cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Stein's method for functions of multivariate normal random variables
Creators: name: Gaunt, Robert E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60F05

description: By the continuous mapping theorem, if a sequence of $d$-dimensional random vectors $(\mathbf{W}_n)_{n\geq1}$ converges in distribution to a multivariate normal random variable $Σ^{1/2}\mathbf{Z}$, then the sequence of random variables $(g(\mathbf{W}_n))_{n\geq1}$ converges in distribution to $g(Σ^{1/2}\mathbf{Z})$ if $g:\mathbb{R}^d\rightarrow\mathbb{R}$ is continuous. In this paper, we develop Stein's method for the problem of deriving explicit bounds on the distance between $g(\mathbf{W}_n)$ and $g(Σ^{1/2}\mathbf{Z})$ with respect to smooth probability metrics. We obtain several bounds for the case that the $j$-component of $\mathbf{W}_n$ is given by $W_{n,j}=\frac{1}{\sqrt{n}}\sum_{i=1}^nX_{ij}$, where the $X_{ij}$ are independent. In particular, provided $g$ satisfies certain differentiability and growth rate conditions, we obtain an order $n^{-(p-1)/2}$ bound, for smooth test functions, if the first $p$ moments of the $X_{ij}$ agree with those of the normal distribution. If $p$ is an even integer and $g$ is an even function, this convergence rate can be improved further to order $n^{-p/2}$. These convergence rates are shown to be of optimal order. We apply our general bounds to some examples, which include the distributional approximation of asymptotically chi-square distributed statistics; the approximation of expectations of smooth functions of binomial and Poisson random variables; rates of convergence in the delta method; and a quantitative variance-gamma approximation of the $D_2^*$ statistic for alignment-free sequence comparison in the case of binary sequences.
description: 32 pages. To appear in Annales de l'Institut Henri Poincare (B) Probabilites et Statistiques, 2019+
Alfacalcidol enhances collagen quality in ovariectomized rat bones: VITAMIN D IMPROVES BONE COLLAGEN QUALITY
Creators: name: Yamauchi, Mitsuo
name: Nagaoka, Hideaki
name: Chida, Takayuki
name: Yamada, Shizuka
name: Terajima, Masahiko
name: Azuma, Yoshiaki
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The aim of this study was to investigate the effects of alfacalcidol (1α(OH)D3 : ALF) on bone collagen employing an ovariectomized rat model. Thirty-five 16-week-old female Sprague-Dawley rats were divided into five groups: SHAM (sham-operated + vehicle), OVX (ovariectomy + vehicle), and three ALF-treated groups, that is, ovariectomy + 0.022 µg/kg/day ALF, ovariectomy + 0.067 µg/kg/day ALF, and ovariectomy + 0.2 µg/kg/day ALF. After 12 weeks of treatment, tibiae were subjected to histological, biochemical and immunohistochemical analyses. Collagen matrices in OVX bone appeared as immature and poorly organized; however, with the ALF treatment, it was improved in a dose-dependent manner. Contents of collagen and pyridinoline cross-link were decreased in OVX compared with SHAM, but they increased to the level comparable to SHAM in ALF-treated groups. The total aldehyde, that is, a sum of free and those involved cross-links, in the highest dose of ALF was significantly higher than the rest of the groups (p < 0.05). In addition, the expression of lysyl oxidase was increased in the all ALF-treated groups compared with OVX (p < 0.05). In conclusion, ALF increases not only the amount of collagen but also enhances the maturation of collagen in ovariectomy-induced osteoporotic bones, which likely contributes to the improvement of bone quality.
Detailed methodology for utilising coccospheres and producing reconstructions from Warm plankton soup and red herrings: calcareous nannoplankton cellular communities and the Palaeocene–Eocene Thermal Maximum
Creators: name: Gibbs, Samantha J.
name: Sheward, Rosie
name: Bown, Paul R.
name: Poulton, Alex J.
name: Alvarez, Sarah
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences
subject: Geochemistry
subject: 40308 Palaeontology (incl. Palynology)

description: Constraining cell geometries and estimates of cellular PIC and POC levels for different groups of calcareous nannoplankton
(400451) Alexander Gall
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Exploring Parameters of Magnetic Particles in 1D Field Excitation
Creators: name: Klemme, Tobias
name: Buzug, Thorsten M.
