cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Role of hPHF1 in H3K27 Methylation and Hox Gene Silencing
Creators: name: Zhang, Y.
name: He, J.
name: Cao, R.
name: Erdjument-Bromage, H.
name: Tempst, P.
name: Wang, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Polycomb group (PcG) proteins are required for maintaining the silent state of the homeotic genes and other important developmental regulators. The silencing function of the PcG proteins has been linked to their intrinsic histone modifying enzymatic activities. The EED-EZH2 complex, containing the core subunits EZH2, EED, SUZ12, and RbAp48, functions as a histone H3K27-specific methyltransferase. Here we describe the identification and characterization of a related EED-EZH2 protein complex which is distinguished from the previous complex by the presence of another PcG protein, hPHF1. Consistent with the ability of hPHF1 to stimulate the enzymatic activity of the core EED-EZH2 complex in vitro, manipulation of mPcl1, the mouse counterpart of hPHF1, in NIH 3T3 cells and cells of the mouse male germ cell line GC1spg results in global alteration of H3K27me2 and H3K27me3 levels and Hox gene expression. Small interfering RNA-mediated knockdown of mPcl1 affects association of the Eed-Ezh2 complex with certain Hox genes, such as HoxA10, as well as Hox gene expression concomitant with an alteration on the H3K27me2 levels of the corresponding promoters. Therefore, our results reveal hPHF1 as a component of a novel EED-EZH2 complex and demonstrate its important role in H3K27 methylation and Hox gene silencing.
In-orbit Performance of the Near-Infrared Spectrograph NIRSpec on the James Webb Space Telescope
Creators: name: Böker, T.
name: Beck, T. L.
name: Birkmann, S. M.
name: Giardino, G.
name: Keyes, C.
name: Kumari, N.
name: Muzerolle, J.
name: Rawle, T.
name: Zeidler, P.
name: Abul-Huda, Y.
name: de Oliveira, C. Alves
name: Arribas, S.
name: Bechtold, K.
name: Bhatawdekar, R.
name: Bonaventura, N.
name: Bunker, A. J.
name: Cameron, A. J.
name: Carniani, S.
name: Charlot, S.
name: Curti, M.
name: Espinoza, N.
name: Ferruit, P.
name: Franx, M.
name: Jakobsen, P.
name: Karakla, D.
name: López-Caniego, M.
name: Lützgendorf, N.
name: Maiolino, R.
name: Manjavacas, E.
name: Marston, A. P.
name: Moseley, S. H.
name: Ogle, P.
name: Perna, M.
name: Peña-Guerrero, M.
name: Pirzkal, N.
name: Plesha, R.
name: Proffitt, C. R.
name: Rauscher, B. J.
name: Rix, H. -W.
name: del Pino, B. Rodríguez
name: Rustamkulov, Z.
name: Sabbi, E.
name: Sing, D. K.
name: Sirianni, M.
name: Plate, M. te
name: Úbeda, L.
name: Wahlgren, G. M.
name: Wislowski, E.
name: Wu, R.
name: Willott, C. J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: The Near-Infrared Spectrograph (NIRSpec) is one of the four focal plane instruments on the James Webb Space Telescope. In this paper, we summarize the in-orbit performance of NIRSpec, as derived from data collected during its commissioning campaign and the first few months of nominal science operations. More specifically, we discuss the performance of some critical hardware components such as the two NIRSpec Hawaii-2RG (H2RG) detectors, wheel mechanisms, and the micro-shutter array. We also summarize the accuracy of the two target acquisition procedures used to accurately place science targets into the slit apertures, discuss the current status of the spectro-photometric and wavelength calibration of NIRSpec spectra, and provide the as measured sensitivity in all NIRSpec science modes. Finally, we point out a few important considerations for the preparation of NIRSpec science programs.
description: accepted by PASP for special issue on JWST in-orbit performance
หลักการบริหารศูนย์การเรียนเพื่อส่งเสริมการเรียนรู้ตลอดชีวิต
Creators: name: เมธชนนท์ ประจวบลาภ
Publisher: name: Department of Strategics for Improving Education Quality, Surindra Rajabhat University
Year: 2023
Subjects: ศูนย์การเรียน
การบริหาร
การเรียนรู้ตลอดชีวิต

description: วารสารราชภัฏสุรินทร์วิชาการ, 1, 5, 97-112
Thermodynamics of black holes and the symmetric generalized uncertainty principle
Creators: name: Dutta, Abhijit
name: Gangopadhyay, Sunandan
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper, we have investigated the thermodynamics of Schwarzschild black holes using the symmetric generalized uncertainty principle which contains correction terms involving momentum and position uncertainty. We obtain the mass-temperature relation and the heat capacity of the black hole using which we compute the critical and remnant masses. The entropy is found to satisfy the area law upto leading order corrections from the symmetric generalized uncertainty principle.
