MRI intensity inhomogeneity correction by combining intensity and spatial information

We propose a novel fully automated method for retrospective correction of intensity inhomogeneity, which is an undesired phenomenon in many automatic image analysis tasks, especially if quantitative analysis is the final goal. Besides most commonly used intensity features, additional spatial image features are incorporated to improve inhomogeneity correction and to make it more dynamic, so that local intensity variations can be corrected more efficiently. The proposed method is a four-step iterative procedure in which a non-parametric inhomogeneity correction is conducted. First, the probability distribution of image intensities and corresponding second derivatives is obtained. Second, intensity correction forces, condensing the probability distribution along the intensity feature, are computed for each voxel. Third, the inhomogeneity correction field is estimated by regularization of all voxel forces, and fourth, the corresponding partial inhomogeneity correction is performed. The degree of inhomogeneity correction dynamics is determined by the size of regularization kernel. The method was qualitatively and quantitatively evaluated on simulated and real MR brain images. The obtained results show that the proposed method does not corrupt inhomogeneity-free images and successfully corrects intensity inhomogeneity artefacts even if these are more dynamic.     

Telomerase reactivation is an early event in laryngeal carcinogenesis.

The exact role and timing of reactivation of telomerase, a key enzyme implicated in cellular immortalization and transformation in the multistep process of laryngeal carcinogenesis, is still unknown. We attempted to (1) determine that quantitative differences exist in the levels of telomerase catalytic subunit (hTERT) mRNA expression among different grades of laryngeal epithelial abnormalities classified according to the Ljubljana classification; (2) determine that telomerase reactivation is an important, most probably early event in laryngeal carcinogenesis; and (3) analyze whether the relative quantity of hTERT mRNA can be used as a molecular biomarker in the early detection of precancerous lesions. The relative quantity of hTERT mRNA, expressed as an hTERT index, was analyzed in 140 frozen laryngeal tissue specimens representing different morphological stages of laryngeal carcinogenesis by using a commercially available LightCycler Telo TAGGG hTERT Quantification kit. The presence and relative quantity of hTERT mRNA in laryngeal epithelium increases progressively with the degree of epithelial abnormalities. hTERT mRNA was detectable in 1/15 normal laryngeal epithelia (7%, mean hTERT index 0.02), 3/15 simple hyperplasias (20%, mean hTERT index 0.09), 10/27 abnormal hyperplasias (37%, mean hTERT index 0.18), 9/12 atypical hyperplasias (75%, mean hTERT index 0.74), 8/9 intraepithelial carcinomas (89%, mean hTERT index 1.82), and 53/62 invasive laryngeal squamous cell carcinomas (85%, mean hTERT index 2.51). Statistical analysis revealed two groups of laryngeal epithelial changes with significant differences in the levels of hTERT mRNA expression (P <.0033): (1) normal and reactive hyperplastic laryngeal epithelium (simple and abnormal hyperplasia) and (2) atypical hyperplasia (precancerous lesion), intraepithelial and invasive laryngeal squamous cell carcinoma. The results of the present study suggest that telomerase reactivation is an early event in laryngeal carcinogenesis, detectable already at the stage of precancerous laryngeal epithelial changes. Nevertheless, other genetic abnormalities appear to be necessary for progression of these epithelial abnormalities toward invasive laryngeal squamous cell carcinoma.     

Human telomerase catalytic subunit gene re-expression is an early event in oral carcinogenesis

AIMS: Detection of telomerase catalytic subunit (hTERT) mRNA has been used as a surrogate marker for estimation of telomerase activity. The exact role and timing of telomerase re-activation, a key enzyme implicated in cellular immortalization and transformation, in the multistep process of oral carcinogenesis is still unknown. The aim was to test the hypothesis that (i) quantitative rather than qualitative differences exist in the level of hTERT mRNA expression between normal oral mucosa, different grades of oral epithelial abnormalities and squamous cell carcinomas of the oral cavity, and that (ii) hTERT gene re-expression is an important, probably early event in oral carcinogenesis. METHODS AND RESULTS: The relative quantity of hTERT mRNA was analysed in 45 frozen oral epithelia representing different morphological stages of oral carcinogenesis classified according to the Ljubljana classification and in 37 oral squamous cell carcinomas, using a commercially available LightCycler Telo TAGGG hTERT Quantification kit. hTERT mRNA was not detected in normal or reactive hyperplastic oral epithelia, but was present in 43% of atypical hyperplasias (premalignant lesions), 60% of intraepithelial carcinomas and 68% of oral squamous cell carcinomas. Statistical analysis revealed two groups of oral epithelial changes, with significant differences in the levels of hTERT mRNA expression: 1, normal and reactive hyperplastic oral epithelium, and 2, atypical hyperplasia, intraepithelial carcinomas and squamous cell carcinomas. CONCLUSION: These data suggest that hTERT gene re-expression represents an early event in the multistep process of oral carcinogenesis, already detectable at the stage of precancerous oral epithelial changes. Nevertheless, other genetic aberrations appear to be necessary for progression of oral epithelial abnormalities towards invasive squamous cell carcinoma.     

