cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Magnetic Flux Tuning of Spin Chirality in Mott Insulators with Ring Exchanges
Creators: name: Wang, Yi-Fei
name: Gong, Chang-De
Publisher: name: arXiv
Year: 2009
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: A manifestation of the many-body Aharonov-Bohm effect in the magnetic-flux-tuned Mott insulators with three-spin and four-spin ring exchanges, presents as an effective tool to manipulate the ground-state spin chirality, such as, tune the magnitude continuously, switch an abrupt jump, or even reverse its sign. Such a mechanism is demonstrated explicitly in both quasi-one-dimensional ladders and two-dimensional lattices with triangles as elementary plaquettes.
description: 4 pages, 5 figures
Scoparone attenuates PD-L1 expression in human breast cancer cells by MKP-3 upregulation
Creators: name: Kim, Seung-Woo
name: Kim, Chan Woo
name: Kim, Hong Seok
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Biophysics
Biological Sciences not elsewhere classified
Cancer

description: Breast cancer is a frequently occurring malignant tumor that is one of the leading causes of cancer-related deaths in women worldwide. Monoclonal antibodies that block programed cell death 1 (PD-1)/programed cell death ligand 1 (PD-L1) – a typical immune checkpoint – are currently the recommended standard therapies for many advanced and metastatic tumors such as triple-negative breast cancer. However, some patients develop drug resistance, leading to unfavorable treatment outcomes. Therefore, other approaches are required for anticancer treatments, such as downregulation of PD-L1 expression and promotion of degradation of PD-L1. Scoparone (SCO) is a bioactive compound isolated from Artemisia capillaris that exhibits antitumor activity. However, the effect of SCO on PD-L1 expression in cancer has not been confirmed yet. This study aimed to evaluate the role of SCO in PD-L1 expression in breast cancer cells in vitro. Our results show that SCO downregulated PD-L1 expression in a dose-dependent manner, via AKT inhibition. Interestingly, SCO treatment did not alter PTEN expression, but increased the expression of mitogen-activated protein kinase phosphatase-3 (MKP-3). In addition, the SCO-induced decrease in PD-L1 expression was reversed by siRNA-mediated MKP-3 knockdown. Collectively, these findings suggest that SCO inhibited the expression of PD-L1 in breast cancer cells by upregulating MKP-3 expression. Therefore, SCO may serve as an innovative combinatorial agent for cancer immunotherapy.
Verifying Real-Time Systems using Explicit-time Description Methods
Creators: name: Wang, Hao
name: MacCaull, Wendy
Publisher: name: arXiv
Year: 2009
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: Timed model checking has been extensively researched in recent years. Many new formalisms with time extensions and tools based on them have been presented. On the other hand, Explicit-Time Description Methods aim to verify real-time systems with general untimed model checkers. Lamport presented an explicit-time description method using a clock-ticking process (Tick) to simulate the passage of time together with a group of global variables for time requirements. This paper proposes a new explicit-time description method with no reliance on global variables. Instead, it uses rendezvous synchronization steps between the Tick process and each system process to simulate time. This new method achieves better modularity and facilitates usage of more complex timing constraints. The two explicit-time description methods are implemented in DIVINE, a well-known distributed-memory model checker. Preliminary experiment results show that our new method, with better modularity, is comparable to Lamport's method with respect to time and memory efficiency.
Strange stars properties calculated in the framework of the Field Correlator Method
Creators: name: Pereira, F. I. M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We calculate the strange star properties in the framework of the Field Correlator Method. We find that for the values of the gluon condensate $G_2=0.006\;{\rm GeV}^4$ and $G_2=0.0068\;{\rm GeV}^4$, which give a critical temperature $T_c\sim170\;{\rm MeV}$ at $μ_c=0$, the sequences of strange stars are compatible with some of the semi-empirical mass-radius relations and data obtained from astrophysical observations.
description: 26 pages, 10 figures
The Local Isometric Embedding in R^3 of Two-Dimensional Riemannian Manifolds With Gaussian Curvature Changing Sign to Finite Order on a Curve
Creators: name: Khuri, Marcus A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Analysis of PDEs (math.AP)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: We consider two natural problems arising in geometry which are equivalent to the local solvability of specific equations of Monge-Ampere type. These two problems are: the local isometric embedding problem for two-dimensional Riemannian manifolds, and the problem of locally prescribed Gaussian curvature for surfaces in R^3. We prove a general local existence result for a large class of Monge-Ampere equations in the plane, and obtain as corollaries the existence of regular solutions to both problems, in the case that the Gaussian curvature vanishes to arbitrary finite order on a single smooth curve.
