pinecone/core-2020-05-10-deduplication huggingface dataset:
Comparative analysis of RNA sequencing methods for degraded or low-input samples

RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers. Recent studies have proposed several methods for RNA-seq of low-quality and/or low-quantity samples, but the relative merits of these methods have not been systematically analyzed. Here we compare five such methods using metrics relevant to transcriptome annotation, transcript discovery and gene expression. Using a single human RNA sample, we constructed and sequenced ten libraries with these methods and compared them against two control libraries. We found that the RNase H method performed best for chemically fragmented, low-quality RNA, and we confirmed this through analysis of actual degraded samples. RNase H can even effectively replace oligo(dT)-based methods for standard RNA-seq. SMART and NuGEN had distinct strengths for measuring low-quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.available in PMC 2014 January 01.National Institutes of Health (U.S.) (Pioneer Award DP1-OD003958-01)National Human Genome Research Institute (U.S.) ((NHGRI) 1P01HG005062-01)National Human Genome Research Institute (U.S.) (NHGRI Center of Excellence in Genome Science Award 1P50HG006193-01)Howard Hughes Medical InstituteMerkin Family Foundation for Stem Cell ResearchBroad Institute of MIT and Harvard (Klarman Cell Observatory)National Human Genome Research Institute (U.S.) (grant HG03067)Fonds voor Wetenschappelijk Onderzoek--Vlaanderen (postdoctoral research fellowship
Spontaneous R-Parity Breaking and Left-Right Symmetry

We propose a simple renormalizable left-right theory where R-parity is
spontaneously broken and neutrino masses are generated through the Type I
seesaw mechanism and R-parity violation. In this theory R-parity and the gauge
symmetry are broken by the sneutrino vacuum expectation values and there is no
Majoron problem. The SU(2)_R and R-parity violation scales are determined by
the SUSY breaking scale making the model very predictive. We discuss the
spectrum and possible tests of the theory through the neutralinos, charginos,
Z^' and W_R decays at the Large Hadron Collider.Comment: 4 pages, minor corrections, title changed, to appear in Physics
  Letters
Dark Matter Search Using Chandra Observations of Willman 1, and a
  Spectral Feature Consistent with a Decay Line of a 5 keV Sterile Neutrino

We report the results of a search for an emission line from radiatively
decaying dark matter in the Chandra X-ray Observatory spectrum of the
ultra-faint dwarf spheroidal galaxy Willman 1. 99% confidence line flux upper
limits over the 0.4-7 keV Chandra bandpass are derived and mapped to an allowed
region in the sterile neutrino mass-mixing angle plane that is consistent with
recent constraints from Suzaku X-ray Observatory and Chandra observations of
the Ursa Minor and Draco dwarf spheroidals. A significant excess to the
continuum, detected by fitting the particle-background-subtracted source
spectrum, indicates the presence of a narrow emission feature with energy 2.51
+/- 0.07 (0.11) keV and flux [3.53 +/- 1.95 (2.77)] X 10^(-6) photons/cm^2/s at
68% (90%) confidence. Interpreting this as an emission line from sterile
neutrino radiative decay, we derive the corresponding allowed range of sterile
neutrino mass and mixing angle using two approaches. The first assumes that
dark matter is solely composed of sterile neutrinos, and the second relaxes
that requirement. The feature is consistent with the sterile neutrino mass of
5.0 +/- 0.2 keV and a mixing angle in a narrow range for which neutrino
oscillations can produce all of the dark matter and for which sterile neutrino
emission from the cooling neutron stars can explain pulsar kicks, thus
bolstering both the statistical and physical significance of our measurement.Comment: 34 pages, including 20 figures; accepted for publication in ApJ;
  substantially expanded discussion session, results unchange
Search for high mass dilepton resonances in pp collisions at sqrt{s}=7
  TeV with the ATLAS experiment

This article presents a search for high mass e e or mu mu resonances in pp
collisions at sqrt{s} = 7 TeV at the LHC. The data were recorded by the ATLAS
experiment during 2010 and correspond to a total integrated luminosity of
~40/pb. No statistically significant excess above the Standard Model
expectation is observed in the search region of dilepton invariant mass above
110 GeV. Upper limits at the 95% confidence level are set on the cross section
times branching ratio of Z' resonances decaying to dielectrons and dimuons as a
function of the resonance mass. A lower mass limit of 1.048 TeV on the
Sequential Standard Model Z' boson is derived, as well as mass limits on Z* and
E(6)-motivated Z' models.Comment: 7 pages (+12 for author list), 5 figures, 6 tables, submitted to
  Physics Letter
Quantum ergodicity for electrons in two dimensions

