TINA manual landmarking tool: software for the precise digitization of 3D landmarks

Background: Interest in the placing of landmarks and subsequent morphometric analyses of shape for 3D data has increased with the increasing accessibility of computed tomography (CT) scanners. However, current computer programs for this task suffer from various practical drawbacks. We present here a free software tool that overcomes many of these problems. Results: The TINA Manual Landmarking Tool was developed for the digitization of 3D data sets. It enables the generation of a modifiable 3D volume rendering display plus matching orthogonal 2D cross-sections from DICOM files. The object can be rotated and axes defined and fixed. Predefined lists of landmarks can be loaded and the landmarks identified within any of the representations. Output files are stored in various established formats, depending on the preferred evaluation software. Conclusions: The software tool presented here provides several options facilitating the placing of landmarks on 3D objects, including volume rendering from DICOM files, definition and fixation of meaningful axes, easy import, placement, control, and export of landmarks, and handling of large datasets. The TINA Manual Landmark Tool runs under Linux and can be obtained for free from http://www.tina-vision.net/tarballs/

Quantitative shape analysis with weighted covariance estimates for increased statistical efficiency

BACKGROUND: The introduction and statistical formalisation of landmark-based methods for analysing biological shape has made a major impact on comparative morphometric analyses. However, a satisfactory solution for including information from 2D/3D shapes represented by ‘semi-landmarks’ alongside well-defined landmarks into the analyses is still missing. Also, there has not been an integration of a statistical treatment of measurement error in the current approaches. RESULTS: We propose a procedure based upon the description of landmarks with measurement covariance, which extends statistical linear modelling processes to semi-landmarks for further analysis. Our formulation is based upon a self consistent approach to the construction of likelihood-based parameter estimation and includes corrections for parameter bias, induced by the degrees of freedom within the linear model. The method has been implemented and tested on measurements from 2D fly wing, 2D mouse mandible and 3D mouse skull data. We use these data to explore possible advantages and disadvantages over the use of standard Procrustes/PCA analysis via a combination of Monte-Carlo studies and quantitative statistical tests. In the process we show how appropriate weighting provides not only greater stability but also more efficient use of the available landmark data. The set of new landmarks generated in our procedure (‘ghost points’) can then be used in any further downstream statistical analysis. CONCLUSIONS: Our approach provides a consistent way of including different forms of landmarks into an analysis and reduces instabilities due to poorly defined points. Our results suggest that the method has the potential to be utilised for the analysis of 2D/3D data, and in particular, for the inclusion of information from surfaces represented by multiple landmark points

Reciclagem de nitrogênio em pastagem consorciada de Calopogonium mucunoides com Brachiaria decumbens.

O trabalho estuda a reciclagem de nitrogênio (N) de Calopogonium mucunoides associado com Brachiaria decumbens, sob pastejo continuo, com lotação de 2,5 U.A/ha. As avaliações foram efetuadas através da medida de crescimento da matéria seca (MS) da gramínea e da leguminosa e da quantidade de N em Kg/ha, mobilizada pelo crescimento para a biomassa das plantas da pastagem. Efetuaram-se avaliações do N total e N assimilável (amônia + nitrato) no perfil do solo, a profundidade de 0 a 250 cm, bem como do desempenho do Rhizobium associado a leguminosa. Pode-se determinar que, a consorciação, o crescimento da gramínea, que mobilizou do solo para a vegetação 105,47 kg de N/ha, foi acrescido de mais 81,37 kg de N/ha por ano, mobilizado pelo crescimento da leguminosa.Na pastagem de gramínea pura, o N mobilizado do solo foi de 123,10 kg de N/ha. e uma diferença significativa (P<0,05) de 63,84 kg de N/ha por ano foi adicionada ao sistema da pastagem, sendo atribuída em sua maior parte a fixação simbiótica, realizada pelo Calopogonium mucunoides. O N reciclado resultou um aumento significativo (P<0,05) na oferta de N e proteína bruta na forragem disponível do pasto consociado, ao longo do ano. A leguminosa foi responsável também por um aumento significativo (P<0,05) da percentagem de N total na camada superficial do solo e aumentou significativamente (P<0,05) o conteúdo de N assimilável no perfil. Os estudos realizados em casa de vegetação, com Rhizobium isolado de plantas da pastagem, indicaram que a estirpe associada...bitstream/item/104558/1/Reciclagem-de-nitrogenio-em-pastagem.pd

