Database Archive Research Articles

Stuttering attitudes among Turkish family generations and neighbors from representative samples

Purpose Attitudes toward stuttering, measured by the Public Opinion Survey of Human Attributes-Stuttering ( POSHA-S), are compared among (a) two different representative samples; (b) family generations (children, parents, and either grandparents or uncles and aunts) and neighbors; (c) children, parents, grandparents/adult relatives, and neighbors of the same family/neighbor units vs. individuals from different family/neighbor units; and (d) attitudes from one Turkish city with an international database archive. Methods Following a school-based, three-stage, cluster probability sampling scheme, two sets of children, parents, grandparents/adult relatives, and neighbors (50 each) in Eskişehir, Turkey (PROB1 and PROB2) completed Turkish translations of the POSHA-S. The POSHA-S measures attitudes toward stuttering within the context of other attributes, such as obesity and mental illness. Results Both replicates of the sampling procedure yielded strikingly similar attitudes for stuttering between children, parents, grandparents/adult relatives, and neighbors in PROB1 vs. PROB2, and between all pair-wise comparisons within PROB1 and PROB2. By contrast, attitudes toward obesity and mental illness were dissimilar. Correlations were small to moderate among attitudes of the same family/neighbor units but were essentially nonexistent between different family/neighbor units. Attitudes toward stuttering in Eskişehir were estimated to be less positive than attitudes from a wide range of samples around the world, although exceptions occurred. Conclusions A school-based probability sampling procedure yielded consistent findings that are likely different from results from convenience samples. Families appear to be an important influence in determining public attitudes toward stuttering and other human attributes. Educational objectives : The reader will be able to: (i) identify similarities and differences among attitudes toward stuttering across generations; (ii) identify similarities and differences among attitudes toward stuttering in Turkey vs. other places in the world; (iii) describe a school-based probability sampling scheme; (iv) describe advantages of using a standard instrument to measure public attitudes toward stuttering.

SU‐E‐T‐26: Automated Plan Evaluation System: Design and Implementation

Purpose: To present software for a Radiation therapy facility that will simplify the process of dosimetric plan evaluation and will help clinicians and physicists to review the plan. Materials and method: Every treatment plan requires certain dosimetric characteristics or parameters to be evaluated, which are essential for the assessment of a treatment plan. One can automate this process with the software that can understand the treatment plan and DVH data and gives you the desired results. This software accepts DICOM RT data from IHE‐RO compliant Varian Eclipse v 8.6 and computes DVH. There is also a facility to define disease site, technique and fractionation specific templates for dose volume constraints. This software helps you to analyze the normal tissue tolerances with the data given in the literature and also gives user the freedom to use α/β ratios to modify the tolerance values in accordance with dose‐fractionation scheme. The dosimetric indices such as conformity index and homogeneity index can also be calculated and compared with the user defined criteria in the template. Results: The prototype system has been used to design various templates for different treatment sites such as head and neck and breast. These templates are used to evaluate plan and dosimetric parameters for several patients. Conclusion: This prototype software provides a simplified solution for an automated dosimetric plan evaluation. The dosimetric parameters used in the plan evaluation is stored in an database archive for all the patients and this data is intended to used for further analysis.

The Public Opinion Survey of Human Attributes-Stuttering ( POSHA-S): Summary framework and empirical comparisons

Purpose The Public Opinion Survey of Human Attributes-Stuttering (POSHA-S) was developed to make available worldwide a standard measure of public attitudes toward stuttering that is practical, reliable, valid, and translatable. Mean data from past field studies as comparisons for interpretation of POSHA-S results are reported. Method Means for POSHA-S items (converted to −100 to +100 scales), components comprising clusters of items, subscores comprising clusters of components, and Overall Stuttering Scores comprising two subscores for stuttering were generated from 64 samples, totaling 2876 respondents who completed experimental versions of the POSHA-S. Discussion Lowest, highest, and median sample values, which vary with the addition of new sample data to the growing POSHA-S database archive, provide points of comparison for any potential sample rather than predetermined values. Conclusions The final POSHA-S, together with an ongoing and growing archive, can provide increasingly meaningful comparisons for stakeholders measuring public attitudes toward stuttering. Educational objectives: (1) Describe the subscores and components of the POSHA-S, (2) describe the Overall Stuttering Score of the POSHA-S, and (3) describe the format for interpretation of the POSHA-S.

