophysics Data System (ADS)

    Gratier, Jean-Pierre; Noiriel, Catherine; Renard, Francois

    2015-04-01

    Natural deformation of rocks is often associated with stress-driven differentiation processes leading to irreversible transformations of their microstructures. The development mechanisms of such processes during diagenesis, tectonic, metamorphism or fault differentiation are poorly known as they are difficult to reproduce experimentally due to the very slow kinetics of stress-driven chemical processes. Here, we show that experimental compaction with development of differentiated layering, similar to what happens in natural deformation, can be obtained by indenter techniques in laboratory conditions. Samples of plaster mixed with clay and of diatomite loosely interbedded with volcanic dust were loaded in presence of their saturated aqueous solutions during several months at 40°C and 150°C, respectively. High-resolution X-ray microtomography and scanning electron microscopy observations show that the layering development is a pressure solution self-organized process. Stress-driven dissolution of the soluble minerals (either gypsum or silica) is initiated in the areas initially richer in insoluble minerals (clays or volcanic dust) because the kinetics of diffusive mass transfer along the soluble/insoluble mineral interfaces is much faster than along the healed boundaries of the soluble minerals. The passive concentration of insoluble minerals amplifies the localization of dissolution along some layers oriented perpendicular to the maximum compressive stress. Conversely, in the areas with initial low content in insoluble minerals and clustered soluble minerals, dissolution is slower. Consequently, these areas are less deformed, they host the re-deposition of the soluble species and they act as rigid objects that concentrate the dissolution near their boundaries thus amplifying the differentiation. A crucial parameter required for self-organized process of pressure solution is the presence of a fluid that is a good solvent of at least some of the rock-forming minerals

  18. Ultrasound contrast agents

    PubMed Central

    Ignee, Andre; Atkinson, Nathan S. S.; Schuessler, Gudrun; Dietrich, Christoph F.

    2016-01-01

    Endoscopic ultrasound (EUS) plays an important role in imaging of the mediastinum and abdominal organs. Since the introduction of US contrast agents (UCA) for transabdominal US, attempts have been made to apply contrast-enhanced US techniques also to EUS. Since 2003, specific contrast-enhanced imaging was possible using EUS. Important studies have been published regarding contrast-enhanced EUS and the characterization of focal pancreatic lesions, lymph nodes, and subepithelial tumors. In this manuscript, we describe the relevant UCA, their application, and specific image acquisition as well as the principles of image tissue characterization using contrast-enhanced EUS. Safety issues, potential future developments, and EUS-specific issues are reviewed. PMID:27824024

  19. Insights Into Precipitation Processes As Revealed By Profiling Radar, Disdrometer and Aircraft Observations During The MC3E Campaign.

    NASA Astrophysics Data System (ADS)

    Giangrande, S. E.; Toto, T.; Mishra, S.; Ryzhkov, A.; Bansemer, A.; Kumjian, M.

    2014-12-01

    The Midlatitude Continental Convective Clouds Experiment (MC3E) was a collaborative campaign led by the National Aeronautic and Space Administration's (NASA's) Global Precipitation Measurement (GPM) mission and the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program. This campaign was held at the DOE ARM Southern Great Plains (SGP) Central Facility (CF) in north-central Oklahoma, with the programs joining forces to deploy an extensive array of airborne, radiosonde and ground-based instrumentation towards an unprecedented set of deep convective environment and cloud property observations. An overarching motivation was to capitalize on the wealth of aircraft observations and new multi-frequency dual-polarization radars to provide insights for improving the treatments of cloud processes in convective models. This study considers a coupled aircraft, radar and surface disdrometer approach for identifying key cloud processes and linking those to possible radar-based microphysical fingerprints and/or cloud properties. Our emphasis is on the MC3E observations collected during aircraft spirals over the column of the ARM CF. We focus on those spirals associated with radar 'bright band' signatures and Doppler spectral anomalies observed within trailing stratifrom precipitation. Two cases are highlighted, one following a weaker convective event, and one following a stronger squall line. For each event, we investigate the usefulness of radar to inform on processes including aggregation and riming as viewed by the vertically-pointing ARM wind profiler (915 MHz) and cloud radar Doppler spectral observations (35 GHz). Matching dual-polarization radar signatures from nearby cm-wavelength radar are also consulted for complementary insights. For one event, the successive Citation II aircraft spirals through the melting layer and associated ground observations indicate a fortunate capture of the transition from a region of riming to one favoring aggregation

  20. Network Analysis of Postharvest Senescence Process in Citrus Fruits Revealed by Transcriptomic and Metabolomic Profiling1[OPEN

    PubMed Central

    Ding, Yuduan; Chang, Jiwei; Ma, Qiaoli; Chen, Lingling; Liu, Shuzhen; Jin, Shuai; Han, Jingwen; Xu, Rangwei; Zhu, Andan; Guo, Jing; Luo, Yi; Xu, Juan; Xu, Qiang; Zeng, YunLiu; Deng, Xiuxin

    2015-01-01

    Citrus (Citrus spp.), a nonclimacteric fruit, is one of the most important fruit crops in global fruit industry. However, the biological behavior of citrus fruit ripening and postharvest senescence remains unclear. To better understand the senescence process of citrus fruit, we analyzed data sets from commercial microarrays, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry and validated physiological quality detection of four main varieties in the genus Citrus. Network-based approaches of data mining and modeling were used to investigate complex molecular processes in citrus. The Citrus Metabolic Pathway Network and correlation networks were constructed to explore the modules and relationships of the functional genes/metabolites. We found that the different flesh-rind transport of nutrients and water due to the anatomic structural differences among citrus varieties might be an important factor that influences fruit senescence behavior. We then modeled and verified the citrus senescence process. As fruit rind is exposed directly to the environment, which results in energy expenditure in response to biotic and abiotic stresses, nutrients are exported from flesh to rind to maintain the activity of the whole fruit. The depletion of internal substances causes abiotic stresses, which further induces phytohormone reactions, transcription factor regulation, and a series of physiological and biochemical reactions. PMID:25802366

  1. Age Effects in L2 Grammar Processing as Revealed by ERPs and How (Not) to Study Them.

    PubMed

    Meulman, Nienke; Wieling, Martijn; Sprenger, Simone A; Stowe, Laurie A; Schmid, Monika S

    2015-01-01

    In this study we investigate the effect of age of acquisition (AoA) on grammatical processing in second language learners as measured by event-related brain potentials (ERPs). We compare a traditional analysis involving the calculation of averages across a certain time window of the ERP waveform, analyzed with categorical groups (early vs. late), with a generalized additive modeling analysis, which allows us to take into account the full range of variability in both AoA and time. Sixty-six Slavic advanced learners of German listened to German sentences with correct and incorrect use of non-finite verbs and grammatical gender agreement. We show that the ERP signal depends on the AoA of the learner, as well as on the regularity of the structure under investigation. For gender agreement, a gradual change in processing strategies can be shown that varies by AoA, with younger learners showing a P600 and older learners showing a posterior negativity. For verb agreement, all learners show a P600 effect, irrespective of AoA. Based on their behavioral responses in an offline grammaticality judgment task, we argue that the late learners resort to computationally less efficient processing strategies when confronted with (lexically determined) syntactic constructions different from the L1. In addition, this study highlights the insights the explicit focus on the time course of the ERP signal in our analysis framework can offer compared to the traditional analysis.

  2. Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite.

    PubMed

    Farasin, Julien; Koechler, Sandrine; Varet, Hugo; Deschamps, Julien; Dillies, Marie-Agnès; Proux, Caroline; Erhardt, Mathieu; Huber, Aline; Jagla, Bernd; Briandet, Romain; Coppée, Jean-Yves; Arsène-Ploetze, Florence

    2017-02-07

    Bacteria of the genus Thiomonas are found ubiquitously in arsenic contaminated waters such as acid mine drainage (AMD), where they contribute to the precipitation and the natural bioremediation of arsenic. In these environments, these bacteria have developed a large range of resistance strategies among which the capacity to form particular biofilm structures. The biofilm formation is one of the most ubiquitous adaptive response observed in prokaryotes to various stresses, such as those induced in the presence of toxic compounds. This study focused on the process of biofilm formation in three Thiomonas strains (CB1, CB2 and CB3) isolated from the same AMD. The results obtained here show that these bacteria are all capable of forming biofilms, but the architecture and the kinetics of formation of these biofilms differ depending on whether arsenite is present in the environment and from one strain to another. Indeed, two strains favoured biofilm formation, whereas one favoured motility in the presence of arsenite. To identify the underlying mechanisms, the patterns of expression of some genes possibly involved in the process of biofilm formation were investigated in Thiomonas sp. CB2 in the presence and absence of arsenite, using a transcriptomic approach (RNA-seq). The findings obtained here shed interesting light on how the formation of biofilms, and the motility processes contribute to the adaptation of Thiomonas strains to extreme environments.

  3. Design of experiments reveals critical parameters for pilot-scale freeze-and-thaw processing of L-lactic dehydrogenase.

    PubMed

    Roessl, Ulrich; Humi, Sebastian; Leitgeb, Stefan; Nidetzky, Bernd

    2015-09-01

    Freezing constitutes an important unit operation of biotechnological protein production. Effects of freeze-and-thaw (F/T) process parameters on stability and other quality attributes of the protein product are usually not well understood. Here a design of experiments (DoE) approach was used to characterize the F/T behavior of L-lactic dehydrogenase (LDH) in a 700-mL pilot-scale freeze container equipped with internal temperature and pH probes. In 24-hour experiments, target temperature between -10 and -38°C most strongly affected LDH stability whereby enzyme activity was retained best at the highest temperature of -10°C. Cooling profile and liquid fill volume also had significant effects on LDH stability and affected the protein aggregation significantly. Parameters of the thawing phase had a comparably small effect on LDH stability. Experiments in which the standard sodium phosphate buffer was exchanged by Tris-HCl and the non-ionic surfactant Tween 80 was added to the protein solution showed that pH shift during freezing and protein surface exposure were the main factors responsible for LDH instability at the lower freeze temperatures. Collectively, evidence is presented that supports the use of DoE-based systematic analysis at pilot scale in the identification of F/T process parameters critical for protein stability and in the development of suitable process control strategies.

  4. The dominance of cold and dry alteration processes on recent Mars, as revealed through pan-spectral orbital analyses

    NASA Astrophysics Data System (ADS)

    Salvatore, M. R.; Mustard, J. F.; Head, J. W.; Rogers, A. D.; Cooper, R. F.

    2014-10-01

    Classic low-albedo regions of the martian surface are investigated using combined reflectance and emission (“pan-spectral”) data to constrain the types of alteration mineral phases that are present at spectrally significant abundances (>10-15%). The lack of hydrated mineral species observed using near-infrared data suggests that anhydrous chemical alteration dominates at the regional scale. Spectral characteristics in the VNIR and TIR are consistent with those associated with weathering processes identified in the hyper-arid, hypo-thermal, and geologically stable McMurdo Dry Valleys of Antarctica, where oxidative weathering processes dominate and significant aqueous alteration does not occur. In addition, the spectral trends associated with oxidative weathering processes are similar to regional trends in VNIR spectral characteristics observed on Mars and potentially complicate the spectral interpretation of basaltic terrains. Collectively, these relationships suggest that the martian surface has been dominated by cold, dry, and stable conditions since the formation of these low-albedo regions. While significant at regional scales early in martian history, aqueous alteration appears to be predominantly absent from large-scale basaltic regions on Mars.

  5. Metaproteomics and metabolomics analyses of chronically petroleum‐polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

    PubMed Central

    Bargiela, Rafael; Herbst, Florian‐Alexander; Martínez‐Martínez, Mónica; Seifert, Jana; Rojo, David; Cappello, Simone; Genovese, María; Crisafi, Francesca; Denaro, Renata; Chernikova, Tatyana N.; Barbas, Coral; von Bergen, Martin; Yakimov, Michail M.; Golyshin, Peter N.

    2015-01-01

    Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi‐enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large‐scale chronic pollution is yet to be defined, particularly in anaerobic and micro‐aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen‐depleted petroleum‐polluted sediments. PMID:26201687

  6. Quantitative proteome analysis of an antibiotic resistant Escherichia coli exposed to tetracycline reveals multiple affected metabolic and peptidoglycan processes.