description: References added
Crowdsourced Doppler Measurements of Time Standard Stations Demonstrating Ionospheric Variability (Poster)
Creators: name: Collins, Kristina
name: Gibbons, John
name: Kazdan, David
name: Boedicker, Rachel
name: Montare, Aidan
name: Benedict, Robert
name: Romanek, Veronica
name: Frissell, Nathaniel
Publisher: name: Zenodo
Year: 2022

description: Abstract: Ionospheric variability due to atmospheric coupling produces measurable effects in Doppler shift of HF (high frequency, 3-30 MHz) skywave signals. These effects are straightforward to measure with low-cost equipment and are conducive to citizen science campaigns. The Ham Radio Science Citizen Investigation (HamSCI) Personal Space Weather Station (PSWS) network is a modular network of community-maintained, open-source receivers, which measure Doppler shift in the precise carrier signals of time standard stations WWV and WWVH. Here, data from the first prototype of the Low-Cost PSWS, also known as the Grape receiver, are presented for a period of time spanning late 2019 to early 2022. Software tools for the visualization and analysis of this living dataset are also discussed and provided. These tools are robust to data interruptions and to the addition, removal or modification of stations, allowing both short- and long-term visualization at higher density and faster cadence than other methods. We show two years' worth of Doppler observations from one station showing observed diurnal and seasonal variations in the dawn/dusk terminators. We highlight a solar flare observation. We also discuss our plans to use and extend this network for observations of upcoming solar eclipses.
Two Schwarzschild-like black holes balanced by their scalar hair
Creators: name: Herdeiro, Carlos A. R.
name: Radu, Eugen
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We show that, unlike vacuum General Relativity, Einstein-scalar theories allow balanced static, neutral, asymptotically flat, double-black hole solutions, for scalar field models minimally coupled to gravity, with appropriate self-interactions. These are scalar hairy versions of the double-Schwarzschild (or Bach-Weyl) solution, but regular on and outside the two (topologically spherical) horizons. The balancing repulsive force is provided by the scalar field. An explicit illustration is presented, using a Weyl-type construction adapted to numerical solutions, requiring no partial linearisation, or integrability structure, of the Einstein-scalar equations. Fixing the couplings of the model, the balanced configurationsform a one-parameter family of solutions, labelled by the proper distance between the black holes.
description: 22 pages, 8 figures
Roles for Ctk1 and Spt6 in Regulating the Different Methylation States of Histone H3 Lysine 36
Creators: name: Duro, E.
name: Youdell, M. L.
name: Fuchs, S. M.
name: Mellor, J.
name: Kisseleva-Romanova, E.
name: Kizer, K. O.
name: Strahl, B. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Set2 (KMT3)-dependent methylation (me) of histone H3 at lysine 36 (H3K36) promotes deacetylation of transcribed chromatin and represses cryptic promoters within genes. Although Set2 is the only methyltransferase (KMTase) for H3K36 in yeast, it is not known if Set2 is regulated or whether the different methylation states at H3K36 are functionally distinct. Here we show that the N-terminal 261 residues of Set2 (Set21-261), containing the SET KMTase domain, are sufficient for H3K36me2, histone deacetylation, and repression of cryptic promoters at STE11. Set2-catalyzed H3K36me2 does not require either Ctk1-dependent phosphorylation of RNA polymerase II (RNAPII) or the presence of the phospho-C-terminal domain (CTD) interaction (SRI) domain of Set2. This finding is consistent with a known correlation between H3K36me2 and whether a gene is on or off, but not the level of activity of a gene. By contrast, H3K36me3 requires Spt6, proline 38 on histone H3 (H3P38), the CTD of RNAPII, Ctk1, and the C-terminal SRI domain of Set2. We suggest that the C-terminal region of Set2, in conjunction with the phosphorylated CTD of RNAPII, influences the KMTase activity to promote H3K36me3 during transcription elongation.
Shared information in classical mean-field models
Creators: name: Cohen, Or
name: Rittenberg, Vladimir
name: Sadhu, Tridib
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Universal scaling of entanglement estimators of critical quantum systems has drawn a lot of attention in the past. Recent studies indicate that similar universal properties can be found for bipartite information estimators of classical systems near phase transitions, opening a new direction in the study of critical phenomena. We explore this subject by studying the information estimators of classical spin chains with general mean-field interactions. In our explicit analysis of two different bipartite information estimators in the canonical ensemble we find that, away from criticality both the estimators remain finite in the thermodynamic limit. On the other hand, along the critical line there is a logarithmic divergence with increasing system-size. The coefficient of the logarithm is fully determined by the mean-field interaction and it is the same for the class of models we consider. The scaling function, however, depends on the details of each model. In addition, we study the information estimators in the micro-canonical ensemble, where they are shown to exhibit a different universal behavior. We verify our results using numerical calculations of two specific cases of the general Hamiltonian.
description: 7 figures, 37 pages, submitted to J. Phys. A
Additional file 2 of Immunotherapy in patients with metastatic castration-resistant prostate cancer: a meta-analysis of data from 7 phase III studies and 3 phase II studies
Creators: name: Zhang, Anqiang
name: Tong, Dali
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Cancer

description: Additional file 2: Table S1. Ongoing III phase randomized trials with immunotherapy in mCRPC.
