pinecone/core-2020-05-10-deduplication huggingface dataset:
Signal Integration by the I kappa B Protein Pickle Shapes Drosophila Innate Host Defense

Pattern recognition receptors are activated following infection and trigger transcriptional programs important for host defense. Tight regulation of NF-kappa B activation is critical to avoid detrimental and misbalanced responses. We describe Pickle, a Drosophila nuclear I kappa B that integrates signaling inputs from both the Imd and Toll pathways by skewing the transcriptional output of the NF-kappa B dimer repertoire. Pickle interacts with the NF-kappa B protein Relish and the histone deacetylase dHDAC1, selectively repressing Relish homodimers while leaving other NF-kappa B dimer combinations unscathed. Pickle's ability to selectively inhibit Relish homodimer activity contributes to proper host immunity and organismal health. Although loss of pickle results in hyper-induction of Relish target genes and improved host resistance to pathogenic bacteria in the short term, chronic inactivation of pickle causes loss of immune tolerance and shortened lifespan. Pickle therefore allows balanced immune responses that protect from pathogenic microbes while permitting the establishment of beneficial commensal hostmicrobe relationships
IP-10 Kinetics in the First Week of Therapy are Strongly Associated with Bacteriological Confirmation of Tuberculosis Diagnosis in HIV-Infected Patients.

Simple effective tools to monitor the long treatment of tuberculosis (TB) are lacking. Easily measured host derived biomarkers have been identified but need to be validated in larger studies and different population groups. Here we investigate the early response in IP-10 levels (between day 0 and day 7 of TB therapy) to identify bacteriological status at diagnosis among 127 HIV-infected patients starting TB treatment. All participants were then classified as responding or not responding to treatment blindly using a previously described IP-10 kinetic algorithm. There were 77 bacteriologically confirmed cases and 41 Xpert MTB/RIF® and culture negative cases. Most participants had a measurable decline in IP-10 during the first 7 days of therapy. Bacteriologically confirmed cases were more likely to have high IP-10 levels at D0 and had a steeper decline than clinically diagnosed cases (mean decline difference 2231 pg/dl, 95% CI: 897-3566, p = 0.0013). Bacteriologically confirmed cases were more likely to have a measurable decline in IP-10 at day 7 than clinically diagnosed cases (48/77 (62.3%) vs 13/41 (31.7%), p < 0.001). This study confirms the association between a decrease in IP-10 levels during the first week of treatment and a bacteriological confirmation at diagnosis in a large cohort of HIV positive patients
Primary nodal anthracosis identified by EBUS-TBNA as a cause of FDG PET/CT positive mediastinal lymphadenopathy.

Isolated mediastinal lymphadenopathy can result from a number of potentially serious aetiologies. Traditionally those presenting with mediastinal lymphadenopathy would undergo mediastinoscopy to elucidate a final diagnosis or receive empirical treatment. There is now increased utilization of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA), in this setting. Five cases of mediastinal lymphadenopathy are presented here in which lymph node anthracosis was identified as the primary diagnosis using EBUS-TBNA. They were female, non-smokers presenting with non-specific symptoms, who retrospectively reported cooking over wood fires. Four were from South Asia. Three were investigated by F-18-fluorodeoxyglucose positron emission tomography/computed tomography (FDG PET/CT) scanning and increased signal was identified in the anthracotic nodes sampled. With expansion of PET/CT and EBUS-TBNA services it is likely that primary nodal anthracosis will be encountered more frequently and should be considered in the differential diagnosis of those with PET/CT positive lymphadenopathy. It may mimic pathologies including tuberculosis and malignancy, thus accurate sampling and follow-up are essential
Characterization of the spore surface and exosporium proteins of Clostridium sporogenes; implications for Clostridium botulinum group I strains.

