Federated ontology-based queries over cancer data

Background Personalised medicine provides patients with treatments that are specific to their genetic profiles. It requires efficient data sharing of disparate data types across a variety of scientific disciplines, such as molecular biology, pathology, radiology and clinical practice. Personalised medicine aims to offer the safest and most effective therapeutic strategy based on the gene variations of each subject. In particular, this is valid in oncology, where knowledge about genetic mutations has already led to new therapies. Current molecular biology techniques (microarrays, proteomics, epigenetic technology and improved DNA sequencing technology) enable better characterisation of cancer tumours. The vast amounts of data, however, coupled with the use of different terms - or semantic heterogeneity - in each discipline makes the retrieval and integration of information difficult. Results Existing software infrastructures for data-sharing in the cancer domain, such as caGrid, support access to distributed information. caGrid follows a service-oriented model-driven architecture. Each data source in caGrid is associated with metadata at increasing levels of abstraction, including syntactic, structural, reference and domain metadata. The domain metadata consists of ontology-based annotations associated with the structural information of each data source. However, caGrid's current querying functionality is given at the structural metadata level, without capitalising on the ontology-based annotations. This paper presents the design of and theoretical foundations for distributed ontology-based queries over cancer research data. Concept-based queries are reformulated to the target query language, where join conditions between multiple data sources are found by exploiting the semantic annotations. The system has been implemented, as a proof of concept, over the caGrid infrastructure. The approach is applicable to other model-driven architectures. A graphical user interface has been developed, supporting ontology-based queries over caGrid data sources. An extensive evaluation of the query reformulation technique is included. Conclusions To support personalised medicine in oncology, it is crucial to retrieve and integrate molecular, pathology, radiology and clinical data in an efficient manner. The semantic heterogeneity of the data makes this a challenging task. Ontologies provide a formal framework to support querying and integration. This paper provides an ontology-based solution for querying distributed databases over service-oriented, model-driven infrastructures

Analysis of DDM into Gamma Radiation

We are interested in the purpose of a dipolar fermionic particle as a viable candidate of Dark Matter (DDM). Then, we study the annihilation of dark matter into photons, considering it as a neutral particle with non-vanishing magnetic (M) and electric (D) dipolar moments. The total annihilation cross section σ(χ → γ) is computed by starting from a general form of coupling χγ in a framework beyond to Standard Model (BSM). We found that candidates with O(mχ )∽102GeV, D≈10−16 e cm are required in order to satisfy the current cosmic relic density

Using Green Fluorescent Protein to Correlate Temperature and Fluorescence Intensity into Bacterial Systems

The unique and stunning spectroscopic properties of Green Fluorescent Protein (GFP) from the jellyfish Aequorea victoria, not to mention of its remarkable structural stability, have made it one of the most widely studied and used molecular tool in medicine, biochemistry, and cell biology. Its high fluorescent quantum yield is due to its chromophore, structure responsible of emitting green visible light when excited at 395 nm. Although it is noteworthy that there is enormous available information of the wonderful luminescent properties of GFP, the fact is that there are features and properties unexplored yet, particulary about its capabilities as molecular reporter in several biological processes. In this work, we used recombinant DNA technology to express the protein in bacteria; prepared the bacterial system both in liquid and solid media, and assembled an experimental set to expose those media to a laser beam; thereby we excited the protein chromophore and used emission spectroscopy in order to observe variations in fluorescence when the bacterial system is exposed to different temperatures

Protostellar Outflows at the EarliesT Stages (POETS). II. A possible radio synchrotron jet associated with the EGO G035.02+0.35

Centimeter continuum observations of protostellar jets have revealed the presence of knots of shocked gas where the flux density decreases with frequency. This spectrum is characteristic of nonthermal synchrotron radiation and implies the presence of both magnetic fields and relativistic electrons in protostellar jets. Here, we report on one of the few detections of nonthermal jet driven by a young massive star in the star-forming region G035.02$+$0.35. We made use of the NSF's Karl G. Jansky Very Large Array (VLA) to observe this region at C, Ku, and K bands with the A- and B-array configurations, and obtained sensitive radio continuum maps down to a rms of 10 $\mu$Jy beam$^{-1}$. These observations allow for a detailed spectral index analysis of the radio continuum emission in the region, which we interpret as a protostellar jet with a number of knots aligned with extended 4.5 $\mu$m emission. Two knots clearly emit nonthermal radiation and are found at similar distances, of approximately 10,000 au, each side of the central young star, from which they expand at velocities of hundreds km s$^{-1}$. We estimate both the mechanical force and the magnetic field associated with the radio jet, and infer a lower limit of $0.4\times10^{-4}$M$_{\odot}$ yr$^{-1}$ km s$^{-1}$ and values in the range $0.7-1.3$mG, respectively.Comment: 10 pages, 4 figures, 5 tables, accepted by Astronomy & Astrophysic

