bluuebunny/crossref_metadata_2025 huggingface dataset:
oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA
Authors: Xu Zongli , Taylor Jack A. , Leung Yuet-Kin , Ho Shuk-Mei , Niu Liang
Published: August 2016

Motivation: 5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are important epigenetic regulators of gene expression. 5mC and 5hmC levels can be computationally inferred at single base resolution using sequencing or array data from paired DNA samples that have undergone bisulfite and oxidative bisulfite conversion. Current estimation methods have been shown to produce irregular estimates of 5hmC level or are extremely computation intensive.

Results: We developed an efficient method oxBS-MLE based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that it outperformed alternative methods in estimate accuracy and computation speed.

Availability and Implementation: oxBS-MLE is implemented in Bioconductor package ENmix.

Contact:  niulg@ucmail.uc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CGDM: collaborative genomic data model for molecular profiling data using NoSQL
Authors: Wang Shicai , Mares Mihaela A. , Guo Yi-ke
Published: August 2016

Motivation: High-throughput molecular profiling has greatly improved patient stratification and mechanistic understanding of diseases. With the increasing amount of data used in translational medicine studies in recent years, there is a need to improve the performance of data warehouses in terms of data retrieval and statistical processing. Both relational and Key Value models have been used for managing molecular profiling data. Key Value models such as SeqWare have been shown to be particularly advantageous in terms of query processing speed for large datasets. However, more improvement can be achieved, particularly through better indexing techniques of the Key Value models, taking advantage of the types of queries which are specific for the high-throughput molecular profiling data.

Results: In this article, we introduce a Collaborative Genomic Data Model (CGDM), aimed at significantly increasing the query processing speed for the main classes of queries on genomic databases. CGDM creates three Collaborative Global Clustering Index Tables (CGCITs) to solve the velocity and variety issues at the cost of limited extra volume. Several benchmarking experiments were carried out, comparing CGDM implemented on HBase to the traditional SQL data model (TDM) implemented on both HBase and MySQL Cluster, using large publicly available molecular profiling datasets taken from NCBI and HapMap. In the microarray case, CGDM on HBase performed up to 246 times faster than TDM on HBase and 7 times faster than TDM on MySQL Cluster. In single nucleotide polymorphism case, CGDM on HBase outperformed TDM on HBase by up to 351 times and TDM on MySQL Cluster by up to 9 times.

Availability and Implementation: The CGDM source code is available at https://github.com/evanswang/CGDM.

Contact:  y.guo@imperial.ac.uk
Extensive complementarity between gene function prediction methods
Authors: Vidulin Vedrana , Šmuc Tomislav , Supek Fran
Published: August 2016

Motivation: The number of sequenced genomes rises steadily but we still lack the knowledge about the biological roles of many genes. Automated function prediction (AFP) is thus a necessity. We hypothesized that AFP approaches that draw on distinct genome features may be useful for predicting different types of gene functions, motivating a systematic analysis of the benefits gained by obtaining and integrating such predictions.

Results: Our pipeline amalgamates 5 133 543 genes from 2071 genomes in a single massive analysis that evaluates five established genomic AFP methodologies. While 1227 Gene Ontology (GO) terms yielded reliable predictions, the majority of these functions were accessible to only one or two of the methods. Moreover, different methods tend to assign a GO term to non-overlapping sets of genes. Thus, inferences made by diverse genomic AFP methods display a striking complementary, both gene-wise and function-wise. Because of this, a viable integration strategy is to rely on a single most-confident prediction per gene/function, rather than enforcing agreement across multiple AFP methods. Using an information-theoretic approach, we estimate that current databases contain 29.2 bits/gene of known Escherichia coli gene functions. This can be increased by up to 5.5 bits/gene using individual AFP methods or by 11 additional bits/gene upon integration, thereby providing a highly-ranking predictor on the Critical Assessment of Function Annotation 2 community benchmark. Availability of more sequenced genomes boosts the predictive accuracy of AFP approaches and also the benefit from integrating them.

Availability and Implementation: The individual and integrated GO predictions for the complete set of genes are available from http://gorbi.irb.hr/.

Contact:  fran.supek@irb.hr

Supplementary information:  Supplementary materials are available at Bioinformatics online.
Using recurrent neural network models for early detection of heart failure onset
Authors: Choi Edward , Schuetz Andy , Stewart Walter F , Sun Jimeng
Published: August 2016

Objective: We explored whether use of deep learning to model temporal relations among events in electronic health records (EHRs) would improve model performance in predicting initial diagnosis of heart failure (HF) compared to conventional methods that ignore temporality.

Materials and Methods: Data were from a health system’s EHR on 3884 incident HF cases and 28 903 controls, identified as primary care patients, between May 16, 2000, and May 23, 2013. Recurrent neural network (RNN) models using gated recurrent units (GRUs) were adapted to detect relations among time-stamped events (eg, disease diagnosis, medication orders, procedure orders, etc.) with a 12- to 18-month observation window of cases and controls. Model performance metrics were compared to regularized logistic regression, neural network, support vector machine, and K-nearest neighbor classifier approaches.