SLIP1, a Factor Required for Activation of Histone mRNA Translation by the Stem-Loop Binding Protein
Creators: name: Marzluff, W. F.
name: Cakmakci, N. G.
name: Lerner, R. S.
name: Zheng, L.
name: Wagner, E. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Replication-dependent histone mRNAs are the only eukaryotic cellular mRNAs that are not polyadenylated, ending instead in a conserved stem-loop. The 3′ end of histone mRNA is required for histone mRNA translation, as is the stem-loop binding protein (SLBP), which binds the 3′ end of histone mRNA. We have identified five conserved residues in a 15-amino-acid region in the amino-terminal portion of SLBP, each of which is required for translation. Using a yeast two-hybrid screen, we identified a novel protein, SLBP-interacting protein 1 (SLIP1), that specifically interacts with this region. Mutations in any of the residues required for translation reduces SLIP1 binding to SLBP. The expression of SLIP1 in Xenopus oocytes together with human SLBP stimulates translation of a reporter mRNA ending in the stem-loop but not a reporter with a poly(A) tail. The expression of SLIP1 in HeLa cells also stimulates the expression of a green fluorescent protein reporter mRNA ending in a stem-loop. RNA interference-mediated downregulation of endogenous SLIP1 reduces the rate of translation of endogenous histone mRNA and also reduces cell viability. SLIP1 may function by bridging the 3′ end of the histone mRNA with the 5′ end of the mRNA, similar to the mechanism of translation of polyadenylated mRNAs.
Formation of young massive clusters from turbulent molecular clouds
Creators: name: Fujii, Michiko S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Young massive clusters are as young as open clusters but more massive and compact compared with typical open clusters. The formation process of young massive clusters is still unclear, and it is an open question whether the formation process is the same as typical open clusters or not. We perform a series of $N$-body simulations starting from initial conditions constructed from the results of hydrodynamical simulations of turbulent molecular clouds. In our simulations, both open clusters and young massive clusters form when we assume a density-dependent star formation efficiency. We find that a local star formation efficiency higher than 50 % is necessary for the formation of young massive clusters, but open clusters forms from less dense regions with a local star formation efficiency of $<50$ %. We confirm that the young massive clusters formed in our simulations have mass, size, and density profile similar to those of observed young massive clusters such as NGC 3603 and Trumpler 14. We also find that these simulated clusters evolve via hierarchical mergers of sub-clusters within a few Myr, as is suggested by recent simulations and observations. Although we do not assume initial mass segregation, we observe that the simulated massive clusters show a shallower slope of the mass function ($Γ\sim-1$) in the cluster center compared to that of the entire cluster ($Γ\sim-1.3$). These values are consistent with those of some young massive clusters in the Milky Way such as Westerlund 1 and Arches.
description: 9 pages, 5 figures, accepted for publication in PASJ
Additional file 3 of Immunotherapy in patients with metastatic castration-resistant prostate cancer: a meta-analysis of data from 7 phase III studies and 3 phase II studies
Creators: name: Zhang, Anqiang
name: Tong, Dali
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Cancer

description: Additional file 3: Three phase II clinical trials were included about Ipilimumab and Nivolumab after screening. In detail, most prostate cancer immunotherapy studies are still in phase II clinical trials, and the number of clinical trials above phase III is very limited. We further screened 86 phase II clinical trials about ICBs, and three trials about Ipilimumab and Nivolumab were included based on maintenance therapy.
Spatial and Temporal Regulation of Focal Adhesion Kinase Activity in Living Cells
Creators: name: Eck, M. J.
name: Rajfur, Z.
name: Schaller, M. D.
name: Jacobson, K.
name: Lietha, D.
name: Cai, X.
name: Ceccarelli, D. F.
name: Hahn, K. M.
name: Karginov, A. V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Focal adhesion kinase (FAK) is an essential kinase that regulates developmental processes and functions in the pathology of human disease. An intramolecular autoinhibitory interaction between the FERM and catalytic domains is a major mechanism of regulation. Based upon structural studies, a fluorescence resonance energy transfer (FRET)-based FAK biosensor that discriminates between autoinhibited and active conformations of the kinase was developed. This biosensor was used to probe FAK conformational change in live cells and the mechanism of regulation. The biosensor demonstrates directly that FAK undergoes conformational change in vivo in response to activating stimuli. A conserved FERM domain basic patch is required for this conformational change and for interaction with a novel ligand for FAK, acidic phospholipids. Binding to phosphatidylinositol 4,5-bisphosphate (PIP2)-containing phospholipid vesicles activated and induced conformational change in FAK in vitro, and alteration of PIP2 levels in vivo changed the level of activation of the conformational biosensor. These findings provide direct evidence of conformational regulation of FAK in living cells and novel insight into the mechanism regulating FAK conformation.
TAZ Promotes Cell Proliferation and Epithelial-Mesenchymal Transition and Is Inhibited by the Hippo Pathway
Creators: name: Bai, F.
name: Zhang, H.
name: Xiong, Y.
name: Zhao, B.
name: Guan, K.-L.
name: Pei, X.-H.
name: Lei, Q.-Y.
name: Zha, Z.-Y.
name: Zhao, S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: TAZ is a WW domain containing a transcription coactivator that modulates mesenchymal differentiation and development of multiple organs. In this study, we show that TAZ is phosphorylated by the Lats tumor suppressor kinase, a key component of the Hippo pathway, whose alterations result in organ and tissue hypertrophy in Drosophila and contribute to tumorigenesis in humans. Lats phosphorylates TAZ on several serine residues in the conserved HXRXXS motif and creates 14-3-3 binding sites, leading to cytoplasmic retention and functional inactivation of TAZ. Ectopic expression of TAZ stimulates cell proliferation, reduces cell contact inhibition, and promotes epithelial-mesenchymal transition (EMT). Elimination of the Lats phosphorylation sites results in a constitutively active TAZ, enhancing the activity of TAZ in promoting cell proliferation and EMT. Our results elucidate a molecular mechanism for TAZ regulation and indicate a potential function of TAZ as an important target of the Hippo pathway in regulating cell proliferation tumorigenesis.