name: Neumann, Alexander
Publisher: name: International Journal on Magnetic Particle Imaging
Year: 2020

description: This work explores how different parameters, e.g. magnetic anisotropy and core radius, influence the signal/spectrum of magnetic particles in a one-dimensional excitation field. Simulations are performed using a model considering both the mechanical and magnetization dynamics of the particle. The performed simulations show an increase of amplitude at higher harmonics for anisotropy constants within a certain range. This increase is also observed for different magnetic radii. The obtained knowledge can help to improve the performance of magnetic particles in magnetic particle imaging. Int. J. Mag. Part. Imag. 6(2), 2020, Article ID: 2004001, DOI: 10.18416/IJMPI.2020.2004001
description: International Journal on Magnetic Particle Imaging, Vol 6 No 2 (2020)
Low-rank tensor approximations for solving multi-marginal optimal transport problems
Creators: name: Strössner, Christoph
name: Kressner, Daniel
Publisher: name: arXiv
Year: 2022
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: By adding entropic regularization, multi-marginal optimal transport problems can be transformed into tensor scaling problems, which can be solved numerically using the multi-marginal Sinkhorn algorithm. The main computational bottleneck of this algorithm is the repeated evaluation of marginals. Recently, it has been suggested that this evaluation can be accelerated when the application features an underlying graphical model. In this work, we accelerate the computation further by combining the tensor network dual of the graphical model with additional low-rank approximations. We provide an example for the color transfer between several images, in which these additional low-rank approximations save more than 96% of the computation time.
A Brief Report of Caregiver Needs and Resource Utilization During Pediatric Hematopoietic Stem Cell Transplantation
Creators: name: Parsons, Susan K.
name: Jeruss, Stefanie
name: tcomes at the Institute for Clinical Research and Health Policy Studies at Tufts Medical Center, Tufts University School of Medicine
name: Stewart, Susan
name: Peterson, Emily
name: Tighiouart, Hocine
name: Terrin, Norma
name: Mayer, Deborah K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Hematopoietic stem cell transplantation (HSCT) is used to eradicate disease and restore normal hematopoietic, immunologic, and/or metabolic functioning. HSCT is a complex treatment that is physiologically and psychologically demanding on the recipient, caregiver, and family. The purpose of this study was to identify needs and resources of family caregivers of pediatric HSCT recipients during the first year after transplant. Parental caregivers (n = 161) completed an online survey. The most cited sources of information were the HSCT team (87.7%), books and other print materials (83.1%), and the Internet (81.5%). However, more than half of the respondents reported that finding resources and services was a problem. More than half identified managing the emotional and social impact of the transplant on their child, posttransplant and follow-up care, practical strategies for caregiving, maintaining the family, and taking care of themselves during this first year as important topics to address. Adequately and regularly assessing caregiver and family needs and providing resources to meet those needs, especially during transitions in care, are important components of transplant care.
Supplementary Analysis, Experiments, and Tables from Perceptual teleology: expectations of action efficiency bias social perception.
Creators: name: Hudson, Matthew
name: McDonough, Katrina L.
name: Edwards, Rhys
name: Bach, Patric
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology

description: Response time analysis, Non-Biological bject Experiment, Probe Experiment, Mask Experiment, Descriptive Tables for Main and Supplementary Experiments.
Association of interleukin-1 gene variations with moderate to severe chronic periodontitis in multiple ethnicities
Creators: name: Doucette-Stamm, L.
name: Wu, X.
name: Kornman, K.
name: Rogus, J.
name: Zhou, J.
name: Offenbacher, S.
name: Lόpez, N. J.
name: Wilkins, L.
name: Beck, J.
name: Bao, X.
name: Chen, D.
name: Jiang, S.
name: Wang, H.-Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Background and ObjectiveGenetic markers associated with disease are often non-functional and generally tag one or more functional “causative” variants in linkage disequilibrium. Markers may not show tight linkage to the causative variants across multiple ethnicities due to evolutionary divergence, and therefore may not be informative across different population groups. Validated markers of disease suggest causative variants exist in the gene and, if the causative variants can be identified, it is reasonable to hypothesize that such variants will be informative across diverse populations. The aim of this study was to test that hypothesis using functional Interleukin-1 (IL-1) gene variations across multiple ethnic populations to replace the non-functional markers originally associated with chronic adult periodontitis in Caucasians.Material and MethodsAdult chronic periodontitis cases and controls from four ethnic groups (Caucasians, African Americans, Hispanics and Asians) were recruited in the USA, Chile and China. Genotypes of IL1B gene single nucleotide polymorphisms (SNPs), including three functional SNPs (rs16944, rs1143623, rs4848306) in the promoter and one intronic SNP (rs1143633), were determined using a single base extension method or TaqMan 5′ nuclease assay. Logistic regression and other statistical analyses were used to examine the association between moderate to severe periodontitis and IL1B gene variations, including SNPs, haplotypes and composite genotypes. Genotype patterns associated with disease in the discovery study were then evaluated in independent validation studies.ResultsSignificant associations were identified in the discovery study, consisting of Caucasians and African Americans, between moderate to severe adult chronic periodontitis and functional variations in the IL1B gene, including a pattern of four IL1B SNPs (OR = 1.87, p < 0.0001). The association between the disease and this IL1B composite genotype pattern was validated in two additional studies consisting of Hispanics (OR = 1.95, p = 0.04) or Asians (OR = 3.27, p = 0.01). A meta-analysis of the three populations supported the association between the IL-1 genotype pattern and moderate to severe periodontitis (OR 1.95; p < 0.001). Our analysis also demonstrated that IL1B gene variations had added value to conventional risk factors in predicting chronic periodontitis.ConclusionThis study validated the influence of IL-1 genetic factors on the severity of chronic periodontitis in four different ethnicities.