Results: Using a 12-month observation window, the area under the curve (AUC) for the RNN model was 0.777, compared to AUCs for logistic regression (0.747), multilayer perceptron (MLP) with 1 hidden layer (0.765), support vector machine (SVM) (0.743), and K-nearest neighbor (KNN) (0.730). When using an 18-month observation window, the AUC for the RNN model increased to 0.883 and was significantly higher than the 0.834 AUC for the best of the baseline methods (MLP).

Conclusion: Deep learning models adapted to leverage temporal relations appear to improve performance of models for detection of incident heart failure with a short observation window of 12–18 months.
The nuts and bolts of hypothesis testing
Authors: Pugh Stephanie L. , Molinaro Annette
Published: August 2016

When reading an article published in a medical journal, statistical tests are mentioned and the results are often supported by a P value. What are these tests? What is a P value and what is its meaning? P values are used to interpret the result of a statistical test. Both are intrinsic parts of hypothesis testing, which is a decision-making tool based on probability. Most medical and epidemiological studies are designed using a hypothesis test so understanding the key principles of a hypothesis test are crucial to interpreting results of a study. From null and alternative hypotheses to the issue of multiple tests, this paper introduces concepts related to hypothesis testing that are crucial to its implementation and interpretation.
In-vitro and in-vivo inhibition of melanoma growth and metastasis by the drug combination of celecoxib and dacarbazine
Authors: Sadhu Satya S. , Wang Shenggang , Averineni Ranjith K. , Seefeldt Teresa , Yang Yang , Guan Xiangming
Published: August 2016

Celecoxib has been found to be effective in cancer prevention and treatment. Its combination with other chemotherapeutic agents was reported to produce synergistic/additive effects on various cancers. Dacarbazine (DTIC) is one of the most commonly used drugs in the treatment of metastatic melanoma. This investigation aimed to determine the in-vitro and in-vivo effects of the drug combination of celecoxib and DTIC on melanoma growth and metastasis. Melanoma cells B16-F10 and SK-MEL-28, and female C57BL/6 mice were used for the study. Our in-vitro data showed that significant synergistic effects were obtained when celecoxib was used together with various concentrations of DTIC. A study with B16-F10 cells using flow cytometry analysis showed that the drug combination induced significantly more apoptosis than each drug used individually. Our in-vivo results showed that the drug combination was much more effective than each drug used alone for the inhibition of both melanoma growth and metastasis in the B16-F10+C57BL/6 mouse models. For melanoma growth, the median survival rates for phosphate-buffered saline (PBS) (control), celecoxib (30 mg/kg), DTIC-1 (10 mg/kg), DTIC-2 (positive control, 50 mg/kg), and the drug combination (DTIC 10 mg/kg+celecoxib 30 mg/kg) were 6, 6.5, 7.5, 7.5, and 9 days, respectively. For melanoma metastasis, the average number of metastatic tumors in murine lungs was 53.7±10.7, 31.8±18.6, 21.2±21.7, 7.0±9.0, and 0.8±2.0 for PBS, DTIC-1, celecoxib, the drug combination, and DTIC-2. Our results warrant further investigation of the combination as an effective treatment for melanoma patients.
RETINAL ARTERIOVENOUS MALFORMATION
Authors: Patel Kevin H. , Kalevar Ananda , McDonald H. Richard , Johnson Robert N.
Published: August 2016

Purpose:

To describe a case of an isolated Group 3 retinal arteriovenous malformation (AVM).

Methods:

Observational case report.

Results:

A 15-year-old girl with no significant medical history presented with no light perception vision in her right eye and gradually decreasing vision in her left eye over several years. She was found to have a large AVM in the posterior pole of the right eye with associated perivascular sheathing in the periphery. Her left eye seemed totally unremarkable. Neuroimaging revealed no intracranial or intraorbital abnormalities. A diagnosis of isolated Group 3 retinal AVM was made.

Conclusion:

Retinal AVMs are congenital, nonhereditary, and sporadic vascular anomalies that develop in the posterior pole. A number of patients with this finding can have coexisting AVMs in the brain, mandible, skin, or orbit, which comprises the Wyburn–Mason syndrome. Because of these systemic associations, neuroimaging should always be considered when a retinal AVM is seen. Severe vision loss can occur from these AVMs secondary to a number of ocular complications, including central retinal vein occlusions.
ACUTE MACULAR NEURORETINOPATHY WITHOUT NEAR-INFRARED REFLECTANCE—AN ATYPICAL CASE PRESENTATION
Authors: Kalevar Ananda , Patel Kevin H. , Fu Arthur D.
Published: August 2016

Background:

Acute macular neuroretinopathy is a rare disease that with the help of multimodal imaging is being diagnosed more frequently.

Methods:

An atypical case is presented and followed by multimodal imaging.

