cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Computer aided drug discovery (CADD) of a thieno[2,3-d]pyrimidine derivative as a new EGFR inhibitor targeting the ribose pocket
Creators: name: Sobh, Eman A.
name: Dahab, Mohammed A.
name: Elkaeed, Eslam B.
name: Alsfouk, Aisha A.
name: Ibrahim, Ibrahim M.
name: Metwaly, Ahmed M.
name: Eissa, Ibrahim H.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Depending on the pharmacophoric characteristics of EGFR inhibitors, a new thieno[2,3-d]pyrimidine derivative has been developed. Firstly, the potential inhibitory effect of the designed compound against EGFR has been proven by docking experiments that showed correct binding modes and excellent binding energies of −98.44 and −88.00 kcal/mol, against EGFR wild-type and mutant type, respectively. Furthermore, MD simulations studies confirmed the precise energetic, conformational, and dynamic alterations that occurred after binding to EGFR. The correct binding was also confirmed by essential dynamics studies. To further investigate the general drug-like properties of the developed candidate, in silico ADME and toxicity studies have also been carried out. The thieno[2,3-d]pyrimidine derivative was synthesized following the earlier promising findings. Fascinatingly, the synthesized compound (4) showed promising inhibitory effects against EGFRWT and EGFRT790M with IC50 values of 25.8 and 182.3 nM, respectively. Also, it exhibited anticancer potentialities against A549 and MCF-7cell lines with IC50 values of 13.06 and 20.13 µM, respectively. Interestingly, these strong activities were combined with selectivity indices of 2.8 and 1.8 against the two cancer cell lines, respectively. Further investigations indicated the ability of compound 4 to arrest the cancer cells’ growth at the G2/M phase and to increase early and late apoptosis percentages from 2.52% and 2.80 to 17.99% and 16.72%, respectively. Additionally, it was observed that compound 4 markedly increased the levels of caspase-3 and caspase-9 by 4 and 3-fold compared to the control cells. Moreover, it up-regulated the level of BAX by 3-fold and down-regulated the level of Bcl-2 by 3-fold affording a BAX/Bcl-2 ratio of 9. Communicated by Ramaswamy H. Sarma
Podocalyxin promotes vascular barrier function
Creators: name: Cait, Jessica
Publisher: name: University of British Columbia
Year: 2019

description: The CD34-family sialomucin, podocalyxin (Podxl), is broadly expressed on the luminal face of blood vessels in adult mammals; however, its biological function on vascular endothelial cells (vEC) is not well-defined. Here, we reveal specific functions for podocalyxin in maintaining endothelial barriers using HUVEC monolayers as a model in vitro. Detailed analysis of barrier HUVEC characteristics using electrical cell-substrate impedance sensing (ECIS) and live cell imaging revealed essential roles for podocalyxin in maintaining cell-cell and cell-matrix interactions. Thus, podocalyxin-deficient HUVEC fail to form a functional barrier when plated on several extracellular matrix (ECM) substrates. Regardless of ECM substrate, these monolayers lack adherens junctions and focal adhesions; and display a disorganized cortical actin cytoskeleton. To explore an in vivo function of podocalyxin, we conditionally deleted Podxl in vEC using the Tie2Cre strain (PodxlΔTie2Cre). Although we did not detect altered permeability in naïve mice at steady state, systemic priming with lipopolysaccharides (LPS) disrupted the blood-brain barrier (BBB) in PodxlΔTie2Cre but not WT mice. To study the potential consequence of this BBB breach, we used a selective agonist of PAR-1, a thrombin receptor expressed by neurons and glial cells. As a polar peptide, the PAR-1 agonist (TFLLRN), is normally excluded from CNS parenchyma by the BBB. In response to systemic administration of TFLLRN, LPS-primed PodxlΔTie2Cre mice experienced a dramatic behavioral change marked by a severely dampened neurological electrical activity. We conclude that podocalyxin expression by CNS vECs is required to maintain BBB integrity under inflammatory conditions.
Bound state solutions of the Dirac-Rosen-Morse potential with spin and pseudospin symmetry
Creators: name: Oyewumi, K. J.
name: Akoshile, C. O.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The energy spectra and the corresponding two- component spinor wavefunctions of the Dirac equation for the Rosen-Morse potential with spin and pseudospin symmetry are obtained. The $s-$wave ($κ= 0$ state) solutions for this problem are obtained by using the basic concept of the supersymmetric quantum mechanics approach and function analysis (standard approach) in the calculations. Under the spin symmetry and pseudospin symmetry, the energy equation and the corresponding two-component spinor wavefunctions for this potential and other special types of this potential are obtained. Extension of this result to $κ\neq 0$ state is suggested.
description: 18 pages
Cucurbitacin-B inhibits cancer cell migration by targeting mortalin and HDM2: computational and in vitro experimental evidence
Creators: name: Huifu, He
name: Shefrin, Seyad
name: Yang, Shi
name: Zhang, Zhenya
name: Kaul, Sunil C.