On the anomalous mass defect of strange stars in the Field Correlator Method
Creators: name: Pereira, F. I. M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We investigate general aspects of the mass defects of strange stars in the context of the Field Correlator Method, without magnetic field. The main parameters of the model that enter the corresponding nonperturbative equation of state of the quark gluon plasma are the gluon condensate $G_2$ and the large distance static $Q{\bar Q}$ potential $V_1$. We calculate mass defects of stellar configurations in the central density range $11<\logρ_c<18$. In general, the mass defects are strongly dependent on the model parameters. For a large range of values of $G_2$ and $V_1$, we obtain anomalous mass defects with magnitudes around $10^{53}\,$erg\,, of the same order of the observed energies of gamma-ray bursts and neutrino emissions in SN1987A, and of the theoretically predicted energies of the quark-novae explosions.
description: 24 pages, 6 figures
title: Mary F. Donovan, MA, MFA Oral History Interview Transcript
Creators: name: Uniformed Services University of the Health Sciences
Publisher: name: University Archives, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
Year: 2018
Subjects: classificationCode: 3
subject: FOS: Medical and health sciences
classificationCode: 6.1
subject: FOS: History and archaeology

description: USU Oral History Interview Transcript
Mary F. Donovan, MA, MFA
First Standardized Patient (SP), Val G. Hemming Simulation Center
08-15-2018
Interviewed by Emelie Rubin
Sonic vibration ameliorates inflammatory diseases via the up-regulation of IL-10
Creators: name: Ahn, Huijeong
name: Jung, Eui-Man
name: Cho, Min-Woo
name: Shin, Meoung-Geun
name: Choi, Jae-Yeong
name: Lee, Geun-Shik
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Mental Health

description: Sonic vibration (SV), or vibroacoustic therapy, is applied to enhance local and systemic blood circulation and alleviate pain using low-frequency sine wave vibrations. However, there is limited scientific data on the mechanisms through which the benefits are achieved. In this study, we investigated the impact of SV on inflammatory responses by assessing cytokine secretion in both in vivo and in vitro models. After inducing inflammatory responses in mice and macrophages, we studied cytokine expression and the symptoms of inflammatory diseases in response to three frequencies (14, 45, or 90 Hz) of SV stimulation at 0.5 m/s2 of amplitude. The results showed that SV at 90 Hz significantly increased interelukin-10 (IL-10) secretion in mice who were administered lipopolysaccharides (LPS) and increased the expression of IL-10 transcripts in peritoneal exudate cells and macrophages. Furthermore, SV at 90 Hz improved LPS-induced lethality and alleviated symptoms in a colitis model. In conclusion, this study scientifically proves the anti-inflammatory effects of vibration therapy through its ability to increase IL-10 expression.
The Dark Universe Riddle
Creators: name: Capistrano, A. J. S.
name: Odon, P. I.
Publisher: name: arXiv
Year: 2008
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: In this work we review some of the theoretical efforts and experimental evidences related to Dark matter and Dark energy problems in the universe. These dilemmas show us how incomplete our knowledge of gravity is, and how our concepts about the universe must at least be revised. Mainly, on the Wilkinson Microwave Anisotropy Probe (WMAP) fifth year, the data indicates that more than 90% of the total energy density of the universe is dark. Here we discuss the impact of these phenomena imprint on gravitational and quantum field theory's standard history. Moreover, we point out some recent and upcoming projects on Cosmology intended to shed light on these problems.
description: 39 pages, corrected typos, additional references, no figures
A Mysterious Cluster Expansion Associated to the Expectation Value of the Permanent of 0-1 Matrices
Creators: name: Federbush, Paul
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mathematical Physics (math-ph)
subject: Combinatorics (math.CO)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We consider two ensembles of nxn matrices. The first is the set of all nxn matrices with entries zeroes and ones such that all column sums and all row sums equal r, uniformly weighted. The second is the set of nxn matrices with zero and one entries where the probability that any given entry is one is r/n, the probabilities of the set of individual entries being i.i.d.'s. Calling the two expectation values E and EB respectively, we develop a formal relation E(perm(A)) = EB(perm (A)) x exp{sum Ti}. We also use a well-known approximating ensemble to E, E1. We prove using E or E1 one obtains the same value of Ti for i < 21. (THE PUBLISHED VERSION OF THIS PAPER ONLY OBTAINS RESULTS FOR i < 8. We go beyond the results of the published version by taking much more advantage of recent work of Pernici and of Wanless on i-matchings on regular bipartite graphs.)These terms Ti, i < 21, have amazing properties. We conjecture that these properties hold also for all i.
description: 8 pages, exegesis of eq(16), great progress in theory and computation compared to published version
Relative Algebro-Geometric stabilities of Toric Manifolds
Creators: name: Yotsutani, Naoto
name: Zhou, Bin
Publisher: name: arXiv
Year: 2016
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C55, 14L24, 14M25

description: In this paper we study the relative Chow and $K$-stability of toric manifolds in the toric sense. First, we give a criterion for relative $K$-stability and instability of toric Fano manifolds in the toric sense. The reduction of relative Chow stability on toric manifolds will be investigated using the Hibert-Mumford criterion in two ways. One is to consider the maximal torus action and its weight polytope. We obtain a reduction by the strategy of Ono [Ono13], which fits into the relative GIT stability detected by Székelyhidi. The other way relies on $\mathbb{C}^*$-actions and Chow weights associated to toric degenerations following Donaldson and Ross-Thomas [D02, RT07]. As applications of our main theorem, we partially determine the relative $K$-stability of toric Fano threefolds and present counter-examples which are relatively $K$-stable in the toric sense but which are asymptotically relatively Chow unstable. In the end, we explain the erroneous parts of the published version of this article (corresponding to Sections 1-5), which provides some inconclusive results for relative $K$-stability in Table 6.
