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PubMed1993

Fourier analysis of blood pressure profiles.

This short review deals with the use of the Fourier technique to analyze diurnal blood pressure (BP) profiles obtained by noninvasive ambulatory monitoring. A Fourier series with four harmonics strikes an acceptable balance between the accuracy and complexity required to model the diurnal profile accurately in most subjects. A weighting procedure makes it possible to allow for the varying time intervals between consecutive pressure readings. Studies based on a single recording are insufficient to characterize an individual with respect to the statistical parameters describing the diurnal BP profile, regardless of whether they are obtained by Fourier analysis or by other methods. The Fourier approach provides the means to translate 24 h BP profiles into interpretable statistical parameters, such as the amplitude and acrophase of the overall model and the harmonics. These parameters can subsequently be used in further statistical analyses. In conclusion, the Fourier approach makes the description of complex, asymmetrical, and multiphasic BP profiles possible. By using the procedures of linear multiple regression, commonly provided by software packages, the calculations can be readily implemented on microcomputers without requiring advanced skills in mathematics or programming techniques.

Blood Pressure↗

PubMed1998

Profile hidden Markov models.

The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.

Humans↗

PubMed1990

Quantitative analysis of one-dimensional gel electrophoresis profiles.

A general method for the one-dimensional quantitative analysis of band profiles from an autoradiographed or stained gel is described. Curved lanes may be tracked, noise across the width of the band reduced by local averaging of densities within a selected window, and background-corrected density profiles produced. Sections of each profile can be subjected to a choice of three methods of peak-area determination, depending on the type of gel and the requirements of the analysis being carried out. In the first method, simple integration is used to measure the area under the profile between any two positions. The second method integrates a Gaussian distribution fitted to a single peak. Where bands overlap, the third method resolves peaks into their component areas, taking into account the observed increase in the width of the band in the direction of electrophoretic migration. This is incorporated into a least-squares profile-fitting method, which is shown to be both accurate and efficient.

Electrophoresis↗

PubMed2005

Profile-based direct kernels for remote homology detection and fold recognition.

MOTIVATION: Protein remote homology detection is a central problem in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for remote homology detection. The performance of these methods depends on how the protein sequences are modeled and on the method used to compute the kernel function between them. RESULTS: We introduce two classes of kernel functions that are constructed by combining sequence profiles with new and existing approaches for determining the similarity between pairs of protein sequences. These kernels are constructed directly from these explicit protein similarity measures and employ effective profile-to-profile scoring schemes for measuring the similarity between pairs of proteins. Experiments with remote homology detection and fold recognition problems show that these kernels are capable of producing results that are substantially better than those produced by all of the existing state-of-the-art SVM-based methods. In addition, the experiments show that these kernels, even when used in the absence of profiles, produce results that are better than those produced by existing non-profile-based schemes. AVAILABILITY: The programs for computing the various kernel functions are available on request from the authors.

Algorithms↗

PubMedDate not supplied

A spatiotemporal profile of visual system activation revealed by current source density analysis in the awake macaque.

We investigated the spatiotemporal activation pattern, produced by one visual stimulus, across cerebral cortical regions in awake monkeys. Laminar profiles of postsynaptic potentials and action potentials were indexed with current source density (CSD) and multiunit activity profiles respectively. Locally, we found contrasting activation profiles in dorsal and ventral stream areas. The former, like V1 and V2, exhibit a 'feedforward' profile, with excitation beginning at the depth of Lamina 4, followed by activation of the extragranular laminae. The latter often displayed a multilaminar/columnar profile, with initial responses distributed across the laminae and reflecting modulation rather than excitation; CSD components were accompanied by either no changes or by suppression of action potentials. System-wide, response latencies indicated a large dorsal/ventral stream latency advantage, which generalizes across a wide range of methods. This predicts a specific temporal ordering of dorsal and ventral stream components of visual analysis, as well as specific patterns of dorsal-ventral stream interaction. Our findings support a hierarchical model of cortical organization that combines serial and parallel elements. Critical in such a model is the recognition that processing within a location typically entails multiple temporal components or 'waves' of activity, driven by input conveyed over heterogeneous pathways from the retina.

Animals↗

PubMed1993

Velocity profiles and phasic flow patterns in the non-stenotic human left anterior descending coronary artery during cardiac surgery.