Results:

A typical acute macular neuroretinopathy lesion was seen on biomicroscopic examination and spectral domain optical coherence tomography examination. However, near-infrared imaging revealed a lack of the characteristic finding along with a relative afferent pupillary defect and a widespread depressed multifocal electroretinogram which has not been reported previously.

Conclusion:

This patient exhibits photoreceptor and outer retinal findings commonly described in acute macular neuroretinopathy lesion without classic near-infrared findings. This case may represent a severe form of acute macular neuroretinopathy.
Diagnostic Value of Visual Examination of Cervical Polypoid Lesions and Predictors of Misdiagnosis
Authors: Uçar Mustafa Gazi , İlhan Tolgay Tuyan , Uçar Rahime Merve , Karabağli Pinar , Çelik Çetin
Published: August 2016

Objectives

This study reviews occasions when cervical polyps removed in an outpatient setting proved not to be cervical polyps histologically. We aimed to identify any anatomical and/or clinical characteristics that predict "incorrect diagnosis” in general practice.

Methods

A retrospective study of consecutive 345 patients who were initially diagnosed with cervical polyps based on a routine gynecological examination in an outpatient setting was included. After histopathological examination, the patients were divided into 2 groups: those with cervical (correct diagnosis, n = 307) and falsely diagnosed with cervical polyps (FDP, n = 38). These 2 groups were compared in terms of age, signs and symptoms, and size of the polypoid lesions.

Results

The initial clinical diagnosis was correct in 307, giving a positive predictive value of 89%. There were no significant difference between the groups with respect to age of patients (p = 0.59) and the size of the lesions (p = 0.42). According to our study, among misdiagnosed patients, nabothian cysts and cervicitis were the most common histological findings; FDPs were more often symptomatic (p < 0.001) and coexisted more frequently with inflammation or ulceration (p < 0.001). All FDPs were developing within the endocervical canal. There were no instances of FDPs that arise from ectocervix. Symptomatic polypoids have a higher risk of preliminary misdiagnosis (OR = 13.0; 95% confidence interval, 3.0–55.1).

Conclusions

All cervical polypoid lesions must be sent to pathology because visual diagnosis is not sufficiently accurate to direct patient care.
Measurement of Symptoms Pre- and Post-treatment of Dry Eye Syndromes
Authors: McMonnies Charles W.
Published: August 2016

Valid assessment of dry eye syndrome symptoms is essential for diagnosis and for making treatment decisions and monitoring responses to treatment. Notwithstanding the desirability of being able to measure across several assessment domains to gauge the influence of symptom burden on the quality of life, the time-consuming nature of such assessments may make them unsuitable for routine clinical use. This review of symptom assessment methods examines the relative merits of visual analogue and Likert scales. Also examined are ways in which symptoms can be influenced by comorbid diseases and associated medications, and how the validity of assessing treatment efficacy could be compounded by natural progression of a dry eye syndrome apart from either favorable, neutral, or adverse responses to treatment. Follow-up assessments may also be biased by patient expectations. How validity of responses could be improved by the instructional use of a demonstration scale is described and illustrated. Personal instruction is suggested for patients anticipated to have age- or language-related difficulties but for some patients instruction could be successfully self-directed. A comparison of methods used to monitor dry eye syndrome treatment has allowed recommendations to be made for a method of using visual analogue scales which incorporates features which have been demonstrated to be advantageous in previous studies. The continuous nature of a visual analogue scale allows for smaller changes to be recorded with associated better discriminating capacity. More powerful statistical analysis of findings is possible when using visual analogue scales. Reference to previous assessment scores and exactly the same scale anchors improve the reliability of measurements of change in symptoms over time.
scater:pre-processing, quality control, normalisation and visualisation of single-cell RNA-seq data in R
Authors: McCarthy Davis J. , Campbell Kieran R. , Lun Aaron T. L. , Wills Quin F.
Published: August 2016

Motivation

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts, and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalisation.

Results

We have developed the R/Bioconductor packagescaterto facilitate rigorous pre-processing, quality control, normalisation and visualisation of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis.scaterprovides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development.

Availability

The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor athttp://bioconductor.org/packages/scater.

Supplementary information

Supplementary material is available online atbioRxivaccompanying this manuscript, and all materials required to reproduce the results presented in this paper are available at dx.doi.org/10.5281/zenodo.60139.
Twitter user tagging method based on burst time series
Authors: Yamamoto Shuhei , Wakabayashi Kei , Kando Noriko , Satoh Tetsuji
Published: August 2016

Purpose

Many Twitter users post tweets that are related to their particular interests. Users can also collect information by following other users. One approach clarifies user interests by tagging labels based on the users. A user tagging method is important to discover candidate users with similar interests. This paper aims to propose a new user tagging method using the posting time series data of the number of tweets.

