Science.gov

Sample records for morphometry reveals reduced

  1. Voxel-based morphometry reveals reduced grey matter volume in the temporal cortex of developmental prosopagnosics

    PubMed Central

    Furl, Nicholas; Draganski, Bogdan; Weiskopf, Nikolaus; Stevens, John; Tan, Geoffrey Chern-Yee; Driver, Jon; Dolan, Ray J.; Duchaine, Bradley

    2009-01-01

    Individuals with developmental prosopagnosia exhibit severe and lasting difficulties in recognizing faces despite the absence of apparent brain abnormalities. We used voxel-based morphometry to investigate whether developmental prosopagnosics show subtle neuroanatomical differences from controls. An analysis based on segmentation of T1-weighted images from 17 developmental prosopagnosics and 18 matched controls revealed that they had reduced grey matter volume in the right anterior inferior temporal lobe and in the superior temporal sulcus/middle temporal gyrus bilaterally. In addition, a voxel-based morphometry analysis based on the segmentation of magnetization transfer parameter maps showed that developmental prosopagnosics also had reduced grey matter volume in the right middle fusiform gyrus and the inferior temporal gyrus. Multiple regression analyses relating three distinct behavioural component scores, derived from a principal component analysis, to grey matter volume revealed an association between a component related to facial identity and grey matter volume in the left superior temporal sulcus/middle temporal gyrus plus the right middle fusiform gyrus/inferior temporal gyrus. Grey matter volume in the lateral occipital cortex was associated with component scores related to object recognition tasks. Our results demonstrate that developmental prosopagnosics have reduced grey matter volume in several regions known to respond selectively to faces and provide new evidence that integrity of these areas relates to face recognition ability. PMID:19887506

  2. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping.

    PubMed

    Luders, Eileen; Kurth, Florian; Toga, Arthur W; Narr, Katherine L; Gaser, Christian

    2013-01-01

    Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators-perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

  3. Tensor-Based Morphometry Reveals Volumetric Deficits in Moderate=Severe Pediatric Traumatic Brain Injury.

    PubMed

    Dennis, Emily L; Hua, Xue; Villalon-Reina, Julio; Moran, Lisa M; Kernan, Claudia; Babikian, Talin; Mink, Richard; Babbitt, Christopher; Johnson, Jeffrey; Giza, Christopher C; Thompson, Paul M; Asarnow, Robert F

    2016-05-01

    Traumatic brain injury (TBI) can cause widespread and prolonged brain degeneration. TBI can affect cognitive function and brain integrity for many years after injury, often with lasting effects in children, whose brains are still immature. Although TBI varies in how it affects different individuals, image analysis methods such as tensor-based morphometry (TBM) can reveal common areas of brain atrophy on magnetic resonance imaging (MRI), secondary effects of the initial injury, which will differ between subjects. Here we studied 36 pediatric moderate to severe TBI (msTBI) participants in the post-acute phase (1-6 months post-injury) and 18 msTBI participants who returned for their chronic assessment, along with well-matched controls at both time-points. Participants completed a battery of cognitive tests that we used to create a global cognitive performance score. Using TBM, we created three-dimensional (3D) maps of individual and group differences in regional brain volumes. At both the post-acute and chronic time-points, the greatest group differences were expansion of the lateral ventricles and reduction of the lingual gyrus in the TBI group. We found a number of smaller clusters of volume reduction in the cingulate gyrus, thalamus, and fusiform gyrus, and throughout the frontal, temporal, and parietal cortices. Additionally, we found extensive associations between our cognitive performance measure and regional brain volume. Our results indicate a pattern of atrophy still detectable 1-year post-injury, which may partially underlie the cognitive deficits frequently found in TBI. PMID:26393494

  4. Tensor-Based Morphometry Reveals Volumetric Deficits in Moderate=Severe Pediatric Traumatic Brain Injury

    PubMed Central

    Hua, Xue; Villalon-Reina, Julio; Moran, Lisa M.; Kernan, Claudia; Babikian, Talin; Mink, Richard; Babbitt, Christopher; Johnson, Jeffrey; Giza, Christopher C.; Thompson, Paul M.; Asarnow, Robert F.

    2016-01-01

    Abstract Traumatic brain injury (TBI) can cause widespread and prolonged brain degeneration. TBI can affect cognitive function and brain integrity for many years after injury, often with lasting effects in children, whose brains are still immature. Although TBI varies in how it affects different individuals, image analysis methods such as tensor-based morphometry (TBM) can reveal common areas of brain atrophy on magnetic resonance imaging (MRI), secondary effects of the initial injury, which will differ between subjects. Here we studied 36 pediatric moderate to severe TBI (msTBI) participants in the post-acute phase (1–6 months post-injury) and 18 msTBI participants who returned for their chronic assessment, along with well-matched controls at both time-points. Participants completed a battery of cognitive tests that we used to create a global cognitive performance score. Using TBM, we created three-dimensional (3D) maps of individual and group differences in regional brain volumes. At both the post-acute and chronic time-points, the greatest group differences were expansion of the lateral ventricles and reduction of the lingual gyrus in the TBI group. We found a number of smaller clusters of volume reduction in the cingulate gyrus, thalamus, and fusiform gyrus, and throughout the frontal, temporal, and parietal cortices. Additionally, we found extensive associations between our cognitive performance measure and regional brain volume. Our results indicate a pattern of atrophy still detectable 1-year post-injury, which may partially underlie the cognitive deficits frequently found in TBI. PMID:26393494

  5. Tensor-Based Morphometry and Stereology Reveal Brain Pathology in the Complexin1 Knockout Mouse

    PubMed Central

    Kielar, Catherine; Sawiak, Stephen J.; Navarro Negredo, Paloma; Tse, Desmond H. Y.; Morton, A. Jennifer

    2012-01-01

    Complexins (Cplxs) are small, soluble, regulatory proteins that bind reversibly to the SNARE complex and modulate synaptic vesicle release. Cplx1 knockout mice (Cplx1−/−) have the earliest known onset of ataxia seen in a mouse model, although hitherto no histopathology has been described in these mice. Nevertheless, the profound neurological phenotype displayed by Cplx1−/− mutants suggests that significant functional abnormalities must be present in these animals. In this study, MRI was used to automatically detect regions where structural differences were not obvious when using a traditional histological approach. Tensor-based morphometry of Cplx1−/− mouse brains showed selective volume loss from the thalamus and cerebellum. Stereological analysis of Cplx1−/− and Cplx1+/+ mice brain slices confirmed the volume loss in the thalamus as well as loss in some lobules of the cerebellum. Finally, stereology was used to show that there was loss of cerebellar granule cells in Cplx1−/− mice when compared to Cplx1+/+ animals. Our study is the first to describe pathological changes in Cplx1−/− mouse brain. We suggest that the ataxia in Cplx1−/− mice is likely to be due to pathological changes in both cerebellum and thalamus. Reduced levels of Cplx proteins have been reported in brains of patients with neurodegenerative diseases. Therefore, understanding the effects of Cplx depletion in brains from Cplx1−/− mice may also shed light on the mechanisms underlying pathophysiology in disorders in which loss of Cplx1 occurs. PMID:22393426

  6. Reduced cortical thickness, surface area in patients with chronic obstructive pulmonary disease: a surface-based morphometry and neuropsychological study.

    PubMed

    Chen, Ji; Lin, In-Tsang; Zhang, Haiyan; Lin, Jianzhong; Zheng, Shili; Fan, Ming; Zhang, Jiaxing

    2016-06-01

    Neural impairments accompanying chronic obstructive pulmonary disease (COPD) have received growing research attention. Previous neuroimaging studies exclusively used volumetric methods to measure cortical volume as a whole rather than focusing on anatomical and neuropathological distinct indices. Here we decomposed the cortical architecture into cortical thickness (CTh), surface area (SA), and gyrification, for the first time, to provide a more integrative profile of brain damage in COPD. Clinical T1-weighted MRI scans were acquired in 25 stable COPD patients (mean age 69) and 25 age-matched controls. Images were processed using surface-based morphometry to obtain cortical parameters enabling more accurate measurement in deep sulci and localized regional mapping. Demographic, physiological, and cognitive assessments were made and correlated with cortical indices. Compared to controls, COPD patients showed significantly reduced CTh broadly distributed in motor, parietal, and prefrontal cortices, together with more circumscribed SA reduction in dorsomedial prefrontal cortex and Broca's area (cluster-level P < 0.05 corrected). No abnormal gyrification was detected. Decreased CTh in parietofrontal networks strongly correlated with visuospatial construction impairment in COPD patients. Furthermore, thinner dorsolateral prefrontal cortex (DLPFC) best predicted poorer performance (r (2)  = 0.315, P = 0.004), and was associated with lower arterial oxygen saturation. These data indicate that cortical thinning is a key morphologic feature associated with COPD that could be partly attributed to oxygen desaturation and contributes to COPD visual memory and drawing deficits. Surface-based morphometry provides valuable information concerning COPD, and could ultimately help us to characterize the neurodegenerative pattern and to clarify neurologic mechanisms underlying cognitive dysfunction in COPD patients. PMID:25986304

  7. Voxel-based morphometry reveals increased gray matter density in Broca's area in male symphony orchestra musicians.

    PubMed

    Sluming, Vanessa; Barrick, Thomas; Howard, Matthew; Cezayirli, Enis; Mayes, Andrew; Roberts, Neil

    2002-11-01

    Broca's area is a major neuroanatomical substrate for spoken language and various musically relevant abilities, including visuospatial and audiospatial localization. Sight reading is a musician-specific visuospatial analysis task, and spatial ability is known to be amenable to training effects. Musicians have been reported to perform significantly better than nonmusicians on spatial ability tests, which is supported by our findings with the Benton judgement of line orientation (JOL) test (P < 0.001). We hypothesised that use-dependent adaptation would lead to increased gray matter density in Broca's area in musicians. Voxel-based morphometry (VBM) and stereological analyses were applied to high-resolution 3D MR images in male orchestral musicians (n = 26) and sex, handedness, and IQ-matched nonmusicians (n = 26). The wide age range (26 to 66 years) of volunteers permitted a secondary analysis of age-related effects. VBM with small volume correction (SVC) revealed a significant (P = 0.002) region of increased gray matter in Broca's area in the left inferior frontal gyrus in musicians. We observed significant age-related volume reductions in cerebral hemispheres, dorsolateral prefrontal cortex subfields bilaterally and gray matter density in the left inferior frontal gyrus in controls but not musicians; a positive correlation between JOL test score and age in musicians but not controls; a positive correlation between years of playing and the volume of gray matter in a significant region identified by VBM in under-50-year-old musicians. We suggest that orchestral musical performance promotes use-dependent retention, and possibly expansion, of gray matter involving Broca's area and that this provides further support for shared neural substrates underpinning expressive output in music and language. PMID:12414299

  8. Sexual dimorphism of sulcal morphology of the ferret cerebrum revealed by MRI-based sulcal surface morphometry

    PubMed Central

    Sawada, Kazuhiko; Horiuchi-Hirose, Miwa; Saito, Shigeyoshi; Aoki, Ichio

    2015-01-01

    The present study quantitatively assessed sexual dimorphism of cortical convolution and sulcal morphology in young adult ferrets by MRI-based sulcal surface morphometry. Ex vivo T1-weighted (short TR/TE) MRI of the ferret cerebrum was acquired with high spatial resolution at 7-tesla. The degree of cortical convolution, evaluated quantitatively based on 3D MRI data by sulcation index (SI), was significantly greater in males (0.553 ± 0.036) than in females (0.502 ± 0.043) (p < 0.001). The rostrocaudal distribution of the cortical convolution revealed a greater convolution in the frontal region of the cortex in males than in females and by a posterior extension of the convolution in the temporo-parieto-occipital region of males. Although the cerebral width in the frontal region was not different between sexes, the rhinal fissure and rostral region of splenial sulcus were more infolded in males than in females. On the contrary, the cerebral width was greater in males in the temporo-parieto-occipital region, and male-prominent posterior extension of infolding was noted in the lateral sulcus, caudal suprasylvian sulcus, pesudosylvian sulcus, hippocampal sulcus, and the caudal region of splenial sulcus. Notably, the caudal descending region of lateral sulcus was clearly infolded in males, but obscured in females. The present results suggest a region-related sexual dimorphism of the sulcal infolding, which is reflected by local cortical expansion in the ferret cerebrum. In particular, male-favored sulcal infolding with expansion of the temporo-parieto-occipital neocortex may be relevant to the human cerebral cortex regarding visuo-spatial and emotion processing, which are known to differ between sexes. The present results will provide fundamental information assessing sex-related changes in the regional sulcal infolding, when ferrets with experimentally-induced gyrification abnormality will be used as models for male-prevalent or male-earlier-onset neurodevelopmental

  9. Prospective motion correction with volumetric navigators (vNavs) reduces the bias and variance in brain morphometry induced by subject motion.

    PubMed

    Tisdall, M Dylan; Reuter, Martin; Qureshi, Abid; Buckner, Randy L; Fischl, Bruce; van der Kouwe, André J W

    2016-02-15

    Recent work has demonstrated that subject motion produces systematic biases in the metrics computed by widely used morphometry software packages, even when the motion is too small to produce noticeable image artifacts. In the common situation where the control population exhibits different behaviors in the scanner when compared to the experimental population, these systematic measurement biases may produce significant confounds for between-group analyses, leading to erroneous conclusions about group differences. While previous work has shown that prospective motion correction can improve perceived image quality, here we demonstrate that, in healthy subjects performing a variety of directed motions, the use of the volumetric navigator (vNav) prospective motion correction system significantly reduces the motion-induced bias and variance in morphometry. PMID:26654788

  10. Isotropic 3D Nuclear Morphometry of Normal, Fibrocystic and Malignant Breast Epithelial Cells Reveals New Structural Alterations

    PubMed Central

    Nandakumar, Vivek; Kelbauskas, Laimonas; Hernandez, Kathryn F.; Lintecum, Kelly M.; Senechal, Patti; Bussey, Kimberly J.; Davies, Paul C. W.; Johnson, Roger H.; Meldrum, Deirdre R.

    2012-01-01

    Background Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria. Methodology We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure. Principal Findings We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations. Conclusions Our results provide a new perspective on nuclear structure variations

  11. Vertebral Morphometry.

    PubMed

    Chou, Sharon H; Vokes, Tamara

    2016-01-01

    There is as yet no agreement about the criteria by which to arrive at an imaging diagnosis of a vertebral fracture. Because high-grade fractures result in alterations in vertebral shape, 1 possible avenue of diagnosis has been to quantitate changes in vertebral shape. The result has been a variety of methods for the relative and absolute measurements of vertebral dimensions. Such measurements have also lent themselves to automated computed analysis. The number of techniques reflects the absence of any consensus about the best. The semiquantitative technique proposed by Genant has become the most widely used and has served the field well for comparative purposes. Its use in higher grade fractures has been widely endorsed, if some concepts (e.g., short vertebral height-vertebrae) are at variance with lower grades of fracturing. Vertebral morphometry may be the only recourse in high volume epidemiological and interventional studies. PMID:26349790

  12. Larger mid-dorsolateral prefrontal gray matter volume in young binge drinkers revealed by voxel-based morphometry.

    PubMed

    Doallo, Sonia; Cadaveira, Fernando; Corral, Montserrat; Mota, Nayara; López-Caneda, Eduardo; Holguín, Socorro Rodríguez

    2014-01-01

    Binge drinking or heavy episodic drinking is a high prevalent pattern of alcohol consumption among young people in several countries. Despite increasing evidence that binge drinking is associated with impairments in executive aspects of working memory (i.e. self-ordered working memory), processes known to depend on the mid-dorsolateral prefrontal cortex (Brodmann areas 46 and 9), less is known about the impact of binge drinking on prefrontal gray matter integrity. Here, we investigated the effects of binge drinking on gray matter volume of mid- dorsolateral prefrontal cortex in youths. We used voxel-based morphometry on the structural magnetic resonance images of subjects reporting a persistent (at least three years) binge drinking pattern of alcohol use (n = 11; age 22.43 ± 1.03) and control subjects (n = 21; age 22.18 ± 1.08) to measure differences in gray matter volume between both groups. In a region of interest analysis of the mid-dorsolateral prefrontal cortex, after co-varying for age and gender, we observed significantly larger gray matter volume in the left mid-dorsolateral prefrontal cortex (Brodmann areas 46 and 9) in binge drinkers in comparison with control subjects. Furthermore, there was a significant positive correlation between left mid-dorsolateral prefrontal cortex volume and Self-Ordered Pointing Test (SOPT) total errors score in binge drinkers. The left mid-dorsolateral prefrontal cortex volume also correlated with the quantity and speed of alcohol intake. These findings indicate that a repeated exposure to alcohol -that does not meet criteria for alcohol dependence- throughout post-adolescent years and young adulthood is linked with structural anomalies in mid-dorsolateral prefrontal regions critically involved in executive aspects of working memory. PMID:24789323

  13. Voxel-based morphometry analysis reveals frontal brain differences in participants with ADHD and their unaffected siblings

    PubMed Central

    Bralten, Janita; Greven, Corina U.; Franke, Barbara; Mennes, Maarten; Zwiers, Marcel P.; Rommelse, Nanda N.J.; Hartman, Catharina; van der Meer, Dennis; O’Dwyer, Laurence; Oosterlaan, Jaap; Hoekstra, Pieter J.; Heslenfeld, Dirk; Arias-Vasquez, Alejandro; Buitelaar, Jan K.

    2016-01-01

    Background Data on structural brain alterations in patients with attention-deficit/hyperactivity disorder (ADHD) have been inconsistent. Both ADHD and brain volumes have a strong genetic loading, but whether brain alterations in patients with ADHD are familial has been underexplored. We aimed to detect structural brain alterations in adolescents and young adults with ADHD compared with healthy controls. We examined whether these alterations were also found in their unaffected siblings, using a uniquely large sample. Methods We performed voxel-based morphometry analyses on MRI scans of patients with ADHD, their unaffected siblings and typically developing controls. We identified brain areas that differed between participants with ADHD and controls and investigated whether these areas were different in unaffected siblings. Influences of medication use, age, sex and IQ were considered. Results Our sample included 307 patients with ADHD, 169 unaffected siblings and 196 typically developing controls (mean age 17.2 [range 8–30] yr). Compared with controls, participants with ADHD had significantly smaller grey matter volume in 5 clusters located in the precentral gyrus, medial and orbitofrontal cortex, and (para)cingulate cortices. Unaffected siblings showed intermediate volumes significantly different from controls in 4 of these clusters (all except the precentral gyrus). Medication use, age, sex and IQ did not have an undue influence on the results. Limitations Our sample was heterogeneous, most participants with ADHD were taking medication, and the comparison was cross-sectional. Conclusion Brain areas involved in decision making, motivation, cognitive control and motor functioning were smaller in participants with ADHD than in controls. Investigation of unaffected siblings indicated familiality of 4 of the structural brain differences, supporting their potential in molecular genetic analyses in ADHD research. PMID:26679925

  14. Larger Mid-Dorsolateral Prefrontal Gray Matter Volume in Young Binge Drinkers Revealed by Voxel-Based Morphometry

    PubMed Central

    Doallo, Sonia; Cadaveira, Fernando; Corral, Montserrat; Mota, Nayara; López-Caneda, Eduardo; Holguín, Socorro Rodríguez

    2014-01-01

    Binge drinking or heavy episodic drinking is a high prevalent pattern of alcohol consumption among young people in several countries. Despite increasing evidence that binge drinking is associated with impairments in executive aspects of working memory (i.e. self-ordered working memory), processes known to depend on the mid-dorsolateral prefrontal cortex (Brodmann areas 46 and 9), less is known about the impact of binge drinking on prefrontal gray matter integrity. Here, we investigated the effects of binge drinking on gray matter volume of mid- dorsolateral prefrontal cortex in youths. We used voxel-based morphometry on the structural magnetic resonance images of subjects reporting a persistent (at least three years) binge drinking pattern of alcohol use (n = 11; age 22.43±1.03) and control subjects (n = 21; age 22.18±1.08) to measure differences in gray matter volume between both groups. In a region of interest analysis of the mid-dorsolateral prefrontal cortex, after co-varying for age and gender, we observed significantly larger gray matter volume in the left mid-dorsolateral prefrontal cortex (Brodmann areas 46 and 9) in binge drinkers in comparison with control subjects. Furthermore, there was a significant positive correlation between left mid-dorsolateral prefrontal cortex volume and Self-Ordered Pointing Test (SOPT) total errors score in binge drinkers. The left mid-dorsolateral prefrontal cortex volume also correlated with the quantity and speed of alcohol intake. These findings indicate that a repeated exposure to alcohol −that does not meet criteria for alcohol dependence− throughout post-adolescent years and young adulthood is linked with structural anomalies in mid-dorsolateral prefrontal regions critically involved in executive aspects of working memory. PMID:24789323

  15. Quantitative Morphometry of Electrophysiologically Identified CA3b Interneurons Reveals Robust Local Geometry and Distinct Cell Classes

    PubMed Central

    Ascoli, Giorgio A.; Brown, Kerry M.; Calixto, Eduardo; Card, J. Patrick; Galvan, E. J.; Perez-Rosello, T.; Barrionuevo, Germán

    2010-01-01

    The morphological and electrophysiological diversity of inhibitory cells in hippocampal area CA3 may underlie specific computational roles and is not yet fully elucidated. In particular, interneurons with somata in strata radiatum (R) and lacunosum-moleculare (L-M) receive converging stimulation from the dentate gyrus and entorhinal cortex as well as within CA3. Although these cells express different forms of synaptic plasticity, their axonal trees and connectivity are still largely unknown. We investigated the branching and spatial patterns, plus the membrane and synaptic properties, of rat CA3b R and L-M interneurons digitally reconstructed after intracellular labeling. We found considerable variability within but no difference between the two layers, and no correlation between morphological and biophysical properties. Nevertheless, two cell types were identified based on the number of dendritic bifurcations, with significantly different anatomical and electrophysiological features. Axons generally branched an order of magnitude more than dendrites. However, interneurons on both sides of the R/L-M boundary revealed surprisingly modular axo-dendritic arborizations with consistently uniform local branch geometry. Both axons and dendrites followed a lamellar organization, and axons displayed a spatial preference towards the fissure. Moreover, only a small fraction of the axonal arbor extended to the outer portion of the invaded volume, and tended to return towards the proximal region. In contrast, dendritic trees demonstrated more limited but isotropic volume occupancy. These results suggest a role of predominantly local feedforward and lateral inhibitory control for both R and L-M interneurons. Such role may be essential to balance the extensive recurrent excitation of area CA3 underlying hippocampal autoassociative memory function. PMID:19496174

  16. Patterns of Quaternary uplift of the Corinth rift southern border (N Peloponnese, Greece) revealed by fluvial landscape morphometry

    NASA Astrophysics Data System (ADS)

    Demoulin, A.; Beckers, A.; Hubert-Ferrari, A.

    2015-10-01

    The Rift of Corinth is a world-class example of young active rifting and, as such, is an ideal natural laboratory of continental extension. However, though much investigated for two decades, several aspects of the mechanisms at work are still poorly understood. The aim of this paper is a detailed morphometric study of the fluvial landscape response to the tectonic uplift of the rift southern shoulder in order to reconstruct the rift's Quaternary evolution, with special attention to timing, location, and intensity of uplift episodes. Based on the use of a large set of catchment and long profile metrics complemented by the new R/SR integrative approach of the regional drainage network, we identified three distinct episodes of uplift of the northern Peloponnese coastal tract, of which the intermediate one, dated around 0.35-0.4 Ma, is only recorded in the topography of the central part of the rift shoulder, and the youngest one appears to have propagated from east to west over the last 10-20 ka. While net uplift remained minimum in the eastern part of the study area during the whole Quaternary, it shows a clear maximum in the central part of the rift shoulder since 0.4 Ma and an eastward shift of this maximum in recent times. Maximum uplift rates calculated from the morphometric data are of > 1.05 and 2-5 mm year- 1 for, the mid-Middle Pleistocene and Holocene uplift episodes, respectively. The morphometric evidence reveals an onshore uplift history remarkably consistent with the rift evolution reconstructed from other data sets. In the long term, it shows a stable pattern of maximum activity in the central part of the rift, confirming previous conclusions about the absence of rift propagation. In the short term, it sheds light on a possible E-W migration of the zone of recent uplift, suggesting that in the near future fault activity and seismic hazard might concentrate in the Heliki-Aegion area, at the western tip of this uplift wave.

  17. Dissociations in Cortical Morphometry in Youth with Down Syndrome: Evidence for Reduced Surface Area but Increased Thickness.

    PubMed

    Lee, Nancy Raitano; Adeyemi, Elizabeth I; Lin, Amy; Clasen, Liv S; Lalonde, François M; Condon, Ellen; Driver, David I; Shaw, Philip; Gogtay, Nitin; Raznahan, Armin; Giedd, Jay N

    2016-07-01

    Detailed descriptions of cortical anatomy in youth with Down syndrome (DS), the most common genetic cause of intellectual disability (ID), are scant. Thus, the current study examined deviations in cortical thickness (CT) and surface area (SA), at high spatial resolution, in youth with DS, to identify focal differences relative to typically developing (TD) youth. Participants included 31 youth with DS and 45 age- and sex-matched TD controls (mean age ∼16 years; range = 5-24 years). All participants completed T1-weighted ASSET-calibrated magnetization prepared rapid gradient echo scans on a 3-T magnetic resonance imaging scanner. Replicating prior investigations, cortical volume was reduced in DS compared with controls. However, a novel dissociation for SA and CT was found-namely, SA was reduced (predominantly in frontal and temporal regions) while CT was increased (notably in several regions thought to belong to the default mode network; DMN). These findings suggest that reductions in SA rather than CT are driving the cortical volume reductions reported in prior investigations of DS. Moreover, given the link between DMN functionality and Alzheimer's symptomatology in chromosomally typical populations, future DS studies may benefit from focusing on the cortex in DMN regions, as such investigations may provide clues to the precocious onset of Alzheimer's disease in this at-risk group. PMID:26088974

  18. Pupillometry reveals reduced unconscious emotional reactivity in autism.

    PubMed

    Nuske, Heather J; Vivanti, Giacomo; Hudry, Kristelle; Dissanayake, Cheryl

    2014-09-01

    Recent theoretical conceptualisations have suggested that emotion processing impairments in autism stem from disruption to the sub-cortical, rapid emotion-processing system. We argue that a clear way to ascertain whether this system is affected in autism is by measuring unconscious emotional reactivity. Using backwards masking, we presented fearful expressions non-consciously (subliminally) as well as consciously (supraliminally), and measured pupillary responses as an index of emotional reactivity in 19 children with autism and 19 typically developing children, aged 2-5 years. The pupillary responses of the children with autism revealed reduced unconscious emotional reactivity, with no group differences on consciously presented emotion. Together, these results indicate a hyporesponsiveness to non-consciously presented emotion suggesting a fundamental difference in emotion processing in autism, which requires consciousness and more time. PMID:25017502

  19. Atlas warping for brain morphometry

    NASA Astrophysics Data System (ADS)

    Machado, Alexei M. C.; Gee, James C.

    1998-06-01

    In this work, we describe an automated approach to morphometry based on spatial normalizations of the data, and demonstrate its application to the analysis of gender differences in the human corpus callosum. The purpose is to describe a population by a reduced and representative set of variables, from which a prior model can be constructed. Our approach is rooted in the assumption that individual anatomies can be considered as quantitative variations on a common underlying qualitative plane. We can therefore imagine that a given individual's anatomy is a warped version of some referential anatomy, also known as an atlas. The spatial warps which transform a labeled atlas into anatomic alignment with a population yield immediate knowledge about organ size and shape in the group. Furthermore, variation within the set of spatial warps is directly related to the anatomic variation among the subjects. Specifically, the shape statistics--mean and variance of the mappings--for the population can be calculated in a special basis, and an eigendecomposition of the variance performed to identify the most significant modes of shape variation. The results obtained with the corpus callosum study confirm the existence of substantial anatomical differences between males and females, as reported in previous experimental work.

  20. Object-based morphometry of the cerebral cortex.

    PubMed

    Mangin, J F; Rivière, D; Cachia, A; Duchesnay, E; Cointepas, Y; Papadopoulos-Orfanos, D; Collins, D L; Evans, A C; Régis, J

    2004-08-01

    Most of the approaches dedicated to automatic morphometry rely on a point-by-point strategy based on warping each brain toward a reference coordinate system. In this paper, we describe an alternative object-based strategy dedicated to the cortex. This strategy relies on an artificial neuroanatomist performing automatic recognition of the main cortical sulci and parcellation of the cortical surface into gyral patches. A set of shape descriptors, which can be compared across subjects, is then attached to the sulcus and gyrus related objects segmented by this process. The framework is used to perform a study of 142 brains of the International Consortium for Brain Mapping (ICBM) database. This study reveals some correlates of handedness on the size of the sulci located in motor areas, which was not detected previously using standard voxel based morphometry. PMID:15338731

  1. Object-based strategy for morphometry of the cerebral cortex.

    PubMed

    Mangin, J F; Rivière, D; Cachia, A; Papadopoulos-Orfanos, D; Collins, D L; Evans, A C; Régis, J

    2003-07-01

    Most of the approaches dedicated to automatic morphometry rely on a point-by-point strategy based on warping each brain towards a reference coordinate system. In this paper, we describe an alternative object-based strategy dedicated to the cortex. This strategy relies on an artificial neuroanatomist performing automatic recognition of the main cortical sulci and parcellation of the cortical surface into gyral patches. A set of shape descriptors, which can be compared across subjects, is then attached to the sulcus and gyrus related objects segmented by this process. The framework is used to perform a study of 142 brains of the ICBM database. This study reveals some correlates of handedness on the size of the sulci located in motor areas, which seem to be beyond the scope of the standard voxel based morphometry. PMID:15344455

  2. Cortical morphometry in frontoparietal and default mode networks in math-gifted adolescents.

    PubMed

    Navas-Sánchez, Francisco J; Carmona, Susana; Alemán-Gómez, Yasser; Sánchez-González, Javier; Guzmán-de-Villoria, Juan; Franco, Carolina; Robles, Olalla; Arango, Celso; Desco, Manuel

    2016-05-01

    Math-gifted subjects are characterized by above-age performance in intelligence tests, exceptional creativity, and high task commitment. Neuroimaging studies reveal enhanced functional brain organization and white matter microstructure in the frontoparietal executive network of math-gifted individuals. However, the cortical morphometry of these subjects remains largely unknown. The main goal of this study was to compare the cortical morphometry of math-gifted adolescents with that of an age- and IQ-matched control group. We used surface-based methods to perform a vertex-wise analysis of cortical thickness and surface area. Our results show that math-gifted adolescents present a thinner cortex and a larger surface area in key regions of the frontoparietal and default mode networks, which are involved in executive processing and creative thinking, respectively. The combination of reduced cortical thickness and larger surface area suggests above-age neural maturation of these networks in math-gifted individuals. Hum Brain Mapp 37:1893-1902, 2016. © 2016 Wiley Periodicals, Inc. PMID:26917433

  3. Computer assisted sperm morphometry in mammals: a review.

    PubMed

    Yániz, J L; Soler, C; Santolaria, P

    2015-05-01

    Computer-assisted sperm morphometry analysis (CASMA or ASMA) systems were developed to reduce the subjectivity of sperm morphology assessement. This review focuses on a complete description of the CASMA technique, including recent developments, factors of variation, results in the different species and possible applications. Techniques to study sperm morphometry include light microscopy, phase-contrast microscopy and, more recently, fluorescence microscopy. Most published studies on sperm morphometry have been centered on the whole sperm heads, although some of them also measured other parts of the sperm structure, such as the nucleus, acrosome, midpiece or flagellum. The independent study of sperm components may be more informative than the traditional assessment of the whole sperm head. Morphometric data provided by the CASMA system may be analyzed using classical statistics although, given the heterogeneity of spermatozoa in the ejaculates, the study of sperm subpopulations using clustering procedures may be more informative. Morphometric results may vary depending on factors intrinsic and extrinsic to the semen donor. Intrinsic factors may include, among others, genetic factors, age and sexual maturity. Extrinsic factors may include those related to the influence of environment on the donor, as well as those related with sample processing and the morphometric analysis itself. Once standardized, this technique may provide relevant information in studies focused on evolutionary biology, sperm formation, sperm quality assessment, including prediction of the potential fertility, semen cryopreservation, or the effect of reprotoxicants. PMID:25802026

  4. REVEAL: An Extensible Reduced Order Model Builder for Simulation and Modeling

    SciTech Connect

    Agarwal, Khushbu; Sharma, Poorva; Ma, Jinliang; Lo, Chaomei; Gorton, Ian; Liu, Yan

    2013-04-30

    Many science domains need to build computationally efficient and accurate representations of high fidelity, computationally expensive simulations. These computationally efficient versions are known as reduced-order models. This paper presents the design and implementation of a novel reduced-order model (ROM) builder, the REVEAL toolset. This toolset generates ROMs based on science- and engineering-domain specific simulations executed on high performance computing (HPC) platforms. The toolset encompasses a range of sampling and regression methods that can be used to generate a ROM, automatically quantifies the ROM accuracy, and provides support for an iterative approach to improve ROM accuracy. REVEAL is designed to be extensible in order to utilize the core functionality with any simulator that has published input and output formats. It also defines programmatic interfaces to include new sampling and regression techniques so that users can ‘mix and match’ mathematical techniques to best suit the characteristics of their model. In this paper, we describe the architecture of REVEAL and demonstrate its usage with a computational fluid dynamics model used in carbon capture.

  5. Comparative Minicolumnar Morphometry of Three Distinguished Scientists

    ERIC Educational Resources Information Center

    Casanova, Manuel F.; Switala, Andrew E.; Trippe, Juan; Fitzgerald, Michael

    2007-01-01

    It has been suggested that the cell minicolumn is the smallest module capable of information processing within the brain. In this case series, photomicrographs of six regions of interests (Brodmann areas 4, 9, 17, 21, 22, and 40) were analyzed by computerized image analysis for minicolumnar morphometry in the brains of three distinguished…

  6. The effect of selected staining techniques on bull sperm morphometry.

    PubMed

    Banaszewska, Dorota; Andraszek, Katarzyna; Czubaszek, Magdalena; Biesiada-Drzazga, Barbara

    2015-08-01

    Sperm morphometry has some value as an indicator of reproductive capacity in males. In laboratory practice a variety of slide-staining methods are used during morphological evaluation of semen to predict male fertility. The aim of this study was to determine the effect of staining of semen using four different techniques on the morphometry of the bull sperm cell. The material for the study consisted of semen collected from test bulls of the Black-and-White variety of Holstein-Friesians. The results obtained in the study indicate differences in the dimensions of bull sperm heads when different slide staining techniques were used. The most similar results for sperm head dimensions were obtained in the case of SpermBlue(®) and eosin+gentian violet complex, although statistically significant differences were found between all the staining techniques. Extreme values were noted for the other staining techniques - lowest for the Papanicolaou and highest for silver nitrate, which may indicate more interference in the cell by the reagents used in the staining process. However, silver nitrate staining was best at identifying the structures of the sperm cell. Hence it is difficult to determine which of the staining methods most faithfully reveals the dimensions and shape of the bull sperm. PMID:26149220

  7. Mapping abnormal subcortical brain morphometry in an elderly HIV + cohort

    PubMed Central

    Wade, Benjamin S.C.; Valcour, Victor G.; Wendelken-Riegelhaupt, Lauren; Esmaeili-Firidouni, Pardis; Joshi, Shantanu H.; Gutman, Boris A.; Thompson, Paul M.

    2015-01-01

    Over 50% of HIV + individuals exhibit neurocognitive impairment and subcortical atrophy, but the profile of brain abnormalities associated with HIV is still poorly understood. Using surface-based shape analyses, we mapped the 3D profile of subcortical morphometry in 63 elderly HIV + participants and 31 uninfected controls. The thalamus, caudate, putamen, pallidum, hippocampus, amygdala, brainstem, accumbens, callosum and ventricles were segmented from high-resolution MRIs. To investigate shape-based morphometry, we analyzed the Jacobian determinant (JD) and radial distances (RD) defined on each region's surfaces. We also investigated effects of nadir CD4 + T-cell counts, viral load, time since diagnosis (TSD) and cognition on subcortical morphology. Lastly, we explored whether HIV + participants were distinguishable from unaffected controls in a machine learning context. All shape and volume features were included in a random forest (RF) model. The model was validated with 2-fold cross-validation. Volumes of HIV + participants' bilateral thalamus, left pallidum, left putamen and callosum were significantly reduced while ventricular spaces were enlarged. Significant shape variation was associated with HIV status, TSD and the Wechsler adult intelligence scale. HIV + people had diffuse atrophy, particularly in the caudate, putamen, hippocampus and thalamus. Unexpectedly, extended TSD was associated with increased thickness of the anterior right pallidum. In the classification of HIV + participants vs. controls, our RF model attained an area under the curve of 72%. PMID:26640768

  8. Voxel-based morphometry and epilepsy.

    PubMed

    Yasuda, Clarissa Lin; Betting, Luiz Eduardo; Cendes, Fernando

    2010-06-01

    Voxel-based morphometry is an automated technique for MRI analyses, developed to study differences in brain morphology and frequently used to study patients with diverse disorders. In epilepsy, it has been used to investigate areas with reduction or increase of gray and white matter, in different syndromes (i.e., temporal lobe epilepsy, focal cortical dysplasia and generalized epilepsies). In temporal lobe epilepsy, voxel-based morphometry showed gray/white matter atrophy extending beyond the atrophic hippocampus. These widespread abnormalities have been associated with seizure frequency, epilepsy duration, incidence of precipitating factors, cognitive dysfunction and surgical outcome. In generalized epilepsies, gray matter abnormalities were identified mainly in the thalamus and frontal cortex, reinforcing the role of the thalamocortical network in the mechanisms of generalized seizures. PMID:20518612

  9. Surface Polysaccharide Mutants Reveal that Absence of O Antigen Reduces Biofilm Formation of Actinobacillus pleuropneumoniae

    PubMed Central

    Hathroubi, S.; Hancock, M. A.; Langford, P. R.; Tremblay, Y. D. N.; Labrie, J.

    2015-01-01

    Actinobacillus pleuropneumoniae is a Gram-negative bacterium belonging to the Pasteurellaceae family and the causative agent of porcine pleuropneumonia, a highly contagious lung disease causing important economic losses. Surface polysaccharides, including lipopolysaccharides (LPS) and capsular polysaccharides (CPS), are implicated in the adhesion and virulence of A. pleuropneumoniae, but their role in biofilm formation is still unclear. In this study, we investigated the requirement for these surface polysaccharides in biofilm formation by A. pleuropneumoniae serotype 1. Well-characterized mutants were used: an O-antigen LPS mutant, a truncated core LPS mutant with an intact O antigen, a capsule mutant, and a poly-N-acetylglucosamine (PGA) mutant. We compared the amount of biofilm produced by the parental strain and the isogenic mutants using static and dynamic systems. Compared to the findings for the biofilm of the parental or other strains, the biofilm of the O antigen and the PGA mutants was dramatically reduced, and it had less cell-associated PGA. Real-time PCR analyses revealed a significant reduction in the level of pgaA, cpxR, and cpxA mRNA in the biofilm cells of the O-antigen mutant compared to that in the biofilm cells of the parental strain. Specific binding between PGA and LPS was consistently detected by surface plasmon resonance, but the lack of O antigen did not abolish these interactions. In conclusion, the absence of the O antigen reduces the ability of A. pleuropneumoniae to form a biofilm, and this is associated with the reduced expression and production of PGA. PMID:26483403

  10. Studying ventricular abnormalities in mild cognitive impairment with hyperbolic Ricci flow and tensor-based morphometry.