name: Sundar, Durai
name: Wadhwa, Renu
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 60506 Virology

description: Cancer metastasis, a highly complex process wherein cancer cells move from the primary site to other sites in the body, is a major hurdle in its therapeutics. A large array of synthetic chemotherapeutic molecules used for the treatment of metastatic cancers, besides being extremely expensive and unaffordable, are known to cause severe adverse effects leading to poor quality of life (QOL) of the patients. In this premise, natural compounds (considered safe, easily available and economic) that possess the potential to inhibit migration of cancer cells are deemed useful and hence are on demand. Cucurbitacin-B (19-(10→9β)-abeo-10-lanost-5-ene triterpene, called Cuc-B) is a steroid mostly found in plants of Cucurbitaceae family. It has been shown to possess anticancer activity although the molecular mechanism remains poorly defined. We present evidence that Cuc-B has the ability to interact with mortalin and HDM2 proteins that are enriched in cancer cells, suppress wild type p53 function and promote cancer cell migration. Computational analyses showed that Cuc-B interacts with mortalin similar to MKT077 and Withanone, both have been shown to reactivate p53 function and inhibit cell migration. Furthermore, Cuc-B interacted with HDM2 similar to Y30, a well-known inhibitor of HDM2. Experimental cell and molecular analyses demonstrated the downregulation of several proteins, critically involved in cell migration in Cuc-B (low non-toxic doses)-treated cancer cells and exhibited inhibition of cell migration. The data suggested that Cuc-B is a potential natural drug that warrants further mechanistic and clinical studies for its use in the management of metastatic cancers. Communicated by Ramaswamy H. Sarma
Mutual Friction in Superfluid He^4 Near the λ-line
Creators: name: Kuehn, Kerry
name: Ahlers, Guenter
Publisher: name: arXiv
Year: 2011
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We present experimental results for the thermal resistivity ρ of superfluid He^4 along several isobars between saturated vapor pressure and the melting pressure. The measurements are for the temperature range 1 - T_c(q)/T_λ < t < 2{\times}10^{-5} and the heat-flux range 3 < q < 70 μW/cm^2. Here t {\equiv} 1-T/T_λ, T_λ is the transition temperature in the limit of zero q, and T_c is the transition temperature at finite q. The data suggest that the resistivity has an incipient singularity at T_λ which can be described by the power law ρ = (t/t0)^{-(mν+α)} where t0 = (q/q0)^x. However, the singularity is supplanted by the transition to a more highly dissipative phase at T_c(q) < T_λ. The results suggest a mild dependence of mν + α on P, but can be described quite well by mν + α = 2.76, x = 0.89, and q_0 = q_{0,0} - q_{0,1}P with q_{0,0} = 401 W/cm^2 and q_{0,1} = -5.0 W /{cm^2-bar}. The results imply that the Gorter-Mellink mutual friction exponent m has a value close to 3.46 and is distinctly larger than the classical value m = 3. We suggest that the reason for this may be found in the nature of the counterflow close to T_λ, which is expected to involve turbulent normalfluid flow.
description: 23 pages, 8 figures
Penetration of nonquantized magnetic flux through a domain-wall bend in time-reversal symmetry broken superconductors
Creators: name: Ferguson, David G.
name: Goldbart, Paul M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: It has been proposed that the superconductivity of Sr$_2$RuO$_4$ is characterized by pairing that is unconventional and, furthermore, spontaneously breaks time-reversal symmetry. However, one of the key expected consequences, viz., that the ground state should exhibit chiral charge currents localized near the boundaries of the sample, has not been observed, to date. We explore an alternative implication of time-reversal symmetry breaking: the existence of walls between domains of opposing chirality. Via a general phenomenological approach, we derive an effective description of the superconductivity in terms of the relevant topological variables (i.e., domain walls and vortices). Hence, by specializing to the in the in-plane rotationally invariant limit, we show that a domain wall that is translationally invariant along the z axis and includes a bend through an angle $Θ$ is accompanied by a nonintegral (and possibly nonquantized) magnetic {\it bend flux} of $\big((Θ/π)+n\big)Φ_0$, with integral $n$, that penetrates the superconductor, localized near the bend. We generalize this result to the situation in which gauge transformations and rotations about the z axis are degenerate transformations of the chiral superconducting order. On the basis of the specialized result and its generalization, we note that any observation of localized, nonquantized flux penetrating a z-axis surface (e.g., via scanned-probe magnetic imaging) can be interpreted in terms of the presence of bent walls between domains of opposing chirality, and hence is suggestive of the existence of time-reversal symmetry-breaking superconductivity.
