cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Mouse Papillomavirus L1 and L2 Are Dispensable for Viral Infection and Persistence at Both Cutaneous and Mucosal Tissues
Creators: name: Brendle, Sarah
name: Li, Jingwei J.
name: Cladel, Nancy M.
name: Shearer, Debra A.
name: Budgeon, Lynn R.
name: Balogh, Karla K.
name: Atkins, Hannah
name: Costa-Fujishima, Marina
name: Lopez, Paul
name: Christensen, Neil D.
name: Doorbar, John
name: Murooka, Thomas T.
name: Hu, Jiafen
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: mouse papillomavirus
L1 mutant
L2 mutant
viral production
tumor growth
RCA
ISH
IHC
RNAscope
TEM
viral copy number
qPCR

description: Papillomavirus L1 and L2, the major and minor capsid proteins, play significant roles in viral assembly, entry, and propagation. In the current study, we investigate the impact of L1 and L2 on viral life cycle and tumor growth with a newly established mouse papillomavirus (MmuPV1) infection model. MmuPV1 L1 knockout, L2 knockout, and L1 plus L2 knockout mutant genomes (designated as L1ATGko-4m, L2ATGko, and L1-L2ATGko respectively) were generated. The mutants were examined for their ability to generate lesions in athymic nude mice. Viral activities were examined by qPCR, immunohistochemistry (IHC), in situ hybridization (ISH), and transmission electron microscopy (TEM) analyses. We demonstrated that viral DNA replication and tumor growth occurred at both cutaneous and mucosal sites infected with each of the mutants. Infections involving L1ATGko-4m, L2ATGko, and L1-L2ATGko mutant genomes generally resulted in smaller tumor sizes compared to infection with the wild type. The L1 protein was absent in L1ATGko-4m and L1-L2ATGko mutant-treated tissues, even though viral transcripts and E4 protein expression were robust. Therefore, L1 is not essential for MmuPV1-induced tumor growth, and this finding parallels our previous observations in the rabbit papillomavirus model. Very few viral particles were detected in L2ATGko mutant-infected tissues. Interestingly, the localization of L1 in lesions induced by L2ATGko was primarily cytoplasmic rather than nuclear. The findings support the hypothesis that the L2 gene influences the expression, location, transport, and assembly of the L1 protein in vivo.
An Experimental and Theoretical Determination of Oscillatory Shear-Induced Crystallization Processes in Viscoelastic Photonic Crystal Media
Creators: name: Finlayson, Chris E.
name: Rosetta, Giselle
name: Baumberg, Jeremy J.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: polymers
shear-induced crystallization
photonic crystals
composite materials
viscoelasticity

description: A study is presented of the oscillatory shear-ordering dynamics of viscoelastic photonic crystal media, using an optical shear cell. The hard-sphere/“sticky”-shell design of these polymeric composite particles produces athermal, quasi-solid rubbery media, with a characteristic viscoelastic ensemble response to applied shear. Monotonic crystallization processes, as directly measured by the photonic stopband transmission, are tracked as a function of strain amplitude, oscillation frequency, and temperature. A complementary generic spatio-temporal model is developed of crystallization due to shear-dependent interlayer viscosity, giving propagating crystalline fronts with increasing applied strain, and a gradual transition from interparticle disorder to order. The introduction of a competing shear-induced flow degradation process, dependent on the global shear rate, gives solutions with both amplitude and frequency dependence. The extracted crystallization timescales show parametric trends which are in good qualitative agreement with experimental observations.
Kambrium-Vendi töörühma välipäevik 77
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1981
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores from Estonia.
Auto-WEKA : combined selection and hyperparameter optimization of supervised machine learning algorithms
Creators: name: Thornton, Chris
Publisher: name: University of British Columbia
Year: 2014

