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PubMed2005

Comparative sugar recovery data from laboratory scale application of leading pretreatment technologies to corn stover.

Biological processing of cellulosic biomass to fuels and chemicals would open up major new agricultural markets and provide powerful societal benefits, but pretreatment operations essential to economically viable yields have a major impact on costs and performance of the entire system. However, little comparative data is available on promising pretreatments. To aid in selecting appropriate systems, leading pretreatments based on ammonia explosion, aqueous ammonia recycle, controlled pH, dilute acid, flowthrough, and lime were evaluated in a coordinated laboratory program using a single source of corn stover, the same cellulase enzyme, shared analytical methods, and common data interpretation approaches to make meaningful comparisons possible for the first time. Each pretreatment made it possible to subsequently achieve high yields of glucose from cellulose by cellulase enzymes, and the cellulase formulations used were effective in solubilizing residual xylan left in the solids after each pretreatment. Thus, overall sugar yields from hemicellulose and cellulose in the coupled pretreatment and enzymatic hydrolysis operations were high for all of the pretreatments with corn stover. In addition, high-pH methods were found to offer promise in reducing cellulase use provided hemicellulase activity can be enhanced. However, the substantial differences in sugar release patterns in the pretreatment and enzymatic hydrolysis operations have important implications for the choice of process, enzymes, and fermentative organisms.

Biomass↗

PubMed1999

Application of generalized estimating equations to a dental randomized clinical trial.

Longitudinal data present statistical problems of interest in clinical trials and epidemiologic studies. In this article, we consider a dental clinical trial in which the outcome measurements are taken on each subject at two follow-up times, and the primary interest is in the dependence of the outcome variable on covariates. The common data structure of these studies is the presence of an intraclass or serial correlation within primary sampling units or subjects. Recently generalized linear models have had extensions to methods for generalized estimating equations that take correlations within primary sampling units into account. We review and apply the Liang-Zeger methodology to a dental clinical trial. In this study, 109 adult male and female volunteers with pre-existing dental plaque were randomized to two mouth rinses (A and B) or a control mouth rinse with double blinding. The major research question in this analysis was: Are the two experimental mouth rinses more effective than the control mouth rinse in inhibiting the development of dental plaque? And if so, what is the effect of baseline plaque measurement?

Adult↗

PubMed1998

[Modelling of radiological services in the context of a hospital information system: does the DICOM standard meet the requirements?].

PROBLEM: The data model given in the DICOM standard is examined under the aspect of system integration. Semantic properties of the IODs (information object definitions) and their relationships are investigated. METHOD: Starting from the entities defined in Part 3 of the DICOM standard, we explored how the classes defined there can be integrated into a common data model of the electronic patient record implemented by the HIS (Hospital Information System). Based on the IODs we investigated the definitions and semantics of entities being relevant for structured recording of image data. RESULTS: Because semantic definitions are incomplete, a proposal is made for the core domain of structured radiologic service recording. Its definition of semantics goes beyond the application domain of radiologic imaging to avoid structural conflicts during HIS/RIS/PACS integration. Differentiation between treatment and billing provides an independent temporal mapping of services concerning medical and billing aspects. Two groups of radiologic services are distinguished: radiologic imaging and additional services. CONCLUSION: The incomplete definition of IOD semantics leads to potential conflicts during system integration. Complete covering of this topic is necessary for implementation of the electronic patient record.

Data Interpretation, Statistical↗

PubMed1998

Hip fracture incidence and mortality in an English Region: a study using routine National Health Service data.

BACKGROUND: We investigated the validity of routine hospital and mortality hip fracture data in one English Region and estimated trends in hip fracture between 1978-1981 and 1993-1995. METHODS: We identified from Hospital Episode System (HES) data for 1993-1995 all hip fracture episodes relating to individual patients aged over 65 years resident in Wessex. We determined from the discharge method code whether an individual had died during that admission. The number of individual regional and district admissions and deaths were compared with those presented in the Public Health Common Data Set. We compared regional admission rates with data for 1978-1981 from a previous study. RESULTS: National comparative indicators for hip fracture overestimated individual admissions in Wessex by 17 per cent (in health authorities by 1-56 per cent). National comparative indicators for hip fracture mortality underestimated individual deaths in Wessex by 48 per cent. Between 1978-1981 and 1993-1995 the age-sex-standardized hip fracture rates rose from 1.90 to 2.63 per 1000 per year for men and from 5.70 to 7.70 per 1000 per year for women. Rates increased in all age groups except those aged 65-69 years. There was also a small fall in absolute mean annual numbers in this age group. The rates also fell in females aged 70-74. CONCLUSIONS: It is possible to adjust routine national HES data to take account of multiple episodes within a single admission. These methods should be applied to national comparative indicators for hip fracture admission and deaths. Hip fracture rates continue to rise in those aged over 70 years. There may be a cohort effect with those born after 1925 showing stable rates which needs further investigation.