Breakdown of PCAC in diffractive neutrino interactions
Creators: name: Kopeliovich, B. Z.
name: Potashnikova, I. K.
name: Schmidt, Ivan
name: Siddikov, M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We test the hypothesis of partially conserved axial current (PCAC) in high energy diffractive neutrino production of pions. Since the pion pole contribution to the Adler relation (AR) is forbidden by conservation of the lepton current, the heavier states, like the a_1 pole, ρ-π-cut, etc., control the lifetime of the hadronic fluctuations of the neutrino. We evaluate the deviation from the AR in diffractive neutrino-production of pions on proton and nuclear targets. At high energies, when all the relevant time scales considerably exceed the size of the target, the AR explicitly breaks down on an absorptive target, such as a heavy nucleus. In this regime, close to the black disc limit, the off-diagonal diffractive amplitudes vanish, while the diagonal one, π->π, which enters the AR, maximizes and saturates the unitarity bound. At lower energies, in the regime of short lifetime of heavy hadronic fluctuations the AR is restored, i.e. it is not altered by the nuclear effects.
description: 10 pages, 5 figures
Equivalent synchronization of chaos in driven and in autonomous systems
Creators: name: Cosenza, M. G.
name: Alvarez-Llamoza, O.
name: Paredes, G.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: It is shown that the synchronization behavior of a system of chaotic maps subject to either an external forcing or a coupling function of their internal variables can be inferred from the behavior of a single element in the system, which can be seen as a single drive-response map. From the conditions for stable synchronization in this single driven-map model with minimal ingredients, we find minimal conditions for the emergence of complete and generalized chaos synchronization in both driven and autonomous associated systems. Our results show that the presence of a common drive or a coupling function for all times is not indispensable for reaching synchronization in a system of chaotic oscillators, nor is the simultaneous sharing of a field, either external or endogenous, by all the elements. In the case of an autonomous system, the coupling function does not need to depend on all the internal variables for achieving synchronization and its functional form is not crucial for generalized synchronization. What becomes essential for reaching synchronization in an extended system is the sharing of some minimal information by its elements, on the average, over long times, independently of the nature (external or internal) of its source.
description: 8 pages, 6 figures
TRAVIATA Project Flyer
Creators: name: Merli, Filippo
name: Göttlich, Emil
Publisher: name: Graz University of Technology
Year: 2019

description: The project TRAVIATA (Turbine Research for Aerodynamical Vane-Frame Improvements in Advanced Two-Spool Arrangements) leading to this application has received funding from the Clean Sky 2 Joint Undertaking under the European Union's Horizon 2020 research and innovation program under grant agreement No 785313.
The end points in the dispersion of Holstein polarons
Creators: name: Goodvin, Glen L.
name: Berciu, Mona
Publisher: name: arXiv
Year: 2010
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We investigate the existence of end points in the dispersion of Holstein polarons in various dimensions, using the Momentum Average approximation which has proved to be very accurate for this model. An end point separates momenta for which the lowest-energy state is a discrete level, i.e., an infinitely-lived polaron, from those where the lowest-energy feature is a continuum in which the "polaron'" is signalled by a resonance with a finite lifetime. While such end points are known to not appear in 1D, we show here that they are generic in 3D if the particle-boson coupling is not too strong. The 2D case is "critical": a pure 2D Holstein model has no end points, like the 1D case. However, any amount of interlayer hopping leads to 3D-like behavior. As a result, such end points are expected to appear in the spectra of layered, quasi-2D systems described by Holstein models. Generalizations to other models are also briefly discussed.
description: 6 pages, 6 figures
Radial standing and self-similar waves for the hyperbolic cubic NLS in 2D
Creators: name: Kevrekidis, P. G.
name: Nahmod, A. R.
name: Zeng, C.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: Mathematical Physics (math-ph)
subject: Analysis of PDEs (math.AP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: In this note we propose a new set of coordinates to study the hyperbolic or non-elliptic cubic nonlinear Schrodinger equation in two dimensions. Based on these coordinates, we study the existence of bounded and continuous hyperbolically radial standing waves, as well as hyperbolically radial self-similar solutions. Many of the arguments can easily be adapted to more general nonlinearities.
description: 19 pages, 1 Figure, to appear in Nonlinearity
Perturbative effects of spinning black holes with applications to recoil velocities
Creators: name: Nakano, Hiroyuki
name: Campanelli, Manuela
name: Lousto, Carlos O.
name: Zlochower, Yosef
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Recently, we proposed an enhancement of the Regge-Wheeler-Zerilli formalism for first-order perturbations about a Schwarzschild background that includes first-order corrections due to the background black-hole spin. Using this formalism, we investigate gravitational wave recoil effects from a spinning black-hole binary system analytically. This allows us to better understand the origin of the large recoils observed in full numerical simulation of spinning black hole binaries.
description: Proceedings of Theory Meets Data Analysis at Comparable and Extreme Mass Ratios (NRDA/Capra 2010), Perimeter Institute, June 2010 - 12 pages
Torus and AGN properties of nearby Seyfert galaxies: Results from fitting IR spectral energy distributions and spectroscopy
Creators: name: Alonso-Herrero, Almudena
name: Almeida, Cristina Ramos
name: Mason, Rachel
name: Ramos, Andres Asensio
name: Roche, Patrick F.
name: Levenson, Nancy A.