    PubMed

    Shi, Jie; Stonnington, Cynthia M; Thompson, Paul M; Chen, Kewei; Gutman, Boris; Reschke, Cole; Baxter, Leslie C; Reiman, Eric M; Caselli, Richard J; Wang, Yalin

    2015-01-01

    Mild Cognitive Impairment (MCI) is a transitional stage between normal aging and dementia and people with MCI are at high risk of progression to dementia. MCI is attracting increasing attention, as it offers an opportunity to target the disease process during an early symptomatic stage. Structural magnetic resonance imaging (MRI) measures have been the mainstay of Alzheimer's disease (AD) imaging research, however, ventricular morphometry analysis remains challenging because of its complicated topological structure. Here we describe a novel ventricular morphometry system based on the hyperbolic Ricci flow method and tensor-based morphometry (TBM) statistics. Unlike prior ventricular surface parameterization methods, hyperbolic conformal parameterization is angle-preserving and does not have any singularities. Our system generates a one-to-one diffeomorphic mapping between ventricular surfaces with consistent boundary matching conditions. The TBM statistics encode a great deal of surface deformation information that could be inaccessible or overlooked by other methods. We applied our system to the baseline MRI scans of a set of MCI subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI: 71 MCI converters vs. 62 MCI stable). Although the combined ventricular area and volume features did not differ between the two groups, our fine-grained surface analysis revealed significant differences in the ventricular regions close to the temporal lobe and posterior cingulate, structures that are affected early in AD. Significant correlations were also detected between ventricular morphometry, neuropsychological measures, and a previously described imaging index based on fluorodeoxyglucose positron emission tomography (FDG-PET) scans. This novel ventricular morphometry method may offer a new and more sensitive approach to study preclinical and early symptomatic stage AD. PMID:25285374

  11. STUDYING VENTRICULAR ABNORMALITIES IN MILD COGNITIVE IMPAIRMENT WITH HYPERBOLIC RICCI FLOW AND TENSOR-BASED MORPHOMETRY

    PubMed Central

    Shi, Jie; Stonnington, Cynthia M.; Thompson, Paul M.; Chen, Kewei; Gutman, Boris; Reschke, Cole; Baxter, Leslie C.; Reiman, Eric M.; Caselli, Richard J.; Wang, Yalin

    2014-01-01

    Mild Cognitive Impairment (MCI) is a transitional stage between normal aging and dementia and people with MCI are at high risk of progression to dementia. MCI is attracting increasing attention, as it offers an opportunity to target the disease process during an early symptomatic stage. Structural magnetic resonance imaging (MRI) measures have been the mainstay of Alzheimer’s disease (AD) imaging research, however, ventricular morphometry analysis remains challenging because of its complicated topological structure. Here we describe a novel ventricular morphometry system based on the hyperbolic Ricci flow method and tensor-based morphometry (TBM) statistics. Unlike prior ventricular surface parameterization methods, hyperbolic conformal parameterization is angle-preserving and does not have any singularities. Our system generates a one-to-one diffeomorphic mapping between ventricular surfaces with consistent boundary matching conditions. The TBM statistics encode a great deal of surface deformation information that could be inaccessible or overlooked by other methods. We applied our system to the baseline MRI scans of a set of MCI subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI: 71 MCI converters vs. 62 MCI stable). Although the combined ventricular area and volume features did not differ between the two groups, our fine-grained surface analysis revealed significant differences in the ventricular regions close to the temporal lobe and posterior cingulate, structures that are affected early in AD. Significant correlations were also detected between ventricular morphometry, neuropsychological measures, and a previously described imaging index based on fluorodeoxyglucose positron emission tomography (FDG-PET) scans. This novel ventricular morphometry method may offer a new and more sensitive approach to study preclinical and early symptomatic stage AD. PMID:25285374

  12. Declining streamflows reveal nonstationary orographic precipitation enhancement driven by reduced westerly flows

    NASA Astrophysics Data System (ADS)

    Luce, Charles; Abatzoglou, John; Holden, Zachary

    2016-04-01

    Although orographic enhancement of precipitation lends mountains an important role in water resources, they are dramatically undersampled by long-term precipitation gages. This has led to the widespread practice of extrapolating trends in low-elevation precipitation gage networks to high elevations via simple climatological precipitation ratios developed from isohyetal maps. An implicit assumption in such a process is non-stationarity in orographic precipitation enhancement, an assumption that can lead to large errors in trend detection and attribution of climate change effects. We show an example from the Northwestern United States where streamflows from mountain watersheds show substantial declines over the last 60 years, even while long-term precipitation gage networks in the region show no trend. We demonstrate that these observed streamflow declines are driven by previously unexplored differential trends in precipitation. November to March westerly winds are strongly correlated with high-elevation precipitation but weakly correlated with low-elevation precipitation. Decreases in winter westerlies across the region from 1950 to 2012 are hypothesized to have reduced orographic precipitation enhancement, yielding differential trends in precipitation across elevations leading to the apparent paradox. Climate projections show continued weakening meridional pressure gradients and westerly flow across the region under greenhouse forcing, highlighting an additional stressor that is relevant for climate change impacts on water resources. This study also reveals the potential of wind speed data from circulation reanalysis products to better inform historical precipitation reconstructions.

  13. Revealing, Reducing, and Representing Uncertainties in New Hydrologic Projections for Climate-changed Futures

    NASA Astrophysics Data System (ADS)

    Arnold, Jeffrey; Clark, Martyn; Gutmann, Ethan; Wood, Andy; Nijssen, Bart; Rasmussen, Roy

    2016-04-01

    The United States Army Corps of Engineers (USACE) has had primary responsibility for multi-purpose water resource operations on most of the major river systems in the U.S. for more than 200 years. In that time, the USACE projects and programs making up those operations have proved mostly robust against the range of natural climate variability encountered over their operating life spans. However, in some watersheds and for some variables, climate change now is known to be shifting the hydroclimatic baseline around which that natural variability occurs and changing the range of that variability as well. This makes historical stationarity an inappropriate basis for assessing continued project operations under climate-changed futures. That means new hydroclimatic projections are required at multiple scales to inform decisions about specific threats and impacts, and for possible adaptation responses to limit water-resource vulnerabilities and enhance operational resilience. However, projections of possible future hydroclimatologies have myriad complex uncertainties that require explicit guidance for interpreting and using them to inform those decisions about climate vulnerabilities and resilience. Moreover, many of these uncertainties overlap and interact. Recent work, for example, has shown the importance of assessing the uncertainties from multiple sources including: global model structure [Meehl et al., 2005; Knutti and Sedlacek, 2013]; internal climate variability [Deser et al., 2012; Kay et al., 2014]; climate downscaling methods [Gutmann et al., 2012; Mearns et al., 2013]; and hydrologic models [Addor et al., 2014; Vano et al., 2014; Mendoza et al., 2015]. Revealing, reducing, and representing these uncertainties is essential for defining the plausible quantitative climate change narratives required to inform water-resource decision-making. And to be useful, such quantitative narratives, or storylines, of climate change threats and hydrologic impacts must sample

  14. Blood-Gene Expression Reveals Reduced Circadian Rhythmicity in Individuals Resistant to Sleep Deprivation

    PubMed Central

    Arnardottir, Erna S.; Nikonova, Elena V.; Shockley, Keith R.; Podtelezhnikov, Alexei A.; Anafi, Ron C.; Tanis, Keith Q.; Maislin, Greg; Stone, David J.; Renger, John J.; Winrow, Christopher J.; Pack, Allan I.

    2014-01-01

    Study Objectives: To address whether changes in gene expression in blood cells with sleep loss are different in individuals resistant and sensitive to sleep deprivation. Design: Blood draws every 4 h during a 3-day study: 24-h normal baseline, 38 h of continuous wakefulness and subsequent recovery sleep, for a total of 19 time-points per subject, with every 2-h psychomotor vigilance task (PVT) assessment when awake. Setting: Sleep laboratory. Participants: Fourteen subjects who were previously identified as behaviorally resistant (n = 7) or sensitive (n = 7) to sleep deprivation by PVT. Intervention: Thirty-eight hours of continuous wakefulness. Measurements and Results: We found 4,481 unique genes with a significant 24-h diurnal rhythm during a normal sleep-wake cycle in blood (false discovery rate [FDR] < 5%). Biological pathways were enriched for biosynthetic processes during sleep. After accounting for circadian effects, two genes (SREBF1 and CPT1A, both involved in lipid metabolism) exhibited small, but significant, linear changes in expression with the duration of sleep deprivation (FDR < 5%). The main change with sleep deprivation was a reduction in the amplitude of the diurnal rhythm of expression of normally cycling probe sets. This reduction was noticeably higher in behaviorally resistant subjects than sensitive subjects, at any given P value. Furthermore, blood cell type enrichment analysis showed that the expression pattern difference between sensitive and resistant subjects is mainly found in cells of myeloid origin, such as monocytes. Conclusion: Individual differences in behavioral effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity. Citation: Arnardottir ES, Nikonova EV, Shockley KR, Podtelezhnikov AA, Anafi RC, Tanis KQ, Maislin G, Stone DJ, Renger JJ, Winrow CJ, Pack AI. Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to

  15. Brain Morphometry using MRI in Schizophrenia Patients

    NASA Astrophysics Data System (ADS)

    Abanshina, I.; Pirogov, Yu.; Kupriyanov, D.; Orlova, V.

    2010-01-01

    Schizophrenia has been the focus of intense neuroimaging research. Although its fundamental pathobiology remains elusive, neuroimaging studies provide evidence of abnormalities of cerebral structure and function in patients with schizophrenia. We used morphometry as a quantitative method for estimation of volume of brain structures. Seventy eight right-handed subjects aged 18-45 years were exposed to MRI-examination. Patients were divided into 3 groups: patients with schizophrenia, their relatives and healthy controls. The volumes of interested structures (caudate nucleus, putamen, ventricles, frontal and temporal lobe) were measured using T2-weighted MR-images. Correlations between structural differences and functional deficit were evaluated.

  16. Neuroanatomical Correlates of Developmental Dyscalculia: Combined Evidence from Morphometry and Tractography

    PubMed Central

    Rykhlevskaia, Elena; Uddin, Lucina Q.; Kondos, Leeza; Menon, Vinod

    2009-01-01

    Poor mathematical abilities adversely affect academic and career opportunities. The neuroanatomical basis of developmental dyscalculia (DD), a specific learning deficit with prevalence rates exceeding 5%, is poorly understood. We used structural MRI and diffusion tensor imaging (DTI) to examine macro- and micro-structural impairments in 7- to 9-year-old children with DD, compared to a group of typically developing (TD) children matched on age, gender, intelligence, reading abilities and working memory capacity. Voxel-based morphometry (VBM) revealed reduced grey matter (GM) bilaterally in superior parietal lobule, intra-parietal sulcus, fusiform gyrus, parahippocampal gyrus and right anterior temporal cortex in children with DD. VBM analysis also showed reduced white matter (WM) volume in right temporal-parietal cortex. DTI revealed reduced fractional anisotropy (FA) in this WM region, pointing to significant right hemisphere micro-structural impairments. Furthermore, FA in this region was correlated with numerical operations but not verbal mathematical reasoning or word reading. Atlas-based tract mapping identified the inferior longitudinal fasciculus, inferior fronto-occipital fasciculus and caudal forceps major as key pathways impaired in DD. DTI tractography suggests that long-range WM projection fibers linking the right fusiform gyrus with temporal-parietal WM are a specific source of vulnerability in DD. Network and classification analysis suggest that DD in children may be characterized by multiple dysfunctional circuits arising from a core WM deficit. Our findings link GM and WM abnormalities in children with DD and they point to macro- and micro-structural abnormalities in right hemisphere temporal-parietal WM, and pathways associated with it, as key neuroanatomical correlates of DD. PMID:20046827

  17. Oligodendrocyte Morphometry and Expression of Myelin – Related mRNA in Ventral Prefrontal White Matter in Major Depressive Disorder

    PubMed Central

    Rajkowska, Grazyna; Mahajan, Gouri; Maciag, Dorota; Sathyanesan, Monica; Iyo, Abiye H.; Moulana, Mohadetheh; Kyle, Patrick B.; Woolverton, William L.; Miguel-Hidalgo, Jose Javier; Stockmeier, Craig A.; Newton, Samuel S.

    2015-01-01

    White matter disturbance in the ventral prefrontal cortex (vPFC) in major depressive disorder (MDD) has been noted with diffusion tensor imaging (DTI). However, the cellular and molecular pathology of prefrontal white matter in MDD and potential influence of antidepressant medications is not fully understood. Oligodendrocyte morphometry and myelin-related mRNA and protein expression was examined in the white matter of the vPFC in MDD. Sections of deep and gyral white matter from the vPFC were collected from 20 subjects with MDD and 16 control subjects. Density and size of CNPase-immunoreactive (−IR) oligodendrocytes were estimated using 3-dimensional cell counting. While neither density nor soma size of oligodendrocytes was significantly affected in deep white matter, soma size was significantly decreased in the gyral white matter in MDD. In rhesus monkeys treated chronically with fluoxetine there was no significant effect on oligodendrocyte morphometry. Using quantitative RTPCR to measure oligodendrocyte-related mRNA for CNPase, PLP1, MBP, MOG, MOBP, Olig1 and Olig2, in MDD there was a significantly reduced expression of PLP1 mRNA (which positively correlated with smaller sizes) and increased expression of mRNA for CNPase, OLIG1 and MOG. The expression of CNPase protein was significantly decreased in MDD. Altered expression of four myelin genes and CNPase protein suggests a mechanism for the degeneration of cortical axons and dysfunctional maturation of oligodendrocytes in MDD. The change in oligodendrocyte morphology in gyral white matter may parallel altered axonal integrity as revealed by DTI. PMID:25930075

  18. Reproducibility in Nerve Morphometry: Comparison between Methods and among Observers

    PubMed Central

    Bilego Neto, Antônio Paulo da Costa; Silveira, Fernando Braga Cassiano; Rodrigues da Silva, Greice Anne; Sanada, Luciana Sayuri; Fazan, Valéria Paula Sassoli

    2013-01-01

    We investigated the reproducibility of a semiautomated method (computerized with manual intervention) for nerve morphometry (counting and measuring myelinated fibers) between three observers with different levels of expertise and experience with the method. Comparisons between automatic (fully computerized) and semiautomated morphometric methods performed by the same computer software using the same nerve images were also performed. Sural nerves of normal adult rats were used. Automatic and semiautomated morphometry of the myelinated fibers were made through the computer software KS-400. Semiautomated morphometry was conducted by three independent observers on the same images, using the semiautomated method. Automatic morphometry overestimated the myelin sheath area, thus overestimating the myelinated fiber size and underestimating the axon size. Fiber distributions overestimation was of 0.5 μm. For the semiautomated morphometry, no differences were found between observers for myelinated fiber and axon size distributions. Overestimation of the myelin sheath size of normal fibers by the fully automatic method might have an impact when morphometry is used for diagnostic purposes. We suggest that not only semiautomated morphometry results can be compared between different centers in clinical trials but it can also be performed by more than one investigator in one single experiment, being a reliable and reproducible method. PMID:23841086

  19. Hemin-functionalized reduced graphene oxide nanosheets reveal peroxynitrite reduction and isomerization activity.

    PubMed

    Vernekar, Amit A; Mugesh, Govindasamy

    2012-11-19

    Facile and efficient reduction of graphene oxide (GO) and novel applications of the reduced graphene oxide (RGO) based materials are of current interest. Herein, we report a novel and facile method for the reduction of GO by using a biocompatible reducing agent dithiothreitol (DTT). Stabilization of DTT by the formation of a six-membered ring with internal disulfide linkage upon oxidation is responsible for the reduction of GO. The reduced graphene oxide is characterized by several spectroscopic and microscopic techniques. Dispersion of RGO in DMF remained stable for several weeks suggesting that the RGO obtained by DTT-mediated reduction is hydrophobic in nature. This method can be considered for large scale production of good quality RGO. Treatment of RGO with hemin afforded a functional hemin-reduced graphene oxide (H-RGO) hybrid material that exhibited remarkable protective effects against the potentially harmful peroxynitrite (PN). A detailed inhibition study on PN-mediated oxidation and nitration reactions indicate that the interaction between hemin and RGO results in a synergistic effect, which leads to an efficient reduction of PN to nitrate. The RGO also catalyzes the isomerization of PN to nitrate as the RGO layers facilitate the rapid recombination of (·)NO(2) with Fe(IV)=O species. In the presence of reducing agents such as ascorbic acid, the Fe(IV)=O species can be reduced to Fe(III), thus helping to maintain the PN reductase cycle. PMID:23042238

  20. Crater studies: Part A: lunar crater morphometry

    USGS Publications Warehouse

    Pike, Richard J.

    1973-01-01

    Morphometry, the quantitative study of shape, complements the visual observation and photointerpretation in analyzing the most outstanding landforms of the Moon, its craters (refs. 32-1 and 32-2). All three of these interpretative tools, which were developed throughout the long history of telescopic lunar study preceding the Apollo Program, will continue to be applicable to crater analysis until detailed field work becomes possible. Although no large (>17.5 km diameter) craters were examined in situ on any of the Apollo landings, the photographs acquired from the command modules will markedly strengthen results of less direct investigations of the craters. For morphometry, the most useful materials are the orbital metric and panoramic photographs from the final three Apollo missions. These photographs permit preparation of contour maps, topographic profiles, and other numerical data that accurately portray for the first time the surface geometry of lunar craters of all sizes. Interpretations of craters no longer need be compromised by inadequate topographic data. In the pre-Apollo era, hypotheses for the genesis of lunar craters usually were constructed without any numerical descriptive data. Such speculations will have little credibility unless supported by accurate, quantitative data, especially those generated from Apollo orbital photographs. This paper presents a general study of the surface geometry of 25 far-side craters and a more detailed study of rim-crest evenness for 15 near-side and far-side craters. Analysis of this preliminary sample of Apollo 15 and 17 data, which includes craters between 1.5 and 275 km in diameter, suggests that most genetic interpretations of craters made from pre-Apollo topographic measurements may require no drastic revision. All measurements were made from topographic profiles generated on a stereoplotter at the Photogrammetric Unit of the U.S. Geological Survey, Center of Astrogeology, Flagstaff, Arizona.

  1. Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As a major component epigenetics, DNA methylation has been proved that widely functions in individual development and various diseases. It has been well studied in model organisms and human but includes limited data for the economic animals. Using reduced representation bisulphite sequencing (RRBS),...

  2. Measured and Modeled Morphometry of Simple Impact Craters

    NASA Astrophysics Data System (ADS)

    Watters, W. A.; Collins, G. S.

    2015-09-01

    We discuss the measured diameter dependence of well-preserved simple crater morphometry on Mars and compare with iSALE simulations. We also describe future work to fully characterize the dependence on impactor velocity and mass, and target properties.

  3. So near and yet so far: harmonic radar reveals reduced homing ability of Nosema infected honeybees.

    PubMed

    Wolf, Stephan; McMahon, Dino P; Lim, Ka S; Pull, Christopher D; Clark, Suzanne J; Paxton, Robert J; Osborne, Juliet L

    2014-01-01

    Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen--Nosema ceranae (Microsporidia)--on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed. PMID:25098331

  4. So Near and Yet So Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees

    PubMed Central

    Wolf, Stephan; McMahon, Dino P.; Lim, Ka S.; Pull, Christopher D.; Clark, Suzanne J.; Paxton, Robert J.; Osborne, Juliet L.

    2014-01-01

    Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed. PMID:25098331

  5. Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium.

    PubMed

    Mazin, Pavel V; Fisunov, Gleb Y; Gorbachev, Alexey Y; Kapitskaya, Kristina Y; Altukhov, Ilya A; Semashko, Tatiana A; Alexeev, Dmitry G; Govorun, Vadim M

    2014-12-01

    The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq and MS-based proteomics to accurately map coding sequences, transcription start sites (TSSs) and transcript 3'-ends (T3Es). We used obtained data to investigate roles of TSSs and T3Es in stress-induced transcriptional responses. We identified 1061 TSSs at a false discovery rate of 10% and showed that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters surrounded by A/T-rich sequences. Our analysis revealed the pronounced operon structure complexity: on average, each coding operon has one internal TSS and T3Es in addition to the primary ones. Our transcriptomic approach based on the intervals between the two nearest transcript ends allowed us to identify two classes of T3Es: strong, unregulated, hairpin-containing T3Es and weak, heat shock-regulated, hairpinless T3Es. Comparing gene expression levels under different conditions revealed widespread and divergent transcription regulation in M. gallisepticum. Modeling suggested that the core promoter structure plays an important role in gene expression regulation. We have shown that the heat stress activation of cryptic promoters combined with the hairpinless T3Es suppression leads to widespread, seemingly non-functional transcription. PMID:25361977

  6. Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium

    PubMed Central

    Mazin, Pavel V.; Fisunov, Gleb Y.; Gorbachev, Alexey Y.; Kapitskaya, Kristina Y.; Altukhov, Ilya A.; Semashko, Tatiana A.; Alexeev, Dmitry G.; Govorun, Vadim M.

    2014-01-01

    The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq and MS-based proteomics to accurately map coding sequences, transcription start sites (TSSs) and transcript 3′-ends (T3Es). We used obtained data to investigate roles of TSSs and T3Es in stress-induced transcriptional responses. We identified 1061 TSSs at a false discovery rate of 10% and showed that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters surrounded by A/T-rich sequences. Our analysis revealed the pronounced operon structure complexity: on average, each coding operon has one internal TSS and T3Es in addition to the primary ones. Our transcriptomic approach based on the intervals between the two nearest transcript ends allowed us to identify two classes of T3Es: strong, unregulated, hairpin-containing T3Es and weak, heat shock-regulated, hairpinless T3Es. Comparing gene expression levels under different conditions revealed widespread and divergent transcription regulation in M. gallisepticum. Modeling suggested that the core promoter structure plays an important role in gene expression regulation. We have shown that the heat stress activation of cryptic promoters combined with the hairpinless T3Es suppression leads to widespread, seemingly non-functional transcription. PMID:25361977

  7. Revealing Optical Properties of Reduced-Dimensionality Materials at Relevant Length Scales.

    PubMed

    Ogletree, D Frank; Schuck, P James; Weber-Bargioni, Alexander F; Borys, Nicholas J; Aloni, Shaul; Bao, Wei; Barja, Sara; Lee, Jiye; Melli, Mauro; Munechika, Keiko; Whitelam, Stephan; Wickenburg, Sebastian

    2015-10-14

    Reduced-dimensionality materials for photonic and optoelectronic applications including energy conversion, solid-state lighting, sensing, and information technology are undergoing rapid development. The search for novel materials based on reduced-dimensionality is driven by new physics. Understanding and optimizing material properties requires characterization at the relevant length scale, which is often below the diffraction limit. Three important material systems are chosen for review here, all of which are under investigation at the Molecular Foundry, to illustrate the current state of the art in nanoscale optical characterization: 2D semiconducting transition metal dichalcogenides; 1D semiconducting nanowires; and energy-transfer in assemblies of 0D semiconducting nanocrystals. For each system, the key optical properties, the principal experimental techniques, and important recent results are discussed. Applications and new developments in near-field optical microscopy and spectroscopy, scanning probe microscopy, and cathodoluminescence in the electron microscope are given detailed attention. Work done at the Molecular Foundry is placed in context within the fields under review. A discussion of emerging opportunities and directions for the future closes the review. PMID:26332202

  8. Multiple electron transfer systems in oxygen reducing biocathodes revealed by different conditions of aeration/agitation.

    PubMed

    Rimboud, Mickaël; Bergel, Alain; Erable, Benjamin

    2016-08-01

    Oxygen reducing biocathodes were formed at -0.2V/SCE (+0.04V/SHE) from compost leachate. Depending on whether aeration was implemented or not, two different redox systems responsible for the electrocatalysis of oxygen reduction were evidenced. System I was observed at low potential (-0.03V/SHE) on cyclic voltammetries (CVs). It appeared during the early formation of the biocathode (few hours) and resisted the hydrodynamic conditions induced by the aeration. System II was observed at higher potential on CV (+0.46V/SHE); it required a longer lag time (up to 10days) and quiescent conditions to produce an electrochemical signal. The hydrodynamic effects produced by the forced aeration led to its extinction. From their different behaviors and examples in the literature, system I was identified as being a membrane-bound cytochrome-related molecule, while system II was identified as a soluble redox mediator excreted by the biofilm. This study highlighted the importance of controlling the local hydrodynamics to design efficient oxygen reducing biocathodes able to operate at high potential. PMID:27035588

  9. Splicing diversity revealed by reduced spliceosomes in C. merolae and other organisms

    PubMed Central

    Hudson, Andrew J; Stark, Martha R; Fast, Naomi M; Russell, Anthony G; Rader, Stephen D

    2015-01-01

    Pre-mRNA splicing has been considered one of the hallmarks of eukaryotes, yet its diversity is astonishing: the number of substrate introns for splicing ranges from hundreds of thousands in humans to a mere handful in certain parasites. The catalytic machinery that carries out splicing, the spliceosome, is similarly diverse, with over 300 associated proteins in humans to a few tens in other organisms. In this Point of View, we discuss recent work characterizing the reduced spliceosome of the acidophilic red alga Cyanidioschyzon merolae, which further highlights the diversity of splicing in that it does not possess the U1 snRNP that is characteristically responsible for 5′ splice site recognition. Comparisons to other organisms with reduced spliceosomes, such as microsporidia, trypanosomes, and Giardia, help to identify the most highly conserved splicing factors, pointing to the essential core of this complex machine. These observations argue for increased exploration of important biochemical processes through study of a wider ranger of organisms. PMID:26400738

  10. Validation of voxel-based morphometry (VBM) based on MRI

    NASA Astrophysics Data System (ADS)

    Yang, Xueyu; Chen, Kewei; Guo, Xiaojuan; Yao, Li

    2007-03-01

    Voxel-based morphometry (VBM) is an automated and objective image analysis technique for detecting differences in regional concentration or volume of brain tissue composition based on structural magnetic resonance (MR) images. VBM has been used widely to evaluate brain morphometric differences between different populations, but there isn't an evaluation system for its validation until now. In this study, a quantitative and objective evaluation system was established in order to assess VBM performance. We recruited twenty normal volunteers (10 males and 10 females, age range 20-26 years, mean age 22.6 years). Firstly, several focal lesions (hippocampus, frontal lobe, anterior cingulate, back of hippocampus, back of anterior cingulate) were simulated in selected brain regions using real MRI data. Secondly, optimized VBM was performed to detect structural differences between groups. Thirdly, one-way ANOVA and post-hoc test were used to assess the accuracy and sensitivity of VBM analysis. The results revealed that VBM was a good detective tool in majority of brain regions, even in controversial brain region such as hippocampus in VBM study. Generally speaking, much more severity of focal lesion was, better VBM performance was. However size of focal lesion had little effects on VBM analysis.

  11. Buried iceberg scours reveal reduced North Atlantic Current during the stage 12 deglacial.

    PubMed

    Newton, Andrew M W; Huuse, Mads; Brocklehurst, Simon H

    2016-01-01

    Reconstructing past ocean-climate environments and heat transport requires proxies from which these conditions can be quantified. This is particularly important for the evaluation of numerical palaeoclimate models. Here we present new evidence for a reduced North Atlantic Current (NAC) at the termination of the third last glacial, for which palaeocurrent information was previously unavailable. This is based on an exquisitely preserved set of buried iceberg scours seen in three-dimensional seismic reflection images from the mid-Norwegian slope. The scours were formed ∼430 ka during the transition from glacial to interglacial conditions. The spiral geometry of the scours suggests that they were carved by grounded icebergs influenced by tidal and geostrophic ocean currents. Using the ratio between the estimated tidal and geostrophic current velocities and comparing them with velocities from the Last Glacial Maximum and the present, we show that the stage 12 NAC velocities may have been ∼50% slower than the present. PMID:26979836

  12. The precision of experienced action video-game players: line bisection reveals reduced leftward response bias.

    PubMed

    Latham, Andrew J; Patston, Lucy L M; Tippett, Lynette J

    2014-11-01

    Twenty-two experienced action video-game players (AVGPs) and 18 non-VGPs were tested on a pen-and-paper line bisection task that was untimed. Typically, right-handers bisect lines 2 % to the left of true centre, a bias thought to reflect the dominance of the right-hemisphere for visuospatial attention. Expertise may affect this bias, with expert musicians showing no bias in line bisection performance. Our results show that experienced-AVGPs also bisect lines with no bias with their right hand and a significantly reduced bias with their left hand compared to non-AVGPs. Bisections by experienced-AVGPs were also more precise than those of non-AVGPs. These findings show the cognitive proficiencies of experienced-AVGPs can generalize beyond computer based tasks, which resemble their training environment. PMID:25341651

  13. Buried iceberg scours reveal reduced North Atlantic Current during the stage 12 deglacial

    PubMed Central

    Newton, Andrew M. W.; Huuse, Mads; Brocklehurst, Simon H.

    2016-01-01

    Reconstructing past ocean-climate environments and heat transport requires proxies from which these conditions can be quantified. This is particularly important for the evaluation of numerical palaeoclimate models. Here we present new evidence for a reduced North Atlantic Current (NAC) at the termination of the third last glacial, for which palaeocurrent information was previously unavailable. This is based on an exquisitely preserved set of buried iceberg scours seen in three-dimensional seismic reflection images from the mid-Norwegian slope. The scours were formed ∼430 ka during the transition from glacial to interglacial conditions. The spiral geometry of the scours suggests that they were carved by grounded icebergs influenced by tidal and geostrophic ocean currents. Using the ratio between the estimated tidal and geostrophic current velocities and comparing them with velocities from the Last Glacial Maximum and the present, we show that the stage 12 NAC velocities may have been ∼50% slower than the present. PMID:26979836

  14. Buried iceberg scours reveal reduced North Atlantic Current during the stage 12 deglacial

    NASA Astrophysics Data System (ADS)

    Newton, Andrew M. W.; Huuse, Mads; Brocklehurst, Simon H.

    2016-03-01

    Reconstructing past ocean-climate environments and heat transport requires proxies from which these conditions can be quantified. This is particularly important for the evaluation of numerical palaeoclimate models. Here we present new evidence for a reduced North Atlantic Current (NAC) at the termination of the third last glacial, for which palaeocurrent information was previously unavailable. This is based on an exquisitely preserved set of buried iceberg scours seen in three-dimensional seismic reflection images from the mid-Norwegian slope. The scours were formed ~430 ka during the transition from glacial to interglacial conditions. The spiral geometry of the scours suggests that they were carved by grounded icebergs influenced by tidal and geostrophic ocean currents. Using the ratio between the estimated tidal and geostrophic current velocities and comparing them with velocities from the Last Glacial Maximum and the present, we show that the stage 12 NAC velocities may have been ~50% slower than the present.

  15. Fish otolith asymmetry: morphometry and modeling.

    PubMed

    Lychakov, D V; Rebane, Y T; Lombarte, A; Fuiman, L A; Takabayashi, A

    2006-09-01

    Mathematical modeling suggests that relatively large values of otolith mass asymmetry in fishes can alter acoustic functionality and may be responsible for abnormal fish behavior when subjected to weightlessness during parabolic or space flight [D.V. Lychakov, Y.T. Rebane, Otolith mass asymmetry in 18 species of fish and pigeon, J. Grav. Physiol. 11 (3) (2004) 17-34; D.V. Lychakov, Y.T. Rebane, Fish otolith mass asymmetry: morphometry and influence on acoustic functionality, Hear. Res. 201 (2005) 55-69]. The results of morphometric studies of otolith mass asymmetry suppose that the absolute value and the sign of the otolith mass asymmetry can change many times during the growth of individual fish within the range +/-20% [D.V. Lychakov, Y.T. Rebane, Otolith mass asymmetry in 18 species of fish and pigeon, J. Grav. Physiol. 11 (3) (2004) 17-34; D.V. Lychakov, Y.T. Rebane, Fish otolith mass asymmetry: morphometry and influence on acoustic functionality, Hear. Res. 201 (2005) 55-69]. This implies that the adverse effects of otolith asymmetry on acoustic and vestibular functionality could change during the lifetime of an individual fish. The aims of the present article were to examine the nature of otolith mass asymmetry fluctuation and to quantify otolith mass asymmetry in a large number of teleost fishes to verify our previous measurements. A dimensionless measure of otolith mass asymmetry, chi, was calculated as the difference between the masses of the right and left paired otoliths divided by average otolith mass. Saccular otolith mass asymmetry was studied in 59 Mediterranean teleost species (395 otolith pairs), 14 Black Sea teleost species (42 otolith pairs), red drum (196 otolith pairs) and guppy (30 otolith pairs). Utricular otolith mass asymmetry was studied in carp (103 otolith pairs) and goldfish (45 otolith pairs). In accordance with our previous results the value of chi did not depend on fish size (length or mass), systematic or ecological position of the

  16. Analysis of RPE morphometry in human eyes

    PubMed Central

    Bhatia, Shagun K.; Rashid, Alia; Chrenek, Micah A.; Zhang, Qing; Bruce, Beau B.; Klein, Mitchel; Boatright, Jeffrey H.; Jiang, Yi; Grossniklaus, Hans E.

    2016-01-01

    Purpose To describe the RPE morphometry of healthy human eyes regarding age and topographic location using modern computational methods with high accuracy and objectivity. We tested whether there were regional and age-related differences in RPE cell area and shape. Methods Human cadaver donor eyes of varying ages were dissected, and the RPE flatmounts were immunostained for F-actin with AF635-phalloidin, nuclei stained with propidium iodide, and imaged with confocal microscopy. Image analysis was performed using ImageJ (NIH) and CellProfiler software. Quantitative parameters, including cell density, cell area, polygonality of cells, number of neighboring cells, and measures of cell shape, were obtained from these analyses to characterize individual and groups of RPE cells. Measurements were taken from selected areas spanning the length of the temporal retina through the macula and the mid-periphery to the far periphery. Results Nineteen eyes from 14 Caucasian donors of varying ages ranging from 29 to 80 years were used. Along a horizontal nasal to temporal meridian, there were differences in several cell shape and size characteristics. Generally, the cell area and shape was relatively constant and regular except in the far periphery. In the outer third of the retina, the cell area and shape differed from the inner two-thirds statistically significantly. In the macula and the far periphery, an overall decreasing trend in RPE cell density, percent hexagonal cells, and form factor was observed with increasing age. We also found a trend toward increasing cell area and eccentricity with age in the macula and the far periphery. When individuals were divided into two age groups, <60 years and ≥60 years, there was a higher cell density, lower cell area, lower eccentricity, and higher form factor in the younger group in the macula and the far periphery (p<0.05 for all measurements). No statistically significant differences in RPE morphometry between age groups were found

  17. DNA Elements Reducing Transcriptional Gene Silencing Revealed by a Novel Screening Strategy

    PubMed Central

    Ueno, Keiichiro; Ohashi, Yuko; Mitsuhara, Ichiro

    2013-01-01

    Transcriptional gene silencing (TGS)–a phenomenon observed in endogenous genes/transgenes in eukaryotes–is a huge hindrance to transgenic technology and occurs mainly when the genes involved share sequence homology in their promoter regions. TGS depends on chromosomal position, suggesting the existence of genomic elements that suppress TGS. However, no systematic approach to identify such DNA elements has yet been reported. Here, we developed a successful novel screening strategy to identify such elements (anti-silencing regions–ASRs), based on their ability to protect a flanked transgene from TGS. A silenced transgenic tobacco plant in which a subsequently introduced transgene undergoes obligatory promoter-homology dependent TGS in trans allowed the ability of DNA elements to prevent TGS to be used as the screening criterion. We also identified ASRs in a genomic library from a different plant species (Lotus japonicus: a perennial legume); the ASRs include portions of Ty1/copia retrotransposon-like and pararetrovirus-like sequences; the retrotransposon-like sequences also showed interspecies anti-TGS activity in a TGS-induction system in Arabidopsis. Anti-TGS elements could provide effective tools to reduce TGS and ensure proper regulation of transgene expression. Furthermore, the screening strategy described here will also facilitate the efficient identification of new classes of anti-TGS elements. PMID:23382937

  18. Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

    PubMed Central

    Zheng, Yunfei; Crawford, Gary W.; Jiang, Leping; Chen, Xugao

    2016-01-01

    Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000–7700 BP), Tianluoshan (7000–6500 BP), Majiabang (6300–6000 BP), and Liangzhu (5300–4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice. PMID:27324699

  19. Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley.

    PubMed

    Zheng, Yunfei; Crawford, Gary W; Jiang, Leping; Chen, Xugao

    2016-01-01

    Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000-7700 BP), Tianluoshan (7000-6500 BP), Majiabang (6300-6000 BP), and Liangzhu (5300-4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice. PMID:27324699

  20. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

    PubMed Central

    Johnston, Eric R.; Rodriguez-R, Luis M.; Luo, Chengwei; Yuan, Mengting M.; Wu, Liyou; He, Zhili; Schuur, Edward A. G.; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong; Konstantinidis, Konstantinos T.

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1–2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100–530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed

  1. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    PubMed

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  2. Voxel-based morphometry in patients with idiopathic generalized epilepsies.

    PubMed

    Betting, Luiz Eduardo; Mory, Susana Barreto; Li, Li Min; Lopes-Cendes, Iscia; Guerreiro, Marilisa M; Guerreiro, Carlos A M; Cendes, Fernando

    2006-08-15

    Idiopathic generalized epilepsies (IGE) are a group of frequent age-related epilepsy syndromes. IGE are clinically characterized by generalized tonic-clonic, myoclonic and absence seizures. According to predominant seizure type and age of onset, IGE are divided in subsyndromes: childhood absence and juvenile absence epilepsy (AE), juvenile myoclonic epilepsy (JME) and generalized tonic-clonic seizures on awakening (GTCS). The limits between these subsyndromes are not well defined, supporting the existence of only one major syndrome. Visual assessment of routine magnetic resonance imaging (MRI) in patients with IGE is normal. MRI voxel-based morphometry (VBM) uses automatically segmented gray and white matter for comparisons, eliminating the investigator bias. We used VBM to study 120 individuals (47 controls, 44 with JME, 24 with AE and 15 with GTCS) to investigate the presence of subtle structural abnormalities in IGE subsyndromes. VBM was performed searching for abnormalities on gray matter concentration (GMC) between patients groups and controls. Compared to controls, JME presented increased GMC in frontobasal region and AE showed increased GMC in the superior mesiofrontal region. The GTCS group did not differ from controls. There were no areas of reduced GMC with the statistical level selected. Region of interest analysis showed increased GMC in the anterior portion of the thalamus in patients with absence seizures. Our results support subtle GMC abnormalities in patients with JME and AE when compared to controls. These findings suggest the existence of different patterns of cortical abnormalities in IGE subsyndromes. PMID:16702001

  3. Problems with six-point vertebral morphometry

    NASA Astrophysics Data System (ADS)

    Gardner, Jill C.; Yaffe, Laurence G.; Johansen, Jennifer M.; von Ingersleben, Gabriel; Chestnut, Charles H., III

    1998-06-01

    In this study we have examined errors in measurements of vertebral heights and vertebral area resulting from spin rotation and projection effects in x-ray images. Measurement errors were evaluated with phantom images, and simulated rotations of a 3D spine model. An active contour model (snake) was used for measurements of vertebral area. The model contained two pressure parameters which were needed to obtain good fits of the snake to upper and lower edges (endplates) of rotated vertebral bodies. Details of the snake model are included in this report. The results of this study indicate that six point vertebral morphometry can result to significant measurement errors, representing an overestimation of vertebral height and area, in cases showing projection effects and concealed endplate contours. In serial studies, such errors could produce the erroneous appearance of `growing' vertebral bodies. One can improve the accuracy of the morphometric analysis by using additional fiducial points placed on corresponding endplate contours. Additional useful information on fracture and vertebral deformity can be obtained by accurately tracking edge contours, using an active contour model, or comparable techniques.

  4. A global database of composite volcano morphometry

    NASA Astrophysics Data System (ADS)

    Grosse, Pablo; Euillades, Pablo A.; Euillades, Leonardo D.; van Wyk de Vries, Benjamin

    2014-01-01

    We present a global database on the subaerial morphometry of composite volcanoes. Data was extracted from the 90-m resolution Shuttle Radar Topography Mission (SRTM) digital elevation model (DEM). The 759 volcanoes included in the database are the composite (i.e., polygenetic) volcanoes listed in the Smithsonian Institution Global Volcanism Program (GVP) database that are covered by the SRTM DEM, have a constructional topography and a basal width larger than 2 km. The extent of each volcano edifice was defined using the NETVOLC algorithm, which computes outlines by minimizing a cost function based on breaks in slope around the edifices. Morphometric parameters were then calculated using the MORVOLC algorithm. The parameters characterize and quantify volcano size (basal width, summit width, height, and volume), profile shape (height/basal width and summit width/basal width ratios), plan shape (ellipticity and irregularity indexes), and slopes. In addition, 104 well-defined and relatively large summit craters/calderas were manually delineated and specific parameters were computed. Most parameters show large variation without clear separations, indicating a continuum of volcano morphologies. Large overlap between the main GVP morphologic types highlights the need for a more rigorous quantitative classification of volcano morphology. The database will be maintained and updated through a website under construction.

  5. On the morphometry of terrestrial shield volcanoes

    NASA Astrophysics Data System (ADS)

    Grosse, Pablo; Kervyn, Matthieu

    2016-04-01

    Shield volcanoes are described as low angle edifices that have convex up topographic profiles and are built primarily by the accumulation of lava flows. This generic view of shields' morphology is based on a limited number of monogenetic shields from Iceland and Mexico, and a small set of large oceanic islands (Hawaii, Galapagos). Here, the morphometry of over 150 monogenetic and polygenetic shield volcanoes, identified inthe Global Volcanism Network database, are analysed quantitatively from 90-meter resolution DEMs using the MORVOLC algorithm. An additional set of 20 volcanoes identified as stratovolcanoes but having low slopes and being dominantly built up by accumulation of lava flows are documented for comparison. Results show that there is a large variation in shield size (volumes range from 0.1 to >1000 km3), profile shape (height/basal width ratios range from 0.01 to 0.1), flank slope gradients, elongation and summit truncation. Correlation and principal component analysis of the obtained quantitative database enables to identify 4 key morphometric descriptors: size, steepness, plan shape and truncation. Using these descriptors through clustering analysis, a new classification scheme is proposed. It highlights the control of the magma feeding system - either central, along a linear structure, or spatially diffuse - on the resulting shield volcano morphology. Genetic relationships and evolutionary trends between contrasted morphological end-members can be highlighted within this new scheme. Additional findings are that the Galapagos-type morphology with a central deep caldera and steep upper flanks are characteristic of other shields. A series of large oceanic shields have slopes systematically much steeper than the low gradients (<4-8°) generally attributed to large Hawaiian-type shields. Finally, the continuum of morphologies from flat shields to steeper complex volcanic constructs considered as stratovolcanoes calls for a revision of this oversimplified

  6. Correlation between Doppler, Manual Morphometry, and Histopathology Based Morphometry of Radial Artery as a Conduit in Coronary Artery Bypass Grafting

    PubMed Central

    Yadava, Om Prakash; Sharma, Vinod; Prakash, Arvind; Ahlawat, Vikas; Mohanty, Bikram K.; Mishra, Rekha; Dinda, Amit K.

