bluuebunny/crossref_metadata_2025 huggingface dataset:
High‐risk CTV delineation for cervix brachytherapy: Application of GEC‐ESTRO guidelines in Australia and New Zealand
Authors: Vinod Shalini K , Lim Karen , Bell Lauren , Veera Jacqueline , Ohanessian Lucy , Juresic Ewa , Borok Nira , Chan Phillip , Chee Raphael , Do Viet , Govindarajulu Geetha , Sridharan Swetha , Johnson Carol , Moses Daniel , Van Dyk Sylvia , Holloway Lois
Published: August 2016

Introduction

Image‐based brachytherapy for cervical cancer using MRI has been implemented in Australia and New Zealand. The aims of this study were to measure variability in High‐risk CTV (HR‐CTV) delineation and evaluate dosimetric consequences of this.

Methods

Nine radiation oncologists, one radiation therapist and two radiologists contoured HR‐CTV on 3T MRI datasets from ten consecutive patients undergoing cervical brachytherapy at a single institution. Contour comparisons were performed using the Dice Similarity Coefficient (DSC) and Mean Absolute Surface Distance (MASD). Two reference contours were created for brachytherapy planning: a Simultaneous Truth and Performance Level Estimation (STAPLE) and a consensus contour (CONSENSUS). Optimized plans (8 Gy) for both these contours were applied to individual participant's contours to assess D90 and D100 coverage of HR CTV. To compare variability in dosimetry, relative standard deviation (rSD) was calculated.

Results

Good concordance (mean DSC≥0.7, MASD≤5 mm) was achieved in 8/10 cases when compared to the STAPLE reference and 6/10 cases when compared to the CONSENSUS reference. Greatest variation was visually seen in the cranio‐caudal direction. The average mean rSD across all patients was 27% and 34% for the STAPLE HR‐CTV D90 and D100, respectively, and 28% and 35% for the CONSENSUS HR‐CTV D90 and D100. Delineation uncertainty resulted in an average dosimetric uncertainty of ±1.5–1.6 Gy per fraction based on an 8 Gy prescribed fraction.

Conclusions

Delineation of HR‐CTV for cervical cancer brachytherapy was consistent amongst observers, suggesting similar interpretation of GEC‐ESTRO guidelines. Despite the good concordance, there was dosimetric variation noted, which could be clinically significant.
Hyperstate matrix models: extending demographic state spaces to higher dimensions
Authors: Roth Gregory , Caswell Hal
Published: August 2016

Demographic models describe population dynamics in terms of the movement of individuals among states (e.g. size, age, developmental stage, parity, frailty, physiological condition). Matrix population models originally classified individuals by a single characteristic. This was enlarged to two characteristics in vec‐permutation models and the closely related megamatrix models. However, it has been recognised that the interplay of more than two characteristics can affect the population dynamics.

Here, we present a framework, called hyperstate matrix model, in which individuals may be classified by any number of characteristics, using the generalisation of the vec‐permutation approach to hypermatrices. These models are constructed from a simple block‐diagonal matrix formulation of the movement of individuals among each dimension of the i‐state.

This framework provides a step‐by‐step construction and makes available the usual demographic analysis developed for classical matrix models. In particular, we derive a general formula for the sensitivity of any output of the hyperstate matrix model, to any vector of parameters. In spite of the technicalities underlying these models, implementation is straightforward and we provide the MATLAB code to carry it out.

We apply this approach to a three‐dimensional example in which individuals are classified by developmental stage, age and heterogeneity classes. The analysis of this model provides insights into how the heritability of the heterogeneity classes affects the long‐term growth rate of the population.

As the questions in conservation biology become more sophisticated and data on threatened species become more detailed, multiple dimensions in demographic models will become increasingly important. Hyperstate matrix methods will make such analyses possible and directly applicable to conservation and population management.
Marginal or conditional regression models for correlated non‐normal data?
Authors: Muff Stefanie , Held Leonhard , Keller Lukas F.
Published: August 2016

Correlated data are ubiquitous in ecological and evolutionary research, and appropriate statistical analysis requires that these correlations are taken into account. For regressions with correlated, non‐normal outcomes, two main approaches are used: conditional and marginal modelling. The former leads to generalized linear mixed models (GLMMs), while the latter are estimated using generalized estimating equations (GEEs), or marginalized multilevel regression models. Differences, advantages and drawbacks of conditional and marginal models have been discussed extensively in the statistical and applied literature, and there is some agreement that the choice of the model must depend on the question under study. Yet, there still appears to be a lot of confusion and disagreement over when to choose which model.

We start with a review of conditional and marginal models, and the differences in the interpretation of the resulting parameter estimates. We highlight that the two types of models propagate different linear relations between the covariates and the response. Moreover, while conditional models explicitly account for heterogeneity among clustered observations, marginal models yield averages over such heterogeneities and are therefore often interpreted as population‐averaged models.