name: Elitzur, Moshe
name: Packham, Christopher
name: Espinosa, Jose Miguel Rodriguez
name: Young, Stuart
name: Diaz-Santos, Tanio
name: Perez-Garcia, Ana M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We used the CLUMPY torus models and a Bayesian approach to fit the infrared spectral energy distributions (SEDs) and ground-based high-angular resolution mid-infrared spectroscopy of 13 nearby Seyfert galaxies. This allowed us to put tight constraints on torus model parameters such as the viewing angle, the radial thickness of the torus Y, the angular size of the cloud distribution sigma_torus, and the average number of clouds along radial equatorial rays N_0. The viewing angle is not the only parameter controlling the classification of a galaxy into a type 1 or a type 2. In principle type 2s could be viewed at any viewing angle as long as there is one cloud along the line of sight. A more relevant quantity for clumpy media is the probability for an AGN photon to escape unabsorbed. In our sample, type 1s have relatively high escape probabilities, while in type 2s, as expected, tend to be low. Our fits also confirmed that the tori of Seyfert galaxies are compact with torus model radii in the range 1-6pc. The scaling of the models to the data also provided the AGN bolometric luminosities, which were found to be in good agreement with estimates from the literature. When we combined our sample of Seyfert galaxies with a sample of PG quasars from the literature to span a range of L_bol(AGN)~10^{43}-10^{47}erg/s, we found plausible evidence of the receding torus. That is, there is a tendency for the torus geometrical covering factor to be lower at high AGN luminosities than at low AGN luminosities. This is because at low AGN luminosities the tori appear to have wider angular sizes and more clouds along radial equatorial rays. We cannot, however rule out the possibility that this is due to contamination by extended dust structures not associated with the dusty torus at low AGN luminosities, since most of these in our sample are hosted in highly inclined galaxies. (Abridged)
description: Accepted for publication in ApJ
Size-dependent rheology of type-I collagen networks
Creators: name: Arevalo, Richard C.
name: Urbach, Jeffrey S.
name: Blair, Daniel L.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We investigate the system size dependent rheological response of branched type I collagen gels. When subjected to a shear strain, the highly interconnected mesh dynamically reorients, resulting in overall stiffening of the network. When a continuous shear strain is applied to a collagen network, we observe that the local apparent modulus, in the strain-stiffening regime, is strongly dependent on the gel thickness. In addition, we demonstrate that the overall network failure is determined by the ratio of the gel thickness to the mesh size. These findings have broad implications for cell-matrix interactions, the interpretation of rheological tissue data, and the engineering of biomimetic scaffolds.
description: 3 pages, 4 figures, to appear in Biophysical Journal Letters, September 2010
"Just add colour" : unintended whiteness in Vancouver theatre and arts and culture policies in Canada
Creators: name: Cheung, Belle Chi-Tung
Publisher: name: University of British Columbia
Year: 2018

description: Common around the world, the arts are considered an expression of culture and are a powerful vehicle for communicating and understanding a nation’s values and collective identity. Diversity is often considered a defining characteristic of Canadian identity, but the arts in Canada has long struggled with its own lack of diversity. This thesis explores the relationship between Canada’s multiculturalism and cultural policies, and how this relationship has resulted in an unintended whiteness in Canadian arts and culture. Focusing on theatre in Greater Vancouver, this relationship is illustrated in two ways: the first, an exploration of artistic expression outside of Canada’s official languages which demonstrate the limiting effects of bilingualism policies on linguistic and cultural expression in Canada, and explores transnationalism as a possible catalyst for new constructions of culture, citizenship, and belonging. The second example explores how theatre practitioners in Greater Vancouver conceptualize, create, and understand diversity in specific ways that perpetuate the invisible hierarchies of whiteness, and make it difficult for diversity to become part of the mainstream. For theatre artists and organizations in Vancouver, diversity has been defined as racialized difference and power dynamics that have resulted in a continued othering. I argue that this relationship ultimately results in a preference for and reproduction of Eurocentric models and artistic values. This thesis questions the role and responsibility of Canadian cultural institutions as accurate representations of “Canadian” identity, and advocates for innovative approaches to cultural policy that would better serve and leverage the unique potential and role of cultural communities in Canada.
Kinetic electrocaloric effect and giant net cooling of lead-free ferroelectric refrigerants
Creators: name: Bai, Yang
name: Zheng, Guang-Ping
name: Shi, San-Qiang
Publisher: name: arXiv
Year: 2010
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Giant electrocaloric (EC) effect is observed in BaTiO3 multilayer thick film structure. The temperature change is as high as 4.0 oC under an applied electric field of 352 kV/cm. Most importantly, the EC effect is found to depend on the varying rate of the applied field. Based on the giant net cooling (~0.37 J/g) resulting from the difference in the varying rates of rising and falling fields, the kinetic EC effect provides an effective solution for the design of refrigeration cycle in ferroelectric micro-refrigerator.