    2016-01-01

    Background. Long-term graft patency is the major factor impacting survival after coronary artery bypass grafting. Arteries are superior in this regard. Radial artery is considered the second best conduit after internal mammary artery. Several studies have shown excellent radial artery patency. We evaluated the morphologic characteristics of radial artery by three modalities, (i) preoperative Doppler ultrasound, (ii) intraoperative manual morphometry, and (iii) postoperative histology-based morphometry, and compared these with the aim of validating Doppler as a noninvasive test of choice for preoperative assessment of radial artery. Methods. This was a prospective study involving 100 patients undergoing coronary artery bypass grafting in which radial artery was used. The radial artery was assessed using preoperative Doppler ultrasound studies, intraoperative morphometry, and postoperative histopathology and morphometry. The morphometric measurements included (i) luminal diameter, (ii) intimal and medial thickness, and (iii) intima-media thickness ratio. Results. Using Bland-Altman plots, there was a 95% limit of agreement between the preoperative Doppler measurements and the postoperative histopathology and morphometry. Conclusion. Doppler ultrasound is an accurate screening test for evaluation of radial artery, in terms of intimal/medial thickness and luminal diameter as a conduit in coronary artery bypass grafting and has been validated by both morphometric and histopathology based studies. PMID:27047699

  7. Correlation between Doppler, Manual Morphometry, and Histopathology Based Morphometry of Radial Artery as a Conduit in Coronary Artery Bypass Grafting.

    PubMed

    Yadava, Om Prakash; Sharma, Vinod; Prakash, Arvind; Ahlawat, Vikas; Kundu, Anirban; Mohanty, Bikram K; Mishra, Rekha; Dinda, Amit K

    2016-01-01

    Background. Long-term graft patency is the major factor impacting survival after coronary artery bypass grafting. Arteries are superior in this regard. Radial artery is considered the second best conduit after internal mammary artery. Several studies have shown excellent radial artery patency. We evaluated the morphologic characteristics of radial artery by three modalities, (i) preoperative Doppler ultrasound, (ii) intraoperative manual morphometry, and (iii) postoperative histology-based morphometry, and compared these with the aim of validating Doppler as a noninvasive test of choice for preoperative assessment of radial artery. Methods. This was a prospective study involving 100 patients undergoing coronary artery bypass grafting in which radial artery was used. The radial artery was assessed using preoperative Doppler ultrasound studies, intraoperative morphometry, and postoperative histopathology and morphometry. The morphometric measurements included (i) luminal diameter, (ii) intimal and medial thickness, and (iii) intima-media thickness ratio. Results. Using Bland-Altman plots, there was a 95% limit of agreement between the preoperative Doppler measurements and the postoperative histopathology and morphometry. Conclusion. Doppler ultrasound is an accurate screening test for evaluation of radial artery, in terms of intimal/medial thickness and luminal diameter as a conduit in coronary artery bypass grafting and has been validated by both morphometric and histopathology based studies. PMID:27047699

  8. Brain morphometry and IQ measurements in preterm children.

    PubMed

    Isaacs, E B; Edmonds, C J; Chong, W K; Lucas, A; Morley, R; Gadian, D G

    2004-12-01

    Although IQ is thought to remain relatively stable in the normal population, a decline in IQ has been noted in children born preterm. It is not clear, however, to what extent the inclusion of children with clear neurological damage has influenced these findings. We examined IQ scores obtained in childhood and then again in adolescence from a group of children born at 30 weeks gestation or less who had been classified as neurologically normal at 7.5-8 years. They showed a significant decline in mean IQ scores over time. MRI scans obtained from a subset of children at adolescence were read as normal in approximately 50% of cases and, in the others, there were no consistent relationships between radiological abnormalities and IQ results. Such children can, however, have relatively subtle brain abnormalities that are not seen on conventional MRI, and we hypothesized that these would be related to declines in IQ. Voxel-based morphometry (VBM) analyses of the MRI scans revealed that absolute IQ scores were related to areas in both the parietal and temporal lobes. The analyses also showed that frontal and temporal lobe regions were associated with the decline in VIQ, while occipital and temporal lobe regions (including the hippocampi) were associated with the decline in PIQ. Hippocampal volume measurements were consistent with the VBM findings. We concluded that preterm children are at risk of declining IQ over time even if they have not suffered obvious neurological damage and that the decline is associated with specific neural regions. Whether this is true of children born at >30 weeks gestation and what other factors predispose to this decline have yet to be determined. PMID:15371289

  9. Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity

    NASA Astrophysics Data System (ADS)

    Woods, Christopher J.; Malaisree, Maturos; Long, Ben; McIntosh-Smith, Simon; Mulholland, Adrian J.

    2013-12-01

    The emergence of a novel H7N9 avian influenza that infects humans is a serious cause for concern. Of the genome sequences of H7N9 neuraminidase available, one contains a substitution of arginine to lysine at position 292, suggesting a potential for reduced drug binding efficacy. We have performed molecular dynamics simulations of oseltamivir, zanamivir and peramivir bound to H7N9, H7N9-R292K, and a structurally related H11N9 neuraminidase. They show that H7N9 neuraminidase is structurally homologous to H11N9, binding the drugs in identical modes. The simulations reveal that the R292K mutation disrupts drug binding in H7N9 in a comparable manner to that observed experimentally for H11N9-R292K. Absolute binding free energy calculations with the WaterSwap method confirm a reduction in binding affinity. This indicates that the efficacy of antiviral drugs against H7N9-R292K will be reduced. Simulations can assist in predicting disruption of binding caused by mutations in neuraminidase, thereby providing a computational `assay.'

  10. Microbial Community Succession during Lactate Amendment and Electron Acceptor Limitation Reveals a Predominance of Metal-Reducing Pelosinus spp.

    PubMed Central

    Mosher, Jennifer J.; Phelps, Tommy J.; Podar, Mircea; Hurt, Richard A.; Campbell, James H.; Drake, Meghan M.; Moberly, James G.; Schadt, Christopher W.; Brown, Steven D.; Hazen, Terry C.; Arkin, Adam P.; Palumbo, Anthony V.; Faybishenko, Boris A.

    2012-01-01

    The determination of the success of in situ bioremediation strategies is complex. By using controlled laboratory conditions, the influence of individual variables, such as U(VI), Cr(VI), and electron donors and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. Triplicate anaerobic, continuous-flow reactors were inoculated with Cr(VI)-contaminated groundwater from the Hanford, WA, 100-H area, amended with lactate, and incubated for 95 days to obtain stable, enriched communities. The reactors were kept anaerobic with N2 gas (9 ml/min) flushing the headspace and were fed a defined medium amended with 30 mM lactate and 0.05 mM sulfate with a 48-h generation time. The resultant diversity decreased from 63 genera within 12 phyla to 11 bacterial genera (from 3 phyla) and 2 archaeal genera (from 1 phylum). Final communities were dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp., with low levels of other organisms, including methanogens. Four new strains of Pelosinus were isolated, with 3 strains being capable of Cr(VI) reduction while one also reduced U(VI). Under limited sulfate, it appeared that the sulfate reducers, including Desulfovibrio spp., were outcompeted. These results suggest that during times of electron acceptor limitation in situ, organisms such as Pelosinus spp. may outcompete the more-well-studied organisms while maintaining overall metal reduction rates and extents. Finally, lab-scale simulations can test new strategies on a smaller scale while facilitating community member isolation, so that a deeper understanding of community metabolism can be revealed. PMID:22267668

  11. Comparative structural morphometry and elemental composition of three marine sponges from western coast of India.

    PubMed

    Kumar, Maushmi S; Shah, Bhaumik

    2014-04-01

    Three marine sponges Halichondria glabrata, Cliono lobata, and Spirastrella pachyspira from the western coastal region of India were compared for their morphometry, biochemical, and elemental composition. One-way analysis of variance was applied for spicule morphometry results. Length, width, and length:width ratio were calculated independently. The ratio of length:width varied from 35 to 42 among the grown samples, which remained in the range of 10-22 in young sample at the beginning of studies. However, no significant change was observed in spicule width compared to length. Elemental compositions of marine sponges were determined by field emission gun-scanning electron microscope. Scanning electron microscopy data revealed that the spicules of all the three sponges were mostly composed of O (47-56%) and Si (30-40%), whereas Al (14.33%) was only detected in the spicules of C. lobata. Apart from these, K, Ni, Ca, Fe, Mg, Na, and S were additionally detected in all the three samples. Presence of heavy metals in the sponges was analyzed by inductively coupled plasma-atomic emission spectroscopy. Results showed that iron was present in a large amount in samples, followed by zinc, lead, and copper. PMID:24500946

  12. The Distribution of Thermophilic Sulfate-reducing Bacteria Along an Estuarine Gradient Reveals Multiple Origins of Endospores in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Bell, E.

    2015-12-01

    Cold marine sediments harbour inactive spores of thermophilic bacteria. These misplaced thermophiles are genetically similar to microorganisms detected in deep biosphere environments, leading to the hypothesis that seabed fluid flow transports thermophiles out of warm subsurface environments and into the ocean. Estuaries form the transition between the marine and the terrestrial biosphere and are influenced by tidal currents, surface run-off and groundwater seepage. Endospores from thermophilic bacteria present in estuarine sediments could therefore originate from a number of sources that may influence the estuary differently. We have therefore tested the hypothesis that this will lead to a gradient in the composition of thermophilic endospore populations in estuarine sediments. The distribution of thermophilic spore-forming sulfate-reducing bacteria along an estuarine gradient from freshwater (River Tyne, UK) to marine (North Sea) was investigated. Microbial community analysis by 16S rRNA gene amplicon sequencing revealed changes in the thermophilic population enriched at different locations within the estuary. Certain species were only detected at the marine end, highlighting possible links to deep marine biosphere habitats such as oil reservoirs that harbour closely related Desulfotomaculum spp. Conversely, other taxa were predominantly observed in the freshwater reaches of the estuary indicating dispersal from an upstream or terrestrial source. Different endospore populations were enriched dependent on incubation temperature and spore heat-resistance. Microcosms incubated at 50, 60 or 70°C showed a shift in the dominant species of Desulfotomaculum enriched as the temperature increased. Microcosms triple-autoclaved at 121°C prior to incubation still showed rapid and reproducible sulfate-reduction and some Desulfotomaculum spp. remained active after autoclaving at 130°C. These results show that temperature physiology and biogeographic patterns can be used to

  13. GATA4 variant interaction with brain limbic structure and relapse risk: A voxel-based morphometry study.

    PubMed

    Zois, Evangelos; Vollstädt-Klein, Sabine; Hoffmann, Sabine; Reinhard, Iris; Bach, Patrick; Charlet, Katrin; Beck, Anne; Treutlein, Jens; Frank, Josef; Jorde, Anne; Kirsch, Martina; Degenhardt, Franziska; Walter, Henrik; Heinz, Andreas; Kiefer, Falk

    2016-09-01

    Atrial natriuretic peptide (ANP) receptors are highly expressed in the amygdala, caudate and hypothalamus. GATA4 gene encodes a transcription factor of ANP associated with the pathophysiology of alcohol dependence. We have previously demonstrated that the GATA4 single nucleotide polymorphism (SNP) rs13273672 revealed stronger alcohol-specific amygdala activation associated with lowered relapse risk to heavy drinking at 90 days in the AA-homozygotes. Our understanding however with respect to GATA4 variation on gray matter (GM) regional amygdala, caudate and hypothalamus volume is limited. We investigated GM differences specific to GATA4 and hypothesized that GM alterations will be predictive of heavy relapse. Eighty-three recently detoxified alcohol dependent patients were included. Neuroimaging data was analyzed using Voxel Based Morphometry (VBM). The main effects of GM volume and genotype as well as their interaction effect on time to heavy relapse (60 and 90 days) were analyzed using cox regression. Significant higher GM volume was found for the AA-genotype group compared with AG/GG-genotype in the hypothalamus and caudate. A significant interaction was revealed between caudate and amygdala GM volume and GATA4 genotype on time to heavy relapse. The interaction was expressed by means of higher GM in the AA genotype group to be associated with reduced risk to relapse whereas in the AG/GG group higher GM was associated with increased risk to relapse. This is the first report on GM regional volume alterations specific to GATA4 genotype [(SNP) rs13273672] and its association with relapse in alcohol dependence. Current findings further support the role of GATA4 in alcoholism. PMID:27397865

  14. Significance of nuclear morphometry in benign and malignant breast aspirates

    PubMed Central

    Narasimha, Aparna; Vasavi, B; Kumar, Harendra ML

    2013-01-01

    Background: Breast carcinoma is one of the most common cancers occurring in the female population world-wide. Normal cells gradually transform to form the cancer cells through several stages. Nuclear changes occurring during these transformational steps need to be assessed objectively. Hence nuclear morphometry can be used as a diagnostic tool. Aim: To compare the nuclear morphometric parameters of benign and malignant breast aspirates. Study Design: Cytology was used to categorize aspirates from the breast lumps in to malignant (30 cases), and benign (30 cases). Nuclear parameters were calculated using the Image J 1.44C morphometric software. Several nuclear size parameters were analyzed. Results: The nuclear area, perimeter, diameter, compactness, and concave points were found to be statistically significant (P < 0.05) parameters in differentiating benign, and malignant aspirates. Conclusion: Nuclear morphometry was thus, a useful objective tool in the differentiating benign, and malignant breast lesions. PMID:23776836

  15. Studies on recombinant single chain Jacalin lectin reveal reduced affinity for saccharides despite normal folding like native Jacalin

    PubMed Central

    Sahasrabuddhe, Anagh A.; Gaikwad, Sushama M.; Krishnasastry, M.V.; Khan, M. Islam

    2004-01-01

    Sugar binding studies, inactivation, unfolding, and refolding of native Jacalin (nJacalin) from Artocarpus integrifolia and recombinant single-chain Jacalin (rJacalin) expressed in Escherichia coli were studied by intrinsic fluorescence and thermal and chemical denaturation approaches. Interestingly, rJacalin does not undergo any proteolytic processing in an E. coli environment. It has 100fold less affinity for methyl-α-galactose (Ka: 2.48 × 102) in comparison to nJacalin (Ka: 1.58 × 104), and it also binds Thomsen-Friedenreich (TF) disaccharide (Galβ1–3GalNAc) with less affinity. Overall sugar binding characteristics of rJacalin are qualitatively similar to that of nJacalin (Galreveal that the rJacalin behaves like nJacalin. Guanidine hydrochloride-induced denaturation, followed by renaturation, yielded total recovery of sugar binding activity of rJacalin in comparison to partial recovery for nJacalin. This signifies the minor changes in the refolding pathways between native and recombinant lectins. The stability of rJacalin is dramatically reduced in the extreme pH range unlike nJacalin. Both lectins do not bind 1-anilino-8-naphthalene sulfonic acid (ANS) in the pH range of 5 to 12 but they do in the pH range of 1–3. Solute quenching studies of the lectin using acrylamide, KI, and CsCl indicated that the tryptophan residues have full accessibility to the neutral quencher and poor accessibility to ionic quenchers. In summary, biophysical and biochemical studies on the native versus recombinant Jacalin suggest that post-translational modification, i.e., the processing of Jacalin into two chains is probably not a prerequisite for sugar binding but may be required for higher affinity. PMID:15557267

  16. Experimentally reduced root–microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus

    PubMed Central

    Lee, Mei-Ho; Comas, Louise H.; Callahan, Hilary S.

    2014-01-01

    Background and Aims Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the magnitude of plasticity relative to differences between species, studies of plasticity can ascertain if plasticity is predictable and whether an environmental factor elicits changes in traits that are functionally advantageous. Methods To compare functional traits and trait plasticities in fine root tissues with natural and reduced levels of colonization by microbial symbionts, trimmed and surface-sterilized root segments of 2-year-old Acer rubrum and Quercus rubra seedlings were manipulated. Segments were then replanted into satellite pots filled with control or heat-treated soil, both originally derived from a natural forest. Mycorrhizal colonization was near zero in roots grown in heat-treated soil; roots grown in control soil matched the higher colonization levels observed in unmanipulated root samples collected from field locations. Key Results Between-treatment comparisons revealed negligible plasticity for root diameter, branching intensity and nitrogen concentration across both species. Roots from treated soils had decreased tissue density (approx. 10–20 %) and increased specific root length (approx. 10–30 %). In contrast, species differences were significant and greater than treatment effects in traits other than tissue density. Interspecific trait differences were also significant in field samples, which generally resembled greenhouse samples. Conclusions The combination of experimental and field approaches was useful for contextualizing trait plasticity in comparison with inter- and intra-specific trait variation. Findings that root traits are largely species dependent, with the exception of root tissue density, are discussed in the context of current literature on root

  17. Morphology, morphometry and ultrastructure of captive six-banded armadillo (Euphractus sexcinctus) sperm.

    PubMed

    Sousa, P C; Santos, E A A; Bezerra, J A B; Lima, G L; Castelo, T S; Fontenele-Neto, J D; Silva, A R

    2013-08-01

    We analyzed the sperm characteristics of captive six-banded armadillos (Euphractus sexcinctus), by the assessment of sperm morphology, morphometry, and ultrastructure. In general, armadillo's ejaculates present more than 80% of sperm within the range considered normal for sperm morphology currently accepted for other mammals. Coiled tails (3.9%) and detached heads (2.8%) were the defects most frequently verified. The morphometric analysis revealed that the total length of six-banded armadillo sperm is 77.6±1.2μm, and the length of the tail is 64.7±1.1μm on average. They also present a big head that corresponds to 16.6% of the entire sperm. Through transmission electron microscopy, we identified the presence of electron lucent points into the nucleus and the presence of about 45 mitochondria spirals in the mitochondrial sheath midpiece as a peculiarity of the six-banded armadillo sperm. PMID:23820069

  18. Persistent Homology in Sparse Regression and Its Application to Brain Morphometry

    PubMed Central

    Hanson, Jamie L.; Ye, Jieping; Davidson, Richard J.; Pollak, Seth D.

    2015-01-01

    Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in drastically speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region. PMID:25823032

  19. Persistent Homology in Sparse Regression and Its Application to Brain Morphometry.

    PubMed

    Chung, Moo K; Hanson, Jamie L; Ye, Jieping; Davidson, Richard J; Pollak, Seth D

    2015-09-01

    Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in drastically speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region. PMID:25823032

  20. The influence of lithium on hippocampal volume in elderly bipolar patients: a study using voxel-based morphometry.

    PubMed

    Zung, S; Souza-Duran, F L; Soeiro-de-Souza, M G; Uchida, R; Bottino, C M; Busatto, G F; Vallada, H

    2016-01-01

    Recent studies have demonstrated that lithium (Li) exerts neuronal protective and regenerative effects both in vitro and in vivo. However, the effects of long-term Li treatment in the brain areas associated with memory impairment of elderly bipolar patients are still unknown. The aim of this study was to compare the hippocampal volumes of elderly bipolar patients using Li, elderly bipolar patients not using Li and healthy controls. Sociodemographic, clinical and magnetic resonance imaging data from 30 elderly euthymic bipolar patients who had been using Li for an average of >61 months; 27 elderly euthymic bipolar patients not taking Li for an average of 45 months; and 22 elderly healthy controls were analyzed. Volumetric differences in the hippocampus between groups were investigated with voxel-based morphometry (VBM) based on the Statistical Parametric Mapping technique. No statistical differences in sociodemographic and clinical characteristics and course of bipolar disorder between the two bipolar groups were observed. Using small volume correction in the VBM analysis (analysis of variance (ANOVA)), one voxel cluster of statistical significance was detected in the left hippocampus (P<0.05 corrected for multiple comparisons, extent threshold >10 voxels). Post hoc unpaired t-tests revealed increased left hippocampal volume in the Li-treated group compared with the non-Li-treated group, and decreased left hippocampal volume in the non-Li group relative to controls. Additional exploratory two-group comparisons indicated trends toward reduced right-hippocampal volumes in the non-Li-treated group relative to both the Li-treated group and controls. The findings suggested that the use of Li may influence the volume of the hippocampus, possibly due to its neuroprotective effects. PMID:27351600

  1. The influence of lithium on hippocampal volume in elderly bipolar patients: a study using voxel-based morphometry

    PubMed Central

    Zung, S; Souza-Duran, F L; Soeiro-de-Souza, M G; Uchida, R; Bottino, C M; Busatto, G F; Vallada, H

    2016-01-01

    Recent studies have demonstrated that lithium (Li) exerts neuronal protective and regenerative effects both in vitro and in vivo. However, the effects of long-term Li treatment in the brain areas associated with memory impairment of elderly bipolar patients are still unknown. The aim of this study was to compare the hippocampal volumes of elderly bipolar patients using Li, elderly bipolar patients not using Li and healthy controls. Sociodemographic, clinical and magnetic resonance imaging data from 30 elderly euthymic bipolar patients who had been using Li for an average of >61 months; 27 elderly euthymic bipolar patients not taking Li for an average of 45 months; and 22 elderly healthy controls were analyzed. Volumetric differences in the hippocampus between groups were investigated with voxel-based morphometry (VBM) based on the Statistical Parametric Mapping technique. No statistical differences in sociodemographic and clinical characteristics and course of bipolar disorder between the two bipolar groups were observed. Using small volume correction in the VBM analysis (analysis of variance (ANOVA)), one voxel cluster of statistical significance was detected in the left hippocampus (P<0.05 corrected for multiple comparisons, extent threshold >10 voxels). Post hoc unpaired t-tests revealed increased left hippocampal volume in the Li-treated group compared with the non-Li-treated group, and decreased left hippocampal volume in the non-Li group relative to controls. Additional exploratory two-group comparisons indicated trends toward reduced right-hippocampal volumes in the non-Li-treated group relative to both the Li-treated group and controls. The findings suggested that the use of Li may influence the volume of the hippocampus, possibly due to its neuroprotective effects. PMID:27351600

  2. APPLYING SPARSE CODING TO SURFACE MULTIVARIATE TENSOR-BASED MORPHOMETRY TO PREDICT FUTURE COGNITIVE DECLINE

    PubMed Central

    Zhang, Jie; Stonnington, Cynthia; Li, Qingyang; Shi, Jie; Bauer, Robert J.; Gutman, Boris A.; Chen, Kewei; Reiman, Eric M.; Thompson, Paul M.; Ye, Jieping; Wang, Yalin

    2016-01-01

    Alzheimer’s disease (AD) is a progressive brain disease. Accurate diagnosis of AD and its prodromal stage, mild cognitive impairment, is crucial for clinical trial design. There is also growing interests in identifying brain imaging biomarkers that help evaluate AD risk presymptomatically. Here, we applied a recently developed multivariate tensor-based morphometry (mTBM) method to extract features from hippocampal surfaces, derived from anatomical brain MRI. For such surface-based features, the feature dimension is usually much larger than the number of subjects. We used dictionary learning and sparse coding to effectively reduce the feature dimensions. With the new features, an Adaboost classifier was employed for binary group classification. In tests on publicly available data from the Alzheimers Disease Neuroimaging Initiative, the new framework outperformed several standard imaging measures in classifying different stages of AD. The new approach combines the efficiency of sparse coding with the sensitivity of surface mTBM, and boosts classification performance. PMID:27499829

  3. A combined massively parallel sequencing indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities

    SciTech Connect

    Cardenas, Erick; Wu, Wei-min; Leigh, Mary Beth; Carley, Jack M; Carroll, Sue L; Gentry, Terry; Luo, Jian; Watson, David B; Gu, Baohua; Ginder-Vogel, Matthew A.; Kitanidis, Peter K.; Jardine, Philip; Kelly, Shelly D; Zhou, Jizhong; Criddle, Craig; Marsh, Terence; Tiedje, James

    2010-08-01

    Massively parallel sequencing has provided a more affordable and high throughput method to study microbial communities, although it has been mostly used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium (VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee, USA. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 {micro}M, and created geochemical gradients in electron donors from the inner loop injection well towards the outer loop and down-gradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical created conditions. Castellaniella, and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity; while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. Abundance of these bacteria as well as the Fe(III)- and U(VI)-reducer Geobacter correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to the electron donor addition and by the groundwater flow path. A false discovery rate approach was implemented to discard false positives by chance given the large amount of data compared.

  4. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach

    SciTech Connect

    Cardenas, Erick; Leigh, Mary Beth; Marsh, Terence; Tiedje, James M.; Wu, Wei-min; Luo, Jian; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Criddle, Craig; Carley, Jack M; Carroll, Sue L; Gentry, Terry J; Watson, David B; Gu, Baohua; Jardine, Philip M; Zhou, Jizhong

    2010-10-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 M and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

  5. Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

    PubMed

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

    2010-10-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

  6. EFFECTS OF LINDANE AND LINURON ON CALCIUM METABOLISM, MORPHOMETRY, AND THE KIDNEY

    EPA Science Inventory

    The effects of lindane and linuron on calcium metabolism, bone morphometry and the kidney. xperiments were performed to investigate the effects of lindane and linuron on calcium metabolism, femur morphometry and nephrotoxicity. ong-Evans hooded rats were dosed daily for 10 weeks ...

  7. Nuclear morphometry and glutathione S-transferase pi expression in breast cancer.

    PubMed

    Huang, J; Bay, B H; Tan, P H

    2000-01-01

    Glutathione S-transferase pi (GST-pi) is a phase II detoxification enzyme whose expression is increased in estrogen receptor (ER)-poor breast cancers and in breast cancers resistant to certain chemotherapeutic agents. The aim of this study was to investigate the immunohistochemical expression of GST-pi in invasive breast carcinoma and to correlate the findings with those of nuclear morphometry. Formalin-fixed paraffin-embedded tissue specimens obtained from 21 invasive breast cancers and 16 adjacent (benign) tissues were immunohistochemically stained using polyclonal anti-human GST-pi antibody. There was positive (defined as >10% immunoreactive tumor cells) but variable expression of GST-pi in 10 (48%) cases. Nuclear morphometry in these 10 tumors revealed immunoreactive malignant cells to be larger (mean area 41.7+/-1.0 microm2) and more rounded in form when compared with non-staining cancer cells (mean area 28.7+/-0.7 microm2). It was also observed that GST-pi immunonegative tumor cells in GST-pi expressing tumors had different morphologies from malignant cells in the remaining 11 (52%) cancers that were regarded as GST-pi negative. Increased GST-pi expression determined by the percentage of positively staining tumor cells, was found to be significantly correlated with increased variability in nuclear area and perimeter (Spearman's rho=0.821, p=0.044 for both) in the subset of node-positive tumors. Our findings suggest that there exists two sub-populations of cancer cells with distinct nuclear morphologies in GST-pi positive tumors; factors other than GST-pi expression are likely to have a phenotypic effect on breast cancer cells; and there may be a special significance of this enzyme in axillary node-positive breast tumors. PMID:10767377

  8. STRUCTURAL CONNECTIVITY VIA THE TENSOR-BASED MORPHOMETRY

    PubMed Central

    Kim, Seung-Goo; Chung, Moo K.; Hanson, Jamie L.; Avants, Brian B.; Gee, James C.; Davidson, Richard J.; Pollak, Seth D.

    2013-01-01

    The tensor-based morphometry (TBM) has been widely used in characterizing tissue volume difference between populations at voxel level. We present a novel computational framework for investigating the white matter connectivity using TBM. Unlike other diffusion tensor imaging (DTI) based white matter connectivity studies, we do not use DTI but only T1-weighted magnetic resonance imaging (MRI). To construct brain network graphs, we have developed a new data-driven approach called the ε-neighbor method that does not need any predetermined parcellation. The proposed pipeline is applied in detecting the topological alteration of the white matter connectivity in maltreated children. PMID:24177222

  9. Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution

    PubMed Central

    Soo, Oi Yoon Michelle; Tan, Wooi Boon; Lim, Lee Hong Susan

    2016-01-01

    Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions. Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams’s Kmult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data. Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root

  10. Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution.

    PubMed

    Khang, Tsung Fei; Soo, Oi Yoon Michelle; Tan, Wooi Boon; Lim, Lee Hong Susan

    2016-01-01

    Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions. Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams's K mult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data. Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root

  11. Morphometry and Morphology of Fresh Craters on Titan

    NASA Astrophysics Data System (ADS)

    Kirk, R. L.; Wood, C. A.; Neish, C.; Lucas, A.; Hayes, A. G.; Cassini Radar Team

    2011-12-01

    Cassini RADAR imagery obtained on Titan flyby T77 revealed a 40-km diameter fresh impact crater at 11.6° N 44.6° W. This is only the 8th crater identified with high confidence (Wood et al., 2010, Icarus 206, 334), and the 3rd (after Sinlap D=79 km and Ksa D=30 km) for which the depth can be estimated by comparing the foreshortening of the near and far walls. This "autostereo" technique yields an estimated depth of 680 m. The T77 image forms a stereo pair with the T17 discovery image of Ksa from which we estimate the depth of Ksa at 750-800 m, in close agreement with SARTopo data. The depth of Sinlap is 760 m based on SARTopo. Depth-diameter ratios for these craters thus range from 0.01 to 0.025 and the depths are comparable to but 200-400 m shallower than fresh craters of the same size on Ganymede (Bray et al., 2008, Met. Planet Sci. 43, 1979). The depth differences could be explained by initial crater morphometry, by relaxation in a different thermal environment, or (perhaps most plausibly given the bland floors of even the freshest Titan craters) to sedimentary infill. In contrast, the 18x36 km elliptical depression at Sotra Facula is much deeper than Ganymede craters of similar size (d=1500 m from stereo), supporting the conclusion that it is not an impact crater. All three craters exhibit a relatively radar-bright annulus around the outer edge of the floor, possibly as the result of mass wasting of blocky materials from the crater walls. The central part of each crater is darker. The central darker floor of the new crater is symmetrical and featureless, whereas Ksa has a bright central ring 7 km in diameter. Stereo spot heights indicate the ring is 350±100 m above the outer floor. This height is in close agreement with the scaling for Ganymede crater central peaks from Bray et al. (2008). The darker floor area of Sinlap is substantially asymmetrical with a small bright central spot whose elevation is unknown. The new crater has continuous, radar

  12. Robust tumor morphometry in multispectral fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Tabesh, Ali; Vengrenyuk, Yevgen; Teverovskiy, Mikhail; Khan, Faisal M.; Sapir, Marina; Powell, Douglas; Mesa-Tejada, Ricardo; Donovan, Michael J.; Fernandez, Gerardo

    2009-02-01

    Morphological and architectural characteristics of primary tissue compartments, such as epithelial nuclei (EN) and cytoplasm, provide important cues for cancer diagnosis, prognosis, and therapeutic response prediction. We propose two feature sets for the robust quantification of these characteristics in multiplex immunofluorescence (IF) microscopy images of prostate biopsy specimens. To enable feature extraction, EN and cytoplasm regions were first segmented from the IF images. Then, feature sets consisting of the characteristics of the minimum spanning tree (MST) connecting the EN and the fractal dimension (FD) of gland boundaries were obtained from the segmented compartments. We demonstrated the utility of the proposed features in prostate cancer recurrence prediction on a multi-institution cohort of 1027 patients. Univariate analysis revealed that both FD and one of the MST features were highly effective for predicting cancer recurrence (p <= 0.0001). In multivariate analysis, an MST feature was selected for a model incorporating clinical and image features. The model achieved a concordance index (CI) of 0.73 on the validation set, which was significantly higher than the CI of 0.69 for the standard multivariate model based solely on clinical features currently used in clinical practice (p < 0.0001). The contributions of this work are twofold. First, it is the first demonstration of the utility of the proposed features in morphometric analysis of IF images. Second, this is the largest scale study of the efficacy and robustness of the proposed features in prostate cancer prognosis.

  13. Pelvic Belt Effects on Pelvic Morphometry, Muscle Activity and Body Balance in Patients with Sacroiliac Joint Dysfunction

    PubMed Central

    Soisson, Odette; Lube, Juliane; Germano, Andresa; Hammer, Karl-Heinz; Josten, Christoph; Sichting, Freddy; Winkler, Dirk; Milani, Thomas L.; Hammer, Niels

    2015-01-01

    Introduction The sacroiliac joint (SIJ) is frequently involved in low back and pelvic girdle pain. However, morphometrical and functional characteristics related to SIJ pain are poorly defined. Pelvic belts represent one treatment option, but evidence still lacks as to their pain-reducing effects and the mechanisms involved. Addressing these two issues, this case-controlled study compares morphometric, functional and clinical data in SIJ patients and healthy controls and evaluates the effects of short-term pelvic belt application. Methods Morphometric and functional data pertaining to pelvic belt effects were compared in 17 SIJ patients and 17 controls. Lumbar spine and pelvis morphometries were obtained from 3T magnetic resonance imaging. Functional electromyography data of pelvis and leg muscles and center of pressure excursions were measured in one-leg stance. The numerical rating scale was used to evaluate immediate pain-reducing effects. Results Pelvic morphometry was largely unaltered in SIJ patients and also by pelvic belt application. The angle of lumbar lateral flexion was significantly larger in SIJ patients without belt application. Muscle activity and center of pressure were unaffected by SIJ pain or by belt application in one-leg stance. Nine of 17 patients reported decreased pain intensities under moderate belt application, four reported no change and four reported increased pain intensity. For the entire population investigated here, this qualitative description was not confirmed on a statistical significant level. Discussion Minute changes were observed in the alignment of the lumbar spine in the frontal plane in SIJ patients. The potential pain-decreasing effects of pelvic belts could not be attributed to altered muscle activity, pelvic morphometry or body balance in a static short-term application. Long-term belt effects will therefore be of prospective interest. PMID:25781325

  14. Cranial morphometry of early hominids: facial region.

    PubMed

    Bilsborough, A; Wood, B A

    1988-05-01

    We report here on early hominid facial diversity, as part of a more extensive morphometric survey of cranial variability in Pliocene and early Pleistocene Hominidae. Univariate and multivariate techniques are used to summarise variation in facial proportions in South and East African hominids, and later Quaternary groups are included as comparators in order to scale the variation displayed. The results indicate that "robust" australopithecines have longer, broader faces than the "gracile" form, but that all australopithecine species show comparable degrees of facial projection. "Robust" crania are characterised by anteriorly situated, deep malar processes that slope forwards and downwards. Smaller hominid specimens, formally or informally assigned to Homo (H. habilis, KNM-ER 1813, etc.), have individual facial dimensions that usually fall within the range of Australopithecus africanus, but which in combination reveal a significantly different morphological pattern; SK 847 shows similarly hominine facial proportions, which differ significantly from those of A. robustus specimens from Swartkrans. KNM-ER 1470 possesses a facial pattern that is basically hominine, but which in some respects mimics that of "robust" australopithecines. Early specimens referred to H. erectus possess facial proportions that contrast markedly with those of other Villafranchian hominids and which suggest differing masticatory forces, possibly reflecting a shift in dietary niche. Overall the results indicate two broad patterns of facial proportions in Hominidae: one is characteristic of Pliocene/basal Pleistocene forms with opposite polarities represented by A. boisei and H. habilis; the other pattern, which typifies hominids from the later Lower Pleistocene onwards, is first found in specimens widely regarded as early representatives of H. erectus, but which differ in which certain respects from the face of later members of that species. PMID:3136656

  15. Deformation-based surface morphometry applied to gray matter deformation.

    PubMed

    Chung, Moo K; Worsley, Keith J; Robbins, Steve; Paus, Tomás; Taylor, Jonathan; Giedd, Jay N; Rapoport, Judith L; Evans, Alan C

    2003-02-01

    We present a unified statistical approach to deformation-based morphometry applied to the cortical surface. The cerebral cortex has the topology of a 2D highly convoluted sheet. As the brain develops over time, the cortical surface area, thickness, curvature, and total gray matter volume change. It is highly likely that such age-related surface changes are not uniform. By measuring how such surface metrics change over time, the regions of the most rapid structural changes can be localized. We avoided using surface flattening, which distorts the inherent geometry of the cortex in our analysis and it is only used in visualization. To increase the signal to noise ratio, diffusion smoothing, which generalizes Gaussian kernel smoothing to an arbitrary curved cortical surface, has been developed and applied to surface data. Afterward, statistical inference on the cortical surface will be performed via random fields theory. As an illustration, we demonstrate how this new surface-based morphometry can be applied in localizing the cortical regions of the gray matter tissue growth and loss in the brain images longitudinally collected in the group of children and adolescents. PMID:12595176

  16. [THE MORPHOMETRY IN CYTOLOGICAL ANALYSIS OF EXUDATIVE FLUIDS].

    PubMed

    Snikhovskaya, K V; Shabalova, I P

    2015-08-01

    The cytological technique takes a leading position in diagnostic of tumor processes according exudative fluids. However, its results depend on large number of subjective factors. The morphometry is one of techniques by virtue of which objectification of data of cytological analysis is possible. The study was carried out to establish differences of morphometric parameters of benign and malignant cells of pleural effusion. The morphometric analysis of cells of mesothelium, breast cancer, adenocarcinoma of lung and adenocarcinoma of stomach was implemented. The parameters characterizing size (area, perimeter) and form (form factor) of nucleus and cell, nucleus-cytoplasm ratio. The results demonstrated that in pleural effusion between cells of proliferating mesothelium and malignant neoplasms exist significant differences in morphometric parameters (p<0.001). The differences between area of nuclei and cells are especially significant. The comparison of data of morphometry of cells of breast cancer; adenocarcinoma of lung and adenocarcinoma of stomach demonstrated that despite of some morphological similarities, analysis of morphometric parameters can provide important data for proper establishment of cytological diagnosis. PMID:26596045

  17. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.

    PubMed

    Hyötyläinen, Tuulia; Jerby, Livnat; Petäjä, Elina M; Mattila, Ismo; Jäntti, Sirkku; Auvinen, Petri; Gastaldelli, Amalia; Yki-Järvinen, Hannele; Ruppin, Eytan; Orešič, Matej

    2016-01-01

    Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD. PMID:26839171

  18. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease

    PubMed Central

    Hyötyläinen, Tuulia; Jerby, Livnat; Petäjä, Elina M.; Mattila, Ismo; Jäntti, Sirkku; Auvinen, Petri; Gastaldelli, Amalia; Yki-Järvinen, Hannele; Ruppin, Eytan; Orešič, Matej

    2016-01-01

    Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD. PMID:26839171

  19. Biosynthetic Pathway of the Reduced Polyketide Product Citreoviridin in Aspergillus terreus var. aureus Revealed by Heterologous Expression in Aspergillus nidulans.

    PubMed

    Lin, Tzu-Shyang; Chiang, Yi-Ming; Wang, Clay C C

    2016-03-18

    Citreoviridin (1) belongs to a class of F1-ATPase β-subunit inhibitors that are synthesized by highly reducing polyketide synthases. These potent mycotoxins share an α-pyrone polyene structure, and they include aurovertin, verrucosidin, and asteltoxin. The identification of the citreoviridin biosynthetic gene cluster in Aspergillus terreus var. aureus and its reconstitution using heterologous expression in Aspergillus nidulans are reported. Two intermediates were isolated that allowed the proposal of the biosynthetic pathway of citreoviridin. PMID:26954888

  20. Ultrastructural and histochemical analysis reveals ethylene-induced responses underlying reduced peel collapse in detached citrus fruit.

    PubMed

    Cajuste, Jacques F; García-Breijo, Francisco J; Reig-Armiñana, José; Lafuente, María T

    2011-10-01

    Fruits from many citrus cultivars develop depressed areas in the flavedo (outer part of the peel) and albedo (inner part) following detachment. Although ultrastructural analysis may provide important information about multiple plant responses to stresses and external stimuli at the cell and tissue levels, and despite the proved efficacy of ethylene in reducing peel damage in citrus fruit, cytological responses of this horticultural crop to protective ethylene concentrations have not yet been reported. We show that applying high ethylene levels (2 μL L(-1) for 14 days) causes sublethal stress as it favored the alteration of cuticle, vacuole, middle lamella and primary wall, especially in the albedo cells, but reduced peel collapse in detached mature "Navelate" oranges (C. sinensis, L. Osbeck) held under nonstressful environmental conditions (22°C and 90-95% RH). Ethylene did not induce relevant changes in lignification but favored the deposition of pectic exudates and the release of sugars from degradation of cell polysaccharides including starch, cellulose, and pectins. In contrast, inhibiting ethylene perception by applying 1-methylcyclopropene (1-MCP) reduced these ethylene-related responses and favored degradation of cell membranes and peel damage. The overall results reflect that mature oranges tolerate high ethylene levels that might favor the activation of defense responses involving oxidative-stress related mechanisms and recycling of nutrients and carbon supply to enable cells to sustain respiration and cope with carbon deprivation stress caused by detachment. PMID:21509903

  1. Morphometry and land cover based multi-criteria analysis for assessing the soil erosion susceptibility of the western Himalayan watershed.