Telomere Loops and Homologous Recombination-Dependent Telomeric Circles in a Kluyveromyces lactis Telomere Mutant Strain
Creators: name: Griffith, J. D.
name: McEachern, M. J.
name: Groff-Vindman, C.
name: Cesare, A. J.
name: Compton, S. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The Kluyveromyces lactis ter1-16T strain contains mutant telomeres that are poorly bound by Rap1, resulting in a telomere-uncapping phenotype and significant elongation of the telomeric DNA. The elongated telomeres of ter1-16T allowed the isolation and examination of native yeast telomeric DNA by electron microscopy. In the telomeric DNA isolated from ter1-16T, looped molecules were observed with the physical characteristics of telomere loops (t-loops) previously described in mammalian and plant cells. ter1-16T cells were also found to contain free circular telomeric DNA molecules (t-circles) ranging up to the size of an entire telomere. When the ter1-16T uncapping phenotype was repressed by overexpression of RAP1 or recombination was inhibited by deletion of rad52, the isolated telomeric DNA contained significantly fewer t-loops and t-circles. These results suggest that disruption of Rap1 results in elevated recombination at telomeres, leading to increased strand invasion of the 3′ overhang within t-loop junctions and resolution of the t-loop junctions into free t-circles.
Additional file 4 of Immunotherapy in patients with metastatic castration-resistant prostate cancer: a meta-analysis of data from 7 phase III studies and 3 phase II studies
Creators: name: Zhang, Anqiang
name: Tong, Dali
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Cancer

description: Additional file 4: Three types of therapy based on ipilimumab, sipuleucel-T and two vaccines respectively for subgroup meta-analysis based on clinical endpoints OS and PFS were performed. In term of OS, immunotherapy based on sipuleucel-T subgroup were able to decrease the risk of death in patients (HR = 0.73; 95%CI, 0.61–0.88; p = 0.001), indicating that sipuleucel-T is effective to improve OS. In term of PFS, in ipilimumab subpopulation, immunotherapy was able to decrease the risk of progression over placebo by 31% (HR = 0.69; 95%CI, 0.61–0.77; p = 0.000), which indicates that ipilimumab is effective to improve PFS.
TRAF6 and the Three C-Terminal Lysine Sites on IRF7 Are Required for Its Ubiquitination-Mediated Activation by the Tumor Necrosis Factor Receptor Family Member Latent Membrane Protein 1
Creators: name: Darnay, B. G.
name: Campos, A. D.
name: Ning, S.
name: Pagano, J. S.
name: Bentz, G. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: We have recently shown that interferon regulatory factor 7 (IRF7) is activated by Epstein-Barr virus latent membrane protein 1 (LMP1), a member of the tumor necrosis factor receptor (TNFR) superfamily, through receptor-interacting protein-dependent K63-linked ubiquitination (L. E. Huye, S. Ning, M. Kelliher, and J. S. Pagano, Mol. Cell. Biol. 27:2910-2918, 2007). In this study, with the use of small interfering RNA and TNFR-associated factor 6 (TRAF6) knockout cells, we first show that TRAF6 and its E3 ligase activity are required for LMP1-stimulated IRF7 ubiquitination. In Raji cells which are latently infected and express high levels of LMP1 and IRF7 endogenously, expression of a TRAF6 small hairpin RNA construct reduces endogenous ubiquitination and endogenous activity of IRF7. In TRAF6−/− mouse embryonic fibroblasts, reconstitution with TRAF6 expression, but not with TRAF6(C70A), which lacks the E3 ligase activity, recovers LMP1's ability to stimulate K63-linked ubiquitination of IRF7. Further, we identify IRF7 as a substrate for TRAF6 E3 ligase and show that IRF7 is ubiquitinated by TRAF6 at multiple sites both in vitro and in vivo. Most important, we determine that the last three C-terminal lysine sites (positions 444, 446, and 452) of human IRF7 variant A are essential for activation of IRF7; these are the first such sites identified. A ubiquitination-deficient mutant of IRF7 with these sites mutated to arginines completely loses transactivational ability in response not only to LMP1 but also to the IRF7 kinase IκB kinase ɛ. In addition, we find that K63-linked ubiquitination of IRF7 occurs independently of its C-terminal functional phosphorylation sites. These data support our hypothesis that regulatory ubiquitination of IRF7 is a prerequisite for its phosphorylation. This is the first evidence to imply that ubiquitination is required for phosphorylation and activation of a transcription factor.
Anomalous features of diffusion in corrugated potentials with spatial correlations: faster than normal, and other surprises
Creators: name: Goychuk, Igor
name: Kharchenko, V. O.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Normal diffusion in corrugated potentials with spatially uncorrelated Gaussian energy disorder famously explains the origin of non-Arrhenius $\exp[-σ^2/(k_BT^2)]$ temperature-dependence in disordered systems. Here we show that unbiased diffusion remains asymptotically normal also in the presence of spatial correlations decaying to zero. However, due to a temporal lack of self-averaging transient subdiffusion emerges on mesoscale, and it can readily reach macroscale even for moderately strong disorder fluctuations of $σ\sim 4-5\, k_BT$. Due to its nonergodic origin such subdiffusion exhibits a large scatter in single trajectory averages. However, at odds with intuition, it occurs essentially faster than one expects from the normal diffusion in the absence of correlations. We apply these results to diffusion of regulatory proteins on DNA molecules and predict that such diffusion should be anomalous, but much faster than earlier expected on a typical length of genes for a realistic energy disorder of several room $k_BT$, or merely $0.05-0.075$ eV.