description: We added the appendix which explains a gap in our article "Relative algebro-geometric stabilities of toric manifolds", published in Tohoku Math. J. (2) 71 (4) 495-524, 2019
Multilevel functional principal component analysis
Creators: name: Di, Chong-Zhi
name: Crainiceanu, Ciprian M.
name: Caffo, Brian S.
name: Punjabi, Naresh M.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: The Sleep Heart Health Study (SHHS) is a comprehensive landmark study of sleep and its impacts on health outcomes. A primary metric of the SHHS is the in-home polysomnogram, which includes two electroencephalographic (EEG) channels for each subject, at two visits. The volume and importance of this data presents enormous challenges for analysis. To address these challenges, we introduce multilevel functional principal component analysis (MFPCA), a novel statistical methodology designed to extract core intra- and inter-subject geometric components of multilevel functional data. Though motivated by the SHHS, the proposed methodology is generally applicable, with potential relevance to many modern scientific studies of hierarchical or longitudinal functional outcomes. Notably, using MFPCA, we identify and quantify associations between EEG activity during sleep and adverse cardiovascular outcomes.
description: Published in at http://dx.doi.org/10.1214/08-AOAS206 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)
China’s health diplomacy and soft power play in Chile and Argentina : a cross-country comparison
Creators: name: Tsang, Hoi Kee
Publisher: name: University of British Columbia
Year: 2024

description: China's growing influence in Latin America has drawn increasing attention in academia. It is often compared to the region's historical ties with North American and European countries. Past studies have focused on Sino-Latin America's cooperation in trade and investment. But during the pandemic, China stepped in and became an alternative for the region in medical assistance. This project has taken a comparative case study approach that contrasts a pair of similarly situated countries that have been on the receiving end of the same Chinese pandemic outreach but with different results: while Chile perceives China relatively positively, Argentina has experienced anti-China protests, and its healthcare practitioners and policymakers have expressed doubts about the effectiveness of Chinese anti-COVID vaccines. The study also aims to demonstrate an effective evaluation of soft power. Despite being frequently studied, what soft power stands for has sparked debates since the concept was coined by American political scientist Joseph Nye three decades ago. A consensus has begun to form about the concept’s resources, actors, and relationship to democracy. But it remains notoriously difficult to measure and even harder to identify the causes of its “success”. In academia, surveys are the most widely used tool for operationalizing soft power to examine general perceptions. However, this research is interested in policy outcomes, so semi-structured interviews with decision-makers are a more effective tool. A field trip was conducted in Chile and Argentina for semi-structured interviews with half a dozen healthcare practitioners in each country. Participants include two former Minister of Health and front-line workers. Unlike previous soft power studies which emphasize generators' capability to produce soft power, this study’s main finding is that the domestic politics of soft power receivers play a significant role. It seems that for practitioners and the general public in the recipient country, if they believe the self-interest of their own politicians reached a level that endangers public interest, they will be warier about future cooperation with a foreign great power, regardless of the soft power that the foreign great power has generated. Findings from the study should shed new light on future global health policy.
Two channel paraunitary filter banks based on linear canonical transform
Creators: name: Shinde, Sudarshan
Publisher: name: arXiv
Year: 2009
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: In this paper a two channel paraunitary filter bank is proposed, which is based on linear canonical transform, instead of discrete Fourier transform. Input-output relation for such a filter bank are derived in terms of polyphase matrices and modulation matrices. It is shown that like conventional filter banks, the LCT based paraunitary filter banks need only one filter to be designed and rest of the filters can be obtained from it. It is also shown that LCT based paraunitary filter banks can be designed by using conventional power-symmetric filter design in Fourier domain.
description: 10 pages, IEEE format
It's Written All Over Your Face: Full-Face Appearance-Based Gaze Estimation
Creators: name: Zhang, Xucong
name: Sugano, Yusuke
name: Fritz, Mario
name: Bulling, Andreas
Publisher: name: arXiv
Year: 2016
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Eye gaze is an important non-verbal cue for human affect analysis. Recent gaze estimation work indicated that information from the full face region can benefit performance. Pushing this idea further, we propose an appearance-based method that, in contrast to a long-standing line of work in computer vision, only takes the full face image as input. Our method encodes the face image using a convolutional neural network with spatial weights applied on the feature maps to flexibly suppress or enhance information in different facial regions. Through extensive evaluation, we show that our full-face method significantly outperforms the state of the art for both 2D and 3D gaze estimation, achieving improvements of up to 14.3% on MPIIGaze and 27.7% on EYEDIAP for person-independent 3D gaze estimation. We further show that this improvement is consistent across different illumination conditions and gaze directions and particularly pronounced for the most challenging extreme head poses.
