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PubMed2005

Differential display in rat livers treated for 13 weeks with phenobarbital implicates a role for metabolic and oxidative stress in nongenotoxic carcinogenicity.

Hepatic enzyme inducers such as phenobarbital are often nongenotoxic rodent hepatocarcinogens. Currently, nongenotoxic hepatocarcinogens can only be definitively identified through costly and extensive long-term, repeat-dose studies (e.g., 2-year rodent carcinogenicity assays). Although liver tumors caused by these compounds are often not found to be relevant to human health, the mechanism(s) by which they cause carcinogenesis are not well understood. Toxicogenomic technologies represent a new approach to understanding the molecular bases of toxicological liabilities such asnongenotoxic carcinogenicity early in the drug discovery/development process. Microarrays have been used to identify mechanistic molecular markers of nongenotoxic rodent hepatocarcinogenesis in short-term, repeat-dose preclinical safety studies. However, the initial "noise" of early adaptive changes may confound mechanistic interpretation of transcription profiling data from short-term studies, and the molecular processes triggered by treatment with a xenobiotic agent are likely to change over the course of long-term treatment. Here, we describe the use of a differential display technology to understand the molecular mechanisms related to 13 weeks of dosing with the prototype rodent nongenotoxic hepatocarcinogen, phenobarbital. These findings implicate a continuing role for oxidative stress in nongenotoxic carcinogenicity.An Excel data file containing raw data is available in full at http://taylorandfrancis.metapress.com/openurl.asp?genre=journal&issn=0192-6233. Click on the issue link for 33(1), then select this article. A download option appears at the bottom of this abstract. The file contains raw data for all gene changes detected by AFLP, including novel genes and genes of unknown function; sequences of detected genes; and animal body and liver weight ratios. In order to access the full article online, you must either have an individual subscription or a member subscription accessed through www.toxpath.org.

Animals↗

PubMed1996

A biochemical protocol for the differentiation of current genomospecies of Aeromonas.

A data file consisting of 40 biochemical and physiological tests for the differentiation of aeromonads was constructed based upon existing published data from various geographical locations and laboratories. The data file covers all the current genomospecies (or hybridisation groups) of Aeromonas and is therefore applicable to bacteriologists from a wide variety of fields. The protocol derived from the data file was adapted for use with a semi-interactive computer identification program. This program was challenged with the type strains of all the currently recognised genomospecies and each genomospecies was correctly identified, with only one strain (ATCC 7966, HG1) having an identification probability of less than 90%. The program was also tested with environmental and clinical isolates and again identifications were achieved with high probabilities. This protocol is designed for use on presumptive isolates of Aeromonas spp. and can be carried out in routine laboratories not equipped to perform the complex DNA hybridisation techniques which are currently used for the differentiation of genomospecies of Aeromonas.

Aeromonas↗

PubMed2005

Confidentiality and spatially explicit data: concerns and challenges.

Recent theoretical, methodological, and technological advances in the spatial sciences create an opportunity for social scientists to address questions about the reciprocal relationship between context (spatial organization, environment, etc.) and individual behavior. This emerging research community has yet to adequately address the new threats to the confidentiality of respondent data in spatially explicit social survey or census data files, however. This paper presents four sometimes conflicting principles for the conduct of ethical and high-quality science using such data: protection of confidentiality, the social-spatial linkage, data sharing, and data preservation. The conflict among these four principles is particularly evident in the display of spatially explicit data through maps combined with the sharing of tabular data files. This paper reviews these two research activities and shows how current practices favor one of the principles over the others and do not satisfactorily resolve the conflict among them. Maps are indispensable for the display of results but also reveal information on the location of respondents and sampling clusters that can then be used in combination with shared data files to identify respondents. The current practice of sharing modified or incomplete data sets or using data enclaves is not ideal for either the advancement of science or the protection of confidentiality. Further basic research and open debate are needed to advance both understanding of and solutions to this dilemma.

Confidentiality↗

PubMed2005

An evaluation of automated neonatal seizure detection methods.