We point out theoretically and with an example that when modelling non‐normal outcomes no unambiguous definition of a marginal model generally exists. Instead, marginal model parameters are marginal only with respect to unaccounted differences among clusters and thus depend on the fixed effects in the model. Therefore, marginal model parameters should not be loosely interpreted as population‐averaged parameters. In addition, we explain how marginal modelling is mathematically analogous to deliberately omitting covariates with explanatory power, and to deliberately introducing a Berkson measurement error into covariates. We also reiterate that marginal modelling is related to a well‐known statistical phenomenon, the Simpson's paradox.

In most cases, therefore, we regard the conditional model as the more powerful choice to explain how covariates are associated with a non‐normal response. Still, marginal models can be useful, given that the scientific question explicitly requires such a model formulation.
Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts
Authors: Mitchell Jonathan S. , Rabosky Daniel L.
Published: August 2016

Understanding variation in rates of speciation and extinction – both among lineages and through time – is critical to the testing of many hypotheses about macroevolutionary processes. Bayesian Analysis of Macroevolutionary Mixtures (BAMM) is a flexible Bayesian framework for inferring the number and location of shifts in macroevolutionary rate across phylogenetic trees and has been widely used in empirical studies. BAMM requires that researchers specify a prior probability distribution on the number of diversification rate shifts before conducting an analysis. The consequences of this ‘model prior’ for inference are poorly known but could potentially influence both the probability of accepting models that are more (high error rate) or less (low power) complex than the generating model.

The hierarchical Poisson process prior in BAMM reduces to a simple geometric distribution on number of rate shifts, and we use this property to increase the efficiency of model selection with Bayes factors. Using BAMM v2.5, we analysed phylogenies simulated with and without diversification heterogeneity across a broad range of prior parameterizations. We also assessed the impact of the model prior on MCMC convergence times and on diversification rate estimates.

For all simulation scenarios, model evidence (Bayes factor support) for the number of shifts is not sensitive to the choice of model prior over the wide range examined here. The best‐supported model found using BAMM rarely includes spurious shifts (<2% of all runs) when diversification models are selected using Bayes factors. BAMM was reliably able to infer the true number of diversification rate shifts across prior expectations that varied by three orders of magnitude. However, we find a strong effect of model prior on MCMC convergence properties: a flatter prior distribution (larger expected number of shifts) can dramatically increase the efficiency of the MCMC simulation.

Our results support the use of a liberal model prior in BAMM, as it reduces computation time without distorting the evidence for rate heterogeneity.
ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Authors: Yu Guangchuang , Smith David K. , Zhu Huachen , Guan Yi , Lam Tommy Tsan‐Yuk
Published: August 2016

We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees.

ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node‐specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree.

The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.

A two‐dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images.

The package ggtree is released under the artistic‐2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).
Adapting Conceptual Frameworks for Patient Engagement in Emergency Department Research
Authors: Wright (née Blackwell) Rebecca , Carden Donna. L. , Hess Erik P. , Booker‐Vaughns Juanita , Dunn Patrick , Kizzie‐Gillett Constance , Vaughan William , Weingarten Gail , Williams Pluscedia , Young‐Brinn Angela , Grudzen Corita
Published: August 2016

For many people the emergency department (ED) is the first point of access to healthcare for acute needs and a recurring location for many with chronic healthcare needs. While the ED is well placed to identify unmet needs it can also be a net that people slip through when faced with uncoordinated and expensive healthcare challenges. Thus the ED has a responsibility to set patients on a safe and meaningful care trajectory, which can only be done in consultation and partnership with the patients themselves. The purpose of this article is to present crucial aspects of patient engagement that are essential for future research to foster an environment of colearning and respect that encourages ongoing involvement by patients, families, and staff.
Human welfare and its connection to nature: What have we learned from crop pollination studies?
Authors: Cunningham Saul A.
Published: August 2016

Human welfare depends on the function of natural systems. This idea is paradigmatic to ecologists and has been the theme of a growing branch of applied ecology. I examine the narrative of human dependence on nature by considering the literature on crop pollination by animals and its importance for food production. Making the connections between human welfare and natural systems is seen as a way to better motivate society to make better decisions, but the debate around crop pollination has been surprisingly contentious. There have been confusing messages, disagreements on the facts, an unfortunate focus on dire projections for the future and a lesser focus on solutions. Most of these problems arise not from poor science but instead from poor communication of complex ideas and differences in perspective, such as the deep disciplinary gap between agricultural scientists and ecologists. By understanding these problems, we can improve the way we do our science and communicate our ideas. I argue that ecologists should continue to communicate the principle that human welfare depends on the function of natural systems and discuss how we can do so in a way that is more genuinely connected to society's needs, such as growing food. If we succeed, we will be changing an intellectually interesting conversation into a dialogue that influences how society interacts with nature.
Comparison of regional fat mass measurement by whole body DXA scans and anthropometric measures to predict insulin resistance in women with polycystic ovary syndrome and controls
Authors: Glintborg Dorte , Petersen Maria Houborg , Ravn Pernille , Hermann Anne Pernille , Andersen Marianne
Published: August 2016

Introduction

Polycystic ovary syndrome (PCOS) is characterized by obesity and insulin resistance. Measures of regional obesity may be used to predict insulin resistance. In the present study we compared fat distribution in patients with PCOS vs. controls and established the best measure of fat mass to predict insulin resistance in patients with PCOS.

