| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are 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 monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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| 4. |
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| 5. |
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| 6. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 7. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 8. |
- Lochner, Michelle, et al.
(författare)
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Optimizing the LSST Observing Strategy for Dark Energy Science : DESC Recommendations for the Wide-Fast-Deep Survey
- 2018
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Cosmology is one of the four science pillars of LSST, which promises to be transformative for our understanding of dark energy and dark matter. The LSST Dark Energy Science Collaboration (DESC) has been tasked with deriving constraints on cosmological parameters from LSST data. Each of the cosmological probes for LSST is heavily impacted by the choice of observing strategy. This white paper is written by the LSST DESC Observing Strategy Task Force (OSTF), which represents the entire collaboration, and aims to make recommendations on observing strategy that will benefit all cosmological analyses with LSST. It is accompanied by the DESC DDF (Deep Drilling Fields) white paper (Scolnic et al.). We use a variety of metrics to understand the effects of the observing strategy on measurements of weak lensing, large-scale structure, clusters, photometric redshifts, supernovae, strong lensing and kilonovae. In order to reduce systematic uncertainties, we conclude that the current baseline observing strategy needs to be significantly modified to result in the best possible cosmological constraints. We provide some key recommendations: moving the WFD (Wide-Fast-Deep) footprint to avoid regions of high extinction, taking visit pairs in different filters, changing the 2x15s snaps to a single exposure to improve efficiency, focusing on strategies that reduce long gaps (>15 days) between observations, and prioritizing spatial uniformity at several intervals during the 10-year survey.
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| 9. |
- Patterson, Nick, et al.
(författare)
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Large-scale migration into Britain during the Middle to Late Bronze Age
- 2022
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; , s. 588-594
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Tidskriftsartikel (refereegranskat)abstract
- Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age1. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain's independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.
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| 10. |
- Ay, Hakan, et al.
(författare)
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Pathogenic Ischemic Stroke Phenotypes in the NINDS-Stroke Genetics Network
- 2014
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Ingår i: Stroke. - 0039-2499. ; 45:12, s. 3589-3596
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND PURPOSE: NINDS (National Institute of Neurological Disorders and Stroke)-SiGN (Stroke Genetics Network) is an international consortium of ischemic stroke studies that aims to generate high-quality phenotype data to identify the genetic basis of pathogenic stroke subtypes. This analysis characterizes the etiopathogenetic basis of ischemic stroke and reliability of stroke classification in the consortium. METHODS: Fifty-two trained and certified adjudicators determined both phenotypic (abnormal test findings categorized in major pathogenic groups without weighting toward the most likely cause) and causative ischemic stroke subtypes in 16954 subjects with imaging-confirmed ischemic stroke from 12 US studies and 11 studies from 8 European countries using the web-based Causative Classification of Stroke System. Classification reliability was assessed with blinded readjudication of 1509 randomly selected cases. RESULTS: The distribution of pathogenic categories varied by study, age, sex, and race (P<0.001 for each). Overall, only 40% to 54% of cases with a given major ischemic stroke pathogenesis (phenotypic subtype) were classified into the same final causative category with high confidence. There was good agreement for both causative (κ 0.72; 95% confidence interval, 0.69-0.75) and phenotypic classifications (κ 0.73; 95% confidence interval, 0.70-0.75). CONCLUSIONS: This study demonstrates that pathogenic subtypes can be determined with good reliability in studies that include investigators with different expertise and background, institutions with different stroke evaluation protocols and geographic location, and patient populations with different epidemiological characteristics. The discordance between phenotypic and causative stroke subtypes highlights the fact that the presence of an abnormality in a patient with stroke does not necessarily mean that it is the cause of stroke.
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| 11. |
- Barnett, R., et al.