OBJECTIVE: To evaluate 3 published automated algorithms for detecting seizures in neonatal EEG. METHODS: One-minute, artifact-free EEG segments consisting of either EEG seizure activity or non-seizure EEG activity were extracted from EEG recordings of 13 neonates. Three published neonatal seizure detection algorithms were tested on each EEG recording. In an attempt to obtain improved detection rates, threshold values in each algorithm were manipulated and the actual algorithms were altered. RESULTS: We tested 43 data files containing seizure activity and 34 data files free from seizure activity. The best results for Gotman, Liu and Celka, respectively, were as follows: sensitivities of 62.5, 42.9 and 66.1% along with specificities of 64.0, 90.2 and 56.0%. CONCLUSIONS: The levels of performance achieved by the seizure detection algorithms are not high enough for use in a clinical environment. The algorithm performance figures for our data set are considerably worse than those quoted in the original algorithm source papers. The overlap of frequency characteristics of seizure and non-seizure EEG, artifacts and natural variances in the neonatal EEG cause a great problem to the seizure detection algorithms. SIGNIFICANCE: This study shows the difficulties involved in detecting seizures in neonates and the lack of a reliable detection scheme for clinical use. It is clear from this study that while each algorithm does produce some meaningful information, the information would only be usable in a reliable neonatal seizure detection process when accompanied by more complex analysis, and more advanced classifiers.

Action Potentials↗

PubMed2003

[Master sample and geoprocessing: technologies for household surveys].

OBJECTIVE: To reduce cost and time associated with household sampling process and to assess the feasibility of shared use of address data file of census enumeration areas in several epidemiological surveys using updated information from the National Survey of Households (PNAD). METHODS: Address data file comprising 72 census enumeration areas was kept as primary sampling units for the city of S o Paulo. During the period 1995-2000, three distinct household samples were drawn using the two-stage cluster sampling procedure. Geographic Information System (GIS) technology allowed delimiting boundaries, blocks and streets for any primary sampling unit and printing updated maps for selected sub-samples. RESULTS: Twenty-five thousand dwellings made up the permanent address data file of the master sample. A cheaper and quicker selection of each sample, plus gathering information on demographic and topographical profiles of census enumeration areas were the main contribution of the study results. CONCLUSIONS: The master sample concept, integrated with GIS technology, is an advantageous alternative sampling design for household surveys in urban areas. Using the list of addresses from the PNAD updated yearly, although limiting its application to the most populated Brazilian cities, avoids the need of creating an independent sampling procedure for each individual survey carried out in the period between demographic censuses, and it is an important contribution for planning sampling surveys in public health.

Censuses↗

PubMed1995

A computer program for the analysis of chromatograms used in pharmacokinetic studies.

An analog/digital (A/D) converter and software written in BASIC language have been developed for the analysis of chromatographic data which are needed for pharmacokinetic (PK) studies in humans and in experimental animals such as dogs and rats. Using an A/D converter, widely sold personal computers produced by NEC or EPSON are applicable to both high-performance liquid-chromatography (HPLC) data analysis and PK analysis. When chromatographic data is taken up by the computer and treated as a variable, a maximum of 12,000 data points are saved by the computer. As 10 digital data points are taken up by the computer per second through the A/D converter, the maximum run time of a chromatogram is 20 min. For the purpose of HPLC analysis, however, five digital data points per second are usually enough for routine analysis. In this software, the program is written to take and save five digital data points/s. Therefore, the maximum run time of this software increased to 40 min per chromatogram. All the digital data through the A/D converter are saved into the data file on a floppy disk or hard disk. For the chromatogram analysis, both automatic peak identification and manual peak identification, which must be selected with the use of the mouse driver, are available. All the data, peak area, peak height, etc. are also saved into the data file. After a calibration curve is produced, following the input of peak analysis data of known spiked samples, the drug concentration for each sample is estimated. These concentration-time data are also saved into the data file.(ABSTRACT TRUNCATED AT 250 WORDS)

Analog-Digital Conversion↗

PubMed1996

Predicting ad libitum dry matter intake and yields of Jersey cows.

