cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 7 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma
Creators: name: Sgro, Agustin
name: Cursons, Joseph
name: Waryah, Charlene
name: Woodward, Eleanor A.
name: Foroutan, Momeneh
name: Lyu, Ruqian
name: Yeoh, George C. T.
name: Leedman, Peter J.
name: Blancafort, Pilar
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 7: Figure S6. Related to Fig. 5. Transcriptional reactivation of HHIP gene by novel CRISPRa combinations does not correlate with changes in promoter DNA methylation in transiently transfected Hep3B cells. A Fold change in HHIP mRNA expression evaluated by qRT-PCR 96 h after transient transfection in Hep3B cells. Cells were transfected with SpdCas9-VPR and MS2-MCP-p65-HSF1, or with SpdCas9-TET1-CD and MS2-MCP-p65-HSF1, along with gRNA G4 or with no gRNA (NO G) as control. Relative gene expression was normalized and compared to cells transfected with empty vector control (EV) for statistical analysis. Data presented as means ± SEM (n = 3), and P-values were determined by unpaired t-test (***P = 0.0001, ****P < 0.0001). B Heatmap showing HHIP promoter DNA methylation in Hep3B cells transiently transfected with the novel CRISPRa combinations. Data from Illumina Infinium 850 K methylation EPIC microarrays. For each probe (listed at left), the difference in β-value from the average is shown (at left; green-purple color map) together with the average probe β-value (at center; blue-yellow color map), and the adjusted P-value for differential methylation between gRNA G4 and NO G for the two combinations tested (at right; white-purple color map).
Sparse Deterministic Approximation of Bayesian Inverse Problems
Creators: name: Schwab, Ch.
name: Stuart, A. M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We present a parametric deterministic formulation of Bayesian inverse problems with input parameter from infinite dimensional, separable Banach spaces. In this formulation, the forward problems are parametric, deterministic elliptic partial differential equations, and the inverse problem is to determine the unknown, parametric deterministic coefficients from noisy observations comprising linear functionals of the solution. We prove a generalized polynomial chaos representation of the posterior density with respect to the prior measure, given noisy observational data. We analyze the sparsity of the posterior density in terms of the summability of the input data's coefficient sequence. To this end, we estimate the fluctuations in the prior. We exhibit sufficient conditions on the prior model in order for approximations of the posterior density to converge at a given algebraic rate, in terms of the number $N$ of unknowns appearing in the parameteric representation of the prior measure. Similar sparsity and approximation results are also exhibited for the solution and covariance of the elliptic partial differential equation under the posterior. These results then form the basis for efficient uncertainty quantification, in the presence of data with noise.
title: การคัดเลือกสายพันธุ์บริสุทธิ์เห็ดถังเช่าทิเบต (Ophiocordyceps sinensis) จากดอกเห็ดถังเช่าทิเบตแห้งที่มาจากประเทศจีน
Creators: name: สุวรรณโฉม ชาตินรินทร์
Publisher: name: สำนักวิจัยและส่งเสริมวิชาการการเกษตร มหาวิทยาลัยแม่โจ้
publisherIdentifierScheme: ROR
Year: 2024
Subjects: การคัดแยกสายพันธุ์
การระบุสายพันธุ์
ลักษณะสัณฐานวิทยา
เห็ดถังเช่า

description: Journal Of Agricultural Research And Extension, 41, 3, 93-102
Investigations into the mechanisms involved in baculovirus nucleocapsid egress
Creators: name: Biswas, Siddhartha
Publisher: name: University of British Columbia
Year: 2018