Design/methodology/approach

Our hypothesis focuses on the relationship between a user’s interests and the posting times of tweets: as users have interests, they will post more tweets at the time when events occur compared with general times. The authors assume that hashtags are labeled tags to users and observe their occurrence counts in each timestamp. The authors extract burst timestamps using Kleinberg’s burst enumeration algorithm and estimate the burst levels. The authors manage the burst levels as term frequency in documents and calculate the score using typical methods such as cosine similarity, Naïve Bayes and term frequency (TF) in a document and inversed document frequency (IDF; TF-IDF).

Findings

From the sophisticated experimental evaluations, the authors demonstrate the high efficiency of the tagging method. Naïve Bayes and cosine similarity are particular suitable for the user tagging and tag score calculation tasks, respectively. Some users, whose hashtags were appropriately estimated by our methods, experienced higher the maximum value of the number of tweets than other users.

Originality/value

Many approaches estimate user interest based on the terms in tweets and apply such graph theory as following networks. The authors propose a new estimation method that uses the time series data of the number of tweets. The merits to estimating user interest using the time series data do not depend on language and can decrease the calculation costs compared with the above-mentioned approaches because the number of features is fewer.
Information privacy disclosure on social network sites
Authors: Li Kai , Wang Xiaowen , Li Kunrong , Che Jianguo
Published: August 2016

Purpose

As social network sites (SNS) have increasingly become one of the most important channels for communication, the related privacy issues gain more and more attention in both industry and academic research fields. This study aims to connect the antecedents of information privacy disclosure on SNS.

Design/methodology/approach

Based on exchange theory, this study tries to investigate the decision-making process for information privacy disclosure on SNS. Factors from both user’s and website’s perspectives are taken into account in the proposed model.

Findings

The results suggest that an individual’s perceived benefits will increase their willingness to disclose information privacy on SNS, but perceived risks decrease this kind of willingness. The authors also find social network size, personal innovativeness and incentive provision positively affect people’s perceived benefits.

Originality/value

Moreover, privacy invasion experience enhances perceived personal risks, but website reputation helps to reduce perceived risks.
Is the Funding of Public National Health Systems Sustainable over the Long Term? Evidence from Eight OECD Countries
Authors: Angelis Aris , Tordrup David , Kanavos Panos
Published: August 2016

This study examines what impact macroeconomic and health‐related factors have on the financial sustainability of health care systems; provides insights on additional financial resources required in order for demand for health care to be met; and reflects on needed reforms by health care systems in the near future. Publicly available data are used to identify the key variables influencing health spending. Statistical analysis is used to provide estimates of future required levels of health spending. Average macroeconomic performance, high debt levels, the need to contain fiscal deficits combined with adverse demographic developments, high outlays on health technologies and competing public sector needs, suggest that a funding gap between required and committed levels of health spending will exist in the next few years. This funding shortfall can be significant and in cumulative terms may range between 39 per cent and 61 per cent of 2012 health expenditure levels over the 2013–2017 period. Health care decision makers will need to place emphasis on outcomes‐based reimbursement, set priorities based on efficiency rules, and implement organisational innovations in order to ensure affordability and sustainability. In the opposite case, contraction of services offered and exclusions from coverage are not unlikely.
Global representation of threatened amphibians ex situ is bolstered by non‐traditional institutions, but gaps remain
Authors: Biega A. , Greenberg D. A. , Mooers A. O. , Jones O. R. , Martin T. E.
Published: August 2016

Ambitious global conservation targets have been set to manage increasing threats to amphibians. Ex situ institutions (broadly, ‘zoos’) are playing an expanding role in meeting these targets. Here, we examine the extent to which zoos house species representing the greatest overall conservation priority by testing how eight variables relating to extinction risk – International Union for the Conservation of Nature status, habitat specialization, obligate stream breeding, geographic range size, body size and island, high‐altitude and tropical endemism – vary between amphibian species held in zoos and their close relatives not held in zoos. Based on 253 species found in zoos that could be confidently paired with close relatives not in zoos, and in contrast to reported patterns for birds and mammals, we find that amphibians currently held in zoos are equally as threatened as their close relatives not found in zoos. This result is entirely driven by the inclusion of data on species holdings from Amphibian Ark (AArk), an organization that helps to coordinate conservation activities in many ‘non‐traditional’ institutions, as well as in ‘traditional’ commercial zoos. Such networks of small non‐traditional institutions thus make meaningful contributions to ex situ conservation, and the establishment of other taxa‐specific organizations modelled on AArk might be considered. That said, our results indicate that the ex situ network is still not prioritizing range‐restricted habitat specialists, species that possess greater overall extinction risk in the near future. We strongly encourage zoos to continue increasing their holdings of amphibian species, but to pay greater attention to these species of particular conservation concern.
Are tourism and conservation compatible for ‘island tame’ species?
Authors: Worrell T. , Admiraal R. , Bateman P. W. , Fleming P. A.
Published: August 2016