    PubMed

    Altaf, Sadaff; Meraj, Gowhar; Romshoo, Shakil Ahmad

    2014-12-01

    Complex mountainous environments such as Himalayas are highly susceptibility to natural hazards particular those that are triggered by the action of water such as floods, soil erosion, mass movements and siltation of the hydro-electric power dams. Among all the natural hazards, soil erosion is the most implicit and the devastating hazard affecting the life and property of the millions of people living in these regions. Hence to review and devise strategies to reduce the adverse impacts of soil erosion is of utmost importance to the planners of watershed management programs in these regions. This paper demonstrates the use of satellite based remote sensing data coupled with the observational field data in a multi-criteria analytical (MCA) framework to estimate the soil erosion susceptibility of the sub-watersheds of the Rembiara basin falling in the western Himalaya, using geographical information system (GIS). In this paper, watershed morphometry and land cover are used as an inputs to the MCA framework to prioritize the sub-watersheds of this basin on the basis of their different susceptibilities to soil erosion. Methodology included the derivation of a set of drainage and land cover parameters that act as the indicators of erosion susceptibility. Further the output from the MCA resulted in the categorization of the sub-watersheds into low, medium, high and very high erosion susceptibility classes. A detailed prioritization map for the susceptible sub-watersheds based on the combined role of land cover and morphometry is finally presented. Besides, maps identifying the susceptible sub-watersheds based on morphometry and land cover only are also presented. The results of this study are part of the watershed management program in the study area and are directed to instigate appropriate measures to alleviate the soil erosion in the study area. PMID:25154685

  2. Deformation-based brain morphometry to track the course of alcoholism: differences between intra-subject and inter-subject analysis.

    PubMed

    Rohlfing, Torsten; Sullivan, Edith V; Pfefferbaum, Adolf

    2006-03-31

    two analyses, e.g., reduction of white matter (including corpus callosum) and increase in CSF volume, and these are in agreement with established effects of alcoholism on brain structure. We conclude that intra-subject morphometry of longitudinal data is preferable to inter-subject morphometry for detecting dynamic changes due to a disease, especially when only small samples are available. Our analysis demonstrates that the distinction between group differences observed at a point in time vs. over time is not merely academic but can substantially reduce the validity of the outcomes of actual morphometric studies. This discrepancy in results underscores the importance of distinguishing between volume differences and volume changes in morphometric analyses. PMID:16500088

  3. X-ray Crystallography Reveals a Reduced Substrate Complex of UDP-Galactopyranose Mutase Poised for Covalent Catalysis by Flavin

    SciTech Connect

    Gruber, Todd D.; Westler, William M.; Kiessling, Laura L.; Forest, Katrina T.

    2009-11-04

    The flavoenzyme uridine 5'-diphosphate galactopyranose mutase (UGM or Glf) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. The latter is a key building block for cell wall construction in numerous pathogens, including Mycobacterium tuberculosis. Mechanistic studies of UGM suggested a novel role for the flavin, and we previously provided evidence that the catalytic mechanism proceeds through a covalent flavin-galactose iminium. Here, we describe 2.3 and 2.5 {angstrom} resolution X-ray crystal structures of the substrate-bound enzyme in oxidized and reduced forms, respectively. In the latter, C1 of the substrate is 3.6 {angstrom} from the nucleophilic flavin N5 position. This orientation is consistent with covalent catalysis by flavin.

  4. Higher Dimensional Meta-State Analysis Reveals Reduced Resting fMRI Connectivity Dynamism in Schizophrenia Patients

    PubMed Central

    Miller, Robyn L.; Yaesoubi, Maziar; Turner, Jessica A.; Mathalon, Daniel; Preda, Adrian; Pearlson, Godfrey; Adali, Tulay; Calhoun, Vince D.

    2016-01-01

    Resting-state functional brain imaging studies of network connectivity have long assumed that functional connections are stationary on the timescale of a typical scan. Interest in moving beyond this simplifying assumption has emerged only recently. The great hope is that training the right lens on time-varying properties of whole-brain network connectivity will shed additional light on previously concealed brain activation patterns characteristic of serious neurological or psychiatric disorders. We present evidence that multiple explicitly dynamical properties of time-varying whole-brain network connectivity are strongly associated with schizophrenia, a complex mental illness whose symptomatic presentation can vary enormously across subjects. As with so much brain-imaging research, a central challenge for dynamic network connectivity lies in determining transformations of the data that both reduce its dimensionality and expose features that are strongly predictive of important population characteristics. Our paper introduces an elegant, simple method of reducing and organizing data around which a large constellation of mutually informative and intuitive dynamical analyses can be performed. This framework combines a discrete multidimensional data-driven representation of connectivity space with four core dynamism measures computed from large-scale properties of each subject’s trajectory, ie., properties not identifiable with any specific moment in time and therefore reasonable to employ in settings lacking inter-subject time-alignment, such as resting-state functional imaging studies. Our analysis exposes pronounced differences between schizophrenia patients (Nsz = 151) and healthy controls (Nhc = 163). Time-varying whole-brain network connectivity patterns are found to be markedly less dynamically active in schizophrenia patients, an effect that is even more pronounced in patients with high levels of hallucinatory behavior. To the best of our knowledge this is

  5. Mesenchymal stem cells from osteoporotic patients reveal reduced migration and invasion upon stimulation with BMP-2 or BMP-7.

    PubMed

    Haasters, Florian; Docheva, Denitsa; Gassner, Christoph; Popov, Cvetan; Böcker, Wolfgang; Mutschler, Wolf; Schieker, Matthias; Prall, Wolf Christian

    2014-09-12

    Fractures to the osteoporotic bone feature a delay in callus formation and reduced enchondral ossification. Human mesenchymal stem cells (hMSC), the cellular source of fracture healing, are recruited to the fracture site by cytokines, such as BMP-2 and BMP-7. Aim of the study was to scrutinize hMSC for osteoporosis associated alterations in BMP mediated migration and invasion as well as in extracellular matrix (ECM) binding integrin expression. HMSC were isolated from 18 healthy or osteoporotic donors. Migration was assessed using a collagen IV coated micro-slide linear gradient chamber and time-lapse microscopy. Invasion was analyzed utilizing an ECM coated transmembrane invasion assay. Quantitative real-time RT PCR was performed for the ECM binding integrins α1, α2, α3, α4, α5, α11, αv and β1. HMSC from osteoporotic patients showed a significant increase of migration upon BMP-2 or FCS stimulation, as well as a significant increase of invasion upon BMP-2, BMP-7 or FCS stimulation. Nevertheless, the migration and invasion capacity was significantly decreased compared to healthy controls. Out of all integrins analyzed, collagen binding integrin α2 was significantly downregulated in hMSC from osteoporotic patients. In conclusion, we here demonstrate for the first time osteoporosis associated alterations in BMP mediated hMSC recruitment. These findings may underlie the reduced healing of osteoporotic fractures. Nevertheless, the maintained migration and invasion response upon BMP stimulation illustrates the therapeutic potential of these clinically approved substances in the treatment of osteoporotic fractures. Another therapeutic target may be the downregulation of the collagen binding integrin α2 in hMSC from osteoporotic patients. PMID:25152406

  6. Higher Dimensional Meta-State Analysis Reveals Reduced Resting fMRI Connectivity Dynamism in Schizophrenia Patients.

    PubMed

    Miller, Robyn L; Yaesoubi, Maziar; Turner, Jessica A; Mathalon, Daniel; Preda, Adrian; Pearlson, Godfrey; Adali, Tulay; Calhoun, Vince D

    2016-01-01

    Resting-state functional brain imaging studies of network connectivity have long assumed that functional connections are stationary on the timescale of a typical scan. Interest in moving beyond this simplifying assumption has emerged only recently. The great hope is that training the right lens on time-varying properties of whole-brain network connectivity will shed additional light on previously concealed brain activation patterns characteristic of serious neurological or psychiatric disorders. We present evidence that multiple explicitly dynamical properties of time-varying whole-brain network connectivity are strongly associated with schizophrenia, a complex mental illness whose symptomatic presentation can vary enormously across subjects. As with so much brain-imaging research, a central challenge for dynamic network connectivity lies in determining transformations of the data that both reduce its dimensionality and expose features that are strongly predictive of important population characteristics. Our paper introduces an elegant, simple method of reducing and organizing data around which a large constellation of mutually informative and intuitive dynamical analyses can be performed. This framework combines a discrete multidimensional data-driven representation of connectivity space with four core dynamism measures computed from large-scale properties of each subject's trajectory, ie., properties not identifiable with any specific moment in time and therefore reasonable to employ in settings lacking inter-subject time-alignment, such as resting-state functional imaging studies. Our analysis exposes pronounced differences between schizophrenia patients (Nsz = 151) and healthy controls (Nhc = 163). Time-varying whole-brain network connectivity patterns are found to be markedly less dynamically active in schizophrenia patients, an effect that is even more pronounced in patients with high levels of hallucinatory behavior. To the best of our knowledge this is the

  7. Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions

    PubMed Central

    Khan, Tahsin; Douglas, Gavin M.; Patel, Priyenbhai; Nguyen Ba, Alex N.; Moses, Alan M.

    2015-01-01

    Intrinsically disordered protein regions are abundant in eukaryotic proteins and lack stable tertiary structures and enzymatic functions. Previous studies of disordered region evolution based on interspecific alignments have revealed an increased propensity for indels and rapid rates of amino acid substitution. How disordered regions are maintained at high abundance in the proteome and across taxa, despite apparently weak evolutionary constraints, remains unclear. Here, we use single nucleotide and indel polymorphism data in yeast and human populations to survey the population variation within disordered regions. First, we show that single nucleotide polymorphisms in disordered regions are under weaker negative selection compared with more structured protein regions and have a higher proportion of neutral non-synonymous sites. We also confirm previous findings that nonframeshifting indels are much more abundant in disordered regions relative to structured regions. We find that the rate of nonframeshifting indel polymorphism in intrinsically disordered regions resembles that of noncoding DNA and pseudogenes, and that large indels segregate in disordered regions in the human population. Our survey of polymorphism confirms patterns of evolution in disordered regions inferred based on longer evolutionary comparisons. PMID:26047845

  8. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

    PubMed Central

    He, Xuesong; McLean, Jeffrey S.; Edlund, Anna; Yooseph, Shibu; Hall, Adam P.; Liu, Su-Yang; Dorrestein, Pieter C.; Esquenazi, Eduardo; Hunter, Ryan C.; Cheng, Genhong; Nelson, Karen E.; Lux, Renate; Shi, Wenyuan

    2015-01-01

    The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. This extremely small coccus (200–300 nm) has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of an Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase, thereby killing its host. This first completed genome (705 kb) for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity. Comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host. Transcriptomic and metabolomic profiles provided the first indications, to our knowledge, that there is signaling interaction between TM7x and XH001. Furthermore, the induction of TNF-α production in macrophages by XH001 was repressed in the presence of TM7x, suggesting its potential immune suppression ability. Overall, our data provide intriguing insights into the uncultivability, pathogenicity, and unique lifestyle of this previously uncharacterized oral TM7 phylotype. PMID:25535390

  9. Absolute pitch: evidence for early cognitive facilitation during passive listening as revealed by reduced P3a amplitudes.

    PubMed

    Rogenmoser, Lars; Elmer, Stefan; Jäncke, Lutz

    2015-03-01

    Absolute pitch (AP) is the rare ability to identify or produce different pitches without using reference tones. At least two sequential processing stages are assumed to contribute to this phenomenon. The first recruits a pitch memory mechanism at an early stage of auditory processing, whereas the second is driven by a later cognitive mechanism (pitch labeling). Several investigations have used active tasks, but it is unclear how these two mechanisms contribute to AP during passive listening. The present work investigated the temporal dynamics of tone processing in AP and non-AP (NAP) participants by using EEG. We applied a passive oddball paradigm with between- and within-tone category manipulations and analyzed the MMN reflecting the early stage of auditory processing and the P3a response reflecting the later cognitive mechanism during the second processing stage. Results did not reveal between-group differences in MMN waveforms. By contrast, the P3a response was specifically associated with AP and sensitive to the processing of different pitch types. Specifically, AP participants exhibited smaller P3a amplitudes, especially in between-tone category conditions, and P3a responses correlated significantly with the age of commencement of musical training, suggesting an influence of early musical exposure on AP. Our results reinforce the current opinion that the representation of pitches at the processing level of the auditory-related cortex is comparable among AP and NAP participants, whereas the later processing stage is critical for AP. Results are interpreted as reflecting cognitive facilitation in AP participants, possibly driven by the availability of multiple codes for tones. PMID:25170790

  10. Reduced mismatch repair of heteroduplexes reveals "non"-interfering crossing over in wild-type Saccharomyces cerevisiae.

    PubMed

    Getz, Tony J; Banse, Stephen A; Young, Lisa S; Banse, Allison V; Swanson, Johanna; Wang, Grace M; Browne, Barclay L; Foss, Henriette M; Stahl, Franklin W

    2008-03-01

    Using small palindromes to monitor meiotic double-strand-break-repair (DSBr) events, we demonstrate that two distinct classes of crossovers occur during meiosis in wild-type yeast. We found that crossovers accompanying 5:3 segregation of a palindrome show no conventional (i.e., positive) interference, while crossovers with 6:2 or normal 4:4 segregation for the same palindrome, in the same cross, do manifest interference. Our observations support the concept of a "non"-interference class and an interference class of meiotic double-strand-break-repair events, each with its own rules for mismatch repair of heteroduplexes. We further show that deletion of MSH4 reduces crossover tetrads with 6:2 or normal 4:4 segregation more than it does those with 5:3 segregation, consistent with Msh4p specifically promoting formation of crossovers in the interference class. Additionally, we present evidence that an ndj1 mutation causes a shift of noncrossovers to crossovers specifically within the "non"-interference class of DSBr events. We use these and other data in support of a model in which meiotic recombination occurs in two phases-one specializing in homolog pairing, the other in disjunction-and each producing both noncrossovers and crossovers. PMID:18385111

  11. Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation

    DOE PAGESBeta

    Garcia-Forner, Nuria; Adams, Henry D.; Sevanto, Sanna; Collins, Adam D.; Dickman, Lee T.; Hudson, Patrick J.; Zeppel, Melanie J. B.; Jenkins, Michael W.; Powers, Heath; Martinez-Vilalta, Jordi; et al

    2015-08-08

    Here, relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P.more » edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.« less

  12. Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation

    SciTech Connect

    Garcia-Forner, Nuria; Adams, Henry D.; Sevanto, Sanna; Collins, Adam D.; Dickman, Lee T.; Hudson, Patrick J.; Zeppel, Melanie J. B.; Jenkins, Michael W.; Powers, Heath; Martinez-Vilalta, Jordi; Mcdowell, Nate G.

    2015-08-08

    Here, relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P. edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.

  13. Metatranscriptome of an Anaerobic Benzene-Degrading, Nitrate-Reducing Enrichment Culture Reveals Involvement of Carboxylation in Benzene Ring Activation

    PubMed Central

    Luo, Fei; Gitiafroz, Roya; Devine, Cheryl E.; Gong, Yunchen; Hug, Laura A.; Raskin, Lutgarde

    2014-01-01

    The enzymes involved in the initial steps of anaerobic benzene catabolism are not known. To try to elucidate this critical step, a metatranscriptomic analysis was conducted to compare the genes transcribed during the metabolism of benzene and benzoate by an anaerobic benzene-degrading, nitrate-reducing enrichment culture. RNA was extracted from the mixed culture and sequenced without prior mRNA enrichment, allowing simultaneous examination of the active community composition and the differential gene expression between the two treatments. Ribosomal and mRNA sequences attributed to a member of the family Peptococcaceae from the order Clostridiales were essentially only detected in the benzene-amended culture samples, implicating this group in the initial catabolism of benzene. Genes similar to each of two subunits of a proposed benzene-carboxylating enzyme were transcribed when the culture was amended with benzene. Anaerobic benzoate degradation genes from strict anaerobes were transcribed only when the culture was amended with benzene. Genes for other benzoate catabolic enzymes and for nitrate respiration were transcribed in both samples, with those attributed to an Azoarcus species being most abundant. These findings indicate that the mineralization of benzene starts with its activation by a strict anaerobe belonging to the Peptococcaceae, involving a carboxylation step to form benzoate. These data confirm the previously hypothesized syntrophic association between a benzene-degrading Peptococcaceae strain and a benzoate-degrading denitrifying Azoarcus strain for the complete catabolism of benzene with nitrate as the terminal electron acceptor. PMID:24795366

  14. Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation.

    PubMed

    Garcia-Forner, Núria; Adams, Henry D; Sevanto, Sanna; Collins, Adam D; Dickman, Lee T; Hudson, Patrick J; Zeppel, Melanie J B; Jenkins, Michael W; Powers, Heath; Martínez-Vilalta, Jordi; Mcdowell, Nate G

    2016-01-01

    Relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P. edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies. PMID:26081870

  15. Multivariate analysis of eigenvalues and eigenvectors in tensor based morphometry

    NASA Astrophysics Data System (ADS)

    Rajagopalan, Vidya; Schwartzman, Armin; Hua, Xue; Leow, Alex; Thompson, Paul; Lepore, Natasha

    2015-01-01

    We develop a new algorithm to compute voxel-wise shape differences in tensor-based morphometry (TBM). As in standard TBM, we non-linearly register brain T1-weighed MRI data from a patient and control group to a template, and compute the Jacobian of the deformation fields. In standard TBM, the determinants of the Jacobian matrix at each voxel are statistically compared between the two groups. More recently, a multivariate extension of the statistical analysis involving the deformation tensors derived from the Jacobian matrices has been shown to improve statistical detection power.7 However, multivariate methods comprising large numbers of variables are computationally intensive and may be subject to noise. In addition, the anatomical interpretation of results is sometimes difficult. Here instead, we analyze the eigenvalues and the eigenvectors of the Jacobian matrices. Our method is validated on brain MRI data from Alzheimer's patients and healthy elderly controls from the Alzheimer's Disease Neuro Imaging Database.

  16. Computed tomography, anatomy and morphometry of the lower extremity

    SciTech Connect

    Hoogewoud, H.M.; Rager, G.; Burch, H.

    1989-01-01

    This book presents up-to-date information on CT imaging of the lower extremity. It includes an atlas correlating new, high-resolution CT scans with identical thin anatomical slices covering the lower extremity from the crista iliaca to the planta pedis. Additional figures, including CT arthrograms of the hip, knee and ankle, depict the anatomy in detail The technique and clinical relevance of CT measurements especially in orthopedic surgery are also clearly explained. Of special interest is the new method developed by the authors for assessing the coverage of the femoral head. The special morphometry software and a 3D program allowing representation in space make it possible to precisely and accurately measure the coverage with normal CT scans of the hip.

  17. Investigations of Martian Impact Crater Morphologies and Morphometries

    NASA Technical Reports Server (NTRS)

    Barlow, Nadine G.

    2002-01-01

    We have made substantial progress towards completion of the original objectives and are continuing to include new data from the Mars Global Surveyor MOC and TES instruments as they become available (the MOLA instrument has ceased operation as of 2002). The project funding has been used to provide salary support to the PI and several undergraduate students, cover publication charges for two papers, reimburse travel expenses to conferences and workshops incurred by the PI and students, and cover a number of other expenses such as software upgrades and production costs of slides and color prints. This study is revising the PI's Catalog of Large Martian Impact Craters with information obtained from MGS and is utilizing data in the revised Catalog to investigate which planetary factors (such as location, elevation, terrain type, etc.) primarily affect the formation of specific ejecta morphologies and morphometries.

  18. New experimental results in atlas-based brain morphometry

    NASA Astrophysics Data System (ADS)

    Gee, James C.; Fabella, Brian A.; Fernandes, Siddharth E.; Turetsky, Bruce I.; Gur, Ruben C.; Gur, Raquel E.

    1999-05-01

    In a previous meeting, we described a computational approach to MRI morphometry, in which a spatial warp mapping a reference or atlas image into anatomic alignment with the subject is first inferred. Shape differences with respect to the atlas are then studied by calculating the pointwise Jacobian determinant for the warp, which provides a measure of the change in differential volume about a point in the reference as it transforms to its corresponding position in the subject. In this paper, the method is used to analyze sex differences in the shape and size of the corpus callosum in an ongoing study of a large population of normal controls. The preliminary results of the current analysis support findings in the literature that have observed the splenium to be larger in females than in males.

  19. Nucleus Morphometry in Cultured Epithelial Cells Correlates with Phenotype.

    PubMed

    Khan, Ayyad Z; Utheim, Tor P; Jackson, Catherine J; Reppe, Sjur; Lyberg, Torstein; Eidet, Jon R

    2016-06-01

    Phenotype of cultured ocular epithelial transplants has been shown to affect clinical success rates following transplantation to the cornea. The purpose of this study was to evaluate the relationship between cell nucleus morphometry and phenotype in three types of cultured epithelial cells. This study provides knowledge for the development of a non-invasive method of determining the phenotype of cultured epithelium before transplantation. Cultured human conjunctival epithelial cells (HCjE), human epidermal keratinocytes (HEK), and human retinal pigment epithelial cells (HRPE) were analyzed by quantitative immunofluorescence. Assessments of nucleus morphometry and nucleus-to-cytoplasm ratio (N/C ratio) were performed using ImageJ. Spearman's correlation coefficient was employed for statistical analysis. Levels of the proliferation marker PCNA in HCjE, HEK, and HRPE correlated positively with nuclear area. Nuclear area correlated significantly with levels of the undifferentiated cell marker ABCG2 in HCjE. Bmi1 levels, but not p63α levels, correlated significantly with nuclear area in HEK. The N/C ratio did not correlate significantly with any of the immunomarkers in HCjE (ABCG2, CK7, and PCNA) and HRPE (PCNA). In HEK, however, the N/C ratio was negatively correlated with levels of the undifferentiated cell marker CK14 and positively correlated with Bmi1 expression. The size of the nuclear area correlated positively with proliferation markers in all three epithelia. Morphometric indicators of phenotype in cultured epithelia can be identified using ImageJ. Conversely, the N/C ratio did not show a uniform relationship with phenotype in HCjE, HEK, or HRPE. N/C ratio therefore, may not be a useful morphometric marker for in vitro assessment of phenotype in these three epithelia. PMID:27329312

  20. Tensor-Based Morphometry as a Neuroimaging Biomarker for Alzheimer’s Disease: An MRI Study of 676 AD, MCI, and Normal Subjects

    PubMed Central

    Hua, Xue; Leow, Alex D.; Parikshak, Neelroop; Lee, Suh; Chiang, Ming-Chang; Toga, Arthur W.; Jack, Clifford R.; Weiner, Michael W.; Thompson, Paul M.

    2011-01-01

    In one of the largest brain MRI studies to date, we used tensor-based morphometry (TBM) to create 3D maps of structural atrophy in 676 subjects with Alzheimer’s disease (AD), mild cognitive impairment (MCI), and healthy elderly controls, scanned as part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Using inverse-consistent 3D non-linear elastic image registration, we warped 676 individual brain MRI volumes to a population mean geometric template. Jacobian determinant maps were created, revealing the 3D profile of local volumetric expansion and compression. We compared the anatomical distribution of atrophy in 165 AD patients (age: 75.6 ± 7.6 years), 330 MCI subjects (74.8 ± 7.5), and 181 controls (75.9 ± 5.1). Brain atrophy in selected regions-of-interest was correlated with clinical measurements - the sum-of-boxes clinical dementia rating (CDR-SB), mini-mental state examination (MMSE), and the logical memory test scores - at voxel level followed by correction for multiple comparisons. Baseline temporal lobe atrophy correlated with current cognitive performance, future cognitive decline, and conversion from MCI to AD over the following year; it predicted future decline even in healthy subjects. Over half of the AD and MCI subjects carried the ApoE4 (apolipoprotein E4) gene, which increases risk for AD; they showed greater hippocampal and temporal lobe deficits than non-carriers. ApoE2 gene carriers - 1/6 of the normal group - showed reduced ventricular expansion, suggesting a protective effect. As an automated image analysis technique, TBM reveals 3D correlations between neuroimaging markers, genes, and future clinical changes, and is highly efficient for large-scale MRI studies. PMID:18691658

  1. Towards fast and routine analyses of volcanic ash morphometry for eruption surveillance applications

    NASA Astrophysics Data System (ADS)

    Leibrandt, Sébastien; Le Pennec, Jean-Luc

    2015-05-01

    The morphometry of volcanic ash produced by explosive eruptions yields ample information on fragmentation processes (e.g. magmatic vs magma-water interactions), and on transport and sedimentation mechanisms. Most previous works on volcanic clast morphometry focused on the Apparent (2D-)Projected shape of ASH grains, here termed APASH, to infer processes and eruptive styles. However, textural analyses of ash grains has remained a long and tedious task that made such approaches inappropriate for eruption surveillance duties. In this work we show that new technological advances on automated dispersion of granular materials imaged with a camera-coupled microscope and enhanced computer capabilities enable fast and high resolution image acquisition of thousands of ash grains that resolve this limitation. With a morpho-grainsizer designed for such fast and routine measurements we perform a series of APASH analyses on selected ash fractions of tephra deposits from known eruptive styles. We record the size, aspect ratio, circularity and convexity of APASH images and assess resolution, reproducibility, minimum population size, and total analytical duration, and offer recommendations for the reporting of APASH data for inter-laboratory comparisons. To avoid fractal geometry concerns, our analyses are carried out at constant size range (250-300 μm) and optical magnification (× 5) on ~ 3000 grains per samples collected from homogenized samples. Results from the andesitic 1999-ongoing eruption of Tungurahua volcano (Ecuador) show that ash particles from the moderate 2001 phase are relatively equant and convex in shape, while the stronger 2006 subplinian phase produced ash grains with more elongated, less circular and less convex APASH signatures. Ash grains from a basaltic scoria cone-forming eruption show even more ragged APASH characteristics. Overall, our protocol allows obtaining accurate and reproducible morphometric measurements that reveal subtle variations of the

  2. Towards fast and routine analyses of volcanic ash morphometry for eruption surveillance applications

    NASA Astrophysics Data System (ADS)

    Leibrandt, Sébastien; Le Pennec, Jean-Luc

    2015-04-01

    The morphometry of volcanic ash produced by explosive eruptions yields ample information on fragmentation processes (e.g. magmatic vs magma-water interactions), and on transport and sedimentation mechanisms. Most previous works on volcanic clast morphometry focused on the Apparent (2D-)Projected shape of ASH grains, here called APASH, to infer processes and eruptive styles. However, textural analyses of ash grains has remained a long and tedious task that made such approaches inappropriate for eruption surveillance duties. In this work we show that new technological advances on automated dispersion of granular materials imaged with a camera-coupled microscope and enhanced computer capabilities enable fast and high resolution image acquisition of thousands of ash grains that solve this limitation. With a morpho-grainsizer designed for such fast and routine measurements we perform a series of APASH analyses on selected ash fractions of tephra deposits from known eruptive styles. We record the size, aspect ratio, circularity and convexity of APASH images and assess resolution, reproducibility, minimum population size, and total analytical duration, and offer recommendations for the reporting of APASH data for interlaboratory comparisons. To avoid fractal geometry concerns, our analyses are carried out at constant size range (250-300 um) and optical magnification (x5) on ~3000 grains/samples collected from homogenized samples. Results from the andesitic 1999-ongoing eruption of Tungurahua volcano (Ecuador) show that ash particles from the moderate 2001 phase are relatively equant and convex in shape, while the stronger 2006 subplinian phase produced ash grains with more elongated, less circular and less convex APASH signatures. Ash grains from a basaltic scoria cone-forming eruption show even more ragged APASH characteristics. Overall, our protocol allows obtaining accurate and reproducible morphometric measurements that reveal subtle variations of the morphological

  3. Morphometry of Left Frontal and Temporal Poles Predicts Analogical Reasoning Abilities.

    PubMed

    Aichelburg, Clarisse; Urbanski, Marika; Thiebaut de Schotten, Michel; Humbert, Frederic; Levy, Richard; Volle, Emmanuelle

    2016-03-01

    Analogical reasoning is critical for making inferences and adapting to novelty. It can be studied experimentally using tasks that require creating similarities between situations or concepts, i.e., when their constituent elements share a similar organization or structure. Brain correlates of analogical reasoning have mostly been explored using functional imaging that has highlighted the involvement of the left rostrolateral prefrontal cortex (rlPFC) in healthy subjects. However, whether inter-individual variability in analogical reasoning ability in a healthy adult population is related to differences in brain architecture is unknown. We investigated this question by employing linear regression models of performance in analogy tasks and voxel-based morphometry in 54 healthy subjects. Our results revealed that the ability to reason by analogy was associated with structural variability in the left rlPFC and the anterior part of the inferolateral temporal cortex. Tractography of diffusion-weighted images suggested that these 2 regions have a different set of connections but may exchange information via the arcuate fasciculus. These results suggest that enhanced integrative and semantic abilities supported by structural variation in these areas (or their connectivity) may lead to more efficient analogical reasoning. PMID:25331605

  4. The correlation between gray matter volume and perceived social support: a voxel-based morphometry study.

    PubMed

    Che, XianWei; Wei, DongTao; Li, WenFu; Li, HaiJiang; Qiao, Lei; Qiu, Jiang; Zhang, QingLin; Liu, YiJun

    2014-01-01

    Social support refers to interpersonal exchanges that include the combinations of aid, affirmation and affection. Perceived social support is a kind of subjective judgment of one's availability of social support. In spite of the importance of perceived social support to health, however, its neural substrate remains unknown. To address this question, voxel-based morphometry was employed to investigate the neural bases of individual differences in responses to the Perceived Social Support Scale (PSSS) in healthy volunteers (144 men and 203 women; mean age = 19.9; SD = 1.33, age range : 17-27). As a result, multiple regression analysis revealed that the PSSS scores were significantly and positively correlated with gray matter volume in a cluster that mainly included areas in posterior parts of posterior cingulate cortex, bilateral lingual cortex, left occipital lobe and cuneus. Highly-supported individuals had larger gray matter volume in these brain regions, implying a relatively high level of ability to engage in self-referential processes and social cognition. Our results provide a biological basis for exploring perceived social support particularly in relationship to various health parameters and outcomes. PMID:24397344

  5. A global database of volcano edifice morphometry using SRTM DEMs

    NASA Astrophysics Data System (ADS)

    Grosse, P.; van Wyk de Vries, B.; Petrinovic, I. A.; Euillades, P. A.

    2009-12-01

    The morphometry of volcanic edifices reflects the aggradational and degradational processes that interact during their evolution. In association with VOGRIPA, a global risk identification project, we are currently constructing a database on the morphometry of volcanic edifices using digital elevation models (DEMs) from the Shuttle Radar Topography Mission (SRTM). Our aim is to compile and make available a global database of morphometric parameters that characterize the shape and size of volcanic edifices. The 90-meter SRTM DEM is presently the best public-access DEM dataset for this task because of its near-global coverage and spatial resolution that is high enough for the analysis of composite volcanic edifices. The Smithsonian Institution database lists 1536 active/potentially active volcanoes worldwide. Of these, ~900 volcano edifices can be analyzed with the SRTM DEMs, discarding volcanoes not covered by the dataset above latitudes 60°N and 56°S, submarine volcanoes, volcanoes with mostly negative topographies (i.e. calderas, maars) and monogenetic cones and domes, which are too small to accurately study with the 90-meter resolution. Morphometric parameters are acquired using an expressly written IDL-language code named MORVOLC. Edifice outline is determined via a semi-automated algorithm that identifies slope-breaks between user-estimated maximum and minimum outlines. Thus, volcanic edifices as topographic entities are considered, excluding aprons or ring plains and other far-reaching volcanic products. Several morphometric parameters are computed which characterize edifice size and shape. Size parameters are height (from base to summit), volume, base and summit areas and widths (average, minimum, maximum). Plan shape is summarized using two independent dimensionless indexes that describe the shape of the elevation contours, ellipticity (quantifies the elongation of each contour) and irregularity (quantifies the irregularity or complexity of each contour

  6. Larger right posterior parietal volume in action video game experts: a behavioral and voxel-based morphometry (VBM) study.

    PubMed

    Tanaka, Satoshi; Ikeda, Hanako; Kasahara, Kazumi; Kato, Ryo; Tsubomi, Hiroyuki; Sugawara, Sho K; Mori, Makoto; Hanakawa, Takashi; Sadato, Norihiro; Honda, Manabu; Watanabe, Katsumi

    2013-01-01

    Recent studies suggest that action video game players exhibit superior performance in visuospatial cognitive tasks compared with non-game players. However, the neural basis underlying this visuospatial cognitive performance advantage remains largely unknown. The present human behavioral and imaging study compared gray matter volume in action video game experts and non-experts using structural magnetic resonance imaging and voxel-based morphometry analysis. The results revealed significantly larger gray matter volume in the right posterior parietal cortex in experts compared with non-experts. Furthermore, the larger gray matter volume in the right posterior parietal cortex significantly correlated with individual performance in a visual working memory task in experts. These results suggest that differences in brain structure may be linked to extensive video game play, leading to superior visuospatial cognitive performance in action video game experts. PMID:23776706

  7. Larger Right Posterior Parietal Volume in Action Video Game Experts: A Behavioral and Voxel-Based Morphometry (VBM) Study

    PubMed Central

    Tanaka, Satoshi; Ikeda, Hanako; Kasahara, Kazumi; Kato, Ryo; Tsubomi, Hiroyuki; Sugawara, Sho K.; Mori, Makoto; Hanakawa, Takashi; Sadato, Norihiro; Honda, Manabu; Watanabe, Katsumi

    2013-01-01

    Recent studies suggest that action video game players exhibit superior performance in visuospatial cognitive tasks compared with non-game players. However, the neural basis underlying this visuospatial cognitive performance advantage remains largely unknown. The present human behavioral and imaging study compared gray matter volume in action video game experts and non-experts using structural magnetic resonance imaging and voxel-based morphometry analysis. The results revealed significantly larger gray matter volume in the right posterior parietal cortex in experts compared with non-experts. Furthermore, the larger gray matter volume in the right posterior parietal cortex significantly correlated with individual performance in a visual working memory task in experts. These results suggest that differences in brain structure may be linked to extensive video game play, leading to superior visuospatial cognitive performance in action video game experts. PMID:23776706

  8. Morphometry, Bite-Force, and Paleobiology of the Late Miocene Caiman Purussaurus brasiliensis

    PubMed Central

    Aureliano, Tito; Ghilardi, Aline M.; Guilherme, Edson; Souza-Filho, Jonas P.; Cavalcanti, Mauro; Riff, Douglas

    2015-01-01

    Purussaurus brasiliensis thrived in the northwestern portion of South America during the Late Miocene. Although substantial material has been recovered since its early discovery, this fossil crocodilian can still be considered as very poorly understood. In the present work, we used regression equations based on modern crocodilians to present novel details about the morphometry, bite-force and paleobiology of this species. According to our results, an adult Purussaurus brasiliensis was estimated to reach around 12.5 m in length, weighing around 8.4 metric tons, with a mean daily food intake of 40.6 kg. It was capable of generating sustained bite forces of 69,000 N (around 7 metric tons-force). The extreme size and strength reached by this animal seems to have allowed it to include a wide range of prey in its diet, making it a top predator in its ecosystem. As an adult, it would have preyed upon large to very large vertebrates, and, being unmatched by any other carnivore, it avoided competition. The evolution of a large body size granted P. brasiliensis many advantages, but it may also have led to its vulnerability. The constantly changing environment on a large geological scale may have reduced its long-term survival, favoring smaller species more resilient to ecological shifts. PMID:25689140

  9. Morphometry, bite-force, and paleobiology of the late miocene caiman Purussaurus brasiliensis.

    PubMed

    Aureliano, Tito; Ghilardi, Aline M; Guilherme, Edson; Souza-Filho, Jonas P; Cavalcanti, Mauro; Riff, Douglas

    2015-01-01

    Purussaurus brasiliensis thrived in the northwestern portion of South America during the Late Miocene. Although substantial material has been recovered since its early discovery, this fossil crocodilian can still be considered as very poorly understood. In the present work, we used regression equations based on modern crocodilians to present novel details about the morphometry, bite-force and paleobiology of this species. According to our results, an adult Purussaurus brasiliensis was estimated to reach around 12.5 m in length, weighing around 8.4 metric tons, with a mean daily food intake of 40.6 kg. It was capable of generating sustained bite forces of 69,000 N (around 7 metric tons-force). The extreme size and strength reached by this animal seems to have allowed it to include a wide range of prey in its diet, making it a top predator in its ecosystem. As an adult, it would have preyed upon large to very large vertebrates, and, being unmatched by any other carnivore, it avoided competition. The evolution of a large body size granted P. brasiliensis many advantages, but it may also have led to its vulnerability. The constantly changing environment on a large geological scale may have reduced its long-term survival, favoring smaller species more resilient to ecological shifts. PMID:25689140

  10. Role of Disgust Proneness in Parkinson’s Disease: A Voxel-Based Morphometry Study

    PubMed Central

    Ille, Rottraut; Wabnegger, Albert; Schwingenschuh, Petra; Katschnig-Winter, Petra; Kögl-Wallner, Mariella; Wenzel, Karoline; Schienle, Anne

    2015-01-01

    The knowledge about personality traits in Parkinson’s disease (PD) is still limited. In particular, disgust proneness has not been investigated as well as its neuronal correlates. Although several morphometric studies demonstrated that PD is associated with gray matter volume (GMV) reduction in olfactory and gustatory regions involved in disgust processing, a possible correlation with disgust proneness has not been investigated. We conducted a voxel-based morphometry analysis to compare GMV between 16 cognitively normal male PD patients with mild to moderate symptoms and 24 matched control subjects. All participants had answered questionnaires for the assessment of disgust proneness, trait anger and trait anxiety. We correlated questionnaire scores with GMV in both groups. The clinical group reported selectively reduced disgust proneness toward olfactory stimuli associated with spoilage. Moreover, they showed GMV reduction in the central olfactory system [orbitofrontal cortex (OFC) and piriform cortex]. Disgust items referring to olfactory processing were positively correlated with OFC volume in PD patients. Our data suggest an association between PD-associated neurodegeneration and olfactory related facets of the personality trait disgust proneness. PMID:25908177

  11. Lung morphometry changes in prevention of airway remodeling by protocatechuic aldehyde in asthmatic mice.

    PubMed

    Zhang, Jiankai; Ma, Mulan; Qin, Dongyun; Huang, Jianping; Cui, Xiaojun; Wu, Yongfu; Yang, Huiling; Fu, Hui; Liao, Cui

    2015-01-01

    Airway remodeling can lead to irreversible airflow obstruction and persistent airway hyper-responsiveness, which is the pathological basis of refractory asthma. To investigate the preventive effect of protocatechuic aldehyde on airway remodeling in asthmatic mice by lung morphometry methods. BALB/c mice were used to establish model of airway remodeling by ovalbumin (OVA) inhalation. Bronchoalveolar lavage fluid (BALF) were collected for eosinophils (EOS) count and detection of interleukin 4 (IL-4), interleukin-13 (IL-13) and interferon (IFN-γ) content. The left lung pathological sections were performed HE, AB-PAS and Masson staining. The epithelial lamina thickness of the left main bronchus (Re), the smooth muscle layer thickness (Rm), the number of goblet cells and goblet cell area percentage (%Ac) and gas side of the road and vascular collagen deposition (%Aco, %Avc) situation were measured. Protocatechuic aldehyde gavage made the reduction of BALF EOS count. IL-4 and IL-13 levels also decreased, while the IFN-γ level increased. The left main bronchus Re, Rm, goblet cell count, Ac% and Aco% and Avc% reduced. Protocatechuic aldehyde can significantly control airway inflammation and prevent airway remodeling. PMID:26221226

  12. Annual research review: progress in using brain morphometry as a clinical tool for diagnosing psychiatric disorders.

    PubMed

    Haubold, Alexander; Peterson, Bradley S; Bansal, Ravi

    2012-05-01

    Brain morphometry in recent decades has increased our understanding of the neural bases of psychiatric disorders by localizing anatomical disturbances to specific nuclei and subnuclei of the brain. At least some of these disturbances precede the overt expression of clinical symptoms and possibly are endophenotypes that could be used to diagnose an individual accurately as having a specific psychiatric disorder. More accurate diagnoses could significantly reduce the emotional and financial burden of disease by aiding clinicians in implementing appropriate treatments earlier and in tailoring treatment to the individual needs. Several methods, especially those based on machine learning, have been proposed that use anatomical brain measures and gold-standard diagnoses of participants to learn decision rules that classify a person automatically as having one disorder rather than another. We review the general principles and procedures for machine learning, particularly as applied to diagnostic classification, and then review the procedures that have thus far attempted to diagnose psychiatric illnesses automatically using anatomical measures of the brain. We discuss the strengths and limitations of extant procedures and note that the sensitivity and specificity of these procedures in their most successful implementations have approximated 90%. Although these methods have not yet been applied within clinical settings, they provide strong evidence that individual patients can be diagnosed accurately using the spatial pattern of disturbances across the brain. PMID:22394424

