Geometry Analysis of an Inverse-Geometry Volumetric CT System With Multiple Detector Arrays

An inverse-geometry volumetric CT (IGCT) system for imaging in a single fast rotation without cone-beam artifacts is being developed. It employs a large scanned source array and a smaller detector array. For a single-source/single-detector implementation, the FOV is limited to a fraction of the source size. Here we explore options to increase the FOV without increasing the source size by using multiple detectors spaced apart laterally to increase the range of radial distances sampled. We also look at multiple source array systems for faster scans. To properly reconstruct the FOV, Radon space must be sufficiently covered and sampled in a uniform manner. Optimal placement of the detectors relative to the source was determined analytically given system constraints (5cm detector width, 25cm source width, 45cm source-to-isocenter distance). For a 1x3 system (three detectors per source) detector spacing (DS) was 18deg and source-to-detector distances (SDD) were 113, 100 and 113cm to provide optimum Radon sampling and a FOV of 44cm. For multiple-source systems, maximum angular spacing between sources cannot exceed 125deg since detectors corresponding to one source cannot be occluded by a second source. Therefore, for 2x3 and 3x3 systems using the above DS and SDD, optimum spacing between sources is 115deg and 61deg respectively, requiring minimum scan rotations of 115deg and 107deg. Also, a 3x3 system can be much faster for full 360deg dataset scans than a 2x3 system (120deg vs. 245deg). We found that a significantly increased FOV can be achieved while maintaining uniform radial sampling as well as a substantial reduction in scan time using several different geometries. Further multi-parameter optimization is underway

Functional Organisation of the Mouse Superior Colliculus

The superior colliculus (SC) is a highly conserved area of the mammalian midbrain that is widely implicated in the organisation and control of behaviour. SC receives input from a large number of brain areas, and provides outputs to a large number of areas. The convergence and divergence of anatomical connections with different areas and systems provides challenges for understanding how SC contributes to behaviour. Recent work in mouse has provided large anatomical datasets, and a wealth of new data from experiments that identify and manipulate different cells within SC, and their inputs and outputs, during simple behaviours. These data offer an opportunity to better understand the roles that SC plays in these behaviours. However, some of the observations appear, at first sight, to be contradictory. Here we review this recent work and hypothesise a simple framework which can capture the observations, that requires only a small change to previous models. Specifically, the functional organisation of SC can be explained by supposing that three largely distinct circuits support three largely distinct classes of simple behaviours–arrest, turning towards, and the triggering of escape or capture. These behaviours are hypothesised to be supported by the optic, intermediate and deep layers, respectively

Visual spatial location influences selection of instinctive behaviours in mouse

Visual stimuli can elicit instinctive approach and avoidance behaviours. In mouse, vision is known to be important for both avoidance of an overhead threat and approach toward a potential terrestrial prey. The stimuli used to characterize these behaviours, however, vary in both spatial location (overhead or near the ground plane) and visual feature (rapidly expanding disc or slowly moving disc). We therefore asked how mice responded to the same visual features presented in each location. We found that a looming black disc induced escape behaviour when presented overhead or to the side of the animal, but the escapes produced by side-looms were less vigorous and often preceded by freezing behaviour. Similarly, small moving discs induced freezing behaviour when presented overhead or to the side of the animal, but side sweeps also elicited approach behaviours, such that mice explored the area of the arena near where the stimulus had been presented. Our observations therefore show that mice combine cues to the location and features of visual stimuli when selecting among potential behaviours

