A pseudoinverse deformation vector field generator and its applications

PURPOSE

To present, implement, and test a self-consistent pseudoinverse displacement vector field (PIDVF) generator, which preserves the location of information mapped back-and-forth between image sets.

METHODS

The algorithm is an iterative scheme based on nearest neighbor interpolation and a subsequent iterative search. Performance of the algorithm is benchmarked using a lung 4DCT data set with six CT images from different breathing phases and eight CT images for a single prostrate patient acquired on different days. A diffeomorphic deformable image registration is used to validate our PIDVFs. Additionally, the PIDVF is used to measure the self-consistency of two nondiffeomorphic algorithms which do not use a self-consistency constraint: The ITK Demons algorithm for the lung patient images and an in-house B-Spline algorithm for the prostate patient images. Both Demons and B-Spline have been QAed through contour comparison. Self-consistency is determined by using a DIR to generate a displacement vector field (DVF) between reference image R and study image S (DVF(R-S)). The same DIR is used to generate DVF(S-R). Additionally, our PIDVF generator is used to create PIDVF(S-R). Back-and-forth mapping of a set of points (used as surrogates of contours) using DVF(R-S) and DVF(S-R) is compared to back-and-forth mapping performed with DVF(R-S) and PIDVF(S-R). The Euclidean distances between the original unmapped points and the mapped points are used as a self-consistency measure.

RESULTS

Test results demonstrate that the consistency error observed in back-and-forth mappings can be reduced two to nine times in point mapping and 1.5 to three times in dose mapping when the PIDVF is used in place of the B-Spline algorithm. These self-consistency improvements are not affected by the exchanging of R and S. It is also demonstrated that differences between DVF(S-R) and PIDVF(S-R) can be used as a criteria to check the quality of the DVF.

CONCLUSIONS

Use of DVF and its PIDVF will improve the self-consistency of points, contour, and dose mappings in image guided adaptive therapy.

Factors associated with bed and room sharing in Chinese school-aged children

BACKGROUND AND OBJECTIVES

Co-sleeping (bed or room sharing) has potential implications for children's development. Previous studies showed that co-sleeping was more prevalent in non-Western countries than in Western countries, which demonstrated that co-sleeping was marked with ethnic and socio-cultural background characteristics. The purpose of this study was to survey the prevalence of bed and room sharing and to examine related factors among school-aged children in an Asian country - China.

METHODS

A cross-sectional questionnaire survey was conducted in 10 districts of Shanghai, China from November to December 2005. A total of 4108 elementary school children, 49.2% boys and 50.8% girls with a mean age of 8.79 years, participated. Parent-administered questionnaires were used to collect information about children's sleeping arrangements and socio-demographic characteristics.

RESULTS

The prevalence of routine bed sharing, room sharing and sleeping alone in Chinese school-aged children was 21.0%, 19.1% and 47.7%, respectively. Bed and room sharing didn't show significant gender difference but gradually decreased with increasing age. Multivariate logistic regression identified those factors associated with bed and room sharing: younger age, large family, children without their own bedroom and parents' approval of a co-sleeping arrangement.

CONCLUSION

Co-sleeping arrangement was a common practice in Chinese school-aged children. Associated factors were characterized by intrinsic socio-cultural values and socio-economic status in China.

Analysis and location of a rice BAC clone containing telomeric DNA sequences

BAC2, a rice BAC clone containing (TTTAGGG)(n) homologous sequences, was analyzed by Southern hybridization and DNA sequencing of its subclones. It was disclosed that there were many tandem repeated satellite DNA sequences, called TA352, as well as simple tandem repeats consisting of TTTAGGG or its variant within the BAC2 insert. A 0. 8 kb (TTTAGGG)(n)-containing fragment in BAC2 was mapped in the telomere regions of at least 5 pairs of rice chromosomes by using fluorescencein situ hybridization (FISH). By RFLP analysis of low copy sequences the BAC2 clone was localized in one terminal region of chromosome 6. All the results strongly suggest that the telomeric DNA sequences of rice are TTTAGGG or its variant, and the linked satellite DNA TA352 sequences belong to telomere-associated sequences.

Controlled release of an antibiotic, gentamicin sulphate, from gravity spun polycaprolactone fibers

The antibiotic, gentamicin sulphate (GS), was incorporated in gravity-spun polycaprolactone (PCL) fibers by spinning from particulate suspensions of the drug in PCL solution to produce a controlled delivery system. The production rate of GS-loaded PCL fibers was confined to the range 1-1.5 m/min and the fiber diameter to 170-220 microm. The kinetics of drug release could be adjusted by varying the GS loading of the fibers and the suspension preparation conditions. Gradual release of approximately 80% of the initial GS content was measured in phosphate buffered saline at 37 degrees C over 50 days from fibers spun from nonhomogenized suspensions, whereas loss of this amount of antibiotic occurred in less than 10 days from fibers spun from homogenized suspensions. Studies of growth inhibition of Stapyhlococcus epidermidis in culture indicated that GS released after 2 weeks from PCL fibers retained antibacterial activity. This behavior recommends further investigation of PCL fibers for local delivery of antibiotics to combat infection associated with periodontal disease, musculoskeletal injuries, and implantation of fiber-based tissue substitutes such as vascular prostheses.

