Developing the Quantitative Histopathology Image Ontology : A case study using the hot spot detection problem

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts

A domain ontology for the non-coding RNA field

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology

The Non-Coding RNA Ontology : a comprehensive resource for the unification of non-coding RNA biology

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users

Bacterially mediated removal of phosphorus and cycling of nitrate and sulfate in the waste stream of a "zero-discharge" recirculating mariculture system

Simultaneous removal of nitrogen and phosphorus by microbial biofilters has been used in a variety of water treatment systems including treatment systems in aquaculture. In this study, phosphorus, nitrate and sulfate cycling in the anaerobic loop of a zero-discharge, recirculating mariculture system was investigated using detailed geochemical measurements in the sludge layer of the digestion basin. High concentrations of nitrate and sulfate, circulating in the overlying water (~15 mM), were removed by microbial respiration in the sludge resulting in a sulfide accumulation of up to 3 mM. Modelling of the observed S and O isotopic ratios in the surface sludge suggested that, with time, major respiration processes shifted from heterotrophic nitrate and sulfate reduction to autotrophic nitrate reduction. The much higher inorganic P content of the sludge relative to the fish feces is attributed to conversion of organic P to authigenic apatite. This conclusion is supported by: (a) X-ray diffraction analyses, which pointed to an accumulation of a calcium phosphate mineral phase that was different from P phases found in the feces, (b) the calculation that the pore waters of the sludge were highly oversaturated with respect to hydroxyapatite (saturation index = 4.87) and (c) there was a decrease in phosphate (and in the Ca/Na molar ratio) in the pore waters simultaneous with an increase in ammonia showing there had to be an additional P removal process at the same time as the heterotrophic breakdown of organic matter

Importance of Suspended Particulates in Riverine Delivery of Bioavailable Nitrogen to Coastal Zones

Total nitrogen (TN) loadings in riverine sediments and their coastal depocenters were compared for Il river systems worldwide to assess the potential impact of riverine particulates on coastal nitrogen budgets. Strong relationships between sediment specific surface area and TN allow these impacts to be estimated without the intense sampling normally required to achieve such budgets. About half of the systems showed higher nitrogen loadings in the riverine sediments than those from the coastal depocenter. In spite of uncertainties, these comparisons indicate that large, turbid rivers, such as the Amazon, Huanghe, and the Mississippi, deliver sediments that in turn release significant or major fractions of the total riverine nitrogen delivery. Riverine particulates must therefore be considered an essential factor in watershed nutrient loading to coastal ecosystems and may affect delivered nutrient ratios as well as total nutrient loading. The relative importance of particulate versus dissolved delivery has decreased over recent decades in the Mississippi as a result of damming and fertilizer use in the watershed

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Hemispheric Sunspot Numbers R_n and R_s: Catalogue and N-S asymmetry analysis

Sunspot drawings are provided on a regular basis at the Kanzelhoehe Solar Observatory, Austria, and the derived relative sunspot numbers are reported to the Sunspot Index Data Center in Brussels. From the daily sunspot drawings, we derived the northern, R_n, and southern, R_s, relative sunspot numbers for the time span 1975-2000. In order to accord with the International Sunspot Numbers R_i, the R_n and R_s have been normalized to the R_i, which ensures that the relation R_n + R_s = R_i is fulfilled. For validation, the derived R_n and R_s are compared to the international northern and southern relative sunspot numbers, which are available from 1992. The regression analysis performed for the period 1992-2000 reveals good agreement with the International hemispheric Sunspot Numbers. The monthly mean and the smoothed monthly mean hemispheric Sunspot Numbers are compiled into a catalogue. Based on the derived hemispheric Sunspot Numbers, we study the significance of N-S asymmetries and the rotational behavior separately for both hemispheres. We obtain that about 60% of the monthly N-S asymmetries are significant at a 95% level, whereas the relative contributions of the northern and southern hemisphere are different for different cycles. From the analysis of power spectra and autocorrelation functions, we derive a rigid rotation with about 27 days for the northern hemisphere, which can be followed for up to 15 periods. Contrary to that, the southern hemisphere reveals a dominant period of about 28 days, whereas the autocorrelation is strongly attenuated after 3 periods. These findings suggest that the activity of the northern hemisphere is dominated by an active zone, whereas the southern activity is mainly dominated by individual long-lived sunspot groups.Comment: 9 pages, 8 figures, data catalogue online available at http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/390/70

Intra-oceanic submarine arc evolution recorded in an ~1-km-thick rear-arc succession of distal volcaniclastic lobe deposits

International Ocean Discovery Program (IODP) Expedition 351 drilled a rear-arc sedimentary succession ~50 km west of the Kyushu-Palau Ridge, an arc remnant formed by rifting during formation of the Shikoku Basin and the Izu-Bonin-Mariana arc. The ~1-km-thick Eocene to Oligocene deep-marine volcaniclastic succession recovered at Site U1438 provides a unique opportunity to study a nearly complete record of intra-oceanic arc development, from a rear-arc perspective on crust created during subduction initiation rather than supra-subduction seafloor spreading. Detailed facies analysis and definition of depositional units allow for broader stratigraphic analysis and definition of lobe elements. Patterns in gravity-flow deposit types and subunits appear to define a series of stacked lobe systems that accumulated in a rear-arc basin. The lobe subdivisions, in many cases, are a combination of a turbidite-dominated subunit and an overlying debris-flow subunit. Debris flow–rich lobe-channel sequences are grouped into four, 1.6–2 m.y. episodes, each roughly the age range of an arc volcano. Three of the episodes contain overlapping lobe facies that may have resulted from minor channel switching or input from a different source. The progressive up-section coarsening of episodes and the increasing channel-facies thicknesses within each episode suggest progressively prograding facies from a maturing magmatic arc. Submarine geomorphology of the modern Mariana arc and West Mariana Ridge provide present-day examples that can be used to interpret the morphology and evolution of the channel (or channels) that fed sediment to Site U1438, forming the sequences interpreted as depositional lobes. The abrupt change from very thick and massive debris flows to fine-grained turbidites at the unit III to unit II boundary reflects arc rifting and progressive waning of turbidity current and ash inputs. This interpretation is consistent with the geochemical record from melt inclusions and detrital zircons. Thus, Site U1438 provides a unique record of the life span of an intra-oceanic arc, from inception through maturation to its demise by intra-arc rifting and stranding of the remnant arc ridge