cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Sex work and HIV/AIDS in Vietnam : addressing mental and emotional needs of trafficking victims
Creators: name: Luu, Man Ky
Publisher: name: University of British Columbia
Year: 2017

description: Poor mental health is a critical factor that can significantly impede reintegration success for many trafficked returnees. Sex trafficking is a highly traumatizing experience, and many victims of the sex trade describe feeling physically, psychologically and emotionally unwell at some stage of their post trafficking lives. These issues often develop during the period of exploitation, and intensify as they struggle to recover and reintegrate back into the society, mainly due to the stigma attached to their record as sex workers. In addition, their mental health worsens if they carry a sexually-transmitted disease, especially HIV/AIDS, which further heightens their distress and prevents successful reintegration efforts. Nonetheless, ensuring psychological support and counselling is not the norm in Vietnam due to the lack of trained professionals, and also cultural prejudice towards people with mental illnesses. Thus, in the absence of formal mechanisms of assistance and counselling, alternative instruments to help victims cope with psychological stress, anxiety, depression, and even suicidal ideation should be promoted and supported. This study seeks to explore religion and spirituality as an alternative instrument to address psychological and emotional needs of HIV-positive victims of sex trafficking in Vietnam.
Teratogenicity and perinatal outcomes associated with epilepsy and the use of antiepileptic drugs
Creators: name: McIntosh, Kristi Anna
Publisher: name: University of British Columbia
Year: 2017

description: Background and Objectives: Epilepsy complicates 0.3 – 0.7% of all pregnancies in developed countries. There is a lack of consensus on appropriate antiepileptic drug (AED) regimens, folic acid supplementation, delivery management, and breastfeeding guidance. This thesis examines how women with epilepsy in British Columbia (BC) and throughout Canada are being managed to concurrently control seizures, decrease teratogenicity and optimize obstetric and perinatal outcomes. Design and Methods: Using BC linked administrative data, I examined utilization of AEDs, teratogenicity and small for gestational age (SGA) outcomes in infants exposed to newer generation AED monotherapy in utero. Using the Canadian Community Health Survey Cycle 3.1, I compared rates of preconceptual folic acid supplementation and breastfeeding among women with and without epilepsy. Using data from the BC Perinatal Data Registry, I compared rates and indications for induction of labour and cesarean section among women with and without epilepsy. Results: Our study on the BC population demonstrates no risk for both major malformations and SGA outcomes with newer generation AED monotherapy such as gabapentin, topiramate and lamotrigine. While pregabalin was not found to increase the risk for major malformations, it is possible that it does increase the risk for SGA outcomes. Newer generation AEDs were less frequently prescribed during pregnancy than older generation AEDs. Women with epilepsy in Canada were no more likely to supplement with folic acid and were significantly less likely to breastfeed when compared to women without epilepsy. In BC, when compared to women without epilepsy, women with epilepsy were significantly more likely to deliver via cesarean section, induction of labour, assisted vaginal delivery, epidural or general anesthesia. Significant differences observed between women with and without epilepsy in the indications provided for cesarean section included breech, fetal malposition and “Other;” and “Maternal Condition” for those undergoing induction of labour. Conclusion: In women with epilepsy, pregnancy management is best implemented preconceptually. This includes planning for sufficient time to transition to the appropriate AED therapy, and to initiate folic acid supplementation. During preconceptual counselling, women with epilepsy of childbearing age should be apprised of delivery options and encouraged to attempt breastfeeding.
Transaction fees and optimal rebalancing in the growth-optimal portfolio
Creators: name: Feng, Yu
name: Medo, Matus
name: Zhang, Liang
name: Zhang, Yi-Cheng
Publisher: name: arXiv
Year: 2010
Subjects: subject: Portfolio Management (q-fin.PM)
subject: FOS: Economics and business

description: The growth-optimal portfolio optimization strategy pioneered by Kelly is based on constant portfolio rebalancing which makes it sensitive to transaction fees. We examine the effect of fees on an example of a risky asset with a binary return distribution and show that the fees may give rise to an optimal period of portfolio rebalancing. The optimal period is found analytically in the case of lognormal returns. This result is consequently generalized and numerically verified for broad return distributions and returns generated by a GARCH process. Finally we study the case when investment is rebalanced only partially and show that this strategy can improve the investment long-term growth rate more than optimization of the rebalancing period.
description: 17 pages, 7 figures
Exploring the CP-Violating Inert-Doublet Model
Creators: name: Grzadkowski, B.
name: Ogreid, O. M.
name: Osland, P.
name: Pukhov, A.
