| 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. |
- 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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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 4. |
- Szatmari, Peter, et al.
(författare)
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Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
- 2007
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:3, s. 319-328
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Tidskriftsartikel (refereegranskat)abstract
- Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,168 families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.
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| 5. |
- Amundadottir, Laufey, et al.
(författare)
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Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer.
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 41, s. 986-990
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Tidskriftsartikel (refereegranskat)abstract
- We conducted a two-stage genome-wide association study of pancreatic cancer, a cancer with one of the lowest survival rates worldwide. We genotyped 558,542 SNPs in 1,896 individuals with pancreatic cancer and 1,939 controls drawn from 12 prospective cohorts plus one hospital-based case-control study. We conducted a combined analysis of these groups plus an additional 2,457 affected individuals and 2,654 controls from eight case-control studies, adjusting for study, sex, ancestry and five principal components. We identified an association between a locus on 9q34 and pancreatic cancer marked by the SNP rs505922 (combined P = 5.37 x 10(-8); multiplicative per-allele odds ratio 1.20; 95% confidence interval 1.12-1.28). This SNP maps to the first intron of the ABO blood group gene. Our results are consistent with earlier epidemiologic evidence suggesting that people with blood group O may have a lower risk of pancreatic cancer than those with groups A or B.
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| 6. |
- Nene, Vishvanath, et al.
(författare)
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Genome sequence of Aedes aegypti, a major arbovirus vector.
- 2007
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5832, s. 1718-23
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Tidskriftsartikel (refereegranskat)abstract
- We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
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| 7. |
- Richards, Stephen, et al.
(författare)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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Ingår i: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Tidskriftsartikel (refereegranskat)abstract
- Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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| 8. |
- Chang, Yu-mei, et al.
(författare)
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A pooled analysis of Melanocytic nevus phenotype and the risk of cutaneous melanoma at different latitudes
- 2009
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 124:2, s. 420-428
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Tidskriftsartikel (refereegranskat)abstract
- An abnormal nevus phenotype is associated with an increased risk of melanoma. We report a pooled analysis conducted using individual nevus data from 15 case-control studies (5,421 melanoma cases and 6,966 controls). The aims were to quantify the risk better and to determine whether relative risk is varied by latitude. Bayesian unconditional logistic random coefficients models were employed to study the risk associated with nevus characteristics. Participants with whole body nevus counts in the highest of 4 population-based categories had a greatly increased risk of melanoma compared with those in the lowest category (pooled odds ratio (pOR) 6.9 (95% confidence interval (CI): 4.4, 1.1.2) for those aged <50 years and pOR 5.1 (95% CI: 3.6, 7.5) for those aged >= 50). The pOR for presence compared with absence of any clinically atypical nevi was 4.0 (95 % CI: 2.8, 5.8). The pORs for 1-2 and >= 3 large nevi on the body compared with none were 2.9 (95% CI: 1.9, 4.3) and 7.1 (95% CI: 4.7, 11.6), respectively. The relative heterogeneities among studies were small for most measures of nevus phenotype, except for the analysis of nevus counts on the arms, which may have been due to methodological differences among studies. The pooled analysis also suggested that an abnormal nevus phenotype is associated most with melanomas on intermittently sun-exposed sites. The presence of increased numbers of nevi, large nevi and clinically atypical nevi on the body are robust risk factors for melanoma showing little variation in relative risk among studies performed at different latitudes. (C) 2008 Wiley-Liss, Inc.
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| 9. |
- Chang, Yu-mei, et al.
