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PubMed1993

Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold.

The three-dimensional profile method expresses the three-dimensional structure of a protein as a table, the profile, which represents the local environment of each residue. The score of an amino acid sequence, aligned with the three-dimensional profile, reflects its compatibility with the profiled structure. In the original implementation, each local environment was characterized by its polarity, the area buried of its side chain, and its secondary structure. Here we describe a modified three-dimensional profile algorithm that characterizes the local environment in terms of the statistical preferences of the profiled residue for neighbors of specific residue types, main-chain conformations, or secondary structure. Combined profiles of the original and the three new types were tested on beta/alpha-barrel protein structures. The method identified the following enzymes of unknown three-dimensional structure as probable beta/alpha-barrels, all of which catalyze reactions in the biosynthesis of aromatic amino acids: anthranilate phosphoribosyltransferase (trpD), glutamine amidotransferase (trpG), and phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA).

Aldose-Ketose Isomerases↗
PubMed2005

Mycobacterium avium with the bird type IS1245 RFLP profile is commonly found in wild and domestic animals, but rarely in humans.

Cervical lymphadenitis is the main manifestation of Mycobacterium avium infection in immunocompetent children. Exposure to birds has been discussed as a source of infection. To clarify from where children acquire the infection, M. avium isolates from different origins were analysed with restriction fragment length polymorphism (RFLP) on insertion sequence IS1245, and compared by computer cluster correlation analysis. This molecular epidemiological tool has previously revealed a distinction between multiband profiles found mainly in strains from humans, and a 3-band/bird type profile in strains isolated mainly from birds. 32 isolates from children were compared with 28 isolates from adults and 45 isolates from animals. We found that 67% of the animal isolates had the bird type profile, also found in 1 sputum isolate from an adult. Strains from children showed only multiband profiles that did not differ significantly from profiles of isolates from adults. All but 2 bird isolates showed the bird type profile. Neither of the remaining 2, which had multiband profiles, clustered with the isolates from children. Our results indicate that the true reservoir of M. avium is unknown. Thus the question of whether or not M. avium can be incriminated as a zoonotic disease remains unanswered.

Adult↗
PubMed2005

Metacarpophalangeal pattern profile analysis as a tool for early diagnosis of Turner syndrome.

PURPOSE: To analyze the metacarpophalangeal pattern profile (MCPP) in a cohort of individuals with Turner syndrome (TS), and to assess its value as a tool for early diagnosis of TS. MATERIAL AND METHODS: Medical records and radiological material were collected of 71 patients with TS aged between 3 and 21 years. Forty-six patients received growth hormone therapy (33-66 microg kg(-1) day(-1)) and 14 of these were also treated with the anabolic steroid oxandrolone (1.25-3.75 mg day(-1)). A total of 233 frontal hand radiographs were studied and pattern profiles were calculated. Profiles of the TS patients were compared with those of 70 normal females. Mean pattern profiles were calculated for different age groups and extrapolated profiles for newborns and infants were developed. RESULTS: Our results confirm that patients with TS have a distinct MCPP which differs significantly from that of normal individuals. A bone-shortening gradient with increasing shortening from distal phalanges to metacarpals was demonstrated. We also showed that the MCPP in TS is a remarkably constant feature from 3 to 18 years. Pattern profiles did not differ significantly between the patients with 45,X and non-45,X karyotype. MCPP was not affected by treatment with growth hormone of growth hormone plus oxandrolone. Discriminant analysis yielded correct classification in 88%, of analyzed cases. CONCLUSION: TS individuals have a distinct hand pattern profile that is not age-related. MCPP analysis can be applied at any age and may facilitate early diagnosis of TS. Our study showed that MCPP analysis is a specific and sensitive method that should be considered as a routinely used tool for early diagnosis of TS in girls with unexplained short stature.

Adolescent↗
PubMed2003

Systems of coping associated with dysphoria, anxiety and depressive illness: a multivariate profile perspective.

