bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Summary

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

Summary

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

AbstractFor 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

AbstractHuman 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

AbstractIntroductionPolycystic 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 methodsThe 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.ResultsWomen 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).ConclusionsWomen 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

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

ObjectivesTo 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 MethodsWe 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.ResultsOverall, 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.ConclusionA 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

AbstractThe 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

AbstractBackgroundTo assess the corneal diameter and its associations in children.DesignCross‐sectional school‐based study.ParticipantsSix thousand twenty‐six children aged 4–18 years were included in the Shandong Children Eye Study.MethodsHorizontal corneal diameter was measured by laser interferometry‐based ocular biometry.Main Outcome MeasuresHorizontal corneal diameter.ResultsCorneal 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.ConclusionsIn 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

AbstractVarious 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

AbstractImplicit 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

AbstractWe 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.