Health problems that influence fitness to drive in the Spanish population: a scoping review
Creators: name: Dinu, Andreea Ionela
name: Frías, Daniel Salazar
name: Szot, Ana Clara
name: Gómez, Lucía Laffarga
name: Cándida Castro Ramírez
name: Bailón, María Rodríguez
name: Aparicio, Pablo Doncel
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Diseases
subject: Medicine and Health Sciences
subject: Pathological Conditions, Signs and Symptoms
subject: fitness to drive
subject: protocol
subject: scoping review
subject: motor vehicle driving
subject: data analytics

description: This scoping review aims to systematically map the research, updated sociodemographic data and documents from official organizations and experts, as well as to identify any existing gaps in knowledge of fitness to drive of Spanish drivers with health problems.
Coupled spin-lattice fluctuations in a compound with orbital degrees of freedom: the Cr based dimer system Sr3Cr2O8
Creators: name: Wulferding, Dirk
name: Lemmens, Peter
name: Choi, Kwang-Yong
name: Gnezdilov, Vladimir
name: Deisenhofer, Joachim
name: Quintero-Castro, Diana
name: Islam, A. T. M. Nazmul
name: Lake, Bella
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report on an extended fluctuation regime in the spin dimer system Sr3Cr2O8 based on anomalies in Raman active phonons and magnetic scattering. The compound has two characteristic temperatures, TS = 275 K, related to a Jahn-Teller transition with structural distortions and orbital ordering and a second, T*= 150 K, which is due to further changes in the orbital sector. Below TS quasielastic scattering marks strong fluctuations and in addition phonon anomalies are observed. For temperatures below T* we observe an exponential decrease of one phonon linewidth and determine a gap of the orbital excitations. At low temperatures the observation of two- and three-magnon scattering allows the determination of the spin excitation gap.
description: 7 pages, 4 figures, 1 table
Gp78 regulation of mitophagy by PINK1 and USP13 is mediated by its CUE domain
Creators: name: Mohammadzadeh, Yahya
Publisher: name: University of British Columbia
Year: 2020

description: Mitophagy is an evolutionarily conserved process by which cells remove damaged mitochondria. Defects in mitophagy lead to mitochondrial dysfunction and are associated with pathological states such as cancer and neurodegenerative disorders. PINK1 protein accumulates in damaged mitochondria, recruits the Parkin ubiquitin ligase and induces mitophagy. We showed in the past that Gp78, an endoplasmic reticulum (ER) membrane E3 ligase localizes to ER-mitochondria contact sites. We also showed that Gp78 induces mitophagy independently of Parkin which is dependent on the presence of an intact Gp78 RING finger domain. We now show that Gp78 mitophagy of damaged mitochondria, induced by the mitochondrial poison CCCP, also requires PINK1. Further, the Gp78 cytoplasmic domain also contains a ubiquitin-binding Coupling of Ubiquitin to ER degradation (CUE) domain. Unlike wild-type Gp78 that induces mitophagy only upon mitochondrial damage, Gp78 with CUE-domain mutation constitutively performs mitophagy regardless of mitochondrial damage and independently of PINK1. This suggests that PINK1 acts upon the CUE domain of Gp78 to promote its mitophagy. The USP13 deubiquitinase has been shown to bind to Gp78 and by co-immunoprecipitation analysis, we found that the USP13-Gp78 interaction is CUE domain-dependent. USP13 knock-down (KD) enhances Gp78 ubiquitination of mitochondria, and like the CUE-mutant Gp78, promotes mitophagy even without induction of mitochondrial damage. We then tested the interdependence of USP13 and PINK1 for Gp78-dependent mitophagy. While PINK1 siRNA KD alone prevents Gp78-mediated mitophagy of damaged mitochondria, knockdown of both PINK1 (siRNA) and USP13 (shRNA), restores the Gp78-dependent mitophagy. This suggests that USP13 inhibition of Gp78-mediated mitophagy is relieved upon mitochondrial damage by PINK1.
Rotational Splitting of Pulsational Modes
Creators: name: Deupree, Robert
name: Beslin, Wilfried
Publisher: name: arXiv
Year: 2010
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Mode splittings produced by uniform rotation and a particular form of differential rotation are computed for two-dimensional rotating 10 Mo ZAMS stellar models. The change in the character of the mode splitting is traced as a function of uniform rotation rate, and it is found that only relatively slow rotation rates are required before the mode splitting becomes asymmetric about the azimuthally symmetric (m=0) mode. Increased rotation produces a progressively altered pattern of the individual modes with respect to each other. Large mode splittings begin to overlap with the mode splittings produced by different radial and latitudinal modes at relatively low rotation rates. The mode splitting pattern for the differentially rotating stars we model is different than that for uniformly rotating stars, making the mode splitting a possible discriminant of the internal angular momentum distribution if one assumes the formidable challenge of mode identification can be overcome.
description: 6 journal pages, 7 Figures, accepted by ApJ
Measurement of jet fragmentation in p + p collision at sqrt(s) = 200 GeV with the PHENIX detector
Creators: name: Lai, Yue-shi
Publisher: name: arXiv
Year: 2010
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Measurement of jet fragmentation property in p + p collisions provides a crucial baseline for the study of a possible, modified fragmentation behavior at the presence of the quark-gluon plasma. We describe the first measurement of jet fragmentation functions in sqrt(s) = 200 GeV p + p collisions at RHIC. This is facilitated by extending the linear least square unfolding technique employed by high energy and nuclear experiments to multidimensional spectra, which allows us to correct the inefficiencies in the jet energy response encountered at detectors such as PHENIX.
