pinecone/core-2020-05-10-deduplication huggingface dataset:
Differentiated, promoter-specific response of [4Fe-4S] NsrR DNA binding to reaction with nitric oxide

© 2016 by The American Society for Biochemistry and Molecular Biology, Inc. NsrR is an iron-sulfur cluster protein that regulates the nitric oxide (NO) stress response of many bacteria. NsrR from Streptomyces coelicolor regulates its own expression and that of only two other genes, hmpA1 and hmpA2, which encode HmpA enzymes predicted to detoxify NO. NsrR binds promoter DNA with high affinity only when coordinating a [4Fe-4S] cluster. Here we show that reaction of [4Fe-4S] NsrR with NO affects DNA binding differently depending on the gene promoter. Binding to the hmpA2 promoter was abolished at ∼2 NO per cluster, although for the hmpA1 and nsrR promoters, ∼4 and ∼8 NO molecules, respectively, were required to abolish DNA binding. Spectroscopic and kinetic studies of the NO reaction revealed a rapid, multi-phase, non-concerted process involving up to 8-10 NO molecules per cluster, leading to the formation of several iron-nitrosyl species. A distinct intermediate was observed at ∼2 NO per cluster, along with two further intermediates at ∼4 and ∼6 NO. The NsrR nitrosylation reaction was not significantly affected by DNA binding. These results show that NsrR regulates different promoters in response to different concentrations of NO. Spectroscopic evidence indicates that this is achieved by different NO-FeS complexes
Experimental verification of the vibro-impact capsule model

This is the author accepted manuscript. The final version is available from Springer Verlag via the DOI in this record.In this paper, an experimental verification of the vibro-impact capsule model proposed by Liu et al. in (Int. J. Mech. Sci, 66:2–11; 2013a, Int. J. Mech. Sci, 72:39–54; 2013b, Int. J. Non-Linear Mech., 70, 30–46; 2015) is presented. The capsule dynamics is investigated experimentally by varying the stiffness of the support spring, and the frequency and the amplitude of excitation. The novel design of the experimental set-up is discussed, and comparisons between the experiments and numerical simulations are presented showing a good agreement. The conducted bifurcation analysis indicates that the behaviour of the system is mainly periodic and that a fine tuning of the control parameters can significantly improve the performance of the system. The main findings provide a better insight into the vibro-impact systems subject to nonlinear friction, and the experimental rig can be used to predict the dynamic behaviour of these systems.The Small Research Grant by the Carnegie Trust for the Universities of Scotlan
Data on the verification and validation of segmentation and registration methods for diffusion MRI.

The verification and validation of segmentation and registration methods is a necessary assessment in the development of new processing methods. However, verification and validation of diffusion MRI (dMRI) processing methods is challenging for the lack of gold-standard data. The data described here are related to the research article entitled "Surface-driven registration method for the structure-informed segmentation of diffusion MR images" [1], in which publicly available data are used to derive golden-standard reference-data to validate and evaluate segmentation and registration methods in dMRI
Search for W' decaying to tau lepton and neutrino in proton-proton collisions at $\sqrt{s} = 8$ TeV

The first search for a heavy charged vector boson in the final state with a tau lepton and a neutrino is reported, using 19.7 fb$^{−1}$ of LHC data at $\sqrt{s} = 8$ TeV . A signal would appear as an excess of events with high transverse mass, where the standard model background is low. No excess is observed. Limits are set on a model in which the W′ decays preferentially to fermions of the third generation. These results substantially extend previous constraints on this model. Masses below 2.0 to 2.7 TeV are excluded, depending on the model parameters. In addition, the existence of a W′ boson with universal fermion couplings is excluded at 95% confidence level, for W′ masses below 2.7 TeV. For further reinterpretation a model-independent limit on potential signals for various transverse mass thresholds is also presented
Search for a Higgs boson decaying into gamma* gamma to ll gamma with low dilepton mass in pp collisions at sqrt(s) = 8 TeV