Aurora-A Kinase Is Essential for Bipolar Spindle Formation and Early Development
Creators: name: Cowley, D. O.
name: O'Quinn, R.
name: Lu, L.
name: Oliver, T. G.
name: Van Dyke, T.
name: Magnuson, T.
name: Salmon, E. D.
name: Rivera-Perez, J. A.
name: Schliekelman, M.
name: He, Y. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Aurora-A is a conserved kinase implicated in mitotic regulation and carcinogenesis. Aurora-A was previously implicated in mitotic entry and spindle assembly, although contradictory results prevented a clear understanding of the roles of Aurora-A in mammals. We developed a conditional null mutation in the mouse Aurora-A gene to investigate Aurora-A functions in primary cells ex vivo and in vivo. We show here that conditional Aurora-A ablation in cultured embryonic fibroblasts causes impaired mitotic entry and mitotic arrest with a profound defect in bipolar spindle formation. Germ line Aurora-A deficiency causes embryonic death at the blastocyst stage with pronounced cell proliferation failure, mitotic arrest, and monopolar spindle formation. Aurora-A deletion in mid-gestation embryos causes an increase in mitotic and apoptotic cells. These results indicate that murine Aurora-A facilitates, but is not absolutely required for, mitotic entry in murine embryonic fibroblasts and is essential for centrosome separation and bipolar spindle formation in vitro and in vivo. Aurora-A deletion increases apoptosis, suggesting that molecular therapies targeting Aurora-A may be effective in inducing tumor cell apoptosis. Aurora-A conditional mutant mice provide a valuable system for further defining Aurora-A functions and for predicting effects of Aurora-A therapeutic intervention.
Why mean $p_{\rm T}$ is interesting
Creators: name: Praszalowicz, Michal
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We discuss energy dependence of mean $p_{\rm T}$ correlation with $N_{\rm ch}$ basing on general features of high energy collisions such as saturation and geometrical scaling. We use Color Glass Condensate calculation of an effective interaction radius that scales as a third root of multiplicity, and then saturates. With this model input we construct scaling variable for $< p_{\rm T} > (N_{\rm ch})$ at different energies both for pp and pPb collisions, and show that recent ALICE data indeed does exhibit this scaling property. We discuss energy dependence of the interaction radius and argue that since the radius cannot grow too large, a universal behavior of $< p_{\rm T} >$ for large multiplicities is expected.
description: 4 pages, 3 figures, talk presented at the International Workshop on Diffraction in High-Energy Physics Primosten (Croatia), September 10 - 16, 2014
CHIP represses myocardin-induced smooth muscle cell differentiation via ubiquitin-mediated proteasomal degradation nabla;
Creators: name: Gu, D.
name: Zhang, H.
name: Zhang, Y.
name: Patterson, C.
name: She, M.
name: Fan, Y.
name: Xie, P.
name: Li, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Myocardin, a coactivator of serum response factor (SRF), plays a critical role in the differentiation of vascular smooth muscle cells (SMCs). However, the molecular mechanisms regulating myocardin stability and activity are not well defined. Here we show that the E3 ligase C terminus of Hsc70-interacting protein (CHIP) represses myocardin-dependent SMC gene expression and transcriptional activity. CHIP interacts with and promotes myocardin ubiquitin-mediated degradation by the proteasome in vivo and in vitro. Furthermore, myocardin ubiquitination by CHIP requires its phosphorylation. Importantly, CHIP overexpression reduces the level of myocardin-dependent SMC contractile gene expression and diminishes arterial contractility ex vivo. These findings for the first time, to our knowledge, demonstrate that CHIP-promoted proteolysis of myocardin plays a key role in the physiological control of SMC phenotype and vessel tone, which may have an important implication for pathophysiological conditions such as atherosclerosis, hypertension, and Alzheimer's disease.
Drosophila Suppressor of Sable Protein [Su(s)] Promotes Degradation of Aberrant and Transposon-Derived RNAs
Creators: name: Searles, L. L.
name: Wilson, C. B.
name: Hunter, C.
name: Bass, S.
name: Wing, J. S.
name: Brewer-Jensen, P.
name: Bai, W.-L.
name: Kuan, Y.-S.
name: Abernethy, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: RNA-binding proteins act at various stages of gene expression to regulate and fine-tune patterns of mRNA accumulation. One protein in this class is Drosophila Su(s), a nuclear protein that has been previously shown to inhibit the accumulation of mutant transcripts by an unknown mechanism. Here, we have identified several additional RNAs that are downregulated by Su(s). These Su(s) targets include cryptic wild-type transcripts from the developmentally regulated Sgs4 and ng1 genes, noncoding RNAs derived from tandemly repeated αβ/αγ elements within an Hsp70 locus, and aberrant transcripts induced by Hsp70 promoter transgenes inserted at ectopic sites. We used the αβ RNAs to investigate the mechanism of Su(s) function and obtained evidence that these transcripts are degraded by the nuclear exosome and that Su(s) promotes this process. Furthermore, we showed that the RNA binding domains of Su(s) are important for this effect and mapped the sequences involved to a 267-nucleotide region of an αβ element. Taken together, these results suggest that Su(s) binds to certain nascent transcripts and stimulates their degradation by the nuclear exosome.