name: Purmohammadi, M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We have explored properties of an extension of the Inert Doublet Model by the addition of an extra non-inert scalar doublet. The model offers a possibility of CP violation in the scalar sector and a candidate for the Dark Matter. Allowed regions in the plane spanned by the mass of the Dark-Matter particle and the lightest neutral Higgs particle have been identified, and constraints from direct and indirect-detection experiments have been studied. For favorable parameter regions one may observe long-lived charged particles produced at the LHC.
description: 39 pages, several figures. v2: Extraneous figures removed, name corrected. v3: version to appear in JHEP
Five Kepler target stars that show multiple transiting exoplanet candidates
Creators: name: Steffen, Jason H.
name: Batalha, Natalie M.
name: Borucki, William J.
name: Buchhave, Lars A.
name: Caldwell, Douglas A.
name: Cochran, William D.
name: Endl, Michael
name: Fabrycky, Daniel C.
name: Fressin, François
name: Ford, Eric B.
name: Fortney, Jonathan J.
name: Haas, Michael J.
name: Holman, Matthew J.
name: Howell, Steve B.
name: Isaacson, Howard
name: Jenkins, Jon M.
name: Koch, David
name: Latham, David W.
name: Lissauer, Jack J.
name: Moorhead, Althea V.
name: Morehead, Robert C.
name: Marcy, Geoffrey
name: MacQueen, Phillip J.
name: Quinn, Samuel N.
name: Ragozzine, Darin
name: Rowe, Jason F.
name: Sasselov, Dimitar D.
name: Seager, Sara
name: Torres, Guillermo
name: Welsh, William F.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present and discuss five candidate exoplanetary systems identified with the Kepler spacecraft. These five systems show transits from multiple exoplanet candidates. Should these objects prove to be planetary in nature, then these five systems open new opportunities for the field of exoplanets and provide new insights into the formation and dynamical evolution of planetary systems. We discuss the methods used to identify multiple transiting objects from the Kepler photometry as well as the false-positive rejection methods that have been applied to these data. One system shows transits from three distinct objects while the remaining four systems show transits from two objects. Three systems have planet candidates that are near mean motion commensurabilities---two near 2:1 and one just outside 5:2. We discuss the implications that multitransiting systems have on the distribution of orbital inclinations in planetary systems, and hence their dynamical histories; as well as their likely masses and chemical compositions. A Monte Carlo study indicates that, with additional data, most of these systems should exhibit detectable transit timing variations (TTV) due to gravitational interactions---though none are apparent in these data. We also discuss new challenges that arise in TTV analyses due to the presence of more than two planets in a system.
description: Accepted to ApJ
Absence of Thermalization in Nonintegrable Systems
Creators: name: Gogolin, Christian
name: Mueller, Markus P.
name: Eisert, Jens
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We establish a link between unitary relaxation dynamics after a quench in closed many-body systems and the entanglement in the energy eigenbasis. We find that even if reduced states equilibrate, they can have memory on the initial conditions even in certain models that are far from integrable. We show that in such situations the equilibrium states are still described by a maximum entropy or generalized Gibbs ensemble, regardless of whether a model is integrable or not, thereby contributing to a recent debate. In addition, we discuss individual aspects of the thermalization process, comment on the role of Anderson localization, and collect and compare different notions of integrability.
description: 5 pages, 2 figures, to appear in PRL, improved presentation of the numerical findings, editorial changes
Holographic fermions in charged Gauss-Bonnet black hole
Creators: name: Wu, Jian-Pin
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study the properties of the Green's functions of the fermions in charged Gauss-Bonnet black hole. What we want to do is to investigate how the presence of Gauss-Bonnet coupling constant $α$ affects the dispersion relation, which is a characteristic of Fermi or non-Fermi liquid, as well as what properties such a system has, for instance, the Particle-hole (a)symmetry. One important result of this research is that we find for $q=1$, the behavior of this system is different from that of the Landau Fermi liquid and so the system can be candidates for holographic dual of generalized non-Fermi liquids. More importantly, the behavior of this system increasingly similar to that of the Landau Fermi liquid when $α$ is approaching its lower bound. Also we find that this system possesses the Particle-hole asymmetry when $q\neq 0$, another important characteristic of this system. In addition, we also investigate briefly the cases of the charge dependence.
description: 22 pages, 6 figures; version published in JHEP
Small x nonlinear evolution with impact parameter and the structure function data
Creators: name: Berger, Jeffrey
name: Stasto, Anna M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The nonlinear Balitsky-Kovchegov equation at small x is solved numerically, incorporating impact parameter dependence. Confinement is modeled by including effective gluon mass in the dipole evolution kernel, which regulates the splitting of dipoles with large sizes. It is shown, that the solution is sensitive to different implementations of the mass in the kernel. In addition, running coupling effects are taken into account in this analysis. Finally, a comparison of the calculations using the dipole framework with the inclusive data from HERA on the structure functions F2 and FL is performed.