description: The mechanism of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) nucleocapsid egress from the nucleus to the plasma membrane leading to the formation of budded virus (BV) is not known. AC141 is a nucleocapsid protein and has been shown to be associated with β-tubulin. We hypothesized that nucleocapsid proteins associate with the lepidopteran microtubule and kinesin-1 during egress. Kinesin-1 is a motor protein that moves along the microtubules and carries cargo. Experiments showed that nucleocapsid proteins associate with kinesin-1 during infection. Downregulation of kinesin-1 by siRNA results in reduced BV production. These studies support that AcMNPV utilizes kinesin-1 and microtubules for nucleocapsid transport and BV production. GP64 (integral membrane protein) and ME53 associate at the plasma membrane and are believed to be at budding foci of nucleocapsids. AC141 was shown to associate with the ME53-GP64 complex at the plasma membrane and potentially facilitates the budding of nucleocapsids. The interaction between AC141, GP64, ME53 may enhance the cellular relocation of ME53. AcMNPV-encoded viral ubiquitin (vUbi) and AC141 (a predicted E3 ubiquitin ligase) have been shown to be required for efficient BV production. We hypothesized that vUbi interacts with AC141 and this interaction is required for BV production. Deletion of both ac141 and vubi restricted the infection to a single cell. AC141 was ubiquitinated by either vUbi or cellular Ubi and this interaction was required for optimal BV production. Virion fractionation showed that a nucleocapsid protein of 100 kDa, potentially AC66, is specifically ubiquitinated with vUbi in BV and but not in occlusion derived virus (ODV). These data suggest ubiquitination of nucleocapsid protein acts as a signal that determines how a nucleocapsid is directed to become a BV or ODV. Polyubiquitin chains are formed by the internal lysines present within the ubiquitin and serve as a signal for various cellular pathways. Mutations of lysines to arginine showed that vUbi is involved in cellular processes mediated by K6 and K27 polyubiquitin chains. The collective results of this study provide significant new data on the role of viral and host proteins and the mechanism by which baculovirus nucleocapsids egress from the nucleus to form BV.
Accelerating universe from F(T) gravity
Creators: name: Myrzakulov, Ratbay
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: It is shown that the acceleration of the universe can be understood by considering a F(T) gravity models. For these F(T) gravity models, a variant of the accelerating cosmology reconstruction program is developed. Some explicit examples of F(T) are reconstructed from the background FRW expansion history.
description: 13 pages, references added
Dense spectrum of resonances and particle capture in a near-black-hole metric
Creators: name: Flambaum, V. V.
name: Gossel, G. H.
name: Gribakin, G. F.
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We show that a quantum scalar particle in the gravitational field of a massive body of radius R which slightly exceeds the Schwarzschild radius r_s, possesses a dense spectrum of narrow resonances. Their lifetimes and density tend to infinity in the limit R -> r_s. We determine the cross section of the particle capture into these resonances and show that it is equal to the absorption cross section for a Schwarzschild black hole. Thus, a non-singular static metric acquires black-hole properties before the actual formation of a black hole.
description: 6 pages, 6 figures, accepted for publication in Physical Review D
title: การศึกษาองค์ประกอบทางเคมีของน้ำมันหอมระเหยจากดอกเอื้องคำสด ด้วยแก๊สโครมาโทกราฟี-แมสสเปกโทรเมตรี/แมสสเปกโทรเมตรี ทริปเปิ้ลควอดรูโพล
Creators: name: รุ่งทิพย์ กาวารี
Publisher: name: สำนักวิจัยและส่งเสริมวิชาการการเกษตร มหาวิทยาลัยแม่โจ้
publisherIdentifierScheme: ROR
Year: 2024
Subjects: เอื้องคำ
องค์ประกอบทางเคมี
น้ำมันหอมระเหย
การกลั่นด้วยน้ำ
แก๊สโครมาโทกราฟ-แมสสเปกโทรมิเตอร์/แมสสเปกโทรมิเตอร์

description: Journal Of Agricultural Research And Extension, 41, 3, 103-112
title: การพัฒนาชุดผลิตภัณฑ์สปาบำรุงเส้นผมสูตรอ่อนโยนจากสารสกัดสมุนไพรไทย
Creators: name: ธนพล กิจพจน์
Publisher: name: สำนักวิจัยและส่งเสริมวิชาการการเกษตร มหาวิทยาลัยแม่โจ้
publisherIdentifierScheme: ROR
Year: 2024
Subjects: สารสกัดสมุนไพร
แชมพูสมุนไพร
ครีมนวดผมสมุนไพร
สารประกอบฟีนอลิก
สารประกอบฟลาโวนอยด์

description: Journal Of Agricultural Research And Extension, 41, 3, 113-126
The KMOS Cluster Survey – KCS: Timing the formation of passive galaxies in clusters with 1.4
Creators: name: Beifiori, Alessandra
Publisher: name: Zenodo
Year: 2019

