Towards data warehousing and mining of protein unfolding simulation data

OBJECTIVES: The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. METHODS: To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. RESULTS: To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. CONCLUSIONS: Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

A Web Map Service implementation for the visualization of multidimensional gridded environmental data

We describe ncWMS, an implementation of the Open Geospatial Consortium’s Web Map Service (WMS) specification for multidimensional gridded environmental data. ncWMS can read data in a large number of common scientific data formats – notably the NetCDF format with the Climate and Forecast conventions – then efficiently generate map imagery in thousands of different coordinate reference systems. It is designed to require minimal configuration from the system administrator and, when used in conjunction with a suitable client tool, provides end users with an interactive means for visualizing data without the need to download large files or interpret complex metadata. It is also used as a “bridging” tool providing interoperability between the environmental science community and users of geographic information systems. ncWMS implements a number of extensions to the WMS standard in order to fulfil some common scientific requirements, including the ability to generate plots representing timeseries and vertical sections. We discuss these extensions and their impact upon present and future interoperability. We discuss the conceptual mapping between the WMS data model and the data models used by gridded data formats, highlighting areas in which the mapping is incomplete or ambiguous. We discuss the architecture of the system and particular technical innovations of note, including the algorithms used for fast data reading and image generation. ncWMS has been widely adopted within the environmental data community and we discuss some of the ways in which the software is integrated within data infrastructures and portals.

Use of an Online Photo Management and Sharing Application to Create a Searchable Digital Dental Radiograph Repository

Problem: Dental radiographs generally display one or more findings/diagnoses, and are linked to a unique set of patient demographics, medical history and other findings not represented by the image. However, this information is not associated with radiographs in any type of meta format, and images are not searchable based on any clinical criteria (1,2). The purpose of this pilot study is to create an online, searchable data repository of dental radiographs to be used for patient care, teaching and research. [See PDF for complete abstract]

The identification of child abuse in Harris County in 1998

Characteristics of child abuse cases are not well known. In this study I collected data on 70 child abuse cases that were reported to Children's Protective Services in Harris County in 1998. The purpose of this study was to determine the factors in Harris County that lead to the identification of physical and sexual abuse. In order to answer the questions of who, what, where and when relative to the discovery of abuse I applied the same questionnaire (see Appendix) to each of 35 Sexual Abuse case reports and to each of 35 Physical Abuse/Neglect case reports. Answers to the first four questions were arranged by frequency distribution to show the predominant reporter, the 10 most common indicators, the most common locale, and the most frequent timing. Tables of the age, sex, and ethnicity of the children indicate the identity of those whose victimization was most reported. In addition the relationship between the form questions and the characteristics of the children was explored. A comparison of Sexual Abuse cases with Physical Abuse/Neglect cases was conducted and the results were analyzed and recorded in the Tables. ^ Child maltreatment often has negative short and long term effects on children's mental health and development. Suicide, violence, delinquency, drug and alcohol abuse and other forms of criminality are frequently child abuse related. Early detection and treatment helps to alleviate the myriad mental and physical ailments that untreated victims present as adults. This translates into medical dollar savings. ^ The long term objectives of my research were to reduce the number of undetected and unreported child abuse cases in Harris County by formulating better educational programs and literature for medical professionals and other personnel who are in contact with children. ^

Pigment data set from the SeaWiFS Bio-optical Archive and Storage System (1961-1996)

The oceans play a critical role in the Earth's climate, but unfortunately, the extent of this role is only partially understood. One major obstacle is the difficulty associated with making high-quality, globally distributed observations, a feat that is nearly impossible using only ships and other ocean-based platforms. The data collected by satellite-borne ocean color instruments, however, provide environmental scientists a synoptic look at the productivity and variability of the Earth's oceans and atmosphere, respectively, on high-resolution temporal and spatial scales. Three such instruments, the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) onboard ORBIMAGE's OrbView-2 satellite, and two Moderate Resolution Imaging Spectroradiometers (MODIS) onboard the National Aeronautic and Space Administration's (NASA) Terra and Aqua satellites, have been in continuous operation since September 1997, February 2000, and June 2002, respectively. To facilitate the assembly of a suitably accurate data set for climate research, members of the NASA Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project and SeaWiFS Project Offices devote significant attention to the calibration and validation of these and other ocean color instruments. This article briefly presents results from the SIMBIOS and SeaWiFS Project Office's (SSPO) satellite ocean color validation activities and describes the SeaWiFS Bio-optical Archive and Storage System (SeaBASS), a state-of-the-art system for archiving, cataloging, and distributing the in situ data used in these activities.

Strontium isotope data from DSDP Sites 32-305 and 62-463 and ODP Sites 113-689 and 113-690

Fluctuations in oxygen (d18O) and carbon (d13C) isotope values of benthic foraminiferal calcite from the tropical Pacific and Southern Oceans indicate rapid reversals in the dominant mode and direction of the thermohaline circulation during a 1 m.y. interval (71-70 Ma) in the Maastrichtian. At the onset of this change, benthic foraminiferal d18O values increased and were highest in low-latitude Pacific Ocean waters, whereas benthic and planktic foraminiferal d13C values decreased and benthic values were lowest in the Southern Ocean. Subsequently, benthic foraminiferal d18O values in the Indo-Pacific decreased, and benthic and planktic d13C values increased globally. These isotopic patterns suggest that cool intermediate-depth waters, derived from high-latitude regions, penetrated temporarily to the tropics. The low benthic d13C values at the Southern Ocean sites, however, suggest that these cool waters may have been derived from high northern rather than high southern latitudes. Correlation with eustatic sea-level curves suggests that sea-level change was the most likely mechanism to change the circulation and/or source(s) of intermediate-depth waters. We thus propose that oceanic circulation during the latest Cretaceous was vigorous and that competing sources of intermediate- and deep-water formation, linked to changes in climate and sea level, may have alternated in importance.