A search is described for a Higgs boson decaying into two photons, one of which has an internal conversion to a muon or an electron pair (ll gamma). The analysis is performed using proton-proton collision data recorded with the CMS detector at the LHC at a centre-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 19.7 inverse femtobarns. The events selected have an opposite-sign muon or electron pair and a high transverse momentum photon. No excess above background has been found in the three-body invariant mass range 120 &lt; m[ll gamma] &lt; 150 GeV, and limits have been derived for the Higgs boson production cross section times branching fraction for the decay H to gamma* gamma to ll gamma, where the dilepton invariant mass is less than 20 GeV. For a Higgs boson with m[H] = 125 GeV, a 95% confidence level (CL) exclusion observed (expected) limit is 6.7 (5.9 +2.8/-1.8) times the standard model prediction. Additionally, an upper limit at 95% CL on the branching fraction of H to J/Psi gamma for the 125 GeV Higgs boson is set at 1.5E-3
Centrality and rapidity dependence of inclusive jet production in √sNN =5.02  TeV proton-lead collisions with the ATLAS detector

Measurements of the centrality and rapidity dependence of inclusive jet production in √sNN=5.02  TeV proton--lead (p +Pb) collisions and the jet cross-section in √s =2.76  TeV proton--proton collisions are presented. These quantities are measured in datasets corresponding to an integrated luminosity of 27.8 nb⁻¹ and 4.0 pb⁻¹, respectively, recorded with the ATLAS detector at the Large Hadron Collider in 2013. The p +Pb collision centrality was characterised using the total transverse energy measured in the pseudorapidity interval −4.9<η<−3.2  in the direction of the lead beam. Results are presented for the double-differential per-collision yields as a function of jet rapidity and transverse momentum (p T  ) for minimum-bias and centrality-selected p +Pb collisions, and are compared to the jet rate from the geometric expectation. The total jet yield in minimum-bias events is slightly enhanced above the expectation in a p T-dependent manner but is consistent with the expectation within uncertainties. The ratios of jet spectra from different centrality selections show a strong modification of jet production at all p T at forward rapidities and for large p T at mid-rapidity, which manifests as a suppression of the jet yield in central events and an enhancement in peripheral events. These effects imply that the factorisation between hard and soft processes is violated at an unexpected level in proton-nucleus collisions. Furthermore, the modifications at forward rapidities are found to be a function of the total jet energy only, implying that the violations may have a simple dependence on the hard parton-parton kinematics
Brief Report: Intestinal dysbiosis in ankylosing spondylitis

Objective Ankylosing spondylitis (AS) is a common, highly heritable immune-mediated arthropathy that occurs in genetically susceptible individuals exposed to an unknown but likely ubiquitous environmental trigger. There is a close relationship between the gut and spondyloarthritis, as exemplified in patients with reactive arthritis, in whom a typically self-limiting arthropathy follows either a gastrointestinal or urogenital infection. Microbial involvement in AS has been suggested; however, no definitive link has been established. The aim of this study was to determine whether the gut in patients with AS carries a distinct microbial signature compared with that in the gut of healthy control subjects. Methods Microbial profiles for terminal ileum biopsy specimens obtained from patients with recent-onset tumor necrosis factor antagonist-naive AS and from healthy control subjects were generated using culture-independent 16S ribosomal RNA gene sequencing and analysis techniques. Results Our results showed that the terminal ileum microbial communities in patients with AS differ significantly (P < 0.001) from those in healthy control subjects, driven by a higher abundance of 5 families of bacteria (Lachnospiraceae [P = 0.001], Ruminococcaceae [P = 0.012], Rikenellaceae [P = 0.004], Porphyromonadaceae [P = 0.001], and Bacteroidaceae [P = 0.001]) and a decrease in the abundance of 2 families of bacteria (Veillonellaceae [P = 0.01] and Prevotellaceae [P = 0.004]). Conclusion We show evidence for a discrete microbial signature in the terminal ileum of patients with AS compared with healthy control subjects. The microbial composition was demonstrated to correlate with disease status, and greater differences were observed between disease groups than within disease groups. These results are consistent with the hypothesis that genes associated with AS act, at least in part, through effects on the gut microbiome
Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3.

