pinecone/core-2020-05-10-deduplication huggingface dataset:
Lipid binding attenuates channel closure of the outer membrane protein OmpF.

Strong interactions between lipids and proteins occur primarily through association of charged headgroups and amino acid side chains, rendering the protonation status of both partners important. Here we use native mass spectrometry to explore lipid binding as a function of charge of the outer membrane porin F (OmpF). We find that binding of anionic phosphatidylglycerol (POPG) or zwitterionic phosphatidylcholine (POPC) to OmpF is sensitive to electrospray polarity while the effects of charge are less pronounced for other proteins in outer or mitochondrial membranes: the ferripyoverdine receptor (FpvA) or the voltage-dependent anion channel (VDAC). Only marginal charge-induced differences were observed for inner membrane proteins: the ammonia channel (AmtB) or the mechanosensitive channel. To understand these different sensitivities, we performed an extensive bioinformatics analysis of membrane protein structures and found that OmpF, and to a lesser extent FpvA and VDAC, have atypically high local densities of basic and acidic residues in their lipid headgroup-binding regions. Coarse-grained molecular dynamics simulations, in mixed lipid bilayers, further implicate changes in charge by demonstrating preferential binding of anionic POPG over zwitterionic POPC to protonated OmpF, an effect not observed to the same extent for AmtB. Moreover, electrophysiology and mass-spectrometry–based ligand-binding experiments, at low pH, show that POPG can maintain OmpF channels in open conformations for extended time periods. Since the outer membrane is composed almost entirely of anionic lipopolysaccharide, with similar headgroup properties to POPG, such anionic lipid binding could prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways
Optimized Diffusion-Weighting Gradient Waveform Design (ODGD) formulation for motion compensation and concomitant gradient nulling

Producción CientíficaPurpose: To present a novel Optimized Diffusion-weighting Gradient waveform Design (ODGD) method for the design of minimum echo time (TE), bulk motion-compensated, and concomitant gradient (CG)-nulling  waveforms for diffusion MRI.

Methods: ODGD motion-compensated waveforms were designed for various moment-nullings Mn (n=0,1,2), for a range of b-values, and spatial resolutions, both without (ODGD-Mn) and with CG-nulling (ODGD-Mn-CG). Phantom and in-vivo (brain and liver) experiments were conducted with various ODGD waveforms to compare motion robustness, signal-to-noise ratio (SNR), and apparent diffusion coefficient (ADC) maps with state-of-the-art waveforms.

Results:ODGD-Mn and ODGD-Mn-CG waveforms reduced the TE of state-of-the-art waveforms. This TE reduction resulted in significantly higher SNR (P < 0.05) in both phantom and in-vivo experiments. ODGD-M1 improved the SNR of BIPOLAR (42.8+-5.3 versus 32.9+-3.3) in the brain, and ODGD-M2 the SNR of motion-compensated (MOCO) and Convex Optimized Diffusion Encoding-M2 (CODE-M2) (12.3+-3.6 versus 9.7+-2.9 and 10.2+-3.4, respectively) in the liver. Further, ODGD-M2 also showed excellent motion robustness in the liver. ODGD-M2-CG waveforms reduced the CG-related dephasing effects of non CG-nulling waveforms in phantom and in-vivo experiments, resulting in accurate ADC maps.

Conclusions: ODGD waveforms enable motion-robust diffusion MRI with reduced TEs, increased SNR, and reduced ADC bias compared to state-of-the-art waveforms in theoretical results, simulations, phantoms and in-vivo experiments.TEC2013-44194-PVA069U1
FINANCIAL RISK AND FINANCIAL RISK MANAGEMENT TECHNOLOGY (RMT):  ISSUES AND ADVANCES

