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PubMed2006

The origin of the diversity of leaf venation pattern.

The leaf venation pattern of plants shows remarkable diversity and species-specificity. However, the mechanism underlying the pattern formation and pattern diversity remains unclear. We developed a mathematical model that is based on the positive feedback regulation between plant hormone auxin and its efflux carrier. This system can generate auxin flow pathways by self-organization from an almost homogeneous state. This result explains a well-known experimental phenomenon referred as to "polar auxin transport." The model can produce diverse leaf venation patterns with spatial regularity under similar conditions to those of leaf development, that is, in the presence of leaf expansion and auxin sink. Final venation patterns are strikingly affected by leaf shape and leaf expansion. These results indicate that the positive feedback regulation between auxin and its efflux carrier is a central dynamic in leaf venation pattern formation. The diversity of leaf venation patterns in plant species is probably due to the differences of leaf shape and leaf expansion pattern.

Algorithms↗
PubMed1986

Isocitrate dehydrogenase in D. melanogaster imaginal discs: pattern development and alteration by homoeotic mutant genes.

The distribution of the soluble form of NADP+-dependent isocitrate dehydrogenase (ICDH) was examined in Drosophila melanogaster imaginal discs. Development of the enzyme patterns and the specific transformations of the patterns by homoeotic mutants were studied. ICDH pattern formation was followed in eye-antennal discs and wing discs from the late 2nd instar stage through 3rd instar and 8 hours into prepupal development. The patterns formed gradually in both disc types. The most interesting pattern developed in the eye portion of the eye-antennal disc complex. ICDH distribution as well as staining intensity correlated well with differentiation of the ommatidia. The spatial distribution of ICDH within the discs was under genetic control. The patterns reflected the state of determination of the disc. When the presumptive tissue type was transformed via mutant homoeotic genes to different determinative states, the ICDH pattern likewise transformed to the pattern characteristic of the newly acquired structure.

Animals↗
PubMed1997

Patterns of lymphokine secretion amongst mouse gamma delta T cell clones.

Although the patterns of lymphokine (LK) secretion by CD4 and CD8 alpha beta T cells have been extensively studied, the question of whether gamma delta T cells display patterns of restricted LK production and whether these patterns are the same as seen in conventional alpha beta T cells has not been previously addressed. In this study we generated panels of gamma delta T cell clones from normal C57BL/6 and BALB/c mice using a lectin-driven system and compared their patterns of secretion of nine LK with those of CD4 and CD8 alpha beta T cell clones generated in the same system. The results showed that gamma delta T cell clones displayed nonrandom patterns of highly restricted LK production with a strong bias towards the production of type 1 LK. The dominant pattern was one of high level secretion of interferon-gamma and tumor necrosis factor (TNF), with variable production of interleukin (IL)-2, and little or none of the type 2 LK IL-4, IL-5, IL-6, and IL-10. This pattern differed significantly from that of CD4 Th1 clones in that gamma delta clones showed a striking deficiency in the production of IL-3 and granulocyte/macrophage colony-stimulating factor. A small subset of gamma delta clones displayed a novel pattern, in which the only LK produced in substantial quantity were TNF and variable amounts of IL-2. The bias of gamma delta T cells towards type 1 LK production was not an artefact associated with cloning because bulk populations of splenic gamma delta T cells behaved in the same way, even when activated in the presence of high concentrations of IL-4.

Animals↗
PubMed1994

Classification of wheat varieties by isoelectric focusing patterns of gliadins and neural network.

Classification of wheat varieties, using isoelectric focusing patterns of the gliadins, image processing and neural networks, is described. The method was compared to a statistical classification method, discriminant analysis. The isoelectric point and the area of each band were calculated by image processing. Different methods of presenting the electrophoretic patterns to the neural network were studied. The most effective method was transformation of the electrophoretic pattern to a small (11 x 47 pixels) representation of the original digitized image, which was presented to the neural network as a vector. The neural network was trained with a number of patterns and tested with new patterns from different electrophoretic runs of the same wheat varieties. In this study we used ten different wheat varieties and the neural network was able to classify 95.5% of the patterns correctly. The statistical classification method classified the same data set 91.8% correctly. We conclude that both the neural network and discriminant analysis were able to classify the patterns correctly with a high degree of certainty. The patterns that were misclassified were indistinguishable by visual inspection.

Discriminant Analysis↗
PubMed2005

Dietary patterns and risk of pancreatic cancer.