Enlargement of subgraphs of infinite graphs by Bernoulli percolation
Creators: name: Okamura, Kazuki
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60K35, 82B41, 82B43, 05C63, 05C80, 05C81

description: We consider changes in properties of a subgraph of an infinite graph resulting from the addition of open edges of Bernoulli percolation on the infinite graph to the subgraph. We give the triplet of an infinite graph, one of its subgraphs, and a property of the subgraphs. Then, in a manner similar to the way Hammersley's critical probability is defined, we can define two values associated with the triplet. We regard the two values as certain critical probabilities, and compare them with Hammersley's critical probability. In this paper, we focus on the following cases of a graph property: being a transient subgraph, having finitely many cut points or no cut points, being a recurrent subset, or being connected. Our results depend heavily on the choice of the triplet. Most results of this paper are announced in \cite{O16} without proofs. This paper gives full details of them.
description: 23 pages, 3 figures, reorganized, final version, to appear in Indagationes Mathematicae
Observation of long-range orbital transport and giant orbital torque
Creators: name: Hayashi, Hiroki
name: Jo, Daegeun
name: Go, Dongwook
name: Gao, Tenghua
name: Haku, Satoshi
name: Mokrousov, Yuriy
name: Lee, Hyun-Woo
name: Ando, Kazuya
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Modern spintronics relies on the generation of spin currents through spin-orbit coupling. The spin-current generation has been believed to be triggered by current-induced orbital dynamics, which governs the angular momentum transfer from the lattice to the electrons in solids. The fundamental role of the orbital response in the angular momentum dynamics suggests the importance of the orbital counterpart of spin currents: orbital currents. However, evidence for its existence has been elusive. Here, we demonstrate the generation of giant orbital currents and uncover fundamental features of the orbital response. We experimentally and theoretically show that orbital currents propagate over longer distances than spin currents by more than an order of magnitude in a ferromagnet and nonmagnets. Furthermore, we find that the orbital current enables electric manipulation of magnetization with efficiencies significantly higher than the spin counterpart. These findings open the door to orbitronics that exploits orbital transport and spin-orbital coupled dynamics in solid-state devices.
Supplementary Analysis, Experiments, and Tables from Perceptual teleology: expectations of action efficiency bias social perception
Creators: name: Hudson, Matthew
name: McDonough, Katrina L.
name: Edwards, Rhys
name: Bach, Patric
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology

description: Response time analysis, Non-Biological bject Experiment, Probe Experiment, Mask Experiment, Descriptive Tables for Main and Supplementary Experiments.
Colloquium: Quantum anomalous Hall effect
Creators: name: Chang, Cui-Zu
name: Liu, Chao-Xing
name: MacDonald, Allan H.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The quantum Hall (QH) effect, quantized Hall resistance combined with zero longitudinal resistance, is the characteristic experimental fingerprint of Chern insulators - topologically non-trivial states of two-dimensional matter with broken time-reversal symmetry. In Chern insulators, non-trivial bulk band topology is expressed by chiral states that carry current along sample edges without dissipation. The quantum anomalous Hall (QAH) effect refers to QH effects that occur in the absence of external magnetic fields due to spontaneously broken time-reversal symmetry. The QAH effect has now been realized in four different classes of two-dimensional materials: (i) thin films of magnetically (Cr- and/or V-) doped topological insulators in the (Bi,Sb)2Te3 family, (ii) thin films of the intrinsic magnetic topological insulator MnBi2Te4, (iii) moiré materials formed from graphene, and (iv ) moiré materials formed from transition metal dichalcogenides. In this Article, we review the physical mechanisms responsible for each class of QAH insulator, highlighting both differences and commonalities, and comment on potential applications of the QAH effect.
description: 39 pages, 18 figures, comments are welcome
Medium composition testing with live/dead staining from Porous poly-l-lactide-co-ε-caprolactone scaffold: a novel biomaterial for vaginal tissue engineering.
