Quick Navigation Research Articles

An effective Key Frame Extraction technique based on Feature Fusion and Fuzzy-C means clustering with Artificial Hummingbird

Key frame extraction is very important in video summarization and content-based video analysis to address the problem of data redundancy in a video. Key frame extraction enables quick navigation and expert video arrangement in many applications. The visually impaired can benefit from the use of key frame extraction for rapid object recognition and tracking. Most key frame extraction techniques consider only a single visual feature instead of multiple features or full pictorial information of the video. This study proposes a key frame extraction method from a video that (i) first removes insignificant frames by pre-processing, (ii) second, four visual and structural feature differences among the consecutive frames are extracted and aggregated to identify informative frames, (iii) third, to cluster the obtained frames, a hybrid FCM-AHA method is proposed by combining Fuzzy C-means(FCM) with artificial hummingbird optimization algorithm (AHA) to circumvent the local minima trapping problem of FCM, and finally, from each cluster, the two frames having greatest Euclidean distance from all the other frames within a cluster is selected as key frames to remove redundant frames. Experimental results on the Open video and YouTube datasets show that the suggested method outperforms state-of-the-art methods both in terms of subjective qualitative analysis and objective quantitative evaluation, e.g., Precision, Recall, and F-score. Further, results are also taken on real video to demonstrate its applicability in real-life applications.

Practical guideline on obesity care in patients with gastrointestinal and liver diseases – Joint ESPEN/UEG guideline

Patients with chronic gastrointestinal disease such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), celiac disease, gastroesophageal reflux disease (GERD), pancreatitis, and chronic liver disease (CLD) often suffer from obesity because of coincidence (IBD, IBS, celiac disease) or related pathophysiology (GERD, pancreatitis and CLD). It is unclear if such patients need a particular diagnostic and treatment that differs from the needs of lean gastrointestinal patients. The present guideline addresses this question according to current knowledge and evidence. The present practical guideline is intended for clinicians and practitioners in general medicine, gastroenterology, surgery and other obesity management, including dietitians and focuses on obesity care in patients with chronic gastrointestinal diseases. The present practical guideline is the shortened version of a previously published scientific guideline developed according to the standard operating procedure for ESPEN guidelines. The content has been re-structured and transformed into flow-charts that allow a quick navigation through the text. In 100 recommendations (3× A, 33× B, 24×0, 40× GPP, all with a consensus grade of 90% or more) care of gastrointestinal patients with obesity - including sarcopenic obesity - is addressed in a multidisciplinary way. A particular emphasis is on CLD, especially metabolic associated liver disease, since such diseases are closely related to obesity, whereas liver cirrhosis is rather associated with sarcopenic obesity. A special chapter is dedicated to obesity care in patients undergoing bariatric surgery. The guideline focuses on adults, not on children, for whom data are scarce. Whether some of the recommendations apply to children must be left to the judgment of the experienced pediatrician. The present practical guideline offers in a condensed way evidence-based advice how to care for patients with chronic gastrointestinal diseases and concomitant obesity, an increasingly frequent constellation in clinical practice.

New concept in neurovascular navigation: technical description and preclinical experience with the Bendit 17 and Bendit 21 microcatheters in a rabbit aneurysm model

BackgroundEndovascular treatment of intracranial vascular diseases, such as aneurysms, is often challenged by unfavorable vascular anatomy. The Bendit Steerable Microcatheter (Bendit Technologies, Tel Aviv, Israel) has bending and torqueing capabilities...

Robust algorithmic binding to arbitrary fragment of program code

When solving a task, a programmer actively interacts with a finite set of code fragments. The information about their locations is important for quick navigation, for other developers, and as a kind of documentation. Integrated development environments (IDEs) provide tools for marking code fragments with labels, displaying lists of labels, and using these labels for quick navigation. However, they often lose the correspondence between the label and the marked place when the code is edited, in particular when changes are made outside the IDE. In previous works, the authors propose a tool to be integrated into various IDEs for “binding” to large syntactic entities of a program and building a markup that is robust to code editing. The description of the marked element is built on the basis of the abstract syntax tree (AST) of the program. Later it is used to algorithmically search for the element in an edited code. The search has a success rate from 99 to 100%. This article aims at robust algorithmic binding to an arbitrary section of the code. For binding to a single-line code fragment, we propose an extension of the model describing the marked fragment, and an additional search algorithm. We also propose an algorithm for embedding nodes corresponding to multi-line fragments in an AST. We show that the correctness of the AST is not violated by these embeddings. Bindings to randomly selected lines were made in the code of three large C# projects. Manual check of these lines search results in the edited code has confirmed that the bindings are robust to code editing.