  13. Comparison of Prostatic Tissue Processed by Microwave and Conventional Technique Using Morphometry

    PubMed Central

    Jain, Promil; Kumar, Sanjay; Arora, B; Singh, Sneh; Chabbra, Sonia; Sen, Rajeev

    2015-01-01

    Background and Objectives: Rapid processing of histopathological specimens and decreased turnaround time is important to fulfill the needs of clinicians treating sick patients, so the present study was conducted to compare the time taken and quality of sections in processing of prostatic tissue by rapid microwave and conventional techniques using morphometry. Methods: Four to five mm thick paired prostate tissue pieces of fifty cases of prostatectomy specimens were taken. One tissue piece of the pair was processed routinely overnight by conventional tissue processing and the other by microwave processing. Time taken for processing by both conventional technique and microwave technique was noted and compared. Then, both were stained with conventional method of hematoxylin and eosin staining and examined for histological typing and grading. Morphometric study was done on slides of prostatic tissue processed by both conventional and microwave technique. Result: The prostatectomy specimens included both benign (86%) and malignant (14%) prostatic lesions in the age range of 46-85 years. The time taken for steps of dehydration, clearing and impregnation in microwave technique was significantly less as compared to histoprocessing done by conventional technique. Morphology, staining patterns of prostatic tissue processed within minutes by microwave technique, whether benign or malignant, were comparable to those sections which were processed in days using standard technique. Conclusion: Domestic microwave oven can be used for histoprocessing to accelerate the processing with preservation of morphology and is cheaper than commercially available microwave ovens and processing time was considerably reduced from days to minutes. PMID:26516319

  14. Lung morphometry changes in prevention of airway remodeling by protocatechuic aldehyde in asthmatic mice

    PubMed Central

    Zhang, Jiankai; Ma, Mulan; Qin, Dongyun; Huang, Jianping; Cui, Xiaojun; Wu, Yongfu; Yang, Huiling; Fu, Hui; Liao, Cui

    2015-01-01

    Airway remodeling can lead to irreversible airflow obstruction and persistent airway hyper-responsiveness, which is the pathological basis of refractory asthma. To investigate the preventive effect of protocatechuic aldehyde on airway remodeling in asthmatic mice by lung morphometry methods. BALB/c mice were used to establish model of airway remodeling by ovalbumin (OVA) inhalation. Bronchoalveolar lavage fluid (BALF) were collected for eosinophils (EOS) count and detection of interleukin 4 (IL-4), interleukin-13 (IL-13) and interferon (IFN-γ) content. The left lung pathological sections were performed HE, AB-PAS and Masson staining. The epithelial lamina thickness of the left main bronchus (Re), the smooth muscle layer thickness (Rm), the number of goblet cells and goblet cell area percentage (%Ac) and gas side of the road and vascular collagen deposition (%Aco, %Avc) situation were measured. Protocatechuic aldehyde gavage made the reduction of BALF EOS count. IL-4 and IL-13 levels also decreased, while the IFN-γ level increased. The left main bronchus Re, Rm, goblet cell count, Ac% and Aco% and Avc% reduced. Protocatechuic aldehyde can significantly control airway inflammation and prevent airway remodeling. PMID:26221226

  15. Computational Morphometry for Detecting Changes in Brain Structure Due to Development, Aging, Learning, Disease and Evolution

    PubMed Central

    Mietchen, Daniel; Gaser, Christian

    2009-01-01

    The brain, like any living tissue, is constantly changing in response to genetic and environmental cues and their interaction, leading to changes in brain function and structure, many of which are now in reach of neuroimaging techniques. Computational morphometry on the basis of Magnetic Resonance (MR) images has become the method of choice for studying macroscopic changes of brain structure across time scales. Thanks to computational advances and sophisticated study designs, both the minimal extent of change necessary for detection and, consequently, the minimal periods over which such changes can be detected have been reduced considerably during the last few years. On the other hand, the growing availability of MR images of more and more diverse brain populations also allows more detailed inferences about brain changes that occur over larger time scales, way beyond the duration of an average research project. On this basis, a whole range of issues concerning the structures and functions of the brain are now becoming addressable, thereby providing ample challenges and opportunities for further contributions from neuroinformatics to our understanding of the brain and how it changes over a lifetime and in the course of evolution. PMID:19707517

  16. Emotional empathy in amyotrophic lateral sclerosis: a behavioural and voxel-based morphometry study.

    PubMed

    Cerami, Chiara; Dodich, Alessandra; Canessa, Nicola; Crespi, Chiara; Iannaccone, Sandro; Corbo, Massimo; Lunetta, Christian; Consonni, Monica; Scola, Elisa; Falini, Andrea; Cappa, Stefano F

    2014-03-01

    Amyotrophic lateral sclerosis (ALS) is a multisystem condition, in which executive and/or behavioural symptoms can occur. Deficits of social cognition, including defective cognitive and emotional empathy, have been recently reported in ALS subjects. The neurostructural correlates of these disorders in ALS are still unknown. The aims of this study were to evaluate two components of empathy in non-demented ALS subjects, and to associate performance with regional grey-matter density using voxel-based morphometry (VBM). Twenty non-demented sporadic probable or definite ALS patients and 56 matched healthy controls (HC) participated in a non-verbal task requiring the attribution of emotional versus cognitive states to identify the correct ending of comic strips, compared with a control condition requiring identifying causal relationships devoid of social components. A subgroup of 14 ALS and 20 HC joined the VBM study. Results demonstrated that, compared with controls, ALS patients showed defective emotional empathy attribution, related with reduced grey-matter density in the anterior cingulate cortex and right inferior frontal gyrus. Our study provided evidence of a specific impairment of emotional empathy in ALS patients, reflecting neural damage in a limbic prefrontal network involved in emotional processing. Social cognition disorders may represent a marker of cognitive dysfunction in ALS. PMID:23586919

  17. Regional gray matter abnormalities in patients with schizophrenia determined with optimized voxel-based morphometry

    NASA Astrophysics Data System (ADS)

    Guo, XiaoJuan; Yao, Li; Jin, Zhen; Chen, Kewei

    2006-03-01

    This study examined regional gray matter abnormalities across the whole brain in 19 patients with schizophrenia (12 males and 7 females), comparing with 11 normal volunteers (7 males and 4 females). The customized brain templates were created in order to improve spatial normalization and segmentation. Then automated preprocessing of magnetic resonance imaging (MRI) data was conducted using optimized voxel-based morphometry (VBM). The statistical voxel based analysis was implemented in terms of two-sample t-test model. Compared with normal controls, regional gray matter concentration in patients with schizophrenia was significantly reduced in the bilateral superior temporal gyrus, bilateral middle frontal and inferior frontal gyrus, right insula, precentral and parahippocampal areas, left thalamus and hypothalamus as well as, however, significant increases in gray matter concentration were not observed across the whole brain in the patients. This study confirms and extends some earlier findings on gray matter abnormalities in schizophrenic patients. Previous behavior and fMRI researches on schizophrenia have suggested that cognitive capacity decreased and self-conscious weakened in schizophrenic patients. These regional gray matter abnormalities determined through structural MRI with optimized VBM may be potential anatomic underpinnings of schizophrenia.

  18. Brain structure in post-traumatic stress disorder: A voxel-based morphometry analysis.

    PubMed

    Tan, Liwen; Zhang, Li; Qi, Rongfeng; Lu, Guangming; Li, Lingjiang; Liu, Jun; Li, Weihui

    2013-09-15

    This study compared the difference in brain structure in 12 mine disaster survivors with chronic post-traumatic stress disorder, 7 cases of improved post-traumatic stress disorder symptoms, and 14 controls who experienced the same mine disaster but did not suffer post-traumatic stress disorder, using the voxel-based morphometry method. The correlation between differences in brain structure and post-traumatic stress disorder symptoms was also investigated. Results showed that the gray matter volume was the highest in the trauma control group, followed by the symptoms-improved group, and the lowest in the chronic post-traumatic stress disorder group. Compared with the symptoms-improved group, the gray matter volume in the lingual gyrus of the right occipital lobe was reduced in the chronic post-traumatic stress disorder group. Compared with the trauma control group, the gray matter volume in the right middle occipital gyrus and left middle frontal gyrus was reduced in the symptoms-improved group. Compared with the trauma control group, the gray matter volume in the left superior parietal lobule and right superior frontal gyrus was reduced in the chronic post-traumatic stress disorder group. The gray matter volume in the left superior parietal lobule was significantly positively correlated with the State-Trait Anxiety Inventory subscale score in the symptoms-improved group and chronic post-traumatic stress disorder group (r = 0.477, P = 0.039). Our findings indicate that (1) chronic post-traumatic stress disorder patients have gray matter structural damage in the prefrontal lobe, occipital lobe, and parietal lobe, (2) after post-traumatic stress, the disorder symptoms are improved and gray matter structural damage is reduced, but cannot recover to the trauma-control level, and (3) the superior parietal lobule is possibly associated with chronic post-traumatic stress disorder. Post-traumatic stress disorder patients exhibit gray matter abnormalities. PMID:25206550

  19. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap

    NASA Astrophysics Data System (ADS)

    Gu, Shuang; Sushko, Oleksandr; Deery, Evelyne; Warren, Martin J.; Pickersgill, Richard W.

    2015-11-01

    CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel β-sheets have swapped their last β-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release.

  20. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap

    PubMed Central

    Gu, Shuang; Sushko, Oleksandr; Deery, Evelyne; Warren, Martin J.; Pickersgill, Richard W.

    2015-01-01

    CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel β-sheets have swapped their last β-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release. PMID:26616290

  1. Shape Classification Using Wasserstein Distance for Brain Morphometry Analysis.

    PubMed

    Su, Zhengyu; Zeng, Wei; Wang, Yalin; Lu, Zhong-Lin; Gu, Xianfeng

    2015-01-01

    Brain morphometry study plays a fundamental role in medical imaging analysis and diagnosis. This work proposes a novel framework for brain cortical surface classification using Wasserstein distance, based on uniformization theory and Riemannian optimal mass transport theory. By Poincare uniformization theorem, all shapes can be conformally deformed to one of the three canonical spaces: the unit sphere, the Euclidean plane or the hyperbolic plane. The uniformization map will distort the surface area elements. The area-distortion factor gives a probability measure on the canonical uniformization space. All the probability measures on a Riemannian manifold form the Wasserstein space. Given any 2 probability measures, there is a unique optimal mass transport map between them, the transportation cost defines the Wasserstein distance between them. Wasserstein distance gives a Riemannian metric for the Wasserstein space. It intrinsically measures the dissimilarities between shapes and thus has the potential for shape classification. To the best of our knowledge, this is the first. work to introduce the optimal mass transport map to general Riemannian manifolds. The method is based on geodesic power Voronoi diagram. Comparing to the conventional methods, our approach solely depends on Riemannian metrics and is invariant under rigid motions and scalings, thus it intrinsically measures shape distance. Experimental results on classifying brain cortical surfaces with different intelligence quotients demonstrated the efficiency and efficacy of our method. PMID:26221691

  2. Investigation of mindfulness meditation practitioners with voxel-based morphometry.

    PubMed

    Hölzel, Britta K; Ott, Ulrich; Gard, Tim; Hempel, Hannes; Weygandt, Martin; Morgen, Katrin; Vaitl, Dieter

    2008-03-01

    Mindfulness meditators practice the non-judgmental observation of the ongoing stream of internal experiences as they arise. Using voxel-based morphometry, this study investigated MRI brain images of 20 mindfulness (Vipassana) meditators (mean practice 8.6 years; 2 h daily) and compared the regional gray matter concentration to that of non-meditators matched for sex, age, education and handedness. Meditators were predicted to show greater gray matter concentration in regions that are typically activated during meditation. Results confirmed greater gray matter concentration for meditators in the right anterior insula, which is involved in interoceptive awareness. This group difference presumably reflects the training of bodily awareness during mindfulness meditation. Furthermore, meditators had greater gray matter concentration in the left inferior temporal gyrus and right hippocampus. Both regions have previously been found to be involved in meditation. The mean value of gray matter concentration in the left inferior temporal gyrus was predictable by the amount of meditation training, corroborating the assumption of a causal impact of meditation training on gray matter concentration in this region. Results suggest that meditation practice is associated with structural differences in regions that are typically activated during meditation and in regions that are relevant for the task of meditation. PMID:19015095

  3. Voxel Based Morphometry in Optical Coherence Tomography: Validation & Core Findings

    PubMed Central

    Antony, Bhavna J.; Chen, Min; Carass, Aaron; Jedynak, Bruno M.; Al-Louzi, Omar; Solomon, Sharon D.; Saidha, Shiv; Calabresi, Peter A.; Prince, Jerry L.

    2016-01-01

    Optical coherence tomography (OCT) of the human retina is now becoming established as an important modality for the detection and tracking of various ocular diseases. Voxel based morphometry (VBM) is a long standing neuroimaging analysis technique that allows for the exploration of the regional differences in the brain. There has been limited work done in developing registration based methods for OCT, which has hampered the advancement of VBM analyses in OCT based population studies. Following on from our recent development of an OCT registration method, we explore the potential benefits of VBM analysis in cohorts of healthy controls (HCs) and multiple sclerosis (MS) patients. Specifically, we validate the stability of VBM analysis in two pools of HCs showing no significant difference between the two populations. Additionally, we also present a retrospective study of age and sex matched HCs and relapsing remitting MS patients, demonstrating results consistent with the reported literature while providing insight into the retinal changes associated with this MS subtype. PMID:27199503

  4. Shape Classification Using Wasserstein Distance for Brain Morphometry Analysis

    PubMed Central

    Su, Zhengyu; Zeng, Wei; Wang, Yalin; Lu, Zhong-Lin; Gu, Xianfeng

    2015-01-01

    Brain morphometry study plays a fundamental role in medical imaging analysis and diagnosis. This work proposes a novel framework for brain cortical surface classification using Wasserstein distance, based on uniformization theory and Riemannian optimal mass transport theory. By Poincare uniformization theorem, all shapes can be conformally deformed to one of the three canonical spaces: the unit sphere, the Euclidean plane or the hyperbolic plane. The uniformization map will distort the surface area elements. The area-distortion factor gives a probability measure on the canonical uniformization space. All the probability measures on a Riemannian manifold form the Wasserstein space. Given any 2 probability measures, there is a unique optimal mass transport map between them, the transportation cost defines the Wasserstein distance between them. Wasserstein distance gives a Riemannian metric for the Wasserstein space. It intrinsically measures the dissimilarities between shapes and thus has the potential for shape classification. To the best of our knowledge, this is the first work to introduce the optimal mass transport map to general Riemannian manifolds. The method is based on geodesic power Voronoi diagram. Comparing to the conventional methods, our approach solely depends on Riemannian metrics and is invariant under rigid motions and scalings, thus it intrinsically measures shape distance. Experimental results on classifying brain cortical surfaces with different intelligence quotients demonstrated the efficiency and efficacy of our method. PMID:26221691

  5. Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

    PubMed

    Ding, Long-Jun; Su, Jian-Qiang; Xu, Hui-Juan; Jia, Zhong-Jun; Zhu, Yong-Guan

    2015-03-01

    Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In (13)C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils. PMID:25171335

  6. Surface-based morphometry reveals distinct cortical thickness and surface area profiles in Williams syndrome.

    PubMed

    Green, Tamar; Fierro, Kyle C; Raman, Mira M; Saggar, Manish; Sheau, Kristen E; Reiss, Allan L

    2016-04-01

    Morphometric investigations of brain volumes in Williams syndrome (WS) consistently show significant reductions in gray matter volume compared to controls. Cortical thickness (CT) and surface area (SA) are two constituent parts of cortical gray matter volume that are considered genetically distinguishable features of brain morphology. Yet, little is known about the independent contribution of cortical CT and SA to these volumetric differences in WS. Thus, our objectives were: (i) to evaluate whether the microdeletion in chromosome 7 associated with WS has a distinct effect on CT and SA, and (ii) to evaluate age-related variations in CT and SA within WS. We compared CT and SA values in 44 individuals with WS to 49 age- and sex-matched typically developing controls. Between-group differences in CT and SA were evaluated across two age groups: young (age range 6.6-18.9 years), and adults (age range 20.2-51.5 years). Overall, we found contrasting effects of WS on cortical thickness (increases) and surface area (decreases). With respect to brain topography, the between-group pattern of CT differences showed a scattered pattern while the between-group surface area pattern was widely distributed throughout the brain. In the adult subgroup, we observed a cluster of increases in cortical thickness in WS across the brain that was not observed in the young subgroup. Our findings suggest that extensive early reductions in surface area are the driving force for the overall reduction in brain volume in WS. The age-related cortical thickness findings might reflect delayed or even arrested development of specific brain regions in WS. PMID:26852730

  7. Effects of Omega-3 Fatty Acid Supplementation on Cognitive Functions and Neural Substrates: A Voxel-Based Morphometry Study in Aged Mice.

    PubMed

    Cutuli, Debora; Pagani, Marco; Caporali, Paola; Galbusera, Alberto; Laricchiuta, Daniela; Foti, Francesca; Neri, Cristina; Spalletta, Gianfranco; Caltagirone, Carlo; Petrosini, Laura; Gozzi, Alessandro

    2016-01-01

    Human and experimental studies have revealed putative neuroprotective and pro-cognitive effects of omega-3 polyunsaturated fatty acids (n-3 PUFA) in aging, evidencing positive correlations between peripheral n-3 PUFA levels and regional grey matter (GM) volume, as well as negative correlations between dietary n-3 PUFA levels and cognitive deficits. We recently showed that n-3 PUFA supplemented aged mice exhibit better hippocampal-dependent mnesic functions, along with enhanced cellular plasticity and reduced neurodegeneration, thus supporting a role of n-3 PUFA supplementation in preventing cognitive decline during aging. To corroborate these initial results and develop new evidence on the effects of n-3 PUFA supplementation on brain substrates at macro-scale level, here we expanded behavioral analyses to the emotional domain (anxiety and coping skills), and carried out a fine-grained regional GM volumetric mapping by using high-resolution MRI-based voxel-based morphometry. The behavioral effects of 8 week n-3 PUFA supplementation were measured on cognitive (discriminative, spatial and social) and emotional (anxiety and coping) abilities of aged (19 month-old at the onset of study) C57B6/J mice. n-3 PUFA supplemented mice showed better mnesic performances as well as increased active coping skills. Importantly, these effects were associated with enlarged regional hippocampal, retrosplenial and prefrontal GM volumes, and with increased post mortem n-3 PUFA brain levels. These findings indicate that increased dietary n-3 PUFA intake in normal aging can improve fronto-hippocampal GM structure and function, an effect present also when the supplementation starts at late age. Our data are consistent with a protective role of n-3 PUFA supplementation in counteracting cognitive decline, emotional dysfunctions and brain atrophy. PMID:26973513

  8. Effects of Omega-3 Fatty Acid Supplementation on Cognitive Functions and Neural Substrates: A Voxel-Based Morphometry Study in Aged Mice

    PubMed Central

    Cutuli, Debora; Pagani, Marco; Caporali, Paola; Galbusera, Alberto; Laricchiuta, Daniela; Foti, Francesca; Neri, Cristina; Spalletta, Gianfranco; Caltagirone, Carlo; Petrosini, Laura; Gozzi, Alessandro

    2016-01-01

    Human and experimental studies have revealed putative neuroprotective and pro-cognitive effects of omega-3 polyunsaturated fatty acids (n-3 PUFA) in aging, evidencing positive correlations between peripheral n-3 PUFA levels and regional grey matter (GM) volume, as well as negative correlations between dietary n-3 PUFA levels and cognitive deficits. We recently showed that n-3 PUFA supplemented aged mice exhibit better hippocampal-dependent mnesic functions, along with enhanced cellular plasticity and reduced neurodegeneration, thus supporting a role of n-3 PUFA supplementation in preventing cognitive decline during aging. To corroborate these initial results and develop new evidence on the effects of n-3 PUFA supplementation on brain substrates at macro-scale level, here we expanded behavioral analyses to the emotional domain (anxiety and coping skills), and carried out a fine-grained regional GM volumetric mapping by using high-resolution MRI-based voxel-based morphometry. The behavioral effects of 8 week n-3 PUFA supplementation were measured on cognitive (discriminative, spatial and social) and emotional (anxiety and coping) abilities of aged (19 month-old at the onset of study) C57B6/J mice. n-3 PUFA supplemented mice showed better mnesic performances as well as increased active coping skills. Importantly, these effects were associated with enlarged regional hippocampal, retrosplenial and prefrontal GM volumes, and with increased post mortem n-3 PUFA brain levels. These findings indicate that increased dietary n-3 PUFA intake in normal aging can improve fronto-hippocampal GM structure and function, an effect present also when the supplementation starts at late age. Our data are consistent with a protective role of n-3 PUFA supplementation in counteracting cognitive decline, emotional dysfunctions and brain atrophy. PMID:26973513

  9. An evaluation of volume-based morphometry for prediction of mild cognitive impairment and Alzheimer's disease

    PubMed Central

    Schmitter, Daniel; Roche, Alexis; Maréchal, Bénédicte; Ribes, Delphine; Abdulkadir, Ahmed; Bach-Cuadra, Meritxell; Daducci, Alessandro; Granziera, Cristina; Klöppel, Stefan; Maeder, Philippe; Meuli, Reto; Krueger, Gunnar

    2014-01-01

    Voxel-based morphometry from conventional T1-weighted images has proved effective to quantify Alzheimer's disease (AD) related brain atrophy and to enable fairly accurate automated classification of AD patients, mild cognitive impaired patients (MCI) and elderly controls. Little is known, however, about the classification power of volume-based morphometry, where features of interest consist of a few brain structure volumes (e.g. hippocampi, lobes, ventricles) as opposed to hundreds of thousands of voxel-wise gray matter concentrations. In this work, we experimentally evaluate two distinct volume-based morphometry algorithms (FreeSurfer and an in-house algorithm called MorphoBox) for automatic disease classification on a standardized data set from the Alzheimer's Disease Neuroimaging Initiative. Results indicate that both algorithms achieve classification accuracy comparable to the conventional whole-brain voxel-based morphometry pipeline using SPM for AD vs elderly controls and MCI vs controls, and higher accuracy for classification of AD vs MCI and early vs late AD converters, thereby demonstrating the potential of volume-based morphometry to assist diagnosis of mild cognitive impairment and Alzheimer's disease. PMID:25429357

  10. Rhesus macaque brain morphometry: a methodological comparison of voxel-wise approaches.

    PubMed

    McLaren, Donald G; Kosmatka, Kristopher J; Kastman, Erik K; Bendlin, Barbara B; Johnson, Sterling C

    2010-03-01

    Voxel-based morphometry studies have become increasingly common in human neuroimaging over the past several years; however, few studies have utilized this method to study morphometry changes in non-human primates. Here we describe the application of voxel-wise morphometry methods to the rhesus macaque (Macaca mulatta) using the 112RM-SL template and priors (McLaren et al. (2009) [42]) and as an illustrative example we describe age-associated changes in grey matter morphometry. Specifically, we evaluated the unified segmentation routine implemented using Statistical Parametric Mapping (SPM) software and the FMRIB's Automated Segmentation Tool (FAST) in the FMRIB Software Library (FSL); the effect of varying the smoothing kernel; and the effect of the normalization routine. We found that when studying non-human primates, brain images need less smoothing than in human studies, 2-4mm FWHM. Using flow field deformations (DARTEL) improved inter-subject alignment leading to results that were more likely due to morphometry differences as opposed to registration differences. PMID:19883763

  11. Preemptive heme oxygenase-1 gene delivery reveals reduced mortality and preservation of left ventricular function 1 yr after acute myocardial infarction.

    PubMed

    Liu, Xiaoli; Simpson, Jeremy A; Brunt, Keith R; Ward, Christopher A; Hall, Sean R R; Kinobe, Robert T; Barrette, Valerie; Tse, M Yat; Pang, Stephen C; Pachori, Alok S; Dzau, Victor J; Ogunyankin, Kofo O; Melo, Luis G

    2007-07-01

    We reported previously that predelivery of heme oxygenase-1 (HO-1) gene to the heart by adeno-associated virus-2 (AAV-2) markedly reduces ischemia and reperfusion (I/R)-induced myocardial injury. However, the effect of preemptive HO-1 gene delivery on long-term survival and prevention of postinfarction heart failure has not been determined. We assessed the effect of HO-1 gene delivery on long-term survival, myocardial function, and left ventricular (LV) remodeling 1 yr after myocardial infarction (MI) using echocardiographic imaging, pressure-volume (PV) analysis, and histomorphometric approaches. Two groups of Lewis rats were injected with 2 x 10(11) particles of AAV-LacZ (control) or AAV-human HO-1 (hHO-1) in the anterior-posterior apical region of the LV wall. Six weeks after gene transfer, animals were subjected to 30 min of ischemia by ligation of the left anterior descending artery followed by reperfusion. Echocardiographic measurements and PV analysis of LV function were obtained at 2 wk and 12 mo after I/R. One year after acute MI, mortality was markedly reduced in the HO-1-treated animals compared with the LacZ-treated animals. PV analysis demonstrated significantly enhanced LV developed pressure, elevated maximal dP/dt, and lower end-diastolic volume in the HO-1 animals compared with the LacZ animals. Echocardiography showed a larger apical anterior-to-posterior wall ratio in HO-1 animals compared with LacZ animals. Morphometric analysis revealed extensive myocardial scarring and fibrosis in the infarcted LV area of LacZ animals, which was reduced by 62% in HO-1 animals. These results suggest that preemptive HO-1 gene delivery may be useful as a therapeutic strategy to reduce post-MI LV remodeling and heart failure. PMID:17322421

  12. Morphology and digitally aided morphometry of the human paracentral lobule.

    PubMed

    Spasojević, Goran; Malobabic, Slobodan; Pilipović-Spasojević, Olivera; Djukić-Macut, Nataša; Maliković, Aleksandar

    2013-02-01

    The human paracentral lobule, the junction of the precentral and postcentral gyri at the medial hemispheric surface, contains several important functional regions, and its variable morphology requires exact morphological and quantitativedata. In order to obtain precise data we investigated the morphology of the paracentral lobule and quantified its visible (extrasulcal) surface. This surface corresponds to commonly used magnetic resonance imaging scout images. We studied 84 hemispheres of adult persons (42 brains; 26 males and 16 females; 20-65 years) fixed in neutral formalin for at least 4 weeks. The medial hemispheric surface was photographed at standard distance and each digital photo was calibrated. Using the intercommissural line system (commissura anterior-commissura posterior or CA-CP line), we performed standardised measurements of the paracentral lobule. Exact determination of its boundaries and morphological types was followed by digital morphometry of its extrasulcal surface using AutoCAD software. We found two distinct morphological types of the human paracentral lobule: continuous type, which was predominant (95.2%), and rare segmented type (4.8%). In hemispheres with segmented cingulate sulcus we also found the short transitional lobulo-limbic gyrus (13.1%). The mean extrasulcal surface of the left paracentral lobule was significantly larger, both in males (left 6.79 cm2 vs. right 5.76 cm2) and in females (left 6.05 cm2 vs. right 5.16 cm2). However, even larger average surfaces in males were not significantly different than the same in females. Reported morphological and quantitative data will be useful during diagnostics and treatment of pathologies affecting the human paracentral lobule, and in further studies of its cytoarchitectonic and functional parcellations. PMID:23749705

  13. Contribution of glomerular morphometry to the diagnosis of pediatric nephropathies.

    PubMed

    Marini, Mariana Barreto; Rocha, Laura Penna; Machado, Juliana Reis; Ramalho, Fernando Silva; Dos Reis, Marlene Antônia; Corrêa, Rosana Rosa Miranda

    2016-05-01

    Only a few studies describe histopathological changes in renal biopsies performed in pediatric patients. This study was conducted to identify an association between morphometric data in renal biopsies and renal function of these patients. Fifty-nine individuals with ages between 2 and 18 years old were selected, who were divided into six groups consisting of frequent nephropathies in children and adolescents and one control group. Proteinuria, urea, and creatinine values of the patients were recorded. Interactive image analysis software Leica QWin[®]was used for morpho- metric analysis of Bowman's capsule, glomerular capillary tuft, and Bowman's space area. The mean glomerular tuft area was higher in the membranous glomerulopathy group than in the podo- cytopathy group (57,101 ± 25,094 vs. 27,420 c ± 6279 µm(2); P <0.05). The median of Bowman's space area was higher in the control group than in the podocytopathy group and in the thin basement membrane/Alport syndrome group [12,210 (7676-26,945) vs. 5801 (3031-7852) µm(2); P <0.01 and 12210 (7676-26,945) vs. 4183 (3797-7992) µm(2); P <0.01, respectively]. There was a positive and significant correlation between Bowman's capsule area and the levels of proteinuria, creatinine, and urea of the patients, as well as between the glomerular tuft area and the levels of proteinuria, creatinine, and urea in the patients, regardless of their nephropathy. Glomerular morphometry may contribute to the diagnosis of some glomerulopathies and the association between glomerular morphometric parameters, and laboratory data may promote a better understanding of the prognosis of these patients. PMID:27215240

  14. A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry

    PubMed Central

    Wolf, Louis; Scheffer-de Gooyert, Jolanda M.; Monedero, Ignacio; Torroja, Laura; Coromina, Lluis; van der Laak, Jeroen A. W. M.; Schenck, Annette

    2016-01-01

    The morphology of synapses is of central interest in neuroscience because of the intimate relation with synaptic efficacy. Two decades of gene manipulation studies in different animal models have revealed a repertoire of molecules that contribute to synapse development. However, since such studies often assessed only one, or at best a few, morphological features at a given synapse, it remained unaddressed how different structural aspects relate to one another. Furthermore, such focused and sometimes only qualitative approaches likely left many of the more subtle players unnoticed. Here, we present the image analysis algorithm ‘Drosophila_NMJ_Morphometrics’, available as a Fiji-compatible macro, for quantitative, accurate and objective synapse morphometry of the Drosophila larval neuromuscular junction (NMJ), a well-established glutamatergic model synapse. We developed this methodology for semi-automated multiparametric analyses of NMJ terminals immunolabeled for the commonly used markers Dlg1 and Brp and showed that it also works for Hrp, Csp and Syt. We demonstrate that gender, genetic background and identity of abdominal body segment consistently and significantly contribute to variability in our data, suggesting that controlling for these parameters is important to minimize variability in quantitative analyses. Correlation and principal component analyses (PCA) were performed to investigate which morphometric parameters are inter-dependent and which ones are regulated rather independently. Based on nine acquired parameters, we identified five morphometric groups: NMJ size, geometry, muscle size, number of NMJ islands and number of active zones. Based on our finding that the parameters of the first two principal components hardly correlated with each other, we suggest that different molecular processes underlie these two morphometric groups. Our study sets the stage for systems morphometry approaches at the well-studied Drosophila NMJ. PMID:26998933

  15. A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry.

    PubMed

    Nijhof, Bonnie; Castells-Nobau, Anna; Wolf, Louis; Scheffer-de Gooyert, Jolanda M; Monedero, Ignacio; Torroja, Laura; Coromina, Lluis; van der Laak, Jeroen A W M; Schenck, Annette

    2016-03-01

    The morphology of synapses is of central interest in neuroscience because of the intimate relation with synaptic efficacy. Two decades of gene manipulation studies in different animal models have revealed a repertoire of molecules that contribute to synapse development. However, since such studies often assessed only one, or at best a few, morphological features at a given synapse, it remained unaddressed how different structural aspects relate to one another. Furthermore, such focused and sometimes only qualitative approaches likely left many of the more subtle players unnoticed. Here, we present the image analysis algorithm 'Drosophila_NMJ_Morphometrics', available as a Fiji-compatible macro, for quantitative, accurate and objective synapse morphometry of the Drosophila larval neuromuscular junction (NMJ), a well-established glutamatergic model synapse. We developed this methodology for semi-automated multiparametric analyses of NMJ terminals immunolabeled for the commonly used markers Dlg1 and Brp and showed that it also works for Hrp, Csp and Syt. We demonstrate that gender, genetic background and identity of abdominal body segment consistently and significantly contribute to variability in our data, suggesting that controlling for these parameters is important to minimize variability in quantitative analyses. Correlation and principal component analyses (PCA) were performed to investigate which morphometric parameters are inter-dependent and which ones are regulated rather independently. Based on nine acquired parameters, we identified five morphometric groups: NMJ size, geometry, muscle size, number of NMJ islands and number of active zones. Based on our finding that the parameters of the first two principal components hardly correlated with each other, we suggest that different molecular processes underlie these two morphometric groups. Our study sets the stage for systems morphometry approaches at the well-studied Drosophila NMJ. PMID:26998933

  16. Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana

    PubMed Central

    Gao, Ruimin; Liu, Peng; Yong, Yuhan; Wong, Sek-Man

    2016-01-01

    Turnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection, and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways. PMID:27086702

  17. Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana.

    PubMed

    Gao, Ruimin; Liu, Peng; Yong, Yuhan; Wong, Sek-Man

    2016-01-01

    Turnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection, and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways. PMID:27086702

  18. Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect.

    PubMed

    Standage, Daniel S; Berens, Ali J; Glastad, Karl M; Severin, Andrew J; Brendel, Volker P; Toth, Amy L

    2016-04-01

    Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insect Polistes dominula, accompanied by analysis of caste-related transcriptome and methylome sequence data for adult queens and workers. Polistes dominula possesses a fairly typical hymenopteran genome, but shows very low genomewide GC content and some evidence of reduced genome size. We found numerous caste-related differences in gene expression, with evidence that both conserved and novel genes are related to caste differences. Most strikingly, these -omics data reveal a major reduction in one of the major epigenetic mechanisms that has been previously suggested to be important for caste differences in social insects: DNA methylation. Along with a conspicuous loss of a key gene associated with environmentally responsive DNA methylation (the de novo DNA methyltransferase Dnmt3), these wasps have greatly reduced genomewide methylation to almost zero. In addition to providing a valuable resource for comparative analysis of social insect evolution, our integrative -omics data for this important behavioural and evolutionary model system call into question the general importance of DNA methylation in caste differences and evolution in social insects. PMID:26859767

  19. Trigeminal intersubnuclear neurons: morphometry and input-dependent structural plasticity in adult rats.

    PubMed

    Martin, Yasmina B; Negredo, Pilar; Villacorta-Atienza, Jose A; Avendaño, Carlos

    2014-05-01

    Intersubnuclear neurons in the caudal division of the spinal trigeminal nucleus that project to the principal nucleus (Pr5) play an active role in shaping the receptive fields of other neurons, at different levels in the ascending sensory system that processes information originating from the vibrissae. By using retrograde labeling and digital reconstruction, we investigated the morphometry and topology of the dendritic trees of these neurons and the changes induced by long-term experience-dependent plasticity in adult male rats. Primary afferent input was either eliminated by transection of the right infraorbital nerve (IoN), or selectively altered by repeated whisker clipping on the right side. These neurons do not display asymmetries between sides in basic metric and topologic parameters (global number of trees, nodes, spines, or dendritic ends), although neurons on the left tend to have longer terminal segments. Ipsilaterally, both deafferentation (IoN transection) and deprivation (whisker trimming) reduced the density of spines, and the former also caused a global increase in total dendritic length and a relative increase in more complex arbors. Contralaterally, deafferentation reduced more complex dendritic trees, and caused a moderate decline in dendritic length and spatial reach, and a loss of spines in number and density. Deprivation caused a similar, but more profound, effect on spines. Our findings provide original quantitative descriptions of a scarcely known cell population, and show that denervation- or deprivation-derived plasticity is expressed not only by neurons at higher levels of the sensory pathways, but also by neurons in key subcortical circuits for sensory processing. PMID:24178892

  20. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    DOE PAGESBeta

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, whichmore » is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.« less

  1. Surface morphology and morphometry of rat alveolar macrophages after ozone exposure

    SciTech Connect

    Dormans, J.A.; Rombout, P.J.; van Loveren, H. )

    1990-09-01

    As the ultrastructural data on the effects of ozone on pulmonary alveolar macrophages (PAM) are lacking, transmission (TEM) and scanning (SEM) electron microscopy were performed on rat PAM present in alveolar lavages following exposure to ozone. Rats were continuously exposed for 7 d to ozone concentrations ranging from 0.25 to 1.50 mg/m3 for 7 d followed by a 5-d recovery period. Additionally, morphometry on lung sections was performed to quantitate PAM. In a second experiment rats were continuously exposed to 1.50 mg O3/m3 for 1, 3, 5, or 7 d. To study the influence of concurrent ozone exposure and lung infection, due to Listeria monocytogenes, rats were exposed for 7 d to 1.50 mg O3/m3 after a Listeria infection. The surface area of lavaged control PAM was uniformly covered with ruffles as shown by SEM and TEM. Exposure to 0.5 mg ozone/m3 for 7 d resulted in cells partly covered with microvilli and blebs in addition to normal ruffles. The number of large size PAM increased with an increase in ozone concentration. After 1 d of exposure, normal-appearing as well as many small macrophages with ruffles and scattered lymphocytes were seen. Lavage samples taken after 5 or 7 d of exposure showed an identical cell composition to that taken after 3 d of exposure. After Listeria infection alone, lavage samples consisted of mainly lymphocytes and some macrophages. Small quantitative changes, such as an increase in the number of polymorphonuclear neutrophils and large-size PAM, occurred in lavages after ozone exposure and infection with L. monocytogenes. Morphometric examination of lung sections revealed a concentration-related increase in the number of PAM, even in animals exposed to 0.25 mg ozone/m3 for 7 d. Centriacinar regions were more severely affected than other regions of lung tissue.

  2. Brain morphometry shows effects of long-term musical practice in middle-aged keyboard players

    PubMed Central

    Gärtner, H.; Minnerop, M.; Pieperhoff, P.; Schleicher, A.; Zilles, K.; Altenmüller, E.; Amunts, K.

    2013-01-01

    To what extent does musical practice change the structure of the brain? In order to understand how long-lasting musical training changes brain structure, 20 male right-handed, middle-aged professional musicians and 19 matched controls were investigated. Among the musicians, 13 were pianists or organists with intensive practice regimes. The others were either music teachers at schools or string instrumentalists, who had studied the piano at least as a subsidiary subject, and practiced less intensively. The study was based on T1-weighted MR images, which were analyzed using deformation-based morphometry. Cytoarchitectonic probabilistic maps of cortical areas and subcortical nuclei as well as myeloarchitectonic maps of fiber tracts were used as regions of interest to compare volume differences in the brains of musicians and controls. In addition, maps of voxel-wise volume differences were computed and analyzed. Musicians showed a significantly better symmetric motor performance as well as a greater capability of controlling hand independence than controls. Structural MRI-data revealed significant volumetric differences between the brains of keyboard players, who practiced intensively and controls in right sensorimotor areas and the corticospinal tract as well as in the entorhinal cortex and the left superior parietal lobule. Moreover, they showed also larger volumes in a comparable set of regions than the less intensively practicing musicians. The structural changes in the sensory and motor systems correspond well to the behavioral results, and can be interpreted in terms of plasticity as a result of intensive motor training. Areas of the superior parietal lobule and the entorhinal cortex might be enlarged in musicians due to their special skills in sight-playing and memorizing of scores. In conclusion, intensive and specific musical training seems to have an impact on brain structure, not only during the sensitive period of childhood but throughout life. PMID

  3. Morphometry of in situ and lavaged pulmonary alveolar macrophages from control and ozone-exposed rats

    SciTech Connect

    Lum, H.; Tyler, W.S.; Hyde, D.M.; Plopper, C.G.

    1983-07-01

    Effects of ambient levels of ozone on cell size and compartments were determined morphometrically for both in situ and lavaged pulmonary alveolar macrophages from rats exposed to filtered air or to filtered air with 0.60 ppm ozone. The ozone exposure was 8 hr/day for 3 days. Significant exposure-related compartmental volume density changes of in situ centriacinar macrophages were: decreased endoplasm (p less than 0.01); increased lysosome-like structures (p less than 0.01); decreased primary lysosomes (p less than 0.01); increased small and large secondary lysosomes (p less than 0.001); and decreased phagosomes/autophagosomes (p less than 0.05). In lavaged macrophages, the only significant exposure-related change was an increase in the density of large secondary lysosomes (p less than 0.01). Mean profile areas of in situ centriacinar macrophages from control and exposed rats were 86.94 micrometers/sup 2/ and 112.04 micrometers/sup 2/, respectively. The average mean cell volume V and mean caliper diameter D of macrophages lavaged from control rats were 1128.45 micrometers/sup 3/ and 12.92 micrometers, respectively, whereas those from exposed rats were 1583.08 micrometers/sup 3/ and 14.46 micrometers, respectively. Exposure-related increases in cell size were seen in both in situ and lavaged macrophages, but more significant differences in cell compartments were seen in the in situ centriacinar macrophages. Morphometry of pulmonary alveolar macrophages after ambient levels of ozone indicated increased uptake, storage, or both rather than cell damage. Comparison of in situ centriacinar and lavaged macrophages from both control and exposed rats revealed significant differences in their volume fractions of nucleus, cytoplasm, ectoplasm, mitochondria, lysosome-like structures, lipid droplets, vacuoles, and phagosome/autophagosomes. These differences between centriacinar and lavaged macrophages indicate different cell populations are sampled by these two methods.