Strontium and oxygen isotope data for DSDP Hole 44-390A and ODP Leg 171 holes

Differences in regional responses to climate fluctuations are well documented on short time scales (e.g., El Niño-Southern Oscillation), but with the exception of latitudinal temperature gradients, regional patterns are seldom considered in discussions of ancient greenhouse climates. Contrary to the expectation of global warming or global cooling implicit in most treatments of climate evolution over millions of years, this paper shows that the North Atlantic warmed by as much as 6°C (1.5% decrease in d18O values of planktic foraminifera) during the Maastrichtian global cooling interval. We suggest that warming was the result of the importation of heat from the South Atlantic. Decreasing North Atlantic d18O values are also associated with increasing gradients in planktic d13C values, suggesting increasing surface-water stratification and a correlated strengthening of the North Atlantic Polar Front. If correct, this conclusion predicts arctic cooling during the late Maastrichtian. Beyond implications for the Maastrichtian, these data demonstrate that climate does not behave as if there is a simple global thermostat, even on geologic time scales.

Chlorine concentration and isotopic data for sediments and serpentine seamount material from ODP Legs 125, 129, 185, and 195

Chlorine isotope ratios were determined for volcanic gas, geothermal well, ash, and lava samples along the Izu-Bonin-Mariana volcanic front, serpentinite clasts and muds from serpentine seamounts (Conical, South Chamorro, Torishima), basalts from the Guguan cross-chain, and sediments from Ocean Drilling Program (ODP) Sites 800, 801, 802, and 1149. There is no systematic variation in d37Cl values along the volcanic front in either gas or ash samples. In contrast, distinct variations occur across the arc, implying variations in the fluid source at different depths within the subduction zone. Serpentinite clasts and serpentine muds from the seamounts tap a source of ~30 km depth and have d37Cl values of structurally bound chloride of +0.4 per mil +/- 0.4 per mil (n = 24), identical to most seafloor serpentinites, suggesting a serpentinite (chrysotile and/or lizardite to antigorite transition) fluid source. Tapping deeper levels of the subduction zone (~115-130 km depth), volcanic gases and ashes have d37Cl values averaging -1.1 per mil +/- 1.0 per mil (n = 29), precisely overlapping the range measured in sediments from ODP cores (-1.1 per mil +/- +0.7 per mil, n = 11) and limited altered oceanic crust (AOC). Both sediments and AOC are possible Cl sources in the volcanic front. The Guguan cross-chain basalts come from the greatest depths and have an average d37Cl value of +0.2 per mil +/- 0.2 per mil (n = 3), suggesting a second serpentine-derived source, in this case from antigorite breakdown at ~200 km depth.

Foraminiferal oxygen and carbon isotope data for DSDP Sites 32-305 and 62-463 and ODP Sites 171-1049 and 171-1050

Oxygen isotope analyses of well-preserved foraminifera from Blake Nose (30°N paleolatitude, North Atlantic) and globally distributed deep-sea sites provide a long-term paleotemperature record for the late Albian-Maastrichtian interval that is difficult to reconcile with the existence of significant Cretaceous ice sheets. Given reasonable assumptions about the isotopic composition of Cretaceous seawater, our results suggest that middle bathyal water temperatures at Blake Nose increased from ~12°C in the late Albian through middle Cenomanian to a maximum of 20°C during the latest Cenomanian and earliest Turonian. Bottom waters were again ~12°C during the middle Campanian and cooled to a minimum of 9°C during the Maastrichtian. Correlative middle bathyal foraminifera from other ocean basins yield paleotemperature estimates that are very similar to those from Blake Nose. Comparison of global bottom-water temperatures and latitudinal thermal gradients suggests that global climate changed from a warm greenhouse state during the late Albian through late Cenomanian to a hot greenhouse phase during the latest Cenomanian through early Campanian, then to cool greenhouse conditions during the mid-Campanian through Maastrichtian.

Concentrations of Ti, Fe, and Al and radiogenic isotope data for sediments of ODP Leg 177

Identifying terrigenous sources in deep-sea sediments may reveal temporal trends in paleocirculation and the relative role of eolian, upwelled, and hemipelagic Fe sources to surface waters. Bulk elemental and isotopic geochemistry of deep-sea sediments recovered during Ocean Drilling Program Leg 177 in the southeastern Atlantic sector of the Southern Ocean reveal several important aspects of paleocirculation and terrigenous provenance. The sites studied span 43°-53°S and represent different oceanographic settings relative to regional hydrography and sediment type. Bulk sediment geochemistry indicates that terrigenous provenance varied over the past 600 k.y. Site 1089, the northernmost site, exhibits clear glacial-interglacial variability in provenance, while provenance appears to vary regardless of climate state at the more southerly sites (Site 1093 and 1094). Nd and Sr isotopes and Sm/Nd ratios of the terrigenous fraction indicate that study sites have geochemically distinguishable provenance. Nd and Sr isotopes further suggest that Sites 1089 and 1094 both contain detrital components that originated in South America over the past 30 k.y.; however, Site 1089 is also influenced by southern African sources and the strength of the Agulhas Current. The e-Nd data support a more hemipelagic source for the terrigenous material rather than an eolian source based on comparisons with Antarctic ice core data and known sea-ice extent.