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Sample records for contrasting processes revealed

  1. Adaptive Processes in Thalamus and Cortex Revealed by Silencing of Primary Visual Cortex during Contrast Adaptation.

    PubMed

    King, Jillian L; Lowe, Matthew P; Stover, Kurt R; Wong, Aimee A; Crowder, Nathan A

    2016-05-23

    Visual adaptation illusions indicate that our perception is influenced not only by the current stimulus but also by what we have seen in the recent past. Adaptation to stimulus contrast (the relative luminance created by edges or contours in a scene) induces the perception of the stimulus fading away and increases the contrast detection threshold in psychophysical tests [1, 2]. Neural correlates of contrast adaptation have been described throughout the visual system including the retina [3], dorsal lateral geniculate nucleus (dLGN) [4, 5], primary visual cortex (V1) [6], and parietal cortex [7]. The apparent ubiquity of adaptation at all stages raises the question of how this process cascades across brain regions [8]. Focusing on V1, adaptation could be inherited from pre-cortical stages, arise from synaptic depression at the thalamo-cortical synapse [9], or develop locally, but what is the weighting of these contributions? Because contrast adaptation in mouse V1 is similar to classical animal models [10, 11], we took advantage of the optogenetic tools available in mice to disentangle the processes contributing to adaptation in V1. We disrupted cortical adaptation by optogenetically silencing V1 and found that adaptation measured in V1 now resembled that observed in dLGN. Thus, the majority of adaptation seen in V1 neurons arises through local activity-dependent processes, with smaller contributions from dLGN inheritance and synaptic depression at the thalamo-cortical synapse. Furthermore, modeling indicates that divisive scaling of the weakly adapted dLGN input can predict some of the emerging features of V1 adaptation.

  2. First- and second-order contrast sensitivity functions reveal disrupted visual processing following mild traumatic brain injury.

    PubMed

    Spiegel, Daniel P; Reynaud, Alexandre; Ruiz, Tatiana; Laguë-Beauvais, Maude; Hess, Robert; Farivar, Reza

    2016-05-01

    Vision is disrupted by traumatic brain injury (TBI), with vision-related complaints being amongst the most common in this population. Based on the neural responses of early visual cortical areas, injury to the visual cortex would be predicted to affect both 1(st) order and 2(nd) order contrast sensitivity functions (CSFs)-the height and/or the cut-off of the CSF are expected to be affected by TBI. Previous studies have reported disruptions only in 2(nd) order contrast sensitivity, but using a narrow range of parameters and divergent methodologies-no study has characterized the effect of TBI on the full CSF for both 1(st) and 2(nd) order stimuli. Such information is needed to properly understand the effect of TBI on contrast perception, which underlies all visual processing. Using a unified framework based on the quick contrast sensitivity function, we measured full CSFs for static and dynamic 1(st) and 2(nd) order stimuli. Our results provide a unique dataset showing alterations in sensitivity for both 1(st) and 2(nd) order visual stimuli. In particular, we show that TBI patients have increased sensitivity for 1(st) order motion stimuli and decreased sensitivity to orientation-defined and contrast-defined 2(nd) order stimuli. In addition, our data suggest that TBI patients' sensitivity for both 1(st) order stimuli and 2(nd) order contrast-defined stimuli is shifted towards higher spatial frequencies.

  3. Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species.

    PubMed

    McGovern, Tamara M; Keever, Carson C; Saski, Christopher A; Hart, Michael W; Marko, Peter B

    2010-11-01

    Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent-based inferences about demographic processes to reconstruct the population histories of two co-distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation. PMID:21040048

  4. 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

  5. Stimulus Contrast and Retinogeniculate Signal Processing.

    PubMed

    Rathbun, Daniel L; Alitto, Henry J; Warland, David K; Usrey, W Martin

    2016-01-01

    Neuronal signals conveying luminance contrast play a key role in nearly all aspects of perception, including depth perception, texture discrimination, and motion perception. Although much is known about the retinal mechanisms responsible for encoding contrast information, relatively little is known about the relationship between stimulus contrast and the processing of neuronal signals between visual structures. Here, we describe simultaneous recordings from monosynaptically connected retinal ganglion cells and lateral geniculate nucleus (LGN) neurons in the cat to determine how stimulus contrast affects the communication of visual signals between the two structures. Our results indicate that: (1) LGN neurons typically reach their half-maximal response at lower contrasts than their individual retinal inputs and (2) LGN neurons exhibit greater contrast-dependent phase advance (CDPA) than their retinal inputs. Further analyses suggests that increased sensitivity relies on spatial convergence of multiple retinal inputs, while increased CDPA is achieved, in part, on temporal summation of arriving signals. PMID:26924964

  6. Stimulus Contrast and Retinogeniculate Signal Processing

    PubMed Central

    Rathbun, Daniel L.; Alitto, Henry J.; Warland, David K.; Usrey, W. Martin

    2016-01-01

    Neuronal signals conveying luminance contrast play a key role in nearly all aspects of perception, including depth perception, texture discrimination, and motion perception. Although much is known about the retinal mechanisms responsible for encoding contrast information, relatively little is known about the relationship between stimulus contrast and the processing of neuronal signals between visual structures. Here, we describe simultaneous recordings from monosynaptically connected retinal ganglion cells and lateral geniculate nucleus (LGN) neurons in the cat to determine how stimulus contrast affects the communication of visual signals between the two structures. Our results indicate that: (1) LGN neurons typically reach their half-maximal response at lower contrasts than their individual retinal inputs and (2) LGN neurons exhibit greater contrast-dependent phase advance (CDPA) than their retinal inputs. Further analyses suggests that increased sensitivity relies on spatial convergence of multiple retinal inputs, while increased CDPA is achieved, in part, on temporal summation of arriving signals. PMID:26924964

  7. Stimulus Contrast and Retinogeniculate Signal Processing.

    PubMed

    Rathbun, Daniel L; Alitto, Henry J; Warland, David K; Usrey, W Martin

    2016-01-01

    Neuronal signals conveying luminance contrast play a key role in nearly all aspects of perception, including depth perception, texture discrimination, and motion perception. Although much is known about the retinal mechanisms responsible for encoding contrast information, relatively little is known about the relationship between stimulus contrast and the processing of neuronal signals between visual structures. Here, we describe simultaneous recordings from monosynaptically connected retinal ganglion cells and lateral geniculate nucleus (LGN) neurons in the cat to determine how stimulus contrast affects the communication of visual signals between the two structures. Our results indicate that: (1) LGN neurons typically reach their half-maximal response at lower contrasts than their individual retinal inputs and (2) LGN neurons exhibit greater contrast-dependent phase advance (CDPA) than their retinal inputs. Further analyses suggests that increased sensitivity relies on spatial convergence of multiple retinal inputs, while increased CDPA is achieved, in part, on temporal summation of arriving signals.

  8. 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…

  9. Anisotropic MRI contrast reveals enhanced ionic transport in plastic crystals.

    PubMed

    Romanenko, Konstantin; Jin, Liyu; Madsen, Louis A; Pringle, Jennifer M; O'Dell, Luke A; Forsyth, Maria

    2014-11-01

    Organic ionic plastic crystals (OIPCs) are attractive as solid-state electrolytes for electrochemical devices such as lithium-ion batteries and solar and fuel cells. OIPCs offer high ionic conductivity, nonflammability, and versatility of molecular design. Nevertheless, intrinsic ion transport behavior of OIPCs is not fully understood, and their measured properties depend heavily on thermal history. Solid-state magnetic resonance imaging experiments reveal a striking image contrast anisotropy sensitive to the orientation of grain boundaries in polycrystalline OIPCs. Probing triethyl(methyl)phosphonium bis(fluorosulfonyl)imide (P1222FSI) samples with different thermal history demonstrates vast variations in microcrystallite alignment. Upon slow cooling from the melt, microcrystallites exhibit a preferred orientation throughout the entire sample, leading to an order of magnitude increase in conductivity as probed using impedance spectroscopy. This investigation describes both a new conceptual window and a new characterization method for understanding polycrystalline domain structure and transport in plastic crystals and other solid-state conductors. PMID:25312993

  10. 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…

  11. 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…

  12. Combined Whole-Rock to Nano-Scale Investigations Reveal Contrasting Response of Pt-Os and Re-Os Isotope Systematics During Magmatic and Post-Magmatic Processes

    NASA Astrophysics Data System (ADS)

    Coggon, J. A.; Luguet, A.; Lorand, J. P.; Fonseca, R.; Wainwright, A.; Appel, P.; Hoffmann, J. E.; Nowell, G. M.

    2015-12-01

    Advances in single-grain and micro- and nano-analytical techniques in recent years have been particularly important to the study of highly siderophile elements (HSE) and have contributed significantly to our knowledge and understanding of their host phases and behaviour. Furthermore, whole-rock- to nano-scale studies provide new perspectives for investigation of HSE isotope systematics. Recent multi-scale 187Re-187Os and 190Pt-186Os studies facilitate comparison, to a previously unattainable degree, of the differing responses of these two decay systems to magmatic and post-magmatic processes. It is well established that mafic-ultramafic melts are sensitive to disturbance of their Re-Os isotope systematics by crustal assimilation, due to the incompatibility and resulting enrichment of Re in crustal lithologies. In contrast the very long half-life and extremely low atomic abundance of 190Pt, combined with relatively low Pt concentrations in crustal rocks, generally render the Pt-Os isotope system insensitive to modification during assimilation. However, using new single chromite grain data (Coggon et al., 2015) from the >3.811 Ga Ujaragssuit nunât layered ultramafic body, Greenland, we show that it is possible to distinguish two distinct episodes of 187Os/188Os modification; Country rock contamination of the parent melt was followed by later metamorphic disturbance of the isotope system. The Pt-Os data (Coggon et al., 2013) from the same samples show no evidence of crustal assimilation, but preserve signatures of mantle melting at ~4.1 Ga as well as disturbance during metamorphism. Macro- to micro-petrographic study clearly demonstrates that Pt, Re and Os are hosted by different mineral phases, of different origins, in these samples. This, together with the physical parameters of the decay systems reported above, leads to the dissimilar behaviour and response of the 187Re-187Os and 190Pt-186Os isotope systems during both magmatic and post-magmatic processes and

  13. 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.

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

    PubMed

    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.

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

    PubMed

    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. PMID:25603114

  16. 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

  17. 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.

  18. A contrast agent recognizing activated platelets reveals murine cerebral malaria pathology undetectable by conventional MRI

    PubMed Central

    von zur Muhlen, Constantin; Sibson, Nicola R.; Peter, Karlheinz; Campbell, Sandra J.; Wilainam, Panop; Grau, Georges E.; Bode, Christoph; Choudhury, Robin P.; Anthony, Daniel C.

    2008-01-01

    Human and murine cerebral malaria are associated with elevated levels of cytokines in the brain and adherence of platelets to the microvasculature. Here we demonstrated that the accumulation of platelets in the brain microvasculature can be detected with MRI, using what we believe to be a novel contrast agent, at a time when the pathology is undetectable by conventional MRI. Ligand-induced binding sites (LIBS) on activated platelet glycoprotein IIb/IIIa receptors were detected in the brains of malaria-infected mice 6 days after inoculation with Plasmodium berghei using microparticles of iron oxide (MPIOs) conjugated to a single-chain antibody specific for the LIBS (LIBS-MPIO). No binding of the LIBS-MPIO contrast agent was detected in uninfected animals. A combination of LIBS-MPIO MRI, confocal microscopy, and transmission electron microscopy revealed that the proinflammatory cytokine TNF-α, but not IL-1β or lymphotoxin-α (LT-α), induced adherence of platelets to cerebrovascular endothelium. Peak platelet adhesion was found 12 h after TNF-α injection and was readily detected with LIBS-MPIO contrast-enhanced MRI. Temporal studies revealed that the level of MPIO-induced contrast was proportional to the number of platelets bound. Thus, the LIBS-MPIO contrast agent enabled noninvasive detection of otherwise undetectable cerebral pathology by in vivo MRI before the appearance of clinical disease, highlighting the potential of targeted contrast agents for diagnostic, mechanistic, and therapeutic studies. PMID:18274670

  19. 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

  20. 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

  1. 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…

  2. 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.

  3. Contrast reversal of the eyes impairs infants' face processing: a near-infrared spectroscopic study.

    PubMed

    Ichikawa, Hiroko; Otsuka, Yumiko; Kanazawa, So; Yamaguchi, Masami K; Kakigi, Ryusuke

    2013-11-01

    Human can easily detect other's eyes and gaze from early in life. Such sensitivity is supported by the contrast polarity of human eyes, which have a white sclera contrasting with the darker colored iris (Kobayashi & Kohshima, (1997). Nature, 387, 767-768; Kobayashi & Kohshima, (2001). Journal of Human Evolution, 40, 419-435). Recent studies suggest that the contrast polarity around the eyes plays an important role in infants' face processing. Newborns preferred upright face images to inverted ones in contrast-preserved faces, but not in contrast-reversed faces (Farroni et al., (2005). Proceedings of National Academy of Sciences of the United States of America, 102, p. 17245-17250). Seven- to 8-month-old infants failed to discriminate between faces when the contrast polarity of eyes was reversed (Otsuka et al., (2013). Journal of Experimental Child Psychology, 115, 598-606). Neuroimaging study with adults revealed that full-negative faces induced less activation in the right fusiform gyrus than either full-positive faces or negative faces with contrast-preserved eyes (Gilad et al., (2009). Proceedings of National Academy of Sciences of the United States of America, 106, p. 5353-5358). In the present study, we investigated whether contrast-reversed eyes diminish infants' brain activity related to face processing. We measured hemodynamic responses in the bilateral temporal area of 5- to 6-month-old infants. Their hemodynamic responses to faces with positive eyes and those with negative eyes were compared against the baseline activation during the presentation of object images. We found that the presentation of faces with positive eyes increased the concentration of oxy-Hb in the right temporal area and those of total-Hb in the bilateral temporal areas. No such change occurred for faces with negative eyes. Our results suggest the importance of contrast polarity of the eyes in the face-selective neural responses from early development. PMID:24012650

  4. Statistically significant contrasts between EMG waveforms revealed using wavelet-based functional ANOVA.

    PubMed

    McKay, J Lucas; Welch, Torrence D J; Vidakovic, Brani; Ting, Lena H

    2013-01-01

    We developed wavelet-based functional ANOVA (wfANOVA) as a novel approach for comparing neurophysiological signals that are functions of time. Temporal resolution is often sacrificed by analyzing such data in large time bins, increasing statistical power by reducing the number of comparisons. We performed ANOVA in the wavelet domain because differences between curves tend to be represented by a few temporally localized wavelets, which we transformed back to the time domain for visualization. We compared wfANOVA and ANOVA performed in the time domain (tANOVA) on both experimental electromyographic (EMG) signals from responses to perturbation during standing balance across changes in peak perturbation acceleration (3 levels) and velocity (4 levels) and on simulated data with known contrasts. In experimental EMG data, wfANOVA revealed the continuous shape and magnitude of significant differences over time without a priori selection of time bins. However, tANOVA revealed only the largest differences at discontinuous time points, resulting in features with later onsets and shorter durations than those identified using wfANOVA (P < 0.02). Furthermore, wfANOVA required significantly fewer (~1/4;×; P < 0.015) significant F tests than tANOVA, resulting in post hoc tests with increased power. In simulated EMG data, wfANOVA identified known contrast curves with a high level of precision (r(2) = 0.94 ± 0.08) and performed better than tANOVA across noise levels (P < <0.01). Therefore, wfANOVA may be useful for revealing differences in the shape and magnitude of neurophysiological signals (e.g., EMG, firing rates) across multiple conditions with both high temporal resolution and high statistical power. PMID:23100136

  5. Automatic and controlled processing of acoustic and phonetic contrasts.

    PubMed

    Sussman, Elyse; Kujala, Teija; Halmetoja, Jaana; Lyytinen, Heikki; Alku, Paavo; Näätänen, Risto

    2004-04-01

    Changes in the temporal properties of the speech signal provide important cues for phoneme identification. An impairment or inability to detect such changes may adversely affect one's ability to understand spoken speech. The difference in meaning between the Finnish words tuli (fire) and tuuli (wind), for example, lies in the difference between the duration of the vowel /u/. Detecting changes in the temporal properties of the speech signal, therefore, is critical for distinguishing between phonemes and identifying words. In the current study, we tested whether detection of changes in speech sounds, in native Finnish speakers, would vary as a function of the position within the word that the informational changes occurred (beginning, middle, or end) by evaluating how length contrasts in segments of three-syllable Finnish pseudo-words and their acoustic correlates were discriminated. We recorded a combination of cortical components of event-related brain potentials (MMN, N2b, P3b) along with behavioral measures of the perception of the same sounds. It was found that speech sounds were not processed differently than non-speech sounds in the early stages of auditory processing indexed by MMN. Differences occurred only in later stages associated with controlled processes. The effects of position and attention on speech and non-speech stimuli are discussed. PMID:15051135

  6. Diabatic processes and the evolution of two contrasting extratropical cyclones

    NASA Astrophysics Data System (ADS)

    Martinez-Alvarado, Oscar; Gray, Suzanne; Methven, John

    2016-04-01

    Two contrasting extratropical cyclones were observed over the United Kingdom during the summer 2012 field campaign of the DIAMET (DIAbatic influences on Mesoscale structures in ExtraTropical storms) project. The first cyclone, observed in July, was a shallow system typical of summer over west Europe while the second cyclone, observed in August, was a much deeper system which developed a potential vorticity (PV) tower. The evolution of these two cyclones was analysed and compared in terms of diabatic effects with respect to two aspects. The first aspect is the amount and distribution of heat produced during the development of each cyclone, measured by the cross-isentropic motion around the cyclone centre. The second aspect is the modification to the circulation around the cyclones' centres, measured by area-averaged isentropic vorticity. The contributions from individual diabatic processes, such as convection, cloud microphysics and radiation, to these two aspects is also considered. The cyclones were analysed via hindcast simulations with a research version of the Met Office Unified Model, enhanced with on-line tracers of diabatic changes of potential temperature and PV. A new methodology for the interpretation of these tracers was also implemented and used. The hindcast simulations were compared with the available dropsonde observations from the field campaign as well as operational analyses and radar rainfall rates. It is shown that, while boundary layer and turbulent mixing processes and cloud microphysics processes contributed to the development of both cyclones, the main differences between the cyclones in terms of diabatic effects could be attributed to differences in convective activity. It is also shown that the contribution from all these diabatic processes to changes in the circulation was modulated by the characteristics of advection around each cyclone in a highly nonlinear fashion. This research establishes a new framework for a systematic comparison

  7. 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.

  8. Growth and carbon isotopes of Mediterranean trees reveal contrasting responses to increased carbon dioxide and drought.

    PubMed

    Granda, Elena; Rossatto, Davi Rodrigo; Camarero, J Julio; Voltas, Jordi; Valladares, Fernando

    2014-01-01

    Forest dynamics will depend upon the physiological performance of individual tree species under more stressful conditions caused by climate change. In order to compare the idiosyncratic responses of Mediterranean tree species (Quercus faginea, Pinus nigra, Juniperus thurifera) coexisting in forests of central Spain, we evaluated the temporal changes in secondary growth (basal area increment; BAI) and intrinsic water-use efficiency (iWUE) during the last four decades, determined how coexisting species are responding to increases in atmospheric CO2 concentrations (C(a)) and drought stress, and assessed the relationship among iWUE and growth during climatically contrasting years. All species increased their iWUE (ca. +15 to +21%) between the 1970s and the 2000s. This increase was positively related to C(a) for J. thurifera and to higher C(a) and drought for Q. faginea and P. nigra. During climatically favourable years the study species either increased or maintained their growth at rising iWUE, suggesting a higher CO2 uptake. However, during unfavourable climatic years Q. faginea and especially P. nigra showed sharp declines in growth at enhanced iWUE, likely caused by a reduced stomatal conductance to save water under stressful dry conditions. In contrast, J. thurifera showed enhanced growth also during unfavourable years at increased iWUE, denoting a beneficial effect of C(a) even under climatically harsh conditions. Our results reveal significant inter-specific differences in growth driven by alternative physiological responses to increasing drought stress. Thus, forest composition in the Mediterranean region might be altered due to contrasting capacities of coexisting tree species to withstand increasingly stressful conditions. PMID:23928889

  9. 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

  10. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

    PubMed

    Alvarez-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.

  11. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

    PubMed

    Alvarez-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

  12. Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites.

    PubMed

    Foulon, Julie; Zappelini, Cyril; Durand, Alexis; Valot, Benoit; Girardclos, Olivier; Blaudez, Damien; Chalot, Michel

    2016-11-15

    The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments.

  13. 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.

  14. 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…

  15. Contrasting crustal evolution processes in the Dharwar craton

    NASA Astrophysics Data System (ADS)

    Lancaster, Penelope J.; Dey, Sukanta; Storey, Craig D.; Mitra, Anirban; Bhunia, Rakesh K.

    2015-04-01

    Archaean cratons provide a critical window into early Earth dynamics, preserving a record of crustal evolution processes that include the start of 'modern' plate tectonics and the development of supercontinents. However, these same processes can also destroy or rework substantial volumes of crust, and the oldest extant Archaean terrane is only ~3.9 Ga. Where Archaean rocks are exposed, bulk techniques such as Pb and Nd isotopes can provide considerable information about continental formation, but these may have been altered by later metamorphic events. Another method is to examine sedimentary units, which can preserve fragments of the crust that are no longer exposed at the Earth's surface. Resistant detrital minerals such as zircon have particular use in these studies, as they incorporate a range of isotopic and geochemical tracers and can survive multiple crystallisation and/or sedimentary events. In this manner, a more complete record of a craton's evolution may be obtained, with the benefit of contributions from contrasting isotopic systems. The Dharwar craton of southern India is one such Archaean block, comprising >2.7 Ga trondjhemite-tonalite-granodiorite (TTG) gneisses, volcano-sedimentary belts (>3.0 and 2.9-2.6 Ga) and 2.7-2.5 Ga calc-alkaline to potassic granitoids. These rocks preserve evidence for several cycles of supracrustal formation, deformation, metamorphism and granitic activity during the Precambrian. New in situ U-Pb-Hf analyses of detrital zircons from across the craton indicate significant juvenile crustal extraction events at ~3.3 and 2.7 Ga, and continuous extraction from 3.7-3.3 Ga. Reworking in the older western block at ~3.0 Ga marks the onset of cratonisation, most likely due to 'modern' plate tectonic processes, while reworking in both the western and younger eastern block at 2.55-2.50 Ga indicates accretion of the two terranes and final cratonisation much later than in most other Archaean terranes (~2.7 Ga). Different patterns of

  16. 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

  17. 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

  18. 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.

  19. Characterization of the Avian Trojan Gene Family Reveals Contrasting Evolutionary Constraints

    PubMed Central

    Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

    2015-01-01

    “Trojan” is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules. PMID:25803627

  20. Does contrast-enhanced ultrasound reveal tumor angiogenesis in pancreatic ductal carcinoma? A prospective study.

    PubMed

    Nishida, Mutsumi; Koito, Kazumitsu; Hirokawa, Naoki; Hori, Masakazu; Satoh, Taishi; Hareyama, Masato

    2009-02-01

    correlation was found between the EU score and histological grading (p < 0.004). The EU score was higher in subjects who had hepatic metastasis compared with subjects who had no hepatic metastasis (p < 0.05). After chemoradiotherapy, 14 subjects exhibited PR, while 13 showed SD. None of the subjects showed PD. The EU score was smaller in PR than SD (p < 0.05). The EU score significantly decreased after the therapy in PR (p < 0.01) but not in SD. IMD and AVD did not significantly decrease in either PR or SD; however, VEGF decreased significantly in PR (p < 0.01) but not in SD. Contrast-enhanced US could reveal tumor vascularity of pancreatic ductal carcinoma and could be potentially useful to evaluate treatment effect of subjects who receive chemoradiotherapy. Further investigation will be needed to prove the usefulness of contrast-enhanced US.

  1. Distinct kimberlite pipe classes with contrasting eruption processes

    NASA Astrophysics Data System (ADS)

    Skinner, E. M. W.; Marsh, J. S.

    2004-09-01

    Field and Scott Smith [Field, M., Scott Smith, B.H., 1999. Contrasting geology and near-surface emplacement of kimberlite pipes in southern Africa and Canada. Proc. 7th Int. Kimb. Conf. (Eds. Gurney et al.) 1, 214-237.] propose that kimberlite pipes can be grouped into three types or classes. Classical or Class 1 pipes are the only class with characteristic low temperature, diatreme-facies kimberlite in addition to hypabyssal- and crater-facies kimberlite. Class 2 and 3 pipes are characterized only by hypabyssal-and crater-facies kimberlite. In an increasing number of Class 1 pipes a new kimberlite facies, transitional-facies kimberlite, is being found. In most cases this facies forms a zone several metres wide at the interface between the hypabyssal- and diatreme-facies. The transitional-facies exhibits textural and mineralogical features, which are continuously gradational between the hypabyssal and the diatreme types. The textural gradations are from a coherent magmatic texture to one where the rock becomes increasingly magmaclastic and this is accompanied by concomitant mineralogical gradations involving the decline and eventual elimination of primary calcite at the expense of microlitic diopside. Both transitional- and diatreme-facies kimberlites are considered to have formed in situ from intruding hypabyssal kimberlite magma as a consequence of exsolution of initially CO 2-rich volatiles from the volatile-rich kimberlite magma. The transitional-facies is initiated by volatile exsolution at depths of about 3 km below the original surface. With subsequent cracking through to the surface and resultant rapid decompression, the further catastrophic exsolution of volatiles and their expansion leads to the formation of the diatreme facies. Thus diatreme-facies kimberlite and Class 1 pipes are emplaced by essentially magmatic processes rather than by phreatomagmatism. Distinctly different petrographic features characterize crater-facies kimberlite in each of the

  2. 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

  3. Improvement of Speckle Contrast Image Processing by an Efficient Algorithm.

    PubMed

    Steimers, A; Farnung, W; Kohl-Bareis, M

    2016-01-01

    We demonstrate an efficient algorithm for the temporal and spatial based calculation of speckle contrast for the imaging of blood flow by laser speckle contrast analysis (LASCA). It reduces the numerical complexity of necessary calculations, facilitates a multi-core and many-core implementation of the speckle analysis and enables an independence of temporal or spatial resolution and SNR. The new algorithm was evaluated for both spatial and temporal based analysis of speckle patterns with different image sizes and amounts of recruited pixels as sequential, multi-core and many-core code. PMID:26782241

  4. 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

  5. ERPs reveal individual differences in morphosyntactic processing.

    PubMed

    Tanner, Darren; Van Hell, Janet G

    2014-04-01

    We investigated individual differences in the neural substrates of morphosyntactic processing among monolingual English speakers using event-related potentials (ERPs). Although grand-mean analysis showed a biphasic LAN-P600 pattern to grammatical violations, analysis of individuals׳ ERP responses showed that brain responses varied systematically along a continuum between negativity- and positivity-dominant ERP responses across individuals. Moreover, the left hemisphere topography of the negativity resulted from component overlap between a centro-parietal N400 in some individuals and a right hemisphere-dominant P600 in others. Our results show that biphasic ERP waveforms do not always reflect separable processing stages within individuals, and moreover, that the LAN can be a variant of the N400. These results show that there are multiple neurocognitive routes to successful grammatical comprehension in language users across the proficiency spectrum. Our results underscore that understanding and quantifying individual differences can provide an important source of evidence about language processing in the general population.

  6. 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

    2012-01-01

    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

  7. 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.

  8. Integrated processing of contrast pulse sequencing ultrasound imaging for enhanced active contrast of hollow gas filled silica nanoshells and microshells.

    PubMed

    Ta, Casey N; Liberman, Alexander; Paul Martinez, H; Barback, Christopher V; Mattrey, Robert F; Blair, Sarah L; Trogler, William C; Kummel, Andrew C; Wu, Zhe

    2012-03-01

    In recent years, there have been increasing developments in the field of contrast-enhanced ultrasound both in the creation of new contrast agents and in imaging modalities. These contrast agents have been employed to study tumor vasculature in order to improve cancer detection and diagnosis. An in vivo study is presented of ultrasound imaging of gas filled hollow silica microshells and nanoshells which have been delivered intraperitoneally to an IGROV-1 tumor bearing mouse. In contrast to microbubbles, this formulation of microshells provided strong ultrasound imaging signals by shell disruption and release of gas. Imaging of the microshells in an animal model was facilitated by novel image processing. Although the particle signal could be identified by eye under live imaging, high background obfuscated the particle signal in still images and near the borders of the tumor with live images. Image processing techniques were developed that employed the transient nature of the particle signal to selectively filter out the background signal. By applying image registration, high-pass, median, threshold, and motion filtering, a short video clip of the particle signal was compressed into a single image, thereby resolving the silica shells within the tumor. © 2012 American Vacuum Society.

  9. 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.…

  10. Larger receptive fields revealed using Battenberg stimuli to assess contrast summation with moving patterns.

    PubMed

    McDougall, Thomas J; Dickinson, J Edwin; Badcock, David R

    2016-09-01

    This study reevaluated the summation extent for moving stimuli using the Battenberg summation paradigm (Meese, 2010), which aims to circumvent internal noise changes with increasing stimulus size by holding display size constant. In the checkerboard stimulus, the size of the checks (luminance-modulated drifting gratings) was varied to measure dependence on signal area. Experiment 1 was a contrast detection task that used either signal checks alternating with uniform, mean luminance, checks (single-motion) or alternate checks containing gratings moving in opposite directions (opposing-motion). The latter was designed to test whether summation extent changes when segregating regions based on motion direction. Results showed summation over a square summation area with a side length of 3.33°, much larger than previous estimates of less than 1° for similar stimuli (Anderson & Burr, 1991). This was found for both motion combinations, providing no evidence that summation extent differs when segregating patterns based on direction, at contrast detection threshold. These results are in close agreement with those obtained for static patterns (Meese, 2010) and support the same underlying summation model. Experiment 2 was a contrast increment detection task conducted to determine whether differences in summation extent arise under suprathreshold contrast conditions. There was no dependence on check size for either condition across the range of sizes tested. This supports the suggestion that segmentation mechanisms dominate perception under high-contrast conditions, a potential adaptive strategy employed by the visual system. PMID:27604069

  11. New Low-Temperature Thermochronology Reveals Contrasting Modes of Continental Extension Across the Sonoran Rifted Margin

    NASA Astrophysics Data System (ADS)

    Kohn, B. P.; Fletcher, J. M.; Gleadow, A. J.; Calmus, T.; Nourse, J. A.

    2003-12-01

    The Sonoran rifted margin extends 250 km from the western flanks of the Sierra Madre Occidental to the Gulf of California and contains a classic Basin and Range morphology that indicates "broad-rift" mode of continental extension. However, new low-temperature thermochronology reveals that the Sonoran rifted margin is also internally composed of at least two temporally and spatially distinct belts that display other distinct styles of extension. Mountain ranges that lie within a narrow belt (20 km wide) along the coast of the Gulf of California between Puerto Libertad and Bahia Kino yield highly discordant apatite fission track (AFT) ages that range from 5 to 54 Ma and likely reflect the strong tilting of these tectonic blocks. The widespread occurrence of AFT ages between 5 and 7 Ma, which are typically found in the deepest crustal levels of the tilt blocks, and the presence of Quaternary scarps indicate that extension in the coastal region largely occurred from late Miocene to recent times. We infer that this belt is dominated by a "narrow-rift" mode of extension where deformation has been focused to produce the Gulf depression. Well inland from the coast (175 km east) is a belt of metamorphic core complexes that extends more than 200 km from Magdalena to Mazatan and typically yields older and more concordant AFT ages from 14 to 23 Ma. However, the presence of ages as young as 8 to 11 Ma indicate that the "metamorphic-core-complex" mode of extension in this belt likely overlapped in time with the "narrow-rift" mode of extension in the Gulf of California. We conclude that the juxtaposition of major deformation belts each with different modes of continental extension reflects the diverse processes that have affected the Sonoran margin through time.

  12. Generation of superparamagnetic liposomes revealed as highly efficient MRI contrast agents for in vivo imaging.

    PubMed

    Martina, Marie-Sophie; Fortin, Jean-Paul; Ménager, Christine; Clément, Olivier; Barratt, Gillian; Grabielle-Madelmont, Cécile; Gazeau, Florence; Cabuil, Valérie; Lesieur, Sylviane

    2005-08-01

    Maghemite (gamma-Fe2O3) nanocrystals stable at neutral pH and in isotonic aqueous media were synthesized and encapsulated within large unilamellar vesicles of egg phosphatidylcholine (EPC) and distearoyl-SN-glycero-3-phosphoethanolamine-N-[methoxy(poly(ethylene glycol))-2000] (DSPE-PEG(2000), 5 mol %), formed by film hydration coupled with sequential extrusion. The nonentrapped particles were removed by flash gel exclusion chromatography. The magnetic-fluid-loaded liposomes (MFLs) were homogeneous in size (195 +/- 33 hydrodynamic diameters from quasi-elastic light scattering). Iron loading was varied from 35 up to 167 Fe(III)/lipid mol %. Physical and superparamagnetic characteristics of the iron oxide particles were preserved after liposome encapsulation as shown by cryogenic transmission electron microscopy and magnetization curve recording. In biological media, MFLs were highly stable and avoided ferrofluid flocculation while being nontoxic toward the J774 macrophage cell line. Moreover, steric stabilization ensured by PEG-surface-grafting significantly reduced liposome association with the macrophages. The ratios of the transversal (r2) and longitudinal (r1) magnetic resonance (MR) relaxivities of water protons in MFL dispersions (6 < r2/r1 < 18) ranked them among the best T2 contrast agents, the higher iron loading the better the T2 contrast enhancement. Magnetophoresis demonstrated the possible guidance of MFLs by applying a magnetic field gradient. Mouse MR imaging assessed MFLs efficiency as contrast agents in vivo: MR angiography performed 24 h after intravenous injection of the contrast agent provided the first direct evidence of the stealthiness of PEG-ylated magnetic-fluid-loaded liposomes. PMID:16045355

  13. 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.