Material and methods

The study was cross‐sectional in an academic tertiary‐care medical center with 167 premenopausal women with PCOS and 110 controls matched for ethnicity, BMI and age. Total and regional fat and lean body mass were assessed by whole body dual‐energy X‐ray absorptiometry (DXA) scans. Anthropometric measures (BMI, waist) and fasting metabolic analyses [insulin, glucose, lipids, Homeostasis model assessment (HOMA‐IR), lipid accumulation product, and visceral adiposity index] were determined. Trial registration numbers: NCT00451568, NCT00145340.

Results

Women with PCOS had higher central fat mass (waist, waist–hip ratio, and upper/lower fat ratio) compared with controls. In bivariate associations, the strongest associations were found between HOMA‐IR and the fat mass measures trunk fat (r = 0.59), waist (r = 0.57) and BMI (r = 0.56), all p < 0.001. During multiple regression analyses, trunk fat, waist and BMI were the best predictors of HOMA‐IR (R2 = 0.48, 0.49, and 0.47, respectively).

Conclusions

Women with PCOS were characterized by central obesity. Trunk fat, waist and BMI were the best predictors of HOMA‐IR in PCOS, but only limited information regarding insulin resistance was gained by whole body DXA scan.
Review article: the potential of interferon and nucleos(t)ide analogue combination therapy in chronic hepatitis B infection
Authors: Viganò M. , Invernizzi F. , Grossi G. , Lampertico P.
Published: August 2016

Background

A short‐term course of pegylated‐interferon (Peg‐IFN), or a long‐term treatment with a third generation nucleot(s)ide analogue (NUC), of chronic hepatitis B (CHB) infection achieves viral suppression and may prevent disease progression. Owing to different mechanisms of action of the two regimens, a Peg‐IFN and NUC combination treatment may be an attractive approach to enhance the off‐treatment rates of virological and serological response.

Aim

To review the literature on combinations of Peg‐IFN plus NUC, including the simultaneous initiation of Peg‐IFN and NUC in naïve patients; an ‘add‐on’ combination, where Peg‐IFN is started at variable times after the beginning of NUC; or a ‘switch‐to’ strategy usually from NUC to Peg‐IFN.

Methods

We performed a PubMed literature search using the following terms individually or in combination: NUC, hepatitis B virus, chronic hepatitis, interferon, pegylated‐interferon, nucleos(t)ide analogues, entecavir, tenofovir. English‐language articles published up to December 2015, as well as conference proceedings from international meetings were reviewed. References from selected papers were reviewed and used if relevant.

Results

While combination and NUC pre‐treatment failed to increase HBsAg clearance rates, more promising results were achieved in patients under long‐term effective NUC therapy.

Conclusion

While Peg‐IFN and nucleos(t)ide analogue combination therapy should not be recommended currently, the addition of or the switch to Peg‐IFN in nucleos(t)ide analogue‐treated patients with chronic hepatitis B infection may be useful option.
PADUA and R.E.N.A.L. nephrometry scores correlate with perioperative outcomes of robot‐assisted partial nephrectomy: analysis of the Vattikuti Global Quality Initiative in Robotic Urologic Surgery (GQI‐RUS) database
Authors: Schiavina Riccardo , Novara Giacomo , Borghesi Marco , Ficarra Vincenzo , Ahlawat Rajesh , Moon Daniel A. , Porpiglia Francesco , Challacombe Benjamin J. , Dasgupta Prokar , Brunocilla Eugenio , La Manna Gaetano , Volpe Alessandro , Verma Hema , Martorana Giuseppe , Mottrie Alexandre
Published: August 2016

Objectives

To evaluate and compare the correlations between Preoperative Aspects and Dimensions Used for an Anatomical (PADUA) and R.E.N.A.L. [Radius (tumour size as maximal diameter), Exophytic/endophytic properties of the tumour, Nearness of tumour deepest portion to the collecting system or sinus, Anterior (a)/posterior (p) descriptor and the Location relative to the polar line] nephrometry scores and perioperative outcomes and postoperative complications in a multicentre, international series of patients undergoing robot‐assisted partial nephrectomy (RAPN) for masses suspicious for renal cell carcinoma (RCC).

Patients and Methods

We retrospectively evaluated the clinical records of patients who underwent RAPN between 2010 and 2013 for clinical N0M0 renal tumours in four international centres that completed all the data required for the Vattikuti Global Quality Initiative in Robotic Urologic Surgery (GQI‐RUS) database. All patients underwent preoperative computed tomography or magnetic resonance imaging to define the clinical stage and anatomical characteristics of the tumours. PADUA and R.E.N.A.L. scores were retrospectively assessed in each centre. Univariate and multivariate analyses were used to evaluate the correlations between age, gender, Charlson comorbidity index, clinical tumour size, PADUA and R.E.N.A.L. complexity group categories and warm ischaemia time (WIT) of >20 min, urinary calyceal system closure, and grade of postoperative complications.