    PubMed

    Jones-Dias, Daniela; Carvalho, Ana Sofia; Moura, Inês Barata; Manageiro, Vera; Igrejas, Gilberto; Caniça, Manuela; Matthiesen, Rune

    2017-03-06

    Tetracyclines are among the most commonly used antibiotics administrated to farm animals for disease treatment and prevention, contributing to the worldwide increase in antibiotic resistance in animal and human pathogens. Although tetracycline mechanisms of resistance are well known, the role of metabolism in bacterial reaction to antibiotic stress is still an important assignment and could contribute to the understanding of tetracycline related stress response. In this study, spectral counts-based label free quantitative proteomics has been applied to study the response to tetracycline of the environmental-borne Escherichia coli EcAmb278 isolate soluble proteome. A total of 1484 proteins were identified by high resolution mass spectrometry at a false discovery rate threshold of 1%, of which 108 were uniquely identified under absence of tetracycline whereas 126 were uniquely identified in presence of tetracycline. These proteins revealed interesting difference in e.g. proteins involved in peptidoglycan-based cell wall proteins and energy metabolism. Upon treatment, 12 proteins were differentially regulated showing more than 2-fold change and p<0.05 (p value corrected for multiple testing). This integrated study using high resolution mass spectrometry based label-free quantitative proteomics to study tetracycline antibiotic response in the soluble proteome of resistant E. coli provides novel insight into tetracycline related stress.

  7. Manipulations of word frequency reveal differences in the processing of morphologically complex and simple words in German

    PubMed Central

    Bronk, Maria; Zwitserlood, Pienie; Bölte, Jens

    2013-01-01

    We tested current models of morphological processing in reading with data from four visual lexical decision experiments using German compounds and monomorphemic words. Triplets of two semantically transparent noun-noun compounds and one monomorphemic noun were used in Experiments 1a and 1b. Stimuli within a triplet were matched for full-form frequency. The frequency of the compounds' constituents was varied. The compounds of a triplet shared one constituent, while the frequency of the unshared constituent was either high or low, but always higher than full-form frequency. Reactions were faster to compounds with high-frequency constituents than to compounds with low-frequency constituents, while the latter did not differ from the monomorphemic words. This pattern was not influenced by task difficulty, induced by the type of pseudocompounds used. Pseudocompounds were either created by altering letters of an existing compound (easy pseudocompound, Experiment 1a) or by combining two free morphemes into a non-existing, but morphologically legal, compound (difficult pseudocompound, Experiment 1b). In Experiments 2a and 2b, frequency-matched pairs of semantically opaque noun-noun compounds and simple nouns were tested. In Experiment 2a, with easy pseudocompounds (of the same type as in Experiment 1a), a reaction-time advantage for compounds over monomorphemic words was again observed. This advantage disappeared in Experiment 2b, where difficult pseudocompounds were used. Although a dual-route might account for the data, the findings are best understood in terms of decomposition of low-frequency complex words prior to lexical access, followed by processing costs due to the recombination of morphemes for meaning access. These processing costs vary as a function of intrinsic factors such as semantic transparency, or external factors such as the difficulty of the experimental task. PMID:23986731

  8. Summing it up: Semantic activation processes in the two hemispheres as revealed by event-related potentials

    PubMed Central

    Kandhadai, Padmapriya; Federmeier, Kara D.

    2009-01-01

    The coarse coding hypothesis suggests that semantic activation is broader in the right hemisphere, affording it an advantage over the left hemisphere for the activation of distantly related concepts or multiple meanings of lexically ambiguous words. Behavioral studies investigating coarse coding have yielded mixed results, perhaps in part because such measures sum across multiple processing stages. To more directly tap into the semantic activation processes that are the focus of the coarse coding hypothesis, the current study combined a visual half-field summation-priming paradigm with the measurement of event-related potentials (ERPs). Two primes converged onto a lateralized, unambiguous target (e.g., lion–stripes–tiger) or diverged onto different meanings of a lateralized, ambiguous target (e.g., kidney–piano–organ); in both cases, the primes were related to one another only through the target. In two experiments, participants either made lexical decisions to the targets or made a semantic-relatedness judgment between primes and target. Priming was measured as reductions in the amplitude of the N400, an ERP component that has been specifically linked to meaning activation and that showed semantic-level priming patterns in both of the tasks used in the present study. Counter to the predictions of the coarse coding hypothesis, equivalent N400 summation priming was observed for targets in the two visual fields, in both types of triplets and in both experiments. Thus, the current results fail to support the hypothesis that semantic activation patterns differ in the two hemispheres and point, instead, to other sources for observed asymmetries in verbal processing. PMID:18675257

  9. Apocalypto: revealing lost text with XMT

    NASA Astrophysics Data System (ADS)

    Mills, David; Davis, Graham R.; Lai, Yu-kun; Rosin, Paul

    2014-09-01

    "Can brute-force high-contrast tomography techniques and image processing techniques retrieve textual content from damaged heritage materials?" The Dental Institute at Queen Mary University of London (QMUL) is the leading centre for very high contrast X-Ray Microtomography imaging. The Apocalypto Project is our collaboration with the heritage community and experts in Computer Vision systems in the Computer Science Department at Cardiff University. This collaboration has developed techniques and a workflow that allows us to reveal textual content from moisture-damaged parchment rolls. This article will also present some initial results from burned and heat shrunken parchment rolls, an insect damaged Mamluk cap and a birch bark roll.

  10. The genetic potential for key biogeochemical processes in Arctic frost flowers and young sea ice revealed by metagenomic analysis.

    PubMed

    Bowman, Jeff S; Berthiaume, Chris T; Armbrust, E Virginia; Deming, Jody W

    2014-08-01

    Newly formed sea ice is a vast and biogeochemically active environment. Recently, we reported an unusual microbial community dominated by members of the Rhizobiales in frost flowers at the surface of Arctic young sea ice based on the presence of 16S gene sequences related to these strains. Here, we use metagenomic analysis of two samples, from a field of frost flowers and the underlying young sea ice, to explore the metabolic potential of this surface ice community. The analysis links genes for key biogeochemical processes to the Rhizobiales, including dimethylsulfide uptake, betaine glycine turnover, and halocarbon production. Nodulation and nitrogen fixation genes characteristic of terrestrial root-nodulating Rhizobiales were generally lacking from these metagenomes. Non-Rhizobiales clades at the ice surface had genes that would enable additional biogeochemical processes, including mercury reduction and dimethylsulfoniopropionate catabolism. Although the ultimate source of the observed microbial community is not known, considerations of the possible role of eolian deposition or transport with particles entrained during ice formation favor a suspended particle source for this microbial community.

  11. Theta and beta oscillatory dynamics in the dentate gyrus reveal a shift in network processing state during cue encounters

    PubMed Central

    Rangel, Lara M.; Chiba, Andrea A.; Quinn, Laleh K.

    2015-01-01

    The hippocampus is an important structure for learning and memory processes, and has strong rhythmic activity. Although a large amount of research has been dedicated toward understanding the rhythmic activity in the hippocampus during exploratory behaviors, specifically in the theta (5–10 Hz) frequency range, few studies have examined the temporal interplay of theta and other frequencies during the presentation of meaningful cues. We obtained in vivo electrophysiological recordings of local field potentials (LFP) in the dentate gyrus (DG) of the hippocampus as rats performed three different associative learning tasks. In each task, cue presentations elicited pronounced decrements in theta amplitude in conjunction with increases in beta (15–30 Hz) amplitude. These changes were often transient but were sustained from the onset of cue encounters until the occurrence of a reward outcome. This oscillatory profile shifted in time to precede cue encounters over the course of the session, and was not present during similar behaviors in the absence of task relevant stimuli. The observed decreases in theta amplitude and increases in beta amplitude in the DG may thus reflect a shift in processing state that occurs when encountering meaningful cues. PMID:26190979

  12. High-resolution transcript profiling reveals shoot abscission process of spruce dwarf mistletoe Arceuthobium sichuanense in response to ethephon

    PubMed Central

    Wang, Yonglin; Xiong, Dianguang; Jiang, Ning; Li, Xuewu; Yang, Qiqing; Tian, Chengming

    2016-01-01

    Arceuthobium (dwarf mistletoes) are hemiparasites that may cause great damage to infected trees belonging to Pinaceae and Cupressaceae. Currently, dwarf mistletoe control involves the use of the ethylene-producing product ethephon (ETH), which acts by inducing dwarf mistletoe shoot abscission. However, the process by which ETH functions is mostly unknown. Therefore, the transcriptome of the ETH-exposed plants was compared to non-exposed controls to identify genes associated with the response to ethephon. In this study, the reference transcriptome was contained 120,316 annotated unigenes, with a total of 21,764 ETH-responsive differentially expressed unigenes were identified. These ETH-associated genes clustered into 20 distinctly expressed pattern groups, providing a view of molecular events with good spatial and temporal resolution. As expected, the greatest number of unigenes with changed expression were observed at the onset of abscission, suggesting induction by ethylene. ETH also affected genes associated with shoot abscission processes including hormone biosynthesis and signaling, cell wall hydrolysis and modification, lipid transference, and more. The comprehensive transcriptome data set provides a wealth of genomic resources for dwarf mistletoe communities and contributes to a better understanding of the molecular regulatory mechanism of ethylene-caused shoots abscission. PMID:27941945

  13. A high performance biometric signal and image processing method to reveal blood perfusion towards 3D oxygen saturation mapping

    NASA Astrophysics Data System (ADS)

    Imms, Ryan; Hu, Sijung; Azorin-Peris, Vicente; Trico, Michaël.; Summers, Ron

    2014-03-01

    Non-contact imaging photoplethysmography (PPG) is a recent development in the field of physiological data acquisition, currently undergoing a large amount of research to characterize and define the range of its capabilities. Contact-based PPG techniques have been broadly used in clinical scenarios for a number of years to obtain direct information about the degree of oxygen saturation for patients. With the advent of imaging techniques, there is strong potential to enable access to additional information such as multi-dimensional blood perfusion and saturation mapping. The further development of effective opto-physiological monitoring techniques is dependent upon novel modelling techniques coupled with improved sensor design and effective signal processing methodologies. The biometric signal and imaging processing platform (bSIPP) provides a comprehensive set of features for extraction and analysis of recorded iPPG data, enabling direct comparison with other biomedical diagnostic tools such as ECG and EEG. Additionally, utilizing information about the nature of tissue structure has enabled the generation of an engineering model describing the behaviour of light during its travel through the biological tissue. This enables the estimation of the relative oxygen saturation and blood perfusion in different layers of the tissue to be calculated, which has the potential to be a useful diagnostic tool.

  14. C-terminomics Screen for Natural Substrates of Cytosolic Carboxypeptidase 1 Reveals Processing of Acidic Protein C termini*

    PubMed Central

    Tanco, Sebastian; Tort, Olivia; Demol, Hans; Aviles, Francesc Xavier; Gevaert, Kris; Van Damme, Petra; Lorenzo, Julia

    2015-01-01

    Cytosolic carboxypeptidases (CCPs) constitute a new subfamily of M14 metallocarboxypeptidases associated to axonal regeneration and neuronal degeneration, among others. CCPs are deglutamylating enzymes, able to catalyze the shortening of polyglutamate side-chains and the gene-encoded C termini of tubulin, telokin, and myosin light chain kinase. The functions of these enzymes are not entirely understood, in part because of the lack of information about C-terminal protein processing in the cell and its functional implications. By means of C-terminal COFRADIC, a positional proteomics approach, we searched for cellular substrates targets of CCP1, the most relevant member of this family. We here identified seven new putative CCP1 protein substrates, including ribosomal proteins, translation factors, and high mobility group proteins. Furthermore, we showed for the first time that CCP1 processes both glutamates as well as C-terminal aspartates. The implication of these C termini in molecular interactions furthermore suggests that CCP1-mediated shortening of acidic protein tails might regulate protein–protein and protein–DNA interactions. PMID:25381060

  15. Capture of micrococcin biosynthetic intermediates reveals C-terminal processing as an obligatory step for in vivo maturation.

