| 1. |
- 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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| 2. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 3. |
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| 4. |
- Aamodt, K., et al.
(författare)
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The ALICE experiment at the CERN LHC
- 2008
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 3:S08002
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Forskningsöversikt (refereegranskat)abstract
- ALICE (A Large Ion Collider Experiment) is a general-purpose, heavy-ion detector at the CERN LHC which focuses on QCD, the strong-interaction sector of the Standard Model. It is designed to address the physics of strongly interacting matter and the quark-gluon plasma at extreme values of energy density and temperature in nucleus-nucleus collisions. Besides running with Pb ions, the physics programme includes collisions with lighter ions, lower energy running and dedicated proton-nucleus runs. ALICE will also take data with proton beams at the top LHC energy to collect reference data for the heavy-ion programme and to address several QCD topics for which ALICE is complementary to the other LHC detectors. The ALICE detector has been built by a collaboration including currently over 1000 physicists and engineers from 105 Institutes in 30 countries, Its overall dimensions are 16 x 16 x 26 m(3) with a total weight of approximately 10 000 t. The experiment consists of 18 different detector systems each with its own specific technology choice and design constraints, driven both by the physics requirements and the experimental conditions expected at LHC. The most stringent design constraint is to cope with the extreme particle multiplicity anticipated in central Pb-Pb collisions. The different subsystems were optimized to provide high-momentum resolution as well as excellent Particle Identification (PID) over a broad range in momentum, up to the highest multiplicities predicted for LHC. This will allow for comprehensive studies of hadrons, electrons, muons, and photons produced in the collision of heavy nuclei. Most detector systems are scheduled to be installed and ready for data taking by mid-2008 when the LHC is scheduled to start operation, with the exception of parts of the Photon Spectrometer (PHOS), Transition Radiation Detector (TRD) and Electro Magnetic Calorimeter (EMCal). These detectors will be completed for the high-luminosity ion run expected in 2010. This paper describes in detail the detector components as installed for the first data taking in the summer of 2008.
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| 5. |
- Bjartmar, Lisa, 1966-, et al.
(författare)
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Neuronal pentraxins mediate synaptic refinement in the developing visual system
- 2006
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Ingår i: Journal of Neuroscience. - 0270-6474 .- 1529-2401. ; 26:23, s. 6269-6281
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Tidskriftsartikel (refereegranskat)abstract
- Neuronal pentraxins (NPs) define a family of proteins that are homologous to C-reactive and acute-phase proteins in the immune system and have been hypothesized to be involved in activity-dependent synaptic plasticity. To investigate the role of NPs in vivo, we generated mice that lack one, two, or all three NPs. NP1/2 knock-out mice exhibited defects in the segregation of eye-specific retinal ganglion cell (RGC) projections to the dorsal lateral geniculate nucleus, a process that involves activity-dependent synapse formation and elimination. Retinas from mice lacking NP1 and NP2 had cholinergically driven waves of activity that occurred at a frequency similar to that of wild-type mice, but several other parameters of retinal activity were altered. RGCs cultured from these mice exhibited a significant delay in functional maturation of glutamatergic synapses. Other developmental processes, such as pathfinding of RGCs at the optic chiasm and hippocampal long-term potentiation and long-term depression, appeared normal in NP-deficient mice. These data indicate that NPs are necessary for early synaptic refinements in the mammalian retina and dorsal lateral geniculate nucleus. We speculate that NPs exert their effects through mechanisms that parallel the known role of short pentraxins outside the CNS.
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| 6. |
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| 7. |
- Ekstrand, Lisa, 1974, et al.
(författare)
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Characterization of thermally conductive epoxy nano-composites
- 2005
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Ingår i: 28th International Spring Seminar on Electronics Technology: Meeting the Challenges of Electronics Technology Progress, 2005; Wiener Neustadt; Austria; 19 May 2005 through 20 May 2005. - 9780780393240 ; 2005, s. 35-39
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Konferensbidrag (refereegranskat)abstract
- This work aims to develop an Anisotropic Conductive Adhesive (ACA) paste with improved thermal conductivity. ACA consists of a polymer based resin and conductive filler particles. We introduce an electrically insulating but thermally conductive phase into the adhesive. Nano and micro scale particles of alumina oxide, silicon carbide and carbon nanotubes are used with and without surface treatment. The thermal measurements are carried out by transient hot wire method. So far, the thermal conductivity of the epoxy has been increased with more than 100%.
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| 8. |
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| 9. |
- Larsson, Pär, et al.
