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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. PMID:27112300

  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. PMID:27036098

  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 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

  6. 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

  7. 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…

  8. 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

  9. 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…

  10. 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…

  11. Social Class Contrasts in Verbal Processing Styles.

    ERIC Educational Resources Information Center

    Poole, Millicent E.

    1977-01-01

    It was hypothesized that distinctive verbal processing styles would be characteristic of different social classes and different sexes, and that these differences could be largely explained by earlier socialization experiences. (BW)

  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.

    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

  14. 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.

  15. 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

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

    PubMed

    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

    2008-03-01

    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-alpha, but not IL-1beta or lymphotoxin-alpha (LT-alpha), induced adherence of platelets to cerebrovascular endothelium. Peak platelet adhesion was found 12 h after TNF-alpha 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

  17. 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

  18. 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

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

    PubMed

    Liu, Jian K; Gollisch, Tim

    2015-07-01

    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. 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…

  1. 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.

  2. 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

  3. Contrast discrimination: Second responses reveal the relationship between the mean and variance of visual signals

    PubMed Central

    Solomon, Joshua A.

    2007-01-01

    To explain the relationship between first- and second-response accuracies in a detection experiment, Swets, Tanner, and Birdsall [Swets, J., Tanner, W. P., Jr., & Birdsall, T. G. (1961). Decision processes in perception. Psychological Review, 68, 301–340] proposed that the variance of visual signals increased with their means. However, both a low threshold and intrinsic uncertainty produce similar relationships. I measured the relationship between first- and second-response accuracies for suprathreshold contrast discrimination, which is thought to be unaffected by sensory thresholds and intrinsic uncertainty. The results are consistent with a slowly increasing variance. PMID:17961625

  4. Contrast discrimination: second responses reveal the relationship between the mean and variance of visual signals.

    PubMed

    Solomon, Joshua A

    2007-12-01

    To explain the relationship between first- and second-response accuracies in a detection experiment, Swets, Tanner, and Birdsall [Swets, J., Tanner, W. P., Jr., & Birdsall, T. G. (1961). Decision processes in perception. Psychological Review, 68, 301-340] proposed that the variance of visual signals increased with their means. However, both a low threshold and intrinsic uncertainty produce similar relationships. I measured the relationship between first- and second-response accuracies for suprathreshold contrast discrimination, which is thought to be unaffected by sensory thresholds and intrinsic uncertainty. The results are consistent with a slowly increasing variance. PMID:17961625

  5. 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

  6. Isotopes reveal contrasting water use strategies among coexisting plant species in a Mediterranean ecosystem.

    PubMed

    Moreno-Gutiérrez, Cristina; Dawson, Todd E; Nicolás, Emilio; Querejeta, José Ignacio

    2012-10-01

    Variation in the stable carbon and oxygen isotope composition (δ13C, Δ18O) of co-occurring plant species may reflect the functional diversity of water use strategies present in natural plant communities. We investigated the patterns of water use among 10 coexisting plant species representing diverse taxonomic groups and life forms in semiarid southeast Spain by measuring their leaf δ13C and Δ18O, the oxygen isotope ratio of stem water and leaf gas exchange rates. Across species, Δ18O was tightly negatively correlated with stomatal conductance (gs), whereas δ13C was positively correlated with intrinsic water use efficiency (WUEi). Broad interspecific variation in Δ18O, δ13C and WUEi was largely determined by differences in gs, as indicated by a strong positive correlation between leaf δ13C and Δ18O across species The 10 co-occurring species segregated along a continuous ecophysiological gradient defined by their leaf δ13C and Δ18O, thus revealing a wide spectrum of stomatal regulation intensity and contrasting water use strategies ranging from 'profligate/opportunistic' (high gs, low WUEi) to 'conservative' (low gs, high WUEi). Coexisting species maintained their relative isotopic rankings in 2 yr with contrasting rainfall, suggesting the existence of species-specific 'isotopic niches' that reflect ecophysiological niche segregation in dryland plant communities. PMID:22913668

  7. 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

  8. 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.

  9. 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

  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. PMID:24116076

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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…

  16. Ambient illumination switches contrast preference of specific retinal processing streams

    PubMed Central

    Pearson, James T.

    2015-01-01

    Contrast, a fundamental feature of visual scenes, is encoded in a distributed manner by ∼20 retinal ganglion cell (RGC) types, which stream visual information to the brain. RGC types respond preferentially to positive (ONpref) or negative (OFFpref) contrast and differ in their sensitivity to preferred contrast and responsiveness to nonpreferred stimuli. Vision operates over an enormous range of mean light levels. The influence of ambient illumination on contrast encoding across RGC types is not well understood. Here, we used large-scale multielectrode array recordings to characterize responses of mouse RGCs under lighting conditions spanning five orders in brightness magnitude. We identify three functional RGC types that switch contrast preference in a luminance-dependent manner (Sw1-, Sw2-, and Sw3-RGCs). As ambient illumination increases, Sw1- and Sw2-RGCs shift from ONpref to OFFpref and Sw3-RGCs from OFFpref to ONpref. In all cases, transitions in contrast preference are reversible and track light levels. By mapping spatiotemporal receptive fields at different mean light levels, we find that changes in input from ON and OFF pathways in receptive field centers underlie shifts in contrast preference. Sw2-RGCs exhibit direction-selective responses to motion stimuli. Despite changing contrast preference, direction selectivity of Sw2-RGCs and other RGCs as well as orientation-selective responses of RGCs remain stable across light levels. PMID:25995351

  17. 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

  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. 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

  20. 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

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

    PubMed

    Wang, Luming; Schumacher, Petra B

    2013-01-01

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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. High-resolution bathymetry reveals contrasting landslide activity shaping the walls of the Mid-Atlantic Ridge axial valley

    NASA Astrophysics Data System (ADS)

    Cannat, Mathilde; Mangeney, Anne; OndréAs, HéLèNe; Fouquet, Yves; Normand, Alain

    2013-04-01

    Axial valleys are found along most slow-spreading mid-ocean ridges and are one of the most prominent topographic features on Earth. In this paper, we present the first deep-tow swath bathymetry for the axial valley walls of the Mid-Atlantic Ridge. These data allow us to analyze axial valley wall morphology with a very high resolution (0.5 to 1 m compared to ≥ 50 m for shipboard multibeam bathymetry), revealing the role played by landslides. Slow-spreading ridge axial valleys also commonly expose mantle-derived serpentinized peridotites in the footwalls of large offset normal faults (detachments). In our map of the Ashadze area (lat. 13°N), ultramafic outcrops have an average slope of 18° and behave as sliding deformable rock masses, with little fragmentation. By contrast, the basaltic seafloor in the Krasnov area (lat. 16°38'N) has an average slope of 32° and the erosion of the steep basaltic rock faces leads to extensive fragmentation, forming debris with morphologies consistent with noncohesive granular flow. Comparison with laboratory experiments suggests that the repose angle for this basaltic debris is > 25°. We discuss the interplay between the normal faults that bound the axial valley and the observed mass wasting processes. We propose that, along axial valley walls where serpentinized peridotites are exposed by detachment faults, mass wasting results in average slopes ≤ 20°, even in places where the emergence angle of the detachment is larger.

  9. 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.

  10. 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

  11. Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution.

    PubMed

    Guo, Wenhu; Grewe, Felix; Fan, Weishu; Young, Gregory J; Knoop, Volker; Palmer, Jeffrey D; Mower, Jeffrey P

    2016-06-01

    Mitochondrial genomes (mitogenomes) of flowering plants are well known for their extreme diversity in size, structure, gene content, and rates of sequence evolution and recombination. In contrast, little is known about mitogenomic diversity and evolution within gymnosperms. Only a single complete genome sequence is available, from the cycad Cycas taitungensis, while limited information is available for the one draft sequence, from Norway spruce (Picea abies). To examine mitogenomic evolution in gymnosperms, we generated complete genome sequences for the ginkgo tree (Ginkgo biloba) and a gnetophyte (Welwitschia mirabilis). There is great disparity in size, sequence conservation, levels of shared DNA, and functional content among gymnosperm mitogenomes. The Cycas and Ginkgo mitogenomes are relatively small, have low substitution rates, and possess numerous genes, introns, and edit sites; we infer that these properties were present in the ancestral seed plant. By contrast, the Welwitschia mitogenome has an expanded size coupled with accelerated substitution rates and extensive loss of these functional features. The Picea genome has expanded further, to more than 4 Mb. With regard to structural evolution, the Cycas and Ginkgo mitogenomes share a remarkable amount of intergenic DNA, which may be related to the limited recombinational activity detected at repeats in Ginkgo Conversely, the Welwitschia mitogenome shares almost no intergenic DNA with any other seed plant. By conducting the first measurements of rates of DNA turnover in seed plant mitogenomes, we discovered that turnover rates vary by orders of magnitude among species. PMID:26831941

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

    PubMed

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

    2009-03-01

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

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

    PubMed

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

    2015-02-15

    The electrochemical degradation of six of the most widely used iodinated contrast media was investigated. Batch experiments were performed under constant current conditions using two DSA® electrodes (titanium coated with a proprietary and patented mixed metal oxide solution of precious metals such as iridium, ruthenium, platinum, rhodium and tantalum). The degradation removal never fell below 85% (at a current density of 64 mA/cm(2) with a reaction time of 150 min) when perchlorate was used as the supporting electrolyte; however, when sulphate was used, the degradation performance was above 80% (at a current density of 64 mA/cm(2) with a reaction time of 150 min) for all of the compounds studied. Three main degradation pathways were identified, namely, the reductive de-iodination of the aromatic ring, the reduction of alkyl aromatic amides to simple amides and the de-acylation of N-aromatic amides to produce aromatic amines. However, as amidotrizoate is an aromatic carboxylate, this is added via the decarboxylation reaction. The investigation did not reveal toxicity except for the lower current density used, which has shown a modest toxicity, most likely for some reaction intermediates that are not further degraded. In order to obtain total removal of the contrast media, it was necessary to employ a current intensity between 118 and 182 mA/cm(2) with energy consumption higher than 370 kWh/m(3). Overall, the electrochemical degradation was revealed to be a reliable process for the treatment of iodinated contrast media that can be found in contaminated waters such as hospital wastewater or pharmaceutical waste-contaminated streams. PMID:25433384

  14. 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

  15. 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.

  16. Contrasting lithospheric mantle domains beneath the Massif Central (France) revealed by geochemistry of peridotite xenoliths

    NASA Astrophysics Data System (ADS)

    Lenoir, Xavier; Garrido, Carlos J.; Bodinier, Jean-Louis; Dautria, Jean-Marie

    2000-09-01

    We report major and trace element analyses for 82 coarse-grained peridotite xenoliths from 25 Cenozoic volcanic centres throughout the Massif Central (France). These data cover a region of about 150×150 km, allowing an investigation of large scale compositional variations in the subcontinental lithospheric mantle (SCLM). In agreement with textural variations, geochemical data define two contrasting lithospheric domains, situated north and south of latitude 45°30'. Peridotites of the northern domain show protogranular textures, characterised by clustered pyroxene-spinel distributions. They are rather refractory and depleted in MREE relative to HREE, but pervasively enriched in LREE and other highly incompatible elements. The samples show mantle-normalised patterns with negative anomalies of Nb, Ta, Zr and Hf, similar to enriched mantle xenoliths ascribed to carbonatitic metasomatism. In contrast, the peridotites of the southern domain are devoid of pyroxene-spinel clusters and are therefore referred to as coarse-granular. They are distinguished from the northern suite by more fertile compositions and relatively flat MREE-HREE patterns. In addition, only the harzburgites and a few lherzolites are enriched in LREE. Most southern domain lherzolites are depleted in these elements and the average composition of the southern suite is comparable to that of depleted MORB-source mantle (DMM). The main compositional differences between the two domains cannot be accounted for by a secular evolution of the Massif Central SCLM caused by Cenozoic plume upwelling. Instead, these differences record the existence of distinct lithospheric blocks assembled during the Variscan orogeny. To some degree, the northern and southern domains are reminiscent of cratonic and circumcratonic SCLM domains. Being relatively refractory and pervasively enriched in LREE, the northern domain displays similarities with cratonic SCLM. It is interpreted as a relatively ancient (pre

  17. 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

  18. 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. PMID:25423027

  19. 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.

  20. 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

  1. 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.

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

    PubMed Central

    2008-01-01

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

  3. 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

  4. Network analysis reveals contrasting effects of intraspecific competition on individual vs. population diets.

    PubMed

    Araújo, Márcio S; Guimarães, Paulo R; Svanbäck, Richard; Pinheiro, Aluisio; Guimarães, Paulo; Dos Reis, Sérgio F; Bolnick, Daniel I

    2008-07-01

    Optimal foraging theory predicts that individuals should become more opportunistic when intraspecific competition is high and preferred resources are scarce. This density-dependent diet shift should result in increased diet breadth for individuals as they add previously unused prey to their repertoire. As a result, the niche breadth of the population as a whole should increase. In a recent study, R. Svanbäck and D. I. Bolnick confirmed that intraspecific competition led to increased population diet breadth in threespine stickleback (Gasterosteus aculeatus). However, individual diet breadth did not expand as resource levels declined. Here, we present a new method based on complex network theory that moves beyond a simple measure of diet breadth, and we use the method to reexamine the stickleback experiment. This method reveals that the population as a whole added new types of prey as stickleback density was increased. However, whereas foraging theory predicts that niche expansion is achieved by individuals accepting new prey in addition to previously preferred prey, we found that a subset of individuals ceased to use their previously preferred prey, even though other members of their population continued to specialize on the original prey types. As a result, populations were subdivided into groups of ecologically similar individuals, with diet variation among groups reflecting phenotype-dependent changes in foraging behavior as prey density declined. These results are consistent with foraging theory if we assume that quantitative trait variation among consumers affects prey preferences, and if cognitive constraints prevent individuals from continuing to use their formerly preferred prey while adding new prey. PMID:18705384

  5. Dispersal in a patchy landscape reveals contrasting determinants of infection in a wild avian malaria system.

    PubMed

    Knowles, Sarah C L; Wood, Matthew J; Alves, Ricardo; Sheldon, Ben C

    2014-03-01

    Understanding exactly when, where and how hosts become infected with parasites is critical to understanding host-parasite co-evolution in natural populations. However, for host-parasite systems in which hosts or parasites are mobile, for example in vector-borne diseases, the spatial location of infection and the relative importance of parasite exposure at successive host life-history stages are often uncertain. Here, using a 6-year longitudinal data set from a spatially referenced population of blue tits, we test the extent to which infection by avian malaria parasites is determined by conditions experienced at natal or breeding sites, as well as by postnatal dispersal between the two. We show that the location and timing of infection differs markedly between two sympatric malaria parasite species. For one species (Plasmodium circumflexum), our analyses indicate that infection occurs after birds have settled on breeding territories, and because the distribution of this parasite is temporally stable across years, hosts born in malarious areas could in principle alter their exposure and potentially avoid infection through postnatal dispersal. Conversely, the spatial distribution of another parasite species (Plasmodium relictum) is unpredictable and infection probability is positively associated with postnatal dispersal distance, potentially indicating that infection occurs during this major dispersal event. These findings suggest that hosts in this population may be subject to divergent selection pressures from these two parasites, potentially acting at different life-history stages. Because this implies parasite species-specific predictions for many coevolutionary processes, they also illustrate the complexity of predicting such processes in multi-parasite systems. PMID:24117384

  6. 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

  7. 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

  8. VEP contrast sensitivity responses reveal reduced functional segregation of mid and high filters of visual channels in autism.

    PubMed

    Jemel, Boutheina; Mimeault, Daniel; Saint-Amour, Dave; Hosein, Anthony; Mottron, Laurent

    2010-01-01

    Despite the vast amount of behavioral data showing a pronounced tendency in individuals with autism spectrum disorder (ASD) to process fine visual details, much less is known about the neurophysiological characteristics of spatial vision in ASD. Here, we address this issue by assessing the contrast sensitivity response properties of the early visual-evoked potentials (VEPs) to sine-wave gratings of low, medium and high spatial frequencies in adults with ASD and in an age- and IQ-matched control group. Our results show that while VEP contrast responses to low and high spatial frequency gratings did not differ between ASD and controls, early VEPs to mid spatial frequency gratings exhibited similar response characteristics as those to high spatial frequency gratings in ASD. Our findings show evidence for an altered functional segregation of early visual channels, especially those responsible for processing mid- and high-frequency spatial scales. PMID:20884562

  9. 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

  10. Interference Contrast Reveals Debonding

    SciTech Connect

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

    2007-11-01

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

  11. 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

  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. 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.

  14. Dynamic contrast-enhanced magnetic resonance imaging reveals stress-induced angiogenesis in MCF7 human breast tumors.

    PubMed

    Furman-Haran, E; Margalit, R; Grobgeld, D; Degani, H

    1996-06-25

    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. PMID:8692800

  15. 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. PMID:27325651

  16. 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

  17. Nitrate in Ground Waters of the United States: Contrasting Scales and Processes

    NASA Astrophysics Data System (ADS)

    Nolan, B. T.

    2002-12-01

    Nitrate is one of the most ubiquitous compounds in ground water. Studies conducted during 1992 - 1995 by the U.S. Geological Survey's National Water Quality Assessment (NAWQA) Program detected nitrate in 71% of shallow ground water samples, more than 13 times as often as organic nitrogen, ammonia, nitrite, and orthophosphate (based on a common detection threshold of 0.2 mg/L). Nitrate commonly occurs in mixtures with other contaminants. Mixtures of "anthropogenic" nitrate (>3 mg/L as N), atrazine, and deethylatrazine were among the most frequently occurring mixtures in ground water samples from 1,497 domestic and public supply wells. The samples were analyzed for nitrate, 83 pesticides, and 60 volatile organic compounds. Elevated nitrate concentration in ground water has been associated with adverse health effects. Interpretive studies conducted at contrasting spatial scales reveal different processes influencing nitrate behavior in ground water. At the national scale, an empirical model indicates that leaching and water-table position influence nitrate concentration in shallow ground water (typically <5 m deep). The probability of nitrate contamination is greater in areas with high nitrogen loading and well-drained soils overlying unconsolidated sand and gravel deposits. Median nitrate concentration for wells grouped by mapped probability region increases from 0.24 to 8.3 mg/L as the predicted probability of nitrate exceeding 4 mg/L increases from 0.17 or less to >0.83. With these shallow ground-water data, nitrate contamination risk increases with increasing depth to ground water because of reduced denitrification potential. Denitrification commonly occurs under anoxic conditions in areas with very shallow depth to ground water (i.e., high water-table position). A regional study indicates that nitrate reduction and calcite dissolution processes influence nitrate concentration in ground waters of the southeastern United States. Water and sediment of the North

  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. 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.

  20. 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

  1. 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. PMID:18458764

  2. Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards.

    PubMed

    Baptista, Paula; Reis, Francisca; Pereira, Eric; Tavares, Rui M; Santos, Pedro M; Richard, Franck; Selosse, Marc-André; Lino-Neto, Teresa

    2015-12-01

    Fungal diversity in Mediterranean forest soils is poorly documented, particularly when considering saprobic and pathogenic organisms. Next-generation sequencing (NGS) methods applied to soil fungi provide the opportunity to unveil the most inconspicuous functional guilds (e.g. saprobes) and life forms (e.g. Corticiaceae) of this tremendous diversity. We used fruitbody surveys over 2 years and soil 454 metabarcoding in Castanea sativa orchards to evaluate respectively the reproductive (fruitbodies) and vegetative (mycelia) parts of fungal communities in three 100-year-old stands. Analysis of 839 fruitbodies and 210 291 ITS1 reads revealed high fungal diversity, mainly shown by belowground analysis, with high (dominant) abundance of mycorrhizal fruitbodies and reads. Both methods displayed contrasted composition and structure of fungal communities, with Basidio- and Ascomycetes dominating above- and belowground, respectively. For the two dominant fungal guilds (i.e. ectomycorrhizal and saprobic), diversity above- and belowground overlapped weakly. This study is the first assessment of the complementarity of fruitbody surveys and NGS for analysing fungal diversity in Mediterranean ecosystems and shows that belowground methods still need to be completed by fruiting diversity to provide a comprehensive overview of the different fungal guilds. The results shed light on chestnut soil biodiversity and question the spatial distribution and synergies among fungal guilds. PMID:26391727

  3. 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

  4. Active role of lagging chromosomes in spindle collapse as revealed by live phase contrast and tubulin immunostaining in grasshopper spermatocytes.

    PubMed

    Rebollo, E; Arana, P

    2001-08-01

    Univalents, that is, chromosomes lacking an attached partner at the first meiotic division, show extremely faulty transmission. Most segregational errors stem from amphitelic (mitotic-like) orientation at metaphase I followed by anaphase I lagging. Our studies in living grasshopper spermatocytes show that amphitelic orientation may provoke spindle collapse: spindle elongation and cytokinesis are impaired and an unreduced restitution nucleus is formed. This does not prevent meiotic progression and eventually leads to the production of diploid gametes. The morphology and characteristics of spindle collapse in our material, as revealed by in vivo observation and tubulin immunostaining, indicate an active role of the chromosomes in the whole process. PMID:11534821

  5. High contrast and metal-less alignment process for all-polymer optical interconnect devices

    NASA Astrophysics Data System (ADS)

    Ge, Tao; Yang, Jilin; Summitt, Chris; Wang, Sunglin; Johnson, Lee; Zaverton, Melissa; Milster, Tom; Takashima, Yuzuru

    2015-03-01

    A polymer-based flat, flexible and parallel optical interconnect has become an attractive approach for short-range data transfer. For such a device, a low cost fabrication technique is required for light couplers to redirect light from source to waveguides. Recently, we demonstrated a mask-less gray scale lithography process, which used a CMOS compatible polymer for a 45-degree mirror coupler. Polymer materials such as epoclad and AP2210B can be used to fabricate flexible substrates and waveguides, respectively. We propose an all-photopolymer lithography process to fabricate the flexible and parallel optical interconnect in conjunction with the mirror couplers. In the process, a buried polymer structure is used to precisely align the mirror coupler to waveguides, which make it possible to avoid an additional metallization process. However, the contrast of such buried fiducial mark is low since such the structure is a phase structure. As a result, it is not feasible to use the buried polymer structure as an alignment mark with conventional amplitude based imaging modalities. To increase the contrast of these buried alignment marks, we propose a feature specific alignment system for which the shape and depth of the buried alignment marks are optimized for phase-based imaging such as phase contrast and Schlieren imaging. Our results show that an optimized alignment mark provides a significant contrast enhancement while using a phase contrast imaging system compared to that of a conventional imaging system. In addition, we have fabricated an optimized alignment mark specifically for use with a Schlieren imaging system.

  6. 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.

  7. 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.

  8. Integrative Acoustic Mapping Reveals Hudson RIver Sediment Processes an Habitats

    NASA Astrophysics Data System (ADS)

    Nitsche, F. O.; Bell, R.; Carbotte, S. M.; Ryan, W. B. F.; Slagle, A.; Chillrud, S.; Kenna, T.; Flood, R.; Ferrini, V.; Cerrato, R.; McHugh, C.; Strayer, D.

    2005-06-01

    Rivers and estuaries around the world are the focus of human settlements and activities. Needs for clean water, ecosystem preservation, commercial navigation, industrial development, and recreational access compete for the use of estuaries, and management of these resources requires a detailed understanding of estuarine morphology and sediment dynamics. This article presents an overview of the first estuary-wide study of a heavily used estuary, the Hudson River, based on high-resolution acoustic mapping of the river bottom. The integration of three high-resolution acoustic methods with extensive sampling reveals an unexpected complexity of bottom features and allows detailed classification of the benthic environment in terms of riverbed morphology, sediment type, and sedimentary processes.

  9. Effect of varying processing solution temperature on radiographic contrast and relative film speed of dental film.

    PubMed

    Matthee, M J; Becker, P J; Seeliger, J E

    1990-12-01

    The aim of this study was to determine the effect of a stepwise rise in temperature on three film types processed in six different processing solutions and to identify the combinations of film, solution and temperature which produced the best results in terms of radiographic contrast and relative film speed. The film types were Agfa Dentus M2, Flow X-ray and Kodak Ultra Speed while the processing solutions were Agfa, Dürr, EBX, Kolchem, MEMS and Pro-tech. An aluminium step-wedge was exposed under standardised conditions. Processing was carried out in a Dürr 245L automatic processor with variable temperature settings from 25 degrees to 35 degrees C. Unexposed films were processed at each temperature setting to determine the base plus fog values. Densitometric readings were taken using a digital densitometer, and the base plug fog values subtracted from each reading. Radiographic contrast and relative film speed were calculated and the data obtained subjected to statistical analysis using Duncan's Multiple Range Test. It could be concluded that, as the processing solution temperature rose from 25 degrees C to 35 degrees C, both radiographic contrast and relative film speed increased. The highest radiographic contrast was obtained by Agfa film in Kolchem solution at 35 degrees C, while Kodak Ultra Speed film in MEMS solution at 35 degrees C gave the highest relative film speed. An acceptable base plus fog level of 0.25 was obtained in the case of Agfa film in combination with Agfa, Dürr and Pro-tech solutions and Flow X-ray film with Dürr solutions. All the other combinations produced a base plug fog level higher than 0.25. PMID:2098942

  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. 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.