description: Many different machine learning algorithms exist; taking into account each algorithm's set of hyperparameters, there is a staggeringly large number of possible choices. This project considers the problem of simultaneously selecting a learning algorithm and setting its hyperparameters. Previous works attack these issues separately, but this problem can be addressed by a fully automated approach, in particular by leveraging recent innovations in Bayesian optimization. The WEKA software package provides an implementation for a number of feature selection and supervised machine learning algorithms, which we use inside our automated tool, Auto-WEKA. Specifically, we examined the 3 search and 8 evaluator methods for feature selection, as well as all of the classification and regression methods, spanning 2 ensemble methods, 10 meta-methods, 27 base algorithms, and their associated hyperparameters. On 34 popular datasets from the UCI repository, the Delve repository, the KDD Cup 09, variants of the MNIST dataset and CIFAR-10, our method produces classification and regression performance often much better than obtained using state-of-the-art algorithm selection and hyperparameter optimization methods from the literature. Using this integrated approach, users can more effectively identify not only the best machine learning algorithm, but also the corresponding hyperparameter settings and feature selection methods appropriate for that algorithm, and hence achieve improved performance for their specific classification or regression task.
Shape of Clusters as a Probe of Screening Mechanisms in Modified Gravity
Creators: name: Llinares, Claudio
name: Mota, David F.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Scalar fields are crucial components in high energy physics and extensions of General Relativity. The fact they are not observed in the solar system may be due to a mechanism which screens their presence in high dense regions. We show how observations of the ellipticity of galaxy clusters can discriminate between models with and without scalar fields and even between different screening mechanisms. Using nowadays X-ray observations we put novel constraints on the different models.
description: 4 pages, 3 figures, matches version accepted for publication in PRL
Kambrium-Vendi töörühma välipäevik 78
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1982
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores from Estonia.
Exploring the Impact of Terminators on Transgene Expression in Chlamydomonas reinhardtii with a Synthetic Biology Approach
Creators: name: Geisler, Katrin
name: Scaife, Mark A.
name: Mordaka, Paweł M.
name: Holzer, Andre
name: Tomsett, Eleanor V.
name: Mehrshahi, Payam
name: Mendoza Ochoa, Gonzalo I.
name: Smith, Alison G.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: algae
heterologous protein expression
modular assembly
quantification of transgene expression
standardized workflow
terminator
3′ UTR

description: Chlamydomonas reinhardtii has many attractive features for use as a model organism for both fundamental studies and as a biotechnological platform. Nonetheless, despite the many molecular tools and resources that have been developed, there are challenges for its successful engineering, in particular to obtain reproducible and high levels of transgene expression. Here we describe a synthetic biology approach to screen several hundred independent transformants using standardised parts to explore different parameters that might affect transgene expression. We focused on terminators and, using a standardised workflow and quantitative outputs, tested 9 different elements representing three different size classes of native terminators to determine their ability to support high level expression of a GFP reporter gene. We found that the optimal size reflected the median size of element found in the C. reinhardtii genome. The behaviour of the terminator parts was similar with different promoters, in different host strains and with different transgenes. This approach is applicable to the systematic testing of other genetic elements, facilitating comparison to determine optimal transgene design.
Single-laser 32.5 Tbit/s Nyquist WDM transmission
Creators: name: Hillerkuss, David
name: Schmogrow, Rene
name: Meyer, Matthias
name: Wolf, Stefan
name: Jordan, Meinert
name: Kleinow, Philipp
name: Lindenmann, Nicole
name: Schindler, Philipp C.
name: Melikyan, Argishti
name: Yang, Xin
name: Ben-Ezra, Shalva
name: Nebendahl, Bernd
name: Dreschmann, Michael
name: Meyer, Joachim
name: Parmigiani, Francesca
name: Petropoulos, Periklis
name: Resan, Bojan
name: Oehler, Aandreas
name: Weingarten, Kurt
name: Altenhain, Lars
name: Ellermeyer, Tobias
name: Moeller, Matthias
name: Huebner, Michael
name: Becker, Juergen
name: Koos, Christian
name: Freude, Wolfgang
name: Leuthold, Juerg
Publisher: name: arXiv
Year: 2012
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Optics (physics.optics)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: We demonstrate 32.5 Tbit/s 16QAM Nyquist WDM transmission over a total length of 227 km of SMF-28 without optical dispersion compensation. A number of 325 optical carriers are derived from a single laser and encoded with dual-polarization 16QAM data using sinc-shaped Nyquist pulses. As we use no guard bands, the carriers have a spacing of 12.5 GHz equal to the Nyquist bandwidth of the data. We achieve a high net spectral efficiency of 6.4 bit/s/Hz using a software-defined transmitter which generates the electrical modulator drive signals in real-time.
description: (c) 2012 Optical Society of America. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modifications of the content of this paper are prohibited
A Review of Electronic Transport in Superconducting Sr 2 RuO 4 Junctions
Creators: name: Anwar, Muhammad Shahbaz
name: Robinson, Jason W. A.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: unconventional superconductivity
Sr2RuO4
chirality
chiral domain wall
superconducting junctions