description: 19 pages, 11 figures. Minor revision. One reference added, two figures updated
Breakdown of universality for unequal-mass Fermi gases with infinite scattering length
Creators: name: Blume, D.
name: Daily, K. M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We treat small trapped unequal-mass two-component Fermi gases at unitarity within a non-perturbative microscopic framework and investigate the system properties as functions of the mass ratio $κ$, and the numbers $N_{1}$ and $N_2$ of heavy and light fermions. While equal-mass Fermi gases with infinitely large interspecies s-wave scattering length $a_s$ are universal, we find that unequal mass Fermi gases are, for sufficiently large $κ$ and in the regime where Efimov physics is absent, not universal. In particular, the $(N_1,N_2)=(2,1)$ and $(3,1)$ systems exhibit three-body (3b) and four-body (4b) resonances at $κ= 12.314(2)$ and $10.4(2)$, respectively, as well as surprisingly large finite-range (FR) effects. These findings have profound implications for ongoing experimental efforts and quantum simulation proposals that utilize unequal-mass atomic Fermi gases.
description: 4 pages, 2 figures
Coherent optical writing and reading of the exciton spin state in single quantum dots
Creators: name: Benny, Y.
name: Khatsevich, S.
name: Kodriano, Y.
name: Poem, E.
name: Presman, R.
name: Galushko, D.
name: Petroff, P. M.
name: Gershoni, D.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences
subject: 00 -General

description: We demonstrate a one to one correspondence between the polarization state of a light pulse tuned to neutral exciton resonances of single semiconductor quantum dots and the spin state of the exciton that it photogenerates. This is accomplished using two variably polarized and independently tuned picosecond laser pulses. The first "writes" the spin state of the resonantly excited exciton. The second is tuned to biexcitonic resonances, and its absorption is used to "read" the exciton spin state. The absorption of the second pulse depends on its polarization relative to the exciton spin direction. Changes in the exciton spin result in corresponding changes in the intensity of the photoluminescence from the biexciton lines which we monitor, obtaining thus a one to one mapping between any point on the Poincare sphere of the light polarization to a point on the Bloch sphere of the exciton spin.
description: 4 pages, 4 figures accepted for publication in PRL
Additional file 1 of Isotopic signatures reveal zinc cycling in the natural habitat of hyperaccumulator Dichapetalum gelonioides subspecies from Malaysian Borneo
Creators: name: van der Ent, Antony
name: Nkrumah, Philip Nti
name: Aarts, Mark G. M.
name: Baker, Alan J. M.
name: Degryse, Fien
name: Wawryk, Chris
name: Kirby, Jason K.
Publisher: name: figshare
Year: 2021
Subjects: subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Table S1. Soil pH, strontium nitrate- and diethylene triamine pentaacetic acid (DTPA)-extractable Zn concentrations (μg g-1), total Zn concentrations and δ66Zn isotope ratios (‰) of soil profile (0–2cm (O), Soil 2–10cm (A)) and bedrock (30 cm (R)) samples collected from the native habitat of Dichapetalum gelonioides subsp. pilosum. SD = standard deviation (instrumental analysis variability). Supplementary Table S2. Procedure for separating and purifying Zn for isotope measurements by multi-collector inductively coupled plasma-mass spectrometry (MC-ICP-MS).
Additional file 1 of Costs of inpatient hospitalisations in the last year of life in older New Zealanders: a cohort study
Creators: name: Scott, Oliver W.
name: Gott, Merryn
name: Edlin, Richard
name: Moyes, Simon A.
name: Muru-Lanning, Marama
name: Kerse, Ngaire
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Supplementary Table 1. Distribution of the cost, number of admissions, and length of stay in the last year of life variables. Supplementary Table 2. Distribution of the cost, number of admissions, and length of stay in the last year of life variables. Supplementary Table 3. Average costs in the last year of life vs costs for those still living. Supplementary Table 4. Average number of admissions in the last year of life vs admissions for those still living. Supplementary Table 5. Average length of stay in the last year of life vs length of stay for those still living. Supplementary Table 6. Generalised linear regression models predicting costs in the last year of life. Supplementary Figure 1. Distribution of the cost in the last year of life variable. Supplementary Figure 2. Distribution of the length of stay in the last year of life variable.
