An ontological characterization of time-series and state-sequences for data mining

Time-series and sequences are important patterns in data mining. Based on an ontology of time-elements, this paper presents a formal characterization of time-series and state-sequences, where a state denotes a collection of data whose validation is dependent on time. While a time-series is formalized as a vector of time-elements temporally ordered one after another, a state-sequence is denoted as a list of states correspondingly ordered by a time-series. In general, a time-series and a state-sequence can be incomplete in various ways. This leads to the distinction between complete and incomplete time-series, and between complete and incomplete state-sequences, which allows the expression of both absolute and relative temporal knowledge in data mining.

Time-reversal ultrawideband breast imaging: pulse design criteria considering multiple tumors with unknown tissue properties

Pulse design is investigated for time-reversal (TR) imaging as applied to ultrawideband (UWB) breast cancer detection. Earlier it has been shown that a suitably-designed UWB pulse may help to improve imaging performance for a single-tumor breast phantom with predetermined lesion properties. The current work considers the following more general and practical situations: presence of multiple malignancies with unknown tumor size and dielectric properties. Four pulse selection criteria are proposed with each focusing on one of the following aspects: eliminating signal clutter generated by tissue inhomogeneities, canceling mutual interference among tumors, improving image resolution, and suppressing artifacts created by sidelobe of the target response. By applying the proposed criteria, the shape parameters of UWB waveforms with desirable characteristics are identified through search of all the possible pulses. Simulation example using a numerical breast phantom, comprised of two tumors and structured clutter distribution, demonstrates the effectiveness of the proposed approach. Specifically, a tradeoff between the image resolution and signal-to-clutter contrast (SCC) is observed in terms of selection of the excitation waveforms.

Distinguishing between similar tubular objects using pulse reflectometry: a study of trumpet and cornet leadpipes

Acoustic pulse reflectometry is used to reconstruct the internal bore profile of trumpet and cornet leadpipe. The method distinguishes between radii differences as small as 0.03 mm, and has since been used by various UK-based brass instrument manufacturers as a diagnostic tool to detect defects that are significant enough to acoustically alter performance.

rbcL sequences indicate a single evolutionary origin of multinucleate cells in the red algal tribe Callithamnieae.

In the Ceramiaceae, one of the largest families of the red algae, there are from 1 to 4000 nuclei in each vegetative cell, but each tribe is homogeneous with respect to the uninucleate/multinucleate character state, except for the Callithamnieae. The goals of this study were to analyze rbcL gene sequences to clarify the evolution of taxa within the tribe Callithamnieae and to evaluate the potential evolutionary significance of the development of multinucleate cells in certain taxa. The genus Aglaothamnion, segregated from Callithamnion because it is uninucleate, was paraphyletic in all analyses. Callithamnion (including Aristothamnion) was monophyletic although not robustly so, apparently due to variations between taxa in rate of sequence evolution. Morphological synapomorphies were identified at different depths in the tree, supporting the molecular phylogenetic analysis. The uninucleate character state is ancestral in this tribe. The evolution of multinucleate cells has occurred once in the Callithamnieae. Multiple nuclei in each cell may combine the benefits of small C values (rapid cell cycle) with large cells (permitting morphological elaboration) while maintaining a constant ratio of nuclear volume: cytoplasmic volume.

rbcL sequences reveal multiple cryptic introductions of the Japanese red alga Polysiphonia harveyi.

