cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA)
Creators: name: Taruttis, Franziska
name: Spang, Rainer
name: Engelmann, Julia C.
Publisher: name: Universität Regensburg
Year: 2015
Subjects: subject: 004 Informatik

description: Motivation: We address the following question: Does inhibition of the expression of a gene X in a cellular assay affect the expression of another gene Y? Rather than inhibiting gene X experimentally, we aim at answering this question computationally using as the only input observational gene expression data. Recently, a new statistical algorithm called Intervention calculus when the Directed acyclic graph is Absent (IDA), has been proposed for this problem. For several biological systems, IDA has been shown to outcompete regression-based methods with respect to the number of true positives versus the number of false positives for the top 5000 predicted effects. Further improvements in the performance of IDA have been realized by stability selection, a resampling method wrapped around IDA that enhances the discovery of true causal effects. Nevertheless, the rate of false positive and false negative predictions is still unsatisfactorily high. Results: We introduce a new resampling approach for causal discovery called accumulation IDA (aIDA). We show that aIDA improves the performance of causal discoveries compared to existing variants of IDA on both simulated and real yeast data. The higher reliability of top causal effect predictions achieved by aIDA promises to increase the rate of success of wet lab intervention experiments for functional studies.
Properties of a consistent Lorentz-violating Abelian gauge theory
Creators: name: Alexandre, Jean
name: Vergou, Ariadni
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A Lorentz violating modification of massless QED is proposed, with higher order space derivatives for the photon field. The fermion dynamical mass generation is studied with the Schwinger-Dyson approach. Perturbative properties of the model are calculated at one-loop and discussed at higher-order loops, showing the consistency of the model. We explain that there is no contradiction with the definition of the speed of light c, although fermions see an an effective light cone, with a maximum speed smaller than c.
description: 16 pages, comments and references added
Additional file 2 of Perceptions of oncology as a career choice among the early career doctors in Pakistan
Creators: name: Aemaz Ur Rehman, Muhammad
name: Farooq, Hareem
name: Ebaad Ur Rehman, Muhammad
name: Ali, Muhammad Mohsin
name: Zafar, Amjad
name: Khokhar, Muhammad Abbas
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 2. Frequencies and Percentages.
Europe - Totalitarian or Democratic ?
Creators: name: Dr. Alan Wenham-Prosser
Publisher: name: Zenodo
Year: 2019
Subjects: Europe
Totalitarian
Karma
Entrenched thinking
Democracy

description: This paper examines the wide range of topics which centre around the freedom of people to chose the way they are governed and the way their leaders spend tax payers hard earned cash, sometimes without consent of the voters. This discusses those subjects of importance to the electorate, who have handed their power to the few who seek to govern them. But it also points out that politicians forget that they are supposed to represent the people and as a result spend the wealth which does not belong to them on subjects they were not elected to get involved in. We also look to see how the ancient teaching of karma (as you sow so shall you reap) has impacted on entrenched thinking over the centuries. Thinking is the main factor in human decision making and action. Few people look to discover the true source of their thinking.
Crossed-products of Calabi-Yau algebras by finite groups
Creators: name: Meur, Patrick Le
Publisher: name: arXiv
Year: 2010
Subjects: subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 18G20, 16W22, 18E30, 16G20, 16G70

description: Let a finite group G act on a differential graded algebra A. This article presents necessary conditions and sufficient conditions for the skew group algebra A*G to be Calabi-Yau. In particular, when A is the Ginzburg dg algebra of a quiver with an invariant potential, then A*G is Calabi-Yau and Morita equivalent to a Ginzburg dg algebra. Some applications of these results are derived to compare the generalised cluster categories of A and A*G when they are defined and to compare the higher Auslander-Reiten theories of A and A*G when A is a finite dimensional algebra.
description: Subsection 4.2 simplified; bibliography updated; settings in (sub)sections recalled when necessary; equations renumbered; minor corrections and reformulations. To appear in the Journal of Pure and Applied Algebra
Additional file 1 of Analysis of plasma proteins using 2D gels and novel fluorescent probes: in search of blood based biomarkers for Alzheimer’s disease
Creators: name: Laffoon, Scott B.
name: Doecke, James D.
name: Roberts, Anne M.
name: Vance, Jennifer A.
name: Reeves, Benjamin D.
name: Pertile, Kelly K.
name: Rumble, Rebecca L.
name: Fowler, Chris J.
name: Trounson, Brett
name: Ames, David
name: Martins, Ralph
name: Bush, Ashley I.
name: Masters, Colin L.
name: Grieco, Paul A.
name: Dratz, Edward A.
name: Roberts, Blaine R.
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Inorganic Chemistry