  12. 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

  13. 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

  14. Misleading Bias-Driven Expectations in Referential Processing and the Facilitative Role of Contrastive Accent.

    PubMed

    Itzhak, Inbal; Baum, Shari R

    2015-10-01

    Probabilistic preferences are often facilitative in language processing and may assist in discourse prediction. However, occasionally these sources of information may lead to inaccurate expectations. The current study investigated a test case of this scenario. An eye-tracking experiment examined the interpretation of ambiguous personal pronouns in the context of implicit causality biases. We tested whether reference resolution may be facilitated online by contrastive accent in cases of a bias-inconsistent referent. Implicit causality biases directed looks to the biased noun phrase; however, when the name of the bias-inconsistent antecedent was accented (e.g., JOHN envied Bill because he ...), this tendency was modulated. Contrastive accent seems to dampen the occasionally confusing prediction of implicit causality biases in referential processing. This demonstrates one way in which the spoken language comprehension system copes with occasional misguidance of otherwise helpful probabilistic information. PMID:25015025

  15. Comparison on extreme pathways reveals nature of different biological processes

    PubMed Central

    2014-01-01

    Background Constraint-based reconstruction and analysis (COBRA) is used for modeling genome-scale metabolic networks (MNs). In a COBRA model, extreme pathways (ExPas) are the edges of its conical solution space, which is formed by all viable steady-state flux distributions. ExPa analysis has been successfully applied to MNs to reveal their phenotypic capabilities and properties. Recently, the COBRA framework has been extended to transcriptional regulatory networks (TRNs) and transcriptional and translational networks (TTNs), so efforts are needed to determine whether ExPa analysis is also effective on these two types of networks. Results In this paper, the ExPas resulting from the COBRA models of E.coli's MN, TRN and TTN were horizontally compared from 5 aspects: (1) Total number and the ratio of their amount to reaction amount; (2) Length distribution; (3) Reaction participation; (4) Correlated reaction sets (CoSets); (5) interconnectivity degree. Significant discrepancies in above properties were observed during the comparison, which reveals the biological natures of different biological processes. Besides, by demonstrating the application of ExPa analysis on E.coli, we provide a practical guidance of an improved approach to compute ExPas on COBRA models of TRNs. Conclusions ExPas of E.coli's MN, TRN and TTN have different properties, which are strongly connected with various biological natures of biochemical networks, such as topological structure, specificity and redundancy. Our study shows that ExPas are biologically meaningful on the newborn models and suggests the effectiveness of ExPa analysis on them. PMID:24565046

  16. 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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1999-05-01

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

  19. Contrasting Networks for Recognition Memory and Recency Memory Revealed by Immediate-Early Gene Imaging in the Rat

    PubMed Central

    2014-01-01

    The expression of the immediate-early gene c-fos was used to compare networks of activity associated with recency memory (temporal order memory) and recognition memory. In Experiment 1, rats were first familiarized with sets of objects and then given pairs of different, familiar objects to explore. For the recency test group, each object in a pair was separated by 110 min in the time between their previous presentations. For the recency control test, each object in a pair was separated by less than a 1 min between their prior presentations. Temporal discrimination of the objects correlated with c-fos activity in the recency test group in several sites, including area Te2, the perirhinal cortex, lateral entorhinal cortex, as well as the dentate gyrus, hippocampal fields CA3 and CA1. For both the test and control conditions, network models were derived using structural equation modeling. The recency test model emphasized serial connections from the perirhinal cortex to lateral entorhinal cortex and then to the CA1 subfield. The recency control condition involved more parallel pathways, but again highlighted CA1 within the hippocampus. Both models contrasted with those derived from tests of object recognition (Experiment 2), because stimulus novelty was associated with pathways from the perirhinal cortex to lateral entorhinal cortex that then involved both the dentate gyrus (and CA3) and CA1 in parallel. The present findings implicate CA1 for the processing of familiar stimuli, including recency discriminations, while the dentate gyrus and CA3 pathways are recruited when the perirhinal cortex signals novel stimuli. PMID:24933661

  20. Processing of projections containing phase contrast in laboratory micro-computerized tomography imaging

    PubMed Central

    Zápražný, Zdenko; Korytár, Dušan; Mikulík, Petr; Áč, Vladimír

    2013-01-01

    Free-space-propagation-based imaging belongs to several techniques for achieving phase contrast in the hard X-ray range. The basic precondition is to use an X-ray beam with a high degree of coherence. Although the best sources of coherent X-rays are synchrotrons, spatially coherent X-rays emitted from a sufficiently small spot of laboratory microfocus or sub-microfocus sources allow the transfer of some of the modern imaging techniques from synchrotrons to laboratories. Spatially coherent X-rays traverse a sample leading to a phase shift. Beam deflection induced by the local change of refractive index may be expressed as a dark–bright contrast on the edges of the object in an X-ray projection. This phenomenon of edge enhancement leads to an increase in spatial resolution of X-ray projections but may also lead to unpleasant artefacts in computerized tomography unless phase and absorption contributions are separated. The possibilities of processing X-ray images of lightweight objects containing phase contrast using phase-retrieval methods in laboratory conditions are tested and the results obtained are presented. For this purpose, simulated and recorded X-ray projections taken from a laboratory imaging system with a microfocus X-ray source and a high-resolution CCD camera were processed and a qualitative comparison of results was made. PMID:24046501

  1. 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. PMID:24285881

  2. 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.

  3. 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.

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

    PubMed

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

    2014-01-01

    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. PMID:24517772

  5. Sedimentary processes in Zenisu deep-sea channel revealed by side-scan imagery

    NASA Astrophysics Data System (ADS)

    Wu, Shiguo; Guo, Junhua; Hidekazu, Tokuyama

    2005-12-01

    Side-scan sonar data collected by Cruises 99-09 Leg 2 and 00-06 Leg 1 of R/V Yokosuka were used to reveal the sedimentary processes in Zenisu deep-sea channel. The middle and lower segments of the channel are rich in turbidite and other debrite deposits. By high-resolution imaging, three sedimentary processes were distinguished with distinct acoustic features. 1. Slumps and slides occur with contrasting backscatter, rough surface textures, blockings, and acoustic shadows at head walls. They are very extensive and often in lobate form downslope. 2. Debris flow has uniform, general medium backscatter, sometimes showing marbling/lineation in lobate form. 3. Turbidity current is characterized by low backscatter confined to the channel as acoustic signal is attenuated. Regional tectonics must be the dominating factor that controls deposition pattern in this area.

  6. Evolutionary pets: offspring numbers reveal speciation process in domesticated chickens.

    PubMed

    Tiemann, Inga; Rehkämper, Gerd

    2012-01-01

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

  7. 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.

  8. Post-processing methods for high-contrast imaging in the context of the WFIRST-AFTA telescope

    NASA Astrophysics Data System (ADS)

    Ygouf, Marie; Soummer, Remi; Perrin, Marshall D.; Pueyo, Laurent; N'Diaye, Mamadou; Macintosh, Bruce

    2015-01-01

    Direct detection and characterization of Earth-like exoplanets with contrasts of 109 require space-based instruments optimized for high-contrast imaging. In this context, the Wide-Field Infrared Survey Telescope - Astrophysics Focused Telescope Assets (WFIRST-AFTA) project will reach contrasts of about 108, using state-of-the-art starlight suppression and wavefront control techniques. A ten-fold contrast improvement to reach the required contrast of 109 is expected to come from post-processing. But the methods of point spread function (PSF) subtraction techniques currently used on both ground-based and space-based instruments have not yet been demonstrated at such high contrast level. In this communication, we explore new ways of implementing post-processing methods on AFTA-like simulated images, taking into account the presence of deformable mirrors, coronagraph and an IFS.

  9. Revealing the Black Box: Information Processing and Media Effects.

    ERIC Educational Resources Information Center

    Geiger, Seth; Newhagen, John

    1993-01-01

    Addresses some of the fundamental assumptions of an information processing approach to mass media effects and the contributions it brings to mass communication. Traces the conceptual and methodological innovations of an information processing perspective as they have been applied to the study of television since the 1980s. (SR)

  10. 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

  11. Image processing of head CT images using neuro best contrast (NBC) and lesion detection performance

    NASA Astrophysics Data System (ADS)

    Tipnis, Sameer; Vincent, Diana; Rumboldt, Zoran; Huda, Walter

    2011-03-01

    Purpose: The purpose of this study was to objectively compare lesion detection performance of head CT images reconstructed using filtered back projection (FBP) algorithms with those reconstructed using NBC. Method: The observer study was conducted using the 2-AFC methodology. An AFC experiment consists of 128 observer choices and permits the computation of the intensity needed to achieve 92% correct (I92%). High values of I92% corresponds to a poor level of detection performance, and vice versa. Head CT images were acquired at an x-ray tube voltage of 120 kVp with a CTDIvol value of 75 mGy in a helical scan. Nine randomly selected normal images from three patients and at three anatomical head locations were reconstructed using filtered back projection (FBP) and neuro-best-contrast (NBC) processing. Circular lesions were generated by projecting spheres onto the image plane, followed by blurring function, with lesion sizes of 2.8 mm, 6.5 mm and 9.8 mm used in these experiments. Four readers were used, with 18 experiments performed by each observer (2 processing techniques × 3 lesion sizes × 3 repeats). The experimental order of the 18 experiments was randomized to eliminate learning curve and/or observer fatigue. The ratio R of the I92% value for NBC to the corresponding I92% value for FBP was calculated for each observer and each lesion size. Values of R greater than unity indicate that NBC is inferior to FBP, and vice versa. Results: Analysis of data from each observer showed that a total of four data points had R less than unity, and eight data points were greater than unity. Eleven of the twelve individual observer R values with one standard deviation of unity. When data for the four observers were pooled, the resultant average R values were 0.98 +/- 0.38, 0.96 +/- 0.33 and 1.15 +/- 0.45, for the 2.8 mm, 6.5 mm and 9.8 mm lesions respectively. The overall average R for all three lesions sizes was 1.03 +/- 0.67. Conclusion: Our AFC investigation has shown no

  12. Tracking of migrating cells under phase-contrast video microscopy with combined mean-shift processes.

    PubMed

    Debeir, O; Van Ham, P; Kiss, R; Decaestecker, C

    2005-06-01

    In this paper, we propose a combination of mean-shift-based tracking processes to establish migrating cell trajectories through in vitro phase-contrast video microscopy. After a recapitulation on how the mean-shift algorithm permits efficient object tracking we describe the proposed extension and apply it to the in vitro cell tracking problem. In this application, the cells are unmarked (i.e., no fluorescent probe is used) and are observed under classical phase-contrast microscopy. By introducing an adaptive combination of several kernels, we address several problems such as variations in size and shape of the tracked objects (e.g., those occurring in the case of cell membrane extensions), the presence of incomplete (or noncontrasted) object boundaries, partially overlapping objects and object splitting (in the case of cell divisions or mitoses). Comparing the tracking results automatically obtained to those generated manually by a human expert, we tested the stability of the different algorithm parameters and their effects on the tracking results. We also show how the method is resistant to a decrease in image resolution and accidental defocusing (which may occur during long experiments, e.g., dozens of hours). Finally, we applied our methodology on cancer cell tracking and showed that cytochalasin-D significantly inhibits cell motility. PMID:15957594

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  14. 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.

  15. 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

  16. Fetal-Adult Cardiac Transcriptome Analysis in Rats with Contrasting Left Ventricular Mass Reveals New Candidates for Cardiac Hypertrophy

    PubMed Central

    Grabowski, Katja; Riemenschneider, Mona; Schulte, Leonard; Witten, Anika; Schulz, Angela; Stoll, Monika; Kreutz, Reinhold

    2015-01-01

    Reactivation of fetal gene expression patterns has been implicated in common cardiac diseases in adult life including left ventricular (LV) hypertrophy (LVH) in arterial hypertension. Thus, increased wall stress and neurohumoral activation are discussed to induce the return to expression of fetal genes after birth in LVH. We therefore aimed to identify novel potential candidates for LVH by analyzing fetal-adult cardiac gene expression in a genetic rat model of hypertension, i.e. the stroke-prone spontaneously hypertensive rat (SHRSP). To this end we performed genome-wide transcriptome analysis in SHRSP to identify differences in expression patterns between day 20 of fetal development (E20) and adult animals in week 14 in comparison to a normotensive rat strain with contrasting low LV mass, i.e. Fischer (F344). 15232 probes were detected as expressed in LV tissue obtained from rats at E20 and week 14 (p < 0.05) and subsequently screened for differential expression. We identified 24 genes with SHRSP specific up-regulation and 21 genes with down-regulation as compared to F344. Further bioinformatic analysis presented Efcab6 as a new candidate for LVH that showed only in the hypertensive SHRSP rat differential expression during development (logFC = 2.41, p < 0.001) and was significantly higher expressed in adult SHRSP rats compared with adult F344 (+ 76%) and adult normotensive Wistar-Kyoto rats (+ 82%). Thus, it represents an interesting new target for further functional analyses and the elucidation of mechanisms leading to LVH. Here we report a new approach to identify candidate genes for cardiac hypertrophy by combining the analysis of gene expression differences between strains with a contrasting cardiac phenotype with a comparison of fetal-adult cardiac expression patterns. PMID:25646840

  17. 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.

  18. Information Processing Limitations as Revealed by Temporal Discrimination

    ERIC Educational Resources Information Center

    Lavoie, Philippe; Grondin, Simon

    2004-01-01

    Information processing limit is a fundamental issue in cognitive psychology. One particular way of studying it is to adopt a temporal span perspective. In this experiment, Weber fractions based on thresholds for duration discrimination are used for adopting this perspective. The results showed that, contrary to the constant predicted by Weber's…

  19. 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.

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

    PubMed

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

    2014-02-01

    Soil salinity is one of the most severe abiotic stress factors threatening agriculture worldwide. Hence, particular interest exists in unraveling mechanisms leading to salt tolerance and improved crop plant performance on saline soils. Barley is considered to be one of the most salinity-tolerant crops, but varying levels of tolerance are well characterized. A proteomic analysis of the roots of two contrasting cultivars (cv. Steptoe and cv. Morex) is presented. Young plants were exposed to a period of 1, 4, 7, or 10 d at 0, 100, or 150 mM NaCl. The root proteome was analyzed based on two-dimensional gel electrophoresis. A number of cultivar-specific and salinity stress-responsive proteins were identified. Mass spectrometry-based identification was successful for 74 proteins, and a hierarchical clustering analysis grouped these into five clusters based on similarity of expression profile. The rank product method was applied to statistically access the early and late responses, and this delivered a number of new candidate proteins underlying salinity tolerance in barley. Among these were some germin-like proteins, some pathogenesis-related proteins, and numerous as-yet uncharacterized proteins. Notably, proteins involved in detoxification pathways and terpenoid biosynthesis were detected as early responsive to salinity and may function as a means of modulating growth-regulating mechanisms and membrane stability via fine tuning of phytohormone and secondary metabolism in the root. PMID:24004485

  1. 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

  2. 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. PMID:25334062

  3. 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.

  4. 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.

  5. 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

  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. Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China.

    PubMed

    Zhao, Jun; Zhang, Ruifu; Xue, Chao; Xun, Weibing; Sun, Li; Xu, Yangchun; Shen, Qirong

    2014-02-01

    Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems. PMID:24276539

  8. 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.

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

    PubMed

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

    2015-10-01

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

  10. 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

  11. 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. PMID:26599978

  12. 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

  13. Spectral OCT with speckle contrast reduction for evaluation of the healing process after PRK and transepithelial PRK

    PubMed Central

    Kaluzny, Bartlomiej J.; Szkulmowski, Maciej; Bukowska, Danuta M.; Wojtkowski, Maciej

    2014-01-01

    We evaluate Spectral OCT (SOCT) with a speckle contrast reduction technique using resonant scanner for assessment of corneal surface changes after excimer laser photorefractive keratectomy (PRK) and we compare healing process between conventional PRK and transepithelial PRK. The measurements were performed before and after the surgery. Obtained results show that SOCT with a resonant scanner speckle contrast reduction is capable of providing information regarding the healing process after PRK. The main difference between the healing processes of PRK and TransPRK, assessed by SOCT, was the time to cover the stroma with epithelium, which was shorter in the TransPRK group. PMID:24761291

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

    PubMed

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

    2013-03-01

    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 multivoxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was used to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during vocalization, compared with during passive listening. One network of regions appears to encode an "error signal" regardless of acoustic features of the error: this network, including right angular gyrus, right supplementary motor area, and bilateral cerebellum, yielded consistent neural patterns across acoustically different, distorted feedback types, only during articulation (not during passive listening). In contrast, a frontotemporal network appears sensitive to the speech features of auditory stimuli during passive listening; this preference for speech features was diminished when the same stimuli were presented as auditory concomitants of vocalization. A third network, showing a distinct functional pattern from the other two, appears to capture aspects of both neural response profiles. Together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple, interactive, functionally differentiated neural systems. PMID:23467350

  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. 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

  18. Attention in natural scenes: contrast affects rapid visual processing and fixations alike.

    PubMed

    't Hart, Bernard Marius; Schmidt, Hannah Claudia Elfriede Fanny; Klein-Harmeyer, Ingo; Einhäuser, Wolfgang

    2013-10-19

    For natural scenes, attention is frequently quantified either by performance during rapid presentation or by gaze allocation during prolonged viewing. Both paradigms operate on different time scales, and tap into covert and overt attention, respectively. To compare these, we ask some observers to detect targets (animals/vehicles) in rapid sequences, and others to freely view the same target images for 3 s, while their gaze is tracked. In some stimuli, the target's contrast is modified (increased/decreased) and its background modified either in the same or in the opposite way. We find that increasing target contrast relative to the background increases fixations and detection alike, whereas decreasing target contrast and simultaneously increasing background contrast has little effect. Contrast increase for the whole image (target + background) improves detection, decrease worsens detection, whereas fixation probability remains unaffected by whole-image modifications. Object-unrelated local increase or decrease of contrast attracts gaze, but less than actual objects, supporting a precedence of objects over low-level features. Detection and fixation probability are correlated: the more likely a target is detected in one paradigm, the more likely it is fixated in the other. Hence, the link between overt and covert attention, which has been established in simple stimuli, transfers to more naturalistic scenarios. PMID:24018728

  19. 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

  20. 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…

  1. 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.…

  2. Uranium-series disequilibria in Vanuatu arc volcanic rocks: constraints on pre-eruptive processes in contrasting volcanic systems

    NASA Astrophysics Data System (ADS)

    Handley, H. K.; Turner, S.; Reagan, M. K.; Girard, G.; Cronin, S. J.; Firth, C.

    2011-12-01

    Recent and present volcanism in the Vanuatu arc (South West Pacific Ocean) occurs at a variety of volcano types that exhibit a wide range of eruptive behaviour: from post-caldera lava-lake activity and lava flows at shield volcanoes (Ambrym), moderately explosive sub-plinian events and associated pyroclastic-flows and lava flows at stratovolcanoes (Lopevi), to persistent strombolian and vulcanian-style eruptions at scoria cones (Yasur). This precludes a generic model of magmatic and eruptive behaviour for the Vantuatu arc volcanoes and necessitates a detailed study of each system. Uranium-series disequilibria in volcanic rocks offer unique insights into pre-eruptive magmatic systems over process-relevant timescales e.g., 238U-230Th (380Ka), 230Th-226Ra (8Ka) and 226Ra-210Pb (100a). The short half-life of 210Pb (t1/2 = 22.6 years) and the volatile nature of the intermediate isotope, 222Rn, (intermediate between the 226Ra parent and 210Pb daughter) provide valuable information on magma transport, evolution and degassing over a timescale more pertinent to the processes leading up to volcanic eruptions. We present new Uranium-series isotope data (U-Th-Ra-210Pb) for young (< 100 years old) volcanic samples from Ambrym, Lopevi and Yasur volcanoes to investigate the timescales of magmatic evolution and degassing in the contrasting volcanic systems. 210Pb deficits ((210Pb/226Ra)0 < 1) in Ambrym and Yasur volcanic rocks suggest effective open-system magmatic degassing of 222Rn, consistent with the persistent lava-lakes/exposed magma and significant gas emissions observed at both volcanoes. Lopevi, on the other hand, largely displays excess 210Pb ((210Pb/226Ra)0 > 1) suggesting that 222Rn gas accumulation and fluxing preceding and/or during eruption (on a decadal timescale) is responsible for the more explosive-style of eruption witnessed at this volcano. Significant accumulation of recently crystallised plagioclase phenocrysts can also create 210Pb excesses in volcanic

  3. 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…

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  6. 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

  7. 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.

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

    ERIC Educational Resources Information Center

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

    2005-01-01

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

  9. The Lore of Admissions Policies: Contrasting Formal and Informal Understandings of the Residency Selection Process

    ERIC Educational Resources Information Center

    Ginsburg, Shiphra; Schreiber, Martin; Regehr, Glenn

    2004-01-01

    Purpose: The selection process for residency positions is sometimes seen as being "opaque'' and unfair by students, and can be a significant source of student stress. Yet efforts to clarify the process may not have helped reduce student stress for a number of reasons. This paper examines the nature of the knowledge that students possess and…

  10. Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis[C][W][OPEN

    PubMed Central

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

    2013-01-01

    The regulation of gene expression is crucial for an organism’s development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression. PMID:24045022

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. Photochemical processing of organic aerosol at nearby continental sites: contrast between urban plumes and regional aerosol

    NASA Astrophysics Data System (ADS)

    Slowik, J. G.; Brook, J.; Chang, R. Y.-W.; Evans, G. J.; Hayden, K.; Jeong, C.-H.; Li, S.-M.; Liggio, J.; Liu, P. S. K.; McGuire, M.; Mihele, C.; Sjostedt, S.; Vlasenko, A.; Abbatt, J. P. D.

    2011-03-01

    As part of the BAQS-Met 2007 field campaign, Aerodyne time-of-flight aerosol mass spectrometers (ToF-AMS) were deployed at two sites in southwestern Ontario from 17 June to 11 July 2007. One instrument was located at Harrow, ON, a rural, agriculture-dominated area approximately 40 km southeast of the Detroit/Windsor/Windsor urban area and 5 km north of Lake Erie. The second instrument was located at Bear Creek, ON, a rural site approximately 70 km northeast of the Harrow site and 50 km east of Detroit/Windsor. Positive matrix factorization analysis of the combined organic mass spectral dataset yields factors related to secondary organic aerosol (SOA), direct emissions, and a factor tentatively attributed to the reactive uptake of isoprene and/or condensation of its early generation reaction products. This is the first application of PMF to simultaneous AMS measurements at different sites, an approach which allows for self-consistent, direct comparison of the datasets. Case studies are utilized to investigate processing of SOA from (1) fresh emissions from Detroit/Windsor and (2) regional aerosol during periods of inter-site flow. A strong correlation is observed between SOA/excess CO and photochemical age as represented by the NOx/NOy ratio for Detroit/Windsor outflow. Although this correlation is not evident for more aged air, measurements at the two sites during inter-site transport nevertheless show evidence of continued atmospheric processing by SOA production. However, the rate of SOA production decreases with airmass age from an initial value of ~10.1 μg m-3 ppmvCO-1 h-1 for the first ~10 h of plume processing to near-zero in an aged airmass (i.e. after several days). The initial SOA production rate is comparable to the observed rate in Mexico City over similar timescales.

  17. Fourier transform image processing techniques for grid-based phase contrast imaging

    NASA Astrophysics Data System (ADS)

    Tahir, Sajjad; Bashir, Sajid; Petruccelli, Jonathan C.; MacDonald, C. A.

    2014-09-01

    A recently developed technique for phase imaging using table top sources is to use multiple fine-pitch gratings. However, the strict manufacturing tolerences and precise alignment required have limited the widespread adoption of grating-based techniques. In this work, we employ a technique recently demonstrated by Bennett et al.1 that ultilizes a single grid of much coarser pitch. Phase is extracted using Fourier processing on a single raw image taken using a focused mammography grid. The effects on the final image of varying grid, object, and detector distances, window widths, and of a variety of windowing functions, used to separate the harmonics, were investigated.

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

    PubMed Central

    Kerdelhué, C; Boivin, T; Burban, C

    2014-01-01

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

  19. 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

  20. 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

  1. 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

  2. High spatial resolution (1.1 μm and 20 nm) FTIR polarization contrast imaging reveals pre-rupture disorder in damaged tendon.

    PubMed

    Wiens, Richard; Findlay, Catherine R; Baldwin, Samuel G; Kreplak, Laurent; Lee, J Michael; Veres, Samuel P; Gough, Kathleen M

    2016-06-23

    Collagen is a major constituent in many life forms; in mammals, collagen appears as a component of skin, bone, tendon and cartilage, where it performs critical functions. Vibrational spectroscopy methods are excellent for studying the structure and function of collagen-containing tissues, as they provide molecular insight into composition and organization. The latter is particularly important for collagenous materials, given that a key feature is their hierarchical, oriented structure, organized from molecular to macroscopic length scales. Here, we present the first results of high-resolution FTIR polarization contrast imaging, at 1.1 μm and 20 nm scales, on control and mechanically damaged tendon. The spectroscopic data are supported with parallel SEM and correlated AFM imaging. Our goal is to explore the changes induced in tendon after the application of damaging mechanical stress, and the consequences for the healing processes. The results and possibilities for the application of these high-spatial-resolution FTIR techniques in spectral pathology, and eventually in clinical applications, are discussed. PMID:27048856

  3. Interaction of image noise, spatial resolution, and low contrast fine detail preservation in digital image processing

    NASA Astrophysics Data System (ADS)

    Artmann, Uwe; Wueller, Dietmar

    2009-01-01

    We present a method to improve the validity of noise and resolution measurements on digital cameras. If non-linear adaptive noise reduction is part of the signal processing in the camera, the measurement results for image noise and spatial resolution can be good, while the image quality is low due to the loss of fine details and a watercolor like appearance of the image. To improve the correlation between objective measurement and subjective image quality we propose to supplement the standard test methods with an additional measurement of the texture preserving capabilities of the camera. The proposed method uses a test target showing white Gaussian noise. The camera under test reproduces this target and the image is analyzed. We propose to use the kurtosis of the derivative of the image as a metric for the texture preservation of the camera. Kurtosis is a statistical measure for the closeness of a distribution compared to the Gaussian distribution. It can be shown, that the distribution of digital values in the derivative of the image showing the chart becomes the more leptokurtic (increased kurtosis) the stronger the noise reduction has an impact on the image.