As numerous coping strategies to deal with stressors can be used concurrently or sequentially, it may be productive to consider coping from a broad, systemic perspective. Using profile analysis and multivariate techniques, we demonstrated that coping profiles comprising multiple strategies distinguished between various mood states (dysphoria, anxiety, major depression, dysthymia and obsessive-compulsive disorder (OCD)). Generally, affective disturbances were associated with increased levels of rumination, cognitive distraction and emotion-focused coping (emotional expression, other-blame, self-blame, emotional containment and passive resignation) coupled with diminished problem solving and social support seeking. These coping profiles, however, varied as a function of anxiety vs. dysphoria, and severity of dysphoric symptoms, although the profile of dysphoric individuals was similar to that of clinically diagnosed dysthymic and major depressive patients. While coping profiles were generally stable over time (6 months), improvement or deterioration of mood was accompanied by corresponding alterations of coping profiles. Importantly, coping profile was not simply a correlate of dysphoric mood, but was also found to be an antecedent condition that favored the evolution of more severe affective problems. It is suggested that a multidimensional approach may prove useful in understanding coping as a dynamic system, and may have implications for clinical intervention.

Adaptation, Psychological↗
PubMed2007

WAIS-III index score profiles in the Canadian standardization sample.

Representative index score profiles were examined in the Canadian standardization sample of the Wechsler Adult Intelligence Scale-Third Edition (WAIS-III). The identification of profile patterns was based on the methodology proposed by Lange, Iverson, Senior, and Chelune (2002) that aims to maximize the influence of profile shape and minimize the influence of profile magnitude on the cluster solution. A two-step cluster analysis procedure was used (i.e., hierarchical and k-means analyses). Cluster analysis of the four index scores (i.e., Verbal Comprehension [VCI], Perceptual Organization [POI], Working Memory [WMI], Processing Speed [PSI]) identified six profiles in this sample. Profiles were differentiated by pattern of performance and were primarily characterized as (a) high VCI/POI, low WMI/PSI, (b) low VCI/POI, high WMI/PSI, (c) high PSI, (d) low PSI, (e) high VCI/WMI, low POI/PSI, and (f) low VCI, high POI. These profiles are potentially useful for determining whether a patient's WAIS-III performance is unusual in a normal population.

Canada↗
PubMed1999

Development of velocity profiles and retrograde flow in the porcine abdominal aorta under different haemodynamic conditions.

Low and/or oscillating wall shear stresses are related to the development of atherosclerosis and this oscillation is influenced by changes in basic haemodynamics (exercise). The objective of this study was to provide in vivo data on the development of velocity profiles and oscillating blood velocities in the abdominal aorta under varying haemodynamic conditions. Six anaesthetized, 90-kg pigs were used in the study. Abdominal aortic velocity profiles across the anterior-posterior diameter were acquired at different axial positions using 10 MHz pulsed Doppler ultrasound. Measurements were obtained under normal conditions and during cardiac pacing up to 170 beats/min. Velocity profiles were obtained during heart rates ranging between 58 and 169 beats/min, and during flow rates ranging between 0.57 and 2.89 l/min. Main outcome measures included minimum velocities, frequency index, shape of velocity profiles (velocity distribution index), Reynolds' numbers, and Womersley's frequency parameter. Velocity profiles were blunted, with lowest velocities at the distal posterior vessel wall. Multiple regression analysis showed the development of velocity profiles to be inversely correlated with the pulsatility index, Womersley's frequency parameter and the mean Reynolds' number (r = 0.89, p < 0.0005). Minimum velocities were negatively correlated with the PI, Womersley's frequency parameter and positively with the mean Reynolds' number (r = 0.94, p < 10(-8)). Retrograde velocities (and hence oscillating wall shear stresses) were present at mean Reynolds' number < 1000. The oscillation of blood velocities at the wall in the porcine abdominal aorta was highly dependent on general haemodynamics (i.e. flow, heart rate and vessel diameter as expressed in the Reynolds' numbers and Womersley's frequency parameters). The velocity profiles in the abdominal aorta were found to be far from parabolic. These findings have important implications for the understanding and future modelling of the complex haemodynamics in the abdominal aorta and their relation to the development of atherosclerotic disease.

Animals↗
PubMed2003

The effect of glucocorticosteroid administration on fetal movements and biophysical profile scores in normal pregnancies.

