1,007 research outputs found
De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes
In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences
Charge dependent azimuthal correlations in Pb--Pb collisions at TeV
Separation of charges along the extreme magnetic field created in non-central
relativistic heavy--ion collisions is predicted to be a signature of local
parity violation in strong interactions. We report on results for charge
dependent two particle azimuthal correlations with respect to the reaction
plane for Pb--Pb collisions at TeV recorded in 2010 with
ALICE at the LHC. The results are compared with measurements at RHIC energies
and against currently available model predictions for LHC. Systematic studies
of possible background effects including comparison with conventional
(parity-even) correlations simulated with Monte Carlo event generators of
heavy--ion collisions are also presented.Comment: Published in the proceedings of "Quark Matter 2011", Annecy-Franc
Ultra-wideband radar for simultaneous and unobtrusive monitoring of respiratory and heart rates in early childhood:A Deep Transfer Learning Approach
Unobtrusive monitoring of children’s heart rate (HR) and respiratory rate (RR) can be valuable for promoting the early detection of potential health issues, improving communication with healthcare providers and reducing unnecessary hospital visits. A promising solution for wireless vital sign monitoring is radar technology. This paper presents a novel approach for the simultaneous estimation of children’s RR and HR utilizing ultra-wideband (UWB) radar using a deep transfer learning algorithm in a cohort of 55 children. The HR and RR are calculated by processing radar signals via spectrogram from time epochs of 10 s (25 sample length of hamming window with 90% overlap) and then transforming the resultant representation into 2-dimensional images. These images were fed into a pre-trained Visual Geometry Group-16 (VGG-16) model (trained on ImageNet dataset), with weights of five added layers fine-tuned using the proposed data. The prediction on the test data achieved a mean absolute error (MAE) of 7.3 beats per minute (BPM < 6.5% of average HR) and 2.63 breaths per minute (BPM < 7% of average RR). We also achieved a significant Pearson’s correlation of 77% and 81% between true and extracted for HR and RR, respectively. HR and RR samples are extracted every 10 s.</p
Measurement of an excess in the yield of J/ at very low in Pb-Pb collisions at = 2.76 TeV
We report on the first measurement of an excess in the yield of J/ at
very low transverse momentum ( GeV/) in peripheral hadronic
Pb-Pb collisions at = 2.76 TeV, performed by ALICE at the
CERN LHC. Remarkably, the measured nuclear modification factor of J/ in
the rapidity range reaches about 7 (2) in the range 0-0.3
GeV/ in the 70-90% (50-70%) centrality class. The J/ production cross
section associated with the observed excess is obtained under the hypothesis
that coherent photoproduction of J/ is the underlying physics mechanism.
If confirmed, the observation of J/ coherent photoproduction in Pb-Pb
collisions at impact parameters smaller than twice the nuclear radius opens new
theoretical and experimental challenges and opportunities. In particular,
coherent photoproduction accompanying hadronic collisions may provide insight
into the dynamics of photoproduction and nuclear reactions, as well as become a
novel probe of the Quark-Gluon Plasma.Comment: 18 pages, 3 captioned figures, 1 table, authors from page 13,
published version, figures at
http://aliceinfo.cern.ch/ArtSubmission/node/191
Identification of tumour-associated and germ line p53 mutations in canine mammary cancer
Mutations of the tumour suppressor p53 gene are found in a number of spontaneous canine cancers and may contribute to increased cytogenetic alterations and tumour formation. Using reverse transcription and DNA amplification, we isolated p53 cDNA from normal and tumour tissue of ten canine mammary cancer patients. DNA sequencing identified p53 mutations in three of the ten patients. These included tumour-associated p53 gene mutations within exons 2 and 5 and a germ line deletion of exons 3 to 7. These results support a role for p53 inactivation in canine mammary tumour formation and breed predisposition to cancer. Such information could prove invaluable in the successful outbreeding of inherited predisposition to cancer in the dog. A putative polymorphism was also identified at codon 69 in exon 4 and we discuss the possibility that similar polymorphisms may be associated with human breast cancer. © 1999 Cancer Research Campaig
Measurement of pion, kaon and proton production in proton-proton collisions at TeV
The measurement of primary , K, p and
production at mid-rapidity ( 0.5) in proton-proton collisions at
TeV performed with ALICE (A Large Ion Collider Experiment) at
