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PubMed2005

Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics.

Although two-dimensional gel electrophoresis (2-DE) has long been a favorite experimental method to screen proteomes, its reproducibility is seldom analyzed with the assistance of quantitative error models. The lack of models of residual distributions that can be used to assign likelihood to differential expression reflects the difficulty in tackling the combined effect of variability in spot intensity and uncertain recognition of the same spot in different gels. In this report we have analyzed a series of four triplicate two-dimensional gels of chicken embryo heart samples at two distinct development stages to produce such a model of residual distribution. In order to achieve this reference error model, a nonparametric procedure for consistent spot intensity normalization had to be established, and is also reported here. In addition to variability in normalized intensity due to various sources, the residual variation between replicates was observed to be compounded by failure to identify the spot itself (gel alignment). The mixed effect is reflected by variably skewed bimodal density distributions of residuals. The extraction of a global error model that accommodated such distribution was achieved empirically by machine learning, specifically by bootstrapped artificial neural networks. The model described is being used to assign confidence values to observed variations in arbitrary 2-DE gels in order to quantify the degree of over-expression and under-expression of protein spots.

Animals↗
PubMed2001

Transrectal ultrasonography in male subfertility patients: an intra- and interobserver study.

The purpose of this paper was to examine whether ultrasound abnormalities of the prostate and seminal vesicles, which may be related to male accessory gland infection, are reproducible. Forty-seven men attending an infertility clinic were studied. Imaging findings of transrectal ultrasonography were recorded. Kappa (kappa)-values to determine the intra- and inter-observer variation were assessed. Calcifications have good intra-observer (kappa = 0.77; 95% CI: 0.59-0.96) and good inter-observer reproducibility (kappa = 0.73; 95% CI: 0.54-0.93). Dilatation of the peri-prostatic plexus had moderate intra-observer (kappa = 0.57; 95% CI: 0.33-0.80) and good inter-observer reproducibility (kappa = 0.74; 95% CI: 0.55-0.94). Other ultrasound abnormalities of the prostate were not reproducible. None of the ultrasound abnormalities of the seminal vesicles were reproducible. In our study the prevalence of ultrasound abnormalities which may be related to male accessory gland infection was as high as 96%. However, only calcifications and dilatation of the venous plexus had good reproducibility. Other observed ultrasound abnormalities of the prostate and seminal vesicles were poorly reproducible and are therefore of no use in the diagnosis of male accessory gland infection.

Adult↗
PubMed2006

Parameter identification and sedative sensitivity analysis of an agitation-sedation model.

Sedation administration and agitation management are fundamental activities in any intensive care unit. A lack of objective measures of agitation and sedation, as well as poor understanding of the underlying dynamics, contribute to inefficient outcomes and expensive healthcare. Recent models of agitation-sedation dynamics have enhanced understanding of the underlying dynamics and enable development of advanced protocols for semi-automated sedation administration. In this research, the agitation-sedation model parameters are identified using an integral-based fitting method developed in this work. Parameter variance is then analysed over 37 intensive care unit patients. The parameter identification method is shown to be effective and computationally inexpensive, making it suited to real-time clinical control applications. Sedative sensitivity, an important model parameter, is found to be both patient-specific and time-varying. However, while the variation between patients is observed to be as large as a factor 10, the observed variation in time is smaller, and varies slowly over a period of days rather than hours. The high fitted model performance across all patients show that the agitation-sedation model presented captures the fundamental dynamics of the agitation-sedation system. Overall, these results provide additional insight into the system and clinical dynamics of sedation management.

Computer Simulation↗
PubMed2004

Logistic versus additive EuroSCORE. A comparative assessment of the two models in an independent population sample.