Investigating the transition to BIM-enabled facilities management : a large public owner's perspective
Creators: name: Kim, Soojung
Publisher: name: University of British Columbia
Year: 2017

description: In the architecture, engineering, construction, owner, and operator (AECOO) industry, there is growing interest in the use of building information modeling (BIM) for facilities management (FM). BIM prevents facility information from being lost, eases the access to data, and automates data entry. Despite these advantages, however, the adoption of FM BIM is facing slow growth. To promote the use of FM BIM, we need to understand the challenges of transitioning to BIM for facility owners. The objective of this research is to investigate the process and effort of developing and utilizing FM BIM. The research is based on a case study of a large public owner organization in Canada. The Owner recently completed the construction of an institutional facility that utilized BIM in design and construction. A pilot study was conducted to inform the owner of the effort to develop the handover BIM for FM purposes. The research was conducted in three phases: (1) the pre pilot study revealed the limitations of current FM processes, (2) the pilot study investigated the process to develop a FM BIM, and (3) the post pilot study identified the organizational barriers to utilizing the FM BIM. The pre pilot study revealed the inefficiencies in the daily FM practice and FM information systems, which was due to the poor quality of handover documents, inaccuracy of facility data, and lack of interoperability among the systems. These inefficiencies motivated the owner to consider the opportunities that BIM could provide for efficient data management. The pilot study detailed the process of developing the FM BIM, which included numerous steps: analyzing handover model, obtaining data from handover documents, populating the model, and attaching the O&M files. A significant amount of effort was required due to the poor quality of handover model, unorganized handover documents, and the absence of parameter template. Beyond these challenges, there were barriers to the utilization of the FM BIM, including the absence of BIM experts, lack of training, and lack of proper hardware and software, which emphasized the need for support from high-level management.
Nuclear symmetry energy and proton-rich reactions at intermediate energies
Creators: name: Yong, Gao-Chan
Publisher: name: arXiv
Year: 2010
Subjects: subject: Nuclear Theory (nucl-th)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Based on an isospin dependent transport model IBUU, effects of high density behavior of nuclear symmetry energy in the proton-rich reaction $^{22}$Si+$^{22}$Si at a beam energy of 400 MeV/nucleon are studied. It is found that the symmetry energy affects $π^{+}$ production more than $π^{-}$. More interestingly, comparing with neutron-rich reactions, for $π^{-}/π^{+}$ and dense matter's N/Z ratios, effects of symmetry energy in the proton-rich reaction both show contrary behaviors. The practical experiment by using the proton-rich reaction $^{22}$Si+$^{40}$Ca to study nuclear symmetry energy are also provided.
description: 5 pages, 7 figures; title changed and two figures added. PRC, in production
Finiteness Property of a Bounded Set of Matrices with Uniformly Sub-Peripheral Spectrum
Creators: name: Dai, Xiongping
name: Kozyakin, Victor
Publisher: name: arXiv
Year: 2011
Subjects: subject: Functional Analysis (math.FA)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: Primary 15B52, Secondary 15A60, 93D20, 65F15

description: In the paper, a simple condition guaranteing the finiteness property for a bounded set of matrices is presented. Given a bounded set S of real or complex matrices, it is shown that existence of a sequence of matrix products such that the spectrum of each matrix in this sequence is uniformly sub-peripheral and tends to the joint spectral radius of S, guarantees the spectral finiteness property for S.
description: 8 pages, 29 bibliography references. Minor changes in v3
A self-organizing state-space-model approach for parameter estimation in Hodgkin-Huxley-type models of single neurons
Creators: name: Vavoulis, Dimitrios V.
name: Straub, Volko A.
name: Aston, John A. D.
name: Feng, Jianfeng
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Biological sciences

description: Traditionally, parameter estimation in biophysical neuron and neural network models usually adopts a global search algorithm, often combined with a local search method in order to minimize the value of a cost function, which measures the discrepancy between various features of the available experimental data and model output. In this study, we approach the problem of parameter estimation in conductance-based models of single neurons from a different perspective. By adopting a hidden-dynamical-systems formalism, we expressed parameter estimation as an inference problem in these systems, which can then be tackled using well-established statistical inference methods. The particular method we used was Kitagawa's self-organizing state-space model, which was applied on a number of Hodgkin-Huxley models using simulated or actual electrophysiological data. We showed that the algorithm can be used to estimate a large number of parameters, including maximal conductances, reversal potentials, kinetics of ionic currents and measurement noise, based on low-dimensional experimental data and sufficiently informative priors in the form of pre-defined constraints imposed on model parameters. The algorithm remained operational even when very noisy experimental data were used. Importantly, by combining the self-organizing state-space model with an adaptive sampling algorithm akin to the Covariance Matrix Adaptation Evolution Strategy we achieved a significant reduction in the variance of parameter estimates. The algorithm did not require the explicit formulation of a cost function and it was straightforward to apply on compartmental models and multiple data sets. Overall, the proposed methodology is particularly suitable for resolving high-dimensional inference problems based on noisy electrophysiological data and, therefore, a potentially useful tool in the construction of biophysical neuron models.