Coherence of Symmetry-Protected Rotational Qubits in Cold Polyatomic Molecules
Creators: name: Löw, Maximilian
name: Ibrügger, Martin
name: Rempe, Gerhard
name: Zeppenfeld, Martin
Publisher: name: arXiv
Year: 2024
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Chemical Physics (physics.chem-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Polar polyatomic molecules provide an ideal but largely unexplored platform to encode qubits in rotational states. Here, we trap cold (100-600 mK) formaldehyde (H$_2$CO) inside an electric box and perform a Ramsey-type experiment to observe long-lived (~100 $μ$s) coherences between symmetry-protected molecular states with opposite rotation but identical orientation, representing a quasi-hidden molecular degree of freedom. As a result, the observed qubit is insensitive to the magnitude of an external electric field, and depends only weakly on magnetic fields. Our findings provide a basis for future quantum and precision experiments with trapped cold molecules.
description: Main paper 6 pages, 3 figures; in total 8 pages, 4 figures. Submitted to PRL
The Spin Glass Phase in the Four-State, Three-Dimensional Potts Model
Creators: name: Cruz, A.
name: Fernandez, L. A.
name: Gordillo-Guerrero, A.
name: Guidetti, M.
name: Maiorano, A.
name: Mantovani, F.
name: Marinari, E.
name: Martin-Mayor, V.
name: Sudupe, A. Munoz
name: Navarro, D.
name: Parisi, G.
name: Perez-Gaviro, S.
name: Ruiz-Lorenzo, J. J.
name: Schifano, S. F.
name: Sciretti, D.
name: Tarancon, A.
name: Tripiccione, R.
name: Velasco, J. L.
name: Yllanes, D.
name: Young, A. P.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We perform numerical simulations, including parallel tempering, on the Potts glass model with binary random quenched couplings using the JANUS application-oriented computer. We find and characterize a glassy transition, estimating the location of the transition and the value of the critical exponents. We show that there is no ferromagnetic transition in a large temperature range around the glassy critical temperature. We also compare our results with those obtained recently on the "random permutation" Potts glass.
description: 7 pages and 3 figures. Corrected minor typos
Linear-Time Algorithms for Maximum-Weight Induced Matchings and Minimum Chain Covers in Convex Bipartite Graphs
Creators: name: Klemz, Boris
name: Rote, Günter
Publisher: name: arXiv
Year: 2017
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: Discrete Mathematics (cs.DM)
subject: FOS: Computer and information sciences

description: A bipartite graph $G=(U,V,E)$ is convex if the vertices in $V$ can be linearly ordered such that for each vertex $u\in U$, the neighbors of $u$ are consecutive in the ordering of $V$. An induced matching $H$ of $G$ is a matching such that no edge of $E$ connects endpoints of two different edges of $H$. We show that in a convex bipartite graph with $n$ vertices and $m$ weighted edges, an induced matching of maximum total weight can be computed in $O(n+m)$ time. An unweighted convex bipartite graph has a representation of size $O(n)$ that records for each vertex $u\in U$ the first and last neighbor in the ordering of $V$. Given such a compact representation, we compute an induced matching of maximum cardinality in $O(n)$ time. In convex bipartite graphs, maximum-cardinality induced matchings are dual to minimum chain covers. A chain cover is a covering of the edge set by chain subgraphs, that is, subgraphs that do not contain induced matchings of more than one edge. Given a compact representation, we compute a representation of a minimum chain cover in $O(n)$ time. If no compact representation is given, the cover can be computed in $O(n+m)$ time. All of our algorithms achieve optimal running time for the respective problem and model. Previous algorithms considered only the unweighted case, and the best algorithm for computing a maximum-cardinality induced matching or a minimum chain cover in a convex bipartite graph had a running time of $O(n^2)$.
On the temporal decay for the 2D non-resistive incompressible MHD equations
Creators: name: Wan, Renhui
Publisher: name: arXiv
Year: 2018
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: Califano-Chiuderi \cite{CC} gave the numerical observation that the energy of the MHD equations is dissipated at a rate independent of the ohmic resistivity, which was first proved by \cite{RWXZ}[Ren et al., J. Funct. Anal., 2014] (the initial data near $(0,\vec{e}_1)$, $\vec{e}_1=(1,0)$). Precisely, they showed some explicit decay rates of solutions in $L^2$ norm. So a nature question is whether the obtained decay rates in \cite{RWXZ} is optimal. In this paper, we aim at giving the explicit decay rates of solutions in both $L^2$ norm and $L^\infty$ norm. In particular, our decay rate in terms of $L^2$ norm improves the previous work \cite{RWXZ}.
