bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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.
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

ABSTRACT

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

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

AbstractThis 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

AbstractAmbitious 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

AbstractIslands 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.