(författare)
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Euclid preparation V. Predicted yield of redshift 7 < z < 9 quasars from the wide survey
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 631
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Tidskriftsartikel (refereegranskat)abstract
- We provide predictions of the yield of 7 < z < 9 quasars from the Euclid wide survey, updating the calculation presented in the Euclid Red Book in several ways. We account for revisions to the Euclid near-infrared filter wavelengths; we adopt steeper rates of decline of the quasar luminosity function (QLF; Phi) with redshift, Phi proportional to 10(k(z-6)), k = 0:72, and a further steeper rate of decline, k = 0:92; we use better models of the contaminating populations (MLT dwarfs and compact early-type galaxies); and we make use of an improved Bayesian selection method, compared to the colour cuts used for the Red Book calculation, allowing the identification of fainter quasars, down to J(AB) similar to 23. Quasars at z > 8 may be selected from Euclid OYJH photometry alone, but selection over the redshift interval 7 < z < 8 is greatly improved by the addition of z-band data from, e.g., Pan-STARRS and LSST. We calculate predicted quasar yields for the assumed values of the rate of decline of the QLF beyond z = 6. If the decline of the QLF accelerates beyond z = 6, with k = 0.92, Euclid should nevertheless find over 100 quasars with 7.0 < z < 7.5, and similar to 25 quasars beyond the current record of z = 7.5, including similar to 8 beyond z = 8.0. The first Euclid quasars at z > 7.5 should be found in the DR1 data release, expected in 2024. It will be possible to determine the bright-end slope of the QLF, 7 < z < 8, M-1450 < 25, using 8m class telescopes to confirm candidates, but follow-up with JWST or E-ELT will be required to measure the faint-end slope. Contamination of the candidate lists is predicted to be modest even at J(AB) similar to 23. The precision with which k can be determined over 7 < z < 8 depends on the value of k, but assuming k = 0.72 it can be measured to a 1 sigma uncertainty of 0.07.
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| 12. |
- Di Baldassarre, Giuliano, et al.
(författare)
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An integrative research framework to unravel the interplay of natural hazards and vulnerabilities
- 2018
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Ingår i: Earth's Future. - : John Wiley & Sons. - 2328-4277. ; 6:3, s. 305-310
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Tidskriftsartikel (refereegranskat)abstract
- Climate change, globalization, urbanization, social isolation, and increased interconnectednessbetween physical, human, and technological systems pose major challenges to disaster risk reduction(DRR). Subsequently, economic losses caused by natural hazards are increasing in many regions of theworld, despite scientific progress, persistent policy action, and international cooperation. We argue thatthese dramatic figures call for novel scientific approaches and new types of data collection to integratethe two main approaches that still dominate the science underpinning DRR: the hazard paradigm and thevulnerability paradigm. Building from these two approaches, here we propose a research framework thatspecifies the scope of enquiry, concepts, and general relations among phenomena. We then discuss theessential steps to advance systematic empirical research and evidence-based DRR policy action.
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| 13. |
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| 14. |
- Jackson, Marie, et al.
(författare)
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Time-lapse characterization of hydrothermal seawater and microbial interactions with basaltic tephra at Surtsey volcano
- 2015
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Ingår i: Scientific Drilling. - Copernicus Publications on behalf of the IODP and the ICDP : Copernicus GmbH. - 1816-8957 .- 1816-3459. ; 20, s. 51-58
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Tidskriftsartikel (refereegranskat)abstract
- A new International Continental Drilling Program (ICDP) project will drill through the 50-yearold edifice of Surtsey Volcano, the youngest of the Vestmannaeyjar Islands along the south coast of Iceland, to perform interdisciplinary time-lapse investigations of hydrothermal and microbial interactions with basaltic tephra. The volcano, created in 1963–1967 by submarine and subaerial basaltic eruptions, was first drilled in 1979. In October 2014, a workshop funded by the ICDP convened 24 scientists from 10 countries for 3 and a half days on Heimaey Island to develop scientific objectives, site the drill holes, and organize logistical support. Representatives of the Surtsey Research Society and Environment Agency of Iceland also participated. Scientific themes focus on further determinations of the structure and eruptive processes of the type locality of Surtseyan volcanism, descriptions of changes in fluid geochemistry and microbial colonization of the subterrestrial deposits since drilling 35 years ago, and monitoring the evolution of hydrothermal and biological processes within the tephra deposits far into the future through the installation of a Surtsey subsurface observatory. The tephra deposits provide a geologic analog for developing specialty concretes with pyroclastic rock and evaluating their long-term performance under diverse hydrothermal conditions.
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| 15. |
- Marques, Carolina A., et al.
(författare)
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Spin-orbit coupling induced Van Hove singularity in proximity to a Lifshitz transition in Sr4Ru3O10
- 2024
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Ingår i: npj Quantum Materials. - 2397-4648. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Van Hove singularities (VHss) in the vicinity of the Fermi energy often play a dramatic role in the physics of strongly correlated electron materials. The divergence of the density of states generated by VHss can trigger the emergence of phases such as superconductivity, ferromagnetism, metamagnetism, and density wave orders. A detailed understanding of the electronic structure of these VHss is therefore essential for an accurate description of such instabilities. Here, we study the low-energy electronic structure of the trilayer strontium ruthenate Sr4Ru3O10, identifying a rich hierarchy of VHss using angle-resolved photoemission spectroscopy and millikelvin scanning tunneling microscopy. Comparison of k-resolved electron spectroscopy and quasiparticle interference allows us to determine the structure of the VHss and demonstrate the crucial role of spin-orbit coupling in shaping them. We use this to develop a minimal model from which we identify a mechanism for driving a field-induced Lifshitz transition in ferromagnetic metals.
