cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A Novel Solution of an Elastic Net Regularization for Dementia Knowledge Discovery using Deep Learning
Creators: name: Shrestha, Kshitiz
name: Alsadoon, Omar Hisham
name: Alsadoon, Abeer
name: Rashid, Tarik A.
name: Ali, Rasha S.
name: Prasad, P. W. C.
name: Jerew, Oday D.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Background and Aim: Accurate classification of Magnetic Resonance Images (MRI) is essential to accurately predict Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD) conversion. Meanwhile, deep learning has been successfully implemented to classify and predict dementia disease. However, the accuracy of MRI image classification is low. This paper aims to increase the accuracy and reduce the processing time of classification through Deep Learning Architecture by using Elastic Net Regularization in Feature Selection. Methodology: The proposed system consists of Convolutional Neural Network (CNN) to enhance the accuracy of classification and prediction by using Elastic Net Regularization. Initially, the MRI images are fed into CNN for features extraction through convolutional layers alternate with pooling layers, and then through a fully connected layer. After that, the features extracted are subjected to Principle Component Analysis (PCA) and Elastic Net Regularization for feature selection. Finally, the selected features are used as an input to Extreme Machine Learning (EML) for the classification of MRI images. Results: The result shows that the accuracy of the proposed solution is better than the current system. In addition to that, the proposed method has improved the classification accuracy by 5% on average and reduced the processing time by 30 ~ 40 seconds on average. Conclusion: The proposed system is focused on improving the accuracy and processing time of MCI converters/non-converters classification. It consists of features extraction, feature selection, and classification using CNN, FreeSurfer, PCA, Elastic Net, Extreme Machine Learning. Finally, this study enhances the accuracy and the processing time by using Elastic Net Regularization, which provides important selected features for classification.
description: 20 pages
Analysis of optimal control problems for the incompressible MHD equations and implementation in a finite element 
multiphysics code
Creators: name: Bornia, Giorgio <1984>
Publisher: name: Alma Mater Studiorum - Università di Bologna
Year: 2012
Subjects: ING-IND/19 Impianti nucleari

description: This thesis deals with the study of optimal control problems for the incompressible Magnetohydrodynamics (MHD) equations. 
Particular attention to these problems arises from several applications in science and engineering, such as fission nuclear reactors with liquid metal coolant and aluminum casting in metallurgy.
In such applications it is of great interest to achieve the control on the fluid state variables through the action of the magnetic Lorentz force.
In this thesis we investigate a class of boundary optimal control problems, in which the flow is controlled through the boundary conditions of the magnetic field. 
Due to their complexity, these problems present various challenges in the definition of an adequate solution approach, both from a theoretical and from a computational point of view.
In this thesis we propose a new boundary control approach, based on lifting functions of the boundary conditions,
which yields both theoretical and numerical advantages.
With the introduction of lifting functions, boundary control problems can be formulated as extended distributed problems.
We consider a systematic mathematical formulation of these problems in terms of the minimization of a cost functional constrained by the MHD equations.
The existence of a solution to the flow equations 
and to the optimal control problem are shown. 
The Lagrange multiplier technique is used to derive an optimality system from which candidate solutions for the control problem can be obtained.
In order to achieve the numerical solution of this system,
a finite element approximation is considered for the discretization together with an appropriate gradient-type algorithm.
A finite element object-oriented library has been developed 
to obtain a parallel and multigrid computational implementation of the optimality system based on a multiphysics approach.
Numerical results of two- and three-dimensional computations show that a possible minimum for the control problem can be computed in a robust and accurate manner.
Bistability in two-locus models with selection, mutation, and recombination
Creators: name: Park, Su-Chan
name: Krug, Joachim
Publisher: name: arXiv
Year: 2010
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: The evolutionary effect of recombination depends crucially on the epistatic interactions between linked loci. A paradigmatic case where recombination is known to be strongly disadvantageous is a two-locus fitness landscape dis- playing reciprocal sign epistasis with two fitness peaks of unequal height. Focusing on the occurrence of bistability in the equilibrium solutions, we consider here the deterministic, haploid two-locus model with reversible mu- tations, selection and recombination. We find analytic formulae for the criti- cal recombination probability rc above which two stable stationary solutions appear which are localized on each of the two fitness peaks. We also derive the stationary genotype frequencies in various parameter regimes. When the recombination rate is close to rc and the fitness difference between the two peaks is small, we obtain a compact description in terms of a cubic polyno- mial which is analogous to the Landau theory of physical phase transitions.
description: Sections 3.7 and 3.8 are added. 22 pages, 6 figures. To appear in J. Math. Biol
Anisotropic Pseudospin Tunneling in Two-Dimensional Black Phosphorus Junctions
Creators: name: Choi, Young Woo
name: Choi, Hyoung Joon
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate the role of pseudospin structure of few-layer black phosphorus (BP) in interband tunneling properties in lateral BP junctions. We find that interband tunneling is critically dependent on junction directions because of the anisotropic pseudospin structure of BP. When the armchair direction of BP is normal to the interface, pseudospins of incident and transmitted carriers are nearly aligned so that interband tunneling is highly effective, analogous to the Klein tunneling in graphene. However, when the zigzag direction is normal to the interface, interband tunneling is suppressed by misaligned pseudospins. We also study junctions of band-gap inverted BP where the electronic structure is characterized by two Dirac cones. In this case, intervalley tunneling is prohibited either by momentum conservation or by pseudospin mismatch while intravalley tunneling is Klein-like irrespective of the junction direction. These results provide a foundation for developing high-performance devices from BP and other pseudospin materials.
description: 6 pages, 4 figures
title: Some physiological effects of high environmental temperatures on the laying hen
Creators: name: Kpodo, Daniel
Publisher: name: The University of Edinburgh
Year: 1982
Subjects: subject: Annexe MSc Digitisation Project 2022 Block 48
subject: High temperature
subject: Metabolic heat production
subject: Laying hen
subject: Egg production
subject: Adaptation