(författare)
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Sun exposure and melanoma risk at different latitudes: a pooled analysis of 5700 cases and 7216 controls
- 2009
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Ingår i: International Journal of Epidemiology. - : Oxford University Press (OUP). - 1464-3685 .- 0300-5771. ; 38:3, s. 814-830
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Tidskriftsartikel (refereegranskat)abstract
- Background Melanoma risk is related to sun exposure; we have investigated risk variation by tumour site and latitude. Methods We performed a pooled analysis of 15 case-control studies (5700 melanoma cases and 7216 controls), correlating patterns of sun exposure, sunburn and solar keratoses (three studies) with melanoma risk. Pooled odds ratios (pORs) and 95% Bayesian confidence intervals (CIs) were estimated using Bayesian unconditional polytomous logistic random-coefficients models. Results Recreational sun exposure was a risk factor for melanoma on the trunk (pOR 1.7; 95% CI: 1.4-2.2) and limbs (pOR 1.4; 95% CI: 1.1-1.7), but not head and neck (pOR 1.1; 95% CI: 0.8-1.4), across latitudes. Occupational sun exposure was associated with risk of melanoma on the head and neck at low latitudes (pOR 1.7; 95% CI: 1.0-3.0). Total sun exposure was associated with increased risk of melanoma on the limbs at low latitudes (pOR 1.5; 95% CI: 1.0-2.2), but not at other body sites or other latitudes. The pORs for sunburn in childhood were 1.5 (95% CI: 1.3-1.7), 1.5 (95% CI: 1.3-1.7) and 1.4 (95% CI: 1.1-1.7) for melanoma on the trunk, limbs, and head and neck, respectively, showing little variation across latitudes. The presence of head and neck solar keratoses was associated with increased risk of melanoma on the head and neck (pOR 4.0; 95% CI: 1.7-9.1) and limbs (pOR 4.0; 95% CI: 1.9-8.4). Conclusion Melanoma risk at different body sites is associated with different amounts and patterns of sun exposure. Recreational sun exposure and sunburn are strong predictors of melanoma at all latitudes, whereas measures of occupational and total sun exposure appear to predict melanoma predominately at low latitudes. Keywords Melanoma, recreational sun exposure, occupational sun exposure, total sun exposure, sunburn, solar keratoses
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| 10. |
- 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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| 11. |
- Stanishev, Vallery, et al.
(författare)
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SN 2003du: 480 days in the life of a normal type Ia supernova
- 2007
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 469:2, s. 645-661
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Tidskriftsartikel (refereegranskat)abstract
- Aims.We present a study of the optical and near-infrared (NIR) properties of the Type Ia Supernova (SN Ia) 2003du.Methods: An extensive set of optical and NIR photometry and low-resolution long-slit spectra was obtained using a number of facilities. The observations started 13 days before B-band maximum light and continued for 480 days with exceptionally good time sampling. The optical photometry was calibrated through the S-correction technique.Results: The {UBVRIJHK} light curves and the color indices of SN 2003du closely resemble those of normal SNe Ia. SN 2003du reached a B-band maximum of 13.49 ± 0.02 mag on JD2 452 766.38 ± 0.5. We derive a B-band stretch parameter of 0.988 ±0.003, which corresponds to Δ m15=1.02 ±0.05, indicative of a SN Ia of standard luminosity. The reddening in the host galaxy was estimated by three methods, and was consistently found to be negligible. Using an updated calibration of the V and {JHK} absolute magnitudes of SNe Ia, we find a distance modulus μ=32.79±0.15 mag to the host galaxy, UGC 9391. We measure a peak {uvoir} bolometric luminosity of 1.35(±0.20)×1043 erg s-1 and Arnett's rule implies that M56Ni≃0.68 ±0.14 Mȯ of 56Ni was synthesized during the explosion. Modeling of the {uvoir} bolometric light curve also indicates M56Ni in the range 0.6-0.8 Mȯ. The spectral evolution of SN 2003du at both optical and NIR wavelengths also closely resembles normal SNe Ia. In particular, the Si II ratio at maximum R(Si II) = 0.22 ±0.02 and the time evolution of the blueshift velocities of the absorption line minima are typical. The pre-maximum spectra of SN 2003du showed conspicuous high-velocity features in the Ca II H&K doublet and infrared triplet, and possibly in Si II λ6355, lines. We compare the time evolution of the profiles of these lines with other well-observed SNe Ia and we suggest that the peculiar pre-maximum evolution of Si II λ6355 line in many SNe Ia is due to the presence of two blended absorption components.