Brief stimuli cast a persistent long-term trace in visual cortex

Visual processing is strongly influenced by the recent stimulus history - a phenomenon termed adaptation. Prominent theories cast adaptation as a consequence of optimized encoding of visual information, by exploiting the temporal statistics of the world. However, this would require the visual system to track the history of individual briefly experienced events, within a stream of visual input, to build up statistical representations over longer timescales. Here, using an openly available dataset from the Allen Brain Observatory, we show that neurons in the early visual cortex of the mouse indeed maintain long-term traces of individual past stimuli that persist despite the presentation of several intervening stimuli, leading to long-term and stimulus-specific adaptation over dozens of seconds. Long-term adaptation was selectively expressed in cortical, but not in thalamic neurons, which only showed short-term adaptation. Early visual cortex thus maintains concurrent stimulus-specific memory traces of past input, enabling the visual system to build up a statistical representation of the world to optimize the encoding of new information in a changing environment.SIGNIFICANCE STATEMENTIn the natural world, previous sensory input is predictive of current input over multi-second timescales. The visual system could exploit these predictabilities by adapting current visual processing to the long-term history of visual input. However, it is unclear whether the visual system can track the history of individual briefly experienced images, within a stream of input, to build up statistical representations over such long timescales. Here, we show that neurons in early visual cortex of the mouse brain exhibit remarkably long-term adaptation to brief stimuli, persisting over dozens of seconds, and despite the presentation of several intervening stimuli. The visual cortex thus maintains long-term traces of individual briefly experienced past images, enabling the formation of statistical representations over extended timescales

Heavy Metals Contamination of Soil in the Vicinity of Hawassa Industrial Zone, Ethiopia

Industrial effluents, containing heavy metals, drain directly into downstream water sources within the Hawassa Industrial Zone. These, water sources are used for irrigation, drinking water and other domestic purposes. The load of pollutants, environmental risks and potential human impacts are generally, unknown for soil in Ethiopia. Therefore, the aim of this study was to determine the extent of heavy metal pollution of soil within the Hawassa Industrial Zone and to evaluate environmental impacts using contamination factor (CF), degree of contamination (Cd), modified degree of contamination (mCd), ecological risk factor (Er), ecological risk index (ERI) and pollution load index (PLI) analyses. Seven heavy metals: Cr, Ni, Cu, Zn, As, Cd and Pb were determined in soil samples from three different sites by inductively coupled plasma mass spectrometry (ICP-MS). Average concentration of metals decreased in the order of Zn>Cu>Cr>Ni>Pb>As>Cd consistent with the normal order of abundance in non-polluted soils. One way ANOVA revealed significant differences (P<0.05) in the concentrations of Cu, As, Cd and Pb among the sampling sites. Pearson\u2019s correlation, principal component and cluster analyses revealed that heavy metals are originating from different sources. Within the industrial area, the CF increased in the order of Pb<Cd<Zn<As<Cu<Cr<Ni. The result of Cd revealed that there was considerable to very high contamination of the soil. The mCd index showed moderate contamination of the soils. The Er increased in the order of Zn<Cr<Pb<Cu<Ni<As<Cd and the result of the ERI value revealed considerable ecological risk for the soils. Overall, the study showed that the soils within the Hawassa Industrial Zone are highly contaminated with heavy metals. Therefore, regular monitoring of heavy metals concentration in soil and policy interventions with respect to waste disposal are recommended

Activated platelets form protected zones of adhesion on fibrinogen and fibronectin-coated surfaces.

Leukocytes form zones of close apposition when they adhere to ligand-coated surfaces. Because plasma proteins are excluded from these contact zones, we have termed them protected zones of adhesion. To determine whether platelets form similar protected zones of adhesion, gel-filtered platelets stimulated with thrombin or ADP were allowed to adhere to fibrinogen- or fibronectin-coated surfaces. The protein-coated surfaces with platelets attached were stained with either fluorochrome-conjugated goat anti-human fibrinogen or anti-human fibronectin antibodies, or with rhodamine-conjugated polyethylene glycol polymers. Fluorescence microscopy revealed that F(ab')2 anti-fibrinogen (100 kD) did not penetrate into the contact zones between stimulated platelets and the underlying fibrinogen-coated surface, while Fab antifibrinogen (50 kD) and 10 kD polyethylene glycol readily penetrated and stained the substrate beneath the platelets. Thrombin- or ADP-stimulated platelets also formed protected zones of adhesion on fibronectin-coated surfaces. F(ab')2 anti-fibronectin and 10 kD polyethylene glycol were excluded from these adhesion zones, indicating that they are much less permeable than those formed by platelets on fibrinogen-coated surfaces. The permeability properties of protected zones of adhesion formed by stimulated platelets on surfaces coated with both fibrinogen and fibronectin were similar to the zones of adhesion formed on fibronectin alone. mAb 7E3, directed against the alpha IIb beta 3 integrin blocked the formation of protected adhesion zones between thrombin-stimulated platelets and fibrinogen or fibronectin coated surfaces. mAb C13 is directed against the alpha 5 beta 1 integrin on platelets. Stimulated platelets treated with this mAb formed protected zones of adhesion on surfaces coated with fibronectin. These protected zones were impermeable to F(ab')2 antifibronectin but were permeable to 10 kD polyethylene glycol. These results show that activated platelets form protected zones of adhesion and that the size of molecules excluded from these zones depends upon the composition of the matrix proteins to which the platelets adhere. They also show that formation of protected zones of adhesion by platelets requires alpha IIb beta 3 integrins while the permeability properties of these zones of adhesion are regulated by both alpha IIb beta 3 and alpha 5 beta 1 integrins