  14. 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

  15. Biochemical and biophysical characterization of four EphB kinase domains reveals contrasting thermodynamic, kinetic and inhibition profiles

    PubMed Central

    Overman, Ross C.; Debreczeni, Judit E.; Truman, Caroline M.; McAlister, Mark S.; Attwood, Teresa K.

    2013-01-01

    The Eph (erythropoietin-producing hepatocellular carcinoma) B receptors are important in a variety of cellular processes through their roles in cell-to-cell contact and signalling; their up-regulation and down-regulation has been shown to have implications in a variety of cancers. A greater understanding of the similarities and differences within this small, highly conserved family of tyrosine kinases will be essential to the identification of effective therapeutic opportunities for disease intervention. In this study, we have developed a route to production of multi-milligram quantities of highly purified, homogeneous, recombinant protein for the kinase domain of these human receptors in Escherichia coli. Analyses of these isolated catalytic fragments have revealed stark contrasts in their amenability to recombinant expression and their physical properties: e.g., a >16°C variance in thermal stability, a 3-fold difference in catalytic activity and disparities in their inhibitor binding profiles. We find EphB3 to be an outlier in terms of both its intrinsic stability, and more importantly its ligand-binding properties. Our findings have led us to speculate about both their biological significance and potential routes for generating EphB isozyme-selective small-molecule inhibitors. Our comprehensive methodologies provide a template for similar in-depth studies of other kinase superfamily members. PMID:23627399

  16. Biochemical and biophysical characterization of four EphB kinase domains reveals contrasting thermodynamic, kinetic and inhibition profiles.

    PubMed

    Overman, Ross C; Debreczeni, Judit E; Truman, Caroline M; McAlister, Mark S; Attwood, Teresa K

    2013-01-01

    The Eph (erythropoietin-producing hepatocellular carcinoma) B receptors are important in a variety of cellular processes through their roles in cell-to-cell contact and signalling; their up-regulation and down-regulation has been shown to have implications in a variety of cancers. A greater understanding of the similarities and differences within this small, highly conserved family of tyrosine kinases will be essential to the identification of effective therapeutic opportunities for disease intervention. In this study, we have developed a route to production of multi-milligram quantities of highly purified, homogeneous, recombinant protein for the kinase domain of these human receptors in Escherichia coli. Analyses of these isolated catalytic fragments have revealed stark contrasts in their amenability to recombinant expression and their physical properties: e.g., a >16°C variance in thermal stability, a 3-fold difference in catalytic activity and disparities in their inhibitor binding profiles. We find EphB3 to be an outlier in terms of both its intrinsic stability, and more importantly its ligand-binding properties. Our findings have led us to speculate about both their biological significance and potential routes for generating EphB isozyme-selective small-molecule inhibitors. Our comprehensive methodologies provide a template for similar in-depth studies of other kinase superfamily members. PMID:23627399

  17. 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

  18. Satellite Solar-induced Chlorophyll Fluorescence Reveals Drought Onset Mechanisms: Insights from Two Contrasting Extreme Events

    NASA Astrophysics Data System (ADS)

    Sun, Y.; Fu, R.; Dickinson, R. E.; Joiner, J.; Frankenberg, C.; Gu, L.; Xia, Y.; Fernando, N.

    2015-12-01

    This study uses the droughts of 2011 in Texas and 2012 over the central Great Plains as case studies to explore the potential of satellite-observed solar-induced chlorophyll fluorescence (SIF) for monitoring drought dynamics. We find that the spatial patterns of negative SIF anomalies from the Global Ozone Monitoring Instrument 2 (GOME-2) closely resembled drought intensity maps from the US Drought Monitor for both events. The drought-induced suppression of SIF occurred throughout 2011 but was exacerbated in summer in the Texas drought. This event was characterized by a persistent depletion of root-zone soil moisture caused by year-long below-normal precipitation. In contrast, for the central Great Plains drought, warmer temperatures and ample precipitation boosted SIF in the spring of 2012; however, a sudden drop in precipitation coupled with unusually high temperatures rapidly depleted soil moisture through evapotranspiration, leading to a rapid onset of drought in early summer. Accordingly, SIF reversed from above to below normal. For both regions, the GOME-2 SIF anomalies were significantly correlated with those of root-zone soil moisture, indicating that the former can potentially be used as proxy of the latter for monitoring agricultural droughts with different onset mechanisms. Further analyses indicate that the contrasting dynamics of SIF during these two extreme events were caused by changes in both fraction of absorbed photosynthetically active radiation (fPAR) and fluorescence yield, suggesting that satellite SIF is sensitive to both structural and physiological/biochemical variations of vegetation. We conclude that the emerging satellite SIF has excellent potential for dynamic drought monitoring.

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

    PubMed

    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

    2015-05-01

    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.

  20. 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.

  1. Active methanotrophs in two contrasting North American peatland ecosystems revealed using DNA-SIP.

    PubMed

    Gupta, Varun; Smemo, Kurt A; Yavitt, Joseph B; Basiliko, Nathan

    2012-02-01

    The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and (13)C-DNA stable-isotope probing (SIP) to measure methane (CH(4)) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH(4) oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phylogenetic diversity of organisms that had assimilated (13)C, including methanotrophs from both the Alpha- and Gammaproteobacteria classes and other potentially non-methanotrophic organisms that were similar to bacteria detected in a UK and Finnish fen. Based on similarities between bacteria in our sites and those in Europe, including Russia, we conclude that site physicochemical characteristics rather than biogeography controlled the phylogenetic diversity of active methanotrophs and that differences in phylogenetic diversity between the bog and fen did not relate to measured CH(4) oxidation rates. A single crenarchaeon in the bog site appeared to be assimilating (13)C in 16S rDNA; however, its phylogenetic similarity to other CO(2)-utilizing archaea probably indicates that this organism is not directly involved in CH(4) oxidation in peat.

  2. 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

  3. Phase-contrast magnetic resonance imaging reveals net retrograde aqueductal flow in idiopathic normal pressure hydrocephalus.

    PubMed

    Ringstad, Geir; Emblem, Kyrre Eeg; Eide, Per Kristian

    2016-06-01

    OBJECT The objective of this study was to assess the net aqueductal stroke volume (ASV) and CSF aqueductal flow rate derived from phase-contrast MRI (PC-MRI) in patients with probable idiopathic normal pressure hydrocephalus (iNPH) before and after ventriculoperitoneal shunt surgery, and to compare observations with intracranial pressure (ICP) scores. METHODS PC-MRI at the level of the sylvian aqueduct was undertaken in patients undergoing assessment for probable iNPH. Aqueductal flow in the craniocaudal direction was defined as positive, or antegrade flow, and net ASV was calculated by subtracting retrograde from antegrade aqueductal flow. Aqueductal flow rate per minute was calculated by multiplying net ASV by heart rate. During the same hospital admission, clinical examination was performed using NPH score and overnight continuous ICP monitoring. Twelve patients were followed prospectively 12 months after shunt placement with clinical assessment and a second PC-MRI. The study also included 2 healthy controls. RESULTS Among 21 patients examined for iNPH, 17 (81%) received a shunt (shunt group), and 4 were treated conservatively (conservative group). Among the patients with shunts, a clinical improvement was observed in 16 (94%) of the 17. Net ASV was negative in 16 (76%) of 21 patients before shunt placement and in 5 (42%) of 12 patients after shunt placement, and increased from a median of -5 μl (range -175 to 27 μl) to a median of 1 μl (range -61 to 30 μl; p = 0.04). Among the 12 patients with PC-MRI after shunt placement, 11 were shunt responders, and in 9 of these 11 either a reduced magnitude of retrograde aqueductal flow, or a complete reversal from retrograde to antegrade flow, occurred. Net ASV was significantly lower in the shunt group than in the conservative group (p = 0.01). The aqueductal flow rate increased from -0.56 ml/min (range -12.78 to 0.58 ml/min) to 0.06 ml/min (range -4.51 to 1.93 ml/min; p = 0.04) after shunt placement. CONCLUSIONS In

  4. 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.

  5. Contrasting behavior of oxygen and iron isotopes in banded iron formation revealed by in situ analysis

    NASA Astrophysics Data System (ADS)

    Beard, B.; Li, W.; Kita, N.; Valley, J. W.; Johnson, C.

    2012-12-01

    Banded iron formations (BIFs) record a period of dramatic secular change in Earth's geologic history, when abundant aqueous Fe(II) was removed from Archean and Proterozoic oceans by oxidation. BIFs are characterized by co-existing of quartz and iron minerals, including oxides and carbonates, and alternating iron-rich and iron-poor layers range from m to contrast, lowest δ18O values were measured from magnetite that contains less than 1 wt% SiO2. Individual magnetite grains can have up to 6 ‰ variation in δ18O values between low-Si core and Si-rich overgrowth. Iron

  6. Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes.

    PubMed

    Dametto, Andressa; Sperotto, Raul A; Adamski, Janete M; Blasi, Édina A R; Cargnelutti, Denise; de Oliveira, Luiz F V; Ricachenevsky, Felipe K; Fregonezi, Jeferson N; Mariath, Jorge E A; da Cruz, Renata P; Margis, Rogério; Fett, Janette P

    2015-09-01

    Rice productivity is largely affected by low temperature, which can be harmful throughout plant development, from germination to grain filling. Germination of indica rice cultivars under cold is slow and not uniform, resulting in irregular emergence and small plant population. To identify and characterize novel genes involved in cold tolerance during the germination stage, two indica rice genotypes (sister lines previously identified as cold-tolerant and cold-sensitive) were used in parallel transcriptomic analysis (RNAseq) under cold treatment (seeds germinating at 13 °C for 7 days). We detected 1,361 differentially expressed transcripts. Differences in gene expression found by RNAseq were confirmed for 11 selected genes using RT-qPCR. Biological processes enhanced in the cold-tolerant seedlings include: cell division and expansion (confirmed by anatomical sections of germinating seeds), cell wall integrity and extensibility, water uptake and membrane transport capacity, sucrose synthesis, generation of simple sugars, unsaturation of membrane fatty acids, wax biosynthesis, antioxidant capacity (confirmed by histochemical staining of H2O2), and hormone and Ca(2+)-signaling. The cold-sensitive seedlings respond to low temperature stress increasing synthesis of HSPs and dehydrins, along with enhanced ubiquitin/proteasome protein degradation pathway and polyamine biosynthesis. Our findings can be useful in future biotechnological approaches aiming to cold tolerance in indica rice.

  7. Mutation and Recombination Frequencies Reveal a Biological Contrast within Strains of Cucumber Mosaic Virus

    PubMed Central

    Pita, Justin S.; Morris, Viktoriya

    2015-01-01

    ABSTRACT Recent in planta studies have shown that strains Fny and LS of Cucumber mosaic virus (CMV) display differential genetic diversities, Fny and LS having higher and lower mutation frequencies, respectively (J. S. Pita and M. J. Roossinck, J Virol 87:790–797, 2012 http://dx.doi.org/10.1128/JVI.01891-12). In this article, we show that these virus strains have differential recombination frequencies as well. However, the high-diversity Fny strain is a low-recombination virus, whereas the very-low-diversity LS strain is instead a high-recombination virus. Unlike the mutation frequency that was determined by both RNAs 1 and 2, the control elements of recombination frequency reside predominantly within RNA 2, specifically within the 2a gene. IMPORTANCE Recombination is an important mechanism in virus evolution that can lead to increased or decreased variation and is a major player in virus speciation events that can lead to emerging viruses. Although viral genomes show very frequent evidence of recombination, details of the mechanism involved in these events are still poorly understood. We show here that the reciprocal effects of high mutation frequency and low recombination frequency (and vice versa) involve the RNA-dependent RNA polymerase of the virus, and we speculate that these evolutionary events are related to differences in processivity for two strains of the same virus. PMID:25903331

  8. Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes.

    PubMed

    Dametto, Andressa; Sperotto, Raul A; Adamski, Janete M; Blasi, Édina A R; Cargnelutti, Denise; de Oliveira, Luiz F V; Ricachenevsky, Felipe K; Fregonezi, Jeferson N; Mariath, Jorge E A; da Cruz, Renata P; Margis, Rogério; Fett, Janette P

    2015-09-01

    Rice productivity is largely affected by low temperature, which can be harmful throughout plant development, from germination to grain filling. Germination of indica rice cultivars under cold is slow and not uniform, resulting in irregular emergence and small plant population. To identify and characterize novel genes involved in cold tolerance during the germination stage, two indica rice genotypes (sister lines previously identified as cold-tolerant and cold-sensitive) were used in parallel transcriptomic analysis (RNAseq) under cold treatment (seeds germinating at 13 °C for 7 days). We detected 1,361 differentially expressed transcripts. Differences in gene expression found by RNAseq were confirmed for 11 selected genes using RT-qPCR. Biological processes enhanced in the cold-tolerant seedlings include: cell division and expansion (confirmed by anatomical sections of germinating seeds), cell wall integrity and extensibility, water uptake and membrane transport capacity, sucrose synthesis, generation of simple sugars, unsaturation of membrane fatty acids, wax biosynthesis, antioxidant capacity (confirmed by histochemical staining of H2O2), and hormone and Ca(2+)-signaling. The cold-sensitive seedlings respond to low temperature stress increasing synthesis of HSPs and dehydrins, along with enhanced ubiquitin/proteasome protein degradation pathway and polyamine biosynthesis. Our findings can be useful in future biotechnological approaches aiming to cold tolerance in indica rice. PMID:26259169

  9. Comparison of phase-difference and complex-difference processing in phase-contrast MR angiography.

    PubMed

    Bernstein, M A; Ikezaki, Y

    1991-01-01

    The two main phase-contrast reconstruction methods are phase difference and complex difference. The signal-to-noise ratio properties and relative advantages of the two techniques are discussed. It is argued that each processing method has applications in which it is superior, and guidelines are provided to determine those applications. It is demonstrated theoretically and experimentally that only the complex-difference method is well suited for processing phase-contrast slabs with use of a projection dephaser gradient.

  10. Contrasting styles of deep-marine pyroclastic eruptions revealed from Axial Seamount push core records

    NASA Astrophysics Data System (ADS)

    Portner, Ryan A.; Clague, David A.; Helo, Christoph; Dreyer, Brian M.; Paduan, Jennifer B.

    2015-08-01

    A comprehensive understanding of explosive basaltic eruption processes in the deep-sea relies upon detailed analysis and comparison of the variety of volcaniclastic lithologies on the seafloor, which has been challenged by insufficient sample recovery. A dedicated ROV-based sampling approach using long push cores offers an unparalleled opportunity to fully characterize the diversity of unconsolidated volcaniclastic lithofacies on a recently active seamount. Lithofacies from Axial Seamount record two styles of pyroclastic eruptions, strombolian and phreatomagmatic, at 1.5 km water depth. Strombolian eruptions are represented by abundant fluidal and highly vesicular (up to 50%) vitriclasts within limu o Pele lapilli tuff and tuffaceous mud lithofacies. Lapilli-ash grain size, normal grading, good sorting, rip-up clasts and homogeneous glass geochemistry characterize individual limu o Pele lapilli tuff beds, and imply proximal deposition from a turbidity flow associated with a single eruption (i.e. event bed). Limu o Pele lapilli tuff beds are interbedded with poorly sorted, chemically heterogeneous and bioturbated tuffaceous mud units that preserve reworking and biologic habitation of more distal pyroclastic fallout and dilute turbidity flows. The phreatomagmatic eruption style is preserved by hydrothermal mineral-bearing muddy tuff that exhibits characteristics distinct from lapilli ash and tuffaceous mud lithofacies. Hydrothermal muddy tuff lithofacies are well-sorted and fine-grained with notable components of non-fluidal basaltic ash (∼45%), fluidal ash (∼30%) and accessory lithics (∼25%). Heterogeneous geochemistry of ash shards implies that juvenile components are minimal. The abundance, mineralogy and texture of lithic components (Fe-Mg clays, pyrite, epidote, actinolite, altered glass, basalt/diabase, hydrothermal breccia and agglutinate), and very fine-grain size of basaltic ash, are consistent with phreatomagmatic eruption deposits. A lack of

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

    PubMed

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

    2008-04-01

    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.

  12. VIP: Vortex Image Processing pipeline for high-contrast direct imaging of exoplanets

    NASA Astrophysics Data System (ADS)

    Gomez Gonzalez, Carlos Alberto; Wertz, Olivier; Christiaens, Valentin; Absil, Olivier; Mawet, Dimitri

    2016-03-01

    VIP (Vortex Image Processing pipeline) provides pre- and post-processing algorithms for high-contrast direct imaging of exoplanets. Written in Python, VIP provides a very flexible framework for data exploration and image processing and supports high-contrast imaging observational techniques, including angular, reference-star and multi-spectral differential imaging. Several post-processing algorithms for PSF subtraction based on principal component analysis are available as well as the LLSG (Local Low-rank plus Sparse plus Gaussian-noise decomposition) algorithm for angular differential imaging. VIP also implements the negative fake companion technique coupled with MCMC sampling for rigorous estimation of the flux and position of potential companions.

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

    PubMed Central

    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. PMID:24550876

  14. 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.

  15. 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.

  16. Functional Flow Patterns and Static Blood Pooling in Tumors Revealed by Combined Contrast-Enhanced Ultrasound and Photoacoustic Imaging.

    PubMed

    Bar-Zion, Avinoam; Yin, Melissa; Adam, Dan; Foster, F Stuart

    2016-08-01

    Alterations in tumor perfusion and microenvironment have been shown to be associated with aggressive cancer phenotypes, raising the need for noninvasive methods of tracking these changes. Dynamic contrast-enhanced ultrasound (DCEUS) and photoacoustic (PA) imaging serve as promising candidates-one has the ability to measure tissue perfusion, whereas the other can be used to monitor tissue oxygenation and hemoglobin concentration. In this study, we investigated the relationship between the different functional parameters measured with DCEUS and PA imaging, using two morphologically different hind-limb tumor models and drug-induced alterations in an orthotopic breast tumor model. Imaging results showed some correlation between perfusion and oxygen saturation maps and the ability to sensitively monitor antivascular treatment. In addition, DCEUS measurements revealed different vascular densities in the core of specific tumors compared with their rims. Noncorrelated perfusion and hemoglobin concentration measurements facilitated discrimination between blood lakes and necrotic areas. Taken together, our results illustrate the utility of a combined contrast-enhanced ultrasound method with photoacoustic imaging to visualize blood flow patterns in tumors. Cancer Res; 76(15); 4320-31. ©2016 AACR.

  17. Do conscious perception and unconscious processing rely on independent mechanisms? A meta-contrast study.

    PubMed

    Peremen, Ziv; Lamy, Dominique

    2014-02-01

    There is currently no consensus regarding what measures are most valid to demonstrate perceptual processing without awareness. Likewise, whether conscious perception and unconscious processing rely on independent mechanisms or lie on a continuum remains a matter of debate. Here, we addressed these issues by comparing the time courses of subjective reports, objective discrimination performance and response priming during meta-contrast masking, under similar attentional demands. We found these to be strikingly similar, suggesting that conscious perception and unconscious processing cannot be dissociated by their time course. Our results also demonstrate that unconscious processing, indexed by response priming, occurs, and that objective discrimination performance indexes the same conscious processes as subjective visibility reports. Finally, our results underscore the role of attention by showing that how much attention the stimulus receives relative to the mask, rather than whether processing is measured by conscious discrimination or by priming, determines the time course of meta-contrast masking. PMID:24398259

  18. Processing deficits of motion of contrast-modulated gratings in anisometropic amblyopia.

    PubMed

    Tang, Yong; Liu, Caiyuan; Liu, Zhongjian; Hu, Xiaopeng; Yu, Yong-Qiang; Zhou, Yifeng

    2014-01-01

    Several studies have indicated substantial processing deficits for static second-order stimuli in amblyopia. However, less is known about the perception of second-order moving gratings. To investigate this issue, we measured the contrast sensitivity for second-order (contrast-modulated) moving gratings in seven anisometropic amblyopes and ten normal controls. The measurements were performed with non-equated carriers and a series of equated carriers. For comparison, the sensitivity for first-order motion and static second-order stimuli was also measured. Most of the amblyopic eyes (AEs) showed reduced sensitivity for second-order moving gratings relative to their non-amblyopic eyes (NAEs) and the dominant eyes (CEs) of normal control subjects, even when the detectability of the noise carriers was carefully controlled, suggesting substantial processing deficits of motion of contrast-modulated gratings in anisometropic amblyopia. In contrast, the non-amblyopic eyes of the anisometropic amblyopes were relatively spared. As a group, NAEs showed statistically comparable performance to CEs. We also found that contrast sensitivity for static second-order stimuli was strongly impaired in AEs and part of the NAEs of anisometropic amblyopes, consistent with previous studies. In addition, some amblyopes showed impaired performance in perception of static second-order stimuli but not in that of second-order moving gratings. These results may suggest a dissociation between the processing of static and moving second-order gratings in anisometropic amblyopia. PMID:25409477

  19. 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

  20. 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.

  1. Neural processes involved with perception of non-native durational contrasts.

    PubMed

    Callan, Akiko M; Callan, Daniel E; Tajima, Keiichi; Akahane-Yamada, Reiko

    2006-08-21

    Neural processes underlying identification of durational contrasts were studied by comparing English and Japanese speakers for Japanese short/long vowel identification relative to consonant identification. Enhanced activities for non-native contrast (Japanese short/long vowel identification by English speakers) were observed in brain regions involved with articulatory-auditory mapping (Broca's area, superior temporal gyrus, planum temporale, and cerebellum), but not in the supramarginal gyrus. Greater activity in the supramarginal gyrus found for the consonant identification over short/long vowel identification by Japanese speakers implies that it is more important for phonetic contrasts differing in place of articulation than for vowel duration. These results support the hypothesis that neural processes used to facilitate perception depend on the relative contribution of information important for articulatory planning control.

  2. 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.

  3. [Information processing in the human brain revealed by eyeblink].

    PubMed

    Nakano, Tamami

    2014-01-01

    People spontaneously generate an eyeblink every few seconds. It is generally accepted that eyeblinks are necessary for ocular lubrication, but spontaneous eyeblinks actually occur several times more frequently than necessary for lubrication. Thus, the functional role of most spontaneous eyeblinks has remained unclear. We found that peoples blinked in synchrony while viewing the same video stories. This blink synchronization specifically occured at the implicit breakpoints of the video stories. Moreover, in face-to-face communication, the listeners blinked with a delay of 0.25-0.5 s after the speaker blinked at the end and during pauses in speech. In contrast, the individuals with autism spectrum disorders, which are characterized by impaired social communication, did not show any eyeblink synchronization with the speaker. These facts demonstrate that spontaneous eyeblink is involved in the contextual segmentation of information, and that eyeblinks have a social function to share the contextual segmentation with others. Futhermore, our neuroimaging study revealed that, while viewing videos, cortical activity momentarily decreases in the dorsal attention network after blink onset but increases in the default-mode network. These results suggest that the spontaneous eyeblink is involved in the disengagement of attention at an implicit contextual breakpoint by controlling the balance between the two competing networks. PMID:24371126

  4. Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species

    PubMed Central

    Zhan, X; Dixon, A; Batbayar, N; Bragin, E; Ayas, Z; Deutschova, L; Chavko, J; Domashevsky, S; Dorosencu, A; Bagyura, J; Gombobaatar, S; Grlica, I D; Levin, A; Milobog, Y; Ming, M; Prommer, M; Purev-Ochir, G; Ragyov, D; Tsurkanu, V; Vetrov, V; Zubkov, N; Bruford, M W

    2015-01-01

    Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species. PMID:25074575

  5. Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species.

    PubMed

    Zhan, X; Dixon, A; Batbayar, N; Bragin, E; Ayas, Z; Deutschova, L; Chavko, J; Domashevsky, S; Dorosencu, A; Bagyura, J; Gombobaatar, S; Grlica, I D; Levin, A; Milobog, Y; Ming, M; Prommer, M; Purev-Ochir, G; Ragyov, D; Tsurkanu, V; Vetrov, V; Zubkov, N; Bruford, M W

    2015-01-01

    Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species. PMID:25074575

  6. Phosphate/Zinc Interaction Analysis in Two Lettuce Varieties Reveals Contrasting Effects on Biomass, Photosynthesis, and Dynamics of Pi Transport

    PubMed Central

    Bouain, Nadia; Kisko, Mushtak; Rouached, Aida; Dauzat, Myriam; Lacombe, Benoit; Belgaroui, Nibras; Ghnaya, Tahar; Davidian, Jean-Claude; Berthomieu, Pierre; Abdelly, Chedly

    2014-01-01

    Inorganic phosphate (Pi) and Zinc (Zn) are essential nutrients for normal plant growth. Interaction between these elements has been observed in many crop plants. Despite its agronomic importance, the biological significance and genetic basis of this interaction remain largely unknown. Here we examined the Pi/Zn interaction in two lettuce (Lactuca sativa) varieties, namely, “Paris Island Cos” and “Kordaat.” The effects of variation in Pi and Zn supply were assessed on biomass and photosynthesis for each variety. Paris Island Cos displayed better growth and photosynthesis compared to Kordaat under all the conditions tested. Correlation analysis was performed to determine the interconnectivity between Pi and Zn intracellular contents in both varieties. Paris Island Cos showed a strong negative correlation between the accumulation levels of Pi and Zn in shoots and roots. However, no relation was observed for Kordaat. The increase of Zn concentration in the medium causes a decrease in dynamics of Pi transport in Paris Island Cos, but not in Kordaat plants. Taken together, results revealed a contrasting behavior between the two lettuce varieties in terms of the coregulation of Pi and Zn homeostasis and provided evidence in favor of a genetic basis for the interconnection of these two elements. PMID:25025059

  7. Temporal contrast improvement based on the self-diffraction process with a cylinder mirror

    NASA Astrophysics Data System (ADS)

    Li, Fangjia; Shen, Xiong; Wang, Peng; Li, Yanyan; Liu, Jun; Wang, Zhanshan; Li, Ruxin

    2016-05-01

    A cylinder reflective mirror was used to increase incident pulse energy to multi-millijoules in the research of temporal contrast enhancement based on a self-diffraction (SD) process. A 170 μJ first-order SD pulse with temporal contrast improved by 4 orders of magnitude was obtained when incident pulse energy was 5.1 mJ. In order to improve energy-conversion efficiency, a 67/33 beam splitter was used to replace the original 50/50 one. A 265 μJ first-order SD signal was achieved without damage of the glass plate at 3.7 mJ input pulse energy with an energy-conversion efficiency of about 7.1%. The generated SD pulse is expected to be used as the seed of high-contrast and high-power laser systems.

  8. 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.

  9. [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.

  10. 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

  11. 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

  12. 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

  13. Major mouse placental compartments revealed by diffusion-weighted MRI, contrast-enhanced MRI, and fluorescence imaging

    PubMed Central

    Solomon, Eddy; Avni, Reut; Hadas, Ron; Raz, Tal; Garbow, Joel Richard; Bendel, Peter; Frydman, Lucio; Neeman, Michal

    2014-01-01

    Mammalian models, and mouse studies in particular, play a central role in our understanding of placental development. Magnetic resonance imaging (MRI) could be a valuable tool to further these studies, providing both structural and functional information. As fluid dynamics throughout the placenta are driven by a variety of flow and diffusion processes, diffusion-weighted MRI could enhance our understanding of the exchange properties of maternal and fetal blood pools—and thereby of placental function. These studies, however, have so far been hindered by the small sizes, the unavoidable motions, and the challenging air/water/fat heterogeneities, associated with mouse placental environments. The present study demonstrates that emerging methods based on the spatiotemporal encoding (SPEN) of the MRI information can robustly overcome these obstacles. Using SPEN MRI in combination with albumin-based contrast agents, we analyzed the diffusion behavior of developing placentas in a cohort of mice. These studies successfully discriminated the maternal from the fetal blood flows; the two orders of magnitude differences measured in these fluids’ apparent diffusion coefficients suggest a nearly free diffusion behavior for the former and a strong flow-based component for the latter. An intermediate behavior was observed by these methods for a third compartment that, based on maternal albumin endocytosis, was associated with trophoblastic cells in the interphase labyrinth. Structural features associated with these dynamic measurements were consistent with independent intravital and ex vivo fluorescence microscopy studies and are discussed within the context of the anatomy of developing mouse placentas. PMID:24969421

  14. Major mouse placental compartments revealed by diffusion-weighted MRI, contrast-enhanced MRI, and fluorescence imaging.

    PubMed

    Solomon, Eddy; Avni, Reut; Hadas, Ron; Raz, Tal; Garbow, Joel Richard; Bendel, Peter; Frydman, Lucio; Neeman, Michal

    2014-07-15

    Mammalian models, and mouse studies in particular, play a central role in our understanding of placental development. Magnetic resonance imaging (MRI) could be a valuable tool to further these studies, providing both structural and functional information. As fluid dynamics throughout the placenta are driven by a variety of flow and diffusion processes, diffusion-weighted MRI could enhance our understanding of the exchange properties of maternal and fetal blood pools--and thereby of placental function. These studies, however, have so far been hindered by the small sizes, the unavoidable motions, and the challenging air/water/fat heterogeneities, associated with mouse placental environments. The present study demonstrates that emerging methods based on the spatiotemporal encoding (SPEN) of the MRI information can robustly overcome these obstacles. Using SPEN MRI in combination with albumin-based contrast agents, we analyzed the diffusion behavior of developing placentas in a cohort of mice. These studies successfully discriminated the maternal from the fetal blood flows; the two orders of magnitude differences measured in these fluids' apparent diffusion coefficients suggest a nearly free diffusion behavior for the former and a strong flow-based component for the latter. An intermediate behavior was observed by these methods for a third compartment that, based on maternal albumin endocytosis, was associated with trophoblastic cells in the interphase labyrinth. Structural features associated with these dynamic measurements were consistent with independent intravital and ex vivo fluorescence microscopy studies and are discussed within the context of the anatomy of developing mouse placentas. PMID:24969421

  15. Major mouse placental compartments revealed by diffusion-weighted MRI, contrast-enhanced MRI, and fluorescence imaging.

    PubMed

    Solomon, Eddy; Avni, Reut; Hadas, Ron; Raz, Tal; Garbow, Joel Richard; Bendel, Peter; Frydman, Lucio; Neeman, Michal

    2014-07-15

    Mammalian models, and mouse studies in particular, play a central role in our understanding of placental development. Magnetic resonance imaging (MRI) could be a valuable tool to further these studies, providing both structural and functional information. As fluid dynamics throughout the placenta are driven by a variety of flow and diffusion processes, diffusion-weighted MRI could enhance our understanding of the exchange properties of maternal and fetal blood pools--and thereby of placental function. These studies, however, have so far been hindered by the small sizes, the unavoidable motions, and the challenging air/water/fat heterogeneities, associated with mouse placental environments. The present study demonstrates that emerging methods based on the spatiotemporal encoding (SPEN) of the MRI information can robustly overcome these obstacles. Using SPEN MRI in combination with albumin-based contrast agents, we analyzed the diffusion behavior of developing placentas in a cohort of mice. These studies successfully discriminated the maternal from the fetal blood flows; the two orders of magnitude differences measured in these fluids' apparent diffusion coefficients suggest a nearly free diffusion behavior for the former and a strong flow-based component for the latter. An intermediate behavior was observed by these methods for a third compartment that, based on maternal albumin endocytosis, was associated with trophoblastic cells in the interphase labyrinth. Structural features associated with these dynamic measurements were consistent with independent intravital and ex vivo fluorescence microscopy studies and are discussed within the context of the anatomy of developing mouse placentas.

  16. 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.

  17. 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.

  18. Enhancement of gamma oscillations indicates preferential processing of native over foreign phonemic contrasts in infants.

    PubMed

    Ortiz-Mantilla, Silvia; Hämäläinen, Jarmo A; Musacchia, Gabriella; Benasich, April A

    2013-11-27

    Young infants discriminate phonetically relevant speech contrasts in a universal manner, that is, similarly across languages. This ability fades by 12 months of age as the brain builds language-specific phonemic maps and increasingly responds preferentially to the infant's native language. However, the neural mechanisms that underlie the development of infant preference for native over non-native phonemes remain unclear. Since gamma-band power is known to signal infants' preference for native language rhythm, we hypothesized that it might also indicate preference for native phonemes. Using high-density electroencephalogram/event-related potential (EEG/ERP) recordings and source-localization techniques to identify and locate the ERP generators, we examined changes in brain oscillations while 6-month-old human infants from monolingual English settings listened to English and Spanish syllable contrasts. Neural dynamics were investigated via single-trial analysis of the temporal-spectral composition of brain responses at source level. Increases in 4-6 Hz (theta) power and in phase synchronization at 2-4 Hz (delta/theta) were found to characterize infants' evoked responses to discrimination of native/non-native syllable contrasts mostly in the left auditory source. However, selective enhancement of induced gamma oscillations in the area of anterior cingulate cortex was seen only during native contrast discrimination. These results suggest that gamma oscillations support syllable discrimination in the earliest stages of language acquisition, particularly during the period in which infants begin to develop preferential processing for linguistically relevant phonemic features in their environment. Our results also suggest that by 6 months of age, infants already treat native phonemic contrasts differently from non-native, implying that perceptual specialization and establishment of enduring phonemic memory representations have been initiated.