Clostridium sporogenes is a non-pathogenic close relative and surrogate for Group I (proteolytic) neurotoxin-producing Clostridium botulinum strains. The exosporium, the sac-like outermost layer of spores of these species, is likely to contribute to adhesion, dissemination, and virulence. A paracrystalline array, hairy nap, and several appendages were detected in the exosporium of C. sporogenes strain NCIMB 701792 by EM and AFM. The protein composition of purified exosporium was explored by LC-MS/MS of tryptic peptides from major individual SDS-PAGE-separated protein bands, and from bulk exosporium. Two high molecular weight protein bands both contained the same protein with a collagen-like repeat domain, the probable constituent of the hairy nap, as well as cysteine-rich proteins CsxA and CsxB. A third cysteine-rich protein (CsxC) was also identified. These three proteins are also encoded in C. botulinum Prevot 594, and homologues (75-100% amino acid identity) are encoded in many other Group I strains. This work provides the first insight into the likely composition and organization of the exosporium of Group I C. botulinum spores
The effect of the OPRMI and DRDY polymorphisms on the relation between attentional bias and alcohol use in adolescence and young adulthood

Contains fulltext :
                  103188.pdf (publisher's version ) (Open Access)Background
The incentive sensitization theory posits that in the transition from sporadic to problematic alcohol use, the incentive value of alcohol increases (wanting) while its hedonic effects (liking) do not change or decreases. The effect of the OPRM1 c.118A>G polymorphism, associated with liking and wanting, and the DRD4-VNTR polymorphism, related to wanting, on the relation between attentional bias and alcohol use was investigated.
Methods
A total of 195 young adolescents (Study 1) and 86 young adult male heavy drinkers (Study 2) completed a visual probe test. Saliva samples were collected to test both polymorphisms.
Results
In Study 1, attentional bias was positively associated with adolescent alcohol use only for OPRM1 G-allele carriers. In Study 2, attentional bias was positively associated with problem drinking for carriers of a DRD4 long allele.
Discussion
It is tentatively proposed that an attentional bias for alcohol is related most strongly to liking and wanting in early adolescents, while in young adults, an attentional bias may reflect wanting. In addition, individual differences associated with two both genetic markers should be taken into account when examining the relation between attentional bias and alcohol use
Subtomogram averaging of COPII assemblies reveals how coat organization dictates membrane shape

Eukaryotic cells employ membrane-bound carriers to transport cargo between compartments in a process essential to cell functionality. Carriers are generated by coat complexes that couple cargo capture to membrane deformation. The COPII coat mediates export from the endoplasmic reticulum by assembling in inner and outer layers, yielding carriers of variable shape and size that allow secretion of thousands of diverse cargo. Despite detailed understanding of COPII subunits, the molecular mechanisms of coat assembly and membrane deformation are unclear. Here we present a 4.9 Å cryo-tomography subtomogram averaging structure of in vitro-reconstituted membrane-bound inner coat. We show that the outer coat (Sec13-Sec31) bridges inner coat subunits (Sar1-Sec23-Sec24), promoting their assembly into a tight lattice. We directly visualize the membrane-embedded Sar1 amphipathic helix, revealing that lattice formation induces parallel helix insertions, yielding tubular curvature. We propose that regulators like the procollagen receptor TANGO1 modulate this mechanism to determine vesicle shape and size
慢性腎臓病合併妊婦における分娩後腎機能増悪関連因子に関する臨床的検討

博士(医学) 乙第2962号(主論文の要旨、要約、審査結果の要旨、本文)，著者名:Yuko FUKASAWA・Yasuo MAKINO・Masaki OGAWA・Keiko UCHIDA・Hideo MATSUI，タイトル:Factors related to deterioration of renal function after singleton delivery in pregnant women with chronic kidney disease，掲載誌:Taiwanese Journal of Obstetrics and Gynecology(1028-4559)，巻・頁・年:55巻2号 p.166～170(2016)，著作権関連情報:Copyright © 2016, Taiwan Association of Obstetrics & Gynecology. Published by Elsevier Taiwan LLC. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)，DOI:10.1016/j.tjog.2016.02.003博士(医学)東京女子医科大
Dysregulation in level of goal and action identification across psychological disorders.