description: The effects of exposure to a constant temperature of 32°C for 3 weeks upon metabolic heat production and some physiological systems implicated in the control of thermogenesis were examined. The deep body temperature of the birds was slightly elevated during the high temperature treatment but some adaptation was achieved by a significant reduction in metabolic heat production particularly the day-time component. The circadian rhythm of metabolic heat production observed in control conditions was markedly reduced by exposure to 32°C. At the beginning of the exposure period there was a transient decrease in locomotor activity but this returned to control levels after 24 hours and probably had little effect upon heat production. Food intake was reduced by approximately 50% during the first 24 hours and remained low throughout the experimental period. This reduced energy intake was accompanied by a decrease in body weight probably due to metabolism of fat reserves as reflected in the decreased respiratory quotient (RQ). Despite this response, plasma free fatty acid concentrations were reduced below control levels during the high temperature exposure. This may be a reflection of the sequestration of plasma free fatty acids for egg lipoprotein production even during the environmental temperature stress. The concentration of plasma glucose was maintained at control levels throughout the experimental period. The exposure at 32 °C did not appear to affect the plasma levels of thyroxine and triiodothyronine. Despite maintaining a near-normal rate of egg production throughout the study the birds were found to produce smaller eggs with thinner shells in response to the high ambient temperature. Most of the observed effects of high temperature were found to be reversible within a short period when birds were returned to 20°C at the end of the experiment. The general indications were that provided husbandry practices could be adapted to cater for the hen's metabolic and production requirements it is possible to encourage profitable poultry production in most hot climates of the world. Conclusions arising out of this experiment call for future climatic studies to be undertaken in conjunction with nutritional formulation programmes so that results from such joint studies could find direct application in the field.
Constraints on the ultra-fast outflows in the narrow-line Seyfert 1 galaxy Mrk 1044 from high-resolution time- and flux-resolved spectroscopy
Creators: name: Xu, Yerong
name: Pinto, Ciro
name: Rogantini, Daniele
name: Bianchi, Stefano
name: Guainazzi, Matteo
name: Kara, Erin
name: Jin, Chichuan
name: CUsumano, Giancarlo
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Ultra-fast outflows (UFOs) have been revealed in a large number of active galactic nuclei (AGN) and are regarded as promising candidates for AGN feedback on the host galaxy. The nature and launching mechanism of UFOs are not yet fully understood. Here we perform a time- and flux-resolved X-ray spectroscopy on four XMM-Newton observations of a highly accreting narrow-line Seyfert 1 (NLS1) galaxy, Mrk 1044, to study the dependence of the outflow properties on the source luminosity. We find that the UFO in Mrk 1044 responds to the source variability quickly and its velocity increases with the X-ray flux, suggesting a high-density ($10^{9}-4.5\times10^{12}\,\mathrm{cm}^{-3}$) and radiatively driven outflow, launched from the region within a distance of $98-6600\, R_\mathrm{g}$ from the black hole. The kinetic energy of the UFO is conservatively estimated ($L_\mathrm{UFO}\sim4.4\%L_\mathrm{Edd}$), reaching the theoretical criterion to affect the evolution of the host galaxy. We also find emission lines, from a large-scale region, have a blueshift of $2700-4500$ km/s in the spectra of Mrk 1044, which is rarely observed in AGN. By comparing with other sources, we propose a correlation between the blueshift of emission lines and the source accretion rate, which can be verified by a future sample study.
description: 14 pages, 13 figures, 3 tables, accepted for publication in MNRAS
Tensor network decompositions in the presence of a global symmetry
Creators: name: Singh, Sukhwinder
name: Pfeifer, Robert N. C.
name: Vidal, Guifre
Publisher: name: arXiv
Year: 2009
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Tensor network decompositions offer an efficient description of certain many-body states of a lattice system and are the basis of a wealth of numerical simulation algorithms. We discuss how to incorporate a global symmetry, given by a compact, completely reducible group G, in tensor network decompositions and algorithms. This is achieved by considering tensors that are invariant under the action of the group G. Each symmetric tensor decomposes into two types of tensors: degeneracy tensors, containing all the degrees of freedom, and structural tensors, which only depend on the symmetry group. In numerical calculations, the use of symmetric tensors ensures the preservation of the symmetry, allows selection of a specific symmetry sector, and significantly reduces computational costs. On the other hand, the resulting tensor network can be interpreted as a superposition of exponentially many spin networks. Spin networks are used extensively in loop quantum gravity, where they represent states of quantum geometry. Our work highlights their importance also in the context of tensor network algorithms, thus setting the stage for cross-fertilization between these two areas of research.
description: 4 pages, 4 figures, RevTeX 4-1
Interaction of bioactive compounds on capillary inner surfaces bearing a dense thermoresponsive polymer brush
Creators: name: Koriyama, Takuya
name: Takayama, Yosuke
name: Hisatsune, Chiho
name: Taka-Aki Asoh
name: Kikuchi, Akihiko
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Inorganic Chemistry
subject: 60506 Virology