Disparities and guideline adherence for HPV testing among patients with oropharyngeal squamous cell carcinoma, NCDB, and SEER

BACKGROUND: Human papilloma virus testing for oropharyngeal squamous-cell carcinoma has been recommended by the National Comprehensive Cancer Network since 2012. We examine disparities, reported rates of human papillomavirus (HPV) testing, and the impact on these findings of limitations with the variable in database registries. METHODS: The HPV variable was queried for patients with oropharyngeal squamous carcinoma (OPSCC) from 2013 to 2016 in National Cancer Data Base (NCDB) and Surveillance, Epidemiology, and End Results (SEER). Multivariable regression was used to identify disparities based on sociodemographic variables. Sensitivity analyses were used to investigate limitations of the variable. RESULTS: Despite limitations in the HPV variable in the databases, there was less than 100% adherence to recommended testing, and there were significant disparities in multiple sociodemographic variables. For example, in NCDB 70% of white versus 60.4% of black patients were tested (odds ratio [OR] 0.75, confidence interval [CI] 0.66-0.85, p ≤ 0.0001); in SEER 59.8% of white and 47.6% of black patients were tested (OR 0.73, CI 0.67-0.81; p ≤ 0.0001). CONCLUSIONS: Disparities exist among patients undergoing testing for HPV-associated OPSCC and adherence to guideline recommended HPV testing has been suboptimal. In addition, the HPV variable definition, especially as it relates to p16 positivity, and use in these two registries should be improved

fMRI adaptation revisited

Adaptation has been widely used in functional magnetic imaging (fMRI) studies to infer neuronal response properties in human cortex. fMRI adaptation has been criticised because of the complex relationship between fMRI adaptation effects and the multiple neuronal effects that could underlie them. Many of the longstanding concerns about fMRI adaptation have received empirical support from neurophysiological studies over the last decade. We review these studies here, and also consider neuroimaging studies that have investigated how fMRI adaptation effects are influenced by high-level perceptual processes. The results of these studies further emphasize the need to interpret fMRI adaptation results with caution, but they also provide helpful guidance for more accurate interpretation and better experimental design. In addition, we argue that rather than being used as a proxy for measurements of neuronal stimulus selectivity, fMRI adaptation may be most useful for studying population-level adaptation effects across cortical processing hierarchies

The Effect of Interocular Phase Difference on Perceived Contrast

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

Technology generation to dissemination:lessons learned from the tef improvement project

Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional- and molecular-breeding techniques to improve tef\u2014an orphan crop important to the food security in the Horn of Africa, a region of the world with recurring devastating famines. We have established an efficient pipeline to bring improved tef lines from the laboratory to the farmers of Ethiopia. Of critical importance to the long-term success of this project is the cooperation among participants in Ethiopia and Switzerland, including donors, policy makers, research institutions, and farmers. Together, European and African scientists have developed a pipeline using breeding and genomic tools to improve the orphan crop tef and bring new cultivars to the farmers in Ethiopia. We highlight a new variety, Tesfa, developed in this pipeline and possessing a novel and desirable combination of traits. Tesfa\u2019s recent approval for release illustrates the success of the project and marks a milestone as it is the first variety (of many in the pipeline) to be released