  19. An oculomotor decision process revealed by functional magnetic resonance imaging.

    PubMed

    Heinen, Stephen J; Rowland, Jess; Lee, Byeong-Taek; Wade, Alex R

    2006-12-27

    It is not known how the brain decides to act on moving objects. We demonstrated previously that neurons in the macaque supplementary eye field (SEF) reflect the rule of ocular baseball, a go/nogo task in which eye movements signal the rule-guided interpretation of the trajectory of a target. In ocular baseball, subjects must decide whether to pursue a moving spot target with an eye movement after discriminating whether the target will cross a distal, visible line segment. Here we identify cortical regions active during the ocular baseball task using event-related human functional magnetic resonance imaging (fMRI) and concurrent eye-movement monitoring. Task-related activity was observed in the SEF, the frontal eye field (FEF), the superior parietal lobule (SPL), and the right ventrolateral prefrontal cortex (VLPFC). The SPL and right VLPFC showed heightened activity only during ocular baseball, despite identical stimuli and oculomotor demands in the control task, implicating these areas in the decision process. Furthermore, the right VLPFC but not the SPL showed the greatest activation during the nogo decision trials. This suggests both a functional dissociation between these areas and a role for the right VLPFC in rule-guided inhibition of behavior. In the SEF and FEF, activity was similar for ocular baseball and a control eye-movement task. We propose that, although the SEF reflects the ocular baseball rule, both areas in humans are functionally closer to motor processing than the SPL and the right VLPFC. By recording population activity with fMRI during the ocular baseball task, we have revealed the cortical substrate of an oculomotor decision process.

  20. 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.

  1. Improved algorithm for processing grating-based phase contrast interferometry image sets

    SciTech Connect

    Marathe, Shashidhara Assoufid, Lahsen Xiao, Xianghui; Ham, Kyungmin; Johnson, Warren W.; Butler, Leslie G.

    2014-01-15

    Grating-based X-ray and neutron interferometry tomography using phase-stepping methods generates large data sets. An improved algorithm is presented for solving for the parameters to calculate transmissions, differential phase contrast, and dark-field images. The method takes advantage of the vectorization inherent in high-level languages such as Mathematica and MATLAB and can solve a 16 × 1k × 1k data set in less than a second. In addition, the algorithm can function with partial data sets. This is demonstrated with processing of a 16-step grating data set with partial use of the original data chosen without any restriction. Also, we have calculated the reduced chi-square for the fit and notice the effect of grating support structural elements upon the differential phase contrast image and have explored expanded basis set representations to mitigate the impact.

  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. 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.

  4. Reach tracking reveals dissociable processes underlying cognitive control.

    PubMed

    Erb, Christopher D; Moher, Jeff; Sobel, David M; Song, Joo-Hyun

    2016-07-01

    The current study uses reach tracking to investigate how cognitive control is implemented during online performance of the Stroop task (Experiment 1) and the Eriksen flanker task (Experiment 2). We demonstrate that two of the measures afforded by reach tracking, initiation time and reach curvature, capture distinct patterns of effects that have been linked to dissociable processes underlying cognitive control in electrophysiology and functional neuroimaging research. Our results suggest that initiation time reflects a response threshold adjustment process involving the inhibition of motor output, while reach curvature reflects the degree of co-activation between response alternatives registered by a monitoring process over the course of a trial. In addition to shedding new light on fundamental questions concerning how these processes contribute to the cognitive control of behavior, these results present a framework for future research to investigate how these processes function across different tasks, develop across the lifespan, and differ among individuals. PMID:27045465

  5. [Metabolomics analysis revealing multiple compounds changed in rhubarb after processing].

    PubMed

    Zhao, Nan; Zhang, Xiao-Zhe; Hu, Chang-Jiang; Jia, Tian-Zhu; Xiao, Hong-Bin

    2014-05-01

    Untargeted metabolomics analysis of rhubarb and stewed rhubarb samples shows that the determined samples clearly clustered in to two groups, indicating that the processing procedures caused changes in the composition and/or content of components in rhubarb. Ten components were identified by UHPLC-Q-TOF-MS/MS and references, which intensity declined in rhubarb after processing. Targeted metabolomics analysis of rhubarb and stewed rhubarb samples indicated that aloe-emodin, rhein, emodin and physcion were detected with lower intensity in stewed rhubarb samples than in rhubarb samples. Metabolomics analysis of rhubarb and stewed rhubarb indicated the various components of rhubarb changed after processing.

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

    PubMed

    Ramu, Vemanna S; Paramanantham, Anjugam; Ramegowda, Venkategowda; Mohan-Raju, Basavaiah; Udayakumar, Makarla; Senthil-Kumar, Muthappa

    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.

  7. Drought onset mechanisms revealed by satellite solar-induced chlorophyll fluorescence: Insights from two contrasting extreme events

    NASA Astrophysics Data System (ADS)

    Sun, Ying; Fu, Rong; Dickinson, Robert; Joiner, Joanna; Frankenberg, Christian; Gu, Lianhong; Xia, Youlong; Fernando, Nelun

    2015-11-01

    This study uses the droughts of 2011 in Texas and 2012 over the central Great Plains as case studies to explore the potential of satellite-observed solar-induced chlorophyll fluorescence (SIF) for monitoring drought dynamics. We find that the spatial patterns of negative SIF anomalies from the Global Ozone Monitoring Experiment 2 (GOME-2) closely resembled drought intensity maps from the U.S. Drought Monitor for both events. The drought-induced suppression of SIF occurred throughout 2011 but was exacerbated in summer in the Texas drought. This event was characterized by a persistent depletion of root zone soil moisture caused by yearlong below-normal precipitation. In contrast, for the central Great Plains drought, warmer temperatures and relatively normal precipitation boosted SIF in the spring of 2012; however, a sudden drop in precipitation coupled with unusually high temperatures rapidly depleted soil moisture through evapotranspiration, leading to a rapid onset of drought in early summer. Accordingly, SIF reversed from above to below normal. For both regions, the GOME-2 SIF anomalies were significantly correlated with those of root zone soil moisture, indicating that the former can potentially be used as proxy of the latter for monitoring agricultural droughts with different onset mechanisms. Further analyses indicate that the contrasting dynamics of SIF during these two extreme events were caused by changes in both fraction of absorbed photosynthetically active radiation fPAR and fluorescence yield, suggesting that satellite SIF is sensitive to both structural and physiological/biochemical variations of vegetation. We conclude that the emerging satellite SIF has excellent potential for dynamic drought monitoring.

  8. 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

  9. Clarifying the role of rigidity contrasts and rock interface strength in sill formation processes

    NASA Astrophysics Data System (ADS)

    Kavanagh, J.; Pavier, M.; Menand, T.; Sparks, R. S. J.

    2012-04-01

    Field observations, numerical and analogue models suggest rigidity contrasts may play an important role in sill formation processes. We present results from analogue experiments and rock strength tests which explore the additional role that rock interface strength could have on the geometry and propagation dynamics of magmatic intrusions. Dyed water (a magma analogue) was injected into layers of solidified gelatine (a crustal analogue) to form experimental dykes and sills. The intrusions were pressure-driven and injected under initially hydrostatic conditions. From 4 to ~15 °C gelatine deforms elastically, and under these conditions the tensile strength of the gelatine (Youngs Modulus) evolves following a power-law relationship that plateaus with time. Varying the concentration of the gelatine allows layer strength contrasts as low as 1% to be created. Our results show that in a two-layered system the upper layer needs to be at least 10% more rigid than the lower layer to cause dyke arrest. An experimental sill then forms if the interface between the layers is weak; otherwise a lateral dyke forms. To test rock interface strength variation in nature we used a 1 kN servo hydraulic test machine to test 5 mm thick cuboidal specimens of sandstone-siltstone rock core where the interface between the strata is preserved. By measuring the load required to grow a starter crack running along the lithological contact between the layers we can calculate its fracture toughness (a measure of the material resistance to the growth of a crack). The results show the rock interfaces have intermediate fracture toughness to their parent units. These results bring into question the relative roles of magma viscosity versus rock fracturing in controlling the nature and propagation dynamics of magmatic intrusions.

  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. 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.

  12. 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

  13. Process-based approach reveals directional effects of environmental factors on movement between habitats.

    PubMed

    Nakayama, Shinnosuke; Ojanguren, Alfredo F; Fuiman, Lee A

    2011-11-01

    1. Understanding the effects of environmental factors on animal distributions is a central issue in ecology. However, movement rules inferred from distribution patterns do not reveal the processes through which animal distribution is realized. 2. We investigated individual movement rules using a process-based approach. In experiments, coastal fish larvae (red drum, Sciaenops ocellatus) were matched with an intraspecific competitor of different sizes, and time series of habitat transition of individuals were fitted with a continuous-time Markov chain model to evaluate the effects of the presence of a competitor, behavioural interactions and habitat quality on the likelihoods of habitat transition. 3. The process-based approach revealed that these factors did not simply act as a 'slope' between habitats that makes it easier to go in one direction and more difficult to return. Rather, these factors modify the movement rules differently depending on the directions of the movement. 4. Individuals were less likely to enter a better habitat in the presence of a larger conspecific, more likely to shift to a poorer habitat when they received aggressive behaviour and more likely to stay in a better habitat in the presence of food. However, no effect was found on the transition intensity for moving in the opposite direction. 5. The process-based approach to evaluating movement rules of animals allowed us to see the contrasting directional effects of different factors on the underlying movement rules used by animals, as opposed to pattern-based fitting of observed distributions. Consideration of these rules would improve the existing habitat-choice models. PMID:21569030

  14. 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.

  15. Protein profiles reveal diverse responsive signaling pathways in kernels of two maize inbred lines with contrasting drought sensitivity.

    PubMed

    Yang, Liming; Jiang, Tingbo; Fountain, Jake C; Scully, Brian T; Lee, Robert D; Kemerait, Robert C; Chen, Sixue; Guo, Baozhu

    2014-01-01

    Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964) with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP), and protein profiles were investigated in developing kernels (35 DAP) using iTRAQ (isobaric tags for relative and absolute quantitation). Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels.

  16. Protein Profiles Reveal Diverse Responsive Signaling Pathways in Kernels of Two Maize Inbred Lines with Contrasting Drought Sensitivity

    PubMed Central

    Yang, Liming; Jiang, Tingbo; Fountain, Jake C.; Scully, Brian T.; Lee, Robert D.; Kemerait, Robert C.; Chen, Sixue; Guo, Baozhu

    2014-01-01

    Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964) with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP), and protein profiles were investigated in developing kernels (35 DAP) using iTRAQ (isobaric tags for relative and absolute quantitation). Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels. PMID:25334062

  17. 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

  18. Contrasting patterns of survival and dispersal in multiple habitats reveal an ecological trap in a food-caching bird.

    PubMed

    Norris, D Ryan; Flockhart, D T Tyler; Strickland, Dan

    2013-11-01

    A comprehensive understanding of how natural and anthropogenic variation in habitat influences populations requires long-term information on how such variation affects survival and dispersal throughout the annual cycle. Gray jays Perisoreus canadensis are widespread boreal resident passerines that use cached food to survive over the winter and to begin breeding during the late winter. Using multistate capture-recapture analysis, we examined apparent survival and dispersal in relation to habitat quality in a gray jay population over 34 years (1977-2010). Prior evidence suggests that natural variation in habitat quality is driven by the proportion of conifers on territories because of their superior ability to preserve cached food. Although neither adults (>1 year) nor juveniles (<1 year) had higher survival rates on high-conifer territories, both age classes were less likely to leave high-conifer territories and, when they did move, were more likely to disperse to high-conifer territories. In contrast, survival rates were lower on territories that were adjacent to a major highway compared to territories that did not border the highway but there was no evidence for directional dispersal towards or away from highway territories. Our results support the notion that natural variation in habitat quality is driven by the proportion of coniferous trees on territories and provide the first evidence that high-mortality highway habitats can act as an equal-preference ecological trap for birds. Reproductive success, as shown in a previous study, but not survival, is sensitive to natural variation in habitat quality, suggesting that gray jays, despite living in harsh winter conditions, likely favor the allocation of limited resources towards self-maintenance over reproduction.

  19. UAS and Distributed Temperature Sensing Reveal Previously Unseen Atmospheric Processes

    NASA Astrophysics Data System (ADS)

    Higgins, C. W.; Liu, Z.; Holmes, H.; Wing, M.; Predosa, R. A.; Blunck, D.

    2015-12-01

    The frontier of atmospheric boundary layer research lies in times and places of complexity. Transitions between atmospheric states, buoyant flows over complex terrain, and times with only weak forcing mechanisms all have rich physical expressions of atmospheric flow that are not fully understood. These motions often span a large range of scales and are nonstationary. Traditional atmospheric measurement approaches are inadequate in these situations as they do not have the data density or the physical extent to capture the full range of motions. An unmanned aerial system (UAS) is used to lift distributed temperature sensing (DTS) technologies to observe the early morning transition from stable to unstably stratified conditions. The UAS/DTS combination yielded observations of temperature and humidity in the lower atmosphere with never-seen-before resolution and extent. The data reveal a complex interplay of motions that occur during the morning transition that ultimately results in the propagation and growth of unstable wave modes. The observations have given new insight into the appropriate scaling variables for the morning transition time.

  20. Image contrast enhancement of Ni/YSZ anode during the slice-and-view process in FIB-SEM.

    PubMed

    Liu, Shu-Sheng; Takayama, Akiko; Matsumura, Syo; Koyama, Michihisa

    2016-03-01

    Focused ion beam-scanning electron microscopy (FIB-SEM) is a widely used and easily operational equipment for three-dimensional reconstruction with flexible analysis volume. It has been using successfully and increasingly in the field of solid oxide fuel cell. However, the phase contrast of the SEM images is indistinct in many cases, which will bring difficulties to the image processing. Herein, the phase contrast of a conventional Ni/yttria stabilized zirconia anode is tuned in an FIB-SEM with In-Lens secondary electron (SE) and backscattered electron detectors. Two accessories, tungsten probe and carbon nozzle, are inserted during the observation. The former has no influence on the contrast. When the carbon nozzle is inserted, best and distinct contrast can be obtained by In-Lens SE detector. This method is novel for contrast enhancement. Phase segmentation of the image can be automatically performed. The related mechanism for different images is discussed.

  1. 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

    2004-11-01

    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.

  2. Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

    PubMed

    Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

    2016-08-01

    Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.

  3. Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

    PubMed

    Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

    2016-08-01

    Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. PMID:27156744

  4. 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. PMID:22876319

  5. Contamination Revealed by Indicator Microorganism Levels during Veal Processing.

    PubMed

    Bosilevac, Joseph M; Wang, Rong; Luedtke, Brandon E; Wheeler, Tommy L; Koohmaraie, Mohammad

    2016-08-01

    During site visits of veal processors, the U.S. Department of Agriculture, Food Safety Inspection Service (FSIS) has reported processing deficiencies that likely contribute to increased levels of veal contamination. Here, we report the results of measuring aerobic plate count bacteria (APC), Enterobacteriaceae, coliforms (CF), and Escherichia coli during eight sample collections at five veal processors to assess contamination during the harvest of bob veal and formula-fed veal before (n = 5 plants) and after (n = 3 plants) changes to interventions and processing practices. Hides of veal calves at each plant had mean log CFU/100 cm(2) APC, Enterobacteriaceae, CF, and E. coli of 6.02 to 8.07, 2.95 to 5.24, 3.28 to 5.83, and 3.08 to 5.59, respectively. Preintervention carcasses had mean log CFU/100 cm(2) APC, Enterobacteriaceae, CF, and E. coli of 3.08 to 5.22, 1.16 to 3.47, 0.21 to 3.06, and -0.07 to 3.10, respectively, before and 2.72 to 4.50, 0.99 to 2.76, 0.69 to 2.26, and 0.33 to 2.12, respectively, after changes were made to improve sanitary dressing procedures. Final veal carcasses had mean log CFU/100 cm(2) APC, Enterobacteriaceae, CF, and E. coli of 0.36 to 2.84, -0.21 to 1.59, -0.23 to 1.59, and -0.38 to 1.45 before and 0.44 to 2.64, -0.16 to 1.33, -0.42 to 1.20, and 0.48 to 1.09 after changes were made to improve carcass-directed interventions. Whereas the improved dressing procedures resulted in improved carcass cleanliness, the changes to carcass-directed interventions were less successful, and veal processors are urged to use techniques that ensure uniform and consistent delivery of antimicrobials to carcasses. Analysis of results comparing bob veal to formula-fed veal found bob veal hides, preintervention carcasses, and final carcasses to have increased (P < 0.05) APC, Enterobacteriaceae, CF, and E. coli (with the exception of hide Enterobacteriaceae; P > 0.05) relative to formula fed veal. When both veal categories were harvested at the same plant on

  6. Contamination Revealed by Indicator Microorganism Levels during Veal Processing.

    PubMed

    Bosilevac, Joseph M; Wang, Rong; Luedtke, Brandon E; Wheeler, Tommy L; Koohmaraie, Mohammad

    2016-08-01

    During site visits of veal processors, the U.S. Department of Agriculture, Food Safety Inspection Service (FSIS) has reported processing deficiencies that likely contribute to increased levels of veal contamination. Here, we report the results of measuring aerobic plate count bacteria (APC), Enterobacteriaceae, coliforms (CF), and Escherichia coli during eight sample collections at five veal processors to assess contamination during the harvest of bob veal and formula-fed veal before (n = 5 plants) and after (n = 3 plants) changes to interventions and processing practices. Hides of veal calves at each plant had mean log CFU/100 cm(2) APC, Enterobacteriaceae, CF, and E. coli of 6.02 to 8.07, 2.95 to 5.24, 3.28 to 5.83, and 3.08 to 5.59, respectively. Preintervention carcasses had mean log CFU/100 cm(2) APC, Enterobacteriaceae, CF, and E. coli of 3.08 to 5.22, 1.16 to 3.47, 0.21 to 3.06, and -0.07 to 3.10, respectively, before and 2.72 to 4.50, 0.99 to 2.76, 0.69 to 2.26, and 0.33 to 2.12, respectively, after changes were made to improve sanitary dressing procedures. Final veal carcasses had mean log CFU/100 cm(2) APC, Enterobacteriaceae, CF, and E. coli of 0.36 to 2.84, -0.21 to 1.59, -0.23 to 1.59, and -0.38 to 1.45 before and 0.44 to 2.64, -0.16 to 1.33, -0.42 to 1.20, and 0.48 to 1.09 after changes were made to improve carcass-directed interventions. Whereas the improved dressing procedures resulted in improved carcass cleanliness, the changes to carcass-directed interventions were less successful, and veal processors are urged to use techniques that ensure uniform and consistent delivery of antimicrobials to carcasses. Analysis of results comparing bob veal to formula-fed veal found bob veal hides, preintervention carcasses, and final carcasses to have increased (P < 0.05) APC, Enterobacteriaceae, CF, and E. coli (with the exception of hide Enterobacteriaceae; P > 0.05) relative to formula fed veal. When both veal categories were harvested at the same plant on

  7. Video image processing greatly enhances contrast, quality, and speed in polarization-based microscopy

    PubMed Central

    1981-01-01

    Video cameras with contrast and black level controls can yield polarized light and differential interference contrast microscope images with unprecedented image quality, resolution, and recording speed. The theoretical basis and practical aspects of video polarization and differential interference contrast microscopy are discussed and several applications in cell biology are illustrated. These include: birefringence of cortical structures and beating cilia in Stentor, birefringence of rotating flagella on a single bacterium, growth and morphogenesis of echinoderm skeletal spicules in culture, ciliary and electrical activity in a balancing organ of a nudibranch snail, and acrosomal reaction in activated sperm. PMID:6788777

  8. Video image processing greatly enhances contrast, quality, and speed in polarization-based microscopy.

    PubMed

    Inoué, S

    1981-05-01

    Video cameras with contrast and black level controls can yield polarized light and differential interference contrast microscope images with unprecedented image quality, resolution, and recording speed. The theoretical basis and practical aspects of video polarization and differential interference contrast microscopy are discussed and several applications in cell biology are illustrated. These include: birefringence of cortical structures and beating cilia in Stentor, birefringence of rotating flagella on a single bacterium, growth and morphogenesis of echinoderm skeletal spicules in culture, ciliary and electrical activity in a balancing organ of a nudibranch snail, and acrosomal reaction in activated sperm. PMID:6788777

  9. Crevasse-splay sedimentation processes revealed through high resolution modelling

    NASA Astrophysics Data System (ADS)

    Hackney, Christopher; Darby, Stephen; Parsons, Daniel; Leyland, Julian; Aalto, Rolf; Nicholas, Andrew; Best, Jim

    2015-04-01

    During rapid rise flood events, crevasse-splay complexes are a dominant conduit through which sediment and water are passed from the main channel onto the floodplain, particularly for large rivers. These crevasse-splay systems are, therefore, key in controlling rates of floodplain sedimentation, as well as conditioning the location of avulsions. Despite recent advances in our capabilities to model the development and evolution of these systems, our understanding of the passage, storage and reworking of water and sediment across them remains relatively poor. A key limitation concerns the point that, since floodplain topography is a first-order control on the hydrodynamics of crevasse-splays, publicly available topographic data sets (e.g. SRTM) are currently unable to resolve key processes at the necessary spatial resolution. Here we employ Structure-from-Motion (SfM) on low-level aerial photography to obtain high-resolution (3m grid cell) georectified topographic data (horizontal error = 0.02 m; vertical error = 0.5 m) for a series of three representative crevasse-splay complexes located along the Mekong River, Cambodia. We use the coupled hydrodynamic and morphodynamic model, Delft-3D to simulate sedimentation patterns for a series of flood events. We model floodplain deposition and erosion and validate simulated spatial and temporal variations against observed patterns. We show how the spatial and temporal patterns of floodplain development via crevasse-splays are conditioned by key hydrological characteristics.

  10. 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

  11. 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

  12. Hearing Without Listening: Functional Connectivity Reveals the Engagement of Multiple Nonauditory Networks During Basic Sound Processing

    PubMed Central

    Melcher, Jennifer R.

    2011-01-01

    Abstract The present functional magnetic resonance imaging (fMRI) study presents data challenging the traditional view that sound is processed almost exclusively in the classical auditory pathway unless imbued with behavioral significance. In a first experiment, subjects were presented with broadband noise in on/off fashion as they performed an unrelated visual task. A conventional analysis assuming predictable sound-evoked responses demonstrated a typical activation pattern that was confined to classical auditory centers. In contrast, spatial independent component analysis (sICA) disclosed multiple networks of acoustically responsive brain centers. One network comprised classical auditory centers, but four others included nominally “nonauditory” areas: cingulo-insular cortex, mediotemporal limbic lobe, basal ganglia, and posterior orbitofrontal cortex, respectively. Functional connectivity analyses confirmed the sICA results by demonstrating coordinated activity between the involved brain structures. In a second experiment, fMRI data obtained from unstimulated (i.e., resting) subjects revealed largely similar networks. Together, these two experiments suggest the existence of a coordinated system of multiple acoustically responsive intrinsic brain networks, comprising classical auditory centers but also other brain areas. Our results suggest that nonauditory centers play a role in sound processing at a very basic level, even when the sound is not intertwined with behaviors requiring the well-known functionality of these regions. PMID:22433051

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

    PubMed Central

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

    2014-01-01

    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. PMID:25150068

  14. 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.

  15. Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes.

    PubMed

    Martin, Guiomar; Soy, Judit; Monte, Elena

    2016-01-01

    Members of the PIF quartet (PIFq; PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes. However, a comprehensive definition of the PIFq-regulated transcriptome under SD is still lacking. We have recently shown that SD and free-running (LL) conditions correspond to "growth" and "no growth" conditions, respectively, correlating with greater abundance of PIF protein in SD. Here, we present a genomic analysis whereby we first define SD-regulated genes at dawn compared to LL in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. By using this sequential strategy, we have identified 349 PIF/SD-regulated genes, approximately 55% induced and 42% repressed by both SD and PIFq. Comparison with available databases indicates that PIF/SD-induced and PIF/SD-repressed sets are differently phased at dawn and mid-morning, respectively. In addition, we found that whereas rhythmicity of the PIF/SD-induced gene set is lost in LL, most PIF/SD-repressed genes keep their rhythmicity in LL, suggesting differential regulation of both gene sets by the circadian clock. Moreover, we also uncovered distinct overrepresented functions in the induced and repressed gene sets, in accord with previous studies in other examined PIF-regulated processes. Interestingly, promoter analyses showed that, whereas PIF/SD-induced genes are enriched in direct PIF targets, PIF/SD-repressed genes are mostly indirectly regulated by the PIFs and might be more enriched in ABA-regulated genes. PMID:27458465

  16. Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes

    PubMed Central

    Martin, Guiomar; Soy, Judit; Monte, Elena

    2016-01-01

    Members of the PIF quartet (PIFq; PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes. However, a comprehensive definition of the PIFq-regulated transcriptome under SD is still lacking. We have recently shown that SD and free-running (LL) conditions correspond to “growth” and “no growth” conditions, respectively, correlating with greater abundance of PIF protein in SD. Here, we present a genomic analysis whereby we first define SD-regulated genes at dawn compared to LL in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. By using this sequential strategy, we have identified 349 PIF/SD-regulated genes, approximately 55% induced and 42% repressed by both SD and PIFq. Comparison with available databases indicates that PIF/SD-induced and PIF/SD-repressed sets are differently phased at dawn and mid-morning, respectively. In addition, we found that whereas rhythmicity of the PIF/SD-induced gene set is lost in LL, most PIF/SD-repressed genes keep their rhythmicity in LL, suggesting differential regulation of both gene sets by the circadian clock. Moreover, we also uncovered distinct overrepresented functions in the induced and repressed gene sets, in accord with previous studies in other examined PIF-regulated processes. Interestingly, promoter analyses showed that, whereas PIF/SD-induced genes are enriched in direct PIF targets, PIF/SD-repressed genes are mostly indirectly regulated by the PIFs and might be more enriched in ABA-regulated genes. PMID:27458465

  17. Simple Image Processing Techniques For The Contrast Enhancement Of Real-Time Digital Speckle Pattern Interferometry Fringes

    NASA Astrophysics Data System (ADS)

    Ganesan, A. R.; Kothiyal, M. P.; Sirohi, Rajpal S.

    1989-09-01

    Some simple image processing techniques are suggested that can be used for enhancing the contrast of real-time digital speckle pattern interferometry fringes. The techniques have been developed for the commercial Intellect 100 image processing system interfaced to a PDP-1 1 /23+ microcomputer, but they can be adapted to any commercial image processing system with slight modifications, if necessary, depending on the hardware configuration of the system.

  18. Multi-voxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

    PubMed Central

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

    2013-01-01

    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 multi-voxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was employed 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 to during passive listening. One network of regions appears to encode an ‘error signal’ irrespective 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 fronto-temporal 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. Taken together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple, interactive, functionally differentiated neural systems. PMID:23467350

  19. High-fidelity photometry and astrometry of high-contrast imaged companions using LOCI processing.

    NASA Astrophysics Data System (ADS)

    Maire, Jérôme; Gagné, Jonathan; Lafrenière, David; Graham, James R.; Doyon, René

    2014-01-01

    abstract-type="normal"> Résumé Direct imaging and spectroscopy of exoplanets is a key element for understanding planet formation and migration. Such direct detections and characterizations remains technologically challenging, since a very high contrast ratio and small angular separation are involved, and futhermore speckle noise limits the high-contrast imaging performance. We further discuss a speckle subtraction and suppression technique that fully takes advantage of spectral and time-domain information on quasi-static speckles to measure the highest-fidelity photometry as well as accurate astrometry of detected companions.

  20. 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

  1. Discrimination Training of Phonemic Contrasts Enhances Phonological Processing in Mainstream School Children

    ERIC Educational Resources Information Center

    Moore, D.R.; Rosenberg, J.F.; Coleman, J.S.

    2005-01-01

    Auditory perceptual learning has been proposed as effective for remediating impaired language and for enhancing normal language development. We examined the effect of phonemic contrast discrimination training on the discrimination of whole words and on phonological awareness in 8- to 10-year-old mainstream school children. Eleven phonemic contrast…

  2. 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.…

  3. 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

  4. 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.

  5. 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. PMID:24904076

  6. 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.

  7. 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.

  8. Contrasting emotion processing and executive functioning in attention-deficit/hyperactivity disorder and bipolar disorder.

    PubMed

    Soncin, Stephen; Brien, Donald C; Coe, Brian C; Marin, Alina; Munoz, Douglas P

    2016-10-01

    Attention-deficit/hyperactivity disorder (ADHD) and bipolar disorder (BD) are highly comorbid and share executive function and emotion processing deficits, complicating diagnoses despite distinct clinical features. We compared performance on an oculomotor task that assessed these processes to capture subtle differences between ADHD and BD. The interaction between emotion processing and executive functioning may be informative because, although these processes overlap anatomically, certain regions that are compromised in each network are different in ADHD and BD. Adults, aged 18-62, with ADHD (n = 22), BD (n = 20), and healthy controls (n = 21) performed an interleaved pro- and antisaccade task (looking toward vs. looking away from a visual target, respectively). Task irrelevant emotional faces (fear, happy, sad, neutral) were presented on a subset of trials either before or with the target. The ADHD group made more direction errors (looked in the wrong direction) than controls. Presentation of negatively valenced (fear, sad) and ambiguous (neutral) emotional faces increased saccadic reaction time in BD only compared to controls, whereas longer presentation of sad faces modestly increased group differences. The antisaccade task differentiated ADHD from controls. Emotional processing further impaired processing speed in BD. We propose that the dorsolateral prefrontal cortex is critical in both processing systems, but the inhibitory signal this region generates is impacted by dysfunction in the emotion processing network, possibly at the orbitofrontal cortex, in BD. These results suggest there are differences in how emotion processing and executive functioning interact, which could be utilized to improve diagnostic specificity. (PsycINFO Database Record

  9. 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

  10. Toward clinical differential phase contrast mammography: preliminary evaluations and image processing schemes

    NASA Astrophysics Data System (ADS)

    Stampanoni, M.; Wang, Z.; Thüring, T.; David, C.; Rössl, E.; van Stevendaal, U.; Köhler, T.; Trippel, M.; Singer, G.; Kubik-Huch, R. A.; Hohl, M. K.; Hauser, N.

    2013-05-01

    Phase contrast and scattering-based X-ray imaging are very promising tools for medical diagnostics because they are able to provide additional and complementary information to traditional absorption-based methods. In this work, we discuss the investigation of three native breast samples with a grating interferometer equipped with a conventional X-ray tube, the full study being published in ref. [1]. We briefly introduce a method to fuse absorption, differential phase and scattering signals into a unique image with improved diagnostic contents. Our approach yields complementary and inaccessible information on the electron density distribution and the small-angle scattering power of the sample which could potentially answer clinically relevant, yet unresolved questions such as the capability to unequivocally discern between (pre-) malignant changes and post-operative scars or to distinguish cancer-invaded regions within healthy tissue.

  11. 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…

  12. Equal Protection and Due Process: Contrasting Methods of Review under Fourteenth Amendment Doctrine.

    ERIC Educational Resources Information Center

    Hughes, James A.

    1979-01-01

    Argues that the Court has, at times, confused equal protection and due process methods of review, primarily by employing interest balancing in certain equal protection cases that should have been subjected to due process analysis. Available from Harvard Civil Rights-Civil Liberties Law Review, Harvard Law School, Cambridge, MA 02138; sc $4.00.…

  13. Contrasting emotion processing and executive functioning in attention-deficit/hyperactivity disorder and bipolar disorder.

    PubMed

    Soncin, Stephen; Brien, Donald C; Coe, Brian C; Marin, Alina; Munoz, Douglas P

    2016-10-01

    Attention-deficit/hyperactivity disorder (ADHD) and bipolar disorder (BD) are highly comorbid and share executive function and emotion processing deficits, complicating diagnoses despite distinct clinical features. We compared performance on an oculomotor task that assessed these processes to capture subtle differences between ADHD and BD. The interaction between emotion processing and executive functioning may be informative because, although these processes overlap anatomically, certain regions that are compromised in each network are different in ADHD and BD. Adults, aged 18-62, with ADHD (n = 22), BD (n = 20), and healthy controls (n = 21) performed an interleaved pro- and antisaccade task (looking toward vs. looking away from a visual target, respectively). Task irrelevant emotional faces (fear, happy, sad, neutral) were presented on a subset of trials either before or with the target. The ADHD group made more direction errors (looked in the wrong direction) than controls. Presentation of negatively valenced (fear, sad) and ambiguous (neutral) emotional faces increased saccadic reaction time in BD only compared to controls, whereas longer presentation of sad faces modestly increased group differences. The antisaccade task differentiated ADHD from controls. Emotional processing further impaired processing speed in BD. We propose that the dorsolateral prefrontal cortex is critical in both processing systems, but the inhibitory signal this region generates is impacted by dysfunction in the emotion processing network, possibly at the orbitofrontal cortex, in BD. These results suggest there are differences in how emotion processing and executive functioning interact, which could be utilized to improve diagnostic specificity. (PsycINFO Database Record PMID:27537826

  14. 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

  15. 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

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

    PubMed

    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

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

    PubMed

    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.

  18. Contrasting effects of strong ties on SIR and SIS processes in temporal networks

    NASA Astrophysics Data System (ADS)

    Sun, Kaiyuan; Baronchelli, Andrea; Perra, Nicola

    2015-12-01

    Most real networks are characterized by connectivity patterns that evolve in time following complex, non-Markovian, dynamics. Here we investigate the impact of this ubiquitous feature by studying the Susceptible-Infected-Recovered (SIR) and Susceptible-Infected-Susceptible (SIS) epidemic models on activity driven networks with and without memory (i.e., Markovian and non-Markovian). We find that memory inhibits the spreading process in SIR models by shifting the epidemic threshold to larger values and reducing the final fraction of recovered nodes. On the contrary, in SIS processes memory reduces the epidemic threshold and, for a wide range of disease parameters, increases the fraction of nodes affected by the disease in the endemic state. The heterogeneity in tie strengths, and the frequent repetition of strong ties it entails, allows in fact less virulent SIS-like diseases to survive in tightly connected local clusters that serve as reservoir for the virus. We validate this picture by studying both processes on two real temporal networks.

  19. High-Resolution Secondary Ion Mass Spectrometry Reveals the Contrasting Subcellular Distribution of Arsenic and Silicon in Rice Roots1[C][W][OA

    PubMed Central

    Moore, Katie L.; Schröder, Markus; Wu, Zhongchang; Martin, Barry G.H.; Hawes, Chris R.; McGrath, Steve P.; Hawkesford, Malcolm J.; Feng Ma, Jian; Zhao, Fang-Jie; Grovenor, Chris R.M.

    2011-01-01

    Rice (Oryza sativa) takes up arsenite mainly through the silicic acid transport pathway. Understanding the uptake and sequestration of arsenic (As) into the rice plant is important for developing strategies to reduce As concentration in rice grain. In this study, the cellular and subcellular distributions of As and silicon (Si) in rice roots were investigated using high-pressure freezing, high-resolution secondary ion mass spectrometry, and transmission electron microscopy. Rice plants, both the lsi2 mutant lacking the Si/arsenite efflux transporter Lsi2 and its wild-type cultivar, with or without an iron plaque, were treated with arsenate or arsenite. The formation of iron plaque on the root surface resulted in strong accumulation of As and phosphorous on the epidermis. The lsi2 mutant showed stronger As accumulation in the endodermal vacuoles, where the Lsi2 transporter is located in the plasma membranes, than the wild-type line. As also accumulated in the vacuoles of some xylem parenchyma cells and in some pericycle cells, particularly in the wild-type mature root zone. Vacuolar accumulation of As is associated with sulfur, suggesting that As may be stored as arsenite-phytochelatin complexes. Si was localized in the cell walls of the endodermal cells with little apparent effect of the Lsi2 mutation on its distribution. This study reveals the vacuolar sequestration of As in rice roots and contrasting patterns of As and Si subcellular localization, despite both being transported across the plasma membranes by the same transporters. PMID:21490163

  20. 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

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

    PubMed

    Kerdelhué, C; Boivin, T; Burban, C

    2014-11-01

    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

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

    PubMed

    Kerdelhué, C; Boivin, T; Burban, C

    2014-11-01

    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.

  3. 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.

  4. 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. PMID:27457982

  5. 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

  6. Contrasted sediment processes and morphological adjustments in three successive cutoff meanders of the Danube delta

    NASA Astrophysics Data System (ADS)

    Tiron Duţu, Laura; Provansal, Mireille; Le Coz, Jérôme; Duţu, Florin

    2014-01-01

    Since the 1980s intensive anthropogenic disturbances have affected the channel of the St. George branch, the southern distributary of the Danube River. The meander cutoff programme since 1984-1988 induced different hydrosedimentary impacts on the local distribution of river flow velocities, discharge, and sediment fluxes between the former meanders and the man-made canals (Ichim and Radoane, 1986; Popa, 1997; Panin, 2003). This paper selects three large cutoff meander reaches of the St. George branch (the Mahmudia, Dunavăţ de Sus, and Dunavăţ de Jos meanders noted here as M1, M2, and M3, respectively) as an example to analyse the human impact in the Danube River delta. The diversion of the flow induces strong modifications by acceleration of the fluxes through the artificial canals combined with dramatically enhanced deposition in the former meander where it was observed in two cases (M1 and M3) with slight modifications in M2. An exceptional flood that occurred in April 2006 offered a good opportunity for scanning different cross sections of the meander systems. Bathymetry, flow velocity, suspended-load concentration, and liquid and solid discharge data were acquired throughout several cross sections of both natural channels and artificial canals of the three cutoffs, using acoustic Doppler current profiler (ADCP) technology, in order to investigate the distribution of the flow and sediment and its impact on the hydrosedimentary processes in each channelized reach and adjacent former meander. Therefore, the results obtained during the 2006 flood were referred to a long-term evolution (1970-2006), analysed by GIS techniques.

  7. 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. PMID:26524454

  8. 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.

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

    PubMed

    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

  10. 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

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

    PubMed

    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

  12. Contrasted enzymatic cocktails reveal the importance of cellulases and hemicellulases activity ratios for the hydrolysis of cellulose in presence of xylans.

    PubMed

    Dondelinger, Eve; Aubry, Nathalie; Ben Chaabane, Fadhel; Cohen, Céline; Tayeb, Jean; Rémond, Caroline

    2016-03-01

    Various enzymatic cocktails were produced from two Trichoderma reesei strains, a cellulase hyperproducer strain and a strain with β-glucosidase activity overexpression. By using various carbon sources (lactose, glucose, xylose, hemicellulosic hydrolysate) for strains growth, contrasted enzymatic activities were obtained. The enzymatic cocktails presented various levels of efficiency for the hydrolysis of cellulose Avicel into glucose, in presence of xylans, or not. These latter were also hydrolyzed with different extents according to cocktails. The most efficient cocktails (TR1 and TR3) on Avicel were richer in filter paper activity (FPU) and presented a low ratio FPU/β-glucosidase activity. Cocktails TR2 and TR5 which were produced on the higher amount of hemicellulosic hydrolysate, possess both high xylanase and β-xylosidase activities, and were the most efficient for xylans hydrolysis. When hydrolysis of Avicel was conducted in presence of xylans, a decrease of glucose release occurred for all cocktails compared to hydrolysis of Avicel alone. Mixing TR1 and TR5 cocktails with two different ratios of proteins (1/1 and 1/4) resulted in a gain of efficiency for glucose release during hydrolysis of Avicel in presence of xylans compared to TR5 alone. Our results demonstrate the importance of combining hemicellulase and cellulase activities to improve the yields of glucose release from Avicel in presence of xylans. In this context, strategies involving enzymes production with carbon sources comprising mixed C5 and C6 sugars or combining different cocktails produced on C5 or on C6 sugars are of interest for processes developed in the context of lignocellulosic biorefinery. PMID:27001439

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

    PubMed Central

    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. PMID:26656497

  14. Distinct deformational history of two contrasting tectonic domains in the Chinese Altai: Their significance in understanding accretionary orogenic process

    NASA Astrophysics Data System (ADS)

    Zhang, Jian; Sun, Min; Schulmann, Karel; Zhao, Guochun; Wu, Qihang; Jiang, Yingde; Guy, Alexandra; Wang, Yuejun

    2015-04-01

    The Chinese Altai, a key component of the western Central Asian Orogenic Belt, is considered to be formed through multiple accretions of different terranes. However, the deformational histories of each terrane (tectonic domain), i.e. structural records before and after the accretion, are rarely studied, which has hindered our understanding of the accretionary processes. To fill the gap, a systematic macro- and microscopic structural analysis was carried out on two contrasting litho-tectonic units, i.e. the early Paleozoic low-grade Alegedayi Ophiolitic Complex (AOC) juxtaposed to the high grade Tarlang Granitic Massif (TGM). Selected rock samples were analyzed using zircon U-Pb isotopic dating to constrain the timing of polyphase deformation. Our structural and geochronological data suggest that the two litho-tectonic units were initially detached and located in different crustal levels and experienced distinct phases of deformation under contrasting P-T conditions. They were mutually accreted with each other in the early Devonian and jointly underwent a WNW-ESE-directed shortening deformational event (D1) at ∼390 Ma. The change of tectonic regime was further enhanced by a subsequent NNE-SSW-directed shortening deformation (D2) after ∼ 380 Ma. The shortening process ended before the crustal-scale sinistral strike-slip shearing deformation along the Erqis fault zone at 290 - 240 Ma. Results of this study provide solid field-based evidence for a model that the Chinese Altai initially underwent a nearly E-W-oriented subduction-accretional event in the middle Paleozoic, before it was reoriented to a nearly N-S-oriented convergence.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. An acido-triggered reversible luminescent and nonlinear optical switch based on a substituted styrylpyridine: EFISH measurements as an unusual method to reveal a protonation-deprotonation NLO contrast.

    PubMed

    Cariati, Elena; Dragonetti, Claudia; Lucenti, Elena; Nisic, Filippo; Righetto, Stefania; Roberto, Dominique; Tordin, Elisa

    2014-02-14

    Diphenyl-(4-{2-[4-(2-pyridin-4-yl-vinyl)-phenyl]-vinyl}-phenyl)-amine (DPVPA) constitutes a novel acido-triggered reversible luminescent and nonlinear optical switch. Remarkably, for the first time the Electric-Field Induced Second Harmonic generation (EFISH) technique is used to reveal a protonation-deprotonation NLO contrast.

  20. 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. PMID:24122158

  1. Using regression to measure holistic face processing reveals a strong link with face recognition ability.

    PubMed

    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 variance. Regressing, rather than subtracting, a control condition from a condition of interest corrects this validity problem by statistically removing all control condition variance, thereby producing a specific measure that is uncorrelated with the control measure. Using 43 participants, we measured the relationships amongst the Cambridge Face Memory Test (CFMT) and two holistic processing measures, the composite task (CT) and the part-whole task (PW). For the holistic processing measures (CT and PW), we contrasted the results for regressing vs. subtracting the control conditions (parts for PW; misaligned congruency effect for CT) from the conditions of interest (wholes for PW; aligned congruency effect for CT). The regression-based holistic processing measures correlated with each other and with CFMT, supporting the idea of a unitary holistic processing mechanism that is involved in skilled face recognition. Subtraction scores yielded weaker correlations, especially for the PW. Together, the regression-based holistic processing measures predicted more than twice the amount of variance in CFMT (R(2)=.21) than their respective subtraction measures (R(2)=.10). We conclude that holistic processing is robustly linked to skilled face recognition. In addition to confirming this theoretically significant link, these results provide a case in point for the inappropriateness of subtraction scores when requiring a specific individual differences measure that removes the variance of a control task.

  2. 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. PMID:26160662

  3. 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.

  4. 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

  5. Spatial frequency filtered images reveal differences between masked and unmasked processing of emotional information.

    PubMed

    Rohr, Michaela; Wentura, Dirk

    2014-10-01

    High and low spatial frequency information has been shown to contribute differently to the processing of emotional information. In three priming studies using spatial frequency filtered emotional face primes, emotional face targets, and an emotion categorization task, we investigated this issue further. Differences in the pattern of results between short and masked, and short and long unmasked presentation conditions emerged. Given long and unmasked prime presentation, high and low frequency primes triggered emotion-specific priming effects. Given brief and masked prime presentation in Experiment 2, we found a dissociation: High frequency primes caused a valence priming effect, whereas low frequency primes yielded a differentiation between low and high arousing information within the negative domain. Brief and unmasked prime presentation in Experiment 3 revealed that subliminal processing of primes was responsible for the pattern observed in Experiment 2. The implications of these findings for theories of early emotional information processing are discussed. PMID:25286124

  6. 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.

  7. Event related potentials reveal differences between morphological (prefixes) and phonological (syllables) processing of words.

    PubMed

    Domínguez, Alberto; Alija, Maira; Cuetos, Fernando; de Vega, Mauel

    2006-11-01

    Behavioral measures in visual priming tasks show opposite effects for syllables and morphemes, which indicate that they are processed by two independent systems. We used event related potentials (ERPs) to explore two priming situations in Spanish: prefix related words (reacción-REFORMA [reaction-reform]), in which prime and target words shared a first syllable that was also a prefix, and syllable related words (regalo-REFORMA [gift-reform.]), in which the shared first syllable was a pseudoprefix in the prime word. Prefix related pairs, unlike syllable related pairs, evoked a very early positivity in reaction to the target (at 150-250ms window), suggesting that the prefix information is immediately available, at a prelexical stage. By contrast, syllable related pairs showed a larger N400 effect. This late negativity may be caused by lateral inhibition among lexical candidates activated in the lexicon by the prime's first syllable. PMID:16996688

  8. 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

  9. Event related potentials reveal differences between morphological (prefixes) and phonological (syllables) processing of words.

    PubMed

    Domínguez, Alberto; Alija, Maira; Cuetos, Fernando; de Vega, Mauel

    2006-11-01

    Behavioral measures in visual priming tasks show opposite effects for syllables and morphemes, which indicate that they are processed by two independent systems. We used event related potentials (ERPs) to explore two priming situations in Spanish: prefix related words (reacción-REFORMA [reaction-reform]), in which prime and target words shared a first syllable that was also a prefix, and syllable related words (regalo-REFORMA [gift-reform.]), in which the shared first syllable was a pseudoprefix in the prime word. Prefix related pairs, unlike syllable related pairs, evoked a very early positivity in reaction to the target (at 150-250ms window), suggesting that the prefix information is immediately available, at a prelexical stage. By contrast, syllable related pairs showed a larger N400 effect. This late negativity may be caused by lateral inhibition among lexical candidates activated in the lexicon by the prime's first syllable.

  10. Acting without seeing: Eye movements reveal visual processing without awareness Miriam Spering & Marisa Carrasco

    PubMed Central

    Spering, Miriam; Carrasco, Marisa

    2015-01-01

    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. We review converging evidence revealing dissociations between the contents of perceptual awareness and different types of eye movements. 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. PMID:25765322

  11. 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.

  12. Target consolidation under high temporal processing demands as revealed by MEG.

    PubMed

    Kessler, Klaus; Schmitz, Frank; Gross, Joachim; Hommel, Bernhard; Shapiro, Kimron; Schnitzler, Alfons

    2005-07-15

    We investigated the nature of resource limitations during visual target processing by imposing high temporal processing demands on the cognitive system. This was achieved by embedding target stimuli into rapid-serial-visual-presentation-streams (RSVP). In RSVP streams, it is difficult to report the second of two targets (T2) if the second follows the first (T1) within 500 ms. This effect is known as the attentional blink (AB). For the AB to occur, it is essential that T1 is followed by a mask, as without such a stimulus, the AB is significantly attenuated. Usually, it is thought that T1 processing is delayed by the mask, which in turn delays T2 processing, increasing the likelihood for T2 failures (AB). Predictions regarding amplitudes and latencies of cortical responses (M300, the magnetic counterpart to the P300) to targets were tested by investigating the neurophysiological effects of the post-T1 item (mask) by means of magnetoencephalography (MEG). Cortical M300 responses to targets drawn from prefrontal sources--areas associated with working memory--revealed accelerated T1 yet delayed T2 processing with an intervening mask. The explanation we are proposing assumes that "protection" of ongoing T1 processing necessitated by the occurrence of the mask suppresses other activation patterns, which boosts T1 yet also hinders further processing. Our data shed light on the mechanisms employed by the human brain for ensuring visual target processing under high temporal processing demands, which is hypothesized to occur at the expense of subsequently presented information.

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

    PubMed

    Novák, Martin; Mitchell, Myron J; Jacková, Iva; Buzek, Frantisek; Schweigstillová, Jana; Erbanová, Lucie; Prikryl, Richard; Fottová, Daniela

    2007-02-01

    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 delta18O-SO4 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(-1) yr(-1), respectively). The second catchment, Na Lizu, was 10 times less polluted. In both catchments, delta18O-SO4 decreased in the following order: open-area precipitation > throughfall > runoff. The delta18O-SO4 values of throughfall exhibited a seasonal pattern at both sites, with maxima in summer and minima in winter. This seasonal pattern paralleled delta18O-H2O values, which were offset by -18 per thousand. Sulfate in throughfall was predominantly formed by heterogeneous (aqueous) oxidation of SO2. Wet-deposited sulfate in an open area did not show systematic delta18O-SO4 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 18O-rich sulfate was not detected, which contrasts with North American industrial sites.

  14. Functional group composition of organic aerosol from combustion emissions and secondary processes at two contrasted urban environments

    NASA Astrophysics Data System (ADS)

    El Haddad, Imad; Marchand, Nicolas; D'Anna, Barbara; Jaffrezo, Jean Luc; Wortham, Henri

    2013-08-01

    The quantification of major functional groups in atmospheric organic aerosol (OA) provides a constraint on the types of compounds emitted and formed in atmospheric conditions. This paper presents functional group composition of organic aerosol from two contrasted urban environments: Marseille during summer and Grenoble during winter. Functional groups were determined using a tandem mass spectrometry approach, enabling the quantification of carboxylic (RCOOH), carbonyl (RCOR‧), and nitro (RNO2) functional groups. Using a multiple regression analysis, absolute concentrations of functional groups were combined with those of organic carbon derived from different sources in order to infer the functional group contents of different organic aerosol fractions. These fractions include fossil fuel combustion emissions, biomass burning emissions and secondary organic aerosol (SOA). Results clearly highlight the differences between functional group fingerprints of primary and secondary OA fractions. OA emitted from primary sources is found to be moderately functionalized, as about 20 carbons per 1000 bear one of the functional groups determined here, whereas SOA is much more functionalized, as in average 94 carbons per 1000 bear a functional group under study. Aging processes appear to increase both RCOOH and RCOR‧ functional group contents by nearly one order of magnitude. Conversely, RNO2 content is found to decrease with photochemical processes. Finally, our results also suggest that other functional groups significantly contribute to biomass smoke and SOA. In particular, for SOA, the overall oxygen content, assessed using aerosol mass spectrometer measurements by an O:C ratio of 0.63, is significantly higher than the apparent O:C* ratio of 0.17 estimated based on functional groups measured here. A thorough examination of our data suggests that this remaining unexplained oxygen content can be most probably assigned to alcohol (ROH), organic peroxides (ROOH

  15. Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations

    PubMed Central

    Badro, Danielle A.; Youhanna, Sonia C.; Salloum, Angélique; Ghassibe-Sabbagh, Michella; Johnsrud, Brian; Khazen, Georges; Matisoo-Smith, Elizabeth; Soria-Hernanz, David F.; Wells, R. Spencer; Tyler-Smith, Chris; Platt, Daniel E.; Zalloua, Pierre A.

    2013-01-01

    The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations. PMID:23382925

  16. In-gel imaging of RNA processing using Broccoli reveals optimal aptamer expression strategies

    PubMed Central

    Filonov, Grigory S.; Kam, Christina W.; Song, Wenjiao; Jaffrey, Samie R.

    2015-01-01

    SUMMARY RNA aptamers can be expressed in cells to influence and image cellular processes. Aptamer folding is maintained by inserting the aptamers into highly structured RNA scaffolds. Here we show that commonly used RNA scaffolds exhibit unexpected instability and cleavage in bacterial and mammalian cells. Using an in-gel staining approach for rapid and simple detection of Spinach- or Broccoli-tagged RNAs in cells, we monitored the processing of RNAs tagged with scaffolded aptamers, revealing endonucleolytic cleavage, RNA instability and poor expression. We reengineered a natural three-way junction structure to generate an alternative scaffold that enables stable aptamer expression in cells. This scaffold was used to create cassettes containing up to four Broccoli units, markedly enhancing the brightness of mammalian cells expressing cassette-tagged RNAs. These experiments describe methods for screening RNA cleavage events in cells, and identify cell-compatible scaffolds that enable efficient tagging of RNAs with aptamers for cellular expression. PMID:26000751

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

    PubMed

    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

  18. 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

  19. Optical Brain Imaging Reveals General Auditory and Language-Specific Processing in Early Infant Development

    PubMed Central

    Minagawa-Kawai, Yasuyo; van der Lely, Heather; Ramus, Franck; Sato, Yutaka; Mazuka, Reiko; Dupoux, Emmanuel

    2011-01-01

    This study uses near-infrared spectroscopy in young infants in order to elucidate the nature of functional cerebral processing for speech. Previous imaging studies of infants’ speech perception revealed left-lateralized responses to native language. However, it is unclear if these activations were due to language per se rather than to some low-level acoustic correlate of spoken language. Here we compare native (L1) and non-native (L2) languages with 3 different nonspeech conditions including emotional voices, monkey calls, and phase scrambled sounds that provide more stringent controls. Hemodynamic responses to these stimuli were measured in the temporal areas of Japanese 4 month-olds. The results show clear left-lateralized responses to speech, prominently to L1, as opposed to various activation patterns in the nonspeech conditions. Furthermore, implementing a new analysis method designed for infants, we discovered a slower hemodynamic time course in awake infants. Our results are largely explained by signal-driven auditory processing. However, stronger activations to L1 than to L2 indicate a language-specific neural factor that modulates these responses. This study is the first to discover a significantly higher sensitivity to L1 in 4 month-olds and reveals a neural precursor of the functional specialization for the higher cognitive network. PMID:20497946

  20. 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

  1. 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)…

  2. 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

  3. Revealing Dynamic Processes of Materials in Liquids Using Liquid Cell Transmission Electron Microscopy

    PubMed Central

    Niu, Kai-Yang; Liao, Hong-Gang; Zheng, Haimei

    2012-01-01

    The recent development for in situ transmission electron microscopy, which allows imaging through liquids with high spatial resolution, has attracted significant interests across the research fields of materials science, physics, chemistry and biology. The key enabling technology is a liquid cell. We fabricate liquid cells with thin viewing windows through a sequential microfabrication process, including silicon nitride membrane deposition, photolithographic patterning, wafer etching, cell bonding, etc. A liquid cell with the dimensions of a regular TEM grid can fit in any standard TEM sample holder. About 100 nanoliters reaction solution is loaded into the reservoirs and about 30 picoliters liquid is drawn into the viewing windows by capillary force. Subsequently, the cell is sealed and loaded into a microscope for in situ imaging. Inside the TEM, the electron beam goes through the thin liquid layer sandwiched between two silicon nitride membranes. Dynamic processes of nanoparticles in liquids, such as nucleation and growth of nanocrystals, diffusion and assembly of nanoparticles, etc., have been imaged in real time with sub-nanometer resolution. We have also applied this method to other research areas, e.g., imaging proteins in water. Liquid cell TEM is poised to play a major role in revealing dynamic processes of materials in their working environments. It may also bring high impact in the study of biological processes in their native environment. PMID:23287885

  4. Event-related potentials reveal early activation of syntax information in Chinese verb processing.

    PubMed

    Deng, Yuan; Wu, Qiuyan; Wang, Jin; Feng, Liping; Xiao, Qing

    2016-09-19

    By taking advantage of the semantic-syntactic characteristics of Chinese verbs, the current study examined the brain activity of automatic activation of syntactic features at the single word level. Both syntactic (transitivity) and semantic (integrity) features of the verb were manipulated. Event-related potentials were measured while subjects performed lexical decision tasks on visually presented verbs at the single word level. The results showed that there was a significant transitivity effect in both lateral and midline areas for the 150-200ms time window (N200 effect), indicating the retrieval of the syntactic feature. There was also a significant syntactic-semantic interaction at the late stage of verb processing (N400 effect) in the midline central-parietal region, reflecting syntactic influences on semantic processing. These findings suggest that transitivity is an integral part of the mental representation of Chinese verbs and such information can be retrieved at the early stage of single verb processing and can influence subsequent semantic integration. These results also reveal the special features of Chinese language processing. PMID:27466021

  5. Event-related potentials reveal early activation of syntax information in Chinese verb processing.

    PubMed

    Deng, Yuan; Wu, Qiuyan; Wang, Jin; Feng, Liping; Xiao, Qing

    2016-09-19

    By taking advantage of the semantic-syntactic characteristics of Chinese verbs, the current study examined the brain activity of automatic activation of syntactic features at the single word level. Both syntactic (transitivity) and semantic (integrity) features of the verb were manipulated. Event-related potentials were measured while subjects performed lexical decision tasks on visually presented verbs at the single word level. The results showed that there was a significant transitivity effect in both lateral and midline areas for the 150-200ms time window (N200 effect), indicating the retrieval of the syntactic feature. There was also a significant syntactic-semantic interaction at the late stage of verb processing (N400 effect) in the midline central-parietal region, reflecting syntactic influences on semantic processing. These findings suggest that transitivity is an integral part of the mental representation of Chinese verbs and such information can be retrieved at the early stage of single verb processing and can influence subsequent semantic integration. These results also reveal the special features of Chinese language processing.

  6. Flexibility and Stability in Sensory Processing Revealed Using Visual-to-Auditory Sensory Substitution

    PubMed Central

    Hertz, Uri; Amedi, Amir

    2015-01-01

    The classical view of sensory processing involves independent processing in sensory cortices and multisensory integration in associative areas. This hierarchical structure has been challenged by evidence of multisensory responses in sensory areas, and dynamic weighting of sensory inputs in associative areas, thus far reported independently. Here, we used a visual-to-auditory sensory substitution algorithm (SSA) to manipulate the information conveyed by sensory inputs while keeping the stimuli intact. During scan sessions before and after SSA learning, subjects were presented with visual images and auditory soundscapes. The findings reveal 2 dynamic processes. First, crossmodal attenuation of sensory cortices changed direction after SSA learning from visual attenuations of the auditory cortex to auditory attenuations of the visual cortex. Secondly, associative areas changed their sensory response profile from strongest response for visual to that for auditory. The interaction between these phenomena may play an important role in multisensory processing. Consistent features were also found in the sensory dominance in sensory areas and audiovisual convergence in associative area Middle Temporal Gyrus. These 2 factors allow for both stability and a fast, dynamic tuning of the system when required. PMID:24518756

  7. Eye-movements and ERPs reveal the time course of processing negation and remitting counterfactual worlds.

    PubMed

    Ferguson, Heather J; Sanford, Anthony J; Leuthold, Hartmut

    2008-10-21

    The ability to update our current knowledge using contextual information is a vital process during every-day language comprehension. To understand a negated statement, readers are required to cancel real-world expectations, but are not explicitly provided with an alternative model. Thus, the question of how and when a negative context influences interpretation of later events arises. We report one eye-movement study (Exp. 1) and one ERP study (Exp. 2) investigating the effects of negation on discourse processing. Prior context depicted a real-world (RW), or negated-world (NW), while the second sentence was manipulated to create RW anomalous continuations, where events included a violation of RW knowledge, and RW-congruent continuations, where the events described were congruent with RW knowledge. Results from Experiment 1 showed that the negated discourse context did not influence initial processing of the target sentence, as reflected in participants' eye-movement behaviour. Similarly, Experiment 2 revealed that the typical N400 effect to semantic violations has not been reversed by introducing a negated-world context. However, in later processing, Experiment 1 demonstrated that the negated-world context is eventually incorporated into the representation of the sentence meaning. Thus, we suggest that discourse does not always have an immediate effect on language comprehension and discuss the results in terms of a variety of accounts of representing negation.

  8. 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.

  9. Water distributions in PS-b-P(S-g-PEO) block grafted copolymer system in aqueous solutions revealed by contrast variation SANS study

    SciTech Connect

    Chen, Wei-Ren; Hong, Kunlun; Li, Xin; Liu, Emily; Liu, Yun; Shew, Chwen-Yang; Smith, Gregory Scott

    2010-01-01

    In this report, we present a contrast variation small angle neutron scattering (SANS) study of PS-b-P(S-g-PEO) block graft copolymers in aqueous media at a concentration of 10 mg/ml. Through varying the solvent D2O/H2O ratio, the scattering contributions from the water molecules and the micellar constituent components can be determined. Based on the commonly used core-shell model, a theoretical coherent scattering cross section incorporating the effect of water penetration is developed and used to analyze the SANS I(Q), we have successfully quantified the micellar structure and the number of - water molecules associated with the core and corona. We have found that the overall micellar hydration level increase with the increase in the molecular weight of hydrophilic PEO side chains. This study provides key information in understanding solvent distributions within self-assembled amphiphilic block grafted copolymers.

  10. Water distributions in polystyrene-block-poly[styrene-g-poly(ethylene oxide)] block grafted copolymer system in aqueous solutions revealed by contrast variation small angle neutron scattering study

    NASA Astrophysics Data System (ADS)

    Li, Xin; Hong, Kunlun; Liu, Yun; Shew, Chwen-Yang; Liu, Emily; Herwig, Kenneth W.; Smith, Gregory S.; Zhao, Junpeng; Zhang, Guangzhao; Pispas, Stergios; Chen, Wei-Ren

    2010-10-01

    We develop an experimental approach to analyze the water distribution around a core-shell micelle formed by polystyrene-block-poly[styrene-g-poly(ethylene oxide (PEO)] block copolymers in aqueous media at a fixed polymeric concentration of 10 mg/ml through contrast variation small angle neutron scattering (SANS) study. Through varying the D2O/H2O ratio, the scattering contributions from the water molecules and the micellar constituent components can be determined. Based on the commonly used core-shell model, a theoretical coherent scattering cross section incorporating the effect of water penetration is developed and used to analyze the SANS I(Q ). We have successfully quantified the intramicellar water distribution and found that the overall micellar hydration level increases with the increase in the molecular weight of hydrophilic PEO side chains. Our work presents a practical experimental means for evaluating the intramacromolecular solvent distributions of general soft matter systems.

  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 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

  15. 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. PMID:26261317

  16. Automatic processing of grammar in the human brain as revealed by the mismatch negativity.

    PubMed

    Pulvermüller, Friedemann; Shtyrov, Yury

    2003-09-01

    The Mismatch Negativity (MMN), a neurophysiological indicator of cognitive processing, was used to investigate grammatical processes in the absence of focused attention to language. Subjects instructed to watch a silent video film and to ignore speech stimuli heard grammatical and ungrammatical spoken word strings that were physically identical up to a divergence point where they differed between each other by a minimal acoustic event, the presence or the absence of a final -s sound. The sentence we come was presented as a rare deviant stimulus against the background of frequently occurring ungrammatical strings, and, in a different experiment, the ungrammatical string *we comes was the deviant in the reverse design. To control for effects related to differences between the critical words, come and comes, control conditions were used in which the same words were presented out of linguistic context. At 100-150 ms after the divergence point, the ungrammatical deviant stimulus elicited a larger MMN than the correct sentence at left-anterior recording sites. This difference was not seen under the out-of-context conditions. In the time range 100-400 ms after stimulus divergence, a spatiotemporal pattern of grammatically related effects was documented by statistically significant interactions of the word and context variables. Minimum-Norm Current Estimates of the cortical sources of the grammaticality effects revealed a main source in the left frontal cortex. We use a neurobiological model of serial order processing to provide a tentative explanation for the data. PMID:14527578

  17. 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.

  18. 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.

  19. Microtopography: What does it reveal about landscape structure, organization and processes?

    NASA Astrophysics Data System (ADS)

    Kumar, Praveen; Goodwell, Allison; Le, Phong; Dutta, Debsunder

    2013-04-01

    High resolution Lidar topography and Airborne Visible/Infrared Imaging Sprectrometer (AVIRIS) remote sensing data are becoming increasingly available over large regions of the Earth's surface. These data sets can be linked to reveal processes and landscape features that cannot be detected at lower resolutions. In May 2011, the Bird's Point New Madrid Floodway in southeastern Missouri was intentionally breached during extreme Mississippi and Ohio River flooding. Pre- and post-flood Lidar and post-flood AVIRIS data enable study of flood geomorphic impacts and the biogeochemical state of the floodplain. Differential Lidar quantifies erosion and deposition, while empirical, statistical and data mining techniques are employed to investigate soil properties from AVIRIS. Vegetation, soil properties, and flood exposure are linked to observed geomorphic impacts to indicate landscape vulnerability to flood events. Additionally, we develop an approach to characterize and link the spatial distribution of microtopographic depressions using the same high resolution Lidar data sets. Topographical floodplain legacies such as former meander scar ridges correlate to soil characteristics and vegetation within the floodplain, and also dictate much of the geomorphic impacts of the levee breach and subsequent inundation. At the location of one extremely eroded meander scar ridge, AVIRIS data shows a high clay content, increased iron concentration and decreased soil organic matter, all in accordance with the erosion of silty and sandy topsoil. This study highlights approaches in which high-resolution data sets can be linked to reveal important landscape properties and analyze impacts of extreme events and long-term legacy effects.

  20. 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

  1. Contrasting strategies used by lichen microalgae to cope with desiccation-rehydration stress revealed by metabolite profiling and cell wall analysis.

    PubMed

    Centeno, Danilo C; Hell, Aline F; Braga, Marcia R; Del Campo, Eva M; Casano, Leonardo M

    2016-05-01

    Most lichens in general, and their phycobionts in particular, are desiccation tolerant, but their mechanisms of desiccation tolerance (DT) remain obscure. The physiological responses and cell wall features of two putatively contrasting lichen-forming microalgae, Trebouxia sp. TR9 (TR9), isolated from Ramalina farinacea (adapted to frequent desiccation-rehydration cycles), and Coccomyxa solorina-saccatae (Csol), obtained from Solorina saccata (growing in usually humid limestone crevices, subjected to seasonal dry periods) was characterized. Microalgal cultures were desiccated under 25%-30% RH and then rehydrated. Under these conditions, RWC and ψw decreased faster and simultaneously during dehydration in Csol, whereas TR9 maintained its ψw until 70% RWC. The metabolic profile indicated that polyols played a key role in DT of both microalgae. However, TR9 constitutively accumulated higher amounts of polyols, whereas Csol induced the polyol synthesis under desiccation-rehydration. Csol also accumulated ascorbic acid, while TR9 synthesized protective raffinose-family oligosaccharides (RFOs) and increased its content of phenolics. Additionally, TR9 exhibited thicker and qualitatively different cell wall and extracellular polymeric layer compared with Csol, indicating higher water retention capability. The findings were consistent with the notion that lichen microalgae would have evolved distinct strategies to cope with desiccation-rehydration stress in correspondence with the water regime of their respective habitats. PMID:26914009

  2. 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.