To investigate associations between broad dietary patterns and pancreatic cancer risk, we conducted a case-control study of 585 histologically confirmed pancreatic cancer cases and 4,779 population-based controls in 8 Canadian provinces between 1994 and 1997. Dietary intake was assessed using a FFQ. Major dietary patterns were identified by factor analysis. Unconditional logistic regression was used to describe associations between dietary pattern scores and risk of pancreatic cancer. Three dietary patterns were identified: Western, characterized by high intake of processed meats, sweets and desserts, refined grains and potatoes; fruits and vegetables, characterized by high intake of fresh fruits and cruciferous vegetables; drinker, characterized by high consumption of liquor, wine and beer. After adjustment for age, BMI, smoking, physical activity, province, educational attainment and total energy intake, the fruits and vegetables pattern was associated with a 49% reduction in pancreatic risk among men (OR = 0.51, 95% CI 0.29-0.90, p = 0.004) when comparing the highest and lowest quartiles of dietary pattern scores. No significant relationship was observed with the Western and drinker patterns. Although the response rate for eligible, recruited subjects was relatively low, our results suggest that the fruits and vegetables dietary pattern reduces pancreatic cancer risk among men.

Adult↗
PubMed2005

Dietary patterns and subsequent colorectal cancer risk by subsite: a prospective cohort study.

In order to investigate the associations between dietary patterns and the risk of colorectal cancer by subsite in Japan, the baseline data from a population-based cohort study of 20,300 men and 21,812 women were analyzed. We conducted factor analysis and identified 3 major dietary patterns, "healthy," "traditional" and "Western," and calculated the factor scores of each pattern for individuals. During 10 years of follow-up, 370 colorectal cancer cases were identified. We found a positive association between the traditional pattern and colon cancer risk in women [rate ratio for highest quartile (RR) = 2.06; 95% CI = 1.10-3.84; p for trend = 0.11], but not in men. This positive association was slightly stronger for proximal colon cancer (RR = 2.07; 95% CI = 0.84-5.12) than for distal colon cancer (RR = 1.84; 95% CI = 0.75-4.50). After multivariate adjustment, the Western dietary pattern was also positively associated with colon cancer risk in females (RR = 2.21; 95% CI = 1.10-4.45), with the strongest associations being observed for females with distal colon cancer (RR = 3.48; 95% CI = 1.25-9.65). We did not observe any significant association between the healthy dietary pattern and colon cancer risk. For rectal cancer, no significant associations were found for the 3 dietary patterns. In conclusion, we found that the traditional and the Western dietary patterns were positively associated with colon cancer risk in females.

Adult↗
PubMed1995

X-ray powder diffraction patterns of calcium phosphates analyzed by the Rietveld method.

Least-square refinement of x-ray powder diffraction patterns analyzed by the Rietveld method can yield structural information which had been unattainable or at least elaborate to obtain by conventional pattern analysis. The Rietveld method calculates a powder pattern on the basis of a structural model as well as the characteristics of the instrument used, and minimizes the differences between the intensities observed and the intensities calculated. The method is applied on patterns produced powders or polycrystalline solids on conventional powder diffractometers. For materials containing more than one crystalline phase with known structures such as hydroxyapatite (HA) and whitlockite (beta-TCP), pattern analysis yields phase quantification without internal or external standards. Refinement of the lattice parameters a0 and c0 determines the degree of dehydroxylation in plasma-sprayed HA coatings. The presence of amorphous Ca phosphates in HA coatings is detected by background modeling. The calculation of entire powder patterns allows discrimination of small concentrations of poorly crystallized Ca phosphate phases against the background, and prevents gross aberrations in estimating secondary phases. Even detect structures such as an OH-deficient HA lattice can be detected through slight differences in diffracted intensity by which the pattern calculated deviates from the pattern observed.

Biocompatible Materials↗
PubMed1993

Chronic liver disease: comparison of ultrasound patterns with laparoscopy and biopsy.

We studied the correlation of ultrasound patterns with laparoscopy and biopsy results in 140 patients with chronic liver disease (CLD). Of the 23 patients with a normal ultrasound pattern (N), biopsies revealed CLD in 18; in the 22 patients with unspecified hepatomegaly (H), biopsies disclosed CLD in 20; and in the 64 patients with a homogeneous bright pattern (HB), biopsies showed CLD in 62. All 22 cases of heterogeneous bright pattern (HTB) and all 9 patients with nodular pattern (ND) had CLD. In conclusion, it appears that the HTB and nodular ultrasound patterns confirm the presence of CLD, the HB pattern is suggestive of CLD, but diagnosis of CLD cannot be made from N and H patterns.

Adult↗
PubMed1982

Mechanisms of G6PD isozyme pattern changes at fertilization.