description: To confirm the modification of a dense thermoresponsive polymer brush on a silica surface by surface-initiated (SI) atom transfer radical polymerization (ATRP), poly(N-isopropylacrylamide) (PNIPAAm) was polymerized from a free ATRP initiator and an ATRP initiator immobilized silica particle (SiP) via ATRP under various initiator concentrations. The obtained PNIPAAm exhibited a well-controlled molecular weight and modification of the concentrated PNIPAAm brush on the SiP surface was confirmed. Based on the optimal ATRP conditions, the PNIPAAm- and poly(NIPAAm-co-butyl methacrylate [BMA]) (PIB)-grafted capillary lumen were prepared by SI-ATRP and used as capillary columns for micro high-performance liquid chromatography for the modulation of biomolecular interactions. The hydrophobic interactions of steroids on the thermoresponsive polymer brush grafted capillary lumens increased with increasing polymer length above the lower critical solution temperature for each polymer. In addition, an increase in the retention factor of steroids with the PIB-grafted capillary began at lower temperatures than that observed for the PNIPAAm-grafted capillary. Thus, the separation of steroids was achieved using a stepwise temperature gradient and was enhanced by modulating the aqueous eluent flow rate during thermoresponsive capillary chromatography. These results indicated that the chain lengths of the concentrated thermoresponsive polymer brushes on the capillary lumen have a crucial influence on the interaction and separation of bioactive compounds in an aqueous mobile phase.
title: Role of the military veterinarian in the maintenance of veterinary public health in war and in the aftermath with particular reference to the role of the military veterinarian of the British army
title: The role of the military veterinarian in the maintenance of veterinary public health in war and in the aftermath with particular reference to the role of the military veterinarian of the British army
titleType: AlternativeTitle
Creators: name: McLaren, William Peter
Publisher: name: The University of Edinburgh
Year: 1982
Subjects: subject: Annexe MSc Digitisation Project 2022 Block 49
subject: Military veterinarian
subject: Veterinary public health
subject: Conventional war
subject: Biological war
subject: Nuclear war

description: The role of the military veterinarian in the maintenance of veterinary public health in conventional war, counter insurgency war biological war and nuclear war is reviewed and discussed. It is concluded that his role in counter insurgency war and, initially in biological war, is limited. He has, however, a major role to play in conventional and nuclear war.
Intuizione e visualizzazione in matematica con particolare riferimento a Felix Klein
Intuition and visualization in mathematics with particular reference to Felix Klein
Creators: name: Muttini, Daniele <1976>
Publisher: name: Alma Mater Studiorum - Università di Bologna
Year: 2012
Subjects: M-FIL/02 Logica e filosofia della scienza