description: We review electronic transport in superconducting junctions with Sr2RuO4. Transport measurements provide evidence for chiral domain walls and, therefore, chiral superconductivity in superconducting Sr2RuO4, but so far, the symmetry of the underlying superconducting state remains inconclusive. Further studies involving density of states measurements and spin-polarised transport in local/non-local Sr2RuO4 junctions with magnetic materials could lead to fundamental discoveries and a better understanding of the superconducting state.
Diffusion phenomena for partially dissipative hyperbolic systems
Creators: name: Wirth, Jens
Publisher: name: arXiv
Year: 2011
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: In this note we provide some precise estimates explaining the diffusive structure of partially dissipative systems with time-dependent coefficients satisfying a uniform Kalman rank condition. Precisely, we show that under certain (natural) conditions solutions to a partially dissipative hyperbolic system are asymptotically equivalent to solutions of a corresponding parabolic equation. The approach is based on an elliptic WKB analysis for small frequencies in combination with exponential stability for large frequencies due to results of Beauchard and Zuazua and arguments of perturbation theory.
description: 13 pages
Einflussfaktoren auf die Arbeitszufriedenheit: Eine quantitative Kano-Studie in einem Schweizer Medienunternehmen
Creators: name: Gubser, Christoph
name: Voss, Rödiger
Publisher: name: e-Journal of Practical Business Research
Year: 2013
Subjects: managementScience

description: e-Journal of Practical Business Research, Ausgabe 14 (12/2013)
One-Loop BPS amplitudes as BPS-state sums
Creators: name: Angelantonj, Carlo
name: Florakis, Ioannis
name: Pioline, Boris
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Number Theory (math.NT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Recently, we introduced a new procedure for computing a class of one-loop BPS-saturated amplitudes in String Theory, which expresses them as a sum of one-loop contributions of all perturbative BPS states in a manifestly T-duality invariant fashion. In this paper, we extend this procedure to all BPS-saturated amplitudes of the form \int_F Γ_{d+k,d} Φ, with Φ being a weak (almost) holomorphic modular form of weight -k/2. We use the fact that any such Φ can be expressed as a linear combination of certain absolutely convergent Poincaré series, against which the fundamental domain F can be unfolded. The resulting BPS-state sum neatly exhibits the singularities of the amplitude at points of gauge symmetry enhancement, in a chamber-independent fashion. We illustrate our method with concrete examples of interest in heterotic string compactifications.
description: 42 pages; v4: a few misprints corrected
Kambrium-Vendi töörühma välipäevik 79
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1983
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores in Estonia (descriptions 1983 and 1985).
Gaussian semiparametric estimates on the unit sphere
Creators: name: Durastanti, Claudio
name: Lan, Xiaohong
name: Marinucci, Domenico
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistics Theory (math.ST)
subject: Probability (math.PR)
subject: FOS: Mathematics

description: We study the weak convergence (in the high-frequency limit) of the parameter estimators of power spectrum coefficients associated with Gaussian, spherical and isotropic random fields. In particular, we introduce a Whittle-type approximate maximum likelihood estimator and we investigate its asympotic weak consistency and Gaussianity, in both parametric and semiparametric cases.
description: Published in at http://dx.doi.org/10.3150/12-BEJ475 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm)
Additional file 1 of Leucine-rich α2-glycoprotein-1 upregulation in plasma and kidney of patients with lupus nephritis
Creators: name: Yang, Yi
name: Luo, Ran
name: Cheng, Yichun
name: Liu, Tingting
name: Dai, Wei
name: Li, Yueqiang
name: Ge, Shuwang
name: Xu, Gang
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: Hematology

description: Additional file 1: Table S1. Primers for quantitative real time reverse transcription polymerase chain reaction.
Kambrium-Vendi töörühma välipäevik 80
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1977
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores in Russia.
Kambrium-Vendi töörühma välipäevik 82
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1977
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores in Latvia.
List Decoding Algorithm based on Voting in Groebner Bases for General One-Point AG Codes
Creators: name: Matsumoto, Ryutaroh
name: Ruano, Diego
name: Geil, Olav
Publisher: name: arXiv
Year: 2012
Subjects: subject: Information Theory (cs.IT)
subject: Symbolic Computation (cs.SC)
subject: Commutative Algebra (math.AC)
subject: Algebraic Geometry (math.AG)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: E.4; F.2.1; I.1.2; I.1.4
subject: 94B35 (Primary), 13P10, 94B27, 14G50 (Secondary)