OBJECTIVE: To evaluate and quantify the effect of glucocorticosteroid administration on fetal movements and biophysical profile scores. METHODS: Eighteen women at 32-34 weeks' gestation were enrolled. Inclusion criterion was an uncomplicated singleton pregnancy not considered to be at high risk. Patients participated for 3 consecutive days. On day 1, the patients underwent a baseline biophysical profile including a non-stress test followed by a 12-mg betamethasone intramuscular injection. On day 2, the patients received a non-stress test and a second dose of betamethasone. On day 3, a biophysical profile with non-stress test was performed. Maternal counts of fetal kicks were also recorded before, during and after the study period. Each test was conducted at approximately the same time of day to control for diurnal variation. Comparison was made between pre-betamethasone biophysical profile scores and fetal movement and post-betamethasone biophysical profile scores and fetal movement. RESULTS: Biophysical profile scores were reduced in 28% of the study population after betamethasone administration (p < 0.05). Amniotic fluid index on day 3 was decreased from baseline in 72% of patients after betamethasone administration (p < 0.05). Forty-four per cent of patients reported a decrease in fetal movement. Of these patients, 87% had a decreased amniotic fluid index when compared to baseline (p < 0.05). CONCLUSIONS: Fetal movements and breathing motion were decreased after glucocorticosteroid administration, as evidenced by biophysical profile scores and kick counts. The decrease in the amniotic fluid index observed after glucocorticosteroid administration may have been the result of decreased fetal breathing and, therefore, decreased efflux of alveolar fluid into the amniotic sac.

Amniotic Fluid↗
PubMed1994

Facial profile changes during and after Herbst appliance treatment.

The short- and long-term effects of the Herbst appliance on the facial profile were determined in 69 Class II, division 1 malocclusions treated for 7 months and followed for 5-10 years post-treatment. Forty-nine subjects exhibited a stable long-term treatment result, while 20 cases relapsed. Lateral cephalometric radiographs from before treatment, after treatment, 6 months post-treatment, and 5-10 years post-treatment were analysed. As a rule Herbst treatment resulted in a reduction of the facial hard and soft tissue profile convexity. In relation to the E-line, the upper lip became retrusive, while the lower lip remained, on average, unchanged. During the post-treatment period of 5-10 years the hard tissue profile convexity was, on average, reduced in both the stable and relapse groups. When excluding the nose in the soft tissue profile evaluation, the facial profile convexity was, on average, reduced in the stable group while it remained unchanged in the relapse group. When including the nose in the evaluation, an average increase in the profile convexity occurred in both examination groups. Furthermore, the upper and lower lips became retrusive in both groups. For all the variables, however, large individual variations existed. In conclusion, it can be said that the Herbst appliance improves the facial hard and soft tissue profiles. Due to post-treatment growth changes the long-term effects of therapy are, however, variable and unpredictable.

Adolescent↗
PubMed2003

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure.

ORFeus is a fully automated, sensitive protein sequence similarity search server available to the academic community via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/). The goal of the development of ORFeus was to increase the sensitivity of the detection of distantly related protein families. Predicted secondary structure information was added to the information about sequence conservation and variability, a technique known from hybrid threading approaches. The accuracy of the meta profiles created this way is compared with profiles containing only sequence information and with the standard approach of aligning a single sequence with a profile. Additionally, the alignment of meta profiles is more sensitive in detecting remote homology between protein families than if aligning two sequence-only profiles or if aligning a profile with a sequence. The specificity of the alignment score is improved in the lower specificity range compared with the robust sequence-only profiles.

Algorithms↗
PubMed2002

Designing gene libraries from protein profiles for combinatorial protein experiments.