  4. Sperm ultrastructure, morphometry, and abnormal morphology in American black bears (Ursus americanus).

    PubMed

    Brito, L F C; Sertich, P L; Stull, G B; Rives, W; Knobbe, M

    2010-11-01

    The objective of this study was to describe sperm ultrastructure, morphometry, and abnormal morphology in American black bears. Electroejaculation was successful in 53.8% (7/13) of the attempts, but urine contamination was common. Epididymal sperm samples were also obtained from five bears. Sperm had a paddle-like head shape and the ultrastructure was similar to that of most other mammals. The most striking particularity of black bear sperm ultrastructure was a tightening of the nucleus in the equatorial region. Although the differences were not significant in all bears, the overall decrease in sperm nucleus dimensions during transport from the caput epididymis to the cauda suggested increasing compaction of the nucleus during maturation. For ejaculated sperm, nucleus length, width, and base width were 4.9, 3.7, and 1.8 μm, respectively, whereas sperm head length, width, and base width were 6.6, 4.8, and 2.3 μm, and midpiece, tail (including midpiece), and total sperm lengths were 9.8, 68.8, and 75.3 μm. Evaluation of sperm cytoplasmic droplets in the epididymis revealed that proximal droplets start migrating toward a distal position in the caput epididymis and that the process was mostly completed by the time sperm reached the cauda epididymis. The proportion of morphologically normal sperm in the ejaculate was 35.6%; the most prevalent sperm defects were distal cytoplasmic droplets and bent/coiled tails. The morphology of abnormal sperm and the underlying ultrastructural defects were similar to that in other large domestic animals thus suggesting similar underlying pathogenesis of specific sperm defects and similar effects on fertility. PMID:20708230

  5. Sports and brain morphology - a voxel-based morphometry study with endurance athletes and martial artists.

    PubMed

    Schlaffke, L; Lissek, S; Lenz, M; Brüne, M; Juckel, G; Hinrichs, T; Platen, P; Tegenthoff, M; Schmidt-Wilcke, T

    2014-02-14

    Physical exercises and motor skill learning have been shown to induce changes in regional brain morphology, this has been demonstrated for various activities and tasks. Also individuals with special skills show differences in regional brain morphology. This has been indicated for professional musicians, London taxi drivers, as well as for athletes like dancers, golfers and judokas. However little is known about whether sports with different metabolic profiles (aerobic vs. anaerobic) are associated with different patterns of altered brain morphology. In this cross-sectional study we investigated two groups of high-performance athletes, one group performing sports that are thought to be mainly aerobic, and one group performing sports known to have intermittent phases of anaerobic metabolism. Using high-resolution structural imaging and voxel-based morphometry (VBM), we investigated a group of 26 male athletes consisting of 13 martial artists and 13 endurance athletes as well as a group of non-exercising men (n=13). VBM analyses revealed higher gray matter (GM) volumes in the supplementary motor area/dorsal premotor cortex (BA 6) in both athlete groups as compared to the control group. In addition, endurance athletes showed significantly higher GM volume in the medial temporal lobe (MTL), specifically in the hippocampus and parahippocampal gyrus, which was not seen in the martial arts group. Our data suggest that high-performance sports are associated with changes in regional brain morphology in areas implicated in motor planning and motor learning. In addition high-level endurance sports seem to affect MTL structures, areas that have previously been shown to be modulated by aerobic exercise. PMID:24291669

  6. Comparative skeletal muscle fibre morphometry among wild birds with different locomotor behaviour

    PubMed Central

    TORRELLA, J. R.; FOUCES, V.; PALOMEQUE, J.; VISCOR, G.

    1998-01-01

    Six muscles of the mallard duck (Anas platyrhynchos), the common coot (Fulica atra) and the yellow-legged gull (Larus cachinnans) were analysed morphometrically, with special emphasis on their functional implications and physiological needs. Oxidative fibres always had significantly smaller size than anaerobic fibres, although no differences in the number of capillaries per fibre were found. This resulted in greater capillary counts per unit of fibre area and perimeter in oxidative than anaerobic fibres, which indicates that the greater demand for oxygen supply may be achieved by decreasing the size of the muscle fibre rather than by increasing the number of associated capillaries. Fast oxidative fibres of the pectoralis and the triceps of the gull had greater sizes than the fast oxidative fibres of the mallard and the coot, which correlates with the difference in energetic demands between flapping and gliding flight. Greater fibre cross-sectional areas and perimeters seem suited to afford the long-lasting activity with low metabolic demands required during gliding. By contrast, mallards and coots attain a high oxidative metabolism, during sustained flapping flight, by reducing fibre size at the expense of a diminished ability for force generation. Between-species comparisons of the hindlimb muscles only yielded differences for the anaerobic fibres of the gastrocnemius, as an important adaptive response to force generation during burst locomotion. The need to manage sustained swimming abilities effectively may result in similar FOG fibre morphometry of the hindlimb muscles studied, indicating that a compromise between the oxygen flux to the muscle cell and the development of power is highly optimised in oxidative fibres of the bird species studied. PMID:9643422

  7. 3D PATTERN OF BRAIN ABNORMALITIES IN WILLIAMS SYNDROME VISUALIZED USING TENSOR-BASED MORPHOMETRY

    PubMed Central

    Chiang, Ming-Chang; Reiss, Allan L.; Lee, Agatha D.; Bellugi, Ursula; Galaburda, Albert M.; Korenberg, Julie R.; Mills, Debra L.; Toga, Arthur W.; Thompson, Paul M.

    2009-01-01

    Williams syndrome (WS) is a neurodevelopmental disorder associated with deletion of ~20 contiguous genes in chromosome band 7q11.23. Individuals with WS exhibit mild to moderate mental retardation, but are relatively more proficient in specific language and musical abilities. We used tensor-based morphometry (TBM) to visualize the complex pattern of gray/white matter reductions in WS, based on fluid registration of structural brain images. Methods 3D T1-weighted brain MRIs of 41 WS subjects (age: 29.2±9.2SD years; 23F/18M) and 39 age-matched healthy controls (age: 27.5±7.4 years; 23F/16M) were fluidly registered to a minimum deformation target. Fine-scale volumetric differences were mapped between diagnostic groups. Local regions were identified where regional structure volumes were associated with diagnosis, and with intelligence quotient (IQ) scores. Brain asymmetry was also mapped and compared between diagnostic groups. Results WS subjects exhibited widely distributed brain volume reductions (~10–15% reduction; P < 0.0002, permutation test). After adjusting for total brain volume, the frontal lobes, anterior cingulate, superior temporal gyrus, amygdala, fusiform gyrus and cerebellum were found to be relatively preserved in WS, but parietal and occipital lobes, thalamus and basal ganglia, and midbrain were disproportionally decreased in volume (P < 0.0002). These regional volumes also correlated positively with performance IQ in adult WS subjects (age ≥ 30 years, P = 0.038). Conclusion TBM facilitates 3D visualization of brain volume reductions in WS. Reduced parietal/occipital volumes may be associated with visuospatial deficits in WS. By contrast, frontal lobes, amygdala, and cingulate gyrus are relatively preserved or even enlarged, consistent with unusual affect regulation and language production in WS. PMID:17512756

  8. Morphometry of impact craters on Mercury from MESSENGER altimetry and imaging

    NASA Astrophysics Data System (ADS)

    Susorney, Hannah C. M.; Barnouin, Olivier S.; Ernst, Carolyn M.; Johnson, Catherine L.

    2016-06-01

    Data acquired by the Mercury Laser Altimeter and the Mercury Dual Imaging System on the MESSENGER spacecraft in orbit about Mercury provide a means to measure the geometry of many of the impact craters in Mercury's northern hemisphere in detail for the first time. The combination of topographic and imaging data permit a systematic evaluation of impact crater morphometry on Mercury, a new calculation of the diameter Dt at which craters transition with increasing diameter from simple to complex forms, and an exploration of the role of target properties and impact velocity on final crater size and shape. Measurements of impact crater depth on Mercury confirm results from previous studies, with the exception that the depths of large complex craters are typically shallower at a given diameter than reported from Mariner 10 data. Secondary craters on Mercury are generally shallower than primary craters of the same diameter. No significant differences are observed between the depths of craters within heavily cratered terrain and those of craters within smooth plains. The morphological attributes of craters that reflect the transition from simple to complex craters do not appear at the same diameter; instead flat floors first appear with increasing diameter in craters at the smallest diameters, followed with increasing diameter by reduced crater depth and rim height, and then collapse and terracing of crater walls. Differences reported by others in Dt between Mercury and Mars (despite the similar surface gravitational acceleration on the two bodies) are confirmed in this study. The variations in Dt between Mercury and Mars cannot be adequately attributed to differences in either surface properties or mean projectile velocity.

  9. Determination of the Relationship between Hydrologic Processes and Basin Morphometry - The Lamos Basin (Mersin, Turkey)

    NASA Astrophysics Data System (ADS)

    Yıldırım, Ümit; Güler, Cüneyt

    2016-04-01

    This study has been carried out to determine the relationship between hydrologic processes and basin morphometry in the Lamos Basin, which is located at the northern part of the Mersin (SE Turkey). The morphometric parameters of the basin was derived from the 1:25K scale topographic map sheets that were digitized using ArcGIS 9.3.1 geographic information system (GIS) software. Morphometric parameters considered in this study include basin area, basin length, basin perimeter length, stream order, stream number, stream length, mean stream length, basin relief, drainage density, stream frequency, drainage texture, bifurcation ratio, form factor, elongation ratio, overland flow length, relief ratio, and hypsometric integral. The results have shown that there are 1252 individual stream reaches with a total length of 1414.1 km in the Lamos basin, which covers an area of 1358 km2 and has a length of 103 km in the N-S direction. Furthermore, the basin has a medium drainage density of 1.04 1/km with a stream frequency and drainage texture values of 0.92 and 4.33, respectively. The basin can be classified as elongated because of the low values of elongation ratio (0.48) and form factor (0.12). The hypsometric integral of the basin (0.58) indicates that it is in the youth period and thus reasonably sensitive to erosion. The values of drainage texture, drainage density, and stream frequency indicate that the Lamos basin is moderately well drained, therefore overland flow in the basin is not expected to be so quick. Thus, in case of occurrence of sudden peak flows, sensitivity to the land sliding and erosion may increase further. As a result, it is suggested that human activities in the basin should be limited in areas in fairly close proximity to the present day stream network to prevent or reduce the risk to life and property.

  10. Computed Tomographic Morphometry of the Internal Anatomy of Mandibular Second Primary Molars

    PubMed Central

    Sharma, Pranjal; Swamy, Dinesh Francis; Shashidara, R; Swamy, Elaine Barretto

    2015-01-01

    ABSTRACT Need for the study: The most important procedure for a successful endodontic treatment is the cleaning and shaping of the canal system. Understanding the internal anatomy of teeth provides valuable information to the clinician that would help him achieve higher clinical success during endodontic therapy. Aims: To evaluate by computed tomography—the internal anatomy of mandibular second primary molars with respect to the number of canals, cross-sectional shape of canals, cross-sectional area of canals and the root dentin thickness. Materials and methods: A total of 31 mandibular second primary molars were subjected to computed-tomographic evaluation in the transverse plane, after mounting them in a prefabricated template. The images, thus, obtained were analyzed using De-winter Bio-wizard® software. Results: All the samples demonstrated two canals in the mesial root, while majority of the samples (65.48%) demonstrated two canals in the distal root. The cross-sectional images of the mesial canals demonstrated a round shape, while the distal canals demonstrated an irregular shape. The root dentin thickness was highly reduced on the distal aspect of mesial and mesial aspect of distal canals. Conclusion: The mandibular second primary molars demonstrated wide variation and complexities in their internal anatomy. A thorough understanding of the complexity of the root canal system is essential for understanding the principles and problems of shaping and cleaning, determining the apical limits and dimensions of canal preparations, and for performing successful endodontic procedures. How to cite this article: Kurthukoti AJ, Sharma P, Swamy DF, Shashidara R, Swamy EB. Computed Tomographic Morphometry of the Internal Anatomy of Mandibular Second Primary Molars. Int J Clin Pediatr Dent 2015;8(3):202-207. PMID:26628855

  11. Cortical abnormalities in bipolar disorder investigated with MRI and voxel-based morphometry.

    PubMed

    Nugent, Allison C; Milham, Michael P; Bain, Earle E; Mah, Linda; Cannon, Dara M; Marrett, Sean; Zarate, Carlos A; Pine, Daniel S; Price, Joseph L; Drevets, Wayne C

    2006-04-01

    Bipolar disorder (BD) has been associated with abnormalities of brain structure. Specifically, in vivo volumetric MRI and/or post mortem studies of BD have reported abnormalities of gray matter (GM) volume in the medial prefrontal cortex (PFC), amygdala, hippocampal subiculum and ventral striatum. These structures share anatomical connections with each other and form part of a "visceromotor" network modulating emotional behavior. Areas of the lateral orbital, superior temporal and posterior cingulate cortices project to this network, but morphometric abnormalities in these areas have not been established in BD. The current study assessed tissue volumes within these areas in BD using MRI and voxel-based morphometry (VBM). MRI images were obtained from 36 BD subjects and 65 healthy controls. To account for possible neurotrophic and neuroprotective effects of psychotropic medications, BD subjects were divided into medicated and unmedicated groups. Images were segmented into tissue compartments, which were examined on a voxel-wise basis to determine the location and extent of morphometric changes. The GM was reduced in the posterior cingulate/retrosplenial cortex and superior temporal gyrus of unmedicated BD subjects relative to medicated BD subjects and in the lateral orbital cortex of medicated BD subjects relative to controls. White matter (WM) was increased in the orbital and posterior cingulate cortices, which most likely reflected alterations in gyral morphology resulting from the reductions in the associated GM. The morphometric abnormalities in the posterior cingulate, superior temporal and lateral orbital cortices in BD support the hypothesis that the extended network of neuroanatomical structures subserving visceromotor regulation contains structural alterations in BD. Additionally, localization of morphometric abnormalities to areas known to exhibit increased metabolism in depression supports the hypothesis that repeated stress and elevated glucocorticoid

  12. STATISTICAL APPROACH TO BRAIN MORPHOMETRY DATA REQUIRED IN DEVELOPMENTAL NEUROTOXICITY (DNT) TESTING GUIDELINES: PROFILE ANALYSIS.

    EPA Science Inventory

    Brain morphometry measurements are required in test guidelines proposed by the USEPA to screen chemicals for developmental neurotoxicity. Because the DNT is a screening battery, the analysis of this data should be sensitive to dose-related changes in the pattern of brain growt...

  13. Annual Research Review: Progress in Using Brain Morphometry as a Clinical Tool for Diagnosing Psychiatric Disorders

    ERIC Educational Resources Information Center

    Haubold, Alexander; Peterson, Bradley S.; Bansal, Ravi

    2012-01-01

    Brain morphometry in recent decades has increased our understanding of the neural bases of psychiatric disorders by localizing anatomical disturbances to specific nuclei and subnuclei of the brain. At least some of these disturbances precede the overt expression of clinical symptoms and possibly are endophenotypes that could be used to diagnose an…

  14. Neural Correlates of Communication Skill and Symptom Severity in Autism: A Voxel-Based Morphometry Study

    ERIC Educational Resources Information Center

    Parks, Lauren K.; Hill, Dina E.; Thoma, Robert J.; Euler, Matthew J.; Lewine, Jeffrey D.; Yeo, Ronald A.

    2009-01-01

    Although many studies have compared the brains of normal controls and individuals with autism, especially older, higher-functioning individuals with autism, little is known of the neural correlates of the vast clinical heterogeneity characteristic of the disorder. In this study, we used voxel-based morphometry (VBM) to examine gray matter…

  15. POLYCHLORINATED BIPHENYL (AROCLOR 1254) INDUCED NEPHROTOXICITY, CHANGES IN FEMUR MORPHOMETRY AND CALCIUM METABOLISM

    EPA Science Inventory

    Experiments were performed to investigate the effects of polychlorinated biphenyl (PCB) on calcium metabolism, femur morphometry, and nephrotoxicity. ischer 344 rats Here dosed daily 1G for 5, 10 or 15 weeks with 0, 0.1, 1, 10 or 25 mg PCB/kg body weight. fter 5, 10 and 15 weeks,...

  16. Reduced occipital and prefrontal brain volumes in dysbindin-associated schizophrenia.

    PubMed

    Donohoe, Gary; Frodl, Thomas; Morris, Derek; Spoletini, Ilaria; Cannon, Dara M; Cherubini, Andrea; Caltagirone, Carlo; Bossù, Paola; McDonald, Colm; Gill, Michael; Corvin, Aiden P; Spalletta, Gianfranco

    2010-01-01

    A three-marker C-A-T dysbindin haplotype identified by Williams et al (PMID: 15066891) is associated with increased risk for schizophrenia, decreased mRNA expression, poorer cognitive performance, and early sensory processing deficits. We investigated whether this same dysbindin risk haplotype was also associated with structural variation in the gray matter volume (GMV). Using voxel-based morphometry, whole-volume analysis revealed significantly reduced GMVs in both the right dorsolateral prefrontal and left occipital cortex, corresponding to the behavioral findings of impaired spatial working memory and EEG findings of impaired visual processing already reported. These data provide important evidence of the influence of dysbindin risk variants on brain structure, and suggest a possible mechanism by which disease risk is being increased. PMID:19794403

  17. Analysis of the ability of pramlintide to inhibit amyloid formation by human islet amyloid polypeptide reveals a balance between optimal recognition and reduced amyloidogenicity.

    PubMed

    Wang, Hui; Ridgway, Zachary; Cao, Ping; Ruzsicska, Bela; Raleigh, Daniel P

    2015-11-10

    The hormone human islet amyloid polypeptide (hIAPP or amylin) plays a role in glucose metabolism, but forms amyloid in the pancreas in type 2 diabetes (T2D) and is associated with β-cell death and dysfunction in the disease. Inhibitors of islet amyloid have therapeutic potential; however, there are no clinically approved inhibitors, and the mode of action of existing inhibitors is not well understood. Rat IAPP (rIAPP) differs from hIAPP at six positions, does not form amyloid, and is an inhibitor of amyloid formation by hIAPP. Five of the six differences are located within the segment of residues 20-29, and three of them are Pro residues, which are well-known disruptors of β-sheet structure. rIAPP is thus a natural example of a "β-breaker inhibitor", a molecule that combines a recognition element with an entity that inhibits β-sheet formation. Pramlintide (PM) is a peptide drug approved for use as an adjunct to insulin therapy for treatment of diabetes. PM was developed by introducing the three Pro substitutions found in rIAPP into hIAPP. Thus, it more closely resembles the human peptide than does rIAPP. Here we examine and compare the ability of rIAPP, PM, and a set of designed analogues of hIAPP to inhibit amyloid formation by hIAPP, to elucidate the factors that lead to effective peptide-based inhibitors. Our results reveal, for this class of molecules, a balance between the reduced amyloidogenicity of the inhibitory sequence on one hand and its ability to recognize hIAPP on the other. PMID:26407043

  18. Voxel Based Morphometry Alterations in Mal de Debarquement Syndrome

    PubMed Central

    Cha, Yoon-Hee; Chakrapani, Shruthi

    2015-01-01

    Background Mal de debarquement syndrome (MdDS) is a disorder of chronic self-motion perception that occurs though entrainment to rhythmic background motion, such as from sea voyage, and involves the perception of low-frequency rocking that can last for months or years. The neural basis of this persistent sensory perception abnormality is not well understood. Methods We investigated grey matter volume differences underlying persistent MdDS by performing voxel-based morphometry on whole brain and pre-specified ROIs in 28 individuals with MdDS and comparing them to 18 age, sex, and handedness matched controls. Results MdDS participants exhibited greater grey matter volume in the left inferior parietal lobule, right inferior occipital gyrus (area V3v), right temporal pole, bilateral cerebellar hemispheric lobules VIII/IX and left lobule VIIa/VIIb. Grey matter volumes were lower in bilateral inferior frontal, orbitofrontal, pregenual anterior cingulate cortex (pgACC) and left superior medial gyri (t = 3.0, p<0.005uncorr). In ROI analyses, there were no volume differences in the middle occipital gyrus (region of V5/MT) or parietal operculum 2 (region of the parietoinsular vestibular cortex). Illness duration was positively related to grey matter volume in bilateral inferior frontal gyrus/anterior insula (IFG/AI), right posterior insula, superior parietal lobule, left middle occipital gyrus (V5/MT), bilateral postcentral gyrus, anterior cerebellum, and left cerebellar hemisphere and vermian lobule IX. In contrast, illness duration was negatively related to volume in pgACC, posterior middle cingulate gyrus (MCC), left middle frontal gyrus (dorsolateral prefrontal cortex-DLPFC), and right cerebellar hemispheric lobule VIIIb (t = 3.0, p<0.005uncorr). The most significant differences were decreased volume in the pgACC and increased volume in the left IFG/AI with longer illness duration (qFDRcorr <0.05). Concurrent medication use did not correlate with these findings or have a

  19. Identifying neural correlates of memory and language disturbances in herpes simplex encephalitis: a voxel-based morphometry (VBM) study.

    PubMed

    Frisch, Stefan; Thiel, Friederike; Marschhauser, Anke; Villringer, Arno; Horstmann, Annette; Schroeter, Matthias L

    2015-03-01

    Herpes simplex encephalitis (HSE) is a severe neurological disease that often leads to persistent cognitive deficits in survivors. Memory and naming impairments have been reported most, although direct association between memory and naming performance and disease-related atrophy has not yet been demonstrated in vivo for a larger sample of patients. In the present work, a voxel-based morphometry (VBM) analysis was conducted on 3T magnetic resonance imaging (MRI) of 13 HSE survivors. The gray matter density values were correlated with scores indicating verbal memory decline, as well as errors/omissions in picture naming; both were obtained through neuropsychological assessment. Analysis of individual lesion patterns revealed a considerable inter-individual variability, mainly with atrophy in the basal forebrain, adjacent frontal cortex, medial and lateral temporal cortex, insula and thalamus. The neuropsychological data analysis revealed correlation between verbal memory decline and atrophy especially in the left hippocampal region, whereas naming problems were associated with gray matter loss especially in the lateral temporal lobe, the thalamus and the left insula. These results confirm, for the first time, the assumptions of earlier studies about the considerable variability of individual lesion patterns in HSE in a whole-brain approach in vivo, and thus the anatomical validity of VBM. PMID:25488475

  20. Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders.

    PubMed

    Wang, Ou; Liang, Guanxiang; McAllister, Tim A; Plastow, Graham; Stanford, Kim; Selinger, Brent; Guan, Le Luo

    2016-01-01

    Super-shedder cattle are a major disseminator of E. coli O157:H7 into the environment, and the terminal rectum has been proposed as the primary E. coli O157:H7 colonization site. This study aimed to identify host factors that are associated with the super-shedding process by comparing transcriptomic profiles in rectal tissue collected from 5 super-shedder cattle and 4 non-shedder cattle using RNA-Seq. In total, 17,859 ± 354 genes and 399 ± 16 miRNAs were detected, and 11,773 genes were expressed in all animals. Fifty-eight differentially expressed (DE) genes (false discovery rate < 0.05) including 11 up-regulated and 47 down-regulated (log 2 (fold change) ranged from -5.5 to 4.2), and 2 up-regulated DE miRNAs (log 2 (fold change) = 2.1 and 2.5, respectively) were identified in super-shedders compared to non-shedders. Functional analysis of DE genes revealed that 31 down-regulated genes were potentially associated with reduced innate and adaptive immune functions in super-shedders, including 13 lymphocytes membrane receptors, 3 transcription factors and 5 cytokines, suggesting the decreased key host immune functions in the rectal tissue of super-shedders, including decreased quantity and migration of immune cells such as lymphocytes, neutrophils and dendritic cells. The up-regulation of bta-miR-29d-3p and the down regulation of its predicted target gene, regulator of G-protein signaling 13, suggested a potential regulatory role of this miRNA in decreased migration of lymphocytes in super-shedders. Based on these findings, the rectal tissue of super-shedders may inherently exhibit less effective innate and adaptive immune protection. Further study is required to confirm if such effect on host immunity is due to the nature of the host itself or due to actions mediated by E. coli O157:H7. PMID:26959367

  1. Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders

    PubMed Central

    Wang, Ou; Liang, Guanxiang; McAllister, Tim A.; Plastow, Graham; Stanford, Kim; Selinger, Brent; Guan, Le Luo

    2016-01-01

    Super-shedder cattle are a major disseminator of E. coli O157:H7 into the environment, and the terminal rectum has been proposed as the primary E. coli O157:H7 colonization site. This study aimed to identify host factors that are associated with the super-shedding process by comparing transcriptomic profiles in rectal tissue collected from 5 super-shedder cattle and 4 non-shedder cattle using RNA-Seq. In total, 17,859 ± 354 genes and 399 ± 16 miRNAs were detected, and 11,773 genes were expressed in all animals. Fifty-eight differentially expressed (DE) genes (false discovery rate < 0.05) including 11 up-regulated and 47 down-regulated (log 2 (fold change) ranged from -5.5 to 4.2), and 2 up-regulated DE miRNAs (log 2 (fold change) = 2.1 and 2.5, respectively) were identified in super-shedders compared to non-shedders. Functional analysis of DE genes revealed that 31 down-regulated genes were potentially associated with reduced innate and adaptive immune functions in super-shedders, including 13 lymphocytes membrane receptors, 3 transcription factors and 5 cytokines, suggesting the decreased key host immune functions in the rectal tissue of super-shedders, including decreased quantity and migration of immune cells such as lymphocytes, neutrophils and dendritic cells. The up-regulation of bta-miR-29d-3p and the down regulation of its predicted target gene, regulator of G-protein signaling 13, suggested a potential regulatory role of this miRNA in decreased migration of lymphocytes in super-shedders. Based on these findings, the rectal tissue of super-shedders may inherently exhibit less effective innate and adaptive immune protection. Further study is required to confirm if such effect on host immunity is due to the nature of the host itself or due to actions mediated by E. coli O157:H7. PMID:26959367

  2. Penalized Fisher Discriminant Analysis and Its Application to Image-Based Morphometry

    PubMed Central

    Wang, Wei; Mo, Yilin; Ozolek, John A.; Rohde, Gustavo K.

    2011-01-01

    Image-based morphometry is an important area of pattern recognition research, with numerous applications in science and technology (including biology and medicine). Fisher Linear Discriminant Analysis (FLDA) techniques are often employed to elucidate and visualize important information that discriminates between two or more populations. We demonstrate that the direct application of FLDA can lead to undesirable errors in characterizing such information and that the reason for such errors is not necessarily the ill conditioning in the resulting generalized eigenvalue problem, as usually assumed. We show that the regularized eigenvalue decomposition often used is related to solving a modified FLDA criterion that includes a least-squares-type representation penalty, and derive the relationship explicitly. We demonstrate the concepts by applying this modified technique to several problems in image-based morphometry, and build discriminant representative models for different data sets. PMID:22140290

  3. Effect of Cocaine on Structural Changes in Brain: MRI Volumetry using Tensor-Based Morphometry

    PubMed Central

    Narayana, Ponnada A.; Datta, Sushmita; Tao, Guozhi; Steinberg, Joel L.; Moeller, F. Gerard

    2010-01-01

    Magnetic resonance imaging (MRI) was performed in cocaine dependent subjects to determine the structural changes in brain compared to non-drug using controls. Cocaine dependent subjects and controls were carefully screened to rule out brain pathology of undetermined origin. Magnetic resonance images were analyzed using tensor-based morphometry (TBM) and voxel-based morphometry (VBM) without and with modulation to adjust for volume changes during normalization. For TBM analysis, unbiased atlases were generated using two different inverse consistent and diffeomorphic nonlinear registration techniques. Two different control groups were used for generating unbiased atlases. Independent of the nonlinear registration technique and normal cohorts used for creating the unbiased atlases, our analysis failed to detect any statistically significant effect of cocaine on brain volumes. These results show that cocaine dependent subjects do not show differences in regional brain volumes compared to non-drug using controls. PMID:20570057

  4. The relationship between trait positive empathy and brain structure: a voxel-based morphometry study.

    PubMed

    Yue, Tong; Pan, Weigang; Huang, Xiting

    2016-04-13

    Although studies relating to positive empathy have received increased attention in recent years, no studies have been carried out to explore the neural basis of positive empathy. Using a voxel-based morphometry analysis, this study investigates the relationship between trait positive empathy (as measured by the Positive Empathy Scale) and its association with brain structure in 86 healthy college students. The results indicate that an individual's ability to show positive empathy is positively correlated with the volume of gray matter in the right insula, left anterior cingulate cortex, dorsolateral prefrontal cortex, and medial prefrontal cortex. It may be suggested that the differences between the abilities of emotion processing and regulating play important roles in shaping an individual's positive empathy traits from the perspective of brain morphometry. PMID:26963166

  5. A new monoclonal antibody DAG-6F4 against human alpha-dystroglycan reveals reduced core protein in some, but not all, dystroglycanopathy patients.

    PubMed

    Humphrey, Emma L; Lacey, Erica; Le, Lam T; Feng, Lucy; Sciandra, Francesca; Morris, Charlotte R; Hewitt, Jane E; Holt, Ian; Brancaccio, Andrea; Barresi, Rita; Sewry, Caroline A; Brown, Susan C; Morris, Glenn E

    2015-01-01

    We generated a novel monoclonal antibody, DAG-6F4, against alpha-dystroglycan which immunolabels the sarcolemma in human muscle biopsies. Its seven amino-acid epitope, PNQRPEL, was identified using phage-displayed peptides and is located immediately after the highly-glycosylated mucin domain of alpha-dystroglycan. On Western blots of recombinant alpha-dystroglycan, epitope accessibility was reduced, but not entirely prevented, by glycosylation. DAG-6F4 immunolabelling was markedly reduced in muscle biopsies from Duchenne muscular dystrophy patients consistent with disruption of the dystroglycan complex. In a range of dystroglycanopathy patients with reduced/altered glycosylation, staining by DAG-6F4 was often less reduced than staining by IIH6 (antibody against the glycan epitope added by LARGE and commonly used to identify glycosylated alpha-dystroglycan). Whereas IIH6 was reduced in all patients, DAG-6F4 was hardly changed in a LARGE patient, less reduced than IIH6 in limb-girdle muscular dystrophy type 2I, but as reduced as IIH6 in some congenital muscular dystrophy patients. Although absence of the LARGE-dependent laminin-binding site appears not to affect alpha-dystroglycan stability at the sarcolemma, the results suggest that further reduction in aDG glycosylation may reduce its stability. These studies suggest that DAG-6F4 may be a useful addition to the antibody repertoire for evaluating the dystroglycan complex in neuromuscular disorders. PMID:25387694

  6. Transient elastography compared to liver biopsy and morphometry for predicting fibrosis in pediatric chronic liver disease: Does etiology matter?

    PubMed Central

    Behairy, Behairy El-Sayed; Sira, Mostafa Mohamed; Zalata, Khaled Refat; Salama, El-Sayed Ebrahem; Abd-Allah, Mohamed Ahmed

    2016-01-01

    AIM: To evaluate transient elastography (TE) as a noninvasive tool in staging liver fibrosis compared with liver biopsy and morphometry in children with different chronic liver diseases. METHODS: A total of 90 children [50 with chronic hepatitis C virus (HCV), 20 with autoimmune hepatitis (AIH) and 20 with Wilson disease] were included in the study and underwent liver stiffness measurement (LSM) using TE. Liver biopsies were evaluated for fibrosis, qualitatively, by Ishak score and quantitatively by fibrosis area fraction (FAF) using digital image analysis (morphometry). LSM was correlated with fibrosis and other studied variables using spearman correlation. A stepwise multiple regression analysis was also performed to examine independent factors associated with LSM. Different cut-off values of LSM were calculated for predicting individual fibrosis stages using receiver-operating characteristic curve. Cut-off values with optimal clinical performance (optimal sensitivity and specificity simultaneously) were selected. RESULTS: The majority of HCV group had minimal activity (80%) and no/mild fibrosis (72%). On the other hand, the majority of AIH group had mild to moderate activity (70%) and moderate to severe fibrosis (95%) and all Wilson disease group had mild to moderate activity (100%) and moderate to severe fibrosis (100%). LSM correlated significantly with both FAF and Ishak scores and the correlation appeared better with the latter (r = 0.839 vs 0.879, P < 0.0001 for both). LSM discriminated individual stages of fibrosis with high performance. Sensitivity ranged from 81.4% to 100% and specificity ranged from 75.0% to 97.2%. When we compared LSM values for the same stage of fibrosis, they varied according to the different etiologies. Higher values were in AIH (16.15 ± 7.23 kPa) compared to Wilson disease (8.30 ± 0.84 kPa) and HCV groups (7.43 ± 1.73 kPa). Multiple regression analysis revealed that Ishak fibrosis stage was the only independent variable

  7. A reexamination of age-related variation in body weight and morphometry of Maryland nutria

    USGS Publications Warehouse

    Sherfy, M.H.; Mollett, T.A.; McGowan, K.R.; Daugherty, S.L.

    2006-01-01

    Age-related variation in morphometry has been documented for many species. Knowledge of growth patterns can be useful for modeling energetics, detecting physiological influences on populations, and predicting age. These benefits have shown value in understanding population dynamics of invasive species, particularly in developing efficient control and eradication programs. However, development and evaluation of descriptive and predictive models is a critical initial step in this process. Accordingly, we used data from necropsies of 1,544 nutria (Myocastor coypus) collected in Maryland, USA, to evaluate the accuracy of previously published models for prediction of nutria age from body weight. Published models underestimated body weights of our animals, especially for ages <3. We used cross-validation procedures to develop and evaluate models for describing nutria growth patterns and for predicting nutria age. We derived models from a randomly selected model-building data set (n = 192-193 M, 217-222 F) and evaluated them with the remaining animals (n = 487-488 M, 642-647 F). We used nonlinear regression to develop Gompertz growth-curve models relating morphometric variables to age. Predicted values of morphometric variables fell within the 95% confidence limits of their true values for most age classes. We also developed predictive models for estimating nutria age from morphometry, using linear regression of log-transformed age on morphometric variables. The evaluation data set corresponded with 95% prediction intervals from the new models. Predictive models for body weight and length provided greater accuracy and less bias than models for foot length and axillary girth. Our growth models accurately described age-related variation in nutria morphometry, and our predictive models provided accurate estimates of ages from morphometry that will be useful for live-captured individuals. Our models offer better accuracy and precision than previously published models

  8. Morphometry of scoria cones, and their relation to geodynamic setting: A DEM-based analysis

    NASA Astrophysics Data System (ADS)

    Fornaciai, Alessandro; Favalli, Massimiliano; Karátson, Dávid; Tarquini, Simone; Boschi, Enzo

    2012-03-01

    The morphometry of a great number of scoria cones, belonging to volcanic fields of various geodynamic settings, has been measured and analyzed, addressing the question whether there is a relation between the prevalent cone shape in a given field and the geodynamic setting of the field itself. Morphometric analysis was carried out on freely downloadable digital elevation models (DEMs). The accuracy of the used DEMs and the associated error in scoria cone morphometry were determined by cross-comparing high-resolution LIDAR-derived DEMs, USGS NED, TINITALY DEM and ASTER GDEM. The 10-m TINITALY/01 and USGS NED DEMs are proven to be suitable for scoria cone morphometry, whereas ASTER GDEM can be used reliably for cones with volume greater than 30 × 106 m3. According to a detailed morphometry of all scoria cones, we propose that the cones related to subductional setting show relatively higher values of Hco/Wco and lower values of Wcr/Wco than the cones related to extensional setting. The detected differences can be imputable to peculiar eruption dynamics resulting in slight but systematic changes in shape, and differences in lithological and sedimentological characteristics that govern post-eruptive erosion. To constrain the pathway of scoria cone erosion, the detected morphometric changes were also interpreted using a simple linear degradation model. Utilizing the obtained simulation results, the inferred initial cone base, and the age of scoria cones, we calculated a diffusion coefficient (K) for several dated cones, which are related to the prevalent climate. Our results, despite the high error associated, allow to assess the median K for all volcanic fields. Due to the complexity of the factors behind, it is not easy to understand if the prevalent shape characterizing a certain volcanic field is due mainly to sin-eruptive or post-eruptive mechanisms; however, our distinction between the two main geodynamic settings may be the first step to decipher these factors.

  9. Widespread structural brain changes in OCD: a systematic review of voxel-based morphometry studies.

    PubMed

    Piras, Federica; Piras, Fabrizio; Chiapponi, Chiara; Girardi, Paolo; Caltagirone, Carlo; Spalletta, Gianfranco

    2015-01-01

    The most widely accepted model of obsessive-compulsive disorder (OCD) assumes brain abnormalities in the "affective circuit", mainly consisting of volume reduction in the medial orbitofrontal, anterior cingulate and temporolimbic cortices, and tissue expansion in the striatum and thalamus. The advent of whole-brain, voxel-based morphometry (VBM) has provided increasing evidence that regions outside the "affective" orbitofronto-striatal circuit are involved in OCD. Nevertheless, potential confounds from the different image analysis methods, as well as other factors, such as patients' medication and comorbidity status, may limit generalization of results. In the present paper, we systematically reviewed the whole-brain VBM literature on OCD by focussing specifically on degree of consistency between studies, extent to which findings have been replicated and interrelation between clinical variables and OCD anatomy, a potentially crucial factor that has been systematically examined only in a limited number of studies. The PubMed database was searched through February 2012. A total of 156 studies were identified; 18 of them fulfilled the inclusion/exclusion criteria and included 511 patients and 504 controls. Results support the notion that the brain alterations responsible for OCD are represented at the network level, and that widespread structural abnormalities may contribute to neurobiological vulnerability to OCD. Apart from defects in regions within the classic "affective" circuit, volume reduction of the cortical source of the dorsolateral (DL) prefronto-striatal "executive" circuit (dorsomedial, DL, ventrolateral and frontopolar prefrontal cortices), and of reciprocally connected regions (temporo-parieto-occipital associative areas) is consistently described in OCD patients. Moreover, increased volume of the internal capsule and reduced frontal and parietal white matter volumes may account for altered anatomical connectivity in fronto-subcortical circuitry

  10. Use of MODIS satellite images for detailed lake morphometry: Application to basins with large water level fluctuations

    NASA Astrophysics Data System (ADS)

    Ovakoglou, George; Alexandridis, Thomas K.; Crisman, Thomas L.; Skoulikaris, Charalampos; Vergos, George S.

    2016-09-01

    Lake morphometry is essential for managing water resources and limnetic ecosystems. For reservoirs that receive high sediment loads, frequent morphometric mapping is necessary to define both the effective life of the reservoir and its water storage capacity for irrigation, power generation, flood control and domestic water supply. The current study presents a methodology for updating the digital depth model (DDM) of lakes and reservoirs with wide intra and interannual fluctuations of water levels using satellite remote sensing. A time series of Terra MODIS satellite images was used to map shorelines formed during the annual water level change cycle, and were validated with concurrent Landsat ETM+ satellite images. The shorelines were connected with in-situ observation of water levels and were treated as elevation contours to produce the DDM using spatial interpolation. The accuracy of the digitized shorelines is within the mapping accuracy of the satellite images, while the resulting DDM is validated using in-situ elevation measurements. Two versions of the DDM were produced to assess the influence of seasonal water fluctuation. Finally, the methodology was applied to Lake Kerkini (Greece) to produce an updated DDM, which was compared with the last available bathymetric survey (1991) and revealed changes in sediment distribution within the lake.

  11. Brain changes associated with postural training in patients with cerebellar degeneration: a voxel-based morphometry study.

    PubMed

    Burciu, Roxana Gabriela; Fritsche, Nicole; Granert, Oliver; Schmitz, Lutz; Spönemann, Nina; Konczak, Jürgen; Theysohn, Nina; Gerwig, Marcus; van Eimeren, Thilo; Timmann, Dagmar

    2013-03-01

    Recent research indicates that physiotherapy can improve motor performance of patients with cerebellar degeneration. Given the known contributions of the cerebellum to motor learning, it remains unclear whether such observable changes in performance are mediated by the cerebellum or cerebral brain areas involved in motor control and learning. The current study addressed this question by assessing the increase in gray matter volume due to sensorimotor training in cerebellar patients using voxel-based morphometry. Nineteen human subjects with pure cerebellar degeneration and matched healthy controls were trained for 2 weeks on a balance task. Postural and clinical assessments along with structural magnetic resonance imaging were performed pretraining and post-training. The main findings were as follows. First, training enhanced balance performance in cerebellar patients. Second, in contrast to controls patients revealed significantly more post-training gray matter volume in the dorsal premotor cortex. Third, training-related increase in gray matter volume was observed within the cerebellum and was more pronounced in controls than in patients. However, statistically cerebellar changes were at the trend level and thus require additional, independent confirmation. We conclude that sensorimotor training of patients with cerebellar neurodegeneration induces gray matter changes primarily within nonaffected neocortical regions of the cerebellar-cortical loop. Residual function of the cerebellum appears to be exploited suggesting either a recovery from degeneration or intact processes of cerebellar plasticity in the remaining healthy tissue. PMID:23467375

  12. A Large Scale (N=400) Investigation of Gray Matter Differences in Schizophrenia Using Optimized Voxel-based Morphometry

    PubMed Central

    Meda, Shashwath A.; Giuliani, Nicole R.; Calhoun, Vince D.; Jagannathan, Kanchana; Schretlen, David J.; Pulver, Anne; Cascella, Nicola; Keshavan, Matcheri; Kates, Wendy; Buchanan, Robert; Sharma, Tonmoy; Pearlson, Godfrey D.