Two data files were used that contained weekly mean values for ad libitum DMI of lactating Jersey cows along with appropriate cow, ration, and environmental traits for predicting DMI. One data file (n = 666) was used to develop prediction equations for DMI because that file represented a number of separate experiments and contained more diversity in potential predictors, especially those related to ration, such as forage type. The other data file (n = 1613) was used primarily to verify these equations. Milk protein yield displaced 4% FCM output as a prediction variable and improved the R2 by several units but was not used in the final equations, however, for the sake of simplicity. All equations contained adjustments for the effects of heat stress, parity (1 vs. > 1), DIM > 15, BW, use of recombinant bST, and other significant independent variables. Equations were developed to predict DMI of cows fed individually or in groups and to predict daily yields of 4% FCM and milk protein; equations accounted for 0.69, 0.74, 0.81, and 0.76 of the variation in the dependent variables with standard deviations of 1.7, 1.6, 2.7, and 0.084 kg/ d, respectively. These equations should be applied to the development of software for computerized dairy ration balancing.

Animal Feed↗

PubMed1998

Managing data for a randomised controlled clinical trial: experience from the WHO Antenatal Care Trial. WHO Antenatal Care Trial Research Group.

The World Health Organisation, in collaboration with four developing countries, is conducting a randomised controlled clinical trial to evaluate a new programme of antenatal care. In a city or region in Argentina, Cuba, Saudi Arabia and Thailand, 53 clinical units were randomly allocated to provide either the new programme or the programme currently in use. This paper describes the organisation of the data management system used to collect the data. Each woman participating in the trial is uniquely identified, and information such as her name, address and expected delivery date is recorded in the trial 'subject number list'. If the clinic belongs to the intervention group, information about the woman's eligibility is recorded on the classification form. Details of the outcome of the pregnancy are indicated on two additional case report forms: the antenatal hospital admission form and the summary form. When forms are completed by the investigators, they are submitted to the country data coordinating centre (CDCC). The CDCCs are responsible for the processing of the country study forms. This includes verification of the batch of forms, data capture into computer files, data verification, data validation, production of query sheets for data problems, maintenance and updating of study master files. All operations on data such as additions or modifications are performed using transaction processing. At monthly intervals, recruitment reports and transaction files are sent to the trial coordinating centre in Geneva. All transaction files are processed to accumulate data on the trial's consolidated master files. A monthly report including number of women recruited in the trial, adverse events reported by the countries, recruitment charts by clinic and analyses on eligible women in the intervention group is prepared and submitted to the data safety and monitoring committee. A workshop was organised in 1995, before the start of the trial, to introduce the data management system to the four participating countries. Annual site visits were made to each CDCC to monitor progress. Additional visits were made when major or critical problems could not be solved by the CDCC. At the closure of data collection, a visit is made to review and assess all data management procedures including form filling, maintenance of registers, computer files, query sheets, data modifications. In addition, final cleaning of the data is performed, and an analysis file is produced for inclusion in the centralised trial analyses and in the country-specific analyses. Based on the experience gained in this trial, the decentralised data management model can be advocated only if CDCCs that will be involved in the trial are already in place with competent and experienced staff. Uniformity of the data management system and of standard operating procedures across countries is also a crucial issue for the effective management of the data collection phase.

Argentina↗

PubMed2006

Characteristics and profile of boys and girls with emotional and behavioural disorders in Flanders mental health institutes: a quantitative study.

BACKGROUND: In this article, we search for gender differences and outline a detailed gender profile for children and youngsters with emotional and behavioural disorders who are placed in Flemish residential care institutes. METHODS: Data were collected of all placements (517 children) in six residential and semi-residential mental health care centres for children and youngsters with emotional and behavioural disorders in East Flanders, Belgium. File data (gender, age, retention, current treatment, type of referral, education, intelligence, Diagnostic and Statistical Manual IV-diagnoses and medication use) were gathered. The Child Behaviour Check List (CBCL) was implemented and completed for each child. On the basis of the CBCL, a behaviour profile was developed by means of correlation tables (Pearson correlation coefficient) and cross tabulations. Finally, the profile was compared with the file data of the boys and the girls. RESULTS: Significant gender differences were found for type of referral, intelligence and diagnoses. The same profile was developed for both genders separately, based on variables Externalizing and Social Problems. The file data associated with the profile groups differ for boys and girls. CONCLUSIONS: The results of our study show the complexity and diversity of the needs of boys and girls with disruptive behaviour in Flemish residential care institutes. Flemish government has to be aware of the fact that the current referral system selects the children with outspoken externalizing and problematic behaviour towards special health care and special schools. They are relegated because the mainstream system is not equipped well enough to cope with their disruptive, aggressive behaviour. Even if governments are in favour of inclusive education, it seems that in practice a rest group is created, in which girls are selected through the same mechanisms as boys, in this case for the same reasons of negative externalizing behaviour and social problems. For this it seems appropriate that school and (semi)-residential institutes apply a specific and adapted methodology.

