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PubMed2005

Association of nonreassuring fetal heart rate patterns and subsequent cerebral palsy in pregnancies with intrauterine bacterial infection.

We evaluated an association of nonreassuring fetal heart rate (FHR) patterns and subsequent cerebral palsy (CP) in pregnancies with intrauterine bacterial infection. Among 10,030 infants born during 1995 to 2000, 139 were complicated with acute intrauterine bacterial infection in labor. The FHR patterns 2 hours immediately before delivery were interpreted according to the guidelines of the National Institute of Child Health and Human Development. The correlations between the FHR patterns and umbilical blood gases, as well as FHR patterns and CP were studied. Statistics included unpaired t test, contingency table with chi (2) and Fisher test, and one-way analysis of variance with Bonferroni/Dunn test. Fifteen infants (11%) developed CP at 2 years or older. Nonreassuring FHR patterns including recurrent late deceleration, severe variable deceleration, and prolonged deceleration occurred in 24% of pregnancies with intrauterine infection. Incidence of CP was not different according to the FHR deceleration patterns or umbilical pH values. Multiple logistic regression analysis revealed that fetal tachycardia (OR, 11; 95% CI, 1.8 to 67) and lower gestational age (< 34 weeks; OR, 9.4; 95% CI, 0.96 to 93) was associated with CP in intrauterine infection. Nonreassuring FHR patterns were increased in intrauterine infection. CP occurred more frequently and was associated with tachycardia and lower gestational age, but not with FHR deceleration patterns or acidemia, suggesting different pathophysiology from acute hypoxia-ischemia.

Cerebral Palsy↗
PubMed2005

Turing pattern formation in coupled reaction-diffusion system with distributed delays.

Turing pattern formation in coupled two-layer system with distributed delayed is investigated. Numerical simulations prove that, when the coupling is weak, it can apparently accelerate the formation process and enhance the spatial amplitude of the pattern. When it is strong, it will prolong the formation process or even inhibit the pattern and turn the whole system into bulk oscillatory state by its influence on the transient oscillatory state. If the coupling covers only part of the system, Turing pattern can be prominently oriented according to the shape of the coupling area at tiny coupling strength. However, if the coupling is too strong, the Turing pattern may also be destroyed. This means that in coupled systems, the delay effect in the cross-layer signal transfer may significantly influence the spatial character and/or the evolution dynamics in Turing pattern formation, even to destroy the pattern. This work is of practical significance in the study of Turing pattern in biosystems, where bilayer membranes or multilayer tissues are often found.

Chemistry, Physical↗
PubMed2000

Power spectral analysis of R-R interval variability before and during the sinusoidal heart rate pattern in fetal lambs.

OBJECTIVE: The appearance of the sinusoidal heart rate pattern found on fetal cardiotocograms has not been fully explained, either physiologically or clinically. In this study we performed power spectral analysis on the sinusoidal heart rate pattern obtained by administration of arginine vasopressin and atropine sulfate to investigate its frequency components in fetal lambs with long-term instrument implantation. STUDY DESIGN: Eleven tests were performed in 4 fetal lambs at 120 to 130 days' gestation. An artificial sinusoidal heart rate pattern was obtained by administration of atropine sulfate and arginine vasopressin in 9 tests. An autoregression model was used to compare the spectral patterns before and during the sinusoidal heart rate pattern. RESULTS: Marked decreases in low-frequency (0.025-0.125 cycles/beat) and high-frequency (0.2-0.5 cycles/beat) areas were observed in the presence of the sinusoidal heart rate pattern. However, there were no significant changes in the very-low-frequency area (0.01-0.025 cycles/beat), which corresponds to the frequency of the sinusoidal heart rate pattern. CONCLUSION: The sinusoidal heart rate pattern may represent a very low-frequency component inherent in fetal heart rate variability that appears when low- and high-frequency components are reduced as a result of strongly suppressed autonomic nervous activity.

Animals↗
PubMed2003

Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices.

The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.

Base Sequence↗
PubMed1990

Automatic generation of primary sequence patterns from sets of related protein sequences.

