REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes

Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of experimental protein synthesis evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation (https://github.com/Biobix/ REPARATION). REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs and >70% of all (variants of) annotated protein coding ORFs were predicted by REPARATION to be translated. Our predictions are supported by matching mass spectrometry proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to intrinsically perform a de novo ORF delineation in bacterial genomes irrespective of the sequence features linked to open reading frames

Semantic user profiling techniques for personalised multimedia recommendation

Due to the explosion of news materials available through broadcast and other channels, there is an increasing need for personalised news video retrieval. In this work, we introduce a semantic-based user modelling technique to capture users’ evolving information needs. Our approach exploits implicit user interaction to capture long-term user interests in a profile. The organised interests are used to retrieve and recommend news stories to the users. In this paper, we exploit the Linked Open Data Cloud to identify similar news stories that match the users’ interest. We evaluate various recommendation parameters by introducing a simulation-based evaluation scheme

Interoperability in IoT through the semantic profiling of objects

The emergence of smarter and broader people-oriented IoT applications and services requires interoperability at both data and knowledge levels. However, although some semantic IoT architectures have been proposed, achieving a high degree of interoperability requires dealing with a sea of non-integrated data, scattered across vertical silos. Also, these architectures do not fit into the machine-to-machine requirements, as data annotation has no knowledge on object interactions behind arriving data. This paper presents a vision of how to overcome these issues. More specifically, the semantic profiling of objects, through CoRE related standards, is envisaged as the key for data integration, allowing more powerful data annotation, validation, and reasoning. These are the key blocks for the development of intelligent applications.Portuguese Science and Technology Foundation (FCT) [UID/MULTI/00631/2013

Finding co-solvers on Twitter, with a little help from Linked Data

In this paper we propose a method for suggesting potential collaborators for solving innovation challenges online, based on their competence, similarity of interests and social proximity with the user. We rely on Linked Data to derive a measure of semantic relatedness that we use to enrich both user profiles and innovation problems with additional relevant topics, thereby improving the performance of co-solver recommendation. We evaluate this approach against state of the art methods for query enrichment based on the distribution of topics in user profiles, and demonstrate its usefulness in recommending collaborators that are both complementary in competence and compatible with the user. Our experiments are grounded using data from the social networking service Twitter.com

Semantic data mining and linked data for a recommender system in the AEC industry

Even though it can provide design teams with valuable performance insights and enhance decision-making, monitored building data is rarely reused in an effective feedback loop from operation to design. Data mining allows users to obtain such insights from the large datasets generated throughout the building life cycle. Furthermore, semantic web technologies allow to formally represent the built environment and retrieve knowledge in response to domain-specific requirements. Both approaches have independently established themselves as powerful aids in decision-making. Combining them can enrich data mining processes with domain knowledge and facilitate knowledge discovery, representation and reuse. In this article, we look into the available data mining techniques and investigate to what extent they can be fused with semantic web technologies to provide recommendations to the end user in performance-oriented design. We demonstrate an initial implementation of a linked data-based system for generation of recommendations

Capturing the Visitor Profile for a Personalized Mobile Museum Experience: an Indirect Approach

An increasing number of museums and cultural institutions around the world use personalized, mostly mobile, museum guides to enhance visitor experiences. However since a typical museum visit may last a few minutes and visitors might only visit once, the personalization processes need to be quick and efficient, ensuring the engagement of the visitor. In this paper we investigate the use of indirect profiling methods through a visitor quiz, in order to provide the visitor with specific museum content. Building on our experience of a first study aimed at the design, implementation and user testing of a short quiz version at the Acropolis Museum, a second parallel study was devised. This paper introduces this research, which collected and analyzed data from two environments: the Acropolis Museum and social media (i.e. Facebook). Key profiling issues are identified, results are presented, and guidelines towards a generalized approach for the profiling needs of cultural institutions are discussed

Blood-based bioenergetic profiling is related to differences in brain morphology in African Americans with Type 2 diabetes.

Blood-based bioenergetic profiling has promising applications as a minimally invasive biomarker of systemic bioenergetic capacity. In the present study, we examined peripheral blood mononuclear cell (PBMC) mitochondrial function and brain morphology in a cohort of African Americans with long-standing Type 2 diabetes. Key parameters of PBMC respiration were correlated with white matter, gray matter, and total intracranial volumes. Our analyses indicate that these relationships are primarily driven by the relationship of systemic bioenergetic capacity with total intracranial volume, suggesting that systemic differences in mitochondrial function may play a role in overall brain morphology

All about that - a URI profiling tool for monitoring and preserving linked data

All About That (AAT) is a URI Profiling tool which allows users to monitor and preserve Linked Data in which they are interested. Its design is based upon the principle of adapting ideas from hypermedia link integrity in order to apply them to the Semantic Web. As the Linked Data Web expands it will become increasingly important to maintain links such that the data remains useful and therefore this tool is presented as a step towards providing this maintenance capability

Computerized crime linkage systems: A critical review and research agenda

Computerized crime linkage systems are meant to assist the police in determining whether crimes have been committed by the same offender. In this article, the authors assess these systems critically and identify four assumptions that affect the effectiveness of these systems. These assumptions are that (a) data in the systems can be coded reliably, (b) data in the systems are accurate, (c) violent serial offenders exhibit consistent but distinctive patterns of behavior, and (d) analysts have the ability to use the data in the systems to link crimes accurately. The authors argue that there is no compelling empirical support for any of the four assumptions, and they outline a research agenda for testing each assumption. Until evidence supporting these assumptions becomes available, the value of linkage systems will remain open to debate