description: Questo lavoro trae spunto da un rinnovato interesse per l’«intuizione» e il «pensiero visivo» in matematica, e intende offrire un contributo alla discussione contemporanea su tali questioni attraverso lo studio del caso storico di Felix Klein. Dopo una breve ricognizione di alcuni dei saggi più significativi al riguardo, provenienti sia dalla filosofia della matematica, sia dalla pedagogia, dalle neuroscienze e dalle scienze cognitive, l’attenzione si concentra sulla concezione epistemologia di Klein, con particolare riferimento al suo uso del concetto di ‘intuizione’. Dai suoi lavori e dalla sua riflessione critica si ricavano non solo considerazioni illuminanti sulla fecondità di un approccio «visivo», ma argomenti convincenti a sostegno del ruolo cruciale dell’intuizione in matematica.
description: Arising from the renewed interest in ‘intuition’ and ‘visual thinking’ in mathematics, this work intends to take part to the contemporary debate on these topics by investigating the ‘historical case’ of Felix Klein. After a brief survey of studies both from philosophy of mathematics and from neuroscience, pedagogy, and cognitive sciences, that have contributed to such revival, the attention is focused on Klein’s epistemological views, with particular reference to his use of the concept of intuition. The analysis aims at clarifying how his reflections provide not only ingenious observations on the effectiveness of a ‘visual’ approach, but also convincing arguments to support the crucial role of intuition in mathematics.
Entanglement degradation in the solid state: interplay of adiabatic and quantum noise
Creators: name: Bellomo, B.
name: Compagno, G.
name: D'Arrigo, A.
name: Falci, G.
name: Franco, R. Lo
name: Paladino, E.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study entanglement degradation of two non-interacting qubits subject to independent baths with broadband spectra typical of solid state nanodevices. We obtain the analytic form of the concurrence in the presence of adiabatic noise for classes of entangled initial states presently achievable in experiments. We find that adiabatic (low frequency) noise affects entanglement reduction analogously to pure dephasing noise. Due to quantum (high frequency) noise, entanglement is totally lost in a state-dependent finite time. The possibility to implement on-chip both local and entangling operations is briefly discussed.
description: Replaced with published version. Minor changes
Efficient Sparse Spherical k-Means for Document Clustering
Creators: name: Knittel, Johannes
name: Koch, Steffen
name: Ertl, Thomas
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Computer and information sciences

description: Spherical k-Means is frequently used to cluster document collections because it performs reasonably well in many settings and is computationally efficient. However, the time complexity increases linearly with the number of clusters k, which limits the suitability of the algorithm for larger values of k depending on the size of the collection. Optimizations targeted at the Euclidean k-Means algorithm largely do not apply because the cosine distance is not a metric. We therefore propose an efficient indexing structure to improve the scalability of Spherical k-Means with respect to k. Our approach exploits the sparsity of the input vectors and the convergence behavior of k-Means to reduce the number of comparisons on each iteration significantly.
description: ACM DocEng 2021
Friedel Oscillations in Microwave Billiards
Creators: name: Baecker, A.
name: Dietz, B.
name: Friedrich, T.
name: Miski-Oglu, M.
name: Richter, A.
name: Schaefer, F.
name: Tomsovic, S.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: Friedel oscillations of electron densities near step edges have an analog in microwave billiards. A random plane wave model, normally only appropriate for the eigenfunctions of a purely chaotic system, can be applied and is tested for non-purely-chaotic dynamical systems with measurements on pseudo-integrable and mixed dynamics geometries. It is found that the oscillations in the pseudo-integrable microwave cavity matches the random plane-wave modeling. Separating the chaotic from the regular states for the mixed system requires incorporating an appropriate phase space projection into the modeling in multiple ways for good agreement with experiment.
Efficient photon sorter in a high-dimensional Hilbert space
Creators: name: Miller, Warner A.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: An increase in the dimension of state space for quantum key distribution (QKD) can decrease its fidelity requirements while also increasing its bandwidth. A significant obstacle for QKD with qudits (d>2) has been an efficient and practical quantum state sorter for photons whose complex fields are modulated in both amplitude and phase. We propose such a sorter based on a multiplexed thick hologram, constructed e.g. from photo-thermal refractive (PTR) glass. We validate this approach using coupled-mode theory with parameters consistent with PTR glass to simulate a holographic sorter. The model assumes a three-dimensional state space spanned by three tilted planewaves. The utility of such a sorter for broader quantum information processing applications can be substantial.
description: 10 pages (revtex4), 3 figures (eps), 1 table; Substantial revision, new sections, new figures. published
A Krylov subspace algorithm for evaluating the phi-functions appearing in exponential integrators
Creators: name: Niesen, Jitse
name: Wright, Will M.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 65F30 (Primary) 65F50, 65L99 (Secondary)

