5,340 research outputs found
EST analysis of gene expression in early cleavage-stage sea urchin embryos
A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts
The Price of Anarchy in Transportation Networks: Efficiency and Optimality Control
Uncoordinated individuals in human society pursuing their personally optimal
strategies do not always achieve the social optimum, the most beneficial state
to the society as a whole. Instead, strategies form Nash equilibria which are
often socially suboptimal. Society, therefore, has to pay a price of anarchy
for the lack of coordination among its members. Here we assess this price of
anarchy by analyzing the travel times in road networks of several major cities.
Our simulation shows that uncoordinated drivers possibly waste a considerable
amount of their travel time. Counterintuitively,simply blocking certain streets
can partially improve the traffic conditions. We analyze various complex
networks and discuss the possibility of similar paradoxes in physics.Comment: major revisions with multicommodity; Phys. Rev. Lett., accepte
Appearance of Half-Metallicity in the Quaternary Heusler Alloys
I report systematic first-principle calculations of the quaternary Heusler
alloys like Co[CrMn]Al, CoMn[AlSn] and
[FeCo]MnAl. I show that when the two limiting cases (x=0 or 1)
correspond to a half-metallic compound, so do the intermediate cases. Moreover
the total spin moment in scales linearly with the total number of
valence electrons (and thus with the concentration ) following the
relation , independently of the origin of the extra valence
electrons, confirming the Slater-Pauling behavior of the normal Heusler alloys.
Finally I discuss in all cases the trends in the atomic projected DOSs and in
the atomic spin moments.Comment: 4 pages, 3 figures, 2 Table
The falling chain of Hopkins, Tait, Steele and Cayley
A uniform, flexible and frictionless chain falling link by link from a heap
by the edge of a table falls with an acceleration if the motion is
nonconservative, but if the motion is conservative, being the
acceleration due to gravity. Unable to construct such a falling chain, we use
instead higher-dimensional versions of it. A home camcorder is used to measure
the fall of a three-dimensional version called an -slider. After
frictional effects are corrected for, its vertical falling acceleration is
found to be . This result agrees with the theoretical
value of for an ideal energy-conserving -slider.Comment: 17 pages, 5 figure
Fermi surface of the colossal magnetoresistance perovskite La_{0.7}Sr_{0.3}MnO_{3}
Materials that exhibit colossal magnetoresistance (CMR) are currently the
focus of an intense research effort, driven by the technological applications
that their sensitivity lends them to. Using the angular correlation of photons
from electron-positron annihilation, we present a first glimpse of the Fermi
surface of a material that exhibits CMR, supported by ``virtual crystal''
electronic structure calculations. The Fermi surface is shown to be
sufficiently cubic in nature that it is likely to support nesting.Comment: 5 pages, 5 PS figure
Modelling stochastic bivariate mortality
Stochastic mortality, i.e. modelling death arrival via a jump process with stochastic intensity, is gaining increasing reputation as a way to represent mortality risk. This paper represents a first attempt to model the mortality risk of couples of individuals, according to the stochastic intensity approach.
On the theoretical side, we extend to couples the Cox processes set up, i.e. the idea that mortality is driven by a jump process whose intensity is itself a stochastic process, proper of a particular generation within each gender. Dependence between the survival times of the members of a couple is captured by an Archimedean copula.