description: In this talk I will discuss recent progress studying the rest-frame optical properties of quiescent galaxies at 1.4 < z < 1.8 using KMOS. I will highlight recent results form the KMOS Custer Survey (KCS), whose aim is to provide a census of quiescent galaxy kinematics at 1.4 < z < 1.8 in know overdensities. The combination of kinematic measurements from KMOS and structural parameters measured from deep HST imaging allowed us to place constraints on the formation ages of passive galaxies at 1.4 < z <1.8 and on the evolution of galaxy properties and scaling relations at high redshift.
Additional file 8 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma
Creators: name: Sgro, Agustin
name: Cursons, Joseph
name: Waryah, Charlene
name: Woodward, Eleanor A.
name: Foroutan, Momeneh
name: Lyu, Ruqian
name: Yeoh, George C. T.
name: Leedman, Peter J.
name: Blancafort, Pilar
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 8: Figure S7. Related to Fig. 5. Lentiviral transduction of SpdCas9-TET1-CD or SpdCas9-VPR targeting HHIP or MT1M genes in Hep3B cells. A Schematic representation of the “all-in-one” lentiviral vectors, SpdCas9-TET1-CD and SpdCas9-VPR, for the constitutive co-expression of a gRNA and TET1-CD or VPR, C-terminally fused to SpdCas9. B Fold change in HHIP mRNA expression assessed by qRT-PCR at 18, 30, and 40 days in Hep3B cells constitutively co-expressing SpdCas9-TET1-CD and the combination of four gRNAs (MIX 4G) targeting HHIP promoter. C Fold change in MT1M mRNA expression assessed by qRT-PCR at 20 days in Hep3B cells lentivirally co-transduced with SpdCas9-TET1-CD and individual gRNAs (G1, G2, G3, and G4) or the MIX 4G; or with SpdCas9-VPR and the most potent gRNA (G1). Data presented as means ± SEM (n = 3), compared to SpdCas9-TET1-CD NO G, and P-values were determined by two-way ANOVA with Šídák's multiple comparisons test for panel (B), and by two-way ANOVA with Dunnett's multiple comparisons test for panel (C) (****P < 0.0001). SpdCas9 Streptococcus pyogenes deactivated Cas9 protein adopted for epigenome engineering, TET1-CD Ten-Eleven Translocation methylcytosine dioxygenase 1-catalytic domain, VPR VP64, p65, Rta, hU6 RNA polymerase III promoter for human U6 snRNA, hUbC human ubiquitin C promoter, 3xFLAG three tandem FLAG® epitope tags, followed by an enterokinase cleavage site, SV40NLS nuclear localization signal of SV40 (simian virus 40) large T antigen, T2A 2A peptide from Thosea asigna virus capsid protein, cleavable linker, PuroR puromycin N-acetyltransferase gene that confers resistance to puromycin, MIX 4G combination of four gRNAs, ns not significant.
Hidden time-reversal in driven XXZ spin chains: exact solutions and new dissipative phase transitions
Creators: name: Yao, Mingxing
name: Lingenfelter, Andrew
name: Belyansky, Ron
name: Roberts, David
name: Clerk, Aashish A.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We show that several models of interacting XXZ spin chains subject to boundary driving and dissipation possess a subtle kind of time-reversal symmetry, making their steady states exactly solvable. We focus on a model with a coherent boundary drive, showing that it exhibits a unique continuous dissipative phase transition as a function of the boundary drive amplitude. This transition has no analogue in the bulk closed system, or in incoherently driven models. We also show the steady state magnetization exhibits a surprising fractal dependence on interaction strength, something previously associated with less easily measured infinite-temperature transport quantities (the Drude weight). Our exact solution also directly yields driven-dissipative double-chain models that have pure, entangled steady states that are also current carrying.
description: 6 pages, 4 figures + 16 pages, 7 figures
The thermodynamic evolution of the cosmological event horizon
Creators: name: Funkhouser, Scott
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Physics (physics.gen-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: By manipulating the integral expression for the proper radius $R_e$ of the cosmological event horizon (CEH) in a Friedmann-Robertson-Walker (FRW) universe, we obtain an analytical expression for the change $\dd R_e$ in response to a uniform fluctuation $\ddρ$ in the average cosmic background density $ρ$. We stipulate that the fluctuation arises within a vanishing interval of proper time, during which the CEH is approximately stationary, and evolves subsequently such that $\ddρ/ρ$ is constant. The respective variations $2πR_e \dd R_e$ and $\dd E_e$ in the horizon entropy $S_e$ and enclosed energy $E_e$ should be therefore related through the cosmological Clausius relation. In that manner we find that the temperature $T_e$ of the CEH at an arbitrary time in a flat FRW universe is $E_e/S_e$, which recovers asymptotically the usual static de Sitter temperature. Furthermore, it is proven that during radiation-dominance and in late times the CEH conforms to the fully dynamical First Law $T_e \drv S_e = P\drv V_e - \drv E_e$, where $V_e$ is the enclosed volume and $P$ is the average cosmic pressure.
description: 6 pages
Additional file 9 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma
Creators: name: Sgro, Agustin
name: Cursons, Joseph
name: Waryah, Charlene
name: Woodward, Eleanor A.
name: Foroutan, Momeneh
name: Lyu, Ruqian
name: Yeoh, George C. T.
name: Leedman, Peter J.
name: Blancafort, Pilar
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 9: Figure S8. Related to Fig. 7. Phenotypic reprogramming in Hep3B HCC cells lentivirally transduced with SpdCas9-VPR targeting and upregulating MT1M with G1, PZP with G2, TTC36 with G3, or with NO G as control. A-C Cell viability determined using a luminescence assay (CellTiter-Glo®). Data shown as fold change compared to SpdCas9-VPR NO G at 24, 48, and 72 h, presented as means ± SEM (n = 3), and P-values were determined by unpaired t-test with Welch's correction (From left to right: (A), ***P = 0.0001, **P = 0.0056; (B), **P = 0.0024, **P = 0.0011; and (C), ****P < 0.0001, *P = 0.0310). D Cell migration assessed by the Boyden chamber assay. Data normalized to SpdCas9-VPR NO G, presented as means ± SEM (n = 3), and P-values were determined by unpaired t-test. ns not significant.
Geometric Phase: a Diagnostic Tool for Entanglement
Creators: name: Sandhya, S. N.
name: Banerjee, Subhashish
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Using a kinematic approach we show that the non-adiabatic, non-cyclic, geometric phase corresponding to the radiation emitted by a three level cascade system provides a sensitive diagnostic tool for determining the entanglement properties of the two modes of radiation. The nonunitary, noncyclic path in the state space may be realized through the same control parameters which control the purity/mixedness and entanglement. We show analytically that the geometric phase is related to concurrence in certain region of the parameter space. We further show that the rate of change of the geometric phase reveals its resilience to fluctuations only for pure Bell type states. Lastly, the derivative of the geometric phase carries information on both purity/mixedness and entanglement/separability.
description: 13 pages 6 figures
Quantum Corrections to Fidelity Decay in Chaotic Systems
Creators: name: Gutkin, Boris
name: Waltner, Daniel
name: Gutierrez, Martha
name: Kuipers, Jack
name: Richter, Klaus
Publisher: name: Universität Regensburg
Year: 2010
Subjects: subject: 530 Physik
subject: 05.45.Mt, 03.65.Sq