description: We develop an algorithm for computing the solution of a large system of linear ordinary differential equations (ODEs) with polynomial inhomogeneity. This is equivalent to computing the action of a certain matrix function on the vector representing the initial condition. The matrix function is a linear combination of the matrix exponential and other functions related to the exponential (the so-called phi-functions). Such computations are the major computational burden in the implementation of exponential integrators, which can solve general ODEs. Our approach is to compute the action of the matrix function by constructing a Krylov subspace using Arnoldi or Lanczos iteration and projecting the function on this subspace. This is combined with time-stepping to prevent the Krylov subspace from growing too large. The algorithm is fully adaptive: it varies both the size of the time steps and the dimension of the Krylov subspace to reach the required accuracy. We implement this algorithm in the Matlab function phipm and we give instructions on how to obtain and use this function. Various numerical experiments show that the phipm function is often significantly more efficient than the state-of-the-art.
description: 20 pages, 3 colour figures, code available from http://www.maths.leeds.ac.uk/~jitse/software.html . v2: Various changes to improve presentation as suggested by the referee
Electrochemistry of pyrite and other sulfides in acid oxygen pressure leaching
Creators: name: Bailey, Leonard Keith
Publisher: name: University of British Columbia
Year: 2010

description: The oxygen pressure leaching of pyrite has been studied in sulfuric and perchloric acid using an oxygen-18 tracer technique. The results are consistent with an entirely electrochemical mechanism. The leaching potential of a pyrite pulp has been measured as 0.699V SHET*(110°C, 1M H2S04, 176 psi 02) and potentiostatic experiments at that potential have yielded the same reaction product ratios as observed in oxygen pressure leaching. The ratio of sulfate to elemental sulfur produced during pyrite leaching has been found to be a function of the leaching mixed potential. The yield of sulfate is increased with increasing potential until all the mineral sulfur is converted to the sulfate form at potentials above 1.0V. A mechanistic model of pyrite leaching has been advanced, which includes the electrochemical formation of a protective sulfur film as its basis. The theory has been supported by polarization studies in combination with Eh-pH diagrams. Chalcopyrite leaching has been studied using the same 0¹⁸ technique. Again the results are consistent with an electrochemical mechanism. The ratio of the sulfate to elemental sulfur in the reaction products has been observed to increase with higher oxygen pressures. The mixed potential of leaching is also increased at higher pressure indicating that the same type of mechanism observed in the pyrite work is operational for chalcopyrite. Molybdenite leaching has also been discussed in terms of the electrochemical model derived for pyrite with good results, and the mechanism therefore appears to have applications in many, if not most, sulfide systems.
title: Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Creators: name: Brackmann, Lara Kim
name: Poplawski, Alicia
name: Grandt, Caine Lucas
name: Schwarz, Heike
name: Hankeln, Thomas
name: Rapp, Steffen
name: Zahnreich, Sebastian
name: Galetzka, Danuta
name: Schmitt, Iris
name: Grad, Christian
name: Eckhard, Lukas
name: Mirsch, Johanna
name: Blettner, Maria
name: Scholz-Kreisel, Peter
name: Hess, Moritz
name: Binder, Harald
name: Schmidberger, Heinz
name: Marron, Manuela
Publisher: name: BioMed Central
Year: 2024

description: Background: Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points.

Methods: Fibroblasts from skin biopsies of 15 cell donors were exposed to a high (2Gy) and a low (0.05Gy) dose of X-rays. RNA was extracted and sequenced 2 h and 4 h after exposure. Differentially expressed genes with an adjusted p-value < 0.05 were flagged and used for pathway analyses including prediction of upstream and downstream effects. Principal component analyses were used to examine the effect of two different sequencing runs on quality metrics and variation in expression and alignment and for explorative analysis of the radiation dose and time point of analysis.

Results: More genes were differentially expressed 4 h after exposure to low and high doses of radiation than after 2 h. In experiments with high dose irradiation and RNA sequencing after 4 h, inactivation of the FAT10 cancer signaling pathway and activation of gluconeogenesis I, glycolysis I, and prostanoid biosynthesis was observed taking p-value (< 0.05) and (in) activating z-score (≥2.00 or ≤ − 2.00) into account. Two hours after high dose irradiation, inactivation of small cell lung cancer signaling was observed. For low dose irradiation experiments, we did not detect any significant (p < 0.05 and z-score ≥ 2.00 or ≤ − 2.00) activated or inactivated pathways for both time points.