  4. 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.

  5. 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

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

    PubMed Central

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

    2015-01-01

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

  7. 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

  8. 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

  9. 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

  10. Contrast studies.

    PubMed

    Anderson, Susan M

    2006-01-01

    Contrast media plays an important role in imaging soft tissues and organs. Though contrast imaging is considered safe, radiologic technologists can improve the safety of contrast examinations by reviewing institutional safety procedures, safe practices for different methods of contrast administration and possible complications. The need for efficient communication and attention to detail during contrast procedures is essential for patient safety. PMID:16998193

  11. Developmental Dyslexia With and Without Language Impairment: ERPs Reveal Qualitative Differences in Morphosyntactic Processing.

    PubMed

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

    2015-01-01

    This study aimed to characterize neuropsychological and linguistic skills in children with Developmental Dyslexia (DD) with and without Language Impairment (LI). Behavioral tests of short-term memory, phonemic awareness, and morphosyntactic processing and electrophysiological responses to agreement violations were administered to 32 DD children (16 with additional LI) and 16 controls. Behavioral data revealed quantitative differences among groups: DD+LI children showed the worst performance, followed by DD-only children and controls. Event-related potential results confirmed atypical morphosyntactic processing in the DD-only group, highlighting qualitative differences between groups. These results support multifactor models of learning disabilities, where different patterns of deficits characterize different subgroups. PMID:26285096

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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

  18. DNA polymerase beta reveals enhanced activity and processivity in reverse micelles.

    PubMed

    Anarbaev, Rashid O; Rogozina, Anastasia L; Lavrik, Olga I

    2009-04-01

    Water is essential for the stability and functions of proteins and DNA. Reverse micelles are simple model systems where the structure and dynamics of water are controlled. We have estimated the size of complex reverse micelles by light scattering technique and examined the local microenvironment using fluorescein as molecular probe. The micelle size and water polarity inside reverse micelles depend on water volume fraction. We have investigated the different hydration and confinement effects on activity, processivity, and stability of mammalian DNA polymerase beta in reverse micelles. The enzyme displays high processivity on primed single-stranded M13mp19 DNA with maximal activity at 10% of water content. The processivity and activity of DNA polymerase strongly depend on the protein concentration. The enzyme reveals also the enhanced stability in the presence of template-primer and at high protein concentration. The data provide direct evidence for strong influence of microenvironment on DNA polymerase activity. PMID:19138815

  19. Utilizing contrast enhancement material as a topside antireflective coating (TARC) for maximizing an i-line 0.35-um process window

    NASA Astrophysics Data System (ADS)

    Moynihan, Matthew L.; Markowski, Mark S.

    1995-06-01

    As critical dimensions become smaller, a greater demand is being placed on existing i-line lithographic capability to support 0.35 micrometers technology. One method that is gaining wider acceptance is the use of a top side anti reflective coating (TARC). The effect of the TARC is to reduce the interference effects occurring in the film stack so that critical dimension (CD) variation as a result of topography is minimized. Unfortunately, the TARC provides no improvement with other lithographic responses that define the process window of a resist. Another approach is to use a contrast enhancement material (CEM). It is well known that a CEM can improve the depth of focus and resolution of a given resist system, and it is suspected that it may also possess some of the interference reduction properties of conventional TARCs. The purpose of this work is to investigate how effective the CEM acts as a TARC, and to determine any additional lithographic improvements which will increase the overall 0.35 micrometers process window. Process optimization of the CEM and TARC revealed that similar processing schemes could be used for both materials, but that it was necessary to remove the CEM (w/ a water rinse) prior to post exposure bake (PEB). The bulk photospeed swing ratio of the SPR3000 alone, was compared to SPR3000/Aquatar and SPR3000/CEM. Results showed that the Aquatar reduced the Eo swing ratio by 75%, while the CEM reduced the Eo swing ratio by about 55%. Similar improvements were seen with 0.35 micrometers CD swing ratio data. Exposure latitude and focus latitude (0.35 micrometers lines/spaces) data was generated using the same resist/enhancement schemes mentioned above at thicknesses corresponding to an Emax and Emin. Results of the lithography at each thickness were overlaid to determine the process window. Results showed the Aquatar and CEM processes to provide improved 0.35 micrometers windows, and that using a contrast enhancement material as a TARC is another

  20. 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

  1. Franck-Condon processes in pentacene monolayers revealed in resonance Raman scattering

    NASA Astrophysics Data System (ADS)

    He, Rui; Tassi, Nancy G.; Blanchet, Graciela B.; Pinczuk, Aron

    2011-03-01

    Franck-Condon processes in pentacene monolayers are revealed in resonance Raman scattering from intramolecular vibrations. The Raman intensities from a totally symmetric vibrational mode display resonance enhancement double peaks when incident or scattered photon energies overlap the free exciton (FE) optical emission. The two resonances are of about equal strength. This remarkable symmetry in the resonance Raman profile suggests that Franck-Condon overlap integrals for the respective vibronic transitions have the same magnitude, which could be explained by the small displacement of potential energy curves along the configuration coordinate upon the FE excitation. The interference between scattering amplitudes in the Raman resonance reveals quantum coherence of the symmetry-split states (Davydov doublet) of the lowest intrinsic singlet exciton in pentacene monolayers.

  2. 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

  3. 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

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

    PubMed Central

    Dickson, Danielle S.; Federmeier, Kara D.

    2015-01-01

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

  5. Contribution of psychoacoustics and neuroaudiology in revealing correlation of mental disorders with central auditory processing disorders

    PubMed Central

    Iliadou, V; Iakovides, S

    2003-01-01

    Background Psychoacoustics is a fascinating developing field concerned with the evaluation of the hearing sensation as an outcome of a sound or speech stimulus. Neuroaudiology with electrophysiologic testing, records the electrical activity of the auditory pathways, extending from the 8th cranial nerve up to the cortical auditory centers as a result of external auditory stimuli. Central Auditory Processing Disorders may co-exist with mental disorders and complicate diagnosis and outcome. Design A MEDLINE search was conducted to search for papers concerning the association between Central Auditory Processing Disorders and mental disorders. The research focused on the diagnostic methods providing the inter-connection of various mental disorders and central auditory deficits. Measurements and Main Results The medline research revealed 564 papers when using the keywords 'auditory deficits' and 'mental disorders'. 79 papers were referring specifically to Central Auditory Processing Disorders in connection with mental disorders. 175 papers were related to Schizophrenia, 126 to learning disabilities, 29 to Parkinson's disease, 88 to dyslexia and 39 to Alzheimer's disease. Assessment of the Central Auditory System is carried out through a great variety of tests that fall into two main categories: psychoacoustic and electrophysiologic testing. Different specialties are involved in the diagnosis and management of Central Auditory Processing Disorders as well as the mental disorders that may co-exist with them. As a result it is essential that they are all aware of the possibilities in diagnostic procedures. Conclusions Considerable evidence exists that mental disorders may correlate with CAPD and this correlation could be revealed through psychoacoustics and neuroaudiology. Mental disorders that relate to Central Auditory Processing Disorders are: Schizophrenia, attention deficit disorders, Alzheimer's disease, learning disabilities, dyslexia, depression, auditory

  6. Feedforward and quick recurrent processes in early visual cortex revealed by TMS?

    PubMed

    de Graaf, Tom A; Goebel, Rainer; Sack, Alexander T

    2012-07-01

    Transcranial magnetic stimulation (TMS) can be applied to occipital cortex to abolish (conscious) perception of visual stimuli. TMS research has revealed several time windows of masking relative to visual stimulus onset, most consistently a time window around 100ms post-stimulus. However, the exact nature of visual processing in this 'classical' time window, e.g. whether it represents the feedforward processing of the visual information, or rather a feedback projection from higher visual areas, remains unclear. Here, we used TMS to mask in the same participants two types of stimuli of different complexities (orientation Gratings and Faces) over different time windows. Interestingly, the masking functions were not the same for both stimulus types. We found an earlier peak masking latency for orientation stimuli, and a slower recovery for Faces. In a second, follow-up experiment, we superimposed both types of stimuli to create one composite stimulus set. Depending on the instruction, participants could then perform orientation or face discrimination tasks on the exact same stimuli. In addition, for each participant, stimuli were calibrated to equate task difficulties. The peak masking latency was now identical for both tasks, but the masking function revealed again a slower recovery during the face discrimination task, suggesting top-down (recurrent) effects in the second half of the masking function. Hence, rather than this masking window reflecting either feedforward or feedback processing, the early part of what is traditionally considered one masking window may reflect feedforward processing, while the latter part may already reflect recurrent processing. These findings shed new light on recurrent models of vision and related theoretical accounts of visual awareness. PMID:22032946

  7. MHC class II variation in a rare and ecological specialist mouse lemur reveals lower allelic richness and contrasting selection patterns compared to a generalist and widespread sympatric congener.

    PubMed

    Pechouskova, Eva; Dammhahn, Melanie; Brameier, Markus; Fichtel, Claudia; Kappeler, Peter M; Huchard, Elise

    2015-04-01

    The polymorphism of immunogenes of the major histocompatibility complex (MHC) is thought to influence the functional plasticity of immune responses and, consequently, the fitness of populations facing heterogeneous pathogenic pressures. Here, we evaluated MHC variation (allelic richness and divergence) and patterns of selection acting on the two highly polymorphic MHC class II loci (DRB and DQB) in the endangered primate Madame Berthe's mouse lemur (Microcebus berthae). Using 454 pyrosequencing, we examined MHC variation in a total of 100 individuals sampled over 9 years in Kirindy Forest, Western Madagascar, and compared our findings with data obtained previously for its sympatric congener, the grey mouse lemur (Microcebus murinus). These species exhibit a contrasting ecology and demography that were expected to affect MHC variation and molecular signatures of selection. We found a lower allelic richness concordant with its low population density, but a similar level of allelic divergence and signals of historical selection in the rare feeding specialist M. berthae compared to the widespread generalist M. murinus. These findings suggest that demographic factors may exert a stronger influence than pathogen-driven selection on current levels of allelic richness in M. berthae. Despite a high sequence similarity between the two congeners, contrasting selection patterns detected at DQB suggest its potential functional divergence. This study represents a first step toward unravelling factors influencing the adaptive divergence of MHC genes between closely related but ecologically differentiated sympatric lemurs and opens new questions regarding potential functional discrepancy that would explain contrasting selection patterns detected at DQB. PMID:25687337

  8. 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

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

    PubMed

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

    2016-01-01

    Brain metastases outnumber the incidence of brain tumors by a factor of ten. Patients with brain metastases have a dismal prognosis and current treatment modalities achieve only a modest clinical benefit. We discuss the process of brain metastasis with respect to mechanisms and involved targets to outline options for therapeutic intervention and focus on breast and lung cancer, as well as melanoma. We describe the process of penetration of the blood-brain-barrier (BBB) by disseminated tumor cells, establishment of a metastatic niche, colonization and outgrowth in the brain parenchyma. Furthermore, the role of angiogenesis in colonization of the brain parenchyma, interactions of extravasated tumor cells with microglia and astrocytes, as well as their propensity for neuromimicry, is discussed. We outline targets suitable for prevention of metastasis and summarize targets suitable for treatment of established brain metastases. Finally, we highlight the implications of findings revealing druggable mutations in brain metastases that cannot be identified in matching primary tumors. PMID:27365375

  10. 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

  11. 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

  12. 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

  13. 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)…

  14. 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

  15. 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

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

    PubMed

    Hertz, Uri; Amedi, Amir

    2015-08-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  18. 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

  19. 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.

  20. TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage.

    PubMed

    Prudova, Anna; Serrano, Katherine; Eckhard, Ulrich; Fortelny, Nikolaus; Devine, Dana V; Overall, Christopher M

    2014-12-18

    Proteases, and specifically metalloproteinases, have been linked to the loss of platelet function during storage before transfusion, but the underlying mechanisms remain unknown. We used a dedicated N-terminomics technique, iTRAQ terminal amine isotopic labeling of substrates (TAILS), to characterize the human platelet N-terminome, proteome, and posttranslational modifications throughout platelet storage over 9 days under blood-banking conditions. From the identified 2938 proteins and 7503 unique peptides, we characterized N-terminal methionine excision, co- and posttranslational Nα acetylation, protein maturation, and proteolytic processing of proteins in human platelets. We also identified for the first time 10 proteins previously classified by the Human Proteome Organization as "missing" in the human proteome. Most N termini (77%) were internal neo-N termini (105 were novel potential alternative translation start sites, and 2180 represented stable proteolytic products), thus highlighting a prominent yet previously uncharacterized role of proteolytic processing during platelet storage. Protease inhibitor studies revealed metalloproteinases as being primarily responsible for proteolytic processing (as opposed to degradation) during storage. System-wide identification of metalloproteinase and other proteinase substrates and their respective cleavage sites suggests novel mechanisms of the effect of proteases on protein activity and platelet function during storage. All data sets and metadata are available through ProteomeXchange with the data set identifier PXD000906. PMID:25331112

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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. PMID:25707867

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. Saccharomyces cerevisiae a-Factor Mutants Reveal Residues Critical for Processing, Activity, and Export

    PubMed Central

    Huyer, Gregory; Kistler, Amy; Nouvet, Franklin J.; George, Carolyn M.; Boyle, Meredith L.; Michaelis, Susan

    2006-01-01

    The Saccharomyces cerevisiae mating pheromone a-factor provides a paradigm for understanding the biogenesis of prenylated fungal pheromones. The biogenesis of a-factor involves multiple steps: (i) C-terminal CAAX modification (where C is cysteine, A is aliphatic, and X is any residue) which includes prenylation, proteolysis, and carboxymethylation (by Ram1p/Ram2p, Ste24p or Rce1p, and Ste14p, respectively); (ii) N-terminal processing, involving two sequential proteolytic cleavages (by Ste24p and Axl1p); and (iii) nonclassical export (by Ste6p). Once exported, mature a-factor interacts with the Ste3p receptor on MATα cells to stimulate mating. The a-factor biogenesis machinery is well defined, as is the CAAX motif that directs C-terminal modification; however, very little is known about the sequence determinants within a-factor required for N-terminal processing, activity, and export. Here we generated a large collection of a-factor mutants and identified residues critical for the N-terminal processing steps mediated by Ste24p and Axl1p. We also identified mutants that fail to support mating but do not affect biogenesis or export, suggesting a defective interaction with the Ste3p receptor. Mutants significantly impaired in export were also found, providing evidence that the Ste6p transporter recognizes sequence determinants as well as CAAX modifications. We also performed a phenotypic analysis of the entire set of isogenic a-factor biogenesis machinery mutants, which revealed information about the dependency of biogenesis steps upon one another, and demonstrated that export by Ste6p requires the completion of all processing events. Overall, this comprehensive analysis will provide a useful framework for the study of other fungal pheromones, as well as prenylated metazoan proteins involved in development and aging. PMID:16963638

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Timing of posterior parahippocampal gyrus activity reveals multiple scene processing stages.

    PubMed

    Bastin, Julien; Committeri, Giorgia; Kahane, Philippe; Galati, Gaspare; Minotti, Lorella; Lachaux, Jean-Philippe; Berthoz, Alain

    2013-06-01

    Posterior parahippocampal gyrus (PPHG) is strongly involved during scene recognition and spatial cognition. How PPHG electrophysiological activity could underlie these functions, and whether they share similar timing mechanisms is unknown. We addressed this question in two intracerebral experiments which revealed that PPHG neural activity dissociated an early stimulus-driven effect (>200 and <500 ms) and a late task-related effect (>600 and <800 ms). Strongest PPHG gamma band (50-150 Hz) activities were found early when subjects passively viewed scenes (scene selectivity effect) and lately when they had to estimate the position of an object relative to the environment (allocentric effect). Based on single trial analyses, we were able to predict when patients viewed scenes (compared to other visual categories) and when they performed allocentric judgments (compared to other spatial judgments). The anatomical location corresponding to the strongest effects was in the depth of the collateral sulcus. Our findings directly affect current theories of visual scene processing and spatial orientation by providing new timing constraints and by demonstrating the existence of separable information processing stages in the functionally defined parahippocampal place area. PMID:22287281

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

    PubMed

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

    2007-08-01

    Improvement in source memory performance throughout childhood is thought to be mediated by the development of executive control. As postretrieval control processes may be better time-locked to the recognition response rather than the retrieval cue, the development of processes underlying source memory was investigated with both stimulus- and response-locked event-related potentials (ERPs). These were recorded in children, adolescents, and adults during a recognition memory exclusion task. Green- and red-outlined pictures were studied, but were tested in black outline. The test requirement was to endorse old items shown in one study color ("targets") and to reject new items along with old items shown in the alternative study color ("nontargets"). Source memory improved with age. All age groups retrieved target and nontarget memories as reflected by reliable parietal episodic memory (EM) effects, a stimulus-locked ERP correlate of recollection. Response-locked ERPs to targets and nontargets diverged in all groups prior to the response, although this occurred at an increasingly earlier time point with age. We suggest these findings reflect the implementation of attentional control mechanisms to enhance target memories and facilitate response selection with the greatest and least success, respectively, in adults and children. In adults only, response-locked ERPs revealed an early-onsetting parietal negativity for nontargets, but not for targets. This was suggested to reflect adults' ability to consistently inhibit prepotent target responses for nontargets. The findings support the notion that the development of source memory relies on the maturation of control processes that serve to enhance accurate selection of task-relevant memories. PMID:17651003

  2. 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

  3. 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

  4. 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

  5. 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.

  6. Flow cytometric analysis and microsatellite genotyping reveal extensive DNA content variation in Trypanosoma cruzi populations and expose contrasts between natural and experimental hybrids

    PubMed Central

    Lewis, Michael D.; Llewellyn, Martin S.; Gaunt, Michael W.; Yeo, Matthew; Carrasco, Hernán J.; Miles, Michael A.

    2009-01-01

    Trypanosoma cruzi exhibits remarkable genetic heterogeneity. This is evident at the nucleotide level but also structurally, in the form of karyotypic variation and DNA content differences between strains. Although natural populations of T. cruzi are predominantly clonal, hybrid lineages (TcIId and TcIIe) have been identified and hybridisation has been demonstrated in vitro, raising the possibility that genetic exchange may continue to shape the evolution of this pathogen. The mechanism of genetic exchange identified in the laboratory is unusual, apparently involving fusion of diploid parents followed by genome erosion. We investigated DNA content diversity in natural populations of T. cruzi in the context of its genetic subdivisions by using flow cytometric analysis and multilocus microsatellite genotyping to determine the relative DNA content and estimate the ploidy of 54 cloned isolates. The maximum difference observed was 47.5% between strain Tu18 cl2 (TcIIb) and strain C8 cl1 (TcI), which we estimated to be equivalent to ∼73 Mb of DNA. Large DNA content differences were identified within and between discrete typing units (DTUs). In particular, the mean DNA content of TcI strains was significantly less than that for TcII strains (P < 0.001). Comparisons of hybrid DTUs TcIId/IIe with corresponding parental DTUs TcIIb/IIc indicated that natural hybrids are predominantly diploid. We also measured the relative DNA content of six in vitro-generated TcI hybrid clones and their parents. In contrast to TcIId/IIe hybrid strains these experimental hybrids comprised populations of sub-tetraploid organisms with mean DNA contents 1.65–1.72 times higher than the parental organisms. The DNA contents of both parents and hybrids were shown to be relatively stable after passage through a mammalian host, heat shock or nutritional stress. The results are discussed in the context of hybridisation mechanisms in both natural and in vitro settings. PMID:19393242

  7. 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…

  8. Real-time single-molecule tethered particle motion analysis reveals mechanistic similarities and contrasts of Flp site-specific recombinase with Cre and λ Int

    PubMed Central

    Fan, Hsiu-Fang; Ma, Chien-Hui; Jayaram, Makkuni

    2013-01-01

    Flp, a tyrosine site-specific recombinase coded for by the selfish two micron plasmid of Saccharomyces cerevisiae, plays a central role in the maintenance of plasmid copy number. The Flp recombination system can be manipulated to bring about a variety of targeted DNA rearrangements in its native host and under non-native biological contexts. We have performed an exhaustive analysis of the Flp recombination pathway from start to finish by using single-molecule tethered particle motion (TPM). The recombination reaction is characterized by its early commitment and high efficiency, with only minor detraction from ‘non-productive’ and ‘wayward’ complexes. The recombination synapse is stabilized by strand cleavage, presumably by promoting the establishment of functional interfaces between adjacent Flp monomers. Formation of the Holliday junction intermediate poses a rate-limiting barrier to the overall reaction. Isomerization of the junction to the conformation favoring its resolution in the recombinant mode is not a slow step. Consistent with the completion of nearly every initiated reaction, the chemical steps of strand cleavage and exchange are not reversible during a recombination event. Our findings demonstrate similarities and differences between Flp and the mechanistically related recombinases λ Int and Cre. The commitment and directionality of Flp recombination revealed by TPM is consistent with the physiological role of Flp in amplifying plasmid DNA. PMID:23737451

  9. Systems Genetics Analysis of GWAS reveals Novel Associations between Key Biological Processes and Coronary Artery Disease

    PubMed Central

    Ghosh, Sujoy; Vivar, Juan; Nelson, Christopher P; Willenborg, Christina; Segrè, Ayellet V; Mäkinen, Ville-Petteri; Nikpay, Majid; Erdmann, Jeannette; Blankenberg, Stefan; O'Donnell, Christopher; März, Winfried; Laaksonen, Reijo; Stewart, Alexandre FR; Epstein, Stephen E; Shah, Svati H; Granger, Christopher B; Hazen, Stanley L; Kathiresan, Sekar; Reilly, Muredach P; Yang, Xia; Quertermous, Thomas; Samani, Nilesh J; Schunkert, Heribert; Assimes, Themistocles L; McPherson, Ruth

    2016-01-01

    Objective Genome-wide association (GWA) studies have identified multiple genetic variants affecting the risk of coronary artery disease (CAD). However, individually these explain only a small fraction of the heritability of CAD and for most, the causal biological mechanisms remain unclear. We sought to obtain further insights into potential causal processes of CAD by integrating large-scale GWA data with expertly curated databases of core human pathways and functional networks. Approaches and Results Employing pathways (gene sets) from Reactome, we carried out a two-stage gene set enrichment analysis strategy. From a meta-analyzed discovery cohort of 7 CADGWAS data sets (9,889 cases/11,089 controls), nominally significant gene-sets were tested for replication in a meta-analysis of 9 additional studies (15,502 cases/55,730 controls) from the CARDIoGRAM Consortium. A total of 32 of 639 Reactome pathways tested showed convincing association with CAD (replication p<0.05). These pathways resided in 9 of 21 core biological processes represented in Reactome, and included pathways relevant to extracellular matrix integrity, innate immunity, axon guidance, and signaling by PDRF, NOTCH, and the TGF-β/SMAD receptor complex. Many of these pathways had strengths of association comparable to those observed in lipid transport pathways. Network analysis of unique genes within the replicated pathways further revealed several interconnected functional and topologically interacting modules representing novel associations (e.g. semaphorin regulated axonal guidance pathway) besides confirming known processes (lipid metabolism). The connectivity in the observed networks was statistically significant compared to random networks (p<0.001). Network centrality analysis (‘degree’ and ‘betweenness’) further identified genes (e.g. NCAM1, FYN, FURIN etc.) likely to play critical roles in the maintenance and functioning of several of the replicated pathways. Conclusions These findings

  10. 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.

  11. 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.

  12. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

    PubMed Central

    Hackl, Hubert; Burkard, Thomas Rainer; Sturn, Alexander; Rubio, Renee; Schleiffer, Alexander; Tian, Sun; Quackenbush, John; Eisenhaber, Frank; Trajanoski, Zlatko

    2005-01-01

    Background Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene products has not been done and global mechanisms have not been investigated. We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development. Results Mouse microarrays with more than 27,000 elements were developed, and transcriptional profiles of 3T3-L1 cells (pre-adipocyte cells) were monitored during differentiation. In total, 780 differentially expressed expressed sequence tags (ESTs) were subjected to in-depth bioinformatics analyses. The analysis of 3'-untranslated region sequences from 395 ESTs showed that 71% of the differentially expressed genes could be regulated by microRNAs. A molecular atlas of fat cell development was then constructed by de novo functional annotation on a sequence segment/domain-wise basis of 659 protein sequences, and subsequent mapping onto known pathways, possible cellular roles, and subcellular localizations. Key enzymes in 27 out of 36 investigated metabolic pathways were regulated at the transcriptional level, typically at the rate-limiting steps in these pathways. Also, coexpressed genes rarely shared consensus transcription-factor binding sites, and were typically not clustered in adjacent chromosomal regions, but were instead widely dispersed throughout the genome. Conclusions Large-scale transcription profiling in conjunction with sophisticated bioinformatics analyses can provide not only a list of novel players in a particular setting but also a global view on biological processes and molecular networks. PMID:16420668

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

    PubMed

    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

  14. 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

  15. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  18. 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

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

    PubMed

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

    2013-12-01

    Native speakers of languages with transparent gender systems can use gender cues to anticipate upcoming words. To examine whether this also holds true for a non-transparent two-way gender system, i.e. Dutch, eye movements were monitored as participants followed spoken instructions to click on one of four displayed items on a screen (e.g., Klik op [Formula: see text] rode appel [Formula: see text], 'Click on the[Formula: see text] red apple[Formula: see text]'). The items contained the target, a colour- and/or gender-matching competitor, and two unrelated distractors. A mixed-effects regression analysis revealed that the presence of a colour-matching and/or gender-matching competitor significantly slowed the process of finding the target. The gender effect, however, was only observed for common nouns, reflecting the fact that neuter gender-marking cannot disambiguate as all Dutch nouns become neuter when used as diminutives. The gender effect for common nouns occurred before noun onset, suggesting that gender information is, at least partially, activated automatically before encountering the noun. PMID:23229089

  20. 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

  1. 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

  2. Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance

    PubMed Central

    Wong, Chui E; Bhalla, Prem L; Ottenhof, Harald; Singh, Mohan B

    2008-01-01

    Background Despite the importance of the shoot apical meristem (SAM) in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum) is a well-established classic model species for genetics studies that has been used since the Mendel era. In addition, the availability of a plethora of developmental mutants makes pea an ideal crop legume for genomics studies. This study aims to utilise genomics tools in isolating genes that play potential roles in the regulation of SAM activity. Results In order to identify genes that are differentially expressed in the SAM, we generated 2735 ESTs from three cDNA libraries derived from freshly micro-dissected SAMs from 10-day-old garden peas (Pisum sativum cv Torsdag). Custom-designed oligonucleotide arrays were used to compare the transcriptional profiles of pea SAMs and non-meristematic tissues. A total of 184 and 175 transcripts were significantly up- or down-regulated in the pea SAM, respectively. As expected, close to 61% of the transcripts down-regulated in the SAM were found in the public database, whereas sequences from the same source only comprised 12% of the genes that were expressed at higher levels in the SAM. This highlights the under-representation of transcripts from the meristematic tissues in the current public pea protein database, and demonstrates the utility of our SAM EST collection as an essential genetic resource for revealing further information on the regulation of this developmental process. In addition to unknowns, many of the up-regulated transcripts are known to encode products associated with cell division and proliferation, epigenetic regulation, auxin

  3. 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 ...