Age Distribution↗

PubMed1983

The National Traumatic Coma Data Bank. Part 1: Design, purpose, goals, and results.

This paper describes the pilot phase of the National Traumatic Coma Data Bank, a cooperative effort of six clinical head-injury centers in the United States. Data were collected on 581 hospitalized patients with severe non-penetrating traumatic head injury. Severe head injury was defined on the basis of a Glasgow Coma Scale (GCS) score of 8 or less following nonsurgical resuscitation or deterioration to a GCS score of 8 or less within 48 hours after head injury. A common data collection protocol, definitions, and data collection instruments were developed and put into use by all centers commencing in June, 1979. Extensive information was collected on pre-hospital, emergency room, intensive care, and recovery phases of patient care. Data were obtained on all patients from the time of injury until the end of the pilot study. The pilot phase of the Data Bank provides data germane to questions of interest to neurosurgeons and to the lay public. Questions are as diverse as: what is the prognosis of severe brain injury; what is the impact of emergency care; and what is the role of rehabilitation in the recovery of the severely head-injured patient?

Accidents↗

PubMed1995

[Gene pool of residents of northeastern Eurasia in light of data on polymorphism of mitochondrial DNA. I. New data on polymorphism of restriction sites of the D-loop of mtDNA in aboriginal populations of the Caucasus and Siberia].

New data about eleven polymorphic sites of restriction in the D-loop of mtDNA revealed with the Ava II, BamH I, EcoR V, Hae III, Kpn I, Rsa I, and Sau3A I restriction enzymes in native populations of the Caucasus (N = 40) and Siberia (N = 44) are presented. A comparison of these groups with each other and with common data for western and eastern Europe as well as for central and eastern Asia reveals a large similarity of all the population groups of Eurasia in respect to the frequency of each polymorphic site separately. The interpopulation differentiation of frequency of polymorphic restriction sites in Eurasia is low and identical at such different hierarchical levels of population structure as ethnic group and extended regional population group. An analysis of differences between sites in the frequency of the presence of restriction sites for BamH I, EcoR V, Hae III, and Sau3A I and the absence of sites for Ava II, Kpn I, and Rsa I at definite loci of the nucleotide chain allowed determination of the region of equilibrium between direct, site-generating, and reverse mutations to be 0.43q. Among eleven polymorphic restriction sites analyzed here, only polymorphism in the Hae III site at the position 16,517 in the population of Eurasia was characterized with frequencies close to equilibrium that determined the extremely large evolutionary age of this polymorphism.

Base Sequence↗

PubMed2006

ProteomeCommons.org JAF: reference information and tools for proteomics.

SUMMARY: Analysis of proteomics data, specifically mass spectrometry data, commonly relies on libraries of known information such as atomic masses, known stable isotopes, atomic compositions of amino acids, observed modifications of known amino acids and ion masses that directly correspond to known amino acid sequences. The Java Analysis Framework (JAF) for proteomics provides a freely usable, open-source library of Java code that abstracts all of the aforementioned data, enabling more rapid development of proteomics tools. The JAF also includes several user tools that can be run directly from a web browser. AVAILABILITY: The current version and an archive of all older versions of the Java Analysis Framework for Proteomics is freely available, including complete source-code, at http://www.proteomecommons.org/current/511/.

Database Management Systems↗

PubMed2002

Quality of life in advanced non-small-cell lung cancer: results of a Southwest Oncology Group randomized trial.