Additional file 5 of Immunotherapy in patients with metastatic castration-resistant prostate cancer: a meta-analysis of data from 7 phase III studies and 3 phase II studies
Creators: name: Zhang, Anqiang
name: Tong, Dali
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Cancer

description: Additional file 5: The trials about pembrolizumab approved to use for advanced solid tumors with the multiple genetic abnormalities (MSI-H or dMMR or TMB-H) were reviewed based on objective response rate (ORR), PFS and complete responses (CRs).
ErbB4 Splice Variants Cyt1 and Cyt2 Differ by 16 Amino Acids and Exert Opposing Effects on the Mammary Epithelium In Vivo
Creators: name: Earp, H. S.
name: Strunk, K. E.
name: Elenius, K.
name: Hunter, D. M.
name: Sandahl, M. A.
name: Miraglia, L. C.
name: Muraoka-Cook, R. S.
name: Husted, C.
name: Chodosh, L. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Data concerning the prognostic value of ErbB4 in breast cancer and effects on cell growth have varied in published reports, perhaps due to the unknown signaling consequences of expression of the intracellular proteolytic ErbB4 s80HER4 fragment or due to differing signaling capabilities of alternatively spliced ErbB4 isoforms. One isoform (Cyt1) contains a 16-residue intracellular sequence that is absent from the other (Cyt2). We expressed s80Cyt1 and s80Cyt2 in HC11 mammary epithelial cells, finding diametrically opposed effects on the growth and organization of colonies in three-dimensional matrices. Whereas expression of s80Cyt1 decreased growth and increased the rate of three-dimensional lumen formation, that of s80Cyt2 increased proliferation without promoting lumen formation. These results were recapitulated in vivo, using doxycycline-inducible, mouse breast-transgenic expression of s80Cyt1 amd s80Cyt2. Expression of s80Cyt1 decreased growth of the mammary ductal epithelium, caused precocious STAT5a activation and lactogenic differentiation, and increased cell surface E-cadherin levels. Remarkably, ductal growth inhibition by s80Cyt1 occurred simultaneously with lobuloalveolar growth that was unimpeded by s80Cyt1, suggesting that the response to ErbB4 may be influenced by the epithelial subtype. In contrast, expression of s80Cyt2 caused epithelial hyperplasia, increased Wnt and nuclear β-catenin expression, and elevated expression of c-myc and cyclin D1 in the mammary epithelium. These results demonstrate that the Cyt1 and Cyt2 ErbB4 isoforms, differing by only 16 amino acids, exhibit markedly opposing effects on mammary epithelium growth and differentiation.
An optimal real-time controller for vertical plasma stabilization
Creators: name: Cruz, N.
name: Moret, J-M.
name: Coda, S.
name: Duval, B. P.
name: Le, H. B.
name: Rodrigues, A. P.
name: Varandas, C. A. F.
name: Correia, C. M. B. A.
name: Goncalves, B. S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Modern Tokamaks have evolved from the initial axisymmetric circular plasma shape to an elongated axisymmetric plasma shape that improves the energy confinement time and the triple product, which is a generally used figure of merit for the conditions needed for fusion reactor performance. However, the elongated plasma cross section introduces a vertical instability that demands a real-time feedback control loop to stabilize the plasma vertical position and velocity. At the Tokamak à Configuration Variable (TCV) in-vessel poloidal field coils driven by fast switching power supplies are used to stabilize highly elongated plasmas. TCV plasma experiments have used a PID algorithm based controller to correct the plasma vertical position. In late 2013 experiments a new optimal real-time controller was tested improving the stability of the plasma. This contribution describes the new optimal real-time controller developed. The choice of the model that describes the plasma response to the actuators is discussed. The high order model that is initially implemented demands the application of a mathematical order reduction and the validation of the new reduced model. The lower order model is used to derive the time optimal control law. A new method for the construction of the switching curves of a bang-bang controller is presented that is based on the state-space trajectories that optimize the time to target of the system. A closed loop controller simulation tool was developed to test different possible algorithms and the results were used to improve the controller parameters. The final control algorithm and its implementation are described and preliminary experimental results are discussed.
