| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Jiang, Jingting, et al.
(författare)
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Clinical Evaluation of Serum Alpha-Fetoprotein-IgM Immune Complexes on the Diagnosis of Primary Hepatocellular Carcinoma
- 2009
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Ingår i: Journal of Clinical Laboratory Analysis. - : Wiley. - 1098-2825 .- 0887-8013. ; 23:4, s. 213-218
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Tidskriftsartikel (refereegranskat)abstract
- We evaluated clinical significance of serum alpha-fetoprotein (AFP)-IgM immune complexes, in comparison with free AFP, on the diagnosis of primary hepatocellular carcinoma (HCC). Serum levels of AFP-IgM immune complexes and free AFP were determined by the ELISA method and electrochemiluminescence, respectively, in 103 healthy controls, 74 patients suffering from primary HCC, 27 patients suffering from liver cirrhosis, and 63 patients suffering from chronic hepatitis. The best cut-off value of AFP-IgM and free AFP for diagnosis of primary HCC were 300 AU/mL and 10 mu g/L respectively, according to the area under the curve (AUC) in this study. The sensitivity of AFP-IgM and free AFP were 64.9 and 79.7%, and the specificity were 75.6 and 80.3%, respectively, when all cases of primary HCC were analyzed, and the AUC of free AFP was larger than that of AFP-IgM (0.85 vs. 0.72, Z = 3.21). However, in case of primary HCC at early stages (stages I and II) were analyzed, the AUC of AFP-IgM was larger than that of free AFP (0.91 vs. 0.82, Z = 1.73), which demonstrated that the sensitivity of AFP-IgM and free AFP were 94.4 and 72.2%, and the specificity were 81.9 and 79.9%, respectively. When both AFP-IgM and free AFP were positive, the specificity of diagnosis of primary HCC was 89.1%, and the efficacy was 79.0%. It is concluded that either sensitivity or specificity of serum level of AFP-IgM immune complexes was higher than that of free AFP in the diagnosis of primary HCC at early stages. As there was false positive AFP-IgM existed in the patients suffering from cirrhosis and chronic hepatitis, the combination of free AFP and AFP-IgM could significantly increase specificity and decrease false negative and/or false positive in the primary HCC at early stages. J. Clin. Lab. Anal. 23:213-218, 2009. (C) 2009 Wiley-Liss, Inc.
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| 3. |
- Lundström, Linda, et al.
(författare)
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A galanin receptor subtype 1 specific agonist
- 2005
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Ingår i: International Journal of Peptide Research and Therapeutics. - : Springer Science and Business Media LLC. - 1573-3904 .- 1573-3149. ; 11:1, s. 17-27
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Tidskriftsartikel (refereegranskat)abstract
- The chimeric peptide M617, galanin(1–13)-Gln14-bradykinin(2–9)amide, is a novel galanin receptor ligand with increased subtype specificity for GalR1 and agonistic activity in cultured cells as well as in vivo. Displacement studies on cell membranes expressing hGalR1 or hGalR2 show the presence of a high affinity binding site for M617 on GalR1 (K i=0.23±.12 nM) while lower affinity was seen towards GalR2 (K i=5.71±1.28 nM) resulting in 25-fold specificity for GalR1. Activation of GalR1 upon stimulation with M617 is further confirmed by internalization of a GalR1-EGFP conjugate. Intracellular signaling studies show the ability of M617 to inhibit forskolin stimulated cAMP formation with 57% and to produce a 5-fold increase in inositol phosphate (IP) accumulation. Agonistic effects on signal transduction are shown on both receptors studied after treatment with M617 in the presence of galanin. In noradrenergic locus coeruleus neurons, M617 induces an outward current even in the presence of TTX plus Ca2+, high Mg2+, suggesting a postsynaptic effect. Intracerebroventricular (i.c.v.) administration of M617 dose-dependently stimulates food uptake in rats while, in contrast, M35 completely fails to affect the feeding behavior. Spinal cord flexor reflex is facilitated by intrathecal (i.t.) administration of M617 as well as galanin with no significant change upon pre-treatment with M617. M617 dose dependently antagonizes the spinal cord hyperexcitablility induced by C-fiber conditioning stimulus and does neither enhance nor antagonize the effect of galanin. These data demonstrate a novel galanin receptor ligand with subtype specificity for GalR1 and agonistic activity, both in vitro and in vivo.