    PubMed

    Bewley, Kathryn D; Bennallack, Philip R; Burlingame, Mark A; Robison, Richard A; Griffitts, Joel S; Miller, Susan M

    2016-11-01

    Thiopeptides, including micrococcins, are a growing family of bioactive natural products that are ribosomally synthesized and heavily modified. Here we use a refactored, modular in vivo system containing the micrococcin P1 (MP1) biosynthetic genes (TclIJKLMNPS) from Macrococcus caseolyticus str 115 in a genetically tractable Bacillus subtilis strain to parse the processing steps of this pathway. By fusing the micrococcin precursor peptide to an affinity tag and coupling it with catalytically defective enzymes, biosynthetic intermediates were easily captured for analysis. We found that two major phases of molecular maturation are separated by a key C-terminal processing step. Phase-I conversion of six Cys residues to thiazoles (TclIJN) is followed by C-terminal oxidative decarboxylation (TclP). This TclP-mediated oxidative decarboxylation is a required step for the peptide to progress to phase II. In phase II, Ser/Thr dehydration (TclKL) and peptide macrocycle formation (TclM) occurs. A C-terminal reductase, TclS, can optionally act on the substrate peptide, yielding MP1, and is shown to act late in the pathway. This comprehensive characterization of the MP1 pathway prepares the way for future engineering efforts.

  16. Capture of micrococcin biosynthetic intermediates reveals C-terminal processing as an obligatory step for in vivo maturation

    PubMed Central

    Bewley, Kathryn D.; Bennallack, Philip R.; Burlingame, Mark A.; Robison, Richard A.; Griffitts, Joel S.

    2016-01-01

    Thiopeptides, including micrococcins, are a growing family of bioactive natural products that are ribosomally synthesized and heavily modified. Here we use a refactored, modular in vivo system containing the micrococcin P1 (MP1) biosynthetic genes (TclIJKLMNPS) from Macrococcus caseolyticus str 115 in a genetically tractable Bacillus subtilis strain to parse the processing steps of this pathway. By fusing the micrococcin precursor peptide to an affinity tag and coupling it with catalytically defective enzymes, biosynthetic intermediates were easily captured for analysis. We found that two major phases of molecular maturation are separated by a key C-terminal processing step. Phase-I conversion of six Cys residues to thiazoles (TclIJN) is followed by C-terminal oxidative decarboxylation (TclP). This TclP-mediated oxidative decarboxylation is a required step for the peptide to progress to phase II. In phase II, Ser/Thr dehydration (TclKL) and peptide macrocycle formation (TclM) occurs. A C-terminal reductase, TclS, can optionally act on the substrate peptide, yielding MP1, and is shown to act late in the pathway. This comprehensive characterization of the MP1 pathway prepares the way for future engineering efforts. PMID:27791142

  17. Domestication Process of the Goat Revealed by an Analysis of the Nearly Complete Mitochondrial Protein-Encoding Genes

    PubMed Central

    Nomura, Koh; Yonezawa, Takahiro; Mano, Shuhei; Kawakami, Shigehisa; Shedlock, Andrew M.; Hasegawa, Masami; Amano, Takashi

    2013-01-01

    Goats (Capra hircus) are one of the oldest domesticated species, and they are kept all over the world as an essential resource for meat, milk, and fiber. Although recent archeological and molecular biological studies suggested that they originated in West Asia, their domestication processes such as the timing of population expansion and the dynamics of their selection pressures are little known. With the aim of addressing these issues, the nearly complete mitochondrial protein-encoding genes were determined from East, Southeast, and South Asian populations. Our coalescent time estimations suggest that the timing of their major population expansions was in the Late Pleistocene and significantly predates the beginning of their domestication in the Neolithic era (≈10,000 years ago). The ω (ratio of non-synonymous rate/synonymous substitution rate) for each lineage was also estimated. We found that the ω of the globally distributed haplogroup A which is inherited by more than 90% of goats examined, turned out to be extremely low, suggesting that they are under severe selection pressure probably due to their large population size. Conversely, the ω of the Asian-specific haplogroup B inherited by about 5% of goats was relatively high. Although recent molecular studies suggest that domestication of animals may tend to relax selective constraints, the opposite pattern observed in our goat mitochondrial genome data indicates the process of domestication is more complex than may be presently appreciated and cannot be explained only by a simple relaxation model. PMID:23936295

  18. Complex network models reveal correlations among network metrics, exercise intensity and role of body changes in the fatigue process

    NASA Astrophysics Data System (ADS)

    Pereira, Vanessa Helena; Gama, Maria Carolina Traina; Sousa, Filipe Antônio Barros; Lewis, Theodore Gyle; Gobatto, Claudio Alexandre; Manchado-Gobatto, Fúlvia Barros

    2015-05-01

    The aims of the present study were analyze the fatigue process at distinct intensity efforts and to investigate its occurrence as interactions at distinct body changes during exercise, using complex network models. For this, participants were submitted to four different running intensities until exhaustion, accomplished in a non-motorized treadmill using a tethered system. The intensities were selected according to critical power model. Mechanical (force, peak power, mean power, velocity and work) and physiological related parameters (heart rate, blood lactate, time until peak blood lactate concentration (lactate time), lean mass, anaerobic and aerobic capacities) and IPAQ score were obtained during exercises and it was used to construction of four complex network models. Such models have both, theoretical and mathematical value, and enables us to perceive new insights that go beyond conventional analysis. From these, we ranked the influences of each node at the fatigue process. Our results shows that nodes, links and network metrics are sensibility according to increase of efforts intensities, been the velocity a key factor to exercise maintenance at models/intensities 1 and 2 (higher time efforts) and force and power at models 3 and 4, highlighting mechanical variables in the exhaustion occurrence and even training prescription applications.

  19. Complex network models reveal correlations among network metrics, exercise intensity and role of body changes in the fatigue process.

    PubMed

    Pereira, Vanessa Helena; Gama, Maria Carolina Traina; Sousa, Filipe Antônio Barros; Lewis, Theodore Gyle; Gobatto, Claudio Alexandre; Manchado-Gobatto, Fúlvia Barros

    2015-05-21

    The aims of the present study were analyze the fatigue process at distinct intensity efforts and to investigate its occurrence as interactions at distinct body changes during exercise, using complex network models. For this, participants were submitted to four different running intensities until exhaustion, accomplished in a non-motorized treadmill using a tethered system. The intensities were selected according to critical power model. Mechanical (force, peak power, mean power, velocity and work) and physiological related parameters (heart rate, blood lactate, time until peak blood lactate concentration (lactate time), lean mass, anaerobic and aerobic capacities) and IPAQ score were obtained during exercises and it was used to construction of four complex network models. Such models have both, theoretical and mathematical value, and enables us to perceive new insights that go beyond conventional analysis. From these, we ranked the influences of each node at the fatigue process. Our results shows that nodes, links and network metrics are sensibility according to increase of efforts intensities, been the velocity a key factor to exercise maintenance at models/intensities 1 and 2 (higher time efforts) and force and power at models 3 and 4, highlighting mechanical variables in the exhaustion occurrence and even training prescription applications.

  20. Transition of the Taiwan-Ryukyu collision-subduction process as revealed by ocean-bottom seismometer observations

    NASA Astrophysics Data System (ADS)

    Chin, Shao-Jinn; Lin, Jing-Yi; Chen, Yen-Fu; Wu, Wen-Nan; Liang, Chin-Wei

    2016-10-01

    Located at the arc-continental collision region between the Eurasian (EP) and Philippine Sea Plates (PSP), Taiwan is usually considered to have a complex tectonic environment, particularly along the eastern coast of the island. To gain a better understanding of the geological evolution of the east Taiwan area, the data from 8 Ocean Bottom Seismometers (OBS) acquired during the Across Taiwan Strait Explosion Experiment in 2012 and 14 inland seismic stations were used to determine a more detailed and accurate distribution of marine earthquakes. Based on the 333 relocated earthquakes and available geophysical data, we suggest two main tectonic boundaries for eastern Taiwan. South of 23.25°N, the homogeneous distribution of earthquakes in the crustal portion for both the inland and offshore areas suggests an ongoing collisional process. North of this location, between approximately 23.25°N and 23.8°N, the abrupt increasing of seismicity depth infers that the underthrusted arc/fore-arc material is deforming due to the collisional compression at depth. In this segment, the subsidence of the arc/fore-arc area determines the transition from collision to subduction. North of 23.8°N, the northwestern dipping PSP is well illustrated by the seismicity both onshore and offshore, indicating a dominant subduction process.

  1. Rise of dinosaurs reveals major body-size transitions are driven by passive processes of trait evolution

    PubMed Central

    Sookias, Roland B.; Butler, Richard J.; Benson, Roger B. J.

    2012-01-01

    A major macroevolutionary question concerns how long-term patterns of body-size evolution are underpinned by smaller scale processes along lineages. One outstanding long-term transition is the replacement of basal therapsids (stem-group mammals) by archosauromorphs, including dinosaurs, as the dominant large-bodied terrestrial fauna during the Triassic (approx. 252–201 million years ago). This landmark event preceded more than 150 million years of archosauromorph dominance. We analyse a new body-size dataset of more than 400 therapsid and archosauromorph species spanning the Late Permian–Middle Jurassic. Maximum-likelihood analyses indicate that Cope's rule (an active within-lineage trend of body-size increase) is extremely rare, despite conspicuous patterns of body-size turnover, and contrary to proposals that Cope's rule is central to vertebrate evolution. Instead, passive processes predominate in taxonomically and ecomorphologically more inclusive clades, with stasis common in less inclusive clades. Body-size limits are clade-dependent, suggesting intrinsic, biological factors are more important than the external environment. This clade-dependence is exemplified by maximum size of Middle–early Late Triassic archosauromorph predators exceeding that of contemporary herbivores, breaking a widely-accepted ‘rule’ that herbivore maximum size greatly exceeds carnivore maximum size. Archosauromorph and dinosaur dominance occurred via opportunistic replacement of therapsids following extinction, but were facilitated by higher archosauromorph growth rates. PMID:22298850

  2. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics.

    PubMed

    Williams, Timothy J; Wilkins, David; Long, Emilie; Evans, Flavia; DeMaere, Mathew Z; Raftery, Mark J; Cavicchioli, Ricardo

    2013-05-01

    Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.

  3. Compressive Phase Contrast Tomography

    SciTech Connect

    Maia, Filipe; MacDowell, Alastair; Marchesini, Stefano; Padmore, Howard A.; Parkinson, Dula Y.; Pien, Jack; Schirotzek, Andre; Yang, Chao

    2010-09-01

    When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. Interference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher contrast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).

  4. Deciphering Piperidine Formation in Polyketide-Derived Indolizidines Reveals a Thioester Reduction, Transamination, and Unusual Imine Reduction Process.

    PubMed

    Peng, Haidong; Wei, Erman; Wang, Jiali; Zhang, Yanan; Cheng, Lin; Ma, Hongmin; Deng, Zixin; Qu, Xudong

    2016-12-16

    Piperidine and indolizidine are two basic units of alkaloids that are frequently observed in natural and synthetic compounds. Their biosynthesis in natural products is highly conserved and mostly derived from the incorporation of lysine cyclization products. Through in vitro reconstitution, we herein identified a novel pathway involving a group of polyketide-derived indolizidines, which comprises the processes of tandem two-electron thioester reduction, transamination, and imine reduction to convert acyl carrier protein (ACP)-tethered polyketide chains into the piperidine moieties of their indolizidine scaffolds. The enzymes that catalyze the imine reduction are distinct from previous known imine reductases, which have a fold of acyl-CoA dehydrogenase but do not require flavin for reduction. Our results not only provide a new way for the biosynthesis of the basic units of alkaloids but also show a novel class of imine reductases that may benefit the fields of biocatalysis and biomanufacturing.

  5. The N400 reveals how personal semantics is processed: Insights into the nature and organization of self-knowledge.

    PubMed

    Coronel, Jason C; Federmeier, Kara D

    2016-04-01

    There is growing recognition that some important forms of long-term memory are difficult to classify into one of the well-studied memory subtypes. One example is personal semantics. Like the episodes that are stored as part of one's autobiography, personal semantics is linked to an individual, yet, like general semantic memory, it is detached from a specific encoding context. Access to general semantics elicits an electrophysiological response known as the N400, which has been characterized across three decades of research; surprisingly, this response has not been fully examined in the context of personal semantics. In this study, we assessed responses to congruent and incongruent statements about people's own, personal preferences. We found that access to personal preferences elicited N400 responses, with congruency effects that were similar in latency and distribution to those for general semantic statements elicited from the same participants. These results suggest that the processing of personal and general semantics share important functional and neurobiological features.