description: Additional file 1.
Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data
Creators: name: Lottaz, Claudio
name: Spang, Rainer
Publisher: name: Universität Regensburg
Year: 2005
Subjects: subject: "Databases, Genetic", "Gene Expression Profiling", "Genetic Testing", "Humans", "Natural Language Processing", "Neoplasm Proteins", "Neoplasms", "Oligonucleotide Array Sequence Analysis", "Phenotype", "Reproducibility of Results", "Sensitivity and Specificity", "Structure-Activity Relationship", "Tumor Markers, Biological"
subject: 004 Informatik
subject: 610 Medizin

description: MOTIVATION: Today, the characterization of clinical phenotypes by gene-expression patterns is widely used in clinical research. If the investigated phenotype is complex from the molecular point of view, new challenges arise and these have not been addressed systematically. For instance, the same clinical phenotype can be caused by various molecular disorders, such that one observes different characteristic expression patterns in different patients. RESULTS: In this paper we describe a novel algorithm called Structured Analysis of Microarrays (StAM), which accounts for molecular heterogeneity of complex clinical phenotypes. Our algorithm goes beyond established methodology in several aspects: in addition to the expression data, it exploits functional annotations from the Gene Ontology database to build biologically focussed classifiers. These are used to uncover potential molecular disease subentities and associate them to biological processes without compromising overall prediction accuracy. AVAILABILITY: Bioconductor compliant R package SUPPLEMENTARY INFORMATION: Complete analyses are available at http://compdiag.molgen.mpg.de/supplements/lottaz05.
Europe - Totalitarian or Democratic ?
Creators: name: Dr. Alan Wenham-Prosser
Publisher: name: Zenodo
Year: 2019
Subjects: Europe
Totalitarian
Karma
Entrenched thinking
Democracy

description: This paper examines the wide range of topics which centre around the freedom of people to chose the way they are governed and the way their leaders spend tax payers hard earned cash, sometimes without consent of the voters.  This discusses those subjects of importance to the electorate, who have handed their power to the few who seek to govern them.  But it also points out that politicians forget that they are supposed to represent the people and as a result spend the wealth which does not belong to them on subjects they were not elected to get involved in.

We also look to see how the ancient teaching of karma (as you sow so shall you reap) has impacted on entrenched thinking over the centuries.  Thinking is the main factor in human decision making and action.

Few people look to discover the true source of their thinking.
Additional file 3 of Perceptions of oncology as a career choice among the early career doctors in Pakistan
Creators: name: Aemaz Ur Rehman, Muhammad
name: Farooq, Hareem
name: Ebaad Ur Rehman, Muhammad
name: Ali, Muhammad Mohsin
name: Zafar, Amjad
name: Khokhar, Muhammad Abbas
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 3. Demographics.
Redundant baseline calibration in CHIME : a first implementation & application as beam probe
Creators: name: Good, Deborah C.
Publisher: name: University of British Columbia
Year: 2017

description: The nature of dark energy is one of the most intriguing scientific questions of the twenty-first century. There are many ways to probe dark energy, but one method involves detecting baryon acoustic oscillations (BAO) throughout the universe's history. BAO have a characteristic size scale and therefore act as a ``standard ruler,'' an advantageous property for a method of tracking the universe's expansion history. While baryon acoustic oscillations can be probed in many ways, one of the most intriguing and promising methods is through twenty-one centimeter hydrogen intensity mapping. Several experiments devoted to twenty-one centimeter hydrogen mapping will be coming on line in coming years, and these experiments have stringent calibration requirements due to the need to remove bright foreground signals. These calibration requirements necessitate new and improved methods for calibration. One proposed method is redundant baseline calibration, a self-calibration method which takes advantage of the massively redundant designs of many hydrogen intensity mapping experiments. With the Canadian Hydrogen Intensity Mapping Experiment as a test case, we demonstrate that the redundant baseline method is effective in even its simplest implementation for an idealized version of a real telescope. We then show that redundant baseline calibration fails in real CHIME Pathfinder data in a way that is consistent with deviations from redundancy observed in processed CHIME Pathfinder data. These deviations from redundancy are themselves consistent with the effects of feed-to-feed beam pattern variations, a possibility not considered in the conventional redundant baseline calibration algorithm. We simulate the CHIME Pathfinder including beam width perturbations and verify that similar failures in the redundant baseline calibration can be generated with beam perturbations. We then use the principles of redundant baseline calibration to solve for our simulated beam perturbations. Finally, we compare redundant baseline calibration results to point source holography results and show that the two are equivalent probes of relative feed-to-feed beam variation. We conclude that redundant baseline calibration is a promising path forward in calibrating hydrogen intensity mapping experiments, both as a conventional calibration method and as a probe of beam structure
Length functions of Hitchin representations
Creators: name: Dreyer, Guillaume
Publisher: name: arXiv
Year: 2011
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: es: 57M50 (primary), 57M05 (secondary), 37F30 (secondary), 22E40 (secondary)