OBJECTIVE: The aim was to investigate the phasic characteristics of normal human left coronary artery flow and velocity profiles across the vessel. METHODS: The phasic characteristics of flow in the human left anterior descending coronary artery, the centreline flow velocities, and the velocity profiles were measured in 10 patients during corrective surgery for atrial septal defect after closure of the defect. None of these patients had any detectable coronary artery stenosis or left ventricular hypertrophy. Measurements were made with a 20 MHz 80 channel pulsed Doppler velocimeter. RESULTS: The velocity waveform displayed a diastolic-predominant pattern with a systolic to diastolic velocity ratio of 0.29(SD 0.17). Reverse flow was observed in early systole in five patients and in mid to late systole in six patients. The values of peak Reynolds number, unsteadiness parameter, and pulsatility index were 504(198), 2.5(0.6), and 5.9(4.4) respectively. The velocity profiles during diastole showed considerable variability in shape, ranging from symmetrical to skewed to M shaped patterns. The peak wall shear rate was 765(250) s-1 on the epicardial wall of the vessel and 712(301) s-1 on the myocardial wall; the difference was not statistically significant. CONCLUSIONS: The velocity waveform displayed a diastolic-predominant pattern. Considerable variability in shape of the velocity profile was found and was perhaps due to the time evolution of the velocity profile within the diastolic time period.

Adolescent↗

PubMed1996

Identification and cloning of neuroblastoma-specific and nerve tissue-specific genes through compiled expression profiles.

An expression profile of active genes in a human neuroblastoma cell line CHP134 was obtained by collecting 1222 partial sequences from a 3'-directed cDNA library representing a non-biased mRNA population. By comparing this expression profile with the compiled profiles of multiple tissues, several novel gene transcripts that appeared only in the profile of the neuroblastoma cell line were identified. Further analyses by Northern blotting revealed two specific cDNA clones that are expressed in most of the human neuroblastomas examined, and three that are in some of the human neuroblastoma cell lines as well as in the adult human brain. Full-size cDNAs were cloned using these five partial cDNA sequences as probes and sequenced. A database search revealed that they are all novel and unique sequences: one sharing some amino acid sequence similarities with a cytoskeletal protein, two clones likely to be transcriptional factors, a clone that has characteristic potassium channel properties, and a clone that is non-homologous to any one of the known proteins. Thus, we argue that the collection of 3'-directed cDNA sequences in combination with the compiled expression profiles of active genes in multiple tissues is a powerful tool for discovering novel genes that are specifically expressed in a given cell or tissue, in this case neuroblastomas and/or nerve tissue.

Amino Acid Sequence↗

PubMed2003

Morbidity profiles of centenarians: survivors, delayers, and escapers.

BACKGROUND: The compression of morbidity hypothesis predicts that, in order to achieve their extreme old age, centenarians markedly delay or even escape diseases that would otherwise be lethal at younger ages. Phenotypic studies have not adequately characterized the prevalence and timing of age-related illnesses among those who achieve exceptional old age. Thus, we conducted a retrospective cohort study of centenarians to explore the timing of such diseases among centenarians. METHODS: Health history questionnaires were completed by 424 centenarians (aged 97-119 years) or their proxies. Lifetime (to-date) diagnoses of 10 major lethal illnesses (hypertension, heart disease, diabetes, stroke, nonskin cancer, skin cancer, osteoporosis, thyroid condition, Parkinson's disease, and chronic obstructive pulmonary disease) and one ocular disease (cataracts) that befall the elderly population, approximate age of diagnosis, level of alcohol and tobacco use, and presence or absence of cognitive impairment were assessed. Because of the retrospective nature of the study, the typically imprecise age of onset of cognitive impairment negated the ability to include age of onset of cognitive impairment in this aspect of the analyses. RESULTS: Examining the ages of onset for the 10 age-associated diseases and excluding cognitive impairment, we found that the centenarians fit into three morbidity profiles-Survivors, Delayers, and Escapers. 24% of male subjects and 43% of female subjects fit the Survivor profile, or those who had a diagnosis of an age-associated illness prior to the age of 80. Delayers were individuals who delayed the onset of age-associated illness until at least the age of 80, and 44% of male and 42% of female subjects fit this profile. Escapers were individuals who attained their 100th year of life without the diagnosis of common age-associated illnesses, and 32% of male and 15% of female subjects fit the Escaper profile. When examining only the most lethal diseases of the elderly population, heart disease, nonskin cancer, and stroke, we found that 87% of male and 83% of female subjects delayed or escaped these diseases. Subjects with and without cognitive impairment did not differ in terms of the profile to which they belonged. CONCLUSIONS: These results suggest there may be multiple routes to achieving exceptional longevity and that there are sex differences according to which route is taken. These routes represent different phenotypes and thus likely different genotypes of centenarians. The identification of three types of centenarians, Survivors, Delayers, and Escapers, provides direction for future study into the factors that determine exceptional longevity.

