The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

Automated integration of real-time and non-real-time defense systems

Various application domains require the integration of distributed real-time or near-real-time systems with non-real-time systems. Smart cities, smart homes, ambient intelligent systems, or network-centric defense systems are among these application domains. Data Distribution Service (DDS) is a communi-cation mechanism based on Data-Centric Publish-Subscribe (DCPS) model. It is used for distributed systems with real-time operational constraints. Java Message Service (JMS) is a messaging standard for enterprise systems using Service Oriented Architecture (SOA) for non-real-time operations. JMS allows Java programs to exchange messages in a loosely coupled fashion. JMS also supports sending and receiving messages using a messaging queue and a publish-subscribe interface. In this article, we pro -pose an architecture enabling the automated integration of distributed real-time and non-real-time systems. We test our proposed architecture using a distributed Command, Control, Communications, Computers, and Intelligence (C4I) system. The system has DDS-based real-time Combat Management System components deployed to naval warships, and SOA-based non-real-time Command and Control components used at headquarters. The proposed solution enables the exchange of data between these two systems efficiently. We compare the proposed solution with a similar study. Our solution is superior in terms of automation support, ease of implementation, scalability, and performance

The determination of total protein, total soluble carbohydrate and pigment contents of some macroalgae collected from Gemlik-Karacaali (Bursa) and Erdek-Ormanli (Balikesir) in the Sea of Marmara, Turkey

In this study, 12 taxa from the Chlorophyta, Phaeophyta and Rhodophyta were collected from different depths at Gemlik-Karacaali and Erdek-Ormanlı. A total of 175 specimens from these divisions were used to determine Total Protein (TP), Total Soluble Carbohydrate (TSCH) and Chlorophyll a (Chl a), Chlorophyll b (Chl b), Chlorophyll c (Chl c), total carotenoid (Car) contents and Chl b/Chl a, Chl c/Chl a, Car/Chl a, Car/Chl b, Car/Chl c ratios. TP, TSCH and pigment contents varied significantly with respect to the algal taxa, stations and depth distribution. In addition, individual differences were important in all of the measured parameters. The maximum TP contents (0.94%–31.03%) were determined in some of the Rhodophyta. In some green seaweeds belonging to the genus Ulva L., the TP content was determined between 2.9%–28.1%. Lower TP contents were determined in Cystoseira barbata (Good) C. Agardh (1.1%–4.3%). In contrast to TP contents, TSCH values were very low; maximum TSCH were determined in Ulva species, as were protein contents. In conclusion, the variations in TP, TSCH and pigment in 12 taxa of macroalgae were analysed according to station, depth, and environment

The influences of depression and venlafaxine use at therapeutic doses on atrial conduction

Patients with depression have increases risk of cardiac mortality. Overdose with venlafaxine has been accused of supraventricular tachycardia, atrial fibrillation and other cardiac effects. Discontinuous and inhomogeneous propagation of sinus impulses in atrium plays a major role in atrial fibrillation. We aimed to measure the effects of venlafaxine therapy on propagation of sinus impulses reflections in electrocardiography in depression. Eligible 19 participants were outpatients with depression. 75 mg/day dose of venlafaxine was administered to the patients. The patients were asked to complete both Beck Depression and Anxiety Inventories. 17 healthy participants enrolled in the study. The electrocardiography records were obtained while patients were drug naive and one week after treatment. The baseline durations of P(minimum) and P(maximum) in the patient group were significantly shorter than controls (p < 0,05). The differences between baseline and after venlafaxine therapy among electrocardiographical variables were statistically insignificant. There were no significant correlations between age, sex, body mass index, clinical inventories and electrocardiographical variables in both patients and controls. Autonomic dysregulation in myocardium is still inconclusive in depression. Venlafaxine at therapeutic dose of 75 mg/day does not seem to be associated with myocardial conduction dysregulation