  6. Chaotic and stochastic processes in the accretion flows of the black hole X-ray binaries revealed by recurrence analysis

    NASA Astrophysics Data System (ADS)

    Suková, Petra; Grzedzielski, Mikolaj; Janiuk, Agnieszka

    2016-02-01

    Aims: Both the well known microquasar GRS 1915+105, as well as its recently discovered analogue, IGR J17091-3624, exhibit variability that is characteristic of a deterministic chaotic system. Their specific kind of quasi-periodic flares that are observed in some states is intrinsically connected with the global structure of the accretion flow, which are governed by the nonlinear hydrodynamics. One plausible mechanism that is proposed to explain this kind of variability is the thermal-viscous instability that operates in the accretion disk. The purely stochastic variability that occurs because of turbulent conditions in the plasma, is quantified by the power density spectra and appears in practically all types of sources and their spectral states. Methods: We pose a question as to whether these two microquasars are one of a kind, or if the traces of deterministic chaos, and hence the accretion disk instability, may also be hidden in the observed variability of other sources. We focus on the black hole X-ray binaries that accrete at a high rate and are, therefore, theoretically prone to the development of radiation pressure-induced instability. To study the nonlinear behaviour of the X-ray sources and distinguish between the chaotic and stochastic nature of their emission, we propose a novel method, which is based on recurrence analysis. Widely known in other fields of physics, this powerful method is used here for the first time in an astrophysical context. We estimate the indications of deterministic chaos quantitatively, such as the Rényi's entropy for the observed time series, and we compare them with surrogate data. Results: Using the observational data collected by the RXTE satellite, we reveal the oscillations pattern and the observable properties of six black hole systems. For five of them, we confirm the signatures of deterministic chaos being the driver of their observed variability. Conclusions: We test the method and confirm the deterministic nature of

  7. Sedimentary processes of the Kusawa Lake torrent system, Yukon, Canada, as revealed by the September 16, 1982 flood event

    NASA Astrophysics Data System (ADS)

    Lowey, Grant W.

    2002-08-01

    The Kusawa Lake torrent system is located in the northern Canadian Cordillera of southwestern Yukon. It is Holocene in age and consists of a catchment area, gorge and alluvial fan complex. The north compartment of the catchment is a third-order basin covering an area of 13.2 km 2. It is characterized by active slumping of Quaternary glacial deposits that supply sediment for the torrent system. The gorge is approximately 800 m long and distinguished by 10 m high vertical walls cut into granitic bedrock. The fan complex is semiconical in shape and covers an area of 1.52 km 2. The active part of the fan is plano-convex in longitudinal profile, covers an area of 0.75 km 2, and is subdivided into an upper, middle and lower fan, based on the occurrence of seven sedimentary facies that were deposited by a catastrophic flood in 1982. The upper fan is characterized by boulder gravel levees and boulder gravel lobes that were deposited by debris flows. It is also characterized by sandy boulder gravel that may represent a transition from debris flow to dominantly hyperconcentrated flow processes. The middle fan is distinguished by sandy cobble gravel and sandy pebble gravel that is interbedded with horizontally laminated sand. These sediments were deposited by hyperconcentrated flows. The lower fan is characterized by horizontally bedded and laminated sand that may represent a transition from hyperconcentrated flow to sheetflood dominant processes, and by sand channels that represent rechannelized waning-flood discharge. The fan displays downfan trends in grain size (boulders to sand), slope style (plano-concave), and slope value (4-1°) typical of sheetflood-dominated fans. The initiation of sedimentation in the Kusawa Lake torrent system was due to a combination of rainfall flooding and flooding related to catastrophic slope failure in the catchment area. Slope failure leads to the formation of a landslide dam and lake, and when the dam fails, the draining lake results in a

  8. List blocking and longer retention intervals reveal an influence of gist processing for lexically ambiguous critical lures

    PubMed Central

    McNabb, Jaimie; Hutchison, Keith A.

    2016-01-01

    In two experiments, we examined veridical and false memory for lists of associates from two meanings (e.g., stumble, trip, harvest, pumpkin, etc.) that converged upon a single, lexically ambiguous critical lure (e.g., fall), in order to compare the activation-monitoring and fuzzy-trace false memory accounts. In Experiment 1, we presented study lists that were blocked or alternated by meaning (within subjects), followed by a free recall test completed immediately or after a 2.5-min delay. Correct recall was greater for blocked than for alternated lists. Critical-lure false recall was greater for blocked lists on an immediate test, whereas both list types produced equivalent false recall on a delayed test. In Experiment 2, lists blocked and alternated by meaning were presented via a between-subjects design, in order to eliminate possible list-type carryover effects. Correct recall replicated the result from Experiment 1; however, blocking lists increased false recall on delayed, but not on immediate, tests. Across the experiments, clustering correct recall by meaning increased across the delay selectively for the alternated lists. Our results suggest that thematic (i.e., gist) processes are influential for false recall, especially following a delay, a pattern consistent with fuzzy-trace theory. PMID:26105976

  9. Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes

    PubMed Central

    2011-01-01

    Background Down syndrome (DS; trisomy 21) is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information. Results We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies. We identified 324 genes with significant genome-wide dosage effects, including well investigated genes like SOD1, APP, RUNX1 and DYRK1A as well as a large proportion of novel genes (N = 62). Furthermore, we characterized these genes using gene ontology, molecular interactions and promoter sequence analysis. In order to judge relevance of the 324 genes for more general cerebral pathologies we used independent publicly available microarry data from brain studies not related with DS and identified a subset of 79 genes with potential impact for neurocognitive processes. All results have been made available through a web server under http://ds-geneminer.molgen.mpg.de/. Conclusions Our study represents a comprehensive integrative analysis of heterogeneous data including genome-wide transcript levels in the domain of trisomy 21. The detected dosage effects build a resource for further studies of DS pathology and the development of new therapies. PMID:21569303

  10. The N400 reveals how personal semantics is processed: Insights into the nature and organization of self-knowledge

    PubMed Central

    Federmeier, Kara D.

    2017-01-01

    There is growing recognition that some important forms of long-term memory are difficult to classify into one of the well-studied memory subtypes. One example is personal semantics. Like the episodes that are stored as part of one’s autobiography, personal semantics is linked to an individual, yet, like general semantic memory, it is detached from a specific encoding context. Access to general semantics elicits an electrophysiological response known as the N400, which has been characterized across three decades of research; surprisingly, this response has not been fully examined in the context of personal semantics. In this study, we assessed responses to congruent and incongruent statements about people’s own, personal preferences. We found that access to personal preferences elicited N400 responses, with congruency effects that were similar in latency and distribution to those for general semantic statements elicited from the same participants. These results suggest that the processing of personal and general semantics share important functional and neurobiological features. PMID:26825011

  11. Crystal Structure of E. coli RecE Protein Reveals a Toroidal Tetramer for Processing Double-Stranded DNA Breaks

    SciTech Connect

    Zhang, Jinjin; Xing, Xu; Herr, Andrew B.; Bell, Charles E.

    2009-07-21

    Escherichia coli RecE protein is part of the classical RecET recombination system that has recently been used in powerful new methods for genetic engineering. RecE binds to free double-stranded DNA (dsDNA) ends and processively digests the 5{prime}-ended strand to form 5{prime}-mononucleotides and a 3{prime}-overhang that is a substrate for single strand annealing promoted by RecT. Here, we report the crystal structure of the C-terminal nuclease domain of RecE at 2.8 {angstrom} resolution. RecE forms a toroidal tetramer with a central tapered channel that is wide enough to bind dsDNA at one end, but is partially plugged at the other end by the C-terminal segment of the protein. Four narrow tunnels, one within each subunit of the tetramer, lead from the central channel to the four active sites, which lie about 15 {angstrom} from the channel. The structure, combined with mutational studies, suggests a mechanism in which dsDNA enters through the open end of the central channel, the 5{prime}-ended strand passes through a tunnel to access one of the four active sites, and the 3{prime}-ended strand passes through the plugged end of the channel at the back of the tetramer.

  12. Looking, seeing and believing in autism: Eye movements reveal how subtle cognitive processing differences impact in the social domain.

    PubMed

    Benson, Valerie; Castelhano, Monica S; Howard, Philippa L; Latif, Nida; Rayner, Keith

    2016-08-01

    Adults with High Functioning Autism Spectrum Disorders (ASD) viewed scenes with people in them, while having their eye movements recorded. The task was to indicate, using a button press, whether the pictures were normal, or in some way weird or odd. Oddities in the pictures were categorized as violations of either perceptual or social norms. Compared to a Typically Developed (TD) control group, the ASD participants were equally able to categorize the scenes as odd or normal, but they took longer to respond. The eye movement patterns showed that the ASD group made more fixations and revisits to the target areas in the odd scenes compared with the TD group. Additionally, when the ASD group first fixated the target areas in the scenes, they failed to initially detect the social oddities. These two findings have clear implications for processing difficulties in ASD for the social domain, where it is important to detect social cues on-line, and where there is little opportunity to go back and recheck possible cues in fast dynamic interactions. Autism Res 2016, 9: 879-887. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

  13. Rhythm evokes action: early processing of metric deviances in expressive music by experts and laymen revealed by ERP source imaging.

    PubMed

    James, Clara E; Michel, Christoph M; Britz, Juliane; Vuilleumier, Patrik; Hauert, Claude-Alain

    2012-12-01

    To examine how musical expertise tunes the brain to subtle metric anomalies in an ecological musical context, we presented piano compositions ending on standard and deviant cadences (endings) to expert pianists and musical laymen, while high-density EEG was recorded. Temporal expectancies were manipulated by substituting standard "masculine" cadences at metrically strong positions with deviant, metrically unaccented, "feminine" cadences. Experts detected metrically deviant cadences better than laymen. Analyses of event-related potentials demonstrated that an early P3a-like component (~150-300 ms), elicited by musical closure, was significantly enhanced at frontal and parietal electrodes in response to deviant endings in experts, whereas a reduced response to deviance occurred in laymen. Putative neuronal sources contributing to the modulation of this component were localized in a network of brain regions including bilateral supplementary motor areas, middle and posterior cingulate cortex, precuneus, associative visual areas, as well as in the right amygdala and insula. In all these regions, experts showed enhanced responses to metric deviance. Later effects demonstrated enhanced activations within the same brain network, as well as higher processing speed for experts. These results suggest that early brain responses to metric deviance in experts may rely on motor representations mediated by the supplementary motor area and motor cingulate regions, in addition to areas involved in self-referential imagery and relevance detection. Such motor representations could play a role in temporal sensory prediction evolved from musical training and suggests that rhythm evokes action more strongly in highly trained instrumentalists.

  14. In vivo two-photon microscopy reveals immediate microglial reaction to implantation of microelectrode through extension of processes

    PubMed Central

    Kozai, Takashi D Yoshida; Vazquez, Alberto L; Weaver, Cassandra L; Kim, Seong-Gi; Cui, X Tracy

    2012-01-01

    Objective Penetrating cortical neural probe technologies allow investigators to record electrical signals in the brain. Implantation of probes results in acute tissue damage, and microglia density increases around implanted devices over weeks. However, the mechanisms underlying this encapsulation are not well understood in the acute temporal domain. The objective here was to evaluate dynamic microglial response to implanted probes using two-photon microscopy. Approach Using two-photon in vivo microscopy, cortical microglia ~200 µm below the surface of the visual cortex were imaged every minute in mice with green fluorescent protein-expressing microglia. Main results Following probe insertion, nearby microglia immediately extended processes toward the probe at (1.6 ± 1.3) µmmin−1 during the first 30–45 min, but showed negligible cell body movement for the first 6 h. Six hours following probe insertion, microglia at distances <130.0 µm (p = 0.5) from the probe surface exhibit morphological characteristics of transitional stage (T-stage) activation, similar to the microglial response observed with laser-induced blood–brain barrier damage. T-stage morphology and microglia directionality indexes were developed to characterize microglial response to implanted probes. Evidence suggesting vascular reorganization after probe insertion and distant vessel damage was also observed hours after probe insertion. Significance A precise temporal understanding of the cellular response to microelectrode implantation will facilitate the search for molecular cues initiating and attenuating the reactive tissue response. PMID:23075490

  15. Transition from distributional to ergodic behavior in an inhomogeneous diffusion process: Method revealing an unknown surface diffusivity.