description: 53 pages, we do some changes including the title and abstract
Optical conductivity in cluster dynamical mean field theory: formalism and application to high temperature superconductors
Creators: name: Lin, Nan
name: Gull, Emanuel
name: Millis, A. J.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The optical conductivity of the one-band Hubbard model is calculated using the 'Dynamical Cluster Approximation' implementation of dynamical mean field theory for parameters appropriate to high temperature copper-oxide superconductors. The calculation includes vertex corrections and the result demonstrates their importance. At densities of one electron per site, an insulating state is found with gap value and above-gap absorption consistent with measurements. As carriers are added the above gap conductivity rapidly weakens and a three component structure emerges, with a low frequency 'Drude' peak, a mid-infrared absorption, and a remnant of the insulating gap. The mid-infrared feature obtained at intermediate dopings is shown to arise from a pseudogap structure in the density of states. On further doping the conductivity evolves to the Drude peak plus weakly frequency dependent tail structure expected for less strongly correlated metals.
description: 5 pages, 3 figures
To understand sQGP through non-topological FL model
Creators: name: Shu, Song
name: Li, Jia-Rong
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: The non-topological FL model is studied at finite temperature and density. The soliton solutions of the FL model in deconfinement phase transition are solved and thoroughly discussed for different boundary conditions. We indicate that the solitons before and after the deconfinement have different physical meanings: the soliton before deconfinement represents hadron, while the soliton after the deconfinement represents the bound state of quarks which leads to a sQGP phase. The corresponding phase diagram is given.
description: 7 pages, 8 figures
Forest pathology in the genomics era : combining comparative genomics and CRISPR-Cas9 gene editing to gain new insights into the genetics of filamentous plant pathogens
Creators: name: Dort, Erika
Publisher: name: University of British Columbia
Year: 2024

description: Filamentous plant pathogens, comprising fungi and oomycetes, are some of the most economically and ecologically damaging species in agriculture, horticulture, and forestry. These pathogens are well-suited to invade novel ecosystems, and the current era of globalization and climate change has facilitated the global spread of invasive filamentous pathogens. The introduction of invasive pathogens is particularly problematic in forestry as native host trees have no co-evolved defense mechanisms against novel invaders, which can lead some invasive pathogens to spread rapidly through forest ecosystems and cause landscape-level impacts. Significant efforts are therefore being directed towards improving the management and mitigation of forest invasive pathogens. As next generation sequencing technologies and molecular techniques have evolved and improved, management research has shifted to elucidating the genetic and genomic mechanisms that filamentous pathogens employ to infect their plant hosts, cause disease, and spread through ecosystems. The purpose of the research presented in this dissertation was to apply modern genomics methods in a forest pathology context with the goal of creating foundational techniques that can be used to further our understanding of the molecular mechanisms driving phytopathogenic lifestyles and traits in filamentous forest pathogens. In the first part of this work, large-scale comparative genomic analyses were performed on fungal genomes using a novel machine-learning method that was able to uncover distinct genomic patterns associated with phytopathogenic lifestyles and traits. These results provided a proof of concept for the use of predictive genomics in the biosurveillance of forest invasive filamentous pathogens. The second part of this work focused on developing molecular techniques for filamentous forest pathogens in the oomycete genus Phytophthora. First, a polyethylene glycol-mediated plasmid transformation method was tested in five forest Phytophthoras to determine which species was most amenable to further molecular method development. Next, CRISPR-Cas9 gene editing was tested in two forest Phytophthoras, P. cactorum and P. ramorum, using a plasmid-ribonucleoprotein co-transformation approach. The results from the plasmid transformations and CRISPR-Cas9 gene editing demonstrated both the potential and challenges for developing molecular techniques in Phytophthora species and provide a foundation for future genomic research in forest Phytophthoras.