Standardizing Rodent Trimming and Embedding Guidelines for Histology: Improving Efficiency in the Laboratory

This poster will outline a process created in the histology laboratory to standardize trimming and embedding guidelines to maintain consistency throughout all studies. Pathologists requested that each tissue be assigned a fixed number for more-efficient slide evaluations. For example, all brains are numbered as cassette one and all pituitary glands are numbered cassette two, etc. To achieve this, a template was created for both the rat and mouse for the histology technicians to use. The template consists of photographs demonstrating tissue trimming and grouping in the order of how the pathologists evaluate the hematoxylin and eosin (H&E) slides. A trim form is created in the web-based client application system, listing the tissues requested for each individual animal. Once this has been completed, the system sorts the original trim form to group all cassettes according to tissue. For example, all cassettes numbered one are grouped together (brains) and all cassettes numbered two are grouped together (pituitary glands), etc. By following this process, improved consistency and efficiency has been noticed by the pathologists. In the future, this template system has the potential to facilitate histopathology digital image database archive and search processes.

Database archiving: how to keep lots of data for a very long time

With the amount of data a business accumulates now doubling every 12 to 18 months, IT professionals need to know how to develop a system for archiving important database data, in a way that both satisfies regulatory requirements and is durable and secure. This important and timely new book explains how to solve these challenges without compromising the operation of current systems. It shows how to do all this as part of a standardized archival process that requires modest contributions from team members throughout an organization, rather than the superhuman effort of a dedicated team. * Exhaustively considers the diverse set of issues--legal, technological, and financial--affecting organizations faced with major database archiving requirements. * Shows how to design and implement a database archival process that is integral to existing procedures and systems. * Explores the role of players at every level of the organization--in terms of the skills they need and the contributions they can make. * Presents its ideas from a vendor-neutral perspective that can benefit any organization, regardless of its current technological investments. * Provides detailed information on building the business case for all types of archiving projects

Development and implementation of real-time data acquisition systems for fusion devices with Open Source software

To improve the plasma position and shape control system in ASDEX Upgrade, it is constantly expanded by the integration of data acquisition systems of important and interesting diagnostics. Usually the main responsibility of data acquisition systems is to collect data and subsequently put it into a data base archive system from where it is later analysed. The obligation now is also to simultaneously process the acquired data with an appropriate algorithm and send the pre-processed data in real-time to the plasma control system during a discharge. To achieve this requirements the used hardware must provide enough processing power and the operating system has to meet some real-time constraints. To avoid the burden of using proprietary real-time operating systems the trend is to use Open Source variants mainly based on Linux. Some of these solutions also allow us doing real-time capable communication using standard Ethernet hardware. By way of an example the implementation process of a prototype of a real-time data acquisition system based on a multi-core processor and Xenomai is demonstrated. Other possible solutions like Realtime Linux and their differences to Xenomai which we propose as the most sophisticated real-time framework for Linux are discussed in this paper.

Technical and Policy Approaches to Balancing Patient Privacy and Data Sharing in Clinical and Translational Research

IntroductionClinical researchers need to share data to support scientific validation and information reuse and to comply with a host of regulations and directives from funders. Various organizations are constructing informatics...

Landscape composition influences local pattern of fire size in the eastern Canadian boreal forest: role of weather and landscape mosaic on fire size distribution in mixedwood boreal forest using the Prescribed Fire Analysis System