(författare)
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The complete genome sequence of Francisella tularensis, the causative agent of tularemia
- 2005
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 37:2, s. 153-159
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Tidskriftsartikel (refereegranskat)abstract
- Francisella tularensis is one of the most infectious human pathogens known. In the past, both the former Soviet Union and the US had programs to develop weapons containing the bacterium. We report the complete genome sequence of a highly virulent isolate of F. tularensis (1,892,819 bp). The sequence uncovers previously uncharacterized genes encoding type IV pili, a surface polysaccharide and iron-acquisition systems. Several virulence-associated genes were located in a putative pathogenicity island, which was duplicated in the genome. More than 10% of the putative coding sequences contained insertion-deletion or substitution mutations and seemed to be deteriorating. The genome is rich in IS elements, including IS630 Tc-1 mariner family transposons, which are not expected in a prokaryote. We used a computational method for predicting metabolic pathways and found an unexpectedly high proportion of disrupted pathways, explaining the fastidious nutritional requirements of the bacterium. The loss of biosynthetic pathways indicates that F. tularensis is an obligate host-dependent bacterium in its natural life cycle. Our results have implications for our understanding of how highly virulent human pathogens evolve and will expedite strategies to combat them.
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| 10. |
- Liu, Yuanhua, 1971, et al.
(författare)
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Considering the importance of user profiles in interface design
- 2009
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Ingår i: User Interfaces. ; , s. 23-
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- User profile is a popular term widely employed during product design processes by industrial companies. Such a profile is normally intended to represent real users of a product. The ultimate purpose of a user profile is actually to help designers to recognize or learn about the real user by presenting them with a description of a real user’s attributes, for instance; the user’s gender, age, educational level, attitude, technical needs and skill level. The aim of this chapter is to provide information on the current knowledge and research about user profile issues, as well as to emphasize the importance of considering these issues in interface design. In this chapter, we mainly focus on how users’ difference in expertise affects their performance or activity in various interaction contexts. Considering the complex interaction situations in practice, novice and expert users’ interactions with medical user interfaces of different technical complexity will be analyzed as examples: one focuses on novice and expert users’ difference when interacting with simple medical interfaces, and the other focuses on differences when interacting with complex medical interfaces. Four issues will be analyzed and discussed: (1) how novice and expert users differ in terms of performance during the interaction; (2) how novice and expert users differ in the perspective of cognitive mental models during the interaction; (3) how novice and expert users should be defined in practice; and (4) what are the main differences between novice and expert users’ implications for interface design. Besides describing the effect of users’ expertise difference during the interface design process, we will also pinpoint some potential problems for the research on interface design, as well as some future challenges that academic researchers and industrial engineers should face in practice.
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| 11. |
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| 12. |
- Liu, Yuanhua, 1971, et al.
(författare)
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Learning From Experienced User in Real Life.
- 2007
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Ingår i: 39th Annual Congress of the Nordic Ergonomics Society (NES), Oct 1-3 2007, Lysekil, Sweden.
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Konferensbidrag (refereegranskat)abstract
- User-centered design (UCD) has become a popular design philosophy and process in recent years. According to this design philosophy, end users’ needs, expectations and limitations when interacting with interfaces or systems are also taken into consideration at each stage of the design process. At the practical usability evaluation stage, how to select test subjects as end users always concerns the reliability of the evaluation results. In a small pilot study, three usability evaluation methods were employed to evaluate the experienced users’ performance on a simple interface, the interface of a Whirlpool microwave oven in a lunchroom at a working-place. The purpose of the study was to investigate how well experienced users handled the interface by performing casual tasks. The aim was to obtain proposals from the evaluation results for future redesign issues. Three usability evaluation methods were used in the study; i.e. Heuristic evaluation (HE), Thinking-Aloud method (TA), and Co-discovery method (CO). Seven typical task scenarios which reflect the typical main functions in practical daily usage of a microwave oven were selected for the evaluation. Altogether sixteen staff members of the working-place participated in the empirical tests. The results from the three methods were compared to each other, in terms of prediction on problem severity, task completion time, and satisfaction. Subjective assessment on task scenarios was also made in the end of each evaluation session. Statistical T-test and Mann-Whitney test were used in the analysis of the results. The results showed that all the test subjects failed in completing several task scenarios, which promotes designers and human factors engineers to reconsider the practical usage and efficiency of multi-functionality on product design and users’ expectations on interface design. In addition, the results also implied some interesting findings and differences among the three evaluation methods, which provide useful information for selecting usability evaluation methods.
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| 13. |
- Liu, Yuanhua, 1971, et al.
(författare)
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Usability Evaluation of a GUI Prototype for a Ventilator Machine.