The Ks-band Tully-Fisher Relation - A Determination of the Hubble Parameter from 218 ScI Galaxies and 16 Galaxy Clusters
Creators: name: Russell, David G.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The value of the Hubble Parameter (H0) is determined using the morphologically type dependent Ks-band Tully-Fisher Relation (K-TFR). The slope and zero point are determined using 36 calibrator galaxies with ScI morphology. Calibration distances are adopted from direct Cepheid distances, and group or companion distances derived with the Surface Brightness Fluctuation Method or Type Ia Supernova. Distances are determined to 16 galaxy clusters and 218 ScI galaxies with minimum distances of 40.0 Mpc. From the 16 galaxy clusters a weighted mean Hubble Parameter of H0=84.2 +/-6 km s-1 Mpc-1 is found. From the 218 ScI galaxies a Hubble Parameter of H0=83.4 +/-8 km s-1 Mpc-1 is found. When the zero point of the K-TFR is corrected to account for recent results that find a Large Magellanic Cloud distance modulus of 18.39 +/-0.05 a Hubble Parameter of 88.0 +/-6 km s-1 Mpc-1 is found. A comparison with the results of the Hubble Key Project (Freedman et al 2001) is made and discrepancies between the K-TFR distances and the HKP I-TFR distances are discussed. Implications for Lamda-CDM cosmology are considered with H0=84 km s-1 Mpc-1. (Abridged)
description: 37 pages including 12 tables and 7 figures. Final version accepted for publication in the Journal of Astrophysics & Astronomy
Physical Uplink Control Channel Design for 5G New Radio
Creators: name: Kundu, Lopamudra
name: Xiong, Gang
name: Cho, Joonyoung
Publisher: name: arXiv
Year: 2018
Subjects: subject: Signal Processing (eess.SP)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The next generation wireless communication system, 5G, or New Radio (NR) will provide access to information and sharing of data anywhere, anytime by various users and applications with diverse multi-dimensional requirements. Physical Uplink Control Channel (PUCCH), which is mainly utilized to convey Uplink Control Information (UCI), is a fundamental building component to enable NR system. Compared to Long Term Evolution (LTE), more flexible PUCCH structure is specified in NR, aiming to support diverse applications and use cases. This paper describes the design principles of various NR PUCCH formats and the underlying physical structures. Further, extensive simulation results are presented to explain the considerations behind the NR PUCCH design.
description: 6 pages, 11 figures, accepted in IEEE 5G World Forum 2018
Yang-Mills flow on special-holonomy manifolds
Creators: name: Oliveira, Goncalo
name: Waldron, Alex
Publisher: name: arXiv
Year: 2018
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: This paper develops Yang-Mills flow on Riemannian manifolds with special holonomy. By analogy with the second-named author's thesis, we find that a supremum bound on a certain curvature component is sufficient to rule out finite-time singularities. Assuming such a bound, we prove that the infinite-time bubbling set is calibrated by the defining $(n-4)$-form.
description: Small edits, formulae in section 4.4 corrected, submitted. 40 pages
Helioseismic Signature of Chromospheric Downflows in Acoustic Travel-Time Measurements from Hinode
Creators: name: Nagashima, Kaori
name: Sekii, Takashi
name: Kosovichev, Alexander G.
name: Zhao, Junwei
name: Tarbell, Theodore D.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We report on a signature of chromospheric downflows in two emerging-flux regions detected by time-distance helioseismology analysis. We use both chromospheric intensity oscillation data in the Ca II H line and photospheric Dopplergrams in the Fe I 557.6nm line obtained by Hinode/SOT for our analyses. By cross-correlating the Ca II oscillation signals, we have detected a travel-time anomaly in the plage regions; outward travel times are shorter than inward travel times by 0.5-1 minute. However, such an anomaly is absent in the Fe I data. These results can be interpreted as evidence of downflows in the lower chromosphere. The downflow speed is estimated to be below 10 km/s. This result demonstrates a new possibility of studying chromospheric flows by time-distance analysis.
description: 9 pages, 4 figures, accepted for publication in ApJL
Local duality for connected Z-algebras
Creators: name: Mori, Izuru
name: Nyman, Adam
Publisher: name: arXiv
Year: 2019
Subjects: subject: Rings and Algebras (math.RA)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 16S38, 16W50

description: We develop basic homological machinery for Z-algebras in order to prove a version of local duality for Ext-finite connected Z-algebras. As an application, we compare two notions of regularity for such algebras.
description: The statements of Theorem 6.11 and Theorem 7.8 in the published paper are not correct: each have a missing hypothesis which is needed for their proof. In an attached corrigendum, we restate both theorems (with the required extra hypothesis), and give corrected proofs of each
Machine Learning Analysis of Anomalous Diffusion
Creators: name: Cai, Wenjie
name: Hu, Yi
name: Qu, Xiang
name: Zhao, Hui
name: Wang, Gongyi
name: Li, Jing
name: Huang, Zihan
Publisher: name: arXiv
Year: 2024
Subjects: subject: Machine Learning (cs.LG)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: The rapid advancements in machine learning have made its application to anomalous diffusion analysis both essential and inevitable. This review systematically introduces the integration of machine learning techniques for enhanced analysis of anomalous diffusion, focusing on two pivotal aspects: single trajectory characterization via machine learning and representation learning of anomalous diffusion. We extensively compare various machine learning methods, including both classical machine learning and deep learning, used for the inference of diffusion parameters and trajectory segmentation. Additionally, platforms such as the Anomalous Diffusion Challenge that serve as benchmarks for evaluating these methods are highlighted. On the other hand, we outline three primary strategies for representing anomalous diffusion: the combination of predefined features, the feature vector from the penultimate layer of neural network, and the latent representation from the autoencoder, analyzing their applicability across various scenarios. This investigation paves the way for future research, offering valuable perspectives that can further enrich the study of anomalous diffusion and advance the application of artificial intelligence in statistical physics and biophysics.
description: 44 pages, 10 figures
Additional file 2 of Silica nanoparticles promote wheat growth by mediating hormones and sugar metabolism
Creators: name: Li, Yiting
name: Xi, Keyong
name: Liu, Xi
name: Han, Shuo
name: Han, Xiaowen
name: Li, Gang
name: Yang, Lijun
name: Ma, Dongfang
name: Fang, Zhengwu
name: Gong, Shuangjun
name: Yin, Junliang
name: Zhu, Yongxing
Publisher: name: figshare
Year: 2023
Subjects: subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Rht genotype analysis of wheat cv. Changnuomai 1.