    PubMed

    Akimoto, Takuma; Seki, Kazuhiko

    2015-08-01

    Diffusion of molecules in cells plays an important role in providing a biological reaction on the surface by finding a target on the membrane surface. The water retardation (slow diffusion) near the target assists the searching molecules to recognize the target. Here, we consider effects of the surface diffusivity on the effective diffusivity, where diffusion on the surface is slower than that in bulk. We show that the ensemble-averaged mean-square displacements increase linearly with time when the desorption rate from the surface is finite, which is valid even when the diffusion on the surface is anomalous (subdiffusion). Moreover, this slow diffusion on the surface affects the fluctuations of the time-averaged mean-square displacements (TAMSDs). We find that fluctuations of the TAMSDs remain large when the measurement time is smaller than a characteristic time, and decays according to an increase of the measurement time for a relatively large measurement time. Therefore, we find a transition from nonergodic (distributional) to ergodic diffusivity in a target search process. Moreover, this fluctuation analysis provides a method to estimate an unknown surface diffusivity.

  16. Consecutive TMS-fMRI reveals an inverse relationship in BOLD signal between object and scene processing.

    PubMed

    Mullin, Caitlin R; Steeves, Jennifer K E

    2013-12-04

    The human visual system is capable of recognizing an infinite number of scenes containing an abundance of rich visual information. There are several cortical regions associated with the representation of a scene, including those specialized for object processing (the lateral occipital area [LO]) and for the spatial layout of scenes (the parahippocampal place area). Although behavioral studies have demonstrated that these image categories (scenes and objects) exert an influence on each other such that scene context can facilitate object identification or that scene categorization can be impaired by the presence of a salient object, little is known about the apparent cortical interactions involved in building the conscious representation of a complete scene. It has been shown that transcranial magnetic stimulation (TMS) to the left LO disrupts object categorization but facilitates scene categorization. Here, we show that this effect is also reflected by changes in the BOLD signal such that TMS to the left LO decreases BOLD signal at the stimulation site (LO) while viewing objects and increases BOLD signal in the left PPA when viewing scenes. This suggests that these regions, although likely not on a strict hierarchy of bottom-up coding, share functional communication likely in the form of inhibitory connections.

  17. Genetic, morphological, and acoustic evidence reveals lack of diversification in the colonization process in an island bird.

    PubMed

    Illera, Juan Carlos; Palmero, Ana M; Laiolo, Paola; Rodríguez, Felipe; Moreno, Ángel C; Navascués, Miguel

    2014-08-01

    Songbirds with recently (i.e., early Holocene) founded populations are suitable models for studying incipient differentiation in oceanic islands. On such systems each colonization event represents a different evolutionary episode that can be studied by addressing sets of diverging phenotypic and genetic traits. We investigate the process of early differentiation in the spectacled warbler (Sylvia conspicillata) in 14 populations separated by sea barriers from three Atlantic archipelagos and from continental regions spanning from tropical to temperate latitudes. Our approach involved the study of sexual acoustic signals, morphology, and genetic data. Mitochondrial DNA did not provide clear population structure. However, microsatellites analyses consistently identified two genetic groups, albeit without correspondence to subspecies classification and little correspondence to geography. Coalescent analyses showed significant evidence for gene flow between the two genetic groups. Discriminant analyses could not correctly assign morphological or acoustic traits to source populations. Therefore, although theory predicting that in isolated populations genetic, morphological, or acoustic traits can lead to radiation, we have strikingly failed to document differentiation on these attributes in a resident passerine throughout three oceanic archipelagos.

  18. Connectivity Reveals Sources of Predictive Coding Signals in Early Visual Cortex During Processing of Visual Optic Flow.

    PubMed

    Schindler, Andreas; Bartels, Andreas

    2016-05-24

    Superimposed on the visual feed-forward pathway, feedback connections convey higher level information to cortical areas lower in the hierarchy. A prominent framework for these connections is the theory of predictive coding where high-level areas send stimulus interpretations to lower level areas that compare them with sensory input. Along these lines, a growing body of neuroimaging studies shows that predictable stimuli lead to reduced blood oxygen level-dependent (BOLD) responses compared with matched nonpredictable counterparts, especially in early visual cortex (EVC) including areas V1-V3. The sources of these modulatory feedback signals are largely unknown. Here, we re-examined the robust finding of relative BOLD suppression in EVC evident during processing of coherent compared with random motion. Using functional connectivity analysis, we show an optic flow-dependent increase of functional connectivity between BOLD suppressed EVC and a network of visual motion areas including MST, V3A, V6, the cingulate sulcus visual area (CSv), and precuneus (Pc). Connectivity decreased between EVC and 2 areas known to encode heading direction: entorhinal cortex (EC) and retrosplenial cortex (RSC). Our results provide first evidence that BOLD suppression in EVC for predictable stimuli is indeed mediated by specific high-level areas, in accord with the theory of predictive coding.

  19. The modulation of causal contexts in motion processes judgment as revealed by P2 and P3.

    PubMed

    Chen, Qingfei; Liang, Xiuling; Peng, Xiaozhe; Liu, Yang; Lei, Yi; Li, Hong

    2017-02-01

    The evoked response potential (ERP) procedure was used to investigate the representation of motion processes in different causal contexts, such as the collision of two squares or the repulsion of two magnets with like poles facing. Participants were required to judge whether each movement was plausible according to the causal context depicted by the cover story. Three main differences after the movement of the second object were found. First, the amplitudes at 70-170ms (N1) and 170-370ms (P2) elicited by a no-contact condition were more negative than a contact condition in the square context, whereas larger N1 and more positive amplitudes at 370-670ms were elicited by a no-contact condition in the magnet context. Second, larger P2 and more positive amplitudes at 370-670ms were elicited by inconsistent direction relative to consistent condition in the square context, whereas smaller N1 and more positive amplitudes at 370-670ms were elicited by inconsistent direction in the magnet context. Finally, larger P2 and more negative amplitudes at 370-470ms were elicited by plausible conditions relative to implausible conditions in a square context, whereas larger N1 and more positive amplitudes at 370-670ms were elicited by plausible conditions in the magnet context. These results suggested that the conceptual knowledge with different causal contexts have distinct effects on the judgment of objects interactions.

  20. Vestibular influences on human postural control in combinations of pitch and roll planes reveal differences in spatiotemporal processing.

    PubMed

    Carpenter, M G; Allum, J H; Honegger, F

    2001-09-01

    destabilize the body. As a result of these changes in response amplitudes, BVL patients had reduced balance correcting ankle torque between 160 and 260 ms and increased torque between 280 and 380 ms compared to normals. There were no differences in the orientation of the resultant ankle torque vectors between BVL and normals, both of which were oriented primarily along the pitch plane. For combinations of backward (toe-up) and roll perturbations BVL patients had larger balance correcting and stabilizing reactions (between 350 and 700 ms) in PARAS than normals and these corresponded to excessive trunk pitch and roll velocities. During roll perturbations, trunk velocities in BVL subjects after 200 ms were directed along directions different from those of normals. Furthermore, roll instabilities appeared later than those of pitch particularly for backward roll perturbations. The results of the study show that combinations of roll and pitch surface rotations yield important spatiotemporal information, especially with respect to trunk response strategies changed by BVL which are not revealed by pitch plane perturbations alone. Our results indicate that vestibular influences are earlier for the pitch plane and are directed to leg muscles, whereas roll control is later and focused on trunk muscles.

  1. Phase-contrast radiography.

    PubMed

    Gao, D; Pogany, A; Stevenson, A W; Wilkins, S W

    1998-01-01

    For the past 100 years, the paradigm for radiography has been premised on absorption as the sole means of contrast formation and on ray optics as the basis for image interpretation. A new conceptual approach to radiography has been developed that includes phase (ie, refractive) contrast and requires wave optics for proper treatment. This new approach greatly increases the amount of information that can be obtained with radiographic techniques and is particularly well suited to the imaging of soft tissue and of very small features in biologic samples. A key feature of the present technique of phase-contrast radiography is the use of a microfocus x-ray source about an order of magnitude (< or = 20 microm) smaller than that used in conventional radiography. Phase-contrast radiography offers a number of improvements over conventional radiography in a clinical setting, especially in soft-tissue imaging. These improvements include increased contrast resulting in improved visualization of anatomic detail, reduced absorbed dose to the patient, inherent image magnification and high spatial resolution, use of harder x rays, and relative ease of implementation. More technologically advanced detectors are currently being developed and commercialized, which will help fully realize the considerable potential of phase-contrast imaging.

  2. Quantitative Proteomic and Transcriptomic Study on Autotetraploid Paulownia and Its Diploid Parent Reveal Key Metabolic Processes Associated with Paulownia Autotetraploidization

    PubMed Central

    Dong, Yanpeng; Deng, Minjie; Zhao, Zhenli; Fan, Guoqiang

    2016-01-01

    Polyploidy plays a very important role in speciation and plant evolution by way of genomic merging and doubling. In the process of polyploidy, rapid genomic, and transcriptomic changes have been observed and researched. However, proteomic divergence caused by the effects of polyploidization is still poorly understood. In the present study, we used iTRAQ coupled with mass spectrometry to quantitatively analyze proteomic changes in the leaves of autotetraploid Paulownia and its diploid parent. A total of 2963 proteins were identified and quantified. Among them, 463 differentially abundant proteins were detected between autotetraploid Paulownia and its diploid parent, and 198 proteins were found to be non-additively abundant in autotetraploid Paulownia, suggesting the presence of non-additive protein regulation during genomic merger and doubling. We also detected 1808 protein-encoding genes in previously published RNA sequencing data. We found that 59 of the genes that showed remarkable changes at mRNA level encoded proteins with consistant changes in their abundance levels, while a further 48 genes that showed noteworthy changes in their expression levels encoded proteins with opposite changes in their abundance levels. Proteins involved in posttranslational modification, protein turnover, and response to stimulus, were significantly enriched among the non-additive proteins, which may provide some of the driving power for variation and adaptation in autopolyploids. Quantitative real-time PCR analysis verified the expression patterns of related protein-coding genes. In addition, we found that the percentage of differentially abundant proteins that matched previously reported differentially expressed genes was relatively low. PMID:27446122

  3. Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi

    PubMed Central

    Greif, Gonzalo; Rodriguez, Matias; Alvarez-Valin, Fernando

    2017-01-01

    American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also, a general down-regulation of surface glycoprotein coding genes was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, and also express a specific subset of surface glycoprotein coding genes. In addition, these results allowed us to improve the annotation of the Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions. PMID:28286708

  4. RNA interference to reveal roles of β-N-acetylglucosaminidase gene during molting process in Locusta migratoria.

    PubMed

    Rong, Shuo; Li, Da-Qi; Zhang, Xue-Yao; Li, Sheng; Zhu, Kun Yan; Guo, Ya-Ping; Ma, En-Bo; Zhang, Jian-Zhen

    2013-02-01

    β-N-acetylglucosaminidases are crucial enzymes involved in chitin degradation in insects. We identified a β-N-acetylglucosaminidase gene (LmNAG1) from Locusta migratoria. The full-length complementary DNA (cDNA) of LmNAG1 consists of 2 667 nucleotides, including an open reading frame (ORF) of 1 845 nucleotides encoding 614 amino acid residues, and 233- and 589-nucleotide non-coding regions at the 5'- and 3'-ends, respectively. Phylogenetic analysis grouped the cDNA-deduced LmNAG1 protein with the enzymatically characterized β-N-acetylglucosaminidases in group I. Analyses of stage- and tissue-dependent expression patterns of LmNAG1 were carried out by real-time quantitative polymerase chain reaction. Our results showed that LmNAG1 transcript level in the integument was significantly high in the last 2 days of the fourth and fifth instar nymphs. LmNAG1 was highly expressed in foregut and hindgut. RNA interference of LmNAG1 resulted in an effective silence of the gene and a significantly reduced total LmNAG enzyme activity at 48 and 72 h after the injection of LmNAG1 double-stranded RNA (dsRNA). As compared with the control nymphs injected with GFP dsRNA, 50% of the dsLmNAG1-injected nymphs were not able to molt successfully and eventually died. Our results suggest that LmNAG1 plays an essential role in molting process of L. migratoria.