description: We generalize the unique decoding algorithm for one-point AG codes over the Miura-Kamiya Cab curves proposed by Lee, Bras-Amorós and O'Sullivan (2012) to general one-point AG codes, without any assumption. We also extend their unique decoding algorithm to list decoding, modify it so that it can be used with the Feng-Rao improved code construction, prove equality between its error correcting capability and half the minimum distance lower bound by Andersen and Geil (2008) that has not been done in the original proposal except for one-point Hermitian codes, remove the unnecessary computational steps so that it can run faster, and analyze its computational complexity in terms of multiplications and divisions in the finite field. As a unique decoding algorithm, the proposed one is empirically and theoretically as fast as the BMS algorithm for one-point Hermitian codes. As a list decoding algorithm, extensive experiments suggest that it can be much faster for many moderate size/usual inputs than the algorithm by Beelen and Brander (2010). It should be noted that as a list decoding algorithm the proposed method seems to have exponential worst-case computational complexity while the previous proposals (Beelen and Brander, 2010; Guruswami and Sudan, 1999) have polynomial ones, and that the proposed method is expected to be slower than the previous proposals for very large/special inputs.
description: Accepted for publication in J. Symbolic Computation. LaTeX2e article.cls, 42 pages, 4 tables, no figures. Ver. 6 added an illustrative example of the algorithm execution
title: Exploring the relationships between terrain, structural foot morphology, and adaptive foot morphology
Creators: name: Bargeman, Fiep
Publisher: name: University of Kent
Year: 2025

description: The arch of the foot is considered a principal element of the structure and function of the foot, and its claimed causative relationship with injuries has been commonly researched. The impact of terrain (Natural and Developed) on the development of the arch has not yet been clearly researched and could be a critical part in the structure-function-injury discussion. Collecting postcodes and Foot Flexibilities (FF) from a range of participants and data gathered using smart insoles allowed for relationships between terrain, foot structure, dynamic response, and the biophysics of the foot to be examined.
Young participants growing up on a Natural terrain were found to have a more flexible arch; however, the same was not observed in an adult population. High FF feet and low FF feet did not yield significantly different values for walking characteristics, nor did they show a difference in adaptability to walking on varying terrains. Moreover, no correlations could be found between FF and walking characteristics. It was found, however, that the dynamic response of the foot differs between varying terrains. Few correlations were observed between terrains per walking characteristic, and the characteristics themselves did not appear interrelated either. Lastly, it was shown that a more deforming arch stores more energy than a rigid arch.
Terrain has been shown to influence the foot structure of a developing foot, but a standardised protocol to classify terrains is required to observe this trend consistently. Pronation was often found to be the outlier in general trends, facilitating development of the theory that pronation is inherent to the foot, undecided by environmental factors or correlated to certain intrinsic classifications. The vertical displacement of the arch was found to be the main cause of higher energy storage in flexible arches, although calculations leading to this observation were based on simplifications of the mechanisms.
Kambrium-Vendi töörühma välipäevik 83
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1985
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores from Estonia (descriptions 1985 and 1986).
Testing over a continuum of null hypotheses with False Discovery Rate control
Creators: name: Blanchard, Gilles
name: Delattre, Sylvain
name: Roquain, Etienne
Publisher: name: arXiv
Year: 2011
Subjects: subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: We consider statistical hypothesis testing simultaneously over a fairly general, possibly uncountably infinite, set of null hypotheses, under the assumption that a suitable single test (and corresponding $p$-value) is known for each individual hypothesis. We extend to this setting the notion of false discovery rate (FDR) as a measure of type I error. Our main result studies specific procedures based on the observation of the $p$-value process. Control of the FDR at a nominal level is ensured either under arbitrary dependence of $p$-values, or under the assumption that the finite dimensional distributions of the $p$-value process have positive correlations of a specific type (weak PRDS). Both cases generalize existing results established in the finite setting. Its interest is demonstrated in several non-parametric examples: testing the mean/signal in a Gaussian white noise model, testing the intensity of a Poisson process and testing the c.d.f. of i.i.d. random variables.
Kambrium-Vendi töörühma välipäevik 84
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1986
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores in Estonia (descriptions 1986 and 1987).
Kambrium-Vendi töörühma välipäevik 85
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1986
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores from Estonia (descriptions 1986 and 1987).
Pooled Association Tests for Rare Genetic Variants: A Review and Some New Results
Creators: name: Derkach, Andriy
name: Lawless, Jerry F.
name: Sun, Lei
Publisher: name: arXiv
Year: 2012
Subjects: subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: In the search for genetic factors that are associated with complex heritable human traits, considerable attention is now being focused on rare variants that individually have small effects. In response, numerous recent papers have proposed testing strategies to assess association between a group of rare variants and a trait, with competing claims about the performance of various tests. The power of a given test in fact depends on the nature of any association and on the rareness of the variants in question. We review such tests within a general framework that covers a wide range of genetic models and types of data. We study the performance of specific tests through exact or asymptotic power formulas and through novel simulation studies of over 10,000 different models. The tests considered are also applied to real sequence data from the 1000 Genomes project and provided by the GAW17. We recommend a testing strategy, but our results show that power to detect association in plausible genetic scenarios is low for studies of medium size unless a high proportion of the chosen variants are causal. Consequently, considerable attention must be given to relevant biological information that can guide the selection of variants for testing.
description: Published in at http://dx.doi.org/10.1214/13-STS456 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Strong convergence for reduced free products (Remarks on a result by Paul Skoufranis)
Creators: name: Pisier, Gilles
Publisher: name: arXiv
Year: 2012
Subjects: subject: Operator Algebras (math.OA)
subject: FOS: Mathematics
subject: 46L64, 46M07