    2008-01-01

    Background Many studies have employed voxel-based morphometry (VBM) of MRI images as an automated method of investigating cortical gray matter differences in schizophrenia. However, results from these studies vary widely, likely due to different methodological or statistical approaches. Objective To use VBM to investigate gray matter differences in schizophrenia in a sample significantly larger than any published to date, and to increase statistical power sufficiently to reveal differences missed in smaller analyses. Methods Magnetic resonance whole brain images were acquired from four geographic sites, all using the same model 1.5T scanner and software version, and combined to form a sample of 200 patients with both first episode and chronic schizophrenia and 200 healthy controls, matched for age, gender and scanner location. Gray matter concentration was assessed and compared using optimized VBM. Results Compared to the healthy controls, schizophrenia patients showed significantly less gray matter concentration in multiple cortical and subcortical regions, some previously unreported. Overall, we found lower concentrations of gray matter in regions identified in prior studies, most of which reported only subsets of the affected areas. Conclusions Gray matter differences in schizophrenia are most comprehensively elucidated using a large, diverse and representative sample. PMID:18378428

  13. A New Method for Automated Identification and Morphometry of Myelinated Fibers Through Light Microscopy Image Analysis.

    PubMed

    Novas, Romulo Bourget; Fazan, Valeria Paula Sassoli; Felipe, Joaquim Cezar

    2016-02-01

    Nerve morphometry is known to produce relevant information for the evaluation of several phenomena, such as nerve repair, regeneration, implant, transplant, aging, and different human neuropathies. Manual morphometry is laborious, tedious, time consuming, and subject to many sources of error. Therefore, in this paper, we propose a new method for the automated morphometry of myelinated fibers in cross-section light microscopy images. Images from the recurrent laryngeal nerve of adult rats and the vestibulocochlear nerve of adult guinea pigs were used herein. The proposed pipeline for fiber segmentation is based on the techniques of competitive clustering and concavity analysis. The evaluation of the proposed method for segmentation of images was done by comparing the automatic segmentation with the manual segmentation. To further evaluate the proposed method considering morphometric features extracted from the segmented images, the distributions of these features were tested for statistical significant difference. The method achieved a high overall sensitivity and very low false-positive rates per image. We detect no statistical difference between the distribution of the features extracted from the manual and the pipeline segmentations. The method presented a good overall performance, showing widespread potential in experimental and clinical settings allowing large-scale image analysis and, thus, leading to more reliable results. PMID:25986589

  14. A voxel-based morphometry study of gray matter correlates of facial emotion recognition in bipolar disorder.

    PubMed

    Neves, Maila de Castro L; Albuquerque, Maicon Rodrigues; Malloy-Diniz, Leandro; Nicolato, Rodrigo; Silva Neves, Fernando; de Souza-Duran, Fábio Luis; Busatto, Geraldo; Corrêa, Humberto

    2015-08-30

    Facial emotion recognition (FER) is one of the many cognitive deficits reported in bipolar disorder (BD) patients. The aim of this study was to investigate neuroanatomical correlates of FER impairments in BD type I (BD-I). Participants comprised 21 euthymic BD-I patients without Axis I DSM IV-TR comorbidities and 21 healthy controls who were assessed using magnetic resonance imaging and the Penn Emotion Recognition Test (ER40). Preprocessing of images used DARTEL (diffeomorphic anatomical registration through exponentiated Lie algebra) for optimized voxel-based morphometry in SPM8. Compared with healthy subjects, BD-I patients performed poorly in on the ER40 and had reduced gray matter volume (GMV) in the left orbitofrontal cortex, superior portion of the temporal pole and insula. In the BD-I group, the statistical maps indicated a direct correlation between FER on the ER40 and right middle cingulate gyrus GMV. Our findings are consistent with the previous studies regarding the overlap of multiple brain networks of social cognition and BD neurobiology, particularly components of the anterior-limbic neural network. PMID:26123449

  15. Voxel-based morphometry (VBM) studies in schizophrenia—can white matter changes be reliably detected with VBM?

    PubMed Central

    Melonakos, Eric; Shenton, Martha; Rathi, Yogesh; Terry, Doug; Bouix, Sylvain; Kubicki, Marek

    2012-01-01

    Voxel-Based Morphometry (VBM) is a hypothesis-free, whole-brain, voxel-by-voxel analytic method that attempts to compare imaging data between populations. Schizophrenia studies have utilized this method to localize differences in Diffusion Tensor Imaging (DTI) derived Fractional Anisotropy (FA), a measure of white matter integrity, between patients and healthy controls. The number of publications has grown, although it is unclear how reliable and reproducible this method is, given the subtle white matter abnormalities expected in schizophrenia. Here we analyze and combine results from 23 studies published to date that use VBM to study schizophrenia in order to evaluate the reproducibility of this method in DTI analysis. Coordinates of each region reported in DTI VBM studies published thus far in schizophrenia were plotted onto a Montreal Neurological Institute atlas, and their anatomical locations were recorded. Results indicated that the reductions of FA in patients with schizophrenia were scattered across the brain. Moreover, even the most consistently reported regions were reported independently in less than 35% of the papers studied. Other instances of reduced FA were replicated at an even lower rate. Our findings demonstrate striking inconsistency, with none of the regions reported in much more than a third of the published papers. Poor replication rate suggests that the application of VBM to DTI data may not be the optimal way for studying the subtle microstructural abnormalities that are being hypothesized in schizophrenia. PMID:21684124

  16. Stem Transcriptome Reveals Mechanisms to Reduce the Energetic Cost of Shade-Avoidance Responses in Tomato1[C][W][OA

    PubMed Central

    Cagnola, Juan Ignacio; Ploschuk, Edmundo; Benech-Arnold, Tomás; Finlayson, Scott A.; Casal, Jorge José

    2012-01-01

    While the most conspicuous response to low red/far-red ratios (R:FR) of shade light perceived by phytochrome is the promotion of stem growth, additional, less obvious effects may be discovered by studying changes in the stem transcriptome. Here, we report rapid and reversible stem transcriptome responses to R:FR in tomato (Solanum lycopersicum). As expected, low R:FR promoted the expression of growth-related genes, including those involved in the metabolism of cell wall carbohydrates and in auxin responses. In addition, genes involved in flavonoid synthesis, isoprenoid metabolism, and photosynthesis (dark reactions) were overrepresented in clusters showing reduced expression in the stem of low R:FR-treated plants. Consistent with these responses, low R:FR decreased the levels of flavonoids (anthocyanin, quercetin, kaempferol) and selected isoprenoid derivatives (chlorophyll, carotenoids) in the stem and severely reduced the photosynthetic capacity of this organ. However, lignin contents were unaffected. Low R:FR reduced the stem levels of jasmonate, which is a known inducer of flavonoid synthesis. The rate of stem respiration was also reduced in low R:FR-treated plants, indicating that by downsizing the stem photosynthetic apparatus and the levels of photoprotective pigments under low R:FR, tomato plants reduce the energetic cost of shade-avoidance responses. PMID:22872775

  17. Global and regional brain volumes normalization in weight-recovered adolescents with anorexia nervosa: preliminary findings of a longitudinal voxel-based morphometry study

    PubMed Central

    Bomba, Monica; Riva, Anna; Morzenti, Sabrina; Grimaldi, Marco; Neri, Francesca; Nacinovich, Renata

    2015-01-01

    The recent literature on anorexia nervosa (AN) suggests that functional and structural abnormalities of cortico-limbic areas might play a role in the evolution of the disease. We explored global and regional brain volumes in a cross-sectional and follow-up study on adolescents affected by AN. Eleven adolescents with AN underwent a voxel-based morphometry study at time of diagnosis and immediately after weight recovery. Data were compared to volumes carried out in eight healthy, age and sex matched controls. Subjects with AN showed increased cerebrospinal fluid volumes and decreased white and gray matter volumes, when compared to controls. Moreover, significant regional gray matter decrease in insular cortex and cerebellum was found at time of diagnosis. No regional white matter decrease was found between samples and controls. Correlations between psychological evaluation and insular volumes were explored. After weight recovery gray matter volumes normalized while reduced global white matter volumes persisted. PMID:25834442

  18. Individual differences in regional prefrontal gray matter morphometry and fractional anisotropy are associated with different constructs of executive function

    PubMed Central

    Smolker, H. R.; Reineberg, A. E.; Orr, J. M.; Banich, M. T.

    2015-01-01

    Although the relationship between structural differences within the prefrontal cortex (PFC) and executive function (EF) has been widely explored in cognitively impaired populations, little is known about this relationship in healthy young adults. Using optimized voxel-based morphometry (VBM), surface-based morphometry (SBM), and fractional anisotropy (FA) we determined the association between regional PFC grey matter (GM) morphometry and white matter tract diffusivity with performance on tasks that tap different aspects of EF as drawn from Miyake et al.’s three-factor model of EF. Reductions in both GM volume (VBM) and cortical folding (SBM) in the ventromedial PFC (vmPFC), ventrolateral PFC (vlPFC), and dorsolateral PFC (dlPFC) predicted better common EF, shifting-specific, and updating-specific performance, respectively. Despite capturing different components of GM morphometry, voxel- and surface-based findings were highly related, exhibiting regionally overlapping relationships with EF. Increased white matter FA in fiber tracts that connect the vmPFC and vlPFC with posterior regions of the brain also predicted better common EF and shifting-specific performance, respectively. These results suggest that the neural mechanisms supporting distinct aspects of EF may differentially rely on distinct regions of the PFC, and at least in healthy young adults, are influenced by regional morphometry of the PFC and the FA of major white matter tracts that connect the PFC with posterior cortical and subcortical regions. PMID:24562372

  19. Morphometry of an Ischemic Lesion of Cat Spinal Cord

    PubMed Central

    Shay, Jonathan

    1973-01-01

    Profiles in random electron micrographs of anterior gray matter of normal and ischemic cat spinal cord were measured with a planimetric computer. Analysis of 5600 area measurements revealed the following differences. Mitochondria of neuron cell bodies, axons, axon terminals and astrocytic processes were two to three times larger after ischemia. However, only 15% of mitochondria of axons and axon terminals and 5% of astrocytic processes lost their matrix density and pattern of cristae, compared to 49% of mitochondria of neuron cell bodies. Ischemia caused no significant changes in mean sizes of axons or axon terminals. Lysosomes in neurons were unchanged. The mean size of astrocytic processes increased more than threefold. PMID:4728890

  20. Exploring the brains of Baduk (Go) experts: gray matter morphometry, resting-state functional connectivity, and graph theoretical analysis

    PubMed Central

    Jung, Wi Hoon; Kim, Sung Nyun; Lee, Tae Young; Jang, Joon Hwan; Choi, Chi-Hoon; Kang, Do-Hyung; Kwon, Jun Soo

    2013-01-01

    One major characteristic of experts is intuitive judgment, which is an automatic process whereby patterns stored in memory through long-term training are recognized. Indeed, long-term training may influence brain structure and function. A recent study revealed that chess experts at rest showed differences in structure and functional connectivity (FC) in the head of caudate, which is associated with rapid best next-move generation. However, less is known about the structure and function of the brains of Baduk experts (BEs) compared with those of experts in other strategy games. Therefore, we performed voxel-based morphometry (VBM) and FC analyses in BEs to investigate structural brain differences and to clarify the influence of these differences on functional interactions. We also conducted graph theoretical analysis (GTA) to explore the topological organization of whole-brain functional networks. Compared to novices, BEs exhibited decreased and increased gray matter volume (GMV) in the amygdala and nucleus accumbens (NA), respectively. We also found increased FC between the amygdala and medial orbitofrontal cortex (mOFC) and decreased FC between the NA and medial prefrontal cortex (mPFC). Further GTA revealed differences in measures of the integration of the network and in the regional nodal characteristics of various brain regions activated during Baduk. This study provides evidence for structural and functional differences as well as altered topological organization of the whole-brain functional networks in BEs. Our findings also offer novel suggestions about the cognitive mechanisms behind Baduk expertise, which involves intuitive decision-making mediated by somatic marker circuitry and visuospatial processing. PMID:24106471

  1. Uranium Bio-accumulation and Cycling as revealed by Uranium Isotopes in Naturally Reduced Sediments from the Upper Colorado River Basin

    NASA Astrophysics Data System (ADS)

    Lefebvre, Pierre; Noël, Vincent; Jemison, Noah; Weaver, Karrie; Bargar, John; Maher, Kate

    2016-04-01

    Uranium (U) groundwater contamination following oxidized U(VI) releases from weathering of mine tailings is a major concern at numerous sites across the Upper Colorado River Basin (CRB), USA. Uranium(IV)-bearing solids accumulated within naturally reduced zones (NRZs) characterized by elevated organic carbon and iron sulfide compounds. Subsequent re-oxidation of U(IV)solid to U(VI)aqueous then controls the release to groundwater and surface water, resulting in plume persistence and raising public health concerns. Thus, understanding the extent of uranium oxidation and reduction within NRZs is critical for assessing the persistence of the groundwater contamination. In this study, we measured solid-phase uranium isotope fractionation (δ238/235U) of sedimentary core samples from four study sites (Shiprock, NM, Grand Junction, Rifle and Naturita, CO) using a multi-collector inductively coupled plasma mass spectrometer (MC-ICP-MS). We observe a strong correlation between U accumulation and the extent of isotopic fractionation, with Δ238U up to +1.8 ‰ between uranium-enriched and low concentration zones. The enrichment in the heavy isotopes within the NRZs appears to be especially important in the vadose zone, which is subject to variations in water table depth. According to previous studies, this isotopic signature is consistent with biotic reduction processes associated with metal-reducing bacteria. Positive correlations between the amount of iron sulfides and the accumulation of reduced uranium underline the importance of sulfate-reducing conditions for U(IV) retention. Furthermore, the positive fractionation associated with U reduction observed across all sites despite some variations in magnitude due to site characteristics, shows a regional trend across the Colorado River Basin. The maximum extent of 238U enrichment observed in the NRZ proximal to the water table further suggests that the redox cycling of uranium, with net release of U(VI) to the groundwater by

  2. Ion Mobility-Mass Spectrometry Reveals Highly-Compact Intermediates in the Collision Induced Dissociation of Charge-Reduced Protein Complexes

    NASA Astrophysics Data System (ADS)

    Bornschein, Russell E.; Niu, Shuai; Eschweiler, Joseph; Ruotolo, Brandon T.

    2016-01-01

    Protocols that aim to construct complete models of multiprotein complexes based on ion mobility and mass spectrometry data are becoming an important element of integrative structural biology efforts. However, the usefulness of such data is predicated, in part, on an ability to measure individual subunits removed from the complex while maintaining a compact/folded state. Gas-phase dissociation of intact complexes using collision induced dissociation is a potentially promising pathway for acquiring such protein monomer size information, but most product ions produced are possessed of high charge states and elongated/string-like conformations that are not useful in protein complex modeling. It has previously been demonstrated that the collision induced dissociation of charge-reduced protein complexes can produce compact subunit product ions; however, their formation mechanism is not well understood. Here, we present new experimental evidence for the avidin (64 kDa) and aldolase (157 kDa) tetramers that demonstrates significant complex remodeling during the dissociation of charge-reduced assemblies. Detailed analysis and modeling indicates that highly compact intermediates are accessed during the dissociation process by both complexes. Here, we present putative pathways that describe the formation of such ions, as well as discuss the broader significance of such data for structural biology applications moving forward.

  3. Brain Morphometry on Congenital Hand Deformities based on Teichmüller Space Theory

    PubMed Central

    Peng, Hao; Wang, Xu; Duan, Ye; Frey, Scott H.; Gu, Xianfeng

    2016-01-01

    Congenital Hand Deformities (CHD) are usually occurred between fourth and eighth week after the embryo is formed. Failure of the transformation from arm bud cells to upper limb can lead to an abnormal appearing/functioning upper extremity which is presented at birth. Some causes are linked to genetics while others are affected by the environment, and the rest have remained unknown. CHD patients develop prehension through the use of their hands, which affect the brain as time passes. In recent years, CHD have gain increasing attention and researches have been conducted on CHD, both surgically and psychologically. However, the impacts of CHD on brain structure are not well-understood so far. Here, we propose a novel approach to apply Teichmüller space theory and conformal welding method to study brain morphometry in CHD patients. Conformal welding signature reflects the geometric relations among different functional areas on the cortex surface, which is intrinsic to the Riemannian metric, invariant under conformal deformation, and encodes complete information of the functional area boundaries. The computational algorithm is based on discrete surface Ricci flow, which has theoretic guarantees for the existence and uniqueness of the solutions. In practice, discrete Ricci flow is equivalent to a convex optimization problem, therefore has high numerically stability. In this paper, we compute the signatures of contours on general 3D surfaces with surface Ricci flow method, which encodes both global and local surface contour information. Then we evaluated the signatures of pre-central and post-central gyrus on healthy control and CHD subjects for analyzing brain cortical morphometry. Preliminary experimental results from 3D MRI data of CHD/control data demonstrate the effectiveness of our method. The statistical comparison between left and right brain gives us a better understanding on brain morphometry of subjects with Congenital Hand Deformities, in particular, missing

  4. MicroCT Morphometry Analysis of Mouse Cancellous Bone: Intra- and Inter-system Reproducibility

    PubMed Central

    Verdelis, K.; Lukashova, L.; Atti, E.; Mayer-Kuckuk, P.; Peterson, M.G.E.; Tetradis, S.; Boskey, A.L.; van der Meulen, M.C.H.

    2012-01-01

    The agreement between measurements and the relative performance reproducibility among different microcomputed tomography (microCT) systems, especially at voxel sizes close to the limit of the instruments, is not known. To compare this reproducibility 3D morphometric analyses of mouse cancellous bone from distal femoral epiphyses were performed using three different ex vivo microCT systems: GE eXplore Locus SP, Scanco μCT35 and Skyscan 1172. Scans were completed in triplicate at 12μm and 8μm voxel sizes and morphometry measurements, from which relative values and dependence on voxel size were examined. Global and individual visually assessed thresholds were compared. Variability from repeated scans at 12μm voxel size was also examined. Bone volume fraction and trabecular separation values were similar, while values for relative bone surface, trabecular thickness and number varied significantly across the three systems. The greatest differences were measured in trabecular thickness (up to 236%) and number (up to 218%). The relative dependence of measurements on voxel size was highly variable for the trabecular number (from 0% to 20% relative difference between measurements from 12μm and 8μm voxel size scans, depending on the system). The intra-system reproducibility of all trabecular measurements was also highly variable across the systems and improved for BV/TV in all the systems when a smaller voxel size was used. It improved using a smaller voxel size in all the other parameters examined for the Scanco system, but not consistently so for the GE or the Skyscan system. Our results indicate trabecular morphometry measurements should not be directly compared across microCT systems. In addition, the conditions, including voxel size, for trabecular morphometry studies in mouse bone should be chosen based on the specific microCT system and the measurements of main interest. PMID:21621659

  5. The Morphometry of Lake Palmas, a Deep Natural Lake in Brazil

    PubMed Central

    Barroso, Gilberto F.; Gonçalves, Monica A.; Garcia, Fábio da C.

    2014-01-01

    Lake Palmas (A = 10.3km2) is located in the Lower Doce River Valley (LDRV), on the southeastern coast of Brazil. The Lake District of the LDRV includes 90 lakes, whose basic geomorphology is associated with the alluvial valleys of the Barreiras Formation (Cenozoic, Neogene) and with the Holocene coastal plain. This study aimed to investigate the relationship of morphometry and thermal pattern of a LDRV deep lake, Lake Palmas. A bathymetric survey carried out in 2011 and the analysis of hydrographic and wind data with a geographic information system allowed the calculation of several metrics of lake morphometry. The vertical profiling of physical and chemical variables in the water column during the wet/warm and dry/mild cold seasons of 2011 to 2013 has furnished a better understanding of the influence of the lake morphometry on its structure and function. The overdeepened basin has a subrectangular elongated shape and is aligned in a NW-SE direction in an alluvial valley with a maximum depth (Zmax) of 50.7m, a volume of 2.2×108 m3 (0.22km3) and a mean depth (Zmv) of 21.4m. These metrics suggest Lake Palmas as the deepest natural lake in Brazil. Water column profiling has indicated strong physical and chemical stratification during the wet/warm season, with a hypoxic/anoxic layer occupying one-half of the lake volume. The warm monomictic pattern of Lake Palmas, which is in an accordance to deep tropical lakes, is determined by water column mixing during the dry and mild cold season, especially under the influence of a high effective fetch associated with the incidence of cold fronts. Lake Palmas has a very long theoretical retention time, with a mean of 19.4 years. The changes observed in the hydrological flows of the tributary rivers may disturb the ecological resilience of Lake Palmas. PMID:25406062

  6. The morphometry of Lake Palmas, a deep natural lake in Brazil.

    PubMed

    Barroso, Gilberto F; Gonçalves, Monica A; Garcia, Fábio da C

    2014-01-01

    Lake Palmas (A = 10.3km2) is located in the Lower Doce River Valley (LDRV), on the southeastern coast of Brazil. The Lake District of the LDRV includes 90 lakes, whose basic geomorphology is associated with the alluvial valleys of the Barreiras Formation (Cenozoic, Neogene) and with the Holocene coastal plain. This study aimed to investigate the relationship of morphometry and thermal pattern of a LDRV deep lake, Lake Palmas. A bathymetric survey carried out in 2011 and the analysis of hydrographic and wind data with a geographic information system allowed the calculation of several metrics of lake morphometry. The vertical profiling of physical and chemical variables in the water column during the wet/warm and dry/mild cold seasons of 2011 to 2013 has furnished a better understanding of the influence of the lake morphometry on its structure and function. The overdeepened basin has a subrectangular elongated shape and is aligned in a NW-SE direction in an alluvial valley with a maximum depth (Zmax) of 50.7 m, a volume of 2.2×10(8) m3 (0.22 km3) and a mean depth (Zmv) of 21.4m. These metrics suggest Lake Palmas as the deepest natural lake in Brazil. Water column profiling has indicated strong physical and chemical stratification during the wet/warm season, with a hypoxic/anoxic layer occupying one-half of the lake volume. The warm monomictic pattern of Lake Palmas, which is in an accordance to deep tropical lakes, is determined by water column mixing during the dry and mild cold season, especially under the influence of a high effective fetch associated with the incidence of cold fronts. Lake Palmas has a very long theoretical retention time, with a mean of 19.4 years. The changes observed in the hydrological flows of the tributary rivers may disturb the ecological resilience of Lake Palmas. PMID:25406062

  7. Some fundamental aspects of morphometry in clinical pathology, demonstrated on a simple, multipurpose analysis system.

    PubMed

    Oberholzer, M; Christen, H; Ettlin, R; Buser, M; Oestreicher, M; Gschwind, R

    1991-10-01

    The aim of this study was (1) to investigate the value of morphometry, (2) to fix a set of parameters suitable for analyzing diagnostic problems, and (3) to create a general strategy for data storage and for user-friendly data management. The intrinsic value of morphometry lies in the fact that in contrast to other morphologic methods, it permits the presentation of findings in the form of numbers. The following set of morphometric parameters, in the broad sense of the term morphometry, is standard in our laboratory: planimetric parameters (shape descriptors), parameters of the gray value histogram (descriptors of the general gray value distribution), texture parameters (descriptors of the correlation between various image segments), invariant moments (descriptors of the size and localization of textural image segments) and densitometric parameters. The introduction of morphometric procedures into the daily routine is facilitated if data registration and evaluation are performed separately. Original data generated by direct measurement are primary or raw data, which are stored as such. In a separate, second step these raw data are used to compare more or less complex morphometric parameters, which are called "secondary data". A system designed for separate data registration and evaluation can easily be adapted to new methodologic developments. For instance, primary data on objects (gray values, coordinates of the contour) measured one time in the past can be reused at any other time for computing new features from these data. This procedure is comparable to the possibilities in immunohistochemical staining: new immunohistochemical stains can be applied to newly prepared sections of old tissue blocks. PMID:1801829

  8. Combining the boundary shift integral and tensor-based morphometry for brain atrophy estimation

    NASA Astrophysics Data System (ADS)

    Michalkiewicz, Mateusz; Pai, Akshay; Leung, Kelvin K.; Sommer, Stefan; Darkner, Sune; Sørensen, Lauge; Sporring, Jon; Nielsen, Mads

    2016-03-01

    Brain atrophy from structural magnetic resonance images (MRIs) is widely used as an imaging surrogate marker for Alzheimers disease. Their utility has been limited due to the large degree of variance and subsequently high sample size estimates. The only consistent and reasonably powerful atrophy estimation methods has been the boundary shift integral (BSI). In this paper, we first propose a tensor-based morphometry (TBM) method to measure voxel-wise atrophy that we combine with BSI. The combined model decreases the sample size estimates significantly when compared to BSI and TBM alone.

  9. Facial morphometry of Ecuadorian patients with growth hormone receptor deficiency/Laron syndrome.

    PubMed Central

    Schaefer, G B; Rosenbloom, A L; Guevara-Aguirre, J; Campbell, E A; Ullrich, F; Patil, K; Frias, J L

    1994-01-01

    Facial morphometry using computerised image analysis was performed on patients with growth hormone receptor deficiency (Laron syndrome) from an inbred population of southern Ecuador. Morphometrics were compared for 49 patients, 70 unaffected relatives, and 14 unrelated persons. Patients with growth hormone receptor deficiency showed significant decreases in measures of vertical facial growth as compared to unaffected relatives and unrelated persons with short stature from other causes. This report validates and quantifies the clinical impression of foreshortened facies in growth hormone receptor deficiency. Images PMID:7815422

  10. [Possibility of the morphometry of the neuronal body and nucleus in cryostat sections of nerve tissue].

    PubMed

    Krasnov, I B

    1982-02-01

    A method of fixation by the Carnoy liquid and of gallocyanine staining is proposed in order to obtain clear-cut boundaries of the neuron body, nucleus and nucleolus in cryostat sections of non-fixed frozen nerve tissue, for subsequent morphometry of the body and nucleus of nerve cells. In the resulting sections, the clearness of boundaries of the body and nucleus in a neuron is sufficient for measuring its diameter with the coefficient of variation not exceeding 2.5%. PMID:7041376

  11. Extraction of sandy bedforms features through geodesic morphometry

    NASA Astrophysics Data System (ADS)

    Debese, Nathalie; Jacq, Jean-José; Garlan, Thierry

    2016-09-01

    State-of-art echosounders reveal fine-scale details of mobile sandy bedforms, which are commonly found on continental shelfs. At present, their dynamics are still far from being completely understood. These bedforms are a serious threat to navigation security, anthropic structures and activities, placing emphasis on research breakthroughs. Bedform geometries and their dynamics are closely linked; therefore, one approach is to develop semi-automatic tools aiming at extracting their structural features from bathymetric datasets. Current approaches mimic manual processes or rely on morphological simplification of bedforms. The 1D and 2D approaches cannot address the wide ranges of both types and complexities of bedforms. In contrast, this work attempts to follow a 3D global semi-automatic approach based on a bathymetric TIN. The currently extracted primitives are the salient ridge and valley lines of the sand structures, i.e., waves and mega-ripples. The main difficulty is eliminating the ripples that are found to heavily overprint any observations. To this end, an anisotropic filter that is able to discard these structures while still enhancing the wave ridges is proposed. The second part of the work addresses the semi-automatic interactive extraction and 3D augmented display of the main lines structures. The proposed protocol also allows geoscientists to interactively insert topological constraints.

  12. Ultrastructural morphometry of the myocardium of Thunnus alalunga.

    PubMed

    Breisch, E A; White, F; Jones, H M; Laurs, R M

    1983-01-01

    The common ventricle in the heart of the Thunnus alalunga was studied. The ventricular myocardium consists of an outer compact layer and a thick inner spongy layer. The compact layer has slightly larger cells (4-6 microns diameter) than the spongy layer (2.5-5 microns diameter). Ultrastructurally the myocardium displays normal arrangements of myofibrils and mitochondria. The sarcoplasmic reticulum is poorly developed. The intercalated discs are simple with the fascia adherens being the most frequent junctional type observed; occasionally a desmosome was seen. Nexus type junctions are present but are unassociated with the intercalated discs. There are no t-tubules evident but the plasmalemma exhibits numerous caveolae which rarely form couplings with the sarcoplasmic reticulum. A morphometric analysis of the volume percent of mitochondria and myofibrils showed that the myocardial cells in the spongy layer of the heart have a significantly greater volume percentage of mitochondria than the compact layer. No significant differences were found between myocardial regions when the volume percentages of myofibrils were compared. The physiological studies revealed that the albacore tuna has heart rates (120 bpm) and ventricular blood pressures (100 mmHg) that are among the highest reported for fish. PMID:6616575

  13. Multidetector Computed Tomography-Based Microstructural Analysis Reveals Reduced Bone Mineral Content and Trabecular Bone Changes in the Lumbar Spine after Transarterial Chemoembolization Therapy for Hepatocellular Carcinoma

    PubMed Central

    Takasu, Miyuki; Yamagami, Takuji; Nakamura, Yuko; Komoto, Daisuke; Kaichi, Yoko; Tani, Chihiro; Date, Shuji; Kiguchi, Masao; Awai, Kazuo

    2014-01-01

    Purpose It is well recognized that therapeutic irradiation can result in bone damage. However, long-term bone toxicity associated with computed tomography (CT) performed during interventional angiography has received little attention. The purpose of this study was to determine the prevalence of osteoporosis and trabecular microstructural changes in patients after transarterial chemoembolization (TACE) for hepatocellular carcinoma therapy using an interventional-CT system. Materials and Methods Spinal microarchitecture was examined by 64-detector CT in 81 patients who underwent TACE, 35 patients with chronic hepatitis, and 79 controls. For each patient, the volumetric CT dose index (CTDIv) during TACE (CTDIv (TACE)), the dose-length product (DLP) during TACE (DLP (TACE)), and CTDIv and DLP of routine dynamic CT scans (CTDIv (CT) and DLP (CT), respectively), were calculated as the sum since 2008. Using a three dimensional (3D) image analysis system, the tissue bone mineral density (tBMD) and trabecular parameters of the 12th thoracic vertebra were calculated. Using tBMD at a reported cutoff value of 68 mg/cm3, the prevalence of osteoporosis was assessed. Results The prevalence of osteoporosis was significantly greater in the TACE vs. the control group (39.6% vs. 18.2% for males, P<0.05 and 60.6% vs. 34.8% for females, P<0.01). Multivariate regression analysis demonstrated that sex, age, and CTDIv (CT) significantly affected the risk of osteoporosis. Of these indices, CTDIv (CT) had the highest area under the curve (AUC) (0.735). Correlation analyses of tBMD with cumulative radiation dose revealed weak correlations between tBMD and CTDIv (CT) (r2 = 0.194, P<0.001). Conclusion The prevalence of osteoporosis was significantly higher in post TACE patients than in control subjects. The cumulative radiation dose related to routine dynamic CT studies was a significant contributor to the prevalence of osteoporosis. PMID:25329933

  14. Microarray Analysis Reveals Increased Transcriptional Repression and Reduced Metabolic Activity but Not Major Changes in the Core Apoptotic Machinery during Maturation of Sympathetic Neurons

    PubMed Central

    Raba, Mikk; Palgi, Jaan; Lehtivaara, Maria; Arumäe, Urmas

    2016-01-01

    Postnatal maturation of the neurons whose main phenotype and basic synaptic contacts are already established includes neuronal growth, refinement of synaptic contacts, final steps of differentiation, programmed cell death period (PCD) etc. In the sympathetic neurons, postnatal maturation includes permanent end of the PCD that occurs with the same time schedule in vivo and in vitro suggesting that the process could be genetically determined. Also many other changes in the neuronal maturation could be permanent and thus based on stable changes in the genome expression. However, postnatal maturation of the neurons is poorly studied. Here we compared the gene expression profiles of immature and mature sympathetic neurons using Affymetrix microarray assay. We found 1310 significantly up-regulated and 1151 significantly down-regulated genes in the mature neurons. Gene ontology analysis reveals up-regulation of genes related to neuronal differentiation, chromatin and epigenetic changes, extracellular factors and their receptors, and cell adhesion, whereas many down-regulated genes were related to metabolic and biosynthetic processes. We show that termination of PCD is not related to major changes in the expression of classical genes for apoptosis or cell survival. Our dataset is deposited to the ArrayExpress database and is a valuable source to select candidate genes in the studies of neuronal maturation. As an example, we studied the changes in the expression of selected genes Igf2bp3, Coro1A, Zfp57, Dcx, and Apaf1 in the young and mature sympathetic ganglia by quantitative PCR and show that these were strongly downregulated in the mature ganglia. PMID:27013977

  15. Dune Morphometry in the Age of Digital Elevation Models

    NASA Astrophysics Data System (ADS)

    Lancaster, N.

    2014-12-01

    Dune patterns can be characterized in many different ways. Relationships between dune height, width and spacing, and the spatial variation in these parameters have been widely employed to provide quantitative information that can be used to describe dune patterns and make comparisons between dunes in widely separated areas, as well as to identify different generations of dunes. Digital elevation models (e.g. ASTER GDEM) provide a rich resource of data for analyses of dune patterns at landscape scales in several ways, including: (1) more extensive analyses using traditional measures, such as relationships between dune height and spacing, and the spatial variation in these parameters; and (2) estimation of sediment thickness on a regional scale. Analyses of data for Arabian and Namibian sand seas and dune fields show that dune height and spacing relationships are much more variable than previously reported and call into question existing models. Regional patterns of sediment thickness reveal areas of erosion, bypass, and accumulation that can be related to transport pathways and wind regimes. The widespread occurrence of complex dune patterns as well as the magnitude of the newly available data sets however requires more sophisticated analyses than simple extraction of dune morphometric parameters using GIS approaches. Geostatistical analyses using spatial autocorrelation, Fourier, and Wavelet methods have been employed in analyses of sub-aqueous bedforms and show promise for dune systems. Automated or semi-automated identification of dune length, width, spacing, and trends using advanced image analysis techniques such as linear segment detection is a potentially transformative approach. The strengths and weaknesses of these methods to provide pertinent geomorphic information are currently being evaluated, but they have the potential to provide new insights into the nature of dune patterns.

  16. Multispectral brain morphometry in Tourette syndrome persisting into adulthood

    PubMed Central

    Martino, Davide; Cavanna, Andrea E.; Hutton, Chloe; Orth, Michael; Robertson, Mary M.; Critchley, Hugo D.; Frackowiak, Richard S.

    2010-01-01

    Tourette syndrome is a childhood-onset neuropsychiatric disorder with a high prevalence of attention deficit hyperactivity and obsessive-compulsive disorder co-morbidities. Structural changes have been found in frontal cortex and striatum in children and adolescents. A limited number of morphometric studies in Tourette syndrome persisting into adulthood suggest ongoing structural alterations affecting frontostriatal circuits. Using cortical thickness estimation and voxel-based analysis of T1- and diffusion-weighted structural magnetic resonance images, we examined 40 adults with Tourette syndrome in comparison with 40 age- and gender-matched healthy controls. Patients with Tourette syndrome showed relative grey matter volume reduction in orbitofrontal, anterior cingulate and ventrolateral prefrontal cortices bilaterally. Cortical thinning extended into the limbic mesial temporal lobe. The grey matter changes were modulated additionally by the presence of co-morbidities and symptom severity. Prefrontal cortical thickness reduction correlated negatively with tic severity, while volume increase in primary somatosensory cortex depended on the intensity of premonitory sensations. Orbitofrontal cortex volume changes were further associated with abnormal water diffusivity within grey matter. White matter analysis revealed changes in fibre coherence in patients with Tourette syndrome within anterior parts of the corpus callosum. The severity of motor tics and premonitory urges had an impact on the integrity of tracts corresponding to cortico-cortical and cortico-subcortical connections. Our results provide empirical support for a patho-aetiological model of Tourette syndrome based on developmental abnormalities, with perturbation of compensatory systems marking persistence of symptoms into adulthood. We interpret the symptom severity related grey matter volume increase in distinct functional brain areas as evidence of ongoing structural plasticity. The convergence of

  17. Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis.

    PubMed

    Falentin, Hélène; Rault, Lucie; Nicolas, Aurélie; Bouchard, Damien S; Lassalas, Jacques; Lamberton, Philippe; Aubry, Jean-Marc; Marnet, Pierre-Guy; Le Loir, Yves; Even, Sergine

    2016-01-01

    Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq) to one or several clinical mastitis events (Mastitic quarter, Mq). Several quarters whose status was unclear (possible history of subclinical mastitis) were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively). Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively). Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc.), the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc.), and the Bifidobacteriales order (Bifidobacterium), whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus) and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the infectious episode

  18. Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis

    PubMed Central

    Falentin, Hélène; Rault, Lucie; Nicolas, Aurélie; Bouchard, Damien S.; Lassalas, Jacques; Lamberton, Philippe; Aubry, Jean-Marc; Marnet, Pierre-Guy; Le Loir, Yves; Even, Sergine

    2016-01-01

    Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq) to one or several clinical mastitis events (Mastitic quarter, Mq). Several quarters whose status was unclear (possible history of subclinical mastitis) were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively). Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively). Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc.), the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc.), and the Bifidobacteriales order (Bifidobacterium), whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus) and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the infectious episode

  19. From Cortical and Subcortical Grey Matter Abnormalities to Neurobehavioral Phenotype of Angelman Syndrome: A Voxel-Based Morphometry Study.

    PubMed

    Aghakhanyan, Gayane; Bonanni, Paolo; Randazzo, Giovanna; Nappi, Sara; Tessarotto, Federica; De Martin, Lara; Frijia, Francesca; De Marchi, Daniele; De Masi, Francesco; Kuppers, Beate; Lombardo, Francesco; Caramella, Davide; Montanaro, Domenico

    2016-01-01

    Angelman syndrome (AS) is a rare neurogenetic disorder due to loss of expression of maternal ubiquitin-protein ligase E3A (UBE3A) gene. It is characterized by severe developmental delay, speech impairment, movement or balance disorder and typical behavioral uniqueness. Affected individuals show normal magnetic resonance imaging (MRI) findings, although mild dysmyelination may be observed. In this study, we adopted a quantitative MRI analysis with voxel-based morphometry (FSL-VBM) method to investigate disease-related changes in the cortical/subcortical grey matter (GM) structures. Since 2006 to 2013 twenty-six AS patients were assessed by our multidisciplinary team. From those, sixteen AS children with confirmed maternal 15q11-q13 deletions (mean age 7.7 ± 3.6 years) and twenty-one age-matched controls were recruited. The developmental delay and motor dysfunction were assessed using Bayley III and Gross Motor Function Measure (GMFM). Principal component analysis (PCA) was applied to the clinical and neuropsychological datasets. High-resolution T1-weighted images were acquired and FSL-VBM approach was applied to investigate differences in the local GM volume and to correlate clinical and neuropsychological changes in the regional distribution of GM. We found bilateral GM volume loss in AS compared to control children in the striatum, limbic structures, insular and orbitofrontal cortices. Voxel-wise correlation analysis with the principal components of the PCA output revealed a strong relationship with GM volume in the superior parietal lobule and precuneus on the left hemisphere. The anatomical distribution of cortical/subcortical GM changes plausibly related to several clinical features of the disease and may provide an important morphological underpinning for clinical and neurobehavioral symptoms in children with AS. PMID:27626634

  20. Childhood adversity is linked to differential brain volumes in adolescents with alcohol use disorder: a voxel-based morphometry study.