Additional file 1 of Novel multivalent design of a monoclonal antibody improves binding strength to soluble aggregates of amyloid beta
Creators: name: Rofo, Fadi
name: Buijs, Jos
name: Falk, Ronny
name: Honek, Ken
name: Lannfelt, Lars
name: Lilja, Anna M.
name: Metzendorf, Nicole G.
name: Gustavsson, Tobias
name: Sehlin, Dag
name: Söderberg, Linda
name: Hultqvist, Greta
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Fig. S1. IgG antibody and 12-mer Aβ oligomer binding. Fig. S2. Sandwich ELISA displaying the binding properties of each antibody to different cross-linked fractions of Aβ 1-42 generated in Fig. 6. Fig. S3. Sandwich ELISA displaying the binding curves of the different antibodies to another batch of cross-linked Aβ 1-42 fractions.
Generalizations of teleparallel gravity and local Lorentz symmetry
Creators: name: Sotiriou, Thomas P.
name: Li, Baojiu
name: Barrow, John D.
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 - Theory (hep-th)
subject: FOS: Physical sciences

description: We analyze the relation between teleparallelism and local Lorentz invariance. We show that generic modifications of the teleparallel equivalent to general relativity will not respect local Lorentz symmetry. We clarify the reasons for this and explain why the situation is different in general relativity. We give a prescription for constructing teleparallel equivalents for known theories. We also explicitly consider a recently proposed class of generalized teleparallel theories, called f(T) theories of gravity, and show why restoring local Lorentz symmetry in such theories cannot lead to sensible dynamics, even if one gives up teleparallelism.
description: 6 pages; v2: minor edits to match published version
Quantization of Integrable Systems and a 2d/4d Duality
Creators: name: Dorey, Nick
name: Hollowood, Timothy J.
name: Lee, Sungjay
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We present a new duality between the F-terms of supersymmetric field theories defined in two- and four-dimensions respectively. The duality relates N=2 supersymmetric gauge theories in four dimensions, deformed by an Omega-background in one plane, to N=(2,2) gauged linear sigma-models in two dimensions. On the four dimensional side, our main example is N=2 SQCD with gauge group SU(L) and 2L fundamental flavours. Using ideas of Nekrasov and Shatashvili, we argue that the Coulomb branch of this theory provides a quantization of the classical Heisenberg SL(2) spin chain. Agreement with the standard quantization via the Algebraic Bethe Ansatz implies the existence of an isomorphism between the chiral ring of the 4d theory and that of a certain two-dimensional theory. The latter can be understood as the worldvolume theory on a surface operator/vortex string probing the Higgs branch of the same 4d theory. We check the proposed duality by explicit calculation at low orders in the instanton expansion. One striking consequence is that the Seiberg-Witten solution of the 4d theory is captured by a one-loop computation in two dimensions. The duality also has interesting connections with the AGT conjecture, matrix models and topological string theory where it corresponds to a refined version of the geometric transition.
description: 51 pages, 7 figures. Additional comments, minor improvements and references added
Galaxy Bias and non-Linear Structure Formation in General Relativity
Creators: name: Baldauf, Tobias
name: Seljak, Uros
name: Senatore, Leonardo
name: Zaldarriaga, Matias
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Length scales probed by large scale structure surveys are becoming closer to the horizon scale. Further, it has been recently understood that non-Gaussianity in the initial conditions could show up in a scale dependence of the bias of galaxies at the largest distances. It is therefore important to include General Relativistic effects. Here we provide a General Relativistic generalization of the bias, valid both for Gaussian and non-Gaussian initial conditions. The collapse of objects happens on very small scales, while long-wavelength modes are always in the quasi linear regime. Around every collapsing region, it is therefore possible to find a reference frame that is valid for all times and where the space time is almost flat: the Fermi frame. Here the Newtonian approximation is applicable and the equations of motion are the ones of the N-body codes. The effects of long-wavelength modes are encoded in the mapping from the cosmological frame to the local frame. For the linear bias, the effect of the long-wavelength modes on the dynamics is encoded in the local curvature of the Universe, which allows us to define a General Relativistic generalization of the bias in the standard Newtonian setting. We show that the bias due to this effect goes to zero as the squared ratio of the physical wavenumber with the Hubble scale for modes longer than the horizon, as modes longer than the horizon have no dynamical effects. However, the bias due to non-Gaussianities does not need to vanish for modes longer than the Hubble scale, and for non-Gaussianities of the local kind it goes to a constant. As a further application, we show that it is not necessary to perform large N-body simulations to extract information on long-wavelength modes: N-body simulations can be done on small scales and long-wavelength modes are encoded simply by adding curvature to the simulation and rescaling the coordinates.