description: By considering correlations between classical orbits we derive semiclassical expressions for the decay of the quantum fidelity amplitude for classically chaotic quantum systems, as well as for its squared modulus, the fidelity or Loschmidt echo. Our semiclassical results for the fidelity amplitude agree with random matrix theory (RMT) and supersymmetry predictions in the universal Fermi golden rule regime. The calculated quantum corrections can be viewed as arising from a static random perturbation acting on nearly self-retracing interfering paths, and hence will be suppressed for time-varying perturbations. Moreover, using trajectory-based methods we show a relation, recently obtained in RMT, between the fidelity amplitude and the cross-form factor for parametric level correlations. Beyond RMT, we compute Ehrenfest-time effects on the fidelity amplitude. Furthermore our semiclassical approach allows for a unified treatment of the fidelity, both in the Fermi golden rule and Lyapunov regimes, demonstrating that quantum corrections are suppressed in the latter.
The KMOS view of cluster disk galaxies at z~1.5
Creators: name: Boehm, Asmus
Publisher: name: Zenodo
Year: 2019

description: I will present first results from our KMOS H-band spectroscopy of ~50 galaxies in two assembling clusters at redshift z=1.47. Our targets were selected from narrow-band imaging of the HyperSuprimeCam Survey and are following the star formation main sequence at their redshift. We combine our analysis with own studies in various environments at lower redshifts.  Based on the spatially resolved Halpha emission, we find a high fraction of kinematically disturbed objects at z=1.47: only approx. 1/3 of the galaxies are regular rotators for which the maximum rotation velocities Vmax can be derived. This is a similar fraction as has been found in the field regime at these redshifts but much lower than in any environment at z<1. In the high-redshift clusters, disturbed kinematics occur at all cluster-centric radii and all galaxy masses, different from what is found in lower-redshift clusters, where disturbances are found preferentially in lower-mass galaxies and closer to the cluster centers. I will also discuss the stellar mass - Vmax (Tully-Fisher) relation as well as an alternate scaling relation combining Vmax and velocity dispersion (aka S_0.5 parameter).
Theory of anisotropic exchange in laterally coupled quantum dots
Creators: name: Baruffa, Fabio
name: Stano, Peter
name: Fabian, Jaroslav
Publisher: name: Universität Regensburg
Year: 2010
Subjects: subject: 530 Physik

description: The effects of spin-orbit coupling on the two-electron spectra in lateral coupled quantum dots are investigated analytically and numerically. It is demonstrated that in the absence of magnetic field, the exchange interaction is practically unaffected by spin-orbit coupling, for any interdot coupling, boosting prospects for spin-based quantum computing. The anisotropic exchange appears at finite magnetic fields. A numerically accurate effective spin Hamiltonian for modeling spin-orbit-induced two-electron spin dynamics in the presence of magnetic field is proposed.
Optimized surface ion trap design for tight confinement and separation of ion chains
Creators: name: Gerasin, Ilya
name: Zhadnov, Nikita
name: Kudeyarov, Konstantin
name: Khabarova, Ksienia
name: Kolachevsky, Nikolay
name: Semerikov, Ilya
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Qubit systems based on trapped ultracold ions win one of the leading positions in the quantum computing field, demonstrating quantum algorithms with the highest complexity to date. Surface Paul traps for ion confinement open the opportunity to scale quantum processors to hundreds of qubits and enable high-connectivity manipulations on ions. To fabricate such a system with certain characteristics, the special design of a surface electrode structure is required. The depth of the trapping potential, the stability parameter, the secular frequency and the distance between an ion and the trap surface should be optimized for better performance. Here we present the optimized design of a relatively simple surface trap that allows several important high-fidelity primitives: tight ion confinement, laser cooling, and wide optical access. The suggested trap design also allows to perform an important basic operation, namely, splitting an ion chain into two parts.
Future surveys of the bulge stellar populations
Creators: name: Origlia, Livia
Publisher: name: Zenodo
Year: 2019

description: In this talk I will highlight open questions and future observational perspectives to unveil the chemical, kinematic and evolutionary properties of the complex stellar populations of the barred Bulge and towards the Galactic center.   Their comprehension is of fundamental importance to interpret and model formation and evolution of the nuclear region of galaxies at large, and the assembling process of massive bulges at high redshift.
Discrete spherical means of directional derivatives and Veronese maps
Creators: name: Belyaev, Alexander
name: Khesin, Boris
name: Tabachnikov, Serge
Publisher: name: arXiv
Year: 2011
Subjects: subject: Numerical Analysis (math.NA)
subject: Metric Geometry (math.MG)
subject: FOS: Mathematics

