ResearchPad - radii https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Mesh smoothing algorithm based on exterior angles split]]> https://www.researchpad.co/article/elastic_article_13823 Since meshes of poor quality give rise to low accuracy in finite element analysis and kinds of inconveniences in many other applications, mesh smoothing is widely used as an essential technique for the improvement of mesh quality. With respect to this issue, the main contribution of this paper is that a novel mesh smoothing method based on an exterior-angle-split process is proposed. The proposed method contains three main stages: the first stage is independent element geometric transformation performed by exterior-angle-split operations, treating elements unconnected; the second stage is to offset scaling and displacement induced by element transformation; the third stage is to determine the final positions of nodes with a weighted strategy. Theoretical proof describes the regularity of this method and many numerical experiments illustrate its convergence. Not only is this method applicable for triangular mesh, but also can be naturally extended to arbitrary polygonal surface mesh. Quality improvements of demonstrations on triangular and quadrilateral meshes show the effectiveness of this method.

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<![CDATA[Automated localization and quality control of the aorta in cine CMR can significantly accelerate processing of the UK Biobank population data]]> https://www.researchpad.co/article/5c6f151bd5eed0c48467adda

Introduction

Aortic distensibility can be calculated using semi-automated methods to segment the aortic lumen on cine CMR (Cardiovascular Magnetic Resonance) images. However, these methods require visual quality control and manual localization of the region of interest (ROI) of ascending (AA) and proximal descending (PDA) aorta, which limit the analysis in large-scale population-based studies. Using 5100 scans from UK Biobank, this study sought to develop and validate a fully automated method to 1) detect and locate the ROIs of AA and PDA, and 2) provide a quality control mechanism.

Methods

The automated AA and PDA detection-localization algorithm followed these steps: 1) foreground segmentation; 2) detection of candidate ROIs by Circular Hough Transform (CHT); 3) spatial, histogram and shape feature extraction for candidate ROIs; 4) AA and PDA detection using Random Forest (RF); 5) quality control based on RF detection probability. To provide the ground truth, overall image quality (IQ = 0–3 from poor to good) and aortic locations were visually assessed by 13 observers. The automated algorithm was trained on 1200 scans and Dice Similarity Coefficient (DSC) was used to calculate the agreement between ground truth and automatically detected ROIs.

Results

The automated algorithm was tested on 3900 scans. Detection accuracy was 99.4% for AA and 99.8% for PDA. Aorta localization showed excellent agreement with the ground truth, with DSC ≥ 0.9 in 94.8% of AA (DSC = 0.97 ± 0.04) and 99.5% of PDA cases (DSC = 0.98 ± 0.03). AA×PDA detection probabilities could discriminate scans with IQ ≥ 1 from those severely corrupted by artefacts (AUC = 90.6%). If scans with detection probability < 0.75 were excluded (350 scans), the algorithm was able to correctly detect and localize AA and PDA in all the remaining 3550 scans (100% accuracy).

Conclusion

The proposed method for automated AA and PDA localization was extremely accurate and the automatically derived detection probabilities provided a robust mechanism to detect low quality scans for further human review. Applying the proposed localization and quality control techniques promises at least a ten-fold reduction in human involvement without sacrificing any accuracy.

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<![CDATA[A simple approximation algorithm for the diameter of a set of points in an Euclidean plane]]> https://www.researchpad.co/article/5c673069d5eed0c484f37a9c

Approximation algorithms with linear complexities are required in the treatments of big data, however, present algorithms cannot output the diameter of a set of points with arbitrary accuracy and near-linear complexity. By introducing the partition technique, we introduce a very simple approximation algorithm with arbitrary accuracy ε and a complexity of O(N + ε−1 log ε−1) for the cases that all points are located in an Euclidean plane. The error bounds are proved strictly, and are verified by numerical tests. This complexity is better than existing algorithms, and the present algorithm is also very simple to be implemented in applications.