  5. Upland Reticulate Mottling Reveals Soil Biophysical Processes across Scales: Development of Structured Heterogeneity in a Marine Terrace Chronosequence

    NASA Astrophysics Data System (ADS)

    Stonestrom, D. A.; Schulz, M. S.; Lawrence, C. R.; Bullen, T. D.; Fitzpatrick, J.; Kyker-Snowman, E.; Manning, J. E.; Mnich, M.

    2015-12-01

    Soils of the Santa Cruz (California, USA) marine terrace chronosequence display an evolving sequence of reticulate mottling from the youngest soil (65 ka) without mottles to the oldest soil (225 ka) with well-developed mottles. Mottles develop in soils forming from relatively uniform shoreline sediments, below the depth of bioturbation. Mottles consist of an interconnected network of low-chroma clay-and-carbon enriched central regions (gray; 2.5Y 6/1) bordered by bleached parent material (white; 2.5Y 8/1) within a diminishing matrix of high-chroma oxidized parent material (orange; 7.5YR 5/8). To explore the nature of mottle development, physical and chemical characteristics of mottle separates (orange, gray, and white) were compared through the deep time represented by the chronosequence. Mineralogical, isotopic, and surface-area differences among mottle separates indicate that centimeter-scale mass-transfer acting across millennia is an integral part of pedogenesis, weathering-front propagation, and carbon and nutrient transfer. Elemental analysis, electron microscopy, and iron-isotope systematics indicate that mottle development is driven by deep roots together with their fungal and microbial symbionts. The current work extends the known realm of upland mottling and shows that such features may be more common than previously recognized in semi-humid to arid regions. Deep soil horizons on old stable landforms develop reticulate mottling as the long-term imprint of rhizospheric processes that control pedogenesis, plant-community sustenance, and sequestration of carbon at depth in unsaturated zones.

  6. Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi.

    PubMed

    Berná, Luisa; Chiribao, Maria Laura; Greif, Gonzalo; Rodriguez, Matias; Alvarez-Valin, Fernando; Robello, Carlos

    2017-01-01

    American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also, a general down-regulation of surface glycoprotein coding genes was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, and also express a specific subset of surface glycoprotein coding genes. In addition, these results allowed us to improve the annotation of the Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions.

  7. Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes.

    PubMed

    de Groot, Marco J L; Daran-Lapujade, Pascale; van Breukelen, Bas; Knijnenburg, Theo A; de Hulster, Erik A F; Reinders, Marcel J T; Pronk, Jack T; Heck, Albert J R; Slijper, Monique

    2007-11-01

    Saccharomyces cerevisiae is unique among yeasts in its ability to grow rapidly in the complete absence of oxygen. S. cerevisiae is therefore an ideal eukaryotic model to study physiological adaptation to anaerobiosis. Recent transcriptome analyses have identified hundreds of genes that are transcriptionally regulated by oxygen availability but the relevance of this cellular response has not been systematically investigated at the key control level of the proteome. Therefore, the proteomic response of S. cerevisiae to anaerobiosis was investigated using metabolic stable-isotope labelling in aerobic and anaerobic glucose-limited chemostat cultures, followed by relative quantification of protein expression. Using independent replicate cultures and stringent statistical filtering, a robust dataset of 474 quantified proteins was generated, of which 249 showed differential expression levels. While some of these changes were consistent with previous transcriptome studies, many of the responses of S. cerevisiae to oxygen availability were, to our knowledge, previously unreported. Comparison of transcriptomes and proteomes from identical cultivations yielded strong evidence for post-transcriptional regulation of key cellular processes, including glycolysis, amino-acyl-tRNA synthesis, purine nucleotide synthesis and amino acid biosynthesis. The use of chemostat cultures provided well-controlled and reproducible culture conditions, which are essential for generating robust datasets at different cellular information levels. Integration of transcriptome and proteome data led to new insights into the physiology of anaerobically growing yeast that would not have been apparent from differential analyses at either the mRNA or protein level alone, thus illustrating the power of multi-level studies in yeast systems biology.

  8. Stable Isotopic Signatures in the Isolated Brine Cyroecosystem of Lake Vida Reveal Evidence of both Abiotic and Biotic Processes

    NASA Astrophysics Data System (ADS)

    Murray, A. E.; Ostrom, N. E.; Glazer, B. T.; McKay, C.; Kenig, F.; Loeffler, F. E.; Fritsen, C. H.; Doran, P. T.

    2011-12-01

    Lake Vida in the Victoria Valley of East Antarctica harbors ice-entrained brine that has been isolated from surface processes for several thousand years. The brine conditions (permanently dark, temperature of -13.4 °C, lack of oxygen, and pH of 6.2) and geochemistry are highly unusual. As an example, the brine contains excessive quantities of both reduced and oxidized nitrogen in nearly all forms, which in several cases are the highest levels found among natural ecosystems on Earth. Though this cryoecosystem appears to be relatively inhospitable, we have evidence that microbial life persists in abundance (cell levels over 107 cells per mL), is capable of protein production at in situ temperatures, and harbors a unique, but not necessarily novel, assemblage of bacterial phylotypes spanning at least eight phyla. In order to assess in situ microbial activities occurring today and in the past, and test hypotheses concerning energy generation in the brine cryoecosystem, the stable isotope signatures of nitrogen, oxygen, and hydrogen have been characterized in liquid and dissolved gas phases of the brine. The data provide evidence for both biotic and potentially abiotic formation of different fractions. The site preference of 15N-nitrous oxide (-3.64) suggests that the primary source of this dissolved gas, which is found at levels as high as 86 μM, is biologically produced by denitrification pathways. This appears to be consistent with detection of Marinobacter and Psychrobacter-related bacterial rRNA gene sequences and isolates in the brine microbial community. On the other hand, dissolved hydrogen present in the brine harbors an δH-H2 isotope signature suggesting that abiotic (potentially via serpentinization) or biotic production is equivocal based on the significant levels of fractionation observed. We postulate however, that a serpentinization production route is more favorable in this system that lies in a basin comprised of Ferrar dolerite sills and granite

  9. RNA-Seq Reveals Age- and Species Differences of CAR-targeted Drug-Processing Genes in Liver.

    PubMed

    Cheng, Sunny Lihua; Bammler, Theo K; Cui, Julia Yue

    2017-02-23

    The constitutive androstane receptor (CAR/Nr1i3) is an important xenobiotic-sensing nuclear receptor that is highly expressed in liver, and is well known to have species differences. During development, age-specific activation of CAR may lead to modified pharmacokinetics and toxicokinetics of drugs and environmental chemicals, leading to higher risks for adverse drug reactions in newborns and children. The goal of this study was to systematically investigate the age- and species-specific regulation of various drug-processing genes (Li et al.) following neonatal or adult CAR activation in livers of wild-type (WT), CAR-null, and humanized CAR-transgenic (hCAR-TG) mice. At either 5- or 60-days of age, the 3 genotypes of mice were administered a species-appropriate CAR ligand or vehicle once daily for 4-days (i.p.). The majority of DPGs were differentially regulated by age and/or CAR activation, and they partitioned into 3 patterns: DPGs in Pattern-1 (up-regulated with age) and Pattern-2 (down-regulated with age) were predominantly regulated by age, whereas DPGs in Pattern 3 were predominantly regulated by CAR activation. There were 36 DPGs that were commonly up-regulated by CAR activation regardless of age or species of CAR; however, the fold-induction in the mRNA expression of these genes was profoundly modified by age. Although the cumulative mRNAs of uptake transporters were not readily altered by CAR, the cumulative Phase-I and -II enzymes as well as efflux transporters were all increased following CAR activation in both species. In general, mCAR activation produced comparable or even greater fold-increases of many DPGs in newborns than in adults; conversely, hCAR activation produced weaker induction in newborns than in adults. Western blotting and enzyme activity assays confirmed the age- and species-specificities of selected CAR-targeted DPGs. In conclusion, neonatal livers appear to be more sensitive to CAR-activators, whereas hCAR and mCAR produce overlapping

  10. Improvement for the multi-scale periodic characteristics revealing of precipitation signals and its impact assessment on soil hydrological process by combining HHT and CWT approaches

    NASA Astrophysics Data System (ADS)

    Yu, S. P.; Yang, J. S.; Liu, G. M.; Yao, R. J.; Wang, X. P.

    2014-06-01

    This study conducts a detailed analysis of the multi-scale periodic features involved in the annual and seasonal precipitation signals at the Chinese coastal reclamation region by selecting the suitable Continuous Wavelet Transform (CWT) and innovatively combining the improved Hilbert Huang Transform (HHT), and further deduces the precipitation trend and its impact on the future soil hydrological process. The Morlet wavelet transform is proved suitable in revealing the precipitation signals broad-scale periodicities, however, the critical mode mixing problem in the CWT causes the poor significances of the fine-scale periodicities, which can not well match the climate background. By combining the HHT approach, the fine-scale mode mixing drawback in the CWT is effectively eliminated, and the multi-scale periodicities of the studied precipitation signals are accurately revealed, based on which an overall decreasing trend of the annual and seasonal precipitation in the future years is demonstrated. Furthermore, by novelly using the Cross Wavelet Transform (XWT) and Wavelet Transform Coherence (WTC) approaches the prominent correlations between the precipitation dynamics and soil and groundwater salinities dynamics, that the precipitation increase can effectively leach the surface soil salt downwards into the deeper soil layers and groundwater with 5-7 days lag, in the new cultivated tidal land are demonstrated. The revealed future decreasing trend of precipitation especially in spring and summer may aggravate the soil salinization at the coastal reclamation region, thus we suggest reasonable salt leaching and evaporation suppression measures to prevent the possible soil secondary salinization process.

  11. Improvement for the multi-scale periodic characteristics revealing of precipitation signals and its impact assessment on soil hydrological process by combining HHT and CWT approaches

    NASA Astrophysics Data System (ADS)

    Yu, S.; Yang, J.; Liu, G.; Yao, R.; Wang, X.

    2015-03-01

    This study conducts a detailed analysis of multi-scale periodic features involved in the annual and seasonal precipitation signals at the typical coastal reclamation region in China by selecting the suitable continuous wavelet transform (CWT) and innovatively combining the improved Hilbert-Huang transform (HHT), and further deduces the precipitation trend and its impacts on the future soil hydrological process. The Morlet wavelet transform is proved suitable in revealing the precipitation signals broad-scale periodicities, however, the critical mode mixing problem in CWT causes the poor significance in the fine-scale periodicities, which cannot well match the climate background. By combining the HHT approach, the fine-scale mode mixing drawback in CWT is effectively eliminated, and the the studied precipitation signals multi-scale periodicities are accurately revealed. Consequently, an overall decreasing trend of annual and seasonal precipitation in future years is demonstrated. Furthermore, by novelly using the cross wavelet transform (XWT) and wavelet transform coherence (WTC) approaches, the prominent correlations between the precipitation dynamics and soil and groundwater salinities dynamics, it is demonstrated that the precipitation increase can effectively leach the surface soil salt downwards into the deeper soil layers and groundwater with 5-7-day lag in the new cultivated tidal land. The revealed future decreasing trend of precipitation, especially in spring and summer, may aggravate the soil salinization at the coastal reclamation region, thus some reasonable salt leaching and evaporation suppression measures need to be taken to prevent the possible soil secondary salinization process.

  12. Revealing Chemical Processes Involved in Electrochemical (De)Lithiation of Al with in Situ Neutron Depth Profiling and X-ray Diffraction.

    PubMed

    Liu, Danny X; Co, Anne C

    2016-01-13

    Herein we report a direct measurement of Li transport in real-time during charge and discharge process within an Al matrix using neutron depth profiling (NDP). In situ NDP was used to reveal and quantify parasitic losses during the first 25 mAhr/g of lithiation, followed by the formation of LiAl protrusions from the surface of pristine Al. Evidence of Li entrapment is also reported during delithiation. Subsequent lithiation and delithiation showed electrochemical charge passed to be equivalent to the amount of lithium incorporated into the Al matrix with negligible difference, suggesting that the parasitic losses including the formation of the solid electrolyte layer may be confined to the first lithiation. Parallel in situ XRD measurements also confirm the transformation of β-LiAl from a solid solution of α-LiAl, revealing solid solution-mediated crystallization of β-LiAl.