description: We describe and study geometric properties of discrete circular and spherical means of directional derivatives of functions, as well as discrete approximations of higher order differential operators. For an arbitrary dimension we present a general construction for obtaining discrete spherical means of directional derivatives. The construction is based on using the Minkowski's existence theorem and Veronese maps. Approximating the directional derivatives by appropriate finite differences allows one to obtain finite difference operators with good rotation invariance properties. In particular, we use discrete circular and spherical means to derive discrete approximations of various linear and nonlinear first- and second-order differential operators, including discrete Laplacians. A practical potential of our approach is demonstrated by considering applications to nonlinear filtering of digital images and surface curvature estimation.
Essays in corporate finance, labour economics, and political economy
Creators: name: Xu, Sheng-Jun
Publisher: name: University of British Columbia
Year: 2017

description: This thesis presents a collection of essays on the intersection of finance, labour, and political economy. In Chapter 2, I exploit the 2003 reduction in the legislative cap for the H-1B visa program to show that a firm’s ability to hire skilled workers affects corporate investment. U.S. firms use the H-1B program to recruit foreign skilled (college-educated) workers, and I find that the reduction in the cap caused a significant decrease in investment for firms that were more reliant on H-1B workers as a source of skilled labour. The effect persists for several years, and is more pronounced for firms hiring workers in “industrial” occupations compared with firms hiring workers in “knowledge” occupations. The remaining essays examine how political incentives affect the policies of U.S. public-sector defined benefit pension plans. In Chapter 3, I present novel empirical evidence that “pension deficits”—the difference between liability accrual rates and asset accumulation rates—are systematically higher in gubernatorial election years. This electoral cycle pattern is explained by systematic dips in governmental contributions, and plans that exhibit larger electoral cycles tend to experience deteriorating funding levels and lower economic growth. Falsification tests, including analysis of private-sector DB pension plans and unexpected Governor transitions, indicate that non-political factors are unlikely to explain the documented electoral cycles. In Chapter 4, I present a theoretical model detailing how electoral incentives induce incumbent politicians to borrow from public pension plans in a short-sighted manner at the expense of taxpayers. Using a career concerns model framework, I show this conflict is rooted in (1) moral hazard stemming from protections that insulate employees from the costs of unfunded pension liabilities, and (2) information asymmetry stemming from the opacity of public pension plans. The model generates predictions consistent with empirical findings from Chapter 3. Specifically, electoral cycles in pension deficits are more pronounced for states that place the burden of funding unfunded pension liabilities on taxpayers, and for states with less transparent public pension systems. Furthermore, pension deficits are larger during elections that are more closely contested and during gubernatorial terms in which the incumbent remains eligible to run for re-election.
Additional file 10 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma
Creators: name: Sgro, Agustin
name: Cursons, Joseph
name: Waryah, Charlene
name: Woodward, Eleanor A.
name: Foroutan, Momeneh
name: Lyu, Ruqian
name: Yeoh, George C. T.
name: Leedman, Peter J.
name: Blancafort, Pilar
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 10: Table S1. Related to Figs. 3–7 and Figures S4-S8. gRNAs designed for gene reactivation by CRISPRa technology. Details include gRNA and PAM sequences, the DNA strand targeted, the distance from the TSS, and the genomic annotations.
Strange quark suppression and strange hadron production in pp collisions at RHIC and LHC
Creators: name: Long, Hai-Yan
name: Feng, Sheng-Qin
name: Zhou, Dai-Mei
name: Yan, Yu-Liang
name: Ma, Hai-Liang
name: Sa, Ben-Hao
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The parton and hadron cascade model PACIAE based on PYTHIA was utilized to systematically investigate the strange particle production in pp collisions at the RHIC and LHC energies. Taking the mechanism of reduction of the strange quark suppression into account the STAR and ALICE data of strange particle production in pp collisions are well reproduced. It turned out that the K/π ratio as a function of reaction energy in pp collisions shows slightly increasing from sqrt(s)=0.2 to 0.9 TeV and then turning to saturation.
Orbital properties of the Bulge giants with Gaia DR2
Creators: name: Simion, Iulia
name: Fernandez-Trincado, J.G.
Publisher: name: Zenodo
Year: 2019

description: Gaia DR2 is set to revolutionize our understanding of the Milky Way's past. I built a catalog of Bulge stars with 6D phase space information and metallicity from existing large-scale Bulge spectroscopic surveys (e.g. ARGOS), which provide line-of-sight velocities and metallicity measurements for 2MASS Red Giant Branch stars, and from Gaia DR2, which provides accurate proper motions. Using this information it was possible to integrate their orbits and thus, gain insight into their origin, opening a small window into the history of formation of the Galactic Bulge/Milky Way.
Is there a relationship between response to total sleep deprivation and efficacy of clomipramine treatment in depressed patients?
Creators: name: Höchli, D.
name: Riemann, D.
name: Zulley, Jürgen
name: Berger, M.
Publisher: name: Universität Regensburg
Year: 1986
Subjects: subject: 610 Medizin
subject: Adolescent
subject: Adult
subject: Bipolar Disorder/drug therapy
subject: Clomipramine/therapeutic use
subject: Depressive Disorder/psychology
subject: Humans
subject: Middle Aged
subject: Prognosis
subject: Psychiatric Status Rating Scales