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<![CDATA[Influence of vertical wind shear on wind- and rainfall areas of tropical cyclones making landfall over South Korea]]> https://www.researchpad.co/article/5c3d0173d5eed0c48403b75a

The wind- and rainfall areas of tropical cyclones (TCs) making landfall over South Korea were examined for the period 1998–2013 by using the Modern Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2) and Tropical Rainfall Measuring Mission (TRMM) 3B42 data. Here, the wind- and rainfall areas were defined as the regions where wind speeds and precipitation rates exceed 14 m s-1 and 80 mm day-1 within 1000 km from the TC center, respectively. In general, TCs show significantly asymmetric wind and rainfall structures, with strong vertical wind shear appearing over South Korea during the landfall period. The rainfall area significantly increases with environmental vertical wind shear while the wind area is not sensitive to it. Composite analyses of the cases of strong and weak vertical wind shear confirm that the increase of rainfall area is related to the asymmetric convection (rising/sinking motion in the downshear-left/upshear-right side) induced by the vertical wind shear. This work highlights the importance of local atmospheric environment in determining the area primarily affected by strong winds or heavy rainfall during TC landfalls.

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<![CDATA[Optimizing community screening for tuberculosis: Spatial analysis of localized case finding from door-to-door screening for TB in an urban district of Ho Chi Minh City, Viet Nam]]> https://www.researchpad.co/article/5c22a0c3d5eed0c4849ec15b

Background

Tuberculosis (TB) is the deadliest infectious disease globally. Current case finding approaches may miss many people with TB or detect them too late.

Data and methods

This study was a retrospective, spatial analysis of routine TB surveillance and cadastral data in Go Vap district, Ho Chi Minh City. We geocoded TB notifications from 2011 to 2015 and calculated theoretical yields of simulated door-to-door screening in three concentric catchment areas (50m, 100m, 200m) and three notification window scenarios (one, two and four quarters) for each index case. We calculated average yields, compared them to published reference values and fit a GEE (Generalized Estimating Equation) linear regression model onto the data.

Results

The sample included 3,046 TB patients. Adjusted theoretical yields in 50m, 100m and 200m catchment areas were 0.32% (95%CI: 0.27,0.37), 0.21% (95%CI: 0.14,0.29) and 0.17% (95%CI: 0.09,0.25), respectively, in the baseline notification window scenario. Theoretical yields in the 50m-catchment area for all notification window scenarios were significantly higher than a reference yield from literature. Yield was positively associated with treatment failure index cases (beta = 0.12, p = 0.001) and short-term inter-province migrants (beta = 0.06, p = 0.022), while greater distance to the DTU (beta = -0.02, p<0.001) was associated with lower yield.

Conclusions

This study is an example of inter-departmental collaboration and application of repurposed cadastral data to progress towards the end TB objectives. The results from Go Vap showed that the use of spatial analysis may be able to identify areas where targeted active case finding in Vietnam can help improve TB case detection.

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<![CDATA[Patterns of brown bear damages on apiaries and management recommendations in the Cantabrian Mountains, Spain]]> https://www.researchpad.co/article/5c0841c1d5eed0c484fcaa7a

Large carnivores are often persecuted due to conflict with human activities, making their conservation in human-modified landscapes very challenging. Conflict-related scenarios are increasing worldwide, due to the expansion of human activities or to the recovery of carnivore populations. In general, brown bears Ursus arctos avoid humans and their settlements, but they may use some areas close to people or human infrastructures. Bear damages in human-modified landscapes may be related to the availability of food resources of human origin, such as beehives. However, the association of damage events with factors that may predispose bears to cause damages has rarely been investigated. We investigated bear damages to apiaries in the Cantabrian Mountains (Spain), an area with relatively high density of bears. We included spatial, temporal and environmental factors and damage prevention measures in our analyses, as factors that may influence the occurrence and intensity of damages. In 2006–2008, we located 61 apiaries, which included 435 beehives damaged in the study area (346 km2). The probability of an apiary being attacked was positively related to both the intensity of the damage suffered the year before and the distance to the nearest damaged apiary, and negatively related to the number of prevention measures employed as well as the intensity of the damage suffered by the nearest damage apiary. The intensity of damage to apiaries was positively related to the size of the apiary and to vegetation cover in the surroundings, and negatively related to the number of human settlements. Minimizing the occurrence of bear damages to apiaries seems feasible by applying and maintaining proper prevention measures, especially before an attack occurs and selecting appropriate locations for beehives (e.g. away from forest areas). This applies to areas currently occupied by bears, and to neighbouring areas where dispersing individuals may expand their range.