Methods for sound risk management are of increasing interest among Wall Street investment banking and
brokerage firms in the aftermath of the October 1987 crash of the stock market. We present an overview of the
basic definitions and issues related to risk, and the management of financial risk and financial risk management
technology (RMT) for information systems (IS) technology professionals. We discuss of the content of risk
management technology, including the models, the software and hardware, and the market data required to track
risk. We also discuss the identification of risky events, alternative approaches to the measurement of risk, and
how investment firms go about formulating strategies to control financial risk.
We next show how changes in the information technologies supporting these tasks have led to improvements in
the control of risk and in the design of products which involve financial risk. Advances in five areas that are
of interest are: communications software, object-oriented programming, the use of parallel processors and
supercomputers, and the application of artificial intelligence and neural nets. Although these new information
technologies create significant opportunities to improve global and departmental risk management, a basic
question that must be addressed involves the costs associated with their implementation. Thus, a third
contribution of this paper is to analyze the extent to which the implementation of these technologies will affect
firm costs. To this end, we evaluate the components of the cost function for risk management, and consider
some ways that the new technologies can be applied to reduce overall costs.Information Systems Working Papers Serie
Observations and a model for the infrared continuum of Centaurus A

The definitive version is available at www.blackwell-synergy.com. Copyright Blackwell Publishing DOI : 10.1046/j.1365-8711.1999.02908.xWe present ISOPHOT S, ISOSWS and 8 to 13 mi- cron ground based observations of Centaurus A that show prominent PAH and silicate features. These and other data are used to construct a model for the infrared continuum. We find that in a nuclear sized aperture (~4 arcsec,~60 pc) the SED is characteris- tic of emission from a starburst and AGN torus; in larger apertures an additional component of cirrus emission is required. Based on our model, the torus diameter is estimated to be 3.6 pc and the best fit- ting inclination angle of the torus is 45 degrees. This result has implications for the detectability of tori in low power AGN and in particular for the use of the IRAS 60/25 micron flux ratio as an indicator of the torus inclination
On straight words and minimal permutators in finite transformation semigroups.

???The original publication is available at www.springerlink.com???. Copyright SpringerMotivated by issues arising in computer science, we investigate the loop-free paths from the identity transformation and corresponding straight words in the Cayley graph of a finite transformation semigroup with a fixed generator set. Of special interest are words that permute a given subset of the state set. Certain such words, called minimal permutators, are shown to comprise a code, and the straight ones comprise a finite code. Thus, words that permute a given subset are uniquely factorizable as products of the subset's minimal permutators, and these can be further reduced to straight minimal permutators. This leads to insight into structure of local pools of reversibility in transformation semigroups in terms of the set of words permuting a given subset. These findings can be exploited in practical calculations for hierarchical decompositions of finite automata. As an example we consider groups arising in biological systems
Evolutionary and Functional Analyses of the Interaction between the Myeloid Restriction Factor SAMHD1 and the Lentiviral Vpx Protein.

SAMHD1 has recently been identified as an HIV-1 restriction factor operating in myeloid cells. As a countermeasure, the Vpx accessory protein from HIV-2 and certain lineages of SIV have evolved to antagonize SAMHD1 by inducing its ubiquitin-proteasome-dependent degradation. Here, we show that SAMHD1 experienced strong positive selection episodes during primate evolution that occurred in the Catarrhini ancestral branch prior to the separation between hominoids (gibbons and great apes) and Old World monkeys. The identification of SAMHD1 residues under positive selection led to mapping the Vpx-interaction domain of SAMHD1 to its C-terminal region. Importantly, we found that while SAMHD1 restriction activity toward HIV-1 is evolutionarily maintained, antagonism of SAMHD1 by Vpx is species-specific. The distinct evolutionary signature of SAMHD1 sheds light on the development of its antiviral specificity
The Castalia mission to Main Belt Coment 133P/Elst-Pizarro

We describe Castalia, a proposed mission to rendezvous with a Main Belt Comet (MBC), 133P/Elst-Pizarro. MBCs are a recently discovered population of apparently icy bodies within the main asteroid belt between Mars and Jupiter, which may represent the remnants of the population which supplied the early Earth with water. Castalia will perform the first exploration of this population by characterising 133P in detail, solving the puzzle of the MBC’s activity, and making the first in situ measurements of water in the asteroid belt. In many ways a successor to ESA’s highly successful Rosetta mission, Castalia will allow direct comparison between very different classes of comet, including measuring critical isotope ratios, plasma and dust properties. It will also feature the first radar system to visit a minor body, mapping the ice in the interior. Castalia was proposed, in slightly different versions, to the ESA M4 and M5 calls within the Cosmic Vision programme. We describe the science motivation for the mission, the measurements required to achieve the scientific goals, and the proposed instrument payload and spacecraft to achieve these
Signaling pathway of ginsenoside-Rg1 leading to nitric oxide production in endothelial cells.

