Identification Of Characteristic Patterns Research Articles

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions

BackgroundCharacterizing recurring sequence patterns in human promoters has been a challenging undertaking even nowadays where a near-complete overview of promoters exists. However, with the more recent availability of genomic location (ChIP-seq) data, one can approach that question through the identification of characteristic patterns of transcription factor occupancy and histone modifications.ResultsBased on the ENCODE annotation and integration of sequence motifs as well as three-dimensional chromatin data, we have undertaken a re-analysis of occupancy and sequence patterns in human promoters. We identify clear groups of CAAT-box and E-box sequence motif containing promoters, as well as a group of promoters whose interaction with an enhancer appears to be mediated by CCCTC-binding factor (CTCF) binding on the promoter. We also extend our analysis to inactive promoters, showing that only a surprisingly small number of inactive promoters is repressed by the polycomb complex. We also identify combinatorial patterns of transcription factor interactions indicated by the ChIP-seq signals.ConclusionOur analysis defines subgroups of promoters characterized by stereotypic patterns of transcription factor occupancy, and combinations of specific sequence patterns which are required for their binding. This grouping provides new hypotheses concerning the assembly and dynamics of transcription factor complexes at their respective promoter groups, as well as questions on the evolutionary origin of these groups.

Sonoelastography of parotid gland tumours: initial experience and identification of characteristic patterns

The aim of this study was to investigate B-mode and elastographical ultrasound criteria capable of differentiating between benign and malignant parotid tumours and to define characteristic elastographical patterns for pleomorphic adenomas and Warthin's tumours. Fifty-seven patients with parotid gland tumours were examined using a combination of B-mode and elastographic ultrasounds. The data acquired were analysed retrospectively by two experienced ultrasound operators to identify specific sonographical features of benign and malignant lesions. Additionally, elastographical patterns were defined and analysed for their specificity. A blurred margin proved to be the only significant criterion in B-mode ultrasound capable of differentiating between malignant and benign tumours. The garland sign was defined as an elastographical pattern found significantly more frequently in malignant tumours, improving sonographical prediction of the benign or malignant nature of a parotid lesion. A logistic regression model was developed that achieved a correct prediction in 87.7% of cases. A "dense core" sign was also specifically defined for pleomorphic adenomas and a "half-half" sign for Warthin's tumours. Elastography is an innovative and powerful diagnostic tool that can improve the sonographical examination of parotid gland tumours by revealing easily recognised and characteristic patterns of tissue distribution. • Elastography can help differentiate benign from malignant parotid tumours during parotid ultrasound. • The elastographical "garland sign" is more frequent in malignant than benign parotid tumours. • Pleomorphic adenomas show an elastographical "dense core sign". • Warthin's tumours show an elastographical "half-half sign". • Parotid cysts show an elastographical "bull's-eye sign".

Placental mesenchymal dysplasia: can early diagnosis ensure a good materno-foetal outcome? A case report

Placental mesenchymal dysplasia is a rare disorder characterized by an increased size placenta with cystic villi and ectasic vessels. The correct diagnosis is very important, because placental mesenchymal dysplasia is usually compatible with a normal foetal morphology and a good materno-foetal outcome. An accurate ultrasound evaluation can help in the identification of characteristic patterns associated to this trophoblastic disease, particularly to distinguish it from its main differential diagnosis, i.e. hydatidiform mole. We report an early second-trimester ultrasound diagnosis of placental mesenchymal dysplasia complicated by foetal growth restriction, but with normal female karyotype and good healthy baby.

Induction Motor Diagnosis Based on a Transient Current Analytic Wavelet Transform via Frequency B-Splines

In this paper, a new induction motor diagnosis methodology is proposed. The approach is based on obtaining a 2-D time-frequency plot representing the time-frequency evolution of the main components in an electrical machine transient current. The identification of characteristic patterns in the time-frequency plane caused by many of the fault-related components enables a reliable machine diagnosis. Unlike other continuous-wavelet-transform-based methods, this work uses frequency B-spline (FBS) wavelets. It is shown that these wavelets enable an efficient filtering in the region neighboring the main frequency, as well as enable a high level of detail in the time-frequency maps. As a consequence, the evolution of the most important current components is precisely traced. These characteristics make it easy to identify the patterns related to the fault components. The technique is applied to the experimental no-load start-up current of motors in a healthy state and with broken bars; the FBS capabilities are revealed. One of the novelties of this paper is the fact that the diagnosis is carried out via the identification not only of the traditional lower sideband harmonic but also of the upper sideband harmonic and four additional fault-related components.