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| 16. |
- McMahon, Colin J, et al.
(författare)
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Paediatric and adult congenital cardiology education and training in Europe.
- 2022
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Ingår i: Cardiology in the young. - 1467-1107. ; 32:12, s. 1966-1983
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Tidskriftsartikel (refereegranskat)abstract
- Limited data exist on training of European paediatric and adult congenital cardiologists.A structured and approved questionnaire was circulated to national delegates of Association for European Paediatric and Congenital Cardiology in 33 European countries.Delegates from 30 countries (91%) responded. Paediatric cardiology was not recognised as a distinct speciality by the respective ministry of Health in seven countries (23%). Twenty countries (67%) have formally accredited paediatric cardiology training programmes, seven (23%) have substantial informal (not accredited or certified) training, and three (10%) have very limited or no programme. Twenty-two countries have a curriculum. Twelve countries have a national training director. There was one paediatric cardiology centre per 2.66 million population (range 0.87-9.64 million), one cardiac surgical centre per 4.73 million population (range 1.63-10.72 million), and one training centre per 4.29 million population (range 1.63-10.72 million population). The median number of paediatric cardiology fellows per training programme was 4 (range 1-17), and duration of training was 3 years (range 2-5 years). An exit examination in paediatric cardiology was conducted in 16 countries (53%) and certification provided by 20 countries (67%). Paediatric cardiologist number is affected by gross domestic product (R2 = 0.41).Training varies markedly across European countries. Although formal fellowship programmes exist in many countries, several countries have informal training or no training. Only a minority of countries provide both exit examination and certification. Harmonisation of training and standardisation of exit examination and certification could reduce variation in training thereby promoting high-quality care by European congenital cardiologists.
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| 17. |
- Setlur, Sunita R., et al.
(författare)
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Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer
- 2008
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Ingår i: Journal of the National Cancer Institute. - Oxford : Oxford University Press. - 0027-8874 .- 1460-2105. ; 100:11, s. 815-825
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The majority of prostate cancers harbor gene fusions of the 5'-untranslated region of the androgen-regulated transmembrane protease serine 2 (TMPRSS2) promoter with erythroblast transformation-specific transcription factor family members. The common fusion between TMPRESS2 and v-ets erythroblastosis virus E26 oncogene homolog (avian) (ERG) is associated with a more aggressive clinical phenotype, implying the existence of a distinct subclass of prostate cancer defined by this fusion. METHODS: We used complementary DNA-mediated annealing, selection, ligation, and extension to determine the expression profiles of 6144 transcriptionally informative genes in archived biopsy samples from 455 prostate cancer patients in the Swedish Watchful Waiting cohort (1987-1999) and the United States-based Physicians(') Health Study cohort (1983-2003). A gene expression signature for prostate cancers with the TMPRSS2-ERG fusion was determined using partitioning and classification models and used in computational functional analysis. Cell proliferation and TMPRSS2-ERG expression in androgen receptor-negative (NCI-H660) prostate cancer cells after treatment with vehicle or estrogenic compounds were assessed by viability assays and quantitative polymerase chain reaction, respectively. All statistical tests were two-sided. RESULTS: We identified an 87-gene expression signature that distinguishes TMPRSS2-ERG fusion prostate cancer as a discrete molecular entity (area under the curve = 0.80, 95% confidence interval [CI] = 0.792 to 0.81; P < .001). Computational analysis suggested that this fusion signature was associated with estrogen receptor (ER) signaling. Viability of NCI-H660 cells decreased after treatment with estrogen (viability normalized to day 0, estrogen vs vehicle at day 8, mean = 2.04 vs 3.40, difference = 1.36, 95% CI = 1.12 to 1.62) or ERbeta agonist (ERbeta agonist vs vehicle at day 8, mean = 1.86 vs 3.40, difference = 1.54, 95% CI = 1.39 to 1.69) but increased after ERalpha agonist treatment (ERalpha agonist vs vehicle at day 8, mean = 4.36 vs 3.40, difference = 0.96, 95% CI = 0.68 to 1.23). Similarly, expression of TMPRSS2-ERG decreased after ERbeta agonist treatment (fold change over internal control, ERbeta agonist vs vehicle at 24 hours, NCI-H660, mean = 0.57- vs 1.0-fold, difference = 0.43-fold, 95% CI = 0.29- to 0.57-fold) and increased after ERalpha agonist treatment (ERalpha agonist vs vehicle at 24 hours, mean = 5.63- vs 1.0-fold, difference = 4.63-fold, 95% CI = 4.34- to 4.92-fold). CONCLUSIONS: TMPRSS2-ERG fusion prostate cancer is a distinct molecular subclass. TMPRSS2-ERG expression is regulated by a novel ER-dependent mechanism.