  3. Structure-function relationship of biological gels revealed by multiple-particle tracking and differential interference contrast microscopy: The case of human lamin networks

    NASA Astrophysics Data System (ADS)

    Panorchan, Porntula; Wirtz, Denis; Tseng, Yiider

    2004-10-01

    Lamin B1 filaments organize into a thin dense meshwork underlying the nucleoplasmic side of the nuclear envelope. Recent experiments in vivo suggest that lamin B1 plays a key structural role in the nuclear envelope, but the intrinsic mechanical properties of lamin B1 networks remain unknown. To assess the potential mechanical contribution of lamin B1 in maintaining the integrity and providing structural support to the nucleus, we measured the micromechanical properties and examined the ultrastructural distribution of lamin B1 networks in vitro using particle tracking methods and differential interference contrast (DIC) microscopy. We exploit various surface chemistries of the probe microspheres (carboxylated, polyethylene glycol-coated, and amine-modified) to differentiate lamin-rich from lamin-poor regions and to rigorously extract local viscoelastic moduli from the mean-squared displacements of noninteracting particles. Our results show that human lamin B1 can, even in the absence of auxiliary proteins, form stiff and yet extremely porous networks that are well suited to provide structural strength to the nuclear lamina. Combining DIC microscopy and particle tracking allows us to relate directly the local organization of a material to its local mechanical properties, a general methodology that can be extended to living cells.

  4. 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.

  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. 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…

  7. 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

  8. 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.

  9. 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.

  10. 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.

  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. 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

    2015-01-01

    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

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

    PubMed Central

    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. PMID:27023442

  14. 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

  15. Preserved reward outcome processing in ASD as revealed by event-related potentials

    PubMed Central

    2012-01-01

    Background Problems with reward system function have been posited as a primary difficulty in autism spectrum disorders. The current study examined an electrophysiological marker of feedback monitoring, the feedback-related negativity (FRN), during a monetary reward task. The study advanced prior understanding by focusing exclusively on a developmental sample, applying rigorous diagnostic characterization and introducing an experimental paradigm providing more subtly different feedback valence (reward versus non-reward instead of reward versus loss). Methods Twenty-six children with autism spectrum disorder and 28 typically developing peers matched on age and full-scale IQ played a guessing game resulting in monetary gain (“win”) or neutral outcome (“draw”). ERP components marking early visual processing (N1, P2) and feedback appraisal (FRN) were contrasted between groups in each condition, and their relationships to behavioral measures of social function and dysfunction, social anxiety, and autism symptomatology were explored. Results FRN was observed on draw trials relative to win trials. Consistent with prior research, children with ASD exhibited a FRN to suboptimal outcomes that was comparable to typical peers. ERP parameters were unrelated to behavioral measures. Conclusions Results of the current study indicate typical patterns of feedback monitoring in the context of monetary reward in ASD. The study extends prior findings of normative feedback monitoring to a sample composed exclusively of children and demonstrates that, as in typical development, individuals with autism exhibit a FRN to suboptimal outcomes, irrespective of neutral or negative valence. Results do not support a pervasive problem with reward system function in ASD, instead suggesting any dysfunction lies in more specific domains, such as social perception, or in response to particular feedback-monitoring contexts, such as self-evaluation of one’s errors. PMID:22958616

  16. Landscape structure, organization and processes revealed through micro-topographic features

    NASA Astrophysics Data System (ADS)

    Kumar, Praveen; Le, Phong; Dutta, Debsunder; Goodwell, Allison

    2014-05-01

    High-resolution Lidar topography and Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) remote sensing data are becoming increasingly available over large regions of the Earth's surface. These data sets can be linked to reveal processes and landscape features that cannot be detected at lower resolutions. In May 2011, the Bird's Point New Madrid Floodway in southeastern Missouri was intentionally breached during extreme Mississippi and Ohio River flooding. Pre- and post-flood Lidar and post-flood AVIRIS data enable study of flood geomorphic impacts and the biogeochemical state of the floodplain. Differential Lidar quantifies erosion and deposition, while empirical, statistical and data mining techniques are employed to investigate soil properties from AVIRIS. Vegetation, soil properties, and flood exposure are linked to observed geomorphic impacts that indicate landscape vulnerability to flood events. We find that the distribution of micro-topographic depressions in the landscape, such as surface area, volume storage, and the distance to the nearest neighbor follows a power scaling law. Additionally, we develop an approach to characterize and quantify the spatial correlations of different surface textural properties and chemical constituents with the distribution of depressions using the same high resolution Lidar and AVIRIS data sets. Topographical floodplain legacies such as former meander scar ridges correlate to soil characteristics and vegetation within the floodplain, and also dictate much of the geomorphic impacts of the levee breach and subsequent inundation. This study highlights approaches in which high-resolution data sets can be linked to reveal important landscape properties and analyze impacts of extreme events and long-term legacy effects.

  17. Dunes on Titan: A major landform revealing atmospheric and surface processes

    NASA Astrophysics Data System (ADS)

    Radebaugh, Jani; Lorenz, Ralph; Arnold, Karl; Savage, Christopher; Williams, Brigitte

    The surface of Saturn’s moon Titan is covered in features that herald an active atmosphere and perhaps interior, such as dunes, rivers, lakes, mountain chains, and possible cryovolcanoes. Examining the geomorphology of these features helps us approach an understanding of the processes that are occurring or have occurred in the atmosphere and subsurface. A major landform on Titan is dunes, composed of organic sands ultimately derived from upper atmospheric processing of methane, subsequently perhaps eroded from organic sedimentary layers by methane rainfall and fluvial flow. Dunes fill vast fields, termed sand seas, similar to those observed in the Sahara, Namibia, and the Arabian peninsula. The equatorial region of Titan contains five separate sand seas as observed by the Cassini Synthetic Aperture Radar (SAR), Imaging Science Subsystem (ISS) and Visual and Infrared Mapping Spectrometer (VIMS) instruments. Together these sand seas cover 14 percent of the surface, totaling 12 million km2, and each have areas on the scale of the Saharan Great Sand Sea. They adjoin each other through sediment pathways around landmasses, and these large-scale connections as well as individual dune interactions with topography indicate a general transport of sediment from west to east. Measurements of dune height, width and spacing in Cassini SAR images reveal all of Titan’s thousands of linear dunes are of the same population. This indicates there was general uniformity in the wind and sediment supply conditions that led to the current dune forms. Variations in the parametric values result from deviations from these conditions, in some locations where elevated terrains have deflected winds. Dunes and sand seas are among the stratigraphically youngest features on Titan, showing little evidence of being affected by impact cratering or fluvial flow. However, individual dunes may be relatively stable, as the reorganization time scale for these features on Earth can be tens to hundreds

  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 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

  19. Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

    PubMed

    Gladden; Ferguson; Friesen; Clayton

    1999-03-01

    Beluga whales (Delphinapterus leucas) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples (n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations. PMID:10199005

  20. Contrast Materials

    MedlinePlus

    ... or other reactions to contrast materials are rare, radiology departments are well-equipped to deal with them. ... is given. However, both the American College of Radiology (ACR) and the European Society of Urogenital Radiology ...

  1. Can pH and electrical conductivity monitoring reveal spatial and temporal patterns in wetland geochemical processes?

    NASA Astrophysics Data System (ADS)

    Gerla, P. J.

    2013-01-01

    Carbonate reactions and equilibria play a dominant role in the biogeochemical function of many wetlands. The US Geological Survey PHREEQC computer code was used to model geochemical reactions that may be typical for wetlands with water budgets characterized by: (a) input dominated by direct precipitation, (b) interaction with groundwater, (c) variable degrees of reaction with organic carbon, and (d) different rates of evapotranspiration. Rainfall with a typical composition was progressively reacted with calcite and organic carbon at various rates and proportions using PHREEQC. Contrasting patterns of the results suggest that basic water quality data collected in the field can reveal differences in the geochemical processes in wetlands. Given a temporal record, these can signal subtle changes in surrounding land cover and use. To demonstrate this, temperature, pH, and electrical conductivity (EC) were monitored for three years in five large wetlands comprising 48 sample sites in northwest Minnesota. EC and pH of samples ranged greatly - from 23 to 1300 μS cm-1 and 5.5 to 9. The largest range in pH was observed in small beach ridge wetlands, where two clusters are apparent: (1) low EC and a wide range of pH and (2) higher pH and EC. Large marshes within a glacial lake - till plain have a broad range of pH and EC, but depend on the specific wetland. Outlying data typically occurred in altered or disturbed areas. The inter-annual and intra-wetland consistency of the results suggests that each wetland system hosts characteristic geochemical conditions.

  2. 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.

  3. Visualization of Neuregulin 1 ectodomain shedding reveals its local processing in vitro and in vivo

    PubMed Central

    Kamezaki, Aosa; Sato, Fuminori; Aoki, Kazuhiro; Asakawa, Kazuhide; Kawakami, Koichi; Matsuzaki, Fumio; Sehara-Fujisawa, Atsuko

    2016-01-01

    Neuregulin1 (NRG1) plays diverse developmental roles and is likely involved in several neurological disorders including schizophrenia. The transmembrane NRG1 protein is proteolytically cleaved and released as a soluble ligand for ErbB receptors. Such post-translational processing, referred to as ‘ectodomain shedding’, is thought to be crucial for NRG1 function. However, little is known regarding the regulatory mechanism of NRG1 cleavage in vivo. Here, we developed a fluorescent probe, NRG1 Cleavage Indicating SenSOR (N-CISSOR), by fusing mCherry and GFP to the extracellular and intracellular domains of NRG1, respectively. N-CISSOR mimicked the subcellular localization and biochemical properties of NRG1 including cleavage dynamics and ErbB phosphorylation in cultured cells. mCherry/GFP ratio imaging of phorbol-12-myristate-13-acetate-stimulated N-CISSOR-expressing HEK293T cells enabled to monitor rapid ectodomain shedding of NRG1 at the subcellular level. Utilizing N-CISSOR in zebrafish embryos revealed preferential axonal NRG1 ectodomain shedding in developing motor neurons, demonstrating that NRG1 ectodomain shedding is spatially regulated at the subcellular level. Thus, N-CISSOR will be a valuable tool for elucidating the spatiotemporal regulation of NRG1 ectodomain shedding, both in vitro and in vivo. PMID:27364328

  4. 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. PMID:23163969

  5. The snooze of lose: Rapid reaching reveals that losses are processed more slowly than gains.

    PubMed

    Chapman, Craig S; Gallivan, Jason P; Wong, Jeremy D; Wispinski, Nathan J; Enns, James T

    2015-08-01

    Decision making revolves around weighing potential gains and losses. Research in economic decision making has emphasized that humans exercise disproportionate caution when making explicit choices involving loss. By comparison, research in perceptual decision making has revealed a processing advantage for targets associated with potential gain, though the effects of loss have been explored less systematically. Here, we use a rapid reaching task to measure the relative sensitivity (Experiment 1) and the time course (Experiments 2 and 3) of rapid actions with regard to the reward valence and probability of targets. We show that targets linked to a high probability of gain influence actions about 100 ms earlier than targets associated with equivalent probability and value of loss. These findings are well accounted for by a model of stimulus response in which reward modulates the late, postpeak phase of the activity. We interpret our results within a neural framework of biased competition that is resolved in spatial maps of behavioral relevance. As implied by our model, all visual stimuli initially receive positive activation. Gain stimuli can build off of this initial activation when selected as a target, whereas loss stimuli have to overcome this initial activation in order to be avoided, accounting for the observed delay between valences. Our results bring clarity to the perceptual effects of losses versus gains and highlight the importance of considering the timeline of different biasing factors that influence decisions. PMID:26097977

  6. 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

  7. 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

  8. Contrasting mechanisms for CO2 absorption and regeneration processes in aqueous amine solutions: Insights from density-functional tight-binding molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nakai, Hiromi; Nishimura, Yoshifumi; Kaiho, Takeaki; Kubota, Takahito; Sato, Hiroshi

    2016-03-01

    CO2 chemical absorption and regeneration processes in aqueous amine solutions were investigated using density-functional tight-binding molecular dynamics simulations. Extensive analyses of the structural, electronic, and dynamical properties of 100 independent trajectories supported the contrasting mechanisms in the absorption and regeneration processes. In the CO2 absorption process, bicarbonate formed where the hydroxyl anion migrated through the hydrogen-bond network of water molecules, namely, by a Grotthuss-type mechanism. On the other hand, direct proton transfer from the protonated amine to the hydroxyl group of bicarbonate, which is called the ion-pair mechanism, was the key step to the release of CO2.

  9. 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.

  10. 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.

  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. 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.

  13. On the Contrastive Analysis of Features in Second Language Acquisition: Uninterpretable Gender on Past Participles in English-French Processing

    ERIC Educational Resources Information Center

    Dekydtspotter, Laurent; Renaud, Claire

    2009-01-01

    Lardiere's discussion raises important questions about the use of features in second language (L2) acquisition. This response examines predictions for processing of a feature-valuing model vs. a frequency-sensitive, associative model in explaining the acquisition of French past participle agreement. Results from a reading-time experiment support…

  14. 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.

  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

    2015-01-01

    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.

  16. 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

    2015-01-01

    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

  17. Auditory sequence processing reveals evolutionarily conserved regions of frontal cortex in macaques and humans

    PubMed Central

    Wilson, Benjamin; Kikuchi, Yukiko; Sun, Li; Hunter, David; Dick, Frederic; Smith, Kenny; Thiele, Alexander; Griffiths, Timothy D.; Marslen-Wilson, William D.; Petkov, Christopher I.

    2015-01-01

    An evolutionary account of human language as a neurobiological system must distinguish between human-unique neurocognitive processes supporting language and evolutionarily conserved, domain-general processes that can be traced back to our primate ancestors. Neuroimaging studies across species may determine whether candidate neural processes are supported by homologous, functionally conserved brain areas or by different neurobiological substrates. Here we use functional magnetic resonance imaging in Rhesus macaques and humans to examine the brain regions involved in processing the ordering relationships between auditory nonsense words in rule-based sequences. We find that key regions in the human ventral frontal and opercular cortex have functional counterparts in the monkey brain. These regions are also known to be associated with initial stages of human syntactic processing. This study raises the possibility that certain ventral frontal neural systems, which play a significant role in language function in modern humans, originally evolved to support domain-general abilities involved in sequence processing. PMID:26573340

  18. 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…

  19. EEG Theta and Alpha Responses Reveal Qualitative Differences in Processing Taxonomic versus Thematic Semantic Relationships

    ERIC Educational Resources Information Center

    Maguire, Mandy J.; Brier, Matthew R.; Ferree, Thomas C.

    2010-01-01

    Despite the importance of semantic relationships to our understanding of semantic knowledge, the nature of the neural processes underlying these abilities are not well understood. In order to investigate these processes, 20 healthy adults listened to thematically related (e.g., leash-dog), taxonomically related (e.g., horse-dog), or unrelated…

  20. 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…

  1. 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

  2. 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...

  3. Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

    PubMed

    Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

    2016-10-20

    The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

  4. Inversion effects reveal dissociations in facial expression of emotion, gender, and object processing

    PubMed Central

    Pallett, Pamela M.; Meng, Ming

    2015-01-01

    To distinguish between high-level visual processing mechanisms, the degree to which holistic processing is involved in facial identity, facial expression, and object perception is often examined through measuring inversion effects. However, participants may be biased by different experimental paradigms to use more or less holistic processing. Here we take a novel psychophysical approach to directly compare human face and object processing in the same experiment, with face processing broken into two categories: variant properties and invariant properties as they were tested using facial expressions of emotion and gender, respectively. Specifically, participants completed two different perceptual discrimination tasks. One involved making judgments of stimulus similarity and the other tested the ability to detect differences between stimuli. Each task was completed for both upright and inverted stimuli. Results show significant inversion effects for the detection of differences in facial expressions of emotion and gender, but not for objects. More interestingly, participants exhibited a selective inversion deficit when making similarity judgments between different facial expressions of emotion, but not for gender or objects. These results suggest a three-way dissociation between facial expression of emotion, gender, and object processing. PMID:26283983

  5. 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

  6. 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

  7. Contrast Between the Sources and Atmospheric Processing of Fine Particles from Asia and North America Measured During INTEX B

    NASA Astrophysics Data System (ADS)

    Weber, R.; Peltier, R.; Hecobian, A.; Blake, D.; Atlas, E.; Riemer, D.; Karl, T.; Apel, E.; Campos, T.; Stohl, A.

    2007-12-01

    During the Intercontinental Chemical Transport Experiment, Phase B (INTEX B), conducted in the spring of 2006, airborne measurements were made in the United States Pacific Northwest of the major inorganic ions and the water-soluble organic carbon (WSOC) of submicron (PM1.0) aerosol. An atmospheric trajectory and a particle dispersion model for CO sources (Flexpart) was used to segregate air masses into those of primarily Asian influence (greater than 75 percent Asian CO) or North American influence (greater than 75 percent North American CO). Measured components of fine particle mass mostly consisted of water-soluble organic carbon and sulfate, with highest median WSOC and sulfate concentrations in North American air masses. Curiously, the fraction of sulfate to WSOC was significantly higher at altitudes above 3 km, opposite to what has been observed closer to Asia and in the northeastern United States. The observations could be explained by loss of sulfate and organic aerosol due to precipitation scavenging near Asia, with reformation of only sulfate during advection from Asia to North America. WSOC sources were investigated by multivariate linear regression analyses of volatile organic compounds (VOCs). In Asian air masses detected over the Pacific Northwest, of the WSOC variability that could be explained (49 percent), most was related to fossil fuel combustion VOCs, compared to North American air masses, where 75 percent of the WSOC variability was explained through a nearly equal combination of fossil fuel combustion and biogenic VOCs. The most distinct WSOC plumes of the mission were from the California Central Valley, where WSOC variability was related to a mix of biogenic and anthropogenic VOCs. These plumes appeared to be related to secondary organic aerosol formation associated with cloud processing.

  8. The phosphoproteome of Aspergillus nidulans reveals functional association with cellular processes involved in morphology and secretion.

    PubMed

    Ramsubramaniam, Nikhil; Harris, Steven D; Marten, Mark R

    2014-11-01

    We describe the first phosphoproteome of the model filamentous fungus Aspergillus nidulans. Phosphopeptides were enriched using titanium dioxide, separated using a convenient ultra-long reverse phase gradient, and identified using a "high-high" strategy (high mass accuracy on the parent and fragment ions) with higher-energy collisional dissociation. Using this approach 1801 phosphosites, from 1637 unique phosphopeptides, were identified. Functional classification revealed phosphoproteins were overrepresented under GO categories related to fungal morphogenesis: "sites of polar growth," "vesicle mediated transport," and "cytoskeleton organization." In these same GO categories, kinase-substrate analysis of phosphoproteins revealed the majority were target substrates of CDK and CK2 kinase families, indicating these kinase families play a prominent role in fungal morphogenesis. Kinase-substrate analysis also identified 57 substrates for kinases known to regulate secretion of hydrolytic enzymes (e.g. PkaA, SchA, and An-Snf1). Altogether this data will serve as a benchmark that can be used to elucidate regulatory networks functionally associated with fungal morphogenesis and secretion. All MS data have been deposited in the ProteomeXchange with identifier PXD000715 (http://proteomecentral.proteomexchange.org/dataset/PXD000715).

  9. 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

  10. Theta phase coherence in affective picture processing reveals dysfunctional sensory integration in psychopathic offenders.

    PubMed

    Tillem, Scott; Ryan, Jonathan; Wu, Jia; Crowley, Michael J; Mayes, Linda C; Baskin-Sommers, Arielle

    2016-09-01

    Psychopathic offenders are described as emotionally cold, displaying deficits in affective responding. However, research demonstrates that many of the psychopathy-related deficits are moderated by attention, such that under conditions of high attentional and perceptual load psychopathic offenders display deficits in affective responses, but do not in conditions of low load. To date, most studies use measures of defensive reflex (i.e., startle) and conditioning manipulations to examine the impact of load on psychopathy-related processing, but have not examined more direct measures of attention processing. In a sample of adult male offenders, the present study examined time-frequency EEG phase coherence in response to a picture-viewing paradigm that manipulated picture familiarity to assess neural changes in processing based on perceptual demands. Results indicated psychopathy-related differences in the theta response, an index of readiness to perceive and integrate sensory information. These data provide further evidence that psychopathic offenders have disrupted integration of sensory information.

  11. 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. PMID:27295362

  12. 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.

  13. 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.

  14. Closely Related Mycobacterial Strains Demonstrate Contrasting Levels of Efficacy as Antitumor Vaccines and Are Processed for Major Histocompatibility Complex Class I Presentation by Multiple Routes in Dendritic Cells

    PubMed Central

    Cheadle, Eleanor J.; O'Donnell, Dearbhaile; Selby, Peter J.; Jackson, Andrew M.

    2005-01-01

    Mycobacteria expressing recombinant antigens are already being developed as vaccines against both infections and tumors. Little is known about how dendritic cells might process such antigens. Two different mycobacterial species, the fast-growing Mycobacterium smegmatis and the slow-growing M. bovis M. bovis BCG, were engineered to express a model tumor antigen, the Kb-restricted dominant cytotoxic T-lymphocyte epitope OVA257-264. Recombinant M. bovis BCG but not recombinant M. smegmatis conferred protection to mice challenged with the B16-OVA tumor cell line. We went on to investigate whether the contrast in antitumor efficacy could be due to differences in how dendritic cells process antigen from the two mycobacterial strains for class I presentation. Both strains of mycobacteria caused phenotypic maturation of dendritic cells, but recombinant M. smegmatis infection led to a greater degree of dendritic cell maturation than recombinant M. bovis BCG infection. Antigen from recombinant M. smegmatis was processed and presented as OVA257-264 on Kb molecules by the dendritic cell line DC2.4 but not by bone marrow-derived dendritic cells (BMDC) or splenic dendritic cells. In contrast, antigen from recombinant M. bovis BCG was presented by all three dendritic cell types as long as the mycobacteria were viable. Such presentation was dependent on proteasome function and nascent major histocompatibility complex (MHC) class I molecules in DC2.4 cells but independent of the proteasome and transporter associated with antigen processings (TAP) in BMDC and splenic dendritic cells. These data demonstrate for the first time that antigen vectored by the slow-growing M. bovis BCG but not that vectored by fast-growing, readily destroyed M. smegmatis is processed and presented on MHC class I by in vitro-generated dendritic cells, which has implications for recombinant microbial vaccine development. PMID:15664917

  15. 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

  16. 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.

  17. Auditory information processing during human sleep as revealed by event-related brain potentials.

    PubMed

    Atienza, M; Cantero, J L; Escera, C

    2001-11-01

    The main goal of this review is to elucidate up to what extent pre-attentive auditory information processing is affected during human sleep. Evidence from event-related brain potential (ERP) studies indicates that auditory information processing is selectively affected, even at early phases, across the different stages of sleep-wakefulness continuum. According to these studies, 3 main conclusions are drawn: (1) the sleeping brain is able to automatically detect stimulus occurrence and trigger an orienting response towards that stimulus if its degree of novelty is large; (2) auditory stimuli are represented in the auditory system and maintained for a period of time in sensory memory, making the automatic-change detection during sleep possible; and (3) there are specific brain mechanisms (sleep-specific ERP components associated with the presence of vertex waves and K-complexes) by which information processing can be improved during non-rapid eye movement sleep. However, the remarkably affected amplitude and latency of the waking-ERPs during the different stages of sleep suggests deficits in the building and maintenance of a neural representation of the stimulus as well as in the process by which neural events lead to an orienting response toward such a stimulus. The deactivation of areas in the dorsolateral pre-frontal cortex during sleep contributing to the generation of these ERP components is hypothesized to be one of the main causes for the attenuated amplitude of these ERPs during human sleep. PMID:11682341

  18. The Thatcher Illusion Reveals Orientation Dependence in Brain Regions Involved in Processing Facial Expressions

    PubMed Central

    Psalta, Lilia; Young, Andrew W.; Thompson, Peter; Andrews, Timothy J.

    2015-01-01

    Although the processing of facial identity is known to be sensitive to the orientation of the face, it is less clear whether orientation sensitivity extends to the processing of facial expressions. To address this issue, we used functional MRI (fMRI) to measure the neural response to the Thatcher illusion. This illusion involves a local inversion of the eyes and mouth in a smiling face—when the face is upright, the inverted features make it appear grotesque, but when the face is inverted, the inversion is no longer apparent. Using an fMRI-adaptation paradigm, we found a release from adaptation in the superior temporal sulcus—a region directly linked to the processing of facial expressions—when the images were upright and they changed from a normal to a Thatcherized configuration. However, this release from adaptation was not evident when the faces were inverted. These results show that regions involved in processing facial expressions display a pronounced orientation sensitivity. PMID:24264941

  19. 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…

  20. 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…

  1. 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…

  2. 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…

  3. Inside the Black Box: Revealing the Process in Applying a Grounded Theory Analysis

    ERIC Educational Resources Information Center

    Rich, Peter

    2012-01-01

    Qualitative research methods have long set an example of rich description, in which data and researchers' hermeneutics work together to inform readers of findings in specific contexts. Among published works, insight into the analytical process is most often represented in the form of methodological propositions or research results. This paper…

  4. Explicit Processing Demands Reveal Language Modality-Specific Organization of Working Memory

    ERIC Educational Resources Information Center

    Rudner, Mary; Ronnberg, Jerker

    2008-01-01

    The working memory model for Ease of Language Understanding (ELU) predicts that processing differences between language modalities emerge when cognitive demands are explicit. This prediction was tested in three working memory experiments with participants who were Deaf Signers (DS), Hearing Signers (HS), or Hearing Nonsigners (HN). Easily nameable…

  5. Caught in the act: revealing the metastatic process by live imaging

    PubMed Central

    Fein, Miriam R.; Egeblad, Mikala

    2013-01-01

    The prognosis of metastatic cancer in patients is poor. Interfering with metastatic spread is therefore important for achieving better survival from cancer. Metastatic disease is established through a series of steps, including breaching of the basement membrane, intravasation and survival in lymphatic or blood vessels, extravasation, and growth at distant sites. Yet, although we know the steps involved in metastasis, the cellular and molecular mechanisms of dissemination and colonization of distant organs are incompletely understood. Here, we review the important insights into the metastatic process that have been gained specifically through the use of imaging technologies in murine, chicken embryo and zebrafish model systems, including high-resolution two-photon microscopy and bioluminescence. We further discuss how imaging technologies are beginning to allow researchers to address the role of regional activation of specific molecular pathways in the metastatic process. These technologies are shedding light, literally, on almost every step of the metastatic process, particularly with regards to the dynamics and plasticity of the disseminating cancer cells and the active participation of the microenvironment in the processes. PMID:23616077

  6. The Thatcher illusion reveals orientation dependence in brain regions involved in processing facial expressions.

    PubMed

    Psalta, Lilia; Young, Andrew W; Thompson, Peter; Andrews, Timothy J

    2014-01-01

    Although the processing of facial identity is known to be sensitive to the orientation of the face, it is less clear whether orientation sensitivity extends to the processing of facial expressions. To address this issue, we used functional MRI (fMRI) to measure the neural response to the Thatcher illusion. This illusion involves a local inversion of the eyes and mouth in a smiling face-when the face is upright, the inverted features make it appear grotesque, but when the face is inverted, the inversion is no longer apparent. Using an fMRI-adaptation paradigm, we found a release from adaptation in the superior temporal sulcus-a region directly linked to the processing of facial expressions-when the images were upright and they changed from a normal to a Thatcherized configuration. However, this release from adaptation was not evident when the faces were inverted. These results show that regions involved in processing facial expressions display a pronounced orientation sensitivity.

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

    PubMed Central

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

    2008-01-01

    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. PMID:18456840

  8. 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.

  9. Spatiotemporal dynamics of affective picture processing revealed by intracranial high-gamma modulations.

    PubMed

    Boucher, Olivier; D'Hondt, Fabien; Tremblay, Julie; Lepore, Franco; Lassonde, Maryse; Vannasing, Phetsamone; Bouthillier, Alain; Nguyen, Dang Khoa

    2015-01-01

    Our comprehension of the neural mechanisms underlying emotional information processing has largely benefited from noninvasive electrophysiological and functional neuroimaging techniques in recent years. However, the spatiotemporal dynamics of the neural events occurring during emotional processing remain imprecise due to the limited combination of spatial and temporal resolution provided by these techniques. This study examines the modulations of high-frequency activity of intracranial electroencephalography recordings associated with affective picture valence, in epileptic patients awaiting neurosurgery. Recordings were obtained from subdural grids and depth electrodes in eight patients while they viewed a series of unpleasant, pleasant and neutral pictures from the International Affective Picture System. Broadband high-gamma (70-150 Hz) power was computed for separate 100-ms time windows and compared according to ratings of emotional valence. Compared to emotionally neutral or pleasant pictures, unpleasant stimuli were associated with an early and long-lasting (≈200-1,000 ms) bilateral increase in high-gamma activity in visual areas of the occipital and temporal lobes, together with a late and transient (≈500-800 ms) decrease found bilaterally in the lateral prefrontal cortex (PFC). Pleasant pictures were associated with increased gamma activity in the occipital cortex, compared to the emotionally neutral stimuli. Consistent with previous studies, our results provide direct evidence of emotion-related modulations in the visual ventral pathway during picture processing. Results in the lateral PFC also shed light on the neural mechanisms underlying its role in negative emotions processing. This study demonstrates the utility of intracranial high-gamma modulations to study emotional process with a high spatiotemporal precision.

  10. Transcriptomic changes during tuber dormancy release process revealed by RNA sequencing in potato.

    PubMed

    Liu, Bailin; Zhang, Ning; Wen, Yikai; Jin, Xin; Yang, Jiangwei; Si, Huaijun; Wang, Di

    2015-03-20

    Potato tuber dormancy release is a critical development process that allows potato to produce new plant. The first Illumina RNA sequencing to generate the expressed mRNAs at dormancy tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) was performed. We identified 26,639 genes including 5,912 (3,450 up-regulated while 2,462 down-regulated) and 3,885 (2,141 up-regulated while 1,744 down-regulated) genes were differentially expressed from DT vs DRT and DRT vs ST. The RNA-Seq results were further verified using qRT-PCR. We found reserve mobilization events were activated before the bud emergence (DT vs DRT) and highlighted after dormancy release (DRT vs ST). Overexpressed genes related to metabolism of auxin, gibberellic acid, cytokinin and barssinosteriod were dominated in DT vs DRT, whereas overexpressed genes involved in metabolism of ethylene, jasmonate and salicylate were prominent in DRT vs ST. Various histone and cyclin isoforms associated genes involved in cell division/cycle were mainly up-regulated in DT vs DRT. Dormancy release process was also companied by stress response and redox regulation, those genes related to biotic stress, cell wall and second metabolism was preferentially overexpressed in DRT vs ST, which might accelerate dormancy breaking and sprout outgrowth. The metabolic processes activated during tuber dormancy release were also supported by plant seed models. These results represented the first comprehensive picture of a large number of genes involved in tuber dormancy release process.

  11. The Intrinsic Dynamics and Unfolding Process of an Antibody Fab Fragment Revealed by Elastic Network Model.

    PubMed

    Su, Ji-Guo; Zhang, Xiao; Han, Xiao-Ming; Zhao, Shu-Xin; Li, Chun-Hua

    2015-01-01

    Antibodies have been increasingly used as pharmaceuticals in clinical treatment. Thermal stability and unfolding process are important properties that must be considered in antibody design. In this paper, the structure-encoded dynamical properties and the unfolding process of the Fab fragment of the phosphocholine-binding antibody McPC603 are investigated by use of the normal mode analysis of Gaussian network model (GNM). Firstly, the temperature factors for the residues of the protein were calculated with GNM and then compared with the experimental measurements. A good result was obtained, which provides the validity for the use of GNM to study the dynamical properties of the protein. Then, with this approach, the mean-square fluctuation (MSF) of the residues, as well as the MSF in the internal distance (MSFID) between all pairwise residues, was calculated to investigate the mobility and flexibility of the protein, respectively. It is found that the mobility and flexibility of the constant regions are higher than those of the variable regions, and the six complementarity-determining regions (CDRs) in the variable regions also exhibit relative large mobility and flexibility. The large amplitude motions of the CDRs are considered to be associated with the immune function of the antibody. In addition, the unfolding process of the protein was simulated by iterative use of the GNM. In our method, only the topology of protein native structure is taken into account, and the protein unfolding process is simulated through breaking the native contacts one by one according to the MSFID values between the residues. It is found that the flexible regions tend to unfold earlier. The sequence of the unfolding events obtained by our method is consistent with the hydrogen-deuterium exchange experimental results. Our studies imply that the unfolding behavior of the Fab fragment of antibody McPc603 is largely determined by the intrinsic dynamics of the protein.

  12. 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.

  13. Theta phase coherence in affective picture processing reveals dysfunctional sensory integration in psychopathic offenders.

    PubMed

    Tillem, Scott; Ryan, Jonathan; Wu, Jia; Crowley, Michael J; Mayes, Linda C; Baskin-Sommers, Arielle

    2016-09-01

    Psychopathic offenders are described as emotionally cold, displaying deficits in affective responding. However, research demonstrates that many of the psychopathy-related deficits are moderated by attention, such that under conditions of high attentional and perceptual load psychopathic offenders display deficits in affective responses, but do not in conditions of low load. To date, most studies use measures of defensive reflex (i.e., startle) and conditioning manipulations to examine the impact of load on psychopathy-related processing, but have not examined more direct measures of attention processing. In a sample of adult male offenders, the present study examined time-frequency EEG phase coherence in response to a picture-viewing paradigm that manipulated picture familiarity to assess neural changes in processing based on perceptual demands. Results indicated psychopathy-related differences in the theta response, an index of readiness to perceive and integrate sensory information. These data provide further evidence that psychopathic offenders have disrupted integration of sensory information. PMID:27373371

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

    PubMed

    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.