We study the effect of electron-electron interaction on a two dimensional
(2D) disordered lattice. For the case of two electrons the analytical estimates
are presented showing a transition from localized to delocalized states in a
way similar to the Anderson transition in 3D. The localized phase corresponds
to large values of the parameter r_s, which is determined by the ratio of the
Coulomb and Fermi energies. The numerical investigations of the spectral
statistics P(s) in a system with up to N_p=30 spin polarized electrons show the
transition from the Poisson to the Wigner-Dyson distribution at a total
electron energy independent of N_p. The relation to experiments on the
metal-insulator transition in 2D is also discussed.Comment: invited talk at Localisation 99, Hamburg; to appear at Ann. Phys.
  (Leipzig); small corrections are adde
Affleck-Dine leptogenesis via right-handed sneutrino fields in a
  supersymmetric hybrid inflation model

The onset of inflation in hybrid models require fine tuning in the initial
conditions. The inflaton field should have an initial value close to the Planck
scale $M_{P}$, whereas the auxiliary "orthogonal" field must be close to zero
with an extreme accuracy. This problem can be alleviated if the orthogonal
field fastly decays into some states not coupled to the inflaton. Natural
candidates for such states can be the right-handed neutrinos. We show that a
non-trivial evolution of the classic sneutrino fields after inflation offers an
interesting mechanism for generating a correct amount of lepton asymmetry,
which being reprocessed by sphalerons can explain the observed baryon asymmetry
of the Universe. Our scenario implies interesting bounds for the neutrino
masses in the context of seesaw mechanism.Comment: 9 pages, no figure
Crystal planes and reciprocal space in Clifford geometric algebra

This paper discusses the geometry of $k$D crystal cells given by $(k+1)$
points in a projective space $\R^{n+1}$. We show how the concepts of
barycentric and fractional (crystallographic) coordinates, reciprocal vectors
and dual representation are related (and geometrically interpreted) in the
projective geometric algebra $Cl(\R^{n+1})$ (see Grassmann H., edited by Engel
F., Die Ausdehnungslehre von 1844 und die Geom. Anal., vol. 1, part 1, Teubner:
Leipzig, 1894.) and in the conformal algebra $Cl(\R^{n+1,1})$. The
crystallographic notions of $d$-spacing, phase angle, structure factors,
conditions for Bragg reflections, and the interfacial angles of crystal planes
are obtained in the same context.
  Keywords: Clifford geometric algebra, crystallography, reciprocal space,
$d$-spacing, phase angle, structure factors, Bragg reflections, interfacial
anglesComment: 9 pages, 6 figure
The Orthogonal 2D Planes Split of Quaternions and Steerable Quaternion
  Fourier Transformations

The two-sided quaternionic Fourier transformation (QFT) was introduced in
\cite{Ell:1993} for the analysis of 2D linear time-invariant
partial-differential systems. In further theoretical investigations
\cite{10.1007/s00006-007-0037-8, EH:DirUP_QFT} a special split of quaternions
was introduced, then called $\pm$split. In the current \change{chapter} we
analyze this split further, interpret it geometrically as \change{an}
\emph{orthogonal 2D planes split} (OPS), and generalize it to a freely
steerable split of $\H$ into two orthogonal 2D analysis planes. The new general
form of the OPS split allows us to find new geometric interpretations for the
action of the QFT on the signal. The second major result of this work is a
variety of \emph{new steerable forms} of the QFT, their geometric
interpretation, and for each form\change{,} OPS split theorems, which allow
fast and efficient numerical implementation with standard FFT software.Comment: 25 pages, 5 figure
Review of the anisotropy working group at UHECR-2012

The study of ultra-high energy cosmic rays (UHECRs) has recently experienced
a jump in statistics as well as improved instrumentation. This has allowed a
better sensitivity in searching for anisotropies in the arrival directions of
cosmic rays. In this written version of the presentation given by the
inter-collaborative "Anisotropy Working Group" at the International Symposium
on Future Directions in UHECR physics at CERN in February 2012, we report on
the current status for anisotropy searches in the arrival directions of UHECRs.Comment: Working Group report given at UHECR 2012 Symposium, CERN, Feb. 201
Gravitational Dynamics From Entanglement "Thermodynamics"