description: Preprint submitted to IEEE Transactions on Nuclear Science
Few-photon single ionization of cold rubidium in the over-the-barrier regime
Creators: name: Ma, Huanyu
name: Wang, Xincheng
name: Zhang, Linxuan
name: Zou, Zhihan
name: Yuan, Junyang
name: Ma, Yixuan
name: Lv, Rujin
name: Shen, Zhenjie
name: Yan, Tianmin
name: Weidemüller, Matthias
name: Ye, Difa
name: Jiang, Yuhai
Publisher: name: arXiv
Year: 2023
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Photoionization of the rubidium (Rb) atoms cooled in a magneto-optical trap, characterized by the coexistence of the ground 5$S_{1/2}$ and the excited 5$P_{3/2}$ states, is investigated experimentally and theoretically with the 400 nm femtosecond laser pulses at intensities of $I=3\times10^9$ W/cm$^2$ - $4.5\times10^{12}$ W/cm$^2$. Recoil-ion momentum distribution (RIMD) of Rb$^+$ exhibits rich ring-like structures and their energies correspond to one-photon ionization of the 5$P_{3/2}$ state, two-photon and three-photon ionizations of the 5$S_{1/2}$ state, respectively. With the increasing of $I$, we find that experimental signals near zero-momentum (NZM) in RIMDs resulted from the 5$P_{3/2}$ state enhance dramatically and its peaked Rb$^+$ momenta dwindle obviously while that from the 5$S_{1/2}$ state is maintained. Meanwhile, the ion-yield ratio of the 5$S_{1/2}$ over the 5$P_{3/2}$ states varies from $I$ to $I^{1.5}$ as $I$ increases. These features indicate a transition from perturbative ionization to strong-perturbative ionization for the 5$P_{3/2}$ state. Numerical simulations by solving the time-dependent Schrödinger equation (TDSE) can qualitatively explain the measurements of RIMD, photoion angular distributions, as well as ion-yield ratio. However, some discrepancies still exist, especially for the NZM dip, which could stem from the electron-electron correlation that is neglected in the present TDSE simulations since we have adopted the single-active-electron approximation.
Studies of the 5' Exonuclease and Endonuclease Activities of CPSF-73 in Histone Pre-mRNA Processing
Creators: name: Sullivan, K. D.
name: Dominski, Z.
name: Marzluff, W. F.
name: Yang, X.-c.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Processing of histone pre-mRNA requires a single 3′ endonucleolytic cleavage guided by the U7 snRNP that binds downstream of the cleavage site. Following cleavage, the downstream cleavage product (DCP) is rapidly degraded in vitro by a nuclease that also depends on the U7 snRNP. Our previous studies demonstrated that the endonucleolytic cleavage is catalyzed by the cleavage/polyadenylation factor CPSF-73. Here, by using RNA substrates with different nucleotide modifications, we characterize the activity that degrades the DCP. We show that the degradation is blocked by a 2′-O-methyl nucleotide and occurs in the 5′-to-3′ direction. The U7-dependent 5′ exonuclease activity is processive and continues degrading the DCP substrate even after complete removal of the U7-binding site. Thus, U7 snRNP is required only to initiate the degradation. UV cross-linking studies demonstrate that the DCP and its 5′-truncated version specifically interact with CPSF-73, strongly suggesting that in vitro, the same protein is responsible for the endonucleolytic cleavage of histone pre-mRNA and the subsequent degradation of the DCP. By using various RNA substrates, we define important space requirements upstream and downstream of the cleavage site that dictate whether CPSF-73 functions as an endonuclease or a 5′ exonuclease. RNA interference experiments with HeLa cells indicate that degradation of the DCP does not depend on the Xrn2 5′ exonuclease, suggesting that CPSF-73 degrades the DCP both in vitro and in vivo.
Investigation of Force-Freeness of Solar Emerging Magnetic Field via Application of the Virial Theorem to MHD Simulations
Creators: name: Kang, Jihye
name: Magara, Tetsuya
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Force-freeness of a solar magnetic field is a key to reconstructing invisible coronal magnetic structure of an emerging flux region on the Sun where active phenomena such as flares and coronal mass ejections frequently occur. We have performed magnetohydrodynamic (MHD) simulations which are adjusted to investigate force-freeness of an emerging magnetic field by using the virial theorem. Our focus is on how the force-free range of an emerging flux region develops and how it depends on the twist of a pre-emerged magnetic field. As an emerging flux region evolves, the upper limit of the force-free range continuously increases while the lower limit is asymptotically reduced to the order of a photospheric pressure scale height above the solar surface. As the twist becomes small the lower limit increases and then seems to be saturated. We also discuss the applicability of the virial theorem to an evolving magnetic structure on the Sun.
description: 21 pages including 9 figures
Chemical diversity of gas in distant galaxies: The metal and dust enrichment and variations within absorbing galaxies
Creators: name: Ramburuth-Hurt, T.
name: De Cia, A.
name: Krogager, J. -K.
name: Ledoux, C.
name: Petitjean, P.
name: Péroux, C.
name: Dessauges-Zavadsky, M.
name: Fynbo, J.
name: Wendt, M.
name: Bouché, N. F.
name: Konstantopoulou, C.
name: Jermann, I.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The chemical composition of gas in galaxies can be measured in detail from absorption spectroscopy. By studying gas in galaxies in this way, it is possible to investigate the small and faint galaxies, which are the most numerous in the universe. In particular, the chemical distribution of gas in absorbing systems gives us insight into cycles of gas in and around galaxies. Here we study chemical enrichment within 64 Damped Lyman-alpha Absorption (DLA) systems between $1.7 < z < 4.2$. We use high-resolution spectra from VLT/UVES to infer dust depletion from relative abundances of several metals. We perform a component-by-component analysis within DLAs, and characterise variations in their chemical enrichment. Unlike hydrogen, the metal columns can be characterised for individual components. We use them to derive the dust depletion ([Zn/Fe]fit), as an indicator for chemical enrichment. We find that some DLAs are chemically diverse within themselves, with [Zn/Fe]fit ranging up to 0.62 dex within a single system. This suggests that absorbing gas within these galaxies is chemically diverse. Although we do not find a clear trend of decreasing dust depletion with redshift, we do see that the most chemically enriched systems are at lower redshifts. We also observe evidence for dust-poor components at all redshifts, which may be due to the accretion of pristine gas onto galaxies. We combine the chemical and kinematic properties of the individual gas components and observe potential signatures of infalling gas, with low depletion at velocities below $\sim$100km/s, and outflows, with high depletion and velocities of $\sim$600km/s. We find over-abundances of alpha-elements (an enhancement of $\sim$0.3dex) and under-abundances of Mn in several components, which is likely a signature of core-collapse SNe nucleosythesis in the ISM. We observe these effects mostly at lower levels of chemical enrichment.