Sonic Visualiser: Visualisation, Analysis, and Annotation of Music Audio Recordings

Sonic Visualiser: Visualisation, Analysis, and Annotation of Music Audio Recordings

COVIDium: a COVID-19 resource compendium.

The severe acute respiratory syndrome coronavirus 2 that causes coronavirus disease 2019 (COVID-19) disrupted the normal functioning throughout the world since early 2020 and it continues to do so. Nonetheless, the global pandemic was taken up as a challenge by researchers across the globe to discover an effective cure, either in the form of a drug or vaccine. This resulted in an unprecedented surge of experimental and computational data and publications, which often translated their findings in the form of databases (DBs) and tools. Over 160 such DBs and more than 80 software tools were developed, which are uncharacterized, unannotated, deployed at different universal resource locators and are challenging to reach out through a normal web search. Besides, most of the DBs/tools are present on preprints and are either underutilized or unrecognized because of their inability to make it to top Google search hits. Henceforth, there was a need to crawl and characterize these DBs and create a compendium for easy referencing. The current article is one such concerted effort in this direction to create a COVID-19 resource compendium (COVIDium) that would facilitate the researchers to find suitable DBs and tools for their research studies. COVIDium tries to classify the DBs and tools into 11 broad categories for quick navigation. It also provides end-users some generic hit terms to filter the DB entries for quick access to the resources. Additionally, the DB provides Tracker Dashboard, Neuro Resources, references to COVID-19 datasets and protein–protein interactions. This compendium will be periodically updated to accommodate new resources. Database URL: The COVIDium is accessible through http://kraza.in/covidium/

Exploiting Social Networks as a Live Mass Media Channel During Disasters for Reactions

Social networks, e.g. Twitter, have been proved to be almost real-time systems for spreading information, that provide a valuable information channel in emergencies, e.g. disasters. This paper presents a framework designed to distill actionable tweets. The framework tackles the diversity, large volume, and noise of tweets for providing users live information for quick responses. To do that, our framework first retrieves a large number of tweets to ensure the diversity. It next removes irrelevant and indirect tweets for reducing the volume, divides informative tweets into predefined classes for quick navigation, and groups tweets in a class into topics to preserve the diversity. Finally, it ranks tweets in each topic to extract important tweets for the user’s quick scan. For ranking, the framework utilizes event extraction to enrich the semantics and reduce the noise of tweets. After that, the framework builds event graphs for ranking to find out important tweets. To validate the efficiency of our framework, we took Twitter as a case study. Experimental results on five disaster datasets show that our framework achieves promising results compared to strong methods in disaster scenarios.

#59: Launching a Network-based Platform for Clinical Case Discussions of Infections in Immunocompromised Pediatric Patients Worldwide

BackgroundInfectious in pediatric patients with cancer are common and can be life-threatening. Understanding risks for infections, mechanisms of progression, and diagnostic and therapeutic interventions is essential for quality care. Clinical guidance emerges frequently from high-income countries and dissemination of information using traditional methods takes time to reach resource-limited settings. By using case-based learning (CBL) strategies, we sought to expedite this process to improve practices worldwide. We report the implementation of a network-based platform for discussion of infections in the immunocompromised child in resource-limited settings and the potential for dynamic sharing of best care practices.MethodsUsing a virtual meeting platform, we established a weekly appointment and invited members of our regional networks, mainly comprising pediatricians with training / interest in infection care and prevention who care for children with cancer. We solicited cases for discussion by providing an electronic case submission form, a presentation template, a presentation checklist, and a protected health information reminder sheet. Materials were prepared in Spanish and English, launching initially in Spanish (October 2019), then expanding to English (September 2020) alternating between Spanish and English-led discussions. Based on the case of the week, a panel of experts, worldwide infectious disease experts, provided recommendations for care based on published evidence, standardized guidelines, and best practices. Detailed written summaries were captured and shared with case submitters. We recorded attendance and evaluated participant satisfaction and the use of discussed information. Additional CBL materials were developed post-launch to support and expand CBL beyond the live meeting sessions.ResultsFrom October 2019 to December 2020, we hosted 45 online meetings with clinical cases presented from 15 countries and 23 institutions across the globe. We have had a total of 1054 attendees, with an average of 28 participants per live meeting. Discussions included complications grouped by viral, fungal, and mycobacterial infection. A quarterly survey revealed that participants found the case discussions most beneficial for reviewing recent literature and learning practices from invited guest experts. Most respondents have very often or always adopted the recommendations discussed during online meetings for the management of patients locally. Additional materials include: a protected virtual community space for storing all CBL materials and promoting continued participant engagement; a growing index of infections with prepared PubMed searches for quick and easy navigation to peer-reviewed literature (n=9); and, written case summary reports, indexed by infection, made available to all audience members for reference (5=in draft, 12=published). During the first part of the COVID-19 pandemic, we incorporated a journal club structure to discuss emerging literature on the virus, and specifically the implications for children with / without cancer. Participants indicated that COVID-19 activities were extremely useful for discussing and digesting the rapidly evolving scientific literature for SARS-CoV-2 and being able to apply lessons learned in real-time.ConclusionsA virtual platform for CBL provides a critical resource that expedites information-sharing and can potentially improve patient care by expanding access to expertise and experience for best care practices beyond geographic boundaries.