We have developed a computer algorithm that can extract the pattern of conserved primary sequence elements common to all members of a homologous protein family. The method involves clustering the pairwise similarity scores among a set of related sequences to generate a binary dendrogram (tree). The tree is then reduced in a stepwise manner by progressively replacing the node connecting the two most similar termini by one common pattern until only a single common "root" pattern remains. A pattern is generated at a node by (i) performing a local optimal alignment on the sequence/pattern pair connected by the node with the use of an extended dynamic programming algorithm and then (ii) constructing a single common pattern from this alignment with a nested hierarchy of amino acid classes to identify the minimal inclusive amino acid class covering each paired set of elements in the alignment. Gaps within an alignment are created and/or extended using a "pay once" gap penalty rule, and gapped positions are converted into gap characters that function as 0 or 1 amino acid of any type during subsequent alignment. This method has been used to generate a library of covering patterns for homologous families in the National Biomedical Research Foundation/Protein Identification Resource protein sequence data base. We show that a covering pattern can be more diagnostic for sequence family membership than any of the individual sequences used to construct the pattern.

Amino Acid Sequence↗
PubMed2004

Dietary patterns, insulin sensitivity and adiposity in the multi-ethnic Insulin Resistance Atherosclerosis Study population.

Epidemiological investigations increasingly employ dietary-pattern techniques to fully integrate dietary data. The present study evaluated the relationship of dietary patterns identified by cluster analysis with measures of insulin sensitivity (SI) and adiposity in the multi-ethnic, multi-centre Insulin Resistance Atherosclerosis Study (IRAS, 1992-94). Cross-sectional data from 980 middle-aged adults, of whom 67 % had normal and 33 % had impaired glucose tolerance, were analysed. Usual dietary intake was obtained by an interviewer-administered, validated food-frequency questionnaire. Outcomes included SI, fasting insulin (FI), BMI and waist circumference. The relationship of dietary patterns to log(SI+1), log(FI), BMI and waist circumference was modelled with multivariable linear regressions. Cluster analysis identified six distinct diet patterns--'dark bread', 'wine', 'fruits', 'low-frequency eaters', 'fries' and 'white bread'. The 'white bread' and the 'fries' patterns over-represented the Hispanic IRAS population predominantly from two centres, while the 'wine' and 'dark bread' groups were dominated by non-Hispanic whites. The dietary patterns were associated significantly with each of the outcomes first at the crude, clinical level (P<0.001). Furthermore, they were significantly associated with FI, BMI and waist circumference independent of age, sex, race or ethnicity, clinic, family history of diabetes, smoking and activity (P<0.004), whereas significance was lost for SI. Studying the total dietary behaviour via a pattern approach allowed us to focus both on the qualitative and quantitative dimensions of diet. The present study identified highly consistent associations of distinct dietary patterns with measures of insulin resistance and adiposity, which are risk factors for diabetes and heart disease.

Adipose Tissue↗
PubMed2005

Consistent dietary patterns identified from childhood to adulthood: the cardiovascular risk in Young Finns Study.

Dietary patterns are useful in nutritional epidemiology, providing a comprehensive alternative to the traditional approach based on single nutrients. The Cardiovascular Risk in Young Finns Study is a prospective cohort study with a 21-year follow-up. At baseline, detailed quantitative information on subjects' food consumption was obtained using a 48 h dietary recall method (n 1768, aged 3-18 years). The interviews were repeated after 6 and 21 years (n 1200 and n 1037, respectively). We conducted a principal component analysis to identify major dietary patterns at each study point. A set of two similar patterns was recognised throughout the study. Pattern 1 was positively correlated with consumption of traditional Finnish foods, such as rye, potatoes, milk, butter, sausages and coffee, and negatively correlated with fruit, berries and dairy products other than milk. Pattern 1 type of diet was more common among male subjects, smokers and those living in rural areas. Pattern 2, predominant among female subjects, non-smokers and in urban areas, was characterised by more health-conscious food choices such as vegetables, legumes and nuts, tea, rye, cheese and other dairy products, and also by consumption of alcoholic beverages. Tracking of the pattern scores was observed, particularly among subjects who were adolescents at baseline. Of those originally belonging to the uppermost quintile of pattern 1 and 2 scores, 41 and 38 % respectively, persisted in the same quintile 21 years later. Our results suggest that food behaviour and concrete food choices are established already in childhood or adolescence and may significantly track into adulthood.

Adolescent↗
PubMed2000

Genetic patterning of embryonic inner ear development.