description: Using an inequality due to Ricard and Xu, we give a different proof of Paul Skoufranis's recent result showing that the strong convergence of possibly non-commutative random variables $X^{(k)}\to X$ is stable under reduced free product with a fixed non-commutative random variable $Y$. In fact we obtain a more general fact: assuming that the families $X^{(k)}=\{X_i^{(k)}\}$ and $Y^{(k)}=\{Y_j^{(k)}\}$ are $*$-free as well as their limits (in moments) $X =\{X_i \}$ and $Y =\{Y_j\}$, the strong convergences $X^{(k)}\to X$ and $Y^{(k)}\to Y$ imply that of $\{X^{(k)},Y^{(k)} \}$ to $\{X ,Y\}$. Phrased in more striking language: the reduced free product is "continuous" with respect to strong convergence. The analogue for weak convergence (i.e. convergence of all moments) is obvious. Our approach extends to the amalgamated free product, left open by Skoufranis.
description: Several corrections and additions were made. A notable addition is the case of amalgamated free products. To appear in IDAQP (Infinite Dimensional Analysis, Quantum Probability and Related Topics)
Viral Evolution and Adaptation as a Multivariate Branching Process
Creators: name: Antoneli, Fernando
name: Bosco, Francisco
name: Castro, Diogo
name: Janini, Luiz Mario
Publisher: name: arXiv
Year: 2011
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Probability (math.PR)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 92Dxx

description: In the present work we analyze the problem of adaptation and evolution of RNA virus populations, by defining the basic stochastic model as a multivariate branching process in close relation with the branching process advanced by Demetrius, Schuster and Sigmund ("Polynucleotide evolution and branching processes", Bull. Math. Biol. 46 (1985) 239-262), in their study of polynucleotide evolution. We show that in the absence of beneficial forces the model is exactly solvable. As a result it is possible to prove several key results directly related to known typical properties of these systems like (i) proof, in the context of the theory of branching processes, of the lethal mutagenesis criterion proposed by Bull, Sanjuán and Wilke ("Theory of lethal mutagenesis for viruses", J. Virology 18 (2007) 2930-2939); (ii) a new proposal for the notion of relaxation time with a quantitative prescription for its evaluation and (iii) the quantitative description of the evolution of the expected values in four distinct regimes: transient, "stationary" equilibrium, extinction threshold and lethal mutagenesis. Moreover, new insights on the dynamics of evolving virus populations can be foreseen.
description: 39 pages, 3 figures. International Symposium on Mathematical and Computational Biology, Tempe, Arizona, USA, 6 - 10 November 2012. Fernando Antoneli, Francisco Bosco, Diogo Castro, And Luiz Mario Janini (2013) Viral Evolution and Adaptation as a Multivariate Branching Process. Biomat 2012: pp. 217-243. Ed.: R. P. Mondaini. World Scientific, Singapore
Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Creators: name: Scherer, Michael
name: Gasparoni, Gilles
name: Rahmouni, Souad
name: Shashkova, Tatiana
name: Arnoux, Marion
name: Louis, Edouard
name: Nostaeva, Arina
name: Avalos, Diana
name: Dermitzakis, Emmanouil T.
name: Aulchenko, Yurii S.
name: Lengauer, Thomas
name: Lyons, Paul A.
name: Georges, Michel
name: Walter, Jörn
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Research
Quantitative trait loci
DNA methylation
Tissue specificity
Computational biology