description: Given a Hitchin representation $ρ\colon π_1(S) \to \PSL_n(\mathbb{R})$, we construct $n$ continuous functions $\ell_i^ρ\colon \mathcal \CH(S) \to \mathbb{R}$ defined on the space of Hölder geodesic currents $\CH(S)$ such that, for a closed, oriented curve $γ$ in $S$, the $i$--th eigenvalue of the matrix $ρ(γ)\in \PSL_n(\mathbb{R})$ is of the form $\pm \mathrm{exp}\, \ell_i^ρ(γ)$: such functions generalize to higher rank Thurston's length function of Fuchsian re\presentations. Identities, diffe\rentiability properties of these lengths $\ell_i^ρ$, as well as applications to eigenvalue estimates, are also considered.
description: 16 pages, 2 figures, final version to appear in Algebraic and Geometric Topology
A mild Ito formula for SPDEs
Creators: name: Da Prato, Giuseppe
name: Jentzen, Arnulf
name: Roeckner, Michael
Publisher: name: arXiv
Year: 2010
Subjects: subject: Probability (math.PR)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 60H15, 35R60

description: This article introduces a certain class of stochastic processes, which we suggest to call mild Ito processes, and a new - somehow mild - Ito type formula for such processes. Examples of mild Ito processes are mild solutions of SPDEs and their numerical approximation processes.
description: 39 pages, 0 figures
CloudIDEA: A Malware Defense Architecture for Cloud Data Centers
Creators: name: Fischer, Andreas
name: Kittel, Thomas
name: Kolosnjaji, Bojan
name: Lengyel, Tamas
name: Mandarawi, Waseem
name: de Meer, Hermann
name: Müller, Tilo
name: Protsenko, Mykola
name: Reiser, Hans
name: Taubmann, Benjamin
name: Weishäupl, Eva
Publisher: name: Universität Regensburg
Year: 2015
Subjects: subject: 004 Informatik

description: Due to the proliferation of cloud computing, cloud-based systems are becoming an increasingly attractive target for malware. In an Infrastructure-as-a-Service (IaaS) cloud, malware located in a customer’s virtual machine (VM) affects not only this customer, but may also attack the cloud infrastructure and other co-hosted customers directly. This paper presents CloudIDEA, an architecture that provides a security service for malware defens in cloud environments. It combines lightweight intrusion monitoring with on-demand isolation, evidence collection, and in-depth analysis of VMs on dedicated analysis hosts. A dynamic decision engine makes on-demand decisions on how to handle suspicious events considering cost-efficiency and quality-of-service constraints.
description: Title: On the Move to Meaningful Internet Systems: OTM 2015 Conferences
Bone health and osteoporosis in women diagnosed with breast cancer in British Columbia
Creators: name: Tseng, Ling-I Olivia
Publisher: name: University of British Columbia
Year: 2017

description: Background: Women diagnosed with breast cancer are at higher risk of osteoporosis and osteoporotic fractures. Information is lacking on utilization of bone mineral density testing in British Columbia, and fracture risks associated with tamoxifen and aromatase inhibitors to plan care. Methods: Three studies were conducted on women diagnosed with breast cancer. Study 1, a retrospective cross-sectional study evaluated the utilization of bone mineral density testing in 1995-2008 and identified factors associated with different testing rates using secondary data-linkage in older women aged ≥65 and diagnosed with breast cancer for ≥3 years in British Columbia, Canada. Study 2, a pilot randomized controlled trial, assessed the feasibility of a protocol designed to improve bone health management, especially bone mineral density testing rates, with educational material in older women aged ≥65 and diagnosed with breast cancer for ≥3 years. And study 3, a systematic review with meta-analysis, estimated fracture risks associated with tamoxifen and aromatase inhibitors in younger women aged ≤65. Results: In older women aged ≥65, proportions of women with ≥1 bone mineral density test per calendar year increased from 1.0% in 1995 to 10.1% in 2008. Women with lower socio-economic status or rural residence were significantly less likely to have a bone mineral density test. The study protocol is feasible with a promising effect of educational material on bone mineral density testing rates (17%, 95%CI=6 to 33) in the 54 participants during the pilot study six-month follow-up period. In younger women aged ≤65, fracture risk did not differ between the tamoxifen and no-tamoxifen groups. Aromatase inhibitor-associated fracture risk was 17% and 35% higher than the risks in the no-aromatase inhibitor group and tamoxifen group respectively. The higher aromatase inhibitor-associated fracture risk compared with tamoxifen descreased slowly over time. The risk was significantly higher during the treatment period, but not the post-treatment period. Conclusions: Increased risk of fractures is reported in women diagnosed with breast cancer and treated with aromatase inhibitors, while screening for osteoporosis with bone mineral density testing is sub-optimal. There is a need to improve bone health management programs which should include educational materials.
Many-Body Effects in a Model of Electromagnetically Induced Transparency
Creators: name: Reslen, Jose
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the effect of inter-band interactions in the absorption profile of a semi-classical model describing electromagnetically induced transparency. We develop a consistent approach using a non-hermitian Hamiltonian to model particle decay. This allow us to characterize the system response for different number of particles so that the effect of particle-interaction on the transmission profile can be studied over a wide range of characteristic parameters.
description: 5+ pages, 4 figures
On the $p$-supports of a holonomic $\mathcal{D}$-module
Creators: name: Bitoun, Thomas
Publisher: name: arXiv
Year: 2010
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: For a smooth variety $Y$ over a perfect field of positive characteristic, the sheaf $D_Y$ of crystalline differential operators on $Y$ (also called the sheaf of $PD$-differential operators) is known to be an Azumaya algebra over $T^*_{Y'},$ the cotangent space of the Frobenius twist $Y'$ of $Y.$ Thus to a sheaf of modules $M$ over $D_Y$ one can assign a closed subvariety of $T^*_{Y'},$ called the $p$-support, namely the support of $M$ seen as a sheaf on $T^*_{Y'}.$ We study here the family of $p$-supports assigned to the reductions modulo primes $p$ of a holonomic $\mathcal{D}$-module. We prove that the Azumaya algebra of differential operators splits on the regular locus of the $p$-support and that the $p$-support is a Lagrangian subvariety of the cotangent space, for $p$ large enough. The latter was conjectured by Kontsevich. Our approach also provides a new proof of the involutivity of the singular support of a holonomic $\mathcal{D}$-module, by reduction modulo $p.$
description: The article has been rewritten with much improved exposition as well as some additional results, e.g. Corollary 6.3.1. This is the final version, accepted for publication in Inventiones Mathematicae
Additional file 1 of Retrieval practice and spaced learning: preventing loss of knowledge in Dutch medical sciences students in an ecologically valid setting
Creators: name: Donker, Stijn C. M.
name: Vorstenbosch, Marc A. T. M.
name: Gerhardus, Martin J. T.
name: Thijssen, Dick H. J.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Additional file 1.
Methods to identify research misconduct and its impact in medical research: A systematic review protocol
Creators: name: Naidu, Jatin S
name: Leung, On Kwok Jeffrey
name: Gurusamy, Kurinchi
Publisher: name: Zenodo
Year: 2023
Subjects: Research misconduct
Falsification
Fabrication
Plagiarism
Detection

