| 1. |
|
|
| 2. |
|
|
| 3. |
- Imanishi, T., et al.
(author)
-
Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
-
In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
-
Journal article (peer-reviewed)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.
|
|
| 4. |
|
|
| 5. |
- Lockwood, M, et al.
(author)
-
Coordinated Cluster and ground-based instrument observations of transient changes in the magnetopause boundary layer during an interval of predominantly northward IMF : relation to reconnection pulses and FTE signatures
- 2001
-
In: Annales Geophysicae. - : Copernicus GmbH. - 0992-7689 .- 1432-0576. ; 19:10-12, s. 1613-1640
-
Research review (peer-reviewed)abstract
- We study a series of transient entries into the low-latitude boundary layer (LLBL) of all four Cluster spacecraft during an outbound pass through the mid-afternoon magnetopause ([X(GSM), Y(GSM), Z(GSM)] approximate to [2, 7, 9] R(E)). The events take place during an interval of northward IMF, as seen in the data from the ACE satellite and lagged by a propagation delay of 75 min that is well-defined by two separate studies: (1) the magnetospheric variations prior to the northward turning (Lockwood et al., 2001, this issue) and (2) the field clock angle seen by Cluster after it had emerged into the magnetosheath (Opgenoorth et al., 2001, this issue). With an additional lag of 16.5 min, the transient LLBL events cor-relate well with swings of the IMF clock angle (in GSM) to near 90degrees. Most of this additional lag is explained by ground-based observations, which reveal signatures of transient reconnection in the pre-noon sector that then take 10-15 min to propagate eastward to 15 MLT, where they are observed by Cluster. The eastward phase speed of these signatures agrees very well with the motion deduced by the cross-correlation of the signatures seen on the four Cluster spacecraft. The evidence that these events are reconnection pulses includes: transient erosion of the noon 630 nm (cusp/cleft) aurora to lower latitudes; transient and travelling enhancements of the flow into the polar cap, imaged by the AMIE technique; and poleward-moving events moving into the polar cap, seen by the EISCAT Svalbard Radar (ESR). A pass of the DMSP-F15 satellite reveals that the open field lines near noon have been opened for some time: the more recently opened field lines were found closer to dusk where the flow transient and the poleward-moving event intersected the satellite pass. The events at Cluster have ion and electron characteristics predicted and observed by Lockwood and Hapgood (1998) for a Flux Transfer Event (FTE), with allowance for magnetospheric ion reflection at Alfvenic disturbances in the magnetopause reconnection layer. Like FTEs, the events are about 1 R(E) in their direction of motion and show a rise in the magnetic field strength, but unlike FTEs, in general, they show no pressure excess in their core and hence, no characteristic bipolar signature in the boundary-normal component. However, most of the events were observed when the magnetic field was southward, i.e. on the edge of the interior magnetic cusp, or when the field was parallel to the magnetic equatorial plane. Only when the satellite begins to emerge from the exterior boundary (when the field was northward), do the events start to show a pressure excess in their core and the consequent bipolar signature. We identify the events as the first observations of FTEs at middle altitudes.
|
|
| 6. |
|
|
| 7. |
- Andreyev, A. N., et al.
(author)
-
New microsecond isomers in Bi-189,Bi-190
- 2001
-
In: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-6001 .- 1434-601X. ; 10:2, s. 129-133
-
Journal article (peer-reviewed)abstract
- New microsecond isomers in the neutron-deficient isotopes Bi-189g,Bi-190 have been identified after in-flight separation by the velocity filter SHIP. The evaporation residues were identified on the basis of delayed recoil-gamma /X-ray, recoil-gamma /X-ray-alpha and excitation function measurements. The systematics of the [pi 1i(13/2)]13/2(+) excited states in the odd-mass Bi nuclei is discussed.
|
|
| 8. |
- Andreyev, A. N., et al.
(author)
-
The discovery of a prolate-oblate-spherical shape triple of spin 0(+) states in the atomic nucleus Pb-186
- 2001
-
In: Nuclear Physics A. - : Elsevier BV. - 0375-9474 .- 1873-1554. ; 682, s. 482C-486C
-
Journal article (peer-reviewed)abstract
- Two excited J(pi)=0(+) states in Pb-186 populated in the a-decay of Po-190 have been identified through alpha -particle/conversion electron coincidences in an experiment at the velocity filter SHIP. The parent Po-190 nuclei have been produced in the Nd-142(Cr-52,4n)Po-190 complete fusion reaction, alpha -particle energies and branching ratios have been measured and hindrance factors were deduced. The observed states have been interpreted as the band heads of the known prolate and (yet unobserved) oblate rotational bands in Pb-186.
|
|
| 9. |
- Hillier, Ladeana W, et al.