In a general conformal field theory, perturbations to the vacuum state obey
the relation \delta S = \delta E, where \delta S is the change in entanglement
entropy of an arbitrary ball-shaped region, and \delta E is the change in
"hyperbolic" energy of this region. In this note, we show that for holographic
conformal field theories, this relation, together with the holographic
connection between entanglement entropies and areas of extremal surfaces and
the standard connection between the field theory stress tensor and the boundary
behavior of the metric, implies that geometry dual to the perturbed state
satisfies Einstein's equations expanded to linear order about pure AdS.Comment: v2: references added, problematic section on Radon transform remove
[CII] and 12CO(1-0) Emission Maps in HLSJ091828.6+514223: A Strongly
  Lensed Interacting System at z=5.24

We present Submillimeter Array (SMA) [CII] 158um and Jansky Very Large Array
(JVLA) $^{12}$CO(1-0) line emission maps for the bright, lensed, submillimeter
source at $z=5.2430$ behind Abell 773: HLSJ091828.6+514223 (HLS0918). We
combine these measurements with previously reported line profiles, including
multiple $^{12}$CO rotational transitions, [CI], water and [NII], providing
some of the best constraints on the properties of the interstellar medium (ISM)
in a galaxy at $z>5$. HLS0918 has a total far-infrared (FIR) luminosity
L_FIR(8-1000um) = (1.6$\pm$0.1)x10^14 L_sun/mu, where the total magnification
mu_total = 8.9$\pm$1.9, via a new lens model from the [CII] and continuum maps.
Despite a HyLIRG luminosity, the FIR continuum shape resembles that of a local
LIRG. We simultaneously fit all of the observed spectral line profiles, finding
four components which correspond cleanly to discrete spatial structures
identified in the maps. The two most redshifted spectral components occupy the
nucleus of a massive galaxy, with a source plane separation <1 kpc. The reddest
dominates the continuum map (de-magnified L_FIR = (1.1$\pm$0.2)x10^13 L_sun),
and excites strong water emission in both nuclear components via a powerful FIR
radiation field from the intense star formation. A third star-forming component
is most likely a region of a merging companion (dV ~ 500 km/s) exhibiting
generally similar gas properties. The bluest component originates from a
spatially distinct region, and photo-dissociation region (PDR) analysis
suggests that it is lower density, cooler and forming stars less vigorously
than the other components. Strikingly, it has very strong [NII] emission which
may suggest an ionized, molecular outflow. This comprehensive view of gas
properties and morphology in HLS0918 previews the science possible for a large
sample of high-redshift galaxies once ALMA attains full sensitivity.Comment: 28 pages, 9 figures, accepted in Ap
Charged R\'enyi Entropies in CFTs with Einstein-Gauss-Bonnet Holographic
  Duals

We calculate the R\'enyi entropy $S_q(\mu,\lambda)$, for a spherical
entangling surface in CFT's with Einstein-Gauss-Bonnet-Maxwell holographic
duals. R\'enyi entropies must obey some interesting inequalities by definition.
However, for Gauss-Bonnet couplings $\lambda$, larger than a specific value,
but still allowed by causality, we observe a violation of the inequality
$\frac{\partial}{{\partial q}}\left({\frac{{q - 1}}{q}S_q(\mu,\lambda)} \right)
\ge 0$, which is related to the existence of negative entropy black holes,
providing interesting restrictions in the bulk theory. Moreover, we find an
interesting distinction of the behaviour of the analytic continuation of
$S_q(\mu,\lambda)$ for imaginary chemical potential, between negative and
non-negative $\lambda$.Comment: 50 pages, 16 figures. v3: Version to appear in JHE
Genetic Algorithms and the Search for Viable String Vacua

Genetic Algorithms are introduced as a search method for finding string vacua
with viable phenomenological properties. It is shown, by testing them against a
class of Free Fermionic models, that they are orders of magnitude more
efficient than a randomised search. As an example, three generation, exophobic,
Pati-Salam models with a top Yukawa occur once in every 10^{10} models, and yet
a Genetic Algorithm can find them after constructing only 10^5 examples. Such
non-deterministic search methods may be the only means to search for Standard
Model string vacua with detailed phenomenological requirements.Comment: 10 figures, 24 pages, JHEP versio
A new method to search for high redshift clusters using photometric
  redshifts