OBJECTIVE: Validation of EuroSCORE outside the boundaries of the original database has been limited to the additive model and has occasionally shown inconsistencies. Therefore we sought to validate the logistic model and assess its predictive performance compared to the additive approach. METHODS: Twenty-four hundred and twenty-six consecutive patients were prospectively assigned individual expected risks of dying calculated by the logistic and the additive EuroSCORE algorithms. Discriminating ability of the two models was tested by Receiver Operating Characteristic (ROC) curves. Calibration was assessed by the Hosmer-Lemeshow (H-T) test and further explored by additional cross-tabulations. A percent difference among the estimates was calculated and plotted across score groups. The series was then sorted by date of operation and split in halves to separately explore the potential effect of variation of performance. RESULTS: Observed mortality (5.6%) was not significantly different from the additive (5.3%) and the logistic estimates (6.9%). Both models satisfactorily discriminated outcomes (ROC areas of 0.80 and 0.79 for the logistic and the additive model, respectively). The H-T test showed that calibration was good for the logistic model (P=0.12) but turned out being inadequate for the additive model (P<0.0001). Further cross-tabulations confirmed a good correlation among observed and predicted death rates by the logistic model across all groups. The additive model, on the other hand, revealed a propensity to over-predict in medium-risk categories and under-predict in the very high-risk cases. Direct comparison of additive vs logistic estimates showed a similar behaviour demonstrating it as an intrinsic property of the additive approach. The split-file analysis revealed a significantly improved outcome for patients treated in the second half of the series though the predictive performance of the two models was unaltered. CONCLUSIONS: Logistic EuroSCORE reliably predicted outcomes in our series despite the higher risk profile compared to the reference EuroSCORE sample and the observed variation in clinical performance during the study period. The additive model was less precise, exhibiting a predictive distortion which should be accounted for, particularly when employing it at the individual patient level.

Aged↗
PubMed2005

Added surfactant can change the phase behavior of aqueous polymer-particle mixtures.

The phase behavior of aqueous mixtures of the "clouding" polymer ethyl(hydroxyethyl)cellulose (EHEC) mixed with colloidal particles and surfactants has been studied. These types of mixtures are important in many technical formulations. Two types of particles, polystyrene latex and silica, and two types of EHEC, nonmodified EHEC (N-EHEC) and hydrophobically modified EHEC (HM-EHEC), were studied. The EHECs adsorb to both kinds of particles. Both the amount and the type of added surfactant were seen to dramatically influence the partitioning of the particles between the EHEC-rich and EHEC-poor phases of phase-separated mixtures (above the cloud point temperature). Surfactants that are known not to associate with the EHEC backbone, that is, nonionic surfactants and short-chain cationic surfactants, changed the interaction between EHEC and the colloidal particles from attraction to repulsion above a specific surfactant concentration, resulting in a change in the partitioning of the particles from the EHEC-rich to the EHEC-poor phase. No such particle inversion was observed for ionic surfactants that bind to the EHEC backbone. An analysis considering both the binding of surfactant to EHEC and the competitive adsorption of surfactant to the particle surfaces could rationalize all observations, including the large variations observed, among the studied mixtures, in the surfactant concentration required for particle inversion.

Cellulose↗
PubMed1998

Secular trends in blood pressure levels in Denmark 1964-1991.

BACKGROUND: Hypertension is an essential risk factor for development of cardiovascular diseases. Prospective studies show a reduction in risk of myocardial infarction with reduction of blood pressure. In Denmark there was a decrease in ischaemic heart disease mortality during the period (1968-1992) with around 34% in 30-65 year old men and 30% in women. OBJECTIVE: To assess the changes in casual blood pressure between 1964 and 1991 in seven cross-sectional population studies. SETTING: Centre of Preventive Medicine, University of Copenhagen, DK-2600 Glostrup. POPULATION: 10359 subjects, equal numbers of men and women, age exactly 30, 40, 50 and 60 years drawn as random samples from a background population of 300000 inhabitants and surveyed in 1964-1974 and five cross-sectional studies 1976, 1978, 1982-1984, 1986-1987 and 1991. METHODS: Blood pressure was measured according to WHO criteria by one technician in each survey. Alcohol consumption and physical activity were measured by a self-administered questionnaire. The weight and height were measured by standardized methods. Data on mortality from ischaemic heart disease were obtained from death certificates recorded by the National Board of Health. RESULTS: Blood pressure increased with increasing age in both genders and was significantly higher in men than in women. Median blood pressure in 50 year old men in 1964 was 135/85 mmHg and in 1991 it was 123/79, whereas in women in 1964 it was 140/85, against 119/74 in 1991. The prevalence of hypertensives among 30 and 40 year olds declined throughout the period. The performance of blood pressure measurements, technical variation, examination programme, seasonal variation and inter-observer variation were potential bias sources and influenced blood pressure levels, but cannot be shown to be responsible for the declining trend in blood pressure and hypertension. Women became a little more physical active in leisure time and men less active. Women consumed less alcohol than men, but the amounts slightly increased by the end of the period. Body mass index >25 was seen less frequently in women than in men and this increased in men over the period. Sale of antihypertensive drugs increased in Denmark over the 1964-1991 period. There seems to be good agreement between the changes in blood pressure in the population and the decline in mortality from stroke and coronary heart disease in Denmark, which is influenced by other risk factors as well. CONCLUSION: Blood pressure distributions have shifted towards lower values in 1964-1991. Prevalence of hypertension declined up to 1983. Risk factor changes as well as treatment for hypertension contribute to this.