description: 56 pages, 99 figures, Accepted for publication in A&A, Abstract abridged for arXiv
Study of RPC bakelite electrodes and detector performance for INO-ICAL
Creators: name: Kumar, Ashok
name: Gaur, Ankit
name: Hasbuddin, Md.
name: Kumar, Praveen
name: Kumar, Purnendu
name: Kaur, Daljeet
name: Mishra, Swati
name: Naimuddin, Md.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The Resistive Plate Chambers (RPCs) are going to be used as the active detectors in the India-based Neutrino Observatory (INO)-Iron Calorimeter (ICAL) experiment for the detection and study of atmospheric neutrinos. In this paper, an extensive study of structural and electrical properties for different kind of bakelite RPC electrodes is presented. RPCs fabricated from these electrodes are tested for their detector efficiency and noise rate. The study concludes with the variation of efficiency, leakage current and counting rate over the period of operation with different gas compositions and operational conditions like temperature and relative humidity.
description: 8 pages, 8 Figures, matches version to appear in JINST
The E3 Ubiquitin Ligase WWP1 Selectively Targets HER4 and Its Proteolytically Derived Signaling Isoforms for Degradation
Creators: name: Hunter, D.
name: Miyazawa, K.
name: Feng, S.-M.
name: Caskey, L. S.
name: Atfi, A.
name: Muraoka-Cook, R. S.
name: Earp, H. S.
name: Sandahl, M. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: In general, epidermal growth factor receptor family members stimulate cell proliferation. In contrast, at least one HER4 isoform, JM-a/Cyt1, inhibits cell growth after undergoing a two-step proteolytic cleavage that first produces a membrane-anchored 80-kDa fragment (m80HER4) and subsequently liberates a soluble 80-kDa fragment, s80HER4. Here we report that s80HER4 Cyt1 action increased the expression of WWP1 (for WW domain-containing protein 1), an E3 ubiquitin ligase, but not other members of the Nedd4 E3 ligase family. The HER4 Cyt1 isoform contains three proline-rich tyrosine (PY) WW binding motifs, while Cyt2 has only two. WWP1 binds to all three Cyt1 PY motifs; the interaction with PY2 found exclusively in Cyt1 was strongest. WWP1 ubiquitinated and caused the degradation of HER4 but not of EGFR, HER2, or HER3. The HER4-WWP1 interaction also accelerated WWP1 degradation. Membrane HER4 (full length and m80HER4, the product of the first proteolytic cleavage) were the preferred targets of WWP1, correlating with the membrane localization of WWP1. Conversely s80HER4, a poorer WWP1 substrate, was found in the cell nucleus, while WWP1 was not. Deletion of the C2 membrane association domain of WWP1 allowed more efficient s80HER4 degradation, suggesting that WWP1 is normally part of a membrane complex that regulates HER4 membrane species levels, with a predilection for the growth-inhibitory Cyt1 isoform. Finally, WWP1 expression diminished HER4 biologic activity in MCF-7 cells. We previously showed that nuclear s80HER4 is ubiquitinated and degraded by the anaphase-promoting complex, suggesting that HER4 ubiquitination within specific cellular compartments helps regulate the unique HER4 signaling capabilities.
The H3K4 Demethylase Lid Associates with and Inhibits Histone Deacetylase Rpd3
Creators: name: Zhang, Y.
name: Lee, N.
name: Jones, R. S.
name: Erdjument-Bromage, H.
name: Tempst, P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: JmjC domain-containing proteins have been shown to possess histone demethylase activity. One of these proteins is the Drosophila histone H3 lysine 4 demethylase Little imaginal discs (Lid), which has been genetically classified as a Trithorax group protein. However, contrary to the supposed function of Lid in gene activation, the biochemical activity of this protein entails the removal of a histone mark that is correlated with active transcription. To understand the molecular mechanism behind the function of Lid, we have purified a Lid-containing protein complex from Drosophila embryo nuclear extracts. In addition to Lid, the complex contains Rpd3, CG3815/Drosophila Pf1, CG13367, and Mrg15. Rpd3 is a histone deacetylase, and along with Polycomb group proteins, which antagonize the function of Trithorax group proteins, it negatively regulates transcription. By reconstituting the Lid complex, we demonstrated that the demethylase activity of Lid is not affected by its association with other proteins. However, the deacetylase activity of Rpd3 is greatly diminished upon incorporation into the Lid complex. Thus, our finding that Lid antagonizes Rpd3 function provides an explanation for the genetic classification of Lid as a positive transcription regulator.