  4. An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection.

    PubMed

    Forni, Diego; Cagliani, Rachele; Tresoldi, Claudia; Pozzoli, Uberto; De Gioia, Luca; Filippi, Giulia; Riva, Stefania; Menozzi, Giorgia; Colleoni, Marta; Biasin, Mara; Lo Caputo, Sergio; Mazzotta, Francesco; Comi, Giacomo P; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2014-03-01

    The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes

  5. 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.

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

    PubMed

    McAllister Byun, Tara; 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 neutralised. 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 neutralised 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 in this article. PMID:26325303

  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. Magma Reservoir Processes Revealed by Geochemistry of the Ongoing East Rift Zone Eruption, Kilauea Volcano, Hawaii

    NASA Astrophysics Data System (ADS)

    Thornber, C. R.

    2002-12-01

    Geochemical data were examined for a suite of 1,000 near-vent lava samples from the Pu`u `O`o-Kupaianaha eruption of Kilauea, collected from January 1983 through October 2001. Bulk lava and glass compositions reveal short- and long-term changes in pre-eruptive magma conditions that can be correlated with changes in edifice deformation, shallow magma transfer and eruptive behavior. Two decades of eruption on Kilauea's east rift zone has yielded ~2 km3 of lava, 97% of which is sparsely olivine-phyric with an MgO range of 6.8 to 9.6 wt%. During separate brief intervals of low-volume, fissure eruption (episodes 1 to 3 and 54), isolated rift-zone reservoirs with lower-MgO and olv-cpx-plg-phryic magma were incorporated by more mafic magma immediately prior to eruption. During prolonged, near-continuous eruption(e.g.,episodes 48-53 and most of 55), steady-state effusion is marked by cyclic variations in olivine-saturated magma chemistry. Bulk lava MgO and eruption temperature vary in cycles of monthly to bi-annual frequency, while olivine-incompatible elements vary inversely to these cycles. However, MgO-normalized values and ratios of highly to moderately incompatible elements (HINCE/MINCE), which nullify olivine fractionation effects, reveal cycles in magma chemistry that occur prior to olivine crystallization over the magmatic temperature range that is tapped by this eruption (1205-1155°C). These short-term cycles are superimposed on a long-term decrease of HINCE/MINCE, which is widely thought to reflect a 20-year change in mantle-source conditions. While HINCE/MINCE variation in primitive recharge magma cannot be ruled out, the short-term fluctuations of this signature may require unreasonably complex mantle variations. Alternatively, the correspondence of HINCE/MINCE cycles with edifice deformation and eruptive behavior suggests that the long-term evolving magmatic condition is a result of prolonged succession of short-term shallow magmatic events. The consistent

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  10. 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

  11. 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.

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

    PubMed

    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

  13. 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

  14. 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

  15. 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…

  16. 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…

  17. 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

  18. 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…

  19. 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. PMID:26298249

  20. 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.

  1. 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

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

    PubMed Central

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

    2015-01-01

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

  3. 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…

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

    PubMed

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

    2016-08-01

    Survival motor neuron (SMN) functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) that catalyze pre-mRNA splicing. Here, we used disruptions in Smn and two additional snRNP biogenesis genes, Phax and Ars2, to classify RNA processing differences as snRNP-dependent or gene-specific in Drosophila Phax and Smn mutants exhibited comparable reductions in snRNAs, and comparison of their transcriptomes uncovered shared sets of RNA processing changes. In contrast, Ars2 mutants displayed only small decreases in snRNA levels, and RNA processing changes in these mutants were generally distinct from those identified in Phax and Smn animals. Instead, RNA processing changes in Ars2 mutants support the known interaction of Ars2 protein with the cap-binding complex, as splicing changes showed a clear bias toward the first intron. Bypassing disruptions in snRNP biogenesis, direct knockdown of spliceosomal proteins caused similar changes in the splicing of snRNP-dependent events. However, these snRNP-dependent events were largely unaltered in three Smn mutants expressing missense mutations that were originally identified in human spinal muscular atrophy (SMA) patients. Hence, findings here clarify the contributions of Phax, Smn, and Ars2 to snRNP biogenesis in Drosophila, and loss-of-function mutants for these proteins reveal differences that help disentangle cause and effect in SMA model flies. PMID:27268418

  5. 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...

  6. Psychophysical "blinding" methods reveal a functional hierarchy of unconscious visual processing.

    PubMed

    Breitmeyer, Bruno G

    2015-09-01

    Numerous non-invasive experimental "blinding" methods exist for suppressing the phenomenal awareness of visual stimuli. Not all of these suppressive methods occur at, and thus index, the same level of unconscious visual processing. This suggests that a functional hierarchy of unconscious visual processing can in principle be established. The empirical results of extant studies that have used a number of different methods and additional reasonable theoretical considerations suggest the following tentative hierarchy. At the highest levels in this hierarchy is unconscious processing indexed by object-substitution masking. The functional levels indexed by crowding, the attentional blink (and other attentional blinding methods), backward pattern masking, metacontrast masking, continuous flash suppression, sandwich masking, and single-flash interocular suppression, fall at progressively lower levels, while unconscious processing at the lowest levels is indexed by eye-based binocular-rivalry suppression. Although unconscious processing levels indexed by additional blinding methods is yet to be determined, a tentative placement at lower levels in the hierarchy is also given for unconscious processing indexed by Troxler fading and adaptation-induced blindness, and at higher levels in the hierarchy indexed by attentional blinding effects in addition to the level indexed by the attentional blink. The full mapping of levels in the functional hierarchy onto cortical activation sites and levels is yet to be determined. The existence of such a hierarchy bears importantly on the search for, and the distinctions between, neural correlates of conscious and unconscious vision. PMID:25704454

  7. Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

    PubMed Central

    Zywicki, Marek; Bakowska-Zywicka, Kamilla; Polacek, Norbert

    2012-01-01

    The exploration of the non-protein-coding RNA (ncRNA) transcriptome is currently focused on profiling of microRNA expression and detection of novel ncRNA transcription units. However, recent studies suggest that RNA processing can be a multi-layer process leading to the generation of ncRNAs of diverse functions from a single primary transcript. Up to date no methodology has been presented to distinguish stable functional RNA species from rapidly degraded side products of nucleases. Thus the correct assessment of widespread RNA processing events is one of the major obstacles in transcriptome research. Here, we present a novel automated computational pipeline, named APART, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data. The major features include efficient handling of non-unique reads, detection of novel stable ncRNA transcripts and processing products and annotation of known transcripts based on multiple sources of information. To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. By employing the APART pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable RNA molecules differentially processed from well known ncRNAs, like rRNAs, tRNAs or snoRNAs, in a stress-dependent manner. PMID:22266655

  8. 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

  9. 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

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

    NASA Astrophysics Data System (ADS)

    Sharma, Rakesh

    2010-07-01

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

  11. The Stimulus Selectivity and Connectivity of Layer Six Principal Cells Reveals Cortical Microcircuits Underlying Visual Processing

    PubMed Central

    Vélez-Fort, Mateo; Rousseau, Charly V.; Niedworok, Christian J.; Wickersham, Ian R.; Rancz, Ede A.; Brown, Alexander P.Y.; Strom, Molly; Margrie, Troy W.

    2014-01-01

    Summary Sensory computations performed in the neocortex involve layer six (L6) cortico-cortical (CC) and cortico-thalamic (CT) signaling pathways. Developing an understanding of the physiological role of these circuits requires dissection of the functional specificity and connectivity of the underlying individual projection neurons. By combining whole-cell recording from identified L6 principal cells in the mouse primary visual cortex (V1) with modified rabies virus-based input mapping, we have determined the sensory response properties and upstream monosynaptic connectivity of cells mediating the CC or CT pathway. We show that CC-projecting cells encompass a broad spectrum of selectivity to stimulus orientation and are predominantly innervated by deep layer V1 neurons. In contrast, CT-projecting cells are ultrasparse firing, exquisitely tuned to orientation and direction information, and receive long-range input from higher cortical areas. This segregation in function and connectivity indicates that L6 microcircuits route specific contextual and stimulus-related information within and outside the cortical network. PMID:25175879

  12. 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

  13. 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

  14. 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.

  15. Mechanical Unfolding of an Autotransporter Passenger Protein Reveals the Secretion Starting Point and Processive Transport Intermediates.

    PubMed

    Baclayon, Marian; Ulsen, Peter van; Mouhib, Halima; Shabestari, Maryam Hashemi; Verzijden, Timo; Abeln, Sanne; Roos, Wouter H; Wuite, Gijs J L

    2016-06-28

    The backbone of secreted autotransporter passenger proteins generally attains a stable β-helical structure. The secretion of passengers across the outer membrane was proposed to be driven by sequential folding of this structure at the cell surface. This mechanism would require a relatively stable intermediate as starting point. Here, we investigated the mechanics of secreted truncated versions of the autotransporter hemoglobin protease (Hbp) of Escherichia coli using atomic force microscopy. The data obtained reveal a β-helical structure at the C terminus that is very stable. In addition, several other distinct metastable intermediates are found which are connected during unfolding by multiroute pathways. Computational analysis indicates that these intermediates correlate to the β-helical rungs in the Hbp structure which are clamped by stacked aromatic residues. Our results suggest a secretion mechanism that is initiated by a stable C-terminal structure and driven forward by several folding intermediates that build up the β-helical backbone. PMID:27219538

  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. 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…

  19. 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…

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

    PubMed Central

    Giglione, Carmela; Serero, Alexandre; Pierre, Michèle; Boisson, Bertrand; Meinnel, Thierry

    2000-01-01

    The N-terminal protein processing pathway is an essential mechanism found in all organisms. However, it is widely believed that deformylase, a key enzyme involved in this process in bacteria, does not exist in eukaryotes, thus making it a target for antibacterial agents such as actinonin. In an attempt to define this process in higher eukaryotes we have used Arabidopsis thaliana as a model organism. Two deformylase cDNAs, the first identified in any eukaryotic system, and six distinct methionine aminopeptidase cDNAs were cloned. The corresponding proteins were characterized in vivo and in vitro. Methionine aminopeptidases were found in the cytoplasm and in the organelles, while deformylases were localized in the organelles only. Our work shows that higher plants have a much more complex machinery for methionine removal than previously suspected. We were also able to identify deformylase homologues from several animals and clone the corresponding cDNA from human cells. Our data provide the first evidence that lower and higher eukaryotes, as well as bacteria, share a similar N-terminal protein processing machinery, indicating universality of this system. PMID:11060042

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

    ERIC Educational Resources Information Center

    Mynatt, Barbee T.; Smith, Kirk H.

    1977-01-01

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

  2. 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

  3. 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…

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

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  5. 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…

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

    PubMed

    Cruse, Damian; Wilding, Edward L

    2011-06-01

    In a pair of recent studies, frontally distributed event-related potential (ERP) indices of two distinct post-retrieval processes were identified. It has been proposed that one of these processes operates over any kinds of task relevant information in service of task demands, while the other operates selectively over recovered contextual (episodic) information. The experiment described here was designed to test this account, by requiring retrieval of different kinds of contextual information to that required in previous relevant studies. Participants heard words spoken in either a male or female voice at study and ERPs were acquired at test where all words were presented visually. Half of the test words had been spoken at study. Participants first made an old/new judgment, distinguishing via key press between studied and unstudied words. For words judged 'old', participants indicated the voice in which the word had been spoken at study, and their confidence (high/low) in the voice judgment. There was evidence for only one of the two frontal old/new effects that had been identified in the previous studies. One possibility is that the ERP effect in previous studies that was tied specifically to recollection reflects processes operating over only some kinds of contextual information. An alternative is that the index reflects processes that are engaged primarily when there are few contextual features that distinguish between studied stimuli. PMID:21382387

  7. 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

  8. Contrasting Li and Mg isotope behaviour in small Alpine rivers: tracing seasonal changes in weathering processes (Invited)

    NASA Astrophysics Data System (ADS)

    Tipper, E.; Hindshaw, R. S.; Bourdon, B.; Lemarchand, E.

    2013-12-01

    Seasonal changes in river chemistry offer the potential to assess how weathering processes respond to changing meteorological parameters and ultimately how chemical weathering might respond to climatic parameters. A key observation with time-series data on river waters is that variations in elemental concentrations (typically less than an order of magnitude) are damped compared to variations in discharge (up to several orders of magnitude). This behavior is referred to as chemostatic. However, both radiogenic and stable isotope ratios of the solutes show significant, systematic temporal variations than indicate that there is not a chemostasis in the elemental release of solutes during dissolution. Here we discuss systematic seasonal variations in lithium and magnesium isotope ratios (the 7Li/6Li 26Mg/24Mg ratio expressed as delta7Li and delta26Mg in per mil units) in stream waters from a mono-lithological granitic, weathering-limited, first order catchment from the Swiss Alps (Damma glacier). Rain, ground, and pore-waters, in addition to plants, rocks, mineral separates and soil are also reported. Whilst the concentration response of Li and Mg in the river waters is attenuated compared to the large changes in discharge that occur over an annual cycle the systematic trends in both the Mg and Li isotope data imply that either the source of the Li and Mg changes in a systematic manner, or that the process by which Mg and Li are released into solution changes as a function of discharge. In the first order the Mg and Li isotope data appear to show similar trends. However, when examined in more detail, it is difficult to reconcile the data by one pair of fractionation factors for Li and Mg. This provides an additional constraint on how weathering processes vary over a seasonal cycle, and perhaps indications an incomplete equilibrium or kinetic limitation to weathering. The reasons behind these trends will be discussed in the context of the apparent chemostatic behavior

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

    PubMed Central

    Rönnberg, 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 pictures were used as stimuli to avoid confounds relating to sensory modality. Performance was largely similar for DS, HS, and HN, suggesting that previously identified intermodal differences may be due to differences in retention of sensory information. When explicit processing demands were high, differences emerged between DS and HN, suggesting that although working memory storage in both groups is sensitive to temporal organization, retrieval is not sensitive to temporal organization in DS. A general effect of semantic similarity was also found. These findings are discussed in relation to the ELU model. PMID:18353759

  10. Frequency-specific disruptions of neuronal oscillations reveal aberrant auditory processing in schizophrenia.

    PubMed

    Hayrynen, Lauren K; Hamm, Jordan P; Sponheim, Scott R; Clementz, Brett A

    2016-06-01

    Individuals with schizophrenia exhibit abnormalities in evoked brain responses in oddball paradigms. These could result from (a) insufficient salience-related cortical signaling (P300), (b) insufficient suppression of irrelevant aspects of the auditory environment, or (c) excessive neural noise. We tested whether disruption of ongoing auditory steady-state responses at predetermined frequencies informed which of these issues contribute to auditory stimulus relevance processing abnormalities in schizophrenia. Magnetoencephalography data were collected for 15 schizophrenia and 15 healthy subjects during an auditory oddball paradigm (25% targets; 1-s interstimulus interval). Auditory stimuli (pure tones: 1 kHz standards, 2 kHz targets) were administered during four continuous background (auditory steady-state) stimulation conditions: (1) no stimulation, (2) 24 Hz, (3) 40 Hz, and (4) 88 Hz. The modulation of the auditory steady-state response (aSSR) and the evoked responses to the transient stimuli were quantified and compared across groups. In comparison to healthy participants, the schizophrenia group showed greater disruption of the ongoing aSSR by targets regardless of steady-state frequency, and reduced amplitude of both M100 and M300 event-related field components. During the no-stimulation condition, schizophrenia patients showed accentuation of left hemisphere 40 Hz response to both standard and target stimuli, indicating an effort to enhance local stimulus processing. Together, these findings suggest abnormalities in auditory stimulus relevance processing in schizophrenia patients stem from insufficient amplification of salient stimuli. PMID:26933842

  11. 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

  12. 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

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

    PubMed Central

    Wang, Quanxin; Sporns, Olaf; Burkhalter, Andreas

    2012-01-01

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

  14. Eyetracking of social preference choices reveals normal but faster processing in autism.

    PubMed

    Gharib, Alma; Mier, Daniela; Adolphs, Ralph; Shimojo, Shinsuke

    2015-06-01

    People with Autism Spectrum Disorder (ASD) have been reported to show atypical attention and evaluative processing, in particular for social stimuli such as faces. The usual measure in these studies is an explicit, subjective judgment, which is the culmination of complex-temporally extended processes that are not typically dissected in detail. Here we addressed a neglected aspect of social decision-making in order to gain further insight into the underlying mechanisms: the temporal evolution of the choice. We investigated this issue by quantifying the alternating patterns of gaze onto faces, as well as nonsocial stimuli, while subjects had to decide which of the two stimuli they preferred. Surprisingly, the temporal profile of fixations relating to choice (the so-called "gaze cascade") was entirely normal in ASD, as were the eventual preference choices. Despite these similarities, we found two key abnormalities: people with ASD made choices more rapidly than did control subjects across the board, and their reaction times for social preference judgments were insensitive to choice difficulty. We suggest that ASD features an altered decision-making process when basing choice on social preferences. One hypothesis motivated by these data is that a choice criterion is reached in ASD regardless of the discriminability of the options. PMID:25921868

  15. Eyetracking of social preference choices reveals normal but faster processing in autism

    PubMed Central

    Gharib, Alma; Mier, Daniela; Adolphs, Ralph; Shimojo, Shinsuke

    2015-01-01

    People with Autism Spectrum Disorder (ASD) have been reported to show atypical attention and eva luative processing, in particular for social stimuli such as faces. The usual measure in these studies is an explicit, subjective judgment, which is the culmination of complex-temporally extended processes that are not typically dissected in detail. Here we addressed a neglected aspect of social decision-making in order to gain further insight into the underlying mechanisms: the temporal evolution of the choice. We investigated this issue by quantifying the alternating patterns of gaze onto faces, as well as nonsocial stimuli, while subjects had to decide which of the two stimuli they preferred. Surprisingly, the temporal profile of fixations relating to choice (the so-called “gaze cascade”) was entirely normal in ASD, as were the eventual preference choices. Despite these similarities, we found two key abnormalities: people with ASD made choices more rapidly than did control subjects across the board, and their reaction times for social preference judgments were insensitive to choice difficulty. We suggest that ASD features an altered decision-making process when basing choice on social preferences. One hypothesis motivated by these data is that a choice criterion is reached in ASD regardless of the discriminability of the options. PMID:25921868

  16. 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

  17. 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

  18. Gadofullerene MRI contrast agents.

    PubMed

    Bolskar, Robert D

    2008-04-01

    A promising new class of MRI contrast-enhancing agents with high relaxivities is based on gadolinium-containing metallofullerenes, which are also termed gadofullerenes. Detailed study of the water-proton relaxivity properties and intermolecular nanoclustering behavior of gadofullerene derivatives has revealed valuable information about their relaxivity mechanisms and given a deeper understanding of this new class of paramagnetic contrast agent. Here, the latest findings on water-solubilized gadofullerene materials and how these findings relate to their future applications in MRI are reviewed and discussed. PMID:18373426

  19. Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy

    PubMed Central

    Andrecka, Joanna; Ortega Arroyo, Jaime; Takagi, Yasuharu; de Wit, Gabrielle; Fineberg, Adam; MacKinnon, Lachlan; Young, Gavin; Sellers, James R; Kukura, Philipp

    2015-01-01

    Myosin 5a is a dual-headed molecular motor that transports cargo along actin filaments. By following the motion of individual heads with interferometric scattering microscopy at nm spatial and ms temporal precision we found that the detached head occupies a loosely fixed position to one side of actin from which it rebinds in a controlled manner while executing a step. Improving the spatial precision to the sub-nm regime provided evidence for an ångstrom-level structural transition in the motor domain associated with the power stroke. Simultaneous tracking of both heads revealed that consecutive steps follow identical paths to the same side of actin in a compass-like spinning motion demonstrating a symmetrical walking pattern. These results visualize many of the critical unknown aspects of the stepping mechanism of myosin 5 including head–head coordination, the origin of lever-arm motion and the spatiotemporal dynamics of the translocating head during individual steps. DOI: http://dx.doi.org/10.7554/eLife.05413.001 PMID:25748137

  20. Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

    PubMed Central

    Underwood, Anthony; Gielbert, Adriana; Woodward, Martin J.

    2014-01-01

    The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified Clostridiales, Bacteroidaceae, and Lactobacillaceae species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to Lactobacillus spp., 155 belonged to Clostridium spp., and 66 belonged to Streptococcus spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed. PMID:24212578

  1. High-Resolution Crack Imaging Reveals Degradation Processes in Nuclear Reactor Structural Materials

    SciTech Connect

    Olszta, Matthew J.; Schreiber, Daniel K.; Thomas, Larry E.; Bruemmer, Stephen M.

    2012-04-01

    Corrosion and cracking represent critical failure mechanisms for structural materials in many applications. Although a crack can often be seen with the unaided eye, higher resolution imaging techniques are required to understand the nature of the crack tips and underlying degradation processes. Researchers at Pacific Northwest National Laboratory (PNNL) employ a suite of microscopy techniques and site-specific material sampling to analyze corrosion and crack structures, producing images and compositional analyses with near-atomic spatial resolution. The samples are cracked components removed from commercial light-water reactor service or laboratory samples tested in simulated reactor environments.

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

    PubMed Central

    2012-01-01

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

  3. Photo-induced processes in collagen-hypericin system revealed by fluorescence spectroscopy and multiphoton microscopy.

    PubMed

    Hovhannisyan, V; Guo, H W; Hovhannisyan, A; Ghukasyan, V; Buryakina, T; Chen, Y F; Dong, C Y

    2014-05-01

    Collagen is the main structural protein and the key determinant of mechanical and functional properties of tissues and organs. Proper balance between synthesis and degradation of collagen molecules is critical for maintaining normal physiological functions. In addition, collagen influences tumor development and drug delivery, which makes it a potential cancer therapy target. Using second harmonic generation, two-photon excited fluorescence microscopy, and spectrofluorimetry, we show that the natural pigment hypericin induces photosensitized destruction of collagen-based tissues. We demonstrate that hypericin-mediated processes in collagen fibers are irreversible and may be used for the treatment of cancer and collagen-related disorders. PMID:24877000

  4. 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

  5. Subduction processes along the Peruvian Margin revealed by wide angle seismic studies

    NASA Astrophysics Data System (ADS)

    Krabbenhoeft, A.; Bialas, J.; Kopp, H.; Kukowski, N.

    2002-12-01

    Within the scope of the GEOPECO (Geophysical Experiments at the Peruvian Continental Margin) project, seismic investigations along the Pacific margin of Peru were carried out using ocean bottom hydrophones (OBH) and seismometers (OBS) recording marine airgun shots. The structure and the P-wave velocity of the oblique subducting Nazca and overriding South-American Plates from 8 °S to 15 °S were determined by forward modeling and tomographic inversion of the wide-angle seismic data combined with the analysis of reflection seismic data. The oceanic Nazca Plate is divided by Mendana Fracture Zone (MFZ) which marks a transition zone of a different crustal age of approximately 28 Ma in the north to 38 Ma in the south at the Peruvian trench. North of MFZ the oceanic crust is influenced by Trujillo Trough trending N15E and the surrounding extensional stresses leading to a crustal thinning as can be seen in the northernmost refraction seismic model. The oceanic crust south of MFZ is overall homogeneous with a thin pelagic sedimentary layer and normal oceanic crustal layers. The P-wave velocity of the mantle is overall 7.9-8.1 km/s. The Peruvian Continental Margin is characterized by the continental slope and several basins, Trujillo and Yaquina basin, Lima basin and Pisco basin, which are partly affected by the southward migration of the subducting Nazca Ridge. This caused uplift and subsidence along the margin leading to erosional tectonic features. The basins and continental basement could be mapped with forward modeling and tomographic inversion as well as the continental backstop on each profile. An accretionary prism is set up with a width of 20 to 30 km and 4 to 5 km thickness which does not further increase in size as revealed by the profiles recorded further north of Nazca Ridge. This and a taper of 14 ° -17 ° at the collision zone indicates that current subduction along the Peruvian Margin is non-accreting.

