| 1. |
- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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| 2. |
- Beral, V, et al.
(författare)
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Alcohol, tobacco and breast cancer - collaborative reanalysis of individual data from 53 epidemiological studies, including 58515 women with breast cancer and 95067 women without the disease
- 2002
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Ingår i: British Journal of Cancer. - : Springer Science and Business Media LLC. - 1532-1827 .- 0007-0920. ; 87, s. 1234-45
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Tidskriftsartikel (refereegranskat)abstract
- Alcohol and tobacco consumption are closely correlated and published results on their association with breast cancer have not always allowed adequately for confounding between these exposures. Over 80% of the relevant information worldwide on alcohol and tobacco consumption and breast cancer were collated, checked and analysed centrally. Analyses included 58515 women with invasive breast cancer and 95067 controls from 53 studies. Relative risks of breast cancer were estimated, after stratifying by study, age, parity and, where appropriate, women's age when their first child was born and consumption of alcohol and tobacco. The average consumption of alcohol reported by controls from developed countries was 6.0 g per day, i.e. about half a unit/drink of alcohol per day, and was greater in ever-smokers than never-smokers, (8.4 g per day and 5.0 g per day, respectively). Compared with women who reported drinking no alcohol, the relative risk of breast cancer was 1.32 (1.19 - 1.45, P < 0.00001) for an intake of 35 - 44 g per day alcohol, and 1.46 (1.33 - 1.61, P < 0.00001) for greater than or equal to 45 g per day alcohol. The relative risk of breast cancer increased by 7.1% (95% CI 5.5-8.7%; P<0.00001) for each additional 10 g per day intake of alcohol, i.e. for each extra unit or drink of alcohol consumed on a daily basis. This increase was the same in ever-smokers and never-smokers (7.1 % per 10 g per day, P < 0.00001, in each group). By contrast, the relationship between smoking and breast cancer was substantially confounded by the effect of alcohol. When analyses were restricted to 22 255 women with breast cancer and 40 832 controls who reported drinking no alcohol, smoking was not associated with breast cancer (compared to never-smokers, relative risk for ever-smokers= 1.03, 95% CI 0.98 - 1.07, and for current smokers=0.99, 0.92 - 1.05). The results for alcohol and for tobacco did not vary substantially across studies, study designs, or according to 15 personal characteristics of the women; nor were the findings materially confounded by any of these factors. If the observed relationship for alcohol is causal, these results suggest that about 4% of the breast cancers in developed countries are attributable to alcohol. In developing countries, where alcohol consumption among controls averaged only 0.4 g per day, alcohol would have a negligible effect on the incidence of breast cancer. In conclusion, smoking has little or no independent effect on the risk of developing breast cancer; the effect of alcohol on breast cancer needs to be interpreted in the context of its beneficial effects, in moderation, on cardiovascular disease and its harmful effects on cirrhosis and cancers of the mouth, larynx, oesophagus and liver. (C) 2002 Cancer Research UK.
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| 3. |
- Gisselsson, D, et al.
(författare)
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Centrosomal abnormalities, multipolar mitoses, and chromosomal instability in head and neck tumours with dysfunctional telomeres.
- 2002
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Ingår i: British Journal of Cancer. - : Springer Science and Business Media LLC. - 1532-1827 .- 0007-0920. ; 87:2, s. 202-207
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Tidskriftsartikel (refereegranskat)abstract
- Carcinomas of the head and neck typically exhibit complex chromosome aberrations but the underlying mutational mechanisms remain obscure. Evaluation of cell division dynamics in low-passage cell lines from three benign and five malignant head and neck tumours revealed a strong positive correlation between multipolarity of the mitotic spindle and the formation of bridges at anaphase in both benign and malignant tumours. Cells exhibiting a high rate of mitotic abnormalities also showed several chromosome termini lacking TTAGGG repeats and a high frequency of dicentric chromosomes. Multicolour karyotyping demonstrated a preferential involvement in structural rearrangements of chromosomes with deficient telomeres. The majority of malignant, mitotically unstable tumours expressed the reverse transcriptase subunit of telomerase. These data indicate that some of the genomic instability in head and neck tumours is initiated by telomere dysfunction, leading to the formation of dicentric chromosomes. These form chromosome bridges at mitosis that could prevent the normal anaphase-telophase transition. In turn, this may cause an accumulation of centrosomes and mitotic multipolarity. Telomerase expression does not confer total stability to the tumour genome but could be crucial for moderating the rate of chromosomal evolution.