Islands play an important conservation role due to high rates of speciation as well as providing a predator‐free refuge environment for species that are vulnerable to terrestrial predation on the mainland. Many animals show marked ‘island tameness’ on predator‐free islands, reducing costly escape responses in the absence of predation threat. Island tameness also translates to altered responses toward humans, making many island species attractive for wildlife tourism. We explored temporal and spatial differences in behavioral responses in the Rottnest Island quokka Setonix brachyurus. This marsupial is an excellent species to test for the effects of ecotourism, as well as of being conservation significance (IUCN‐listed as vulnerable). Comparing escape responses for n = 339 individuals in high tourism and low tourism seasons, quokkas at tourism sites allowed a person to approach closer before moving away compared with non‐tourisms sites, and two‐thirds of individuals around tourism sites allowed a person to approach within 1 m (compared with 14% of individuals at non‐tourism sites). For n = 67 ad hoc interactions with tourists, quokkas would only move away from an interaction with a tourist when the tourist group was noisy or there was an attempt to touch the animal. Time budgets (n = 379 individuals) showed that quokkas spent more time in group behavior and locomotion, but less in vigilance and feeding for tourism sites compared with non‐tourism sites. Understanding the impact of ecotourism on animal behavior will help to frame conservation management actions to ensure persistence of threatened wildlife species. We propose two models describing animal responses toward ecotourism: spatial separation according to animal temperament or temporal adjustment due to learned habituation. These models are not mutually exclusive and we suggest that both spatial separation and habitation are likely evident for Rottnest quokkas. We discuss the implications of these results for protection of animals on the island as well as for species conservation.
The frequency of small saccades during fixation is age independent in children between 5 and 16 years of age
Authors: Larsen Dorte Ancher , Bek Toke
Published: August 2016

Purpose

Fixational eye movements are necessary for maintaining normal vision by preventing a stabilized image on the retina that would result in visual fading. The movements can be divided into tremor, drifts and saccades that may be related to movements of gaze and to fixation. It has previously been shown that the frequency of fixational saccades with an amplitude larger than 3° depends on age. The purpose of this study was to investigate whether other parameters describing fixational saccades also depend on age which necessitates age correction in studies of fixation during visual development.

Methods

Fixational eye movements were recorded in 36 normal children aged 5–16 years. Parameters describing fixational saccades were characterized using a standardized algorithm and were correlated with age.

Results

There was a significant linear relation between the amplitude and duration of fixational saccades (r2 = 0.37, p < 0.0001). The relation between the number of saccadic movements and the amplitude was unimodal and showed no correlation with age. However, the number of saccades per examination with an amplitude larger than 1° showed a negative correlation with age (r2 = 0.23, p = 0.003).

Conclusions

The overall frequency and amplitude of fixational saccades show no correlation with age that necessitates correction in clinical studies of visual development. The decreasing frequency of large saccadic eye movements with increasing child age may be due to improved attention.
Calming cycle theory: the role of visceral/autonomic learning in early mother and infant/child behaviour and development
Authors: Welch Martha G.
Published: August 2016

Results from a randomised controlled trial of Family Nurture Intervention (FNI) showed significantly improved maternal behaviours and infant neurodevelopment and behaviour through 18 months, including a significantly reduced risk for autism. Preliminary results from a pilot study of FNI in preschool children found significant reduction in adverse behaviour. Conclusion: Calming cycle theory proposes that early emotional behaviour is shaped by subcortical visceral/autonomic co‐conditioning between mother and infant. Two new constructs, emotional connection and visceral/autonomic co‐regulation, are defined within a functional Pavlovian conditioning framework and are theorised to be part of an evolutionarily conserved mammalian phenomenon first identified by Pavlov.
RNA toxicity induced by expanded CAG repeats in Huntington's disease
Authors: Martí Eulàlia
Published: August 2016

Huntington's disease (HD) belongs to the group of inherited polyglutamine (PolyQ) diseases caused by an expanded CAG repeat in the coding region of the Huntingtin (HTT) gene that results in an elongated polyQ stretch. Abnormal function and aggregation of the mutant protein has been typically delineated as the main molecular cause underlying disease development. However, the most recent advances have revealed novel pathogenic pathways directly dependent on an RNA toxic gain‐of‐function. Expanded CAG repeats within exon 1 of the HTT mRNA induce toxicity through mechanisms involving, at least in part, gene expression perturbations. This has important implications not only for basic and translational research in HD, but also for other types of diseases carrying the expanded CAG in other genes, which likely share pathogenic aspects. Here I will review the evidence and mechanisms underlying RNA toxicity in CAG repeat expansions, with particular focus on HD. These comprise abnormal subcellular localization of the transcripts containing the expanded CAG repeats; sequestration of several types of proteins by the expanded CAG repeat which results in defects of alternative splicing events and gene expression; and aberrant biogenesis and detrimental activity of small CAG repeated RNAs (sCAG) that produce altered gene silencing. Although these altered pathways have been detected in HD models, their contribution to disease development and progress requires further study.
Iterative Closest Conformal Maps between Planar Domains
Authors: Segall Aviv , Ben‐Chen Mirela
Published: August 2016