  6. 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

  7. Single-molecule assay reveals strand switching and enhanced processivity of UvrD

    NASA Astrophysics Data System (ADS)

    Dessinges, Marie-Noëlle; Lionnet, Timothée; Xi, Xu Guang; Bensimon, David; Croquette, Vincent

    2004-04-01

    DNA helicases are enzymes capable of unwinding double-stranded DNA (dsDNA) to provide the single-stranded DNA template required in many biological processes. Among these, UvrD, an essential DNA repair enzyme, has been shown to unwind dsDNA while moving 3'-5' on one strand. Here, we use a single-molecule manipulation technique to monitor real-time changes in extension of a single, stretched, nicked dsDNA substrate as it is unwound by a single enzyme. This technique offers a means for measuring the rate, lifetime, and processivity of the enzymatic complex as a function of ATP, and for estimating the helicase step size. Strikingly, we observe a feature not seen in bulk assays: unwinding is preferentially followed by a slow, enzyme-translocation-limited rezipping of the separated strands rather than by dissociation of the enzymatic complex followed by quick rehybridization of the DNA strands. We address the mechanism underlying this phenomenon and propose a fully characterized model in which UvrD switches strands and translocates backwards on the other strand, allowing the DNA to reanneal in its wake. helicase | DNA replication | DNA repair | magnetic tweezers

  8. Single-molecule assay reveals strand switching and enhanced processivity of UvrD.

    PubMed

    Dessinges, Marie-Noëlle; Lionnet, Timothée; Xi, Xu Guang; Bensimon, David; Croquette, Vincent

    2004-04-27

    DNA helicases are enzymes capable of unwinding double-stranded DNA (dsDNA) to provide the single-stranded DNA template required in many biological processes. Among these, UvrD, an essential DNA repair enzyme, has been shown to unwind dsDNA while moving 3'-5' on one strand. Here, we use a single-molecule manipulation technique to monitor real-time changes in extension of a single, stretched, nicked dsDNA substrate as it is unwound by a single enzyme. This technique offers a means for measuring the rate, lifetime, and processivity of the enzymatic complex as a function of ATP, and for estimating the helicase step size. Strikingly, we observe a feature not seen in bulk assays: unwinding is preferentially followed by a slow, enzyme-translocation-limited rezipping of the separated strands rather than by dissociation of the enzymatic complex followed by quick rehybridization of the DNA strands. We address the mechanism underlying this phenomenon and propose a fully characterized model in which UvrD switches strands and translocates backwards on the other strand, allowing the DNA to reanneal in its wake. PMID:15079074

  9. 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

  10. 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

  11. 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

  12. Phagosome maturation during endosome interaction revealed by partial rhodopsin processing in retinal pigment epithelium

    PubMed Central

    Wavre-Shapton, Silène T.; Meschede, Ingrid P.; Seabra, Miguel C.; Futter, Clare E.

    2014-01-01

    ABSTRACT Defects in phagocytosis and degradation of photoreceptor outer segments (POS) by the retinal pigment epithelium (RPE) are associated with aging and retinal disease. The daily burst of rod outer segment (ROS) phagocytosis by the RPE provides a unique opportunity to analyse phagosome processing in vivo. In mouse retinae, phagosomes containing stacked rhodopsin-rich discs were identified by immuno-electron microscopy. Early apical phagosomes stained with antibodies against both cytoplasmic and intradiscal domains of rhodopsin. During phagosome maturation, a remarkably synchronised loss of the cytoplasmic epitope coincided with movement to the cell body and preceded phagosome–lysosome fusion and disc degradation. Loss of the intradiscal rhodopsin epitope and disc digestion occurred upon fusion with cathepsin-D-positive lysosomes. The same sequential stages of phagosome maturation were identified in cultured RPE and macrophages challenged with isolated POS. Loss of the cytoplasmic rhodopsin epitope was insensitive to pH but sensitive to protease inhibition and coincided with the interaction of phagosomes with endosomes. Thus, during pre-lysosomal maturation of ROS-containing phagosomes, limited rhodopsin processing occurs upon interaction with endosomes. This potentially provides a sensitive readout of phagosome–endosome interactions that is applicable to multiple phagocytes. PMID:25074813

  13. 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

  14. 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

  15. Eye movements reveal differences in children's referential processing during narrative comprehension.

    PubMed

    Engelen, Jan A A; Bouwmeester, Samantha; de Bruin, Anique B H; Zwaan, Rolf A

    2014-02-01

    Children differ in their ability to build referentially coherent discourse representations. Using a visual world paradigm, we investigated how these differences might emerge during the online processing of spoken discourse. We recorded eye movements of 69 children (6-11 years of age) as they listened to a 7-min story and concurrently viewed a display containing line drawings of the protagonists. Throughout the story, the protagonists were referenced by either a name (e.g., rabbit) or an anaphoric pronoun (e.g., he). Results showed that the probability of on-target fixations increased after children heard a proper name, but not after they heard an anaphoric pronoun. However, differences in the probability of on-target fixation at word onset indicate that the referents of anaphoric pronouns were anticipated by good comprehenders, but less so by poor comprehenders. These findings suggest that comprehension outcomes are related to the online processing of discourse-level cues that regulate the accessibility of entities. PMID:24182944

  16. 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

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

    PubMed

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

    2016-01-01

    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

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

    PubMed Central

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

    2016-01-01

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

  19. Congruency proportion reveals asymmetric processing of irrelevant physical and numerical dimensions in the size congruity paradigm.

    PubMed

    Borgmann, Karl; Fugelsang, Jonathan; Ansari, Daniel; Besner, Derek

    2011-06-01

    When the proportion of congruent trials in conflict tasks is manipulated (e.g., Stroop, Simon), the typical result is that the magnitude of the conflict effect increases as the proportion of congruent trials increases. The present experiment investigated the influence of Congruency Proportion in the context of the Size Congruity Paradigm. Congruency Proportion had a significant impact on the Numerical Judgement Task (judging which of two numbers is numerically larger), but not on the Physical Judgement Task (judging which of two numbers is printed in a larger font). These data support the inference that physical size information is processed before, and more fluently than, numerical size information. The implications of this asymmetry are discussed in terms of the relative role of semantic and physical size information in representations of magnitude, and the role they play in both of these tasks. PMID:21668091

  20. 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.

  1. 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

  2. Biogeochemical Processes in Late Archean Marine Biosphere Revealed by Isotopic and Molecular Records

    NASA Astrophysics Data System (ADS)

    Eigenbrode, J. L.; Freeman, K. H.; Summons, R. E.

    2004-12-01

    The presence of shallow-marine oxygen oases and associated aerobic ecosystems in an otherwise anoxic and anaerobic world has been proposed by researchers to explain the anomalous 40 permil spread in organic-carbon isotope values during the late Archean. To test this hypothesis, we studied isotopic, molecular, and lithologic records of 2.7-2.5 Ga rocks of different depositional facies from the Hamersley Province, Western Australia. Kerogen carbon-isotopic compositions indicate that extreme 13C-depletion (more than -45 permil) was associated with shallow-marine-carbonate environments at 2.72 Ga and with deepwater environments thereafter. Moreover, kerogen-carbon-isotope values associated with carbonate environments became enriched by more than 10 permil over 100-150 Ma. These observations suggest that microbial processes responsible for extreme 13C-depletion became less significant in shallow carbonate environments, but remained important in deeper settings. Molecular biomarker ratios determined for associated bitumens: 1) strongly correlate to kerogen carbon-isotope values and other biomarker ratios, and, 2) show relationships with depositional facies and dolomite abundance giving credence to a syngenetic relationship with host rocks. The biomarker data confirm aerobic methanotrophs in the Late Archean biosphere, but not in strong association with extreme 13C-depletion. Biomarker patterns reflect a greater association of aerobic respiration and oxygenic photosynthesis in shallow carbonate environments compared to deeper settings. Collectively, the data record dramatic changes in carbon cycling associated with environmental partitioning of microbial processes and ecosystems over 100-150 Ma. Most likely, this represents increased bioavailability of strong electron acceptors with the expansion of oxidant-rich oases prior to rise in atmospheric oxygen.

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

    NASA Astrophysics Data System (ADS)

    Zhou, Zhenjun; Zhang, Jie; Chintzoglou, Georgios

    2015-04-01

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

  4. Analysis of spliceosomal proteins in Trypanosomatids reveals novel functions in mRNA processing.

    PubMed

    Tkacz, Itai Dov; Gupta, Sachin Kumar; Volkov, Vadim; Romano, Mali; Haham, Tomer; Tulinski, Pawel; Lebenthal, Ilana; Michaeli, Shulamit

    2010-09-01

    In trypanosomatids, all mRNAs are processed via trans-splicing, although cis-splicing also occurs. In trans-splicing, a common small exon, the spliced leader (SL), which is derived from a small SL RNA species, is added to all mRNAs. Sm and Lsm proteins are core proteins that bind to U snRNAs and are essential for both these splicing processes. In this study, SmD3- and Lsm3-associated complexes were purified to homogeneity from Leishmania tarentolae. The purified complexes were analyzed by mass spectrometry, and 54 and 39 proteins were purified from SmD3 and Lsm complexes, respectively. Interestingly, among the proteins purified from Lsm3, no mRNA degradation factors were detected, as in Lsm complexes from other eukaryotes. The U1A complex was purified and mass spectrometry analysis identified, in addition to U1 small nuclear ribonucleoprotein (snRNP) proteins, additional co-purified proteins, including the polyadenylation factor CPSF73. Defects observed in cells silenced for U1 snRNP proteins suggest that the U1 snRNP functions exclusively in cis-splicing, although U1A also participates in polyadenylation and affects trans-splicing. The study characterized several trypanosome-specific nuclear factors involved in snRNP biogenesis, whose function was elucidated in Trypanosoma brucei. Conserved factors, such as PRP19, which functions at the heart of every cis-spliceosome, also affect SL RNA modification; GEMIN2, a protein associated with SMN (survival of motor neurons) and implicated in selective association of U snRNA with core Sm proteins in trypanosomes, is a master regulator of snRNP assembly. This study demonstrates the existence of trypanosomatid-specific splicing factors but also that conserved snRNP proteins possess trypanosome-specific functions. PMID:20592024

  5. 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

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

    PubMed

    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 δ(13)C-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

  7. Redox processes as revealed by voltammetry in the surface sediments of the Gotland Basin, Baltic Sea

    NASA Astrophysics Data System (ADS)

    Yücel, Mustafa; Dale, Andy; Sommer, Stefan; Pfannkuche, Olaf

    2014-05-01

    Sulfur cycling in marine sediments undergoes dramatic changes with changing redox conditions of the overlying waters. The upper sediments of the anoxic Gotland Basin, central Baltic Sea represent a dynamic redox environment with extensive mats of sulfide oxidizing bacteria covering the seafloor beneath the chemocline. In order to investigate sulfur redox cycling at the sediment-water interface, sediment cores were sampled over a transect covering 65 - 174 m water depth in August-September 2013. High resolution (0.25 mm minimum) vertical microprofiles of electroactive redox species including dissolved sulfide and iron were obtained with solid state Au-Hg voltammetric microelectrodes. This approach enabled a fine-scale comparison of porewater profiles across the basin. The steepest sulfide gradients (i.e. the highest sulfide consumption) occurred within the upper 10 mm in sediments covered by surficial mats (2.10 to 3.08 mmol m-2 day-1). In sediments under permanently anoxic waters (>140m), voltammetric signals for Fe(II) and aqueous FeS were detected below a subsurface maximum in dissolved sulfide, indicating a Fe flux originating from older, deeper sedimentary layers. Our results point to a unique sulfur cycling in the Gotland basin seafloor where sulfide accumulation is moderated by sulfide oxidation at the sediment surface and by FeS precipitation in deeper sediment layers. These processes may play an important role in minimizing benthic sulfide fluxes to bottom waters around the major basins of the Baltic Sea.

  8. Sub-processes of motor learning revealed by a robotic manipulandum for rodents.

    PubMed

    Lambercy, O; Schubring-Giese, M; Vigaru, B; Gassert, R; Luft, A R; Hosp, J A

    2015-02-01

    Rodent models are widely used to investigate neural changes in response to motor learning. Usually, the behavioral readout of motor learning tasks used for this purpose is restricted to a binary measure of performance (i.e. "successful" movement vs. "failure"). Thus, the assignability of research in rodents to concepts gained in human research - implying diverse internal models that constitute motor learning - is still limited. To solve this problem, we recently introduced a three-degree-of-freedom robotic platform designed for rats (the ETH-Pattus) that combines an accurate behavioral readout (in the form of kinematics) with the possibility to invasively assess learning related changes within the brain (e.g. by performing immunohistochemistry or electrophysiology in acute slice preparations). Here, we validate this platform as a tool to study motor learning by establishing two forelimb-reaching paradigms that differ in degree of skill. Both conditions can be precisely differentiated in terms of their temporal pattern and performance levels. Based on behavioral data, we hypothesize the presence of several sub-processes contributing to motor learning. These share close similarities with concepts gained in humans or primates. PMID:25446755

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

    PubMed

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

    2015-12-01

    Acute myeloid leukemia (AML) is a heterogeneous disease characterized by myeloid precursor proliferation in the bone marrow, apoptosis reduction and differentiation arrest. Although there are several studies in this field, events related to disease initiation and progression remain unknown. The malignant transformation of hematopoietic stem cells (HSC) is thought to generate leukemic stem cells, and this transformation could be related to changes in mesenchymal stromal cell (hMSC) signaling. Thus, the aim of this work was to analyze the gene expression profile of hMSC from AML patients (hMSC-AML) compared to healthy donors hMSCs (hMSC-HD). The results showed a common molecular signature for all hMSC-AML. Other assays were performed with a large number of patients and the results confirmed a molecular signature that is capable of distinguishing hMSC-AML from hMSC-HD. Moreover, CCL2 and BMP4 genes encode secreted proteins that could affect HSCs. To verify whether these proteins are differentially expressed in AML patients, ELISA was performed with plasma samples. CCL2 and BMP4 proteins are differentially expressed in AML patients, indicating changes in hMSC-AML signaling. Altogether, hMSCs-AML signaling alterations could be an important factor in the leukemic transformation process. PMID:26279521

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

    PubMed

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

    2014-01-01

    The pattern of epileptic seizures is often considered unpredictable and the interval between events without correlation. A number of studies have examined the possibility that seizure activity respects a power-law relationship, both in terms of event magnitude and inter-event intervals. Such relationships are found in a variety of natural and man-made systems, such as earthquakes or Internet traffic, and describe the relationship between the magnitude of an event and the number of events. We postulated that human inter-seizure intervals would follow a power-law relationship, and furthermore that evidence for the existence of a long-memory process could be established in this relationship. We performed a post hoc analysis, studying eight patients who had long-term (up to 2 years) ambulatory intracranial EEG data recorded as part of the assessment of a novel seizure prediction device. We demonstrated that a power-law relationship could be established in these patients (β = - 1.5). In five out of the six subjects whose data were sufficiently stationary for analysis, we found evidence of long memory between epileptic events. This memory spans time scales from 30 min to 40 days. The estimated Hurst exponents range from 0.51 to 0.77 ± 0.01. This finding may provide evidence of phase-transitions underlying the dynamics of epilepsy. PMID:25386160

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

    PubMed

    Bidelman, Gavin M; Syed Khaja, Ameenuddin

    2014-06-20

    Auditory filter theory dictates a physiological compromise between frequency and temporal resolution of cochlear signal processing. We examined neurophysiological correlates of these spectrotemporal tradeoffs in the human auditory system using auditory evoked brain potentials and psychophysical responses. Temporal resolution was assessed using scalp-recorded auditory brainstem responses (ABRs) elicited by paired clicks. The inter-click interval (ICI) between successive pulses was parameterized from 0.7 to 25 ms to map ABR amplitude recovery as a function of stimulus spacing. Behavioral frequency difference limens (FDLs) and auditory filter selectivity (Q10 of psychophysical tuning curves) were obtained to assess relations between behavioral spectral acuity and electrophysiological estimates of temporal resolvability. Neural responses increased monotonically in amplitude with increasing ICI, ranging from total suppression (0.7 ms) to full recovery (25 ms) with a temporal resolution of ∼3-4 ms. ABR temporal thresholds were correlated with behavioral Q10 (frequency selectivity) but not FDLs (frequency discrimination); no correspondence was observed between Q10 and FDLs. Results suggest that finer frequency selectivity, but not discrimination, is associated with poorer temporal resolution. The inverse relation between ABR recovery and perceptual frequency tuning demonstrates a time-frequency tradeoff between the temporal and spectral resolving power of the human auditory system. PMID:24793771

  12. Heterochromatin dynamics during the differentiation process revealed by the DNA methylation reporter mouse, MethylRO.

    PubMed

    Ueda, Jun; Maehara, Kazumitsu; Mashiko, Daisuke; Ichinose, Takako; Yao, Tatsuma; Hori, Mayuko; Sato, Yuko; Kimura, Hiroshi; Ohkawa, Yasuyuki; Yamagata, Kazuo

    2014-06-01

    In mammals, DNA is methylated at CpG sites, which play pivotal roles in gene silencing and chromatin organization. Furthermore, DNA methylation undergoes dynamic changes during development, differentiation, and in pathological processes. The conventional methods represent snapshots; therefore, the dynamics of this marker within living organisms remains unclear. To track this dynamics, we made a knockin mouse that expresses a red fluorescent protein (RFP)-fused methyl-CpG-binding domain (MBD) protein from the ROSA26 locus ubiquitously; we named it MethylRO (methylation probe in ROSA26 locus). Using this mouse, we performed RFP-mediated methylated DNA immunoprecipitation sequencing (MeDIP-seq), whole-body section analysis, and live-cell imaging. We discovered that mobility and pattern of heterochromatin as well as DNA methylation signal intensity inside the nuclei can be markers for cellular differentiation status. Thus, the MethylRO mouse represents a powerful bioresource and technique for DNA methylation dynamics studies in developmental biology, stem cell biology, as well as in disease states. PMID:24936475

  13. Heterochromatin Dynamics during the Differentiation Process Revealed by the DNA Methylation Reporter Mouse, MethylRO

    PubMed Central

    Ueda, Jun; Maehara, Kazumitsu; Mashiko, Daisuke; Ichinose, Takako; Yao, Tatsuma; Hori, Mayuko; Sato, Yuko; Kimura, Hiroshi; Ohkawa, Yasuyuki; Yamagata, Kazuo

    2014-01-01

    Summary In mammals, DNA is methylated at CpG sites, which play pivotal roles in gene silencing and chromatin organization. Furthermore, DNA methylation undergoes dynamic changes during development, differentiation, and in pathological processes. The conventional methods represent snapshots; therefore, the dynamics of this marker within living organisms remains unclear. To track this dynamics, we made a knockin mouse that expresses a red fluorescent protein (RFP)-fused methyl-CpG-binding domain (MBD) protein from the ROSA26 locus ubiquitously; we named it MethylRO (methylation probe in ROSA26 locus). Using this mouse, we performed RFP-mediated methylated DNA immunoprecipitation sequencing (MeDIP-seq), whole-body section analysis, and live-cell imaging. We discovered that mobility and pattern of heterochromatin as well as DNA methylation signal intensity inside the nuclei can be markers for cellular differentiation status. Thus, the MethylRO mouse represents a powerful bioresource and technique for DNA methylation dynamics studies in developmental biology, stem cell biology, as well as in disease states. PMID:24936475

  14. 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.

  15. 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

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

    PubMed

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

    2012-01-01

    Normal aging is accompanied by changes in both structural and functional cerebral organization. Although verbal knowledge seems to be relatively stable across the lifespan, there are age-related changes in the rapid use of that knowledge during on-line language processing. In particular, aging has been linked to reduce effectiveness in preparing for upcoming words and building an integrated sentence-level representation. The current study assessed whether such age-related changes extend even to much simpler language units, such as modification relations between a centrally presented adjective and a lateralized noun. Adjectives were used to elicit concrete and abstract meanings of the same, polysemous lexical items (e.g., "green book" vs. "interesting book"). Consistent with findings that lexical information is preserved with age, older adults, like younger adults, exhibited concreteness effects at the adjectives, with more negative responses to concrete adjectives over posterior (300-500 ms; N400) and frontal (300-900 ms) channels. However, at the noun, younger adults exhibited concreteness-based predictability effects linked to left hemisphere processing and imagery effects linked to right hemisphere processing, contingent on whether the adjectives and nouns formed a cohesive conceptual unit. In contrast, older adults showed neither effect, suggesting that they were less able to rapidly link the adjective-noun meaning to form an integrated conceptual representation. Age-related changes in language processing may thus be more pervasive than previously realized. PMID:22044648

  17. 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. PMID:24936174

  18. 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

  19. 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

  20. 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

  1. Paleotethyan subduction process revealed from Triassic blueschists in the Lancang tectonic belt of Southwest China

    NASA Astrophysics Data System (ADS)

    Fan, Weiming; Wang, Yuejun; Zhang, Yanhua; Zhang, Yuzhi; Jourdan, Fred; Zi, Jianwei; Liu, Huichuan

    2015-11-01

    The subduction of the Paleotethyan Ocean and subsequent continental collision along the Lancang tectonic belt of the southeastern Paleotethyan belt is a major tectonic event in Southwest China, but the event of the subduction preceding the final collision is still not well-constrained. The mafic blueschists exposed in the Lancang accretionary complex provide crucial records of the Paleotethyan subduction process. In this paper, we present a set of new petrologic, geochronological and geochemical data for the Suyi mafic blueschists in the Lancang metamorphic zone. The mineral assemblage of these blueschists consists of zoned sodic amphibole (25-30%), albite (15-20%), epidote (25-30%), phengite (5-10%), chlorite (~ 5-10%), and minor amounts of actinolite, apatite, sphene, zircon, ilmenite, quartz and secondary limonite. This suggests a prograde metamorphism from ~ 0.5 to ~ 0.9 GPa and retrograde metamorphic overprinting (back to ~ 0.6 GPa) within the temperature range of 300-450 °C. The Suyi blueschists give a zircon U-Pb age of 260 ± 4 Ma and glaucophane minerals formed during prograde metamorphism yield a 40Ar/39Ar plateau age of 242 ± 5 Ma (MSWD = 0.77; P = 0.54). The blueschists have geochemical compositions of subalkaline basalt and show typical OIB-type REE and multi-elemental patterns and εNd(t) values ranging from + 3.35 to + 4.85. Based on available data, it is inferred that the protolith formed at 260 Ma and originated from a basaltic seamount. The basaltic rocks subducted down to 30-35 km depths beneath the Lincang arc to form the epidote blueschists at ~ 242 Ma. The blueschists were subsequently transported to shallower crustal levels in response to the continuous underthrust of the subducted slab and the continent-continent collision in the middle-late Triassic. These results provide a systematic constraint on the tectonic evolution and temporal framework of the southeastern Paleotethyan belt in Southwest China.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    transported debris was about 30 - 90 m thick, covered on the preexisting debris deposit hill and around the river channel. The debris formed a dammed lake, with a maximum volume of 45 Mm3. Based on DTMs data sets, field observations, the discrete element method - PFC3D is adapts to analyze the triggering mechanism and sling dynamic process. The presence and the coupling effect from the strong ground excitation and high pore water pressure is the essential factor to triggering the landslide event. The results shows that the best fit between the deposit topography of the post-event DTM and numerical simulations, the fictional coefficient of the sliding surface is as low as 0.087. The maximum sliding speed is as high as 87.2 m/s, the result coincide with the seismic record from the nearby strong motion seismic record.

  4. Improved vessel morphology measurements in contrast-enhanced multi-detector computed tomography coronary angiography with non-linear post-processing.

    PubMed

    Ferencik, Maros; Lisauskas, Jennifer B; Cury, Ricardo C; Hoffmann, Udo; Abbara, Suhny; Achenbach, Stephan; Karl, W Clem; Brady, Thomas J; Chan, Raymond C

    2006-03-01

    Multi-detector computed tomography (MDCT) permits detection of coronary plaque. However, noise and blurring impair accuracy and precision of plaque measurements. The aim of the study was to evaluate MDCT post-processing based on non-linear image deblurring and edge-preserving noise suppression for measurements of plaque size. Contrast-enhanced MDCT coronary angiography was performed in four subjects (mean age 55 +/- 5 years, mean heart rate 54 +/- 5 bpm) using a 16-slice scanner (Siemens Sensation 16, collimation 16 x 0.75 mm, gantry rotation 420 ms, tube voltage 120 kV, tube current 550 mAs, 80 mL of contrast). Intravascular ultrasound (IVUS; 40 MHz probe) was performed in one vessel in each patient and served as a reference standard. MDCT vessel cross-sectional images (1 mm thickness) were created perpendicular to centerline and aligned with corresponding IVUS images. MDCT images were processed using a deblurring and edge-preserving noise suppression algorithm. Then, three independent blinded observers segmented lumen and outer vessel boundaries in each modality to obtain vessel cross-sectional area and wall area in the unprocessed MDCT cross-sections, post-processed MDCT cross-sections and corresponding IVUS. The wall area measurement difference for unprocessed and post-processed MDCT images relative to IVUS was 0.4 +/- 3.8 mm2 and -0.2 +/- 2.2 mm2 (p < 0.05), respectively. Similarly, Bland-Altman analysis of vessel cross-sectional area from unprocessed and post-processed MDCT images relative to IVUS showed a measurement difference of 1.0 +/- 4.4 and 0.6 +/- 4.8 mm2, respectively. In conclusion, MDCT permitted accurate in vivo measurement of wall area and vessel cross-sectional area as compared to IVUS. Post-processing to reduce blurring and noise reduced variability of wall area measurements and reduced measurement bias for both wall area and vessel cross-sectional area. PMID:16442768

  5. 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.

  6. New Geochemical Analyses Reveal Crustal Accretionary Processes at The Overlapping Spreading Center Near 3 N East Pacific Rise

    NASA Astrophysics Data System (ADS)

    Smithka, I. N.; Perfit, M. R.