description: 48 pages, 4 figures; v2: added references, JCAP published version
Quantum walks on complex networks with connection instabilities and community structure
Creators: name: Tsomokos, Dimitris I.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Social and Information Networks (cs.SI)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: A continuous-time quantum walk is investigated on complex networks with the characteristic property of community structure, which is shared by most real-world networks. Motivated by the prospect of viable quantum networks, I focus on the effects of network instabilities in the form of broken links, and examine the response of the quantum walk to such failures. It is shown that the reconfiguration of the quantum walk is determined by the community structure of the network. In this context, quantum walks based on the adjacency and Laplacian matrices of the network are compared, and their responses to link failures is analyzed.
description: 5.1 pages, 4 figures; Shift of focus towards quantum networks (published version)
Perfect Fluids and Bad Metals: Transport Analogies Between Ultracold Fermi Gases and High $T_c$ Superconductors
Creators: name: Guo, Hao
name: Wulin, Dan
name: Chien, Chih-Chun
name: Levin, K.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: In this paper, we examine in a unified fashion dissipative transport in strongly correlated systems. We thereby demonstrate the connection between "bad metals" (such as the high temperature superconductors) and "perfect fluids" (such as the ultracold Fermi gases, near unitarity). One motivation of this work is to communicate to the high energy physics community some of the central unsolved problems in high $T_c$ superconductors. Because of interest in the nearly perfect fluidity of the cold gases and because of new tools such as the AdS/CFT correspondence, this better communication may lead to important progress in a variety of different fields. A second motivation is to draw attention to the great power of transport measurements which more directly reflect the excitation spectrum than, say, thermodynamics and thus strongly constrain microscopic theories of correlated fermionic superfluids. Our calculations show that bad metal and perfect fluid behavior is associated with the presence of a normal state excitation gap which suppresses the effective number of carriers leading to anomalously low conductivity and viscosity above the transition temperature $T_c$. Below $T_c$ we demonstrate that the condensate collective modes ("phonons") do not couple to transverse probes such as the shear viscosity. As a result, our calculated shear viscosity at low $T$ becomes arbitrarily small as observed in experiments. In both homogeneous and trap calculations we do not find the upturn in $η$ or $η/s$ (where $s$ is the entropy density) found in most theories. In the process of these studies we demonstrate compatibility with the transverse sum rule and find reasonable agreement with both viscosity and cuprate conductivity experiments.
description: 21 pages, 11 figures
Recombinant expression and band-gap engineering of the bacterial photosynthetic reaction centre
Creators: name: Jun, Daniel Young
Publisher: name: University of British Columbia
Year: 2017

description: The Rhodobacter sphaeroides photosynthetic reaction centre (RC) is a pigment-protein complex that efficiently captures and converts photon energy into a charge-separated state. Given the conversion efficiency and the high electric potential of the electron, the major focus of my project was to deliver/extract electrons to/from various cofactors along the charge-separation pathway in the RC, including the special pair of bacteriochlorophylls (P), the bacteriopheophytin (HA), the primary quinone (QA), and the secondary quinone (QB). An over-expression system was created to produce RCs, using the R. sphaeroides RCx strain, pIND4 plasmid, a modified culture medium, and changes to growth conditions. These changes resulted in a 35-fold increase in protein levels compared to the previous system. To extract electrons from the quinone region of the RC, this region was made more accessible to the solvent by deleting portions of the H subunit cytoplasmic globular domain. The results indicated that the truncated RC mutants assembled stably and thereby reduced the electron transfer distance between the quinone and an external electron acceptor. Photochronoamperometry measurements on mutant RCs designed to test the feasibility of delivering electrons from an electrode to P showed photocurrent generation and direction that were consistent with the binding of the RC P-side to the electrode surface. Similar experiments on the feasibility of extracting electrons from HA, QA and QB, for delivery to highly ordered pyrolytic graphite (HOPG) or gold electrodes, also showed photocurrent generation and direction consistent with the binding of the RC HA-side or Q-side to the electrode surface. Finally, the thermal stability of complexes was studied by in vivo addition of light harvesting complex 1 (LH1) from the thermophile Thermochromatium tepidum to the RC. A hybrid core complex consisting of an R. sphaeroides RC surrounded by T. tepidum TLH1 conferred greater tolerance to thermal energies, compared to the analogous R. sphaeroides RC-LH1 core complex, at temperatures up to 70 °C. The combination of these results show that, in principle, the RC can be modified to extract electrons at different energy levels, or band gaps, with possible applications in heat-stabile biohybrid solar cell technologies.