Conformal maps between planar domains are an important tool in geometry processing, used for shape deformation and image warping. The Riemann mapping theorem guarantees that there exists a conformal map between any two simply connected planar domains, yet computing this map efficiently remains challenging. In practice, one of the main algorithmic questions is the correspondence between the boundaries of the domains. On the one hand, there exist a number of conformal maps between any two domains, thus many potential boundary correspondences, yet on the other, given full boundary prescription a conformal map might not exist. Furthermore, an approximate boundary fitting can be enough for many applications. We therefore propose an alternating minimization algorithm for finding a boundary‐approximating conformal map given only an initial global alignment of the two input domains. We utilize the Cauchy‐Green complex barycentric coordinates to parameterize the space of conformal maps from the source domain, and thus compute a continuous map without requiring the discretization of the domain, and without mapping to intermediate domains. This yields a very efficient method which allows to interactively modify additional user‐provided constraints, such as point‐to‐point and stroke‐to‐stroke correspondences. Furthermore, we show how to easily generalize this setup to quasi‐conformal maps, thus enriching the space of mappings and reducing the area distortion. We compare our algorithm to state‐of‐the‐art methods for mapping between planar domains, and demonstrate that we achieve less distorted maps on the same inputs. Finally, we show applications of our approach to stroke based deformation and constrained texture mapping.
Crawl through Neighbors: A Simple Curve Reconstruction Algorithm
Authors: Parakkat Amal Dev , Muthuganapathy Ramanathan
Published: August 2016

Given a planar point set sampled from an object boundary, the process of approximating the original shape is called curve reconstruction. In this paper, a novel non‐parametric curve reconstruction algorithm based on Delaunay triangulation has been proposed and it has been theoretically proved that the proposed method reconstructs the original curve under ε‐sampling. Starting from an initial Delaunay seed edge, the algorithm proceeds by finding an appropriate neighbouring point and adding an edge between them. Experimental results show that the proposed algorithm is capable of reconstructing curves with different features like sharp corners, outliers, multiple objects, objects with holes, etc. The proposed method also works for open curves. Based on a study by a few users, the paper also discusses an application of the proposed algorithm for reconstructing hand drawn skip stroke sketches, which will be useful in various sketch based interfaces.
Identifying Style of 3D Shapes using Deep Metric Learning
Authors: Lim Isaak , Gehre Anne , Kobbelt Leif
Published: August 2016

We present a method that expands on previous work in learning human perceived style similarity across objects with different structures and functionalities. Unlike previous approaches that tackle this problem with the help of hand‐crafted geometric descriptors, we make use of recent advances in metric learning with neural networks (deep metric learning). This allows us to train the similarity metric on a shape collection directly, since any low‐ or high‐level features needed to discriminate between different styles are identified by the neural network automatically. Furthermore, we avoid the issue of finding and comparing sub‐elements of the shapes. We represent the shapes as rendered images and show how image tuples can be selected, generated and used efficiently for deep metric learning. We also tackle the problem of training our neural networks on relatively small datasets and show that we achieve style classification accuracy competitive with the state of the art. Finally, to reduce annotation effort we propose a method to incorporate heterogeneous data sources by adding annotated photos found online in order to expand or supplant parts of our training data.
Exploration of Empty Space among Spherical Obstacles via Additively Weighted Voronoi Diagram
Authors: Manak M.
Published: August 2016

Properties of granular materials or molecular structures are often studied on a simple geometric model – a set of 3D balls. If the balls simultaneously change in size by a constant speed, topological properties of the empty space outside all these balls may also change. Capturing the changes and their subsequent classification may reveal useful information about the model. This has already been solved for balls of the same size, but only an approximate solution has been reported for balls of different sizes. These solutions work on simplicial complexes derived from the dual structure of the ordinary Voronoi diagram of ball centers and use the mathematical concept of simplicial homology groups. If the balls have different radii, it is more appropriate to use the additively weighted Voronoi diagram (also known as the Apollonius diagram) instead of the ordinary diagram, but the dual structure is no longer a simplicial complex, so the previous approaches cannot be used directly. In this paper, a method is proposed to overcome this problem. The method works with Voronoi edges and vertices instead of the dual structure. Additional bridge edges are introduced to overcome disconnected cases. The output is a tree graph of events where cavities are created or merged during a simulated shrinking of the balls. This graph is then reorganized and filtered according to some criteria to get a more concise information about the development of the empty space in the model.
Voice and ageing: clinical, endoscopic and acoustic investigation
Authors: Pessin A.B.B. , Tavares E.L.M. , Gramuglia A.C.J. , de Carvalho L.R. , Martins R.H.G.
Published: August 2016

Vocal symptoms are frequent in the elderly and are consequences of structural changes in the larynx that occur with ageing.

Objective

To identify the voice alterations in elderly patients attending a voice clinic.