    2013-12-01

    Mid-ocean ridges (MORs) are the sites of oceanic lithosphere creation and construction. Ridge discontinuities are a global phenomenom but are not as well understood as ridge axes. Geochemical analyses provide insights into upper mantle processes since elements fractionate with melting and freezing as well as reside in material to retain source signature. Lavas collected from ridge discontinuities consist of greater chemical diversity and represent variations in source, melting parameters, and local crustal processes. The small overlapping spreading center (OSC) near the third parallel north on the East Pacific Rise has been superficially analyzed previously, but here we present new isotope analyses and expand our understanding of MOR processes and processes near OSCs. Initial analyses of lavas collected in 2000 on AHA-NEMO2 revealed normal MOR basalt trends in rare earth element enrichments as well as in major element concentrations. Crystal fractionation varies along the tips of both axes, with MgO and TiO2 concentrations increasing towards the OSC basin. Newly analyzed Sr, Nd, and Pb isotope ratios will further constrain the nature of geochemical diversity along axis. As the northern tip seems to be propagating and the southern tip dying, lavas collected from each may reflect two different underlying mantle melting and magma storage processes.

  7. 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

  8. Early activation of Broca's area in grammar processing as revealed by the syntactic mismatch negativity and distributed source analysis.

    PubMed

    Hanna, Jeff; Mejias, Sandrine; Schelstraete, Marie-Anne; Pulvermüller, Friedemann; Shtyrov, Yury; Van der Lely, Heather K J

    2014-01-01

    Though activation of Broca's region in the combinatorial processing of symbols (language, music) has been revealed by neurometabolic studies, most previous neurophysiological research found the earliest grammar indices in the temporal cortex, with inferior-frontal generators becoming active at relatively late stages. We use the attention- and task-free syntactic mismatch negativity (sMMN) event-related potential (ERP) to measure rapid and automatic sensitivity of the human brain to grammatical information in participants' native language (French). Further, sources underlying the MMN were estimated by applying the Parametrical Empirical Bayesian (PEB) approach, with the Multiple Sparse Priors (MSP) technique. Results showed reliable grammar-related activation focused on Broca's region already in the 150-190 ms time window, providing robust documentation of its involvement in the first stages of syntactic processing. PMID:24279717

  9. The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing

    SciTech Connect

    Jackson, R.N.; Robinson, H.; Klauer, A. A.; Hintze, B. J.; van Hoof, A.; Johnson, S. J.

    2010-07-01

    The essential RNA helicase, Mtr4, performs a critical role in RNA processing and degradation as an activator of the nuclear exosome. The molecular basis for this vital function is not understood and detailed analysis is significantly limited by the lack of structural data. In this study, we present the crystal structure of Mtr4. The structure reveals a new arch-like domain that is specific to Mtr4 and Ski2 (the cytosolic homologue of Mtr4). In vivo and in vitro analyses demonstrate that the Mtr4 arch domain is required for proper 5.8S rRNA processing, and suggest that the arch functions independently of canonical helicase activity. In addition, extensive conservation along the face of the putative RNA exit site highlights a potential interface with the exosome. These studies provide a molecular framework for understanding fundamental aspects of helicase function in exosome activation, and more broadly define the molecular architecture of Ski2-like helicases.

  10. 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

  11. Extroversion-related differences in speed of premotor and motor processing as revealed by lateralized readiness potentials.

    PubMed

    Stahl, Jutta; Rammsayer, Thomas

    2008-03-01

    To further elucidate extroversion-related differences in speed of sensorimotor processing, the authors obtained behavioral and psychophysiological measures as participants (16 introverts and 16 extroverts) performed a visual go/no-go task. Although no extroversion-related differences in reaction time emerged, introverts showed faster premotor processing but slower central and peripheral motor processing--as indicated by latencies of the lateralized readiness potential (LRP) and electromyographic (EMG) data, respectively--than extroverts did. Additional regression analyses revealed that stimulus-locked LRP latency, response-locked LRP latency, and Nl EMG amplitude accounted for 40% of overall variability in individual extroversion scores. On the basis of the present results, the authors introduce a compensation hypothesis that accounts for the common failure of researchers to demonstrate extroversion-related differences in reaction time. The present results challenge J. Brebner and C. Cooper's (1985) model of extroversion in which stimulus analysis is not slower in introverts than in extroverts. However, the present findings support the assumption of faster motor processing in extroverts. PMID:18400680

  12. 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

  13. TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level

    PubMed Central

    2014-01-01

    Background The TGF-β signaling pathway is a fundamental pathway in the living cell, which plays a key role in many central cellular processes. The complex and sometimes contradicting mechanisms by which TGF-β yields phenotypic effects are not yet completely understood. In this study we investigated and compared the transcriptional response profile of TGF-β1 stimulation in different cell types. For this purpose, extensive experiments are performed and time-course microarray data are generated in human and mouse parenchymal liver cells, human mesenchymal stromal cells and mouse hematopoietic progenitor cells at different time points. We applied a panel of bioinformatics methods on our data to uncover common patterns in the dynamic gene expression response in respective cells. Results Our analysis revealed a quite variable and multifaceted transcriptional response profile of TGF-β1 stimulation, which goes far beyond the well-characterized classical TGF-β1 signaling pathway. Nonetheless, we could identify several commonly affected processes and signaling pathways across cell types and species. In addition our analysis suggested an important role of the transcription factor EGR1, which appeared to have a conserved influence across cell-types and species. Validation via an independent dataset on A549 lung adenocarcinoma cells largely confirmed our findings. Network analysis suggested explanations, how TGF-β1 stimulation could lead to the observed effects. Conclusions The analysis of dynamical transcriptional response to TGF-β treatment experiments in different human and murine cell systems revealed commonly affected biological processes and pathways, which could be linked to TGF-β1 via network analysis. This helps to gain insights about TGF-β pathway activities in these cell systems and its conserved interactions between the species and tissue types. PMID:24886091

  14. Geochemistry of river-borne clays entering the East China Sea indicates two contrasting types of weathering and sediment transport processes

    NASA Astrophysics Data System (ADS)

    Bi, Lei; Yang, Shouye; Li, Chao; Guo, Yulong; Wang, Quan; Liu, James T.; Yin, Ping

    2015-09-01

    The East China Sea is characterized by wide continental shelf receiving a huge input of terrigenous matter from both large rivers and mountainous rivers, which makes it an ideal natural laboratory for studying sediment source-to-sink transport processes. This paper presents mineralogical and geochemical data of the clays and bulk sediments from the rivers entering the East China Sea, aiming to investigate the general driving mechanism of silicate weathering and sediment transport processes in East Asian continental margin. Two types of river systems, tectonically stable continental rivers and tectonically active mountainous rivers, coexist in East Asia. As the direct weathering products, clays can better reflect the silicate weathering regimes within the two river systems. Provenance rock types are not the dominant factor causing silicate weathering intensity difference existed in the East Asian rivers. The silicate weathering intensity of tectonically stable river basins is primarily driven by monsoon climate, and the sediment transfer is relatively slow because of natural trapping process and increasing damming effect. The geochemistry of these river-borne sediments can thus indicate paleo-weathering intensities in East Asian continent. In contrast, silicate weathering intensity in tectonically active mountainous rivers is greatly limited by strong physical erosion despite the high temperature and highest monsoon rainfall. The factors controlling silicate weathering in tectonically active catchments are complex and thus, it should be prudent to use river sediment records to decipher paleoclimate change. These two different silicate weathering regimes and sediment transport processes are manifestations of the landscape evolution and overall dominate the sedimentation in Asian continental margin.

  15. Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis

    PubMed Central

    Huang, Shu; Wang, Jun; Yue, Wucheng; Chen, Jiao; Gaughan, Sarah; Lu, Weiqun; Lu, Guoqing; Wang, Chenghui

    2015-01-01

    Molting is a critical developmental process for crustaceans, yet the underlying molecular mechanism is unknown. In this study, we used RNA-Seq to investigate transcriptomic profiles of the hepatopancreas and identified differentially expressed genes at four molting stages of Chinese mitten crab (Eriocheir sinensis). A total of 97,398 transcripts were assembled, with 31,900 transcripts annotated. Transcriptomic comparison revealed 1,189 genes differentially expressed amongst different molting stages. We observed a pattern associated with energy metabolism and physiological responses during a molting cycle. In specific, differentially expressed genes enriched in postmolt were linked to energy consumption whereas genes enriched in intermolt were related to carbohydrates, lipids metabolic and biosynthetic processes. In premolt, a preparation stage for upcoming molting and energy consumption, highly expressed genes were enriched in response to steroid hormone stimulus and immune system development. The expression profiles of twelve functional genes detected via RNA-Seq were corroborated through real-time RT-PCR assay. Together, our results, including assembled transcriptomes, annotated functional elements and enriched differentially expressed genes amongst different molting stages, provide novel insights into the functions of the hepatopancreas in energy metabolism and biological processes pertaining to molting in crustaceans. PMID:26369734

  16. Looking at the evidence in visual world: eye-movements reveal how bilingual and monolingual Turkish speakers process grammatical evidentiality.

    PubMed

    Arslan, Seçkin; Bastiaanse, Roelien; Felser, Claudia

    2015-01-01

    This study presents pioneering data on how adult early bilinguals (heritage speakers) and late bilingual speakers of Turkish and German process grammatical evidentiality in a visual world setting in comparison to monolingual speakers of Turkish. Turkish marks evidentiality, the linguistic reference to information source, through inflectional affixes signaling either direct (-DI) or indirect (-mIş) evidentiality. We conducted an eye-tracking-during-listening experiment where participants were given access to visual 'evidence' supporting the use of either a direct or indirect evidential form. The behavioral results indicate that the monolingual Turkish speakers comprehended direct and indirect evidential scenarios equally well. In contrast, both late and early bilinguals were less accurate and slower to respond to direct than to indirect evidentials. The behavioral results were also reflected in the proportions of looks data. That is, both late and early bilinguals fixated less frequently on the target picture in the direct than in the indirect evidential condition while the monolinguals showed no difference between these conditions. Taken together, our results indicate reduced sensitivity to the semantic and pragmatic function of direct evidential forms in both late and early bilingual speakers, suggesting a simplification of the Turkish evidentiality system in Turkish heritage grammars. We discuss our findings with regard to theories of incomplete acquisition and first language attrition. PMID:26441762

  17. Looking at the evidence in visual world: eye-movements reveal how bilingual and monolingual Turkish speakers process grammatical evidentiality

    PubMed 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

  18. The Organization of Right Prefrontal Networks Reveals Common Mechanisms of Inhibitory Regulation Across Cognitive, Emotional, and Motor Processes.

    PubMed

    Depue, B E; Orr, J M; Smolker, H R; Naaz, F; Banich, M T

    2016-04-01

    Inhibitory control/regulation is critical to adapt behavior in accordance with changing environmental circumstances. Dysfunctional inhibitory regulation is ubiquitous in neurological and psychiatric populations. These populations exhibit dysfunction across psychological domains, including memory/thought, emotion/affect, and motor response. Although investigation examining inhibitory regulation within a single domain has begun outlining the basic neural mechanisms supporting regulation, it is unknown how the neural mechanisms of these domains interact. To investigate the organization of inhibitory neural networks within and across domains, we used neuroimaging to outline the functional and anatomical pathways that comprise inhibitory neural networks regulating cognitive, emotional, and motor processes. Networks were defined at the group level using an array of analyses to indicate their intrinsic pathway structure, which was subsequently assessed to determine how the pathways explained individual differences in behavior. Results reveal how neural networks underlying inhibitory regulation are organized both within and across domains, and indicate overlapping/common neural elements. PMID:25601236

  19. 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

  20. 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.

  1. 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

  2. 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. PMID:24312283

  3. A GFP endometriosis model reveals important morphological characteristics of the angiogenic process that govern benign and malignant diseases.

    PubMed

    Machado, Daniel Escorsim; Palumbo, Antônio; Santos, João Marcos; Mattos, Rômulo Medina; dos Santos, Thiago Alves; Seabra, Sergio Henrique; Boldrini, Leonardo da Cunha; Perini, Jamila Alessandra; Nasciutti, Luiz Eurico

    2014-07-01

    Endometriosis involves the growth of endometriotic tissue outside the uterine cavity, and is frequently associated with different malignancies. A well-reported alteration in the disease microenvironment is the proliferation of new blood vessels around the lesions, as part of a necessary repertory to contribute to the invasiveness and development of infiltrating endometriosis. Therefore, the establishment of a reliable experimental model is essential to elucidate the contribution of angiogenesis and to develop new therapeutic approaches to endometriosis treatment. For this purpose we transplanted endometrial fragments from green fluorescent protein (GFP)-mice (n=20) into the peritoneal cavity of wild-type mice (n=20), and then analyzed the morphological changes and the process of angiogenesis. The lesions were cystic and vascularized, and showed morphological hallmarks such as endometrial glands and stroma. An increase in endometriotic lesion vascular density was revealed by immunostaining and RNAm expression for Vegf and its receptor Flk-1, and the lesions were confirmed as a tissue-donor source by GFP fluorescent cells. The same pattern was observed through staining of activated macrophages and an increase of about 25% in the number of macrophage-positive cells was also demonstrated in endometriotic lesions by flow cytometry, which concords with previous data that correlate endometriosis, angiogenesis and inflammation. According to our understanding, this is the first demonstration that the pattern of the angiogenic process in the GFP endometriosis model is very similar to that of cancer. These observations will be useful for investigation of the process of angiogenesis involved in the attachment and invasion of endometrial cells, as well as an in vivo platform model to study the effects of antiangiogenic drugs. PMID:24385307

  4. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing

    PubMed Central

    Tang, Thean Hock; Rozhdestvensky, Timofey S.; d’Orval, Béatrice Clouet; Bortolin, Marie-Line; Huber, Harald; Charpentier, Bruno; Branlant, Christiane; Bachellerie, Jean-Pierre; Brosius, Jürgen; Hüttenhofer, Alexander

    2002-01-01

    The bulge–helix–bulge (BHB) motif recognised by the archaeal splicing endonuclease is also found in the long processing stems of archaeal rRNA precursors in which it is cleaved to generate pre-16S and pre-23S rRNAs. We show that in two species, Archaeoglobus fulgidus and Sulfolobus solfataricus, representatives from the two major archaeal kingdoms Euryarchaeota and Crenarchaeota, respectively, the pre-rRNA spacers cleaved at the BHB motifs surrounding pre-16S and pre-23S rRNAs subsequently become ligated. In addition, we present evidence that this is accompanied by circularisation of ribosomal pre-16S and pre-23S rRNAs in both species. These data reveal a further link between intron splicing and pre-rRNA processing in Archaea, which might reflect a common evolutionary origin of the two processes. One spliced RNA species designated 16S-D RNA, resulting from religation at the BHB motif of 16S pre-rRNA, is a highly abundant and stable RNA which folds into a three-stem structure interrupted by two single-stranded regions as assessed by chemical probing. It spans a region of the pre-rRNA 5′ external transcribed spacer exhibiting a highly conserved folding pattern in Archaea. Surprisingly, 16S-D RNA contains structural motifs found in archaeal C/D box small RNAs and binds to the L7Ae protein, a core component of archaeal C/D box RNPs. This supports the notion that it might have an important but still unknown role in pre-rRNA biogenesis or might even target RNA molecules other than rRNA. PMID:11842103

  5. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    PubMed

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2016-02-01

    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

  6. 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

  7. Analysis of gene expression dynamics revealed delayed and abnormal epidermal repair process in aged compared to young skin.

    PubMed

    Sextius, Peggy; Marionnet, Claire; Tacheau, Charlotte; Bon, François-Xavier; Bastien, Philippe; Mauviel, Alain; Bernard, Bruno A; Bernerd, Françoise; Dubertret, Louis

    2015-05-01

    With aging, epidermal homeostasis and barrier function are disrupted. In a previous study, we analyzed the transcriptomic response of young skin epidermis after stratum corneum removal, and obtained a global kinetic view of the molecular processes involved in barrier function recovery. In the present study, the same analysis was performed in aged skin in order to better understand the defects which occur with aging. Thirty healthy male volunteers (67 ± 4 years old) were involved. Tape-strippings were carried out on the inner face of one forearm, the other unstripped forearm serving as control. At 2, 6, 18, 30 and 72 h after stripping, TEWL measurements were taken, and epidermis samples were collected. Total RNA was extracted and analyzed using DermArray(®) cDNA microarrays. The results highlighted that barrier function recovery and overall kinetics of gene expression were delayed following stripping in aged skin. Indeed, the TEWL measurements showed that barrier recovery in the young group appeared to be dramatically significant during the overall kinetics, while there were no significant evolution in the aged group until 30 h. Moreover, gene expression analysis revealed that the number of modulated genes following tape stripping increased as a function of time and reached a peak at 6 h after tape stripping in young skin, while it was at 30 h in aged skin, showing that cellular activity linked to the repair process may be engaged earlier in young epidermis than in aged epidermis. A total of 370 genes were modulated in the young group. In the aged group, 382 genes were modulated, whose 184 were also modulated in the young group. Only eight genes that were modulated in both groups were significantly differently modulated. The characterization of these genes into 15 functional families helped to draw a scenario for the aging process affecting epidermal repair capacity. PMID:25740152

  8. A pattern of perseveration in cocaine addiction may reveal neurocognitive processes implicit in the Wisconsin Card Sorting Test.

    PubMed

    Woicik, Patricia A; Urban, Catherine; Alia-Klein, Nelly; Henry, Ashley; Maloney, Thomas; Telang, Frank; Wang, Gene-Jack; Volkow, Nora D; Goldstein, Rita Z

    2011-06-01

    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 behavior in individuals with cocaine use disorders (CUD) and healthy controls (CON) during performance of the Wisconsin Card Sorting Test (WCST) (N=107 in each group). By examining perseverative errors within each of the 6 blocks of the WCST, we uniquely test two forms of set switching that are differentiated by either the presence (extradimensional set shifting (EDS) - first 3 blocks) or absence (task-set switching - last 3 blocks) of new contingency learning. We also explore relationships between perseveration and select cognitive and drug use factors including verbal learning and memory, trait inhibitory control, motivational state, and urine status for cocaine (in CUD). Results indicate greater impairment for CUD than CON on the WCST, even in higher performing CUD who completed all 6 blocks of the WCST. Block by block analysis conducted on completers' scores indicate a tendency for greater perseveration in CUD than CON but only during the first task-set switch; no such deficits were observed during EDS. This task-set switching impairment was modestly associated with two indices of immediate recall (r=-.32, -.29) and urine status for cocaine [t (134)=2.3, p<.03]. By distinguishing these two forms of switching on the WCST, the current study reveals a neurocognitive context (i.e. initial stage of task-set switching) implicit in the WCST that possibly relies upon intact dopaminergic function, but that is impaired in CUD, as associated with worse recall and possibly withdrawal from cocaine. Future studies should investigate whether dopaminergically innervated pathways alone, or in combination with other monoamines

  9. A Pattern of Perseveration in Cocaine Addiction May Reveal Neurocognitive Processes Implicit in the Wisconsin Card Sorting Test

    PubMed Central

    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 behavior in individuals with cocaine use disorders (CUD) and healthy controls (CON) during performance of the Wisconsin Card Sorting Test (WCST) (N = 107 in each group). By examining perseverative errors within each of the 6 blocks of the WCST, we uniquely test two forms of set switching that are differentiated by either the presence (extradimensional set shifting (EDS) – first 3 blocks) or absence (task-set switching – last 3 blocks) of contingency learning. We also explore relationships between perseveration and select cognitive and drug use factors including verbal learning and memory, trait inhibitory control, motivational state, and urine status for cocaine (in CUD). Results indicate greater impairment for CUD than CON on the WCST, even in higher performing CUD who completed all 6 blocks of the WCST. Block by block analysis conducted on completers’ scores indicate a tendency for greater perseveration in CUD than CON but only during the first task-set switch; no such deficits were observed during EDS. This task-set switching impairment was modestly associated with two indices of immediate recall (r = −.32, −.29) and urine status for cocaine [t (134) = 2.3, p <.03]. By distinguishing these two forms of switching on the WCST, the current study reveals a neurocognitive context (i.e. initial stage of task-set switching) implicit in the WCST that possibly relies upon intact dopaminergic function, but that is impaired in CUD, as associated with worse recall and possibly withdrawal from cocaine. Future studies should investigate whether dopaminergically innervated pathways alone, or in combination with other

  10. ERPs reveal atypical processing of subject versus object Wh-questions in children with specific language impairment

    PubMed Central

    Epstein, Baila; Hestvik, Arild; Shafer, Valerie L.; Schwartz, Richard G.

    2013-01-01

    Background Children with specific language impairment (SLI) show particular difficulty comprehending and producing object (Who did the bear follow?) relative to subject (Who followed the tiger?) wh-questions. Aims To determine if school-age children with SLI, relative to children with typical development (TD), show a more distinct unevenness, or asymmetry, in the comprehension of these questions. In addition, this study examined whether the sustained left-anterior negativity (LAN) in event-related potentials (ERP) could be used as a marker for atypical processing of these questions in children with SLI. The LAN effect signals the greater working memory processes for maintaining in memory the dislocated object in object wh-questions and reflects working memory capacity in adults. It was predicted that the amplitude of the LAN would be greater in children with SLI, reflecting the characteristic low working memory capacity in this population. The concomitance of these behavioural and electrophysiological effects would suggest that the subject–object asymmetry in SLI should be investigated in relation to poor working memory skills. Methods & Procedures Groups including 13 children with SLI, 17 same-age TD children and 18 normal adults completed an auditory sentence comprehension task requiring button responses while continuous electroencephalography (EEG) was collected. Accuracy for subject and object questions was calculated. The mean amplitude values of the ERP data for the wh-questions were examined to identify differential processing of subject and object questions. Outcomes & Results TD children demonstrated asymmetrical comprehension of subject and object wh-questions, whereas children with SLI comprehended both question types poorly and adults did not show subject–object asymmetry. ERP waveforms spanning the wh-dependency revealed a large and widespread sustained anterior positivity for object relative to subject questions in the TD group, indicating

  11. 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.

  12. A two-step ICT process for solvatochromic betaine pyridinium revealed by ultrafast spectroscopy, multivariate curve resolution, and TDDFT calculations.

    PubMed

    Aloïse, Stéphane; Pawlowska, Zuzanna; Ruckebusch, Cyril; Sliwa, Michel; Dubois, Julien; Poizat, Olivier; Buntinx, Guy; Perrier, Aurélie; Maurel, François; Jacques, Patrice; Malval, Jean-Pierre; Poisson, Lionel; Piani, Giovanni; Abe, Jiro

    2012-02-14

    This work deals with the photophysics of a pyridinium betaine, 2-pyridin-1-yl-1H-benzimidazole (SBPa), based on a combination of steady-state, femtosecond photoionization (gas phase) and femtosecond transient absorption (solution) spectroscopic measurements, supported by (LR)-PCM-(TD)DFT calculations. Preliminary and new electrochemical results have revealed a strongly negative solvatochromic charge transfer (CT) absorption due to a S(0) → S(2) vertical transition and a weakly-solvatochromic emission due to S(1) → S(0) transition. Advanced TDDFT optimizations of the Franck-Condon states S(2)(FC) and S(1)(FC) led to two additional CT levels with planar geometry, S(2)(CT) and S(1)(CT), respectively, allowing prediction of a two-step photoinduced ICT process, i.e., S(0) → S(2)(FC) and S(2)(CT) → S(1)(CT), separated by a S(2)(FC) → S(2)(CT) back charge transfer relaxation. While the pyridinium ring is the acceptor group in both steps, two different donor groups, the benzene ring and the imidazole bridge, are involved in the excitation and internal conversion processes, respectively. Femtosecond transient absorption experiments supported by MCR-ALS decomposition confirmed indeed the contribution of two distinct CT states in the photophysics of SBPa: following excitation to the S(2)(CT) state, ultrafast production of the emissive S(1) state (the only channel observable in the gas phase) was observed to occur in competition with a further ICT process toward the S(1)(CT) state, with a time constant ranging from 300 fs to 20 ps depending on the solvent. While in aprotic media this ICT process was found to be purely solvent controlled (double polarity and viscosity dependency), in protic solvents, the influence of the hydrogen bond network has to be taken into account. Comparison with data obtained for a pre-twisted SBPa analogue led us to exclude the presence of any large-amplitude geometrical change during ICT. Analyzing the solvent dependency using the power law

  13. Reconstruction of a probable ancestral form of conger eel galectins revealed their rapid adaptive evolution process for specific carbohydrate recognition.

    PubMed

    Konno, Ayumu; Ogawa, Tomohisa; Shirai, Tsuyoshi; Muramoto, Koji

    2007-11-01

    Recently, many cases of rapid adaptive evolution, which is characterized by the higher substitution rates of nonsynonymous substitutions to synonymous ones, have been identified in the various genes of venomous and biodefense proteins, including the conger eel galectins, congerins I and II (ConI and ConII). To understand the evolutionary process of congerins, we prepared a probable ancestral form, Con-anc, corresponding to the putative amino acid sequence at the divergence of ConI and ConII in phylogenetic tree with 76% and 61% sequence identities to the current proteins, respectively. Con-anc and ConII had comparable thermostability and similar carbohydrate specificities in general, whereas ConI was more thermostable and showed different carbohydrate specificities. Con-anc showed decreased specificity to oligosaccharides with alpha 2,3-sialyl galactose moieties. These suggest that ConI and ConII have evolved via accelerated evolution under significant selective pressure to increase the thermostability and to acquire the activity to bind to alpha2,3-sialyl galactose present in pathogenic bacteria, respectively. Furthermore, comparative mutagenesis analyses of Con-anc and congerins revealed the structural basis for specific recognition of ConII to alpha2,3-sialyl galactose moiety, and strong binding ability of ConI to oligosaccharides including lacto-N-biosyl (Galbeta1-3GlcNAc) or lacto-N-neobiosyl (Galbeta1-4GlcNAc) residues, respectively. Thus, protein engineering using a probable ancestral form presented here is a powerful approach not only to determine the evolutionary process but also to investigate the structure-activity relationships of proteins. PMID:17827170

  14. 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

  15. Nuclear localization signal deletion mutants of lamin A and progerin reveal insights into lamin A processing and emerin targeting.