Protein combinatorial libraries provide new ways to probe the determinants of folding and to discover novel proteins. Such libraries are often constructed by expressing an ensemble of partially random gene sequences. Given the intractably large number of possible sequences, some limitation on diversity must be imposed. A non-uniform distribution of nucleotides can be used to reduce the number of possible sequences and encode peptide sequences having a predetermined set of amino acid probabilities at each residue position, i.e., the amino acid sequence profile. Such profiles can be determined by inspection, multiple sequence alignment or physically-based computational methods. Here we present a computational method that takes as input a desired sequence profile and calculates the individual nucleotide probabilities among partially random genes. The calculated gene library can be readily used in the context of standard DNA synthesis to generate a protein library with essentially the desired profile. The fidelity between the desired profile and the calculated one coded by these partially random genes is quantitatively evaluated using the linear correlation coefficient and a relative entropy, each of which provides a measure of profile agreement at each position of the sequence. On average, this method of identifying such codon frequencies performs as well or better than other methods with regard to fidelity to the original profile. Importantly, the method presented here provides much better yields of complete sequences that do not contain stop codons, a feature that is particularly important when all or large fractions of a gene are subject to combinatorial mutation.

Amino Acids↗
PubMed1996

Biotechnology in profiled dialysis.

Profiled dialysis is a new conceptual approach to patient intradialytic vascular instability. It is based on the continuous modulation of dialysis operative parameters, such as dialysate sodium and UF rate, according to pre-established profiles. The points to be defined for profiled dialysis are: (a) the patient's individual sodium and masses already stated; (b) the patient's individual algorithms to fit the clinically effective intradialytic variations in plasma sodium and sodium mass; (c) a mathematical model from which sodium and UF profiles are automatically worked out at the beginning of each session. The basic concept of profiled dialysis should evolve towards an ongoing "profiling' programme. This is based on the continuous on-line intradialytic adjustment of profiles according to the patient's emerging clinical requirements.

Biotechnology↗
PubMed1990

Effects of electromyographic processing methods on computer-averaged surface electromyographic profiles for the gluteus medius muscle.

The objective of this study was to demonstrate how two different linear envelope detectors, as used in the quantification of surface electromyographic (EMG) signals, can lead to differences in the properties of observed computer-averaged EMG profiles. Eight healthy male subjects, aged 24 to 32 years, participated in the study. Computer-averaged EMG profiles for the gluteus medius muscle were recorded at a free-walking cadence and at stepping frequencies of 78 and 120 steps/min, using detectors with 3- and 25-Hz cutoff frequencies simultaneously. The 3-Hz filtered EMG profiles proved to be smoother, to exhibit a significantly lower cycle-to-cycle variability, and to have a greater time lag with respect to the original unprocessed EMG signal than the 25-Hz filtered EMG profiles. The observed intersubject variability also was lower for the 3-Hz filtered EMG profiles than for the 25-Hz filtered EMG profiles. The results indicate that comparison of EMG profiles recorded with different detectors is difficult. A standard detector may solve this difficulty.

Adult↗
PubMed2000

Acoustic reflectometry profiles of endotracheal and esophageal intubation.

BACKGROUND: Acoustic reflectometry can be used to create a "one-dimensional image" of a cavity, such as the airway and lung, with the image displayed as an area-length curve. This pilot study was undertaken to determine whether acoustic reflectometry could be used to distinguish between an endotracheal and an esophageal intubation. METHODS: Ten adult patients underwent general endotracheal anesthesia and neuromuscular blockade. The reflectometer wavetube was attached to an endotracheal tube, and a reflectometric profile was obtained of the endotracheal tube and the airway and lung cavity. After confirmation of tracheal intubation, a second endotracheal tube was placed in the esophagus. After four breaths were administered, a reflectometric profile of the endotracheal tube-esophagus cavity was obtained. RESULTS: The acoustic reflectometric profiles for tracheal and esophageal intubation profiles were distinctive and characteristic. For an endotracheal tube-airway cavity, the profile shows a constant cross-sectional area throughout the length of the endotracheal tube, followed by a rapid rise in the area past the carina. For an esophageal intubation, the profile shows constant cross-sectional area throughout the length of the endotracheal tube, followed by a sudden decrease in the cross-sectional area to zero. CONCLUSIONS: In this pilot study, acoustic reflectometry within seconds, and without resort to capnography, was able to generate characteristic and distinctive area-length profiles for both endotracheal and esophageal intubation. Acoustic reflectometry may have a role in the emergency imaging of the airway, and in the immediate detection of esophageal intubations, particularly in cases of cardiopulmonary arrest in which the usual techniques for confirmation of breathing tube placement fail.