notes: PMCID: PMC3043255types: Journal Article; ReviewThis is an open access article that is freely available in ORE or from the publisher's web site. Please cite the published version.Copyright © 2010 Elsevier Ltd. All rights reserved.Goals, events, and actions can be mentally represented within a hierarchical framework that ranges from more abstract to more concrete levels of identification. A more abstract level of identification involves general, superordinate, and decontextualized mental representations that convey the meaning of goals, events, and actions, "why" an action is performed, and its purpose, ends, and consequences. A more concrete level of identification involves specific and subordinate mental representations that include contextual details of goals, events, and actions, and the specific "how" details of an action. This review considers three lines of evidence for considering that dysregulation of level of goal/action identification may be a transdiagnostic process. First, there is evidence that different levels of identification have distinct functional consequences and that in non-clinical samples level of goal/action identification appears to be regulated in a flexible and adaptive way to match the level of goal/action identification to circumstances. Second, there is evidence that level of goal/action identification causally influences symptoms and processes involved in psychological disorders, including emotional response, repetitive thought, impulsivity, problem solving and procrastination. Third, there is evidence that the level of goal/action identification is biased and/or dysregulated in certain psychological disorders, with a bias towards more abstract identification for negative events in depression, GAD, PTSD, and social anxiety
Prosthetic foot design: the significance of the normalized ground reaction force

This study maps bones and joints, relate them to the vertical ground reaction forces on gait. Their localities are charted in the form of graph. This is then being exploited as arguments to reason the design of prosthetic foot. The mathematical model is developed and is based on the relationship among the anatomy of bones and joints, the vertical ground reaction forces on certain points as well as the sequence when these points experience the vertical ground reaction forces. Using the model, a custom design prosthetic foot is built using a male subject of size 5 scanned foot image. It is concluded that proper mappings and modeling of foot structure can be used as reference in design and development of prosthetic feet
Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME

This review encompasses the most important advances in liver functions and hepatotoxicity and analyzes which mechanisms can be studied in vitro. In a complex architecture of nested, zonated lobules, the liver consists of approximately 80 % hepatocytes and 20 % non-parenchymal cells, the latter being involved in a secondary phase that may dramatically aggravate the initial damage. Hepatotoxicity, as well as hepatic metabolism, is controlled by a set of nuclear receptors (including PXR, CAR, HNF-4α, FXR, LXR, SHP, VDR and PPAR) and signaling pathways. When isolating liver cells, some pathways are activated, e.g., the RAS/MEK/ERK pathway, whereas others are silenced (e.g. HNF-4α), resulting in up- and downregulation of hundreds of genes. An understanding of these changes is crucial for a correct interpretation of in vitro data. The possibilities and limitations of the most useful liver in vitro systems are summarized, including three-dimensional culture techniques, co-cultures with non-parenchymal cells, hepatospheres, precision cut liver slices and the isolated perfused liver. Also discussed is how closely hepatoma, stem cell and iPS cell-derived hepatocyte-like-cells resemble real hepatocytes. Finally, a summary is given of the state of the art of liver in vitro and mathematical modeling systems that are currently used in the pharmaceutical industry with an emphasis on drug metabolism, prediction of clearance, drug interaction, transporter studies and hepatotoxicity. One key message is that despite our enthusiasm for in vitro systems, we must never lose sight of the in vivo situation. Although hepatocytes have been isolated for decades, the hunt for relevant alternative systems has only just begun
Exactly solvable D_N-type quantum spin models with long-range
  interaction

We derive the spectra of the D_N-type Calogero (rational) su(m) spin model,
including the degeneracy factors of all energy levels. By taking the strong
coupling limit of this model, in which its spin and dynamical degrees of
freedom decouple, we compute the exact partition function of the su(m)
Polychronakos-Frahm spin chain of D_N type. With the help of this partition
function we study several statistical properties of the chain's spectrum, such
as the density of energy levels and the distribution of spacings between
consecutive levels.Comment: 12 pages, 2 figure
Pseudo-Newtonian Potential for Charged Particle in Kerr-Newman Geometry

We consider the equatorial circular motion of a test particle of specific
charge q/m << 1 in the Kerr-Newman geometry of a rotating charged black hole.
We find the particle's conserved energy and conserved projection of the angular
momentum on the black hole's axis of rotation as corrections, in leading order
of q/m, to the corresponding energy and angular momentum of a neutral particle.
We determine the centripetal force acting on the test particle and,
consequently, we find a classical pseudo-Newtonian potential with which one can
mimic this general relativistic problem.Comment: 8 page
Thermal evolution of the chiral condensate in SU(2) and SU(3) Chiral
  Perturbation Theory