Methods

Elderly patients of both genders were divided into two groups: 60–75 and above 76 years. All patients completed a questionnaire with identification data, profession, vocal symptoms, hearing, habits and addictions, and systemic diseases. All participants were submitted to video laryngoscopy and acoustic and auditory‐perceptual vocal analysis.

Results

In this study, women predominated (40 F versus 32 M). Hoarseness was reported by 34.72% of the participants. Other symptoms included singing difficulty (17%) and phonatory effort (15.28%). Maximum phonation time showed lower values and scores 2 and 3 of perceptual analysis were registered in 33% of the elderly participants, but without statistical significance. The fundamental frequency values were inferior in older man and high in women and acoustic parameters showed high values in both groups, but without statistical significance. Videolaryngoscopies demonstrated alterations in 47% of the participants, especially bowed and atrophic vocal folds.

Conclusions

We described the vocal symptoms, vocal perceptual and acoustic analysis and endoscopic findings of an elderly population, characterising the presbyphonia. Therapeutic measures must involve speech therapy and/or surgery to reduce the glottal gap, allowing less air leakage and, consequently, better vocal performance.
Reconciling Biodiversity Indicators to Guide Understanding and Action
Authors: Hill Samantha L.L. , Harfoot Mike , Purvis Andy , Purves Drew W. , Collen Ben , Newbold Tim , Burgess Neil D. , Mace Georgina M.
Published: August 2016

Many metrics can be used to capture trends in biodiversity and, in turn, these metrics inform biodiversity indicators. Sampling biases, genuine differences between metrics, or both, can often cause indicators to appear to be in conflict. This lack of congruence confuses policy makers and the general public, hindering effective responses to the biodiversity crisis. We show how different and seemingly inconsistent metrics of biodiversity can, in fact, emerge from the same scenario of biodiversity change. We develop a simple, evidence‐based narrative of biodiversity change and implement it in a simulation model. The model demonstrates how, for example, species richness can remain stable in a given landscape, whereas other measures (e.g. compositional similarity) can be in sharp decline. We suggest that linking biodiversity metrics in a simple model will support more robust indicator development, enable stronger predictions of biodiversity change, and provide policy‐relevant advice at a range of scales.
Evaluation of image quality in carotid and cerebrovascular disease: a comparative study between subtraction and routine computed tomography angiography
Authors: Zhao De‐Li , Wan Yong , Wang Guo‐Kun , Wang Hai‐Bo , Liang Hong‐Wei , Zhou Hai‐Ting , Gao Li , Zhang Jin‐Ling
Published: August 2016

Objective

Few data exist comparing the image quality and diagnostic accuracy of subtraction computed tomography (CT) angiography (SCTA) in carotid and cerebrovascular arteries with routine CT angiography (RCTA).

Patients and methods

In this study, 56 patients underwent 128‐row CT angiography of these vessels with review by two radiologists using routine, nonsubtracted, and SCTA protocols. Comparisons were made using a 4‐point subjective rating scale in all patients. Eighteen patients were examined with both SCTA and invasive digital subtraction angiography (DSA). The accuracy of SCTA and routine CTA reformations was assessed and compared by both patient‐based and vessel‐based analyses of intracranial aneurysms and intracranial and extracranial arterial stenotic lesions using DSA results as the reference standard.

Results

Diagnostic accuracy in the adjacent skull base portion of the internal carotid artery (ICA) and reading time for cerebral aneurysms and vessel stenoses were obviously improved with SCTA protocol, but the accuracy in vertebro‐basilar arteries was no different. The diagnostic accuracy in general was slightly increased compared with routine CTA.

Conclusion

Review of SCTA images is an effective means to remove bone close to vessels as seen on routine CTA and has good image quality and diagnostic accuracy. SCTA is superior to routine CTA in the visualization and diagnostic accuracy of adjacent skull base part of the ICA and decreases reading time for carotid and cerebrovascular arterial imaging.
Cardiac iron load and function in transfused patients treated with deferasirox (the MILE study)
Authors: Ho P. Joy , Tay Lay , Teo Juliana , Marlton Paula , Grigg Andrew , St Pierre Tim , Brown Greg , Badcock Caro‐Anne , Traficante Robert , Gervasio Othon L. , Bowden Donald K.
Published: August 2016

Objectives

To assess the effect of iron chelation therapy with deferasirox on cardiac iron and function in patients with transfusion‐dependent thalassemia major, sickle cell disease (SCD), and myelodysplastic syndromes (MDS).

Methods

This phase IV, single‐arm, open‐label study over 53 wk evaluated the change in cardiac and liver iron load with deferasirox (up to 40 mg/kg/d), measured by magnetic resonance imaging (MRI).