Wildfire simulations were carried out using the Prescribed Fire Analysis System (PFAS) to study the effect of landscape composition on fire sizes in eastern Canadian boreal forests. We used the Lake Duparquet forest as reference, plus 13 forest mosaic scenarios whose compositions reflected lengths of fire cycle. Three fire weather risks based on duff moisture were used. We performed 100 simulations per risk and mosaic, with topography and hydrology set constant for the reference. Results showed that both weather and landscape composition significantly influenced fire sizes. Weather related to fire propagation explained almost 79% of the variance, while landscape composition and weather conditions for ignition explained ∼14 and 2% respectively. In terms of landscape, burned area increased with increasing presence of shade-tolerant species, which are related to long fire cycles. Comparisons among the distributions of cumulated area burned from scenarios plus those from the Société de Protection des Forêts contre le Feu database archives showed that PFAS simulated realistic fire sizes using the 80–100% class of probable fire extent. Future analyses would best be performed on a larger region as the limited size of the study area could not capture fires larger than 11 000 ha, which represent 3% of fires but 65% of the total area burned at the provincial scale.

Treatment of conjunctival melanocytic neoplasms: the Liverpool experience

Abstract Purpose To audit the results of treatment of conjunctival melanoma in Liverpool. Methods Patients treated between 1993 and 2006 were identified by searching the Ocular Oncology Service database and pathology archives. The casenotes were reviewed. Patients were included if their conjunctival tumour was histologically diagnosed as invasive melanoma. Tumour extent and location were defined using a mapping system we developed. During the course of this study, cryotherapy was abandoned in favour of topical chemotherapy for intra‐epithelial melanocytic neoplasia and brachytherapy for invasive disease. Results Forty patients with invasive conjunctival melanoma were initially treated at our centre and another 36 were referred to us for salvage therapy after a surgical intervention elsewhere (11 with no visible tumour, 9 with intra‐epithelial disease and 16 with invasive melanoma). The patients we initially treated all retained the eye, most without significant visual loss. Recurrence occurred in six patients, none of whom had adjunctive brachytherapy. Four patients died of metastasis, all with caruncular involvement. After salvage therapy in 16 patients referred with recurrent or persistent invasive disease, two eyes were lost and five patients died, only one of whom had caruncular involvement. Conclusion Excision of invasive conjunctival melanoma with adjunctive brachytherapy and topical chemotherapy achieved high rates of local tumour control with little ocular morbidity. Without caruncular involvement, disease‐specific mortality was rare unless the patient was referred with invasive disease after a surgical procedure elsewhere. Our results suggest that inexpert surgical intervention increases the risk of local tumour recurrence and metastatic death.

Fungal cytochrome P450 database

BackgroundCytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.ResultsThe Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.ConclusionThe FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site .

Sorting hierarchical data in external memory for archiving

Sorting hierarchical data in external memory is necessary for a wide variety of applications including archiving scientific data and dealing with large XML datasets. The topic of sorting hierarchical data, however, has received little attention from the research community so far. In this paper we focus on sorting arbitrary hierarchical data that far exceed the size of physical memory. We propose HErMeS, an algorithm that generalizes the most widely-used techniques for sorting flat data in external memory. HErMeS efficiently exploits the hierarchical structure to minimize the number of disk accesses and optimize the use of available memory. We extract the theoretical bounds of the algorithm with respect to the structure of the hierarchical dataset. We then show how the algorithm can be used to support efficient archiving. We have conducted an experimental study using several workloads and comparing HErMeS to the state-of-the-art approaches. Our results show that our algorithm ( a ) meets its theoretical expectations, ( b ) allows for scalable database archiving, and ( c ) outperforms the competition by a significant factor. These results, we believe, prove our technique to be a viable and scalable solution to the problem of sorting hierarchical data in external memory.