On the calibration side, we fit the joint survival function by calibrating separately the (analytical) copula and the (analytical) margins. First, we select the best fit copula according to the methodology of Wang and Wells (2000) for censored data. Then, we provide a sample-based calibration for the intensity, using a time-homogeneous, non mean-reverting, affine process: this gives the analytical marginal survival functions. Coupling the best fit copula with the calibrated margins we obtain, on a sample generation, a joint survival function which incorporates the stochastic nature of mortality improvements and is far from representing independency.On the contrary, since the best fit copula turns out to be a Nelsen one, dependency is increasing with age and long-term dependence exists
Fate and transport of volatile organic compounds in glacial till and groundwater at an industrial site in Northern Ireland
Volatile organic compound (VOC) contamination of subsurface geological material and groundwater was discovered on the Nortel Monkstown industrial site, Belfast, Northern Ireland. The objectives of this study were to (1) investigate the characteristics of the geological material and its influences on contaminated groundwater flow across the site using borehole logs and hydrological evaluations, and (2) identify the contaminants and examine their distribution in the subsurface geological material and groundwater using chemical analysis. This report focuses on the eastern car park (ECP) which was a former storage area associated with trichloroethene (TCE) degreasing operations. This is where the greatest amount of volatile organic compounds (VOCs), particularly TCE, were detected. The study site is on a complex deposit of clayey glacial till with discontinuous coarser grained lenses, mainly silts, sands and gravel, which occur at 0.45-7.82 m below ground level (bgl). The lenses overall form an elongated formation that acts as a small unconfined shallow aquifer. There is a continuous low permeable stiff clayey till layer beneath the lenses that performs as an aquitard to the groundwater. Highest concentrations of VOCs, mainly TCE, in the geological material and groundwater are in these coarser lenses at similar to 4.5-7 m bgl. Highest TCE measurements at 390,000 mu g L-1 for groundwater and at 39,000 mu g kg(-1) at 5.7 m for geological material were in borehole GA19 in the coarse lens zone. It is assumed that TCE gained entrance to the subsurface near this borehole where the clayey till was thin to absent above coarse lenses which provided little retardation to the vertical migration of this dense non-aqueous phase liquid (DNAPL) into the groundwater. However, TCE is present in low concentrations in the geological material overlying the coarse lens zone. Additionally, VOCs appear to be associated with poorly drained layers and in peat < 3.0 m bgl in the ECP. Some indication of natural attenuation as VOCs degradation products vinyl chloride (VC) and dichloromethane (DCM) also occur on the site
Transcript-indexed ATAC-seq for precision immune profiling.
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy
Morphine activates neuroinflammation in a manner parallel to endotoxin
Opioids create a neuroinflammatory response within the CNS, compromising opioid-induced analgesia and contributing to various unwanted actions. How this occurs is unknown but has been assumed to be via classic opioid receptors. Herein, we provide direct evidence that morphine creates neuroinflammation via the activation of an innate immune receptor and not via classic opioid receptors. We demonstrate that morphine binds to an accessory protein of Toll-like receptor 4 (TLR4), myeloid differentiation protein 2 (MD-2), thereby inducing TLR4 oligomerization and triggering proinflammation. Small-molecule inhibitors, RNA interference, and genetic knockout validate the TLR4/MD-2 complex as a feasible target for beneficially modifying morphine actions. Disrupting TLR4/MD-2 protein–protein association potentiated morphine analgesia in vivo and abolished morphine-induced proinflammation in vitro, the latter demonstrating that morphine-induced proinflammation only depends on TLR4, despite the presence of opioid receptors. These results provide an exciting, nonconventional avenue to improving the clinical efficacy of opioids.Xiaohui Wang, Lisa C. Loram, Khara Ramos, Armando J. de Jesus, Jacob Thomas, Kui Cheng, Anireddy Reddy, Andrew A. Somogyi, Mark R. Hutchinson, Linda R. Watkins and Hang Yi
Large Orbital Magnetic Moment and Coulomb Correlation effects in FeBr2
We have performed an all-electron fully relativistic density functional
calculation to study the magnetic properties of FeBr2. We show for the first
time that the correlation effect enhances the contribution from orbital degrees
of freedom of electrons to the total magnetic moment on Fe as
opposed to common notion of nearly total quenching of the orbital moment on
Fe site. The insulating nature of the system is correctly predicted when
the Hubbard parameter U is included. Energy bands around the gap are very
narrow in width and originate from the localized Fe-3 orbitals, which
indicates that FeBr2 is a typical example of the Mott insulator.Comment: 4 pages, 3 figures, revtex4, PRB accepte
- …