Quantitative Sensory Testing in adults with Tourette syndrome

INTRODUCTION: Abnormal sensory perceptions, for instance hypersensitivity to certain external stimuli or premonitory urges preceding tics, are core features in Gilles de la Tourette syndrome (GTS). Aberrant awareness of externally applied stimuli in terms of altered sensory perception thresholds might contribute to these sensory phenomena in GTS. METHODS: We used the well-established and standardized “Quantitative Sensory Testing” (QST) battery (German Research Network on Neuropathic Pain) to investigate 13 sensory parameters including thermal, mechanical/tactile and pain thresholds in 14 GTS patients without clinically significant comorbidities and 14 healthy controls matched for age and gender. RESULTS: There were no relevant group differences in any of the 13 QST parameters and no specific QST pattern in GTS patients. There was no correlation between QST parameters and “Premonitory Urge for Tics scale” (PUTS) scores. CONCLUSION: Our data show that the perceptual threshold detection of externally applied sensory stimuli is normal in adults with GTS. This indicates that other perceptual mechanisms, such as abnormal central sensorimotor processing and/or aberrant interoceptive awareness might underlie the clinically significant sensory abnormalities in GTS

Erosion during extreme flood events dominates Holocene canyon evolution in northeast Iceland

Extreme flood events have the potential to cause catastrophic landscape change in short periods of time (10(0) to 10(3) h). However, their impacts are rarely considered in studies of long-term landscape evolution (>10(3) y), because the mechanisms of erosion during such floods are poorly constrained. Here we use topographic analysis and cosmogenic (3)He surface exposure dating of fluvially sculpted surfaces to determine the impact of extreme flood events within the Jökulsárgljúfur canyon (northeast Iceland) and to constrain the mechanisms of bedrock erosion during these events. Surface exposure ages allow identification of three periods of intense canyon cutting about 9 ka ago, 5 ka ago, and 2 ka ago during which multiple large knickpoints retreated large distances (>2 km). During these events, a threshold flow depth was exceeded, leading to the toppling and transportation of basalt lava columns. Despite continuing and comparatively large-scale (500 m(3)/s) discharge of sediment-rich glacial meltwater, there is no evidence for a transition to an abrasion-dominated erosion regime since the last erosive event because the vertical knickpoints have not diffused over time. We provide a model for the evolution of the Jökulsárgljúfur canyon through the reconstruction of the river profile and canyon morphology at different stages over the last 9 ka and highlight the dominant role played by extreme flood events in the shaping of this landscape during the Holocene

Stronger Neural Modulation by Visual Motion Intensity in Autism Spectrum Disorders

Theories of autism spectrum disorders (ASD) have focused on altered perceptual integration of sensory features as a possible core deficit. Yet, there is little understanding of the neuronal processing of elementary sensory features in ASD. For typically developed individuals, we previously established a direct link between frequency-specific neural activity and the intensity of a specific sensory feature: Gamma-band activity in the visual cortex increased approximately linearly with the strength of visual motion. Using magnetoencephalography (MEG), we investigated whether in individuals with ASD neural activity reflect the coherence, and thus intensity, of visual motion in a similar fashion. Thirteen adult participants with ASD and 14 control participants performed a motion direction discrimination task with increasing levels of motion coherence. A polynomial regression analysis revealed that gamma-band power increased significantly stronger with motion coherence in ASD compared to controls, suggesting excessive visual activation with increasing stimulus intensity originating from motion-responsive visual areas V3, V6 and hMT/V5. Enhanced neural responses with increasing stimulus intensity suggest an enhanced response gain in ASD. Response gain is controlled by excitatory-inhibitory interactions, which also drive high-frequency oscillations in the gamma-band. Thus, our data suggest that a disturbed excitatoryinhibitory balance underlies enhanced neural responses to coherent motion in ASD

Bulk ion heating with ICRH in JET DT plasmas

Reactor relevant ICRH scenarios have been assessed during DT experiments on the JET tokamak using H mode divertor discharges with ITER-like shapes and safety factors. Deuterium minority heating in tritium plasmas was demonstrated for the first time. For 9% deuterium, an ICRH power of 6 MW gave 1.66 MW of fusion power from reactions between suprathermal deuterons and thermal tritons. The Q value of the steady state discharge reached 0.22 for the length of the RF flat-top (2.7 s), corresponding to three plasma energy replacement times. The Doppler broadened neutron spectrum showed a deuteron energy of 125 keV, which was optimum for fusion and close to the critical energy. Thus, strong bulk ion heating was obtained at the same time as high fusion efficiency. Deuterium fractions around 20% produced the strongest ion heating together with a strong reduction of the suprathermal deuteron tail. The ELMs had low amplitude and high frequency and each ELM transported less plasma energy content than the 1% required by ITER. The energy confinement time, on the ITERH97-P scale, was 0.90, which is sufficient for ignition in ITER. 3He minority heating, in approximately 50:50 D:T plasmas with up to 10% 3He, also demonstrated strong bulk ion heating. Central ion temperatures up to 13 keV were achieved, together with central electron temperatures up to 12 keV. The normalized H mode confinement time was 0.95. Second harmonic tritium heating produced energetic tritons above the critical energy. This scheme heats the electrons in JET, unlike in ITER where the lower power density will allow mainly ion heating. The inverted scenario of tritium minority ICRH in a deuterium plasma was demonstrated as a successful heating method producing both suprathermal neutrons and bulk ion heating. Theoretical calculations of the DT reactivity mostly give excellent agreement with the measured reaction rates

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome