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PubMed1996

Relationships between polymorphism for mitochondrial deoxyribonucleic acid and yield traits of Holstein cows.

Two independent data files from the breeding herd of Iowa State University and six North Carolina herds were used to examine relationships between yield traits and mtDNA polymorphism. Maternal lineages were established by tracing ancestry of cows to founder females in the herd book of the Holstein Association. Data from Iowa State University were 1476 records from 602 cows from 29 maternal lineages. The nucleotides of mtDNA encoding rRNA were sequenced. Eleven sites of polymorphism were found. An animal model for gene substitution was used to examine the relationship between sequence differences and yield traits. Traits analyzed were mature equivalent yield of milk, fat, SNF, and milk energy as well as concentrations of fat, SNF, and milk energy. Effects of sequence differences were significant for most traits. Sequence information from the D-loop was available for 12 lineages from North Carolina. The effect of polymorphism at 4 sites was examined using 1472 records from 668 cows. Traits measured were the same, except that protein replaced SNF. No significant relationships existed between any of the traits and D-loop polymorphism, but results suggested that an association might exist between polymorphism and concentrations of milk yield, fat percentage, and energy. Whenever a significant relationship was detected, the effect of mutation (rare genotype) was detrimental.

Animals↗
PubMed2000

Umbilical artery catheters in the newborn: effects of heparin.

BACKGROUND: This section is under preparation and will be included in the next issue. OBJECTIVES: To determine whether the use of heparin in fluids infused through an umbilical arterial catheter in newborn infants influences the frequency of clinical ischemic events, catheter occlusion, aortic thrombosis, intraventricular hemorrhage, hypertension, death, or the duration of catheter usability. SEARCH STRATEGY: Randomized and quasi randomized controlled trials of umbilical catheterization use were obtained from the following sources: 1. Effective Care of the Newborn Infant, edited by JC Sinclair and MB Bracken. 2. Medline Search using Melvyl Medline Plus and the keyword headings 'Umbilic#', 'Catheter#' and subject heading 'Infant, Newborn' 3. Search of personal data files SELECTION CRITERIA: Randomized trials in newborn infants of any birthweight or gestation. Comparison of heparinised to non heparinised infusion fluids, including comparison of heparin in the infusate to heparin just in the flush solution. Clinically important end points such as catheter occlusion or aortic thrombosis. DATA COLLECTION AND ANALYSIS: There were five randomized controlled trials retrieved. All gave details of the incidence of catheter occlusion. Two also reported the incidence of aortic thrombosis. The intervention was reasonably consistent: heparin in the infusate at a concentration of 1 unit/mL was investigated in all trials except one which used a concentration of 0.25 units/mL. Studies generally included both term and preterm infants. MAIN RESULTS: Heparinization of the infusate decreases the incidence of catheter occlusion but does not affect the frequency of aortic thrombosis. Heparinization of the flush solution is not an adequate alternative. There does not appear to be an effect on frequency of intraventricular hemorrhage, death or clinical ischemic phenomena. REVIEWER'S CONCLUSIONS: Heparinization of the fluid infused through an umbilical arterial catheter decreases the likelihood of umbilical arterial catheters occluding. The lowest concentration tested so far (0.25 units/mL) has been shown to be effective. Heparinization of flushes without heparinizing the infusate is ineffective. The frequency of aortic thrombosis has not been shown to be affected; however, the confidence intervals for this effect are very wide. The frequency of intraventricular hemorrhage has not been shown to be affected by heparinization of the infusate, but again the confidence intervals are very wide and even a major increase in the incidence of grade 3 and 4 intraventricular hemorrhage would not have been detected.

Anticoagulants↗
PubMed2005

Efficient unsupervised algorithms for the detection of seizures in continuous EEG recordings from rats after brain injury.

Long-term EEG monitoring in chronically epileptic animals produces very large EEG data files which require efficient algorithms to differentiate interictal spikes and seizures from normal brain activity, noise, and, artifact. We compared four methods for seizure detection based on (1) EEG power as computed using amplitude squared (the power method), (2) the sum of the distances between consecutive data points (the coastline method), (3) automated spike frequency and duration detection (the spike frequency method), and (4) data range autocorrelation combined with spike frequency (the autocorrelation method). These methods were used to analyze a randomly selected test set of 13 days of continuous EEG data in which 75 seizures were imbedded. The EEG recordings were from eight different rats representing two different models of chronic epilepsy (five kainate-treated and three hypoxic-ischemic). The EEG power method had a positive predictive value (PPV, or true positives divided by the sum of true positives and false positives) of 18% and a sensitivity (true positives divided by the sum of true positives and false negatives) of 95%, the coastline method had a PPV of 78% and sensitivity of 99.59, the spike frequency method had a PPV of 78% and a sensitivity of 95%, and the autocorrelation method yielded a PPV of 96% and a sensitivity of 100%. It is possible to detect seizures automatically in a prolonged EEG recording using computationally efficient unsupervised algorithms. Both the quality of the EEG and the analysis method employed affect PPV and sensitivity.

Algorithms↗
PubMed1982

Microcomputer assisted interpretative reporting of protein electrophoresis data.

A microcomputer based system for interpretative reporting of protein electrophoretic data has been developed. Data for serum urine, and cerebrospinal fluid protein electrophoreses as well as immunoelectrophoresis can be entered. Patient demographic information is entered through the keyboard, followed by manual entry of total and fractionated protein levels obtained after densitometer scanning of the electrophoretic strip. Protein patterns are coded, interpreted, and final reports generated. In most cases, interpretation time is less than one second. Computer misinterpretation is uncommon and easily corrected by edit functions within the system. Discrepancies between computer and pathologist interpretation are automatically stored in a separate data file for later review and possible program modification. Any or all previous tests on a patient may be reviewed, with graphic display of the electrophoretic pattern. The system is well-accepted by the laboratory staff, and allows rapid storage, retrieval, and analysis of protein electrophoretic data.

Blood Protein Electrophoresis↗
PubMed2004

Dialyser reuse-associated mortality and hospitalization risk in incident Medicare haemodialysis patients, 1998-1999.

BACKGROUND: The reuse of haemodialysers has been practiced in the United States for >20 years. We investigated mortality and hospitalization risk according to various reuse practices, testing the hypothesis that outcomes are improved in patients treated with dialysers cleaned with bleach and sterilized with formaldehyde. METHODS: We studied 1998 and 1999 incident Medicare haemodialysis patients, with follow-up through December 31, 2000 (49 273 patients). Clinical conditions and dialysis therapy were characterized from Medicare claims data. Included were patients who could be linked to a dialysis provider. Demographic characteristics were obtained from the Centers for Medicare and Medicaid Services (CMS) Medical Evidence Report. Mortality information was obtained from the CMS ESRD Death Notification; hospitalization information, from Medicare in-patient claims files. Data on reuse practices were obtained from the annual survey of haemodialysis units conducted by the Centers for Disease Control and Prevention. RESULTS: Cox regression analyses found no significant differences in mortality or first-hospitalization risk for patients in dialysis units not using bleach as a cleaning agent. Outcomes for patients treated in units using glutaraldehyde did not vary according to use of bleach. In the analysis of first-hospitalization risk, there was no difference according to various germicide/bleach combinations. Overall, there was no significant difference in relative risk of death or in hospitalization risk among the reuse groups (including the no-reuse group). CONCLUSIONS: For the 1998-1999 period, reuse practices were not associated with a survival advantage or disadvantage. Our findings may reflect the National Kidney Foundation's 1997 introduction of clinical practice guidelines, the intent of which was to bring about increased consistency of care within the dialysis community in the United States.

Equipment Reuse↗
PubMed2005

Functioning, problem behavior and health services use among nursing home residents with alcohol-use disorders: nationwide data from the VA minimum data set.

OBJECTIVE: We examined (1) whether nursing home residents with alcohol-use disorders (AUDs) function more poorly, have more behavioral problems and use more health services than do demographically matched controls without such disorders, and (2) whether AUDs interact with alcohol consumption to predict poorer behavioral and health services outcomes among nursing home residents. METHOD: We used Department of Veterans Affairs (VA) Patient Treatment File data to identify a nationwide sample of older VA nursing home residents with recent AUD diagnoses (n = 3,336) and a demographically matched sample without such diagnoses (n = 3,336). The groups were compared on the Resident Assessment Instrument Minimum Data Set indices of health-related functioning, substance use, problem behavior and health services use. We conducted two-way analyses of variance to determine interactions between presence of an AUD and alcohol consumption on problem behavior and health services use. RESULTS: Residents with AUD diagnoses functioned somewhat better than demographically matched controls. However, they were more likely to have falls and fractures, difficulties in social functioning and to use more health services. AUD diagnoses interacted with alcohol consumption to predict an elevated risk of falls and fractures and more mental health services use. CONCLUSIONS: Older residents with an AUD form a distinct nursing home population that functions somewhat better than residents without such disorders but they may pose more challenges to staff and use more health care services. Residents' drinking histories should be considered in formulating nursing home policies about alcohol consumption.

Aged↗
PubMed1998

Computer assisted neurophysiology by a distributed Java program.

We have developed a distributed software package which allows neurophysiologists to have at hand a set of network and graphic tools in order to perform the analysis of data collected from the electrical activity of neurons, studied in the experimental laboratory. This system is built around three major components. First, the experimental data are processed in order to select specific data files from the networked computer and display the spike trains as raster dots. The second part selects one type of analysis (e.g., cross-correlation, out of a set of possible choices) after configuration of some specific parameters. Finally, the third component deals with the results of data analyses, which are selected and displayed on a multi-parameter graphic "ring binder." We have used the Java programming language to implement this application. This recent object-oriented language offers platform-independent software tools including graphic package and standard network protocols.

Algorithms↗
PubMedDate not supplied

Software for efficient visualization and analysis of multiple, large, multi-dimensional data sets from magnetic resonance imaging.

Comprehensive magnetic resonance imaging (MRI) protocols create multiple, large, multi-dimensional data sets that are challenging to review and interpret in an efficient manner. We report on a program called CliniViewer that uses a common data file format to display all files originating from the scanner and other post-processing programs in an integrated display matrix. The five rows of images and maps have general themes of Anatomic Images, Echo-Planar Images, Parametric Maps (derived from echo-planar images), Metabolic Images, and Non-Image Data, respectively. Each row of the matrix contains related image windows of individual MR acquisitions or maps derived from such acquisitions.An interpreter can quickly screen all images and then select any image from the display to create a separate daughter window incorporating a set of analysis tools for in-depth examination. Given that the images can be acquired in the same co-registered planes without moving the subject, regional analysis can be performed simultaneously across multiple MR image types and the corresponding maps, thereby integrating anatomic features with parametric properties. Color can be used to highlight parametric values that fall outside normal ranges to quickly identify abnormalities on each map. CliniViewer is an efficient environment for analyzing multiple images and maps from comprehensive clinical imaging protocols, aiding the neuroradiologist in providing an integrated interpretation of all available MR data for efficient clinical decision making. CliniViewer is compared to AnalyzeAVW and NIH Image, two popular MR image analysis tools. CliniViewer allows efficient clinical analysis of multiple images and maps from comprehensive clinical imaging protocols.

Brain↗
PubMed2004

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

MOTIVATION: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. RESULTS: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. AVAILABILITY: http://www.molgenis.nl

Computational Biology↗
PubMed1988

A peak detector program for event-related potentials.

A computer program, developed for peak detection of averaged evoked potential waveforms, is described. The program is able to automatically score up to 200 data files in a single session. The user is asked to define intervals (windows) in which a maximum peak is to be detected. The program can optionally search each EEG channel or a single 'reference' channel from which all other channels will be compared. The mean amplitude of several data points can also be computed within a particular window. When evoked potentials are particularly noisy, it is possible to estimate the 'signal' in the higher frequency background 'noise'. Because the program is written in BASIC, it can be readily transferred to many different computer systems.

Arousal↗
PubMedDate not supplied

[The mortality of a retrospective cohort of workers in a Spanish iron and steel plant. The methodological problems in defining the cohort].

The work environment of an iron foundry involved a large number of exposures related to several health problems, mainly lung cancer. "Altos Hornos del Mediterráneo (AHM)" fron Sagunto is an iron industry that stopped its foundry plant production in 1984. The present paper shows the methodological problems merged during the reconstruction of AHM workers' cohort. From personnel files a male cohort was defined for 7,018 males who worked at least one year and started work between 1950 and 1970, following them through 1991. The cause of death was obtained from de Civil register, Life insurance and reference hospitals. By means of experts the work areas were rated in three exposure levels. 6% of cohort members were lost during the follow-up. 2786 deaths were reported and 88% causes of death were retrieved. The enterprise data files let us to reconstruct the cohort, but the availability of a National Death Index, as there is in other countries would have made easier the job and would have improved the data quality.

Cause of Death↗
PubMed2001

Using force analysis to target collection and analysis of environmental information.

Knowledge of the forces driving and modifying ecosystems can be employed in concert with signal analysis to target the data most likely to yield sensitivity and resilience information. One can optimize return of information per investment of resources by targeting segments of signals that are dominated by the force of interest, coupled with scientific understanding of the system of interest. This force analysis approach is an effective means both to design efficient new monitoring programs and to target relevant information in large data files. We present five example applications of force analysis. Three examples illustrate this approach for an evaluation of whether Canadian rivers might be sensitive to changes in climate. It was concluded that Canadian rivers appear to be sensitive to changing climate. A fourth example illustrates how automated snow pillow data may be evaluated to ascertain the sensitivity of snow accumulation to change in climate. It was concluded that snow accumulation at the site evaluated did appear to be sensitive to changing climate. The fifth example illustrates the assessment of whether a river recovers with the elimination of inputs of iron from an abandoned mine. It was concluded that resilience remained unproven since the river had not as yet restabilized. The force analysis approach focuses data collection or data evaluation on those data required to answer specific resource management questions, greatly reducing collection or consideration of data that are not relevant to that question. This approach is potentially very cost-efficient and therefore is likely to be of interest to hydrologists, climatologists, and environmental data managers.

British Columbia↗
PubMed2006

[Management of in utero foetal death: Which assessment to undertake?].

OBJECTIVE: To assess the value of para-clinical exams prescribed in case of in utero foetal death, to result in the establishment of a new algorithm of diagnostic tests. MATERIALS AND METHODS: A retrospective analysis on a series of 106 stillbirths gathered between September 1989 and December 1998 in the obstetrical and gynaecological department of the Lausanne University Hospital which is a tertiary centre. Stillbirth was defined as foetal death occurring as from the date of foetal viability. Thus, only pregnancies from 24 weeks and onwards were included in this series. We excluded all stillbirths occurring during medical termination of pregnancy and cases with incomplete data files. The Fretts' classification was used. The different exams asked by the physician were screened and we analysed their pertinence to determine the aetiological diagnosis for each case. The search for significant risk factors was also taken into account. We compared our management of in utero foetal death with data from the literature to propose a new algorithm. RESULTS: The aetiology of in utero foetal death could be attributed in ninety percent of the cases. The principal causes were in utero growth retardation (19.8%), foetal congenital and chromosomal anomalies (18.9%), infections (15.1%), placental abruption (7.5%), preeclampsia (5.6%), maternal diabetes (3.8%). The remaining 18.9% are divided in to miscellaneous causes. In 10.4% of the cases we could not find any explanation to the death of the foetus. The exams that yielded the most information when done were: foetal autopsy which was abnormal in 92.7%, placental investigation which was abnormal in 93% and the babygramme (X-ray of the foetal skeleton) which was abnormal in 53%. Maternal serology for infections was informative in 6.6% of the cases. CONCLUSION: We present here a protocol for the diagnostic management of stillbirth which is differentiated according to the circumstances surrounding the event. This should prove useful to reduce superfluous tests.

Abruptio Placentae↗
PubMed2003

Probing conformation and conformational change in proteins is optimally undertaken in relative mode.

Hydrodynamic bead modelling has been widely used in attempts to assess the 3D conformation of proteins in solution. Initially, simple models employing only a small number of beads were used, with a considerable degree of success. Latterly, high-resolution bead models based upon atomic coordinates have been developed, and much more sophisticated questions can in principle be addressed. A detailed analysis is presented of the errors involved in the generation of such models and associated prediction of (translational friction) parameters, and in the practical measurement of these parameters for comparison. It is shown that in most cases, for a particle of only moderate asymmetry, the errors are such that it is not feasible to determine, on an absolute basis, which of a range of candidate conformers is the "correct" one. However, when the properties of the candidate conformers can be compared in relation to those of a "paradigm conformer", whose structure in solution, on the basis of external evidence, can be accepted as correct, then errors cancel and very precise comparisons become possible. The generation of 3D bead models (and hence 3D data files) for a range of candidate conformers is a simple matter, using the existing program MacBEADS, further facilitated by a 3D display module (pro Fit).

Centrifugation, Density Gradient↗
PubMed1997

The National Cancer Data Base and physician network.