Adolescent↗

PubMed1992

The development and use of industry data by the Social Security Administration.

Over the past few years the Social Security Bulletin has published a series of technical articles that describe various Social Security Administration (SSA) data files. This article provides an overview of SSA's industry-related data files and statistical systems from both a current and a historical perspective. The author begins by explaining how SSA first collected business data from employers (starting in 1937) as a by-product of the requirement that employers report employee wages for benefit computation purposes. She describes the administrative methods by which the data are collected, SSA's coordination of its activities with other agencies, the data collection forms used, the scheme by which the data are coded, and the employer files into which the data are classified. In her closing, the author provides examples of the various uses of the industry data and the ways that these data relate to SSA's statistical program needs and to those of other agencies as well.

Data Collection↗

PubMed1990

Managing clinical research data: software tools for hypothesis exploration.

Data representation, data file specification, and the communication of data between software systems are playing increasingly important roles in clinical data management. This paper describes the concept of a self-documenting file that contains annotations or comments that aid visual inspection of the data file. We describe access of data from annotated files and illustrate data analysis with a few examples derived from the UNIX operating environment. Use of annotated files provides the investigator with both a useful representation of the primary data and a repository of comments that describe some of the context surrounding data capture.

Data Interpretation, Statistical↗

PubMed2000

Nitric oxide for respiratory failure in infants born at or near term.

BACKGROUND: This section is under preparation and will be included in the next issue. OBJECTIVES: To determine whether treatment of hypoxemic newborn infants with inhaled nitric oxide (INO) improves oxygenation and reduces the rates of death, or the requirement for ECMO. SEARCH STRATEGY: Electronic and hand searching of pediatric/neonatal literature and personal data files. In addition we contacted the principal investigators of articles which have been published as abstracts to ascertain the necessary information. SELECTION CRITERIA: Randomized and quasi randomized studies in term and near term infants. Administration of inhaled nitric oxide. Clinically relevant outcomes, including death, requirement for ECMO, and oxygenation. DATA COLLECTION AND ANALYSIS: Eight randomized controlled studies were found in term and near term infants with hypoxia. Entry criteria were reasonably consistent except for the one trial that studied only infants with congenital diaphragmatic hernia (Ninos 1997). MAIN RESULTS: Inhaled nitric oxide appears to improve outcome in hypoxemic term and near term infants by reducing the incidence of the combined endpoint of death or need for ECMO. The reduction seems to be entirely a reduction in need for ECMO; mortality is not reduced. Oxygenation improves in approximately 50% of infants receiving nitric oxide. The Oxygenation Index decreases by a (weighted) mean of 15.1 within 30 to 60 minutes after commencing therapy and PaO2 increases by a mean of 53 mmHg. It does not appear to affect outcome whether infants have clear echocardiographic evidence of PPHN or not. The outcome of infants with diaphragmatic hernia was not improved; indeed there is a suggestion that outcome was slightly worsened. REVIEWER'S CONCLUSIONS: On the evidence presently available, it appears reasonable to use inhaled nitric oxide in a concentration of 20 ppm for term and near term infants with hypoxic respiratory failure who do not have a diaphragmatic hernia. Longterm neurodevelopmental and pulmonary followup of surviving infants enrolled in randomized trials of INO are required to establish more firmly the role of INO in the treatment of neonatal respiratory failure.

Fetal Hypoxia↗

PubMedDate not supplied

[Intraoperative complications in extracapsular extraction with a posterior-chamber lens implant. Medical record data].

