2,416 research outputs found
Globally increased ultraconserved noncoding RNA expression in pancreatic adenocarcinoma
This is the final version of the article. Available from the publisher via the DOI in this record.Transcribed ultraconserved regions (T-UCRs) are a class of non-coding RNAs with 100% sequence conservation among human, rat and mouse genomes. T-UCRs are differentially expressed in several cancers, however their expression in pancreatic adenocarcinoma (PDAC) has not been studied. We used a qPCR array to profile all 481 T-UCRs in pancreatic cancer specimens, pancreatic cancer cell lines, during experimental pancreatic desmoplasia and in the pancreases of P48Cre/wt; KrasLSL-G12D/wt mice. Fourteen, 57 and 29% of the detectable T-UCRs were differentially expressed in the cell lines, human tumors and transgenic mouse pancreases, respectively. The vast majority of the differentially expressed T-UCRs had increased expression in the cancer. T-UCRs were monitored using an in vitro model of the desmoplastic reaction. Twenty-five % of the expressed T-UCRs were increased in the HPDE cells cultured on PANC-1 cellular matrix. UC.190, UC.233 and UC.270 were increased in all three human data sets. siRNA knockdown of each of these three T-UCRs reduced the proliferation of MIA PaCa-2 cells up to 60%. The expression pattern among many T-UCRs in the human and mouse pancreases closely correlated with one another, suggesting that groups of T-UCRs are co-activated in PDAC. Successful knockout of the transcription factor EGR1 in PANC-1 cells caused a reduction in the expression of a subset of T-UCRs suggesting that EGR1 may control T-UCR expression in PDAC. We report a global increase in expression of T-UCRs in both human and mouse PDAC. Commonalties in their expression pattern suggest a similar mechanism of transcriptional upregulation for T-UCRs in PDAC.Supported by grants R21/R33CA114304 and
U01CA111294. G.A.C. is supported as a Fellow at The
University of Texas MD Anderson Research Trust, as a
University of Texas System Regents Research Scholar
and by the CLL Global Research Foundation. Work in Dr.
Calin’s laboratory is supported in part by a 2009 Seena
Magowitz–Pancreatic Cancer Action Network AACR Pilot
Grant, the Laura and John Arnold Foundation, the RGK
Foundation and the Estate of C. G. Johnson, Jr. A.C.P.A.P.
was supported by NIH fellowship 5F31CA142238
Demonstration of entanglement-by-measurement of solid state qubits
Projective measurements are a powerful tool for manipulating quantum states.
In particular, a set of qubits can be entangled by measurement of a joint
property such as qubit parity. These joint measurements do not require a direct
interaction between qubits and therefore provide a unique resource for quantum
information processing with well-isolated qubits. Numerous schemes for
entanglement-by-measurement of solid-state qubits have been proposed, but the
demanding experimental requirements have so far hindered implementations. Here
we realize a two-qubit parity measurement on nuclear spins in diamond by
exploiting the electron spin of a nitrogen-vacancy center as readout ancilla.
The measurement enables us to project the initially uncorrelated nuclear spins
into maximally entangled states. By combining this entanglement with
high-fidelity single-shot readout we demonstrate the first violation of Bells
inequality with solid-state spins. These results open the door to a new class
of experiments in which projective measurements are used to create, protect and
manipulate entanglement between solid-state qubits.Comment: 6 pages, 4 figure
Mapping Exoplanets
The varied surfaces and atmospheres of planets make them interesting places
to live, explore, and study from afar. Unfortunately, the great distance to
exoplanets makes it impossible to resolve their disk with current or near-term
technology. It is still possible, however, to deduce spatial inhomogeneities in
exoplanets provided that different regions are visible at different
times---this can be due to rotation, orbital motion, and occultations by a
star, planet, or moon. Astronomers have so far constructed maps of thermal
emission and albedo for short period giant planets. These maps constrain
atmospheric dynamics and cloud patterns in exotic atmospheres. In the future,
exo-cartography could yield surface maps of terrestrial planets, hinting at the
geophysical and geochemical processes that shape them.Comment: Updated chapter for Handbook of Exoplanets, eds. Deeg & Belmonte. 17
pages, including 6 figures and 4 pages of reference
Decoherence-protected quantum gates for a hybrid solid-state spin register
Protecting the dynamics of coupled quantum systems from decoherence by the
environment is a key challenge for solid-state quantum information processing.