Computing the distance distribution of systematic non-linear codes
Creators: name: Guerrini, Eleonora
name: Orsini, Emmanuela
name: Sala, Massimiliano
Publisher: name: arXiv
Year: 2009
Subjects: subject: Discrete Mathematics (cs.DM)
subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: The most important families of non-linear codes are systematic. A brute-force check is the only known method to compute their weight distribution and distance distribution. On the other hand, it outputs also all closest word pairs in the code. In the black-box complexity model, the check is optimal among closest-pair algorithms. In this paper we provide a Groebner basis technique to compute the weight/distance distribution of any systematic non-linear code. Also our technique outputs all closest pairs. Unlike the check, our method can be extended to work on code families.
Tidally Heated Terrestrial Exoplanets: Viscoelastic Response Models
Creators: name: Henning, Wade G.
name: O'Connell, Richard J.
name: Sasselov, Dimitar D.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Tidal friction in exoplanet systems, driven by orbits that allow for durable nonzero eccentricities at short heliocentric periods, can generate internal heating far in excess of the conditions observed in our own solar system. Secular perturbations or a notional 2:1 resonance between a Hot Earth and Hot Jupiter can be used as a baseline to consider the thermal evolution of convecting bodies subject to strong viscoelastic tidal heating. We compare results first from simple models using a fixed Quality factor and Love number, and then for three different viscoelastic rheologies: the Maxwell body, the Standard Anelastic Solid, and the Burgers body. The SAS and Burgers models are shown to alter the potential for extreme tidal heating by introducing the possibility of new equilibria and multiple response peaks. We find that tidal heating tends to exceed radionuclide heating at periods below 10-30 days, and exceed insolation only below 1-2 days. Extreme cases produce enough tidal heat to initiate global-scale partial melting, and an analysis of tidal limiting mechanisms such as advective cooling for earthlike planets is discussed. To explore long term behaviors, we map equilibria points between convective heat loss and tidal heat input as functions of eccentricity. For the periods and magnitudes discussed, we show that tidal heating, if significant, is generally detrimental to the width of habitable zones.
description: 18 pages, 9 figures
Artinian and non-artinian local cohomology modules
Creators: name: Dibaei, Mohammad T.
name: Vahidi, Alireza
Publisher: name: arXiv
Year: 2008
Subjects: subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics
subject: 13D45; 13E10

description: Let $M$ be a finite module over a commutative noetherian ring $R$. For ideals $\fa$ and $\fb$ of $R$, the relations between cohomological dimensions of $M$ with respect to $\fa, \fb$, $\fa\cap\fb$ and $\fa+ \fb$ are studied. When $R$ is local, it is shown that $M$ is generalized Cohen-Macaulay if there exists an ideal $\fa$ such that all local cohomology modules of $M$ with respect to $\fa$ have finite lengths. Also, when $r$ is an integer such that $0\leq r< \dim_R(M)$, any maximal element $\fq$ of the non-empty set of ideals $\{\fa$ : $\H_\fa^i(M)$ is not artinian for some $i$, $i\geq r$$\}$ is a prime ideal and that all Bass numbers of $\H_\fq^i(M)$ are finite for all $i\geq r$.
description: 10 pages, to appear in Canadian Mathematical Bulletin
PL Morse theory in low dimensions
Creators: name: Grunert, Romain
name: Kühnel, Wolfgang
name: Rote, Günter
Publisher: name: arXiv
Year: 2019
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57R70, 57Q99, 52B70, 68Q17

description: We discuss a PL analogue of Morse theory for PL manifolds. There are several notions of regular and critical points. A point is homologically regular if the homology does not change when passing through its level, it is strongly regular if the function can serve as one coordinate in a chart. Several criteria for strong regularity are presented. In particular we show that in low dimensions $d \leq 4$ a homologically regular point on a PL $d$-manifold is always strongly regular. Examples show that this fails to hold in higher dimensions $d \geq 5$. One of our constructions involves an 8-vertex embedding of the dunce hat into a polytopal 4-sphere with 8 vertices such that a regular neighborhood is Mazur's contractible 4-manifold.