This scientific work includes the retrospective study of the intra-operatory complications in 150 cases of cataract operated eyes, using extracapsular implant of artificial crystalline in the posterior chamber; the study is based on the operatory data file, filled in by the surgeon immediately after the operation. The data file we are submitting to your attention can be registered on a floppy disk; it includes the most important data concerning the patient, the type of the cataract, the operatory techniques, the incidents that might occur and the most appropriate method to solve them. The registration on file of the operatory data has proven its efficiency while grouping, inventorying and processing data, but also while determining the conclusions of the prophylactic measures. The rupture of the anterior capsula till the zonular zone occurred in 0.66% of the cases; capsular rests--2%; sphincter lesions--1.33%; iris lesions--0.66%, endothelium lesions--1.33%; posterior capsula rupture--2.66%, followed by anterior vitrectomy and implant of an artificial crystalline in the anterior chamber.

Cataract Extraction↗

PubMed2004

A suitable method for identifying cell aggregates in laser scanning cytometry listmode data for analyzing disaggregated cell suspensions obtained from human cancers.

BACKGROUND: The presence of cell aggregates in cell suspensions obtained from human solid tumors can interfere with the measurement of cell DNA content of cell singlets, and can confound multiparameter analysis of other measurements on the same cells. Flow cytometric corrections for cell aggregates based on signal pulse shape have not proven to be reliable. Mathematical models have been developed to correct for cell aggregates in binned DNA histogram data, but they are not suitable for the correction of correlated non-DNA measurements obtained on the same cells. METHODS: A total of 21 samples representing a variety of normal and malignant human cell types, including normal lymphocytes, normal sputum, human breast cancer cell lines, and mechanically disaggregated cell suspensions from primary breast cancers and nonsmall cell lung cancers, were studied by laser scanning cytometry (LSC) using the CompuCyte laser scanning cytometer (Cambridge, MA). Nuclear area, nuclear perimeter, and an LSC-based cell texture parameter were measured on approximately 400 cells in each sample, using an air-cooled, violet laser emitting at a wavelength of 405 nm for DAPI excitation, and each cell was classified as a singlet or aggregate by its appearance under direct observation. A "saddle function" provided by CompuCyte was used, together with an algorithm based on the measurements of nuclear area, perimeter, and cell texture (the APT algorithm), to identify cell aggregates and exclude them from the listmode data file. RESULTS: Proportions of cell aggregates in the uncorrected samples ranging from 6 to 56% (mean, 20%) were reduced to proportions ranging from 0 to 7% (mean, 2.4%) after correction. The discriminant function was "tuned" to maintain both average cell singlet purity and average cell singlet yield at >70% over a broad range of cell DNA contents. CONCLUSIONS: A combined approach to cell aggregate detection, which utilizes both the saddle function and the APT algorithm, produces list mode data files that exclude >80% of cell aggregates from samples of disaggregated cell suspensions of human tumors and other sources of clinical material. Such data files are suitable for multiparameter analysis.

Algorithms↗

PubMed1995

Preparing for health care reform and an LCME site visit: addressing the generalist-non-generalist imbalance.

PURPOSE: The purpose of the present study was to evaluate primary care outcomes for the Loma Linda University School of Medicine (LLUSM), using Association of American Medical Colleges (AAMC) data files. The two principal objectives were to estimate the percentages of LLUSM graduates who are practicing or will practice primary care medicine and to determine what information available on application to LLUSM is useful in predicting graduates' specialty choices (i.e., primary versus non-primary care). METHOD: In 1993-94 data were taken from several AAMC data files (available to all medical schools), including the Graduate Medical Education (GME) Tracking Census and the American Medical College Application Service (AMCAS) Applicant Master File. The second and fourth years after graduation were used as points of evaluation. Primary care (generalist) was defined as taking or having completed a residency in family practice, internal medicine, or pediatrics, and not having taken any fellowship training. RESULTS: Fourth year after graduation: 42.4% of the 1,064 LLUSM graduates (1983 to 1990) were training in or had completed residencies in family practice (19.8%), internal medicine (16.2%), or pediatrics (6.4%). Second year of GME: of the 1,365 LLUSM graduates (1983 to 1992), 49.3% were in the primary care pipeline (19.8% in family practice, 21.9% in internal medicine, and 7.6% in pediatrics). Two variables available on admission to medical school were associated with being in the primary care pipeline (second-year GME generalist): being a woman and being a member of a non-underrepresented minority. One variable was associated with being in the non-primary care pipeline: having a rural county code. Undergraduate grades and Medical College Admission Test scores were not good predictors. CONCLUSION: The AAMC data files, available to all medical schools, are useful for estimating and evaluating primary care outcomes.