Exploring interaction techniques for 360 panoramas inside a 3D reconstructed scene for mixed reality remote collaboration

Remote collaboration using mixed reality (MR) enables two separated workers to collaborate by sharing visual cues. A local worker can share his/her environment to the remote worker for a better contextual understanding. However, prior techniques were using either 360 video sharing or a complicated 3D reconstruction configuration. This limits the interactivity and practicality of the system. In this paper we show an interactive and easy-to-configure MR remote collaboration technique enabling a local worker to easily share his/her environment by integrating 360 panorama images into a low-cost 3D reconstructed scene as photo-bubbles and projective textures. This enables the remote worker to visit past scenes on either an immersive 360 panoramic scenery, or an interactive 3D environment. We developed a prototype and conducted a user study comparing the two modes of how 360 panorama images could be used in a remote collaboration system. Results suggested that both photo-bubbles and projective textures can provide high social presence, co-presence and low cognitive load for solving tasks while each have its advantage and limitations. For example, photo-bubbles are good for a quick navigation inside the 3D environment without depth perception while projective textures are good for spatial understanding but require physical efforts.

CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances.

In recent years, the ability to generate genomic data has increased dramatically along with the demand for easily personalized and customizable genome browsers for effective visualization of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provides means for creating multiple visualization instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customizable web application for interactive visualization of genomic data. Once deployed, CRAMER supports seamless creation of multiple visualization instances in parallel while allowing users to control and customize multiple tracks. The application is deployed on a Node.js server and is supported by a MongoDB database which stored all customizations made by the users allowing quick navigation between instances. Currently, the browser supports visualizing a large number of file formats for genome annotation, variant calling, reads coverage and gene expression. Additionally, the browser supports direct Javascript coding for personalized tracks, providing a whole new level of customization both functionally and visually. Tracks can be added via direct file upload or processed in real-time via links to files stored remotely on an FTP repository. Furthermore, additional tracks can be added by users via simple drag and drop to an existing visualization instance. CRAMER is implemented in JavaScript and is publicly available on GitHub on https://github.com/FadyMohareb/cramer. The application is released under an MIT licence and can be deployed on any server running Linux or Mac OS. f.mohareb@cranfield.ac.uk. Supplementary data are available at Bioinformatics online.

CHRONOscope: Application for the Interactive Visualization of Carbon-14 and Beryllium-10 Atmospheric data

ABSTRACTInformation about the global climate, the carbon cycle, changes in solar activity, and a number of other atmospheric processes are preserved in the carbon-14 and the beryllium-10 records. However, these isotope datasets are large and cumbersome to work with. We have designed a self-contained, easy-to-use application that allows for more efficient analysis of different periods and patterns of interest. For several applications in atmospheric modelling, a pre-processing stage is applied to the isotope datasets in order to interpolate the data and mitigate their low temporal resolution. In CHRONOscope, we included linear and non-linear methods of interpolation with interactive parameter optimization. The resultant interpolated data can be extracted for further use. The main functionalities of CHRONOscope include the importation and superimposition of external data, quick navigation through the data with the use of markers, expression of the carbon-14 results in both Δ14C and yr BP form, separation of the data by source, and the visualization of associated error bars. We make this free software available in standalone applications for both Windows and Mac operating systems.