(author)
-
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
-
In: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
-
Journal article (peer-reviewed)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
|
|
| 10. |
- Hoff, P, et al.
(author)
-
Nuclear spectroscopy at Sn-133
- 2000
-
In: HYPERFINE INTERACTIONS. - : BALTZER SCI PUBL BV. - 0304-3843. ; 129:1-4, s. 141-148
-
Journal article (other academic/artistic)abstract
- It is described how the measurement of n gamma -coincidences can be used to identify single-particle states in Sn-133. This method, in combination with the improved yields at ISOLDE, has facilitated firm determination of three excited single-particle stat
|
|
| 11. |
|
|
| 12. |
|
|
| 13. |
|
|
| 14. |
- Lockwood, M., Fazakerley, A., Opgenoorth, H., Moen, J., van Eyken, A.P., Dunlop, M., Bosqued, J.M., Lu, G., Cully, C., Eglitis, P., McCrea, I., Hapgood, M. A., Wild, M.N., Stamper, R., Denig, W., Taylor, M., . Wild, J.A., Provan, G., Amm, O., Kauristie
(author)
-
Coordinated Cluster, ground-based instrumentation and low-altitude satellite observations of transient poleward-moving events in the ionosphere and in the tail lobe
- 2001
-
In: Annales Geophysicae. ; 19:10, s. 1589-1612
-
Journal article (peer-reviewed)abstract
- During the interval between 8:00–9:30 on 14 January 2001, the four Cluster spacecraft were moving from the central magnetospheric lobe, through the dusk sector mantle, on their way towards intersecting the magnetopause near 15:00 MLT and 15:00 UT. Throug
|
|
| 15. |
- Marklund, G.T., Ivchenko, N., Karlsson, T., Fazakerley, A., Dunlop, M., Lindqvist, P.A., Buchert, S., Owen, C., Taylor, M., Vaivalds, A., Carter, P., Andre, M. and Balogh, A.
(author)
-
Temporal evolution of the electric field accelerating electrons away from the auroral ionosphere.
- 2001
-
In: Nature. ; 414:6865, s. 724-727
-
Journal article (peer-reviewed)abstract
- The bright night-time aurorae that are visible to the unaided eye are caused by electrons accelerated towards Earth by an upward-pointing electric field(1-3). On adjacent geomagnetic field lines the reverse process occurs: a downward-pointing electric fie
|
|
| 16. |
|
|
| 17. |
|
|
| 18. |
|
|
| 19. |
- Pavey, S, et al.
(author)
-
Microarray expression profiling in melanoma reveals a BRAF mutation signature
- 2004
-
In: Oncogene. - : Springer Science and Business Media LLC. - 1476-5594 .- 0950-9232. ; 23:23, s. 4060-4067
-
Journal article (peer-reviewed)abstract
- We have used microarray gene expression pro. ling and machine learning to predict the presence of BRAF mutations in a panel of 61 melanoma cell lines. The BRAF gene was found to be mutated in 42 samples (69%) and intragenic mutations of the NRAS gene were detected in seven samples (11%). No cell line carried mutations of both genes. Using support vector machines, we have built a classifier that differentiates between melanoma cell lines based on BRAF mutation status. As few as 83 genes are able to discriminate between BRAF mutant and BRAF wild-type samples with clear separation observed using hierarchical clustering. Multidimensional scaling was used to visualize the relationship between a BRAF mutation signature and that of a generalized mitogen-activated protein kinase ( MAPK) activation ( either BRAF or NRAS mutation) in the context of the discriminating gene list. We observed that samples carrying NRAS mutations lie somewhere between those with or without BRAF mutations. These observations suggest that there are gene-specific mutation signals in addition to a common MAPK activation that result from the pleiotropic effects of either BRAF or NRAS on other signaling pathways, leading to measurably different transcriptional changes.
|
|
| 20. |
|
|
| 21. |
- Baeckström, Dan, 1956, et al.
(author)
-
Activation of the alpha2beta1 integrin prevents c-erbB2-induced scattering and apoptosis of human mammary epithelial cells in collagen.