Information - Disturbance Tradeoff in the Estimation of a Unitary Transformation
Creators: name: Bisio, Alessandro
name: Chiribella, Giulio
name: D'Ariano, Giacomo Mauro
name: Perinotti, Paolo
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We address the problem of the information-disturbance trade-off associated to the estimation of a quantum transformation, and show how the extraction of information about the a black box causes a perturbation of the corresponding input-output evolution. In the case of a black box performing a unitary transformation, randomly distributed according to the invariant measure, we give a complete solution of the problem, deriving the optimal trade-off curve and presenting an explicit construction of the optimal quantum network.
description: 10 pages, 4 figures
Plasma-like Vacuum in Podolsky Regularized Classical Electrodynamics
Creators: name: Santos, Roberto Baginski B.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: We analyze wave propagation in the vacuum of Podolsky regularized electrodynamics. Two kinds of waves were found in the theory: the traditional non-dispersive waves of Maxwell electrodynamics, and a dispersive wave reminiscent of wave propagation in a collisionless plasma. Charged particle concentration was determined, and found to be huge in this vacuum. We interpret the results in terms of vacuum polarization effects induced in an otherwise classical theory.
description: 7 pages, 1 figure, corrected typos, accepted for publication in Modern Physics Letters A
Additional file 1 of Reasons for SARS-CoV-2 infection in children and their role in the transmission of infection according to age: a case-control study
Creators: name: Calvani, Mauro
name: Cantiello, Giulia
name: Cavani, Maria
name: Lacorte, Eleonora
name: Mariani, Bruno
name: Panetta, Valentina
name: Parisi, Pasquale
name: Parisi, Gabriella
name: Roccabella, Federica
name: Silvestri, Paola
name: Vanacore, Nicola
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1. .
Ground-State Phase Diagram of the 1D t-J model
Creators: name: Moreno, Alexander
name: Muramatsu, Alejandro
name: Manmana, Salvatore R.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We examine the ground-state phase diagram of the t-J model in one dimension by means of the Density Matrix Renormalization Group. This model is characterized by a rich phase diagram as a function of the exchange interaction J and the density n, displaying Luttinger-liquid (LL) behavior both of repulsive and attractive (i.e. superconducting) nature, a spin-gap phase, and phase-separation. The phase boundaries separating the repulsive from the attractive LL phase as J is increased, and also the boundaries of the spin-gap region at low densities, and phase-separation at even larger J, are determined on the basis of correlation functions and energy-gaps. In particular, we shed light on a contradiction between variational and renormalization-group (RG) results about the extent of the spin-gap phase, that results larger than the variational but smaller than the RG one. Furthermore, we show that the spin gap can reach a sizable value (~ 0.1 t) at low enough filling, such that preformed pairs should be observable at temperatures below these energy scales. No evidence for a phase with clustering of more than two particles is found on approaching phase separation.
description: 14 pages
On the Minimal Length Uncertainty Relation and the Foundations of String Theory
Creators: name: Chang, Lay Nam
name: Lewis, Zachary
name: Minic, Djordje
name: Takeuchi, Tatsu
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We review our work on the minimal length uncertainty relation as suggested by perturbative string theory. We discuss simple phenomenological implications of the minimal length uncertainty relation and then argue that the combination of the principles of quantum theory and general relativity allow for a dynamical energy-momentum space. We discuss the implication of this for the problem of vacuum energy and the foundations of non-perturbative string theory.
description: 19 pages, revtex4, 6 pdf figures, updated references
Chiral asymmetry and axial anomaly in magnetized relativistic matter
Creators: name: Gorbar, E. V.
name: Miransky, V. A.
name: Shovkovy, I. A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The induced axial current and the chiral anomaly are studied in the normal phase of magnetized relativistic matter. A special attention is paid to the role of the chiral shift parameter Delta, leading to a relative shift of the longitudinal momenta in the dispersion relations of opposite chirality fermions. In the Nambu-Jona-Lasinio model, it is shown directly from the form of the gap equation that Delta necessarily exists in the normal phase in a magnetic field. By making use of the gauge invariant point-splitting regularization, we then show that the presence of Delta essentially modifies the form of the axial current, but does not affect the conventional axial anomaly relation. By recalculating the axial current with the proper-time regularization, we conclude that the result is robust with respect to a specific regularization scheme used.
description: 7 pages, published version: several refferences added and discussions extended
How does the earth system generate and maintain thermodynamic disequilibrium and what does it imply for the future of the planet?