description: Total sleep deprivation (TSD) and tricyclic medication are successful treatment modalities for patients with a major depressive disorder. Recent studies have suggested a positive relationship between TSD response and succeeding tricyclic treatment, even on a very specific level, thus supporting the assumption of two distinct biochemical subtypes of depression. The present study tested this hypothesis by treating 10 inpatients with a major depressive disorder first with TSD and succeedingly with clomipramine. Contrary to expectation, a negative relationship between clinical response to the two treatment modalities was found.
Phase shift in the REM sleep rhythm
Creators: name: Schulz, Hartmut
name: Dirlich, Gerhard
name: Zulley, Jürgen
Publisher: name: Universität Regensburg
Year: 1975
Subjects: subject: 610 Medizin
subject: Adult
subject: Circadian Rhythm
subject: Female
subject: Humans
subject: Male
subject: Sleep, REM/physiology

description: The periodic alternation between REM and NREM sleep was analyzed. Usually, sleep records of consecutive nights of a subject are regarded to be independent events. However, it may be that consecutive nights are realizations of a continuously ongoing rhythm. This was tested in the present study. The temporal patterns of REM and NREM sleep in sequences of about 30 consecutive nights for 3 subjects were analyzed. The results show that only the onset of the first REM sleep phase during any one night may be predicted from the sleep onset time, whereas a systematic phase shift between consecutive nights was observed in the later REM sleep phases. Thus, the onset of later REM sleep phases is better predicted by assuming a rhythm with stable period length which controls the appearance of REM sleep phases in successive nights. Under the experimental conditions the phase shift was between 5 and 10 min per 24 hrs for the 3 subjects. The result is accordance with Kleitman's basic rest activity cycle (BRAC) hypothesis.
Two distinct Mott-Insulator to Bose-glass transitions and breakdown of self averaging in the disordered Bose-Hubbard model
Creators: name: Krüger, Frank
name: Hong, Seungmin
name: Phillips, Philip
Publisher: name: arXiv
Year: 2010
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We investigate the instabilities of the Mott-insulating phase of the weakly disordered Bose-Hubbard model within a renormalization group analysis of the replica field theory obtained by a strong-coupling expansion around the atomic limit. We identify a new order parameter and associated correlation length scale that is capable of capturing the transition from a state with zero compressibility, the Mott insulator, to one in which the compressibility is finite, the Bose glass. The order parameter is the relative variance of the disorder-induced mass distribution. In the Mott insulator, the relative variance renormalizes to zero, whereas it diverges in the Bose glass. The divergence of the relative variance signals the breakdown of self-averaging. The length scale governing the breakdown of self-averaging is the distance between rare regions. This length scale is finite in the Bose glass but diverges at the transition to the Mott insulator with an exponent of $ν=1/D$ for incommensurate fillings. Likewise, the compressibility vanishes with an exponent of $γ=4/D-1$ at the transition. At commensurate fillings, the transition is controlled by a different fixed point at which both the disorder and interaction vertices are relevant.
description: Extended, published version
Additional file 11 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma
Creators: name: Sgro, Agustin
name: Cursons, Joseph
name: Waryah, Charlene
name: Woodward, Eleanor A.
name: Foroutan, Momeneh
name: Lyu, Ruqian
name: Yeoh, George C. T.
name: Leedman, Peter J.
name: Blancafort, Pilar
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 11: Table S2. Related to Figs. 2–7 and Figures S4-S7. TaqMan gene expression assays utilized for qRT-PCR experiments.
Annotation of the human odontoblast cell layer and dental pulp proteomes and N-terminomes
Creators: name: Abbey, Simon
Publisher: name: University of British Columbia
Year: 2017

description: The proteome and N-terminome of the human odontoblast cell layer was identified for the first time by shotgun proteomic and terminal amine isotopic labeling of substrates (TAILS) N terminomic analyses, respectively, and compared with that of human dental pulp stroma from 3rd molar teeth. After reverse-phase liquid chromatography-tandem mass spectrometry, >170,000 spectra from the shotgun and TAILS analyses were matched by four search engines to 4,888 and 12,063 peptides in the odontoblast cell layer and pulp stroma, respectively. Using the Trans-Proteomic Pipeline, I identified 895 and 2,423 unique proteins in these tissues at an FDR of ≤ 1 %. In the odontoblast cell layer proteome I found proteomic evidence for dentin sialophosphoprotein, which is cleaved into dentin phosphoprotein and dentin sialoprotein, proteins that are important in dentin mineralization. Further, 222 proteins of the odontoblast cell layer were not found in the pulp, suggesting many of these proteins are synthesized preferentially by odontoblasts. I also found minor differences in the odontoblast cell layer between the dental pulp proteomes of older and younger donors. The human dental pulp stroma proteome was expanded by 974 new proteins, not previously identified among the 4,123 proteins identified in our previous dental pulp study (Eckhard et al., 2015). Thus, by exploring the proteome of the odontoblast cell layer and expanding the known dental pulp proteome, we found distinct proteome differences when compared with each other and with dentin. The mass spectrometry raw data and metadata have been deposited to ProteomeXchange with the PXD identifier ˂PXD006557˃.
Estimating Form Factors of $B_s\rightarrow D_s^{(*)}$ and their Applications to Semi-leptonic and Non-leptonic Decays
Creators: name: Chen, Xiang-Jun
name: Fu, Hui-feng
name: Kim, C. S.
name: Wang, Guo-Li
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: $B_s^0\rightarrow D_s^{-}$ and $B_s^0\rightarrow D_s^{*-}$ weak transition form factors are estimated for the whole physical region with a method based on an instantaneous approximated Mandelstam formulation of transition matrix elements and the instantaneous Bethe-Salpeter equation. We apply the estimated form factors to branching ratios, CP asymmetries and polarization fractions of non-leptonic decays within the factorization approximation. And we study the non-factorizable effects and annihilation contributions with the perturbative QCD approach. The branching ratios of semi-leptonic $B_s^0\rightarrow D_s^{(*)-}l^+ν_l$ decays are also evaluated. We show that the calculated decay rates agree well with the available experimental data. The longitudinal polarization fraction of $B_s\rightarrow D_s^*V(A)$ decays are $\sim0.8$ when $V(A)$ denotes a light meson, and are $\sim0.5$ when $V(A)$ denotes a $D_q$ ($q=d,s$) meson.
description: Final version published in J Phys. G 39 (2012) 045002 (Title also changed)
The SIRIUS code: Statistical Inference of physical paRameters of sIngle and mUltiple populations in Stellar clusters
Creators: name: Souza, Stefano
name: Oliveira, R.A.P.
name: Kerber, L. O.
name: Barbuy, B.
Publisher: name: Zenodo
Year: 2019