Creators: name: Sartoneva, Reetta
name: Kuismanen, Kirsi
name: Juntunen, Miia
name: Karjalainen, Sanna
name: Hannula, Markus
name: Kyllönen, Laura
name: Hyttinen, Jari
name: Huhtala, Heini
name: Paakinaho, Kaarlo
name: Miettinen, Susanna
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Biological Engineering
subject: 90301 Biomaterials
subject: FOS: Medical engineering
subject: 90399 Biomedical Engineering not elsewhere classified

description: Figure S1: Medium testing live/dead images at day 7. The epithelial cells (A-D), stromal cells (E-H) and their co-cultures (I-P) were cultured in different medium compositions; EpiLife (A,I,M) or 5% HS in DMEM/F12 (E), 3 % HS in EpiLife (B,F,J,N), EpiLife and BM 1:1 (C,G,K,O) and CnT prime CC (D,H,L,P). Scale bar 1 mm.
Disordered Protein Diffusion under Crowded Conditions
Creators: name: Benton, Laura A.
name: Pielak, Gary J.
name: Singh, Vishavpreet
name: Wang, Yaqiang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Intrinsically disordered proteins are important in signaling, regulation, and translocation. Understanding their diffusion under physiologically relevant conditions will yield insight into their functions. We used NMR to quantify the translational diffusion of a globular and a disordered protein in dilute solution and under crowded conditions. In dilute solution, the globular protein chymotrypsin inhibitor 2 (CI2, 7.4 kDa) diffuses faster than the disordered protein α-synuclein (14 kDa). Surprisingly, the opposite occurs under crowded conditions; α-synuclein diffuses faster than CI2, even though α-synuclein is larger than CI2. These data show that shape is a key parameter determining protein diffusion under crowded conditions, adding to the properties known to be affected by macromolecular crowding. The results also offer a clue about why many signaling proteins are disordered.
Signal prediction by anticipatory relaxation dynamics
Creators: name: Voss, Henning U.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: Real-time prediction of signals is a task often encountered in control problems as well as by living systems. Here a model-free prediction approach based on the coupling of a linear relaxation-delay system to a smooth, stationary signal is described. The resulting anticipatory relaxation dynamics (ARD) is a frequency-dependent predictor of future signal values. ARD not only approximately predicts signals on average but can anticipate the occurrence of signal peaks, too. This can be explained by recognizing ARD as an input/output system with negative group delay. It is completely characterized, including its prediction horizon, by its analytically given frequency response function.
description: 2 figures included in text. Second revision
(400452) William Gall
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Weak Antiferromagnetic Coupling via a Superexchange Interaction between Mn(II)–Mn(II) Ions: A QM/MM Study of the Active Site of Human Cytosolic X-Propyl Aminopeptidase P
Creators: name: Wu, Sangwook
name: Liu, Shubin
name: Pedersen, Lee G.
name: Sim, Sooyeon
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: We investigate the dinuclear manganese, Mn(II)-Mn(II), active site of human cytosolic X-propyl aminopeptidase (XPNPEP1) employing the QM/MM method. The optimized structure supports two manganese atoms at the active site and excludes the possibility of a single Mn(II) atom or other combination of divalent metal ions: Ca(II), Fe(II), Mg(II). A broken symmetry solution verifies an antiferromagnetically coupled state between the Mn(II)-Mn(II) pair, which is the ground state. From the energy difference between the high spin state (HS) and the broken symmetry state (BS), we estimate the exchange coupling constant, J, to be 5.15 cm-1. Also, we observe multiple bridges (p orbitals) from solvent and two carboxylate linking to the Mn(II)-Mn(II), which leads to the weakly antiferromagnetic interaction of d5-d5 electrons through superexchange coupling.
Non-trivial matrix actions preserve normality for continued fractions
Creators: name: Vandehey, Joseph
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11K16, 11K50

description: A seminal result due to Wall states that if $x$ is normal to a given base $b$ then so is $rx+s$ for any rational numbers $r,s$ with $r\neq 0$. We show that a stronger result is true for normality with respect to the continued fraction expansion. In particular, suppose $a,b,c,d\in \mathbb{Z}$ with $ad-bc\neq 0$. Then if $x$ is continued fraction normal, so is $(ax+b)/(cx+d)$.