the Large Hadron Collider (LHC) is reported. Particle identification is
performed using the specific ionization energy loss and time-of-flight
information, the ring-imaging Cherenkov technique and the kink-topology
identification of weak decays of charged kaons. Transverse momentum spectra are
measured from 0.1 up to 3 GeV/ for pions, from 0.2 up to 6 GeV/ for kaons
and from 0.3 up to 6 GeV/ for protons. The measured spectra and particle
ratios are compared with QCD-inspired models, tuned to reproduce also the
earlier measurements performed at the LHC. Furthermore, the integrated particle
yields and ratios as well as the average transverse momenta are compared with
results at lower collision energies.Comment: 33 pages, 19 captioned figures, 3 tables, authors from page 28,
published version, figures at
http://aliceinfo.cern.ch/ArtSubmission/node/156
Detection of mutations within exons 4 to 8 of the p53 tumor suppressor gene in canine mammary glands
IL-33 Induces IL-9 Production in Human CD4+ T Cells and Basophils
IL-33, an IL-1 family member and ligand for the IL-1 receptor-related protein ST2, has been associated with induction of Th2 cytokines such as IL-4, IL-5, and IL-13. Here, we report that IL-33 can initiate IL-9 protein secretion in vitro in human CD4+ T cells and basophils isolated from peripheral blood. TGF-β has been described as a critical factor for IL-9 induction in Th2 cells; however, we found that TGF-β also induces co-production of IL-9 in purified, naïve (>99%) CD4+CD45RA+CD45RO−CD25− T cells differentiated towards a Th1 profile. Subsequently, it was demonstrated that TGF-β is important, although not an absolute requirement, for IL-9 production in CD4+ T cells. IL-9 production by purified (>95%) human basophils, cultured for 24 h with IL-3 or IL-33, was found, with a strong synergy between the two, likely to be explained by the IL-3 upregulated ST2 expression. Collectively, these data indicate that barrier functioning cells are important for the regulation of IL-9 production by immune cells in inflamed tissue
Microbial Community Analysis of a Methane-Producing Biocathode in a Bioelectrochemical System
A methane-producing biocathode that converts CO2 into methane was studied electrochemically and microbiologically. The biocathode produced methane at a maximum rate of 5.1 L CH4/m2 projected cathode per day (1.6 A/m2) at −0.7 V versus NHE cathode potential and 3.0 L CH4/m2 projected cathode per day (0.9 A/m2) at −0.6 V versus NHE cathode potential. The microbial community at the biocathode was dominated by three phylotypes of Archaea and six phylotypes of bacteria. The Archaeal phylotypes were most closely related to Methanobacterium palustre and Methanobacterium aarhusense. Besides methanogenic Archaea, bacteria seemed to be associated with methane production, producing hydrogen as an intermediate. Biomass density varied greatly with part of the carbon electrode covered with a dense biofilm, while only clusters of cells were found on other parts. Based on our results, we discuss how inoculum enrichment and changing operational conditions may help to increase biomass density and to select for microorganisms that produce methane
Multiplicity dependence of jet-like two-particle correlations in p-Pb collisions at = 5.02 TeV
Two-particle angular correlations between unidentified charged trigger and
associated particles are measured by the ALICE detector in p-Pb collisions at a
nucleon-nucleon centre-of-mass energy of 5.02 TeV. The transverse-momentum
range 0.7 5.0 GeV/ is examined,
to include correlations induced by jets originating from low
momen\-tum-transfer scatterings (minijets). The correlations expressed as
associated yield per trigger particle are obtained in the pseudorapidity range
. The near-side long-range pseudorapidity correlations observed in
high-multiplicity p-Pb collisions are subtracted from both near-side
short-range and away-side correlations in order to remove the non-jet-like
components. The yields in the jet-like peaks are found to be invariant with
event multiplicity with the exception of events with low multiplicity. This
invariance is consistent with the particles being produced via the incoherent
fragmentation of multiple parton--parton scatterings, while the yield related
to the previously observed ridge structures is not jet-related. The number of
uncorrelated sources of particle production is found to increase linearly with
multiplicity, suggesting no saturation of the number of multi-parton
interactions even in the highest multiplicity p-Pb collisions. Further, the
number scales in the intermediate multiplicity region with the number of binary
nucleon-nucleon collisions estimated with a Glauber Monte-Carlo simulation.Comment: 23 pages, 6 captioned figures, 1 table, authors from page 17,
published version, figures at
http://aliceinfo.cern.ch/ArtSubmission/node/161
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