State-space modelling of geolocation data reveals sex differences in the use of management areas by breeding northern fulmars

We thank Orkney Islands Council for access to Eynhallow and Talisman Energy (UK) Ltd and Marine Scotland for fieldwork and equipment support. Handling and tagging of fulmars was conducted under licences from the British Trust for Ornithology and the UK Home Office. EE was funded by a Marine Alliance for Science and Technology for Scotland/University of Aberdeen College of Life Sciences and Medicine studentship and LQ was supported by a NERC Studentship. Thanks also to the many colleagues who assisted with fieldwork during the project, and to Helen Bailey and Arliss Winship for advice on implementing the state-space model.

Mining dynamic databases for frequent closed itemsets

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Semi-parametric geolocation estimation in NLOS environments

The position of a stationary target can be determined using triangulation in combination with time of arrival measurements at several sensors. In urban environments, none-line-of-sight (NLOS) propagation leads to biased time estimation and thus to inaccurate position estimates. Here, a semi-parametric approach is proposed to mitigate the effects of NLOS propagation. The degree of contamination by NLOS components in the observations, which result in asymmetric noise statistics, is determined and incorporated into the estimator. The proposed method is adequate for environments where the NLOS error plays a dominant role and outperforms previous approaches that assume a symmetric noise statistic.

Research databases page usability test - August 2016

During the summer of 2016, Duke University Libraries staff began a project to update the way that research databases are displayed on the library website. The new research databases page is a customized version of the default A-Z list that Springshare provides for its LibGuides content management system. Duke Libraries staff made adjustments to the content and interface of the page. In order to see how Duke users navigated the new interface, usability testing was conducted on August 9th, 2016.

Mining dynamic databases for frequent closed itemsets

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

The epidemiology, healthcare and societal burden and costs of asthma in the UK and its member nations: analyses of standalone and linked national databases

Background: There are a lack of reliable data on the epidemiology and associated burden and costs of asthma. We sought to provide the first UK-wide estimates of the epidemiology, healthcare utilisation and costs of asthma. 

Methods: We obtained and analysed asthma-relevant data from 27 datasets: these comprised national health surveys for 2010-11, and routine administrative, health and social care datasets for 2011-12; 2011-12 costs were estimated in pounds sterling using economic modelling. 

Results: The prevalence of asthma depended on the definition and data source used. The UK lifetime prevalence of patient-reported symptoms suggestive of asthma was 29.5 % (95 % CI, 27.7-31.3; n = 18.5 million (m) people) and 15.6 % (14.3-16.9, n = 9.8 m) for patient-reported clinician-diagnosed asthma. The annual prevalence of patient-reported clinician-diagnosed-and-treated asthma was 9.6 % (8.9-10.3, n = 6.0 m) and of clinician-reported, diagnosed-and-treated asthma 5.7 % (5.7-5.7; n = 3.6 m). Asthma resulted in at least 6.3 m primary care consultations, 93,000 hospital in-patient episodes, 1800 intensive-care unit episodes and 36,800 disability living allowance claims. The costs of asthma were estimated at least £1.1 billion: 74 % of these costs were for provision of primary care services (60 % prescribing, 14 % consultations), 13 % for disability claims, and 12 % for hospital care. There were 1160 asthma deaths. 

Conclusions: Asthma is very common and is responsible for considerable morbidity, healthcare utilisation and financial costs to the UK public sector. Greater policy focus on primary care provision is needed to reduce the risk of asthma exacerbations, hospitalisations and deaths, and reduce costs.

Protecting databases from schema disclosure: a CRUD-based protection model

Database schemas, in many organizations, are considered one of the critical assets to be protected. From database schemas, it is not only possible to infer the information being collected but also the way organizations manage their businesses and/or activities. One of the ways to disclose database schemas is through the Create, Read, Update and Delete (CRUD) expressions. In fact, their use can follow strict security rules or be unregulated by malicious users. In the first case, users are required to master database schemas. This can be critical when applications that access the database directly, which we call database interface applications (DIA), are developed by third party organizations via outsourcing. In the second case, users can disclose partially or totally database schemas following malicious algorithms based on CRUD expressions. To overcome this vulnerability, we propose a new technique where CRUD expressions cannot be directly manipulated by DIAs any more. Whenever a DIA starts-up, the associated database server generates a random codified token for each CRUD expression and sends it to the DIA that the database servers can use to execute the correspondent CRUD expression. In order to validate our proposal, we present a conceptual architectural model and a proof of concept.

