Abstract
Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Abstract
The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila), a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.

Abstract
S-RNase-based gametophytic self-incompatibility evolved once before the split of the Asteridae and Rosidae. In Prunus (tribe Amygdaloideae of Rosaceae), the self-incompatibility S-pollen is a single F-box gene that presents the expected evolutionary signatures. In Malus and Pyrus (subtribe Pyrinae of Rosaceae), however, clusters of F-box genes (called SFBBs) have been described that are expressed in pollen only and are linked to the S-RNase gene. Although polymorphic, SFBB genes present levels of diversity lower than those of the S-RNase gene. They have been suggested as putative S-pollen genes, in a system of non-self recognition by multiple factors. Subsets of allelic products of the different SFBB genes interact with non-self S-RNases, marking them for degradation, and allowing compatible pollinations. This study performed a detailed characterization of SFBB genes in Sorbus aucuparia (Pyrinae) to address three predictions of the non-self recognition by multiple factors model. As predicted, the number of SFBB genes was large to account for the many S-RNase specificities. Secondly, like the S-RNase gene, the SFBB genes were old. Thirdly, amino acids under positive selectionuthose that could be involved in specificity determinationuwere identified when intra-haplotype SFBB genes were analysed using codon models. Overall, the findings reported here support the non-self recognition by multiple factors model.

Abstract
Patients' privacy is critical in healthcare but users of Electronic Health Records (EHR) frequently circumvent existing security rules to perform their daily work. Users are so-called the weakest link in security but they are, many times, part of the solution when they are involved in systems' design. In the healthcare domain, the focus is to treat patients (many times with scarce technological, time and human resources) and not to secure their information. Therefore, security must not interfere with this process but be present, nevertheless. Security usability issues must also be met with interdisciplinary knowledge from human-computer-interaction, social sciences and psychology. The main goal of this paper is to raise security and usability awareness with the analysis of users' interaction logs of a BreakTheGlass (BTG) feature. This feature is used to restrict access to patient reports to a group of healthcare professionals within an EHR but also permit access control override in emergency and/or unexpected situations. The analysis of BTG user interaction logs allows, in a short time span and transparently to the user, revealing security and usability problems. This log analysis permits a better choice of methodologies to further apply in the investigation and resolution of the encountered problems.

Abstract
The goal of the OPTIM project is to optimize the graphical user interface of an electronic health record (EHR) by predicting clinical documents' relevance and provide a ranked list of relevant documents for the given user at a certain time. This paper describes the architecture of the relevance assignment and ranking prototype and some implementation issues. The prototype's design is based on two components: OPTIM Core, with logical representation, estimation server's integration and the webservice layer, and the OPTIM WebUI, with the user interface for presenting the results. The prototype was tested in integration with an EHR using a simulated environment. The results were encouraging but yet they revealed a certain lack of security (confidentiality). It has now the capacity of rating 10 documents per second. Nonetheless, the integration of features such as rating clinical relevance based on mathematical models can be included in existing EHR potentially improving their usability.

Abstract
Traditional follow-up of patients with cardiovascular devices is still an activity that, in addition to serving an increasing population, requires a considerable amount of time and specialized human and technical resources. Our aim was to evaluate the applicability of the CareLink (R) (Medtronic, Minneapolis, MN) remote monitoring system as a complementary option to the follow-up of patients with implanted devices, between in-office visits. Evaluated outcomes included both clinical (event detection and time to diagnosis) and nonclinical (patient's satisfaction and economic costs) aspects. An observational, longitudinal, prospective study was conducted with patients from a Portuguese central hospital sampled by convenience during 1 week (43 patients). Data were collected in four moments: two in-office visits and two remote evaluations, reproducing 1 year of clinical follow-up. Data sources included health records, implant reports, initial demographic data collection, follow-up printouts, and a questionnaire. After selection criteria were verified, 15 patients (11 men [73%]) were included, 63.4 +/- 10.8 years old, re-presenting 14.0 +/- 6.3 implant months. Clinically, 15 events were detected (9 by remote monitoring and 6 by patient-initiated activation), of which only 9 were symptomatic. We verified that remote monitoring could detect both symptomatic and asymptomatic events, whereas patient-initiated activation only detected symptomatic ones (p = 0.028). Moreover, the mean diagnosis anticipation in patients with events was approximately 58 days (p < 0.001). In nonclinical terms, we observed high or very high satisfaction (67% and 33%, respectively) with using remote monitoring technology, but still 8 patients (53%) stated they preferred in-office visits. Finally, the introduction of remote monitoring technology has the ability to reduce total follow-up costs for patients by 25%. We conclude that the use of this system constitutes a viable complementary option to the follow-up of patients with implantable devices, between in-office visits.