description: A systematic review protocol describing methods to identify research misconduct and its impact in medical research
Modeling sequencing errors by combining Hidden Markov models
Creators: name: Lottaz, Claudio
name: Iseli, Christian
name: Jongeneel, C. Victor
name: Bucher, Philipp
Publisher: name: Universität Regensburg
Year: 2003
Subjects: subject: coding region prediction, sequencing errors, expressed sequence tags, hidden Markov models
subject: 004 Informatik

description: Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.
On jets, extensions and characteristic classes II
Creators: name: Maakestad, Helge Øystein
Publisher: name: arXiv
Year: 2010
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14F10, 14F40

description: In this paper we define and study generalized Atiyah classes for quasi coherent sheaves relative to arbitrary morphisms of schemes. We use derivations and quasi coherent sheaves of left and right O-modules to define a generalized first order jet bundle J(E) and a generalized Atiyah sequence for E. The generalized jet bundle J(E) is a left and right module over a sheaf J of associative rings on X. The sheaf J is an extension of O with a sheaf I of two sided ideals of square zero. The Atiyah sequence gives rise to a generalized Atiyah class c(E) with the property that c(E)=0 if and only if the left structure on J(E) is O-isomorphic to the right structure on J(E). We give examples where c(E)=0 and c(E)\neq 0 hence the class c(E) is a non trivial characteristic class.
description: This paper is a revised and extended version of a section in the paper "On jets, extensions and characteristic classes". A section with explicit examples is added. Some proofs are shortened
Current advances in the synthesis and biological potencies of tri- and tetra-substituted 1H-imidazoles
Creators: name: Mommahed Heravi, Majid
name: Daraie, Mansoureh
name: Zadsirjan, Vahideh
Publisher: name: figshare
Year: 2022
Subjects: subject: 30303 Optical Properties of Materials
subject: FOS: Chemical sciences
subject: 30302 Nanochemistry and Supramolecular Chemistry
subject: 30701 Quantum Chemistry
subject: 39904 Organometallic Chemistry
subject: Organic Chemistry
subject: 30502 Natural Products Chemistry
subject: 30599 Organic Chemistry not elsewhere classified
subject: 30205 Non-metal Chemistry
subject: Computational Chemistry
subject: Nuclear Chemistry
subject: 30504 Organic Green Chemistry

