469 research outputs found
Early star-forming galaxies and the reionization of the Universe
Star forming galaxies represent a valuable tracer of cosmic history. Recent
observational progress with Hubble Space Telescope has led to the discovery and
study of the earliest-known galaxies corresponding to a period when the
Universe was only ~800 million years old. Intense ultraviolet radiation from
these early galaxies probably induced a major event in cosmic history: the
reionization of intergalactic hydrogen. New techniques are being developed to
understand the properties of these most distant galaxies and determine their
influence on the evolution of the universe.Comment: Review article appearing in Nature. This posting reflects a submitted
version of the review formatted by the authors, in accordance with Nature
publication policies. For the official, published version of the review,
please see http://www.nature.com/nature/archive/index.htm
Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.
BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed.MethodsTen CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.ResultsAn average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value <0.05, minimum inclusion level difference >0.1).ConclusionThe RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis
Testing the theory of immune selection in cancers that break the rules of transplantation
Modification of cancer cells likely to reduce their immunogenicity, including loss or down-regulation of MHC molecules, is now well documented and has become the main support for the concept of immune surveillance. The evidence that these modifications, in fact, result from selection by the immune system is less clear, since the possibility that they may result from reorganized metabolism associated with proliferation or from cell de-differentiation remains. Here, we (a) survey old and new transplantation experiments that test the possibility of selection and (b) survey how transmissible tumours of dogs and Tasmanian devils provide naturally evolved tests of immune surveillance
Adaptive multi-polling scheduler for QoS support of video transmission in IEEE 802.11e WLANs
The 802.11E Task Group has been established to enhance quality of service (QoS) provision for time-bounded services in the current IEEE 802.11 medium access control protocol. The QoS is introduced throughout hybrid coordination function controlled channel access (HCCA) for the rigorous QoS provision. In HCCA, the station is allocated a fixed transmission opportunity (TXOP) based on its TSPEC parameters so that it is efficient for constant bit rate streams. However, as the profile of variable bit rate traffics is inconstant, they are liable to experience a higher delay especially in bursty traffic case. In this paper, we present a dynamic TXOP assignment algorithm called adaptive multi-polling TXOP scheduling algorithm (AMTXOP) for supporting the video traffics transmission over IEEE 802.11e wireless networks. This scheme invests a piggybacked information about the size of the subsequent video frames of the uplink streams to assist the hybrid coordinator accurately assign the TXOP according to actual change in the traffic profile. The proposed scheduler is powered by integrating multi-polling scheme to further reduce the delay and polling overhead. Extensive simulation experiments have been carried out to show the efficiency of the AMTXOP over the existing schemes in terms of the packet delay and the channel utilization
Variational Methods for Biomolecular Modeling
Structure, function and dynamics of many biomolecular systems can be
characterized by the energetic variational principle and the corresponding
systems of partial differential equations (PDEs). This principle allows us to
focus on the identification of essential energetic components, the optimal
parametrization of energies, and the efficient computational implementation of
energy variation or minimization. Given the fact that complex biomolecular
systems are structurally non-uniform and their interactions occur through
contact interfaces, their free energies are associated with various interfaces
as well, such as solute-solvent interface, molecular binding interface, lipid
domain interface, and membrane surfaces. This fact motivates the inclusion of
interface geometry, particular its curvatures, to the parametrization of free
energies. Applications of such interface geometry based energetic variational
principles are illustrated through three concrete topics: the multiscale
modeling of biomolecular electrostatics and solvation that includes the
curvature energy of the molecular surface, the formation of microdomains on
lipid membrane due to the geometric and molecular mechanics at the lipid
interface, and the mean curvature driven protein localization on membrane
surfaces. By further implicitly representing the interface using a phase field
function over the entire domain, one can simulate the dynamics of the interface
and the corresponding energy variation by evolving the phase field function,
achieving significant reduction of the number of degrees of freedom and
computational complexity. Strategies for improving the efficiency of
computational implementations and for extending applications to coarse-graining
or multiscale molecular simulations are outlined.Comment: 36 page
Physics of leptoquarks in precision experiments and at particle colliders
We present a comprehensive review of physics effects generated by leptoquarks
(LQs), i.e., hypothetical particles that can turn quarks into leptons and vice
versa, of either scalar or vector nature. These considerations include
discussion of possible completions of the Standard Model that contain LQ
fields. The main focus of the review is on those LQ scenarios that are not
problematic with regard to proton stability. We accordingly concentrate on the
phenomenology of light leptoquarks that is relevant for precision experiments
and particle colliders. Important constraints on LQ interactions with matter
are derived from precision low-energy observables such as electric dipole
moments, (g-2) of charged leptons, atomic parity violation, neutral meson
mixing, Kaon, B, and D meson decays, etc. We provide a general analysis of
indirect constraints on the strength of LQ interactions with the quarks and
leptons to make statements that are as model independent as possible. We
address complementary constraints that originate from electroweak precision
measurements, top, and Higgs physics. The Higgs physics analysis we present
covers not only the most recent but also expected results from the Large Hadron
Collider (LHC). We finally discuss direct LQ searches. Current experimental
situation is summarized and self-consistency of assumptions that go into
existing accelerator-based searches is discussed. A progress in making
next-to-leading order predictions for both pair and single LQ productions at
colliders is also outlined.Comment: 136 pages, 22 figures, typographical errors fixed, the Physics
Reports versio
Is There Any Association between Use of Smokeless Tobacco Products and Coronary Heart Disease in Bangladesh?