description: To be published in the proceedings of the 2010 Winter Workshop on Nuclear Dynamics, Jan. 3-9, 2010, Ochos Rios, Jamaica
Evidence for Low Black Hole Spin and Physically Motivated Accretion Models from Millimeter VLBI Observations of Sagittarius A*
Creators: name: Broderick, Avery E.
name: Fish, Vincent L.
name: Doeleman, Sheperd S.
name: Loeb, Abraham
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Millimeter very-long baseline interferometry (mm-VLBI) provides the novel capacity to probe the emission region of a handful of supermassive black holes on sub-horizon scales. For Sagittarius A* (Sgr A*), the supermassive black hole at the center of the Milky Way, this provides access to the region in the immediate vicinity of the horizon. Broderick et al. (2009) have already shown that by leveraging spectral and polarization information as well as accretion theory, it is possible to extract accretion-model parameters (including black hole spin) from mm-VLBI experiments containing only a handful of telescopes. Here we repeat this analysis with the most recent mm-VLBI data, considering a class of aligned, radiatively inefficient accretion flow (RIAF) models. We find that the combined data set rules out symmetric models for Sgr A*'s flux distribution at the 3.9-sigma level, strongly favoring length-to-width ratios of roughly 2.4:1. More importantly, we find that physically motivated accretion flow models provide a significantly better fit to the mm-VLBI observations than phenomenological models, at the 2.9-sigma level. This implies that not only is mm-VLBI presently capable of distinguishing between potential physical models for Sgr A*'s emission, but further that it is sensitive to the strong gravitational lensing associated with the propagation of photons near the black hole. Based upon this analysis we find that the most probable magnitude, viewing angle, and position angle for the black hole spin are a=0.0(+0.64+0.86), theta=68(+5+9)(-20-28) degrees, and xi=-52(+17+33)(-15-24) east of north, where the errors quoted are the 1-sigma and 2-sigma uncertainties.
description: 15 pages, 10 figures, submitted to ApJ
Physarum rubiginosum Fr. & Palmquist, Symb.
Creators: name: Treviño-Zevallos, Italo
name: García-Cunchillos, Iván
name: Basanta, Diana Wrigley De
name: Lado, Carlos
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Protozoa
Mycetozoa
Myxomycetes
Physarales
Physaraceae
Physarum
Physarum rubiginosum

description: 146. º Physarum rubiginosum Fr. & Palmquist, Symb. gasteromyc., fasc. 3: 21 (1818)
 Specimen examined. PERU. Cusco: Anta, Chinchaypujio, Parccotica, Chinchipuya, Km 8,650, 3608 m, 13º34′07”S, 72º14′27”W, 17 Apr 2016, leaves of Alnus acuminata, Lado 24423 (MA-Fungi 95762).
 Notes. Physarum rubiginosum has orange scales in the peridium and capillitium (Fig. 4C) with angular, calcareous concretions. Similar to Ph. lateritium (Berk. & Ravenel) Morgan, differing by its capillitium with calcareous concretions with rounded borders.
 Known from Europe and North America (Poulain et al. 2011), in the Neotropics, it has been recorded from the Windward Islands, Jamaica, and Mexico (Lado & Wrigley de Basanta 2008). It is the first record for South America, inhabiting the litter of Alnus acuminata trees.
description: Published as part of Treviño-Zevallos, Italo, García-Cunchillos, Iván, Basanta, Diana Wrigley De & Lado, Carlos, 2023, Diversity of Myxomycetes from Peru Part III: The high Andes and the altiplano, pp. 1-92 in Phytotaxa 624 (1) on page 72, DOI: 10.11646/phytotaxa.624.1.1, http://zenodo.org/record/10150721
The most distant radio quasars at the highest resolution
Creators: name: Frey, S.
name: Paragi, Z.
name: Gurvits, . L. I.
name: Gabányi, K. É.
name: Cseh, D.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: There are about 50 quasars known at redshifts z>5.7 to date. Only three of them are detected in the radio (J0836+0054, z=5.77; J1427+3312, z=6.12; J1429+5447, z=6.21). The highest-redshift quasars are in the forefront of current astrophysical and cosmological research since they provide important constraints on the growth of the earliest supermassive black holes in the Universe, and on the physical conditions in their environment. These sources are indeed associated with active galactic nuclei as revealed by high-resolution Very Long Baseline Interferometry (VLBI) observations. It is still unclear whether the physical properties of the few z~6 radio quasars are in general similar to those of their lower-redshift cousins. In the case of J1427+3312, the 100-pc scale double morphology suggests a young radio source. Here we report on the recent European VLBI Network (EVN) imaging observations of J1429+5447, the most distant radio quasar known. Based on its milli-arcsecond-scale structural and spectral properties, this quasar is similar to J0836+0054 and J1427+3312. This raises the question if the compact steep-spectrum radio emission is a "universal" feature of the most distant radio quasars. It could only be answered after many more objects at z>6 are discovered and studied.