The commitment of the otocyst to form balance (pars superior) and hearing (pars inferior) receptors is under the control of patterning genes. Intersecting patterns of gene expression has been proposed to explain the regionalization of inner ear sensory receptor development. Insights into the roles of patterning genes is being acquired from the analysis of inner ear development of null mutation mice. An example of the consequences of the loss of expression of a single patterning gene is the effect of a null mutation of paired-box gene 2 (Pax2) on formation of the cochlea. Pax2 transcripts are expressed in the pars inferior of the otocyst and null mutant inner ears show agenesis of the cochlea. This is an example of the profound effect that loss of a single patterning gene can have on inner ear development. However, more typically there is redundancy of gene action during inner ear development as exemplified by the overlapping pattern of expression of two closely related homeobox-containing genes (i.e. Hmx2 and Hmx3) in the pars superior of the otocyst. Hmx2 and Hmx3 genes are both expressed early in otic development with Hmx3 transcripts present in the placode. However, null mutation of the Hmx3 patterning gene produced only a limited vestibular defect, and did not result in the agenesis of the vestibule. This result suggests that there is redundancy in genes that have similar patterns of regional expression in the otic anlagen.

Animals↗
PubMed1992

Dietary patterns and colon cancer in western New York.

Seven dietary patterns were identified among control subjects in the Western New York Diet Study (1975-1986) by application of principal components analysis to data from a 95-item food frequency interview. The results of case-control analyses of colon cancer risk for these patterns are presented. Cases were matched with neighborhood controls on the bases of age and sex; 205 colon case-control male and 223 female pairs were obtained. The dietary patterns and intakes of energy, total fat, and dietary fiber were examined with logistic regression for their individual contributions to risk. In males, three of these dietary patterns were associated positively with fat and energy consumption; they elevated risk for colon cancer and accounted for more risk than did the specific nutrients. Control for energy and fat intakes allowed the protective influences of additional dietary patterns to be expressed. No patterns elevated risk in women; two patterns were protective for colon cancer. Controlling for energy and fat intake enhanced the protection afforded by one of these patterns but had no influence on that of the other. Measures of foods rather than single nutrients may be more inclusive of dietary exposures to risk as well as being related more directly to underlying health behaviors. Therefore they may be better able to account for risk in diseases with multiple causation.

Case-Control Studies↗
PubMed2000

Is a dense mammographic parenchymal pattern a contraindication to hormonal replacement therapy?

The aim of the study was to find out whether the effect of hormonal replacement therapy (HRT) is modified by the mammographic parenchymal patterns on the risk of breast cancer. Subjects were 4163 Finnish women aged 40-47 years at entry who were invited to breast cancer screening every second year from 1982 to 1990. Mammographic parenchymal patterns (Wolfe's classification) were recorded at each screening round. The information, on use of HRT, was recorded from 1984. The follow-up ended in 1993 and up until that time 68 new breast cancers were diagnosed. A Poisson regression model was used in the analysis of the data. Use of HRT was not related to the risk of breast cancer (RR = 0.7, 95% CI 0.4-1.4), whereas mammographic parenchymal pattern was statistically significantly associated with risk of breast cancer. The age-adjusted relative risk of breast cancer among women with P2 versus N1 pattern was 2.5 (95% CI 1.3-4.8) and with DY versus N1 pattern 4.9 (951% CI 1.6-15.1). Women using HRT and with DY pattern were at substantially increased risk of breast cancer (RR = 11.6, 95% CI 2.5-53.6) compared with women not using HRT and with N1 pattern. There was an increased risk of breast cancer among women with DY mammographic parenchymal pattern who used HRT, which was consistent with a synergistic joint effect.

Adult↗
PubMed2005

Dietary patterns of Korean Americans described by factor analysis.

OBJECTIVES: This study tested the hypothesis that the dietary behaviors of Korean Americans (KAs) can be grouped into dietary patterns and subsequently examined relations between major dietary patterns and sociodemographic characteristics. METHODS: A cross-sectional study was conducted with KAs residing in Michigan using a mail survey. Of 1,860 questionnaires mailed to KAs in Michigan, 637 (34%) responded and 497 first-generation KAs (263 men, 234 women, aged 30-87 y) were included in the final analyses. A factor analysis was used to identify dietary patterns from a 93-item food frequency questionnaire developed for KAs (KFFQ). RESULTS: Major dietary patterns of KAs were labeled "vegetable/fruit," and "traditional Korean" in both men and women and "acculturated American" in men and "traditional American" in women. The "traditional Korean" dietary pattern was negatively associated with length of residence in the U.S. for both men and women (p < 0.01). The other major dietary patterns were not associated with other sociodemographic variables examined in men; however, the "vegetable/fruit" dietary pattern was positively associated with length of residence in the U.S. (p < 0.05) and education level (p < 0.05) in women. CONCLUSIONS: Dietary pattern analysis can be used to understand dietary behaviors regarding health risks of ethnically different immigrants including KAs.