  15. Integration of Consonant and Pitch Processing as Revealed by the Absence of Additivity in Mismatch Negativity

    PubMed Central

    Gong, Diankun; Chen, Sifan; Kendrick, Keith M.; Yao, Dezhong

    2012-01-01

    Consonants, unlike vowels, are thought to be speech specific and therefore no interactions would be expected between consonants and pitch, a basic element for musical tones. The present study used an electrophysiological approach to investigate whether, contrary to this view, there is integrative processing of consonants and pitch by measuring additivity of changes in the mismatch negativity (MMN) of evoked potentials. The MMN is elicited by discriminable variations occurring in a sequence of repetitive, homogeneous sounds. In the experiment, event-related potentials (ERPs) were recorded while participants heard frequently sung consonant-vowel syllables and rare stimuli deviating in either consonant identity only, pitch only, or in both dimensions. Every type of deviation elicited a reliable MMN. As expected, the two single-deviant MMNs had similar amplitudes, but that of the double-deviant MMN was also not significantly different from them. This absence of additivity in the double-deviant MMN suggests that consonant and pitch variations are processed, at least at a pre-attentive level, in an integrated rather than independent way. Domain-specificity of consonants may depend on higher-level processes in the hierarchy of speech perception. PMID:22693614

  16. 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.

  17. 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

  18. 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. PMID:25802366

  19. 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.

  20. Transcriptome analysis of poplar rust telia reveals overwintering adaptation and tightly coordinated karyogamy and meiosis processes.

    PubMed

    Hacquard, Stéphane; Delaruelle, Christine; Frey, Pascal; Tisserant, Emilie; Kohler, Annegret; Duplessis, Sébastien

    2013-01-01

    Most rust fungi have a complex life cycle involving up to five different spore-producing stages. The telial stage that produces melanized overwintering teliospores is one of these and plays a fundamental role for generating genetic diversity as karyogamy and meiosis occur at that stage. Despite the importance of telia for the rust life cycle, almost nothing is known about the fungal genetic programs that are activated in this overwintering structure. In the present study, the transcriptome of telia produced by the poplar rust fungus Melampsora larici-populina has been investigated using whole genome exon oligoarrays and RT-qPCR. Comparative expression profiling at the telial and uredinial stages identifies genes specifically expressed or up-regulated in telia including osmotins/thaumatin-like proteins (TLPs) and aquaporins that may reflect specific adaptation to overwintering as well numerous lytic enzymes acting on plant cell wall, reflecting extensive cell wall remodeling at that stage. The temporal dynamics of karyogamy was followed using combined RT-qPCR and DAPI-staining approaches. This reveals that fusion of nuclei and induction of karyogamy-related genes occur simultaneously between the 25 and 39 days post inoculation time frame. Transcript profiling of conserved meiosis genes indicates a preferential induction right after karyogamy and corroborates that meiosis begins prior to overwintering and is interrupted in Meiosis I (prophase I, diplonema stage) until teliospore germination in early spring.

  1. Transcriptome analysis of poplar rust telia reveals overwintering adaptation and tightly coordinated karyogamy and meiosis processes

    PubMed Central

    Hacquard, Stéphane; Delaruelle, Christine; Frey, Pascal; Tisserant, Emilie; Kohler, Annegret; Duplessis, Sébastien

    2013-01-01

    Most rust fungi have a complex life cycle involving up to five different spore-producing stages. The telial stage that produces melanized overwintering teliospores is one of these and plays a fundamental role for generating genetic diversity as karyogamy and meiosis occur at that stage. Despite the importance of telia for the rust life cycle, almost nothing is known about the fungal genetic programs that are activated in this overwintering structure. In the present study, the transcriptome of telia produced by the poplar rust fungus Melampsora larici-populina has been investigated using whole genome exon oligoarrays and RT-qPCR. Comparative expression profiling at the telial and uredinial stages identifies genes specifically expressed or up-regulated in telia including osmotins/thaumatin-like proteins (TLPs) and aquaporins that may reflect specific adaptation to overwintering as well numerous lytic enzymes acting on plant cell wall, reflecting extensive cell wall remodeling at that stage. The temporal dynamics of karyogamy was followed using combined RT-qPCR and DAPI-staining approaches. This reveals that fusion of nuclei and induction of karyogamy-related genes occur simultaneously between the 25 and 39 days post inoculation time frame. Transcript profiling of conserved meiosis genes indicates a preferential induction right after karyogamy and corroborates that meiosis begins prior to overwintering and is interrupted in Meiosis I (prophase I, diplonema stage) until teliospore germination in early spring. PMID:24312107

  2. Transcriptome analysis of poplar rust telia reveals overwintering adaptation and tightly coordinated karyogamy and meiosis processes.

    PubMed

    Hacquard, Stéphane; Delaruelle, Christine; Frey, Pascal; Tisserant, Emilie; Kohler, Annegret; Duplessis, Sébastien

    2013-01-01

    Most rust fungi have a complex life cycle involving up to five different spore-producing stages. The telial stage that produces melanized overwintering teliospores is one of these and plays a fundamental role for generating genetic diversity as karyogamy and meiosis occur at that stage. Despite the importance of telia for the rust life cycle, almost nothing is known about the fungal genetic programs that are activated in this overwintering structure. In the present study, the transcriptome of telia produced by the poplar rust fungus Melampsora larici-populina has been investigated using whole genome exon oligoarrays and RT-qPCR. Comparative expression profiling at the telial and uredinial stages identifies genes specifically expressed or up-regulated in telia including osmotins/thaumatin-like proteins (TLPs) and aquaporins that may reflect specific adaptation to overwintering as well numerous lytic enzymes acting on plant cell wall, reflecting extensive cell wall remodeling at that stage. The temporal dynamics of karyogamy was followed using combined RT-qPCR and DAPI-staining approaches. This reveals that fusion of nuclei and induction of karyogamy-related genes occur simultaneously between the 25 and 39 days post inoculation time frame. Transcript profiling of conserved meiosis genes indicates a preferential induction right after karyogamy and corroborates that meiosis begins prior to overwintering and is interrupted in Meiosis I (prophase I, diplonema stage) until teliospore germination in early spring. PMID:24312107

  3. 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. PMID:25051274

  4. Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process

    PubMed Central

    Chandran, Uma R; Ma, Changqing; Dhir, Rajiv; Bisceglia, Michelle; Lyons-Weiler, Maureen; Liang, Wenjing; Michalopoulos, George; Becich, Michael; Monzon, Federico A

    2007-01-01

    Background Prostate cancer is characterized by heterogeneity in the clinical course that often does not correlate with morphologic features of the tumor. Metastasis reflects the most adverse outcome of prostate cancer, and to date there are no reliable morphologic features or serum biomarkers that can reliably predict which patients are at higher risk of developing metastatic disease. Understanding the differences in the biology of metastatic and organ confined primary tumors is essential for developing new prognostic markers and therapeutic targets. Methods Using Affymetrix oligonucleotide arrays, we analyzed gene expression profiles of 24 androgen-ablation resistant metastatic samples obtained from 4 patients and a previously published dataset of 64 primary prostate tumor samples. Differential gene expression was analyzed after removing potentially uninformative stromal genes, addressing the differences in cellular content between primary and metastatic tumors. Results The metastatic samples are highly heterogenous in expression; however, differential expression analysis shows that 415 genes are upregulated and 364 genes are downregulated at least 2 fold in every patient with metastasis. The expression profile of metastatic samples reveals changes in expression of a unique set of genes representing both the androgen ablation related pathways and other metastasis related gene networks such as cell adhesion, bone remodelling and cell cycle. The differentially expressed genes include metabolic enzymes, transcription factors such as Forkhead Box M1 (FoxM1) and cell adhesion molecules such as Osteopontin (SPP1). Conclusion We hypothesize that these genes have a role in the biology of metastatic disease and that they represent potential therapeutic targets for prostate cancer. PMID:17430594

  5. Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia.

    PubMed

    Torkamani, Ali; Dean, Brian; Schork, Nicholas J; Thomas, Elizabeth A

    2010-04-01

    We performed integrated gene coexpression network analysis on two large microarray-based brain gene expression data sets generated from the prefrontal cortex obtained post-mortem from 101 subjects, 47 subjects with schizophrenia and 54 normal control subjects, ranging in age from 19 to 81 years. Twenty-eight modules of coexpressed genes with functional interpretations were detected in both normal subjects and those with schizophrenia. Significant overlap of "case" and "control" module composition was observed, indicating that extensive differences in underlying molecular connectivity are not likely driving pathology in schizophrenia. Modules of coexpressed genes were characterized according to disease association, cell type specificity, and the effects of aging. We find that genes with altered expression in schizophrenia clustered into distinct coexpression networks and that these were associated primarily with neurons. We further identified a robust effect of age on gene expression modules that differentiates normal subjects from those with schizophrenia. In particular, we report that normal age-related decreases in genes related to central nervous system developmental processes, including neurite outgrowth, neuronal differentiation, and dopamine-related cellular signaling, do not occur in subjects with schizophrenia during the aging process. Extrapolating these findings to earlier stages of development supports the concept that schizophrenia pathogenesis begins early in life and is associated with a failure of normal decreases in developmental-related gene expression. These findings provide a novel mechanism for the "developmental" hypothesis of schizophrenia on a molecular level.

  6. 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.

  7. Magnetoencephalography reveals altered auditory information processing in youth with obsessive-compulsive disorder.

    PubMed

    Korostenskaja, Milena; Harris, Elana; Giovanetti, Cathy; Horn, Paul; Wang, Yingying; Rose, Douglas; Fujiwara, Hisako; Xiang, Jing

    2013-05-30

    Patients with obsessive-compulsive disorder (OCD) often report sensory intolerances which may lead to significant functional impairment. This study used auditory evoked fields (AEFs) to address the question of whether neural correlates of sensory auditory information processing differ in youth with OCD compared with healthy comparison subjects (HCS). AEFs, recorded with a whole head 275-channel magnetoencephalography system, were elicited in response to binaural auditory stimuli from 10 pediatric subjects with OCD (ages 8-13, mean 11 years, 6 males) and 10 age- and gender-matched HCS. Three major neuromagnetic responses were studied: M70 (60-80 ms), M100 (90-120 ms), and M150 (130-190 ms). When compared with HCS, subjects with OCD demonstrated delayed latency of the M100 response. In subjects with OCD the amplitude of the M100 and M150 responses was significantly greater in the right hemisphere compared with the left hemisphere. Current results suggest that when compared with HCS, subjects with OCD have altered auditory information processing, evident from the delayed latency of the M100 response, which is thought to be associated with the encoding of physical stimulus characteristics. Interhemispheric asymmetry with increased M100 and M150 amplitudes over the right hemisphere compared with the left hemisphere was found in young OCD subjects. These results should be interpreted with caution due to the high variability rate of responses in both HCS and OCD subjects, as well as the possible effect of medication in OCD subjects.

  8. Tracking individual secretory vesicles during exocytosis reveals an ordered and regulated process

    PubMed Central

    Donovan, Kirk W.

    2015-01-01

    Post-Golgi secretory vesicle trafficking is a coordinated process, with transport and regulatory mechanisms to ensure appropriate exocytosis. While the contributions of many individual regulatory proteins to this process are well studied, the timing and dependencies of events have not been defined. Here we track individual secretory vesicles and associated proteins in vivo during tethering and fusion in budding yeast. Secretory vesicles tether to the plasma membrane very reproducibly for ∼18 s, which is extended in cells defective for membrane fusion and significantly lengthened and more variable when GTP hydrolysis of the exocytic Rab is delayed. Further, the myosin-V Myo2p regulates the tethering time in a mechanism unrelated to its interaction with exocyst component Sec15p. Two-color imaging of tethered vesicles with Myo2p, the GEF Sec2p, and several exocyst components allowed us to document a timeline for yeast exocytosis in which Myo2p leaves 4 s before fusion, whereas Sec2p and all the components of the exocyst disperse coincident with fusion. PMID:26169352

  9. 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. PMID:20388591

  10. Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia

    PubMed Central

    Torkamani, Ali; Dean, Brian; Schork, Nicholas J.; Thomas, Elizabeth A.

    2010-01-01

    We performed integrated gene coexpression network analysis on two large microarray-based brain gene expression data sets generated from the prefrontal cortex obtained post-mortem from 101 subjects, 47 subjects with schizophrenia and 54 normal control subjects, ranging in age from 19 to 81 years. Twenty-eight modules of coexpressed genes with functional interpretations were detected in both normal subjects and those with schizophrenia. Significant overlap of “case” and “control” module composition was observed, indicating that extensive differences in underlying molecular connectivity are not likely driving pathology in schizophrenia. Modules of coexpressed genes were characterized according to disease association, cell type specificity, and the effects of aging. We find that genes with altered expression in schizophrenia clustered into distinct coexpression networks and that these were associated primarily with neurons. We further identified a robust effect of age on gene expression modules that differentiates normal subjects from those with schizophrenia. In particular, we report that normal age-related decreases in genes related to central nervous system developmental processes, including neurite outgrowth, neuronal differentiation, and dopamine-related cellular signaling, do not occur in subjects with schizophrenia during the aging process. Extrapolating these findings to earlier stages of development supports the concept that schizophrenia pathogenesis begins early in life and is associated with a failure of normal decreases in developmental-related gene expression. These findings provide a novel mechanism for the “developmental” hypothesis of schizophrenia on a molecular level. PMID:20197298

  11. ERPs reveal comparable syntactic sentence processing in native and non-native readers of English

    PubMed Central

    Kotz, Sonja A.; Holcomb, Phillip J.; Osterhout, Lee

    2009-01-01

    L2 syntactic processing has been primarily investigated in the context of syntactic anomaly detection, but only sparsely with syntactic ambiguity. In the field of event-related potentials (ERPs) syntactic anomaly detection and syntactic ambiguity resolution is linked to the P600. The current ERP experiment examined L2 syntactic processing in highly proficient L1 Spanish-L2 English readers who had acquired English informally around the age of 5 years. Temporary syntactic ambiguity (induced by verb subcategorization information) was tested as a language-specific phenomenon of L2, while syntactic anomaly resulted from phrase structure constraints that are similar in L1 and L2. Participants judged whether a sentence was syntactically acceptable or not. Native readers of English showed a P600 in the temporary syntactically ambiguous and syntactically anomalous sentences. A comparable picture emerged in the non-native readers of English. Both critical syntactic conditions elicited a P600, however, the distribution and latency of the P600 varied in the syntactic anomaly condition. The results clearly show that early acquisition of L2 syntactic knowledge leads to comparable online sensitivity towards temporal syntactic ambiguity and syntactic anomaly in early and highly proficient non-native readers of English and native readers of English. PMID:18061129

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

    PubMed

    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

  13. Vibrotactile masking experiments reveal accelerated somatosensory processing in congenitally blind Braille readers

    PubMed Central

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

    2010-01-01

    Braille reading is a demanding task that requires the identification of rapidly varying tactile patterns. During proficient reading, neighboring characters impact the fingertip at about 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 to 100-micron 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-micron; 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. PMID:20980584

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  16. Magnetoencephalography reveals altered auditory information processing in youth with obsessive-compulsive disorder.

    PubMed

    Korostenskaja, Milena; Harris, Elana; Giovanetti, Cathy; Horn, Paul; Wang, Yingying; Rose, Douglas; Fujiwara, Hisako; Xiang, Jing

    2013-05-30

    Patients with obsessive-compulsive disorder (OCD) often report sensory intolerances which may lead to significant functional impairment. This study used auditory evoked fields (AEFs) to address the question of whether neural correlates of sensory auditory information processing differ in youth with OCD compared with healthy comparison subjects (HCS). AEFs, recorded with a whole head 275-channel magnetoencephalography system, were elicited in response to binaural auditory stimuli from 10 pediatric subjects with OCD (ages 8-13, mean 11 years, 6 males) and 10 age- and gender-matched HCS. Three major neuromagnetic responses were studied: M70 (60-80 ms), M100 (90-120 ms), and M150 (130-190 ms). When compared with HCS, subjects with OCD demonstrated delayed latency of the M100 response. In subjects with OCD the amplitude of the M100 and M150 responses was significantly greater in the right hemisphere compared with the left hemisphere. Current results suggest that when compared with HCS, subjects with OCD have altered auditory information processing, evident from the delayed latency of the M100 response, which is thought to be associated with the encoding of physical stimulus characteristics. Interhemispheric asymmetry with increased M100 and M150 amplitudes over the right hemisphere compared with the left hemisphere was found in young OCD subjects. These results should be interpreted with caution due to the high variability rate of responses in both HCS and OCD subjects, as well as the possible effect of medication in OCD subjects. PMID:23545237

  17. 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.

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

    PubMed

    Küper, Kristina; Heil, Martin

    2009-04-01

    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.

  19. 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

  20. ERPs reveal comparable syntactic sentence processing in native and non-native readers of English.

    PubMed

    Kotz, Sonja A; Holcomb, Phillip J; Osterhout, Lee

    2008-07-01

    L2 syntactic processing has been primarily investigated in the context of syntactic anomaly detection, but only sparsely with syntactic ambiguity. In the field of event-related potentials (ERPs) syntactic anomaly detection and syntactic ambiguity resolution is linked to the P600. The current ERP experiment examined L2 syntactic processing in highly proficient L1 Spanish-L2 English readers who had acquired English informally around the age of 5 years. Temporary syntactic ambiguity (induced by verb subcategorization information) was tested as a language-specific phenomenon of L2, while syntactic anomaly resulted from phrase structure constraints that are similar in L1 and L2. Participants judged whether a sentence was syntactically acceptable or not. Native readers of English showed a P600 in the temporary syntactically ambiguous and syntactically anomalous sentences. A comparable picture emerged in the non-native readers of English. Both critical syntactic conditions elicited a P600, however, the distribution and latency of the P600 varied in the syntactic anomaly condition. The results clearly show that early acquisition of L2 syntactic knowledge leads to comparable online sensitivity towards temporal syntactic ambiguity and syntactic anomaly in early and highly proficient non-native readers of English and native readers of English.

  1. Second language syntactic processing revealed through event-related potentials: an empirical review.

    PubMed

    Caffarra, Sendy; Molinaro, Nicola; Davidson, Doug; Carreiras, Manuel

    2015-04-01

    Learning a second language (L2) can be crucial in the present globalized society. However, reaching the level of L1 performance of native speakers is still a challenge for many. Distinct factors could account for the persistent gap observed between natives' and non-natives' syntactic abilities: L1-L2 differences, AoA, proficiency, L2 immersion duration, L2 training duration. Although different theoretical approaches described the role of these several factors, not all studies using on-line measures have investigated them comprehensively and consistently. The present work reviews available ERP studies on L2 syntactic analysis in order to establish the relative weight of each factor on the time course of L2 processing. Logistic regression analyses were performed on the presence or absence of ERP effects reported in response to L2 syntactic violations, including all the influential factors as categorical independent variables. The results showed that immersion duration has an influence on the ERP correlates linked to early mechanisms of syntactic processing, while the global proficiency level has an impact on the ERP correlates related to late, language-monitoring activity.

  2. Behavior Reveals Selective Summation and Max Pooling among Olfactory Processing Channels.

    PubMed

    Bell, Joseph S; Wilson, Rachel I

    2016-07-20

    The olfactory system is divided into processing channels (glomeruli), each receiving input from a different type of olfactory receptor neuron (ORN). Here we investigated how glomeruli combine to control behavior in freely walking Drosophila. We found that optogenetically activating single ORN types typically produced attraction, although some ORN types produced repulsion. Attraction consisted largely of a behavioral program with the following rules: at fictive odor onset, flies walked upwind, and at fictive odor offset, they reversed. When certain pairs of attractive ORN types were co-activated, the level of the behavioral response resembled the sum of the component responses. However, other pairs of attractive ORN types produced a response resembling the larger component (max pooling). Although activation of different ORN combinations produced different levels of behavior, the rules of the behavioral program were consistent. Our results illustrate a general method for inferring how groups of neurons work together to modulate behavioral programs. PMID:27373835

  3. 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

  4. 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.

  5. 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

  6. Petrogenetic Processes in a Deep Arc Section: A MASH Zone Revealed

    NASA Astrophysics Data System (ADS)

    Bergantz, G. W.; Walker, B. A.; Otamendi, J.; Ducea, M. N.

    2013-12-01

    The Sierra Valle Fértil section of the Ordovician Famatina arc in west central Argentina exposes the plutonic roots and associated host rocks in a 100 km long, nearly continuous section with paleo-depths of >25 km to 8 km or less. This tilted section exposes identifiable end-member components of a juvenile continental arc: large bodies of granodiorite and tonalites in the mid-to-upper crust, a mafic- and ultramafic- dominated lower crust, which is interlayered with a lithologically homogenous sequence of metapelites and other supracrustal compositions. The 'circulatory system' of the arc is continuous and decipherable: all units described above are physically linked via hyper-solidus and migmatitic domains, veins and dikes that connect source rocks to plutons. The preservation is exceptional as arc magmatism was largely arrested by a soft collision during the prograde peak, before long-lasting magmatism had obliterated the architecture of a complete 'compositional cycle' that occurred over a span of 4-5 Ma. Hence much as volcanic systems are a ';snapshot' of a magmatic system, the Sierra Valle Fértil provides a ';snapshot' of a juvenile, but crustal-scale plutonic system, without significant over-print of high temperature structures and very long-lived repeated magmatic processing. Of special interest is the ';engine room' of the arc: mafic to ultra-mafic cumulates (pyx, olv, amp, plag), dunites to mafic tonalites which are also cumulates. These occur as a composite, heterogeneous, variably cumulate complex up to 15 km thick. The compositional variability is consistent with a fractionation model but one that requires a changing cumulate assemblage (gabbros) reflecting discrete episodes of extraction of daughter magmas (tonalites). Field identification of distinct mafic plutons is difficult as hyper-solidus conditions prevailed throughout the construction of the complex, blending new intrusions of mafic magma with existing cumulate mush. Based on Sr, Nd and O

  7. 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.

  8. 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

  9. Repetition-related reductions in neural activity reveal component processes of mental simulation

    PubMed Central

    St. Jacques, Peggy L.; Robbins, Clifford A.; Wig, Gagan S.; Schacter, Daniel L.

    2014-01-01

    In everyday life, people adaptively prepare for the future by simulating dynamic events about impending interactions with people, objects and locations. Previous research has consistently demonstrated that a distributed network of frontal–parietal–temporal brain regions supports this ubiquitous mental activity. Nonetheless, little is known about the manner in which specific regions of this network contribute to component features of future simulation. In two experiments, we used a functional magnetic resonance (fMR)-repetition suppression paradigm to demonstrate that distinct frontal–parietal–temporal regions are sensitive to processing the scenarios or what participants imagined was happening in an event (e.g. medial prefrontal, posterior cingulate, temporal–parietal and middle temporal cortices are sensitive to the scenarios associated with future social events), people (medial prefrontal cortex), objects (inferior frontal and premotor cortices) and locations (posterior cingulate/retrosplenial, parahippocampal and posterior parietal cortices) that typically constitute simulations of personal future events. This pattern of results demonstrates that the neural substrates of these component features of event simulations can be reliably identified in the context of a task that requires participants to simulate complex, everyday future experiences. PMID:23482621

  10. Activity profiling of vacuolar processing enzymes reveals a role for VPE during oomycete infection.

    PubMed

    Misas-Villamil, Johana C; Toenges, Gerrit; Kolodziejek, Izabella; Sadaghiani, Amir M; Kaschani, Farnusch; Colby, Thomas; Bogyo, Matthew; van der Hoorn, Renier A L

    2013-02-01

    Vacuolar processing enzymes (VPEs) are important cysteine proteases that are implicated in the maturation of seed storage proteins, and programmed cell death during plant-microbe interactions and development. Here, we introduce a specific, cell-permeable, activity-based probe for VPEs. This probe is highly specific for all four Arabidopsis VPEs, and labeling is activity-dependent, as illustrated by sensitivity for inhibitors, pH and reducing agents. We show that the probe can be used for in vivo imaging and displays multiple active isoforms of VPEs in various tissues and in both monocot and dicot plant species. Thus, VPE activity profiling is a robust, simple and powerful tool for plant research for a wide range of applications. Using VPE activity profiling, we discovered that VPE activity is increased during infection with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa). The enhanced VPE activity is host-derived and EDS1-independent. Sporulation of Hpa is reduced on vpe mutant plants, demonstrating a role for VPE during compatible interactions that is presumably independent of programmed cell death. Our data indicate that, as an obligate biotroph, Hpa takes advantage of increased VPE activity in the host, e.g. to mediate protein turnover and nutrient release.

  11. The Dynamics of the Epileptic Brain Reveal Long-Memory Processes

    PubMed Central

    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. PMID:25386160

  12. 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.

  13. Rapid emotional processing in relation to trauma-related symptoms as revealed by magnetic source imaging

    PubMed Central

    2014-01-01

    Background Traumatic stress leads to functional reorganization in the brain and may trigger an alarm response. However, when the traumatic event produces severe helplessness, the predominant peri-traumatic response may instead be marked by a dissociative shutdown reaction. The neural correlates of this dissociative shutdown were investigated by presenting rapidly presented affective pictures to female participants with posttraumatic stress disorder (PTSD), and comparing responses to a Non-PTSD control group. Methods Event-related-magnetic-fields were recorded during rapid visual serial presentation of emotionally arousing stimuli (unpleasant or pleasant), which alternated with pictures with low affective content (neutral). Neural sources, based on the L2-surface-minimum-norm, correlated with the severity of the symptom clusters: PTSD, depression and shutdown dissociation. Results For the early cortical response (60 to 110 ms), dissociation and PTSD symptom severity show similar spatial distributions of correlates for unpleasant stimuli. Cortical networks that could be involved in the relationships seem to be widespread. Conclusion We conclude that shutdown dissociation, PTSD and depression all have distinct effects on early processing of emotional stimuli. PMID:24997778

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

    PubMed

    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.

  15. 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

  16. Proteomic changes during tuber dormancy release process revealed by iTRAQ quantitative proteomics in potato.

    PubMed

    Liu, Bailin; Zhang, Ning; Zhao, Shuo; Chang, Jing; Wang, Zemin; Zhang, Guodong; Si, Huaijun; Wang, Di

    2015-01-01

    Given that limited information is available with regard to tuber dormancy release related proteome, we conducted proteome analysis of tuber dormancy release process at dormant tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) using the iTRAQ technology. A total of 1,752 proteins were identified. Among them, a subset of 316 proteins was screened as significant up- (137) and down regulated (179) between DT vs DRT. A subset of 120 proteins experienced significant up- (40) or down-regulation (80) between DRT vs ST. The differentially expressed proteins were grouped into 11 functional categories. Proteins enriched in functional categories of major carbohydrate (CHO) metabolism, glycolysis, fermentation, amino acid metabolism, protein and transport were highly up-regulated, while functional categories of photosynthesis and RNA were down-regulated between DT vs DRT. Proteins enriched in functional groups of protein, cell wall, lipid metabolism, miscellaneous, and signaling were strongly up-regulated, while functional categories of photosynthesis, hormone metabolism and protein were down-regulated between DRT vs ST. Consistent with previous documented differentially expressed genes, most of differentially expressed proteins were also identified between DT and DRT, indicating the metabolism shift from growth suspension to growth activation as tubers dormancy breaking. The changes in protein profiles showed lower concordance with corresponding alterations in transcript levels, indicating possible transcriptional and posttranscriptional regulation. Furthermore, the possible mechanism of tuber dormancy release was discussed in relation to what was known in transcripts change and other plant models from carbohydrate metabolism, protein metabolism, stress response, redox regulation, transcription regulation, DNA metabolism, amino acid metabolism, development, signaling as well as hormone metabolism.

  17. Human demographic processes and genetic variation as revealed by mtDNA simulations.

    PubMed

    Miró-Herrans, Aida T; Mulligan, Connie J

    2013-02-01

    Humans' ability for rapid dispersal and adaptation has allowed us to colonize diverse geographic and climatic regions of the planet, creating a complex evolutionary history. This complexity can be understood, at least partially, by modeling the underlying demographic parameters in the evolutionary process. In this study, we analyze a model of human evolution in which population size, gene flow (GF), and time are varied. Specifically, we simulate mitochondrial DNA for 42 demographic scenarios, represented by 42 parameter combinations, to describe the initial dispersal of modern humans out of Africa. The analyses include three values for colonization size (CS; 1%, 10%, and 30% of the African population), seven values for rate of GF (10(-6)-0.5), and two values for time of colonization (50,000 and 100,000 years ago). We then estimate summary statistics for the simulated data sets to calculate the percent of explained variation by each parameter and to identify which parameter combinations generate distinct differences in genetic variation, that is, which demographic scenarios can be distinguished from each other. On the basis of these results, we make recommendations about which summary statistics to use according to the parameter of interest. Our results show that CS, GF, and their interaction have the largest effect on genetic variation under our model of human evolution. Comparison with empirical data suggests that 1% of the existing African mitochondrial genetic variation left and colonized the rest of the world (i.e., CS = 1%) and bidirectional GF continued at a level of ∼10 individuals per generation (i.e., GF = 10(-3)) after the initial colonization. Our study serves as a model to bridge the gap between the use of simulations for theoretical population genetics and empirical data analysis such as approximate bayesian computation approaches and is, thus, applicable to the study of molecular evolution in any organism.

  18. Nanoanalytical Electron Microscopy Reveals a Sequential Mineralization Process Involving Carbonate-Containing Amorphous Precursors.

    PubMed

    Nitiputri, Kharissa; Ramasse, Quentin M; Autefage, Hélène; McGilvery, Catriona M; Boonrungsiman, Suwimon; Evans, Nicholas D; Stevens, Molly M; Porter, Alexandra E

    2016-07-26

    A direct observation and an in-depth characterization of the steps by which bone mineral nucleates and grows in the extracellular matrix during the earliest stages of maturation, using relevant biomineralization models as they grow into mature bone mineral, is an important research goal. To better understand the process of bone mineralization in the extracellular matrix, we used nanoanalytical electron microscopy techniques to examine an in vitro model of bone formation. This study demonstrates the presence of three dominant CaP structures in the mineralizing osteoblast cultures: <80 nm dense granules with a low calcium to phosphate ratio (Ca/P) and crystalline domains; calcium phosphate needles emanating from a focus: "needle-like globules" (100-300 nm in diameter) and mature mineral, both with statistically higher Ca/P compared to that of the dense granules. Many of the submicron granules and globules were interspersed around fibrillar structures containing nitrogen, which are most likely the signature of the organic phase. With high spatial resolution electron energy loss spectroscopy (EELS) mapping, spatially resolved maps were acquired showing the distribution of carbonate within each mineral structure. The carbonate was located in the middle of the granules, which suggested the nucleation of the younger mineral starts with a carbonate-containing precursor and that this precursor may act as seed for growth into larger, submicron-sized, needle-like globules of hydroxyapatite with a different stoichiometry. Application of analytical electron microscopy has important implications in deciphering both how normal bone forms and in understanding pathological mineralization. PMID:27383526

  19. 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

  20. Structure and expression of the human L-myc gene reveal a complex pattern of alternative mRNA processing

    SciTech Connect

    Kaye, F.; Battey, J.; Nau, M.; Brooks, B.; Seifter, E.; De Greve, J.; Birrer, M.; Sausville, E.; Minna, J.

    1988-01-01

    The authors' analyzed in detail the structure of the L-myc gene isolated from human placental DNA and characterized its expression in several small-cell lung cancer cell lines. The gene is composed of three exons and two introns spanning 6.6 kilobases in human DNA. Several distinct mRNA species are produced in all small-cell lung cancer cell lines that express L-myc. These transcripts are generated from a single gene by alternative splicing of introns 1 and 2 and by use of alternative polyadenylation signals. In some mRNAs that is a long open reading frame with a predicted translated protein of 364 residues. Amino acid sequence comparison with c-myc and N-myc demonstrated multiple discrete regions with extensive homology. In contrast, other mRNA transcripts, generated by alternative processing, could encode a truncated protein with a novel carboxy-terminal end.

  1. Cortical activation during word processing in late bilinguals: similarities and differences as revealed by functional magnetic resonance imaging.

    PubMed

    Marian, Viorica; Shildkrot, Yevgeniy; Blumenfeld, Henrike K; Kaushanskaya, Margarita; Faroqi-Shah, Yasmeen; Hirsch, Joy

    2007-04-01

    Functional magnetic resonance imaging was used to compare cortical organization of the first (L1, Russian) and second (L2, English) languages. Six fluent Russian-English bilinguals who acquired their second language postpuberty were tested with words and nonwords presented either auditorily or visually. Results showed that both languages activated similar cortical networks, including the inferior frontal, middle frontal, superior temporal, middle temporal, angular, and supramarginal gyri. Within the inferior frontal gyrus (IFG), L2 activated a larger cortical volume than L1 during lexical and phonological processing. For both languages, the left IFG was more active than the right IFG during lexical processing. Within the left IFG, the distance between centers of activation associated with lexical processing of translation equivalents across languages was larger than the distance between centers of activation associated with lexical processing of different words in the same language. Results of phonological processing analyses revealed different centers of activation associated with the first versus the second language in the IFG, but not in the superior temporal gyrus (STG). These findings are discussed within the context of the current literature on cortical organization in bilinguals and suggest variation in bilingual cortical activation associated with lexical, phonological, and orthographic processing.