The electrophoretic pattern of G6PD changes in sea urchin egg supernatants, gels, and pellets (homogenized in 0.01 M MgCl2, 0.01 M Tris, pH8, and centrifuged at 4 X 10(4)g) within the first minute following sperm penetration. Therefore, the changes in pattern are an early event of egg activation and are not changes in gene activity. Calcium ionophore activation causes similar changes in G6PD in unfertilized eggs, so calcium is probably involved directly or indirectly. Treatment with 1 mg/ml of G6P and/or NADP, DTT, or papain also causes changes in the isozyme patterns, but the resulting patterns are different from patterns obtained from the fertilized fractions, and each treatment produces a unique pattern. The results lead to the conclusion that the different patterns of unfertilized and fertilized eggs are due to enzyme posttranslational modification. Different patterns may result from intrinsic differences in 1) -SH reduction or levels of glutathione, 2) substrate and cofactor levels, or 3) proteolytic enzymes released naturally or as a result of homogenization.

Animals↗
PubMed2006

Developmental mechanisms underlying tooth patterning in continuously replacing osteichthyan dentitions.

The dentition of osteichthyans presents an astonishing diversity with regard to the distribution of teeth in the oral cavity, tooth numbers, arrangements, shapes, and sizes. Taking examples from three unrelated teleosts--the most speciose group of osteichthyans--and from the literature, this study explores how the initial tooth pattern is set up, and how this relates to the establishment and maintenance (or modification) of the tooth replacement pattern. In teleosts, first-generation teeth (the very first teeth in ontogeny to develop at a particular locus) are commonly initiated in adjacent or in alternate (odd and even) positions. The mechanisms responsible for these divergent developmental patterns remain to be elucidated, in particular, whether they reflect a field or local type of control. However, patterns of adjacent or alternate tooth initiation, set up by the first-generation teeth, can easily turn into replacement patterns where new teeth are initiated simultaneously every second, or even every third position, by synchronizing the formation of new first-generation teeth to the formation of replacement teeth at older loci. Our observations suggest that, once established, the replacement pattern appears to be maintained, as a kind of "default" state. Variations and modifications in this pattern are nevertheless common and suggest that tooth replacement is under local control, exerted at the level of the initiation of replacement teeth. Further studies are needed to test the hypothesis that regular replacement patterns are more frequent in association with the plesiomorphic condition of extramedullary replacement (replacement on the surface of the dentigerous bone) and more rare in the derived condition of intramedullary replacement (replacement within the medullary cavity of the dentigerous bone).

Animals↗
PubMed1993

Patterns of sensory nerve conduction abnormalities in demyelinating and axonal peripheral nerve disorders.

The pattern of an abnormal median-normal sural (AMNS) sensory response is associated with acute and chronic inflammatory demyelinating polyradiculoneuropathy (AIDP and CIDP) and considered unusual in other types of neuropathy, although specificity and sensitivity of this pattern have not been evaluated. We compared sensory responses (patterns and absolute values) in patients with AIDP, CIDP, diabetic polyneuropathy (DP), and motor neuron disease (MND). Using strict criteria, the AMNS pattern occurred more frequently in recent onset AIDP (39%) compared with CIDP (28%), DP (14%-23%), or MND (22%) patients. This pattern was found in 3% of control subjects. The extreme pattern of an absent median-present sural response occurred only in AIDP and CIDP patients and in no other groups. Abnormalities of both nerves were more common in long-standing polyneuropathies such as CIDP and DP compared with AIDP or MND. Median nerve amplitudes were reduced significantly in AIDP, CIDP, and DP patients compared with MND patients, whereas sural nerve amplitudes were significantly reduced only in DP and CIDP patients. These findings may reflect early distal nerve involvement particularly in AIDP patients which is highlighted by differences in median and sural nerve recording electrode placement. We conclude that, in the appropriate clinical setting, the AMNS pattern, an absent median-present sural response pattern, or a reduced median amplitude compared with the sural amplitude supports a diagnosis of a primary demyelinating polyneuropathy.

Adolescent↗
PubMed1997

Semiautomated resolution of overlapping stutter patterns in genomic microsatellite analysis.