Conclusions: Compared to 2 h after irradiation, a higher number of differentially expressed genes were found 4 h after exposure to low and high dose ionizing radiation. Differences in gene expression were related to signal transduction pathways of the DNA damage response after 2 h and to metabolic pathways, that might implicate cellular senescence, after 4 h. The time point 4 h will be used to conduct further irradiation experiments in a larger sample.
Massive black holes lurking in Milky Way satellites
Creators: name: Van Wassenhove, S.
name: Volonteri, M.
name: Walker, M. G.
name: Gair, J. R.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: As massive black holes (MBHs) grow from lower-mass seeds, it is natural to expect that a leftover population of progenitor MBHs should also exist in the present universe. Dwarf galaxies undergo a quiet merger history, and as a result, we expect that dwarfs observed in the local Universe retain some `memory' of the original seed mass distribution. Consequently, the properties of MBHs in nearby dwarf galaxies may provide clean indicators of the efficiency of MBH formation. In order to examine the properties of MBHs in dwarf galaxies, we evolve different MBH populations within a Milky Way halo from high-redshift to today. We consider two plausible MBH formation mechanisms: `massive seeds' formed via gas-dynamical instabilities and a Population III remnant seed model. `Massive seeds' have larger masses than PopIII remnants, but form in rarer hosts. We dynamically evolve all halos merging with the central system, taking into consideration how the interaction modifies the satellites, stripping their outer mass layers. We compute different properties of the MBH population hosted in these satellites. We find that for the most part MBHs retain the original mass, thus providing a clear indication of what the properties of the seeds were. We derive the black hole occupation fraction (BHOF) of the satellite population at z=0. MBHs generated as `massive seeds' have large masses that would favour their identification, but their typical BHOF is always below 40 per cent and decreases to less than per cent for observed dwarf galaxy sizes. In contrast, Population III remnants have a higher BHOF, but their masses have not grown much since formation, inhibiting their detection.
description: revised version, MNRAS in press
Alexander invariants of links
Creators: name: Bailey, James Leonard
Publisher: name: University of British Columbia
Year: 2010

description: In the three main sections of this thesis (chapters II, III, and IV; chapter I consists of definitions) we explore three methods of studying Alexander polynomials of links which are alternatives to Fox' free differential calculus. In chapter II we work directly with a presentation of the link group and show how to obtain a presentation for the Alexander invariant. From this we deduce that the order ideal of the Alexander invariant is principal for links of two or three components (the case of one component is well known) but nonprincipal in general for links of four or more components. In any event we show that only one determinant is needed to obtain the Alexander polynomial. In chapter III we use surgery techniques to characterize Alexander invariants of links of two components in terms of their presentation matrices. We then use this to show that the Torres conditions characterize link polynomials when the linking number of the two components is zero or both components are unknotted and the linking number is two. Chapter IV uses Seifert surfaces to prove a generalization of a theorem of Kidwell which relates the individual degrees of the Alexander polynomial to the linking complexity, to present an algorithm for calculating the Alexander polynomial of a two-bridge link from a two-bridge diagram and to prove a conjecture of Kidwell in the special case of two-bridge links. These results are then used to generate link polynomials from allowable pairs (a concept introduced in chapter III) and these results in turn are used to produce methods of generating allowable pairs.
A Class of Graph-Geodetic Distances Generalizing the Shortest-Path and the Resistance Distances
Creators: name: Chebotarev, Pavel
Publisher: name: arXiv
Year: 2008
Subjects: subject: Combinatorics (math.CO)
subject: Discrete Mathematics (cs.DM)
subject: Metric Geometry (math.MG)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 05C12, 05C50, 05C05, 15A48

description: A new class of distances for graph vertices is proposed. This class contains parametric families of distances which reduce to the shortest-path, weighted shortest-path, and the resistance distances at the limiting values of the family parameters. The main property of the class is that all distances it comprises are graph-geodetic: $d(i,j)+d(j,k)=d(i,k)$ if and only if every path from $i$ to $k$ passes through $j$. The construction of the class is based on the matrix forest theorem and the transition inequality.
description: 14 pages. Discrete Applied Mathematics
The relative tensor product and a minimal fiber product in the setting of $C^{*}$-algebras
Creators: name: Timmermann, Thomas
Publisher: name: arXiv
Year: 2009
Subjects: subject: Operator Algebras (math.OA)
subject: FOS: Mathematics
subject: 46L08 (Primary) 46L06, 46L55 (Secondary)