Medium composition testing with live/dead staining from Porous poly-l-lactide-co-∑-caprolactone scaffold: a novel biomaterial for vaginal tissue engineering
Creators: name: Sartoneva, Reetta
name: Kuismanen, Kirsi
name: Juntunen, Miia
name: Karjalainen, Sanna
name: Hannula, Markus
name: Kyllönen, Laura
name: Hyttinen, Jari
name: Huhtala, Heini
name: Paakinaho, Kaarlo
name: Miettinen, Susanna
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Biological Engineering
subject: 90301 Biomaterials
subject: FOS: Medical engineering
subject: 90399 Biomedical Engineering not elsewhere classified

description: Figure S1: Medium testing live/dead images at day 7. The epithelial cells (A-D), stromal cells (E-H) and their co-cultures (I-P) were cultured in different medium compositions; EpiLife (A,I,M) or 5% HS in DMEM/F12 (E), 3 % HS in EpiLife (B,F,J,N), EpiLife and BM 1:1 (C,G,K,O) and CnT prime CC (D,H,L,P). Scale bar 1 mm.
(400453) Mary Gall
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Topological properties of Floquet winding bands in a photonic lattice
Creators: name: Adiyatullin, Albert F.
name: Upreti, Lavi K.
name: Lechevalier, Corentin
name: Evain, Clement
name: Copie, Francois
name: Suret, Pierre
name: Randoux, Stephane
name: Delplace, Pierre
name: Amo, Alberto
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The engineering of synthetic materials characterised by more than one class of topological invariants is one of the current challenges of solid-state based and synthetic materials. Using a synthetic photonic lattice implemented in a two-coupled ring system we engineer an anomalous Floquet metal that is gapless in the bulk and shows simultaneously two different topological properties. On the one hand, this synthetic lattice presents bands characterised by a winding number. The winding emerges from the breakup of inversion symmetry and it directly relates to the appearance of Bloch suboscillations within its bulk. On the other hand, the Floquet nature of the lattice results in well-known anomalous insulating phases with topological edge states. The combination of broken inversion symmetry and periodic time modulation studied here enrich the variety of topological phases available in lattices subject to Floquet driving and suggest the possible emergence of novel phases when periodic modulation is combined with the breakup of spatial symmetries.
description: Published version. Includes supplementary information
Supplementary Figures and Parameter Table from Mosquito-borne transmission in urban landscapes: the missing link between vector abundance and human density.
Creators: name: Romeo-Aznar, Victoria
name: Paul, Richard
name: Telle, Olivier
name: Pascual, Mercedes
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: Health Care
subject: Diseases
subject: 111706 Epidemiology
subject: FOS: Health sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Table of parameters used in simulations. Supplementary Figures.
Separating weak lensing and intrinsic alignments using radio observations
Creators: name: Whittaker, Lee
name: Brown, Michael L.
name: Battye, Richard A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We discuss methods for performing weak lensing using radio observations to recover information about the intrinsic structural properties of the source galaxies. Radio surveys provide unique information that can benefit weak lensing studies, such as HI emission, which may be used to construct galaxy velocity maps, and polarized synchrotron radiation; both of which provide information about the unlensed galaxy and can be used to reduce galaxy shape noise and the contribution of intrinsic alignments. Using a proxy for the intrinsic position angle of an observed galaxy, we develop techniques for cleanly separating weak gravitational lensing signals from intrinsic alignment contamination in forthcoming radio surveys. Random errors on the intrinsic orientation estimates introduce biases into the shear and intrinsic alignment estimates. However, we show that these biases can be corrected for if the error distribution is accurately known. We demonstrate our methods using simulations, where we reconstruct the shear and intrinsic alignment auto and cross-power spectra in three overlapping redshift bins. We find that the intrinsic position angle information can be used to successfully reconstruct both the lensing and intrinsic alignment power spectra with negligible residual bias.
description: 17 pages, 10 figures, submitted to MNRAS
Ensembles of Vision Transformers as a New Paradigm for Automated Classification in Ecology
Creators: name: Kyathanahally, S.
name: Hardeman, T.
name: Reyes, M.
name: Merz, E.
name: Bulas, T.
name: Brun, P.
name: Pomati, F.
name: Baity-Jesi, M.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Monitoring biodiversity is paramount to manage and protect natural resources. Collecting images of organisms over large temporal or spatial scales is a promising practice to monitor the biodiversity of natural ecosystems, providing large amounts of data with minimal interference with the environment. Deep learning models are currently used to automate classification of organisms into taxonomic units. However, imprecision in these classifiers introduces a measurement noise that is difficult to control and can significantly hinder the analysis and interpretation of data. {We overcome this limitation through ensembles of Data-efficient image Transformers (DeiTs), which not only are easy to train and implement, but also significantly outperform} the previous state of the art (SOTA). We validate our results on ten ecological imaging datasets of diverse origin, ranging from plankton to birds. On all the datasets, we achieve a new SOTA, with a reduction of the error with respect to the previous SOTA ranging from 29.35% to 100.00%, and often achieving performances very close to perfect classification. Ensembles of DeiTs perform better not because of superior single-model performances but rather due to smaller overlaps in the predictions by independent models and lower top-1 probabilities. This increases the benefit of ensembling, especially when using geometric averages to combine individual learners. While we only test our approach on biodiversity image datasets, our approach is generic and can be applied to any kind of images.
description: To appear in Scientific Reports
Das Deutsche Burgenmuseum
Creators: name: Großmann, Ulrich G.