Acculturation↗
PubMed1997

Brain proton magnetic resonance spectroscopy in HIV-related encephalopathy: identification of evolving metabolic patterns in relation to dementia and therapy.

Proton MRS has proved useful in the early diagnosis of HIV-related encephalopathy. The modifications of brain metabolism in HIV-related encephalopathy can be classified according to different metabolic patterns (Vion-Dury J et al. CR Acad Sci 1994;317:833-840). The present study describes the relative occurrence of these patterns and evaluates their evolution under zidovudine treatment. We have examined 112 HIV patients--35 neuroasymptomatic patients and 77 patients with ADC (AIDS dementia complex)--with localized proton MRS, using the PRESS 135-msec sequence. We have found the same metabolic modifications in N-acetylaspartate and choline-containing compounds as described in the literature. In addition, 14% of HIV patients with normal MRI displayed abnormal MRS, whatever their neurological status. The MRS-added diagnostic value in neuroasymptomatic patients reaches 30 %. The occurrence of undifferentiated (modification of NAA/Cho ratio only) and Cho (mainly an increase in choline signal) patterns is not significantly different in neuroasymptomatic and ADC patients. The NAA pattern (mainly a significant loss of NAA) is more frequent in ADC patients. Only ADC patients display the double pattern (with a significant increase in choline signal and a significant loss of NAA). Quantitated cerebral atrophy (bifrontal ratio) is related to the occurrence of NAA loss (in NAA and double patterns). An MRS follow-up study of 11 HIV patients showed that the clinical outcome was favorable after a 1000-mg/day zidovudine treatment in patients displaying an NAA pattern whereas this treatment had no effect on the patients displaying the Cho pattern. Consequently, MRS appears to be of great interest in predicting responsiveness to antiretroviral drugs and detecting early any resistance to treatment.

AIDS Dementia Complex↗
PubMed1998

Approaches to the automatic discovery of patterns in biosequences.

This paper surveys approaches to the discovery of patterns in biosequences and places these approaches within a formal framework that systematises the types of patterns and the discovery algorithms. Patterns with expressive power in the class of regular languages are considered, and a classification of pattern languages in this class is developed, covering the patterns that are the most frequently used in molecular bioinformatics. A formulation is given of the problem of the automatic discovery of such patterns from a set of sequences, and an analysis is presented of the ways in which an assessment can be made of the significance of the discovered patterns. It is shown that the problem is related to problems studied in the field of machine learning. The major part of this paper comprises a review of a number of existing methods developed to solve the problem and how these relate to each other, focusing on the algorithms underlying the approaches. A comparison is given of the algorithms, and examples are given of patterns that have been discovered using the different methods.

Algorithms↗
PubMedDate not supplied

Cell patterning on biological gels via cell spraying through a mask.

We present an easily applicable and inexpensive method for patterning cells on arbitrary surfaces including biological gels with little loss of viability or function. Single-cell suspensions of human umbilical vein endothelial cells and NIH 3T3 fibroblasts were sprayed with an off-the-shelf airbrush through a mask to create 100-microm scale patterns on collagen gels. Three-dimensional patterns were created by layering a collagen gel on top of the first pattern and patterning the top gel. Coculture of rat hepatocytes with NIH 3T3 patterns on collagen gels resulted in localized increased activity of cytochrome P-450 along the pattern. These results suggest that cell spraying is a useful tool for the study of heterotypic cellular interactions and tissue-engineering applications on biologically relevant matrices, and for the creation of three-dimensional cell patterns in vitro.

Animals↗
PubMed1995

Effects of dietary fat on high-density-lipoprotein subclasses are influenced by both apolipoprotein E isoforms and low-density-lipoprotein subclass patterns.

We examined the effects of replacing dietary fat with carbohydrates on high-density-lipoprotein (HDL) subclasses as measured by nondenaturing polyacrylamide-gradient-gel electrophoresis. One hundred five men received a 6-wk low-fat diet (24% of total energy) and a 6-wk high-fat diet (46% of energy) in a crossover design. Absorbency of protein stain was measured within five HDL subclasses: HDL3c (7.2-7.8 nm), HDL3b (7.8-8.2 nm), HDL3a (8.2-8.8 nm), HDL2a (8.8-9.7 nm), and HDL2b (9.7-12 nm). The low-density-lipoprotein-(LDL) subclass pattern was determined by gradient-gel electrophoresis, with pattern B men defined as having an LDL-predominant peak diameter < or = 25.5 nm and an LDL distribution skewed toward larger size particles. On the high-fat diet, 18 men exhibited LDL-subclass pattern B and 87 men exhibited the alternative LDL pattern A. Twelve men had the apolipoprotein (apo) epsilon 2 allele. Replacing dietary fat with carbohydrates 1) significantly decreased HDL3a, HDL2a, and HDL2b; 2) reduced HDL2b significantly more in pattern A than in pattern B men; and 3) increased plasma HDL3b concentrations significantly more in those men with the epsilon 2 allele. Our results suggest that unfavorable HDL changes were significantly more likely to occur in men who had LDL-subclass pattern A or the apo epsilon allele than in men who had pattern B or lacked the epsilon 2 allele.