Results

Overall, 277 patients were evaluated. The median (interquartile range) tumour size was 33.0 (22.0–43.0) mm. The median PADUA and R.E.N.A.L. scores were eight and seven, respectively; 112 (40.4%), 86 (31.0%) and 79 (28.5%) patients were classified in the low‐, intermediate‐ or high‐complexity group according to PADUA score, while 118 (42.5%), 139 (50.1%) and 20 (7.2%) were classified in the low‐, intermediate‐ or high‐complexity group according to R.E.N.A.L. score, respectively. Both nephrometry tools significantly correlated with perioperative outcomes at univariate and multivariate analyses.

Conclusion

A precise stratification of patients before PN is recommended to consider both the potential threats and benefits of nephron‐sparing surgery. In our present analysis, both PADUA and R.E.N.A.L. were significantly associated with predicting prolonged WIT and high‐grade postoperative complications after RAPN.
Hyperdominance in fruit production in the Brazilian Atlantic rain forest: the functional role of plants in sustaining frugivores
Authors: Staggemeier Vanessa G. , Cazetta Eliana , Morellato Leonor Patrícia Cerdeira
Published: August 2016

The availability of fruits is critical for tropical forests, where the majority of plant species rely upon animal vectors for seed dispersal. However, we do not know how fruit production is temporally distributed over species and families. Two plant families are particularly important in floristic inventories of Atlantic rain forests: Arecaceae, a few species of which are highly abundant; and Myrtaceae, which is abundant and displays outstanding species diversity. In this context, we asked whether hyperdominance occurs in fruit production in the Atlantic rain forest, and whether it occurs in the abundant species of Arecaceae and Myrtaceae. We investigated whether the temporal fruit production patterns differ between Myrtaceae, Arecaceae, and the plant community as a whole. We also applied a functional dispersion index to assess the temporal fruit diversity over a 2‐yr period, with regard to morphological and phenological traits. We found that the phenomenon of hyperdominance occurs in fruit production: five species accounted for more than half of the pulp biomass. Arecaceae fruit biomass peaked at the end of wet season, overlapping with the community peak; whereas Myrtaceae species fruited throughout the year and were an important resource during periods of food scarcity. Myrtaceae filled more of the fruit morphospace over time because their fruits exhibit a large range of morphologies and phenological strategies. Our results demonstrated the importance of combining phenology and fruit morphology in the evaluation of resource availability, which revealed periods of high fruit diversity that could support a range of frugivore sizes and maintain overall ecosystem functionality.
TheAlberta Mental Health Act 2010and Revolving Door Syndrome: Control, Care, and Identity in Making up People
Authors: Barron Gary R.S.
Published: August 2016

In this paper, I describe dividing practices in making up a specific medical‐legal category—the revolving door patient—to identify, label, and direct the actions of particular people living with mental illness. The revolving door patient was a category that had been spoken of for some time, but became a formal legal subject with the introduction of theAlberta Mental Health Act 2010and Community Treatment Orders (CTOs). I demonstrate how a rationale of control over unpredictable and dangerous individuals was primary in creating this new category, and that the characterization of the revolving door patient required a disciplinary technology to reduce danger. I argue that the CTO is a medical‐legal technology that solves the problem of governing a subject in order to produce a patient that manages mental illness. I conclude by reflecting on how the narrative of the revolving door patient, and of mental illness more broadly, has implications for personal identity and tensions between care and control.

Dans cet article, je décris comment des ‘pratiques divisées’ ont créé une catégorie spécifique médico‐légale ‐ le « revolving door patient » ‐ afin d'identifier, d’étiqueter et de contrôler les comportements de certains individus vivants avec une maladie mentale. Le «revolving door patient», une catégorie dont on avait parlé depuis un certain temps, est devenu un sujet juridique formel par l'introduction de la loi de la santé mentale de l'Alberta 2010 et de l'Ordre de Traitement Communautaire (OCT). Je démontre comment une logique de contrôle sur les individus imprévisibles et dangereux eu un rôle prépondérant lors de la création de cette catégorie et que la caractérisation du «revolving door patient», entant que telle, a nécessité une technologie disciplinaire pour réduire le danger social. Je soutiens que le OTC est une technologie médico‐légale qui résout le problème de contrôle d'un sujet en produisant un patient qui gère une maladie mentale. Je conclus en démontrant de quelle façon le «revolving door patient», et la maladie mentale en général, a des répercussions sur l'identité personnelle et produisent des tensions entre les soins et le contrôle.
Corneal diameter and associated parameters in Chinese children: the Shandong Children Eye Study
Authors: Jiang Wen Jun , Wu Hui , Wu Jian Feng , Hu Yuan Yuan , Lu Tai Liang , Sun Wei , Guo Da Dong , Wang Xing Rong , Bi Hong Sheng , Jonas Jost B
Published: August 2016

Background

To assess the corneal diameter and its associations in children.

Design

Cross‐sectional school‐based study.

Participants

Six thousand twenty‐six children aged 4–18 years were included in the Shandong Children Eye Study.

Methods

Horizontal corneal diameter was measured by laser interferometry‐based ocular biometry.

Main Outcome Measures

Horizontal corneal diameter.