    PubMed

    Wu, Di; Flannery, Andrew R; Cai, Helen; Ko, Eunae; Cao, Kan

    2014-01-01

    Lamin A is a major component of the lamina, which creates a dynamic network underneath the nuclear envelope. Mutations in the lamin A gene (LMNA) cause severe genetic disorders, one of which is Hutchinson-Gilford progeria syndrome (HGPS), a disease triggered by a dominant mutant named progerin. Unlike the wild-type lamin A, whose farnesylated C-terminus is excised during post-translational processing, progerin retains its farnesyl tail and accumulates on the nuclear membrane, resulting in abnormal nuclear morphology during interphase. In addition, membrane-associated progerin forms visible cytoplasmic aggregates in mitosis. To examine the potential effects of cytoplasmic progerin, nuclear localization signal (NLS) deleted progerin and lamin A (PGΔNLS and LAΔNLS, respectively) have been constructed. We find that both ΔNLS mutants are farnesylated in the cytosol and associate with a sub-domain of the ER via their farnesyl tails. While the farnesylation on LAΔNLS can be gradually removed, which leads to its subsequent release from the ER into the cytoplasm, PGΔNLS remains permanently farnesylated and membrane-bounded. Moreover, both ΔNLS mutants dominantly affect emerin's nuclear localization. These results reveal new insights into lamin A biogenesis and lamin A-emerin interaction. PMID:24637396

  16. Fluoxetine-induced transactivation of the platelet-derived growth factor type β receptor reveals a novel heterologous desensitization process.

    PubMed

    Kruk, Jeff S; Vasefi, Maryam S; Gondora, Nyasha; Ahmed, Nawaz; Heikkila, John J; Beazely, Michael A

    2015-03-01

    Many G protein-coupled receptors (GPCRs), including serotonin (5-HT) receptors promote the activity of receptor tyrosine kinases (RTKs) via intracellular signaling pathways in a process termed transactivation. Although transactivation pathways are commonly initiated by a GPCR, a recent report demonstrated that serotonin-selective reuptake inhibitors (SSRIs) were able to block 5-HT-induced transactivation of the platelet-derived growth factor (PDGF) type β receptor. We show that a 45 min pretreatment of SH-SY5Y cells with the SSRI fluoxetine indeed blocked 5-HT-induced transactivation of the PDGFβ receptor. However, upon further examination, we discovered that during the pretreatment period, fluoxetine itself was transiently transactivating the PDGFβ receptor via 5-HT2 receptor activation. After 45min, the increase in PDGFβ receptor phosphorylation induced by fluoxetine had returned to baseline, but a subsequent transactivating stimulus (5-HT) failed to "re-transactivate" the PDGFβ receptor. We further demonstrate that 45min, but not 3h, 5-HT pretreatment blocks dopamine-induced PDGFβ receptor transactivation. This did not involve changes in PDGF receptor function, since ligand (PDGF)-induced PDGFβ receptor activation was not inhibited by 5-HT pretreatment. To our knowledge this is the first demonstration of the heterologous desensitization of an RTK transactivation pathway and reveals a previously unknown short-term "blackout" period where no additional transactivation signaling is possible. PMID:25702926

  17. 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

  18. Nuclear localization signal deletion mutants of lamin A and progerin reveal insights into lamin A processing and emerin targeting

    PubMed Central

    Wu, Di; Flannery, Andrew R; Cai, Helen; Ko, Eunae; Cao, Kan

    2014-01-01

    Lamin A is a major component of the lamina, which creates a dynamic network underneath the nuclear envelope. Mutations in the lamin A gene (LMNA) cause severe genetic disorders, one of which is Hutchinson-Gilford progeria syndrome (HGPS), a disease triggered by a dominant mutant named progerin. Unlike the wild-type lamin A, whose farnesylated C-terminus is excised during post-translational processing, progerin retains its farnesyl tail and accumulates on the nuclear membrane, resulting in abnormal nuclear morphology during interphase. In addition, membrane-associated progerin forms visible cytoplasmic aggregates in mitosis. To examine the potential effects of cytoplasmic progerin, nuclear localization signal (NLS) deleted progerin and lamin A (PGΔNLS and LAΔNLS, respectively) have been constructed. We find that both ΔNLS mutants are farnesylated in the cytosol and associate with a sub-domain of the ER via their farnesyl tails. While the farnesylation on LAΔNLS can be gradually removed, which leads to its subsequent release from the ER into the cytoplasm, PGΔNLS remains permanently farnesylated and membrane-bounded. Moreover, both ΔNLS mutants dominantly affect emerin’s nuclear localization. These results reveal new insights into lamin A biogenesis and lamin A-emerin interaction. PMID:24637396

  19. Population-based resequencing revealed an ancestral winter group of cultivated flax: implication for flax domestication processes

    PubMed Central

    Fu, Yong-Bi

    2012-01-01

    Cultivated flax (Linum usitatissimum L.) is the earliest oil and fiber crop and its early domestication history may involve multiple events of domestication for oil, fiber, capsular indehiscence, and winter hardiness. Genetic studies have demonstrated that winter cultivated flax is closely related to oil and fiber cultivated flax and shows little relatedness to its progenitor, pale flax (L. bienne Mill.), but winter hardiness is one major characteristic of pale flax. Here, we assessed the genetic relationships of 48 Linum samples representing pale flax and four trait-specific groups of cultivated flax (dehiscent, fiber, oil, and winter) through population-based resequencing at 24 genomic regions, and revealed a winter group of cultivated flax that displayed close relatedness to the pale flax samples. Overall, the cultivated flax showed a 27% reduction of nucleotide diversity when compared with the pale flax. Recombination frequently occurred at these sampled genomic regions, but the signal of selection and bottleneck was relatively weak. These findings provide some insight into the impact and processes of flax domestication and are significant for expanding our knowledge about early flax domestication, particularly for winter hardiness. PMID:22822439

  20. 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. PMID:26116530

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. Ultrasound Despeckling for Contrast Enhancement

    PubMed Central

    Tay, Peter C.; Garson, Christopher D.; Acton, Scott T.; Hossack, John A.

    2010-01-01

    Images produced by ultrasound systems are adversely hampered by a stochastic process known as speckle. A despeckling method based upon removing outlier is proposed. The method is developed to contrast enhance B-mode ultrasound images. The contrast enhancement is with respect to decreasing pixel variations in homogeneous regions while maintaining or improving differences in mean values of distinct regions. A comparison of the proposed despeckling filter is compared with the other well known despeckling filters. The evaluations of despeckling performance are based upon improvements to contrast enhancement, structural similarity, and segmentation results on a Field II simulated image and actual B-mode cardiac ultrasound images captured in vivo. PMID:20227984

  7. Ultrasound despeckling for contrast enhancement.

    PubMed

    Tay, Peter C; Garson, Christopher D; Acton, Scott T; Hossack, John A

    2010-07-01

    Images produced by ultrasound systems are adversely hampered by a stochastic process known as speckle. A despeckling method based upon removing outlier is proposed. The method is developed to contrast enhance B-mode ultrasound images. The contrast enhancement is with respect to decreasing pixel variations in homogeneous regions while maintaining or improving differences in mean values of distinct regions. A comparison of the proposed despeckling filter is compared with the other well known despeckling filters. The evaluations of despeckling performance are based upon improvements to contrast enhancement, structural similarity, and segmentation results on a Field II simulated image and actual B-mode cardiac ultrasound images captured in vivo. PMID:20227984

  8. 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…

  9. Gender differences in implicit and explicit processing of emotional facial expressions as revealed by event-related theta synchronization.

    PubMed

    Knyazev, Gennady G; Slobodskoj-Plusnin, Jaroslav Y; Bocharov, Andrey V

    2010-10-01

    Emotion information processing may occur in 2 modes that are differently represented in conscious awareness. Fast online processing involves coarse-grained analysis of salient features and is not represented in conscious awareness; offline processing takes hundreds of milliseconds to generate fine-grained analysis and is represented in conscious awareness. These processing modes may be studied using event-related electroencephalogram theta synchronization as a marker of emotion processing. Two experiments were conducted that differed on the mode of emotional information presentation. In the explicit mode, subjects were explicitly instructed to evaluate the emotional content of presented stimuli; in the implicit mode, their attention was directed to other features of the stimulus. In the implicit mode, theta synchronization was most pronounced in the early processing stage, whereas in the explicit mode, it was more pronounced in the late processing stage. The early processing stage was more pronounced in men, whereas the late processing stage was more pronounced in women. Implications of these gender differences in emotion processing for well-documented differences in social behavior are discussed. PMID:21038950

  10. 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

  11. 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…

  12. 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…

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. Earlier timbre processing of instrumental tones compared to equally complex spectrally rotated sounds as revealed by the mismatch negativity.

    PubMed

    Christmann, Corinna A; Lachmann, Thomas; Berti, Stefan

    2014-10-01

    Harmonically rich sounds have been shown to be processed more efficiently by the human brain compared to single sinusoidal tones. To control for stimulus complexity as a potentially confounding factor, tones and equally complex spectrally rotated sounds, have been used in the present study to investigate the role of the overtone series in sensory auditory processing in non-musicians. Timbre differences in instrumental tones with equal pitch elicited a MMN which was earlier compared to that elicited by the spectrally rotated sounds, indicating that harmonically rich tones are processed faster compared to non-musical sounds without an overtone series, even when pitch is not the relevant information. PMID:25173970

  18. fMRI reveals lateralized pattern of brain activity modulated by the metrics of stimuli during auditory rhyme processing.

    PubMed

    Hurschler, Martina A; Liem, Franziskus; Oechslin, Mathias; Stämpfli, Philipp; Meyer, Martin

    2015-08-01

    Our fMRI study investigates auditory rhyme processing in spoken language to further elucidate the topic of functional lateralization of language processing. During scanning, 14 subjects listened to four different types of versed word strings and subsequently performed either a rhyme or a meter detection task. Our results show lateralization to auditory-related temporal regions in the right hemisphere irrespective of task. As for the left hemisphere we report responses in the supramarginal gyrus as well as in the opercular part of the inferior frontal gyrus modulated by the presence of regular meter and rhyme. The interaction of rhyme and meter was associated with increased involvement of the superior temporal sulcus and the putamen of the right hemisphere. Overall, these findings support the notion of right-hemispheric specialization for suprasegmental analyses during processing of spoken sentences and provide neuroimaging evidence for the influence of metrics on auditory rhyme processing. PMID:26025759

  19. 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

  20. Opportunistic proteolytic processing of carbonic anhydrase 1 from Chlamydomonas in Arabidopsis reveals a novel route for protein maturation.

    PubMed

    Juvale, Parijat S; Wagner, Ryan L; Spalding, Martin H

    2016-04-01

    Proteolytic processing of secretory proteins to yield an active form generally involves specific proteolytic cleavage of a pre-protein. Multiple specific proteases have been identified that target specific pre-protein processing sites in animals. However, characterization of site-specific proteolysis of plant pre-proteins is still evolving. In this study, we characterized proteolytic processing of Chlamydomonas periplasmic carbonic anhydrase 1 (CAH1) in Arabidopsis. CAH1 pre-protein undergoes extensive post-translational modification in the endomembrane system, including glycosylation, disulfide bond formation and proteolytic removal of a peptide 'spacer' region, resulting in a mature, heterotetrameric enzyme with two large and two small subunits. We generated a series of small-scale and large-scale modifications to the spacer and flanking regions to identify potential protease target motifs. Surprisingly, we found that the endoproteolytic removal of the spacer from the CAH1 pre-protein proceeded via an opportunistic process apparently followed by further maturation via amino and carboxy peptidases. We also discovered that the spacer itself is not required for processing, which appears to be dependent only on the number of amino acids separating two key disulfide-bond-forming cysteines. Our data suggest a novel, opportunistic route for pre-protein processing of CAH1. PMID:26917556

  1. Opportunistic proteolytic processing of carbonic anhydrase 1 from Chlamydomonas in Arabidopsis reveals a novel route for protein maturation

    PubMed Central

    Juvale, Parijat S.; Wagner, Ryan L.; Spalding, Martin H.

    2016-01-01

    Proteolytic processing of secretory proteins to yield an active form generally involves specific proteolytic cleavage of a pre-protein. Multiple specific proteases have been identified that target specific pre-protein processing sites in animals. However, characterization of site-specific proteolysis of plant pre-proteins is still evolving. In this study, we characterized proteolytic processing of Chlamydomonas periplasmic carbonic anhydrase 1 (CAH1) in Arabidopsis. CAH1 pre-protein undergoes extensive post-translational modification in the endomembrane system, including glycosylation, disulfide bond formation and proteolytic removal of a peptide ‘spacer’ region, resulting in a mature, heterotetrameric enzyme with two large and two small subunits. We generated a series of small-scale and large-scale modifications to the spacer and flanking regions to identify potential protease target motifs. Surprisingly, we found that the endoproteolytic removal of the spacer from the CAH1 pre-protein proceeded via an opportunistic process apparently followed by further maturation via amino and carboxy peptidases. We also discovered that the spacer itself is not required for processing, which appears to be dependent only on the number of amino acids separating two key disulfide-bond-forming cysteines. Our data suggest a novel, opportunistic route for pre-protein processing of CAH1. PMID:26917556

  2. 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

  3. 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

    2016-04-01

    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 sea surface temperature SST anomalies into partial SST 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.

  4. [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

  5. Speech Perception in Tones and Noise via Cochlear Implants Reveals Influence of Spectral Resolution on Temporal Processing

    PubMed Central

    Kreft, Heather A.

    2014-01-01

    Under normal conditions, human speech is remarkably robust to degradation by noise and other distortions. However, people with hearing loss, including those with cochlear implants, often experience great difficulty in understanding speech in noisy environments. Recent work with normal-hearing listeners has shown that the amplitude fluctuations inherent in noise contribute strongly to the masking of speech. In contrast, this study shows that speech perception via a cochlear implant is unaffected by the inherent temporal fluctuations of noise. This qualitative difference between acoustic and electric auditory perception does not seem to be due to differences in underlying temporal acuity but can instead be explained by the poorer spectral resolution of cochlear implants, relative to the normally functioning ear, which leads to an effective smoothing of the inherent temporal-envelope fluctuations of noise. The outcome suggests an unexpected trade-off between the detrimental effects of poorer spectral resolution and the beneficial effects of a smoother noise temporal envelope. This trade-off provides an explanation for the long-standing puzzle of why strong correlations between speech understanding and spectral resolution have remained elusive. The results also provide a potential explanation for why cochlear-implant users and hearing-impaired listeners exhibit reduced or absent masking release when large and relatively slow temporal fluctuations are introduced in noise maskers. The multitone maskers used here may provide an effective new diagnostic tool for assessing functional hearing loss and reduced spectral resolution. PMID:25315376

  6. 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.

  7. 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

  8. Application of Hoffman modulation contrast microscopy coupled with three-wavelength two-beam interferometry to the in situ direct observation of the growth process of a crystal in microgravity

    NASA Technical Reports Server (NTRS)

    Tsukamoto, Katsuo

    1988-01-01

    Direct visualization of three dimensional transfer process of both heat and mass around a growing crystal and mono-molecular growth layers on the surface is possible in situ by means of high resolution Hoffman modulation contrast microscopy coupled with three wavelength two beam Mach-Zehnder interferometry. This in situ observation is very suitable for the verification of the growth mechanism of a crystal in a solution or a melt in microgravity.

  9. 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

  10. 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

  11. 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

  12. Apocalypto: revealing lost text with XMT

    NASA Astrophysics Data System (ADS)

    Mills, David; Davis, Graham R.; Lai, Yu-kun; Rosin, Paul

    2014-09-01

    "Can brute-force high-contrast tomography techniques and image processing techniques retrieve textual content from damaged heritage materials?" The Dental Institute at Queen Mary University of London (QMUL) is the leading centre for very high contrast X-Ray Microtomography imaging. The Apocalypto Project is our collaboration with the heritage community and experts in Computer Vision systems in the Computer Science Department at Cardiff University. This collaboration has developed techniques and a workflow that allows us to reveal textual content from moisture-damaged parchment rolls. This article will also present some initial results from burned and heat shrunken parchment rolls, an insect damaged Mamluk cap and a birch bark roll.

  13. Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes

    PubMed Central

    Tausta, S. Lori; Li, Pinghua; Si, Yaqing; Gandotra, Neeru; Liu, Peng; Sun, Qi; Brutnell, Thomas P.; Nelson, Timothy

    2014-01-01

    The comparison of the cell-specific transcriptomes of bundle sheath (BS) and mesophyll (M) cells from successive developmental stages of maize (Zea mays) leaves reveals that the number of genes preferentially transcribed in one cell type or the other varies considerably from the sink–source transition to mature photosynthetic stages. The number of differentially expressed (DE) genes is maximal at a stage well before full maturity, including those that encode key functions for C4 photosynthesis. The developmental dynamics of BS/M differential expression can be used to identify candidates for other C4-related functions and to simplify the identification of specific pathways members from otherwise complex gene families. A significant portion of the candidates for C4-related transcription factors identified with this developmental DE strategy overlap with those identified in studies using alternative strategies, thus providing independent support for their potential importance. PMID:24790109

  14. 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

  15. 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

  16. 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.

  17. 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. PMID:25632131

  18. 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…

  19. Neural Decoding Reveals Impaired Face Configural Processing in the Right Fusiform Face Area of Individuals with Developmental Prosopagnosia

    PubMed Central

    Zhang, Jiedong; Liu, Jia

    2015-01-01

    Most of human daily social interactions rely on the ability to successfully recognize faces. Yet ∼2% of the human population suffers from face blindness without any acquired brain damage [this is also known as developmental prosopagnosia (DP) or congenital prosopagnosia]). Despite the presence of severe behavioral face recognition deficits, surprisingly, a majority of DP individuals exhibit normal face selectivity in the right fusiform face area (FFA), a key brain region involved in face configural processing. This finding, together with evidence showing impairments downstream from the right FFA in DP individuals, has led some to argue that perhaps the right FFA is largely intact in DP individuals. Using fMRI multivoxel pattern analysis, here we report the discovery of a neural impairment in the right FFA of DP individuals that may play a critical role in mediating their face-processing deficits. In seven individuals with DP, we discovered that, despite the right FFA's preference for faces and it showing decoding for the different face parts, it exhibited impaired face configural decoding and did not contain distinct neural response patterns for the intact and the scrambled face configurations. This abnormality was not present throughout the ventral visual cortex, as normal neural decoding was found in an adjacent object-processing region. To our knowledge, this is the first direct neural evidence showing impaired face configural processing in the right FFA in individuals with DP. The discovery of this neural impairment provides a new clue to our understanding of the neural basis of DP. PMID:25632131

  20. 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…

  1. 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…

  2. 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

  3. The role of fluids in rock layering development: a pressure solution self-organized process revealed by laboratory experiments

    NASA Astrophysics Data System (ADS)

    Gratier, Jean-Pierre; Noiriel, Catherine; Renard, Francois

    2015-04-01

    Natural deformation of rocks is often associated with stress-driven differentiation processes leading to irreversible transformations of their microstructures. The development mechanisms of such processes during diagenesis, tectonic, metamorphism or fault differentiation are poorly known as they are difficult to reproduce experimentally due to the very slow kinetics of stress-driven chemical processes. Here, we show that experimental compaction with development of differentiated layering, similar to what happens in natural deformation, can be obtained by indenter techniques in laboratory conditions. Samples of plaster mixed with clay and of diatomite loosely interbedded with volcanic dust were loaded in presence of their saturated aqueous solutions during several months at 40°C and 150°C, respectively. High-resolution X-ray microtomography and scanning electron microscopy observations show that the layering development is a pressure solution self-organized process. Stress-driven dissolution of the soluble minerals (either gypsum or silica) is initiated in the areas initially richer in insoluble minerals (clays or volcanic dust) because the kinetics of diffusive mass transfer along the soluble/insoluble mineral interfaces is much faster than along the healed boundaries of the soluble minerals. The passive concentration of insoluble minerals amplifies the localization of dissolution along some layers oriented perpendicular to the maximum compressive stress. Conversely, in the areas with initial low content in insoluble minerals and clustered soluble minerals, dissolution is slower. Consequently, these areas are less deformed, they host the re-deposition of the soluble species and they act as rigid objects that concentrate the dissolution near their boundaries thus amplifying the differentiation. A crucial parameter required for self-organized process of pressure solution is the presence of a fluid that is a good solvent of at least some of the rock-forming minerals

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

    PubMed Central

    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 (200-500ms) elicited by unrelated related words was more negative than all related words. Furthermore, the late frontal distributed negativity (500-700ms) 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

  5. Functionally defined white matter reveals segregated pathways in human ventral temporal cortex associated with category-specific processing.

    PubMed

    Gomez, Jesse; Pestilli, Franco; Witthoft, Nathan; Golarai, Golijeh; Liberman, Alina; Poltoratski, Sonia; Yoon, Jennifer; Grill-Spector, Kalanit

    2015-01-01

    It is unknown if the white-matter properties associated with specific visual networks selectively affect category-specific processing. In a novel protocol we combined measurements of white-matter structure, functional selectivity, and behavior in the same subjects. We find two parallel white-matter pathways along the ventral temporal lobe connecting to either face-selective or place-selective regions. Diffusion properties of portions of these tracts adjacent to face- and place-selective regions of ventral temporal cortex correlate with behavioral performance for face or place processing, respectively. Strikingly, adults with developmental prosopagnosia (face blindness) express an atypical structure-behavior relationship near face-selective cortex, suggesting that white-matter atypicalities in this region may have behavioral consequences. These data suggest that examining the interplay between cortical function, anatomical connectivity, and visual behavior is integral to understanding functional networks and their role in producing visual abilities and deficits. PMID:25569351

  6. 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

  7. Functionally defined white matter reveals segregated pathways in human ventral temporal cortex associated with category-specific processing

    PubMed Central

    Gomez, Jesse; Pestilli, Franco; Witthoft, Nathan; Golarai, Golijeh; Liberman, Alina; Poltoratski, Sonia; Yoon, Jennifer; Grill-Spector, Kalanit

    2014-01-01

    Summary It is unknown if the white matter properties associated with specific visual networks selectively affect category-specific processing. In a novel protocol we combined measurements of white matter structure, functional selectivity, and behavior in the same subjects. We find two parallel white matter pathways along the ventral temporal lobe connecting to either face-selective or place-selective regions. Diffusion properties of portions of these tracts adjacent to face- and place-selective regions of ventral temporal cortex correlate with behavioral performance for face or place processing, respectively. Strikingly, adults with developmental prosopagnosia (face blindness) express an atypical structure-behavior relationship near face-selective cortex, suggesting that white matter atypicalities in this region may have behavioral consequences. These data suggest that examining the interplay between cortical function, anatomical connectivity, and visual behavior is integral to understanding functional networks and their role in producing visual abilities and deficits. PMID:25569351

  8. 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

  9. fMRI reveals distinct CNS processing during symptomatic and recovered complex regional pain syndrome in children.

    PubMed

    Lebel, A; Becerra, L; Wallin, D; Moulton, E A; Morris, S; Pendse, G; Jasciewicz, J; Stein, M; Aiello-Lammens, M; Grant, E; Berde, C; Borsook, D

    2008-07-01

    Complex regional pain syndrome (CRPS) in paediatric patients is clinically distinct from the adult condition in which there is often complete resolution of its signs and symptoms within several months to a few years. The ability to compare the symptomatic and asymptomatic condition in the same individuals makes this population interesting for the investigation of mechanisms underlying pain and other symptoms of CRPS. We used fMRI to evaluate CNS activation in paediatric patients (9-18 years) with CRPS affecting the lower extremity. Each patient underwent two scanning sessions: once during an active period of pain (CRPS(+)), and once after symptomatic recovery (CRPS(-)). In each session, mechanical (brush) and thermal (cold) stimuli were applied to the affected region of the involved limb and the corresponding mirror region of the unaffected limb. Two fundamental fMRI analyses were performed: (i) within-group analysis for CRPS(+) state and CRPS(-) state for brush and cold for the affected and unaffected limbs in each case; (ii) between-group (contrast) analysis for activations in affected and unaffected limbs in CRPS or post-CRPS states. We found: (i) in the CRPS(+) state, stimuli that evoked mechanical or cold allodynia produced patterns of CNS activation similar to those reported in adult CRPS; (ii) in the CRPS(+) state, stimuli that evoked mechanical or cold allodynia produced significant decreases in BOLD signal, suggesting pain-induced activation of endogenous pain modulatory systems; (iii) cold- or brush-induced activations in regions such as the basal ganglia and parietal lobe may explain some CNS-related symptoms in CRPS, including movement disorders and hemineglect/inattention; (iv) in the CRPS(-) state, significant activation differences persisted despite nearly complete elimination of evoked pain; (v) although non-noxious stimuli to the unaffected limb were perceived as equivalent in CRPS(+) and CRPS(-) states, the same stimulus produced different

  10. Gene expression signatures in motor neurone disease fibroblasts reveal dysregulation of metabolism, hypoxia-response and RNA processing functions

    PubMed Central

    Raman, R; Allen, S P; Goodall, E F; Kramer, S; Ponger, L-L; Heath, P R; Milo, M; Hollinger, H C; Walsh, T; Highley, J R; Olpin, S; McDermott, C J; Shaw, P J; Kirby, J

    2015-01-01

    Aims Amyotrophic lateral sclerosis (ALS) and primary lateral sclerosis (PLS) are two syndromic variants within the motor neurone disease spectrum. As PLS and most ALS cases are sporadic (SALS), this limits the availability of cellular models for investigating pathogenic mechanisms and therapeutic targets. The aim of this study was to use gene expression profiling to evaluate fibroblasts as cellular models for SALS and PLS, to establish whether dysregulated biological processes recapitulate those seen in the central nervous system and to elucidate pathways that distinguish the clinically defined variants of SALS and PLS. Methods Microarray analysis was performed on fibroblast RNA and differentially expressed genes identified. Genes in enriched biological pathways were validated by quantitative PCR and functional assays performed to establish the effect of altered RNA levels on the cellular processes. Results Gene expression profiling demonstrated that whilst there were many differentially expressed genes in common between SALS and PLS fibroblasts, there were many more expressed specifically in the SALS fibroblasts, including those involved in RNA processing and the stress response. Functional analysis of the fibroblasts confirmed a significant decrease in miRNA production and a reduced response to hypoxia in SALS fibroblasts. Furthermore, metabolic gene changes seen in SALS, many of which were also evident in PLS fibroblasts, resulted in dysfunctional cellular respiration. Conclusions The data demonstrate that fibroblasts can act as cellular models for ALS and PLS, by establishing the transcriptional changes in known pathogenic pathways that confer subsequent functional effects and potentially highlight targets for therapeutic intervention. PMID:24750211

  11. 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

  12. 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

  13. Design of experiments reveals critical parameters for pilot-scale freeze-and-thaw processing of L-lactic dehydrogenase.