The temperature evolution of the chiral condensates in a gas made of pions,
kaons and etas is studied within the framework of SU(2) and SU(3) Chiral
Perturbation Theory. We describe the temperature dependence of the quark
condensates by using the meson meson scattering phase shifts in a second order
virial expansion. We find that the SU(3) formalism yields an extrapolated
melting temperature for the non-strange condensates which is lower by about
20-30 MeV than within SU(2). In addition our results show that the strange
condensate melting is slower than that of the non-strange, due to the different
strange and non-strange quark masses.Comment: 6 pages, two figures. To appear in the Proceedings of QCD02.
  Montpellier, France. July 200
Broken planar Skyrmions -- statics and dynamics

The broken planar Skyrme model is a theory that breaks global O(3) symmetry
to the dihedral group D_N. It has been shown that the single soliton solution
is formed of N constituent parts, named partons, that are topologically
confined. The multi-soliton solutions have already been computed for N = 3 and
were shown to be related to polyiamonds. We extend this for larger N and
demonstrate that this polyform structure continues (planar figures formed by
regular N-gons joined along their edges, of which polyiamonds are the N=3
subset). Furthermore, we numerically simulate the dynamics of this model for
the first time. It will be demonstrated that the time dependent behaviour of
these solutions can be broken down into the interactions of its constituent
partons. The results are then compared with those of the standard planar Skyrme
model.Comment: 20 pages, 10 figure
Ginzburg-Landau phase diagram of QCD near chiral critical point - chiral
  defect lattice and solitonic pion condensate -

We investigate the influence of the isospin asymmetry on the phase structure
of quark matter near the chiral critical point systematically using a
generalized version of Ginzburg-Landau approach. The effect has proven to be so
profound that it brings about not only a shift of the critical point but also a
rich variety of phases in its neighborhood. In particular, there shows up a
phase with spatially varying charged pion condensate which we name the
"solitonic pion condensate" in addition to the "chiral defect lattice" where
the chiral condensate is partially destructed by periodic placements of
two-dimensional wall-like defects. Our results suggest that there may be an
island of solitonic pion condensate in the low temperature and high density
side of QCD phase diagram.Comment: 5 pages, 4 eps figures; v2: version accepted for publication in PL
Young's double slit interference pattern from a twisted beam

The interference pattern of a Laguerre Gaussian beam in a double slit
experiment is reported. Whereas a typical laser beam phase front is planar, a
Laguerre Gaussian beam exhibits a wave front that is twisting along the
direction of propagation. This leads to a distorted interference pattern. The
topological charge also called the order of the twisted beam can be then
readily and simply determined. More precisely, the naked eye resolution of the
distortion shift of the interference pattern directly informs about the number
of twists made as well as on the sign of the twist. These results are in very
good agreement with theoretical calculations that offer a general description
of the double slit interference with twisted beams.Comment: 11 pages, 4 figure
Vacuum condition and the relation between response parameter and anomaly
  coefficient in (1+3) dimensions

The role of Israel-Hartle-Hawking vacuum is discussed for anomalous fluid in
presence of both the gauge and gravitational anomalies in ($1+3$) dimensions. I
show that imposition of this vacuum condition leads to the relation
$\tilde{c}_{4d}=-8\pi^2c_m$ between the response parameter ($\tilde{c}_{4d}$)
and the anomaly coefficient ($c_m$). This establishes a connection between the
coefficients appearing in a first order and a third order derivative terms in
the constitutive relation.Comment: Comments added, to appear in JHE
Integrable S-matrices, massive and massless modes and the AdS_2 x S^2
  superstring