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| 4. |
- Jin, Y, et al.
(författare)
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Cytogenetic and fluorescence in situ hybridization characterization of chromosome 8 rearrangements in head and neck squamous cell carcinomas
- 2001
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Ingår i: Cancer Genetics and Cytogenetics. - 0165-4608. ; 130:2, s. 111-117
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Tidskriftsartikel (refereegranskat)abstract
- Structural rearrangements of chromosome 8 are frequently encountered in squamous cell carcinomas of the head and neck (HNSCC). These aberrations often affect the centromeric region, resulting in the formation of isochromosome i(8q) and whole arm translocations. Some tumors may display structural rearrangements of 8p23. To characterize further the localization of the breakpoints in such rearrangements, 12 HNSCC known to carry pericentromeric rearrangements of chromosome 8 and 8p23 abnormalities were investigated with fluorescence in situ hybridization (FISH) by the use of 15 YAC clones spanning 8p23 and 8p11 to 8q11. FISH confirmed that all, except one, aberrations cytogenetically interpreted to be i(8q) were true, monocentric i(8q). Similarly, all whole-arm translocations appeared as centric fusions. It could thus be concluded that the essential outcome of these rearrangements is genomic imbalances and not rearrangement of genes in the pericentromeric region. By the use of five YAC clones mapping to 8p23, different breakpoints at the molecular level were disclosed in cases with cytogenetically identical 8p23 rearrangements. An evaluation of the genomic imbalances detected in the present series revealed that overrepresentation of 8q material was present in 11 of the 12 tumors. The most commonly gained segment was 8q22 approximately qter, found in all cases with 8q overrepresentation. Loss of parts of or the entire 8p was seen in 10 tumors. The smallest overlapping deleted region was localized to the subtelomeric region of 8p.
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| 5. |
- Brinck, Tore, et al.
(författare)
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Segmental analysis of molecular surface electrostatic potentials : application to enzyme inhibition
- 2003
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Ingår i: Journal of Molecular Modeling. - : Springer Science and Business Media LLC. - 1610-2940 .- 0948-5023. ; 9:2, s. 77-83
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Tidskriftsartikel (refereegranskat)abstract
- We have recently shown that the anti-HIV activities of reverse transcriptase inhibitors can be related quantitatively to properties of the electrostatic potentials on their molecular surfaces. We now introduce the technique of using only segments of the drug molecules in developing such expressions. If an improved correlation is obtained for a given family of compounds, it would suggest that the segment being used plays a key role in the interaction. We demonstrate the procedure for three groups of drugs, two acting on reverse transcriptase and one on HIV protease. Segmental analysis is found to be definitely beneficial in one case, less markedly so in another, and to have a negative effect in the third. The last result indicates that major portions of the molecular surfaces are involved in the interactions and that the entire molecules need to be considered, in contrast to the first two examples, in which certain segments appear to be of primary importance. This initial exploratory study shows that segmental analysis can provide insight into the nature of the process being investigated, as well as possibly enhancing the predictive capability.
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| 6. |
- Hu, Y. C., et al.
(författare)
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HPFBench : A High Performance Fortran benchmark suite
- 2000
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Ingår i: ACM Transactions on Mathematical Software. - : Association for Computing Machinery (ACM). - 0098-3500 .- 1557-7295. ; 26:1, s. 99-149
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Tidskriftsartikel (refereegranskat)abstract
- The High Performance Fortran (HPF) benchmark suite HPFBench is designed for evaluating the HPF language and compilers on scalable architectures. The functionality of the benchmarks covers scientific software library functions and application kernels that reflect the computational structure and communication patterns in fluid dynamic simulations, fundamental physics, and molecular studies in chemistry and biology. The benchmarks are characterized in terms of FLOP count, memory usage, communication pattern, local memory accesses, array allocation mechanism, as well as operation and communication counts per iteration. The benchmarks output performance evaluation metrics in the form of elapsed times, FLOP rates, and communication time breakdowns. We also provide a benchmark guide to aid the choice of subsets of the benchmarks for evaluating particular aspects of an HPF compiler. Furthermore, we report an evaluation of an industry-leading HPF compiler from the Portland Group Inc. using the HPFBench benchmarks on the distributed-memory IBM SP2.