description: In this report, we review the current chemistry progress and in particular the synthesis approaches of tri- and tetra-substituted imidazoles.
Fault-tolerant ancilla preparation and noise threshold lower bounds for the 23-qubit Golay code
Creators: name: Paetznick, Adam
name: Reichardt, Ben W.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In fault-tolerant quantum computing schemes, the overhead is often dominated by the cost of preparing codewords reliably. This cost generally increases quadratically with the block size of the underlying quantum error-correcting code. In consequence, large codes that are otherwise very efficient have found limited fault-tolerance applications. Fault-tolerant preparation circuits therefore are an important target for optimization. We study the Golay code, a 23-qubit quantum error-correcting code that protects the logical qubit to a distance of seven. In simulations, even using a naive ancilla preparation procedure, the Golay code is competitive with other codes both in terms of overhead and the tolerable noise threshold. We provide two simplified circuits for fault-tolerant preparation of Golay code-encoded ancillas. The new circuits minimize error propagation, reducing the overhead by roughly a factor of four compared to standard encoding circuits. By adapting the malignant set counting technique to depolarizing noise, we further prove a threshold above 1.32 x 10^{-3} noise per gate.
description: 47 pages, 19 figures. (v2): added more detailed overhead analysis, fixed clerical error in Fig. 4
Wigner chaos and the fourth moment
Creators: name: Kemp, Todd
name: Nourdin, Ivan
name: Peccati, Giovanni
name: Speicher, Roland
Publisher: name: arXiv
Year: 2010
Subjects: subject: Probability (math.PR)
subject: Operator Algebras (math.OA)
subject: FOS: Mathematics

description: We prove that a normalized sequence of multiple Wigner integrals (in a fixed order of free Wigner chaos) converges in law to the standard semicircular distribution if and only if the corresponding sequence of fourth moments converges to 2, the fourth moment of the semicircular law. This extends to the free probabilistic, setting some recent results by Nualart and Peccati on characterizations of central limit theorems in a fixed order of Gaussian Wiener chaos. Our proof is combinatorial, analyzing the relevant noncrossing partitions that control the moments of the integrals. We can also use these techniques to distinguish the first order of chaos from all others in terms of distributions; we then use tools from the free Malliavin calculus to give quantitative bounds on a distance between different orders of chaos. When applied to highly symmetric kernels, our results yield a new transfer principle, connecting central limit theorems in free Wigner chaos to those in Gaussian Wiener chaos. We use this to prove a new free version of an important classical theorem, the Breuer-Major theorem.
description: Published in at http://dx.doi.org/10.1214/11-AOP657 the Annals of Probability (http://www.imstat.org/aop/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Critical Brownian sheet does not have double points
Creators: name: Dalang, Robert C.
name: Khoshnevisan, Davar
name: Nualart, Eulalia
name: Wu, Dongsheng
name: Xiao, Yimin
Publisher: name: arXiv
Year: 2010
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: We derive a decoupling formula for the Brownian sheet which has the following ready consequence: An $N$-parameter Brownian sheet in $\mathbf{R}^d$ has double points if and only if $d<4N$. In particular, in the critical case where $d=4N$, the Brownian sheet does not have double points. This answers an old problem in the folklore of the subject. We also discuss some of the geometric consequences of the mentioned decoupling, and establish a partial result concerning $k$-multiple points in the critical case $k(d-2N)=d$.
description: Published in at http://dx.doi.org/10.1214/11-AOP665 the Annals of Probability (http://www.imstat.org/aop/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Vanishing of algebraic Brauer-Manin obstructions
Creators: name: Borovoi, Mikhail
Publisher: name: arXiv
Year: 2010
Subjects: subject: Number Theory (math.NT)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14F22 (Primary), 20G30, 14M17, 11G35, 14G25, 14C22 (Secondary)

description: Let X be a homogeneous space of a quasi-trivial k-group G, with geometric stabilizer H, over a number field k. We prove that under certain conditions on the character group of H, certain algebraic Brauer-Manin obstructions to the Hasse principle and weak approximation vanish, because the abelian groups where they take values vanish. When H is connected or abelian, these algebraic Brauer-Manin obstructions to the Hasse principle and weak approximation are the only ones, so we prove the Hasse principle and weak approximation for X under certain conditions. As an application, we obtain new sufficient conditions for the Hasse principle and weak approximation for linear algebraic groups.
description: V.5, 13 pages. Following a suggestion of the referee, the proofs of Lemmas 3.2 and 3.4 were omitted in the published version (see V.4). In this version 5, we give detailed proofs of those lemmas
Giant Rabi splitting in metallic cluster-cavity system
Creators: name: Savenko, I. G.
name: Polozkov, R. G.
name: Shelykh, I. A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate theoretically the photo absorbtion of the cluster of alkali atoms embedded into a single mode quantum microcavity. We show that when the energy of the giant plasmonic resonance lies close to the energy of the cavity mode, the strong coupling between plasmon and cavity photon can occur, which is characterized by mode anticrossing and observation of the doublet structure in ptotoabsorbtion. The characteristic values of the Rabi splitting are expected to be several orders of magnitude larger then those observed in single quantum dot-cavity systems.
description: 6 pages + 7 figures
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations
Creators: name: Roy, Rajarshi
name: Poddar, Sayan
name: Sk, Md Fulbabu
name: Kar, Parimal
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer

description: In the current study, we have investigated the conformational dynamics of a triantennary (N-glycan1) and tetraantennary (N-glycan2) hybrid N-glycans found on the surface of the HIV glycoprotein using 20 μs long all-atom molecular dynamics (MD) simulations. The main objective of the present study is to elucidate the influence of adding a complex branch on the overall glycan structural dynamics. Our investigation suggests that the average RMSD value increases when a complex branch is added to N-glycan1. However, the RMSD distribution is relatively wider in the case of N-glycan1 compared to N-glycan2, which indicates that multiple complex branches restrict the conformational variability of glycans. A similar observation is obtained from the principal component analysis of both glycans. All the puckering states (4C1 to 1C4) of each monosaccharide except mannose are sampled in our simulations, although the 4C1 chair form is energetically more favorable than 1C4. In N-glycan1, the 1–6 linkage in the mannose branch [Man(9)-α(1-6)-Man(5)] stays in the gauche-gauche cluster, whereas it moves towards trans-gauche in N-glycan2. For both glycans, mannose branches are more flexible than the complex branches, and adding a complex branch does not influence the dynamics of the mannose branches. We have noticed that the end-to-end distance of the complex branch shortens by ∼ 10 Å in the presence of another complex branch. This suggests that in the presence of an additional complex branch, the other complex branch adopts a close folded structure. All these conformational changes involve the selective formation of inter-residue and water-mediated hydrogen-bond networks. Communicated by Ramaswamy H. Sarma
The Cytoprotective Effects of E-α-(4-Methoxyphenyl)-2’,3,4,4'-Tetramethoxychalcone (E-α-p-OMe-C6H4-TMC)-A Novel and Non-Cytotoxic HO-1 Inducer
Creators: name: Kaufmann, Kai B.
name: Al-Rifai, Nafisah
name: Ulbrich, Felix
name: Schallner, Nils
name: Rücker, Hannelore
name: Enzinger, Monika
name: Petkes, Hermina
name: Pitzl, Sebastian
name: Goebel, Ulrich
name: Amslinger, Sabine
Publisher: name: Universität Regensburg
Year: 2015
Subjects: subject: 540 Chemie

description: Cell protection against different noxious stimuli like oxidative stress or chemical toxins plays a central role in the treatment of many diseases. The inducible heme oxygenase isoform, heme oxygenase-1 (HO-1), is known to protect cells against a variety of harmful conditions including apoptosis. Because a number of medium strong electrophiles from a series of α-X-substituted 2’,3,4,4’-tetramethoxychalcones (α-X-TMCs, X = H, F, Cl, Br, I, CN, Me, p-NO2-C6H4, Ph, p-OMe-C6H4, NO2, CF3, COOEt, COOH) had proven to activate Nrf2 resulting in HO-1 induction and inhibit NF-κB downstream target genes, their protective effect against staurosporine induced apoptosis and reactive oxygen species (ROS) production was investigated. RAW264.7 macrophages treated with 19 different chalcones (15 α-X-TMCs, chalcone, 2’-hydroxychalcone, calythropsin and 2’-hydroxy-3,4,4’-trimethoxychalcone) prior to staurosporine treatment were analyzed for apoptosis and ROS production, as well as HO-1 protein expression and enzyme activity. Additionally, Nrf2 and NF-κB activity was assessed. We found that amongst all tested chalcones only E-α-(4-methoxyphenyl)-2’,3,4,4'-tetramethoxychalcone (E-α-p-OMe-C6H4-TMC) demonstrated a distinct, statistically significant antiapoptotic effect in a dose dependent manner, showing no toxic effects, while its double bond isomer Z-α-p-OMe-C6H4-TMC displayed no significant activity. Also, E-α-p-OMe-C6H4-TMC induced HO-1 protein expression and increased HO-1 activity, whilst inhibition of HO-1 by SnPP-IX abolished its antiapoptotic effect. The only weakly electrophilic chalcone E-α-p-OMe-C6H4-TMC reduced the staurosporine triggered formation of ROS, while inducing the translocation of Nrf2 into the nucleus. Furthermore, staurosporine induced NF-κB activity was attenuated following E-α-p-OMe-C6H4-TMC treatment. Overall, E-α-p-OMe-C6H4-TMC demonstrated its effective cytoprotective potential via a non-toxic induction of HO-1 in RAW264.7 macrophages. The observed cytoprotective effect may partly be related to both, the activation of the Nrf2- and inhibition of the NF-κB pathway.
Unbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein
Creators: name: Mishra, Lokpati
name: Bandyopadhyay, Tusar
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: The first direful biomolecular event leading to COVID-19 disease is the SARS-CoV-2 virus surface spike (S) protein-mediated interaction with the human transmembrane protein, angiotensin-converting enzyme 2 (hACE2). Prevention of this interaction presents an attractive alternative to thwart SARS-CoV-2 replications. The development of monoclonal antibodies (mAbs) in the convalescent plasma treatment, nanobody, and designer peptides, which recognizes epitopes that overlap with hACE2 binding sites in the receptor-binding domain (RBD) of S protein (S/RBD) and thereby blocking the infection has been the center stage of therapeutic research. Here we report atomistic and reliable in silico structure-energetic features of the S/RBD interactions with hACE2 and its two inhibitors (convalescent mAb, B38, and an alpaca nanobody, Ty1). The discovered potential of mean forces exhibits free energy basin and barriers along the interaction pathways, providing sufficient molecular insights to design a B38 mutant and a Ty1-based peptide with higher binding capacity. While the mutated B38 forms a 60-fold deeper free energy minimum, the designer peptide (Ty1-based) constitutes 38 amino acids and is found to form a 100-fold deeper free energy minimum in the first binding basin than their wild-type variants in complex with S/RBD. Our strategy may help to design more efficacious biologics towards therapeutic intervention against the current raging pandemic. Communicated by Ramaswamy H. Sarma
stam – a Bioconductor compliant R package for structured analysis of microarray data
Creators: name: Lottaz, Claudio
name: Spang, Rainer
Publisher: name: Universität Regensburg
Year: 2005
Subjects: subject: "Calibration", "Cluster Analysis", "Computers, Molecular", "Gene Expression Profiling", "Humans", "Internet", "Phenotype", "Protein Array Analysis", "Software", "User-Computer Interface"
subject: 004 Informatik