description: Funder: Universität des Saarlandes (1036)
description: Abstract: Background: Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects. Results: Here, we present a two-step computational framework MAGAR (https://bioconductor.org/packages/MAGAR), which fully supports the identification of methQTLs from matched genotyping and DNA methylation data, and additionally allows for illuminating cell type-specific methQTL effects. In a pilot analysis, we apply MAGAR on data in four tissues (ileum, rectum, T cells, B cells) from healthy individuals and demonstrate the discrimination of common from cell type-specific methQTLs. We experimentally validate both types of methQTLs in an independent data set comprising additional cell types and tissues. Finally, we validate selected methQTLs located in the PON1, ZNF155, and NRG2 genes by ultra-deep local sequencing. In line with previous reports, we find cell type-specific methQTLs to be preferentially located in enhancer elements. Conclusions: Our analysis demonstrates that a systematic analysis of methQTLs provides important new insights on the influences of genetic variants to cell type-specific epigenomic variation.
High light and temperature reduce photosynthetic efficiency through different mechanisms in the C 4 model Setaria viridis
Creators: name: Anderson, Cheyenne M.
name: Mattoon, Erin M.
name: Zhang, Ningning
name: Becker, Eric
name: McHargue, William
name: Yang, Jiani
name: Patel, Dhruv
name: Dautermann, Oliver
name: McAdam, Scott A. M.
name: Tarin, Tonantzin
name: Pathak, Sunita
name: Avenson, Tom J.
name: Berry, Jeffrey
name: Braud, Maxwell
name: Niyogi, Krishna K.
name: Wilson, Margaret
name: Nusinow, Dmitri A.
name: Vargas, Rodrigo
name: Czymmek, Kirk J.
name: Eveland, Andrea L.
name: Zhang, Ru
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Article
/631/449/2661/2662
/631/449/1734/2689
/631/449/2661/2663
/38/39
/38/91
/38/90
/14/28
/14/63
/64
article

description: Funder: start-up funding from Donald Danforth Plant Science Center (DDPSC)
description: Abstract: C4 plants frequently experience high light and high temperature conditions in the field, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour high light or high temperature treatment at photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in high light or high temperature treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to high light and high temperature. We provide a systematic analysis of high light and high temperature responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.
An evaluation of a rapid conversion to teleSANE in response to COVID-19
Creators: name: Shaw, Jessica
name: Feeney, Hannah
name: Meunier-Sham, Joan
name: Hazard, Karen
name: Plante, Pamela
name: Petricone, Randi
Publisher: name: University of Illinois at Chicago
Year: 2023
Subjects: Uncategorized

description: Sexual Assault Nurse Examiners (SANEs) provide expert, comprehensive medical forensic care to patients who present for services following a sexual assault. Because SANEs are not consistently available, telehealth technology is being explored as a means to provide access to this expert care (i.e., teleSANE). During the COVID-19 pandemic, teleSANE offered additional potential benefits by reducing the length of time spent and number of providers in patient exam rooms, the need for personal protective equipment that was in high demand and short supply, and provider anxiety related to providing in-person care. In the summer of 2020, the Massachusetts SANE program rapidly and temporarily converted five hospitals from in-person SANE care to teleSANE. An evaluation team interviewed 23 providers using a rapid research and evaluation methods approach to assess the temporary model and inform the future of SANE care. Evaluation findings reveal it is possible to rapidly and temporarily convert hospitals from in-person to teleSANE care in a time of broad uncertainty, and that such a change requires intensive and thoughtful planning; a shared commitment to being supportive, flexible, and responsive; and specific experience and expertise. Considerations for communities exploring how best to ensure consistent, equitable access to SANEs are discussed.
From cosmic deceleration to acceleration: new constraints from SN Ia and BAO/CMB
Creators: name: Giostri, R.
name: Santos, M. Vargas dos
name: Waga, I.
name: Reis, R. R. R.
name: Calvão, M. O.
name: Lago, B. L.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We use type Ia supernovae (SN Ia) data in combination with recent baryonic acoustic oscillations (BAO) and cosmic microwave background (CMB) observations to constrain a kink-like parametrization of the deceleration parameter ($q$). This $q$-parametrization can be written in terms of the initial ($q_i$) and present ($q_0$) values of the deceleration parameter, the redshift of the cosmic transition from deceleration to acceleration ($z_t$) and the redshift width of such transition ($τ$). By assuming a flat space geometry, $q_i=1/2$ and adopting a likelihood approach to deal with the SN Ia data we obtain, at the 68% confidence level (C.L.), that: $z_t=0.56^{+0.13}_{-0.10}$, $τ=0.47^{+0.16}_{-0.20}$ and $q_0=-0.31^{+0.11}_{-0.11}$ when we combine BAO/CMB observations with SN Ia data processed with the MLCS2k2 light-curve fitter. When in this combination we use the SALT2 fitter we get instead, at the same C.L.: $z_t=0.64^{+0.13}_{-0.07}$, $τ=0.36^{+0.11}_{-0.17}$ and $q_0=-0.53^{+0.17}_{-0.13}$. Our results indicate, with a quite general and model independent approach, that MLCS2k2 favors Dvali-Gabadadze-Porrati-like cosmological models, while SALT2 favors $Λ$CDM-like ones. Progress in determining the transition redshift and/or the present value of the deceleration parameter depends crucially on solving the issue of the difference obtained when using these two light-curve fitters.
description: 25 pages, 9 figures
Efimov three-body states on top of a Fermi sea
Creators: name: Nygaard, Nicolai Gayle
name: Zinner, Nikolaj Thomas
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Superconductivity (cond-mat.supr-con)
subject: Nuclear Theory (nucl-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The stabilization of Cooper pairs of bound electrons in the background of a Fermi sea is the origin of superconductivity and the paradigmatic example of the striking influence of many-body physics on few-body properties. In the quantum-mechanical three-body problem the famous Efimov effect yields unexpected scaling relations among a tower of universal states. These seemingly unrelated problems can now be studied in the same setup thanks to the success of ultracold atomic gas experiments. In light of the tremendous effect of a background Fermi sea on two-body properties, a natural question is whether a background can modify or even destroy the Efimov effect. Here we demonstrate how the generic problem of three interacting particles changes when one particle is embedded in a background Fermi sea, and show that Efimov scaling persists. It is found in a scaling that relates the three-body physics to the background density of fermionic particles.
description: 15 pages, 2 figures, 2 appendices, revised and updated version, in press
Translating synthetic natural language to database queries with a polyglot deep learning framework
Creators: name: Bazaga, Adrián
name: Gunwant, Nupur
name: Micklem, Gos
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Article
/639/705/117
/639/705/794
article