Age of Onset↗

PubMed2003

Multiple (multicentric and multifocal) cancers in the ipsilateral breast with different histologies: profiles of chromosomal numerical abnormality.

BACKGROUND: Chromosomal numerical abnormality (CNA) is a characteristic of breast cancer as with other common solid cancers. Multiple mammary carcinomas are also sometimes encountered in the ipsilateral breast. Deciding whether they are multicentric (arising independently) or multifocal (of the same origin) has been a continued challenge to clinicians and pathologists. METHODS: We experienced two cases of macroscopically distinct double carcinomas in the ipsilateral breast, in which two cancers had a different histopathological morphology. Centromere probes identifying 17 different and specific centromeres were used to obtain the profile of CNA for each tumor, with a microwave-assisted FISH protocol. For comparison, a case of three lesions, two of which had the same and the other different histology was also studied. RESULTS: Contrary to our expectations, in spite of the particular difference in the histopathological picture of these tumors, the CNA profile was the same in one case and different in the other. The gain of chromosome 1 and loss of chromosome 15 are representative features shared by multifocal cases. On the other hand, the multiple cancers with the same histology had mostly the same CNA profile. CONCLUSIONS: CNA profiling is useful to identify the lineage of multiple breast cancers. As shown here, regardless of the histological features, a certain common CNA profile can define the same origin of some multiple cancers.

Adenocarcinoma, Mucinous↗

PubMed2003

Finding weak similarities between proteins by sequence profile comparison.

To improve the recognition of weak similarities between proteins a method of aligning two sequence profiles is proposed. It is shown that exploring the sequence space in the vicinity of the sequence with unknown properties significantly improves the performance of sequence alignment methods. Consistent with the previous observations the recognition sensitivity and alignment accuracy obtained by a profile-profile alignment method can be as much as 30% higher compared to the sequence-profile alignment method. It is demonstrated that the choice of score function and the diversity of the test profile are very important factors for achieving the maximum performance of the method, whereas the optimum range of these parameters depends on the level of similarity to be recognized.

Algorithms↗

PubMed2006

GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.

In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website http://tubic.tju.edu.cn/GC-Profile/. In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution.

Algorithms↗

PubMed1996

Sodium profiling in elderly haemodialysis patients.

Intradialytic vascular instability continues to be one of the most frequent complications in elderly haemodialysis patients. Signs of impending hypotension such as sweating, apprehension, tachycardia, nausea, or vomiting may be infrequent in the geriatric population. The onset of hypotension in the elderly may be sudden and profound and may lead to serious consequences such as myocardial infarction, stroke, or aspiration if not treated promptly. Prevention of vascular instability is extremely important in the elderly. Avoiding rapid ultrafiltration sedatives, or antihypertensive medications and food intake may be beneficial. Optimal dialysate composition (dialysate sodium, bicarbonate, and calcium concentration) is important. Dialysate sodium profiling may be useful in the elderly to reduce intradialytic hypotension. Step sodium profiles result in better plasma volume refilling in early dialysis, while linear dialysate sodium profiles have greater plasma volume in late dialysis, suggesting that dialysate sodium profiles may need to be individualized for optimal response. Sodium profiling could also result in sodium retention, and long-term studies are needed in the elderly before their widespread use is recommended. Use of newer modalities such as continuous monitoring of plasma volume with Crit Line, and determination and monitoring of body-fluid compartments with bioimpedance may further improve vascular stability in the elderly.

Aged↗

PubMed2005

The effect of sodium profiling and feedback technologies on plasma conductivity and ionic mass balance: a study in hypotension-prone dialysis patients.