description: BACKGROUND: Genome wide microarray studies have the potential to unveil novel disease entities. Clinically homogeneous groups of patients can have diverse gene expression profiles. The definition of novel subclasses based on gene expression is a difficult problem not addressed systematically by currently available software tools. RESULTS: We present a computational tool for semi-supervised molecular disease entity detection. It automatically discovers molecular heterogeneities in phenotypically defined disease entities and suggests alternative molecular sub-entities of clinical phenotypes. This is done using both gene expression data and functional gene annotations. We provide stam, a Bioconductor compliant software package for the statistical programming environment R. We demonstrate that our tool detects gene expression patterns, which are characteristic for only a subset of patients from an established disease entity. We call such expression patterns molecular symptoms. Furthermore, stam finds novel sub-group stratifications of patients according to the absence or presence of molecular symptoms. CONCLUSION: Our software is easy to install and can be applied to a wide range of datasets. It provides the potential to reveal so far indistinguishable patient sub-groups of clinical relevance.
Perfect State Transfer in PT-symmetric Non-Hermitian Networks
Creators: name: Zhang, X. Z.
name: Jin, L.
name: Song, Z.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We systematically study the parity- and time-reversal (PT) symmetric non-Hermitian version of a quantum network proposed in the paper of Christandl et al. [Phys. Rev. Lett. 92, 187902 (2004)]. The nature of this model shows that it is a paradigm to demonstrate the complex relationship between the pseudo-Hermitian Hamiltonian and its Hermitian counterpart as well as a candidate in the experimental realization to simulate PT-symmetry breaking. We also show that this model allows a conditional perfect state transfer within the unbroken PT-symmetry region but not an arbitrary one. This is due to the fact that the evolution operator at a certain period is equivalent to the PT operator for the real-valued wave function in the elaborate PT-symmetric Hilbert space.
description: 7 pages, 3 figures
Interaction of Anagrelide drug molecule on pristine and doped boron nitride nanocages: a DFT, RDG, PCM and QTAIM investigation
Creators: name: Nishat, Maliha
name: Hossain, Md. Rakib
name: Hasan, Md. Mehade
name: Hossain, Md. Kamal
name: Hossain, Md. Abul
name: Ahmed, Farid
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology

description: Nowadays, a nanostructure-based drug delivery system is one of the most noticeable topics to be studied, and in this regard, boron nitride nanoclusters are promising drug carriers for targeted drug delivery systems. In this article, the interaction mechanism of Anagrelide (AG) drug with B12N12 and Al- and Ga-doped B12N12 nanocages have been investigated using DFT with B3LYP/6-31 G (d, p) method in both gas and water media. All our studied complexes are thermodynamically stable, and doped nanocage complexes have higher negative adsorption energy (EAd.) and negative solvation energy than AG/B12N12 complexes which correspond to the stability of these systems in both media. The negative highest EAd value is 64.98 kcal/mol (63.17 kcal/mol) and 65.69 kcal/mol (65.11 kcal/mol) in gas (water) media for complex F (AG/AlB11N12) and complex I (AG/GaB11N12) respectively, which refers to the highest stability of these systems. The enhanced values of dipole moment (from 12.40 (12.65) Debye to 17.21 (17.69) Debye in complex F (complex I)) also confirm their stability. The QTAIM and RDG analysis endorse the strong adsorption nature of the AG drug onto the AlB11N12, and GaB11N12 nanocages, which is consistent with the adsorption energy as chemisorption occurs for these complexes. According to the electronic properties, doped nanocages show high sensitivity that infers their promising nature for drug delivery purposes. Thus, complex F and complex I are promising drug delivery systems, and doped nanocages (AlB11N12 and GaB11N12) are better carriers than pristine nanocages for the AG drug delivery system. Communicated by Ramaswamy H. Sarma
Small area quantile estimation under unit-level models
Creators: name: Zhang, Qiong
Publisher: name: University of British Columbia
Year: 2017