In Europe, the last 20 years have seen a spectacular increase in accidental introductions of marine species, but it has recently been suggested that both the actual number of invaders and their impacts have been seriously underestimated because of the prevalence of sibling species in marine habitats. The red alga Polysiphoniaharveyi is regarded as an alien in the British Isles and Atlantic Europe, having appeared in various locations there during the past 170 years. Similar or conspecific populations are known from Atlantic North America and Japan. To choose between three competing hypotheses concerning the origin of P. harveyi in Europe, we employed rbcL sequence analysis in conjunction with karyological and interbreeding data for samples and isolates of P. harveyi and various congeners from the Pacific and North Atlantic Oceans. All cultured isolates of P. harveyi were completely interfertile, and there was no evidence of polyploidy or aneuploidy. Thus, this biological species is both morphologically and genetically variable: intraspecific rbcL divergences of up to 2.1% are high even for red algae. Seven rbcL haplotypes were identified. The four most divergent haplotypes were observed in Japanese samples from Hokkaido and south-central Honshu, which are linked by hypothetical 'missing' haplotypes that may be located in northern Honshu. These data are consistent with Japan being the centre of diversity and origin for P. harveyi. Two non-Japanese lineages were linked to Hokkaido and Honshu, respectively. A single haplotype was found in all North Atlantic and Mediterranean accessions, except for North Carolina, where the haplotype found was the same as that invading in New Zealand and California. The introduction of P. harveyi into New Zealand has gone unnoticed because P. strictissima is a morphologically indistinguishable native sibling species. The sequence divergence between them is 4–5%, greater than between some morphologically distinct red algal species. Two different types of cryptic invasions of P. harveyi have therefore occurred. In addition to its introduction as a cryptic sibling species in New Zealand, P. harveyi has been introduced at least twice into the North Atlantic from presumed different source populations. These two introductions are genetically and probably also physiologically divergent but completely interfertile.

Methylation status of oestrogen receptor-a-gene promoter sequences in human ovarian epithelial cell lines.

We have determined the methylation status of the CpG island of the oestrogen receptor gene in seven human ovarian cell lines. Cell lines expressing oestrogen receptor showed no evidence of hypermethylation. In three of four cell lines that produced no detectable oestrogen receptor protein, hypermethylation was observed at the NotI site of the CpG island. These results indicate that aberrant hypermethylation may be responsible for a significant proportion of epithelial ovarian tumours in which oestrogen receptor expression is lost.

Three primary kinetic characteristics observed in a pulse-response TAP experiment

The state-by-state transient screening approach based on a pulse-response thin-zone TAP experiment is further developed whereby single-pulse kinetic tests are treated as small perturbations to catalyst compositions and analyzed using integral method of moments. Results on three primary kinetic characteristics, termed basic kinetic coefficients, are presented. These three coefficients were introduced as main observables from experimentally measured TAP-responses in a kinetic-model-free manner. Each was analytically determined from moments of responses with no assumption about the detailed kinetic model. In this paper, the inverse question of how well these coefficients represent the time evolution of the observed responses is addressed. Sets of three basic kinetic coefficients are calculated from model and experimental responses and these calculated values are used to generate 3-coefficient curves in a kinetic-model-free manner. The comparison of these 3-coefficient curves with original responses shows that three basic kinetic coefficients can be sufficient to describe the observed kinetics of exit flow time dependencies with no assumption regarding the detailed kinetic model.

Effect of a COL1A1 Sp1 Binding Site Polymorphism on Arterial Pulse Wave Velocity: An Index of Compliance.

Reduced arterial compliance precedes changes in blood pressure, which may be mediated through alterations in vessel wall matrix composition. We investigated the effect of the collagen type I-1 gene (COL1A1) +2046G>T polymorphism on arterial compliance in healthy individuals. We recruited 489 subjects (251 men and 238 women; mean age, 22.6±1.6 years). COL1A1 genotypes were determined using polymerase chain reaction and digestion by restriction enzyme Bal1. Arterial pulse wave velocities were measured in 3 segments, aortoiliac (PWVA), aortoradial (PWVB), and aorto-dorsalis-pedis (PWVF), as an index of compliance using a noninvasive optical method. Data were available for 455 subjects. The sample was in Hardy-Weinberg equilibrium with genotype distributions and allele frequencies that were not significantly different from those reported previously. The T allele frequency was 0.22 (95% confidence interval, 0.19 to 0.24). Two hundred eighty-three (62.2%) subjects were genotype GG, 148 (35.5%) subjects were genotype GT, and 24 (5.3%) subjects were genotype TT. A comparison of GG homozygotes with GT and TT individuals demonstrated a statistically significant association with arterial compliance: PWVF 4.92±0.03 versus 5.06±0.05 m/s (ANOVA, P=0.009), PWVB 4.20±0.03 versus 4.32±0.04 m/s (ANOVA, P=0.036), and PWVA 3.07±0.03 versus 3.15±0.03 m/s (ANOVA, P=0.045). The effects of genotype were independent of age, gender, smoking, mean arterial pressure, body mass index, family history of hypertension, and activity scores. We report an association between the COL1A1 gene polymorphism and arterial compliance. Alterations in arterial collagen type 1A deposition may play a role in the regulation of arterial compliance