Estimated phosphorous requirement with and without added phytase of starting broiler chicks

For poultry the availability of phosphorus from ingredients of plant origin is limited, because this element is bound to phytates, and birds do not produce the enzyme phytase. Thus, it is necessary to complement their diets with inorganic P. Recently, microbial phytase has been utilized to improve the availability of P from phytates. Two experiments were conducted to calculate the optimal biological level of available P (Pa) with and without phytase, and to evaluate the effect of phytase on body weight gain (WG) and ash content of the tibia (% ASH) of broilers from 1-21 days of age. In Expt. 1 seven levels of Pa were evaluate: 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, and 0.60%; in Expt. 2, four levels of Pa 0.15, 0.27, 0.39, and 0.51%, and four levels of phytase 0, 200, 400, and 600 FTU (units of phytase/kg of diet) were evaluated in a factorial arrangement. In Expt. 1 there were differences (P<.05) in WG and % ASH with the levels of 0.45 and 0.50% Pa being the best. The optimal biological level was 0.46% for WG, similar to the 0.45% proposed by NRC (1994); and 0.49% for%ASH. In Exp. 2 the effect of phytase level onWGand%ASH, followed a linear tendency, the 600 FTU level surpassing the 0 FTU level by 13.5% forWGand 8.5 for%ASH (P<.05). The optimal biological level (P<.05) of Pa forWGwas estimated as 0.47 with 0 FTU and 0.394% with 600 FTU, and for%ASH as 0.47% with 0 FTU and 0.43% with 600 FTU. For maximum WG it is possible to reduce the inorganic P level by 0.75 g/kg diet (0.075%) when supplementing with 600 FTU)

Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.H.L. was supported by an Australian Research Council grant (DP150101875) awarded to M.A. R. and C.X.C. T.G.S. is supported by an Australian Government Research Training Program Scholarship. R.A.G.-P. is supported by an International Postgraduate Research Scholarship and a University of Queensland Centenary Scholarship. This project was supported by the computational resources of the Australian National Computational Infrastructure (NCI) National Facility systems through the NCI Merit Allocation Scheme (Project d85) awarded to M.A.R. and C.X.C. The data used in this project were funded by the Great Barrier Reef Foundation’s Resilient Coral Reefs Successfully Adapting to Climate Change research and development program in collaboration with the Australian Government, Bioplatforms Australia through the National Collaborative Research Infrastructure Strategy (NCRIS), Rio Tinto and a family foundation. The authors also acknowledge the work done by the Reef Future Genomics (ReFuGe) 2020 Consortium. Access to data generated by the consortium can be accessed via reefgenomics.org. In memory of S.F., our friend and colleague who is sorely missed

NETTAB 2012 on “Integrated Bio-Search”

The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, and knowledge with the aim of answering complex bio-medical-molecular questions, i.e. some of the most challenging issues in bioinformatics today. It brought together about 80 researchers working in the field of Bioinformatics, Computational Biology, Biology, Computer Science and Engineering. More than 50 scientific contributions, including keynote and tutorial talks, oral communications, posters and software demonstrations, were presented at the workshop. This preface provides a brief overview of the workshop and shortly introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement

Transient Photoreceptor Deconstruction by CNTF Enhances rAAV-Mediated Cone Functional Rescue in Late Stage CNGB3-Achromatopsia

Achromatopsia is a genetic disorder of cones, and one of the most common forms is a channelopathy caused by mutations in the β-subunit, CNGB3, of the cone cyclic nucleotide-gated (CNG) channel. Recombinant adeno-associated virus of serotype 5 (rAAV5)-mediated gene transfer of human CNGB3 cDNA to mutant dog cones results in functional and structural rescue in dogs \u3c0.5 years of age, but treatment is minimally effective in dogs \u3e1 year. We now test a new therapeutic concept by combining gene therapy with the administration of ciliary neurotrophic factor (CNTF). Intravitreal CNTF causes transient dedifferentiation of photoreceptors, a process called deconstruction, whereby visual cells become immature with short outer segments, and decreased retinal function and gene expression that subsequently return to normal. Cone function was successfully rescued in all mutant dogs treated between 14 and 42 months of age with this strategy. CNTF-mediated deconstruction and regeneration of the photoreceptor outer segments prepares the mutant cones optimally for gene augmentation therapy