Apolipoproteins E↗
PubMed1999

Genetic and environmental influences on eating patterns of twins aged >/=50 y.

BACKGROUND: Clinicians and researchers could benefit from a greater understanding of the role of genetic and environmental factors in human eating behavior. OBJECTIVE: Our aim was to estimate the relative influence of genetic and environmental factors on habitual eating patterns in middle-aged and elderly men and women. DESIGN: Male and female twins (n = 4640) aged >/=50 y completed a mailed version of the National Cancer Institute food-frequency questionnaire. Factor analysis was performed to identify eating patterns among respondents. Estimates of genetic, common environmental (shared by family members), and specific environmental (unique to an individual) influences were obtained for food use, serving size, and consumption frequency by comparing monozygotic and dizygotic twin-pair groups with structural equation analysis. RESULTS: Two independent eating patterns were identified: the first consisted of items high in fat, salt, and sugar, and the second reflected healthful eating habits. Although the influence of environmental factors was larger, between 15% and 38% of the total variation in pattern 1 and between 33% and 40% in pattern 2 were explained by genetic influences. Models accounting for sex differences in genetic and environmental estimates fit the data significantly better for food use and serving size of foods in eating pattern 1 and for food use in eating pattern 2. CONCLUSION: Although 60-85% of the variability in eating patterns was associated with environmental factors, genetic influences were also apparent and there was some evidence of sex specificity. These findings may be important in crafting dietary interventions and predicting adherence to these interventions.

Aged↗
PubMed1987

Recognition of characteristic patterns in sets of functionally equivalent DNA sequences.

An algorithm has been developed for the identification of unknown patterns which are distinctive for a set of short DNA sequences believed to be functionally equivalent. A pattern is defined as being a string, containing fully or partially specified nucleotides at each position of the string. The advantage of this 'vague' definition of the pattern is that it imposes minimum constraints on the characterization of patterns. A new feature of the approach developed here is that it allows a 'fair' simultaneous testing of patterns of all degrees of degeneracy. This analysis is based on an evaluation of inhomogeneity in the empirical occurrence distribution of any such pattern within a set of sequences. The use of the nonparametric kernel density estimation of Parzen allows one to assess small disturbances among the sequence alignments. The method also makes it possible to identify sequence subsets with different characteristic patterns. This algorithm was implemented in the analysis of patterns characteristic of sets of promoters, terminators and splice junction sequences. The results are compared with those obtained by other methods.

Algorithms↗
PubMed2002

Extreme value theory applied to postoperative breathing patterns.

BACKGROUND: There has been little published work on the statistical features of breath times in postoperative patients. We applied extreme value theory (a statistical method) to the variation in the timing of postoperative breathing. METHODS: We observed 49 patients 3-6 h after a variety of surgical procedures, once they had achieved a stable breathing pattern. The breathing patterns could be one of the three types predicted by the extreme value model. 'Finite' breathing patterns (n=30) have a finite upper limit of duration for any apnoea. Patients that displayed one of the other two patterns ('standard' and 'extended') have, potentially, no limit in duration of apnoea. RESULTS: The type of breathing pattern observed in each patient was not reliably identified by most of the commonly used risk factors (age, type of surgery, opioid type, dose, and route of administration). A finite pattern was observed in 13 of 26 patients receiving epidural (vs 17 of 23 parenteral analgesia: P=0.15), and 15 of 19 receiving morphine (vs 15 of 30 other opioids: P=0.05). The patients with 'finite' patterns were also significantly less drowsy (score 1.04 (0.92) vs 1.62 (0.62), P<0.05). CONCLUSIONS: The breathing pattern was not related to mean breath times, suggesting that the prevalence of apnoeas cannot be reliably predicted by measurement of the respiratory rate alone.

Adult↗