The National Cancer Data Base (NCDB) is a nationwide outcomes database for oncology presently including 1,600 hospitals in 50 states. Half of all U.S. cancer cases are accessioned annually. It is important for U.S. clinicians and health information management professionals to become familiar with the NCDB to increase the usefulness of this comparative database in their hospital quality assurance programs. The NCDB's unique characteristics include its implementation by clinicians, its provision of access to data from hospitals participating in the Approvals Program of the Commission on Cancer, and its affiliation with a 2,200-member national physician network. The NCDB annual data are augmented by patient care evaluation studies, which provide a capability for cross-sectional surveys with an expanded data set. The NCDB has participated in the significant data standardization effort for U.S. cancer registries. The procedures used maintain confidentiality of the patient, physician, and participating hospital, and physical access to the data files is limited. The three primary products of the NCDB are hospital comparative reports, state and local reports, and scientific reports.

Cancer Care Facilities↗
PubMed2003

Analysis of pooled data from the randomised controlled trials of endarterectomy for symptomatic carotid stenosis.

BACKGROUND: Endarterectomy reduces risk of stroke in certain patients with recently symptomatic internal carotid stenosis. However, investigators have made different recommendations about the degree of stenosis above which surgery is effective, partly because of differences between trials in the methods of measurement of stenosis. To accurately assess the overall effect of surgery, and to increase power for secondary analyses, we pooled trial data and reassessed carotid angiograms. METHODS: We pooled data from the European Carotid Surgery Trial (ECST), North American Symptomatic Carotid Endarterectomy Trial, and Veterans Affairs trial 309 from the original electronic data files. Outcome events were re-defined, if necessary, to achieve comparability. Pre-randomisation carotid angiograms from ECST were re-measured by the method used in the other two trials. RESULTS: Risks of main outcomes in both treatment groups and effects of surgery did not differ between trials. Data for 6092 patients, with 35000 patient-years of follow-up, were therefore pooled. Surgery increased the 5-year risk of ipsilateral ischaemic stroke in patients with less than 30% stenosis (n=1746, absolute risk reduction -2.2%, p=0.05), had no effect in patients with 30-49% stenosis (1429, 3.2%, p=0.6), was of marginal benefit in those with 50-69% stenosis (1549, 4.6%, p=0.04), and was highly beneficial in those with 70% stenosis or greater without near-occlusion (1095, 16.0%, p<0.001). There was a trend towards benefit from surgery in patients with near-occlusion at 2 years' follow-up (262, 5.6%, p=0.19), but no benefit at 5 years (-1.7%, p=0.9). INTERPRETATION: Re-analysis of the trials with the same measurements and definitions yielded highly consistent results. Surgery is of some benefit for patients with 50-69% symptomatic stenosis, and highly beneficial for those with 70% symptomatic stenosis or greater but without near-occlusion. Benefit in patients with carotid near-occlusion is marginal in the short-term and uncertain in the long-term.

Aged↗
PubMed2005

Automated external defibrillators on board merchant vessels? Preliminary report article for discussion.

OBJECTIVES: Acute heart diseases are the most frequent causes for fatalities on merchant vessels. Presently there is no sufficient therapy available to treat ventricular fibrillation. The aim of this study was to test whether common automated external defibrillators [AED] may be appropriate for the use aboard merchant vessels. METHODS: In 2005, nine seafarers were introduced to four common models of AED (HeartStartFR2+, Lifepak500, AEDplus, FREDeasy) using standard video or DVD presentations. AED handling by the subjects was tested in standardized simulated emergency scenarios. After training, they subjectively rated each AED on 24 factors involved in the introduction and handling of the device. An actual ECG was then obtained with each AED at a site located beside the ship's main engine to test under maximum vibration. The ECG data were extracted and sent as an e-mail attachment via satellite to the German Telemedical Maritime Assistance Service [TMAS] in Cuxhaven. RESULTS AND CONCLUSIONS: All subjects handled the AED correctly. The AED received a total amount of points in the range between 2125 to 2241 (of 2400 possible). The subjects preferred AED with coloured as well as light marked buttons which gave a feedback (e.g. audible tones) when they were pressed. All AED were able to register an ECG in the vibrating ambient. Due to interface problems it was only possible to extract three ECG files, and only two files (data < 300 kB) could be sent as e-mail attachment via satellite to the German TMAS. In noisy areas the AED must guide the user, e.g. by screen massages and/or pictograms. Displays should provide additional data to help assess resuscitation effectiveness. A special procedure is necessary to ensure that ships and TMAS own the same software to read the transmitted ECG files, which are not allowed to exceed a size of 300 kB.

Adolescent↗
PubMed2006

Genome-wide DNA polymorphism analyses using VariScan.

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Algorithms↗