  2. Adaptation to stimulus contrast and correlations during natural visual stimulation

    PubMed Central

    Lesica, Nicholas A.; Jin, Jianzhong; Weng, Chong; Yeh, Chun-I; Butts, Daniel A.; Stanley, Garrett B.; Alonso, Jose-Manuel

    2008-01-01

    Summary In this study, we characterize the adaptation of neurons in the cat lateral geniculate nucleus to changes in stimulus contrast and correlations. By comparing responses to high and low contrast natural scene movie and white noise stimuli, we show that an increase in contrast or correlations results in receptive fields with faster temporal dynamics and stronger antagonistic surrounds, as well as decreases in gain and selectivity. We also observe contrast- and correlation-induced changes in the reliability and sparseness of neural responses. We find that reliability is determined primarily by processing in the receptive field (the effective contrast of the stimulus), while sparseness is determined by the interactions between several functional properties. These results reveal a number of novel adaptive phenomena and suggest that adaptation to stimulus contrast and correlations may play an important role in visual coding in a dynamic natural environment. PMID:17678859

  3. Ionization yield and absorption spectra reveal superexcited Rydberg state relaxation processes in H2O and D2O

    NASA Astrophysics Data System (ADS)

    Fillion, J.-H.; Dulieu, F.; Baouche, S.; Lemaire, J.-L.; Jochims, H. W.; Leach, S.

    2003-07-01

    The absorption cross section and the ionization quantum yield of H2O have been measured using a synchrotron radiation source between 9 and 22 eV. Comparison between the two curves highlights competition between relaxation processes for Rydberg states converging to the first tilde A 2A 1 and to the second tilde B 2B 2 excited states of H2O+. Comparison with D2O absorption and ionization yields, derived from Katayama et al (1973 J. Chem. Phys. 59 4309), reveals specific energy-dependent deuteration effects on competitive predissociation and autoionization relaxation channels. Direct ionization was found to be only slightly affected by deuteration.

  4. 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. PMID:24279717

  5. 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.

  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. PMID:26734990

  7. 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.

  8. 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. PMID:27277404

  9. The hand in motion of liberals and conservatives reveals the differential processing of positive and negative information.

    PubMed

    Carraro, Luciana; Castelli, Luigi; Negri, Paolo

    2016-07-01

    Recent research revealed that political conservatives and liberals differ in the processing of valenced information. In particular, conservatives (vs. liberals) tend to weigh negative information more than positive information in their perception of the physical and social world. In the present work, we further investigated the ideology-based asymmetries in the processing of negative and positive information examining both the attention-grabbing power of negative information and the trajectories of the movements performed by respondents when required to categorize positive and negative stimuli. To this end we employed a modified version of the Mouse-Tracking procedure (Freeman & Ambady, 2010), recording hand movements during the execution of categorization tasks. Results showed that conservatives were indeed slower to start and execute response actions to negative stimuli, and, more specifically, the trajectories of their movements signaled avoidance tendencies aimed at increasing the distance from negative stimuli. In addition, this pattern of findings emerged both when participants were asked to categorize the stimuli according to their valence and when the same stimuli had to be categorized on the basis of irrelevant perceptual features. Overall, results demonstrate that conservatives and liberals process valenced information differently, perform different spontaneous movements when exposed to them, and that such asymmetries are largely independent from current processing goals. PMID:27160061

  10. Naturally processed HLA class II peptides reveal highly conserved immunogenic flanking region sequence preferences that reflect antigen processing rather than peptide-MHC interactions.

    PubMed

    Godkin, A J; Smith, K J; Willis, A; Tejada-Simon, M V; Zhang, J; Elliott, T; Hill, A V

    2001-06-01

    MHC class II heterodimers bind peptides 12-20 aa in length. The peptide flanking residues (PFRs) of these ligands extend from a central binding core consisting of nine amino acids. Increasing evidence suggests that the PFRs can alter the immunogenicity of T cell epitopes. We have previously noted that eluted peptide pool sequence data derived from an MHC class II Ag reflect patterns of enrichment not only in the core binding region but also in the PFRS: We sought to distinguish whether these enrichments reflect cellular processes or direct MHC-peptide interactions. Using the multiple sclerosis-associated allele HLA-DR2, pool sequence data from naturally processed ligands were compared with the patterns of enrichment obtained by binding semicombinatorial peptide libraries to empty HLA-DR2 molecules. Naturally processed ligands revealed patterns of enrichment reflecting both the binding motif of HLA-DR2 (position (P)1, aliphatic; P4, bulky hydrophobic; and P6, polar) as well as the nonbound flanking regions, including acidic residues at the N terminus and basic residues at the C terminus. These PFR enrichments were independent of MHC-peptide interactions. Further studies revealed similar patterns in nine other HLA alleles, with the C-terminal basic residues being as highly conserved as the previously described N-terminal prolines of MHC class II ligands. There is evidence that addition of C-terminal basic PFRs to known peptide epitopes is able to enhance both processing as well as T cell activation. Recognition of these allele-transcending patterns in the PFRs may prove useful in epitope identification and vaccine design.

  11. 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

  12. Automated cell tracking and analysis in phase-contrast videos (iTrack4U): development of Java software based on combined mean-shift processes.

    PubMed

    Cordelières, Fabrice P; Petit, Valérie; Kumasaka, Mayuko; Debeir, Olivier; Letort, Véronique; Gallagher, Stuart J; Larue, Lionel

    2013-01-01

    Cell migration is a key biological process with a role in both physiological and pathological conditions. Locomotion of cells during embryonic development is essential for their correct positioning in the organism; immune cells have to migrate and circulate in response to injury. Failure of cells to migrate or an inappropriate acquisition of migratory capacities can result in severe defects such as altered pigmentation, skull and limb abnormalities during development, and defective wound repair, immunosuppression or tumor dissemination. The ability to accurately analyze and quantify cell migration is important for our understanding of development, homeostasis and disease. In vitro cell tracking experiments, using primary or established cell cultures, are often used to study migration as cells can quickly and easily be genetically or chemically manipulated. Images of the cells are acquired at regular time intervals over several hours using microscopes equipped with CCD camera. The locations (x,y,t) of each cell on the recorded sequence of frames then need to be tracked. Manual computer-assisted tracking is the traditional method for analyzing the migratory behavior of cells. However, this processing is extremely tedious and time-consuming. Most existing tracking algorithms require experience in programming languages that are unfamiliar to most biologists. We therefore developed an automated cell tracking program, written in Java, which uses a mean-shift algorithm and ImageJ as a library. iTrack4U is a user-friendly software. Compared to manual tracking, it saves considerable amount of time to generate and analyze the variables characterizing cell migration, since they are automatically computed with iTrack4U. Another major interest of iTrack4U is the standardization and the lack of inter-experimenter differences. Finally, iTrack4U is adapted for phase contrast and fluorescent cells.

  13. 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. PMID:26441762

  14. 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

  15. 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.

  16. Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity

    PubMed Central

    2015-01-01

    DNA lesion bypass polymerases process different lesions with varying fidelities, but the structural, dynamic, and mechanistic origins of this phenomenon remain poorly understood. Human DNA polymerase κ (Polκ), a member of the Y family of lesion bypass polymerases, is specialized to bypass bulky DNA minor groove lesions in a predominantly error-free manner, by housing them in its unique gap. We have investigated the role of the unique Polκ gap and N-clasp structural features in the fidelity of minor groove lesion processing with extensive molecular modeling and molecular dynamics simulations to pinpoint their functioning in lesion bypass. Here we consider the N2-dG covalent adduct derived from the carcinogenic aromatic amine, 2-acetylaminofluorene (dG-N2-AAF), that is produced via the combustion of kerosene and diesel fuel. Our simulations reveal how the spacious gap directionally accommodates the lesion aromatic ring system as it transits through the stages of incorporation of the predominant correct partner dCTP opposite the damaged guanine, with preservation of local active site organization for nucleotidyl transfer. Furthermore, flexibility in Polκ’s N-clasp facilitates the significant misincorporation of dTTP opposite dG-N2-AAF via wobble pairing. Notably, we show that N-clasp flexibility depends on lesion topology, being markedly reduced in the case of the benzo[a]pyrene-derived major adduct to N2-dG, whose bypass by Polκ is nearly error-free. Thus, our studies reveal how Polκ’s unique structural and dynamic properties can regulate its bypass fidelity of polycyclic aromatic lesions and how the fidelity is impacted by lesion structures. PMID:25148552

  17. Peripheral venous contrast echocardiography.

    PubMed

    Seward, J B; Tajik, A J; Hagler, D J; Ritter, D G

    1977-02-01

    Contrast echocardiography is the technique of injecting various echo-producing agents into the bloodstream and, with standard echocardiographic techniques, observing the blood flow patterns as revealed by the resulting cloud of echoes. These techniques have only recently been utilized to evaluate various cardiac defects. Two physical properties of these agents characterize their usefulness: (1) clouds of echoes can be observed downstream as well as at the injection site, and (2) the echo-producing quality of these agents is completely lost with a single transit through either the pulmonary or the systemic capillary bed. Thus, detection of resultant echoes in both the venous and the arterial blood pool is indicative of abnormal shunting. In 60 patients with a spectrum of cardiac defects and a wide range in age of presentation, studies were made of (1) the feasibility of performing contrast echocardiography with superficial peripheral venous injections, and (2) the clinical usefulness of this relatively noninvasive technique in detecting and localizing intracardiac right ot left shunting. Most superficial peripheral veins could be utilized, and the resultant contrast echograms were reproducible and similar in quality to those obtained more central (caval) injections. Right to left shunts could be localized in the atrial, ventricular or intrapulmonary level. Characteristic flow patterns were also recognized for tricuspid atresia and common ventricle.

  18. The process of S-nitrosation in sGC β1(1-194) revealed by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Li; Wang, Dandan; Xu, Haoran; Mi, Mengdan; Li, Zhengqiang

    2015-06-01

    Soluble guanylate cyclase (sGC) is the most important receptor for the signaling molecule NO. NO activates sGC by binding to its heme cofactor and reacts with free thiols in the protein itself. The S-nitrosation of cysteine thiols affects the activity of soluble guanylate cyclase (sGC). In this study, infrared (IR) spectroscopy and site-directed mutagenesis were used to investigate S-H vibration and the process of S-nitrosation in the β1 subunit (amino acids 1-194) of sGC. Fourier transform IR spectroscopy revealed that wild-type and mutants (C78S and C122S) of sGC β1(1-194) exhibited S-H peaks around 2560 cm-1. The signals were attenuated in the IR spectra of S-nitrosoglutathione-treated mutants, demonstrating that S-nitrosation in sGC β1(1-194) occured at residues C78 and C122, and the process of the reaction was GSNO concentration-dependent.

  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. Phosphoproteomic analysis of induced resistance reveals activation of signal transduction processes by beneficial and pathogenic interaction in grapevine.

    PubMed

    Perazzolli, Michele; Palmieri, Maria Cristina; Matafora, Vittoria; Bachi, Angela; Pertot, Ilaria

    2016-05-20

    Protein phosphorylation regulates several key processes of the plant immune system. Protein kinases and phosphatases are pivotal regulators of defense mechanisms elicited by resistance inducers. However, the phosphorylation cascades that trigger the induced resistance mechanisms in plants have not yet been deeply investigated. The beneficial fungus Trichoderma harzianum T39 (T39) induces resistance against grapevine downy mildew (Plasmopara viticola), but its efficacy could be further improved by a better understanding of the cellular regulations involved. We investigated quantitative changes in the grapevine phosphoproteome during T39-induced resistance to get an overview of regulatory mechanisms of downy mildew resistance. Immunodetection experiments revealed activation of the 45 and 49kDa kinases by T39 treatment both before and after pathogen inoculation, and the phosphoproteomic analysis identified 103 phosphopeptides that were significantly affected by the phosphorylation cascades during T39-induced resistance. Peptides affected by T39 treatment showed comparable phosphorylation levels after P. viticola inoculation, indicating activation of the microbial recognition machinery before pathogen infection. Phosphorylation profiles of proteins related to photosynthetic processes and protein ubiquitination indicated a partial overlap of cellular responses in T39-treated and control plants. However, phosphorylation changes of proteins involved in response to stimuli, signal transduction, hormone signaling, gene expression regulation, and RNA metabolism were exclusively elicited by P. viticola inoculation in T39-treated plants. These results highlighted the relevance of phosphorylation changes during T39-induced resistance and identified key regulator candidates of the grapevine defense against downy mildew. PMID:27010348

  1. 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. PMID:25740152

  2. 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

  3. 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

  4. Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves

    PubMed Central

    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

    2011-01-01

    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

  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. 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

  7. Investigation of metal contamination induced by a through silicon via reveal process using direct Si/Cu grinding and residual metal removal

    NASA Astrophysics Data System (ADS)

    Watanabe, Naoya; Aoyagi, Masahiro; Katagawa, Daisuke; Bandoh, Tsubasa; Mitsui, Takahiko; Yamamoto, Eiichi

    2016-06-01

    We investigated metal contamination induced by a through silicon via (TSV) reveal process using direct Si/Cu grinding and residual metal removal. A complementary metal oxide semiconductor (CMOS) wafer including TSVs was bonded to a glass support substrate, and a TSV reveal process was performed by direct Si/Cu grinding and residual metal removal. Then, metal contamination near the SiO2/Si interface on the front side of the wafer was investigated by using a pulsed-MOS capacitor technique and measuring the effective generation lifetime and effective surface generation velocity before and after this TSV reveal process. The results of Zerbst analysis showed that the changes in average effective generation lifetime and average effective surface generation velocity were ‑5.4 and +4.2%, respectively. These results demonstrate that the effect of metal contamination induced by our TSV reveal process on circuit components is small.

  8. Investigation of metal contamination induced by a through silicon via reveal process using direct Si/Cu grinding and residual metal removal

    NASA Astrophysics Data System (ADS)

    Watanabe, Naoya; Aoyagi, Masahiro; Katagawa, Daisuke; Bandoh, Tsubasa; Mitsui, Takahiko; Yamamoto, Eiichi

    2016-06-01

    We investigated metal contamination induced by a through silicon via (TSV) reveal process using direct Si/Cu grinding and residual metal removal. A complementary metal oxide semiconductor (CMOS) wafer including TSVs was bonded to a glass support substrate, and a TSV reveal process was performed by direct Si/Cu grinding and residual metal removal. Then, metal contamination near the SiO2/Si interface on the front side of the wafer was investigated by using a pulsed-MOS capacitor technique and measuring the effective generation lifetime and effective surface generation velocity before and after this TSV reveal process. The results of Zerbst analysis showed that the changes in average effective generation lifetime and average effective surface generation velocity were -5.4 and +4.2%, respectively. These results demonstrate that the effect of metal contamination induced by our TSV reveal process on circuit components is small.

  9. Analytical strategy to reveal the in vivo process of multi-component herbal medicine: a pharmacokinetic study of licorice using liquid chromatography coupled with triple quadrupole mass spectrometry.

    PubMed

    Qiao, Xue; Ye, Min; Xiang, Cheng; Wang, Qing; Liu, Chun-Fang; Miao, Wen-Juan; Guo, De-An

    2012-10-01

    Although various techniques have been employed to analyze drug metabolites, the metabolism of multi-component herbal medicine has seldom been fully addressed. In contrast to chemical drugs, a number of compounds in herbal medicine could get into circulation and then be metabolized. Moreover, these compounds may have metabolic interactions which make their pharmacokinetics (PK) even more complicated. The present work aims to elucidate the multi-component pharmacokinetics of a herbal medicine, and to demonstrate how PK behaviors were altered by co-existing constituents. Licorice (Glycyrrhiza uralensis Fisch.), a most commonly used herbal medicine, was chosen as a model. A strategy was proposed to compare the PK profiles of licorice extract with those of nine single compounds. These compounds were major bioactive constituents of licorice, and represented various structural types (flavanone, chalcone, isoflavone, saponin, and coumarin). We established a segmented selected reaction monitoring LC/MS/MS method to simultaneously monitor 63 licorice metabolites in rat plasma, and obtained the PK profiles of 55 metabolites. The results indicated that interactions among licorice compounds altered their PK behaviors in 4 aspects: improvement in bioavailability for aglycones (133- and 109-fold increase for liquiritigenin and isoliquiritigenin, respectively), prolongation in system circulation for glycosides (0.3h delay in T(max) for liquiritin apioside and isoliquiritin apioside), decrease of potential toxicity for saponins such as glycyrrhizic acid, and shift in plasma distribution for phase II metabolites. This is the first attempt to systematically reveal the in vivo process of licorice. Moreover, the study indicates noticeable interactions to alter pharmacokinetics among licorice compounds, which may be characteristic for herbal medicines.

  10. 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.

  11. Physical Connectivity Mapping by Circular Permutation of Human Telomerase RNA Reveals New Regions Critical for Activity and Processivity.

    PubMed

    Mefford, Melissa A; Zappulla, David C

    2015-01-01

    Telomerase is a specialized ribonucleoprotein complex that extends the 3' ends of chromosomes to counteract telomere shortening. However, increased telomerase activity is associated with ∼90% of human cancers. The telomerase enzyme minimally requires an RNA (hTR) and a specialized reverse transcriptase protein (TERT) for activity in vitro. Understanding the structure-function relationships within hTR has important implications for human disease. For the first time, we have tested the physical-connectivity requirements in the 451-nucleotide hTR RNA using circular permutations, which reposition the 5' and 3' ends. Our extensive in vitro analysis identified three classes of hTR circular permutants with altered function. First, circularly permuting 3' of the template causes specific defects in repeat-addition processivity, revealing that the template recognition element found in ciliates is conserved in human telomerase RNA. Second, seven circular permutations residing within the catalytically important core and CR4/5 domains completely abolish telomerase activity, unveiling mechanistically critical portions of these domains. Third, several circular permutations between the core and CR4/5 significantly increase telomerase activity. Our extensive circular permutation results provide insights into the architecture and coordination of human telomerase RNA and highlight where the RNA could be targeted for the development of antiaging and anticancer therapeutics. PMID:26503788

  12. Pathway analysis of senescence-associated miRNA targets reveals common processes to different senescence induction mechanisms.

    PubMed

    Lafferty-Whyte, Kyle; Cairney, Claire J; Jamieson, Nigel B; Oien, Karin A; Keith, W Nicol

    2009-04-01

    Multiple mechanisms of senescence induction exist including telomere attrition, oxidative stress, oncogene expression and DNA damage signalling. The regulation of the cellular changes required to respond to these stimuli and create the complex senescent cell phenotype has many different mechanisms. MiRNAs present one mechanism by which genes with diverse functions on multiple pathways can be simultaneously regulated. In this study we investigated 12 miRNAs previously identified as senescence regulators. Using pathway analysis of their target genes we tested the relevance of miRNA regulation in the induction of senescence. Our analysis highlighted the potential of these senescence-associated miRNAs (SA-miRNAs) to regulate the cell cycle, cytoskeletal remodelling and proliferation signalling logically required to create a senescent cell. The reanalysis of publicly available gene expression data from studies exploring different senescence stimuli also revealed their potential to regulate core senescence processes, regardless of stimuli. We also identified stimulus specific apoptosis survival pathways theoretically regulated by the SA-miRNAs. Furthermore the observation that miR-499 and miR-34c had the potential to regulate all 4 of the senescence induction types we studied highlights their future potential as novel drug targets for senescence induction. PMID:19419692

  13. 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.

  14. Processes and time scales of magmatic evolution as revealed by Fe-Mg chemical and isotopic zoning in natural olivines

    NASA Astrophysics Data System (ADS)

    Oeser, Martin; Dohmen, Ralf; Horn, Ingo; Schuth, Stephan; Weyer, Stefan

    2015-04-01

    In this study, we applied high-precision in situ Fe and Mg isotope analyses by femtosecond laser ablation (fs-LA) MC-ICP-MS on chemically zoned olivine xeno- and phenocrysts from intra-plate volcanic regions in order to investigate the magnitude of Fe and Mg isotope fractionation and its suitability to gain information on magma evolution. Our results show that chemical zoning (i.e., Mg#) in magmatic olivines is commonly associated with significant zoning in δ56Fe and δ26Mg (up to 1.7‰ and 0.7‰, respectively). We explored different cases of kinetic fractionation of Fe and Mg isotopes by modeling diffusion in the melt or olivine and simultaneous growth or dissolution. Combining the information of chemical and isotopic zoning in olivine allows to distinguish between various processes that may occur during magma evolution, namely diffusive Fe-Mg exchange between olivine and melt, rapid crystal growth, and Fe-Mg inter-diffusion simultaneous to crystal dissolution or growth. Chemical diffusion in olivine appears to be the dominant process that drives isotope fractionation in magmatic olivine. Simplified modeling of Fe and Mg diffusion is suitable to reproduce both the chemical and the isotopic zoning in most of the investigated olivines and, additionally, provides time information about magmatic processes. For the Massif Central (France), modeling of diffusive re-equilibration of mantle olivines in basanites revealed a short time span (<2 years) between the entrainment of a mantle xenolith in an intra-plate basaltic magma and the eruption of the magma. Furthermore, we determined high cooling rates (on the order of a few tens to hundreds of °C per year) for basanite samples from a single large outcrop in the Massif Central, which probably reflects the cooling of a massive lava flow after eruption. Results from the modeling of Fe and Mg isotope fractionation in olivine point to a systematic difference between βFe and βMg (i.e., βFe/βMg ≈ 2), implying that the

  15. 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

  16. Recognition of infrared images. Part 3: The effect of image processing with a size-contrast box filter on observation performance

    NASA Astrophysics Data System (ADS)

    Alblas, B. P.

    1989-10-01

    The size-contrast box filter (which incorporates contrast and expected size of the target) was used in the detection of military targets in infrared images in order to distinguish clutter from targets and to increase the observation performance. The percentage of detected targets by the computer was between 65 and 93 percent, the percentage of false alarms between 14 and 40 percent. All the images were marked with one or two cues (arrows) at the most probable occupied position(s). The effect of cueing is very significant. The type of algorithm and the number of cues has no effect. On average the detection score increased by 20 percent and the percentage of false alarms decreased by 60 percent. These improvements are maintained, when after performing the runs with cueing, the cues were left out. The human observer supported by cueing appeared to always perform much better than the computer with respect to false alarms.

  17. 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

  18. 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

  19. 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…

  20. Visual maladaptation in contrast domain

    NASA Astrophysics Data System (ADS)

    Pajak, Dawid; Cadík, Martin; Aydin, Tunç O.; Myszkowski, Karol; Seidel, Hans-Peter

    2010-02-01

    In this work we simulate the effect of the human eye's maladaptation to visual perception over time through a supra-threshold contrast perception model that comprises adaptation mechanisms. Specifically, we attempt to visualize maladapted vision on a display device. Given the scene luminance, the model computes a measure of perceived multi-scale contrast by taking into account spatially and temporally varying contrast sensitivity in a maladapted state, which is then processed by the inverse model and mapped to a desired display's luminance assuming perfect adaptation. Our system simulates the effect of maladaptation locally, and models the shifting of peak spatial frequency sensitivity in maladapted vision in addition to the uniform decrease in contrast sensitivity among all frequencies. Through our GPU implementation we demonstrate the visibility loss of scene details due to maladaptation over time at an interactive speed.

  1. 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.

  2. 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

  3. 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.

  4. Contrasting the eastern Pacific El Niño and the central Pacific El Niño: process-based feedback attribution

    NASA Astrophysics Data System (ADS)

    Hu, Xiaoming; Yang, Song; Cai, Ming

    2016-10-01

    This paper examines the roles of radiative and non-radiative air-sea coupled thermodynamic processes in modifying sea surface temperature (SST) anomalies driven by (air-sea coupled) oceanic dynamic processes, focusing on their contributions to the key differences between the eastern Pacific (EP) El Niño and the central Pacific (CP) El Niño. The attribution is achieved by decomposing SST anomalies into partial temperature anomalies due to individual processes using a coupled atmosphere-surface climate feedback-response analysis method. Oceanic processes induce warming from the central to the eastern equatorial Pacific and cooling over the western basin with a maximum warming center in the central Pacific for both types of El Niño. The processes that act to oppose the oceanic process-induced SST anomalies are surface latent heat flux, sensible heat flux, cloud, and atmospheric dynamic feedbacks, referred to as negative-feedback processes. The cooling due to each of the four negative-feedback processes is the strongest in the region where the initial warming due to oceanic processes is the largest. Water-vapor feedback is the sole process that acts to enhance the initial warming induced by oceanic processes. The increase in atmospheric water vapor over the eastern Pacific is much stronger for the EP El Niño than for the CP El Niño. It is the strong water-vapor feedback over the eastern Pacific and the strong negative feedbacks over the central equatorial Pacific that help to relocate the maximum warming center from the central Pacific to the eastern basin for the EP El Niño.

  5. Fluvial connectivity and climate: A comparison of channel pattern and process in two climatically contrasting fluvial sedimentary systems in South Africa

    NASA Astrophysics Data System (ADS)

    Grenfell, S. E.; Grenfell, M. C.; Rowntree, K. M.; Ellery, W. N.

    2014-01-01

    The aim of this research was to investigate the dynamics of valley formation, sediment delivery and channel pattern in two climatically contrasting fluvial sedimentary systems in South Africa. Each system comprised a network of headwater valley fills and floodplains underlain by sedimentary Karoo Supergroup rocks that are intersected by resistant dolerite dykes and sills. The Seekoei River Floodplain and Gordonville valley fill site in the Great Karoo, however, experience less than half the annual precipitation of the Nsonge River Floodplain and Hlatikhulu valley fill in the KwaZulu-Natal Drakensberg Foothills. Furthermore, rainfall is more variable in the Karoo. Despite climatic differences, headwater valley fills were geomorphically similar. In contrast, floodplains in the two regions were vastly different, even when the same downstream control (a resistant dolerite intrusion crossing the drainage line) was considered. Upstream of a dolerite dyke, the Nsonge River is highly sinuous and located in a wide floodplain that has been carved by lateral planation of the underlying bedrock. In comparison, the Seekoei River, located upstream of a dolerite sill, is discontinuous and characterized by floodouts and avulsing distributaries that undergo periods of bedrock incision, followed by infilling.It is likely that this disparity is caused by the inability of infrequent, unsustained flows to develop meanders and, thus, adjust the channel planform to changes in discharge, sediment load and valley slope. Flow variability, thus, exercises a strong control on channel pattern and causes floodouts in headwater settings and the semi-arid Karoo floodplain. As a result, sediment transport in the Seekoei River is likely to be episodic, and net retention of sediment in the semi-arid floodplain is greater than in the sub-humid Nsonge River Floodplain, where sediment depth is limited.

  6. [Contrast sensitivity in glaucoma].

    PubMed

    Bartos, D

    1989-05-01

    Author reports on results of the contrast sensitivity examinations using the Cambridge low-contrast lattice test supplied by Clement Clarke International LTD, in patients with open-angle glaucoma and ocular hypertension. In glaucoma patients there was observed statistically significant decrease of the contrast sensitivity. In patients with ocular hypertension decrease of the contrast sensitivity was in patients affected by corresponding changes of the visual field and of the optical disc. The main advantages of the Cambridge low-contrast lattice test were simplicity, rapidity and precision of its performance. PMID:2743444

  7. 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.

  8. Contrasting the Eastern Pacific El Niño and the Central Pacific El Niño: Process-based Feedback Attribution

    NASA Astrophysics Data System (ADS)

    HU, X.; Yang, S.; Cai, M.

    2015-12-01

    This paper examines the roles of the radiative and non-radiative air-sea coupled thermodynamic processes in modifying the SST anomalies driven by air-sea coupled oceanic dynamic processes. This helps to isolate their contributions to the key differences between the Eastern Pacific (EP) El Niño and the Central Pacific (CP) El Niño. The attribution is achieved by decomposing sea surface temperature (SST) anomalies into partial SST anomalies due to individual processes using a coupled atmosphere-surface climate feedback-responses analysis method. Oceanic processes induce warming from the central to the eastern equatorial Pacific and cooling over the western basin with the maximum warming center in the central Pacific for both types of El Niño. The processes that act to oppose the oceanic process-induced SST anomalies are surface latent flux, sensible heat flux, cloud, and atmospheric dynamic feedbacks. The cooling due to each of the four negative-feedback processes is strongest in the region where the initial warming due to oceanic processes is maximum. Water vapor feedback is the sole process that acts to enhance the initial warming induced by oceanic processes. The increase of atmospheric water vapor over the eastern Pacific is much stronger for EP El Niño than CP El Niño. Therefore, it is the strong water vapor feedback over the eastern Pacific together with the strong negative feedbacks over the central equatorial Pacific that helps to relocate the maximum warming center from the central Pacific to the eastern basin for EP El Niño.This paper examines the roles of the radiative and non-radiative air-sea coupled thermodynamic processes in modifying the SST anomalies driven by air-sea coupled oceanic dynamic processes. This helps to isolate their contributions to the key differences between the Eastern Pacific (EP) El Niño and the Central Pacific (CP) El Niño. The attribution is achieved by decomposing sea surface temperature (SST) anomalies into partial SST

  9. 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. PMID:26771674

  10. 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…

  11. 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…

  12. Indicators of early and late processing reveal the importance of within-trial-time for theories of associative learning.

    PubMed

    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.

  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. 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. PMID:9554844

  15. 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.

  16. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of Pre-rRNA processing factors.

    PubMed

    Tafforeau, Lionel; Zorbas, Christiane; Langhendries, Jean-Louis; Mullineux, Sahra-Taylor; Stamatopoulou, Vassiliki; Mullier, Romain; Wacheul, Ludivine; Lafontaine, Denis L J

    2013-08-22

    Mature ribosomal RNAs (rRNAs) are produced from polycistronic precursors following complex processing. Precursor (pre)-rRNA processing has been extensively characterized in yeast and was assumed to be conserved in humans. We functionally characterized 625 nucleolar proteins in HeLa cells and identified 286 required for processing, including 74 without a yeast homolog. For selected candidates, we demonstrated that pre-rRNA processing defects are conserved in different cell types (including primary cells), defects are not due to activation of a p53-dependent nucleolar tumor surveillance pathway, and they precede cell-cycle arrest and apoptosis. We also investigated the exosome's role in processing internal transcribed spacers (ITSs) and report that 3' end maturation of 18S rRNA involves EXOSC10/Rrp6, a yeast ITS2 processing factor. We conclude that human cells adopt unique strategies and recruit distinct trans-acting factors to carry out essential processing steps, posing fundamental implications for understanding ribosomopathies at the molecular level and developing effective therapeutic agents. PMID:23973377

  17. Switch-like regulation of tissue-specific alternative pre-mRNA processing patterns revealed by customized fluorescence reporters

    PubMed Central

    Kuroyanagi, Hidehito

    2013-01-01

    Alternative processing of precursor mRNAs (pre-mRNAs), including alternative transcription start sites, alternative splicing and alternative polyadenylation, is the major source of protein diversity and plays crucial roles in development, differentiation and diseases in higher eukaryotes. It is estimated from microarray analyses and deep sequencing of mRNAs from synchronized worms that up to 25% of protein-coding genes in Caenorhabditis elegans undergo alternative pre-mRNA processing and that many of them are subject to developmental regulation. Recent progress in visualizing the alternative pre-mRNA processing patterns in living worms with custom-designed fluorescence reporters has enabled genetic analyses of the regulatory mechanisms for alternative processing events of interest in vivo. Expression of the tissue-specific isoforms of actin depolymerising factor (ADF)/cofilin, UNC-60A and UNC-60B, is regulated by a combination of alternative splicing and alternative polyadenylation of pre-mRNA from a single gene unc-60. We recently found that muscle-specific splicing regulators ASD-2 and SUP-12 cooperatively switch the pre-mRNA processing patterns of the unc-60 gene in body wall muscles. Here I summarize the bichromatic fluorescence reporter system utilized for visualizing the tissue-specific alternative processing patterns of the unc-60 pre-mRNA. I also discuss the model for the coordinated regulation of the UNC-60B-type pre-mRNA processing in body wall muscles by ASD-2 and SUP-12. PMID:24778931

  18. fMRI-constrained source analysis reveals early top-down modulations of interference processing using a flanker task.

    PubMed

    Siemann, Julia; Herrmann, Manfred; Galashan, Daniela

    2016-08-01

    Usually, incongruent flanker stimuli provoke conflict processing whereas congruent flankers should facilitate task performance. Various behavioral studies reported improved or even absent conflict processing with correctly oriented selective attention. In the present study we attempted to reinvestigate these behavioral effects and to disentangle neuronal activity patterns underlying the attentional cueing effect taking advantage of a combination of the high temporal resolution of Electroencephalographic (EEG) and the spatial resolution of functional magnetic resonance imaging (fMRI). Data from 20 participants were acquired in different sessions per method. We expected the conflict-related N200 event-related potential (ERP) component and areas associated with flanker processing to show validity-specific modulations. Additionally, the spatio-temporal dynamics during cued flanker processing were examined using an fMRI-constrained source analysis approach. In the ERP data we found early differences in flanker processing between validity levels. An early centro-parietal relative positivity for incongruent stimuli occurred only with valid cueing during the N200 time window, while a subsequent fronto-central negativity was specific to invalidly cued interference processing. The source analysis additionally pointed to separate neural generators of these effects. Regional sources in visual areas were involved in conflict processing with valid cueing, while a regional source in the anterior cingulate cortex (ACC) seemed to contribute to the ERP differences with invalid cueing. Moreover, the ACC and precentral gyrus demonstrated an early and a late phase of congruency-related activity differences with invalid cueing. We discuss the first effect to reflect conflict detection and response activation while the latter more likely originated from conflict monitoring and control processes during response competition. PMID:27181762

  19. 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. PMID:27067362

  20. 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.