We here provide definitive evidence that ginsenoside-Rg1, the pharmacologically active component of ginseng, is a functional ligand of the glucocorticoid receptor (GR) as determined by fluorescence polarization assay. Rg1 increased the phosphorylation of GR, phosphatidylinositol-3 kinase (PI3K), Akt/PKB and endothelial nitric oxide synthase (eNOS) leading to increase nitric oxide (NO) production in human umbilical vein endothelial cell. Rg1-induced eNOS phosphorylation and NO production were significantly reduced by RU486, LY294,002, or SH-6. Also, knockdown of GR completely eliminated the Rg1-induced NO production. This study revealed that Rg1 can indeed serve as an agonist ligand for GR and the activated GR can induce rapid NO production from eNOS via the non-transcriptional PI3K/Akt pathway
Deformation of Dijkgraaf-Vafa Relation via Spontaneously Broken N=2
  Supersymmetry

It is known that the fermionic shift symmetry of the N=1, U(N) gauge model
with a superpotential of an adjoint chiral superfield is replaced by the second
(spontaneously broken) supersymmetry in the N=2, U(N) gauge model with a
prepotential and Fayet-Iliopoulos parameters. Based on a diagrammatic analysis,
we demonstrate how the well-known form of the effective superpotential in the
former model is modified in the latter. A set of two equations on the one-point
functions stating the Konishi anomaly is modified accordingly.Comment: 12 pages, 1 figure; v2: typos corrected and a footnote added; v3:
  minor corrections adde
VLBI observations of jupiter with the initial test station of LOFAR and
  the nancay decametric array

AIMS: To demonstrate and test the capability of the next generation of
low-frequency radio telescopes to perform high resolution observations across
intra-continental baselines. Jupiter's strong burst emission is used to perform
broadband full signal cross-correlations on time intervals of up to hundreds of
milliseconds. METHODS: Broadband VLBI observations at about 20 MHz on a
baseline of ~50000 wavelengths were performed to achieve arcsecond angular
resolution. LOFAR's Initial Test Station (LOFAR/ITS, The Netherlands) and the
Nancay Decametric Array (NDA, France) digitize the measured electric field with
12 bit and 14 bit in a 40 MHz baseband. The fine structure in Jupiter's signal
was used for data synchronization prior to correlation on the time-series data.
RESULTS: Strong emission from Jupiter was detected during snapshots of a few
seconds and detailed features down to microsecond time-scales were identified
in dynamic spectra. Correlations of Jupiter's burst emission returned strong
fringes on 1 ms time-scales over channels as narrow as a hundred kilohertz
bandwidth. CONCLUSIONS: Long baseline interferometry is confirmed at low
frequencies, in spite of phase shifts introduced by variations in ionospheric
propagation characteristics. Phase coherence was preserved over tens to
hundreds of milliseconds with a baseline of ~700 km. No significant variation
with time was found in the correlations and an estimate for the fringe
visibility of 1, suggested that the source was not resolved. The upper limit on
the source region size of Jupiter Io-B S-bursts corresponds to an angular
resolution of ~3 arcsec. Adding remote stations to the LOFAR network at
baselines up to thousand kilometers will provide 10 times higher resolution
down to an arcsecond.Comment: 6 pages, 4 figures. Nigl, A., Zarka, P., Kuijpers, J., Falcke, H.,
  Baehren, L., VLBI observations of Jupiter with the Initial Test Station of
  LOFAR and the Nancay Decametric Array, A&A, 471, 1099-1104, accepted on
  31/05/200
Casimir Effect in Spacetime with Extra Dimensions -- From Kaluza-Klein
  to Randall-Sundrum Models

In this article, we derive the finite temperature Casimir force acting on a
pair of parallel plates due to a massless scalar field propagating in the bulk
of a higher dimensional brane model. In contrast to previous works which used
approximations for the effective masses in deriving the Casimir force, the
formulas of the Casimir force we derive are exact formulas. Our results
disprove the speculations that existence of the warped extra dimension can
change the sign of the Casimir force, be it at zero or any finite temperature.Comment: 9 pages, 3 figure. Final version accepted by Phys. Lett.
Nontrivial Fixed Point in the 4D $\Phi^4$ Lattice Model with Internal
  $O(N)$ Symmetry