Extreme Value Analysis of Tropical Cyclone Trapped-Fetch Waves

Abstract Many of the extreme ocean wave events generated by tropical cyclones (TCs) can be explained by examining one component of the spectral wave field, the trapped-fetch wave (TFW). Using a Lagrangian TFW model, a parametric model representation of the local TC wind fields, and the National Hurricane Center’s hurricane database archive, a dataset of TFWs was created from all TCs in the Atlantic Ocean, Gulf of Mexico, and Caribbean Sea from 1851 to 2005. The wave height at each hourly position along a TFW trajectory was sorted into 2° × 2° latitude–longitude grid squares. Five grid squares (north of Hispaniola, Gulf of Mexico, Carolina coast, south of Nova Scotia, and south of Newfoundland) were used to determine if extreme value theory could be applied to the extremes in the TFW dataset. The statistical results justify accepting that a generalized Pareto distribution (GPD) model with a threshold of 6 m could be fitted to the data: the datasets were mostly modeled adequately, and much of the output information was useful. Additional tests were performed by sorting the TFW data into the marine areas in Atlantic Canada, which are of particular interest to the Meteorological Service of Canada because of the high ocean traffic, offshore drilling activities, and commercial fishery. GPD models were fitted, and return periods and the 95% confidence intervals (CIs) for 10-, 15-, and 20-m return levels were computed. The results further justified the use of the GPD model; hence, extension to the remaining grid squares was warranted. Of the 607 grid squares successfully modeled, the percentage of grid squares with finite lower (upper) values for the 10-, 15-, and 20-m return level CIs were 100 (80), 94 (53), and 90 (16), respectively. The lower success rate of 20-m TFW CIs was expected, given the rarity of 20-m TFWs: of the 5 713 625 hourly TFW points, only 13 958, or 0.24%, were 20 m or higher. Overall, the distribution of the successfully modeled grid squares in the data domain agreed with TFW theory and TC climatology. As a direct result of this study, the summary datasets and return level plots were integrated into application software for use by risk managers. A description of the applications illustrates their use in addressing various questions on extreme TFWs.

A Matlab based framework for the real-time environment at FTU

In this paper we report on recent developments, based on The MathWorks’ Simulink and Real-Time Workshop (RTW) packages, aimed at obtaining a high level environment where a new control law can be easily modelled, simulated with the real-time constraints and then translated in the appropriate executable format. Using this tool, the control designer only needs to specify the control law in the Simulink graphical environment. The arising model is then automatically translated in C code, integrated with control system code and simulated in real-time using the data from the Frascati Tokamak Upgrade (FTU) data base archive. All the necessary steps to adapt the RTW scripts and the control system code to the new simulation/validation environment will be illustrated in this paper. Moreover, we will report on some experimental tests where the actual experiment is compared with the simulations provided by the proposed environment.

International Comparison of Analytical Methods of Determining the Soil Organic Matter Content of Lithuanian Eutric Albeluvisols

Several soil organic matter (SOM) methodologies have been employed to analyze a suite of subsampled soils, and their results have been correlated. This will permit future comparison of the large archive of SOM databases, which widely exist in Lithuania and other Central and Eastern European countries, with those of other international countries. Samples were collected (n=92) from topsoil and subsoil horizons of Eutric Glassoboralfs (Eutric Albeluvisols) at five long‐term monitoring sites (three sites with 8 years' duration and two sites with 20 years' duration) containing a total of 46 experimental field plots. Each soil sample was subsampled and SOM determined by several analytical approaches (namely, dry combustion, Walkley–Black, Tyurin photometric, Tyurin titrimetric, and loss‐on‐ignition methods). Correlation coefficients between multiple sets of results varied between r=0.831 and r=0.965 (n=92, P<0.001). Based on the strength and significance of these relationships, we propose that simple linear regression equations can be confidently employed to recalculate SOM data among various analytical methodologies and thus help resolve the issue of international data comparison.

NOPdb: Nucleolar Proteome Database

The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain structures and relevant protein homologues across species, as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of ∼500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints, highlighted by visualization means in the NOPdb, provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/uncharacterized proteins. The NOPdb () is searchable by either gene names, nucleotide or protein sequences, Gene Ontology terms or motifs, or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink, OMIM and PubMed).

Fully Automated System for Three-Dimensional Bronchial Morphology Analysis Using Volumetric Multidetector Computed Tomography of the Chest

Recent advancements in computed tomography (CT) have enabled quantitative assessment of severity and progression of large airway damage in chronic pulmonary disease. The advent of fast multidetector computed tomography scanning has allowed the acquisition of rapid, low-dose 3D volumetric pulmonary scans that depict the bronchial tree in great detail. Volumetric CT allows quantitative indices of bronchial airway morphology to be calculated, including airway diameters, wall thicknesses, wall area, airway segment lengths, airway taper indices, and airway branching patterns. However, the complexity and size of the bronchial tree render manual measurement methods impractical and inaccurate. We have developed an integrated software package utilizing a new measurement algorithm termed mirror-image Gaussian fit that enables the user to perform automated bronchial segmentation, measurement, and database archiving of the bronchial morphology in high resolution and volumetric CT scans and also allows 3D localization, visualization, and registration.