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| 12. |
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| 13. |
- Axelberg, Peter G.V. 1959, et al.
(författare)
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AUTOMATIC CLASSIFICATION OF VOLTAGE EVENTS USING THE SUPPORT VECTOR MACHINE METHOD
- 2007
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Ingår i: 19th International Conference on Electricity Distribution (SIRED 2007) , Vienna, Austria, 21-24 May, 2007.
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Konferensbidrag (refereegranskat)abstract
- Statistically based classification systems need to be trained on a large number of training data in order to classify unseen data accurately. However, it is difficult to gather enough voltage events for the training purpose from real recordings. Therefore, a classification system trained to accurately classify real voltage events, but based on synthetic training data is highly in demand. This paper therefore proposes the design of a statistically based classification system trained on synthetic data. The paper gives also the results of conducted performance tests when the proposed classification system was trained to classify seven common types of voltage events. The experiments showed an overall detection rate of 81.6%, 91.9% and 99.5% respectively.
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| 14. |
- Axelberg, Peter G.V., et al.
(författare)
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Performance Tests of a Support Vector Machine used for Classification of Voltage Disturbances
- 2006
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Ingår i: in proc. of 12th International conf. on Harmonics and Quality of Power (ICHQP 2006), Cascais, Portugal, Oct.1-5, 2006.
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Konferensbidrag (refereegranskat)abstract
- This paper proposes a novel method for classifying voltage disturbances in electric power systems by using the Support Vector Machine (SVM) method. The proposed SVM classifier is designed to classify five common types of voltage disturbances and experiments have been conducted on recorded disturbances with good classification results. The proposed SVM classifier is also shown to be robust in terms of using training data and testing data that originate from two different power networks.
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| 15. |
- Axelberg, Peter G.V. 1959, et al.
(författare)
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Support Vector Machine for Classification of Voltage Disturbances
- 2007
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Ingår i: accepted for publication in IEEE Transactions on Power Delivery. ; 22:3, s. 1297-1303, July, 2007
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Tidskriftsartikel (refereegranskat)abstract
- The Support Vector Machine (SVM) is a powerful method for statistical classification of data used in a number of different applications. However, the usefulness of the method in a commercial available system is very much dependent on whether the SVM classifier can be pre-trained from a factory since it is not realistic that the SVM classifier must be trained by the customers themselves before it can be used. We first propose a novel SVM classification system for voltage disturbances. Our aim also includes investigating the performance of the proposed SVM classifier when the voltage disturbance data used for training and testing are originated from different sources. The data used in the experiments were originated from both real disturbances recorded in two different power networks and from synthetic data. The experimental results have shown excellent accuracy in classification when training data were originated from one power network and unseen testing data from another. High accuracy was also achieved when the SVM classifier was trained on data from a real power network and test data originated from synthetic data. Slightly less accuracy was achieved when the SVM classifier was trained on synthetic data and test data were originated from the power network.
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| 16. |
- Axelberg, Peter G.V. 1959, et al.
(författare)
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Trace of flicker sources by using the quantity of flicker power
- 2007
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Ingår i: IEEE transactions on Power Delivery. ; 23:1, s. pp.465-471
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Tidskriftsartikel (refereegranskat)abstract
- Industries that produce flicker are often placed close to each other and connected to the same power grid system. This implies that the measured flicker level at the point of common coupling (PCC) is a result of contribution from a number of different flicker sources. In a mitigation process it is essential to know which one of the flicker sources is the dominant one. We propose a method to determine the flicker propagations and trace the flicker sources by using flicker power measurements. Flicker power is considered as a quantity containing both sign and magnitude. The sign determines if a flicker source is placed downstream or upstream with respect to a given monitoring point and the magnitude is used to determine the propagation of flicker power throughout the power network and to trace the dominant flicker source. This paper covers the theoretical background of flicker power and describes a novel method for calculation of flicker power that can be implemented in a power network analyzer. Also conducted simulations and a field test based on the proposed method will be described in the paper.
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| 18. |
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