Acoustics↗
PubMed2003

Vertical profile of tritium concentration in air during a chronic atmospheric HT release.

The vertical profiles of tritium gas and tritiated water concentrations in air, which would have an influence on the assessment of tritium doses as well as on the environmental monitoring of tritium, were measured in a chronic tritium gas release experiment performed in Canada in 1994. While both of the profiles were rather uniform during the day because of atmospheric mixing, large gradients of the profiles were observed at night. The gradient coefficients of the profiles were derived from the measurements. Correlations were analyzed between the gradient coefficients and meteorological conditions: solar radiation, wind speed, and turbulent diffusivity. It was found that the solar radiation was highly correlated with the gradient coefficients of tritium gas and tritiated water profiles and that the wind speed and turbulent diffusivity showed weaker correlations with those of tritiated water profiles. A one-dimensional tritium transport model was developed to analyze the vertical diffusion of tritiated water re-emitted from the ground into the atmosphere. The model consists of processes of tritium gas deposition to soil including oxidation into tritiated water, reemission of tritiated water, dilution of tritiated water in soil by rain, and vertical diffusion of tritiated water in the atmosphere. The model accurately represents the accumulation of tritiated water in soil water and the time variations and vertical profiles of tritiated water concentrations in air.

Air Pollutants, Radioactive↗
PubMed2004

K3 Endo, ProTaper, and ProFile systems: breakage and distortion in severely curved roots of molars.

It was the aim of this study to investigate the incidence of file breakage and distortion when the ProTaper, K3 Endo, and ProFile systems were used to instrument canals in the severely curved roots of extracted molars. Forty-five roots of extracted mandibular and maxillary molars with curvatures between 40 and 75 degrees were chosen for this study. The canals in group 1 were instrumented with the ProFile system. Roots in group 2 were instrumented with the ProTaper system, and those in group 3 were instrumented with the K3 Endo system. The three systems were used according to the manufacturers' instructions. The proportion of files distorted was 15.3% for the ProFile group, 2.4% for the ProTaper group, and 8.3% for the K3 Endo group. There was a statistically significant difference between the ProFile and ProTaper groups (p=0.0079). The percentage of broken files was 1.7% for the ProFile group, 6.0% for the ProTaper group, and 2.1% for the K3 Endo group. No statistically significant differences were found between these three groups (p=0.4243). The results of this study showed that these three rotary tapered systems were not significantly different with regard to breakage. There were significantly more distorted files in the ProFile group when compared with the ProTaper group. With regard to distortion, there was no significant difference between the ProTaper and K3 Endo and the ProFile and K3 Endo groups.

Dental Alloys↗
PubMed1995

Physicians' response to length-of-stay profiling.

One of the techniques adopted recently by certain hospitals to meet the competitive pressure for reducing costs is physician profiling. Profiling produces periodic reports that compare a physician's resource consumption to a benchmark figure. This study analyzes the effectiveness and implications of one hospital's introduction of physician patient length-of-stay profiling. Data for 24,000 patients treated by 400 physicians in 450 diagnosis-related groups over 42 months were analyzed, including both preprofiling and postprofiling periods. Statistical tests examined whether more physicians achieved the length-of-stay benchmark after profiling was introduced, controlling for physician, disease category (diagnosis-related group), and patient severity level. First, the results establish a significant increase in the percentage of physicians who achieve the length-of-stay benchmark after the introduction of profiling. Second, it was found that physicians who had initially failed to meet the benchmark reduced their patients' average length of stay much more than those physicians who initially achieved the benchmark. Further, reductions occurred primarily at intermediate severity levels, and in diagnosis-related groups with a large economic impact for the hospital. Although the profiling program did achieve the objective of reducing patient length of stay, further improvement may be possible. First, providing different benchmarks or targets for different physicians may extend the improvement to a greater percentage of all physicians involved. Second, an analysis of monthly data on total weighted procedures reveals that the reduction in length of stay resulted in an increase in the number of procedures performed per patient day. This finding suggests that to achieve a reduction in hospital costs and charges, profiling programs should be combined with process improvement initiatives.

Diagnosis-Related Groups↗
PubMed2005

Dynamics of the circadian blood pressure profiles after renal transplantation.