Results

Corneal diameter measurements were available for 5970 (99.1%) children. In multivariate analysis, larger horizontal corneal diameter (mean: 12.02 ± 0.38 mm; range: 10.1–15.0 mm) was associated with longer corneal curvature radius longer axial length, male gender, younger maternal age, rural region of habitation and lower intraocular pressure measurements. Higher prevalence of abnormally large corneas (macrocorneas; horizontal diameter ≥ 12.76 mm; mean value +2  ×  standard deviations; mean: 2.6%; 95% CI: 2.2, 3.0) was associated with longer corneal curvature radius, longer axial length, younger maternal age and male gender. Higher prevalence of abnormally small corneas (horizontal diameter ≤ 11.24mm; mean value −2 × standard deviations; mean: 2.4%; 95% CI: 2.0, 2.8) was correlated with shorter corneal curvature radius, shorter axial length and urban region of habitation. Neither abnormally large nor small corneas were correlated with time spent indoors/outdoors.

Conclusions

In 4 to 18‐year‐old children, larger corneal diameter was associated most strongly with flatter corneal curvature, followed by longer axial length and male gender. Corneal diameter was independent of age beyond an age of 4 years. Abnormally large and abnormally small corneas may be defined as being ≥12.76 and ≤11.24 mm in diameter, respectively. Corneal diameter was not correlated with time spent indoors/outdoors.
Scale‐Invariant Directional Alignment of Surface Parametrizations
Authors: Campen Marcel , Ibing Moritz , Ebke Hans‐Christian , Zorin Denis , Kobbelt Leif
Published: August 2016

Various applications of global surface parametrization benefit from the alignment of parametrization isolines with principal curvature directions. This is particularly true for recent parametrization‐based meshing approaches, where this directly translates into a shape‐aware edge flow, better approximation quality, and reduced meshing artifacts. Existing methods to influence a parametrization based on principal curvature directions suffer from scale‐dependence, which implies the necessity of parameter variation, or try to capture complex directional shape features using simple 1D curves. Especially for non‐sharp features, such as chamfers, fillets, blends, and even more for organic variants thereof, these abstractions can be unfit. We present a novel approach which respects and exploits the 2D nature of such directional feature regions, detects them based on coherence and homogeneity properties, and controls the parametrization process accordingly. This approach enables us to provide an intuitive, scale‐invariant control parameter to the user. It also allows us to consider non‐local aspects like the topology of a feature, enabling further improvements. We demonstrate that, compared to previous approaches, global parametrizations of higher quality can be generated without user intervention.
Near‐Isometric Level Set Tracking
Authors: Tao Michael , Solomon Justin , Butscher Adrian
Published: August 2016

Implicit representations of geometry have found applications in shape modeling, simulation, and other graphics pipelines. These representations, however, do not provide information about the paths of individual points as shapes move and undergo deformation. For this reason, we reconsider the problem of tracking points on level set surfaces, with the goal of designing an algorithm that — unlike previous work — can recover rotational motion and nearly isometric deformation. We track points on level sets of a time‐varying function using approximate Killing vector fields (AKVFs), the velocity fields of near‐isometric motions. To this end, we provide suitable theoretical and discrete constructions for computing AKVFs in a narrow band surrounding an animated level set surface. Furthermore, we propose time integrators well‐suited to integrating AKVFs in time to track points. We demonstrate the theoretical and practical advantages of our proposed algorithms on synthetic and practical tasks.
Stenciling: Designing Structurally‐Sound Surfaces with Decorative Patterns
Authors: Schumacher Christian , Thomaszewski Bernhard , Gross Markus
Published: August 2016

We present a novel method to design shells with artistic cutouts in a manner that produces a stable final result. The process of stenciling, removing material with a fixed shape, is a particularly appealing way to introduce a decorative pattern into the design of architectural structures, furniture, or household objects. However, removing material can easily weaken an object to the point where its integrity is compromised, while purely functional distributions of cutouts lack the desired aesthetic component. We tackle this problem by combining aesthetics, stability, and material efficiency in an optimization that determines the distribution and scaling of these stencils in a way that complies as much as possible with both pattern and stability objectives. We demonstrate the capabilities of our system on examples from architecture, furniture design, and decorative items, and show how user interaction can be integrated to guide the aesthetics of the final result.
Stable Region Correspondences Between Non‐Isometric Shapes
Authors: Ganapathi‐Subramanian V. , Thibert B. , Ovsjanikov M. , Guibas L.
Published: August 2016

We consider the problem of finding meaningful correspondences between 3D models that are related but not necessarily very similar. When the shapes are quite different, a point‐to‐point map is not always appropriate, so our focus in this paper is a method to build a set of correspondences between shape regions or parts. The proposed approach exploits a variety of feature functions on the shapes and makes use of the key observation that points in matching parts have similar ranks in the sorting of the corresponding feature values. Our algorithm proceeds in two steps. We first build an affinity matrix between points on the two shapes, based on feature rank similarity over many feature functions. We then define a notion of stability of a pair of regions, with respect to this affinity matrix, obtained as a fixed point of a nonlinear operator. Our method yields a family of corresponding maximally stable regions between the two shapes that can be used to define shape parts. We observe that this is an instance of the biclustering problem and that it is related to solving a constrained maximal eigenvalue problem. We provide an algorithm to solve this problem that mimics the power method. We show the robustness of its output to noisy input features as well its convergence properties. The obtained part correspondences are shown to be almost perfect matches in the isometric case, and also semantically appropriate even in non‐isometric cases. We provide numerous examples and applications of this technique, for example to sharpening correspondences in traditional shape matching algorithms.
Non‐Rigid Puzzles
Authors: Litany O. , Rodolà E. , Bronstein A. M. , Bronstein M. M. , Cremers D.
Published: August 2016