Publisher: name: Burgen und Schlösser - Zeitschrift für Burgenforschung und Denkmalpflege
Year: 2022

description: Burgen und Schlösser - Zeitschrift für Burgenforschung und Denkmalpflege, Bd. 57 Nr. 2 (2016): Burgen und Schlösser. Zeitschrift für Burgenforschung und Denkmalpflege
Mapping the Protein Domain Structures of the Respiratory Mucins: A Mucin Proteome Coverage Study
Creators: name: Kesimer, Mehmet
name: Wang, T. Tiffany
name: DeMaria, Genevieve
name: Sheehan, John K.
name: Cao, Rui
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Mucin genes encode a family of the largest expressed proteins in the human genome. The proteins are highly substituted with O-linked oligosaccharides which greatly restrict access to the peptide backbones. The genomic organization of the N-terminal, O-glycosylated, and C-terminal regions of most of the mucins has been established and is available in the sequence databases. However, much less is known about the fate of their exposed protein regions after translation and secretion, and, to date, detailed proteomic studies complementary to the genomic studies are rather limited. Using mucins isolated from cultured human airway epithelial cell secretions, trypsin digestion and mass spectrometry, we investigated the proteome coverage of the mucins responsible for the maintenance and protection of the airway epithelia. Excluding the heavily glycosylated mucin domains, up to 85% coverage of the N-terminal region of the gel forming mucins MUC5B and MUC5AC was achieved, and up to 60% of the C-terminal regions were covered, suggesting that more N- and sparsely O-glycosylated regions as well as possible other modifications are available at the C-terminus. All possible peptides from the cysteine-rich regions that interrupt the heavily glycosylated mucin domains were identified. Interestingly, 43 cleavage sites from ten different domains of MUC5B and MUC5AC were identified, which possessed a non-tryptic cleavage site on the N-terminal end of the peptide, indicating potential exposure to proteolytic and/or “spontaneous cleavages”. Some of these non-tryptic cleavages may be important for proper maturation of the molecule, before and/or after secretion. Most of the peptides identified from MUC16 were from the SEA region. Surprisingly, three peptides were clearly identified from its heavily glycosylated regions. Up to 25% coverage of MUC4 was achieved covering seven different domains of the molecule. All peptides from the MUC1 cytoplasmic domain were detected along with the three non-tryptic cleavages in the region. Only one peptide was identified from MUC20 which led us to successful antisera raised against the molecule. Taken together, this report represents our current efforts to dissect the complexities of mucin macromolecules. Identification of regions accessible to proteolysis can help in the design of effective antibodies and points to regions that might be available for mucin-protein interactions and identification of cleavage sites will enable understanding of their pre- and post-secretory processing in normal and disease environments.
From indicative to interpretative maps: Dubrovnik urban fabric in the city councils' deliberations 1400‐1450
Creators: name: Škarić, Ana Plosnić
Publisher: name: Zenodo
Year: 2022
Subjects: late medieval, documents, urban fabric, relationships, mapping

description: This paper aims to prompt the visualisation of the research results within the discipline of art history. The core research is documents of a late medieval commune and its relationship with the urban fabric, which is followed by the development of the methodology of mapping and visualizing the research results. The documents studied are the Dubrovnik city councils’ deliberations from 1400 until 1450. They are preserved as manuscripts written in Latin. The manuscripts had been investigated during the DUCAC project (Dubrovnik: Civitas et Acta Consiliorum. Visualizing Development of the Late Medieval Urban Fabric, Croatian Science Foundation, 2014‐2017), which resulted in a collection of 3341 fully transcribed deliberations that reveal the government’s decisions on buildings and spaces in the city. The transcriptions have been published on the project web pages in the form of a map‐searchable database (https://ducac.ipu.hr/project/mapping/). They are organized according to the possibility of locating a building or a space recorded in a document. This database indicates the prospects for further research. The richness of the data allows further research to be conducted from different perspectives and within different disciplines. In this paper, the research is based on the questions which are formulated within the discipline of art history. They tend to disclose the aspects and the extent of the government control over the urban fabric. The questions are: what buildings were recorded in the deliberations, where they are/or were located and how precise we can be in mapping them, who were the owners and to which social group they belonged, what were the government demands and reasons that stood behind these decisions. As a case study, the paper prompts further discussions on the methodology of mapping and visualizing the result of the research on pre-modern cities.