We describe a new method (Poisson Probability Method, PPM) to search for high
redshift galaxy clusters and groups by using photometric redshift information
and galaxy number counts. The method relies on Poisson statistics and is
primarily introduced to search for Mpc-scale environments around a specific
beacon. The PPM is tailored to both the properties of the FR I radio galaxies
in the Chiaberge et al. (2009) sample, that are selected within the COSMOS
survey, and on the specific dataset used. We test the efficiency of our method
of searching for cluster candidates against simulations. Two different
approaches are adopted. i) We use two z~1 X-ray detected cluster candidates
found in the COSMOS survey and we shift them to higher redshift up to z=2. We
find that the PPM detects the cluster candidates up to z=1.5, and it correctly
estimates both the redshift and size of the two clusters. ii) We simulate
spherically symmetric clusters of different size and richness, and we locate
them at different redshifts (i.e. z = 1.0,1.5, and 2.0) in the COSMOS field. We
find that the PPM detects the simulated clusters within the considered redshift
range with a statistical 1-sigma redshift accuracy of ~0.05. The PPM is an
efficient alternative method for high-redshift cluster searches that may also
be applied to both present and future wide field surveys such as SDSS Stripe
82, LSST, and Euclid. Accurate photometric redshifts and a survey depth similar
or better than that of COSMOS (e.g. I<25) are required.Comment: 30 pages, 14 figures, ApJ accepte
Nearby supernova host galaxies from the CALIFA Survey: I. Sample, data
  analysis, and correlation to star-forming regions

[Abridged] We use optical IFS of nearby SN host galaxies provided by the
CALIFA Survey with the goal of finding correlations in the environmental
parameters at the location of different SN types. We recover the sequence in
association of different SN types to the star-forming regions by using several
indicators of the ongoing and recent SF related to both the ionized gas and the
stellar populations. While the total ongoing SF is on average the same for the
three SN types, SNe Ibc/IIb tend to happen closer to star-forming regions and
occur in higher SF density locations compared to SNe II and SNe~Ia, the latter
showing the weakest correlation. SNe~Ia host galaxies have on average masses
that are $\sim$0.3-0.8~dex higher than CC SNe hosts due to a larger fraction of
old stellar populations in the SNe~Ia hosts. Using the recent SN~Ia delay-time
distribution and the SFHs of the galaxies, we show that the SN~Ia hosts in our
sample should presently produce a factor 2 more SNe~Ia than the CC~SN hosts.
Since both types are in hosts with similar SF rate and hence similar CC~SN
rate, this can explain the mass difference between the SN~Ia and CC~SN hosts,
and reinforce the finding that at least part of SNe~Ia should originate from
very old progenitors. Comparing the mean SFH of the eight least massive
galaxies to that of the massive SF SN~Ia hosts we find that the low-mass
galaxies formed their stars over more extended time than the massive SN~Ia
hosts. We estimate that the low-mass galaxies should produce by a factor of 10
less SNe~Ia, and a factor of 3 less CC~SNe than the high-mass group. Therefore
the ratio between the number of CC~SNe and SNe~Ia is expected to increase with
decreasing the galaxy mass. CC~SNe tend to explode at positions with younger
stellar populations than the galaxy average, but the galaxy properties at
SNe~Ia locations are one average the same as the global ones.Comment: (Accepted in A&A, 24 pages, 19 Figures, 9 Tables
Toda fields of SO(3) hyper-Kähler metrics

We examine the Toda frame formulation of the SO(3)-invariant hyper-Kahler 4-metrics, namely Eguchi-Hanson, Taub-NUT and Atiyah-Hitchin. Our method exploits the presence of a rotational SO(2) isometry, leading to the explicit construction of all three complex structures as a singlet plus a doublet. The Atiyah-Hitchin metric on the moduli space of BPS SU(2) monopoles with magnetic charge 2 is purely rotational.We examine the Toda frame formulation of the SO(3)-invariant hyper-Kahler 4-metrics, namely Eguchi-Hanson, Taub-NUT and Atiyah-Hitchin. Our method exploits the presence of a rotational SO(2) isometry, leading to the explicit construction of all three complex structures as a singlet plus a doublet. The Atiyah-Hitchin metric on the moduli space of BPS SU(2) monopoles with magnetic charge 2 is purely rotational
Non-abelian anomalies and effective actions for a homogeneous space G/H