description: We introduce a relative tensor product of $C^{*}$-modules and a spatial fiber product of $C^{*}$-algebras that are analogues of Connes' fusion of correspondences and the fiber product of von Neumann algebras introduced by Sauvageot, respectively, and study their categorical properties. These constructions form the basis for our approach to quantum groupoids in the setting of $C^{*}$-algebras that is published separately.
description: 36 pages; completely rewritten for publication and to be more easily accessible; the main constructions and results remain unaltered; the numbering has changed; beware that existing references in other articles may refer to the (numbering of the) first version
How to understand the cell by breaking it: network analysis of gene perturbation screens
Creators: name: Markowetz, Florian
Publisher: name: arXiv
Year: 2009
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Biological sciences

description: Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental perturbations on a genome-wide scale. This review surveys the current state-of-the-art in analyzing perturbation screens from a network point of view. We describe approaches to make the step from the parts list to the wiring diagram by using phenotypes for network inference and integrating them with complementary data sources. The first part of the review describes methods to analyze one- or low-dimensional phenotypes like viability or reporter activity; the second part concentrates on high-dimensional phenotypes showing global changes in cell morphology, transcriptome or proteome.
description: Review based on ISMB 2009 tutorial; after two rounds of revision
On Markov chains induced by partitioned transition probability matrices
Creators: name: Kaijser, Thomas
Publisher: name: arXiv
Year: 2009
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60J05, 60F05