PURPOSE: The main purpose of this paper is to present the results of a randomized trial comparing the effects of two chemotherapy regimens on the Quality of life (QOL) of patients with advanced non-small-cell lung cancer (NSCLC). Trials in advanced stage disease represent an important treatment context for QOL assessment. A second purpose of this paper is to examine methods for handling the level of missing data commonly observed in the advanced stage disease context. METHODS: Patients were randomized to receive cisplatin plus vinorelbine or carboplatin plus paclitaxel. The QOL of 222 patients was assessed with the Functional Assessment of Cancer Therapy-Lung (FACT-L) prior to randomization; follow-up assessments occurred at 13 and 25 weeks. Three methods were used to analyze the QOL data: (1) cross-sectional analysis of four patient categories (improved, stable, missing, and declined) based on changes in the FACT-L score, (2) a mixed linear model, and (3) a pattern mixture model. The longitudinal analyses addressed two potential data biases. RESULTS: Questionnaire submission rates were 91% at baseline, 68% at 13 weeks, and 47% at 25 weeks. The cross-sectional and mixed linear model analyses did not show significant differences by treatment arm in patient-reported QOL. The pattern mixture model analysis, more appropriate given non-ignorable missing data, also found no statistically significant effect of treatment on patient QOL. CONCLUSION: We present a sensitivity analysis approach with multiple methods for analyzing treatment effects on patient QOL in the presence of substantial, non-ignorable missing data in an advanced stage disease clinical trial. We conclude that the two treatment arms did not differ statistically in their effects on patient QOL over a 25-week treatment period.

Antineoplastic Combined Chemotherapy Protocols↗

PubMed1998

Advanced query mechanisms for biological databases.

Existing query interfaces for biological databases are either based on fixed forms or textual query languages. Users of a fixed form-based query interface are limited to performing some pre-defined queries providing a fixed view of the underlying database, while users of a free text query language-based interface have to understand the underlying data models, specific query languages and application schemas in order to formulate queries. Further, operations on application-specific complex data (e.g., DNA sequences, proteins), which are usually provided by a variety of software packages with their own format requirements and peculiarities, are not available as part of, nor integrated with biological query interfaces. In this paper, we describe generic tools that provide powerful and flexible support for interactively exploring biological databases in a uniform and consistent way, that is via common data models, formats, and notations, in the framework of the Object-Protocol Model (OPM). These tools include (i) a Java graphical query construction tool with support for automatic generation of Web query forms that can be either used for further specifying conditions, or can be saved and customized; (ii) query processors for interpreting and executing queries that may involve complex application-specific objects, and that could span multiple heterogeneous databases and file systems; and (iii) utilities for automatic generation of HTML pages containing query results, that can be browsed using a Web browser. These tools avoid the restrictions imposed by traditional fixed-form query interfaces, while providing users with simple and intuitive facilities for formulating ad-hoc queries across heterogeneous databases, without the need to understand the underlying data models and query languages.

Animals↗

PubMed1992

Computer-assisted generation of multi-leaf collimator settings for conformation therapy.

Techniques for the automatic set up of the individual leaf positions of a Philips multi-leaf collimator system to cover a defined target volume are described. Tumour outline data for multi-field treatments may be obtained from one of two techniques, either from simulator images or from cross-sectional computed tomography (CT) slices. In the first technique, simulator images are digitized directly from image intensifier video signals or from conventional film radiographs using a CCD camera. Corrections for image distortion are carried out before reformatting the digitized images to a common data structure. Target outlines are subsequently traced interactively on the digital image to create an outline file. In the second technique, target volumes are defined on several individual CT slices and these are then used to obtain projected graphical views from any desired angle. In both techniques, a scaled graphical representation of leaf positions is then displayed and set relative to the outer edge of the target outline. Both techniques allow interactive repositioning of single leaves when required, or the operator can specify a margin around the projected target volume. Leaf prescription data files are created and are transferred via a Decnet-OSI-Opennet network link to an Intel microcomputer, which is used to drive the device itself. Examples of both techniques are given.

Humans↗

PubMed1997

Hybrid rendering of multidimensional image data.

The most important rendering methods applied in medical imaging are surface and volume rendering techniques. Each approach has its own advantages and limitations: Fast surface-oriented methods are able to support real-time interaction and manipulation. The underlying representation, however, is dependent on intensive image processing to extract the object surfaces. In contrast, volume visualization is not necessarily based on extensive image processing and interpretation. No data reduction to geometric primitives, such as polygons, is required. Therefore, the process of volume rendering is currently not operating in real time. In order to provide the radiological diagnosis with additional information as well as to enable simulation and preoperative treatment planning we developed a new hybrid rendering method which combines the advantages of surface and volume presentation, and minimizes the limitations of these approaches. We developed a common data representation method for both techniques. A preprocessing module enables the construction of a data volume by interpolation as well as the calculation of object surfaces by semiautomatic image interpretation and surface construction. The hybrid rendering system is based on transparency and texture mapping features. It is embedded in a user-friendly open system which enables the support of new application fields such as virtual reality and stereolithography. The efficiency of our new method is described for 3-D subtraction angiography and the visualization of morpho-functional relationships.