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| 7. |
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| 8. |
- Jin, Kui-Juan, et al.
(författare)
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Terahertz frequency radiation from Bloch oscillations in GaAs/Al0.3Ga0.7As superlattices
- 2003
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 68:15: 153315
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Tidskriftsartikel (refereegranskat)abstract
- We have performed a joint theoretical and experimental study to investigate the terahertz radiation from Bloch oscillations in a GaAs/Al0.3Ga0.7As superlattice under the condition that there is no Zener tunneling. The total radiation intensity has been calculated with a semiclassical approach in the low field regime where the Wannier-Stark ladder (WSL) cannot be resolved, and with an exact numerical solution in the high field regime where the WSL is well formed. With an adjustment of the intensity units, without fitting material parameters, the calculated results agree almost perfectly with the measured data given in arbitrary units. Consequently, our work gives convincing evidence that the measured THz radiation is due to the Bloch oscillations.
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| 9. |
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| 10. |
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| 11. |
- Johansson, Boo, et al.
(författare)
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Sensitivity and specificity of dementia coding in two Swedish disease registries
- 2004
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Ingår i: Neurology. - 0028-3878. ; 63:4, s. 739-41
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Tidskriftsartikel (refereegranskat)abstract
- The authors investigated the sensitivity and specificity of dementia identification in two Swedish disease registries by using clinical diagnoses from two population-based studies as gold standards. The probability of dementia detected by the Inpatient Discharge Registry was 55% for prevalent patients and 31% for incident patients and was higher than detection by the Cause of Death Registry. Specificity was 98% for the Inpatient Discharge Registry and 100% for the Cause of Death Registry.
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| 12. |
- Leon, Rosa, et al.
(författare)
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Dislocation-induced spatial ordering of InAs quantum dots : Effects on optical properties
- 2002
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 91:9, s. 5826-5830
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Tidskriftsartikel (refereegranskat)abstract
- Misfit dislocations were used to modify the surface morphology and to attain spatial ordering of quantum dots (QDs) by molecular beam epitaxy. Effects of anneal time and temperature on strain-relaxed InxGa1-xAs/GaAs layers and subsequent spatial ordering of InAs QDs were investigated. Photoluminescence (PL) and time-resolved PL was used to study the effects of increased QD positional ordering, increased QD uniformity, and their proximity to dislocation arrays on their optical properties. Narrower inhomogeneous PL broadening from the QDs ordered on dislocation arrays were observed, and differences in PL dynamics were found.
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| 13. |
- Lerma, F., et al.
(författare)
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Superdeformed bands in Sr80-83, Y82-84, Zr-83,Zr-84 : Transition quadrupole moments, moments of inertia, and configuration assignments
- 2003
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 67:4, s. 044310-
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Tidskriftsartikel (refereegranskat)abstract
- Multiple superdeformed bands in the nuclei Sr80-83, Y82-84, and Zr-83,Zr-84 have been studied in a backed-target experiment, using the Gammasphere and the Microball 4pi detector arrays. For 15 bands in these nuclei, average transition quadrupole moments have been measured with high accuracy, using the Doppler-shift attenuation method. Among these are the newly observed superdeformed bands in Y-83,Y-84, which are isospectral with the bands in Sr-82,Sr-83. These isospectral bands have nearly identical transition quadrupole moments. Two of the bands in Sr-81 interact and cross transitions between them are observed. The present measurements place stringent conditions on configuration assignments for the bands obtained from two types of mean-field calculations, leading to a consistent understanding of the mass similar to80 superdeformed bands. The assignments for different bands arise from one or more nucleons occupying the N-0=5h(11/2) intruder orbital.
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| 14. |
- Nakao, S, et al.