    PubMed

    Brooks, Samantha J; Dalvie, Shareefa; Cuzen, Natalie L; Cardenas, Valerie; Fein, George; Stein, Dan J

    2014-06-01

    Previous neuroimaging studies link both alcohol use disorder (AUD) and early adversity to neurobiological differences in the adult brain. However, the association between AUD and childhood adversity and effects on the developing adolescent brain are less clear, due in part to the confound of psychiatric comorbidity. Here we examine early life adversity and its association with brain volume in a unique sample of 116 South African adolescents (aged 12-16) with AUD but without psychiatric comorbidity. Participants were 58 adolescents with DSM-IV alcohol dependence and with no other psychiatric comorbidities, and 58 age-, gender- and protocol-matched light/non-drinking controls (HC). Assessments included the Childhood Trauma Questionnaire (CTQ). MR images were acquired on a 3T Siemens Magnetom Allegra scanner. Volumes of global and regional structures were estimated using SPM8 Voxel Based Morphometry (VBM), with analysis of covariance (ANCOVA) and regression analyses. In whole brain ANCOVA analyses, a main effect of group when examining the AUD effect after covarying out CTQ was observed on brain volume in bilateral superior temporal gyrus. Subsequent regression analyses to examine how childhood trauma scores are linked to brain volumes in the total cohort revealed a negative correlation in the left hippocampus and right precentral gyrus. Furthermore, bilateral (but most significantly left) hippocampal volume was negatively associated with sub-scores on the CTQ in the total cohort. These findings support our view that some alterations found in brain volumes in studies of adolescent AUD may reflect the impact of confounding factors such as psychiatric comorbidity rather than the effects of alcohol per se. In particular, early life adversity may influence the developing adolescent brain in specific brain regions, such as the hippocampus. PMID:24496784

  1. A comparison of manual neuronal reconstruction from biocytin histology or 2-photon imaging: morphometry and computer modeling

    PubMed Central

    Blackman, Arne V.; Grabuschnig, Stefan; Legenstein, Robert; Sjöström, P. Jesper

    2014-01-01

    Accurate 3D reconstruction of neurons is vital for applications linking anatomy and physiology. Reconstructions are typically created using Neurolucida after biocytin histology (BH). An alternative inexpensive and fast method is to use freeware such as Neuromantic to reconstruct from fluorescence imaging (FI) stacks acquired using 2-photon laser-scanning microscopy during physiological recording. We compare these two methods with respect to morphometry, cell classification, and multicompartmental modeling in the NEURON simulation environment. Quantitative morphological analysis of the same cells reconstructed using both methods reveals that whilst biocytin reconstructions facilitate tracing of more distal collaterals, both methods are comparable in representing the overall morphology: automated clustering of reconstructions from both methods successfully separates neocortical basket cells from pyramidal cells but not BH from FI reconstructions. BH reconstructions suffer more from tissue shrinkage and compression artifacts than FI reconstructions do. FI reconstructions, on the other hand, consistently have larger process diameters. Consequently, significant differences in NEURON modeling of excitatory post-synaptic potential (EPSP) forward propagation are seen between the two methods, with FI reconstructions exhibiting smaller depolarizations. Simulated action potential backpropagation (bAP), however, is indistinguishable between reconstructions obtained with the two methods. In our hands, BH reconstructions are necessary for NEURON modeling and detailed morphological tracing, and thus remain state of the art, although they are more labor intensive, more expensive, and suffer from a higher failure rate due to the occasional poor outcome of histological processing. However, for a subset of anatomical applications such as cell type identification, FI reconstructions are superior, because of indistinguishable classification performance with greater ease of use

  2. Andean Basins Morphometry: Assesing South American Large Rivers' Source Areas

    NASA Astrophysics Data System (ADS)

    Bean, R. A.; Latrubesse, E. M.

    2014-12-01

    Presently there are no regional-scale morphometric analyses of Andean fluvial basins. Therefore, we created a continental-scale database of these basins. Our data covers over an area 1,000,000 km2 of the Andes, from Venezuela to Argentina. These basins are the source of some of the largest rivers in the world including the Amazon, Orinoco, Parana, and Magdalena. Morphometric parameters including shape factor, relief ratio, longitudinal profiles and different indices of basin elevation were calculated based on the CGIAR SRTM 4.1 DEM (~90 m resolution). FAO Hydrosheds were used to segment the DEM by major catchment and then manually cut at the Andean zone. In the North and Central Andes, this produced over 500,000 subcatchments, which we reduced to 619 by setting minimum catchment area to 100 km2. We then integrate lithologic data from DNPM geologic data. Our results indicate that sedimentary lithologies dominate Central Andean catchments (n=268,k=4), which cover an area 767,00 km2, while the Northern Andean catchments (covering 350,000 km2) are more varied, dominated by volcanics in the Pacific (n=78), a sedimentary (48%) dominant mix in the Caribbean (n=138) and 60% sedimentary in the Amazon-Orinoco subregion catchments (n=138). Elevation averages are smallest in the north Andes and average maximum elevations (6,026 m) in the Argentinian catchments (n=65) of the Central Andes are the highest. Shape factors range from 0.49 to 0.58 in the North and 0.52 to 0.58 in the Central Andes. There are clear differences in all categories between region and subregion, but that difference does not hinge on a single morphometric or geologic parameter. Morphometric parameters at a watershed scale (listed in Table) are analyzed and hydrologic data from gauging stations throughout the Andes (n=100) are used to compare morphometric parameters with lithology and characteristics from the basin hydrograph (peak discharge timing, minimum and maximum discharge, and runoff).

  3. How much is there really? Why stereology is essential in lung morphometry.

    PubMed

    Weibel, Ewald R; Hsia, Connie C W; Ochs, Matthias

    2007-01-01

    Quantitative data on lung structure are essential to set up structure-function models for assessing the functional performance of the lung or to make statistically valid comparisons in experimental morphology, physiology, or pathology. The methods of choice for microscopy-based lung morphometry are those of stereology, the science of quantitative characterization of irregular three-dimensional objects on the basis of measurements made on two-dimensional sections. From a practical perspective, stereology is an assumption-free set of methods of unbiased sampling with geometric probes, based on a solid mathematical foundation. Here, we discuss the pitfalls of lung morphometry and present solutions, from specimen preparation to the sampling scheme in multiple stages, for obtaining unbiased estimates of morphometric parameters such as volumes, surfaces, lengths, and numbers. This is demonstrated on various examples. Stereological methods are accurate, efficient, simple, and transparent; the precision of the estimates depends on the size and distribution of the sample. For obtaining quantitative data on lung structure at all microscopic levels, state-of-the-art stereology is the gold standard. PMID:16973815

  4. Generalized tensor-based morphometry of HIV/AIDS using multivariate statistics on deformation tensors.

    PubMed

    Lepore, N; Brun, C; Chou, Y Y; Chiang, M C; Dutton, R A; Hayashi, K M; Luders, E; Lopez, O L; Aizenstein, H J; Toga, A W; Becker, J T; Thompson, P M

    2008-01-01

    This paper investigates the performance of a new multivariate method for tensor-based morphometry (TBM). Statistics on Riemannian manifolds are developed that exploit the full information in deformation tensor fields. In TBM, multiple brain images are warped to a common neuroanatomical template via 3-D nonlinear registration; the resulting deformation fields are analyzed statistically to identify group differences in anatomy. Rather than study the Jacobian determinant (volume expansion factor) of these deformations, as is common, we retain the full deformation tensors and apply a manifold version of Hotelling's $T(2) test to them, in a Log-Euclidean domain. In 2-D and 3-D magnetic resonance imaging (MRI) data from 26 HIV/AIDS patients and 14 matched healthy subjects, we compared multivariate tensor analysis versus univariate tests of simpler tensor-derived indices: the Jacobian determinant, the trace, geodesic anisotropy, and eigenvalues of the deformation tensor, and the angle of rotation of its eigenvectors. We detected consistent, but more extensive patterns of structural abnormalities, with multivariate tests on the full tensor manifold. Their improved power was established by analyzing cumulative p-value plots using false discovery rate (FDR) methods, appropriately controlling for false positives. This increased detection sensitivity may empower drug trials and large-scale studies of disease that use tensor-based morphometry. PMID:18270068

  5. The effect of cryopreservation on sperm head morphometry in Florida male goat related to sperm freezability.

    PubMed

    Hidalgo, M; Rodríguez, I; Dorado, J M

    2007-07-01

    The Sperm Class Analyzer was used to investigate the effect of freeze-thawing procedure on Florida buck sperm head morphometry, and to relate possible changes in sperm head dimensions to cryopreservation success. Semen samples (n=76) were frozen with tris and milk-based extenders and thawed. Sperm quality samples (motility, morphology, acrosome), and sperm head morphometric values (length, width, area, perimeter, ellipticity) were compared between fresh and frozen-thawed samples. Sperm freezability was judged according to the sperm quality parameters assessed. Fertility data was obtained after artificial insemination with cryopreserved semen. Cryopreservation success was different between freezing methods. Sperm head dimensions were significantly (p<0.05) smaller in cryopreserved tris and milk spermatozoa respectively than in those of the fresh samples. The sperm head morphometric parameters that had changed after cryopreservation were lower in suitable semen samples after thawing and with successful pregnancies after artificial insemination. These data suggest that changes in sperm head morphometry might reflect spermatozoa injury occurred during cryopreservation. PMID:16904275

  6. Analysis of shallow landslides by morphometry parameters derived from terrestrial laser scanning point clouds

    NASA Astrophysics Data System (ADS)

    Mayr, A.; Rutzinger, M.; Bremer, M.; Wiegand, C.; Kringer, K.; Geitner, C.

    2012-04-01

    Erosion by shallow landslides is a widespread and growing phenomenon in mountainous areas. The major consequences are loss of soil and regolith as well as damages on infrastructure and provision of unconsolidated material for secondary processes such as mudflows. In this study we present a concept for extracting morphometry parameters from terrestrial laser scanning (TLS) point clouds in order to investigate the relation between slope surface structure and regolith depth. TLS is used to collect high-resolution point cloud data of an affected slope in the Schmirn Valley (Tyrol, Austria). Regolith depth is considered to be one of the important factors for the development of shallow landslides. However, direct field measurements are labour- and time-consuming. In this study we developed an approach, to investigate the relation between regolith depth and surface morphometry parameters. The reference regolith depth information is derived from lightweight dynamic cone penetrometer tests (DCPT) within the test site. The suggested approach integrates spatial analysis of Geographic Information Systems and point cloud processing algorithms. It will help to enhance the prediction of shallow landslide occurrence by (i) deriving high resolution 3D morphometric parameters and (ii) determining regolith depth with a reasonable effort due to automation. In future we want to be able to contribute with this concept to the detailed modelling of shallow landslide susceptibility on alpine slopes.

  7. Generalized Tensor-Based Morphometry of HIV/AIDS Using Multivariate Statistics on Deformation Tensors

    PubMed Central

    Lepore, Natasha; Brun, Caroline; Chou, Yi-Yu; Chiang, Ming-Chang; Dutton, Rebecca A.; Hayashi, Kiralee M.; Luders, Eileen; Lopez, Oscar L.; Aizenstein, Howard J.; Toga, Arthur W.; Becker, James T.; Thompson, Paul M.

    2009-01-01

    This paper investigates the performance of a new multivariate method for tensor-based morphometry (TBM). Statistics on Riemannian manifolds are developed that exploit the full information in deformation tensor fields. In TBM, multiple brain images are warped to a common neuroanatomical template via 3-D nonlinear registration; the resulting deformation fields are analyzed statistically to identify group differences in anatomy. Rather than study the Jacobian determinant (volume expansion factor) of these deformations, as is common, we retain the full deformation tensors and apply a manifold version of Hotelling’s T 2 test to them, in a Log-Euclidean domain. In 2-D and 3-D magnetic resonance imaging (MRI) data from 26 HIV/AIDS patients and 14 matched healthy subjects, we compared multivariate tensor analysis versus univariate tests of simpler tensor-derived indices: the Jacobian determinant, the trace, geodesic anisotropy, and eigenvalues of the deformation tensor, and the angle of rotation of its eigenvectors. We detected consistent, but more extensive patterns of structural abnormalities, with multivariate tests on the full tensor manifold. Their improved power was established by analyzing cumulative p-value plots using false discovery rate (FDR) methods, appropriately controlling for false positives. This increased detection sensitivity may empower drug trials and large-scale studies of disease that use tensor-based morphometry. PMID:18270068

  8. Pedicle Morphometry for Thoracic Screw Fixation in Ethnic Koreans : Radiological Assessment Using Computed Tomographic Myelography

    PubMed Central

    Choi, Yong Soo; Yi, Hyeong-Joong; Kim, Young-Joon

    2009-01-01

    Objective In the thoracic spine, insertion of a pedicle screw is annoying due to small pedicle size and wide morphological variation between different levels of the spine and between individuals. The aim of our study was to analyze radiologic parameters of the pedicle morphometry from T1 to T8 using computed tomographic myelography (CTM) in Korean population. Methods For evaluation of the thoracic pedicle morphometry, the authors prospectively analyzed a consecutive series of 26 patients with stable thoracic spines. With the consent of patients, thoracic CTM were performed, from T1 to T8. We calculated the transverse outer diameters and the transverse angles of the pedicle, distance from the cord to the inner cortical wall of the pedicle, and distance from the cord to the dura. Results Transverse outer pedicle diameter was widest at T1 (7.66 ± 2.14 mm) and narrowest at T4 (4.38 ± 1.55 mm). Transverse pedicle angle was widest at T1 (30.2 ± 12.0°) and it became less than 9.0° below T6 level. Theoretical safety zone of the medial perforation of the pedicle screw, namely, distance from the cord to inner cortical wall of the pedicle was more than 4.5 mm. Conclusion Based on this study, we suggest that the current pedicle screw system is not always suitable for Korean patients. Computed tomography is required before performing a transpedicular screw fixation at the thoracic levels. PMID:19893719

  9. A case study of morphometry as a more sensitive paleoceanographic tool in Globigerinoides ruber

    NASA Astrophysics Data System (ADS)

    Iwai, F. S.; de Lima Toledo, F. A.; Badaraco Costa, K.

    2013-12-01

    There are a number of paleoceanographic tools that take advantage from the wide geographic and temporal occurrence of planktic foraminifers in marine sediments. These tools comprises since simple visual identification and counting to geochemical analysis. Globigerinoides ruber is specially employed due to its high abundance in addition to the advantages mentioned above. That has been attributed to its broad tolerance to most of ecological factors and due to this fact, for this reason, its abundance fluctuation does not provide a significant paleocenographic data like other species do. Globigerinoides ruber has been largely employed in geochemical analysis which demands a higher number of individuals. However, Globigerinoides ruber from brazilian continental margin core tops sediments presents no significant fluctuation either in its abundance and on two of the main paleoceanographic proxies, oxygen and carbon isotope signals, indicating there is no significant environmental difference along brazilian continental margin. Nevertheless, Globigerinoides ruber specimens morphometry does show a significant change between brazilian continental margin core tops. This indicates that morphometry may be a more sensitive tool, enabling a more detailed exploration of paleoceanographical data than other tools do in this species.

  10. Voxel-based morphometry in eating disorders: correlation of psychopathology with grey matter volume.

    PubMed

    Joos, Andreas; Klöppel, Stefan; Hartmann, Armin; Glauche, Volkmar; Tüscher, Oliver; Perlov, Evgeniy; Saum, Barbara; Freyer, Tobias; Zeeck, Almut; Tebartz van Elst, Ludger

    2010-05-30

    Twenty-nine adult female patients with eating disorders (17 with bulimia nervosa, 12 with restrictive anorexia nervosa) were compared with 18 age-matched female healthy controls, using voxel-based morphometry. Restrictive anorexia nervosa patients showed a decrease of grey matter, particularly affecting the anterior cingulate cortex, frontal operculum, temporoparietal regions and the precuneus. By contrast, patients with bulimia nervosa did not differ from healthy controls. A positive correlation of "drive for thinness" and grey matter volume of the right inferior parietal lobe was found for both eating disorder groups. The strong reduction of grey matter volume in adult patients with restrictive anorexia nervosa is in line with results of adolescent patients. Contrary to other studies, this first voxel-based morphometry report of bulimic patients did not find any structural abnormalities. The inferior parietal cortex is a critical region for sensory integration of body and spatial perception, and the correlation of "drive for thinness" with grey matter volume of this region points to a neural correlate of this core psychopathological feature of eating disorders. PMID:20400273

  11. Neural Correlates of Aggression in Medication-Naive Children with ADHD: Multivariate Analysis of Morphometry and Tractography

    PubMed Central

    Cha, Jiook; Fekete, Tomer; Siciliano, Francesco; Biezonski, Dominik; Greenhill, Laurence; Pliszka, Steven R; Blader, Joseph C; Krain Roy, Amy; Leibenluft, Ellen; Posner, Jonathan

    2015-01-01

    Aggression is widely observed in children with attention deficit/hyperactivity disorder (ADHD) and has been frequently linked to frustration or the unsatisfied anticipation of reward. Although animal studies and human functional neuroimaging implicate altered reward processing in aggressive behaviors, no previous studies have documented the relationship between fronto-accumbal circuitry—a critical cortical pathway to subcortical limbic regions—and aggression in medication-naive children with ADHD. To address this, we collected behavioral measures and parental reports of aggression and impulsivity, as well as structural and diffusion MRI, from 30 children with ADHD and 31 healthy controls (HC) (mean age, 10±2.1 SD). Using grey matter morphometry and probabilistic tractography combined with multivariate statistical modeling (partial least squares regression and support vector regression), we identified anomalies within the fronto-accumbal circuit in childhood ADHD, which were associated with increased aggression. More specifically, children with ADHD showed reduced right accumbal volumes and frontal-accumbal white matter connectivity compared with HC. The magnitude of the accumbal volume reductions within the ADHD group was significantly correlated with increased aggression, an effect mediated by the relationship between the accumbal volume and impulsivity. Furthermore, aggression, but not impulsivity, was significantly explained by multivariate measures of fronto-accumbal white matter connectivity and cortical thickness within the orbitofrontal cortex. Our multi-modal imaging, combined with multivariate statistical modeling, indicates that the fronto-accumbal circuit is an important substrate of aggression in children with ADHD. These findings suggest that strategies aimed at probing the fronto-accumbal circuit may be beneficial for the treatment of aggressive behaviors in childhood ADHD. PMID:25645374

  12. Neural Correlates of Aggression in Medication-Naive Children with ADHD: Multivariate Analysis of Morphometry and Tractography.

    PubMed

    Cha, Jiook; Fekete, Tomer; Siciliano, Francesco; Biezonski, Dominik; Greenhill, Laurence; Pliszka, Steven R; Blader, Joseph C; Roy, Amy Krain; Leibenluft, Ellen; Posner, Jonathan

    2015-06-01

    Aggression is widely observed in children with attention deficit/hyperactivity disorder (ADHD) and has been frequently linked to frustration or the unsatisfied anticipation of reward. Although animal studies and human functional neuroimaging implicate altered reward processing in aggressive behaviors, no previous studies have documented the relationship between fronto-accumbal circuitry-a critical cortical pathway to subcortical limbic regions-and aggression in medication-naive children with ADHD. To address this, we collected behavioral measures and parental reports of aggression and impulsivity, as well as structural and diffusion MRI, from 30 children with ADHD and 31 healthy controls (HC) (mean age, 10±2.1 SD). Using grey matter morphometry and probabilistic tractography combined with multivariate statistical modeling (partial least squares regression and support vector regression), we identified anomalies within the fronto-accumbal circuit in childhood ADHD, which were associated with increased aggression. More specifically, children with ADHD showed reduced right accumbal volumes and frontal-accumbal white matter connectivity compared with HC. The magnitude of the accumbal volume reductions within the ADHD group was significantly correlated with increased aggression, an effect mediated by the relationship between the accumbal volume and impulsivity. Furthermore, aggression, but not impulsivity, was significantly explained by multivariate measures of fronto-accumbal white matter connectivity and cortical thickness within the orbitofrontal cortex. Our multi-modal imaging, combined with multivariate statistical modeling, indicates that the fronto-accumbal circuit is an important substrate of aggression in children with ADHD. These findings suggest that strategies aimed at probing the fronto-accumbal circuit may be beneficial for the treatment of aggressive behaviors in childhood ADHD. PMID:25645374

  13. Effects of Direct-Fed Microbials on Growth Performance, Gut Morphometry, and Immune Characteristics in Broiler Chickens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to compare growth performance, gut morphometry, and parameters of local and systemic immunity in broiler chickens fed for 22 consecutive days with a diet supplemented with one of eight Bacillus spp. as a direct-fed microbial (DFM), a commercial product incorporating three DF...

  14. DEVELOPMENT OF THE SMALL AIRWAYS AND ALVEOLI FROM CHILDHOOD TO ADULT LUNG MEASURED BY AEROSOL-DERIVED AIRWAY MORPHOMETRY

    EPA Science Inventory

    Understanding the human development of pulmonary airspaces is important for calculating the dose from exposure to inhaled materials as a function of age. We have measured, in vivo, the airspace caliber of the small airways and alveoli by aerosol-derived airway morphometry (ADAM) ...

  15. Dyslexia and Voxel-Based Morphometry: Correlations between Five Behavioural Measures of Dyslexia and Gray and White Matter Volumes

    ERIC Educational Resources Information Center

    Tamboer, Peter; Scholte, H. Steven; Vorst, Harrie C. M.

    2015-01-01

    In voxel-based morphometry studies of dyslexia, the relation between causal theories of dyslexia and gray matter (GM) and white matter (WM) volume alterations is still under debate. Some alterations are consistently reported, but others failed to reach significance. We investigated GM alterations in a large sample of Dutch students (37 dyslexics…

  16. GENETIC INFLUENCE OF APOE4 GENOTYPE ON HIPPOCAMPAL MORPHOMETRY - AN N=725 SURFACE-BASED ADNI STUDY

    PubMed Central

    Shi, Jie; Leporé, Natasha; Gutman, Boris A.; Thompson, Paul M.; Baxter, Leslie C.; Caselli, Richard L.; Wang, Yalin

    2014-01-01

    The apolipoprotein E (APOE) e4 allele is the most prevalent genetic risk factor for Alzheimer’s disease (AD). Hippocampal volumes are generally smaller in AD patients carrying the e4 allele compared to e4 non-carriers. Here we examined the effect of APOE e4 on hippocampal morphometry in a large imaging database – the Alzheimer’s Disease Neuroimaging Initiative (ADNI). We automatically segmented and constructed hippocampal surfaces from the baseline MR images of 725 subjects with known APOE genotype information including 167 with AD, 354 with mild cognitive impairment (MCI), and 204 normal controls. High-order correspondences between hippocampal surfaces were enforced across subjects with a novel inverse consistent surface fluid registration method. Multivariate statistics consisting of multivariate tensor-based morphometry (mTBM) and radial distance were computed for surface deformation analysis. Using Hotelling’s T2 test, we found significant morphological deformation in APOE e4 carriers relative to non-carriers in the entire cohort as well as in the non-demented (pooled MCI and control) subjects, affecting the left hippocampus more than the right, and this effect was more pronounced in e4 homozygotes than heterozygotes. Our findings are consistent with previous studies that showed e4 carriers exhibit accelerated hippocampal atrophy; we extend these findings to a novel measure of hippocampal morphometry. Hippocampal morphometry has significant potential as an imaging biomarker of early stage AD. PMID:24453132

  17. Effects of direct-fed microbials on growth performance, gut morphometry, and immune characteristics in broiler chickens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to compare growth performance, gut morphometry, and parameters of local and systemic immunity in broiler chickens fed for 22 consecutive days with a diet supplemented with one of eight Bacillus spp. as a direct-fed microbial (DFM), a commercial product incorporating three DF...

  18. Effects of Hormone Therapy on Brain Volumes Changes of Postmenopausal Women Revealed by Optimally-Discriminative Voxel-Based Morphometry

    PubMed Central

    Zhang, Tianhao; Casanova, Ramon; Resnick, Susan M.; Manson, JoAnn E.; Baker, Laura D.; Padual, Claudia B.; Kuller, Lewis H.; Bryan, R. Nick; Espeland, Mark A.; Davatzikos, Christos

    2016-01-01

    Backgrounds The Women's Health Initiative Memory Study Magnetic Resonance Imaging (WHIMS-MRI) provides an opportunity to evaluate how menopausal hormone therapy (HT) affects the structure of older women’s brains. Our earlier work based on region of interest (ROI) analysis demonstrated potential structural changes underlying adverse effects of HT on cognition. However, the ROI-based analysis is limited in statistical power and precision, and cannot provide fine-grained mapping of whole-brain changes. Methods We aimed to identify local structural differences between HT and placebo groups from WHIMS-MRI in a whole-brain refined level, by using a novel method, named Optimally-Discriminative Voxel-Based Analysis (ODVBA). ODVBA is a recently proposed imaging pattern analysis approach for group comparisons utilizing a spatially adaptive analysis scheme to accurately locate areas of group differences, thereby providing superior sensitivity and specificity to detect the structural brain changes over conventional methods. Results Women assigned to HT treatments had significant Gray Matter (GM) losses compared to the placebo groups in the anterior cingulate and the adjacent medial frontal gyrus, and the orbitofrontal cortex, which persisted after multiple comparison corrections. There were no regions where HT was significantly associated with larger volumes compared to placebo, although a trend of marginal significance was found in the posterior cingulate cortical area. The CEE-Alone and CEE+MPA groups, although compared with different placebo controls, demonstrated similar effects according to the spatial patterns of structural changes. Conclusions HT had adverse effects on GM volumes and risk for cognitive impairment and dementia in older women. These findings advanced our understanding of the neurobiological underpinnings of HT effects. PMID:26974440

  19. Quantification and Comparison of Anti-Fibrotic Therapies by Polarized SRM and SHG-Based Morphometry in Rat UUO Model

    PubMed Central

    Weldon, Steve M.; Matera, Damian; Lee, ChungWein; Yang, Haichun; Fryer, Ryan M.; Fogo, Agnes B.; Reinhart, Glenn A.

    2016-01-01

    Renal interstitial fibrosis (IF) is an important pathologic manifestation of disease progression in a variety of chronic kidney diseases (CKD). However, the quantitative and reproducible analysis of IF remains a challenge, especially in experimental animal models of progressive IF. In this study, we compare traditional polarized Sirius Red morphometry (SRM) to novel Second Harmonic Generation (SHG)-based morphometry of unstained tissues for quantitative analysis of IF in the rat 5 day unilateral ureteral obstruction (UUO) model. To validate the specificity of SHG for detecting fibrillar collagen components in IF, co-localization studies for collagens type I, III, and IV were performed using IHC. In addition, we examined the correlation, dynamic range, sensitivity, and ability of polarized SRM and SHG-based morphometry to detect an anti-fibrotic effect of three different treatment regimens. Comparisons were made across three separate studies in which animals were treated with three mechanistically distinct pharmacologic agents: enalapril (ENA, 15, 30, 60 mg/kg), mycophenolate mofetil (MMF, 2, 20 mg/kg) or the connective tissue growth factor (CTGF) neutralizing antibody, EX75606 (1, 3, 10 mg/kg). Our results demonstrate a strong co-localization of the SHG signal with fibrillar collagens I and III but not non-fibrillar collagen IV. Quantitative IF, calculated as percent cortical area of fibrosis, demonstrated similar response profile for both polarized SRM and SHG-based morphometry. The two methodologies exhibited a strong correlation across all three pharmacology studies (r2 = 0.89–0.96). However, compared with polarized SRM, SHG-based morphometry delivered a greater dynamic range and absolute magnitude of reduction of IF after treatment. In summary, we demonstrate that SHG-based morphometry in unstained kidney tissues is comparable to polarized SRM for quantitation of fibrillar collagens, but with an enhanced sensitivity to detect treatment-induced reductions in

  20. Quantification and Comparison of Anti-Fibrotic Therapies by Polarized SRM and SHG-Based Morphometry in Rat UUO Model.

    PubMed

    Qian, Hu Sheng; Weldon, Steve M; Matera, Damian; Lee, ChungWein; Yang, Haichun; Fryer, Ryan M; Fogo, Agnes B; Reinhart, Glenn A

    2016-01-01

    Renal interstitial fibrosis (IF) is an important pathologic manifestation of disease progression in a variety of chronic kidney diseases (CKD). However, the quantitative and reproducible analysis of IF remains a challenge, especially in experimental animal models of progressive IF. In this study, we compare traditional polarized Sirius Red morphometry (SRM) to novel Second Harmonic Generation (SHG)-based morphometry of unstained tissues for quantitative analysis of IF in the rat 5 day unilateral ureteral obstruction (UUO) model. To validate the specificity of SHG for detecting fibrillar collagen components in IF, co-localization studies for collagens type I, III, and IV were performed using IHC. In addition, we examined the correlation, dynamic range, sensitivity, and ability of polarized SRM and SHG-based morphometry to detect an anti-fibrotic effect of three different treatment regimens. Comparisons were made across three separate studies in which animals were treated with three mechanistically distinct pharmacologic agents: enalapril (ENA, 15, 30, 60 mg/kg), mycophenolate mofetil (MMF, 2, 20 mg/kg) or the connective tissue growth factor (CTGF) neutralizing antibody, EX75606 (1, 3, 10 mg/kg). Our results demonstrate a strong co-localization of the SHG signal with fibrillar collagens I and III but not non-fibrillar collagen IV. Quantitative IF, calculated as percent cortical area of fibrosis, demonstrated similar response profile for both polarized SRM and SHG-based morphometry. The two methodologies exhibited a strong correlation across all three pharmacology studies (r2 = 0.89-0.96). However, compared with polarized SRM, SHG-based morphometry delivered a greater dynamic range and absolute magnitude of reduction of IF after treatment. In summary, we demonstrate that SHG-based morphometry in unstained kidney tissues is comparable to polarized SRM for quantitation of fibrillar collagens, but with an enhanced sensitivity to detect treatment-induced reductions in IF

  1. 3He lung morphometry technique: Accuracy analysis and pulse sequence optimization

    NASA Astrophysics Data System (ADS)

    Sukstanskii, A. L.; Conradi, M. S.; Yablonskiy, D. A.

    2010-12-01

    The 3He lung morphometry technique (Yablonskiy et al., JAP, 2009), based on MRI measurements of hyperpolarized gas diffusion in lung airspaces, provides unique information on the lung microstructure at the alveolar level. 3D tomographic images of standard morphological parameters (mean airspace chord length, lung parenchyma surface-to-volume ratio, and the number of alveoli per unit lung volume) can be created from a rather short (several seconds) MRI scan. These parameters are most commonly used to characterize lung morphometry but were not previously available from in vivo studies. A background of the 3He lung morphometry technique is based on a previously proposed model of lung acinar airways, treated as cylindrical passages of external radius R covered by alveolar sleeves of depth h, and on a theory of gas diffusion in these airways. The initial works approximated the acinar airways as very long cylinders, all with the same R and h. The present work aims at analyzing effects of realistic acinar airway structures, incorporating airway branching, physiological airway lengths, a physiological ratio of airway ducts and sacs, and distributions of R and h. By means of Monte-Carlo computer simulations, we demonstrate that our technique allows rather accurate measurements of geometrical and morphological parameters of acinar airways. In particular, the accuracy of determining one of the most important physiological parameter of lung parenchyma - surface-to-volume ratio - does not exceed several percent. Second, we analyze the effect of the susceptibility induced inhomogeneous magnetic field on the parameter estimate and demonstrate that this effect is rather negligible at B0 ⩽ 3T and becomes substantial only at higher B0 Third, we theoretically derive an optimal choice of MR pulse sequence parameters, which should be used to acquire a series of diffusion-attenuated MR signals, allowing a substantial decrease in the acquisition time and improvement in accuracy of the

  2. Regionally accentuated reversible brain grey matter reduction in ultra marathon runners detected by voxel-based morphometry

    PubMed Central

    2014-01-01

    Background During the 4,487 km ultra marathon TransEurope-FootRace 2009 (TEFR09), runners showed catabolism with considerable reduction of body weight as well as reversible brain volume reduction. We hypothesized that ultra marathon athletes might have developed changes to grey matter (GM) brain morphology due to the burden of extreme physical training. Using voxel-based morphometry (VBM) we undertook a cross sectional study and two longitudinal studies. Methods Prior to the start of the race 13 runners volunteered to participate in this study of planned brain scans before, twice during, and 8 months after the race. A group of matched controls was recruited for comparison. Twelve runners were able to participate in the scan before the start of the race and were taken into account for comparison with control persons. Because of drop-outs during the race, VBM could be performed in 10 runners covering the first 3 time points, and in 7 runners who also had the follow-up scan after 8 months. Volumetric 3D datasets were acquired using an MPRAGE sequence. A level of p < 0.05, family-wise corrected for multiple comparisons was the a priori set statistical threshold to infer significant effects from VBM. Results Baseline comparison of TEFR09 participants and controls revealed no significant differences regarding GM brain volume. During the race however, VBM revealed GM volume decreases in regionally distributed brain regions. These included the bilateral posterior temporal and occipitoparietal cortices as well as the anterior cingulate and caudate nucleus. After eight months, GM normalized. Conclusion Contrary to our hypothesis, we did not observe significant differences between TEFR09 athletes and controls at baseline. If this missing difference is not due to small sample size, extreme physical training obviously does not chronically alter GM. However, during the race GM volume decreased in brain regions normally associated with visuospatial and language tasks. The

  3. Volumetric and Voxel-Based Morphometry Findings in Autism Subjects With and Without Macrocephaly

    PubMed Central

    Bigler, Erin D.; Abildskov, Tracy J.; Petrie, Jo Ann; Johnson, Michael; Lange, Nicholas; Chipman, Jonathan; Lu, Jeffrey; McMahon, William; Lainhart, Janet E.

    2015-01-01

    This study sought to replicate Herbert et al. (2003a), which found increased overall white matter (WM) volume in subjects with autism, even after controlling for head size differences. To avoid the possibility that greater WM volume in autism is merely an epiphenomena of macrocephaly over-representation associated with the disorder, the current study included control subjects with benign macrocephaly. The control group also included subjects with a reading disability to insure cognitive heterogeneity. WM volume in autism was significantly larger, even when controlling for brain volume, rate of macrocephaly, and other demographic variables. Autism and controls differed little on whole-brain WM voxel-based morphometry (VBM) analyses suggesting that the overall increase in WM volume was non-localized. Autism subjects exhibited a differential pattern of IQ relationships with brain volumetry findings from controls. Current theories of brain overgrowth and their importance in the development of autism are discussed in the context of these findings. PMID:20446133

  4. Tensor-based cortical surface morphometry via weighted spherical harmonic representation.

    PubMed

    Chung, Moo K; Dalton, Kim M; Davidson, Richard J

    2008-08-01

    We present a new tensor-based morphometric framework that quantifies cortical shape variations using a local area element. The local area element is computed from the Riemannian metric tensors, which are obtained from the smooth functional parametrization of a cortical mesh. For the smooth parametrization, we have developed a novel weighted spherical harmonic (SPHARM) representation, which generalizes the traditional SPHARM as a special case. For a specific choice of weights, the weighted-SPHARM is shown to be the least squares approximation to the solution of an isotropic heat diffusion on a unit sphere. The main aims of this paper are to present the weighted-SPHARM and to show how it can be used in the tensor-based morphometry. As an illustration, the methodology has been applied in the problem of detecting abnormal cortical regions in the group of high functioning autistic subjects. PMID:18672431

  5. Voxel-based morphometry predicts shifts in dendritic spine density and morphology with auditory fear conditioning

    PubMed Central

    Keifer Jr, O. P.; Hurt, R. C.; Gutman, D. A.; Keilholz, S. D.; Gourley, S. L.; Ressler, K. J.

    2015-01-01

    Neuroimaging has provided compelling data about the brain. Yet the underlying mechanisms of many neuroimaging techniques have not been elucidated. Here we report a voxel-based morphometry (VBM) study of Thy1-YFP mice following auditory fear conditioning complemented by confocal microscopy analysis of cortical thickness, neuronal morphometric features and nuclei size/density. Significant VBM results included the nuclei of the amygdala, the insula and the auditory cortex. There were no significant VBM changes in a control brain area. Focusing on the auditory cortex, confocal analysis showed that fear conditioning led to a significantly increased density of shorter and wider dendritic spines, while there were no spine differences in the control area. Of all the morphology metrics studied, the spine density was the only one to show significant correlation with the VBM signal. These data demonstrate that learning-induced structural changes detected by VBM may be partially explained by increases in dendritic spine density. PMID:26151911

  6. Two-dimensional versus three-dimensional morphometry of monogenoidean sclerites.

    PubMed

    Galli, Paolo; Strona, Giovanni; Villa, Anna Maria; Benzoni, Francesca; Stefani, Fabrizio; Doglia, Silvia Maria; Kritsky, Delane C

    2007-03-01

    A new method of three-dimensional (3-D) analysis of sclerotised structures of monogenoids was performed by processing z-series images using 3D-Doctor. Z-series were obtained from Gomori's trichrome-stained specimens of marine and freshwater monogenoids under laser scanning confocal fluorescence microscopy. Measurements obtained from 3-D images were then compared with those from 2-D images taken from both flattened and unflattened specimens. Data comparison demonstrated that 3-D morphometry allowed avoidance of over-estimation due to deformation and the reduction of errors associated with different spatial orientations. Moreover, study of 3-D images permitted observation of morphological details that are not detectable in 2-D representations. PMID:17254585

  7. Population based analysis of directional information in serial deformation tensor morphometry.

    PubMed

    Studholme, Colin; Cardenas, Valerie

    2007-01-01

    Deformation morphometry provides a sensitive approach to detecting and mapping subtle volume changes in the brain. Population based analyses of this data have been used successfully to detect characteristic changes in different neurodegenerative conditions. However, most studies have been limited to statistical mapping of the scalar volume change at each point in the brain, by evaluating the determinant of the Jacobian of the deformation field. In this paper we describe an approach to spatial normalisation and analysis of the full deformation tensor. The approach employs a spatial relocation and reorientation of tensors of each subject. Using the assumption of small changes, we use a linear modeling of effects of clinical variables on each deformation tensor component across a population. We illustrate the use of this approach by examining the pattern of significance and orientation of the volume change effects in recovery from alcohol abuse. Results show new local structure which was not apparent in the analysis of scalar volume changes. PMID:18044583

  8. Voxel based morphometry in optical coherence tomography: validation and core findings

    NASA Astrophysics Data System (ADS)

    Antony, Bhavna J.; Chen, Min; Carass, Aaron; Jedynak, Bruno M.; Al-Louzi, Omar; Solomon, Sharon D.; Saidha, Shiv; Calabresi, Peter A.; Prince, Jerry L.

    2016-03-01

    Optical coherence tomography (OCT) of the human retina is now becoming established as an important modality for the detection and tracking of various ocular diseases. Voxel based morphometry (VBM) is a long standing neuroimaging analysis technique that allows for the exploration of the regional differences in the brain. There has been limited work done in developing registration based methods for OCT, which has hampered the advancement of VBM analyses in OCT based population studies. Following on from our recent development of an OCT registration method, we explore the potential benefits of VBM analysis in cohorts of healthy controls (HCs) and multiple sclerosis (MS) patients. Specifically, we validate the stability of VBM analysis in two pools of HCs showing no significant difference between the two populations. Additionally, we also present a retrospective study of age and sex matched HCs and relapsing remitting MS patients, demonstrating results consistent with the reported literature while providing insight into the retinal changes associated with this MS subtype.

  9. Evaluation of Pre-Malignant and Malignant Lesions in Cervico Vaginal (PAP) Smears by Nuclear Morphometry

    PubMed Central

    Rani M.N, Divya; Kumar ML, Harendra; SR, Sheela

    2014-01-01

    Background: Cervical cancer is the second most common cancer occurring among women worldwide, with almost half a million new cases each year. Normal cells gradually transform to form cancer cells through several stages. So, the changes occurring during the transformational stages need to be assessed. Aim: Our aim was to study various nuclear parameters useful in evaluating pre-malignant and malignant cervico-vaginal pap smears. Materials and Methods: Bethesda System was used to categorize cervical pap smears into premalignant and malignant lesions. Nuclear parameters were calculated using J 1.44C morphometric software. Several nuclear size parameters were analysed. Results: The nuclear area, perimeter, diameter were found to be statistically significant (p<0.05) parameters in differentiating premalignant from malignant cervical smears. Conclusion: Nuclear morphometry was thus a useful objective tool in differentiating premalignant from malignant cervical smears. PMID:25584229

  10. Reproducibility of Brain Morphometry from Short-Term Repeat Clinical MRI Examinations: A Retrospective Study

    PubMed Central

    Liu, Hon-Man; Chen, Shan-Kai; Chen, Ya-Fang; Lee, Chung-Wei; Yeh, Lee-Ren

    2016-01-01

    Purpose To assess the inter session reproducibility of automatic segmented MRI-derived measures by FreeSurfer in a group of subjects with normal-appearing MR images. Materials and Methods After retrospectively reviewing a brain MRI database from our institute consisting of 14,758 adults, those subjects who had repeat scans and had no history of neurodegenerative disorders were selected for morphometry analysis using FreeSurfer. A total of 34 subjects were grouped by MRI scanner model. After automatic segmentation using FreeSurfer, label-wise comparison (involving area, thickness, and volume) was performed on all segmented results. An intraclass correlation coefficient was used to estimate the agreement between sessions. Wilcoxon signed rank test was used to assess the population mean rank differences across sessions. Mean-difference analysis was used to evaluate the difference intervals across scanners. Absolute percent difference was used to estimate the reproducibility errors across the MRI models. Kruskal-Wallis test was used to determine the across-scanner effect. Results The agreement in segmentation results for area, volume, and thickness measurements of all segmented anatomical labels was generally higher in Signa Excite and Verio models when compared with Sonata and TrioTim models. There were significant rank differences found across sessions in some labels of different measures. Smaller difference intervals in global volume measurements were noted on images acquired by Signa Excite and Verio models. For some brain regions, significant MRI model effects were observed on certain segmentation results. Conclusions Short-term scan-rescan reliability of automatic brain MRI morphometry is feasible in the clinical setting. However, since repeatability of software performance is contingent on the reproducibility of the scanner performance, the scanner performance must be calibrated before conducting such studies or before using such software for retrospective