description: 5 pages, 1 figure
Baryogenesis and Late-Decaying Moduli
Creators: name: Allahverdi, Rouzbeh
name: Dutta, Bhaskar
name: Sinha, Kuver
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Late-decaying string moduli dilute the baryon asymmetry of the universe created in any previous era. The reheat temperature for such moduli is below a GeV, thus motivating baryogenesis at very low temperatures. We present an extension of the minimal supersymmetric standard model with TeV-scale colored fields that can yield the correct baryon asymmetry of the universe in this context. Modulus decay, which reheats the universe at a temperature below GeV, produces the visible sector fields and neutralino dark matter in non-thermal fashion. We discuss various possibilities for baryogenesis from TeV scale colored fields and show that they can generate an acceptable baryon asymmetry, while being compatible with phenomenological constraints like neutron-antineutron oscillation.
description: 8 pages, 3 figures
Local exact exchange potentials within the all-electron FLAPW method and a comparison with pseudopotential results
Creators: name: Betzinger, Markus
name: Friedrich, Christoph
name: Blügel, Stefan
name: Görling, Andreas
Publisher: name: arXiv
Year: 2011
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We present a general numerical approach to construct local Kohn-Sham potentials from orbital-dependent functionals within the all-electron full-potential linearized augmented-plane-wave (FLAPW) method, in which core and valence electrons are treated on an equal footing. As a practical example, we present a treatment of the orbital-dependent exact-exchange (EXX) energy and potential. A formulation in terms of a mixed product basis, which is constructed from products of LAPW basis functions, enables a solution of the optimized-effective-potential (OEP) equation with standard numerical algebraic tools and without shape approximations for the resulting potential. We find that the mixed product and LAPW basis sets must be properly balanced to obtain smooth and converged EXX potentials without spurious oscillations. The construction and convergence of the exchange potential is analyzed in detail for diamond. Our all-electron results for C, Si, SiC, Ge, GaAs semiconductors as well as Ne and Ar noble-gas solids are in very favorable agreement with plane-wave pseudopotential calculations. This confirms the adequacy of the pseudopotential approximation in the context of the EXX-OEP formalism and clarifies a previous contradiction between FLAPW and pseudopotential results.
description: 12 pages, 7 figures, 5 tables
Dissociation of relativistic $^{10}$C nuclei in nuclear track emulsion
Creators: name: Artemenkov, D. A.
name: Alikulov, S. S.
name: Kattabekov, R. R.
name: Mamatkulov, K. Z.
name: Kornegrutsa, N. K.
name: Krivenkov, D. O.
name: Zarubin, P. I.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Dissociation of 1.2 A GeV $^{10}$C nuclei in nuclear track emulsionis is studied. It is shown that most precise angular measurements provided by this technique play a crucial role in the restoration of the excitation spectrum of the 2$α$+2p system. Strong contribution of the cascade process $^{10}$C$\rightarrow ^9$B$\rightarrow ^8$Be identified.
description: 5 pages, 3 figures, conference: The 21st European Conference on Few-Body Problems in Physics, Salamanca, Spain, 29th August - 3rd September, 2010
Characterizing community hoarding cases
Creators: name: Kysow, Kate
Publisher: name: University of British Columbia
Year: 2018

description: Understanding the complexity of hoarding cases is a challenge faced by clinicians and communities alike. Although classified as a mental disorder, the clutter generated by hoarding behaviours does not solely affect the individual; these behaviours are of great concern for society in general. The two approaches to assessing and responding to hoarding disorder taken by research and communities are considerably different. Research has focused on assessing the internal experience of those with hoarding disorder, as well as developing treatments to reduce hoarding behaviours. In contrast, communities across North America have been focused on assessing the public safety threats posed by hoarding cases and responding through a harm reduction approach. The current study bridged the gap between these approaches through a research collaboration with the Vancouver-based Hoarding Action Response Team. Due to the complexity of cases, community-based hoarding teams use a case-by-case approach to address hoarding-related problems. This study conducted a cluster analysis to identify subgroups of hoarding cases and propose intervention targets. Data were collected from the team’s work (e.g., health records, team triage meetings, fire data management system). The current study identified five clusters: Cohabiting in Squalor, Socially Engaged, Isolated at Home, Medically Complex, and Difficult to House. All clusters had a similar degree of clutter, but presented distinct challenges necessitating different interventions. Results from this study will lead to more efficient triaging, network coordination, and evidence-based decision-making on the part of policymakers.
QND Measurement of Large-Spin Ensembles by Dynamical Decoupling
Creators: name: Koschorreck, M.
name: Napolitano, M.
name: Dubost, B.
name: Mitchell, M. W.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum non-demolition (QND) measurement of collective variables by off-resonant optical probing has the ability to create entanglement and squeezing in atomic ensembles. Until now, this technique has been applied to real or effective spin one-half systems. We show theoretically that the build-up of Raman coherence prevents the naive application of this technique to larger spin atoms, but that dynamical decoupling can be used to recover the ideal QND behavior. We experimentally demonstrate dynamical decoupling by using a two-polarization probing technique. The decoupled QND measurement achieves a sensitivity 5.7(6) dB better than the spin projection noise.