  1. Contrast Intravasation During Hysterosalpingography

    PubMed Central

    Bhoil, Rohit; Sood, Dinesh; Sharma, Tanupriya; Sood, Shilpa; Sharma, Jiten; Kumar, Nitesh; Ahluwalia, Ajay; Parekh, Dipen; Mistry, Kewal A.; Sood, Saurav

    2016-01-01

    Summary Hysterosalpingography is an imaging method to evaluate the endometrial and uterine morphology and fallopian tube patency. Contrast intravasation implies backflow of injected contrast into the adjoining vessels mostly the veins and may be related to factors altering endometrial vascularity and permeability. Radiologists and gynaecologists should be well acquainted with the technique of hysterosalpingography, its interpretation, and intravasation of contrast agents for safer procedure and to minimize the associated complications. PMID:27279925

  2. 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. PMID:25491751

  3. Individual differences in skilled adult readers reveal dissociable patterns of neural activity associated with component processes of reading.

    PubMed

    Welcome, Suzanne E; Joanisse, Marc F

    2012-03-01

    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 frontal and temporal regions whereas semantic processing was associated with bilateral middle frontal activation. Individual differences in reading subskills were reflected in differences in the degree to which cortical regions were engaged during reading. Variation in sight word reading efficiency was associated with degree of activation in visual cortex. Increased phonological decoding skill was associated with greater activation in left temporo-parietal cortex. Greater reading comprehension ability was associated with decreased activation in anterior cingulate and temporal regions. Notably, associations between reading ability and neural activation indicate that brain/behavior relationships among skilled readers differ from patterns associated with dyslexia and reading development.

  4. 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.

  5. 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

  6. Striatal and hippocampal entropy and recognition signals in category learning: simultaneous processes revealed by model-based fMRI.

    PubMed

    Davis, Tyler; Love, Bradley C; Preston, Alison R

    2012-07-01

    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. 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

  8. 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…

  9. 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.

  10. Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process

    PubMed Central

    Iacovache, Ioan; De Carlo, Sacha; Cirauqui, Nuria; Dal Peraro, Matteo; van der Goot, F. Gisou; Zuber, Benoît

    2016-01-01

    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. PMID:27405240

  11. Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process.

    PubMed

    Iacovache, Ioan; De Carlo, Sacha; Cirauqui, Nuria; Dal Peraro, Matteo; van der Goot, F Gisou; Zuber, Benoît

    2016-01-01

    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. PMID:27405240

  12. Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process.

    PubMed

    Iacovache, Ioan; De Carlo, Sacha; Cirauqui, Nuria; Dal Peraro, Matteo; van der Goot, F Gisou; Zuber, Benoît

    2016-07-13

    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.

  13. 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.

  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. 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…

  16. 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…

  17. 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. PMID:26482709

  18. 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

  19. 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…

  20. The Processing of Causal and Hierarchical Relations in Semantic Memory as Revealed by N400 and Frontal Negativity.

    PubMed

    Liang, Xiuling; Chen, Qingfei; Lei, Yi; Li, Hong

    2015-01-01

    Most current studies investigating semantic memory have focused on associative (ring-emerald) or taxonomic relations (bird-sparrow). Little is known about the question of how causal relations (virus-epidemic) are stored and accessed in semantic memory. The goal of this study was to examine the processing of causally related, general associatively related and hierarchically related word pairs when participants were required to evaluate whether pairs of words were related in any way. The ERP data showed that the N400 amplitude (200-500 ms) elicited by unrelated related words was more negative than all related words. Furthermore, the late frontal distributed negativity (500-700 ms) elicited by causally related words was smaller than hierarchically related words, but not for general associated words. These results suggested the processing of causal relations and hierarchical relations in semantic memory recruited different degrees of cognitive resources, especially for role binding. PMID:26148338

  1. Behavioral Contrast in Infants.

    ERIC Educational Resources Information Center

    Fagen, Jeffrey W.

    This study used the behavioral contrast paradigm to assess the excitatory and inhibitory capabilities of young infants. Behavioral contrast is described as the phenomenon whereby the rates of responding in the presence of two stimuli, both of which were previously associated with reinforcement, change in opposite directions when only one of them…

  2. 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

  3. Asymmetric processing of mutant factor X Arg386Cys reveals differences between intrinsic and extrinsic pathway activation.

    PubMed

    Baroni, M; Pavani, G; Pinotti, M; Branchini, A; Bernardi, F; Camire, R M

    2015-10-01

    Alterations in coagulation factor X (FX) activation, mediated by the extrinsic VIIa/tissue factor (FVIIa/TF) or the intrinsic factor IXa/factor VIIIa (FIXa/FVIIIa) complexes, can result in hemorrhagic/prothrombotic tendencies. However, the molecular determinants involved in substrate recognition by these enzymes are poorly defined. Here, we investigated the role of arginine 386 (chymotrypsin numbering c202), a surface-exposed residue on the FX catalytic domain. The naturally occurring FX386Cys mutant and FX386Ala variant were characterized. Despite the unpaired cysteine, recombinant (r)FX386Cys was efficiently secreted (88.6±21.3% of rFXwt) and possessed normal clearance in mice. rFX386Cys was also normally activated by FVIIa/TF and displayed intact amidolytic activity. In contrast, rFX386Cys activation by the FIXa/FVIIIa complex was 4.5-fold reduced, which was driven by a decrease in the kcat (1.6∗10(-4) s(-1) vs 5.8∗10(-4) s(-1), rFXwt). The virtually unaltered Km (70.6 nM vs 55.6nM, rFXwt) suggested no major alterations in the FX substrate exosite. Functional assays in plasma supplemented with rFX386Cys indicated a remarkable reduction in the thrombin generation rate and thus in coagulation efficiency. Consistently, the rFX386Ala variant displayed similar biochemical features suggesting that global changes at position 386 impact the intrinsic pathway activation. These data indicate that the FXArg386 is involved in FIXa/FVIIIa-mediated FX activation and help in elucidating the bleeding tendency associated with the FX386Cys in a rare FX deficiency case. Taking advantage of the unpaired cysteine, the rFX386Cys mutant may be efficiently targeted by thiol-specific ligands and represent a valuable tool to study FX structure-function relationships both in vitro and in vivo. PMID:26012870

  4. Environmental surveillance of norovirus in Argentina revealed distinct viral diversity patterns, seasonality and spatio-temporal diffusion processes.

    PubMed

    Fernández, María D Blanco; Torres, Carolina; Poma, Hugo R; Riviello-López, Gabriela; Martínez, Laura C; Cisterna, Daniel M; Rajal, Verónica B; Nates, Silvia V; Mbayed, Viviana A

    2012-10-15

    Norovirus (NoV) contamination was evaluated in five rivers of Argentina between 2005 and 2011. NoV was present in all sampled rivers, with distinct NoV patterns in waters impacted by different-sized communities. In rivers affected by medium-sized populations (Salta and Córdoba cities) only one or two genotypes were present, GII.4 being the main one, with winter seasonality. In contrast, in the much more heavily populated area of Buenos Aires city the prevalent GII.4 was accompanied by several additional genotypes (GII.4, GII.b, GII.2, GII.7, GII.17, GII.e and GII.g) and one ungenotyped GII NoV, with no clear seasonality. GII.4 2006b was the main variant detected (60.9%). Phylogeographic and phylodynamic analyses performed in region D of the VP1 gene showed a most recent common ancestor in 2002 and a substitution rate of 3.7×10(-3) substitutions per site per year (HPD95%=2.3×10(-3)-5.2×10(-3)) for this variant still involving a significant population size with a slight decrease since 2008. The spatio-temporal diffusion analysis proposed Europe as an intermediate path between the American Continent and the rest of the World for NoV dissemination. Given the importance of NoV as a cause of epidemic gastroenteritis and the likelihood of its environmental transmission, the results of this work should increase public and institutional awareness of the health risk involved in sewage discharges into the environment. Environmental surveillance of enteric viruses could be a very useful tool not only to prevent waterborne outbreaks, but also to describe the epidemiology of the viruses. The detailed analysis of the viral genomes disposed into the environment contributed to the characterization of the dissemination, diversity and seasonality of NoV in its natural host population. In future studies, environmental surveillance and molecular analysis should be complemented with a quantitative viral risk assessment for estimating the disease burden from viruses in the

  5. 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.

  6. Age Effects in L2 Grammar Processing as Revealed by ERPs and How (Not) to Study Them

    PubMed Central

    Meulman, Nienke; Wieling, Martijn; Sprenger, Simone 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. PMID:26683335

  7. 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

  8. 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. PMID:26683335

  9. Cerebral hemodynamic response in Chinese (first) and English (second) language processing revealed by event-related functional MRI.

    PubMed

    Pu, Y; Liu, H L; Spinks, J A; Mahankali, S; Xiong, J; Feng, C M; Tan, L H; Fox, P T; Gao, J H

    2001-06-01

    Comparative functional neuroimaging studies using the block design paradigm have previously demonstrated that there are no significant differences in the location of areas of cerebral activation when native Chinese speakers independently process single words or sentences in both the Chinese (first) and English (second) languages. While it has also been documented that significant domains of brain response include the inferior to middle left frontal lobe, the latency, amplitude and duration of the associated hemodynamic changes during isolated neural processing of Chinese and English languages still remain unknown. The aim of this study, therefore, was to examine the characteristics of the hemodynamic alterations in the above-mentioned regions with event-related functional MRI (ER-fMRI) when native Chinese speakers performed verb generation tasks in both the Chinese (first) and English (second) languages. Our results demonstrate the presence of a similar neural activity-induced hemodynamic response in the inferior to middle left frontal lobe during both tasks. Further, there were also no statistically significant differences among the variables that described the hemodynamic response curves. These findings strongly imply that the underlying neural mechanism for Chinese (first) and English (second) language processing may be similar in native Chinese speakers.

  10. Contrasting isotopic signatures between anthropogenic and geogenic Zn and evidence for post-depositional fractionation processes in smelter-impacted soils from Northern France

    NASA Astrophysics Data System (ADS)

    Juillot, Farid; Maréchal, Chloe; Morin, Guillaume; Jouvin, Delphine; Cacaly, Sylvain; Telouk, Philipe; Benedetti, Marc F.; Ildefonse, Philippe; Sutton, Steve; Guyot, François; Brown, Gordon E., Jr.

    2011-05-01

    Zinc isotopes have been studied along two smelter-impacted soil profiles sampled near one of the largest Pb and Zn processing plants in Europe located in northern France, about 50 km south of Lille. Mean δ 66Zn values along these two soil profiles range from +0.22 ± 0.17‰ (2 σ) to +0.34 ± 0.17‰ (2 σ) at the lowest horizons and from +0.38 ± 0.45‰ (2 σ) to +0.76 ± 0.14‰ (2 σ) near the surface. The δ 66Zn values in the lowest horizons of the soils are interpreted as being representative of the local geochemical background (mean value +0.31 ± 0.38‰), whereas heavier δ 66Zn values near the surface of the two soils are related to anthropogenic Zn. This anthropogenic Zn occurs in the form of franklinite (ZnFe 2O 4)-bearing slag grains originating from processing wastes at the smelter site and exhibiting δ 66Zn values of +0.81 ± 0.20‰ (2 σ). The presence of franklinite is indicated by EXAFS analysis of the topsoil samples from both soil profiles as well as by micro-XANES analysis of the surface horizon of a third smelter-impacted soil from a distant site. These results indicate that naturally occurring Zn and smelter-derived Zn exhibit significantly different δ 66Zn values, which suggests that zinc isotopes can be used to distinguish between geogenic and anthropogenic sources of Zn in smelter-impacted soils. In addition to a possible influence of additional past sources of light Zn (likely Zn-sulfides and Zn-sulfates directly emitted by the smelter), the light δ 66Zn values in the surface horizons compared to smelter-derived slag materials are interpreted as resulting mainly from fractionation processes associated with biotic and/or abiotic pedological processes (Zn-bearing mineral precipitation, Zn complexation by organic matter, and plant uptake of Zn). This conclusion emphasizes the need for additional Zn isotopic studies before being able to use Zn isotopes to trace sources and pathways of this element in surface environments.

  11. 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

  12. Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation.

    PubMed

    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; Ferrer, Manuel; Golyshin, Peter N

    2015-10-01

    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.

  13. Positive allosteric modulation reveals a specific role for mGlu2 receptors in sensory processing in the thalamus.

    PubMed

    Copeland, C S; Neale, S A; Salt, T E

    2012-02-15

    Group II metabotropic glutamate receptor (mGlu) modulation of sensory processing in the rat ventrobasal thalamic nucleus (VB) has been extensively studied in vivo. However, it is not yet known what the relative contributions are of the Group II mGlu receptor subtypes (mGlu2 and mGlu3) to this modulation, nor to what extent these receptors may be activated under physiological conditions during this process. Using single-neurone recording in the rat VB in vivo with local application of the selective Group II agonist LY354740 and the subtype selective mGlu2 positive allosteric modulator (PAM) LY487379, our findings were twofold. Firstly, we found that there is an mGlu2 component to the effects of LY354740 on sensory responses in the VB. Secondly, we have demonstrated that application of the PAM alone can modulate sensory responses of single neurones in vivo. This indicates that mGlu2 receptors can be activated by endogenous agonist following physiological sensory stimulation. We speculate that the mGlu2 subtype could be activated under physiological stimulus-evoked conditions by 'glutamate spillover' from synapses between excitatory sensory afferents and VB neurones that can lead to a reduction in sensory-evoked inhibition arising from the thalamic reticular nucleus (TRN). We propose that this potential mGlu2 receptor modulation of inhibition could play an important role in discerning relevant information from background activity upon physiological sensory stimulation. Furthermore, this could be a site of action for mGlu2 PAMs to modulate cognitive processes. PMID:22199165

  14. Cueing effects on semantic and perceptual categorization: ERPs reveal differential effects of validity as a function of processing stage.

    PubMed

    Lai, Grace; Mangels, Jennifer A

    2007-05-15

    Valid cueing has been shown to accelerate target identification and improve decision accuracy. However, the precise nature and extent to which biasing influences the successive stages of target processing remain unclear. The present event-related potential (ERP) study used a "hybrid" task that combined features of standard cued-attention and task-switching paradigms in order to explore the effects of expectation on both identification and categorization of centrally presented stimuli. Subjects made semantic judgments (living/nonliving) on word targets ("bunny"), and perceptual judgments (right/left) on arrow targets ("<"). Target expectancy was manipulated using cues that were valid (60 percent of trials), invalid (10 percent), or neutral (30 percent). Invalidly cued targets required task-set switching before categorization could commence, and resulted in RT costs relative to validly or neutrally cued targets. Additional benefits from valid-cueing were only observed for word targets. Invalid cueing of both arrow and word targets modulated early posterior visual potentials (P1/N1) and elicited a subsequent anterior P3a (270 ms). The temporal relationship of these effects suggests that the P3a indexed domain-general task-set switching processes recruited in response to the detection of unexpected perceptual information. Subsequent to the P3a and immediately preceding the behavioral response, validly cued targets elicited enhanced stimulus-specific waveforms (arrows: parietal positivity [P290], words: inferior temporal negativity [late ITN: 400-600 ms]). The degree of neural enhancement relative to the invalid and neutral conditions mirrored the magnitude of corresponding RT benefits, suggesting that these waveforms indexed categorization, decision processes or both. Together, these results suggest that valid cueing increases the neural efficiency of initial stimulus identification, facilitating transmission of information to subsequent categorization stages, where

  15. 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

  16. Proteomic Analysis of Solid Pseudopapillary Tumor of the Pancreas Reveals Dysfunction of the Endoplasmic Reticulum Protein Processing Pathway*

    PubMed Central

    Zhu, Yi; Xu, Hong; Chen, Hao; Xie, Junjie; Shi, Minmin; Shen, Baiyong; Deng, Xiaxing; Liu, Chao; Zhan, Xi; Peng, Chenghong

    2014-01-01

    Solid pseudopapillary tumor of the pancreas (SPTP) is a low-grade malignant tumor with a favorable prognosis after surgery. Many previous studies have focused on clinical features or pathological biomarkers of the disease, but a better understanding of the molecular mechanisms underlying SPTP may help guide future therapeutic strategies. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify differentially expressed proteins in SPTP specimens. A total of 1171 proteins with a threshold of a 1.5-fold change and a p value ≤ 0.05 between SPTP tissue and matched normal pancreas tissue were identified for bioinformatics analysis. Mass spectrometry results were then further confirmed by assessing six representative proteins (ACADL, EPHX2, MSI2, DKK4, JUP, and DAD1) in individual specimens with immunohistochemistry. Upon mapping of the differentially expressed proteins to the Kyoto Encyclopedia of Genes and Genomes pathways database, we found several new cell-adhesion molecules that could be used as pathologic biomarkers. Furthermore, we observed that many endoplasmic reticulum-associated proteins were altered, suggesting that endoplasmic reticulum stress may play an important role in SPTP tumorigenesis. Seven proteins (ERO1LB, TRIM1, GRP94, BIP, SEC61B, P4HB, and PDIA4) in this pathway were further validated by immunohistochemistry, and six of them (except SEC61B) coincided to the LC-MS/MS results. This first comprehensive analysis of the SPTP proteome confirms proteins that have been implicated in earlier reports and reveals novel candidates and pathways that could be investigated further for clinical applications. PMID:24997997

  17. Rbm20-deficient cardiogenesis reveals early disruption of RNA processing and sarcomere remodeling establishing a developmental etiology for dilated cardiomyopathy.

    PubMed

    Beraldi, Rosanna; Li, Xing; Martinez Fernandez, Almudena; Reyes, Santiago; Secreto, Frank; Terzic, Andre; Olson, Timothy M; Nelson, Timothy J

    2014-07-15

    Dilated cardiomyopathy (DCM) due to mutations in RBM20, a gene encoding an RNA-binding protein, is associated with high familial penetrance, risk of progressive heart failure and sudden death. Although genetic investigations and physiological models have established the linkage of RBM20 with early-onset DCM, the underlying basis of cellular and molecular dysfunction is undetermined. Modeling human genetics using a high-throughput pluripotent stem cell platform was herein designed to pinpoint the initial transcriptome dysfunction and mechanistic corruption in disease pathogenesis. Tnnt2-pGreenZeo pluripotent stem cells were engineered to knockdown Rbm20 (shRbm20) to determine the cardiac-pathogenic phenotype during cardiac differentiation. Intracellular Ca(2+) transients revealed Rbm20-dependent alteration in Ca(2+) handling, coinciding with known pathological splice variants of Titin and Camk2d genes by Day 24 of cardiogenesis. Ultrastructural analysis demonstrated elongated and thinner sarcomeres in the absence of Rbm20 that is consistent with human cardiac biopsy samples. Furthermore, Rbm20-depleted transcriptional profiling at Day 12 identified Rbm20-dependent dysregulation with 76% of differentially expressed genes linked to known cardiac pathology ranging from primordial Nkx2.5 to mature cardiac Tnnt2 as the initial molecular aberrations. Notably, downstream consequences of Rbm20-depletion at Day 24 of differentiation demonstrated significant dysregulation of extracellular matrix components such as the anomalous overexpression of the Vtn gene. By using the pluripotent stem cell platform to model human cardiac disease according to a stage-specific cardiogenic roadmap, we established a new paradigm of familial DCM pathogenesis as a developmental disorder that is patterned during early cardiogenesis and propagated with cellular mechanisms of pathological cardiac remodeling.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. Rise of dinosaurs reveals major body-size transitions are driven by passive processes of trait evolution.

    PubMed

    Sookias, Roland B; Butler, Richard J; Benson, Roger B J

    2012-06-01

    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.

  3. 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

    2015-01-01

    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. PMID:25994386

  4. Development and application of in vivo molecular traps reveals that dynein light chain occupancy differentially affects dynein-mediated processes.

    PubMed

    Varma, Dileep; Dawn, Amrita; Ghosh-Roy, Anindya; Weil, Sarah J; Ori-McKenney, Kassandra M; Zhao, Yanqiu; Keen, James; Vallee, Richard B; Williams, John C

    2010-02-23

    The ability to rapidly and specifically regulate protein activity combined with in vivo functional assays and/or imaging can provide unique insight into underlying molecular processes. Here we describe the application of chemically induced dimerization of FKBP to create nearly instantaneous high-affinity bivalent ligands capable of sequestering cellular targets from their endogenous partners. We demonstrate the specificity and efficacy of these inducible, dimeric "traps" for the dynein light chains LC8 (Dynll1) and TcTex1 (Dynlt1). Both light chains can simultaneously bind at adjacent sites of dynein intermediate chain at the base of the dynein motor complex, yet their specific function with respect to the dynein motor or other interacting proteins has been difficult to dissect. Using these traps in cultured mammalian cells, we observed that induction of dimerization of either the LC8 or TcTex1 trap rapidly disrupted early endosomal and lysosomal organization. Dimerization of either trap also disrupted Golgi organization, but at a substantially slower rate. Using either trap, the time course for disruption of each organelle was similar, suggesting a common regulatory mechanism. However, despite the essential role of dynein in cell division, neither trap had a discernable effect on mitotic progression. Taken together, these studies suggest that LC occupancy of the dynein motor complex directly affects some, but not all, dynein-mediated processes. Although the described traps offer a method for rapid inhibition of dynein function, the design principle can be extended to other molecular complexes for in vivo studies.

  5. 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.

  6. 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.

  7. 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.

  8. Source Processes Revealed at Two Guatemalan Volcanoes: Insights from Multidisciplinary Observations of Harmonic Tremor and Numerical Modeling

    NASA Astrophysics Data System (ADS)

    Brill, K. A.; Waite, G. P.

    2012-12-01

    Tremor signals at volcanoes are typically attributed to fluid movement within the system. Characteristics of harmonic tremor (i.e. duration, frequency content, polarization) can convey detailed information about source processes from which they emanate, but decoding these signals poses great challenges due to the complexity of volcanic environments. We recorded instances of harmonic tremor at both Santiaguito and Fuego volcanoes Guatemala, Central America. The instances of harmonic tremor occur both independent from and contemporaneous with explosions, and last anywhere from 30 seconds to tens of minutes. The signals have fundamental frequencies between 0.3 and 2.5 Hz, with as many as 20 overtones, and exhibit spectral gliding of up to 0.75 Hz over the course of an event, changing as quickly as 0.1 Hz/second. Field observations; video recordings; and time-lapse, ultraviolet, and thermal imagery; collected simultaneously with acoustic and seismic recordings allow us to constrain source locations and processes beyond what would otherwise be possible just acoustic and seismic recordings. We propose that the harmonic tremor signals are generated by nonlinear excitation of fracture walls as gas vents out of the systems. Additionally, we investigate the complex wavefield generated by harmonic tremor and the heterogeneous volcanic media. Particle motions at both volcanoes are typically elliptical, but vary dramatically over time as the fundamental frequency glides up and down (see figure). In addition, the particle motions of harmonics often have different polarities from each other and the fundamental frequency. Through finite difference modeling, we isolate the effects of near-field terms, topography, and source mechanism to explore each of these factors' contribution to the unexpected behavior.

  9. 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).

  10. Ferrimagnetic susceptibility contrast agents.

    PubMed

    Bach-Gansmo, T

    1993-01-01

    Contrast agents based on superparamagnetic particles have been in clinical development for more than 5 years, and the complexity of their effects is still not elucidated. The relaxivities are frequently used to give an idea of their efficacy, but these parameters can only be used if they are concentration independent. For large superparamagnetic systems, the evolution of the transverse magnetization is biexponential, after an initial loss of magnetization. Both these characteristics of large superparamagnetic systems should lead to prudence in using the relaxivities as indicators of contrast medium efficacy. Susceptibility induced artefacts have been associated with the use of superparamagnetic contrast agents since the first imaging evaluation took place. The range of concentrations where good contrast effect was achieved without inducing artefacts, as well as blurring and metal artefacts were evaluated. The influence of motion on the induction of artefacts was studied, and compared to the artefacts induced by a paramagnetic agent subject to motion. With a suitable concentration of a negative contrast agent, a signal void could be achieved in the region prone to motion, and no artefacts were induced. If the concentration was too high, a displacement of the region close to the contrast agent was observed. The artefacts occurred in a volume surrounding the contrast agent, i.e., also outside the imaging plane. In comparison a positive, paramagnetic contrast agent induced heavy artefacts in the phase encoding direction, appearing as both high intensity regions and black holes, in a mosaic pattern. Clinical trials of the oral contrast agent OMP for abdominal MR imaging showed this agent to be safe and efficacious. OMP increased the diagnostic efficacy of abdominal MR imaging in 2 of 3 cases examined, with a significant decrease in motion artefacts. Susceptibility contrast agents may also be of use in the evaluation of small lesions in the liver. Particulate material

  11. 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

  12. 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

  13. A simulation framework for auditory discrimination experiments: Revealing the importance of across-frequency processing in speech perception.

    PubMed

    Schädler, Marc René; Warzybok, Anna; Ewert, Stephan D; Kollmeier, Birger

    2016-05-01

    A framework for simulating auditory discrimination experiments, based on an approach from Schädler, Warzybok, Hochmuth, and Kollmeier [(2015). Int. J. Audiol. 54, 100-107] which was originally designed to predict speech recognition thresholds, is extended to also predict psychoacoustic thresholds. The proposed framework is used to assess the suitability of different auditory-inspired feature sets for a range of auditory discrimination experiments that included psychoacoustic as well as speech recognition experiments in noise. The considered experiments were 2 kHz tone-in-broadband-noise simultaneous masking depending on the tone length, spectral masking with simultaneously presented tone signals and narrow-band noise maskers, and German Matrix sentence test reception threshold in stationary and modulated noise. The employed feature sets included spectro-temporal Gabor filter bank features, Mel-frequency cepstral coefficients, logarithmically scaled Mel-spectrograms, and the internal representation of the Perception Model from Dau, Kollmeier, and Kohlrausch [(1997). J. Acoust. Soc. Am. 102(5), 2892-2905]. The proposed framework was successfully employed to simulate all experiments with a common parameter set and obtain objective thresholds with less assumptions compared to traditional modeling approaches. Depending on the feature set, the simulated reference-free thresholds were found to agree with-and hence to predict-empirical data from the literature. Across-frequency processing was found to be crucial to accurately model the lower speech reception threshold in modulated noise conditions than in stationary noise conditions.

  14. 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.

  15. 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.

  16. Interspecies avian brain chimeras reveal that large brain size differences are influenced by cell-interdependent processes.

    PubMed

    Chen, Chun-Chun; Balaban, Evan; Jarvis, Erich D

    2012-01-01

    Like humans, birds that exhibit vocal learning have relatively delayed telencephalon maturation, resulting in a disproportionately smaller brain prenatally but enlarged telencephalon in adulthood relative to vocal non-learning birds. To determine if this size difference results from evolutionary changes in cell-autonomous or cell-interdependent developmental processes, we transplanted telencephala from zebra finch donors (a vocal-learning species) into Japanese quail hosts (a vocal non-learning species) during the early neural tube stage (day 2 of incubation), and harvested the chimeras at later embryonic stages (between 9-12 days of incubation). The donor and host tissues fused well with each other, with known major fiber pathways connecting the zebra finch and quail parts of the brain. However, the overall sizes of chimeric finch telencephala were larger than non-transplanted finch telencephala at the same developmental stages, even though the proportional sizes of telencephalic subregions and fiber tracts were similar to normal finches. There were no significant changes in the size of chimeric quail host midbrains, even though they were innervated by the physically smaller zebra finch brain, including the smaller retinae of the finch eyes. Chimeric zebra finch telencephala had a decreased cell density relative to normal finches. However, cell nucleus size differences between each species were maintained as in normal birds. These results suggest that telencephalic size development is partially cell-interdependent, and that the mechanisms controlling the size of different brain regions may be functionally independent. PMID:22860132

  17. Interspecies Avian Brain Chimeras Reveal That Large Brain Size Differences Are Influenced by Cell–Interdependent Processes

    PubMed Central

    Chen, Chun-Chun; Balaban, Evan; Jarvis, Erich D.

    2012-01-01

    Like humans, birds that exhibit vocal learning have relatively delayed telencephalon maturation, resulting in a disproportionately smaller brain prenatally but enlarged telencephalon in adulthood relative to vocal non-learning birds. To determine if this size difference results from evolutionary changes in cell-autonomous or cell-interdependent developmental processes, we transplanted telencephala from zebra finch donors (a vocal-learning species) into Japanese quail hosts (a vocal non-learning species) during the early neural tube stage (day 2 of incubation), and harvested the chimeras at later embryonic stages (between 9–12 days of incubation). The donor and host tissues fused well with each other, with known major fiber pathways connecting the zebra finch and quail parts of the brain. However, the overall sizes of chimeric finch telencephala were larger than non-transplanted finch telencephala at the same developmental stages, even though the proportional sizes of telencephalic subregions and fiber tracts were similar to normal finches. There were no significant changes in the size of chimeric quail host midbrains, even though they were innervated by the physically smaller zebra finch brain, including the smaller retinae of the finch eyes. Chimeric zebra finch telencephala had a decreased cell density relative to normal finches. However, cell nucleus size differences between each species were maintained as in normal birds. These results suggest that telencephalic size development is partially cell-interdependent, and that the mechanisms controlling the size of different brain regions may be functionally independent. PMID:22860132

  18. A simulation framework for auditory discrimination experiments: Revealing the importance of across-frequency processing in speech perception.

    PubMed

    Schädler, Marc René; Warzybok, Anna; Ewert, Stephan D; Kollmeier, Birger

    2016-05-01

    A framework for simulating auditory discrimination experiments, based on an approach from Schädler, Warzybok, Hochmuth, and Kollmeier [(2015). Int. J. Audiol. 54, 100-107] which was originally designed to predict speech recognition thresholds, is extended to also predict psychoacoustic thresholds. The proposed framework is used to assess the suitability of different auditory-inspired feature sets for a range of auditory discrimination experiments that included psychoacoustic as well as speech recognition experiments in noise. The considered experiments were 2 kHz tone-in-broadband-noise simultaneous masking depending on the tone length, spectral masking with simultaneously presented tone signals and narrow-band noise maskers, and German Matrix sentence test reception threshold in stationary and modulated noise. The employed feature sets included spectro-temporal Gabor filter bank features, Mel-frequency cepstral coefficients, logarithmically scaled Mel-spectrograms, and the internal representation of the Perception Model from Dau, Kollmeier, and Kohlrausch [(1997). J. Acoust. Soc. Am. 102(5), 2892-2905]. The proposed framework was successfully employed to simulate all experiments with a common parameter set and obtain objective thresholds with less assumptions compared to traditional modeling approaches. Depending on the feature set, the simulated reference-free thresholds were found to agree with-and hence to predict-empirical data from the literature. Across-frequency processing was found to be crucial to accurately model the lower speech reception threshold in modulated noise conditions than in stationary noise conditions. PMID:27250164

  19. Consecutive TMS-fMRI reveals an inverse relationship in BOLD signal between object and scene processing.

    PubMed

    Mullin, Caitlin R; Steeves, Jennifer K E

    2013-12-01

    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.

  20. Atomic model of a nonenveloped virus reveals pH sensors for a coordinated process of cell entry.

    PubMed

    Zhang, Xing; Patel, Avnish; Celma, Cristina C; Yu, Xuekui; Roy, Polly; Zhou, Z Hong

    2016-01-01

    Viruses sense environmental cues such as pH to engage in membrane interactions for cell entry during infection, but how nonenveloped viruses sense pH is largely undefined. Here, we report both high- and low-pH structures of bluetongue virus (BTV), which enters cells via a two-stage endosomal process. The receptor-binding protein VP2 possesses a zinc finger that may function to maintain VP2 in a metastable state and a conserved His866, which senses early-endosomal pH. The membrane-penetration protein VP5 has three domains: dagger, unfurling and anchoring. Notably, the β-meander motif of the anchoring domain contains a histidine cluster that can sense late-endosomal pH and also possesses four putative membrane-interaction elements. Exposing BTV to low pH detaches VP2 and dramatically refolds the dagger and unfurling domains of VP5. Our biochemical and structure-guided-mutagenesis studies support these coordinated pH-sensing mechanisms.

  1. 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.

  2. 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. PMID:24749863

  3. Quantitative Proteomic and Transcriptomic Study on Autotetraploid Paulownia and Its Diploid Parent Reveal Key Metabolic Processes Associated with Paulownia Autotetraploidization.

    PubMed

    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

  4. 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

  5. Developmental roles of Drosophila tRNA processing endonuclease RNase ZL as revealed with a conditional rescue system

    PubMed Central

    Xie, Xie; Dubrovskaya, Veronica; Yacoub, Nancy; Walska, Joanna; Gleason, Tara; Reid, Katherine; Dubrovsky, Edward B.

    2013-01-01

    Drosophila RNase ZL (dRNaseZ) belongs to a family of endoribonucleases with a major role in tRNA 3′-end processing. The biochemical function of RNase ZL is conserved from yeast to human. Here we present a study of its biological function during Drosophila development. In flies, dRNaseZ provides a non-redundant function, as the RNZED24 knockout (KO) mutation causes early larval lethality. Mosaic and conditional rescue techniques were employed to determine dRNaseZ requirements at later stages. We found that dRNaseZ activity is essential for all phases of fly development that involve cell division, including growth of adult tissue progenitors during larval and metamorphic stages, and gametogenesis in adults. At the cellular level, two major phenotypes were identified – cell growth deficiency in endoreplicating tissues and cell cycle arrest in mitotic tissues. While cell growth and proliferation are both dependant on protein synthesis, the two phenotypes displayed reliance on different dRNaseZ functions. We found that dRNaseZ KO completely blocks tRNA maturation without diminishing the abundance of mature tRNA molecules. Our data indicate that growth arrest of endoreplicating cells is primarily attributed to the relocation of the pool of mature tRNAs into the nuclei causing a decrease in translation efficiency. Mitotically dividing cells appear to be less dependent on translation machinery as they maintain their normal size when deprived of dRNaseZ activity, but rather display a cell cycle arrest at the G2-M transition. PMID:23867108

  6. 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.