Efst á síðunni er hægt að nálgast greinina í heild sinni með því að smella á hlekkinn                    To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked FilesCis-acting regulatory SNPs resulting in differential allelic expression (DAE) may, in part, explain the underlying phenotypic variation associated with many complex diseases. To investigate whether common variants associated with DAE were involved in breast cancer susceptibility among BRCA1 and BRCA2 mutation carriers, a list of 175 genes was developed based of their involvement in cancer-related pathways.Using data from a genome-wide map of SNPs associated with allelic expression, we assessed the association of ~320 SNPs located in the vicinity of these genes with breast and ovarian cancer risks in 15,252 BRCA1 and 8211 BRCA2 mutation carriers ascertained from 54 studies participating in the Consortium of Investigators of Modifiers of BRCA1/2.We identified a region on 11q22.3 that is significantly associated with breast cancer risk in BRCA1 mutation carriers (most significant SNP rs228595 p = 7 × 10(-6)). This association was absent in BRCA2 carriers (p = 0.57). The 11q22.3 region notably encompasses genes such as ACAT1, NPAT, and ATM. Expression quantitative trait loci associations were observed in both normal breast and tumors across this region, namely for ACAT1, ATM, and other genes. In silico analysis revealed some overlap between top risk-associated SNPs and relevant biological features in mammary cell data, which suggests potential functional significance.We identified 11q22.3 as a new modifier locus in BRCA1 carriers. Replication in larger studies using estrogen receptor (ER)-negative or triple-negative (i.e., ER-, progesterone receptor-, and HER2-negative) cases could therefore be helpful to confirm the association of this locus with breast cancer risk
Comments on N = (2, 2) supersymmetry on two-manifolds.

We study curved-space rigid supersymmetry for two-dimensional  NN  = (2, 2) supersymmetric fields theories with a vector-like R-symmetry by coupling such theories to background supergravity. The associated Killing spinors can be viewed as holomorphic sections of particular complex line bundles over Euclidean space-time, which severely restricts the allowed supersymmetric couplings on compact orientable Riemann surfaces without boundaries. For genus g > 1, the only consistent non-singular couplings are the ones dictated by the topological A-twist. On spaces with S2 topology, there exist additional supersymmetric backgrounds with m = 0 or ±1 unit of flux for the R-symmetry gauge field. The m = −1 case includes the Ω-background on the sphere. We also systematically work out the curved-space supersymmetry multiplets and supersymmetric Lagrangians
Investigating the measurement of offshore wind turbine blades using coherent laser radar

AbstractLarge-scale offshore wind turbine blades need careful dimensional inspection at the production stage. This paper aims to establish an accurate measurement technique using Coherent Laser Radar technology combined with B-Spline point generation and alignment. Through varying the Degrees of Freedom (DoF), used for data point transformation, within the Spatial Analyser software package, erroneous inspection results generated by unconstrained blade flexing can be eradicated. The paper concludes that implementing a single B-Spline point generation and alignment method, whilst allowing transformation with DoF in X, Y and Rz, provides confidence to wind turbine blade manufacturers that inspection data is accurate. The experimental procedure described in this paper can also be applied to the precision inspection of other large-scale non-rigid, unconstrained objects
Point sets that minimize (≤k)-edges, 3-decomposable drawings, and the rectilinear crossing number of K30

AbstractThere are two properties shared by all known crossing-minimizing geometric drawings of Kn, for n a multiple of 3. First, the underlying n-point set of these drawings minimizes the number of (≤k)-edges, that means, has exactly 3(k+22)(≤k)-edges, for all 0≤k<n/3. Second, all such drawings have the n points divided into three groups of equal size; this last property is captured under the concept of 3-decomposability. In this paper we show that these properties are closely related: every n-point set with exactly 3(k+22)(≤k)-edges for all 0≤k<n/3, is 3-decomposable. The converse, however, is easy to see that it is false. As an application, we prove that the rectilinear crossing number of K30 is 9726
Are adverse effects of antiepileptic drugs different in symptomatic partial and idiopathic generalized epilepsies? The Portuguese–Brazilian validation of the Liverpool Adverse Events Profile