(författare)
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Effect of high-energy Si+ ion irradiation on the crystallization behavior of amorphous strontium titanate films
- 2002
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Ingår i: Nuclear Instruments and Methods in Physics Research Section B. - 0168-583X .- 1872-9584. ; 191, s. 226-229
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Tidskriftsartikel (refereegranskat)abstract
- Amorphous strontium titanate (STO) films deposited on Si substrates by magnetron sputtering at room temperature were irradiated with 2 MeV Si ions at doses of 5 x 10(16)-1.5 x 10(17) Si+/cm(2) and post-annealed at 450 degreesC in vacuum. The compositional and structural changes of STO films after the ion irradiation were examined by Rutherford backscattering spectrometry, scanning electron microscopy and X-ray diffraction measurements. The Sr:Ti:O ratio of the as-deposited films was found to be approximately 0.8:1:3. Ion irradiation did not affect the amount of Sr and Ti significantly and the films remained amorphous. After annealing, however, the formation of STO crystals was observed and Sr and O were slightly lost from the films. As compared to the un-irradiated STO films, the ion-irradiated ones showed significantly enhanced crystallization behaviors upon vacuum annealing. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 15. |
- Nakao, S., et al.
(författare)
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Influence of high-energy Si+ ion irradiation on microstructure and mechanical properties of alumina films
- 2002
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Ingår i: Surface & Coatings Technology. - 0257-8972 .- 1879-3347. ; 158-159, s. 534-537
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Tidskriftsartikel (refereegranskat)abstract
- Amorphous alumina films, approximately 600 nm in thickness, prepared on Si(100) substrates by RF magnetron sputtering were irradiated with 2.0 MeV Si ions at a dose of 1 × 1017 ions/cm2 and the influence on the composition, microstructure, and mechanical properties was examined by Rutherford backscattering. X-ray diffraction and nano-indentation measurements. It was found that the O/Al ratio in the films was approximately 1.5, and there was no significant alteration in this ratio after ion irradiation. However, a structural change from amorphous to the crystalline ?-alumina was observed. Hardness and elastic modulus of the irradiated film were significantly increased from approximately 11 and 181 GPa up to approximately 25 and 246 GPa, respectively. © 2002 Elsevier Science B.V. All rights reserved.
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| 16. |
- Ober, Elke A, et al.
(författare)
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Vegfc is required for vascular development and endoderm morphogenesis in zebrafish.
- 2004
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Ingår i: EMBO Reports. - : EMBO. - 1469-221X .- 1469-3178. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- During embryogenesis, complex morphogenetic events lead endodermal cells to coalesce at the midline and form the primitive gut tube and associated organs. While several genes have recently been implicated in endoderm differentiation, we know little about the genes that regulate endodermal morphogenesis. Here, we show that vascular endothelial growth factor C (Vegfc), an angiogenic as well as a lymphangiogenic factor, is unexpectedly involved in this process in zebrafish. Reducing Vegfc levels using morpholino antisense oligonucleotides, or through overexpression of a soluble form of the VEGFC receptor, VEGFR-3, affects the coalescence of endodermal cells in the anterior midline, leading to the formation of a forked gut tube and the duplication of the liver and pancreatic buds. Further analyses indicate that Vegfc is additionally required for the initial formation of the dorsal endoderm. We also demonstrate that Vegfc is required for vasculogenesis as well as angiogenesis in the zebrafish embryo. These data argue for a requirement of Vegfc in the developing vasculature and, more surprisingly, implicate Vegfc signalling in two distinct steps during endoderm development, first during the initial differentiation of the dorsal endoderm, and second in the coalescence of the anterior endoderm to the midline.
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| 17. |
- Zhang, X. L., et al.
(författare)
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Automatic real-time control for gain-flattened fiber Raman amplifiers
- 2004
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Ingår i: Optics Communications. - : Elsevier BV. - 0030-4018 .- 1873-0310. ; 239:01-3, s. 79-84
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Tidskriftsartikel (refereegranskat)abstract
- An automatic control algorithm for flattening the gain of a fiber Raman amplifier is derived from the Raman scattering equations. A pseudo-inverse gain matrix is introduced to adjust the powers of the pump lasers. The algorithm is simple, fast, effective, robust and insensitive to the length and type of the fiber. It is demonstrated experimentally that the gain flattening for Raman amplifiers comprising various types and lengths of fiber and with different target gains can be achieved automatically with this algorithm. The algorithm converges for both small and large input signal. Flattened Raman gain with a fluctuation less than 0.40 dB over a 50-nm bandwidth for a 50-km SMF or less than 0.20 dB over a 40-nm bandwidth for a 6.6-km dispersion compensated fiber is realized in the experiment.