BACKGROUND: Sodium profiling improves haemodynamic tolerance in haemodialysis (HD) patients but may also influence sodium homeostasis. Changes in blood volume and plasma conductivity (PC) during HD can be modelled by feedback technology, but their effects on sodium homeostasis are not widely studied. METHODS: This randomized crossover study compared PC and ionic mass balance (IMB) as surrogate markers of sodium balance between standard HD [dialysate conductivity (DC) 14.0 mS/cm], sodium profiling (DC 15.0-->14.0 mS/cm), blood volume (BV)-controlled and PC-controlled feedback (target: post-HD PC: 14.0 mS/cm) in 10 HD patients with frequent hypotension. RESULTS: 440 treatments were studied. Pre-dialytic PC was significantly higher during SP (14.4+/-0.2 mS/cm) compared to standard HD (14.2+/-0.3 mS/cm), and was not different between the other manoeuvres: PC-controlled (14.1+/-0.3 mS/cm), and BV-controlled feedback (14.2+/-0.2 mS/cm). Except for the first treatment, during which IMB was lower during the sodium profile, IMB did not differ significantly between the various manoeuvres and was strongly dependent upon ultrafiltration volume and the difference between pre-dialytic PC and DC. Symptomatic hypotensive episodes occurred least frequently during BV-controlled feedback (8%) compared to the other manoeuvres (standard HD, 16%; sodium profile, 14%; PC-controlled feedback, 17%), but differences were not significant. Inter-dialytic weight gain and pre-dialytic systolic blood pressure did not differ. CONCLUSIONS: Pre-dialytic PC increased during the sodium profile, and did not differ between BV- or PC-controlled feedback compared to standard HD. Thus, it appears that both BV- and PC-controlled feedback can be safely prescribed without substantial salt- and water-loading, at least in the short term. Analysis of IMB is useful to assess differences in sodium balance between single treatment sessions but appears of less value in a steady-state situation.

Aged↗

PubMed2003

Two azuki bean XTH genes, VaXTH1 and VaXTH2, with similar tissue-specific expression profiles, are differently regulated by auxin.

To gain insight into the functional diversity of the XTH (xyloglucan endotransglucosylase/hydrolase) gene family, we analyzed the expression profiles of two azuki bean genes, VaXTH1 and VaXTH2, which share a striking resemblance in their amino acid sequences. The two XTH genes exhibit essentially similar tissue-specific expression profiles, in that both mRNAs are found predominantly in the phloem fibers of growing internodes. However, their expression profiles are not identical. Whereas VaXTH1 is expressed in xylem cells in the basal part of the internode, little or no expression of VaXTH2 is found in the xylem. Furthermore, they exhibit spatially divergent RNA distribution profiles along the internode, VaXTH1 being expressed nearer to the top of the internode than VaXTH2. This indicates their temporally divergent expression profiles during development of the phloem fiber. Indole-3-acetic acid (IAA) up-regulates both of the mRNA levels. However, this effect of IAA on the VaXTH1 gene is nullified in 0.25 M mannitol, which prevents cell expansion without affecting auxin action per se. In contrast, the IAA-induced up-regulation of the VaXTH2 gene is not affected by mannitol. Furthermore, fusicoccin, which promotes acidification and growth, up-regulates VaXTH1 expression, but not VaXTH2 expression. Thus, the two XTH genes are committed to different steps of the cell wall dynamics in the same cell type at different stages of phloem fiber development, and are regulated by IAA in different ways.

Fabaceae↗

PubMed2001

The determinants of alpha-amylase pH-activity profiles.

The glycosyl hydrolases present a large family of enzymes that are of great significance for industry. Consequently, there is considerable interest in engineering the enzymes in this family for optimal performance under a range of very diverse conditions. Until recently, tailoring glycosyl hydrolases for specific industrial processes mainly involved stability engineering, but lately there has also been considerable interest in engineering their pH-activity profiles. We mutated four neutral residues (N190, F290, N326 and Q360) in the chimeric Bacillus Ba2 alpha-amylase to both charged and neutral amino acids. The results show that the pH-activity profile of the Ba2 alpha-amylase can be changed by inserting charged residues close to the active site. The changes in the pH-activity profile for these neutral --> charged mutations do not, however, correlate with the predictions from calculations of the p K(a) values of the active site residues. More surprisingly, the neutral --> neutral mutations change the pH-activity profile as much as the neutral --> charged mutations. From these results, it is concluded that factors other than electrostatics, presumably the dynamic aspects of the active site, are important for the shape of the pH-activity profiles of the alpha-amylases.