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<![CDATA[Modelling structural determinants of ventilation heterogeneity: A perturbative approach]]> https://www.researchpad.co/article/5c09944dd5eed0c4842ae9c5

We have developed a computational model of gas mixing and ventilation in the human lung represented as a bifurcating network. We have simulated multiple-breath washout (MBW), a clinical test for measuring ventilation heterogeneity (VH) in patients with obstructive lung conditions. By applying airway constrictions inter-regionally, we have predicted the response of MBW indices to obstructions and found that they detect a narrow range of severe constrictions that reduce airway radius to 10%–30% of healthy values. These results help to explain the success of the MBW test to distinguish obstructive lung conditions from healthy controls. Further, we have used a perturbative approach to account for intra-regional airway heterogeneity that avoids modelling each airway individually. We have found, for random airway heterogeneity, that the variance in MBW indices is greater when indices are already elevated due to constrictions. By quantifying this effect, we have shown that variability in lung structure and mechanical properties alone can lead to clinically significant variability in MBW indices (specifically the Lung Clearance Index—LCI, and the gradient of phase-III slopes—Scond), but only in cases simulating obstructive lung conditions. This method is a computationally efficient way to probe the lung’s sensitivity to structural changes, and to quantify uncertainty in predictions due to random variations in lung mechanical and structural properties.

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<![CDATA[Topographical study of the trapezius muscle, greater occipital nerve, and occipital artery for facilitating blockade of the greater occipital nerve]]> https://www.researchpad.co/article/5b8acdf140307c144d0de05b

The aim of this study was to clarify the topographical relationships between the greater occipital nerve and the trapezius muscle and between the greater occipital nerve and the occipital artery in the occiput in order to increase the success rate of greater occipital nerve blockade. Fifty-six halved heads of 28 cadavers were used in this study. The piercing points and the courses of the greater occipital nerve and occipital artery were analyzed by dividing a line connecting between the external occipital protuberance and mastoid process into three equal parts. A circle with a radius of 2 cm drawn at the medial trisection point of this line was divided into four equal sectors. The greater occipital nerve simply passed the lateral border of the trapezius muscle and then pierced the fascia connecting the cranial attachment of the trapezius muscle with the sternocleidomastoid muscle in 62.5% of the specimens, whereas it pierced the muscle itself in the other 37.5%. The greater occipital nerve and occipital artery pierced the fascia within the 2-cm-radius circle in 85.7% and 98.2% of the specimens, respectively. The piercing points of the greater occipital nerve and occipital artery were observed most frequently in the inferomedial (42.9%) and inferolateral (37.5%) sectors of the circle, respectively. The greater occipital nerve and occipital artery pierced the same sector of the circle and accompanied each other in 51.8% of the specimens. These results are expected to improve the understanding of the topographical relationships between the greater occipital nerve and trapezius muscle and between the greater occipital nerve and occipital artery in the occiput, and thus provide helpful information for the management of occipital neuralgia.

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<![CDATA[Low-resistive vibratory penetration in granular media]]> https://www.researchpad.co/article/5989db53ab0ee8fa60bdca0e

Non-cohesive materials such as sand, dry snow or cereals are encountered in various common circumstances, from everyday situations to industry. The process of digging into these materials remains a challenge to most animals and machines. Within the animal kingdom, different strategies are employed to overcome this issue, including excavation methods used by ants, the two-anchor strategy employed by soft burrowers such as razor-clams, and undulatory motions exhibited by sandfish lizards. Despite the development of technology to mimic these techniques in diggers and robots, the limitations of animals and machines may differ, and mimicry of natural processes is not necessarily the most efficient technological strategy. This study presents evidence that the resisting force for the penetration of an intruder into a dry granular media can be reduced by one order of magnitude with small amplitude (A ≃ 10 μm) and low frequency (f = 50 − 200 Hz) mechanical vibrations. This observed result is attributed to the local fluidization of the granular bed which induces the rupture of force chains. The drop in resistive force on entering dry granular materials may be relevant in technological development in order to increase the efficiency of diggers and robots.