It is shown that the infinite dimensional critical surface of general
euclidean lattice actions in a generic four-dimensional scalar field theory
with $\Phi^4$ interactions has a domain of special multicritical points where
higher dimensional operators play a special role. Renormalized trajectories of
higher derivative continuum field theories with nontrivial interactions are
traced back to special ultraviolet stable fixed points on the manifold of
multicritical points. These fixed points have an infinite number of relevant
directions which identify the universality classes of critical higher
derivative field theories. The relevance of the new fixed point structure is
discussed within the context of the triviality Higgs mass bound.Comment: Plenary talk given at the XII International Symposium on Lattice
  Field Theory, September 27 - October 1, 1994, Bielefeld, Germany. To appear
  in the conference proceedings; uuencoded compressed Postscript file (7
  pages.
Eviction of a 125 GeV "heavy"-Higgs from the MSSM

We prove that the present experimental constraints are already enough to rule
out the possibility of the ~125 GeV Higgs found at LHC being the second
lightest Higgs in a general MSSM context, even with explicit CP violation in
the Higgs potential. Contrary to previous studies, we are able to eliminate
this possibility analytically, using simple expressions for a relatively small
number of observables. We show that the present LHC constraints on the diphoton
signal strength, tau-tau production through Higgs and BR(B -> X_s gamma) are
enough to preclude the possibility of H_2 being the observed Higgs with m_H~125
GeV within an MSSM context, without leaving room for finely tuned
cancellations. As a by-product, we also comment on the difficulties of an MSSM
interpretation of the excess in the gamma-gamma production cross section
recently found at CMS that could correspond to a second Higgs resonance at
m_H~136 GeV.Comment: 38 pages, 9 figures. Final version accepted at JHEP. Sections 2, 3
  and appendices simplified. Experimental results updated, several references
  added. Small typos corrected and a new comparison of approximate formulas
  with full expressions include
On graphs with no induced subdivision of $K_4$

We prove a decomposition theorem for graphs that do not contain a subdivision
of $K_4$ as an induced subgraph where $K_4$ is the complete graph on four
vertices. We obtain also a structure theorem for the class $\cal C$ of graphs
that contain neither a subdivision of $K_4$ nor a wheel as an induced subgraph,
where a wheel is a cycle on at least four vertices together with a vertex that
has at least three neighbors on the cycle. Our structure theorem is used to
prove that every graph in $\cal C$ is 3-colorable and entails a polynomial-time
recognition algorithm for membership in $\cal C$. As an intermediate result, we
prove a structure theorem for the graphs whose cycles are all chordless
On the Fu\v{c}ik spectrum of the wave operator and an asymptotically
  linear problem

We study generalized solutions of the nonlinear wave equation
$$u_{tt}-u_{ss}=au^+-bu^-+p(s,t,u),$$ with periodic conditions in $t$ and
homogeneous Dirichlet conditions in $s$, under the assumption that the ratio of
the period to the length of the interval is two. When $p\equiv 0$ and $\lambda$
is a nonzero eigenvalue of the wave operator, we give a proof of the existence
of two families of curves (which may coincide) in the Fu\v{c}ik spectrum
intersecting at $(\lambda,\lambda)$. This result is known for some classes of
self-adjoint operators (which does not cover the situation we consider here),
but in a smaller region than ours. Our approach is based on a dual variational
formulation and is also applicable to other operators, such as the Laplacian.
In addition, we prove an existence result for the nonhomogeneous situation,
when the pair $(a,b)$ is not `between' the Fu\v{c}ik curves passing through
$(\lambda,\lambda)\neq(0,0)$ and $p$ is a continuous function, sublinear at
infinity
A new sample of X-ray selected narrow emission-line galaxies. I. The
  nature of optically elusive AGN