BACKGROUND: Most epidemiological studies exploring the association between smokeless tobacco (SLT) use and coronary heart disease (CHD) have been in Western populations, and have focused on SLT products used in those countries. Few studies come from South Asian countries. Our objective was to determine the association between SLT use and CHD among non-smoking adults in Bangladesh. METHODS: A matched case-control study of non-smoking Bangladeshi adults aged 40–75 years was conducted in 2010. Incident cases of CHD were selected from two cardiac hospitals. Community controls, matched to CHD cases, were selected from neighbourhoods, and hospital controls were selected from outpatient departments of the same hospitals. The Rose Angina Questionnaire (RAQ) was also used to re-classify cases and controls. RESULTS: The study enrolled 302 cases, 1,208 community controls and 302 hospital controls. Current use was higher among community controls (38%) compared to cases (33%) and hospital controls (32%). Current use of SLT was not significantly associated with an increased risk of CHD when community controls were used (adjusted OR 0.87, 95% CI 0.63–1.19), or when hospital controls were used (adjusted OR 1.00, 95% CI 0.63–1.60), or when both control groups were combined (adjusted OR 1.00, 95% CI 0.74–1.34). Risk of CHD did not increase with use of individual types except gul, frequency, duration, past use of SLT products, or using the RAQ to re-classify cases and controls. There was a significant association between gul use and CHD when both controls were combined (adjusted OR 2.93, 95% CI 1.28–6.70). CONCLUSIONS: There was no statistically significant association between SLT use in general and CHD among non-smoking adults in Bangladesh. Further research on the association between gul use and CHD in Bangladesh along with SLT use and CHD in other parts of the subcontinent will guide public health policy and interventions that focus on SLT-related diseases.Muhammad Azia Rahman, Nicola Spurrier, Mohammad Afzal Mahmood, Mahmudur Rahman, Soehl Reza Choudhury and Stephen Leede
Geometric frustration in compositionally modulated ferroelectrics
Geometric frustration is a broad phenomenon that results from an intrinsic
incompatibility between some fundamental interactions and the underlying
lattice geometry1-7. Geometric frustration gives rise to new fundamental
phenomena and is known to yield intriguing effects, such as the formation of
exotic states like spin ice, spin liquids and spin glasses1-7. It has also led
to interesting findings of fractional charge quantization and magnetic
monopoles5,6. Geometric frustration related mechanisms have been proposed to
understand the origins of relaxor behavior in some multiferroics, colossal
magnetocapacitive coupling and unusual and novel mechanisms of high Tc
superconductivity1-5. Although geometric frustration has been particularly well
studied in magnetic systems in the last 20 years or so, its manifestation in
the important class formed by ferroelectric materials (that are compounds
exhibiting electric rather than magnetic dipoles) is basically unknown. Here,
we show, via the use of a first-principles-based technique, that
compositionally graded ferroelectrics possess the characteristic "fingerprints"
associated with geometric frustration. These systems have a highly degenerate
energy surface and exhibit original critical phenomena. They further reveal
exotic orderings with novel stripe phases involving complex spatial
organization. These stripes display spiral states, topological defects and
curvature. Compositionally graded ferroelectrics can thus be considered as the
"missing" link that brings ferroelectrics into the broad category of materials
able to exhibit geometric frustration. Our ab-initio calculations allow a deep
microscopic insight into this novel geometrically frustrated system.Comment: 14 pages, 5 Figures;
http://www.nature.com/nature/journal/v470/n7335/full/nature09752.htm
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