description: Abstract: The number of databases as well as their size and complexity is increasing. This creates a barrier to use especially for non-experts, who have to come to grips with the nature of the data, the way it has been represented in the database, and the specific query languages or user interfaces by which data are accessed. These difficulties worsen in research settings, where it is common to work with many different databases. One approach to improving this situation is to allow users to pose their queries in natural language. In this work we describe a machine learning framework, Polyglotter, that in a general way supports the mapping of natural language searches to database queries. Importantly, it does not require the creation of manually annotated data for training and therefore can be applied easily to multiple domains. The framework is polyglot in the sense that it supports multiple different database engines that are accessed with a variety of query languages, including SQL and Cypher. Furthermore Polyglotter supports multi-class queries. Good performance is achieved on both toy and real databases, as well as a human-annotated WikiSQL query set. Thus Polyglotter may help database maintainers make their resources more accessible.
Determining Frequentist Confidence Limits Using a Directed Parameter Space Search
Creators: name: Daniel, Scott F.
name: Connolly, Andrew J.
name: Schneider, Jeff
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We consider the problem of inferring constraints on a high-dimensional parameter space with a computationally expensive likelihood function. We propose a machine learning algorithm that maps out the Frequentist confidence limit on parameter space by intelligently targeting likelihood evaluations so as to quickly and accurately characterize the likelihood surface in both low- and high-likelihood regions. We compare our algorithm to Bayesian credible limits derived by the well-tested Markov Chain Monte Carlo (MCMC) algorithm using both multi-modal toy likelihood functions and the 7-year WMAP cosmic microwave background likelihood function. We find that our algorithm correctly identifies the location, general size, and general shape of high-likelihood regions in parameter space while being more robust against multi-modality than MCMC.
description: 24 pages; 16 figures
Kambrium-Vendi töörühma välipäevik 86
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1987
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores in Leningrad Oblast (Osmino area).
Computing the Galois group of some parameterized linear differential equation of order two
Creators: name: Dreyfus, Thomas
Publisher: name: arXiv
Year: 2011
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 34M15, 12H20, 34M03 (Primary)

description: We extend Kovacic's algorithm to compute the differential Galois group of some second order parameterized linear differential equation. In the case where no Liouvillian solutions could be found, we give a necessary and sufficient condition for the integrability of the system. We give various examples of computation.
description: 14 pages, final version. To appear in Proceedings of the American Mathematical Society
Kambrium-Vendi töörühma välipäevik 87
Creators: name: Pirrus, Enn
name: Mens, Kaisa
Publisher: name: Tallinna Tehnikaülikooli Geoloogia Instituut
Year: 1988
Subjects: Cambrian
geological descriptions

description: Field notebook with descriptions of Cambrian and Vendian drill cores in Leningrad Oblast.
VESPA ORIENTALIS (Hymenoptera Vespidae), THE FIRST RECORD IN MARCHE REGION
Creators: name: Ruschioni, Sara
name: Lorenzini, Marco
name: Fontana, Paolo
Publisher: name: Zenodo
Year: 2023