Amino Acids↗

PubMed2000

Does the multidimensional nature of Super Profiles help district health authorities understand the way social capital affects health?

BACKGROUND: Social capital describes the notion that the social processes in an area can lead to benefits in health. As Super Profiles describe the social character of an area and they are easy for health authorities to use, they could provide a simple method for local assessment of how social organization affects health. METHODS: We calculated the expected mean birthweight for the enumeration districts of Birmingham based upon marital status, registration details of the child, year of birth, the mother's country of birth, fetal sex and deprivation as judged by the Townsend score using data from 138,696 live-born singleton births for the years 1986-1996 inclusive. We classified enumeration districts into Target Markets, derived from Super Profiles. For each Target Market, we calculated the observed mean birthweight and the difference and 95 per cent confidence interval between the observed and expected birthweights. We used information in Super Profiles to speculate about the social processes that led to some Target Markets having mean birthweights that were significantly different from those expected. RESULTS: Fifteen of the 40 Target Markets had significant differences between predicted and observed mean birthweight, but these differences were less than 50 g. There were no common characteristics of Target Markets that were consistently advantageous for birthweight and none that were disadvantageous. CONCLUSION: The information in the Super Profiles does not illuminate the way that social processes affect health, and the variation in mean birthweight between areas explained by social processes as measured by Super Profiles is small.

Birth Certificates↗

PubMed1991

Personality profiles and specialty choices of students from two medical school classes.

Changes in the composition of medical school classes, in methods of personality assessment, and in the nature of medical specialties motivated the authors to reexamine the relationship between a student's personality and his or her chosen medical specialty. In the mid-1980s, the authors assessed two consecutive classes of medical school students (120 in each class) on 15 personality measures throughout their four years; usable data were obtained for 199 of the students. The students' specialty choices upon graduation were obtained from the results of the National Resident Matching Program, and were classified as follows: internal medicine, surgery, family practice, pediatrics, psychiatry, obstetrics-gynecology, and hospital-based specialties. The authors constructed personality profiles for the students who had chosen each of these seven specialty groupings, on the basis of t-tests and discriminant function analyses, and discuss these profiles and their associations with the students' specialty choices in the context of earlier research. The personality profiles for surgeons were remarkable for their consistency with reports from the literature from the 1950s and 1960s, while the profiles for obstetricians, psychiatrists, and pediatricians were complex and provocative. Distinctive personality profiles did not emerge for internists or family practitioners.

Career Choice↗

PubMedDate not supplied

Screening to identify patients at risk: profiles of psychological risk factors for early intervention.

There is a serious need to provide effective early interventions that prevent the development of persistent pain and disability. Identifying patients at risk for this development is an important step. Our aim was to explore whether distinct subgroups of individuals with similar response patterns on a screening questionnaire exist. Moreover, the objective was to then relate these groups to future outcomes, for example, sick leave as an impetus for developing tailored interventions that might better prevent chronic problems. A total of 363 patients seeking primary care for acute or subacute spinal pain completed the Orebro Musculoskeletal Pain Screening Questionnaire and were then followed to determine outcome. Cluster analysis was used to identify subgroups. Validity was tested using 3 methods including the split-half technique. The subgroups were compared prospectively on outcome measures obtained 1 year later. Using pain intensity, fear-avoidance beliefs, function, and mood, we found 4 distinct profiles: Fear-Avoidant, Distressed Fear-Avoidant, Low Risk, and Low Risk-Depressed Mood. These 4 subgroups were also robust in all 3 of the validity procedures. The 4 subgroups were clearly related to outcome. Although the low risk profiles had virtually no one developing long-term sick leave, the Fear-Avoidant profile had 35% and the Distressed Fear-Avoidant profile 62% developing long-term sick leave. Our results suggest that fear-avoidance and distress are important factors in the development of pain-related disability and may serve as a key for early identification. Providing interventions specific to the factors isolated in the profiles should enhance the prevention of persistent pain and disability.

Adult↗