Inevitability and Importance of Non-Perturbative Elements in Quantum Field Theory
Creators: name: Bakulev, Alexander P.
name: Shirkov, Dmitry V.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The subject of the first section-lecture is concerned with the strength and the weakness of the perturbation theory (PT) approach, that is expansion in powers of a small parameter $α$, in Quantum Theory. We start with outlining a general troublesome feature of the main quantum theory instrument, the perturbation expansion method. The striking issue is that perturbation series in powers of $α\ll 1$ is not a convergent series. The formal reason is an essential singularity of quantum amplitude (matrix element) $C(α)$ at the origin $α=0$. In many physically important cases one needs some alternative means of theoretical analysis. In particular, this refers to perturbative QCD (pQCD) in the low-energy domain. In the second section-lecture, we discuss the approach of Analytic Perturbation Theory (APT). We start with a short historic preamble and then discuss how combining the Dispersion Relation with the Renormalization Group (RG) techniques yields the APT with \myMath{\displaystyle e^{-1/α}} nonanalyticity. Next we consider the results of APT applications to low-energy QCD processes and show that in this approach the fourth-loop contributions, which appear to be on the asymptotic border in the pQCD approach, are of the order of a few per mil. Then we note that using the RG in QCD dictates the need to use the Fractional APT (FAPT) and describe its basic ingredients. As an example of the FAPT application in QCD we consider the pion form factor $F_π(Q^2)$ calculation. At the end, we discuss the resummation of nonpower series in {(F)APT} with application to the estimation of the Higgs-boson-decay width $Γ_{H\to\bar{b}b}(m_H^2)$.
description: 26 pages, 13 figures, invited talk delivered by the first author at the 6th Mathematical Physics Meeting: Summer School and Conference on Modern Mathematical Physics, Belgrade, Sept 15-23, 2010
DEP Bulletin: Volume 42 Issue 7
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 2018

description: The DEP bulletin is a semi-monthly publication of the New Jersey Department of Environmental Protection. It contains a list of construction permit applications recently filed or acted upon by the Department along with a calendar of events of interest, a schedule of public hearings, and Environmental Impact Statements acted upon during the period.
Entropy rate calculations of algebraic measures
Creators: name: Marchand, Katy
name: Mulherkar, Jaideep
name: Nachtergaele, Bruno
Publisher: name: arXiv
Year: 2011
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences
subject: 94A15

description: Let $K = \{0,1,...,q-1\}$. We use a special class of translation invariant measures on $K^\mathbb{Z}$ called algebraic measures to study the entropy rate of a hidden Markov processes. Under some irreducibility assumptions of the Markov transition matrix we derive exact formulas for the entropy rate of a general $q$ state hidden Markov process derived from a Markov source corrupted by a specific noise model. We obtain upper bounds on the error when using an approximation to the formulas and numerically compute the entropy rates of two and three state hidden Markov models.
Forward modelling to determine the observational signatures of white-light imaging and interplanetary scintillation for the propagation of an interplanetary shock in the ecliptic plane
Creators: name: Xiong, Ming
name: Breen, A. R.
name: Bisi, M. M.
name: Owens, M. J.
name: Fallows, R. A.
name: Dorrian, G. D.
name: Davies, J. A.
name: Thomasson, P.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: Recent coordinated observations of interplanetary scintillation (IPS) and stereoscopic heliospheric imagers (HIs) are significant to continuously track the propagation and evolution of solar eruptions throughout interplanetary space. In order to obtain a better understanding of the observational signatures in these two remote-sensing techniques, the magnetohydrodynamics of the macro-scale interplanetary disturbance and the radio-wave scattering of the micro-scale electron-density fluctuation are coupled and investigated using a newly-constructed multi-scale numerical model. This model is then applied to a case of an interplanetary shock propagation within the ecliptic plane. The shock could be nearly invisible to an HI, once entering the Thomson-scattering sphere of the HI. The asymmetry in the optical images between the western and eastern HIs suggests the shock propagation off the Sun-Earth line. Meanwhile, an IPS signal, strongly dependent on the local electron density, is insensitive to the density cavity far downstream of the shock front. When this cavity (or the shock nose) is cut through by an IPS ray-path, a single speed component at the flank (or the nose) of the shock can be recorded; when an IPS ray-path penetrates the sheath between the shock nose and this cavity, two speed components at the sheath and flank can be detected. Moreover, once a shock front touches an IPS ray-path, the derived position and speed at the irregularity source of this IPS signal, together with an assumption of a radial and constant propagation of the shock, can be used to estimate the later appearance of the shock front in the elongation of the HI field of view. The results of synthetic measurements from forward modelling are helpful in inferring the in-situ properties of coronal mass ejection from real observational data via an inverse approach.
description: 31 pages, 8 figures, Journal of Atmospheric and Solar-Terrestrial Physics, accepted