Computer Graphics↗

PubMed1994

[Modeling and projecting mortality in Chile].

"In a recent paper, Lee and Carter developed a new method for analyzing and forecasting time series of age specific mortality, and applied it to the U.S. population. In this paper, we extend that method to deal with various problems of incomplete data common in Third World populations, and then apply the method to forecast mortality in Chile." (SUMMARY IN ENG)

Americas↗

PubMed2025

ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration.

BACKGROUND: In biomedical research, subjects and biospecimens are commonly tracked using simple IDs or UUIDs, which guarantee uniqueness but convey no embedded semantic information. Contextual metadata (such as tissue type, diagnosis, or assay) is often stored separately, making integration, cohort selection, and downstream analysis cumbersome. While structured barcoding systems exist in large consortia (e.g., TCGA, GTEx) or domain-specific contexts (e.g., SPREC, GOLD), no unified, extensible framework currently spans both subjects and biosamples in a human- and machine-readable way. METHODS: We developed ClarID, a domain-agnostic specification that supports two identifier formats: (i) a human-readable form (e.g., 'CNAG_Test-HomSap-00001-LIV-TUM-RNA-C22.0-TRT-P1W' that encodes key metadata such as project, species, subject_id, tissue, assay, disease, timepoint and duration (from that event); and (ii) a compact version named 'stub' (e.g., 'CT01001LTR0N401T1W') optimized for filenames, pipelines, and labeling.ClarID is implemented through an open-source command-line tool, ClarID-Tools, which processes tabular metadata files (CSV/TSV) and uses a YAML-based codebook to generate, decode, and validate identifiers, as well as to create and read QR codes. The tool supports bulk and single-sample processing and allows easy integration with institutional workflows. RESULTS: To demonstrate ClarID's utility, we applied it to datasets from the Genomic Data Commons (GDC), generating interpretable identifiers for more than 113,000 clinical records (subjects) and 4,255 biospecimen records. All materials, including pre-processing scripts, input and encoded data, are publicly available and fully reproducible via the accompanying GitHub repository and Google Colab. CONCLUSIONS: ClarID fills a critical gap between opaque accession numbers and rich metadata schemas by embedding key context directly into structured identifiers. It enhances traceability, facilitates downstream analysis, and remains adaptable to project-specific needs through a configurable codebook. The accompanying ClarID-Tools software is freely available, together with full documentation and reproducible pipelines, at https://github.com/CNAG-Biomedical-Informatics/clarid-tools.

Biosample identifiers↗

PubMed1994

Acuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1beta.

To assess the accuracy of refined structures, a comparison was made using independently determined structures of the same protein in the same crystal form. The models were re-refined against a common data set to minimize the effects of different data and different refinement protocols. The process did not converge to a single model. Rather the structures differed from each other by 0.84 A which was roughly three times that predicted by a Luzzati analysis [Luzzati (1952). Acta Cryst. 5, 802-810]. The individual structures are equally valid and at least partially independent as evidenced by a reduction of the R factor by 0.013 when a simple linear combination is used. Only 29 solvent molecules were common to all four models.

Journal Article↗

PubMed2006

Structured correlation in models for clustered data.

Correlation is always a concern in the analysis of clustered data. One area of interest is to develop a general correlation modelling approach for high dimensional data with unbalanced hierarchical and heterogeneous data structures, e.g. multilevel data. Commonly used correlation structures might have limitation for such situations. In this paper, we propose two extensions, multiblock and multilayer correlations. These methods are very flexible in modelling correlation and can be incorporated in many multivariate approaches, while the major discussion focuses on the applications under the generalized estimating equations (GEE) methods. The approaches are especially useful in GEE when each cluster is large and complex but the number of clusters is small. If an incorrect correlation is applied to such data, the results are less efficient. Multiblock and multilayer correlations extend GEE methods to model complicated multilevel data with arbitrary number of levels and cluster size. The extended estimating equation for correlation parameters has an orthogonal property, and the computation is very efficient. A simulation study compares the conventional methods versus the proposed methods, and it shows the gain in relative efficiency and the flexibility in modelling various structures.

Adult↗

PubMedDate not supplied

Epidemiology of pediatric EMS practice: a multistate analysis.