description: Sample surveys are widely used as a cost-effective way to collect information on variables of interest in target populations. In applications, we are generally interested in parameters such as population means, totals, and quantiles. Similar parameters for subpopulations or areas, formed by geographic areas and socio-demographic groups, are also of interest in applications. However, the sample size might be small or even zero in subpopulations due to the probability sampling and the budget limitation. There has been intensive research on how to produce reliable estimates for characteristics of interest for subpopulations for which the sample size is small or even zero. We call this line of research Small Area Estimation (SAE). In this thesis, we study the performance of a number of small area quantile estimators based on a popular unit-level model and its variations. When a finite population can be regarded as a sample from some model, we may use the whole sample from the finite population to determine the model structure with a good precision. The information can then be used to produce more reliable estimates for small areas. However, if the model assumption is wrong, the resulting estimates can be misleading and their mean squared errors can be underestimated. Therefore, it is critical to check the robustness of estimators under various model mis-specification scenarios. In this thesis, we first conduct simulation studies to investigate the performance of three small area quantile estimators in the literature. They are found not to be very robust in some likely situations. Based on these observations, we propose an approach to obtain more robust small area quantile estimators. Simulation results show that the proposed new methods have superior performance either when the error distribution in the model is non-normal or the data set contain many outliers.
The 2D AKLT state on the honeycomb lattice is a universal resource for quantum computation
Creators: name: Wei, Tzu-Chieh
name: Affleck, Ian
name: Raussendorf, Robert
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Universal quantum computation can be achieved by simply performing single-qubit measurements on a highly entangled resource state. Resource states can arise from ground states of carefully designed two-body interacting Hamiltonians. This opens up an appealing possibility of creating them by cooling. The family of Affleck-Kennedy-Lieb-Tasaki (AKLT) states are the ground states of particularly simple Hamiltonians with high symmetry, and their potential use in quantum computation gives rise to a new research direction. Expanding on our prior work [T.-C. Wei, I. Affleck, and R. Raussendorf, Phys. Rev. Lett. 106, 070501 (2011)], we give detailed analysis to explain why the spin-3/2 AKLT state on a two-dimensional honeycomb lattice is a universal resource for measurement-based quantum computation. Along the way, we also provide an alternative proof that the 1D spin-1 AKLT state can be used to simulate arbitrary one-qubit unitary gates. Moreover, we connect the quantum computational universality of 2D random graph states to their percolation property and show that these states whose graphs are in the supercritical (i.e. percolated) phase are also universal resources for measurement-based quantum computation.
description: 21 pages, 13 figures, long version of Phys. Rev. Lett. 106, 070501 (2011) or arXiv:1102.5064
Bose–Einstein correlations in hadron-pairs from lepto-production on nuclei ranging from hydrogen to xenon
Creators: name: The Hermes, Collaboration
name: Schäfer, Andreas
Publisher: name: Universität Regensburg
Year: 2015
Subjects: subject: 530 Physik

description: Bose–Einstein correlations of like-sign charged hadrons produced in deep-inelastic electron and positron scattering are studied in the HERMES experiment using nuclear targets of 1 H, 2 H, 3 He, 4 He, N, Ne, Kr, and Xe. A Gaussian approach is used to parametrize a two-particle correlation function determined from events with at least two charged hadrons of the same sign charge. This correlation function is compared to two different empirical distributions that do not include the Bose–Einstein correlations. One distribution is derived from unlike-sign hadron pairs, and the second is derived from mixing like-sign pairs from different events. The extraction procedure used simulations incorporating the experimental setup in order to correct the results for spectrometer acceptance effects, and was tested using the distribution of unlike-sign hadron pairs. Clear signals of Bose–Einstein correlations for all target nuclei without a significant variation with the nuclear target mass are found. Also, no evidence for a dependence on the invariant mass W of the photon-nucleon system is found when the results are compared to those of previous experiments.
description: Projekt SCOAP3
The Ising Susceptibility Scaling Function
Creators: name: Chan, Y.
name: Guttmann, A. J.
name: Nickel, B. G.
name: Perk, J. H. H.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We have dramatically extended the zero field susceptibility series at both high and low temperature of the Ising model on the triangular and honeycomb lattices, and used these data and newly available further terms for the square lattice to calculate a number of terms in the scaling function expansion around both the ferromagnetic and, for the square and honeycomb lattices, the antiferromagnetic critical point.
description: PDFLaTeX, 50 pages, 5 figures, zip file with series coefficients and background data in Maple format provided with the source files. Vs2: Added dedication and made several minor additions and corrections. Vs3: Minor corrections. Vs4: No change to eprint. Added essential square-lattice series input data (used in the calculation) that were removed from University of Melbourne's website