Creators: name: Kleidon, Axel
Publisher: name: arXiv
Year: 2011
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The chemical composition of the earths atmosphere far from equilibrium is unique in the solar system and has been attributed to the presence of widespread life. Here I show that this perspective can be quantified using non-equilibrium thermodynamics. Generating disequilibrium in a thermodynamic variable requires the extraction of power from another thermodynamic gradient, and the second law of thermodynamics imposes fundamental limits on how much power can be extracted. When applied to complex earth system processes, where several irreversible processes compete to deplete the same gradients, it is easily shown that the maximum thermodynamic efficiency is much less than the classic Carnot limit, so that the ability of the earth system to generate power and disequilibrium is limited. This approach is used to quantify how much free energy is generated by various earth system processes to generate chemical disequilibrium. It is shown that surface life generates orders of magnitude more chemical free energy than any abiotic surface process, therefore being the primary driving force for shaping the geochemical environment at the planetary scale. To apply this perspective to the possible future of the planet, we first note that the free energy consumption by human activity is a considerable term in the free energy budget of the planet, and that global changes are closely related to this consumption of free energy. Since human activity and demands for free energy is going to increase in the future, the central question is how human free energy demands can increase sustainably without negatively impacting the ability of the earth system to generate free energy. I illustrate the implications of this thermodynamic perspective by discussing the forms of renewable energy and planetary engineering that would enhance overall free energy generation and thereby "empower" the future of the planet.
description: contribution to Theme Issue "Influence of Nonlinearity and Randomness in Climate Prediction" of Philosophical Transactions of the Royal Society A
Bone strength accrual across adolescent growth and the influences of physical activity and sedentary time
Creators: name: Gabel, Leigh Elizabeth Christine
Publisher: name: University of British Columbia
Year: 2017

description: With recent advances in imaging technologies, we are acquiring a better understanding of the complex hierarchy of bone and how bone adapts its geometry, microarchitecture and ultimately, its strength to withstand the loads imposed upon it during adolescent growth. Thus, in this thesis, I examine the influence of physical activity (PA), sedentary time, maturity and sex on estimated bone strength and its determinants (i.e., microarchitecture, geometry and density) across adolescence. This thesis is based on the UBC Healthy Bones III Study (HBSIII), a mixed longitudinal cohort of healthy girls and boys age 8-12 years at study entry. We assessed bone strength, geometry and density at the tibial shaft using peripheral quantitative computed tomography (pQCT) and bone strength, microarchitecture, geometry and density at the distal tibia and radius using high-resolution pQCT (HR-pQCT). We assessed PA and sedentary time using accelerometry. Four studies comprise this thesis. First, I investigated cross-sectional associations between sedentary time and bone strength and its determinants at the distal tibia by HR-pQCT. I found no associations between sedentary time and bone parameters. Second, I examined maturity- and sex-related adaptations of bone geometry and strength at the tibial shaft using pQCT. I found that larger bone area in boys provided them a greater bone strength advantage compared with girls across adolescence. Third, I examined maturity- and sex-related adaptations of bone strength and its determinants by HR-pQCT at the distal tibia and radius. I found greater bone strength in boys across adolescence was underpinned by greater trabecular bone volume and total bone area. Fourth, I examined prospective associations between PA, sedentary time and bone strength and its determinants at the distal tibia and radius using HR-pQCT. I observed greater bone strength and trabecular bone volume in participants engaging in more PA and lower total bone area in participants engaging in more sedentary time. Collectively, these studies enhance our understanding of how bone is gained during adolescence and add a unique perspective to the benefits of PA for bone strength and its determinants.
Stretching semiflexible filaments with quenched disorder
Creators: name: Benetatos, Panayotis
name: Terentjev, Eugene M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: We study the effect of quenched randomness in the arc-length dependent spontaneous curvature of a wormlike chain under tension. In the weakly bending approximation in two dimensions, we obtain analytic results for the force-elongation curve and the width of transverse fluctuations. We compare quenched and annealed disorder and conclude that the former cannot always be reduced to a simple change in the stiffness of the pure system. We also discuss the effect of a random transverse force on the stretching response of a wormlike chain without spontaneous curvature.
description: 5 pages, minor changes, added references, final version as published in PRE
Additional file 1 of Neuroligin-1 mediates presynaptic maturation through brain-derived neurotrophic factor signaling
Creators: name: Petkova-Tuffy, Andonia
name: Gödecke, Nina
name: Viotti, Julio
name: Korte, Martin
name: Dresbach, Thomas
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Fig. S1. Separation of the three fluorescent channels for the panels in Figure 1 A. Scale bar is 10 μm.