An idle qubit can be efficiently insulated from the outside world via dynamical
decoupling, as has recently been demonstrated for individual solid-state
qubits. However, protection of qubit coherence during a multi-qubit gate poses
a non-trivial problem: in general the decoupling disrupts the inter-qubit
dynamics, and hence conflicts with gate operation. This problem is particularly
salient for hybrid systems, wherein different types of qubits evolve and
decohere at vastly different rates. Here we present the integration of
dynamical decoupling into quantum gates for a paradigmatic hybrid system, the
electron-nuclear spin register. Our design harnesses the internal resonance in
the coupled-spin system to resolve the conflict between gate operation and
decoupling. We experimentally demonstrate these gates on a two-qubit register
in diamond operating at room temperature. Quantum tomography reveals that the
qubits involved in the gate operation are protected as accurately as idle
qubits. We further illustrate the power of our design by executing Grover's
quantum search algorithm, achieving fidelities above 90% even though the
execution time exceeds the electron spin dephasing time by two orders of
magnitude. Our results directly enable decoherence-protected interface gates
between different types of promising solid-state qubits. Ultimately, quantum
gates with integrated decoupling may enable reaching the accuracy threshold for
fault-tolerant quantum information processing with solid-state devices.Comment: This is original submitted version of the paper. The revised and
finalized version is in print, and is subjected to the embargo and other
editorial restrictions of the Nature journa
Observation of anomalous decoherence effect in a quantum bath at room temperature
Decoherence of quantum objects is critical to modern quantum sciences and
technologies. It is generally believed that stronger noises cause faster
decoherence. Strikingly, recent theoretical research discovers the opposite
case for spins in quantum baths. Here we report experimental observation of the
anomalous decoherence effect for the electron spin-1 of a nitrogen-vacancy
centre in high-purity diamond at room temperature. We demonstrate that under
dynamical decoupling, the double-transition can have longer coherence time than
the single-transition, even though the former couples to the nuclear spin bath
as twice strongly as the latter does. The excellent agreement between the
experimental and the theoretical results confirms the controllability of the
weakly coupled nuclear spins in the bath, which is useful in quantum
information processing and quantum metrology.Comment: 22 pages, related paper at http://arxiv.org/abs/1102.557
Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study
BACKGROUND: Quantitative molecular methods (QMMs) such as quantitative real-time polymerase chain reaction (q-PCR), reverse-transcriptase PCR (qRT-PCR) and quantitative nucleic acid sequence-based amplification (QT-NASBA) are increasingly used to estimate pathogen density in a variety of clinical and epidemiological contexts. These methods are often classified as semi-quantitative, yet estimates of reliability or sensitivity are seldom reported. Here, a statistical framework is developed for assessing the reliability (uncertainty) of pathogen densities estimated using QMMs and the associated diagnostic sensitivity. The method is illustrated with quantification of Plasmodium falciparum gametocytaemia by QT-NASBA. RESULTS: The reliability of pathogen (e.g. gametocyte) densities, and the accompanying diagnostic sensitivity, estimated by two contrasting statistical calibration techniques, are compared; a traditional method and a mixed model Bayesian approach. The latter accounts for statistical dependence of QMM assays run under identical laboratory protocols and permits structural modelling of experimental measurements, allowing precision to vary with pathogen density. Traditional calibration cannot account for inter-assay variability arising from imperfect QMMs and generates estimates of pathogen density that have poor reliability, are variable among assays and inaccurately reflect diagnostic sensitivity. The Bayesian mixed model approach assimilates information from replica QMM assays, improving reliability and inter-assay homogeneity, providing an accurate appraisal of quantitative and diagnostic performance. CONCLUSIONS: Bayesian mixed model statistical calibration supersedes traditional techniques in the context of QMM-derived estimates of pathogen density, offering the potential to improve substantially the depth and quality of clinical and epidemiological inference for a wide variety of pathogens
Large tunable valley splitting in edge-free graphene quantum dots on boron nitride
Coherent manipulation of binary degrees of freedom is at the heart of modern
quantum technologies. Graphene offers two binary degrees: the electron spin and
the valley. Efficient spin control has been demonstrated in many solid state
systems, while exploitation of the valley has only recently been started, yet
without control on the single electron level. Here, we show that van-der Waals
stacking of graphene onto hexagonal boron nitride offers a natural platform for
valley control. We use a graphene quantum dot induced by the tip of a scanning
tunneling microscope and demonstrate valley splitting that is tunable from -5
to +10 meV (including valley inversion) by sub-10-nm displacements of the
quantum dot position. This boosts the range of controlled valley splitting by
about one order of magnitude. The tunable inversion of spin and valley states
should enable coherent superposition of these degrees of freedom as a first
step towards graphene-based qubits
The Echinococcus canadensis (G7) genome: A key knowledge of parasitic platyhelminth human diseases
Background: The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools. Results: We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a core set of 881 orthologs shared among five cestode species. Comparative genomics revealed that there are more single nucleotide polymorphisms (SNPs) between E. canadensis (G7) and E. granulosus (G1) than between E. canadensis (G7) and E. multilocularis. This result was unexpected since E. canadensis (G7) and E. granulosus (G1) were considered to belong to the species complex E. granulosus sensu lato. We described SNPs in known drug targets and metabolism genes in the E. canadensis (G7) genome. Regarding gene regulation, we analysed three particular features: CpG island distribution along the three Echinococcus genomes, DNA methylation system and small RNA pathway. The results suggest the occurrence of yet unknown gene regulation mechanisms in Echinococcus. Conclusions: This is the first work that addresses Echinococcus comparative genomics. The resources presented here will promote the study of mechanisms of parasite development as well as new tools for drug discovery. The availability of a high-quality genome assembly is critical for fully exploring the biology of a pathogenic organism. The E. canadensis (G7) genome presented in this study provides a unique opportunity to address the genetic diversity among the genus Echinococcus and its particular developmental features. At present, there is no unequivocal taxonomic classification of Echinococcus species; however, the genome-wide SNPs analysis performed here revealed the phylogenetic distance among these three Echinococcus species. Additional cestode genomes need to be sequenced to be able to resolve their phylogeny.Fil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica; ArgentinaFil: Assis, Juliana. FundaciĂłn Oswaldo Cruz; BrasilFil: Gomes AraĂşjo, Flávio M.. FundaciĂłn Oswaldo Cruz; BrasilFil: Salim, Anna C. M.. FundaciĂłn Oswaldo Cruz; BrasilFil: Macchiaroli, Natalia. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica; ArgentinaFil: Cucher, Marcela Alejandra. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica; ArgentinaFil: Camicia, Federico. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica; ArgentinaFil: Fox, Adolfo. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica; ArgentinaFil: Rosenzvit, Mara Cecilia. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica; ArgentinaFil: Oliveira, Guilherme. Instituto TecnolĂłgico Vale; Brasil. FundaciĂłn Oswaldo Cruz; BrasilFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en MicrobiologĂa y ParasitologĂa MĂ©dica; Argentin
- …