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| 6. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 7. |
- Dominguez, Cecilia A, et al.
(författare)
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Genetic analysis of neuropathic pain-like behavior following peripheral nerve injury suggests a role of the major histocompatibility complex in development of allodynia
- 2008
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Ingår i: Pain. - : Ovid Technologies (Wolters Kluwer Health). - 1872-6623 .- 0304-3959. ; 136:3, s. 313-319
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Tidskriftsartikel (refereegranskat)abstract
- Neuropathic pain is a common consequence of damage to the nervous system. We here report a genetic analysis of development of neuropathic pain-like behaviors after unilateral photochemically-induced ischemic sciatic nerve injury in a panel of inbred rat strains known to display different susceptibility to autoimmune neuroinflammation. Pain behavior was initially characterized in Dark-Agouti (DA; RT1(avl)), Piebald Virol Glaxo (PVG; RT1(c)), and in the major histocompatibility complex (MHC)-congenic strain PVG-RT1(avl). All strains developed mechanical hypersensitivity (allodynia) following nerve injury. However, the extent and duration of allodynia varied significantly among the strains, with PVG displaying more severe allodynia compared to DA rats. Interestingly, the response of PVG-RT1(avR1) was similar to that of DA, suggesting regulation by the MHC locus. This notion was subsequently confirmed in an F2 cohort derived from crossing of the PVG and PVG-RT1(avl) strains, where allodynia was reduced in homozygous or heterozygous carriers of the RT1(avl) allele in comparison to rats homozygous for the RT1(c) allele. These results indicate that certain allelic variants of the MHC could influence susceptibility to develop and maintain neuropathic pain-like behavior following peripheral nerve injury in rats.
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| 8. |
- Holland, Linda Z, et al.
(författare)
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The amphioxus genome illuminates vertebrate origins and cephalochordate biology
- 2008
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 18:7, s. 1100-1111
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Tidskriftsartikel (refereegranskat)abstract
- Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
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| 9. |
- Kapilashrami, Mukes, et al.
(författare)
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On the defect induced ferromagnetic ordering above room-temperature in undoped and Mn doped ZnO thin films
- 2009
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Ingår i: NOVEL MATERIALS AND DEVICES FOR SPINTRONICS. - Warrendale, PA : MATERIALS RESEARCH SOCIETY. ; , s. 3-8
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Konferensbidrag (refereegranskat)abstract
- Evidence for long range ferromagnetic order above room-temperature, RTFM, in pristine ZnO, In2O3, TiO2 nanoparticles and thin films, containing no nominal magnetic elements have been reported recently. This could question the origin of RTFM in doped dilute alloys if for example the ZnO matrix itself develops a defect induced magnetic order with a significant moment per unit cell. In this presentation we report a systematic study of the film thickness dependence of RTFM in pure ZnO deposited by DC Magnetron Sputtering. We observe a maximum in the saturation magnetization, Ms, value of 0.62 emu/g (0,018 ÎŒB/unit cell), for a -480 nm film deposited in an oxygen ambience of appropriate pressure. Above a thickness of around 1 ÎŒm the films are diamagnetic as expected. We thus see a sequential transition from ferromagnetism to para- and eventual diamagnetism as a function of film thickness in ZnO. We also find that in such a ZnO matrix with a maximum intrinsic defect induced moment, on doping with Mn the maximum enhanced Ms value of 0.78 emu/g is obtained for 1 at. % Mn doping. With this approach of appropriate doping in a defect tailored matrix, we routinely obtain RTFM in both undoped and Mn- doped ZnO thin films.
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| 10. |
- Kapilashrami, Mukes, et al.
(författare)
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Transition from ferromagnetism to diamagnetism in undoped ZnO thin films
- 2009
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 95:3
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Tidskriftsartikel (refereegranskat)abstract
- We report a systematic study of the film thickness dependence (0.1-1 mu m) of room-temperature ferromagnetism in pure magnetron-sputtered ZnO thin films wherein a sequential transition from ferromagnetism to paramagnetism and diamagnetism as a function of film thickness is observed. The highest saturation magnetization (M-S) value observed is 0.62 emu/g (0.018 mu(B)/unit cell) for a similar to 480 nm film. On doping the ZnO film with 1 at. % Mn enhances the M-S value by 26%. The ferromagnetic order in ZnO matrix is believed to be defect induced. In addition, on doping with Mn hybridization between the 2p states of O and the 3d states of Mn occurs.
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