  13. Psychophysical contrast calibration

    PubMed Central

    To, Long; Woods, Russell L; Goldstein, Robert B; Peli, Eli

    2013-01-01

    Electronic displays and computer systems offer numerous advantages for clinical vision testing. Laboratory and clinical measurements of various functions and in particular of (letter) contrast sensitivity require accurately calibrated display contrast. In the laboratory this is achieved using expensive light meters. We developed and evaluated a novel method that uses only psychophysical responses of a person with normal vision to calibrate the luminance contrast of displays for experimental and clinical applications. Our method combines psychophysical techniques (1) for detection (and thus elimination or reduction) of display saturating nonlinearities; (2) for luminance (gamma function) estimation and linearization without use of a photometer; and (3) to measure without a photometer the luminance ratios of the display’s three color channels that are used in a bit-stealing procedure to expand the luminance resolution of the display. Using a photometer we verified that the calibration achieved with this procedure is accurate for both LCD and CRT displays enabling testing of letter contrast sensitivity to 0.5%. Our visual calibration procedure enables clinical, internet and home implementation and calibration verification of electronic contrast testing. PMID:23643843

  14. Phonation in Tonal Contrasts

    ERIC Educational Resources Information Center

    Kuang, Jianjing

    2013-01-01

    Phonation is used in many tonal languages, but how it should be incorporated into tonal systems is not well understood. The purpose of this dissertation thus is to examine the role of phonation in tonal contrasts, and to investigate how phonation and pitch interact in the tonal space. This dissertation presents close studies of tonal contrasts…

  15. Simultaneous blur contrast

    NASA Astrophysics Data System (ADS)

    Webster, Shernaaz M.; Webster, Michael A.; Taylor, John; Jaikumar, Jaikishan; Verma, Richa

    2001-06-01

    How well-focused an image appears can be strongly influenced by the surroundings context. A blurred surround can cause a central image to appear too sharp, while sharped surrounds can induce blur. We examined some spatial properties and stimulus selectivities of this 'simultaneous blur contrast.' Observers adjusted the focus of a central test image by a 2AFC staircase procedure that varied the slope of the image amplitude spectrum. The test were surrounded by 8 identical images with biased spectra, that were presented concurrently with the test for 0.5 sec on a uniform gray background. Contrast effects were comparable in magnitude for image sizes ranging from 1-deg to 4-deg in visual angle, but were stronger for test that were viwe4 in the periphery rather than fixated directly. Consistent biases were found for different types of grayscale images, including natural images, filtered noise, and simple edges. However, effects were weaker when surrounds and tests were drawn from different images, or differed in contrast-polarity or color, and thus do not depend on blur or on average spatial- frequency content per se. These induction effects may in part reflect a manifestation of selective contrast gain control

  16. Contrasting Views on Censorship.

    ERIC Educational Resources Information Center

    Riel, Arthur R., Jr.

    This paper asserts that public demands for book censorship are but one aspect of a deep public dissatisfaction with the educational establishment, and develops the thesis that the cause of this dissatisfaction is the contrast in world views and religions of those in the educational establishment and the censors. The educational establishment…

  17. Contrast enhancement via texture region based histogram equalization

    NASA Astrophysics Data System (ADS)

    Singh, Kuldeep; Vishwakarma, Dinesh K.; Singh Walia, Gurjit; Kapoor, Rajiv

    2016-08-01

    This paper presents two novel contrast enhancement approaches using texture regions-based histogram equalization (HE). In HE-based contrast enhancement methods, the enhanced image often contains undesirable artefacts because an excessive number of pixels in the non-textured areas heavily bias the histogram. The novel idea presented in this paper is to suppress the impact of pixels in non-textured areas and to exploit texture features for the computation of histogram in the process of HE. The first algorithm named as Dominant Orientation-based Texture Histogram Equalization (DOTHE), constructs the histogram of the image using only those image patches having dominant orientation. DOTHE categories image patches into smooth, dominant or non-dominant orientation patches by using the image variance and singular value decomposition algorithm and utilizes only dominant orientation patches in the process of HE. The second method termed as Edge-based Texture Histogram Equalization, calculates significant edges in the image and constructs the histogram using the grey levels present in the neighbourhood of edges. The cumulative density function of the histogram formed from texture features is mapped on the entire dynamic range of the input image to produce the contrast-enhanced image. Subjective as well as objective performance assessment of proposed methods is conducted and compared with other existing HE methods. The performance assessment in terms of visual quality, contrast improvement index, entropy and measure of enhancement reveals that the proposed methods outperform the existing HE methods.

  18. Time-frequency analysis of target detection reveals an early interface between bottom-up and top-down processes in the gamma-band.

    PubMed

    Busch, Niko A; Schadow, Jeanette; Fründ, Ingo; Herrmann, Christoph S

    2006-02-15

    The early visual gamma-band response is an oscillatory signal evoked approximately 100 ms after stimulation. While some studies have found effects of various cognitive processes on this signal, such effects could not be replicated in other studies. Accordingly, some authors have claimed that evoked gamma-band activity reflects merely sensory functions. To resolve these conflicting positions, we conducted a target detection experiment in which the feature that defined the target could be distributed over a large or a small part of the entire stimulus. Only targets covering a larger area of the entire stimulus evoked stronger gamma-band activity than standards although the over-all stimulus size was identical for all stimuli. This increase in evoked activity resulted from stronger oscillatory power and not exclusively from stronger phase-locking. In contrast, N1 and P3 amplitudes were larger for target stimuli irrespective of the distribution of the relevant stimulus feature. These results are consistent with the notion that early gamma-band activity is generated by feature-selective neural assemblies the activity of which can in fact be modulated by top-down processes. This interaction, however, may be only detectable in scalp-recorded EEG if it affects a sufficient number of neural assemblies.

  19. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  20. Chromatography: concepts and contrasts

    SciTech Connect

    Miller, J.M.

    1988-01-01

    As the author states in the Preface, this text attempts to provide a unified approach to chromatography (hence the title) by way of contrasting similarities and differences between gas chromatography (GC), column liquid chromatography (LC), and thin-layer chromatography (TLC). This book is also said to be pitched at an elementary level, suitable for most newcomers to the field (e.g., advanced undergraduates and beginning graduate students in the academic world, as well as bench-level chemists in industry).

  1. Optical Measurements Reveal Interplay Between Surface and Bottom Processes Involving Phytoplankton, Organic Carbon, Iron, Light, and Oxygen in Two Stratified Mesotrophic Lakes

    NASA Astrophysics Data System (ADS)

    Hargreaves, B. R.; Vaidya, A.; Wiles, K. A.

    2009-12-01

    Water column distribution of phytoplankton, organic carbon, particulate and dissolved iron are described through detailed vertical optical measurements that include downwelling cosine irradiance, turbidity, dissolved oxygen, fluorescence by CDOM, Chl-a, phycobilin pigments, and diffuse attenuation for several UV wavebands, plus pH, temperature, and specific conductance. These measurements were completed with a group of profiling instruments during summer in two mid-latitude small lakes. Special calibration allowed for correcting the impact of CDOM and turbidity on the pigment fluorescence signals. These in situ data were combined with laboratory analysis of discrete water column samples for methanol-extracted chlorophyll-a, spectral absorbance of particles, concentration of particulates (dry mass and ash-free mass), total particulate and "dissolved" iron, DOC and CDOM (the "dissolved fraction" passes through a GF/F filter). Surface processes revealed by these measurement include solar heating and photobleaching of CDOM (partly distributed by wind-driven mixing), and nonphotochemical quenching of phytoplankton chlorophyll-a fluorescence. Bottom processes revealed by these measurements include oxygen consumption by net heterotrophic metabolism, release of DOC, CDOM, and iron from anoxic bottom sediments, and the development of a biological community structured by the light and temperature gradients and absence or scarcity of dissolved oxygen near the bottom. The iron associated with CDOM and particles in the deep samples substantially increased the latter's DOC-specific absorption once there was an opportunity for oxidation. A model for mass-specific spectral absorption of particulates accounts for the contribution of organic matter and iron associated with the particles. A detailed hydrologic budget for one of the lakes will allow the water column processes to be explored further by accounting for inputs and outputs of water and organic carbon (via precipitation

  2. Combined diffusion-weighted and functional magnetic resonance imaging reveals a temporal-occipital network involved in auditory-visual object processing

    PubMed Central

    Beer, Anton L.; Plank, Tina; Meyer, Georg; Greenlee, Mark W.

    2013-01-01

    Functional magnetic resonance imaging (MRI) showed that the superior temporal and occipital cortex are involved in multisensory integration. Probabilistic fiber tracking based on diffusion-weighted MRI suggests that multisensory processing is supported by white matter connections between auditory cortex and the temporal and occipital lobe. Here, we present a combined functional MRI and probabilistic fiber tracking study that reveals multisensory processing mechanisms that remained undetected by either technique alone. Ten healthy participants passively observed visually presented lip or body movements, heard speech or body action sounds, or were exposed to a combination of both. Bimodal stimulation engaged a temporal-occipital brain network including the multisensory superior temporal sulcus (msSTS), the lateral superior temporal gyrus (lSTG), and the extrastriate body area (EBA). A region-of-interest (ROI) analysis showed multisensory interactions (e.g., subadditive responses to bimodal compared to unimodal stimuli) in the msSTS, the lSTG, and the EBA region. Moreover, sounds elicited responses in the medial occipital cortex. Probabilistic tracking revealed white matter tracts between the auditory cortex and the medial occipital cortex, the inferior occipital cortex (IOC), and the superior temporal sulcus (STS). However, STS terminations of auditory cortex tracts showed limited overlap with the msSTS region. Instead, msSTS was connected to primary sensory regions via intermediate nodes in the temporal and occipital cortex. Similarly, the lSTG and EBA regions showed limited direct white matter connections but instead were connected via intermediate nodes. Our results suggest that multisensory processing in the STS is mediated by separate brain areas that form a distinct network in the lateral temporal and inferior occipital cortex. PMID:23407860

  3. Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing.

    PubMed

    Fang, Ruo-si; Dong, Ya-chen; Chen, Feng; Chen, Qi-he

    2015-10-01

    Rice wine is a traditional Chinese fermented alcohol drink. Spontaneous fermentation with the use of the Chinese starter and wheat Qu lead to the growth of various microorganisms during the complete brewing process. It's of great importance to fully understand the composition of bacteria diversity in rice wine in order to improve the quality and solve safety problems. In this study, a more comprehensive bacterial description was shown with the use of bacteria diversity analysis, which enabled us to have a better understanding. Rarefaction, rank abundance, alpha Diversity, beta diversity and principal coordinates analysis simplified their complex bacteria components and provide us theoretical foundation for further investigation. It has been found bacteria diversity is more abundant at mid-term and later stage of brewing process. Bacteria community analysis reveals there is a potential safety hazard existing in the fermentation, since most of the sequence reads are assigned to Enterobacter (7900 at most) and Pantoea (7336 at most), followed by Staphylococcus (2796 at most) and Pseudomonas (1681 at most). Lactic acid bacteria are rare throughout the fermentation process which is not in accordance with other reports. This work may offer us an opportunity to investigate micro ecological fermentation system in food industry.

  4. miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering.