Shape correspondence is a fundamental problem in computer graphics and vision, with applications in various problems including animation, texture mapping, robotic vision, medical imaging, archaeology and many more. In settings where the shapes are allowed to undergo non‐rigid deformations and only partial views are available, the problem becomes very challenging. To this end, we present a non‐rigid multi‐part shape matching algorithm. We assume to be given a reference shape and its multiple parts undergoing a non‐rigid deformation. Each of these query parts can be additionally contaminated by clutter, may overlap with other parts, and there might be missing parts or redundant ones. Our method simultaneously solves for the segmentation of the reference model, and for a dense correspondence to (subsets of) the parts. Experimental results on synthetic as well as real scans demonstrate the effectiveness of our method in dealing with this challenging matching scenario.
Curve Reconstruction with Many Fewer Samples
Authors: Ohrhallinger S. , Mitchell S.A. , Wimmer M.
Published: August 2016

We consider the problem of sampling points from a collection of smooth curves in the plane, such that the Crust family of proximity‐based reconstruction algorithms can rebuild the curves. Reconstruction requires a dense sampling of local features, i.e., parts of the curve that are close in Euclidean distance but far apart geodesically. We show that ε < 0.47‐sampling is sufficient for our proposed HNN‐Crust variant, improving upon the state‐of‐the‐art requirement of ε < ‐sampling. Thus we may reconstruct curves with many fewer samples. We also present a new sampling scheme that reduces the required density even further than ε < 0.47‐sampling. We achieve this by better controlling the spacing between geodesically consecutive points. Our novel sampling condition is based on the reach, the minimum local feature size along intervals between samples. This is mathematically closer to the reconstruction density requirements, particularly near sharp‐angled features. We prove lower and upper bounds on reach ρ‐sampling density in terms of lfs ε‐sampling and demonstrate that we typically reduce the required number of samples for reconstruction by more than half.
Disk Density Tuning of a Maximal Random Packing
Authors: Ebeida Mohamed S. , Rushdi Ahmad A. , Awad Muhammad A. , Mahmoud Ahmed H. , Yan Dong‐Ming , English Shawn A. , Owens John D. , Bajaj Chandrajit L. , Mitchell Scott A.
Published: August 2016

We introduce an algorithmic framework for tuning the spatial density of disks in a maximal random packing, without changing the sizing function or radii of disks. Starting from any maximal random packing such as a Maximal Poisson‐disk Sampling (MPS), we iteratively relocate, inject (add), or eject (remove) disks, using a set of three successively more‐aggressive local operations. We may achieve a user‐defined density, either more dense or more sparse, almost up to the theoretical structured limits. The tuned samples are conflict‐free, retain coverage maximality, and, except in the extremes, retain the blue noise randomness properties of the input. We change the density of the packing one disk at a time, maintaining the minimum disk separation distance and the maximum domain coverage distance required of any maximal packing. These properties are local, and we can handle spatially‐varying sizing functions. Using fewer points to satisfy a sizing function improves the efficiency of some applications. We apply the framework to improve the quality of meshes, removing non‐obtuse angles; and to more accurately model fiber reinforced polymers for elastic and failure simulations.
Deep Learning for Robust Normal Estimation in Unstructured Point Clouds
Authors: Boulch Alexandre , Marlet Renaud
Published: August 2016

Normal estimation in point clouds is a crucial first step for numerous algorithms, from surface reconstruction and scene understanding to rendering. A recurrent issue when estimating normals is to make appropriate decisions close to sharp features, not to smooth edges, or when the sampling density is not uniform, to prevent bias. Rather than resorting to manually‐designed geometric priors, we propose to learn how to make these decisions, using ground‐truth data made from synthetic scenes. For this, we project a discretized Hough space representing normal directions onto a structure amenable to deep learning. The resulting normal estimation method outperforms most of the time the state of the art regarding robustness to outliers, to noise and to point density variation, in the presence of sharp edges, while remaining fast, scaling up to millions of points.
Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia
Authors: Gatesy John , Meredith Robert W. , Janecka Jan E. , Simmons Mark P. , Murphy William J. , Springer Mark S.
Published: August 2016