description: The presence of Vespa orientalis Linnaeus, 1771 (Hymenoptera Vespidae) was reported for the first time on the eastern side of the Italian peninsula, in Ancona (Marche Region). After an initial sighting by a beekeeper, sampling was carried out directly in the apiary and the identity of the insects captured was subsequently confirmed in the laboratory.
Self-reported oral health and dental service utilization of vulnerable pregnant women registering for the prenatal public health program in Fraser Health, BC, Canada
Creators: name: Jessani, Abbas Ali
Publisher: name: University of British Columbia
Year: 2014

description: Objective: To determine the baseline self-reported oral health and dental service utilization of pregnant women from diverse ethno cultural backgrounds within the geographical are of the Fraser Health Authority in British Columbia, Canada. Method: A prospective 34-item cross-sectional survey was administered to all the women enrolling for a prenatal registration program between October 2012 and January 2013. For data analysis, a two-sample t-test was used, and categorical variables were tested using a chi-square test. Multivariable logistic regressions were used to estimate the odds ratio. Results: A total of 740 pregnant women filled out the questionnaire. The majority (84%) of the respondents rated their oral health as good or excellent. Fifty two percent of the women had visited dental professional during last year. Almost 1/3 of those reporting symptoms of depression rated their oral health as fair or poor. Forty-one percent reported having bleeding gums, 22% experienced tooth sensitivity, and 13% had persistent dry mouth since the beginning of their pregnancy. When asked about the beliefs associated with pregnancy, 37% of the respondents expected bleeding gums, and 34% expected tooth sensitivity. Women born in India had visited a dental professional 2.8 times more often than women who had been born elsewhere. Those with dental insurance were 6.6 times more likely to visit a dentist than those without insurance. Conclusion: The majority of pregnant women considered dental care during pregnancy to be very important and had previously visited a dental professional within the last year. However, more than 1/3 had experienced one or more oral problems while more than half held false beliefs about the effects of pregnancy upon oral health. These reported oral beliefs and problems could be addressed with patient education during routine pre-natal care and subsequent referral to a dentist if needed.
Timiriaseviidae Mandelstam 1960
Creators: name: Mesquita-Joanes, Francesc
name: Gálvez, Ángel
name: Palero, Ferran
name: Rueda, Juan
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Ostracoda
Podocopida
Timiriaseviidae

description: FamilyTimiriaseviidae Mandelstam, 1960
Diagnosis.
[Based on the list of characteristic traits of the subfamily Timiriaseviinae by Martens (1995) and Danielopol et al. (2018) and on the types of hinge and sieve pores respectively by Danielopol et al. (2014) and Danielopol et al. (2018)]. Cytheroid Ostracoda with globular shells, particularly in the females, which are larger than males and have a brood pouch (i. e., shell sexual dimorphism apparent). Hinge lophodont, adont, or protodont (Danielopol et al. 2014). Sieve pores absent or type B if present (Danielopol et al. 2018). Terminal segment of the antennula usually short, not longer than the previous segment. Fused part of the antennula Ya aesthetasc with adjacent seta short or not distinguishable, less than one third the length of the aesthetasc. Ventral seta on the second antennular segment situated in a medial or proximal position, not in the distal margin, or absent. Maxillular palp not subdivided in two segments, and with a reduced number of setae. Distal lobe of hemipenis moveable, not fused to the rest of the hemipenis.
description: Published as part of Mesquita-Joanes, Francesc, Gálvez, Ángel, Palero, Ferran & Rueda, Juan, 2025, A new species of Elpidium Müller, 1880 (Crustacea, Ostracoda) from Hispaniola, with an updated key to the species of the genus, and its molecular phylogenetic positioning within the Cytheroidea, pp. 75-106 in ZooKeys 1233 on pages 75-106, DOI: 10.3897/zookeys.1233.126611
Wormhole Cosmic Censorship
Creators: name: Matos, Tonatiuh
name: Urena-Lopez, L. Arturo
name: Miranda, Galaxia
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We analyze the properties of a Kerr-like wormhole supported by phantom matter, which is an exact solution of the Einstein-phantom field equations. It is shown that the solution has a naked ring singularity which is unreachable to null geodesics falling freely from the outside. Similarly to Roger Penrose's cosmic censorship, that states that all naked singularities in the Universe must be protected by event horizons, here we conjecture from our results that a naked singularity can also be fully protected by the intrinsic properties of a wormhole's throat.