- 2005
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Ingår i: International Journal of Clinical Monitoring and Computing. - : Springer Science and Business Media LLC. - 0167-9945 .- 1387-1307 .- 1573-2614. ; 18:5-6, s. 365-372
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Tidskriftsartikel (refereegranskat)abstract
- Objective. Information presentation on the monitor screen of ventilator machines affects nurses' response and decision-making during ventilation treatment. The purpose of this study is to evaluate whether a new GUI (graphical user interface) prototype, the so-called circular displayprototype can make deviations easy to detect. Method. A numerical display prototype was made and used as a reference displ ay in the evaluation. Six task scenarios that involved parameter changes were selected to simulate a real situation under volume control (VC) mode during ventilation treatment. Usability tests with the two display designs were carried out in a usability laboratory. Twenty medical nursing students participated as test subjects in the usability tests. Results. The objective results showed that the graphical circular display had an advantage over the numerical display in interpreting parameter changes, but not in reducing the error rates for detecting the number of parameter changes or for forming an overall picture of the patient's situation. Furthermore, the circular display prototype did not improve the detection time. Conclusions. Although the majority of the test subjects preferred the graphical circular display, the results implied that several aspects of this prototype should be improved in a future development study.
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| 14. |
- Liu, Yuanhua, 1971, et al.
(författare)
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Usability Tests as a Benchmarking Tool - A Case Study on Complex Medical Ventilators
- 2009
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Ingår i: Contemporary Ergonomics 2009. - 9780415804332 ; , s. 182-188
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Konferensbidrag (refereegranskat)abstract
- Medical ergonomics has become an important topic in the field of ergonomics due to the increasing deficiencies in medical device design. The aim of the present study was to use usability testing as a benchmarking tool of modern and complex ventilator machines in a real hospital setting to propose future redesign ideas for a target machine – SERVO-i. A usability study was carried out at the neonatal intensive care unit (ICU) with 6 expert nurses. During the tests, an artificial lung was used to simulate the real treatment context on a neonatal patient. A number of potential usability problems were detected on SERVO-i. Using Babylog and Stephanie as two reference machines, the strengths and weaknesses of SERVO-i were identified as well. Some valuable lessons were learnt from the study, which could be used as guidance for the choice of test subjects and control of tests in real life human-machine working environments.
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| 15. |
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| 16. |
- Pasche, Boris, et al.
(författare)
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Somatic acquisition and signaling of TGFBR1*6A in cancer
- 2005
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Ingår i: Journal of the American Medical Association (JAMA). - : American Medical Association (AMA). - 0098-7484 .- 1538-3598. ; 294:13, s. 1634-1646
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Tidskriftsartikel (refereegranskat)abstract
- Context: TGFBR1*6A is a common polymorphism of the type I transforming growth factor 0 receptor (TGFBR1). Epidemiological studies suggest that TGFBR1*6A may act as a tumor susceptibility allele. How TGFBR1*6A contributes to cancer development is largely unknown.. Objectives: To determine whether TGFBR1*6A is somatically acquired by primary tumors and metastases during cancer development and whether the 3-amino acid deletion that differentiates TGFBR1*6A from TGFBR1 is part of the mature receptor or part of the signal sequence and to investigate TGFBR1*6A signaling in cancer cells. Design, Setting, and Patients: Tumor And germline tissues from 531 patients with a diagnosis of head and neck, colorectal, or breast cancer recruited from 3 centers in the United States and from 1 center in Spain from June 1, 1994, through June 30, 2004, In vitro translation assays, MCF-7 breast cancer cells stably transfected with TGFBR1*6A, TGFBR1, or the vector alone, DLD-1 colorectal cancer cells that endogenously carry TGFBR1*6A, and SW48 colorectal cancer cells that do not carry TGFBR1*6A. Main Outcome Measures: TGFBR1*6A somatic acquisition in cancer. Determination of the amino terminus of the mature TGFBR1*6A and TGFBR1 receptors. Determination of TGF-beta-dependent cell proliferation. Results: TGFBR1*6A was somatically acquired in 13 of 44 (29.5%) colorectal cancer metastases, in 4 of 157 (2.5%) of colorectal tumors, in 4 of 226 (1.8%) head and neck primary tumors, and in none of the 104 patients with breast cancer. TGFBR1*6A somatic acquisition is not associated with loss of heterozygosity, microsatellite instability, or a mutator phenotype. The signal sequences of TGFBR1 and TGFBR1*6A are cleaved at the same site resulting in identical mature receptors. TGFBR1*6A may switch TGF-beta growth inhibitory signals into growth stimulatory signals in MCF-7 breast cancer cells and in DLD-1 colorectal cancer cells. Conclusions: TGFBR1*6A is somatically acquired in 29.5% of liver metastases from colorectal cancer and may bestow cancer cells with a growth advantage in the presence of TGF-beta. The functional consequences of this conversion appear to be mediated by the TGFBR1*6A signal sequence rather than by the mature receptor. The results highlight a new facet of TGF-beta signaling in cancer and suggest that TGFBR1*6A may represent a potential therapeutic target in cancer.
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