Results

Cardiac iron load (myocardial T2*) significantly improved (P = 0.002) overall (n = 46; n = 36 thalassemia major, n = 4 SCD, n = 6 MDS). Results were significant for patients with normal and moderate baseline cardiac iron (P = 0.017 and P = 0.015, respectively), but not in the five patients with severe cardiac iron load. Liver iron concentration (LIC) significantly decreased overall [mean LIC 10.4 to 8.2 mg Fe/g dry tissue (dw); P = 0.024], particularly in those with baseline LIC >7 mg Fe/g dw (19.9 to 15.6 mg Fe/g dw; P = 0.002). Furthermore, myocardial T2* significantly increased in patients with LIC <7 mg Fe/g dw, but not in those with a higher LIC. Safety was consistent with previous reports.

Conclusions

Once‐daily deferasirox over 1 yr significantly increased myocardial T2* and reduced LIC. This confirms that single‐agent deferasirox is effective in the management of cardiac iron, especially for patients with myocardial T2* >10 ms (Clinicaltrials.gov identifier: NCT00673608).
The course of language functions after temporal lobe epilepsy surgery: a prospective study
Authors: Giovagnoli A. R. , Parente A. , Didato G. , Manfredi V. , Deleo F. , Tringali G. , Villani F.
Published: August 2016

Background and purpose

Anterior temporal lobectomy (ATL) within the language‐dominant hemisphere can impair naming. This prospective study examined the pre‐operative to post‐operative course of different language components, clarifying which changes are relevant within the short‐term and long‐term outcome of language.

Methods

Patients with drug‐resistant temporal lobe epilepsy (TLE) were evaluated using the Token, Boston Naming and Word Fluency tests assessing sentence comprehension and word‐finding on visual, semantic or phonemic cues.

Results

A total of 106 patients were evaluated before and 6 months, 1 and 2 years after ATL; 60 patients were also evaluated after 5 years and 38 controls were assessed at baseline. Seizure outcome was comparable between the left and right TLE patients. Before surgery, naming and word fluency were impaired in the left and right TLE patients, whereas sentence comprehension was normal. After left or right ATL, word fluency progressively improved, naming showed early worsening and late improvement after left ATL and progressive improvement after right ATL, and sentence comprehension did not change. At the 5‐year follow‐up, naming improvement was clinically significant in 31% and 71% of the left and right TLE patients, respectively. Pre‐operative naming, ATL laterality, schooling, and post‐operative seizure frequency and number of antiepileptic drugs predicted post‐operative naming. Pre‐operative word fluency and schooling predicted post‐operative word fluency.

Conclusions

Left or right TLE can impair word‐finding but not sentence comprehension. After ATL, word‐finding may improve for a long time, depending on TLE laterality, seizure control and mental reserve. These findings may clarify prognosis prior to treatment.
Long‐term exposure and safety of lacosamide monotherapy for the treatment of partial‐onset (focal) seizures: Results from a multicenter, open‐label trial
Authors: Vossler David G. , Wechsler Robert T. , Williams Paulette , Byrnes William , Therriault Sheila ,   the ALEX‐MT study group
Published: August 2016

Objective

To assess long‐term use and safety of lacosamide (LCM) ≤800 mg/day monotherapy in patients with partial‐onset seizures (POS) enrolled previously in a historical‐controlled, conversion‐to‐monotherapy study (SP902; NCT00520741).

Methods

Patients completing or exiting SP902 with LCM as monotherapy or as adjunctive therapy were eligible to enter this 2‐year open‐label extension (OLE) trial (SP904; NCT00530855) at a starting dose ±100 mg/day of their final SP902 dose. Investigators could adjust the LCM dose to 100–800 mg/day and add up to two antiepileptic drugs to optimize tolerability and seizure reduction.

Results

Three hundred twenty‐two patients received LCM: 210 patients (65.2%) completed and 112 (34.8%) discontinued, most commonly owing to withdrawal of consent (9.3%). Two hundred fifty‐eight patients (80.1%) had ≥1 year of and 216 (67.1%) had ≥2 years of LCM exposure, of whom 179/258 (69.4%) achieved LCM monotherapy lasting for any 12‐month period, and 126/216 (58.3%) patients exposed for ≥24 months achieved LCM monotherapy for any 24‐month period. Total exposure = 525.5 patient‐years. The median modal dose was 500 mg/day. Two hundred ninety‐two patients (90.7%) achieved LCM monotherapy at some point during the study. Sixty‐five of 87 patients who exited and 193/235 who completed SP902 were exposed for ≥12 months, and 43.1% and 78.2%, respectively, achieved LCM monotherapy for ≥12 months. Median LCM monotherapy duration was 587.0 days (2–791 days); 91.0% of patients reported treatment‐emergent adverse events, of which the most common were dizziness (27.3%), headache (17.1%), and nausea (14.3%). Compared with the SP902 study baseline, 74.2% of patients had a ≥50% seizure reduction and 5.6% were seizure‐free at 24 months.

Significance

The majority of patients were receiving LCM monotherapy at 0, 12, and 24 months in this OLE. Lacosamide monotherapy (median dose of 500 mg/day) had a safety profile similar to that of adjunctive therapy studies. These results support the use of lacosamide as long‐term monotherapy treatment for adults with POS.