Discrimination of outer membrane proteins using a K-nearest neighbor method

Identification of outer membrane proteins (OMPs) from genome is an important task. This paper presents a k-nearest neighbor (K-NN) method for discriminating outer membrane proteins (OMPs). The method makes predictions based on a weighted Euclidean distance that is computed from residue composition. The method achieves 89.1% accuracy with 0.668 MCC (Matthews correlation coefficient) in discriminating OMPs and non-OMPs. The performance of the method is improved by including homologous information into the calculation of residue composition. The final method achieves an accuracy of 96.1%, with 0.873 MCC, 87.5% sensitivity, and 98.2% specificity. Comparisons with multiple recently published methods show that the method proposed in this study outperforms the others.

Variants in the 5q31 cytokine gene cluster are associated with psoriasis

A multitiered genetic association study of 25 215 single-nucleotide polymorphisms (SNPs) in three case-control sample sets (1446 patients and 1432 controls) identified three IL13-linked SNPs (rs1800925, rs20541 and rs848) associated with psoriasis. Although the susceptibility effects at these SNPs were modest (joint allelic odds ratios (ORs): 0.76 to 0.78; P(comb): 1.3E-03 to 2.50E-04), the association patterns were consistent across the sample sets, with the minor alleles being protective. Haplotype analyses identified one common, susceptible haplotype CCG (joint allelic OR=1.27; P(comb)=1.88E-04) and a less common, protective haplotype TTT (joint allelic OR=0.74; P(comb)=7.05E-04). In combination with the other known genetic risk factors, HLA-C, IL12B and IL23R, the variants reported here generate an 11-fold psoriasis-risk differential. Residing in the 5q31 cytokine gene cluster, IL13 encodes an important T-cell-derived cytokine that regulates cell-mediated immunity. These results provide the foundation for additional studies required to fully dissect the associations within this cytokine-rich genomic region, as polymorphisms in closely linked candidate genes, such as IRF1, IL5 or IL4, may be driving these results through linkage disequilibrium.

Transverse beam spin asymmetries in forward-angle elastic electron-proton scattering

We have measured the beam-normal single-spin asymmetry in elastic scattering of transversely polarized 3 GeV electrons from unpolarized protons at Q2=0.15, 0.25 (GeV/c)2. The results are inconsistent with calculations solely using the elastic nucleon intermediate state and generally agree with calculations with significant inelastic hadronic intermediate state contributions. A(n) provides a direct probe of the imaginary component of the 2gamma exchange amplitude, the complete description of which is important in the interpretation of data from precision electron-scattering experiments.

Gene delivery by the hSP-B promoter to lung alveolar type II epithelial cells in LAL-knockout mice through bone marrow mesenchymal stem cells

Tissue damage and inflammation promote bone marrow stem cells (BMSCs) to differentiate into a variety of cell types in residing tissues. BMSCs can stably maintain their plasticity and are an ideal cell population for delivery of therapeutic genes to non-hematopoietic tissues. Using lacZ as a reporter gene, we demonstrated that the lung-specific human surfactant protein B (hSP-B) 1.5-kb promoter is able to deliver the lacZ gene into the lung of lysosomal acid lipase (LAL) gene-knockout (lal-/-) mice by beta-galactosidase staining, flow cytometry and double immunofluorescence staining. Around 10-18% alveolar type II epithelial cells (AT II cells) exhibited positive lacZ gene expression after 8 weeks of BMSC injection in recipient lal-/- mice. The wild-type mice exhibited no expression after the same treatment. BMSCs from hSP-B 1.5-kb lacZ transgenic mice entered and repopulated in lal-/- bone marrow. The study supports a concept that pulmonary inflammation caused by LAL deficiency can trigger BMSC residing in lal-/- bone marrow, migrating into the lung and converting into residential AT II cells. The hSP-B 1.5 kb promoter is an ideal tool to deliver therapeutic genes into AT II cells through BMSCs to cure pulmonary inflammation-triggered diseases.

Proton spin structure in the resonance region

We have examined the spin structure of the proton in the region of the nucleon resonances (1.085 GeV<W<1.910 GeV) at an average four momentum transfer of Q2=1.3 GeV2. Using the Jefferson Lab polarized electron beam, a spectrometer, and a polarized solid target, we measured the asymmetries A|| and A(perpendicular) to high precision, and extracted the asymmetries A1 and A2, and the spin structure functions g1 and g2. We found a notably nonzero A(perpendicular), significant contributions from higher-twist effects, and only weak support for polarized quark-hadron duality.

End-grafted low-molecular-weight PNIPAM does not collapse above the LCST

The interfacial properties of end-grafted temperature-responsive poly(N-isopropylacryamide) (PNIPAM) were quantified by direct force measurements both above and below the lower critical solution temperature (LCST) of 32 degrees C. The forces were measured between identical, opposing PNIPAM films and between a PNIPAM film and a lipid membrane. At the grafting densities and molecular weights investigated, the polymer extension did not change significantly above the LCST, and the polymers did not adhere. Below the LCST, the force-distance profiles suggest a vertical phase separation, which results in a diluter outer layer and a dense surface proximal layer. At large separations, the force profiles agree qualitatively with simple polymer theory but deviate at small separations. Importantly, at these low grafting densities and molecular weights, the end-grafted PNIPAM does not collapse above the LCST. This finding has direct implications for triggering liposomal drug release with end-grafted PNIPAM, but it increases the temperature range where these short PNIPAM chains function as steric stabilizers.