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<![CDATA[Throughput assurance of wireless body area networks coexistence based on stochastic geometry]]> https://www.researchpad.co/article/5989db53ab0ee8fa60bdcbc1

Wireless body area networks (WBANs) are expected to influence the traditional medical model by assisting caretakers with health telemonitoring. Within WBANs, the transmit power of the nodes should be as small as possible owing to their limited energy capacity but should be sufficiently large to guarantee the quality of the signal at the receiving nodes. When multiple WBANs coexist in a small area, the communication reliability and overall throughput can be seriously affected due to resource competition and interference. We show that the total network throughput largely depends on the WBANs distribution density (λp), transmit power of their nodes (Pt), and their carrier-sensing threshold (γ). Using stochastic geometry, a joint carrier-sensing threshold and power control strategy is proposed to meet the demand of coexisting WBANs based on the IEEE 802.15.4 standard. Given different network distributions and carrier-sensing thresholds, the proposed strategy derives a minimum transmit power according to varying surrounding environment. We obtain expressions for transmission success probability and throughput adopting this strategy. Using numerical examples, we show that joint carrier-sensing thresholds and transmit power strategy can effectively improve the overall system throughput and reduce interference. Additionally, this paper studies the effects of a guard zone on the throughput using a Matern hard-core point process (HCPP) type II model. Theoretical analysis and simulation results show that the HCPP model can increase the success probability and throughput of networks.

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<![CDATA[Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production]]> https://www.researchpad.co/article/5989da30ab0ee8fa60b8448a

Myxococcus xanthus, a model organism for studies of multicellular behavior in bacteria, moves exclusively on solid surfaces using two distinct but coordinated motility mechanisms. One of these, social (S) motility is powered by the extension and retraction of type IV pili and requires the presence of exopolysaccharides (EPS) produced by neighboring cells. As a result, S motility requires close cell-to-cell proximity and isolated cells do not translocate. Previous studies measuring S motility by observing the colony expansion of cells deposited on agar have shown that the expansion rate increases with initial cell density, but the biophysical mechanisms involved remain largely unknown. To understand the dynamics of S motility-driven colony expansion, we developed a reaction-diffusion model describing the effects of cell density, EPS deposition and nutrient exposure on the expansion rate. Our results show that at steady state the population expands as a traveling wave with a speed determined by the interplay of cell motility and growth, a well-known characteristic of Fisher’s equation. The model explains the density-dependence of the colony expansion by demonstrating the presence of a lag phase–a transient period of very slow expansion with a duration dependent on the initial cell density. We propose that at a low initial density, more time is required for the cells to accumulate enough EPS to activate S-motility resulting in a longer lag period. Furthermore, our model makes the novel prediction that following the lag phase the population expands at a constant rate independent of the cell density. These predictions were confirmed by S motility experiments capturing long-term expansion dynamics.

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<![CDATA[The Role of Parieto-Occipital Junction in the Interaction between Dorsal and Ventral Streams in Disparity-Defined Near and Far Space Processing]]> https://www.researchpad.co/article/5989d9f9ab0ee8fa60b7178a

Neuropsychological and functional MRI data suggest that two functionally and anatomically dissociable streams of visual processing exist: a ventral perception-related stream and a dorsal action-related stream. However, relatively little is known about how the two streams interact in the intact brain during the production of adaptive behavior. Using functional MRI and a virtual three-dimensional paradigm, we aimed at examining whether the parieto-occipital junction (POJ) acts as an interface for the integration and processing of information between the dorsal and ventral streams in the near and far space processing. Virtual reality three-dimensional near and far space was defined by manipulating binocular disparity, with -68.76 arcmin crossed disparity for near space and +68.76 arcmin uncrossed disparity for near space. Our results showed that the POJ and bilateral superior occipital gyrus (SOG) showed relative increased activity when responded to targets presented in the near space than in the far space, which was independent of the retinotopic and perceived sizes of target. Furthermore, the POJ showed the enhanced functional connectivity with both the dorsal and ventral streams during the far space processing irrespective of target sizes, supporting that the POJ acts as an interface between the dorsal and ventral streams in disparity-defined near and far space processing. In contrast, the bilateral SOG showed the enhanced functional connectivity only with the ventral stream if retinotopic sizes of targets in the near and far spaces were matched, which suggested there was a functional dissociation between the POJ and bilateral SOG.