Microsatellites are polymorphic, short nucleotide repeating units scattered more or less randomly throughout the genome. They are readily detectable by polymerase chain reaction (PCR) and often used as genomic markers. One problem in the analysis of microsatellite data is the appearance of secondary bands during PCR that result in extended banding patterns. These "stutter" patterns may overlap in heterozygous alleles and obscure the overall pattern, severely interfering with analysis. This paper develops a model that successfully predicts the general shape of stutter patterns. It then presents techniques for measuring the intensity of the individual contributing alleles. The model is based on the assumption that there is a certain probability of losing or gaining a microsatellite repeat unit during each PCR cycle. The effect is cumulative, with the chance of losing a repeat unit being much greater than that of gaining one, which leads to a gradual reduction in the mean length of the pattern with increased PCR cycles. This can be modeled quantitatively to predict the shape of the stutter pattern, a prediction borne out by experiment. Next, a least-squares technique is presented that is used to analyze the overlapping stutter patterns and determine the relative concentration of each microsatellite in heterozygous alleles. The technique is based on the observation that, at least for microsatellites of approximately the same length, the relative intensity of each band in the stutter pattern is approximately the same for each allele. The stutter shape is most easily determined from homozygous alleles. It can also be approximated from heterozygous samples if the difference between the lengths of the primary microsatellite bands can be determined.

Algorithms↗
PubMed1999

Evaluation of the human choroidal melanoma rabbit model for studying microcirculation patterns with confocal ICG and histology.

The aim of this study was to develop consistently focal elevated choroidal masses of human choroidal melanoma in immunosuppressed rabbits and to correlate the visualization of prognostically significant microcirculation patterns from confocal indocyanine green angiography with histologic microcirculation patterns. A human choroidal melanoma cell line (OCM1) was implanted in the choroid of 40 rabbit eyes using three different techniques: transscleral choroidal injection of a cell suspension, injection of a cell suspension in a surgically induced cyclodialysis cleft, and implantation of solid tumor fragments in a surgically induced cyclodialysis cleft. The rabbits were immunosuppressed with daily injections of Cyclosporin A to prevent host versus graft reaction. The eyes were studied weekly with indirect ophthalmoscopy and fundus photography to monitor tumor growth and indocyanine green angiography using a confocal scanning laser ophthalmoscope to identify microcirculation patterns in vivo and correlate these findings with the histologic demonstration of tumor microcirculation patterns. A tumor mass was identified by indirect ophthalmoscopy in 16 of the 40 implanted rabbit eyes (40%). Each of these tumors was confirmed histologically to represent a focal elevated choroidal mass. All 16 elevated choroidal masses grow in eyes in which solid tumor fragments were implanted. In total, a melanoma was identified histologically in 28 of the implanted 40 eyes (70%). In addition to the 16 eyes where the melanoma appeared as a focal elevated choroidal mass, 4 eyes contained a focal elevated mass in the sclera and 8 eyes contained a flat choroidal tumor. Histologically, microcirculation patterns were identified only in the 16 eyes with focal elevated choroidal masses. Confocal indocyanine green angiography imaged microcirculation patterns in 13 of these 16 eyes (81%). The surgical implantation of small solid fragments of human choroidal melanoma in immunosuppressed rabbit eyes provides the best method to consistently obtain focal elevated choroidal masses. These focal elevated choroidal masses resemble booth the localization and the growth pattern of choroidal melanomas in humans. In addition, they also contain microcirculation patterns similar to those seen in humans that are detectable with confocal indocyanine green angiography. The use of indocyanine green angiography with this animal model may be especially useful in designing and evaluating anti-microcirculation treatments directed at uveal melanoma.

Angiography↗
PubMed1994

Photostimulation changes the pattern of luteinizing hormone secretion in turkey hens.

Changes in the secretory pattern of luteinizing hormone (LH) were determined in turkey hens during initiation of reproduction. Photosensitive hens were switched from a short day photoschedule of 6L:18D (light:dark) to 14L:10D and serially bled six times during the next 6 weeks of photostimulation and early after ovulatory cycles had begun. The pattern of LH secretion at 0-1 day of photostimulation was characterized by a low baseline concentration of LH with numerous low frequency, high amplitude pulses. This pattern changed at Days 4-5 and 11-12 of photostimulation (hens photostimulated but not yet laying) to a pattern characterized by a high baseline with few ill defined pulses of very short duration. Once the hens had initiated egg production, ovulatory surges of LH (duration of 358 +/- 104 min) were superimposed on the basic pattern seen during photostimulation. The ascending limb of the ovulatory surge was much shorter in duration than the descending limb. No diurnal variation was detected in baseline concentration before or during photostimulation or after egg production had begun. It was concluded that photosensitive turkey hens secrete LH in low frequency; high amplitude pulses superimposed on a low baseline. During photostimulation, this pattern changes to one characterized by a high baseline with few pulses of low amplitude and short duration. This pattern of secretion is stimulatory to the ovary and continues until egg laying begins when it is modified by ovulatory surges of LH, characterized by short duration ascending limbs and longer duration descending limbs, which are superimposed on the high baseline pattern noted during photostimulation.