Abstract 2490: R2: Genomics analysis and visualization platform

Abstract Given the complexity, omics data like RNA-seq are often analyzed by bioinformaticians, and not the wetlab researchers that performed the experiments. With the biomedical researcher (with limited or no bioinformatics skills) in mind as the end-user, we developed the user-friendly, publicly accessible R2 platform (http://r2.amc.nl), enabling biomedical scientists to work with their own data from anywhere at any time. R2 (cited in >850 peer-reviewed scientific publications) consists of an omics database, coupled to an extensive set of interactive tools to analyze/visualize the datasets. Interactive analyses within the software are highly connected, allowing quick navigation between various aspects of the datamining process. Besides password protected private data, R2 also contains an extensive body of publicly available omics data, enabling users to relate their findings to other diseases / tissues, or as validation in integrative analyses. Next to gene expression (bulk as well as single cell), R2 is also being employed for the integration, analysis and visualization of copynumber, SNP, methylation, miRNA, drug response, ChIP-seq, and NGS exome/WGS DNA sequencing data. Analyses include correlation, differential expression, gene sets, gene ontology, transcription factor binding sites, tSNE, PCA, k-means, Kaplan Meier survival scans, signature creation etc. Visualizations include various gene oriented plots, heatmaps, Circos plots, embedded genome browser, Venn diagrams, etc. The real power of the platform lies in the chaining of results of analyses; e.g. the results of a differential expression analysis can be further trimmed down using a Kaplan Meier analysis that in turn can be used for a Gene Ontology over-representation analysis. Furthermore, the webserver allows for overviews across different datasets (such as MegaSampler and 2D distribution), where a user can harness the power of thousands of measurements. Recently, integrated analyses for personalized medicine, where copy number, mRNA expression, methylation and mutation data are combined into a comprehensive overview, occasionally supplemented with PDX/organoid drug response data. These serve clinical decision making for a patient, but as growing cohorts also form a treasure trove for scientific discovery. R2 provides a central starting point from where data mining and analysis paths can be followed within one environment. Data/analyses can be shared between R2-users via our community options, making R2 an outstanding environment for discovery, hypothesis testing and scientific collaboration. Citation Format: Jan Koster, Richard Volckmann, Danny Zwijnenburg, Piet Molenaar, Rogier Versteeg. R2: Genomics analysis and visualization platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2490.

Advanced Optical Materials : Shedding Light on Excellent Research for 5 Years

<i>Advanced Optical Materials</i> : Shedding Light on Excellent Research for 5 Years

Online validity and accuracy of references within drug promotion materials in orthopaedic out-patient department

Background - In the era of evidence based medicine, correct and relevant information should accompany any broadcast of pharmaceutical related knowledge. A substandard piece of information has potential for negative impact on care-giver and patient at large. The claims about any pharmaceutical agent with respect to its action, complications or superiority over other ones should be based on strong level of evidence for better knowledge that is aimed at positive impact on judicious decision making and good outcome of therapy. It is thus important that periodic assessment of claims made by promotional materials should be done to ensure their validity and not rely on marketing noise. A detailed study of drug promotion materials collected in orthopaedic out-patient department within a period of four months (Oct 2015 to Jan 2016) was done with special attention to presence, quality and validity of information or claims made within it. 238 random materials were collected in a defined period, out of which 120 excluded in first and 72 in second evaluation. The remaining 46 materials with 65 references in total were part of study. The references were searched over world wide web for its validity, ease of availability and correctness. Majority (26, 56.52%) of the materials were without proper references. Most of the references were about mechanism of action followed by superiority to other drugs. There was deficiency in the presented references including lack of author name, wrong volume of journal or problem with easy identification over net in most references (32, 49.23%). Pain medication were followed by antibiotics and calcium related agents in number of references present. The wrong referencing and difficult to trace the source were leading problems noted on online assessment. The quality of promotional material should quote well substantiated evidence about mechanism of action, superiority and rationale of its use. The evidence thus garnered should be of highest level or from standard reference text book. The preferable use of digital object identifier (doi) is advisable for better search of the articles to check on internet. For ease of quick navigation through referencing articles use of technology like quick response (QR) codes may be considered in the future.