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<![CDATA[Extending trust to immigrants: Generalized trust, cross-group friendship and anti-immigrant sentiments in 21 European societies]]> https://www.researchpad.co/article/5989db5aab0ee8fa60bdf627

The aim of this study is twofold. First, we expand on the literature by testing whether generalized trust is negatively related to anti-immigrant sentiments in Europe. Second, we examine to what extent the relation between generalized trust and anti-immigrant sentiments is dependent upon cross-group friendships. We apply multilevel linear regression modeling to representative survey data enriched with levels of ethnic diversity covering 21 European countries. Results show that both generalized trust and cross-group friendship are negatively related to anti-immigrant sentiments. However, there is a negligible positive relation between generalized trust and cross-group friendship (r = .10), and we can clearly observe that they operate independently from one another. Hence, trusting actors are not more likely to form more cross-group friendships, and cross-group friendship do not lead to the development of more generalized trust. Instead, the findings show that generalized trust leads immigrants too to be included in the radius of trusted others and, as a consequence, the benign effects of generalized trust apply to them as well. We conclude that the strength of generalized trust is a form of generalization, beyond the confines of individual variations in intergroup experiences.

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<![CDATA[Decision-Making under Ambiguity Is Modulated by Visual Framing, but Not by Motor vs. Non-Motor Context. Experiments and an Information-Theoretic Ambiguity Model]]> https://www.researchpad.co/article/5989da42ab0ee8fa60b8a5ee

A number of recent studies have investigated differences in human choice behavior depending on task framing, especially comparing economic decision-making to choice behavior in equivalent sensorimotor tasks. Here we test whether decision-making under ambiguity exhibits effects of task framing in motor vs. non-motor context. In a first experiment, we designed an experience-based urn task with varying degrees of ambiguity and an equivalent motor task where subjects chose between hitting partially occluded targets. In a second experiment, we controlled for the different stimulus design in the two tasks by introducing an urn task with bar stimuli matching those in the motor task. We found ambiguity attitudes to be mainly influenced by stimulus design. In particular, we found that the same subjects tended to be ambiguity-preferring when choosing between ambiguous bar stimuli, but ambiguity-avoiding when choosing between ambiguous urn sample stimuli. In contrast, subjects’ choice pattern was not affected by changing from a target hitting task to a non-motor context when keeping the stimulus design unchanged. In both tasks subjects’ choice behavior was continuously modulated by the degree of ambiguity. We show that this modulation of behavior can be explained by an information-theoretic model of ambiguity that generalizes Bayes-optimal decision-making by combining Bayesian inference with robust decision-making under model uncertainty. Our results demonstrate the benefits of information-theoretic models of decision-making under varying degrees of ambiguity for a given context, but also demonstrate the sensitivity of ambiguity attitudes across contexts that theoretical models struggle to explain.

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<![CDATA[Transcranial Doppler-Based Surrogates for Cerebral Blood Flow: A Statistical Study]]> https://www.researchpad.co/article/5989daa7ab0ee8fa60ba7ef9

It is commonly assumed that perfusion in a given cerebral territory can be inferred from Blood Flow Velocity (BFV) measurements in the corresponding stem artery. In order to test this hypothesis, we construct a cerebral blood flow (CBF) estimator based on transcranial Doppler (TCD) blood flow velocity and ten other easily available patient characteristics and clinical parameters. A total of 261 measurements were collected from 88 older patients. The estimator is based on local regression (Random Forest). Its performance is analyzed against baseline CBF from 3-D pseudocontinuous arterial spin labeling (pCASL) magnetic resonance imaging (MRI). Patient specific CBF predictions are of poor quality (r = 0.41 and p-value = 4.5 × 10−12); the hypothesis is thus not clearly supported by evidence.

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<![CDATA[Rotatable Small Permanent Magnet Array for Ultra-Low Field Nuclear Magnetic Resonance Instrumentation: A Concept Study]]> https://www.researchpad.co/article/5989daecab0ee8fa60bbf87f

Object

We studied the feasibility of generating the variable magnetic fields required for ultra-low field nuclear magnetic resonance relaxometry with dynamically adjustable permanent magnets. Our motivation was to substitute traditional electromagnets by distributed permanent magnets, increasing system portability.