BACKGROUND: Abnormalities of diurnal blood pressure (BP) rhythm ("nondipping") are well-described in dialysis patients, and have prognostic importance. It is controversial whether successful renal transplantation (RTx) improves diurnal BP rhythm. To date, no study has attempted to define and model the evolution of diurnal BP rhythm profiles from dialysis to engraftment, focusing on the immediate (4-6 weeks) and medium-term (>1 year) postengraftment periods. METHODS: To test if kidney transplantation normalizes the BP profile, ambulatory blood pressure monitoring (ABPM) was performed in 20 living related transplants (age, 30.3+/-5.1 years; 11 males, on dialysis for 25.6 months) 1 month preRTx and repeated 1 month and >1 year (ABPM3) after successful RTx. Dipping was defined as a sleep-to-awake ratio>0.92 (for systolic BP) and >0.90 (for diastolic BP). RESULTS: PreRTx only 15% patients were dippers. At 1 month postRTx (creatinine clearance, 65.8 ml/min), all patients were complete nondippers. However, after >1 year postRTx (creatinine clearance, 70.4 ml/min), 40% were now dippers. Most importantly, overall, 30% of the patients improved significantly their circadian rhythm (35.3% of the initial preRTx nondippers). Despite successful renal transplantation, 55% patients maintained unchanged their nondipping profile throughout all three ABPM recordings. The only determinants of "long-term" postRTx circadian rhythm are the contemporary level of the renal function and the baseline, dialysis dipping profile: SBP3 sleep-to-awake ratio is related with serum creatinine3 (r=0.58, P=0.001), creatinine clearance (r=-0.41, P=0.036) and SBP1 sleep-to-awake ratio (r=0.48, P=0.034); similarly DBP3 sleep-to-awake ratio is related with serum creatinine3 (r=0.63, P=0.001), creatinine clearance (r=-0.471, P=0.036) and SBP1 sleep-to-awake ratio (r=0.53, P=0.016). In all, 57% of the variance in dipping status can be attributed and explained by the contribution of renal function and initial circadian variability. CONCLUSIONS: Half of the nondipper dialysis patients maintain a permanently abnormal circadian rhythm, despite successful RTx. In the short term, RTx is associated with a highly abnormal diurnal profile, exclusively related to ciclosporin dose and levels. However, in the longer term, renal transplantation leads to a significant improvement of the circadian blood pressure profile, influenced by the renal function level and by the pretransplantation dipping profile.

Adult↗
PubMed1994

Variation in outer-membrane protein and lipopolysaccharide profiles of Pasteurella haemolytica isolates of serotypes A1 and A2 obtained from pneumonic and healthy cattle.

The outer-membrane protein (OMP) and lipopolysaccharide (LPS) profiles of 29 isolates of Pasteurella haemolytica serotypes A1 (18 isolates) and A2 (11 isolates), obtained from pneumonic (13 isolates) or healthy (16 isolates) cattle, were compared by SDS-PAGE and Western blot analysis. Coomassie-blue-stained OMP profiles of serotype A1 and A2 isolates could be distinguished from each other by differences in both major and minor proteins. Whereas the OMP profiles of the serotype A1 isolates were extremely uniform in stained gels, there was variation in the mobilities of high-molecular-mass minor proteins and one of the major proteins of serotype A2 isolates. Differences in the OMP profiles of isolates within both the A1 and A2 serotypes were more clearly distinguished by Western blotting than by staining after SDS-PAGE. Thus, by Western blot analysis, four distinct OMP profiles were identified within the serotype A1 and A2 isolates, respectively. The profiles of the serotype A1 isolates were designated OMP types 1.1, 1.2, 1.3 and 1.4; those of the serotype A2 isolates were designated OMP types 2.1, 2.2, 2.3 and 2.4. Three distinct LPS profiles were recognized among the isolates which, by comparison with previously described LPS types, were identified as smooth LPS type 1 and rough LPS types 3 and 5. Isolates of serotype A1 consisted of LPS type 1 only. whereas isolates of serotype A2 consisted of LPS types 3 or 5. OMP and LPS analysis of P. haemolytica has applications in epidemiological and virulence studies.

Animals↗