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| 18. |
- Sigl, Michael, et al.
(författare)
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The WAIS Divide deep ice core WD2014 chronology - Part 2 : Annual-layer counting (0-31 ka BP)
- 2016
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Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 12:3, s. 769-786
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Tidskriftsartikel (refereegranskat)abstract
- We present the WD2014 chronology for the upper part (0-2850 m; 31.2 ka BP) of the West Antarctic Ice Sheet (WAIS) Divide (WD) ice core. The chronology is based on counting of annual layers observed in the chemical, dust and electrical conductivity records. These layers are caused by seasonal changes in the source, transport, and deposition of aerosols. The measurements were interpreted manually and with the aid of two automated methods. We validated the chronology by comparing to two high-accuracy, absolutely dated chronologies. For the Holocene, the cosmogenic isotope records of 10Be from WAIS Divide and 14C for IntCal13 demonstrated that WD2014 was consistently accurate to better than 0.5 % of the age. For the glacial period, comparisons to the Hulu Cave chronology demonstrated that WD2014 had an accuracy of better than 1 % of the age at three abrupt climate change events between 27 and 31 ka. WD2014 has consistently younger ages than Greenland ice core chronologies during most of the Holocene. For the Younger Dryas-Preboreal transition (11.595 ka; 24 years younger) and the Bølling-Allerød Warming (14.621 ka; 7 years younger), WD2014 ages are within the combined uncertainties of the timescales. Given its high accuracy, WD2014 can become a reference chronology for the Southern Hemisphere, with synchronization to other chronologies feasible using high-quality proxies of volcanism, solar activity, atmospheric mineral dust, and atmospheric methane concentrations.
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| 19. |
- Sims, Mark R., et al.
(författare)
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Development status of life marker chip for ExoMars
- 2012
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Ingår i: Planetary and Space Science. - : Elsevier BV. - 0032-0633 .- 1873-5088. ; 72:1, s. 129-137
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Tidskriftsartikel (refereegranskat)abstract
- The Life Marker Chip (LMC) is one of the instruments being developed for possible flight on the 2018 ExoMars mission. The instrument uses solvents to extract organic compounds from samples of martian regolith and to transfer the extracts to dedicated detectors based around the use of antibodies. The scientific aims of the instrument are to detect organics in the form of biomarkers that might be associated with extinct life, extant life or abiotic sources of organics. The instrument relies on a novel surfactant-based solvent system and bespoke, commercial and research-developed antibodies against a number of distinct biomarkers or molecular types. The LMC comprises of a number of subsystems designed to accept up to four discrete samples of martian regolith or crushed rock, implement the solvent extraction, perform microfluidic-based multiplexed antibody-assays for biomarkers and other targets, optically detect the fluorescent output of the assays, control the internal instrument pressure and temperature, in addition to the associated instrument control electronics and software. The principle of operation, the design and the instrument development status as of December 2011 are reported here. The instrument principle can be extended to other configurations and missions as needed.
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| 20. |
- Tomlins, Scott A., et al.
(författare)
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The role of SPINK1 in ETS rearrangement-negative prostate cancers
- 2008
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Ingår i: Cancer Cell. - Amsterdam : Elsevier. - 1535-6108 .- 1878-3686. ; 13:6, s. 519-28
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Tidskriftsartikel (refereegranskat)abstract
- ETS gene fusions have been characterized in a majority of prostate cancers; however, the key molecular alterations in ETS-negative cancers are unclear. Here we used an outlier meta-analysis (meta-COPA) to identify SPINK1 outlier expression exclusively in a subset of ETS rearrangement-negative cancers ( approximately 10% of total cases). We validated the mutual exclusivity of SPINK1 expression and ETS fusion status, demonstrated that SPINK1 outlier expression can be detected noninvasively in urine, and observed that SPINK1 outlier expression is an independent predictor of biochemical recurrence after resection. We identified the aggressive 22RV1 cell line as a SPINK1 outlier expression model and demonstrate that SPINK1 knockdown in 22RV1 attenuates invasion, suggesting a functional role in ETS rearrangement-negative prostate cancers.
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| 21. |
- Yusuf, D, et al.
(författare)
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The transcription factor encyclopedia
- 2012
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906. ; 13:3, s. R24-
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Tidskriftsartikel (refereegranskat)
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