Automatic annotation of lecture videos for multimedia driven pedagogical platforms

Today’s eLearning websites are heavily loaded with multimedia contents, which are often unstructured, unedited, unsynchronized, and lack inter-links among different multimedia components. Hyperlinking different media modality may provide a solution for quick navigation and easy retrieval of pedagogical content in media driven eLearning websites. In addition, finding meta-data information to describe and annotate media content in eLearning platforms is challenging, laborious, prone to errors, and time-consuming task. Thus annotations for multimedia especially of lecture videos became an important part of video learning objects. To address this issue, this paper proposes three major contributions namely, automated video annotation, the 3-Dimensional (3D) tag clouds, and the hyper interactive presenter (HIP) eLearning platform. Combining existing state-of-the-art SIFT together with tag cloud, a novel approach for automatic lecture video annotation for the HIP is proposed. New video annotations are implemented automatically providing the needed random access in lecture videos within the platform, and a 3D tag cloud is proposed as a new way of user interaction mechanism. A preliminary study of the usefulness of the system has been carried out, and the initial results suggest that 70% of the students opted for using HIP as their preferred eLearning platform at Gjøvik University College (GUC).

Retained PTEN Expression Preferentially Identifies Mismatch Repair-Proficient Breast Cancers

Introduction/ Background Loss of phosphatase and tensin homolog (PTEN) expression and alterations in mismatch repair (MMR) genes are regarded as early oncogenic events in breast cancer. It has recently been hypothesized that the polyadenosine tract in PTEN might be a target for mutation in MMR-deficient endometrial tumors. However, the frequency and significance of MMR alterations in breast cancer is debated, and their relationship with PTEN status has not been investigated in the breast. Aims In this study, we sought to explore the relationships between PTEN expression and MMR alterations and to define whether PTEN immunohistochemistry is a predictor of MMR status in breast cancer. Methods 309 cases, including 261 invasive ductal carcinomas, no special type, 32 invasive lobular carcinomas, and 16 invasive ductal carcinomas, mixed types, carefully characterized from clinical and pathological standpoints, were reviewed and used to construct 11 tissue microarrays (TMAs). For each case, a mean of 4.5 tumor tissue cores (range 3 to 6 cores) was sampled, incorporating distinct topographic areas of the tumor, as well as matched non-neoplastic breast tissue, and, when present, associated in situ carcinoma. Taken together, 1381 spots were generated. Each TMA was subjected to immunohistochemical analysis of PTEN and the DNA MMR proteins MLH1, MSH2, MSH6 and PMS2. In order to allow a quick navigation within each TMA, and to minimize human-related biases, each stained slide was digitalized and blindly analyzed by two pathologists using a dedicated software able to segment TMA cores. The pattern of expression was therefore annotated manually on a digital database using a specific add-on module. Results According to clinicopathologic surrogate definition of intrinsic subtypes, PTEN protein loss was more frequent in luminal A-like and triple negative groups compared to luminal B-like carcinomas, as recently observed in other studies. MMR status in Luminal B-like tumors did not differ significantly between PTEN-retained and PTEN-loss groups, regardless HER2 amplification. In particular, retained PTEN expression was a predictor of MMR proficiency in approximately 35% of cases for this group. However, in luminal A-like and triple negative breast cancer groups, retained positive expression of MMR proteins was observed in 100% of cases showing PTEN wild-type immunohistochemical expression. Discussion: The present study is the first to investigate PTEN protein loss in a large set of breast carcinomas based on DNA MMR status by immunohistochemistry. Our findings broaden the understanding of the biology underpinning breast cancer, suggesting that MMR alterations are likely to be independent of PTEN status in the majority of luminal B-like breast cancers and that, in a way akin to endometrial carcinoma, MMR deficiency could play a part in the development of PTEN alterations in luminal A-like and triple negative breast cancers. The integration of traditional pathology with cutting-edge digital tools allowed a rapid quantification of immunohistochemistry and effective data organization in this wide cohort multi-variable study. Conclusion: PTEN immunohistochemistry is a useful adjunct in the clinical evaluation of breast cancer patients, being able to capture all MMR-proficient luminal A-like and triple negative tumors.