AbstractWe report the results of administration of the Portuguese–Brazilian translation of the Liverpool Adverse Events Profile (LAEP) to 100 patients (mean age=34.5, SD=12.12; 56 females), 61 with symptomatic partial epilepsy (SPE) and 39 with idiopathic generalized epilepsy (IGE) (ILAE, 1989) who were on a stable antiepileptic drug (AED) regimen and being treated in a Brazilian tertiary epilepsy center. Carbamazepine was the most commonly used AED (43.0%), followed by valproic acid (32.0%). Two or more AEDs were used by 69.0% of patients. The mean LAEP score (19 questions) was 37.6 (SD=13.35). The most common adverse effects were sleepiness (35.0%), memory problems (35.0%), and difficulty in concentrating (25.0%). Higher LAEP scores were associated with polytherapy with three or more AEDs (P=0.005), female gender (P<0.001), older age (P<0.001), and uncontrolled seizures (P=0.045). The intraclass coefficient (test–retest reliability) for LAEP overall score was 0.848 (95% CI=0.782–0.895), with a range from 0.370 (unsteadiness) to 0.750 (memory problems). Cronbach's α coefficient (internal consistency) was 0.903. The LAEP was highly correlated with Quality of Life in Epilepsy-31 inventory (r=−0.804, P>0.001) and Hospital Anxiety and Depression Scale (Depression: r=0.637, P<0.001; Anxiety: r=0.621, P<0.001) dimensions. LAEP overall scores were similar in people with SPE and IGE and were not helpful in differentiating adverse effects in these two groups. Clinical variables that influenced global LAEP were seizure frequency (P=0.050) and generalized tonic–clonic seizures in the last month (P=0.031) in the IGE group, and polytherapy with three or more AEDs (P=0.003 and P=0.003) in both IGE and SPE groups
Designing a knowledge co-production operating space for urban environmental governance—Lessons from Rotterdam, Netherlands and Berlin, Germany

AbstractChallenges for a sustainable urban development are increasingly important in cities because urbanization and related land take come up with negative challenges for the environment and for city residents. Searching for successful solutions to environmental problems requires combined efforts of different scientific disciplines and an active dialogue between stakeholders from policy and society. In this paper, we present a comparative assessment of the way policy-science dialogues have achieved knowledge co-production about strategic urban environmental governance action using the cities of Berlin in Germany and Rotterdam in the Netherlands as case studies. The ecosystem services framework is applied as a lens for policy–science interaction and a ‘knowledge co-production operating space’ is introduced. We show how policy officers, urban planners, practitioners and scientists learned from each other, and highlight the impact of this knowledge co-production for governance practice. We found that the concerted collaboration and co-creation between researchers and policy officers have led to mutual learning and establishment of relationships and trust in both cities. Not only the policy-relevance of research and its policy uptake were achieved but also new insights for research blind spots were created. In our conclusions we reflect on co-production processes with two types of conditions that we introduced to be most influential in the way knowledge can be co-created. These are conditions that relate to the way knowledge co-production processes are set-up and, conditions that relate to the expected value or benefit that the co-produced knowledge will bring across society, policy and practice
Scale invariance of the η-deformed AdS5×S5 superstring, T-duality and modified type II equations