Materials and Methods

The finite element method (COMSOL®) was employed for the numerical study of a small permanent magnet array to calculate achievable magnetic field strength, homogeneity, switching time and magnetic forces. A manually operated prototype was simulated and constructed to validate the numerical approach and to verify the generated magnetic field.

Results

A concentric small permanent magnet array can be used to generate strong sample pre-polarisation and variable measurement fields for ultra-low field relaxometry via simple prescribed magnet rotations. Using the array, it is possible to achieve a pre-polarisation field strength above 100 mT and variable measurement fields ranging from 20–50 μT with 200 ppm absolute field homogeneity within a field-of-view of 5 x 5 x 5 cubic centimetres.

Conclusions

A dynamic small permanent magnet array can generate multiple highly homogeneous magnetic fields required in ultra-low field nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) instruments. This design can significantly reduce the volume and energy requirements of traditional systems based on electromagnets, improving portability considerably.

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<![CDATA[Cortical porosity not superior to conventional densitometry in identifying hemodialysis patients with fragility fracture]]> https://www.researchpad.co/article/5989db52ab0ee8fa60bdc64c

Hemodialysis (HD) patients face increased fracture risk, which is further associated with elevated risk of hospitalization and mortality. High-resolution peripheral computed tomography (HR-pQCT) has advanced our understanding of bone disease in chronic kidney disease by characterizing distinct changes in both the cortical and trabecular compartments. Increased cortical porosity (Ct.Po) has been shown to be associated with fracture in patients with osteopenia or in postmenopausal diabetic women. We tested whether the degree of Ct.Po identifies hemodialysis patients with prevalent fragility fractures in comparison to bone mineral density (BMD) assessed by dual X-ray absorptiometry (DXA). We performed a post-hoc analysis of a cross-sectional study in 76 prevalent hemodialysis patients. Markers of mineral metabolism, coronary calcification score, DXA-, and HR-pQCT-data were analyzed, and Ct.Po determined at radius and tibia. Ct.Po was significantly higher in patients with fracture but association was lost after adjusting for age and gender (tibia p = 0.228, radius p = 0.5). Instead, femoral (F) BMD neck area (p = 0.03), F T-score neck area (p = 0.03), radius (R) BMD (p = 0.03), R T-score (p = 0.03), and cortical HR-pQCT indices such as cortical area (Ct.Ar) (tibia: p = 0.01; radius: p = 0.02) and cortical thickness (Ct.Th) (tibia: p = 0.03; radius: p = 0.02) correctly classified patients with fragility fractures. Area under receiver operating characteristic curves (AUC) for Ct.Po (tibia AUC: 0.711; p = 0.01; radius AUC: 0.666; p = 0.04), Ct.Ar (tibia AUC: 0.832; p<0.001; radius AUC: 0.796; p<0.001), and F neck BMD (AUC: 0.758; p = 0.002) did not differ significantly among each other. In conclusion, measuring Ct.Po is not superior to BMD determined by DXA for identification of HD patients with fragility fracture.

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<![CDATA[Protruding Features of Viral Capsids Are Clustered on Icosahedral Great Circles]]> https://www.researchpad.co/article/5989daa7ab0ee8fa60ba7cc6