We consider the problem of constructing the fully gauged effective action for Nambu-Goldstone bosons valued in a homogeneous space G/H, with the requirement that the action be invariant under the gauge transformations of H. We show that this can be done whenever G/H is reductive and H is embedded in G so as to be anomaly free, in particular if H is an anomaly safe group. We construct the necessary generalization of the Bardeen counterterm and give explicit forms for the anomaly and the effective action. When G/H is a symmetric space the counterterm and the anomaly decompose into a parity even and a parity odd part. In this case, for the parity even part of the action, one does not need the anomaly free embedding of H
Strange meson enhancement in Pb - Pb collisions

The NA44 Collaboration has measured yields and differential distributions of $K^{+}, K^{-}, \pi^{+}, \pi^{-}$ in transverse kinetic energy and rapidity, around the center-of-mass rapidity in 158 AGeV/c Pb + Pb collisions at the CERN SPS. A considerable enhancement of $K^{+}$ production per $\pi$ is observed, as compared to $p + p$ collisions at this energy. To illustrate the importance of secondary hadron rescattering as an enhancement mechanism, we compare strangeness production at the SPS and AGS with predictions of the transport model RQMD.The NA44 Collaboration has measured yields and differential distributions of K+, K-, pi+, pi- in transverse kinetic energy and rapidity, around the center-of-mass rapidity in 158 A GeV/c Pb+Pb collisions at the CERN SPS. A considerable enhancement of K+ production per pi is observed, as compared to p+p collisions at this energy. To illustrate the importance of secondary hadron rescattering as an enhancement mechanism, we compare strangeness production at the SPS and AGS with predictions of the transport model RQMD.The NA44 Collaboration has measured yields and differential distributions of K + , K − , π + , π − in transverse kinetic energy and rapidity, around the center-of-mass rapidity in 158 A GeV/ c Pb+Pb collisions at the CERN SPS. A considerable enhancement of K + production per π is observed, as compared to p + p collisions at this energy. To illustrate the importance of secondary hadron rescattering as an enhancement mechanism, we compare strangeness production at the SPS and AGS with predictions of the transport model RQMD
Finite-size effects on the phase structure of the Nambu-Jona-Lasinio
  model

The Nambu-Jona-Lasinio (NJL) model is one of the most frequently used
four-fermion models in the study of dynamical symmetry breaking. In particular,
the NJL model is convenient for that analysis at finite temperature, chemical
potential and size effects, as has been explored in the last decade. With this
motivation, we investigate the finite-size effects on the phase structure of
the NJL model in $D = 3$ Euclidean dimensions, in the situations that one, two
and three dimensions are compactified. In this context, we employ the
zeta-function and compactification methods to calculate the effective potential
and gap equation. The critical lines that separate trivial and non-trivial
fermion mass phases in a second order transition are obtained. We also analyze
the system at finite temperature, considering the inverse of temperature as the
size of one of the compactified dimensions.Comment: 12 pages, 3 figures, revtex
M Theory Fivebrane Interpretation for Strong Coupling Dynamics of
  SO(N_c) Gauge Theories

We study M theory fivebranes to understand the moduli space of vacua of N=1
supersymmetric SO(N_c) gauge theory with N_f flavors in four dimensions. We
discuss how the various branches of this theory arise in the string/M theory
brane configurations and compare our results with the ones obtained earlier by
Intriligator and Seiberg in the context of field theory.
  In the M theory approach, we explain the various branches from the asymptotic
position of semi-infinite D4 branes in the $w=x^8+i x^9$ direction, which is
closely related to the eigenvalues of the meson matrix $M^{ij} = Q^{i}_a
Q^{j}_a$ where $Q^{i}_a$ is a squark multiplet ( $i=1, \cdots, 2N_f$ and $ a=1,
\cdots, N_c$).In M theory, these branches are explained by observing a new
phenomena which did not occur for the gauge groups SU(N_c) or Sp(N_c).Comment: 15 pages, Latex, English corrected, Version to Appear in Physics
  Letters
Charm meson production from meson-nucleon scattering

Using an effective hadronic Lagrangian with physical hadron masses and
coupling constants determined either empirically or from SU(4) flavor symmetry,
we study the production cross sections of charm mesons from pion and rho meson
interactions with nucleons. With a cutoff parameter of 1 GeV at interaction
vertices as usually used in studying the cross sections for $J/\psi$ absorption
and charm meson scattering by hadrons, we find that the cross sections for
charm meson production have values of a few tenth of mb and are dominated by
the s channel nucleon pole diagram. Relevance of these reactions to charm meson
production in relativistic heavy ion collisions is discussed.Comment: 8 pages, 4 figures, slight revision and references adde