OBJECTIVE: To describe the epidemiology of pediatric emergency medical services (EMS) practice in a large patient population from several geographic areas. DESIGN: Retrospective computer analysis of EMS databases from four states using a common data set and analysis system. SETTING: Pennsylvania, Tennessee, Mississippi, and Nevada (except Clark County), 1990 through 1992. METHODS: All patient-care reports of patients 14 years old and younger were extracted from the EMS databases and analyzed for the following factors: age, gender, date, elapsed prehospital times, incident type, mechanism of injury, call disposition, illness or injuries encountered, severity of illness/injury (by abnormal vital signs), and basic life support (BLS) and advanced life support (ALS) treatment delivered. RESULTS: A total of 1,512,907 patient care reports were reviewed. Those of 61,132 children were extracted for analysis. These children comprised about 4% of prehospital responses. Male subjects predominated (56%), and children aged 7 through 14 years represented 46% of cases. Most calls occurred in the evening and daylight hours. Children were transported by ambulance in 89% of cases, and care was refused in 7.7%. Mean response time was 9 +/- 16 minutes, mean scene time 12 +/- 14 minutes, and mean transport time 14 +/- 20 minutes. Traumatic incidents predominated at 42%, with motor vehicle accidents and falls the most common mechanisms. Blunt injuries accounted for 94% of trauma, whereas respiratory problems, seizures, and poisoning/overdose were the most common medical problems. Vital signs were obtained in 56% of cases. Abnormal vital signs were noted in 21% of these, and the presumptive causes were similar in distribution to those of the general population, with the addition of cardiac arrest. The most commonly used treatments were spinal immobilization, oxygen administration, intravenous access and several ALS medications. An ALS capability was available in more than half the runs, but ALS treatment was delivered in only 14% of those cases. Outcome data were not available. CONCLUSION: This multistate analysis of pediatric EMS epidemiology confirms findings reported in smaller regional studies, with several exceptions. Excessive scene times were not noted. Few children had serious disorders as evidenced by abnormal vital signs. An ALS treatment, when available, was used infrequently. These findings have implications for EMS planners and educators.

Adolescent↗

PubMed2005

Imputing cross-sectional missing data: comparison of common techniques.

OBJECTIVE: Increasing awareness of how missing data affects the analysis of clinical and public health interventions has led to increasing numbers of missing data procedures. There is little advice regarding which procedures should be selected under different circumstances. This paper compares six popular procedures: listwise deletion, item mean substitution, person mean substitution at two levels, regression imputation and hot deck imputation. METHOD: Using a complete dataset, each was examined under a variety of sample sizes and differing levels of missing data. The criteria were the true t-values for the entire sample. RESULTS: The results suggest important differences. If missing data are from a scale where about half the items are present, hot deck imputation or person mean substitution are best. Because person mean substitution is computationally simpler, similar in its efficiency, advocated by other researchers and more likely to be an option on statistical software packages, it is the method of choice. If the missing data are from a scale where more than half the items are missing, or with single-item measures, then hot deck imputation is recommended. The findings also showed that listwise deletion and item mean substitution performed poorly. CONCLUSIONS: Person mean and hot deck imputation are preferred. Since listwise deletion and item mean substitution performed poorly, yet are the most widely reported methods, the findings have broad implications.

Anxiety↗

PubMedDate not supplied

Vaginal birth after cesarean section: a pilot study of outcomes in women receiving midwifery care.

A recent trend discouraging or not offering women a choice to labor after a cesarean birth has resulted in higher cesarean birth rates and lower rates of vaginal birth after cesarean birth (VBAC). The few studies describing midwifery practice have demonstrated favorable outcomes; however, the studies are too small to thoroughly evaluate critical outcomes. In this retrospective descriptive study, clinical outcome data were obtained from eight midwifery practices. The aims were to collect, aggregate, and analyze data from multiple midwifery practices and then describe outcomes. Usable data representing 649 trials of labor were submitted. Overall, 72% (range 64%-100%) of women gave birth vaginally. Mean infant birth weight was 3,501 (SD = 534) g, and the mean Apgar scores were 7.99 (SD = 1.4; median 8) at 1 minute and 8.84 (SD = 0.8; median 9) at 5 minutes. Only 5.3% (n = 14) of infants were admitted to the neonatal intensive care unit. This small retrospective study demonstrates similar outcomes to those reported in the current literature. A larger prospective study to carefully describe midwifery care outcomes using a common data collection method is needed to provide evidence for determining the continuation of VBAC as part of midwifery care.

Adult↗