Autonomous Navigation for Micro Aerial Vehicles in Complex GNSS-denied Environments

Micro aerial vehicles, such as multirotors, are particular well suited for the autonomous monitoring, inspection, and surveillance of buildings, e.g., for maintenance in industrial plants. Key prerequisites for the fully autonomous operation of micro aerial vehicles in restricted environments are 3D mapping, real-time pose tracking, obstacle detection, and planning of collision-free trajectories. In this article, we propose a complete navigation system with a multimodal sensor setup for omnidirectional environment perception. Measurements of a 3D laser scanner are aggregated in egocentric local multiresolution grid maps. Local maps are registered and merged to allocentric maps in which the MAV localizes. For autonomous navigation, we generate trajectories in a multi-layered approach: from mission planning over global and local trajectory planning to reactive obstacle avoidance. We evaluate our approach in a GNSS-denied indoor environment where multiple collision hazards require reliable omnidirectional perception and quick navigation reactions.

Black blood late gadolinium enhancement using combined T2 magnetization preparation and inversion recovery

Background Late gadolinium enhancement (LGE) imaging allows assessment of focal scar [1]. An inversion recovery based sequence is commonly used to achieve suppression of healthy myocardium signal. However, the blood pool and subendocardial scar typically have similar signal, making it difficult to distinguish subendocardial scar. Several methods have been proposed to increase the blood-scar contrast including a double inversion technique [2], and T2-prepared (T2prep) sequences [3,4]. However, all these approaches suffer from either reduced SNR or reduced scar-myocardium contrast. In this work, we propose a novel pulse sequence that uses an optimized combination of an inversion pulse and a T2prep composite pulse to simultaneously null both the healthy myocardium and blood signals, producing a black-blood LGE (BB-LGE) image without losing significant scar-myocardium contrast. We also developed a quick navigation sequence, analogous to the Look-Locker, to help determine the ideal nulling time before imaging.

Cultivating travellers' revisit intention to e-tourism service: the moderating effect of website interactivity

The research goals of this study were to investigate how the design and service quality of the website of the public sectors affect tourists' satisfaction and continued usage intention. We collected a sample of tourists, using a survey questionnaire, and we tested the model and hypotheses using a structural equation modelling approach. E-tourism websites have unique interactive and multimedia qualities with the potential to create experiences similar to a product trial. In total, invitation messages were mailed to 2000 members of the Taiwanese backpackers' forum, of which 256 were returned completed. The findings of this study indicate that the mission of excellence in travel services will be an important strategy in e-tourism website design; an e-tourism website that allows quick navigation is likely to attract travellers. Moreover, it is important that governments adopt a knowledge-sharing culture in their relationship strategy by developing a competence for building long-term relationships with tourists.

Abstract 2334: Identification of differentially expressed genes and somatic mutations in esophageal adenocarinoma cancer patients

Abstract High throughput sequencing technologies are currently revolutionizing the cancer research area with rapid improvements in sequencing capacity and time consumption. As a result the most time consuming step has moved from being the sequencing process itself to being the bioinformatic data analysis. RNA sequencing (RNA-Seq) is used in an increasing number of transcriptomic studies. The great advantage of using RNA-Seq is its ability to precisely quantify transcript levels and identify novel transcripts, isoforms, and splice junctions, while further providing information of the mutational landscape down to single base resolution. To ease the hurdles associated with RNA-Seq data analysis there is an increasing demand for tools that are specifically tailored to RNA-Seq data. Here we describe how the newly developed CLC Cancer Research Workbench can be used to analyze and visualize RNA-Seq data with ready-to-use workflows that automatically map, quantify, and annotate transcriptomes. We identify differentially expressed genes and transcripts in Illumina HiSeq transcriptomic data from matched tumor and normal samples from four esophageal adenocarinoma cancer patients, and compare the mutational patterns in the samples with the expression values of the corresponding genes. Results are visualized in a track based genome browser view, which provides the means for quick and easy navigation as well as allowing the user to simultaneously view and annotate multiple samples and different data types (e.g. genes, transcript expression levels, and detected variants). Citation Format: Bodil Oster, Anika Joecker, Anne-Mette K. Hein, Patrick Dekker, Robert O'Neill, Adam Krejci, Anne Arens, Naomi Thomson, Cecilie Boysen, Søren Mønsted, Roald Forsberg, Bjarne Knudsen, Thomas Knudsen, Richard Lussier, Ted R. Hupp. Identification of differentially expressed genes and somatic mutations in esophageal adenocarinoma cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2334. doi:10.1158/1538-7445.AM2014-2334