AbstractWe consider the ABF background underlying the η-deformed AdS5×S5 sigma model. This background fails to satisfy the standard IIB supergravity equations which indicates that the corresponding sigma model is not Weyl invariant, i.e. does not define a critical string theory in the usual sense. We argue that the ABF background should still define a UV finite theory on a flat 2d world-sheet implying that the η-deformed model is scale invariant. This property follows from the formal relation via T-duality between the η-deformed model and the one defined by an exact type IIB supergravity solution that has 6 isometries albeit broken by a linear dilaton. We find that the ABF background satisfies candidate type IIB scale invariance conditions which for the R–R field strengths are of the second order in derivatives. Surprisingly, we also find that the ABF background obeys an interesting modification of the standard IIB supergravity equations that are first order in derivatives of R–R fields. These modified equations explicitly depend on Killing vectors of the ABF background and, although not universal, they imply the universal scale invariance conditions. Moreover, we show that it is precisely the non-isometric dilaton of the T-dual solution that leads, after T-duality, to modification of type II equations from their standard form. We conjecture that the modified equations should follow from κ-symmetry of the η-deformed model. All our observations apply also to η-deformations of AdS3×S3×T4and AdS2×S2×T6models
“Semi-realistic” F-term inflation model building in supergravity

AbstractWe describe methods for building “semi-realistic” models of F-term inflation. By semi-realistic we mean that they are built in, and obey the requirements of, “semi-realistic” particle physics models. The particle physics models are taken to be effective supergravity theories derived from orbifold compactifications of string theory, and their requirements are taken to be modular invariance, absence of mass terms and stabilization of moduli. We review the particle physics models, their requirements and tools and methods for building inflation models
Magnetic and quadrupole moments of neutron deficient 58–62Cu isotopes

AbstractThis paper reports on the ground state nuclear moments measured in 58–62Cu using collinear laser spectroscopy at the ISOLDE facility. The quadrupole moments for 58–60Cu have been measured for the first time as Q(Cu58)=−15(3) efm2, Q(Cu59)=−19.3(19) efm2, Q(Cu60)=+11.6(12) efm2 and with higher precision for 61,62Cu as Q(Cu61)=−21.1(10) efm2, Q(Cu62)=−2.2(4) efm2. The magnetic moments of 58,59Cu are measured with a higher precision as μ(Cu58)=+0.570(2)μN and μ(Cu59)=+1.8910(9)μN. The experimental nuclear moments are compared to large-scale shell-model calculations with the GXPF1 and GXPF1A effective interactions, allowing the softness of the 56Ni core to be studied
Mass spectrometry identification of age-associated proteins from the malaria mosquitoes Anopheles gambiae s.s. and Anopheles stephensi

AbstractThis study investigated proteomic changes occurring in Anopheles gambiae and Anopheles stephensi during adult mosquito aging. These changes were evaluated using two-dimensional difference gel electrophoresis (2D-DIGE) and the identities of aging related proteins were determined using capillary high-pressure liquid chromatography (capHPLC) coupled with a linear ion-trap (LTQ)-Orbitrap XL hybrid mass spectrometry (MS). Here, we have described the techniques used to determine age associated proteomic changes occurring in heads and thoraces across three age groups; 1, 9 and 17 d old A. gambiae and 4 age groups; 1, 9, 17 and 34 d old A. stephensi. We have provided normalised spot volume raw data for all protein spots that were visible on 2D-DIGE images for both species and processed Orbitrap mass spectrometry data. For public access, mass spectrometry raw data are available via ProteomeXchange with identifier PXD002153. A detailed description of this study has been described elsewhere [1]
Evolutionary Divergence of Enzymatic Mechanisms for Posttranslational Polyglycylation

SummaryPolyglycylation is a posttranslational modification that generates glycine side chains on proteins. Here we identify a family of evolutionarily conserved glycine ligases that modify tubulin using different enzymatic mechanisms. In mammals, two distinct enzyme types catalyze the initiation and elongation steps of polyglycylation, whereas Drosophila glycylases are bifunctional. We further show that the human elongating glycylase has lost enzymatic activity due to two amino acid changes, suggesting that the functions of protein glycylation could be sufficiently fulfilled by monoglycylation. Depletion of a glycylase in Drosophila using RNA interference results in adult flies with strongly decreased total glycylation levels and male sterility associated with defects in sperm individualization and axonemal maintenance. A more severe RNAi depletion is lethal at early developmental stages, indicating that protein glycylation is essential. Together with the observation that multiple proteins are glycylated, our functional data point towards a general role of glycylation in protein functions