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereasMP‐ESTcoalescence analysis of the same dataset yields a weakly supported tree that conflicts with many traditionally recognized clades. Here, we evaluate this discrepancy via improved coalescence analyses with reference to the rich history of phylogenetic studies on mammals. This integration clearly demonstrates that both supermatrix and coalescence analyses of just 26 loci yield a congruent, well‐supported phylogenetic hypothesis for Mammalia. Discrepancies between published studies are explained by implementation of overly simpleDNAsubstitution models, inadequate tree‐search routines and limitations of theMP‐ESTmethod. We develop a simple measure,partitioned coalescence support(PCS), which summarizes the distribution of support and conflict among gene trees for a given clade. Extremely highPCSscores for outlier gene trees at two nodes in the mammalian tree indicate a troubling bias in theMP‐ESTmethod. We conclude that in this age of phylogenomics, a solid understanding of systematics fundamentals, choice of valid methodology and a broad knowledge of a clade's taxonomic history are still required to yield coherent phylogenetic inferences.
Immunocytochemistry for Claudin‐18 and Maspin in biliary brushing cytology increases the accuracy of diagnosing pancreatobiliary malignancies
Authors: Tokumitsu T. , Sato Y. , Yamashita A. , Moriguchi‐Goto S. , Kondo K. , Nanashima A. , Asada Y.
Published: August 2016

Objective

Biliary brush cytology is an important diagnostic tool in the evaluation of pancreatobiliary malignancies. However, it is difficult to distinguish between malignant and benign cells. The present study evaluated the utility of immunocytochemical expression of Claudin‐18 and Maspin in brushing cytology specimens of pancreatobiliary lesions in the diagnosis of pancreatobiliary malignancies.

Methods

The study retrospectively assessed biliary and pancreatic duct brushing cytology specimens of 43 patients whose pancreatobiliary lesions were histologically diagnosed at the University of Miyazaki Hospital. Scanty cellularity slides and cases with no histological confirmation were excluded. Alcohol‐fixed and Papanicolaou‐stained slides were immunostained with monoclonal antibodies to Claudin‐18 and Maspin.

Results

Of the 43 patients, 35 (81.4%) were finally histologically diagnosed with invasive adenocarcinomas. The sensitivity of routine cytology for the detection of malignancy was 63%, and the specificity was 100%. The sensitivity of cytology in combination with immunocytochemical expression of Claudin‐18 (89%) or Claudin‐18 and/or Maspin (97%) was significantly higher than that of cytology alone (P < 0.01).

Conclusion

Immunocytochemical staining for Claudin‐18 and Maspin improved the diagnostic sensitivity for pancreatobiliary adenocarcinomas.
The Enemy as a Patient: What can be Learned from the Emotional Experience of Physicians and Why does it Matter Ethically?
Authors: Rubinstein Gil , Bentwich Miriam Ethel
Published: August 2016

This qualitative research examines the influence of animosity on physicians during clinical encounters and its ethical implications. Semi‐structured interviews were conducted with ten Israeli‐Jewish physicians: four treated Syrians and six treated Palestinian terrorists/Hezbollah militants or Palestinian civilians. An interpretive phenomenological analysis was used to uncover main themes in these interviews. Whereas the majority of physicians stated they are obligated to treat any patient, physicians who treated Syrians exhibited stronger emotional expression and implicit empathy, while less referring to the presence of the Israeli‐Arab conflict. In contrast, physicians who treated enemy combatants or Palestinian civilians showed the exact opposite. Linking these results to the “Implicit Bias” theory, the role of empathy and the beneficence principle in medical ethics, we argue that: (a) the unconscious decreased emotional involvement among the latter group of physicians is a deficiency that needs to be recognized; and (b) this deficiency undermines the principle of beneficence, thereby possibly influencing the fulfillment of the commitment to treat patients. Acknowledging and addressing the potential emotional and ethical deficiencies entailed in encounters with the so‐called enemy‐patients are of importance to the global medical community, since such encounters are increasingly an integral part of the current political realities faced by both the developed and developing worlds.
Exenatide once weekly improved 24‐hour glucose control and reduced glycaemic variability in metformin‐treated participants with type 2 diabetes: a randomized, placebo‐controlled trial
Authors: Frías Juan P. , Nakhle Samer , Ruggles James A. , Zhuplatov Sergey , Klein Eric , Zhou Rong , Strange Poul
Published: August 2016

Aim

To assess the effects of once‐weekly exenatide on 24‐hour glucose control and variability.

Materials and methods

This double‐blind, placebo‐controlled trial randomized metformin‐treated adults with type 2 diabetes to once‐weekly exenatide 2.0 mg or placebo. Continuous glucose monitoring (CGM) was performed at baseline and weeks 4 and 10. The primary outcome was change in CGM‐measured 24‐hour mean glucose level.

Results

In the once‐weekly exenatide (n = 60) and placebo (n = 56) groups (modified intention‐to‐treat population), the baseline glycated haemoglobin (HbA1c) concentrations were 8.2% and 8.0%, respectively, and the fasting plasma glucose (FPG) concentration was 9.86 and 9.32 mmol/L, respectively. Once‐weekly exenatide significantly (p < 0.001) reduced 24‐hour mean glucose level versus placebo (week 4, −1.44 vs −0.29 mmol/L; week 10, −1.71 vs −0.17 mmol/L), with consistent control throughout the week. Once‐weekly exenatide significantly reduced FPG and 2‐hour postprandial glucose (PPG) levels versus placebo at week 4 (FPG, −1.65 vs −0.11 mmol/L; PPG, −1.79 vs −0.11 mmol/L) and week 10 (FPG, −2.32 vs −0.28 mmol/L; PPG, −2.46 vs −0.33 mmol/L). At week 10, once‐weekly exenatide reduced the mean amplitude of glucose excursions (MAGE; −0.84 vs 0.16 mmol/L) and standard deviation (s.d.) of mean glucose (−0.35 vs 0.04 mmol/L). By week 10, once‐weekly exenatide‐treated participants spent more time in euglycaemia (once‐weekly exenatide, 77% vs placebo, 58%), less time in hyperglycaemia (22% vs 42%), and a similar time in hypoglycaemia (0.7% vs 0.3%). Common adverse events were injection‐site nodule (once‐weekly exenatide, 10.0% vs placebo, 0.0%), urinary tract infection (6.7% vs 8.9%) and nausea (6.7% vs 0.0%).