Career Choice↗

PubMedDate not supplied

A simple automated procedure for the detection and identification of peaks in gas chromatography--continuous scan mass spectrometry. Application to systematic toxicological analysis of drugs in whole human blood.

Gas chromatography-mass spectrometry (GC-MS), which combines the separation power of GC with the power of MS for the identification of unknown compounds, possesses high potential in systematic toxicological analysis (STA). Different factors, however, do not allow this potential to be fully exploited. Between them, the low selectivity of the mass spectrometer operating in continuous scan plays a critical role, in many cases precluding the possibility of selecting mass spectra in the total ion chromatogram (TIC) sufficiently clean for a positive identification by library search, even when using reverse search algorithms. Moreover, the large amount of information contained in GC-MS data file that results from the analysis of a biological extract makes the efforts of manual search almost useless and requires the availability of reliable methods for the automated detection and identification of peaks in a TIC. In this paper, a simple procedure that improves the performance of a bench-top GC-MS system in the purification of mass spectra of coeluting compounds and that can be easily combined with the automated processing of a GC-MS data file is described. It is based on the subtraction of the intensities of successive pairs of scans in the TIC, on the detection of positive and negative peaks in the transformed chromatograms, and on the search of the corresponding background-subtracted electron ionization mass spectra against reference libraries. In order to evaluate the proposed procedure, GC-MS data files obtained for the analysis of extracts of blank whole blood spiked with more than 100 drugs, poisons, and their metabolites at a concentration of 0.5 mg/L were used. Compared with the search of the raw TICs, the proposed procedure increased the number of identified substances and, in many cases, obtained higher match quality values for identification.

Amitriptyline↗

PubMed1991

["MEDDOS", a computer program for constructing treatment plans in pediatric intensive care units].

We attempted to facilitate the establishment of treatment regimens in paediatric intensive care units by means of a computer programme and to increase drug safety by standardization of dosage and avoidance of calculation errors. The programme has the following features: the user can enter drugs, oral nutrition and i.v. solutions into data files. Drugs and solutions can be chosen from these data files for the individual patient. Drug dosage is calculated from preselected dosages and the patient's data for individual dosage regimens. The desired intake of fluid volume and glucose can be chosen. Due to this preselection the quantity and concentration of the glucose solution is calculated. The total daily intake of electrolytes, calories, carbohydrates, protein and fat is shown on a balance sheet. Complete schedules can be saved and, if needed, restored for other patients.

Child↗

PubMed1996

Interobserver variability in the classification of neonatal seizures based on medical record data.

This population-based, retrospective cohort study of neonatal seizures included all 16,428 neonates born to residents of Fayette County, Kentucky, from 1985 to 1989. Eighty potential cases were ascertained by computer search of hospital-based medical record systems, birth certificate data files, and multiple-cause-of-death mortality data files. Medical records for potential cases were abstracted, and relevant portions were reviewed independently by three neurologists using prospectively determined criteria. Both unweighted and weighted kappa statistics were used to measure agreement between each pair of observers in the classification of potential cases as seizures, possible seizures, or not seizures, adjusting for the proportion of agreement expected by chance. Agreement in the classification of potential cases was excellent (kappa = 0.72-0.79, average = 0.76; weighted kappa = 0.85-0.88, average = 0.87). The kappa extension statistic of Kraemer was used to assess agreement in the classification of seizure types by a simplification of the classification scheme of Volpe. This documented excellent agreement between raters in the classification of seizure types (kappa e = 0.72). Experienced raters can reliably classify potential cases of neonatal seizures using seizure descriptions transcribed from medical records.

Cohort Studies↗