Spherical viruses are remarkably well characterized by the Triangulation (T) number developed by Casper and Klug. The T-number specifies how many viral capsid proteins are required to cover the virus, as well as how they are further subdivided into pentamer and hexamer subunits. The T-number however does not constrain the orientations of these proteins within the subunits or dictate where the proteins should place their protruding features. These protrusions often take the form of loops, spires and helices, and are significant because they aid in stability of the capsid as well as recognition by the host organism. Until now there has be no overall understanding of the placement of protrusions for spherical viruses, other than they have icosahedral symmetry. We constructed a set of gauge points based upon the work affine extensions of Keef and Twarock, which have fixed relative angular locations with which to measure the locations of these features. This work adds a new element to our understanding of the geometric arrangement of spherical viral capsid proteins; chiefly that the locations of protruding features are not found stochastically distributed in an icosahedral manner across the viral surface, but instead these features are found only in specific locations along the 15 icosahedral great circles. We have found that this result holds true as the T number and viral capsids size increases, suggesting an underlying geometric constraint on their locations. This is in spite of the fact that the constraints on the pentamers and hexamer orientations change as a function of T-number, as you need to accommodate more hexamers in the same solid angle between pentamers. The existence of this angular constraint of viral capsids suggests that there is a fitness or energetic benefit to the virus placing its protrusions in this manner. This discovery may have profound impacts on identifying and eliminating viral pathogens, understanding evolutionary constraints as well as bioengineering for capsid drug delivery systems. This result also suggests that in addition to biochemical attachment restrictions, there are additional geometric constraints that should be adhered to when modifying protein capsids.

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<![CDATA[What to Do When K-Means Clustering Fails: A Simple yet Principled Alternative Algorithm]]> https://www.researchpad.co/article/5989d9d1ab0ee8fa60b64481

The K-means algorithm is one of the most popular clustering algorithms in current use as it is relatively fast yet simple to understand and deploy in practice. Nevertheless, its use entails certain restrictive assumptions about the data, the negative consequences of which are not always immediately apparent, as we demonstrate. While more flexible algorithms have been developed, their widespread use has been hindered by their computational and technical complexity. Motivated by these considerations, we present a flexible alternative to K-means that relaxes most of the assumptions, whilst remaining almost as fast and simple. This novel algorithm which we call MAP-DP (maximum a-posteriori Dirichlet process mixtures), is statistically rigorous as it is based on nonparametric Bayesian Dirichlet process mixture modeling. This approach allows us to overcome most of the limitations imposed by K-means. The number of clusters K is estimated from the data instead of being fixed a-priori as in K-means. In addition, while K-means is restricted to continuous data, the MAP-DP framework can be applied to many kinds of data, for example, binary, count or ordinal data. Also, it can efficiently separate outliers from the data. This additional flexibility does not incur a significant computational overhead compared to K-means with MAP-DP convergence typically achieved in the order of seconds for many practical problems. Finally, in contrast to K-means, since the algorithm is based on an underlying statistical model, the MAP-DP framework can deal with missing data and enables model testing such as cross validation in a principled way. We demonstrate the simplicity and effectiveness of this algorithm on the health informatics problem of clinical sub-typing in a cluster of diseases known as parkinsonism.

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<![CDATA[GPS Tracking of Free-Ranging Pigs to Evaluate Ring Strategies for the Control of Cysticercosis/Taeniasis in Peru]]> https://www.researchpad.co/article/5989db3fab0ee8fa60bd6443

Background

Taenia solium, a parasitic cestode that affects humans and pigs, is the leading cause of preventable epilepsy in the developing world. T. solium eggs are released into the environment through the stool of humans infected with an adult intestinal tapeworm (a condition called taeniasis), and cause cysticercosis when ingested by pigs or other humans. A control strategy to intervene within high-risk foci in endemic communities has been proposed as an alternative to mass antihelminthic treatment. In this ring strategy, antihelminthic treatment is targeted to humans and pigs residing within a 100 meter radius of a pig heavily-infected with cysticercosis. Our aim was to describe the roaming ranges of pigs in this region, and to evaluate whether the 100 meter radius rings encompass areas where risk factors for T. solium transmission, such as open human defecation and dense pig activity, are concentrated.

Methodology/Principal Findings

In this study, we used Global Positioning System (GPS) devices to track pig roaming ranges in two rural villages of northern Peru. We selected 41 pigs from two villages to participate in a 48-hour tracking period. Additionally, we surveyed all households to record the locations of open human defecation areas. We found that pigs spent a median of 82.8% (IQR: 73.5, 94.4) of their time roaming within 100 meters of their homes. The size of home ranges varied significantly by pig age, and 93% of the total time spent interacting with open human defecation areas occurred within 100 meters of pig residences.

Conclusions/Significance

These results indicate that 100 meter radius rings around heavily-infected pigs adequately capture the average pig’s roaming area (i.e., home range) and represent an area where the great majority of exposure to human feces occurs.

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