Conclusions

In metformin‐treated participants with type 2 diabetes, once‐weekly exenatide significantly improved daily glucose control and reduced glycaemic variability at weeks 4 and 10, as shown by reductions in 24‐hour glucose, FPG and PPG levels, MAGE and s.d., and increased time spent in euglycaemia.
Perioperative echocardiography‐derived right ventricle function parameters and early outcomes after tetralogy of Fallot repair in mid‐childhood: a single‐center, prospective observational study
Authors: Raj Ravi , Puri Goverdhan Dutt , Jayant Aveek , Thingnam Shyam Kumar Singh , Singh Rana Sandip , Rohit Manoj Kumar
Published: August 2016

Background

Right ventricular (RV) function alterations are invariably present in all patients after tetralogy of Fallot (TOF) repair. Unlike the developed world where most of the patients with TOF are corrected in infancy, average age of presentation and thus surgery for these patients in the developing world may be higher. We aimed to study the correlation between RV function parameters such as tricuspid annular peak systolic excursion (TAPSE), fractional area change (FAC), and tricuspid annular peak systolic velocity (S’) with early outcome variables after intracardiac repair for TOF.

Materials and Methods

Fifty patients with a preoperative diagnosis of tetralogy of Fallot scheduled for corrective surgery were included in this single‐center, prospective observational study. A preoperative transthoracic echocardiogram was performed to measure RV function parameters (FAC0, TAPSE0, S'0). Transthoracic echocardiography was repeated postoperatively to measure FAC1, TAPSE1, S'1 (day 1) and FAC2, TAPSE2, and S'2 (day 3). The relationship between preoperative and postoperative RV function parameters with in‐hospital mortality, duration of mechanical ventilation, and intensive care unit stay was studied.

Results

The median age of patients was 6 years (range 1–14 years). Multiple stepwise logistic regression analysis showed RV FAC as best predictor of clinical outcome. Area under the receiver operating characteristic curve for postoperative RV function parameters, that is, FAC, TAPSE, and S’ to predict early or delayed recovery was 0.944, 0.875, and 0.655, respectively.

Conclusions

Among the RV function parameters studied, RV FAC best predicted the early outcome variables after TOF repair, followed by TAPSE while lateral tricuspid annular velocity S’ being the least predictive.
Nutrient patterns and their relationship to metabolic syndrome in Iranian adults
Authors: Khayyatzadeh Sayyed Saeid , Moohebati Mohsen , Mazidi Mohsen , Avan Amir , Tayefi Maryam , Parizadeh Seyed Mohammad Reza , Ebrahimi Mahmoud , Heidari‐Bakavoli Alireza , Azarpazhooh Mahmoud Reza , Esmaily Habibollah , Ferns Gordon A. , Nematy Mohsen , Safarian Mohammad , Ghayour‐mobarhan Majid
Published: August 2016

Background

The prevalence of metabolic syndrome (MetS) is increasing globally. It is associated with a significant risk of developing type 2 diabetes mellitus and cardiovascular disease.

Materials and methods

The relationship between adherence to several different dietary patterns and the presence of MetS was explored in an Iranian population sample of 5764 subjects.

Results

We observed that the prevalence of MetS was 13% and 18% in men and women, respectively. There were three main dietary patterns: the first pattern was characterized by protein, carbohydrate, starch, glucose, fructose, sucrose, maltose, dietary fibre, potassium, calcium, magnesium, phosphorus, iron, zinc, manganese, thiamine, riboflavin, carotene, vitamin c and lactose; second representative of fat, saturated fat, monounsaturated fat, polyunsaturated fat, cholesterol, sodium, calcium, zinc, phosphorus, iodine, vitamin D, chloride, betaine, niacin; third consisting of copper, selenium, vitamin A, riboflavin, vitamin B12. In this dietary pattern, individuals in first quintile had a higher consumption of total fat, saturated fatty acid, monounsaturated fatty acid, polyunsaturated fatty acid, cholesterol and vitamin A. In the second pattern, individuals in the fifth quintile ate less carbohydrate, dietary fibre, glucose, Fructose, potassium compared to first quintile. We found that individuals in the first quintile in pattern 3 had higher intakes of protein, zinc and calcium compared to other quintiles.

Conclusions

We have found that a nutrient pattern which mostly characterized by dietary protein, carbohydrate, starch, glucose, fructose, sucrose, maltose was associated with a higher risk of MetS in both genders, while a pattern which was represent of copper, selenium, Vitamin A, riboflavin, vitamin B12 was associated with greater odds of Mets, in women.