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- Adam, J., et al.
(författare)
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Centrality dependence of high-p(T) D meson suppression in Pb-Pb collisions at root s(NN)=2.76 TeV
- 2015
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear modification factor, R-AA, of the prompt charmed mesons D-0, D+ and D*+, and their antiparticles, was measured with the ALICE detector in Pb-Pb collisions at a centre-of-mass energy root s(NN) = 2 : 76 TeV in two transverse momentum intervals, 5 < p(T) < 8 GeV/c and 8 < p(T) < 16 GeV/c, and in six collision centrality classes. The R-AA shows a maximum suppression of a factor of 5{6 in the 10% most central collisions. The suppression and its centrality dependence are compatible within uncertainties with those of charged pions. A comparison with the R-AA of non-prompt J/psi from B meson decays, measured by the CMS Collaboration, hints at a larger suppression of D mesons in the most central collisions.
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| 5. |
- Miller, R, et al.
(författare)
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On the Relation Between the (Censored) Shifted Wald and the Wiener Distribution as Measurement Models for Choice Response Times
- 2018
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Ingår i: Applied psychological measurement. - : SAGE Publications. - 1552-3497 .- 0146-6216. ; 42:2, s. 116-135
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Tidskriftsartikel (refereegranskat)abstract
- Inferring processes or constructs from performance data is a major hallmark of cognitive psychometrics. Particularly, diffusion modeling of response times (RTs) from correct and erroneous responses using the Wiener distribution has become a popular measurement tool because it provides a set of psychologically interpretable parameters. However, an important precondition to identify all of these parameters is a sufficient number of RTs from erroneous responses. In the present article, we show by simulation that the parameters of the Wiener distribution can be recovered from tasks yielding very high or even perfect response accuracies using the shifted Wald distribution. Specifically, we argue that error RTs can be modeled as correct RTs that have undergone censoring by using techniques from parametric survival analysis. We illustrate our reasoning by fitting the Wiener and (censored) shifted Wald distribution to RTs from six participants who completed a Go/No-go task. In accordance with our simulations, diffusion modeling using the Wiener and the shifted Wald distribution yielded identical parameter estimates when the number of erroneous responses was predicted to be low. Moreover, the modeling of error RTs as censored correct RTs substantially improved the recovery of these diffusion parameters when premature trial timeout was introduced to increase the number of omission errors. Thus, the censored shifted Wald distribution provides a suitable means for diffusion modeling in situations when the Wiener distribution cannot be fitted without parametric constraints.
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- Enge, S., et al.
(författare)
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A REVIEW OF HERBIVORE EFFECTS ON SEAWEED INVASIONS
- 2017
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Ingår i: OCEANOGRAPHY AND MARINE BIOLOGY: AN ANNUAL REVIEW, VOL 55. - BOCA RATON : Taylor and Francis. - 9781138197862 - 9781351987592 ; , s. 421-440
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Almost 300 non-native seaweeds are identified worldwide and an increasing number of these are classified as invasive with potential negative effects on the diversity and functioning of native ecosystems. Marine herbivores affect seaweed biomass and community structure in marine habitats across the globe. Consequently, herbivore-seaweed interactions are expected to be important for the establishment and invasion success of non-native seaweeds. To synthesize current knowledge of consumer effects on non-native seaweeds, we performed a meta-analysis on feeding preferences of native herbivores for non-native versus native seaweeds. Data were included from 35 studies, published from 1992-2015 and comprising 18 non-native seaweeds. Results showed that overall, native herbivores tended to prefer to feed on native rather than non-native seaweeds. Preferences were, however, variable across studies with significant differences between taxonomic and functional groups of seaweeds. In particular, filamentous red non-native seaweeds were of low palatability to native herbivores. No general feeding preferences were apparent between natives and non-natives for brown and green seaweeds, or for leathery and corticated seaweeds. In addition, we reviewed the existing studies on the effects of consumers on the performance of native and non-native seaweeds in invaded communities. This indicated that non-native seaweeds performed better than their native competitors in the presence of grazers, but in many cases had superior competitive abilities also in the absence of herbivory. To achieve a comprehensive evaluation of consumers' role in seaweed invasion success, future research should have a larger focus on manipulative community experiments, ideally on time scales that include seasonal changes and complete life cycles of the seaweeds.
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| 9. |
- Jager, R, et al.
(författare)
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Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
- 2015
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6, s. 6178-
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Tidskriftsartikel (refereegranskat)abstract
- Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer–promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.
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- Jolma, A, et al.
(författare)
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Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
- 2010
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 20:6, s. 861-873
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Tidskriftsartikel (refereegranskat)abstract
- The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the ∼1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers.
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| 17. |
- Zhou, K., et al.
(författare)
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An overlooked subset of Cx3cr1(wt/wt) microglia in the Cx3cr1(CreER-Eyfp/wt) mouse has a repopulation advantage over Cx3cr1(CreER-Eyfp/wt) microglia following microglial depletion
- 2022
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Ingår i: Journal of Neuroinflammation. - : Springer Science and Business Media LLC. - 1742-2094. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Fluorescent reporter labeling and promoter-driven Cre-recombinant technologies have facilitated cellular investigations of physiological and pathological processes, including the widespread use of the Cx3cr1(CreER-Eyfp/wt) mouse strain for studies of microglia. Methods Immunohistochemistry, Flow Cytometry, RNA sequencing and whole-genome sequencing were used to identify the subpopulation of microglia in Cx3cr1(CreER-Eyfp/wt) mouse brains. Genetically mediated microglia depletion using Cx3cr1(CreER-Eyfp/wt)Rosa26(DTA/wt) mice and CSF1 receptor inhibitor PLX3397 were used to deplete microglia. Primary microglia proliferation and migration assay were used for in vitro studies. Results We unexpectedly identified a subpopulation of microglia devoid of genetic modification, exhibiting higher Cx3cr1 and CX3CR1 expression than Cx3cr1(CreER-Eyfp/wt)Cre(+)Eyfp(+) microglia in Cx3cr1(CreER-Eyfp/wt) mouse brains, thus termed Cx3cr1(high)Cre(-)Eyfp(-) microglia. This subpopulation constituted less than 1% of all microglia under homeostatic conditions, but after Cre-driven DTA-mediated microglial depletion, Cx3cr1(high)Cre(-)Eyfp(-) microglia escaped depletion and proliferated extensively, eventually occupying one-third of the total microglial pool. We further demonstrated that the Cx3cr1(high)Cre(-)Eyfp(-) microglia had lost their genetic heterozygosity and become homozygous for wild-type Cx3cr1. Therefore, Cx3cr1(high)Cre(-)Eyfp(-) microglia are Cx3cr1(wt/wt)Cre(-)Eyfp(-). Finally, we demonstrated that CX3CL1-CX3CR1 signaling regulates microglial repopulation both in vivo and in vitro. Conclusions Our results raise a cautionary note regarding the use of Cx3cr1(CreER-Eyfp/wt) mouse strains, particularly when interpreting the results of fate mapping, and microglial depletion and repopulation studies.
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