    PubMed

    Roessl, Ulrich; Humi, Sebastian; Leitgeb, Stefan; Nidetzky, Bernd

    2015-09-01

    Freezing constitutes an important unit operation of biotechnological protein production. Effects of freeze-and-thaw (F/T) process parameters on stability and other quality attributes of the protein product are usually not well understood. Here a design of experiments (DoE) approach was used to characterize the F/T behavior of L-lactic dehydrogenase (LDH) in a 700-mL pilot-scale freeze container equipped with internal temperature and pH probes. In 24-hour experiments, target temperature between -10 and -38°C most strongly affected LDH stability whereby enzyme activity was retained best at the highest temperature of -10°C. Cooling profile and liquid fill volume also had significant effects on LDH stability and affected the protein aggregation significantly. Parameters of the thawing phase had a comparably small effect on LDH stability. Experiments in which the standard sodium phosphate buffer was exchanged by Tris-HCl and the non-ionic surfactant Tween 80 was added to the protein solution showed that pH shift during freezing and protein surface exposure were the main factors responsible for LDH instability at the lower freeze temperatures. Collectively, evidence is presented that supports the use of DoE-based systematic analysis at pilot scale in the identification of F/T process parameters critical for protein stability and in the development of suitable process control strategies. PMID:25820483

  14. 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

  15. 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. PMID:26201687

  16. 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

  17. 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

  18. 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

  19. Contrasting pyroclast density spectra from subaerial and submarine silicic eruptions in the Kermadec arc: implications for eruption processes and dredge sampling

    NASA Astrophysics Data System (ADS)

    Barker, Simon J.; Rotella, Melissa D.; Wilson, Colin J. N.; Wright, Ian C.; Wysoczanski, Richard J.

    2012-08-01

    Pyroclastic deposits from four caldera volcanoes in the Kermadec arc have been sampled from subaerial sections (Raoul and Macauley) and by dredging from the submerged volcano flanks (Macauley, Healy, and the newly discovered Raoul SW). Suites of 16-32 mm sized clasts have been analyzed for density and shape, and larger clasts have been analyzed for major element compositions. Density spectra for subaerial dry-type eruptions on Raoul Island have narrow unimodal distributions peaking at vesicularities of 80-85%, whereas ingress of external water (wet-type eruption) or extended timescales for degassing generate broader distributions, including denser clasts. Submarine-erupted pyroclasts show two different patterns. Healy and Raoul SW dredge samples and Macauley Island subaerial-emplaced samples are dominated by modes at ~80-85%, implying that submarine explosive volcanism at high eruption rates can generate clasts with similar vesicularities to their subaerial counterparts. A minor proportion of Healy and Raoul SW clasts also show a pink oxidation color, suggesting that hot clasts met air despite 0.5 to >1 km of intervening water. In contrast, Macauley dredged samples have a bimodal density spectrum dominated by clasts formed in a submarine-eruptive style that is not highly explosive. Macauley dredged pyroclasts are also the mixed products of multiple eruptions, as shown by pumice major-element chemistry, and the sea-floor deposits reflect complex volcanic and sedimentation histories. The Kermadec calderas are composite features, and wide dispersal of pumice does not require large single eruptions. When coupled with chemical constraints and textural observations, density spectra are useful for interpreting both eruptive style and the diversity of samples collected from the submarine environment.

  20. 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…

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

    PubMed Central

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

    2014-01-01

    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 Ca2+ transients revealed Rbm20-dependent alteration in Ca2+ 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. PMID:24584570

  2. 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

  3. Component analysis and growth process of nasopharyngeal calculus as revealed by Fourier transform infrared (FT-IR) spectroscopy.

    PubMed

    Ogawa, T; Shibata, A; Maeda, Y; Uno, Y; Okano, M; Nishizaki, K; Ohsaki, K

    2003-06-01

    A quite rare case of nasopharyngeal calculus in a woman in her twenties associated with the nasal discharge of pseudomonas infection was reported. As the substance was irregularly large in size, we extracted it partially by piecemeal resection using forceps and also by cracking technique using the holmium yttrium-aluminum-garnet (YAG) laser, under saline irrigation and stereotactic microscopic navigator (SMN) system under endoscopic observation. The substance was firmly fixed to the pharyngeal tonsil bed. The final extract was a small piece of singly folded bandage, which is probably the focal background for calculus formation. In a cross section of calculus specimen removed during surgery, Fourier transform infrared (FT-IR) analysis revealed that a) signal ratio of methylene group (organic substance) to amide I (protein) was 21.6% at the nasal cavity side, gradually decreased toward nasal mucous membrane showing approximate 50%, b) signal ratio of amide I to P04(3-) (inorganic substance) ranged between 17.7% and 26.7% at the different sites and inside the calculus, the protein content was approximate 1/5 of the inorganic substance, and c) signal ratio of the methylene group to amide I at the nasal cavity site showed that their contents were almost equal. The quantity of the organic substance was estimated at approximate 1/2 quantity of the protein at both the central part and the part contacted with the mucous membrane. From these results, it seems that throughout the course of calculus growth, both inorganic substance and protein remain almost constant inside the calculus, while organic substance is released from the internal part of the calculus being probably formed at an early stage. PMID:12899453

  4. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics.

    PubMed

    Williams, Timothy J; Wilkins, David; Long, Emilie; Evans, Flavia; DeMaere, Mathew Z; Raftery, Mark J; Cavicchioli, Ricardo

    2013-05-01

    Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean. PMID:23126454

  5. Topographic representations of object size and relationships with numerosity reveal generalized quantity processing in human parietal cortex

    PubMed Central

    Harvey, Ben M.; Fracasso, Alessio; Petridou, Natalia; Dumoulin, Serge O.

    2015-01-01

    Humans and many animals analyze sensory information to estimate quantities that guide behavior and decisions. These quantities include numerosity (object number) and object size. Having recently demonstrated topographic maps of numerosity, we ask whether the brain also contains maps of object size. Using ultra-high-field (7T) functional MRI and population receptive field modeling, we describe tuned responses to visual object size in bilateral human posterior parietal cortex. Tuning follows linear Gaussian functions and shows surround suppression, and tuning width narrows with increasing preferred object size. Object size-tuned responses are organized in bilateral topographic maps, with similar cortical extents responding to large and small objects. These properties of object size tuning and map organization all differ from the numerosity representation, suggesting that object size and numerosity tuning result from distinct mechanisms. However, their maps largely overlap and object size preferences correlate with numerosity preferences, suggesting associated representations of these two quantities. Object size preferences here show no discernable relation to visual position preferences found in visuospatial receptive fields. As such, object size maps (much like numerosity maps) do not reflect sensory organ structure but instead emerge within the brain. We speculate that, as in sensory processing, optimization of cognitive processing using topographic maps may be a common organizing principle in association cortex. Interactions between object size and numerosity maps may associate cognitive representations of these related features, potentially allowing consideration of both quantities together when making decisions. PMID:26483452

  6. 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

  7. Global Transcriptome Analysis Reveals Acclimation-Primed Processes Involved in the Acquisition of Desiccation Tolerance in Boea hygrometrica.

    PubMed

    Zhu, Yan; Wang, Bo; Phillips, Jonathan; Zhang, Zhen-Nan; Du, Hong; Xu, Tao; Huang, Lian-Cheng; Zhang, Xiao-Fei; Xu, Guang-Hui; Li, Wen-Long; Wang, Zhi; Wang, Ling; Liu, Yong-Xiu; Deng, Xin

    2015-07-01

    Boea hygrometrica resurrection plants require a period of acclimation by slow soil-drying in order to survive a subsequent period of rapid desiccation. The molecular basis of this observation was investigated by comparing gene expression profiles under different degrees of water deprivation. Transcripts were clustered according to the expression profiles in plants that were air-dried (rapid desiccation), soil-dried (gradual desiccation), rehydrated (acclimated) and air-dried after acclimation. Although phenotypically indistinguishable, it was shown by principal component analysis that the gene expression profiles in rehydrated, acclimated plants resemble those of desiccated plants more closely than those of hydrated acclimated plants. Enrichment analysis based on gene ontology was performed to deconvolute the processes that accompanied desiccation tolerance. Transcripts associated with autophagy and α-tocopherol accumulation were found to be activated in both air-dried, acclimated plants and soil-dried non-acclimated plants. Furthermore, transcripts associated with biosynthesis of ascorbic acid, cell wall catabolism, chaperone-assisted protein folding, respiration and macromolecule catabolism were activated and maintained during soil-drying and rehydration. Based on these findings, we hypothesize that activation of these processes leads to the establishment of an optimal physiological and cellular state that enables tolerance during rapid air-drying. Our study provides a novel insight into the transcriptional regulation of critical priming responses to enable survival following rapid dehydration in B. hygrometrica. PMID:25907569

  8. Untangling intra- and interspecific effects on body size clines reveals divergent processes structuring convergent patterns in Anolis lizards.

    PubMed

    Muñoz, Martha M; Wegener, Johanna E; Algar, Adam C

    2014-11-01

    Bergmann's rule-the tendency for body size to increase in colder environments-remains controversial today, despite 150 years of research. Considerable debate has revolved around whether the rule applies within or among species. However, this debate has generally not considered that clade-level relationships are caused by both intra- and interspecific effects. In this article, we implement a novel approach that allows for the separation of intra- and interspecific components of trait-environment relationships. We apply this approach to body size clines in two Caribbean clades of Anolis lizards and discover that their similar body size gradients are constructed in very different ways. We find inverse Bergmann's clines-high-elevation lizards are smaller bodied-for both the cybotes clade on Hispaniola and the sagrei clade on Cuba. However, on Hispaniola, the inverse cline is driven by interspecific differences, whereas intraspecific variation is responsible for the inverse cline on Cuba. Our results suggest that similar body size clines can be constructed through differing evolutionary and ecological processes, namely, through local adaptation or phenotypic plasticity (intraspecific clines) and/or size-ordered spatial sorting (interspecific clines). We propose that our approach can help integrate a divided research program by focusing on how the combined effects of intra- and interspecific processes can enhance or erode clade-level relationships at large biogeographic scales. PMID:25325747

  9. Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes

    PubMed Central

    Saunders, Megan; Glenn, Anthony E; Kohn, Linda M

    2010-01-01

    All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the study of functional trait variation in the host and its fungal consortium. We review studies on crop endophytes that investigate plant and fungal traits likely to be important in endophyte community processes. We focus on approaches that could speed detection of general trends in endophyte community assembly: (i) use of the ‘assembly rules’ concept to identify specific mechanisms that influence endophyte community dynamics, (ii) measurement of functional trait variation in plants and fungi to better understand endophyte community processes and plant–fungal interactions, and (iii) investigation of microbe–microbe interactions, and fungal traits that mediate them. This approach is well suited for research in agricultural systems, where pair-wise host–fungus interactions and mechanisms of fungal–fungal competition have frequently been described. Areas for consideration include the possibility that human manipulation of crop phenotype and deployment of fungal biocontrol species can significantly influence endophyte community assembly. Evaluation of endophyte assembly rules may help to fine-tune crop management strategies. PMID:25567944

  10. Topographic representations of object size and relationships with numerosity reveal generalized quantity processing in human parietal cortex.

    PubMed

    Harvey, Ben M; Fracasso, Alessio; Petridou, Natalia; Dumoulin, Serge O

    2015-11-01

    Humans and many animals analyze sensory information to estimate quantities that guide behavior and decisions. These quantities include numerosity (object number) and object size. Having recently demonstrated topographic maps of numerosity, we ask whether the brain also contains maps of object size. Using ultra-high-field (7T) functional MRI and population receptive field modeling, we describe tuned responses to visual object size in bilateral human posterior parietal cortex. Tuning follows linear Gaussian functions and shows surround suppression, and tuning width narrows with increasing preferred object size. Object size-tuned responses are organized in bilateral topographic maps, with similar cortical extents responding to large and small objects. These properties of object size tuning and map organization all differ from the numerosity representation, suggesting that object size and numerosity tuning result from distinct mechanisms. However, their maps largely overlap and object size preferences correlate with numerosity preferences, suggesting associated representations of these two quantities. Object size preferences here show no discernable relation to visual position preferences found in visuospatial receptive fields. As such, object size maps (much like numerosity maps) do not reflect sensory organ structure but instead emerge within the brain. We speculate that, as in sensory processing, optimization of cognitive processing using topographic maps may be a common organizing principle in association cortex. Interactions between object size and numerosity maps may associate cognitive representations of these related features, potentially allowing consideration of both quantities together when making decisions. PMID:26483452

  11. Distributed Cortical Phase Synchronization in the EEG Reveals Parallel Attention and Working Memory Processes Involved in the Attentional Blink.

    PubMed

    Glennon, Mark; Keane, Michael A; Elliott, Mark A; Sauseng, Paul

    2016-05-01

    Attentional blink (AB) describes a visuo-perceptual phenomenon in which the second of 2 targets within a rapid serial visual presentation stream is not detected. There are several cognitive models attempting to explain the fundamentals of this information processing bottleneck. Here, we used electroencephalographic recordings and the analysis of interregional phase synchronization of rhythmical brain activity to investigate the neural bases of the AB. By investigating the time course of interregional phase synchronization separately for trials in which participants failed to report the second target correctly (AB trials) and trials in which no AB occurred, and by clustering interregional connections based on their functional similarity, it was possible to define several distinct cortical networks. Analyzing these networks comprising phase synchronization-over a large spectrum of brain frequencies from theta to gamma activity-it was possible to identify neural correlates for cognitive subfunctions involved in the AB, such as the encoding of targets into working memory, tuning of attentional filters, and the recruitment of general cognitive resources. This parallel activation of functionally distinct neural processes substantiates the eligibility of several cognitive models on the AB. PMID:25750255

  12. Complex network models reveal correlations among network metrics, exercise intensity and role of body changes in the fatigue process

    PubMed Central

    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

  13. 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.

  14. 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

  15. Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes.

    PubMed

    Saunders, Megan; Glenn, Anthony E; Kohn, Linda M

    2010-09-01

    All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the study of functional trait variation in the host and its fungal consortium. We review studies on crop endophytes that investigate plant and fungal traits likely to be important in endophyte community processes. We focus on approaches that could speed detection of general trends in endophyte community assembly: (i) use of the 'assembly rules' concept to identify specific mechanisms that influence endophyte community dynamics, (ii) measurement of functional trait variation in plants and fungi to better understand endophyte community processes and plant-fungal interactions, and (iii) investigation of microbe-microbe interactions, and fungal traits that mediate them. This approach is well suited for research in agricultural systems, where pair-wise host-fungus interactions and mechanisms of fungal-fungal competition have frequently been described. Areas for consideration include the possibility that human manipulation of crop phenotype and deployment of fungal biocontrol species can significantly influence endophyte community assembly. Evaluation of endophyte assembly rules may help to fine-tune crop management strategies. PMID:25567944

  16. The neural correlates of implicit and explicit sequence learning: Interacting networks revealed by the process dissociation procedure

    PubMed Central

    Destrebecqz, Arnaud; Peigneux, Philippe; Laureys, Steven; Degueldre, Christian; Del Fiore, Guy; Aerts, Joël; Luxen, André; Van Der Linden, Martial; Cleeremans, Axel; Maquet, Pierre

    2005-01-01

    In two H215O 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 contributions to performance during a subsequent sequence generation task. To manipulate the extent to which the repeating sequential pattern was learned explicitly, we varied the pace of the choice reaction time task—a variable that is known to have differential effects on the extent to which sensitivity to sequence structure involves implicit or explicit knowledge. Results showed that activity in the striatum subtends the implicit component of performance during recollection of a learned sequence, whereas the anterior cingulate/mesial prefrontal cortex (ACC/MPFC) supports the explicit component. Most importantly, we found that the ACC/MPFC exerts control on the activity of the striatum during retrieval of the sequence after explicit learning, whereas the activity of these regions is uncoupled when learning had been essentially implicit. These data suggest that implicit learning processes can be successfully controlled by conscious knowledge when learning is essentially explicit. They also supply further evidence for a partial dissociation between the neural substrates supporting conscious and nonconscious components of performance during recollection of a learned sequence. PMID:16166397

  17. Father's Day dike intrusion and eruption reveals interaction between magmatic and tectonic processes at Kilauea Volcano, Hawaii

    NASA Astrophysics Data System (ADS)

    Foster, J. H.; Brooks, B. A.; Sandwell, D. T.; Poland, M.; Miklius, A.; Myer, D.; Okubo, P. G.; Patrick, M.; Wolfe, C.

    2007-12-01

    The June 17-19, 2007, Father's Day dike intrusion and eruption at Kilauea volcano brought to an end a seven- year period of steady state lava effusion at the Pu'u 'O'o vent. The event was observed by an unprecedented number of geophysical instruments, with temporary arrays of GPS and tiltmeters augmenting the continuous monitoring network. Envisat and ALOS SAR scenes were also acquired during this event and provide further information on the surface deformation as the event progressed. Fortuitously, the Envisat acquisition was during a pause in the middle of the sequence, while the ALOS PALSAR scene was acquired at the end of the sequence, allowing us to model each phase separately. Analysis of these data sets indicates that, in addition to three phases of the dike intrusion, a slow earthquake also occurred on the south flank of Kilauea. The slow earthquake apparently began near the end of the second phase of the dike intrusion. It was still underway the following day, when the third phase of the intrusion began and culminated in a small eruption. This suggests the possibility that the slow earthquake was triggered by the initial diking, and then in turn influenced the progression of the intrusion. Two of the largest previous slow earthquakes also hint at a connection between slow earthquakes and eruptive activity on Kilauea. The range of observations of the Father's Day events provides us with a unique opportunity to investigate the complex interactions between the tectonic processes of the south flank and magmatic processes within the summit and rift zones.

  18. 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.

  19. 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

  20. Toward Critical Contrastive Rhetoric

    ERIC Educational Resources Information Center

    Kubota, Ryuko; Lehner, Al

    2004-01-01

    A traditional approach to contrastive rhetoric has emphasized cultural difference in rhetorical patterns among various languages. Despite its laudable pedagogical intentions to raise teachers' and students' cultural and rhetorical awareness in second language writing, traditional contrastive rhetoric has perpetuated static binaries between English…

  1. The Contrast Theory of Negative Input.

    ERIC Educational Resources Information Center

    Saxton, Matthew

    1997-01-01

    Presents an alternative definition of negative evidence, based on the idea that the unique discourse structure created in the juxtaposition of child error and adult correct form can reveal the child in contrast or conflict between the two forms. Findings reveal that children reproduced the correct irregular model more often and persisted with…

  2. Population structure, demographic history, and selective processes: contrasting evidences from mitochondrial and nuclear markers in the European spiny lobster Palinurus elephas (Fabricius, 1787).

    PubMed

    Babbucci, Massimiliano; Buccoli, Simona; Cau, Angelo; Cannas, Rita; Goñi, Raquel; Díaz, David; Marcato, Stefania; Zane, Lorenzo; Patarnello, Tomaso

    2010-09-01

    The European spiny lobster Palinurus elephas (Fabricius, 1787) is an ecologically and economically important species inhabiting a wide geographic range that extends from the North-east Atlantic and Azores to the Eastern Mediterranean. We investigated the population structure and evolutionary history of this species by both mitochondrial and microsatellite markers. Ten population samples covering a large part of the species distribution range (three samples from the Atlantic Ocean and seven from the Mediterranean Sea) were analyzed for a portion of the mitochondrial control region and seven polymorphic microsatellite loci. Both markers rejected the hypothesis of panmixia identifying two differentiated gene pools. The control region clearly distinguished the Atlantic and Mediterranean populations in two genetically separated groups. Microsatellites, also revealed two groups roughly associated to the Atlantic-Mediterranean separation, however, the Azores sample did not conform to this geographic scheme. Discrepancy between mitochondrial and nuclear markers emerged also when reconstructing the history of the species. Neutrality tests of the mitochondrial sequences indicated a departure from mutation-drift equilibrium that, combined to the mismatch analysis, pointed toward a sudden population expansion in both Atlantic and Mediterranean gene pools. Unexpectedly, microsatellites did not identify any signal of population expansion neither in the Atlantic pool nor in the Mediterranean one. PMID:20510378

  3. 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

  4. Looking, seeing and believing in autism: Eye movements reveal how subtle cognitive processing differences impact in the social domain.

    PubMed

    Benson, Valerie; Castelhano, Monica S; Howard, Philippa L; Latif, Nida; Rayner, Keith

    2016-08-01

    Adults with High Functioning Autism Spectrum Disorders (ASD) viewed scenes with people in them, while having their eye movements recorded. The task was to indicate, using a button press, whether the pictures were normal, or in some way weird or odd. Oddities in the pictures were categorized as violations of either perceptual or social norms. Compared to a Typically Developed (TD) control group, the ASD participants were equally able to categorize the scenes as odd or normal, but they took longer to respond. The eye movement patterns showed that the ASD group made more fixations and revisits to the target areas in the odd scenes compared with the TD group. Additionally, when the ASD group first fixated the target areas in the scenes, they failed to initially detect the social oddities. These two findings have clear implications for processing difficulties in ASD for the social domain, where it is important to detect social cues on-line, and where there is little opportunity to go back and recheck possible cues in fast dynamic interactions. Autism Res 2016, 9: 879-887. © 2015 International Society for Autism Research, Wiley Periodicals, Inc. PMID:26614312

  5. 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.

  6. Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes

    PubMed Central

    2011-01-01

    Background Down syndrome (DS; trisomy 21) is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information. Results We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies. We identified 324 genes with significant genome-wide dosage effects, including well investigated genes like SOD1, APP, RUNX1 and DYRK1A as well as a large proportion of novel genes (N = 62). Furthermore, we characterized these genes using gene ontology, molecular interactions and promoter sequence analysis. In order to judge relevance of the 324 genes for more general cerebral pathologies we used independent publicly available microarry data from brain studies not related with DS and identified a subset of 79 genes with potential impact for neurocognitive processes. All results have been made available through a web server under http://ds-geneminer.molgen.mpg.de/. Conclusions Our study represents a comprehensive integrative analysis of heterogeneous data including genome-wide transcript levels in the domain of trisomy 21. The detected dosage effects build a resource for further studies of DS pathology and the development of new therapies. PMID:21569303

  7. Mass spectrometrical analysis of the processed metastasis-inducing anterior gradient protein 2 homolog reveals 100% sequence coverage.

    PubMed

    Myung, J-K; Frischer, T; Afjehi-Sadat, L; Pollak, A; Lubec, G

    2008-08-01

    Anterior gradient protein 2 homolog is a metastasis-inducing protein in a rat model of rat breast cancer and prognostic for outcome in hormonally treated breast cancer patients. Carrying out protein profiling in several mammalian cells and tissues, we detected this protein (synonym: secreted cement gland protein XAG-2 homolog) that was originally described in toad skin, in human bronchial epithelia. Tissues obtained from biopsies were homogenised and extracted proteins were run on two-dimensional gel electrophoresis. Following in-gel digestion with proteases trypsin, AspN, LysC and chymotrypsin, mass spectrometrical analysis was carried out by MALDI-TOF/TOF. The use of MS following multi-enzyme digestion of the protein resulted into 100% sequence coverage. MS/MS analysis enabled sequencing of 87% of the protein structure. This percentage does not include the signal peptide that was not observed in our protein due to processing. No posttranslational modifications were detectable and no sequence conflicts were observed. Complete analysis, unambiguous identification and characterisation of this biologically important protein could be shown, which is relevant for the definition of a marker protein that has been described so far by immunochemical methods only. Complete analysis is of importance as it forms the basis for all future work on this protein and, moreover, may serve as an analytical tool for further studies. PMID:17497304

  8. Acetylome Profiling Reveals Overlap in the Regulation of Diverse Processes by Sirtuins, Gcn5, and Esa1*

    PubMed Central

    Downey, Michael; Johnson, Jeffrey R.; Davey, Norman E.; Newton, Billy W.; Johnson, Tasha L.; Galaang, Shastyn; Seller, Charles A.; Krogan, Nevan; Toczyski, David P.

    2015-01-01

    Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone protein acetylation. To identify HATs that promote acetylation of these sites, we also performed this analysis in gcn5 (SAGA) and esa1 (NuA4) mutants. We observed strong sequence specificity for the sirtuins and for each of these HATs. Although the Gcn5 and Esa1 consensus sequences are entirely distinct, the sirtuin consensus overlaps almost entirely with that of Gcn5, suggesting a strong coordination between these two regulatory enzymes. Furthermore, by examining global acetylation in an ada2 mutant, which dissociates Gcn5 from the SAGA complex, we found that a subset of Gcn5 targets did not depend on an intact SAGA complex for targeting. Our work provides a framework for understanding how HAT and HDAC enzymes collaborate to regulate critical cellular