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| 18. |
- Zheng, WT, et al.
(författare)
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Chemical bonding in carbon nitride films studied by X-ray spectroscopies
- 2001
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Ingår i: DIAMOND AND RELATED MATERIALS. - : ELSEVIER SCIENCE SA. - 0925-9635. ; 10:9-10, s. 1897-1900 Language: English
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Tidskriftsartikel (refereegranskat)abstract
- Carbon nitride films are deposited using dc magnetron sputtering in a N-2 discharge. The nature of chemical bonding of the films is investigated using X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure, and X-ray emission spectros
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| 19. |
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| 20. |
- Zheng, W.T., et al.
(författare)
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Chemical bonding in carbon nitride films studied by X-ray spectroscopies
- 2001
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Ingår i: Diamond and related materials. - 0925-9635 .- 1879-0062. ; 10:9-10, s. 1897-1900
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Tidskriftsartikel (refereegranskat)abstract
- Carbon nitride films are deposited using dc magnetron sputtering in a N2 discharge. The nature of chemical bonding of the films is investigated using X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure, and X-ray emission spectroscopy. X-Ray photoelectron spectroscopy spectra show that N1s binding states depend on substrate temperature, in which two pronounced peaks can be observed. The near edge X-ray absorption fine structure at C1s and N1s exhibits a similar absorption profile in the p* resonance region, but the s* resonance is sharper in the N1s spectra. Resonant N K-emission spectra show a strong dependence on excitation photo energies. Compared XPS N1s spectra with recent theoretical calculations by Johansson and Stafstrom, two main nitrogen sites are assigned in which N bound to sp3 hybridized C and sp2 hybridized C, respectively. The correlation of X-ray photoelectron, X-ray absorption, and X-ray emission spectra for N in carbon nitride films is also discussed. © 2001 Elsevier Science B.V. All rights reserved.
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| 21. |
- Zheng, W.T., et al.
(författare)
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Chemical bonding, structure, and hardness of carbon nitride thin films
- 2000
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Ingår i: Diamond and related materials. - 0925-9635 .- 1879-0062. ; 9:9-10, s. 1790-1794
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Carbon nitride films are deposited on Si(001) substrates by reactive d.c. magnetron sputtering graphite in a pure N2 discharge. The chemical bonding and structure of carbon nitride films were probed using Fourier transformation infrared (FTIR) and near edge X-ray absorption fine structure (NEXAFS), and the hardness was evaluated using nanoindentation experiments. The structure and hardness for the films are dependent on the substrate temperature (T(s)). FTIR and NEXAFS spectra show that N atoms are bound to sp1, sp2 and sp3 hybridized C atoms, and the intensity of p(*) resonance for C1s NEXAFS spectra is the lowest for the film grown at T(s) = 350°C, having a turbostratic-like structure, high hardness and stress. The correlation between the structure and hardness of carbon nitride films is discussed. (C) 2000 Elsevier Science S.A. All rights reserved.Carbon nitride films are deposited on Si(001) substrates by reactive d.c. magnetron sputtering graphite in a pure N2 discharge. The chemical bonding and structure of carbon nitride films were probed using Fourier transformation infrared (FTIR) and near edge X-ray absorption fine structure (NEXAFS), and the hardness was evaluated using nanoindentation experiments. The structure and hardness for the films are dependent on the substrate temperature (Ts). FTIR and NEXAFS spectra show that N atoms are bound to sp1, sp2 and sp3 hybridized C atoms, and the intensity of p* resonance for C1s NEXAFS spectra is the lowest for the film grown at Ts = 350°C, having a turbostratic-like structure, high hardness and stress. The correlation between the structure and hardness of carbon nitride films is discussed.
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