description: Let S be a denumerable state space and let P be a transition probability matrix on S. If a denumerable set M of nonnegative matrices is such that the sum of the matrices is equal to P, then we call M a partition of P. Let K denote the set of probability vectors on S. To every partition M of P we can associate a transition probability function on K defined in such a way that if p in K and m in M are such that ||pm|| > 0, then, with probability ||pm|| the vector p is transferred to the vector pm/||pm||. Here ||.|| denotes the l_1-norm. In this paper we investigate convergence in distribution for Markov chains generated by transition probability functions induced by partitions of transition probability matrices. An important application of the convergence results obtained is to filtering processes of partially observed Markov chains.
description: Version 2 consists of 37 pages, Version 1 of 73 pages. Section 12 of Version 1 is removed. Most proofs in Version 2 are shorter. Some are even omitted. Version 2 is accepted by Acta Math. Sin. (Engl. Ser.)
Non-Equilibrium Statistical Physics of Currents in Queuing Networks
Creators: name: Chernyak, Vladimir Y.
name: Chertkov, Michael
name: Goldberg, David A.
name: Turitsyn, Konstantin
Publisher: name: arXiv
Year: 2010
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Information Theory (cs.IT)
subject: Probability (math.PR)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We consider a stable open queuing network as a steady non-equilibrium system of interacting particles. The network is completely specified by its underlying graphical structure, type of interaction at each node, and the Markovian transition rates between nodes. For such systems, we ask the question ``What is the most likely way for large currents to accumulate over time in a network ?'', where time is large compared to the system correlation time scale. We identify two interesting regimes. In the first regime, in which the accumulation of currents over time exceeds the expected value by a small to moderate amount (moderate large deviation), we find that the large-deviation distribution of currents is universal (independent of the interaction details), and there is no long-time and averaged over time accumulation of particles (condensation) at any nodes. In the second regime, in which the accumulation of currents over time exceeds the expected value by a large amount (severe large deviation), we find that the large-deviation current distribution is sensitive to interaction details, and there is a long-time accumulation of particles (condensation) at some nodes. The transition between the two regimes can be described as a dynamical second order phase transition. We illustrate these ideas using the simple, yet non-trivial, example of a single node with feedback.
description: 26 pages, 5 figures
Mathematical modeling of antigenicity for HIV dynamics
Creators: name: Dubois, François
name: Meur, Hervé Le
name: Reiss, Claude
Publisher: name: arXiv
Year: 2008
Subjects: subject: Numerical Analysis (math.NA)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted lymphocytes. We model the interaction of the immune system and the viral strains by two processes. On the one hand, the presence of a given viral quasi-species generates antigenically adapted lymphocytes. On the other hand, the lymphocytes kill only viruses for which they have been designed. We consider also the mutation and multiplication of the virus. An original infection term is derived. So as to compare our system of differential equations with well-known models, we study some of them and compare their predictions to ours in the reduced case of only one antigenicity. In this particular case, our model does not yield any major qualitative difference. We prove mathematically that, in this case, our model is biologically consistent (positive fields) and has a unique continuous solution for long time evolution. In conclusion, this model improves the ability to simulate more advanced phases of the disease.
Gravity from self-interaction redux
Creators: name: Deser, S.
Publisher: name: arXiv
Year: 2009
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: I correct some recent misunderstandings about, and amplify some details of, an old explicit non-geometrical derivation of GR.
description: Final, amplified, published version; GRG (2009)
Symmetry Factors of Feynman Diagrams for Scalar Fields
Creators: name: Dong, P. V.
name: Hue, L. T.
name: Hung, H. T.
name: Long, H. N.
name: Thao, N. H.
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The symmetry factor of Feynman diagrams for real and complex scalar fields is presented. Being analysis of Wick expansion for Green functions, the mentioned factor is derived in a general form. The symmetry factor can be separated into two ones corresponding to that of connected and vacuum diagrams. The determination of symmetry factors for the vacuum diagrams is necessary as they play a role in the effective action and phase transitions in cosmology. In the complex scalar theory the diagrams different in topology may give the same contribution, hence inverse of the symmetry factor (1/S) for total contribution is a summation of each similar ones (1/S_i), i.e., 1/S = \sum_i (1/S_i).
description: Journal version, new references added
Efficient implementation of bipartite nonlocal unitary gates using prior entanglement and classical communication
Creators: name: Yu, Li
name: Griffiths, Robert B.
name: Cohen, Scott M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Any bipartite nonlocal unitary operation can be carried out by teleporting a quantum state from one party to the other, performing the unitary gate locally, and teleporting a state back again. This paper investigates unitaries which can be carried out using less prior entanglement and classical communication than are needed for teleportation. Large families of such unitaries are constructed using (projective) representations of finite groups. Among the tools employed are: a diagrammatic approach for representing entangled states, a theorem on the necessary absence of information at certain times and locations, and a representation of bipartite unitaries based on a group Fourier transform.
description: Minor corrections so as to agree with the published version
Pseudo-Hermitian Representation of Quantum Mechanics
Creators: name: Mostafazadeh, Ali
Publisher: name: arXiv
Year: 2008
Subjects: subject: Quantum Physics (quant-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: A diagonalizable non-Hermitian Hamiltonian having a real spectrum may be used to define a unitary quantum system, if one modifies the inner product of the Hilbert space properly. We give a comprehensive and essentially self-contained review of the basic ideas and techniques responsible for the recent developments in this subject. We provide a critical assessment of the role of the geometry of the Hilbert space in conventional quantum mechanics to reveal the basic physical principle motivating our study. We then offer a survey of the necessary mathematical tools and elaborate on a number of relevant issues of fundamental importance. In particular, we discuss the role of the antilinear symmetries such as PT, the true meaning and significance of the charge operators C and the CPT-inner products, the nature of the physical observables, the equivalent description of such models using ordinary Hermitian quantum mechanics, the pertaining duality between local-non-Hermitian versus nonlocal-Hermitian descriptions of their dynamics, the corresponding classical systems, the pseudo-Hermitian canonical quantization scheme, various methods of calculating the (pseudo-) metric operators, subtleties of dealing with time-dependent quasi-Hermitian Hamiltonians and the path-integral formulation of the theory, and the structure of the state space and its ramifications for the quantum Brachistochrone problem. We also explore some concrete physical applications of the abstract concepts and tools that have been developed in the course of this investigation. These include applications in nuclear physics, condensed matter physics, relativistic quantum mechanics and quantum field theory, quantum cosmology, electromagnetic wave propagation, open quantum systems, magnetohydrodynamics, quantum chaos, and biophysics.
description: 76 pages, 2 figures, 243 references, published as Int. J. Geom. Meth. Mod. Phys. 7, 1191-1306 (2010)
DNA-Protein Binding Rates: Bending Fluctuation and Hydrodynamic Coupling Effects
Creators: name: von Hansen, Yann
name: Netz, Roland R.
name: Hinczewski, Michael
Publisher: name: arXiv
Year: 2009
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: Chemical Physics (physics.chem-ph)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory focuses on two competing effects: polymer shape fluctuations, which speed up association, and the hydrodynamic coupling between the diffusing particle and the chain, which slows down association. Polymer bending fluctuations are described using a mean field dynamical theory, while the hydrodynamic coupling between polymer and particle is incorporated through a simple heuristic approximation. Both of these we validate through comparison with Brownian dynamics simulations. Neither of the effects has been fully considered before in the biophysical context, and we show they are necessary to form accurate estimates of reaction processes. The association rate depends on the stiffness of the polymer and the particle size, exhibiting a maximum for intermediate persistence length and a minimum for intermediate particle radius. In the parameter range relevant to DNA-protein binding, the rate increase is up to 100% compared to the Smoluchowski result for simple center-of-mass motion. The quantitative predictions made by the theory can be tested experimentally.
description: 21 pages, 11 figures, 1 table