Avirulence and altered physiological properties of cystic fibrosis strains of Pseudomonas aeruginosa

Twenty Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis in good and poor clinical condition were typed by the American Scientific (Difco Laboratories, Detroit, Mich.) Typing Scheme. Only five strains were agglutinated with a single typing serum. Ten strains were agglutinated with more than one serum, and five were not agglutinated with any serum, suggesting some type of lipopolysaccharide alteration in the majority of these strains. Of the strains from patients in good clinical condition, 72% demonstrated proteolytic activity, while 60% of the strains from patients in poor clinical condition demonstrated no proteolytic activity. Twenty-three cystic fibrosis strains of P. aeruginosa examined demonstrated reduced bacteremic virulence when compared with a virulent burn strain with a 50% lethal dose (LD50) of 1.5 X 10(1) CFU in an invasive burned mouse model. Ninety-two percent of the strains tested were avirulent at doses of 10(3) to 10(5) CFU. The LD50s were determined for 10 selected strains which exhibited specific important morphological and physiological deficiencies. Five of the strains tested gave LD50s greater than 10(6) CFU. Reduced virulence of these strains was associated with loss of two or more physiological characteristics associated with virulence. The cystic fibrosis strains of P. aeruginosa which morphologically and physiologically resembled the virulent burn strain were the most virulent (LD50s of 10(2) to 10(4). Results suggest that some degree of virulence is associated only with classic strains prevalent in early infections. The data suggest that a selection transition occurs in the lungs of patients with cystic fibrosis that favors P. aeruginosa avirulence. The avirulent state may be caused by alterations in the cell envelope, including associated factors such as motility and chemotaxis and protease production.     

Change of phonation control after cochlear implantation.

OBJECTIVE: To assess the influence of acquired auditory control on some voice parameters in deaf children and adults after cochlear implantation. STUDY DESIGN: Prospective clinical study. SETTING: Tertiary referral center. PATIENTS: Twenty-nine prelingually deafened children and 11 postlingually deafened adults. INTERVENTIONS: The samples of a vowel /a/ were analyzed with an Multi-Dimensional Voice Program (Kay Elemetrics Corporation, Lincoln Park, NJ) before and 6 to 12 months after the cochlear implantation. MAIN OUTCOME MEASURES: The average fundamental frequency (F0), the short-term variation of F0 (JIT) and the amplitude (SH), the very long-term variation of F0 (vF0) and the amplitude (vAm), and the noise-to-harmonic ratio (NHR) were determined and compared for both age groups. The results of the acoustic analysis performed before the implantation were compared with the results after the implantation for children and adults. RESULTS: Significantly greater JIT, SH, vF0, and vAm were detected in the children than in the adults before and after the implantation. The prelingually deafened children significantly improved the control of their phonation after 6 to 12 months' use of the cochlear implant (JIT: p=0.014, SH: p=0.011, vF0: p=0.014, vAm: p=0.031). In the postlingually deafened adults, no significant improvement was found in any of the studied voice parameters after the implantation. F0 showed little or no change after the implantation in children and adults. CONCLUSION: As expected, the voice quality of the prelingually deafened children was significantly worse than that of the postlingually deafened adults. After cochlear implantation, the children significantly improved their short-term and long-term F0 and amplitude variability. In adults, no significant improvement was detected. We suppose that the improvement is a consequence not only of the acquired hearing control but also of the adaptation ability of neuromuscular phonation control and the maturing of these control mechanisms in children. In adults, better phonation quality in general and lesser improvement after the implantation can be the results of well-developed and stable phonation patterns.     

Structural basis and prediction of substrate specificity in protein serine/threonine kinases

The large number of protein kinases makes it impractical to determine their specificities and substrates experimentally. Using the available crystal structures, molecular modeling, and sequence analyses of kinases and substrates, we developed a set of rules governing the binding of a heptapeptide substrate motif (surrounding the phosphorylation site) to the kinase and implemented these rules in a web-interfaced program for automated prediction of optimal substrate peptides, taking only the amino acid sequence of a protein kinase as input. We show the utility of the method by analyzing yeast cell cycle control and DNA damage checkpoint pathways. Our method is the only available predictive method generally applicable for identifying possible substrate proteins for protein serinethreonine kinases and helps in silico construction of signaling pathways. The accuracy of prediction is comparable to the accuracy of data from systematic large-scale experimental approaches.     

The Effect of Scandium on the Structure,Microstructure and Superconductivity of Equimolar Sc-Hf-Nb-Ta-Ti-Zr Refractory High-Entropy Alloys

In this study, we investigate the scandium-containing Sc-Hf-Nb-Ta-Ti-Zr system of refractory high-entropy alloys (HEAs). Using the arc-melting method, we synthesized nine equimolar alloys (five 4-, three 5- and one 6-component), with all of them containing Sc. The alloys were characterized by XRD, electron microscopy and EDS, while superconductivity was investigated via electrical resistivity, specific heat and the Meissner effect. The results were compared to the parent Hf-Nb-Ta-Ti-Zr refractory HEAs, forming a single-phase body-centered cubic (bcc) structure and quite homogeneous microstructure. The addition of Sc produces a two-phase structure in the Sc-Hf-Nb-Ta-Ti-Zr alloys, with one phase being bcc and the other hexagonal close-packed (hcp). The hcp phase absorbs practically all Sc, whereas the Sc-poor bcc phase is identical to the bcc phase in the Hf-Nb-Ta-Ti-Zr parent system. Upon the Sc addition, the microstructure becomes very inhomogeneous. Large bcc dendrites (10–100 µm) are homogeneous in the central parts, but become a fine dispersion of sub-micron precipitates of the bcc and hcp phases close to the edges. The interdendritic regions are also a fine dispersion of the two phases. Superconductivity of the Sc-Hf-Nb-Ta-Ti-Zr alloys originates from the bcc phase fraction, which demonstrates identical superconducting parameters as the bcc Hf-Nb-Ta-Ti-Zr parent alloys, while the Sc-containing hcp phase fraction is non-superconducting.