description: 24 pages, 3 figures
Effects of maternal nonylphenol exposure on the proliferation of glial cells in the brain of male offspring mice
Creators: name: Lee, Seung Hyun
name: Shin, Hyun Seung
name: So, Yun Hee
name: Lee, Dong Hun
name: Kim, Jin Yeop
name: Lee, Eun-Hee
name: Jung, Eui-Man
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Mental Health

description: Glial cells play a significant role in maintaining brain homeostasis and normal brain development, and their functions can be impaired by exposure to endocrine disruptors. 4-n-Nonylphenol (NP), a representative endocrine disruptor, is widely used in personal care products and industrial materials. NP accumulates in various organs, including the brain, of living organisms and adversely influences brain health. However, studies on the effects of NP on glial cells are limited. This study aims to investigate the effects of NP on glial cells using primary mixed glial cells and offspring mice exposed to NP during gestation and lactation. In vitro experiments revealed that NP exposure stimulated the astrocytes and microglia proliferation but not oligodendrocytes. NP exposure activated microglia and reduced myelin protein expression in oligodendrocytes. Moreover, maternal NP exposure increased the numbers of microglia and oligodendrocytes in the cerebral cortex of adult offspring. NP exposure caused anxiety– and depressive-like behaviors in adult mice. Collectively, these findings suggest that maternal NP exposure negatively affects the brain development in adult offspring mice.
Understanding semantics and geometry of scenes
Creators: name: Suhail, Mohammed
Publisher: name: University of British Columbia
Year: 2024

description: In this dissertation, we present new approaches for structured scene understanding from images and videos. Structured scene understanding finds numerous applications, including in robotics and autonomous vehicles, as well as in 3D content creation and video editing. The focus of this research is on three specific tasks: scene graph generation, novel view synthesis, and layered scene representation. Scene graph generation involves creating a graph structure that represents the objects and their relationships in a scene. Generating a scene graph from an image demands a comprehensive comprehension of constituent objects and their associations. Our exploration delves into integrating the often overlooked structure of the output space into the reasoning framework. Additionally, we extend beyond bounding box granularity by leveraging pixel-level masks to ground objects when such annotations are absent in scene graph datasets. Novel view synthesis involves generating new views of a scene from input images. Achieving this demands a deep comprehension of the scene's underlying geometry to ensure the rendering of pixels aligns seamlessly with the scene's structure. Within this dissertation, our exploration centers on methods capable of accurately rendering scenes, particularly when dealing with non-Lambertian surfaces. Moreover, we address the challenge of developing view-synthesis techniques capable of generating new scene perspectives without necessitating training for each scene. Layered scene representation involves decomposing a scene into different semantically meaningful layers. In our pursuit of this task, we confront the constraints inherent in existing methods when handling videos with parallax effects resulting from homography-based modeling. To address this, our exploration focuses on a methodology aimed at learning a three-dimensional (3D) layered representation. This approach aims to surpass these limitations and facilitate a more comprehensive scene decomposition. The main contributions of this thesis thus include the exploration and advancement of these tasks.
Tracking down the elusive charginos / neutralinos through $τ$ leptons at the Large Hadron Collider
Creators: name: Bhattacharyya, Nabanita
name: Datta, Amitava
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: An unconstrained minimal supersymmetric standard model with the superpartners of the strongly interacting particles very heavy (close to the kinematic reach of the LHC or even beyond it) and a relatively light electroweak sector is considered. Using the event generator Pythia it is shown that the 1$τ$-jet (tagged) + 2$l$ and 2$τ$-jets (tagged) + 1$l$ signals with a reasonably hard $\etslash$ spectrum either by themselves or in combination with the conventional $3l$ signal, which is known to be of rather modest size with a soft $\etslash$ spectrum, may appreciably extend the reach of chargino-neutralino search at the LHC with 10 fb$^{-1}$ of integrated luminosity. This is especially so if the lighter chargino and the second lightest neutralino decays via two body leptonic modes with large BRs. The theoretical motivation of this scenario, yielding large values of the fine-tuning parameters but consistent with various indirect constraints including the dark matter relic density, is briefly discussed. It is shown that in the minimal supergravity (mSUGRA) model with an universal scalar mass at the GUT scale, the signals involving $τ$-jets are not viable. Theoretically well-motivated variations of these boundary conditions are, however, adequate for reviving these signals.
description: 24 pages, 3 figures, only cosmetic changes have been made and new references have been incorporated
$\mathrm{G}_2$-instantons on the 7-sphere
Creators: name: Waldron, Alex
Publisher: name: arXiv
Year: 2020
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C07 (Primary), 53C29 (Secondary)

description: We study the deformation theory of $\mathrm{G}_2$-instantons on the 7-sphere, specifically those obtained from instantons on the 4-sphere via the quaternionic Hopf fibration. We find that the pullback of the standard ASD instanton lies in a smooth, complete, 15-dimensional family of $\mathrm{G}_2$-instantons. In general, the space of infinitesimal $\mathrm{G}_2$-instanton deformations on $S^7$ is identified with three copies of the space of ASD deformations on $S^4.$
description: Final version, appeared in JLMS