Animals↗
PubMed1998

Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution.

Detection of recurring three-dimensional side-chain patterns is a potential means of inferring protein function. This paper presents a new method for detecting such patterns and discusses various implications. The method allows detection of side-chain patterns without any prior knowledge of function, requiring only protein structure data and associated multiple sequence alignments. A recursive, depth-first search algorithm finds all possible groups of identical amino acids common to two protein structures independent of sequence order. The search is highly constrained by distance constraints, and by ignoring amino acids unlikely to be involved in protein function. A weighted root-mean-square deviation (RMSD) between equivalenced groups of amino acids is used as a measure of similarity. The statistical significance of any RMSD is assigned by reference to a distribution fitted to simulated data. Searches with the Ser/His/Asp catalytic triad, a His/His porphyrin binding pattern, and the zinc-finger Cys/Cys/His/His pattern are performed to test the method on known examples. An all-against-all comparison of representatives from the structural classification of proteins (SCOP) is performed, revealing several new examples of evolutionary convergence to common patterns of side-chains within different tertiary folds and in different orders along the sequence. These include a di-zinc binding Asp/Asp/His/His/Ser pattern common to alkaline phosphatase/bacterial aminopeptidase, and an Asp/Glu/His/His/Asn/Asn pattern common to the active sites of DNase I and endocellulase E1. Implications for protein evolution, function prediction and the rational design of functional regulators are discussed.

Acetylglucosaminidase↗
PubMed1997

Evidence-Based Pattern Classification: A Structural Approach to Human Perceptual Learning and Generalization

Models of human pattern classification have been traditionally based on implicit pattern descriptions which involve lists of continuous attribute values or discrete features. Here we propose an alternative approach which makes explicit use of pattern structure in terms of components and their unary (part-specific) and binary (part-relational) properties. Such attributes "evidence" different classes of patterns and allow one to model processes of both perceptual learning and generalization to novel instances. An object in an evidence-based system is represented by a set of rules, where each rule provides a certain amount of class-specific evidence. The accumulated class evidence over all activated rules determines the classification probability. We have examined how well this concept reflects human performance by training observers to classify compound Gabor patterns and then testing them with segmented (grey-level-transformed) versions of the patterns in the original training set. If the observers were to construct rules to define each pattern class in terms of perceived parts and their relations, then it should be expected that classification performance would generalize to these new patterns. Results confirm this hypothesis and the specific feature extraction, learning, and rule generation model used to predict performance. Copyright 1997 Academic Press

Journal Article↗
PubMed2002

Pattern formation of the cone mosaic in the zebrafish retina: a cell rearrangement model.

In fish retinas, cone photoreceptor cells are arranged in two-dimensional regular patterns, called cone mosaics. In the zebrafish retina, four subtypes of cone cells, which are maximally sensitive to different wavelengths of light, appear in quasi-periodic patterns. The pattern formation mechanism is unknown. Here, I develop a mathematical model to examine whether cell adhesion can explain the formation of the zebrafish mosaic. I assume that the movement of differentiated cells is responsible for generating the pattern, and that the movement rate is modified by cell adhesion. The pattern is formed if the magnitudes of cell adhesion between cell types are chosen appropriately. I determine the conditions of cell adhesion for generating the pattern. I also compare this cell rearrangement model with a previously studied model in which the pattern is formed by transitions of cell fate. The condition for obtaining the focal pattern is looser in the cell rearrangement model than in the fate transition model.

Animals↗
PubMed2003

Difference in the retinal cone mosaic pattern between zebrafish and medaka: cell-rearrangement model.

In fish retina, four kinds of photoreceptor cells (or cones) are two-dimensionally arranged in a very regular manner, forming cone mosaics. Mosaic pattern differs between species--two typical patterns are "row mosaic" and "square mosaic", exemplified by the cone mosaics in zebrafish and in medaka, respectively. In this paper, we study a cell-rearrangement model. Cells with pre-fixed fate exchange their locations between nearest neighbors and form regular mosaic patterns spontaneously, if the adhesive force between nearest neighbors and between next-nearest neighbors depend on their cell types in an appropriate manner. The same model can produce both row and square mosaic patterns. However, if the cell-cell interaction is restricted to nearest neighbors only, the square mosaic (medaka pattern) cannot be generated, showing the importance of interaction between next-nearest neighbors. In determining whether row mosaic (zebrafish pattern) or square mosaic (medaka pattern) is to be formed, two shape factors are very important, which control the way adhesions in different geometric relations are combined. We also developed theoretical analysis of the parameter ranges for the row mosaic and the square mosaic to have higher total adhesion than alternative spatial patterns.

Animals↗