description: Globular clusters (GCs) are fundamental pieces to understand the formation and evolution of the Milky Way. From the color-magnitude diagrams it is possible to get physical parameters such as age, distance, reddening, proper motions, among others. The wealth of information available in high quality photometric, spectroscopic and/or astrometric data, allows to perform a comprehensive and self-consistent analysis combining different data and techniques. We are developing a python package based on a Bayesian approach, that we named SIRIUS, to extract as much as possible information of a stellar cluster, in general. In addition, SIRIUS can characterize both simple and multiple stellar populations in a stellar cluster. We have tested the SIRIUS validity, analyzing HST, VLT, Gemini, VVV, and Gaia DR2 data of bulge GCs.
Half-flat structures on decomposable Lie groups
Creators: name: Freibert, Marco
name: Schulte-Hengesbach, Fabian
Publisher: name: arXiv
Year: 2010
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C25 (primary), 53C15, 53C30 (secondary)

description: Half-flat SU(3)-structures are the natural initial values for Hitchin's evolution equations whose solutions define parallel G_2-structures. Together with the results of arXiv:0912.3486v1, the results of this article completely solve the existence problem of left-invariant half-flat SU(3)-structures on decomposable Lie groups. The proof is supported by the calculation of the Lie algebra cohomology for all indecomposable five-dimensional Lie algebras which refines and clarifies the existing classification of five-dimensional Lie algebras.
description: 15 pages, v2: minor corrections and improved presentation
Dynamical energy analysis for built-up acoustic systems at high frequencies
Creators: name: Chappell, D. J.
name: Giani, S.
name: Tanner, G.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Dynamical Systems (math.DS)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Standard methods for describing the intensity distribution of mechanical and acoustic wave fields in the high frequency asymptotic limit are often based on flow transport equations. Common techniques are statistical energy analysis, employed mostly in the context of vibro-acoustics, and ray tracing, a popular tool in architectural acoustics. Dynamical energy analysis makes it possible to interpolate between standard statistical energy analysis and full ray tracing, containing both of these methods as limiting cases. In this work a version of dynamical energy analysis based on a Chebyshev basis expansion of the Perron-Frobenius operator governing the ray dynamics is introduced. It is shown that the technique can efficiently deal with multi-component systems overcoming typical geometrical limitations present in statistical energy analysis. Results are compared with state-of-the-art hp-adaptive discontinuous Galerkin finite element simulations.
Gauge and Lorentz transformation placed on the same foundation
Creators: name: Saar, R.
name: Groote, S.
name: Liivat, H.
name: Ots, I.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this note we show that a "dynamical" interaction for arbitrary spin can be constructed in a straightforward way if gauge and Lorentz transformations are placed on the same foundation. As Lorentz transformations act on space-time coordinates, gauge transformations are applied to the gauge field. Placing these two transformations on the same ground means that all quantized field like spin-1/2 and spin-3/2 spinors are functions not only of the coordinates but also of the gauge field components. This change of perspective solves a couple of problems occuring for higher spin fields like the loss of causality, bad high-energy properties and the deviation of the gyromagnetic ratio from its constant value g=2 for any spin, as caused by applying the minimal coupling. Starting with a "dynamical" interaction, a non-minimal coupling can be derived which is consistent with causality, the expectation for the gyromagnetic ratio, and well-behaved for high energies. As a consequence, on this stage the (elektromagnetic) gauge field has to be considered as classical field. Therefore, standard quantum field theory cannot be applied. Despite this inconvenience, such a common ground is consistent with an old dream of physicists almost a century ago. Our approach, therefore, indicates a straightforward way to realize this dream.
description: 12 pages, no figures, published version. arXiv admin note: substantial text overlap with arXiv:0908.3761
FEAST fundamental framework for electronic structure calculations: Reformulation and solution of the muffin-tin problem
Creators: name: Levin, Alan
name: Zhang, Deyin
name: Polizzi, Eric
Publisher: name: arXiv
Year: 2011
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Chemical Physics (physics.chem-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: In a recent article [1], the FEAST algorithm has been presented as a general purpose eigenvalue solver which is ideally suited for addressing the numerical challenges in electronic structure calculations. Here, FEAST is presented beyond the "black-box" solver as a fundamental modeling framework which can naturally address the original numerical complexity of the electronic structure problem as formulated by Slater in 1937 [2]. The non-linear eigenvalue problem arising from the muffin-tin decomposition of the real-space domain is first derived and then reformulated to be solved exactly within the FEAST framework. This new framework is presented as a fundamental and practical solution for performing both accurate and scalable electronic structure calculations, bypassing the various issues of using traditional approaches such as linearization and pseudopotential techniques. A finite element implementation of this FEAST framework along with simulation results for various molecular systems are also presented and discussed.
description: 20 pages, 7 figures
Computational projection display : towards efficient high brightness projection in cinema
Creators: name: Damberg, Gerwin
Publisher: name: University of British Columbia
Year: 2017