Experiences of Establishing Up-To-Date On-Site Sampler Applications

Spatial problems and spatial decisions are decisive in agricultural-environmental informatics systems and the solutions require systems that can collect, evaluate and display spatial data. The distinctive features of spatial informatics systems therefore have to be considered when establishing integrated spatial informatics systems.However, the prepared spatial evaluations are not the only „added value” elements of a completed informatics system. The method of access can also speed up the work of participants and the whole system, making it more efficient with simple data-handling and the application of open standards. The significance of prepared database archives can also increase, since the accumulated data-assets are easy to utilize and become marketable.

SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design

The Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) is a relatively simple and inexpensive method for genotyping single nucleotide polymorphisms (SNPs). It requires minimal investment in instrumentation. Here, we describe a web application, ‘SNP Cutter,’ which designs PCR–RFLP assays on a batch of SNPs from the human genome. NCBI dbSNP rs IDs or formatted SNPs are submitted into the SNP Cutter which then uses restriction enzymes from a pre-selected list to perform enzyme selection. The program is capable of designing primers for either natural PCR–RFLP or mismatch PCR–RFLP, depending on the SNP sequence data. SNP Cutter generates the information needed to evaluate and perform genotyping experiments, including a PCR primers list, sizes of original amplicons and different allelic fragment after enzyme digestion. Some output data is tab-delimited, therefore suitable for database archiving. The SNP Cut-ter is available at .

A Reanalysis of the Surface Winds for Hurricane Donna of 1960

Hurricane Donna, the only major hurricane to strike the United States during the 1960 Atlantic hurricane season, passed over the middle Florida Keys near Sombrero Key before making landfall southeast of Naples, near Goodland, Florida, on 10 September at approximately 1600 UTC. This study makes detailed retrospective surface wind analyses of Hurricane Donna utilizing the National Oceanic and Atmospheric Administration (NOAA) Hurricane Research Division's (HRD) H*Wind surface wind analysis system. Analyses were produced at intervals of 6 h between 1800 UTC 9 September and 1200 UTC 11 September 1960 while the hurricane was close to and over Florida. These analyses depict the storm track as well as the distribution and extent of tropical storm force, 50 kt (25.7 m s−1), and the hurricane-force wind radii throughout this time period and include new methodologies for adjusting aircraft flight-level data to the surface in the tropical cyclone core environment. Algorithms were developed to account for the effects of eyewall tilt and the warm core structure typical of tropical cyclones. Additional methods were developed using global positioning system (GPS) dropwindsondes (sondes) to more accurately adjust boundary layer winds to equivalent surface winds. The Kaplan–DeMaria Inland Wind Decay Model was also used for the first time to adjust landfall data being input into the H*Wind system. These data were used to generate low-weighted background fields that helped generate postlandfall wind field analyses of Hurricane Donna. Finally, swaths of peak winds, duration of hurricane- and major hurricane–force winds, and wind steadiness were produced to facilitate damage assessment. The information provided by these objective analyses is significantly more detailed than the more limited descriptions of peak winds, storm position, and minimum central pressure available in the National Hurricane Center's (NHC) hurricane database archive (HURDAT).

VIRTUAL2D: A web-accessible predictive database for proteomics analysis.

The available archive of sequence databases compiled from whole genome projects and budding proteomics efforts have enabled us to develop VIRTUAL2D, an interactive system for the assembly of virtual protein expression maps computed on the basis of theoretical isoelectric focusing point, molecular weight, tissue specificity and relative abundance for any set of proteins currently catalogued. This tool will assist in the preliminary, albeit putative, prediction of the identity and location of unknown and/or low abundance proteins in experimentally derived two-dimensional polyacrylamide gel electrophoresis maps.