We derive the exact S-matrix for the scattering of particular representations
of the centrally-extended psu(1|1)^2 Lie superalgebra, conjectured to be
related to the massive modes of the light-cone gauge string theory on AdS_2 x
S^2 x T^6. The S-matrix consists of two copies of a centrally-extended psu(1|1)
invariant S-matrix and is in agreement with the tree-level result following
from perturbation theory. Although the overall factor is left unfixed, the
constraints following from crossing symmetry and unitarity are given. The
scattering involves long representations of the symmetry algebra, and the
relevant representation theory is studied in detail. We also discuss Yangian
symmetry and find it has a standard form for a particular limit of the
aforementioned representations. This has a natural interpretation as the
massless limit, and we investigate the corresponding limits of the massive
S-matrix. Under the assumption that the massless modes of the light-cone gauge
string theory transform in these limiting representations, the resulting
S-matrices would provide the building blocks for the full S-matrix. Finally,
some brief comments are given on the Bethe ansatz.Comment: 33 pages; v2: 37 pages, clarifications, including on the issue of
  double crossing, and comments added, version to appear in JHE
A new AdS_4/CFT_3 Dual with Extended SUSY and a Spectral Flow

We construct a new AdS_4 background in Type IIB supergravity by means of a
non-Abelian T-duality transformation on the Type IIA dual of ABJM. The analysis
of probe and particle-like branes suggests a dual CFT in which each of the
gauge groups is doubled. A common feature of non-Abelian T-duality is that in
the absence of any global information coming from String Theory it gives rise
to non-compact dual backgrounds, with coordinates living in the Lie algebra of
the Lie group involved in the dualization. In backgrounds with CFT duals this
poses obvious problems to the CFTs. In this paper we show that for the new
AdS_4 background the gauge groups of the associated dual CFT undergo a spectral
flow as the non-compact internal direction runs from 0 to infinity, which
resembles Seiberg duality in N=1. This phenomenon, very reminiscent of the
cascade, provides an interpretation in the CFT for the running of the
non-compact coordinate, and suggests that at the end of the flow the extra
charges disappear and the dual CFT is described by a 2-node quiver very similar
to ABJM, albeit with reduced supersymmetry.Comment: 40 pages, published versio
Kaluza-Klein theory for teleparallel gravity

We study teleparallel gravity in the \emph{original} Kaluza-Klein (KK)
scenario. Our calculation of the KK reduction of teleparallel gravity indicates
that the 5-dimensional torsion scalar $^{(5)}T$ generates the non-Brans-Dicke
type effective Lagrangian in 4-dimension due to an additional coupling between
the derivative of the scalar field and torsion, but the result is equivalent to
that in general relativity. We also discuss the cosmological behavior in the
FLRW universe based on the effective teleparallel gravity.Comment: 8 pages, no figure, Phys. Lett. B737 (2014) 248-25
Quantitative study of valence and configuration interaction parameters
  of the Kondo semiconductors CeM2Al10 (M = Ru, Os and Fe) by means of
  bulk-sensitive hard x-ray photoelectron spectroscopy

The occupancy of the 4f^n contributions in the Kondo semiconductors
CeM2Al10(M = Ru, Os and Fe) has been quantitatively determined by means of
bulk-sensitive hard x-ray photoelectron spectroscopy (HAXPES) on the Ce 3d core
levels. Combining a configuration interaction scheme with full multiplet
calculations allowed to accurately describe the HAXPES data despite the
presence of strong plasmon excitations in the spectra. The configuration
interaction parameters obtained from this analysis -- in particular the
hybridization strength V_eff and the effective f binding energy Delta_f --
indicate a slightly stronger exchange interaction in CeOs2Al10 compared to
CeRu2Al10, and a significant increase in CeFe2Al10. This verifies the
coexistence of a substantial amount of Kondo screening with magnetic order and
places the entire CeM2Al10 family in the region of strong exchange
interactions.Comment: 9 pages, 4 figures, submitted to Physical Review
Chern-Simons Couplings for Dielectric F-Strings in Matrix String Theory

We compute the non-abelian couplings in the Chern-Simons action for a set of
coinciding fundamental strings in both the type IIA and type IIB Matrix string
theories. Starting from Matrix theory in a weakly curved background, we
construct the linear couplings of closed string fields to type IIA Matrix
strings. Further dualities give a type IIB Matrix string theory and a type IIA
theory of Matrix strings with winding.Comment: 6 pages. Contribution to the proceedings of the RTN meeting ``The
  Quantum Structure of Spacetime and the Geometric Nature of Fundamental
  Interactions'', (Corfu, 13-20 September 2001). v2: reference adde