Using the 3XMM catalogue of serendipitous X-ray sources, and the SDSS-DR9
spectroscopic catalogue, we have obtained a new sample of X-ray selected narrow
emission line galaxies. The standard optical diagnostic diagram and selection
by hard X-ray luminosity expose a mismatch between the optically-based and
X-ray-based classifications. The nature of these misclassified elusive AGN can
be understood in terms of their broader X-ray and optical properties and leads
to a division of this sub-sample into two groups. A little more than half are
likely to be narrow-line Seyfert 1s (NLS1s), so misclassified because of the
contribution of the Broad Line Region (BLR) to their optical spectra. The
remainder have some of the properties of Seyfert 2 (Sy2) AGN; their optical
elusiveness can be explained by optical dilution from the host galaxy plus a
star-formation contribution and by their underluminous optical emission due to
low accretion rates. Because some of the Sy2 sources have very low accretion
rates, are unabsorbed, plus the fact that they lack broad optical emission
lines, they are good candidates to be True Sy2 AGN.Comment: 13 pages, 13 figues, accepted for publication in A&
Collective flow in ultrarelativistic $^3$He-Au collisions

The triangular flow in ultrarelativistic $^3$He-Au collisions at RHIC
energies is enhanced due to the triangular arrangement of the nucleon
configurations in $^3$He. We study the fireball eccentricities in the Glauber
Monte Carlo model and find that since the configurations of the projectile
$^3$He are elongated triangles, the created fireball has a large ellipticity
and a smaller triangularity. The dependence of the triangularity on centrality
is weak, so it cannot be extracted from the centrality dependence of the
triangular flow $v_3$, as it is dominated by the centrality dependence of the
hydrodynamic response. We propose to look at the centrality dependence of the
ratio $v_n\{4\}/v_n\{2\}$, where the uncertainties from the hydrodynamic
response cancel, and show that the basic signature of the geometry-driven
collective flow is the raise of the ratio $v_3\{4\}/v_3\{2\}$ with the number
of participant nucleons for centralities less than 10%
Compactifications of F-Theory on Calabi-Yau Threefolds at Constant Coupling

Generalizing the work of Sen, we analyze special points in the moduli space of the compactification of the F-theory on elliptically fibered Calabi-Yau threefolds where the coupling remains constant. These contain points where they can be realized as orbifolds of six torus $T^6$ by $Z_m \times Z_n (m, n=2, 3, 4, 6)$. At various types of intersection points of singularities, we find that the enhancement of gauge symmetries arises from the intersection of two kinds of singularities. We also argue that when we take the Hirzebruch surface as a base for the Calabi-Yau threefold, the condition for constant coupling corresponds to the case where the point like instantons coalesce, giving rise to enhanced gauge group of $Sp(k)$
Temperature Instabilities in N=4 Strings

An effective supergravity description of all instabilities of N_4=4 superstrings is derived. The construction is based on the N_4=4 BPS mass formula at finite temperature and uses the properties of N_4=4 gauged supergravity. It provides the boundaries of the various thermal phases in the non-perturbative moduli space. It also draws a precise picture of the dynamics in the high-temperature heterotic phase. This brief contribution summarizes results obtained in collaboration with I. Antoniadis and C. Kounnas
Noncanonical Quantization of Gravity; 1, Foundations of Affine Quantum Gravity

The nature of the classical canonical phase-space variables for gravity suggests that the associated quantum field operators should obey affine commutation relations rather than canonical commutation relations. Prior to the introduction of constraints, a primary kinematical representation is derived in the form of a reproducing kernel and its associated reproducing kernel Hilbert space. Constraints are introduced following the projection operator method which involves no gauge fixing, no complicated moduli space, nor any auxiliary fields. The result, which is only qualitatively sketched in the present paper, involves another reproducing kernel with which inner products are defined for the physical Hilbert space and which is obtained through a reduction of the original reproducing kernel. Several of the steps involved in this general analysis are illustrated by means of analogous steps applied to one-dimensional quantum mechanical models. These toy models help in motivating and understanding the analysis in the case of gravity
Multi-graviton theories: yes-go and no-go results

We report yes-go and no-go results on consistent cross-couplings for a collection of gravitons. Motivated by the search of theories where multiplets of massless spin-two fields cross-interact, we look for all the consistent deformations of a positive sum of Pauli-Fierz actions. We also investigate the problem of deforming a (positive and negative) sum of linearized Weyl gravity actions and show explicitly that there exists multi-Weyl-graviton theories. As the single-graviton Weyl theory, these theories do not have an energy bounded from below