    PubMed

    Stiefel, Fabian; Fischer, Simon; Sczyrba, Alexander; Otte, Kerstin; Hesse, Friedemann

    2016-05-10

    Fed-batch cultivation of recombinant Chinese hamster ovary (CHO) cell lines is one of the most widely used production modes for commercial manufacturing of recombinant protein therapeutics. Furthermore, fed-batch cultivations are often conducted as biphasic processes where the culture temperature is decreased to maximize volumetric product yields. However, it remains to be elucidated which intracellular regulatory elements actually control the observed pro-productive phenotypes. Recently, several studies have revealed microRNAs (miRNAs) to be important molecular switches of cell phenotypes. In this study, we analyzed miRNA profiles of two different recombinant CHO cell lines (high and low producer), and compared them to a non-producing CHO DG44 host cell line during fed-batch cultivation at 37°C versus a temperature shift to 30°C. Taking advantage of next-generation sequencing combined with cluster, correlation and differential expression analyses, we could identify 89 different miRNAs, which were differentially expressed in the different cell lines and cultivation phases. Functional validation experiments using 19 validated target miRNAs confirmed that these miRNAs indeed induced changes in process relevant phenotypes. Furthermore, computational miRNA target prediction combined with functional clustering identified putative target genes and cellular pathways, which might be regulated by these miRNAs. This study systematically identified novel target miRNAs during different phases and conditions of a biphasic fed-batch production process and functionally evaluated their potential for host cell engineering.

  5. Orientation anisotropies in human primary visual cortex depend on contrast.

    PubMed

    Maloney, Ryan T; Clifford, Colin W G

    2015-10-01

    Orientation processing in visual cortex appears matched to the environment, such that larger neural populations are tuned to cardinal (horizontal/vertical) than oblique orientations. This may be manifested perceptually as a cardinal bias: poorer sensitivity to oblique compared to cardinal orientations (the "oblique effect"). However, a growing body of psychophysical data reveals the opposite pattern of anisotropy: a bias towards the oblique over the cardinal orientations (the "horizontal effect"), something matched by recent functional magnetic resonance imaging (fMRI) studies that have found an increased response to the oblique over the cardinal orientations in early visual cortex. This may reveal the operation of an efficient coding strategy optimised to the diet of orientations encountered during natural viewing. From consideration of coding efficiency, it might be expected that the anisotropies would change as the quality/strength of the oriented stimulus changes. In two experiments, fMRI response modulations were measured in retinotopically-defined human early visual cortex as a function of the contrast and orientation of sinusoidal gratings. Both experiments revealed a marked change in the V1 response from a cardinal (vertical) bias at low contrast to an oblique bias at high contrast. In Experiment 2, this was also apparent in areas V2 and V3. On average, there was no systematic "radial bias" (a preference for orientations aligned with the visual field meridian) in V1, although it was present in some individual subjects. The change in orientation anisotropies with contrast is consistent with an adaptive stimulus coding strategy in cortex that shifts according to the strength of the sensory inputs.

  6. Perceived Speed of Compound Stimuli Is Moderated by Component Contrast, Not Overall Pattern Contrast

    PubMed Central

    Thompson, Peter

    2016-01-01

    The perception of speed is susceptible to manipulations of image contrast, both for simple sine wave and more complex stimuli, such that low-contrast patterns generally appear slower than their high-contrast equivalents. It is not known whether the crucial factor is the contrast of the underlying Fourier components or the contrast of the overall complex pattern. Here, two experiments investigate this issue using compound gratings, comprising two vertical sine wave stimuli with equal contrast, but a 3:1 spatial frequency ratio. Component gratings were summed in “peaks add” and in “peaks subtract” phase, creating conditions with either (a) identical component contrasts, despite differences in overall pattern contrast or (b) differences in component contrasts despite identical overall pattern contrast. Experiment 1 demonstrated that the perceived speed is determined by the contrast of the components regardless of relative phase and hence of overall pattern contrast. Experiment 2 replicated this result while eliminating potential explanations based on differences in spatial frequency content. Along with previous compound grating and plaid studies, the data support a two-stage velocity estimation process involving the derivation of separate speed signals for each Fourier component, followed by integration of these signals across spatial scales. PMID:27826408

  7. Transcript and hormone analyses reveal the involvement of ABA-signalling, hormone crosstalk and genotype-specific biological processes in cold-shock response in wheat.

    PubMed

    Kalapos, Balázs; Dobrev, Petre; Nagy, Tibor; Vítámvás, Pavel; Györgyey, János; Kocsy, Gábor; Marincs, Ferenc; Galiba, Gábor

    2016-12-01

    The effect of one-day cold-shock on the transcriptome and phytohormones (auxin, cytokinins, abscisic, jasmonic and salicylic acids) was characterised in freezing-sensitive (Chinese Spring), highly freezing-tolerant (Cheyenne) and moderately freezing-tolerant (Chinese Spring substituted with Cheyenne's 5A chromosome) wheat genotypes. Altogether, 636 differentially expressed genes responding to cold-shock were identified. Defence genes encoding LEA proteins, dehydrins, chaperons and other temperature-stress responsive proteins were up-regulated in a genotype-independent manner. Abscisic acid was up-regulated by cold accompanied by adherent expression of its metabolic genes. Data revealed the involvement of particular routes within ABA-dependent signalling in response to cold-shock in the examined genotypes. Cold-shock affected gene expression along carbohydrate metabolic pathways. In photosynthesis, cold-shock changed the expression of a number of genes in the same way as it was previously reported for ABA. Overrepresentation analysis of the differentially expressed genes supported the ABA-signalling and carbohydrate metabolism results, and revealed some pronounced biological process GO categories associated with the cold-shock response of the genotypes. Protein network analysis indicated differences between the genotypes in the information flow along their signal perception and transduction, suggesting different biochemical and cellular strategies in their reaction to cold-shock.

  8. Deep sequencing analyses of pine wood nematode Bursaphelenchus xylophilus microRNAs reveal distinct miRNA expression patterns during the pathological process of pine wilt disease.

    PubMed

    Ding, XiaoLei; Ye, JianRen; Wu, XiaoQin; Huang, Lin; Zhu, LiHua; Lin, SiXi

    2015-01-25

    Bursaphelenchus xylophilus is known as the causative agent of pine wilt disease with complex life cycles. In this research, four small RNA libraries derived from different infection stages of pine wilt disease were constructed and sequenced. Consequently, we obtained hundreds of evolutionarily conserved miRNAs and novel miRNA candidates. The analysis of miRNA expression patterns showed that most miRNAs were expressed at extraordinarily high levels during the middle stage of pine wilt disease. Functional analysis revealed that expression levels of miR-73 and miR-239 were mutually exclusive with their target GH45 cellulase genes. In addition, another set of atypical miRNAs, termed mirtrons, was also identified in this study. Thus, our research has provided detailed characterization of B. xylophilus miRNA expression patterns during the pathological process of pine wilt disease. These findings would contribute to more in-depth understanding of this devastating plant disease.

  9. High Contrast CRT.

    DTIC Science & Technology

    1980-02-01

    form brown sulfides or sulfates. By con- trast, No. 1720 glass does not acquire a brown coloration . How- ever, preliminary tests with 1723 glass show...TR-77-2639-F NL -mmo mhhmhul IIII,. BwII ---- i 11111--- IIIIIN III i 8’ II.I25 .11111 I .6 MCROCOPY RESOLUTION TEST CHART NATIONAL BUREAU Of...High Contrast Displays Two- Color CRT Laminar Flow Electron Gun Thin Film Phosphor Color Penetration Tube 2% AS~iTACT (ConIlm. a" Pove.. 0fdo if

  10. Contrast adaptation in the Limulus lateral eye

    PubMed Central

    Valtcheva, Tchoudomira M.

    2015-01-01

    Luminance and contrast adaptation are neuronal mechanisms employed by the visual system to adjust our sensitivity to light. They are mediated by an assortment of cellular and network processes distributed across the retina and visual cortex. Both have been demonstrated in the eyes of many vertebrates, but only luminance adaptation has been shown in invertebrate eyes to date. Since the computational benefits of contrast adaptation should apply to all visual systems, we investigated whether this mechanism operates in horseshoe crab eyes, one of the best-understood neural networks in the animal kingdom. The spike trains of optic nerve fibers were recorded in response to light stimuli modulated randomly in time and delivered to single ommatidia or the whole eye. We found that the retina adapts to both the mean luminance and contrast of a white-noise stimulus, that luminance- and contrast-adaptive processes are largely independent, and that they originate within an ommatidium. Network interactions are not involved. A published computer model that simulates existing knowledge of the horseshoe crab eye did not show contrast adaptation, suggesting that a heretofore unknown mechanism may underlie the phenomenon. This mechanism does not appear to reside in photoreceptors because white-noise analysis of electroretinogram recordings did not show contrast adaptation. The likely site of origin is therefore the spike discharge mechanism of optic nerve fibers. The finding of contrast adaption in a retinal network as simple as the horseshoe crab eye underscores the broader importance of this image processing strategy to vision. PMID:26445869

  11. Contrast and depth perception: effects of texture contrast and area contrast.

    PubMed

    Ichihara, Shigeru; Kitagawa, Norimichi; Akutsu, Hiromi

    2007-01-01

    Many objects in natural scenes have textures on their surfaces. Contrast of the texture surfaces (the texture contrast) reduces when the viewing distance increases. Similarly, contrast between the surfaces of the objects and the background (the area contrast) reduces when the viewing distance increases. The texture contrast and the area contrast were defined by the contrast between random dots, and by the contrast between the average luminance of the dot pattern and the luminance of the background, respectively. To examine how these two types of contrast influence depth perception, we ran two experiments. In both experiments two areas of random-dot patterns were presented against a uniform background, and participants rated relative depth between the two areas. We found that the rated depth of the patterned areas increased with increases in texture contrast. Furthermore, the effect of the texture contrast on depth judgment increased when the area contrast became low.

  12. Effects of sex and proficiency in second language processing as revealed by a large-scale fNIRS study of school-aged children.

    PubMed

    Sugiura, Lisa; Ojima, Shiro; Matsuba-Kurita, Hiroko; Dan, Ippeita; Tsuzuki, Daisuke; Katura, Takusige; Hagiwara, Hiroko

    2015-10-01

    Previous neuroimaging studies in adults have revealed that first and second languages (L1/L2) share similar neural substrates, and that proficiency is a major determinant of the neural organization of L2 in the lexical-semantic and syntactic domains. However, little is known about neural substrates of children in the phonological domain, or about sex differences. Here, we conducted a large-scale study (n = 484) of school-aged children using functional near-infrared spectroscopy and a word repetition task, which requires a great extent of phonological processing. We investigated cortical activation during word processing, emphasizing sex differences, to clarify similarities and differences between L1 and L2, and proficiency-related differences during early L2 learning. L1 and L2 shared similar neural substrates with decreased activation in L2 compared to L1 in the posterior superior/middle temporal and angular/supramarginal gyri for both sexes. Significant sex differences were found in cortical activation within language areas during high-frequency word but not during low-frequency word processing. During high-frequency word processing, widely distributed areas including the angular/supramarginal gyri were activated in boys, while more restricted areas, excluding the angular/supramarginal gyri were activated in girls. Significant sex differences were also found in L2 proficiency-related activation: activation significantly increased with proficiency in boys, whereas no proficiency-related differences were found in girls. Importantly, cortical sex differences emerged with proficiency. Based on previous research, the present results indicate that sex differences are acquired or enlarged during language development through different cognitive strategies between sexes, possibly reflecting their different memory functions.

  13. Microarray gene expression analysis reveals major differences between Toxocara canis and Toxocara cati neurotoxocarosis and involvement of T. canis in lipid biosynthetic processes.

    PubMed

    Janecek, Elisabeth; Wilk, Esther; Schughart, Klaus; Geffers, Robert; Strube, Christina

    2015-06-01

    Toxocara canis and Toxocara cati are globally occurring intestinal nematodes of dogs and cats with a high zoonotic potential. Migrating larvae in the CNS of paratenic hosts, including humans, may cause neurotoxocarosis resulting in a variety of neurological symptoms. Toxocara canis exhibits a stronger affinity to the CNS than T. cati, causing more severe neurological symptoms in the mouse model. Pathomechanisms of neurotoxocarosis as well as host responses towards the respective parasite are mostly unknown. Therefore, the aim of this study was to characterise the pathogenesis at a transcriptional level using whole genome microarray expression analysis and identify differences and similarities between T. canis- and T. cati-infected brains. Microarray analysis was conducted in cerebra and cerebella of infected C57Bl/6J mice 42daysp.i. revealing more differentially transcribed genes for T. canis- than T. cati-infected brains. In cerebra and cerebella of T. canis-infected mice, a total of 2304 and 1954 differentially transcribed genes, respectively, were identified whereas 113 and 760 differentially transcribed genes were determined in ce