- 2000
-
In: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 19:40, s. 4592-603
-
Journal article (peer-reviewed)abstract
- Constitutive overexpression of c-erbB2 in the mammary epithelial cell line MTSV1-7 has been shown to result in epithelial-mesenchymal conversion, anchorage-independent growth and loss of organized morphogenesis in collagen. To elucidate the events leading to this drastic change, MTSV1-7 cells and its subclone HB2 (which shows a more strictly epithelial phenotype) were transfected with the hybrid trk-neu receptor consisting of the extracellular domain of the trkA nerve growth factor (NGF) receptor and the transmembrane and cytoplasmic domains of c-erbB2 (neu). In cells expressing this construct, c-erbB2 homodimerization can be mimicked by addition of NGF. In trk-neu transfectants of HB2 cells, modest expression led to increased cell proliferation upon NGF treatment. When clones with higher expression levels were grown in collagen, NGF instead induced cell scattering, diminished viability and dramatically increased apoptosis. Interestingly, both the dissociation of colonies and loss of cell viability could be completely reversed by treatment of the cells with antibodies that activate the adhesive capacity of the alpha2beta1 integrin. Long-term NGF treatment of high-expressing transfectants generated fibroblastic clones displaying a reduced expression of integrin alpha2 and E-cadherin, and extensive apoptosis in collagen. These results, which indicate that strong c-erbB2 signalling may lead to downregulation and/or inactivation of the alpha2beta1 integrin, promoting apoptosis in collagen, provide one possible explanation to the increased apoptosis frequently seen in early tumour development.
|
|
| 22. |
|
|
| 23. |
|
|
| 24. |
- Bernasconi, G, et al.
(author)
-
Evolutionary ecology of the prezygotic stage
- 2004
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 303:5660, s. 971-975
-
Research review (peer-reviewed)abstract
- The life cycles of sexually reproducing animals and flowering plants begin with male and female gametes and their fusion to form a zygote. Selection at this earliest stage is crucial for offspring quality and raises similar evolutionary issues, yet zoology and botany use dissimilar approaches. There are striking parallels in the role of prezygotic competition for sexual selection on males, cryptic female choice, sexual conflict, and against selfish genetic elements and genetic incompatibility. In both groups, understanding the evolution of sex-specific and reproductive traits will require an appreciation of the effects of prezygotic competition on fitness.
|
|
| 25. |
|
|
| 26. |
|
|
| 27. |
|
|
| 28. |
- Kloo, Lars A., et al.
(author)
-
Investigations of the polyiodides H3O center dot I-x (x=3, 5 or 7) as dibenzo-18-crown-6 complexes
- 2000
-
In: Journal of the Chemical Society-Dalton Transactions. - : Royal Society of Chemistry (RSC). - 0300-9246 .- 1470-479X .- 1364-5447. ; 7:7, s. 1061-1065
-
Journal article (peer-reviewed)abstract
- The compounds [H3O(dibenzo-18-crown-6)][I-x] (x = 3,5,7) have been synthesised and investigated by X-ray diffraction as well as Raman and far-IR spectroscopy. The structure of the triiodide contains two independent, slightly asymmetric and bent I-3(-) ions with I-I distances in the range 2.92-2.94 Angstrom. The pentaiodide can be described as composed of (I-3(-)). I-2, where the I-I distances in the asymmetric and slightly bent I-3 unit are 2.894(2) and 2.942(2) Angstrom and in the I-2 unit 2.763(2) Angstrom. The L-shaped I-5(-) ions are linked together forming a chain of I-10 rectangles through van der Waals interactions in the range 3.7-3.8 Angstrom. The structure determination supports a pyramidal geometry of the H3O+ ion in the dibenzo-18-crown-6 moiety of both structures. Because of severe crystal twinning the crystal structure of the heptaiodide could not be determined. However, the results from the spectroscopic investigation are consistent with a heptaiodide of composition (I-3(-)). 2I(2).
|
|
| 29. |
|
|
| 30. |
- Löfgren, Anneli, et al.
(author)
-
Symmetry of Two-Terminal Nonlinear Electric Conduction
- 2004
-
In: Physical Review Letters. - 1079-7114. ; 92:4, s. 1-046803
-
Journal article (peer-reviewed)abstract
- The well-established symmetry relations for linear transport phenomena cannot, in general, be applied in the nonlinear regime. Here we propose a set of symmetry relations with respect to bias voltage and magnetic field for the nonlinear conductance of two-terminal electric conductors. We experimentally confirm these relations using phase-coherent, semiconductor quantum dots.
|
|
| 31. |
- Marinova-Mutafchieva, L, et al.
(author)
-
Mesenchymal cells expressing bone morphogenetic protein receptors are present in the rheumatoid arthritis joint.