A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities
Creators: name: Giddings, Morgan C.
name: Risk, Brian A.
name: Edwards, Nathan J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Peppy, the proteogenomic/proteomic search software, employs a novel method for assessing the match quality between an MS/MS spectrum and a theorized peptide sequence. The scoring system uses three score factors calculated with binomial probabilities: the probability that a fragment ion will randomly align with a peptide ion; the probability that the aligning ions will be selected from the set of most intense peaks; and the probability that the intensities of fragment ions identified as y-ions are greater than those of their counterpart b-ions. The scores produced by the method act as global confidence scores, which facilitate the accurate comparison of results and the estimation of false discovery rates. Peppy has been integrated into the meta-search engine PepArML to produce meaningful comparisons with Mascot, MSGF+, OMSSA, X!Tandem, k-Score and s-Score. For two of the three the data sets examined with the PepArML analysis, Peppy exceeded the accuracy performance of the other scoring systems; for the third set Peppy was outperformed only by MSGF+.
Learning Solution Manifolds for Control Problems via Energy Minimization
Creators: name: Zamora, Miguel
name: Poranne, Roi
name: Coros, Stelian
Publisher: name: arXiv
Year: 2022
Subjects: subject: Robotics (cs.RO)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: A variety of control tasks such as inverse kinematics (IK), trajectory optimization (TO), and model predictive control (MPC) are commonly formulated as energy minimization problems. Numerical solutions to such problems are well-established. However, these are often too slow to be used directly in real-time applications. The alternative is to learn solution manifolds for control problems in an offline stage. Although this distillation process can be trivially formulated as a behavioral cloning (BC) problem in an imitation learning setting, our experiments highlight a number of significant shortcomings arising due to incompatible local minima, interpolation artifacts, and insufficient coverage of the state space. In this paper, we propose an alternative to BC that is efficient and numerically robust. We formulate the learning of solution manifolds as a minimization of the energy terms of a control objective integrated over the space of problems of interest. We minimize this energy integral with a novel method that combines Monte Carlo-inspired adaptive sampling strategies with the derivatives used to solve individual instances of the control task. We evaluate the performance of our formulation on a series of robotic control problems of increasing complexity, and we highlight its benefits through comparisons against traditional methods such as behavioral cloning and Dataset aggregation (Dagger).
description: IEEE Robotics and Automation Letters (RA-L), 2022. Also in: Intelligent Robots and Systems (IROS)
Comparison of the Membrane Proteome of Virulent Mycobacterium tuberculosis and the Attenuated Mycobacterium bovis BCG Vaccine Strain by Label-Free Quantitative Proteomics
Creators: name: Wrobel, John A.
name: Feltcher, Meghan E.
name: Chen, Xian
name: Braunstein, Miriam
name: Gu, Sheng
name: Gunawardena, Harsha P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The Mycobacterium tuberculosis (MTB) membrane is rich in antigens that are potential targets for diagnostics and the development of new vaccines. To better understand the mechanisms underlying MTB virulence and identify new targets for therapeutic intervention we investigated the differential composition of membrane proteomes between virulent M. tuberculosis H37Rv (MTB) and the Mycobacterium bovis BCG vaccine strain. To compare the membrane proteomes, we used LC-MS/MS analysis in combination with label-free quantitative (LFQ) proteomics, utilizing the area-under-curve (AUC) of the extracted ion chromatograms (XIC) of peptides obtained from m/z and retention time alignment of MS1 features. With this approach, we obtained relative abundance ratios for 2,203 identified membrane-associated proteins in high confidence. Of these proteins, 294 showed statistically significant differences of at least 2 fold, in relative abundance between MTB and BCG membrane fractions. Our comparative analysis detected several proteins associated with known genomic regions of difference between MTB and BCG as being absent, which validated the accuracy of our approach. In further support of our label-free quantitative data, we verified select protein differences by immunoblotting. To our knowledge we have generated the first comprehensive and high coverage profile of comparative membrane proteome changes between virulent MTB and its attenuated relative BCG, which helps elucidate the proteomic basis of the intrinsic virulence of the MTB pathogen.