Adult↗
PubMed1990

A procaryotic regulatory factor with a histone H1-like carboxy-terminal domain: clonal variation of repeats within algP, a gene involved in regulation of mucoidy in Pseudomonas aeruginosa.

A novel procaryotic transcriptional regulatory element, AlgP, with a histone H1-like carboxy-terminal domain was identified in Pseudomonas aeruginosa. AlgP is required for transcription of the key biosynthetic gene algD, which is necessary for production of the exopolysaccharide alginate causing mucoidy in P. aeruginosa. Mucoidy is a critical virulence determinant of P. aeruginosa invariably associated with the respiratory infections causing high mortality in cystic fibrosis. Here we show that AlgP and histones H1 both have repeated units of the Lys-Pro-Ala-Ala motif (KPAA) and its variations within their long (over 100 amino acids) carboxy-terminal domains. This region of histone H1 tails has been shown to bind to the linker DNA in eucaryotic chromatin fibers. A synthetic 50-mer peptide consisting of repeats from the AlgP carboxy-terminal domain was found to bind DNA in a mobility shift DNA-binding assay. AlgP is encoded by a gene that contains multiple direct repeats organized as tandem, head-to-tail, 12-base-pair (bp) units overlapping with six highly conserved 75-bp units. The repetitive structure of the algP gene appears to participate in the processes underlying the metastable character of mucoidy in P. aeruginosa. Relatively large DNA rearrangements spanning the region with tandem direct repeats encoding the carboxy-terminal histone H1-like structure of AlgP were detected in several strains upon conversion from the mucoid to the nonmucoid phenotype. The frequency of the detectable algP rearrangements associated with the transition into the nonmucoid state varied from strain to strain and ranged from 0 to 50%. The nonmucoid derivatives with the clearly rearranged chromosomal copy of algP were complemented to mucoidy with plasmids containing algP from P. aeruginosa PAO. When a random collection of mucoid strains, isolated from different cystic fibrosis patients, was analyzed by using polymerase chain reaction, an additional level of strain-dependent sequence variation in algP was observed. Variations in the number of the 12-bp repeats were found; however, they did not appear to influence the mucoid status of the strains examined. Thus, the repeated region of algP appears to be a hot spot for DNA rearrangements and strain-dependent variability.

Amino Acid Sequence↗
PubMed2024

Comparative analysis of chloroplast genomes in ten holly (Ilex) species: insights into phylogenetics and genome evolution.

In order to clarify the chloroplast genomes and structural features of ten Ilex species and provide insights into the phylogeny and genome evolution of the genus Ilex, we conducted a comparative analysis of chloroplast genomes using bioinformatics methods. The chloroplast genomes of ten Ilex species were obtained, and their structural features and variations were compared. The results indicated that all chloroplast genomes in the genus Ilex exhibit a double-stranded circular structure, with sizes ranging from 157,356 to 158,018&#xa0;bp, showing minimal differences in size. The chloroplast genomes of the ten Ilex species have a relatively conservative gene count, with a total of 134 to 135 genes, including 88 or 89 protein-coding genes, and a conserved number of 8 rRNA genes. Each chloroplast genome contains 3 to 123 SSR (Simple Sequence Repeat) sites, predominantly composed of mononucleotide and trinucleotide repeats, with no detection of pentanucleotide or hexanucleotide repeats. The variation in dispersed repeat sequences among Ilex species is minimal, with a total repeat sequence number ranging from 1 to 14, concentrated in the length range of 30 to 42 base pairs. The expansion and contraction of chloroplast genome boundaries among Ilex species are relatively stable, with only minor variations observed in individual species. Variations in non-coding regions are more pronounced than those in coding regions, with the variability in the Large Single Copy region (LSC) being the highest, while the variability in the Inverted Repeat region A (IRa) is the lowest. The divergence time among Ilex species was estimated using the MCMC-tree module, revealing the evolutionary relationships among these species, their common ancestors, and their differentiation throughout the evolutionary process. The research findings provide a valuable reference for the systematic study and molecular marker development of Ilex plants.