description: Cinema projectors need to compete with home theater displays in terms of image quality. High frame rate and high spatial resolution as well as stereoscopic 3D are common features today, but even the most advanced cinema projectors lack in-scene contrast and more importantly high peak luminance, both of which are essential perceptual attributes for images to look realistic. At the same time studies on HDR image statistics suggest that the average image intensity in a controlled ambient viewing environment such as cinema can be as low as 1% for cinematic HDR content and does not often exceed 18%, middle gray in photography. Traditional projection systems form images and colours by blocking the source light from a lamp, therefore attenuating on average between 99% and 82% of light before it reaches the screen. This inefficient use of light poses significant challenges for achieving higher peak brightness levels. We propose a new projector architecture built around commercially available components, in which light can be steered to form images. The gain in system efficiency significantly reduces the total cost of ownership of a projector (fewer components and lower operating cost) and at the same time increases peak luminance and improves black level beyond what is practically achievable with incumbent projector technologies. At the heart of this computational display technology is a new projector hardware design using phase-modulation in combination with new optimization algorithms for real-time phase retrieval. Based on this concept we propose and design a full featured projector prototype. To allow for display of legacy SDR as well as high brightness HDR content on light steering projectors we derive perceptually motivated, calibrated tone mapping and colour appearance models. We develop a calibrated optical forward model of the projector hardware and analyse the impact of content mapping parameters and algorithm choices on (light) power requirements.
Flexible Memory Networks
Creators: name: Curto, Carina
name: Degeratu, Anda
name: Itskov, Vladimir
Publisher: name: arXiv
Year: 2010
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Algebraic Topology (math.AT)
subject: FOS: Biological sciences
subject: FOS: Mathematics

description: Networks of neurons in some brain areas are flexible enough to encode new memories quickly. Using a standard firing rate model of recurrent networks, we develop a theory of flexible memory networks. Our main results characterize networks having the maximal number of flexible memory patterns, given a constraint graph on the network's connectivity matrix. Modulo a mild topological condition, we find a close connection between maximally flexible networks and rank 1 matrices. The topological condition is H_1(X;Z)=0, where X is the clique complex associated to the network's constraint graph; this condition is generically satisfied for large random networks that are not overly sparse. In order to prove our main results, we develop some matrix-theoretic tools and present them in a self-contained section independent of the neuroscience context.
description: Accepted to Bulletin of Mathematical Biology, 11 July 2011
Capacitive Near-field Communication for Ubiquitous Interaction and Perception
Creators: name: Grosse-Puppendahl, Tobias
name: Herber, Sebastian
name: Wimmer, Raphael
name: Englert, Frank
name: Beck, Sebastian
name: von Wilmsdorff, Julian
name: Wichert, Reiner
name: Kuijper, Arjan
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: capacitive communication, capacitive near-field communication, capacitive sensing, intrabody communication
subject: 004 Informatik
subject: 600 Technik
subject: 620 Ingenieurwissenschaften

description: Smart objects within instrumented environments offer an always available and intuitive way of interacting with a system. Connecting these objects to other objects in range or even to smartphones and computers, enables substantially innovative interaction and sensing approaches. In this paper, we investigate the concept of Capacitive Near-Field Communication to enable ubiquitous interaction with everyday objects in a short-range spatial context. Our central contribution is a generic framework describing and evaluating this communication method in Ubiquitous Computing. We prove the relevance of our approach by an open-source implementation of a low-cost object tag and a transceiver offering a high-quality communication link at typical distances up to 15 cm. Moreover, we present three case studies considering tangible interaction for the visually impaired, natural interaction with everyday objects, and sleeping behavior analysis.
Additional file 1 of Imaging the metabolic reprograming of fatty acid synthesis pathway enables new diagnostic and therapeutic opportunity for breast cancer
Creators: name: Wang, Fukai
name: Ma, Shuangshuang
name: Chen, Panpan
name: Han, Yuhao
name: Liu, Zhaoyun
name: Wang, Xinzhao
name: Sun, Chenglong
name: Yu, Zhiyong
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology
subject: Computational Biology

description: Supplementary Material 1