(400454) Mary Kidd
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Analysis of Multipartite Entanglement Distribution using a Central Quantum-Network Node
Creators: name: Avis, Guus
name: Rozpędek, Filip
name: Wehner, Stephanie
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the performance (rate and fidelity) of distributing multipartite entangled states in a quantum network through the use of a central node. Specifically, we consider the scenario where the multipartite entangled state is first prepared locally at a central node, and then transmitted to the end nodes of the network through quantum teleportation. As our first result, we present leading-order analytical expressions and lower bounds for both the rate and fidelity at which a specific class of multipartite entangled states, namely Greenberger-Horne-Zeilinger (GHZ) states, are distributed. Our analytical expressions for the fidelity accurately account for time-dependent depolarizing noise encountered by individual quantum bits while stored in quantum memory, as verified using Monte Carlo simulations. As our second result, we compare the performance to the case where the central node is an entanglement switch and the GHZ state is created by the end nodes in a distributed fashion. Apart from these two results, we outline how the teleportation-based scheme could be physically implemented using trapped ions or nitrogen-vacancy centers in diamond.
description: 19 pages, 12 figures + 20 pages, 2 figures appendix
Peppy: Proteogenomic Search Software
Creators: name: Spitzer, Wendy J.
name: Giddings, Morgan C.
name: Risk, Brian A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have been limited to small genomes, as large genomes can prove impractical due to the required amount of computer memory and computation time. We present Peppy, a software tool designed to perform every necessary task of proteogenomic searches quickly, accurately and automatically. The software generates a peptide database from a genome, tracks peptide loci, matches peptides to MS/MS spectra and assigns confidence values to those matches. Peppy automatically performs a decoy database generation, search and analysis to return identifications at the desired false discovery rate threshold. Written in Java for cross-platform execution, the software is fully multithreaded for enhanced speed. The program can run on regular desktop computers, opening the doors of proteogenomic searching to a wider audience of proteomics and genomics researchers. Peppy is available at http://geneffects.com/peppy.
Abstract SETTLEMENT IN PENEDÈS (CATALONIA) BETWEEN THE 10TH AND THE 13TH CENTURIES
Creators: name: Marçal Díaz Ros
Publisher: name: Zenodo
Year: 2022

description: Penedès is an historical region of Catalonia which was controlled by the Count of Barcelona and its nobility from the 10th century onwards. Using documentary and archaeological sources, the outcoming research has the main objective to achieve the cartographical restitution of the Medieval Penedès settlements (10-13th centuries) and their analysis from a geographical and historical perspective. In this sense, there will be addressed some phenomena from that period as the abandonment of settlements in mountainous areas, the concentration of population around churches, towers and markets or the expansion of farms (masies).Penedès is an historical region of Catalonia which was controlled by the Count of Barcelona and its nobility from the 10th century onwards. Using documentary and archaeological sources, the outcoming research has the main objective to achieve the cartographical restitution of the Medieval Penedès settlements (10-13th centuries) and their analysis from a geographical and historical perspective. In this sense, there will be addressed some phenomena from that period as the abandonment of settlements in mountainous areas, the concentration of population around churches, towers and markets or the expansion of farms (masies). This research has been supported by the Secretary of Universities and Research of the Generalitat de Catalunya and the European Social Fund as part of the PhD project “Poblament i assentaments al Penedès medieval: segles x-xiii”, under the direction of Dr. Marta Sancho Planas and Dr. Maria Soler Sala (University of Barcelona). This investigation has been conducted under the following research projects: “Priores, senyors i prínceps. Els espais de poder a la Catalunya medieval i moderna” and “Paisajes monásticos. Representaciones y virtualizaciones de las realidades espirituales y materiales medievales en el Mediterráneo Occidental (siglos VI-XVI)” [PGC2018-095350-B-I00].
Scanning tunneling potentiometry implemented into a multi-tip setup by software
Creators: name: Lüpke, F.
name: Korte, S.
name: Cherepanov, V.
name: Voigtländer, B.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We present a multi-tip scanning tunneling potentiometry technique that can be implemented into existing multi-tip scanning tunneling microscopes without hardware changes. The resulting setup allows flexible in situ contacting of samples under UHV conditions and subsequent measurement of the sample topography and local electric potential with resolution down to Å and μV, respectively. The performance of the potentiometry feedback is demonstrated by thermovoltage measurements on the Ag/Si$(111)-(\sqrt3\times\sqrt3)\rm R30^{\circ}$ surface by resolving a standing wave pattern. Subsequently, the ability to map the local transport field as a result of a lateral current through the sample surface is shown on Ag/Si$(111)-(\sqrt3\times\sqrt3)\rm R30^{\circ}$ and Si$(111)-(7\times7)$ surfaces.