Genome, Chloroplast↗
PubMed1995

An approach to the development of decision support for diagnosing pathology from radiographs.

OBJECTIVES: Large inter-observer variation has been reported in oral radiology. Providing observers with a checklist prompting them to focus on specific radiographically visible features with known relevance to the diagnosis has been shown to improve diagnostic accuracy. We intended to investigate whether diagnostic accuracy for bony pathology could be improved by a computerized decision aid. The decision support provided the user with radiographic reference images for the degree of presence of a radiographic feature (such as radiopacity) and structured the use of diagnostic knowledge. METHODS: Twenty-seven general dental practitioners participated in the study. They diagnosed seven radiographic cases of bony pathology using a prototype decision aid and seven other cases unaided. For each radiograph the dentists assessed the degree of presence of five radiographically visible features which had been selected from the literature oral radiology because of their use in describing, radiographically visible bony pathology. The dentists' assessments of degree of feature presence, and their diagnoses, were recorded. Histopathology was used as a diagnostic 'gold standard'. The degree of presence of the features in the radiographic images was also assessed by an independently selected panel of expert oral radiologists in a Delphi consensus procedure. RESULTS: Determination of the degree of presence of three radiographically visible features assessed by the dentists using the prototype decision aid was significantly improved (by up to 12%) compared to the results of their unaided assessments. The diagnostic accuracy of one-third of the dentists was also improved. CONCLUSION: The use of reference images can improve dentists' assessments of the degree of feature presence.

Analysis of Variance↗
PubMed2001

Ethnic variations in observance and rationale for postpartum sexual abstinence in Malawi.

Using quantitative and qualitative data from three culturally heterogeneous ethnic groups in Malawi, I show that differences in postpartum sexual abstinence are closely associated with community-specific rationales for the practice, particularly differences in the definition and timing of child-strengthening rituals that couples are required to perform before resuming intercourse. Contrary to conventional wisdom, the primary rationale for abstinence in the study areas is not linked to child spacing. Among Tumbukas in the north, most women perform the ritual immediately after resuming menstruation. Among the other ethnic groups, the rituals can be performed at any time after the end of postpartum bleeding. The study underscores the utility of the complementary micro-level approach in understanding reproductive behavior in sub-Saharan Africa.

Amenorrhea↗
PubMed1983

Variability of arterial blood gas values in stable patients in the ICU.

To establish guidelines for the interpretation of changes in arterial blood gas (ABG) values, we studied 29 clinically stable ICU patients for spontaneous variability in PaO2, PaCO2 and pH. ABGs were sampled six times over a 50-minute period, during which all patients received a fixed FIO2 of 0.5 via endotracheal tube and underwent no therapeutic interventions. Each sample was analyzed in duplicate with careful attention to method of collection and measurement. The range separating the lowest and highest PaO2 varied from 1 to 45 mm Hg (16.2 +/- 10.9 mm Hg [mean +/- SD] ). For PaCO2 this range was from 1 to 8 mm Hg (3.0 +/- 1.9 mm Hg). Coefficient of variation for PaO2 and PaCO2 averaged 5.1 +/- 3.2 percent (mean +/- SD) and 3.0 +/- 1.5 percent respectively. pH varied within 0.03 +/- 0.02 units. Percentage change in PaO2 between sequential intrapatient samples averaged 5.3 +/- 2.8 percent (mean +/- SD) and 7.1 +/- 7.9 percent over ten- and 50-minute intervals, respectively. Various clinical features were analyzed by multiple regression analysis for their relation to PaO2 variation. Only leukocyte count and mean arterial oxygen content were statistically significant associations (p less than 0.05), but together explained less than 35 percent of the variation observed. Because considerable spontaneous variation occurs, even in stable patients, clinicians should base therapeutic decisions on trends in PaO2 values rather than on isolated changes interpreted without appropriate clinical correlation.

Adult↗