Information Analysis and Databases

Means to automate the fact replace the man in their job functions for a man and machines automatic mechanism, ie documentary specialists in computer and computers are the cornerstone of any modern system of documentation and information. From this point of view immediately raises the problem of deciding what resources should be applied to solve the specific problem in each specific case. We will not let alone to propose quick fixes or recipes in order to decide what to do in any case. The solution depends on repeat for each particular problem. What we want is to move some points that can serve as a basis for reflection to help find the best solution possible, once the problem is defined correctly. The first thing to do before starting any automated system project is to define exactly the domain you want to cover and assess with greater precision possible importance.

An investigation of imputation methods for discrete databases and multi-variate time series

When it comes to information sets in real life, often pieces of the whole set may not be available. This problem can find its origin in various reasons, describing therefore different patterns. In the literature, this problem is known as Missing Data. This issue can be fixed in various ways, from not taking into consideration incomplete observations, to guessing what those values originally were, or just ignoring the fact that some values are missing. The methods used to estimate missing data are called Imputation Methods. The work presented in this thesis has two main goals. The first one is to determine whether any kind of interactions exists between Missing Data, Imputation Methods and Supervised Classification algorithms, when they are applied together. For this first problem we consider a scenario in which the databases used are discrete, understanding discrete as that it is assumed that there is no relation between observations. These datasets underwent processes involving different combina- tions of the three components mentioned. The outcome showed that the missing data pattern strongly influences the outcome produced by a classifier. Also, in some of the cases, the complex imputation techniques investigated in the thesis were able to obtain better results than simple ones. The second goal of this work is to propose a new imputation strategy, but this time we constrain the specifications of the previous problem to a special kind of datasets, the multivariate Time Series. We designed new imputation techniques for this particular domain, and combined them with some of the contrasted strategies tested in the pre- vious chapter of this thesis. The time series also were subjected to processes involving missing data and imputation to finally propose an overall better imputation method. In the final chapter of this work, a real-world example is presented, describing a wa- ter quality prediction problem. The databases that characterized this problem had their own original latent values, which provides a real-world benchmark to test the algorithms developed in this thesis.

Mixed Spatial and Nonspatial Problems in Location Based Services

With hundreds of millions of users reporting locations and embracing mobile technologies, Location Based Services (LBSs) are raising new challenges. In this dissertation, we address three emerging problems in location services, where geolocation data plays a central role. First, to handle the unprecedented growth of generated geolocation data, existing location services rely on geospatial database systems. However, their inability to leverage combined geographical and textual information in analytical queries (e.g. spatial similarity joins) remains an open problem. To address this, we introduce SpsJoin, a framework for computing spatial set-similarity joins. SpsJoin handles combined similarity queries that involve textual and spatial constraints simultaneously. LBSs use this system to tackle different types of problems, such as deduplication, geolocation enhancement and record linkage. We define the spatial set-similarity join problem in a general case and propose an algorithm for its efficient computation. Our solution utilizes parallel computing with MapReduce to handle scalability issues in large geospatial databases. Second, applications that use geolocation data are seldom concerned with ensuring the privacy of participating users. To motivate participation and address privacy concerns, we propose iSafe, a privacy preserving algorithm for computing safety snapshots of co-located mobile devices as well as geosocial network users. iSafe combines geolocation data extracted from crime datasets and geosocial networks such as Yelp. In order to enhance iSafe's ability to compute safety recommendations, even when crime information is incomplete or sparse, we need to identify relationships between Yelp venues and crime indices at their locations. To achieve this, we use SpsJoin on two datasets (Yelp venues and geolocated businesses) to find venues that have not been reviewed and to further compute the crime indices of their locations. Our results show a statistically significant dependence between location crime indices and Yelp features. Third, review centered LBSs (e.g., Yelp) are increasingly becoming targets of malicious campaigns that aim to bias the public image of represented businesses. Although Yelp actively attempts to detect and filter fraudulent reviews, our experiments showed that Yelp is still vulnerable. Fraudulent LBS information also impacts the ability of iSafe to provide correct safety values. We take steps toward addressing this problem by proposing SpiDeR, an algorithm that takes advantage of the richness of information available in Yelp to detect abnormal review patterns. We propose a fake venue detection solution that applies SpsJoin on Yelp and U.S. housing datasets. We validate the proposed solutions using ground truth data extracted by our experiments and reviews filtered by Yelp.