- 2000
-
In: Arthritis and rheumatism. - 0004-3591. ; 43:9, s. 2046-55
-
Journal article (peer-reviewed)abstract
- To evaluate the presence of cells of an early mesenchymal lineage, as judged by the expression of bone morphogenetic protein receptors (BMPRs), in the joints of normal individuals and patients with rheumatoid arthritis (RA).Synovial fluids, single cell suspensions of cultured fibroblast-like synoviocytes (FLS), and synovial tissues were examined by immunohistology with antibodies to BMPR type IA (BMPRIA), BMPRIB, and BMPRII and then quantified using computerized image analysis. Other antibodies were evaluated by cytofluorography.In primary cultures of joint effusions from patients with RA and other forms of inflammatory arthritis, there were large adherent cells with the appearance of either fibroblasts or stromal cells that stained with antibodies to mesenchymal elements-CD44, type I collagen, alpha-actin, and vimentin-but not with antibodies to hematopoietic markers. These cells proliferated rapidly, expressed BMPRIA and BMPRII, and soon became the predominant cells in culture. They were retained through multiple passages and persistently displayed surface vascular cell adhesion molecule 1. Immunohistochemical analysis of cultured RA FLS (passages 3, 4, and 6; n = 6) revealed that 11.6% were BMPR-positive, while only 2.0% of osteoarthritis FLS (passage 4; n = 3) were BMPR-positive, and 1 normal synovial culture had no BMPR-positive cells. In all RA synovial membranes examined (n = 9), BMPRI- and BMPRII-expressing cells were identified in the intimal lining and were also scattered in the subintima. These cells constituted approximately 25% and approximately 7% of the cells in each area, respectively. Double immunostaining showed no coexpression of BMPR-positive cells with CD68, CD34, or CD3. Cells expressing BMPR were not seen in any normal synovial samples (n = 4). Strong staining for BMPR was identified on cells at the invasive front of the pannus and at sites of cartilage erosion.The inflamed RA joint contains BMPR-positive mesenchymal cells. Their origin is still speculative, but since their counterparts in the bone marrow are essential for osteoclastogenesis, support lymphocyte development and maturation, and protect T cells and B cells from programmed cell death, the BMPR-positive cells may be essential elements in the pathogenesis of RA and other inflammatory forms of chronic synovitis.
|
|
| 32. |
- Marklund, Göran T., et al.
(author)
-
Temporal evolution of the electric field accelerating electrons away from the auroral ionosphere
- 2001
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 414:6865, s. 724-727
-
Journal article (peer-reviewed)abstract
- The bright night-time aurorae that are visible to the unaided eye are caused by electrons accelerated towards Earth by an upward-pointing electric field(1-3). On adjacent geomagnetic field lines the reverse process occurs: a downward-pointing electric field accelerates electrons away from Earth(4-11). Such magnetic-field-aligned electric fields in the collisionless plasma above the auroral ionosphere have been predicted(12), but how they could be maintained is still a matter for debate(13). The spatial and temporal behaviour of the electric fields-a knowledge of which is crucial to an understanding of their nature-cannot be resolved uniquely by single satellite measurements. Here we report on the first observations by a formation of identically instrumented satellites crossing a beam of upward-accelerated electrons. The structure of the electric potential accelerating the beam grew in magnitude and width for about 200 s, accompanied by a widening of the downward-current sheet, with the total current remaining constant. The 200-s timescale suggests that the evacuation of the electrons from the ionosphere contributes to the formation of the downward-pointing magnetic-field-aligned electric fields. This evolution implies a growing load in the downward leg of the current circuit, which may affect the visible discrete aurorae.
|
|
| 33. |
|
|
| 34. |
- Robinson, SD, et al.
(author)
-
High-spin structures and band termination effects in Cd-104
- 2002
-
In: Journal of Physics G: Nuclear and Particle Physics. - : IOP Publishing. - 0954-3899. ; 28:6, s. 1415-1431
-
Journal article (peer-reviewed)abstract
- High-spin states in the neutron-deficient isotope Cd-104 were populated using the Cr-50(Ni-58,4p)Cd-104 reaction at a beam energy of 250 MeV The level scheme has been extended using triple gamma-ray coincidences to a spin of 29h and an excitation energy of 18.2 MeV. Several collective structures involving the excitation of h(11/2) neutrons have been observed to spins approaching 30h. The high-spin structure has been compared to the results of cranked Nilsson-Strutinsky calculations.
|
|
| 35. |
|
|
| 36. |
|
|