Databases for quantitative history

This paper will propose that, rather than sitting on silos of data, historians that utilise quantitative methods should endeavour to make their data accessible through databases, and treat this as a new form of bibliographic entry. Of course in many instances historical data does not lend itself easily to the creation of such data sets. With this in mind some of the issues regarding normalising raw historical data will be looked at with reference to current work on nineteenth century Irish trade. These issues encompass (but are not limited to) measurement systems, geographic locations, and potential problems that may arise in attempting to unify disaggregated sources. It will discuss the need for a concerted effort by historians to define what is required from digital resources for them to be considered accurate, and to what extent the normalisation requirements for database systems may conflict with the desire for accuracy. Many of the issues that the historian may encounter engaging with databases will be common to all historians, and there would be merit in having defined standards for referencing items, such as people, places, locations, and measurements.

A multiagent based strategy for detecting attacks in databases in a distributed mode

This paper presents a distributed hierarchical multiagent architecture for detecting SQL injection attacks against databases. It uses a novel strategy, which is supported by a Case-Based Reasoning mechanism, which provides to the classifier agents with a great capacity of learning and adaptation to face this type of attack. The architecture combines strategies of intrusion detection systems such as misuse detection and anomaly detection. It has been tested and the results are presented in this paper.

Advancing Bag-of-visual-words Representations For Lesion Classification In Retinal Images.

Diabetic Retinopathy (DR) is a complication of diabetes that can lead to blindness if not readily discovered. Automated screening algorithms have the potential to improve identification of patients who need further medical attention. However, the identification of lesions must be accurate to be useful for clinical application. The bag-of-visual-words (BoVW) algorithm employs a maximum-margin classifier in a flexible framework that is able to detect the most common DR-related lesions such as microaneurysms, cotton-wool spots and hard exudates. BoVW allows to bypass the need for pre- and post-processing of the retinographic images, as well as the need of specific ad hoc techniques for identification of each type of lesion. An extensive evaluation of the BoVW model, using three large retinograph datasets (DR1, DR2 and Messidor) with different resolution and collected by different healthcare personnel, was performed. The results demonstrate that the BoVW classification approach can identify different lesions within an image without having to utilize different algorithms for each lesion reducing processing time and providing a more flexible diagnostic system. Our BoVW scheme is based on sparse low-level feature detection with a Speeded-Up Robust Features (SURF) local descriptor, and mid-level features based on semi-soft coding with max pooling. The best BoVW representation for retinal image classification was an area under the receiver operating characteristic curve (AUC-ROC) of 97.8% (exudates) and 93.5% (red lesions), applying a cross-dataset validation protocol. To assess the accuracy for detecting cases that require referral within one year, the sparse extraction technique associated with semi-soft coding and max pooling obtained an AUC of 94.2 ± 2.0%, outperforming current methods. Those results indicate that, for retinal image classification tasks in clinical practice, BoVW is equal and, in some instances, surpasses results obtained using dense detection (widely believed to be the best choice in many vision problems) for the low-level descriptors.

Growth Curves For Girls With Turner Syndrome.

The objective of this study was to review the growth curves for Turner syndrome, evaluate the methodological and statistical quality, and suggest potential growth curves for clinical practice guidelines. The search was carried out in the databases Medline and Embase. Of 1006 references identified, 15 were included. Studies constructed curves for weight, height, weight/height, body mass index, head circumference, height velocity, leg length, and sitting height. The sample ranged between 47 and 1,565 (total = 6,273) girls aged 0 to 24 y, born between 1950 and 2006. The number of measures ranged from 580 to 9,011 (total = 28,915). Most studies showed strengths such as sample size, exclusion of the use of growth hormone and androgen, and analysis of confounding variables. However, the growth curves were restricted to height, lack of information about selection bias, limited distributional properties, and smoothing aspects. In conclusion, we observe the need to construct an international growth reference for girls with Turner syndrome, in order to provide support for clinical practice guidelines.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.